FIELD OF THE INVENTION

The present invention relates to genetically modified ascomycetous filamentous fungi, in particular of the species Thermothelomyces heterothallica (formerly Myceliophthora thermophila ), in which at least one of the enzymes involved in the nicotinamide riboside biosynthesis pathway has been engineered to increase the production of nicotinamide riboside and/or its precursors.

BACKGROUND OF THE INVENTION

Nicotinamide riboside (NR) is a new form of vitamin B3 that functions as a precursor to nicotinamide adenine dinucleotide (NAD), a key player in the cellular production of energy. NAD oxidized form (NAD ⁺ ) participates in a host of metabolic pathways and is involved in other important processes, such as DNA repair. NAD ⁺ levels naturally decline as people and animals age, and this loss has been proposed as contributing to the underlying physiology of aging. Clinical studies have shown that NR can significantly increase levels of NAD ⁺ and some of its associated metabolites in both whole blood and peripheral blood mononuclear cells. NR is converted into NAD ⁺ through two distinct pathways. The first pathway utilizes the NR kinase, NRK1, to produce nicotinamide mononucleotide (NMN), which is then converted into NAD ⁺ . The second pathway cleaves NR into nicotinamide (Nam) and a ribose, by exploiting two independently acting enzymes uridine hydrolase 1 (URH1) and purine nucleoside phosphorylase (PNP1).

Wild type Thermothelomyces heterothallica ( Th . heterothallica ) Cl (recently renamed from Myceliophthora thermophila , which in turn was renamed from Chrysosporium lucknowense) is a thermotolerant ascomycetous filamentous fungus producing high levels of cellulases, which made it attractive for production of these and other enzymes on a commercial scale.

For example, US Patent Nos. 8,268,585 and 8,871,493 to the Applicant of the present invention disclose a transformation system in the field of filamentous fungal hosts for expressing and secreting heterologous proteins or polypeptides. Also disclosed is a process for producing large amounts of polypeptides or proteins in an economical manner. The system comprises a transformed or transfected fungal strain of the genus Chrysosporium , more particularly of Chrysosporium lucknowense and mutants or derivatives thereof. Also disclosed are transformants containing Chrysosporium coding sequences, as well expressing-regulating sequences of Chrysosporium genes.

Wild type Cl was deposited in accordance with the Budapest Treaty with the number VKM F-3500 D, deposit date August 29, 1996. High Cellulase (HC) and Low Cellulase (LC) strains have also been deposited, as described, for example, in US Patent No. 8,268,585.

Recently, the Applicant of the present has shown that filamentous fungi, particularly Th. heterothallica is highly suitable for the production of secondary metabolites. International (PCT) Application Publication No. WO 2020/161682 discloses that Th. heterothallica is capable of producing cannabinoids and precursors thereof, particularly of producing cannabigerolic acid (CBGA) and/or cannabigerovarinic acid (CBGVA) and products thereof, including tetrahydrocannabinolic acid (THCA), cannabidiolic acid (CBDA) and cannabidivarinic acid (CBDVA), and use thereof for producing said precursors and cannabinoids.

US Patent No. 8,114,626 discloses fungal strain, particularly Saccharomyces strain deficient in nicotinamide riboside import and salvage and use thereof for producing nicotinamide riboside. Methods for producing nicotinamide riboside and a nicotinamide riboside-supplemented food product using the strain of the invention are also provided.

WO 2018/211028 discloses microbial production of nicotinamide riboside and/or nicotinamide mononucleotide using a genetically modified fungus.

There remains a need for a system for producing high amounts of nicotinamide riboside for use in the pharmaceutical industry in an efficient and cost-effective way.

SUMMARY OF THE INVENTION

The present invention provides genetically modified ascomycetous filamentous fungi capable of producing nicotinamide riboside (NR) and precursors thereof. In particular, the present invention provides Thermothelomyces heterothallica strain C1 as an exemplary ascomycetous filamentous fungus genetically modified to enhance the production of nicotinamide riboside. The fungi described herein have been modified to increase the flux of the NR metabolic pathway.

The yeast Saccharomyces is currently the major candidate for the production of nicotinamide riboside in microorganisms. Surprisingly, the present invention shows that Th. heterothallica , exemplifying ascomycetous filamentous fungi, can be genetically modified to significantly increase the outcome of the endogenous pathways naturally producing NR, while blocking natural NR catabolism. The present invention shows that combination of overexpressing enzymes involved in the NR biosynthesis pathway and optionally the blocking of catabolism and/or cellular uptake of NR significantly increases the production of NR. Advantageously, a large portion of the NR is secreted and accumulated in the growth medium, enabling simple recovery and purification procedures. Moreover, the genetically modified ascomycetous filamentous fungus according to the invention significantly increases the ratio of NR to other metabolites, such as nicotinic acid ribose and nicotinic acid, which further simplifies the purification procedure.

The exemplary Th. heterothallica C1 system of the present invention was engineered for production of NR by overexpressing five genes encoding enzymes involved in conversion of quinolinate intermediate to NR (BNA6, NMA1, QNS1, ISN1, and SDT1) and by deleting four genes encoding enzymes that catabolize NR (NRK1, PNP1, and URH1) or that transport excreted NR back into the cells (NRT1). The genetically modified fungi described herein produced 10-20 times more NR compared to their parent strains. Without wishing to be bound by any specific theory or mechanism of action, diverting the resources of the fungus by methods of metabolic engineering increases the potential of this strain to become a more efficient host for production of NR compared to, for example, S. cerevisiae.

Furthermore, several Th. heterothallica C1 strains developed by the Applicant of the present invention are less sensitive to feedback repression by glucose and other fermentable sugars present in the growth medium as carbon source than conventional yeast strains and also most other ascomycetous filamentous fungal hosts, and consequently can tolerate higher feeding rate of the carbon source, leading to high yields production by these fungi. In addition, some of the Th. heterothallica C1 strains developed by the Applicant of the present invention can be grown in liquid cultures with significantly reduced medium viscosity in fermenters, compared to most other ascomycetous filamentous fungal species. The low viscosity cultures of Th. heterothallica C1 are comparable to that of S. cerevisiae and other yeast species. The low viscosity may be attributed to the morphological change of the strain from having long and highly interlaced hyphae in the parental strain(s) to short and less interlaced hyphae in the developed strain(s). Low medium viscosity is highly advantageous in large scale industrial production.

According to an aspect of the present invention there is provided a genetically modified ascomycetous filamentous fungus for producing nicotinamide riboside or a precursor thereof, the genetically modified filamentous fungus comprises at least one cell comprising at least one exogenous polynucleotide selected from the group consisting of (i) an exogenous polynucleotide encoding Nicotinate-nucleotide pyrophosphorylase (BNA6); (ii) an exogenous polynucleotide encoding Nicotinamide Mononucleotide Adenylyltransferase (NMA1); (iii) an exogenous polynucleotide encoding glutamine (Q) dependent Nad ⁺ synthetase (QNS1); (iv) an exogenous polynucleotide encoding Inosine 5'-monophosphate (IMP)-specific 5'-nucleotidase (ISN1); and (v) an exogenous polynucleotide encoding pyrimidine nucleotidase (SDT1).

According to some embodiments, the NR precursor is nicotinamide adenine dinucleotide (NAD) or nicotinamide mononucleotide (NMN).

According to some embodiments, the genetically modified ascomycetous filamentous fungus comprises at least one cell comprising a plurality of exogenous polynucleotides encoding for at least two different proteins selected from the group consisting of BNA6, NMA1, QNS1, ISN1, and SDT1. According to certain embodiments, the genetically modified ascomycetous filamentous fungus comprises at least one cell comprising a plurality of exogenous polynucleotides encoding for at least three different proteins selected from the group consisting of BNA6, NMA1, QNS1, ISN1, and SDT1. According to certain embodiments, the genetically modified ascomycetous filamentous fungus comprises at least one cell comprising a plurality of exogenous polynucleotides encoding for at least four different proteins selected from the group consisting of BNA6, NMA1, QNS1, ISN1, and SDT1. According to specific embodiments, the genetically modified ascomycetous filamentous fungus comprises at least one cell comprising a plurality of exogenous polynucleotides encoding for BNA6, NMA1, QNS1, ISN1, and SDT1.

According to some embodiments, the polynucleotide encodes an enzyme that is endogenous to the genetically modified ascomycetous filamentous fungus.

According to some embodiments, the polynucleotide is endogenous to the genetically modified ascomycetous filamentous fungus. According to other embodiments, the polynucleotide is heterologous to the genetically modified ascomycetous filamentous fungus.

According to certain exemplary embodiments, the polynucleotides of the present invention are designed based on the amino acid sequence of the enzyme to be produced employing a codon usage of a filamentous fungus.

According to some embodiments, the BNA6 protein comprises an amino acid sequence having at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or at least 99%, or 100% identity to the amino acid sequence of Thermothelomyces heterothallica BNA6. According to certain embodiments, the Thermothelomyces heterothallica BNA6 comprises the amino acids of SEQ ID NO: 1.

According to some embodiments, the exogenous polynucleotide encoding BNA6 comprises a nucleotide sequence having at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% identity to the nucleotide sequence of Thermothelomyces heterothallica bna6. According to some embodiments, the Thermothelomyces heterothallica bna6 comprises the nucleotide sequence of SEQ ID NO: 2.

According to some embodiments, the NMA1 protein comprises an amino acid sequence having at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or at least 99%, or 100% identity to the amino acid sequence of Thermothelomyces heterothallica NMA1. According to certain embodiments, the Thermothelomyces heterothallica NMA1 comprises the amino acids of SEQ ID NO: 3.

According to some embodiments, the exogenous polynucleotide encoding NMA1 comprises a nucleotide sequence having at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% identity to the nucleotide sequence of Thermothelomyces heterothallica nmal. According to some embodiments, the Thermothelomyces heterothallica nmal comprises the nucleotide sequence of SEQ ID NO: 4.

According to some embodiments, the QNS1 protein comprises an amino acid sequence having at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or at least 99%, or 100% identity to the amino acid sequence of Thermothelomyces heterothallica QNS1. According to certain embodiment, the Thermothelomyces heterothallica QNS1 comprises the amino acids of SEQ ID NO: 5.

According to some embodiments, the exogenous polynucleotide encoding QNS1 comprises a nucleotide sequence having at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% identity to the nucleotide sequence of Thermothelomyces heterothallica qnsl. According to some embodiments, the Thermothelomyces heterothallica qnsl comprises the nucleotide sequence of SEQ ID NO: 6.

According to some embodiments, the ISN1 protein comprises an amino acid sequence having at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or at least 99%, or 100% identity to the amino acid sequence of Thermothelomyces heterothallica ISN1. According to certain embodiments, the Thermothelomyces heterothallica ISN1 comprises the amino acids of SEQ ID NO: 7.

According to some embodiments, the exogenous polynucleotide encoding ISN1 comprises a nucleotide sequence having at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% identity to the nucleotide sequence of Thermothelomyces heterothallica isnl. According to some embodiments, the Thermothelomyces heterothallica isnl comprises the polynucleotide SEQ ID NO: 8.

According to some embodiments, the SDT1 protein comprises an amino acid sequence having at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or at least 99%, or 100% identity to the amino acid sequence of Thermothelomyces heterothallica SDT1. According to certain embodiments, the Thermothelomyces heterothallica SDT1 comprises the amino acids of SEQ ID NO: 9.

According to some embodiments, the exogenous polynucleotide encoding SDT1 comprises a nucleotide sequence having at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% identity to the nucleotide sequence of Thermothelomyces heterothallica sdtl. According to some embodiments, the Thermothelomyces heterothallica sdtl comprises the nucleotide sequence of SEQ ID NO: 10.

According to some embodiments, the genetically modified ascomycetous filamentous fungus expresses elevated amounts of at least one protein selected from the group consisting of BNA6, NMA1, QNS1, ISN1, and SDT1 compared to the non- modified strain. Each possibility represents a separate embodiment of the present invention.

According to some embodiments, the genetically modified ascomycetous filamentous fungus further comprises at least one cell having reduced expression and/or activity of at least one protein or enzyme that catabolize NR, modify NR or transport NR into the cells’ cytoplasm.

According to some embodiments, the genetically modified ascomycetous filamentous fungus comprises at least one cell having reduced expression and/or activity of at least one protein or enzyme selected from the group consisting of Nicotinamide riboside kinase 1 (NRK1), Uridine hydrolase 1 (URH1), Purine nucleoside phosphorylase (PNPl), and Nicotinamide riboside transporter 1 (NRT1). According to certain embodiments, the genetically modified ascomycetous filamentous fungus comprises at least one cell having reduced expression and/or activity of at least two different proteins or enzymes selected from the group consisting of NRK1, URH1, PNPl, and NRT1. According to certain embodiments, the genetically modified ascomycetous filamentous fungus comprises at least one cell having reduced expression and/or activity of at least three different proteins or enzymes selected from the group consisting of NRK1, URH1, PNPl, and NRT1. According to certain embodiments, the genetically modified ascomycetous filamentous fungus comprises at least one cell having reduced expression and/or activity of NRK1, URH1, PNPl, and NRT1. According to some embodiments, the genetically modified ascomycetous filamentous fungus expresses reduced amounts of at least one protein selected from the group consisting of NRK1, URH1, PNPl, and NRT1, compared to the non-modified strain. Each possibility represents a separate embodiment of the invention.

According to some embodiments, the genetically modified ascomycetous filamentous fungus comprises at least one deleted or disrupted gene selected from the group consisting of nrk1 , urh1, pnp1 , and nrt1. Each possibility represents a separate embodiment of the invention.

According to certain embodiments, the genetically modified ascomycetous filamentous fungus comprises at least one cell comprising at least one exogenous polynucleotide encoding a protein selected from the group consisting of BNA6, NMA1, QNS1, ISN1, and SDT1 and reduced expression and/or activity of at least one protein or enzyme selected from the group consisting NRK1, URH1, PNP1, and NRT1.

According to some embodiments, the genetically modified ascomycetous filamentous fungus is capable of producing an elevated amount of NR, compared to the non-modified fungus.

According to some embodiments, the genetically modified ascomycetous filamentous fungus is capable of producing higher NR amount compared to the produced amount of nicotinic acid ribose (NAR). According to certain embodiments, the genetically modified ascomycetous filamentous fungus is capable of producing at least twice the amount of NR compared to NAR.

According to some embodiments, the genetically modified ascomycetous filamentous fungus is capable of producing higher NR amount compared to the produced amount of nicotinic acid (NA). According to certain embodiments, the genetically modified ascomycetous filamentous fungus is capable of producing at least twice the amount of NR compared to nicotinic acid.

According to some embodiments, the genetically modified ascomycetous filamentous fungus produces nicotinamide ribose in an increased amount compared to the amount produced in a corresponding unmodified ascomycetous filamentous fungus cultured under similar conditions. According to certain embodiments, the genetically modified ascomycetous filamentous fungus is capable of producing at least 5 times more NR compared to its parent strain. According to certain embodiments, the genetically modified ascomycetous filamentous fungus is capable of producing at least 10 times more NR compared to its parent strain.

According to some embodiments, the genetically modified ascomycetous filamentous fungus is capable of increasing the amount of secreted nicotinamide ribose in the growth medium by at least 2, 5, or 10 compared to a non-genetically modified ascomycetous filamentous fungus. According to some embodiments, the genetically modified ascomycetous filamentous fungus is capable of producing at least 10 mg NR /L growth medium. According to some embodiments, the genetically modified ascomycetous filamentous fungus is capable of producing at least 15 mg NR /L growth medium. According to certain embodiments, at least 70%, 80%, or 90% of the produced NR is secreted NR.

The polynucleotides encoding each of the proteins or enzymes may form part of one or more DNA constructs and/or expression vectors. According to certain embodiments, each of the polynucleotide forms part of a separate expression DNA construct/vector. According to other embodiments, part or all the polynucleotides are present within the same DNA construct/expression vector.

According to some embodiments, the at least one exogenous polynucleotide is a DNA construct or an expression vector further comprising at least one regulatory element operable in said ascomycetous filamentous fungus. According to certain embodiments, the regulatory element is selected from the group consisting of a regulatory element endogenous to said fungus and a regulatory element heterologous to said fungus.

According to some embodiments, the ascomycetous filamentous fungus is of a genus within the group Pezizomycotina.

According to some embodiments, the ascomycetous filamentous fungus is of a genus selected from the group consisting of Thermothelomyces, Myceliophthora , Trichoderma, Aspergillus, Penicillium, Rasamsonia, Chrysosporium , Corynascus, Fusarium, Neurospora, and Talaromyces.

According to some embodiments, the ascomycetous filamentous fungus is of a species selected from the group consisting of Thermothelomyces heterothallica (also denoted Myceliophthora thermophila), Myceliophthora lutea , Aspergillus nidulans , Aspergillus funiculosus Aspergillus niger , Aspergillus oryzae, Trichoderma reesei, Trichoderma harzianum, Trichoderma longibrachiatum, Trichoderma viride, Rasamsonia emersonii. Penicillium chrysogenum , Penicillium verrucosum , Sporotrichum thermophile, Corynascus fumimontanus, Corynascus thermophilus, Chrysosporium lucknowense , Fusarium graminearum , Fusarium venenatum , Neurospora crassa, and Talaromyces piniphilus.

According to some embodiments, the ascomycetous filamentous fungus is a Thermothelomyces heterothallica strain comprising rDNA sequence having at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% or 100% identity to the nucleic acid sequence set forth in SEQ ID NO: 15.

According to some embodiments, the ascomycetous filamentous fungus is Thermothelomyces heterothallica C1. According to certain embodiments, the Thermothelomyces heterothallica C1 is of strain UV18-25, deposit No. VKM F-3631 D and derivatives thereof.

According to an additional aspect, the present invention provides a method for producing a fungus capable of producing nicotinamide riboside or a precursor thereof, the method comprising transforming at least one cell of the fungus with at least one exogenous polynucleotide selected from the group consisting of (i) an exogenous polynucleotide encoding BNA6; (ii) an exogenous polynucleotide encoding NMA1; (iii) an exogenous polynucleotide encoding QNS1; (iv) an exogenous polynucleotide encoding ISN1; and (v) an exogenous polynucleotide encoding SDT1. Each possibility represents a separate embodiment of the invention.

According to some embodiments, the NR precursor is nicotinamide adenine dinucleotide (NAD) or nicotinamide mononucleotide (NMN).

According to some embodiments, the method comprises transforming at least one cell of the fungus with at least two, at least three, at least four or five exogenous polynucleotides encoding for different proteins selected from the group consisting of BNA6, NMA1, QNS1, ISN1, and SDT1.

According to some embodiments, the method further comprises engineering the fungus to inhibit the expression and/or activity of NRK1, URH1, PNPl, or NRT1 in the at least one cell. According to certain embodiments, the method further comprises engineering the fungus to inhibit the expression and/or activity of at least two different proteins selected from the group consisting of NRK1, URH1, PNPl, and NRT1 in the at least one cell. According to certain embodiments, the method further comprises engineering the fungus to inhibit the expression and/or activity of at least three different proteins selected from the group consisting of NRK1, URH1, PNPl, and NRT1 in the at least one cell. According to specific exemplary embodiments, the method further comprises engineering the fungus to inhibit the expression and/or activity of NRK1, URH1, PNP1, and NRT1 in the at least one cell.

According to some embodiments, inhibiting the expression of a protein or enzyme comprising deleting or disrupting the endogenous gene encoding for the protein or enzyme.

According to some embodiments, the method further comprises modulating the expression and/or activity of at least one additional endogenous enzyme of the nicotinamide riboside pathway.

According to some embodiments, the genetically modified fungus produces the nicotinamide riboside in an elevated amount compared to the amount produced by a corresponding unmodified fungus not transformed with the at least one polynucleotide.

According to some embodiments, the ascomycetous filamentous fungus is of a genus within Pezizomycotina.

According to some embodiments, the ascomycetous filamentous fungus is of a genus selected from the group consisting of Thermothelomyces, Myceliophthora , Trichoderma, Aspergillus, Penicillium, Rasamsonia, Chrysosporium , Corynascus, Fusarium, Neurospora, and Talaromyces.

According to some embodiments, the ascomycetous filamentous fungus is of a species selected from the group consisting of Thermothelomyces heterothallica or (Myceliophthora thermophila ), Myceliophthora lutea , Aspergillus nidulans , Aspergillus funiculosus, Aspergillus niger , Aspergillus oryzae, Trichoderma reesei, Trichoderma harzianum, Trichoderma longibrachiatum, Trichoderma viride, Rasamsonia emersonii , Penicillium chrysogenum, Penicillium verrucosum , Sporotrichum thermophile, Corynascus fumimontanus, Corynascus thermophilus, Chrysosporium lucknowense Fusarium graminearum , Fusarium venenatum , Neurospora crassa and Talaromyces piniphilus.

According to some embodiments, the ascomycetous filamentous fungus is a Thermothelomyces heterothallica strain comprising rDNA sequence having at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% or 100% identity to the nucleic acid sequence set forth in SEQ ID NO: 15.

According to some embodiments, the ascomycetous filamentous fungus is Thermothelomyces heterothallica C1. According to certain embodiments, the Thermothelomyces heterothallica C1 is of strain UV18-25, deposit No. VKM F-3631 D or a derivative thereof.

According to a further aspect, the present invention provides a method of producing at least one nicotinamide riboside or a precursor thereof, the method comprising culturing the genetically modified fungus as described herein in a suitable medium; and recovering the at least one nicotinamide riboside product.

According to some embodiments, the recovering step comprises recovering the NR from the growth medium, from the fungal mass or both.

According to some embodiments, the NR is recovered from the growth medium. According to certain embodiment, at least 50%, 60%, 70%, 80%, 90% or 95% of the NR is secreted NR.

According to some embodiments, the medium comprises a carbon source selected from the group consisting of glucose, sucrose, xylose, arabinose, galactose, fructose, lactose, cellobiose, glycerol and any combination thereof. Each possibility represents a separate embodiment of the invention.

According to certain embodiments, culturing of the genetically modified fungus in a suitable medium provides for synthesis of nicotinamide riboside in an increased amount compared to the amount produced in a corresponding unmodified fungus cultured under similar conditions.

According to certain embodiments, the corresponding unmodified fungus is of the same species of the genetically modified fungus. According to some embodiments, the corresponding fungus is isogenic to the genetically modified fungus.

It is to be understood explicitly that the scope of the present invention encompasses homologs, analogs, variants and derivatives, including shorter and longer polypeptides, proteins and polynucleotides, as well as polypeptide, protein and polynucleotide analogs with one or more amino acid or nucleic acid substitution, as well as amino acid or nucleic acid derivatives, non-natural amino or nucleic acids and synthetic amino or nucleic acids as are known in the art, with the stipulation that these variants and modifications must preserve the activity of protein or enzymes described herein. Specifically, any active fragments of the active polypeptide or protein as well as extensions, conjugates and mixtures are disclosed according to the principles of the present invention.

It is to be understood that any combination of each of the aspects and the embodiments disclosed herein is explicitly encompassed within the disclosure of the present invention.

Other objects, features and advantages of the present invention will become clear from the following description and drawings.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Enzymatic reactions towards NR formation. The genes marked in bold gray are overexpressed and the ones in light gray and italics are deleted in the final strain.

FIG. 2. A schematic representation of the plasmids constructed in this work. The marker gene nial in pChD004 and amdS in pChD005 and pChDOO are placed between repeated sequences (DR), which enable excision of the marker from the chromosome in the presence of counter selective agents, potassium nitrate or fluoroacetamide, respectively, and isolation of a strain free of the corresponding marker.

FIGs. 3A-3C. Figure 3 A. Extracellular metabolite concentration in cell culture medium of different strains as indicated. Figure 3B. Intracellular metabolites detected following cold methanol extraction of harvested cells. Figure 3C. Extra- and intracellular metabolites detected following cold methanol extraction of samples containing cells and culture medium. Metabolite concentrations are presented for different engineered Cl strains as indicated and detailed in Table 2.

FIGs. 4A-4D. Figure 4A. Extra- and intracellular compounds (mg/L) found in cold methanol extracted cultivation samples containing the fungi and culture medium. Presented are the strains derived from M1889 (detailed in Table 2). Figure 4B. Extracellular NR concentration (mg/L) in culture medium of different samples (corresponding to Figure 4 A samples). Figure 4C. Extracellular compounds (mg/L) found in cold methanol extracted cultivation samples containing the fungi and culture medium. Presented are the strains derived from M1892. Figure 4D. Extracellular NR concentration (mg/L) in culture medium of different samples (corresponding to Figure 4C samples). FIGs. 5A-5B. Extracellular metabolite concentrations (mg/L) produced by M1889 derived (Figure 5 A) or M1892 derived (Figure 5B) modified strains. The relevant genetic modifications are shown below the graphs.

FIGs, 6A-6C NR biosynthesis modifications in selected strains. Figure 6A. mChD042 and mChD045; Δnrk1 :SDT1 Δnrt1 :BNA6 Δpnp 1 :NMA 1. Figure 6B. mChD044 and mChD047; Δnrk1: SDT1 Δnrt1 :BNA6 Δurh 1 :ISN1, QNS1. Figure 6C. mChD071 and mChD073; Δnrk1.SDT1 Δnrt1 :BNA6 Δurh 1 :ISN1, QNS1, Δpnp 1 :NMA1.

FIG. 7. Glucose consumption and NR production during 96 hours at +35°C of strains M1889, M1892, mChD001 and mChD004 in 5 g/L starting glucose production medium. Increased glucose concentrations at 96h are due to evaporation and decreased NR concentrations at 96h due to degradation.

FIG. 8. Glucose consumption and NR production during 192 hours (first 48h at +35°C, then +20°C) of strains M1889, M1892, mChD001 and mChD004 in 5 g/L starting glucose production medium. Values are the lowest glucose and highest NR amounts measured per strain per time-point.

FIGs. 9A-9B. Biomass-normalized Biolector Pro cultivation results. Both supernatant (Figure 9A) and cell + supernatant (Figure 9B) results are shown for each of the strains at two time points (48 and 72h).

FIGs. 10A-10C. Figure 10A. Concentrations of extracellular NR (mg/L), protein (mg/L) and biomass (g/L) in bioreactor cultivation with strain mcChD042-3-1. Figure 10B - Extracellular compounds (mg/L). Figure 10C - Combination of extra- and intracellular compounds (mg/L).

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides alternative, highly efficient system for producing nicotinamide riboside and precursors thereof. The system of the invention is based in part on the filamentous fungus Thermothelomyces heterothallica C1 and particular strains thereof, which have been previously developed as a natural biological factory for protein as well as secondary metabolite production. These strains show high growth rate while keeping low culture viscosity, and are thus highly suitable for continuous growth in fermentation cultures at volumes as high as 100,000-150,000 liters or greater. The present invention in some embodiments provides genetically modified fungi engineered for production of NR by deleting four genes encoding enzymes that catabolize NR (NRK1, PNP1, URH1) or transport of excreted NR back into the cells (NRT1), and by overexpressing five genes encoding enzymes of the nicotinamide riboside pathway (BNA6, NMA1, QNA1, ISN1, SDT1).

Definitions

Ascomycetous filamentous fungi as defined herein refer to any fungal strain belonging to the group Pezizomycotina. The Pezizomycotina comprises, but is not limited to the following groups:

Sordariales, including genera:

Thermothelomyces (including species: heterothallica and thermophila ), Myceliophthora (including the species lutea and unnamed species), Corynascus (including the species fumimontanus ),

Neurospora (including the species crassa );

Hypocreales , including genera:

Fusarium (including the species graminearum and venenatum), Trichoderma (including the species reesei, harzianum, longibrachiatum and viride );

Onygenales, including genera:

Chrysosporium (including the species Iucknowense);

Eurotiales , including genera:

Rasamsonia (including the species emersonii),

Penicillium (including the species verrucosum ),

Aspergillus (including the species funiculosus , nidulans , niger and oryzae) Talaromyces (including the species piniphilus (formerly Penicillium funiculosum).

It is to be understood that the above list is not conclusive, and is meant to provide an incomplete list of industrially relevant filamentous ascomycetous fungal species.

While there may be filamentous ascomycetous species outside Pezizomycotina, that group does not contain Saccharomycotina, which contains most commonly known non- filamentous industrially relevant genera, such as Saccharomyces, Komagataella (including formerly Pichia pastoris), Kluyveromyces or Taphrinomycotina, which contains some other commonly known non-filamentous industrially relevant genera, such as Schizosaccharomyces.

All taxonomical categories above are defined according to the NCBI Taxonomy browser (ncbi.nlm.nih.gov/taxonomy) as of the date of the patent application.

It must be appreciated that fungal taxonomy is in constant move, and the naming and the hierarchical position of taxa may change in the future. However, a skilled person in the art will be able to unambiguously determine if a particular fungal strain belongs to the group as defined above.

According to certain embodiments, the filamentous fungus genus is selected from the group consisting of Myceliophthora, Thermothelomyces, Aspergillus, Penicillium, Trichoderma, Rasamsonia, Chrysosporium , Corynascus, Fusarium, Neurospora, Talaromyces and the like. According to some embodiments, the fungus is selected from the group consisting of Myceliophthora thermophila, Thermothelomyces thermophila (formerly M. thermophila), Thermothelomyces heterothallica (formerly M. thermophila and heterothallica ), Myceliophthora lutea , Aspergillus nidulans , Aspergillus funiculosus Aspergillus niger , Aspergillus oryzae, Penicillium chrysogenum, Penicillium verrucosum, Trichoderma reesei, Trichoderma harzianum, Trichoderma longibrachiatum, Trichoderma viride, Chrysosporium lucknowense , Rasamsonia emersonii , Sporotrichum thermophile, Corynascus fumimontanus, Corynascus thermophilus , Fusarium graminearum , Fusarium venenatum , Neurospora crassa, and Talaromyces piniphilus.

In particular, the present invention provides Thermothelomyces heterothallica strain C1 as model for an ascomycetous filamentous fungus, capable of producing nicotinamide riboside.

The terms “ Thermothelomyces ” and its species “ Thermothelomyces heterothallica and thermophila ” are used herein in the broadest scope as is known in the art. Description of the genus and its species can be found, for example, in Marin-Felix Y (2015. Mycologica 107(3): 619-632 doi.org/10.3852/14-228) and van den Brink J et al. (2012, Fungal Diversity 52(1): 197-207). As used herein " C1" or "Thermothelomyces heterothallica C1" or Th. heterothallica C1, or C1 all refer to Thermothelomyces heterothallica strain C1.

It is noted that the above authors (Marin-Felix et al., 2015) proposed splitting of the genus Myceliophthora based on differences in optimal growth temperature, morphology of the conidiospore, and details of the sexual reproduction cycle. According to the proposed criteria C1 clearly belongs to the newly established genus Thermothelomyces , which contain former thermotolerant Myceliophthora species rather than to the genus Myceliophthora , which remains to include the non-thermotolerant species. As C1 can form ascospores with some other Thermothelomyces (formerly Myceliophthora ) strains with opposite mating type, C1 is best classified as Th. heterothallica strain C1 , rather than Th. thermophila C1.

It must also be appreciated that the fungal taxonomy was also in constant change in the past, so the current names listed above may be preceded by a variety of older names beyond Myceliophthora thermophila (van Oorschot, 1977. Persoonia 9(3):403), which are now considered synonyms. For example, Thermothelomyces heterothallica (Marin- Felix et al., 2015. Mycologica, 3:619-63), is synonymized with Corynascus heterotchallicus , Thielavia heterothallica , Chrysosporium lucknowense and thermophile as well as Sporotrichium thermophile (Alpinis 1963. Nova Hedwigia 5:74).

It is further to be explicitly understood that the present invention encompasses any strain containing a ribosomal DNA (rDNA) sequence that shows 99% homology or more to SEQ ID NO: 15, and all those strains are considered to be conspecific with Thermothelomyces heterothallica.

Th. heterothallica strain C1 (as Chrysosporium lucknowense strain C1) and mutants derived therefrom were deposited in accordance with the Budapest Treaty with the number VKM F-3500 D, deposit date August 29, 1996.

Particularly, the term Th. heterothallica strain C1 encompasses genetically modified sub-strains derived from the wild type strain, which have been mutated, using random or directed approaches, for example, using UV mutagenesis, or by deleting one or more endogenous genes. For example, the Cl strain may refer to a wild type strain modified to delete one or more genes encoding an endogenous protease and/or one or more genes encoding an endogenous chitinase. For example, C1 strains which are encompassed by the present invention include strain UV18-25, deposit No. VKM F-3631 D; strain NG7C-19, deposit No. VKM F-3633 D; and strain UV13-6, deposit No. VKM F-3632 D. Further Cl strain that may be used according to the teachings of the present invention include HC strain UV18-1 OOf deposit No. CBS 141147; HC strain UV18-1 OOf deposit No. CBS141143; LC strain W1L#100I deposit No. CBS141153; and LC strain W1L#100I deposit No. CBS141149 and derivatives thereof.

It is to be explicitly understood that the teachings of the present invention encompass mutants, derivatives, progeny, and clones of the Th. heterothallica C1 strains, as long as these derivatives, progeny, and clones, when genetically modified according to the teachings of the present invention are capable of producing at least one nicotinamide riboside product according to the teachings of the invention.

It is to be explicitly understood that the term “derivative” with reference to fungal line encompasses any fungal parent line with modifications positively affecting product yield, efficiency, or efficacy, or affecting any trait improving the fungal derivative as a tool to produce the nicotinamide riboside. As used herein, the term “progeny" refers to an unmodified descendant from the parent fungal line, such as cell from cell.

Computational models of metabolic networks have been shown to be an effective tool in studying and engineering microbial metabolism for production of valuable chemicals. Due to the fast and ongoing development of the computational tools, the accuracy of such models is increased. The inventors of the present invention have used proprietary data to establish genome-scale metabolic model for Th. heterothallica C1. Simulations of the model were performed to identify metabolic targets to be engineered to improve NR production. Based on the model simulations, primary targets to be up- or down-regulation in order to increase the efficacy of the metabolic fluxes towards formation of the precursors of NR were searched and identified. Many of the precursors are involved in several competing metabolic reactions and therefore, engineering of relevant metabolic branching points may enhance the flux towards NR.

According to an aspect of the present invention there is provided a genetically modified filamentous fungus for producing nicotinamide riboside or a precursor thereof, the genetically modified filamentous fungus comprises at least one cell comprising at least one exogenous polynucleotide selected from the group consisting of (i) an exogenous polynucleotide encoding BNA6; (ii) an exogenous polynucleotide encoding NMAl; (iii) an exogenous polynucleotide encoding QNS1; (iv) an exogenous polynucleotide encoding ISN1; and (v) an exogenous polynucleotide encoding SDT1.

According to some embodiments, the NR precursor is NAD. According to some embodiments, the NR precursor is NMN.

According to some embodiments, the ascomycetous filamentous fungus comprises at least one cell having reduced or abolished expression and/or activity of at least one protein or enzyme that catabolize NR, modify NR or transport NR into the cells’ cytoplasm. According to certain embodiments, the ascomycetous filamentous fungus comprises at least one cell having reduced or abolished expression and/or activity at least two, at least three or at least four proteins or enzymes that catabolize NR, modify NR or transport NR into the cells’ cytoplasm.

According to some embodiments, the ascomycetous filamentous fungus comprises at least two exogenous polynucleotides encoding for an enzyme selected from the group consisting of BNA6, NMAl, QNS1, ISN1, and SDT1, said fungus comprises at least one cell having reduced or abolished expression and/or activity of at least two proteins or enzymes that catabolize NR, modify NR or transport NR into the cells’ cytoplasm. According to some embodiments, the ascomycetous filamentous fungus comprises at least three exogenous polynucleotides encoding for an enzyme selected from the group consisting of BNA6, NMAl, QNS1, ISN1, and SDT1, said fungus comprises at least one cell having reduced or abolished expression and/or activity of at least three proteins or enzymes that catabolize NR, modify NR or transport NR into the cells’ cytoplasm.

According to some embodiments, the ascomycetous filamentous fungus comprises at least one exogenous polynucleotide, the polynucleotide encoding for SDT1, said fungus comprises at least one cell having reduced or abolished expression and/or activity of NRK1. According to additional embodiments, the ascomycetous filamentous fungus comprises at least one exogenous polynucleotide, the polynucleotide encoding for BNA6, said fungus comprises at least one cell having reduced or abolished expression and/or activity of NRT1. According to exemplary embodiments, the ascomycetous filamentous fungus comprises at least two exogenous polynucleotides, the polynucleotides encoding for STD1 and BNA6, said fungus comprises at least one cell having reduced or abolished expression and/or activity of NRK1 and NRT1. According to some embodiments, the genetically modified filamentous fungus comprises at least one cell comprising at least one exogenous polynucleotide encoding for BNA6. According to some embodiments, the genetically modified filamentous fungus comprises at least one cell comprising at least one exogenous polynucleotide encoding for NMA1. According to some embodiments, the genetically modified filamentous fungus comprises at least one cell comprising at least one exogenous polynucleotide encoding for QNS1. According to some embodiments, the genetically modified filamentous fungus comprises at least one cell comprising at least one exogenous polynucleotide encoding for ISN1. According to some embodiments, the genetically modified filamentous fungus comprises at least one cell comprising at least one exogenous polynucleotide encoding for SDT1.

According to some embodiments, the genetically modified filamentous fungus does not express NRK1. According to some embodiments, the genetically modified filamentous fungus does not express URH1. According to some embodiments, the genetically modified filamentous fungus does not express PNP1. According to some embodiments, the genetically modified filamentous fungus does not express NRT1.

According to specific embodiments, the ascomycetous filamentous fungus comprises at least one cell comprising three exogenous polynucleotides encoding for SDT1, BNA6, and NMA1, said fungus comprises at least one cell having reduced or abolished expression and/or activity of NRK1, NRT1 and PNP1.

According to an aspect of the present invention there is provided a genetically modified ascomycetous filamentous fungus for producing nicotinamide riboside, wherein the genetically modified filamentous fungus comprises at least one cell comprising exogenous polynucleotides encoding for BNA6, NMA1, QNS1, ISN1, and SDT1; said genetically modified ascomycetous filamentous fungus do not express or express reduced amount of NRK1, URH1, PNP1, and NRT1.

The bna6 gene encodes for Nicotinate-nucleotide pyrophosphorylase (BNA6 protein), catalyzing the reaction: CO ₂ + diphosphate + nicotinate α-D-ribonucleotide = 5- phospho-α-D-ribose 1 -diphosphate + 2 H ⁺ + quinolinate. The Thermothelomyces heterothallica BNA6 amino acid sequence is set forth in SEQ ID NO: 1 (AE054644.1). The genomic nucleotide sequence set forth in SEQ ID NO: 2 (MYCTH 2297423). According to certain embodiments, the mRNA coding sequence is set forth in SEQ ID NO: 16.

According to some embodiments, the BNA6 comprises an amino acid sequence having at least 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 1.

According to some embodiments, BNA6 is encoded by a nucleic acid sequence having at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% identity to SEQ ID NO: 16.

The nmal gene encodes for Nicotinamide Mononucleotide Adenylyltransferase (NMA1 protein), catalyzes the transfer of the adenylyl moiety of ATP to nicotinamide mononucleotide to form NAD, involved in pathways of NAD biosynthesis, including the de novo, NAD(+) salvage, and nicotinamide riboside salvage pathways. The human homolog of nmal is nmnat. Yeast nmal has a paralog, nma2 , that arose from the whole genome duplication. The Thermothelomyces heterothallica NMA1 amino acid sequence is set forth in SEQ ID NO. 3 (AE058772.1). The genomic nucleotide sequence is set forth in SEQ ID NO: 4 (MYCTH 2306323). According to certain embodiments, the mRNA coding sequence is set forth in SEQ ID NO: 17.

According to some embodiments, the NMA1 protein comprises an amino acid sequence having at least 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 3.

According to some embodiments, NMA1 is encoded by a nucleic acid sequence having at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% identity to SEQ ID NO: 17.

The qnsl gene encodes for glutamine (Q) dependent Nad+ Synthetase (QNS1 protein), which is essential for the formation of NAD(+) from nicotinic acid adenine dinucleotide. The Thermothelomyces heterothallica QNS1 amino acid sequence is set forth in SEQ ID NO: 5 (AE056119.1). The genomic nucleotide sequence is set forth in SEQ ID NO: 6 (MYCTH 79619). According to certain embodiments, the mRNA coding sequence is set forth in SEQ ID NO: 18.

According to some embodiments, the QNS1 protein comprises an amino acid sequence having at least 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 5.

According to some embodiments, QNS1 is encoded by a nucleic acid sequence having at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% identity to SEQ ID NO: 18.

The isnl gene encodes for Inosine 5'-monophosphate (IMP)-specific 5'- nucleotidase (ISN1 protein), which catalyzes the breakdown of IMP to inosine. The ISN1 is responsible for production of nicotinamide riboside. The Thermothelomyces heterothallica ISN1 amino acid sequence is set forth in SEQ ID NO: 7 (AE054982.1). The Genomic nucleotide sequence is set forth in SEQ ID NO: 8 (MYCTH 2137468). According to certain embodiments, the mRNA coding sequence is set forth in SEQ ID NO: 19.

According to some embodiments, the ISN1 comprises an amino acid sequence having at least 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 7.

According to some embodiments, ISN1 is encoded by a nucleic acid sequence having at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% identity to SEQ ID NO: 19.

The sdtl gene encodes for Pyrimidine nucleotidase (SDT1 protein) and responsible for production of nicotinamide riboside. The Thermothelomyces heterothallica SDT1 amino acid sequence is set forth in SEQ ID NO: 9 (AE055395.1). The genomic nucleotide sequence is set forth in SEQ ID NO: 10 (MYCTH 2050929). According to certain embodiments, the mRNA coding sequence is set forth in SEQ ID NO: 20.

According to some embodiments, the SDT1 comprises an amino acid sequence having at least 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 9.

According to some embodiments, SDT1 is encoded by a nucleic acid sequence having at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% identity to SEQ ID NO: 20.

The nrkl gene encodes for Nicotinamide Riboside Kinase 1 (NRK1 protein). It catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). The Thermothelomyces heterothallica sdtl nucleotide sequence (MYCTH 2311889) including 1 kb flanks is set forth in SEQ ID NO: 11.

The urhl gene encodes for Uridine nucleosidase (URH1 protein). It cleaves N- glycosidic bonds in nucleosides and involved in the nicotinamide riboside salvage pathway. The Thermothelomyces heterothallica urhl nucleotide sequence (MYCTH 2295930) including 1 kb flanks is set forth in SEQ ID NO: 12.

The pnpl gene encodes for Purine nucleoside phosphorylase (PNP1 protein). It specifically metabolizes inosine and guanosine nucleosides and involved in the nicotinamide riboside salvage pathway. The Thermothelomyces heterothallica pnpl nucleotide sequence (MYCTH 2306426) including 1 kb flanks is set forth in SEQ ID NO: 13.

The term "transporter protein" as used herein refers to an enzyme capable of catalyzing the transport of nicotinamide riboside for importing nicotinamide riboside from the periplasm to the cytoplasm. The enzyme in S. cerevisiae is known as NRT1. The nrtl gene encodes for Nicotinamide Riboside Transporter (NRT1 protein). The Thermothelomyces heterothallica nrtl nucleotide sequence (MYCTH 2310258) including 1 kb flanks is set forth in SEQ ID NO: 14.

The present invention encompasses amino acid sequences that are substantially homologous to amino acids sequences based on any one of the sequences identified in this application. The terms “sequence identity” and “sequence homology” are considered synonymous in this specification.

There are many established algorithms available to align two amino acid sequences. Typically, one sequence acts as a reference sequence, to which test sequences may be compared. The sequence comparison algorithm calculates the percentage sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters. Alignment of amino acid sequences for comparison may be conducted, for example, by computer implemented algorithms (e.g. GAP, BESTFIT, FASTA or TFASTA), or BLAST and BLAST 2.0 algorithms.

In a comparison, the identity may exist over a region of the sequences that is at least 10 amino acid residues in length (e.g. at least 15, 20, 30, 40, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650 or 685 amino acid residues in length, e.g. up to the entire length of the reference sequence). Each possibility represents a separate embodiment of the invention.

The term "exogenous” as used herein refers to a polynucleotide which is not naturally expressed within the fungus (e.g., heterologous polynucleotide from a different species) or to an endogenous nucleic acid of which overexpression in the fungus is desired. The exogenous polynucleotide may be introduced into the fungus in a stable or transient manner, so as to produce a ribonucleic acid (RNA) molecule and/or a polypeptide molecule. The term “endogenous” as used herein refers to a polynucleotide or polypeptide which is naturally present and/or naturally expressed within a fungus, particularly Th. Heterothallica , e.g., the genetic modified fungus comprises an additional copy of the sequence.

The term “heterologous” as used herein includes a sequence that was inserted to the fungi and is not naturally found in the fungi.

The term “overexpression” as used herein refers to an elevated level of gene product (whether nucleic acid or protein), or any metabolite produced as a result of the catalytic activity of a certain overexpressed gene product or a combination of gene products as compared with the expression of the same in the parental strain.

The terms “DNA construct”, “expression vector”, "expression construct" and "expression cassette" are used to refer to an artificially assembled or isolated nucleic acid molecule which includes a nucleic acid sequence encoding a protein of interest and which is assembled such that the protein of interest is functionally expressed in a target host cell. An expression vector typically comprises appropriate regulatory sequences operably linked to the nucleic acid sequence encoding the protein of interest. An expression vector may further include a nucleic acid sequence encoding a selection marker.

The terms "polynucleotide", "nucleic acid sequence", and "nucleotide sequence" are used herein to refer to polymers of deoxyribonucleotides (DNA), ribonucleotides (RNA), and modified forms thereof in the form of a separate fragment or as a component of a larger construct. A nucleic acid sequence may be a coding sequence, i.e., a sequence that encodes for an end product in the cell, such as a protein. According to certain embodiments of the invention, the protein is an enzyme. According to certain exemplary embodiments, the encoded enzymes include, but are not limited to, BNA6, NMA1, QNS1, SDT1, and ISN1. A nucleic acid sequence may also be a regulatory sequence, such as, for example, a promoter, or a terminator.

The terms "protein" is used herein to refer to a polymer of amino acid residues. The term “protein” usually indicates an amino acid sequence consisting of more than 50 amino acid residues.

A sequence (such as, nucleic acid sequence and amino acid sequence) that is "homologous" to a reference sequence refers herein to percent identity between the sequences, where the percent identity is at least 70%, at least 75%, preferably at least 80%, at least 85%, at least 90%, at least 95%, at least 98% at least 99% or at least 99.5%. Each possibility represents a separate embodiment of the present invention. Homologous nucleic acid sequences include variations related to codon usage and degeneration of the genetic code.

Nucleic acid sequences encoding the polypeptides of the present invention may be optimized for expression. Examples of such sequence modifications include, but are not limited to, an altered G/C content to more closely approach that typically found in filamentous fungi.

The phrase "codon optimization" refers to the selection of appropriate DNA nucleotides for use within a structural gene or fragment thereof that approaches codon usage within the organism of interest, and/or to a process of modifying a nucleic acid sequence for enhanced expression in the host cells of interest by replacing at least one codon (e.g., one or more than about 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more codons) of the native sequence with codons that are more frequently or most frequently used in the genes of that host cell while maintaining the native amino acid sequence. Various species exhibit particular bias for certain codons of a particular amino acid. Codon bias (differences in codon usage between organisms) often correlates with the efficiency of translation of messenger RNA (mRNA), which is in turn believed to be dependent on, among other things, the properties of the codons being translated and the availability of particular transfer RNA (tRNA) molecules. The predominance of selected tRNAs in a cell is generally a reflection of the codons used most frequently in peptide synthesis. Accordingly, genes can be tailored for optimal gene expression in a given organism based on codon optimization. Therefore, an optimized gene or nucleic acid sequence refers to a gene in which the nucleotide sequence of a native or naturally occurring gene has been modified in order to utilize statistically-preferred or statistically-favored codons within the organism.

Sequence identity may be determined using a nucleotide/amino acid sequence comparison algorithm, as known in the art.

The term “coding sequence” is used herein to refer to a sequence of nucleotide starting with a start codon (ATG) containing any number of codons excluding stop codons, and a stop codon (TAA, TGA, TAA), which code for a functional polypeptide.

Any coding sequence, or amino acid sequence listed herein also encompasses truncated sequences, which are missing 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more codons or amino acids from any part of the sequence. Truncated versions of coding sequences or amino sequences can be identified using nucleotide/amino acid sequence comparison algorithm, as known in the art.

Any coding sequence, or amino acid sequence listed herein also encompasses fused sequences, which contain besides the coding sequence provided herein, or a truncation of that sequence as defined above, other sequences. The fused sequences can be sequences as disclosed herein and other sequences. Fused coding sequences or amino sequences can be identified using nucleotide/amino acid sequence comparison algorithm, as known in the art.

DNA sequences are assembled to expression cassettes, selection cassettes and further to DNA constructs and/or expression vectors by conventional molecular biological approaches utilizing restriction endonucleases and ligases, Gibson assembly or yeast recombination. Also, the above can be synthesized by DNA synthesis service providers. As known in the art, several different techniques can achieve the same result.

DNA sequences are assembled to expression cassettes joining a 5’ regulatory regions (promoters), a coding sequence and a 3’ regulatory regions (terminators) as described hereinbelow and as are known in the art. Any combination of these three sequences can form a functional expression cassette.

The list of terminators includes, but are not limited to that of Th. heterothallica genes encoding for uncharacterized protein G2QF75 (XP 003664349); polyubiquitin homologue (G2QHM8, XP 003664133); uncharacterized protein (G2QIA5, XP 003664731); beta-glucosidase (G2QD93, XP 003662704); elongation factor 1-alpha (G2Q129, XP_003660173); chitinase (G2QDD4, XP_003663544) phosphoglycerate kinase (PGK) (Uniprot G2QLD8), glyceraldehyde 3 -phosphate dehydrogenase (GPD) (G2QPQ8), phosphofructokinase (PFK) (G2Q605); or triose phosphate isomerase (TPI) (G2QBR0); actin (ACT) (G2Q7Q5); cbhl (GenBank AX284115) or b-glucosidase 1 bgll (XM 003662656). Exogenous terminators include that of Aspergillus nidulans gpdA terminator.

5’ regulatory regions (promoters) are practically defined as a stretch of up to 2000 base pairs preceding the start codon of the coding sequence of the gene they regulate, provided that the preceding region is non-coding.

3’ regulatory regions (terminators) are practically defined as a stretch of up to 300 base pairs downstream from the end codon of the coding sequence of the gene, provided that the subsequent region is non-coding.

DNA sequences are also assembled to selection marker cassettes, which are expression cassettes where the coding sequence codes for a gene that provides a selective advantage when present in a transformed strain. Such advantage can be utilization of a new carbon or nitrogen source, a resistance to a toxic substance, etc. More specifically, the selection marker used in the expression cassette of the present invention is amdS, which confers to the transformed fungi the ability to use acetamide as sole nitrogen source, where an Aspergillus nidulans gpdA promoter drives an Aspergillus nidulans amdS gene, and the transcription of which is terminated by its natural Aspergillus nidulans amdS terminator. Hygromycin resistance gene is also used as a selection marker.

DNA constructs used for targeted transformation are composed of (a) a suitable vector that allows the maintenance of the DNA construct in a particular host, (b) zero, one or more expression cassettes in any direction, (c) a selection marker cassette in any direction and (d) sequences that are identical to select stretches of the target genomic DNA (also called as targeting arms). These components are placed so, that the two targeting arms encompass any expression cassettes and the selection marker cassette, so that when homologous recombination happens between the targeting arms and the two identical regions in the genomic DNA, the sequence between the targeting arms of the DNA constructs gets inserted into the chromosome, and replaces the sequence originally present on the chromosome. Using this principle, genes can be knocked out from, or inserted into the genome. By placing a sequence downstream of the selection marker cassette, which is identical to the sequence just upstream of the selection marker cassette, it is possible to recycle the marker as known in the art.

The term "regulatory sequences" refer to DNA sequences which control the expression (transcription) of coding sequences, such as promoters, enhancers and terminators.

The term "promoter" is directed to a regulatory DNA sequence which controls or directs the transcription of another DNA sequence in vivo or in vitro. Usually, the promoter is located in the 5' region (that is, precedes, located upstream) of the transcribed sequence. Promoters may be derived in their entirety from a native source, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic nucleotide segments. Promoters can be constitutive (i.e. promoter activation is not regulated by an inducing agent and hence rate of transcription is constant), or inducible (i.e., promoter activation is regulated by an inducing agent or environmental condition). Promoters may also restrict transcription to a certain developmental stage or to a certain morphologically distinct part of the organism. In most cases the exact boundaries of regulatory sequences have not been completely defined, and in some cases, cannot be completely defined, and thus DNA sequences of some variation may have identical promoter activity.

The term "terminator" is directed to another regulatory DNA sequence which regulates transcription termination. A terminator sequence is operably linked to the 3' terminus of the nucleic acid sequence to be transcribed.

The terms "C1 promoter" and "C1 terminator" indicate promoter and terminator sequences suitable for use in C1, i.e., capable of directing gene expression in C1.

However, as known to the skilled artisan, the choice of promoters and terminators may not be critical, and similar results can be obtained with a variety of promoters and terminators providing similar or identical gene expression.

The term "operably linked" means that a selected nucleic acid sequence is in proximity with a regulatory element (promoter, enhancer and/or terminator) to allow the regulatory element to regulate expression of the selected nucleic acid sequence.

The present invention discloses the production of nicotinamide riboside using genetically modified strains of Th. heterothallica C1. As described hereinabove, filamentous fungi of other species sharing endogenous similar pathways of precursor production can be also used.

According to certain embodiments, the polynucleotides of the present invention are designed based on the amino acid sequence of the enzyme to be produced employing a codon usage of a filamentous fungus. According to certain embodiments, the filamentous fungus belongs to the group Pezizomycotina. According to some embodiments, the filamentous fungus belongs to a group selected from the group consisting of Sordariales, Hypocreales Onygenales, and Eurotiales including genera and species as described in the “definition” section hereinabove. According to certain exemplary embodiments, the fungus is Th. heterothallica. According to these embodiments, the polynucleotides of the present invention are polynucleotides identified in Th. heterothallica or homologs thereto. According to certain currently exemplary embodiments, the fungus is Th. heterothallica C1.

According to certain exemplary embodiments, the Th. heterothallica C1 strain is a derivative of strain UV18-25.

According to certain embodiments, the exogenous polynucleotide is endogenous to the fungus, particularly to Th. heterothallica C1. According to certain embodiments, the exogenous polynucleotide is heterologous to the fungus, particularly to Th. heterothallica C1.

The polynucleotides encoding each of the enzymes may form part of one or more DNA constructs and/or expression vectors. According to certain embodiments, each of the polynucleotide forms part of a separate DNA construct/vector. According to other embodiments, part or all the polynucleotides are present within the same DNA construct/expression vector. This means that genes may be introduced one by one, or several of them may also be introduced to the transformed fungi at one time.

The DNA constructs or expression vector or plurality of same each comprises regulatory elements controlling the transcription of the polynucleotides within the at least one fungus cell. The regulatory element can be a regulatory element endogenous to the fungus, particularly to Th. heterothallica C1 or exogenous to the fungus.

According to certain embodiments, the regulatory element is selected from the group consisting of a 5’ regulatory element (collectively referred to as promoter), and 3’ regulatory element (collectively referred to as terminator), even though these nucleotide sequences may contain additional regulatory elements not classified as promoter or terminator sequences in the strict sense.

According to certain embodiments, the DNA construct or expression vector comprises at least one promoter operably linked to at least one polynucleotide containing a coding sequence, operably linked to at least one terminator. According to certain embodiments, the promoter is endogenous promoter of the fungus, particularly to Th. heterothallica. According to additional or alternative embodiments, the promoter is heterologous to the fungus, particularly to Th. heterothallica. According to certain embodiments, the terminator is endogenous terminator of the fungus, particularly to Th. heterothallica. According to additional or alternative embodiments, the terminator is heterologous to the fungus, particularly to Th. heterothallica.

According to certain exemplary embodiments, the DNA constructs contain synthetic regulatory elements called as “synthetic expression system” (SES) essentially as described in International (PCT) Application Publication No. WO 2017/144777.

According to certain embodiments, the one or more polynucleotides is stably integrated into at least one chromosomal locus of the at least one cell of the genetically modified fungus. According to certain embodiments, the one or more polynucleotides is/are stably integrated into one or more defined sites on the fungal chromosomes. According to certain embodiments, the one or more polynucleotides is/are stably integrated into random sites of the chromosome. According to certain embodiments, the polynucleotides may be incorporated in targeted or random fashion as 1, 2, or more copies to 1, 2 or more chromosomal loci.

According to certain alternative embodiments, the one or more polynucleotides is transiently expressed using extrachromosomal expression vectors as is known to a person skilled in the art.

According to certain exemplary embodiments the Th. heterothallica ku70 homologous gene is knocked out by preferentially eliminating the full coding sequence of the ku70 gene as known in the art. The inactivation of the ku70 gene enhances the percentage of targeted transformations as known in the art.

According to certain embodiments, culturing of the genetically modified fungus in a suitable medium provides for synthesis of nicotinamide riboside product, and/or derivatives thereof in an increased amount compared to the amount produced in a corresponding unmodified fungus cultured under similar conditions.

According to certain embodiments, the corresponding unmodified fungus is of the same species of the genetically modified fungus. According to some embodiments, the corresponding fungus is isogenic to the genetically modified fungus.

According to certain exemplary embodiments, the present invention provides a genetically modified Th. heterothallica C1 fungus that enables producing nicotinamide riboside. According to these embodiments, such genetically modified Th. heterothallica Cl fungus comprises at least one cell comprising at least one polynucleotide selected from the group consisting of (i) an exogenous polynucleotide encoding Nicotinate- nucleotide pyrophosphorylase (BNA6); (ii) an exogenous polynucleotide encoding Nicotinamide Mononucleotide Adenylyltransferase (NMA1); (iii) an exogenous polynucleotide encoding glutamine (Q) dependent Nad ⁺ synthetase (QNS1); (iv) an exogenous polynucleotide encoding Inosine 5'-monophosphate (IMP)-specific 5'- nucleotidase (ISN1); and (v) an exogenous polynucleotide encoding pyrimidine nucleotidase (SDT1).

According to certain embodiments, a suitable medium for culturing the genetically modified fungi comprises a carbon source selected from the group consisting of glucose, sucrose, xylose, arabinose, galactose, fructose, lactose, cellobiose, and glycerol. According to some embodiments, the carbon source is provided from waste of ethanol production or other bioproduction from starch, sugar beet and sugar cane such as molasses comprising fermentable sugars, starch, lignocellulosic biomass comprising polymeric carbohydrates such as cellulose and hemicellulose.

According to certain currently exemplary embodiments, the fungus is Th. heterothallica C1. According to certain embodiments, the strain of Th. heterothallica C1 is selected from the group consisting of strain UV18-25, deposit No. VKM F-3631 D; strain NG7C-19, deposit No. VKM F-3633 D; and strain UV13-6, deposit no. VKM F- 3632 D. Additional strains that may be used are HC strain UV18-100f deposit No. CBS141147; HC strain UV18-100f deposit No. CBS141143; LC strain W1L#100I deposit No. CBS141153; and LC strain W1L#100I deposit No. CBS141149 and derivatives thereof. Each possibility represents a separate embodiment of the present invention.

According to another aspect, the present invention provides a method for producing a fungus capable of producing nicotinamide riboside, the method comprising transforming at least one cell of the fungus with at least one polynucleotide selected from the group consisting of (i) an exogenous polynucleotide encoding Nicotinate-nucleotide pyrophosphorylase (BNA6); (ii) an exogenous polynucleotide encoding Nicotinamide Mononucleotide Adenylyltransferase (NMA1); (iii) an exogenous polynucleotide encoding glutamine (Q) dependent Nad ⁺ synthetase (QNS1); (iv) an exogenous polynucleotide encoding Inosine 5 '-monophosphate (IMP)-specific 5 '-nucleotidase (ISN1); and (v) an exogenous polynucleotide encoding pyrimidine nucleotidase (SDT1).

According to some embodiments, the method further comprises deleting, inhibiting, or reducing the expression of an enzyme or protein selected from the group consisting of Nicotinamide riboside kinase 1 (NRK1), Uridine hydrolase 1 (URH1), Purine nucleoside phosphorylase (PNPl), and Nicotinamide riboside transporter 1 (NRT1).

The terms “reduced expression” or “inhibited expression” of a protein or enzyme as described herein are used herein interchangeably and include, but are not limited to, deleting or disrupting the gene that encodes for the protein or enzyme.

The terms “reduced activity” or “inhibited activity” of a protein or enzyme as described herein are used herein interchangeably and include, but are not limited to, posttranslational modifications resulting in reduced or abolished activity of the protein or enzyme.

According to certain embodiments, the genetically modified fungus produces nicotinamide riboside in an elevated amount compared to the amount produced by a corresponding fungus not transformed with the polynucleotides.

Any method as is known in the art for transforming filamentous fungi with at least one polynucleotide can be used according to the teachings of the present invention. The fungus and the polynucleotides are as described hereinabove.

According to yet another aspect, the present invention provides a method of producing nicotinamide riboside, the method comprising culturing the genetically modified fungus, particularly Th. heterothallica C1 fungi of the present invention in a suitable medium; and recovering the produced products.

According to certain embodiments, the medium comprises a carbon source selected from the group consisting of glucose, sucrose, xylose, arabinose, galactose, fructose, lactose, cellobiose, and glycerol. According to certain embodiments the carbon source is waste obtained from ethanol production or other bioproduction from starch, sugar beet and sugar cane such as molasses comprising fermentable sugars, starch, lignocellulosic biomass comprising polymeric carbohydrates such as cellulose and hemicellulose.

According to some embodiment, the nicotinamide ribose is purified from the fungi growth medium.

According to other embodiments, the nicotinamide riboside is extracted from the fungal mass. Any method as is known in the art for extracting metabolites from vegetative tissues can be used.

According to some embodiments, the genetically modified ascomycetous filamentous fungus produces nicotinamide ribose in an increased amount compared to the amount produced in a corresponding unmodified ascomycetous filamentous fungus cultured under similar conditions. According to certain embodiments, the genetically modified ascomycetous filamentous fungus is capable of producing at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 times more NR compared to its parent strain. Each possibility represents a separate embodiment of the invention. According to certain embodiments, the genetically modified ascomycetous filamentous fungus is capable of producing at least 10 times more NR compared to its parent strain.

According to some embodiments, the genetically modified ascomycetous filamentous fungus is capable of increasing the amount of secreted nicotinamide ribose in the growth medium by at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 compared to a non-genetically modified ascomycetous filamentous fungus. Each possibility represents a separate embodiment of the invention. According to some embodiments, the genetically modified ascomycetous filamentous fungus is capable of producing at least 10 mg NR /L growth medium. According to some embodiments, the genetically modified ascomycetous filamentous fungus is capable of producing at least 15 mg NR /L growth medium. According to certain embodiments, at least 70%, 80%, or 90% of the produced NR is secreted NR.

According to a further aspect, the present invention provides nicotinamide and/or precursors thereof produced by the genetically modified fungus, particularly the genetically modified Th. heterothallica C1 of the present invention. The following examples are presented in order to more fully illustrate some embodiments of the invention. They should, in no way be construed, however, as limiting the broad scope of the invention. One skilled in the art can readily devise many variations and modifications of the principles disclosed herein without departing from the scope of the invention.

EXAMPLES

Metabolite extraction protocols: Excreted metabolites

Remove -300 μl aliquot from the cultivation, remove cells by centrifugation and take the supernatant for analysis. Store at +4°C up to one day, or at -80°C for longer periods. Intracellular metabolites

Divide 50% methanol containing 13C-NAM as an internal standard in 5 ml aliquots and cool down to -80°C.

Filter a 3-5 ml aliquot of cell culture through a nylon membrane filter (Whatman, 0.45 pm pore size, 7404-004). Wash 3 x 5 ml DDIW.

Scrape the cells from the membrane, transfer into cold 50% methanol and incubate at -80°C for 1 h.

Vortex and centrifuge at 7800 rpm in 15 ml Greiner tubes for 10 min to remove cell debris. Take 4 ml supernatant for analysis. Store at -80°C up to 1 week.

Extra- and intracellular metabolites

Divide methanol - DDIW (2.5 : 1.5) solution containing 13C-NAM as an internal standard in 4 ml aliquots into 15 ml greiner tubes and cool down to -80°C.

Transfer 1 ml of cell culture into 4ml cold methanol-DDIW (final concentration 50% methanol) and vortex. Incubate at -80°C for 1 h.

Vortex and centrifuge at 7800 rpm in 15 ml Greiner tubes for 10 min to remove cell debris. Take 4 ml supernatant for analysis. Store at -80 °C up to 1 week.

Example 1: Identification of NR biosynthetic genes in Thermothelomyces heterothallica C1 genome

The genes to be deleted or over-expressed in the NR pathway in C1 were identified from Cl genome based on homology to the corresponding genes in Saccharomyces cerevisiae. S. cerevisiae pathway related to NR and other NAD metabolites is described e.g. in Evans et al. (2010, BMC Chem Biol 10:2). The closest homologues of the S. cerevisiae BNA6, QNS1, ISN1, URH1, NRK1, NMA1, NMA2, SDT1, PNP1 and NRT1 were identified in C1 using a bidirectional blast search. The S. cerevisiae protein and genome sequence data used in the search was obtained from SGD database, and in- house/Dyadic genome data was used for C1. A blast search of the amino acid sequences corresponding to the S. cerevisiae bna6, qnsl , isnl , urhl, and nrkl genes showed a single homologue for each of the genes/proteins in the translated genome sequence of C1. This was confirmed by a blast search of the detected C1 counterpart sequences against the S. cerevisiae proteome sequence, which gave the original yeast query sequences as the best hits in the search. The blast search of the amino acid sequences corresponding to NMA1 and NMA2 gave the same protein in C1 as the best hit. The result is expected since nma2 is a duplication of the nmal gene in S. cerevisiae genome. When S. cerevisiae sdtH Sdtlp sequence was blasted against the translated C1 genome, homology to a single protein was detected. When the sequence of the homologue was used as query in a blast search against S. cerevisiae proteome, homology to two proteins, Sdtlp and Phm8p (genes sdtl and pmh8) were detected. Homology of the C1 protein to Sdtlp was slightly higher than to Pmh8p. pmh8 gene is a paralog of sdtl gene as a result of a gene duplication in S. cerevisiae genome. Similarly, when the amino acid sequence corresponding to S. cerevisiae Pnplp was blasted against the translated C1 genome, a single homologue in C1 was found. When this C1 sequence was blasted back against S. cerevisiae proteome, Meulp and Pnplp ( meul and pnpl genes) were found as the best homologues. The homology to Meulp was higher than that to Pnplp. meul gene encodes an enzyme that degrades NR in the same manner as pnpl. When the closest homologue of S. cerevisiae nrtl in C1, was blasted back against S. cerevisiae proteome, three proteins Dal4p, Fur4p and Fuilp (genes dal4,fur4,fuil) were detected to have a higher homology to the C1 protein as compared to the Nrtlp. When S. cerevisiae dal4, fur4 and fuil were blasted against C1 genome same gene was detected. These results may indicate that there is only one gene in C1 representing all these four S. cerevisiae genes.

Example 2: Engineering of Thermothelomyces heterothallica C1 for nicotinamide ribose production

To engineer the C1 to produce elevated amounts of nicotinamide ribose selected enzymatic steps of the native NR biosynthetic pathway were enhanced and genes responsible for NR catabolism or uptake of excreted NR were knocked out. The engineering included several consecutive steps aiming at a strain, which has four deletions in genes encoding enzymes responsible for NR utilization (NRK1, PNPl, URH1) or transport of excreted NR (NRT1) back into the cells, and additional copies of five genes encoding enzymes for conversion of quinolinate intermediate to NR (SDT1, BNA6, NMA1, QNS1, ISN1) (see Fig.1). A synthetic expression system (SES) to strengthen enzyme activities specific for NR biosynthesis was used. Two different C1 strains, a high cellulase strain M1889 and a low cellulase strain M1892, were used as the transformation hosts. Identical procedures were used to engineer the two hosts. Plasmids used for C1 engineering are described in Table 1 and Fig. 2. Hygromycin resistance, pyr5, amdS and nial markers were used in transformations. C1 protoplasts were transformed using linearized plasmids and transformed colonies were selected on agar plates containing acetamide, sodium nitrate or hygromycin as the selective agent as appropriate. The presence of transformed DNA in the target loci was analyzed by PCR using three sets of primers specific for 5’ end, 3’ end, or the deleted region. Initially four transformation lines were carried out simultaneously with both host strains. Sequential transformations were carried out to construct the basic NR producing strain. The strains constructed are listed in Table 2.

Table 1. List of plasmids

* pChD002 and pChD003 split marker Table 2. Engineered Cl strains

The effects of the genetic modifications on the production of NR were assessed by quantification of NR and selected metabolic pathway intermediates by analyzing samples of cells and cell culture medium. Example 3: Analysis of NAD ⁺ metabolome

A quantitative UPLC-MS/MS method for analysis of NR and 10 other intermediates from extra- and intracellular Cl samples was set up. The method is based on an article by Evans et al. (BMC Chemical Biology 2010 10:2).

All extracellular samples were reconstituted in 50% mobile phase B (20 mM ammonium acetate in 80% acetonitrile, pH 9.9) before analysis. Intracellular samples were analyzed directly after extraction. The appropriate dilutions of the samples were done when necessary.

Analysis was performed on an Acquity UHPLC system, Waters (Milford, MA, USA) and Waters Xevo TQ-S MS (Manchester, UK) using an ACQUITY UPLC BEH Amide Column, 130 A, 1.7 pm, 2.1 mm X 100 mm (Waters), kept at 30 °C. Injection volume was 2 pi. Separation was performed using gradient elution with 50 mM ammonium acetate in water, pH 9.9 (A) and 20 mM ammonium acetate in 80% acetonitrile, pH 9.9 (B) at a flow rate of 0.5 ml/min. Gradient program was following: 0 min 80 % B, 3.0 min 65 % B, 3.1 min 80 % B and equilibrium time between runs was 2.0 min.

Mass spectrometry was performed in positive polarity using the capillary voltage of 1,3 kV. Desolvation temperature was 500 °C, and source temperature was 150 °C. The cone gas flow was 150 1/h (nitrogen), desolvation gas was 1000 1/h (nitrogen), and collision gas was 0.15 ml/min. Analytes were detected using multiple reaction monitoring (MRM) using auto dwell time function. Analytes were quantified by internal standard method. Nicotinamide- 13 C6 (Sigma-Aldrich) was used as internal standard. For other details of the method, see Table 3. The targeted UPLC-MS/MS method for NAD ⁺ metabolites analysis, including the sample preparation protocols, was successfully set up and used for analysis.

Table 3. Precursor and product ions used for MRM, retention times, cone voltage and collision energy used for the analyzed compounds and the internal standards. Linearity, recovery, limit of detection (LOD) and limit of quantitation (LOQ) were determined. The calibration curves showed good linearity in the studied range from 0.002 μg/ml to 10 μg/ml with correlation coefficient R ² greater than 0.99. The recoveries were good (> 92 %) for all studied compounds with the exception of NADH which recovery was 73.5%. Limit of detection (LOD) of the method was determined as lowest concentration of the spiked components that could be reliable differentiated from the background level (S/N >3), the limits of quantitation (LOQ) were determined as ratio S/N >10. All results are summarized in Table 4.

The stability of the metabolites was studied at 4°C in cell culture medium. The spiked samples were analyzed on day 1, day 3 and day 7 (data not shown). Most of the compounds were stable for three days. The most notable exception was NADH, which did not give reliable results due to the poor stability.

Table 4. Linearity, recovery, limit of detection and limit of quantitation of the method.

Example 4: NR production by the engineered strains Production of NR and related metabolites in 24-well plate cultivations

For determination of NR production, the different strains were grown in 3.5 ml liquid production medium in 24-well plates at 35°C for three days with 800 rpm in a humidity-controlled shaker. NR and related metabolites were quantified from samples containing cell culture medium, cells harvested by filtration, or cells and culture medium together. Metabolites were released from cells using hot ethanol or cold methanol. The latter method appeared more suitable since some of the metabolites are unstable at high temperatures (data not shown). There were clear differences between excreted and intracellular metabolites (Figures 3A-3C).

Small amounts of NR were detected in the non-modified parental strains M1889 and M1892. NR, NA and NAR were predominately excreted into the culture medium (Fig. 3 A). Engineered strains (mChDx) produced increased amounts of NR. NAD is the predominant intracellular compound (Fig. 3B). Samples containing a combination of culture medium and cells show all the metabolites (Fig. 3C). NR measurement from culture medium appears convenient and sufficient for comparing different strains for their ability to produce the desired compound. However, the consequences of the genetic modifications are not fully revealed by analyzing extracellular metabolites only, since many of the NR precursors are not excreted into the culture medium. Therefore, quantification of both extra- and intracellular compounds provides additional understanding of the NR pathway activities of the modified strains.

Fig. 4. illustrates the NR-related metabolites in a comprehensive set of modified strains. A major improvement of NR production was observed in mChD042-strains and mChD045-strains in which the pnpl gene was deleted along with NMA1 overexpression (Fig. 4B and 4D). The M1889-derived strains produced more NR than the M1892 derived strains. The mChD042-strains excreted clearly more NR, NAD, NMN than their predecessors. In contrast, the mChD044- and mChD047-strains in which the urhl gene was deleted along with the QNS1 and ISN1 overexpression, increased amounts of NA and NAR were produced (Fig. 4A and 4C), while NR production was not increased (Fig. 4B and 4D).

The strains mChD071 and mChD073 containing all the planned modifications, deletion of nrkl, pnpl, urhl and nrtl genes and overexpressing SDT1, BNA6, NMA1, QNS1 and ISN1, were analyzed for excreted NR related metabolites along with their predecessors mChD042, mChD044, mChD045 and mChD047, which lacked the final modifications (Fig. 5). The corresponding modifications in NR biosynthetic pathway are shown in Fig. 6. The M1889 derived strain mChD071 produced more NR and less NAR, a by-product, than any other strain including the previous best strain mChD042-3-1. M1889-derived strains mChD083 and mChD084 contain the same pathway modifications as mChD071 as verified by PCR, but they have different markers (see table 2). Deletion of the pnpl gene rather than NMA1 overexpression was crucial for increasing NR production and decreasing NA production. mChD044-1 was transformed with pChD004 in order to delete pnpl. The resulted colonies also included colonies in which pnpl was intact. In these colonies the concentrations of excreted metabolites resembled that of mChD044-1 (Fig. 5 and data not shown).

Example 5: Automated cultivations and production of NR in 96-well plates

The suitability of a Screening Robot system for this invention was tested. The system, which is a custom set-up by Beckman-Coulter, is able to handle several 96-well format deep-well plates simultaneously. Inoculation, cultivation, centrifugation, supernatant removal and sample storage at +4°C can be all automatically performed. Also, an automated colony picking from Petri dishes to 96-well format prior screening enhances the screening efficiency. This all allows a throughput of more than a thousand mutants per week.

The screening test was performed for four strains. Transformation host strain M1889 (high cellulose strain) and its daughter strain mChD001 (Δnrk1 :SDT1, pyr5), and the transformation host strain M1892 (low cellulose strain) and its daughter strain mChD004 ( Δnrk1 ;SDT1,pyr5) were used. The main goals were to test whether all of the steps work technically with Cl and that NR production improvement is detectable in mother-daughter strains when doing all of the work with robot.

The screening was done as described herein. Colonies were picked from Petri dishes to agar-filled 96-well format plates with a Qpix colony picker and incubated at +35°C. After visible colonies were formed, the wells were washed with a washing buffer, which rinsed off the formed spores from the mycelium. The resulting spore suspension was then used to inoculate 1 mL of production medium (20 or 5 g/L of glucose) in 96-well format deep-well plates. Next, three incubation temperature strategies were tested in order to assess the required time and temperature for optimal screening results. Incubation at +20°C for 3 days did not result in spore germination and growth. Incubation at +35°C for 4 days resulted in spore germination, growth and NR production (up to 0.6 mg/L with mChD001 at 72h; see Fig. 7). A combination of these two incubation temperatures (growth phase of 2 days at +35°C followed by a production phase of 6 days at +20°C) resulted in spore germination, growth and NR production (up to 1.3 mg/L with mChD001 at 192h; see Fig. 8). After the incubation, cells were centrifuged down and supernatant was collected. It was either stored at +4°C and analyzed the following night, or stored at -20°C for 1-3 days, thawed and analyzed for NR and other metabolites.

Although the decreased incubation temperature in the production phase resulted in higher NR production, it did not change the screening result itself. Modified daughter strains produced more NR than the mother strains, and the strain order based on NR production stayed the same between and during the different incubation strategies. These results show that by utilizing a Screening Robot set-up one is able to choose the best producers for upscale tests and for further modifications.

Example 6: NR production of fungi grown in biolector

Biolector Pro by m2p-labs is a microbioreactor device. It hosts one 48-well format flower-shaped-deep-well plate at a time in a humid, shaken, temperature-controlled and oxygen-rich environment. Each of the wells can be monitored for several cultivation parameters through optical chemical sensors or clear well bottom. This enables the online measurement of, for example, dissolved oxygen, pH, biomass and riboflavin or other fluorescent compounds. One proof-of-concept Biolector Pro cultivation was conducted in order to assess its usability for screening. Biolector Pro can be used as an additional step between the Screening Robot and actual bench-top bioreactors.

Biolector Pro was tested for the following strains. Transformation host strain M1889 (high cellulose strain) and its daughter strains mChD001 ( Δnrk1 ;SDT1,pyr5), mChD037-8-B (Δnrk1 :SDT1, Δnrt1 ;BNA6, amdS, Δnial), mChD042-3-1 (Δnrk1 : SDT1, Anrt 1 ;BNA6, Apnpl :NMA1, Nial, HygR, amdS), mChD044-31 (Δnrk1 :SDT1, Δnrt1 ;BNA6, Δurh 1 :ISN1, QNS1, HygR, amdS, Anial) and mChD079 (Δnrk1 :SDT1, Anrt 1 ;BNA6, Apnpl :NMA 7, Nial, HygR). Transformation host strain M1892 (low cellulose strain) and its daughter strains mChD004 ( Δnrk1 ;SDT1,pyr5), mChD041-16-b- 2 (Δnrk1 :SD Tl, Δnrt1 ;BNA6, amdS, Anial), mChD045-7-3 (Δnrk1 :SDT1, Anrt 1 ;BNA6, Apnpl :NMA1, Nial, HygR, amdS), mChD047-1-1 (Δnrk1 :SDT1, Δnrt1 ;BNA6, Aurh 1 :ISN1, QNS1, HygR, amdS, Anial) and mChD082 (Δnrk1 :SDT1 , Anrt 1 ;BNA6, Apnpl :NMA1, Nial, HygR).

Each of the twelve strains were cultivated in four parallels in 1 mL of production medium at +35°C, 800 rpm and head-space oxygen 35% for 72 hours. Half of the samples were removed at 48 hours. Biomass and riboflavin were measured online at 10-minute intervals and samples (48 and 72h) were analyzed for NR and other metabolites both from the supernatant and by cold-methanol extraction (cells + supernatant analysis).

Figure 9 shows the amount of NR normalized to biomass at 48 and 72h. M1889- family strains produced more NR and a clear production improvement trend can be seen between mother and great-granddaughter strains. By normalizing the NR production to biomass, it is evident that a unit of modified cells produce more NR. Amount of up to 3.5 mg/L (strain mChD042-3-1) of NR was present in the supernatant at 72h. Biolector Pro suits for screening C1 strains and it gives a great benefit of online biomass detection although its throughput is not as high as Screening Robot’s.

Example 7: NR production bioreactor cultivation

To optimize and evaluate the NR producing strains in bioreactors, strain mChD42- 3-1 (Δnrk1:SDT1 Δnrt :BNA6 Δpnp 1 :NMA1) was cultivated in a 1 L bioreactor using conditions that are typical C1 protein production conditions.

The inoculum grew in shake flasks more slowly than expected and therefore the initial biomass in bioreactor was relatively low at the early stages of the cultivation. The cultivation temperature was 38°C and pH 6.8. The culture was grown in batch mode for the first 24 hours, where after glucose, mineral salts and vitamins were fed into the reactor.

Samples were collected for the determination of biomass, secreted proteins and NR- related metabolites at 23, 47, 71, 95 and 165 h.

Excreted NR concentration was 15 mg/L, and total NR concentration was 22 mg/L at the end of the cultivation 165 h. The culture parameters are as follows:

• Batch phase: 1 L reactor (Q) - initial volume 800 ml;

• T = 38°C;

• pH = 6.8; pH control = NH ₄ OH (12.5%);

• aeration = 0.6 slpm;

• Agitation = 500-1250 rpm - cascade control;

• Dissolved oxygen tension - >30% during first 8 h, then >25% cascade control needed - adjust manually;

• Antifoam = J647 - manual addition ca. 6 ml, 1 ml each evening • Feed: 503 g/L glucose containing 1x mineral salts for feeding, plus biotin and thiamine

Biomass and secreted protein concentrations at 165 h were 15 g/L and 17 g/L, respectively (Figure 10A). NR concentration increased throughout the cultivation and it was the most abundant NR-related metabolite found in the culture medium from 71 h onwards (Figure 10A-10B). In comparison, NAD was the most abundant metabolite inside the cells (Figure 10C). NAD and NMN are the two immediate precursors of NR biosynthesis. Based on this fact it is contemplated that a significant proportion of NAD and NMN may be converted to NR if strain development is continued.

The foregoing description of the specific embodiments will so fully reveal the general nature of the invention that others can, by applying current knowledge, readily modify and/or adapt for various applications such specific embodiments without undue experimentation and without departing from the generic concept, and, therefore, such adaptations and modifications should and are intended to be comprehended within the meaning and range of equivalents of the disclosed embodiments. It is to be understood that the phraseology or terminology employed herein is for the purpose of description and not of limitation. The means, materials, and steps for carrying out various disclosed functions may take a variety of alternative forms without departing from the invention.