Lysine biosynthesis and metabolism in fungi

To overview the gene content of the important pathogen Phytophthora infestans, large-scale cDNA and genomic sequencing was performed. A set of 75,757 high-quality expressed sequence tags (ESTs) from P. infestans was obtained from 20 cDNA libraries representing a broad range of growth conditions, stress responses, and developmental stages. These included libraries from P. infestans-potato and -tomato interactions, from which 963 pathogen ESTs were identified. To complement the ESTs, onefold coverage of the P. infestans genome was obtained and regions of coding potential identified. A unigene set of 18,256 sequences was derived from the EST and genomic data and characterized for potential functions, stage-specific patterns of expression, and codon bias. Cluster analysis of ESTs revealed major differences between the expressed gene content of mycelial and spore-related stages, and affinities between some growth conditions. Comparisons with databases of fungal pathogenicity genes revealed conserved elements of pathogenicity, such as class III pectate lyases, despite the considerable evolutionary distance between oomycetes and fungi. Thirty-seven genes encoding components of flagella also were identified. Several genes not anticipated to occur in oomycetes were detected, including chitin synthases, phosphagen kinases, and a bacterial-type FtsZ cell-division protein. The sequence data described are available in a searchable public database.

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“…Although true fungi synthesize lysine using the α-aminoadipate (AAA) pathway (Zabriskie and Jackson 2000), oomycetes use the diamino- Fig. 3.…”

Section: Lysine Biosynthetic Pathwaysmentioning

confidence: 99%

Large-Scale Gene Discovery in the Oomycete Phytophthora infestans Reveals Likely Components of Phytopathogenicity Shared with True Fungi

Randall¹,

Dwyer²,

Huitema³

et al. 2005

MPMI

164

134

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“…The S. cerevisiae enzyme has pH optima of 10.0 in the direction of lysine formation, and 7.0 in the direction of saccharopine formation (2). The pH dependence of V/K Lys is bell shaped giving pK a values of 6.3 and 8.0, while the V/K α-Kg profile exhibits a single pK a of 8.4 on the basic side (6).…”

mentioning

confidence: 99%

A Proposed Proton Shuttle Mechanism for Saccharopine Dehydrogenase from Saccharomyces cerevisiae

Alguindigue

West

et al. 2006

Biochemistry

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Saccharopine dehydrogenase (N6-(glutaryl-2)-L-lysine: NAD oxidoreductase (L-lysine forming)) catalyzes the final step in the α-aminoadipate pathway for lysine biosynthesis. It catalyzes the reversible pyridine nucleotide-dependent oxidative deamination of saccharopine to generate α-Kg and lysine using NAD + as an oxidizing agent. Proton shuttle chemical mechanism is proposed on the basis of the pH dependence of kinetic parameters, dissociation constants for competitive inhibitors, and isotope effects. In the direction of lysine formation, once NAD and saccharopine bind, a group with a pK a of 6.2 accepts a proton from the secondary amine of saccharopine as it is oxidized. This protonated general base then does not participate in the reaction again until lysine is formed at the completion of the reaction. A general base with a pK a of 7.2 accepts a proton from H 2 O as it attacks the Schiff base carbon of saccharopine to form the carbinolamine intermediate. The same residue then serves as a general acid and donates a proton to the carbinolamine nitrogen to give the protonated carbinolamine. Collapse of carbinolamine is then facilitated by the same group accepting a proton from the carbinolamine hydroxyl to generate α-Kg and lysine. The amine nitrogen is then protonated by the group that originally accepted a proton from the secondary amine of saccharopine, and products are released. In the reverse reaction direction, finite primary deuterium kinetic isotope effects were observed for all parameters with the exception of V 2 /K NADH , consistent with a steady state random mechanism, and indicative of a contribution from hydride transfer to rate limitation. The pH dependence, as determined from the primary isotope effect of D V 2 and D (V 2 /K Lys ), suggests that a step other than hydride transfer becomes rate-limiting as the pH is increased. This step is likely protonation/deprotonation of the carbinolamine nitrogen formed as an intermediate in imine hydrolysis. The observed solvent isotope effect indicates proton transfer also contributes to rate limitation. A concerted proton and hydride transfer is suggested by multiple substrate/solvent isotope effect, as well as a proton transfer in another step, likely hydrolysis of the carbinolamine. In agreement, dome-shaped proton inventories are observed for V 2 and V 2 /K Lys suggesting proton transfer exists in at least two sequential transition states.Saccharopine dehydrogenase (N6-(glutaryl-2)-L-lysine: NAD oxidoreductase (L-lysine forming); (EC 1.5.1.7)) (SDH 1 ) catalyzes the final step in the α-aminoadipate pathway (AAA) for the de novo synthesis of L-lysine in fungi (1,2). The enzyme catalyzes the reversible † This work is supported by the Grayce B. Kerr Endowment to the University of Oklahoma (to P.F.C.), and a grant (GM 071417) from the National Institute of Health (to P.F.C. and A.H.W.). * Corresponding author: E-mail: pcook@chemdept.chem.ou.edu 1 Abbreviations: SDH, saccharopine dehydrogenase; AAA, α-aminoadipate pathway; α-Kg, α-ketoglutarate; Sacc,...

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“…Some organisms such as bacteria and plants use the so-called diaminopimelic acid pathway for biosynthesis of this amino acid. However, other organisms including filamentous fungi, yeast, some Euglena species (Bhattacharjee, 1985) and the bacteria Thermus thermophilus and Pyrococcus horikoshii (Kosuge & Hoshino, 1998;Kobashi et al, 1999;Jia et al, 2006) use the so-called a-aminoadipate pathway (Zabriskie & Jackson, 2000;Xu et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Transcriptional upregulation of four genes of the lysine biosynthetic pathway by homocitrate accumulation in Penicillium chrysogenum: homocitrate as a sensor of lysine-pathway distress

et al. 2009

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The lysine biosynthetic pathway has to supply large amounts of α-aminoadipic acid for penicillin biosynthesis in Penicillium chrysogenum. In this study, we have characterized the P. chrysogenum L2 mutant, a lysine auxotroph that shows highly increased expression of several lysine biosynthesis genes (lys1, lys2, lys3, lys7). The L2 mutant was found to be deficient in homoaconitase activity since it was complemented by the Aspergillus nidulans lysF gene. We have cloned a gene (named lys3) that complements the L2 mutation by transformation with a P. chrysogenum genomic library, constructed in an autonomous replicating plasmid. The lys3-encoded protein showed high identity to homoaconitases. In addition, we cloned the mutant lys3 allele from the L2 strain that showed a G1534 to A1534 point mutation resulting in a Gly495 to Asp495 substitution. This mutation is located in a highly conserved region adjacent to two of the three cysteine residues that act as ligands to bind the iron–sulfur cluster required for homoaconitase activity. The L2 mutant accumulates homocitrate. Deletion of the lys1 gene (homocitrate synthase) in the L2 strain prevented homocitrate accumulation and reverted expression levels of the four lysine biosynthesis genes tested to those of the parental prototrophic strain. Homocitrate accumulation seems to act as a sensor of lysine-pathway distress, triggering overexpression of four of the lysine biosynthesis genes.

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Lysine biosynthesis and metabolism in fungi

Cited by 152 publications

References 130 publications

Large-Scale Gene Discovery in the Oomycete Phytophthora infestans Reveals Likely Components of Phytopathogenicity Shared with True Fungi

Large-Scale Gene Discovery in the Oomycete Phytophthora infestans Reveals Likely Components of Phytopathogenicity Shared with True Fungi

A Proposed Proton Shuttle Mechanism for Saccharopine Dehydrogenase from Saccharomyces cerevisiae

Transcriptional upregulation of four genes of the lysine biosynthetic pathway by homocitrate accumulation in Penicillium chrysogenum: homocitrate as a sensor of lysine-pathway distress

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