Molecular Evolution of Lysine Biosynthesis in Agaricomycetes

As an indispensable essential amino acid in the human body, lysine is extremely rich in edible mushrooms. The α-aminoadipic acid (AAA) pathway is regarded as the biosynthetic pathway of lysine in higher fungal species in Agaricomycetes. However, there is no deep understanding about the molecular evolutionary relationship between lysine biosynthesis and species in Agaricomycetes. Herein, we analyzed the molecular evolution of lysine biosynthesis in Agaricomycetes. The phylogenetic relationships of 93 species in 34 families and nine orders in Agaricomycetes were constructed with six sequences of LSU, SSU, ITS (5.8 S), RPB1, RPB2, and EF1-α datasets, and then the phylogeny of enzymes involved in the AAA pathway were analyzed, especially homocitrate synthase (HCS), α-aminoadipate reductase (AAR), and saccharopine dehydrogenase (SDH). We found that the evolution of the AAA pathway of lysine biosynthesis is consistent with the evolution of species at the order level in Agaricomycetes. The conservation of primary, secondary, predicted tertiary structures, and substrate-binding sites of the enzymes of HCS, AAR, and SDH further exhibited the evolutionary conservation of lysine biosynthesis in Agaricomycetes. Our results provide a better understanding of the evolutionary conservation of the AAA pathway of lysine biosynthesis in Agaricomycetes.

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Evaluation of Lysine Biosynthesis as an Antifungal Drug Target: Biochemical Characterization of Aspergillus fumigatus Homocitrate Synthase and Virulence Studies

Eukaryotic Cell ◽

10.1128/ec.00020-10 ◽

2010 ◽

Vol 9 (6) ◽

pp. 878-893 ◽

Cited By ~ 44

Author(s):

Felicitas Schöbel ◽

Ilse D. Jacobsen ◽

Matthias Brock

Keyword(s):

Invasive Aspergillosis ◽

Aspergillus Fumigatus ◽

Drug Target ◽

Biochemical Characterization ◽

Fungal Species ◽

Antifungal Drug ◽

Lysine Biosynthesis ◽

Murine Models ◽

Content Type ◽

Homocitrate Synthase

ABSTRACT Aspergillus fumigatus is the main cause of severe invasive aspergillosis. To combat this life-threatening infection, only limited numbers of antifungals are available. The fungal α-aminoadipate pathway, which is essential for lysine biosynthesis, has been suggested as a potential antifungal drug target. Here we reanalyzed the role of this pathway for establishment of invasive aspergillosis in murine models. We selected the first pathway-specific enzyme, homocitrate synthase (HcsA), for biochemical characterization and for study of its role in virulence. A. fumigatus HcsA was specific for the substrates acetyl-coenzyme A (acetyl-CoA) and α-ketoglutarate, and its activity was independent of any metal ions. In contrast to the case for other homocitrate synthases, enzymatic activity was hardly affected by lysine and gene expression increased under conditions of lysine supplementation. An hcsA deletion mutant was lysine auxotrophic and unable to germinate on unhydrolyzed proteins given as a sole nutrient source. However, the addition of partially purified A. fumigatus proteases restored growth, confirming the importance of free lysine to complement auxotrophy. In contrast to lysine-auxotrophic mutants from other fungal species, the mutant grew on blood and serum, indicating the existence of high-affinity lysine uptake systems. In agreement, although the virulence of the mutant was strongly attenuated in murine models of bronchopulmonary aspergillosis, virulence was partially restored by lysine supplementation via the drinking water. Additionally, in contrast to the case for attenuated pulmonary infections, the mutant retained full virulence when injected intravenously. Therefore, we concluded that inhibition of fungal lysine biosynthesis, at least for disseminating invasive aspergillosis, does not appear to provide a suitable target for new antifungals.

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α-Aminoadipate pool concentration and penicillin biosynthesis in strains of Penicillium chrysogenum

Canadian Journal of Microbiology ◽

10.1139/m86-087 ◽

1986 ◽

Vol 32 (6) ◽

pp. 473-480 ◽

Cited By ~ 40

Author(s):

W. M. Jaklitsch ◽

W. Hampel ◽

M. Röhr ◽

C. P. Kubicek ◽

G. Gamerith

Keyword(s):

Amino Acid ◽

Penicillium Chrysogenum ◽

Intracellular Concentration ◽

Lysine Biosynthesis ◽

Penicillin Biosynthesis ◽

Penicillin Production ◽

Saccharopine Dehydrogenase ◽

Two Factors ◽

Homocitrate Synthase ◽

Rate Limiting

Intracellular amino acid pools in four Penicillium chrysogenum strains, which differed in their ability to produce penicillin, were determined under conditions supporting growth without penicillin production and under conditions supporting penicillin production. A significant correlation between the rate of pencillin production and the intracellular concentration of α-aminoadipate was observed, which was not shown with any other amino acid in the pool. In replacement cultivation, penicillin production was stimulated by α-aminoadipate, but not by valine or cysteine. Exogenously added α-aminoadipate (2 or 3 mM) maximally stimulated penicillin synthesis in two strains of different productivity. Under these conditions intracellular concentrations of α-aminoadipate were comparable in the two strains in spite of the higher rate of penicillin production in the more productive strain. Results suggest that the lower penicillin titre of strain Q 176 is due to at least two factors: (i) the intracellular concentration of α-aminoadipate is insufficient to allow saturation of any enzyme which is rate limiting in the conversion of α-aminoadipate to penicillin and (ii) the level of an enzyme, which is rate limiting in the conversion of α-aminoadipate to penicillin, is lower in Q 176 (relative to strain D6/1014/A). Results suggest that the intracellular concentration of α-aminoadipate in strain D6/1014/A is sufficiently high to allow saturation of the rate-limiting penicillin biosynthetic enzyme in that strain. The basis of further correlation of intracellular α-aminoadipate concentration and penicillin titre among strains D6/1014/A, P2, and 389/3, the three highest penicillin producers studied here, remains to be established. Preliminary studies which attempted to explain the differences in intracellular α-aminoadipate concentrations in strains Q 176, D6/1014/A, and P2 in terms of differences in activities or kinetics of two enzymes of lysine biosynthesis (homocitrate synthase and saccharopine dehydrogenase) did not reveal differences in those enzymes among the three strains.

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Paraburkholderia phymatum Homocitrate Synthase NifV Plays a Key Role for Nitrogenase Activity during Symbiosis with Papilionoids and in Free-Living Growth Conditions

Cells ◽

10.3390/cells10040952 ◽

2021 ◽

Vol 10 (4) ◽

pp. 952

Author(s):

Paula Bellés-Sancho ◽

Martina Lardi ◽

Yilei Liu ◽

Sebastian Hug ◽

Marta Adriana Pinto-Carbó ◽

...

Keyword(s):

Nitrogenase Activity ◽

Root Nodules ◽

Growth Conditions ◽

Lysine Biosynthesis ◽

Metabolome Analysis ◽

Plant Host ◽

Free Living ◽

Bacterial Enzyme ◽

Homocitrate Synthase ◽

Iron Molybdenum Cofactor

Homocitrate is an essential component of the iron-molybdenum cofactor of nitrogenase, the bacterial enzyme that catalyzes the reduction of dinitrogen (N2) to ammonia. In nitrogen-fixing and nodulating alpha-rhizobia, homocitrate is usually provided to bacteroids in root nodules by their plant host. In contrast, non-nodulating free-living diazotrophs encode the homocitrate synthase (NifV) and reduce N2 in nitrogen-limiting free-living conditions. Paraburkholderia phymatum STM815 is a beta-rhizobial strain, which can enter symbiosis with a broad range of legumes, including papilionoids and mimosoids. In contrast to most alpha-rhizobia, which lack nifV, P. phymatum harbors a copy of nifV on its symbiotic plasmid. We show here that P. phymatum nifV is essential for nitrogenase activity both in root nodules of papilionoid plants and in free-living growth conditions. Notably, nifV was dispensable in nodules of Mimosa pudica despite the fact that the gene was highly expressed during symbiosis with all tested papilionoid and mimosoid plants. A metabolome analysis of papilionoid and mimosoid root nodules infected with the P. phymatum wild-type strain revealed that among the approximately 400 measured metabolites, homocitrate and other metabolites involved in lysine biosynthesis and degradation have accumulated in all plant nodules compared to uninfected roots, suggesting an important role of these metabolites during symbiosis.

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Identification of DNA Unique to the Tomato Fusarium Wilt and Crown Rot Pathogens

10.32747/1995.7571359.bard ◽

1995 ◽

Author(s):

Harold Corby Kistler ◽

Talma Katan

Keyword(s):

Evolutionary Relationship ◽

Fungal Species ◽

Diagnostic Methods ◽

Crown Rot ◽

Molecular Diagnostic ◽

Disease Development ◽

Optimal Temperature ◽

Formae Speciales ◽

Soil Borne Pathogens ◽

Different Strains

Wilt and crown rot are two important diseases of tomato caused by different strains ("formae speciales") of the fungus, Fusarium oxysporum. While both pathogens are members of the same fungal species, each differs genetically and resistance to the diseases is controlled by different genes in the plant. Additionally, the formae speciales differ in their ecology (e.g. optimal temperature of disease development) and epidemiology. Nevertheless, the distinction between these diseases based on symptoms alone may be unclear due to overlapping symptomatology. We have found in our research that the ambiguity of the pathogens is further confounded because strains causing tomato wilt or crown rot each may belong to several genetically and phylogenetically distinct lineages of F. oxysporum. Furthermore, individual lineages of the pathogen causing wilt or crown rot may themselves be very closely related. The diseases share the characteristic that the pathogen's inoculum may be aerially dispersed. This work has revealed a complex evolutionary relationship among lineages of the pathogens that makes development of molecular diagnostic methods more difficult than originally anticipated. However, the degree of diversity found in these soil-borne pathogens has allowed study of their population genetics and patterns of dispersal in agricultural settings.

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Analysis of the molecular evolution of histone variant H2A.Z using a linker-mediated complex strategy and yeast genetic complementation

Bioscience Biotechnology and Biochemistry ◽

10.1093/bbb/zbab190 ◽

2021 ◽

Author(s):

Saho Kitagawa ◽

Masayuki Kusakabe ◽

Daisuke Takahashi ◽

Takumi Narimiya ◽

Yu Nakabayashi ◽

...

Keyword(s):

Molecular Evolution ◽

Evolutionary Conservation ◽

Histone Variant ◽

Genetic Complementation ◽

Yeast Genetic

Abstract The histone variant H2A.Z is deposited into chromatin by specific machinery and is required for genome functions. Using a linker-mediated complex strategy combined with yeast genetic complementation, we demonstrate evolutionary conservation of H2A.Z together with its chromatin incorporation and functions. This approach is applicable to the evolutionary analyses of proteins that form complexes with interactors.

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Comparative Analyses of Homocitrate Synthase Genes of Ascomycetous Yeasts

International Journal of Evolutionary Biology ◽

10.1155/2012/254941 ◽

2012 ◽

Vol 2012 ◽

pp. 1-4

Author(s):

Hiromi Nishida

Keyword(s):

Gene Duplication ◽

Nucleosome Position ◽

Lysine Biosynthesis ◽

Promoter Regions ◽

Additional Function ◽

Coding Regions ◽

Damage Repair ◽

Homocitrate Synthase ◽

Ascomycetous Yeasts ◽

Regulatory Controls

Most ascomycetous yeasts have 2 homocitrate synthases (HCSs). Among the fungal lysine biosynthesis-related genes, only the HCS gene was duplicated in the course of evolution. It was recently reported that HCS of Saccharomyces cerevisiae has an additional function in nuclear activities involving chromatin regulation related to DNA damage repair, which is not related to lysine biosynthesis. Thus, it is possible that the bifunctionality is associated with HCS gene duplication. Phylogenetic analysis showed that duplication has occurred multiple times during evolution of the ascomycetous yeasts. It is likely that the HCS gene duplication in S. cerevisiae occurred in the course of Saccharomyces evolution. Although the nucleosome position profiles of the two S. cerevisiae HCS genes were similar in the coding regions, they were different in the promoter regions, suggesting that they are subject to different regulatory controls. S. cerevisiae has maintained HCS activity for lysine biosynthesis and has obtained bifunctionality.

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DNA photolyase of enterococci: possible explanation for its low sunlight inactivation rate

Biologia ◽

10.2478/s11756-009-0168-6 ◽

2009 ◽

Vol 64 (5) ◽

Author(s):

Mushtaq Hussain ◽

Syeda Qamarunnissa ◽

Saboohi Raza ◽

Javed Qureshi ◽

Abdul Wajid ◽

...

Keyword(s):

Binding Sites ◽

Light Harvesting ◽

Inactivation Rate ◽

Dna Photolyase ◽

Multiple Sequence ◽

Efficient Energy Transfer ◽

Tertiary Structures ◽

E Coli ◽

The Difference ◽

Substrate Binding Sites

AbstractDNA photolyase is perhaps the most ancient and direct arsenal in curing the UV-induced dimers formed in the microbial genome. Out of two cofactors of the enzyme, catalytic and light harvesting, differences in the latter have provided basis for categorizing photolyases of prokaryotes as folate and deazaflavin types. In the present study, the homology modeling of DNA photolyase of Enterococcus faecalis was undertaken. The predicted models were structurally compared with the crystal structure coordinates of photolyases from Escherichia coli (folate type) and Anacystis nidulans (deazaflavin type). Discrepancies present in the multiple sequence alignment and tertiary structures, particularly at the light harvesting cofactor (methenyltetrahydrofolic acid, MTHF; 8-hydroxy-5-deazaflavin, 8-HDF) binding sites indicated the mechanistic nature of enterococcal photolyase. Concisely, despite the greater holistic homology with folate-type photolyase, enterococcal photolyase was characterized as deazaflavin-type. The presence of 8-HDF binding sites and groove architecture of substrate binding sites were also found supportive in this regard. The inter cofactor distance and/or orientation also implied to the efficient energy transfer in photolyase of Enterococcus in comparison with E. coli. In addition, we observed relatively high protein deformability in the enterococcal genome, which may favors the repair action of photolyase. The findings are expected to provide molecular insights into the difference in sunlight inactivation rate of two important fecal contamination indicators, namely Enterococcus and E. coli.

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Novel Chimeric Spermidine Synthase-Saccharopine Dehydrogenase Gene (SPE3-LYS9) in the Human Pathogen Cryptococcus neoformans

Eukaryotic Cell ◽

10.1128/ec.3.3.752-763.2004 ◽

2004 ◽

Vol 3 (3) ◽

pp. 752-763 ◽

Cited By ~ 31

Author(s):

Joanne M. Kingsbury ◽

Zhonghui Yang ◽

Tonya M. Ganous ◽

Gary M. Cox ◽

John H. McCusker

Keyword(s):

Cryptococcus Neoformans ◽

Lysine Biosynthesis ◽

Temperature Sensitive ◽

Mrna Levels ◽

Spermidine Synthase ◽

Gene Encoding ◽

Saccharopine Dehydrogenase ◽

Dehydrogenase Gene

ABSTRACT The Cryptococcus neoformans LYS9 gene (encoding saccharopine dehydrogenase) was cloned and found to be part of an evolutionarily conserved chimera with SPE3 (encoding spermidine synthase). spe3-lys9, spe3-LYS9, and SPE3-lys9 mutants were constructed, and these were auxotrophic for lysine and spermidine, spermidine, and lysine, respectively. Thus, SPE3-LYS9 encodes functional spermidine synthase and saccharopine dehydrogenase gene products. In contrast to Saccharomyces cerevisiae spe3 mutants, the polyamine auxotrophy of C. neoformans spe3-LYS9 mutants was not satisfied by spermine. In vitro phenotypes of spe3-LYS9 mutants included reduced capsule and melanin production and growth rate, while SPE3-lys9 mutants grew slowly at 30°C, were temperature sensitive in rich medium, and died upon lysine starvation. Consistent with the importance of saccharopine dehydrogenase and spermidine synthase in vitro, spe3-lys9 mutants were avirulent and unable to survive in vivo and both functions individually contributed to virulence. SPE3-LYS9 mRNA levels showed little evidence of being influenced by exogenous spermidine or lysine or starvation for spermidine or lysine; thus, any regulation is likely to be posttranscriptional. Expression in S. cerevisiae of the full-length C. neoformans SPE3-LYS9 cDNA complemented a lys9 mutant but not a spe3 mutant. However, expression in S. cerevisiae of a truncated gene product, consisting of only C. neoformans SPE3, complemented a spe3 mutant, suggesting possible modes of regulation. Therefore, we identified and describe a novel chimeric SPE3-LYS9 gene, which may link spermidine and lysine biosynthesis in C. neoformans.

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