Characterization of bacterial homocitrate synthase involved in lysine biosynthesis

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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Stabilization and characterization of histidine-tagged homocitrate synthase from Saccharomyces cerevisiae

Archives of Biochemistry and Biophysics ◽

10.1016/j.abb.2003.11.005 ◽

2004 ◽

Vol 421 (2) ◽

pp. 243-254 ◽

Cited By ~ 18

Author(s):

Babak Andi ◽

Ann H. West ◽

Paul F. Cook

Keyword(s):

Saccharomyces Cerevisiae ◽

Homocitrate Synthase

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Functional and Phylogenetic Divergence of Fungal Adenylate-Forming Reductases

Applied and Environmental Microbiology ◽

10.1128/aem.01767-14 ◽

2014 ◽

Vol 80 (19) ◽

pp. 6175-6183 ◽

Cited By ~ 18

Author(s):

Daniel Kalb ◽

Gerald Lackner ◽

Dirk Hoffmeister

Keyword(s):

Lysine Biosynthesis ◽

Reduction Step ◽

Content Type ◽

Ceriporiopsis Subvermispora ◽

Major Class ◽

Genes Encoding ◽

Short Chain Dehydrogenase ◽

Phylogenetic Divergence

ABSTRACTA key step in fungall-lysine biosynthesis is catalyzed by adenylate-formingl-α-aminoadipic acid reductases, organized in domains for adenylation, thiolation, and the reduction step. However, the genomes of numerous ascomycetes and basidiomycetes contain an unexpectedly large number of additional genes encoding similar but functionally distinct enzymes. Here, we describe the functionalin vitrocharacterization of four reductases which were heterologously produced inEscherichia coli. TheCeriporiopsis subvermisporaserine reductase Nps1 features a terminal ferredoxin-NADP+reductase (FNR) domain and thus belongs to a hitherto undescribed class of fungal multidomain enzymes. The second major class is characterized by the canonical terminal short-chain dehydrogenase/reductase domain and represented byCeriporiopsis subvermisporaNps3 as the first biochemically characterizedl-α-aminoadipic acid reductase of basidiomycete origin.Aspergillus flavusl-tyrosine reductases LnaA and LnbA are members of a distinct phylogenetic clade. Phylogenetic analysis supports the view that fungal adenylate-forming reductases are more diverse than previously recognized and belong to four distinct classes.

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Characterization of Homoisocitrate Dehydrogenase Involved in Lysine Biosynthesis of an Extremely Thermophilic Bacterium,Thermus thermophilusHB27, and Evolutionary Implication of β-Decarboxylating Dehydrogenase

Journal of Biological Chemistry ◽

10.1074/jbc.m205133200 ◽

2002 ◽

Vol 278 (3) ◽

pp. 1864-1871 ◽

Cited By ~ 36

Author(s):

Junichi Miyazaki ◽

Nobuyuki Kobashi ◽

Makoto Nishiyama ◽

Hisakazu Yamane

Keyword(s):

Thermophilic Bacterium ◽

Lysine Biosynthesis ◽

Evolutionary Implication

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Molecular Evolution of Lysine Biosynthesis in Agaricomycetes

Journal of Fungi ◽

10.3390/jof8010037 ◽

2021 ◽

Vol 8 (1) ◽

pp. 37

Author(s):

Zili Song ◽

Maoqiang He ◽

Ruilin Zhao ◽

Landa Qi ◽

Guocan Chen ◽

...

Keyword(s):

Molecular Evolution ◽

Evolutionary Relationship ◽

Deep Understanding ◽

Evolutionary Conservation ◽

Fungal Species ◽

Lysine Biosynthesis ◽

Tertiary Structures ◽

Saccharopine Dehydrogenase ◽

Homocitrate Synthase ◽

Substrate Binding Sites

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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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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