Evolutionary relationships of bacterial and archaeal glutamine synthetase genes

Brown,; Masuchi, Yaeko; Robb, Frank T.; Doolittle, W. Ford

doi:10.1007/bf00175876

Cited by 183 publications

(166 citation statements)

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“…The second gene ( glnA), encoding glutamine synthetase (GS), has also been used in the past for phylogenetic studies comparing archaea to bacteria [15,16]. GS is an important enzyme involved in nitrogen metabolism and ammonia assimilation in many eukaryotes and prokaryotes.…”

Section: Introductionmentioning

confidence: 99%

recA and glnA sequences separate the Bacteroides fragilis population into two genetic divisions associated with the antibiotic resistance genotypes cepA and cfiA

Gutacker

Valsangiacomo

Bernasconi

et al. 2002

Journal of Medical Microbiology

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The sequences of part of the glutamine synthetase-encoding gene ( glnA) and of the RecA-encoding gene (recA) were determined and aligned for 45 Bacteroides fragilis isolates from different clinical and geographical origin. The patterns of sequence divergence of glnA and recA were very similar. The sequences of a 303-bp fraction of recA showed 45 nucleotide substitutions, 40 of which allowed the separation of B. fragilis into two major divisions, which were not found when the deduced amino acid sequences were considered. The 687-bp sequences analysed for the glnA gene showed 112 nucleotide substitutions, 96 of which separated the population into the same two divisions as those described for recA. In this case, the deduced amino acid sequences showed this subdivision as well: three of the six observed amino acid substitutions were division-speci®c. Within the two divisions, both genes presented a high degree of sequence conservation. Each B. fragilis division was associated with the presence of a different antibiotic resistance gene: cepA encoding a serine-â-lactamase (division I) and c®A encoding a metallo-â-lactamase (division II). No particular clusters associated with geographical or clinical origin, or with the production of an enterotoxin were observed. Sequencing of the c®A gene allowed identi®cation of two different alleles in division II. However, no association of these different c®A alleles with the expression of imipenem resistance was observed. In conclusion, the phylogenetic patterns observed by sequencing recA and glnA are in agreement with those obtained previously by MLEE (multilocus enzyme electrophoresis). Thus, it appears that the evolution of recA and glnA genes is similar to that of the whole chromosome of B. fragilis. Horizontal gene transfer between divisions I and II seems to be low, at best. However, the results of the present study could not clarify de®nitively whether divisions I and II should be considered as two different B. fragilis genospecies.

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Section: Introductionmentioning

confidence: 99%

recA and glnA sequences separate the Bacteroides fragilis population into two genetic divisions associated with the antibiotic resistance genotypes cepA and cfiA

Gutacker

Valsangiacomo

Bernasconi

et al. 2002

Journal of Medical Microbiology

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“…However, trees inferred from protein-coding genes or proteins are not always topologically congruent with the rDNA tree (4,5) or with one another (6,7). Instances of incongruence are often attributed to historical transfers of genetic information from one genealogical lineage to another (8).…”

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confidence: 99%

Highways of gene sharing in prokaryotes

Beiko

Harlow²,

Ragan³

2005

Proc. Natl. Acad. Sci. U.S.A.

455

510

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The extent to which lateral genetic transfer has shaped microbial genomes has major implications for the emergence of community structures. We have performed a rigorous phylogenetic analysis of >220,000 proteins from genomes of 144 prokaryotes to determine the contribution of gene sharing to current prokaryotic diversity, and to identify ''highways'' of sharing between lineages. The inferred relationships suggest a pattern of inheritance that is largely vertical, but with notable exceptions among closely related taxa, and among distantly related organisms that live in similar environments.lateral genetic transfer ͉ microbial genomes ͉ molecular phylogeny B eginning in the 1980s, recognition of the 16S ribosomal RNA gene (rDNA) as a molecular chronometer (1), the development of automated sequencing technology and PCR, and improved phylogenetic methods (2) converged to yield a universal phylogenetic tree (1, 3) that was often interpreted as the ''tree of life.'' However, trees inferred from protein-coding genes or proteins are not always topologically congruent with the rDNA tree (4, 5) or with one another (6, 7). Instances of incongruence are often attributed to historical transfers of genetic information from one genealogical lineage to another (8). Mechanisms for lateral genetic transfer (LGT) are well characterized, and in a laboratory context underpin much of the biotechnology industry. At issue, however, is the extent to which LGT has contributed to the natural diversity of prokaryotes. If LGT has been rampant and consequential, there may in fact be no universal tree of life, and attempts to construct a phylogenetic classification of prokaryotes based on molecular sequence information will ultimately be futile (9).Least controversial among proposed LGT events are transfers that span relatively short evolutionary distances, where the donor and recipient organisms are members of the same species. DNA exchanges between close relatives are likely to be successful because of compatible methods of genetic exchange such as conjugation and the increased likelihood of homologous recombination between the donated DNA and the recipient genome (10). Linkage disequilibrium analysis of environmental samples has revealed extensive homologous recombination within many species of prokaryotes (11). Transfers between distantly related taxa are much less likely to succeed, because conjugation or viral transduction of genes between different species is less common (although not impossible), and foreign DNA must be integrated into the genome via illegitimate rather than homologous recombination (10). However, if organisms in the environment are subjected to a constant ''rain'' of DNA (12), then these rare processes will occur in evolutionary time, and will be fixed in a lineage especially if they confer a selective advantage on the recipient organism.LGT has tremendous implications for the genesis and evolution of microbial communities: if extensive LGT can occur among distantly related organisms, then processes such as niche inv...

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“…The two major GS families, GSI and GSII, are widely distributed in prokaryotes. GSI is largely absent in eukaryotes, but plays a vital role in many microorganisms, existing as α-and β-isoforms that differ in terms of sequence (35-41% identity), regulatory mechanisms (feedback allosteric regulation or adenylylation regulation), and biological functions (catalytic and chaperone activities) (28). Both the GSI-β and GSII enzymes are found in actinomycetes, and are distinguishable from each other by specific 25-amino acid insertion sequences (23).…”

Section: Discussionmentioning

confidence: 99%

Sirtuin-dependent reversible lysine acetylation of glutamine synthetases reveals an autofeedback loop in nitrogen metabolism

You

Yin

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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In cells of all domains of life, reversible lysine acetylation modulates the function of proteins involved in central cellular processes such as metabolism. In this study, we demonstrate that the nitrogen regulator GlnR of the actinomycete Saccharopolyspora erythraea directly regulates transcription of the acuA gene (SACE_5148), which encodes a Gcn5-type lysine acetyltransferase. We found that AcuA acetylates two glutamine synthetases (GlnA1 and GlnA4) and that this lysine acetylation inactivated GlnA4 (GSII) but had no significant effect on GlnA1 (GSI-β) activity under the conditions tested. Instead, acetylation of GlnA1 led to a gain-of-function that modulated its interaction with the GlnR regulator and enhanced GlnR–DNA binding. It was observed that this regulatory function of acetylated GSI-β enzymes is highly conserved across actinomycetes. In turn, GlnR controls the catalytic and regulatory activities (intracellular acetylation levels) of glutamine synthetases at the transcriptional and posttranslational levels, indicating an autofeedback loop that regulates nitrogen metabolism in response to environmental change. Thus, this GlnR-mediated acetylation pathway provides a signaling cascade that acts from nutrient sensing to acetylation of proteins to feedback regulation. This work presents significant new insights at the molecular level into the mechanisms underlying the regulation of protein acetylation and nitrogen metabolism in actinomycetes.

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Evolutionary relationships of bacterial and archaeal glutamine synthetase genes

Cited by 183 publications

References 45 publications

recA and glnA sequences separate the Bacteroides fragilis population into two genetic divisions associated with the antibiotic resistance genotypes cepA and cfiA

recA and glnA sequences separate the Bacteroides fragilis population into two genetic divisions associated with the antibiotic resistance genotypes cepA and cfiA

Highways of gene sharing in prokaryotes

Sirtuin-dependent reversible lysine acetylation of glutamine synthetases reveals an autofeedback loop in nitrogen metabolism

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