scholarly journals Evolution of Aminoacyl-tRNA Synthetases—Analysis of Unique Domain Architectures and Phylogenetic Trees Reveals a Complex History of Horizontal Gene Transfer Events

1999 ◽  
Vol 9 (8) ◽  
pp. 689-710 ◽  
Author(s):  
Yuri I. Wolf ◽  
L. Aravind ◽  
Nick V. Grishin ◽  
Eugene V. Koonin
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Domain Architecture ◽  
Specific Gene ◽  
Trna Synthetases ◽  
Aminoacyl Trna Synthetases ◽  
Eukaryotic Genes ◽  
Multiple Alignments

Phylogenetic analysis of aminoacyl-tRNA synthetases (aaRSs) of all 20 specificities from completely sequenced bacterial, archaeal, and eukaryotic genomes reveals a complex evolutionary picture. Detailed examination of the domain architecture of aaRSs using sequence profile searches delineated a network of partially conserved domains that is even more elaborate than previously suspected. Several unexpected evolutionary connections were identified, including the apparent origin of the β-subunit of bacterial GlyRS from the HD superfamily of hydrolases, a domain shared by bacterial AspRS and the B subunit of archaeal glutamyl-tRNA amidotransferases, and another previously undetected domain that is conserved in a subset of ThrRS, guanosine polyphosphate hydrolases and synthetases, and a family of GTPases. Comparison of domain architectures and multiple alignments resulted in the delineation of synapomorphies—shared derived characters, such as extra domains or inserts—for most of the aaRSs specificities. These synapomorphies partition sets of aaRSs with the same specificity into two or more distinct and apparently monophyletic groups. In conjunction with cluster analysis and a modification of the midpoint-rooting procedure, this partitioning was used to infer the likely root position in phylogenetic trees. The topologies of the resulting rooted trees for most of the aaRSs specificities are compatible with the evolutionary “standard model” whereby the earliest radiation event separated bacteria from the common ancestor of archaea and eukaryotes as opposed to the two other possible evolutionary scenarios for the three major divisions of life. For almost all aaRSs specificities, however, this simple scheme is confounded by displacement of some of the bacterial aaRSs by their eukaryotic or, less frequently, archaeal counterparts. Displacement of ancestral eukaryotic aaRS genes by bacterial ones, presumably of mitochondrial origin, was observed for three aaRSs. In contrast, there was no convincing evidence of displacement of archaeal aaRSs by bacterial ones. Displacement of aaRS genes by eukaryotic counterparts is most common among parasitic and symbiotic bacteria, particularly the spirochaetes, in which 10 of the 19 aaRSs seem to have been displaced by the respective eukaryotic genes and two by the archaeal counterpart. Unlike the primary radiation events between the three main divisions of life, that were readily traceable through the phylogenetic analysis of aaRSs, no consistent large-scale bacterial phylogeny could be established. In part, this may be due to additional gene displacement events among bacterial lineages. Argument is presented that, although lineage-specific gene loss might have contributed to the evolution of some of the aaRSs, this is not a viable alternative to horizontal gene transfer as the principal evolutionary phenomenon in this gene class.[Complete multiple alignments of all aaRSs from complete genomes as well as the alignments of conserved regions used for phylogenetic tree construction are available at ftp://ncbi.nlm.nih.gov/pub/koonin/aaRS]

scholarly journals Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process

2000 ◽  
Vol 64 (1) ◽  
pp. 202-236 ◽  
Author(s):  
Carl R. Woese ◽  
Gary J. Olsen ◽  
Michael Ibba ◽  
Dieter Söll
Keyword(s):  
Genetic Code ◽  
Phylogenetic Trees ◽  
Genetic Material ◽  
Evolutionary Process ◽  
Group Iv ◽  
Evolutionary Relationships ◽  
Evolutionary Stage ◽  
Trna Synthetases ◽  
Aminoacyl Trna Synthetases ◽  
The Individual

SUMMARY The aminoacyl-tRNA synthetases (AARSs) and their relationship to the genetic code are examined from the evolutionary perspective. Despite a loose correlation between codon assignments and AARS evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. Nevertheless, the AARSs are very informative about the evolutionary process. Examination of the phylogenetic trees for each of the AARSs reveals the following. (i) Their evolutionary relationships mostly conform to established organismal phylogeny: a strong distinction exists between bacterial- and archaeal-type AARSs. (ii) Although the evolutionary profiles of the individual AARSs might be expected to be similar in general respects, they are not. It is argued that these differences in profiles reflect the stages in the evolutionary process when the taxonomic distributions of the individual AARSs became fixed, not the nature of the individual enzymes. (iii) Horizontal transfer of AARS genes between Bacteria and Archaea is asymmetric: transfer of archaeal AARSs to the Bacteria is more prevalent than the reverse, which is seen only for the “gemini group.” (iv) The most far-ranging transfers of AARS genes have tended to occur in the distant evolutionary past, before or during formation of the primary organismal domains. These findings are also used to refine the theory that at the evolutionary stage represented by the root of the universal phylogenetic tree, cells were far more primitive than their modern counterparts and thus exchanged genetic material in far less restricted ways, in effect evolving in a communal sense.

scholarly journals CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Sara J. Weaver ◽  
Davi R. Ortega ◽  
Matthew H. Sazinsky ◽  
Triana N. Dalia ◽  
Ankur B. Dalia ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Vibrio Cholerae ◽  
Natural Transformation ◽  
Domain Architecture ◽  
Genetic Material ◽  
Surface Binding ◽  
Exogenous Dna ◽  
Insight Into

Abstract Natural transformation is the process by which bacteria take up genetic material from their environment and integrate it into their genome by homologous recombination. It represents one mode of horizontal gene transfer and contributes to the spread of traits like antibiotic resistance. In Vibrio cholerae, a type IVa pilus (T4aP) is thought to facilitate natural transformation by extending from the cell surface, binding to exogenous DNA, and retracting to thread this DNA through the outer membrane secretin, PilQ. Here, we use a functional tagged allele of VcPilQ purified from native V. cholerae cells to determine the cryoEM structure of the VcPilQ secretin in amphipol to ~2.7 Å. We use bioinformatics to examine the domain architecture and gene neighborhood of T4aP secretins in Proteobacteria in comparison with VcPilQ. This structure highlights differences in the architecture of the T4aP secretin from the type II and type III secretion system secretins. Based on our cryoEM structure, we design a series of mutants to reversibly regulate VcPilQ gate dynamics. These experiments support the idea of VcPilQ as a potential druggable target and provide insight into the channel that DNA likely traverses to promote the spread of antibiotic resistance via horizontal gene transfer by natural transformation.

scholarly journals Phylogenetic Analysis Reveals Multiple Lateral Transfers of Adenosine-5′-Phosphosulfate Reductase Genes among Sulfate-Reducing Microorganisms

2002 ◽  
Vol 184 (1) ◽  
pp. 278-289 ◽  
Author(s):  
Michael W. Friedrich
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
16S Rrna ◽  
Lateral Gene Transfer ◽  
Phylogenetic Trees ◽  
Gram Positive ◽  
Sulfate Reducing ◽  
Wide Range ◽  
Aps Reductase ◽  
Key Enzyme

ABSTRACT Lateral gene transfer affects the evolutionary path of key genes involved in ancient metabolic traits, such as sulfate respiration, even more than previously expected. In this study, the phylogeny of the adenosine-5′-phosphosulfate (APS) reductase was analyzed. APS reductase is a key enzyme in sulfate respiration present in all sulfate-respiring prokaryotes. A newly developed PCR assay was used to amplify and sequence a fragment (∼900 bp) of the APS reductase gene, apsA, from a taxonomically wide range of sulfate-reducing prokaryotes (n = 60). Comparative phylogenetic analysis of all obtained and available ApsA sequences indicated a high degree of sequence conservation in the region analyzed. However, a comparison of ApsA- and 16S rRNA-based phylogenetic trees revealed topological incongruences affecting seven members of the Syntrophobacteraceae and three members of the Nitrospinaceae, which were clearly monophyletic with gram-positive sulfate-reducing bacteria (SRB). In addition, Thermodesulfovibrio islandicus and Thermodesulfobacterium thermophilum, Thermodesulfobacterium commune, and Thermodesulfobacterium hveragerdense clearly branched off between the radiation of the δ-proteobacterial gram-negative SRB and the gram-positive SRB and not close to the root of the tree as expected from 16S rRNA phylogeny. The most parsimonious explanation for these discrepancies in tree topologies is lateral transfer of apsA genes across bacterial divisions. Similar patterns of insertions and deletions in ApsA sequences of donor and recipient lineages provide additional evidence for lateral gene transfer. From a subset of reference strains (n = 25), a fragment of the dissimilatory sulfite reductase genes (dsrAB), which have recently been proposed to have undergone multiple lateral gene transfers (M. Klein et al., J. Bacteriol. 183:6028–6035, 2001), was also amplified and sequenced. Phylogenetic comparison of DsrAB- and ApsA-based trees suggests a frequent involvement of gram-positive and thermophilic SRB in lateral gene transfer events among SRB.

scholarly journals Adaptation by Ancient Horizontal Acquisition of Butyrate Metabolism Genes in Aggregatibacter actinomycetemcomitans

mBio ◽  
2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Ahmed M. Moustafa ◽  
Senthil Kumar Velusamy ◽  
Lidiya Denu ◽  
Apurva Narechania ◽  
Daniel H. Fine ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Strong Association ◽  
Aggregatibacter Actinomycetemcomitans ◽  
Short Chain ◽  
Oral Microbiota ◽  
Content Type ◽  
History Of ◽  
The Impact

ABSTRACT Like the bacterial residents of the human gut, it is likely that many of the species in the human oral microbiota have evolved to better occupy and persist in their niche. Aggregatibacter actinomycetemcomitans (Aa) is both a common colonizer of the oral cavity and has been implicated in the pathogenesis of periodontal disease. Here, we present a whole-genome phylogenetic analysis of Aa isolates from humans and nonhuman primates that revealed an ancient origin for this species and a long history of association with the Catarrhini, the lineage that includes Old World monkeys (OWM) and humans. Further genomic analysis showed a strong association with the presence of a short-chain fatty acid (SCFA) catabolism locus (atoRDAEB) in many human isolates that was absent in almost all nonhuman OWM isolates. We show that this locus was likely acquired through horizontal gene transfer. When grown under conditions that are similar to those at the subgingival site of periodontitis (anaerobic, SCFA replete), Aa strains with atoRDAEB formed robust biofilms and showed upregulation of genes involved in virulence, colonization, and immune evasion. Both an isogenic deletion mutant and nonhuman primate isolates lacking the ato locus failed to grow in a robust biofilm under these conditions, but grew well under the carbohydrate-rich conditions similar to those found above the gumline. We propose that the acquisition of the ato locus was a key evolutionary step allowing Aa to utilize SCFAs, adapt, and modulate subgingival disease. IMPORTANCE There has been considerable interest in the impact of short-chain fatty acids (SCFAs) on inflammatory effects related to the microbiome. Here, we present evidence that SCFAs may also be important in disease by providing an energy source or disease-associated cue for colonizing pathogens. We propose that SCFAs allow Aggregatibacter actinomycetemcomitans (Aa) to adapt to the subgingival anaerobic environment, which is the site of human periodontitis. Under anaerobic, SCFA-rich conditions, human-derived Aa strains that possess butyrate metabolism genes form strong biofilms and upregulate virulence genes. Our phylogenetic analysis highlights a long history of evolution of Aa with its primate hosts and suggests that the acquisition of butyrate metabolism genes may have been a critical step in allowing Aa to colonize a new niche and cause disease in humans. Overall, this study highlights the important role that horizontal gene transfer may play in microbial adaptation and the evolution of infectious disease.

scholarly journals Phylogenetic analysis of genomic islands in closely-related species belonging to Sinorhizobium sp.

2020 ◽  
Author(s):  
M. E. Vladimirova ◽  
V. S. Muntyan ◽  
A. S. Saksaganskaya ◽  
B. V. Simarov ◽  
M. L. Roumiantseva
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Related Species ◽  
Genomic Islands ◽  
Closely Related Species ◽  
Homologous Sequences

Genomic islands of closely related S. meliloti and S. medicae species were evaluated and homologous sequences were identified; it has been suggested that horizontal gene transfer occurs at homologous tRNA sites.

scholarly journals A comprehensive phylogenetic analysis of the serpin superfamily

2020 ◽  
Author(s):  
Matthew A. Spence ◽  
Matthew D. Mortimer ◽  
Ashley M. Buckle ◽  
Bui Quang Minh ◽  
Colin J. Jackson
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Convergent Evolution ◽  
Alternative Hypothesis ◽  
Structural Alignment ◽  
High Homology ◽  
Physiological Processes ◽  
New Directions ◽  
Hub Proteins

Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer (HGT) due to their unexpectedly high homology. Here we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6000-sequence phylogeny that encompasses serpins from all kingdoms of life. We show that in addition to a central “hub” of highly conserved serpins, there has been extensive diversification of the superfamily into many novel functional clades. Our analysis indicates that the hub proteins are ancient and are similar because of convergent evolution, rather than the alternative hypothesis of HGT. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.

scholarly journals Reconstructing the Phylogeny of Corynebacteriales while Accounting for Horizontal Gene Transfer

2020 ◽  
Vol 12 (4) ◽  
pp. 381-395
Author(s):  
Nilson Da Rocha Coimbra ◽  
Aristoteles Goes-Neto ◽  
Vasco Azevedo ◽  
Aïda Ouangraoua
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Bacterial Species ◽  
Gene Tree ◽  
Gene Families ◽  
Common Mechanism ◽  
Species Trees ◽  
Bacterial Phylogeny ◽  
Homologous Genes

Abstract Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. We present a new method for estimating bacterial phylogeny that accounts for the presence of genes acquired by horizontal gene transfer between genomes. The method identifies and corrects putative transferred genes in gene families, before applying a gene tree-based summary method to estimate bacterial species trees. The method was applied to estimate the phylogeny of the order Corynebacteriales, which is the largest clade in the phylum Actinobacteria. We report a collection of 14 phylogenetic trees on 360 Corynebacteriales genomes. All estimated trees display each genus as a monophyletic clade. The trees also display several relationships proposed by past studies, as well as new relevant relationships between and within the main genera of Corynebacteriales: Corynebacterium, Mycobacterium, Nocardia, Rhodococcus, and Gordonia. An implementation of the method in Python is available on GitHub at https://github.com/UdeS-CoBIUS/EXECT (last accessed April 2, 2020).

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