scholarly journals Evolution of Leucyl-tRNA Synthetase Through Eukaryotic Speciation

2017 ◽  
Vol 14 (3) ◽  
Author(s):  
Katelyn Unvert ◽  
Frank Kovacs ◽  
Chi Zhang ◽  
Rachel Hellmann-Whitaker ◽  
Katelin Arndt
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Active Sites ◽  
Sequence Data ◽  
Research Effort ◽  
Trna Synthetase ◽  
Trna Synthetases ◽  
Speciation Process ◽  
Evolutionary Relatedness ◽  
Vertical Gene Transfer

Aminoacyl-tRNA synthetases (aaRSs) are part of the cellular translation machinery and as such, they are essential enzymes for every known cell. Due to their ubiquitous nature, their evolutionary history has been intensely researched to better understand the origins of life on a molecular level. Herein, we examine the evolutionary relatedness of leucyl-tRNA synthetases (LeuRS) from each major eukaryotic branch through the speciation process. This research effort was centered on amino acid sequence data as well as generating homology protein models for each LeuRS enzyme. Comparative analysis of this sequence and structural data for LeuRS amongst eukaryotes has indicated a high level of conservation within the active sites of these enzymes. Phylogenetic analysis confirmed this high degree of conservation as well as established evolutionary relatedness between these LeuRS enzymes. Based on this data, vertical gene transfer propagated LeuRS throughout the eukaryotic domain. Horizontal gene transfer and domain acquisition events were not observed within the eukaryotic organisms studied. Our data also highlighted LeuRS adaptation through the speciation process due to slight variability of scaffolding residues outside of the active site regions. We hypothesize that this variability may be due to mechanistic differences amongst LeuRS enzymes that have assumed non-translational functionality through the evolutionary process. KEYWORDS: tRNA Synthetase; Leucyl-tRNA Synthetase; Eukaryotic Evolution; LeuRS Conservation; Vertical Gene Transfer; Horizontal Gene Transfer; Convergent Evolution; Primordial Enzymes

scholarly journals Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer.

1994 ◽  
Vol 91 (18) ◽  
pp. 8670-8674 ◽  
Author(s):  
V. Lamour ◽  
S. Quevillon ◽  
S. Diriong ◽  
V. C. N'Guyen ◽  
M. Lipinski ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Trna Synthetase

scholarly journals Horizontal transfer in bacterial Methionyl tRNA synthetase is very common shown by Genus and phyla level phylogenetic analysis.

2016 ◽  
Author(s):  
Prabhakar Ghorpade ◽  
Avinash Pange ◽  
Bhaskar Sharma
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Single Copy ◽  
Trna Synthetase ◽  
Species Tree ◽  
Large Trees ◽  
Conserved Gene ◽  
Methionyl Trna Synthetase ◽  
Informational Gene

Methionyl tRNA synthetase is single copy informational gene in Salmonella typhimurium. Informational genes are more conserved than operational genes. In this study we had analyzed HGT events within MetG sequences of different bacterial genera. A species tree based on 16srRNA sequences of the same genus was drawn evaluated against the generally accepted species tree of the bacteria. MetG phylogenetic tree was evaluated against the 16srRNAS tree and HGT event identified. Similarly phyla trees were made and HGT event identified. 24 HGT events were identified between genus and 11 within phyla. MetG is a considered as conserved gene finding so many HGT event in this gene indicate that horizontal gene transfer is very common in this gene. Manual tree making for phyla could help to understand phylogenetic relationships between very large trees.

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 Archaeal Aminoacyl-tRNA Synthesis: Diversity Replaces Dogma

Genetics ◽  
1999 ◽  
Vol 152 (4) ◽  
pp. 1269-1276
Author(s):  
Debra Tumbula ◽  
Ute C Vothknecht ◽  
Hyun-soo Kim ◽  
Michael Ibba ◽  
Bokkee Min ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Transfer ◽  
Molecular Biology ◽  
Genetic Code ◽  
Genome Sequencing ◽  
Protein Biosynthesis ◽  
Methanobacterium Thermoautotrophicum ◽  
Trna Synthetase ◽  
Trna Synthetases ◽  
Field Investigations

Abstract Accurate aminoacyl-tRNA synthesis is essential for faithful translation of the genetic code and consequently has been intensively studied for over three decades. Until recently, the study of aminoacyl-tRNA synthesis in archaea had received little attention. However, as in so many areas of molecular biology, the advent of archaeal genome sequencing has now drawn researchers to this field. Investigations with archaea have already led to the discovery of novel pathways and enzymes for the synthesis of numerous aminoacyl-tRNAs. The most surprising of these findings has been a transamidation pathway for the synthesis of asparaginyl-tRNA and a novel lysyl-tRNA synthetase. In addition, seryl- and phenylalanyl-tRNA synthetases that are only marginally related to known examples outside the archaea have been characterized, and the mechanism of cysteinyl-tRNA formation in Methanococcus jannaschii and Methanobacterium thermoautotrophicum is still unknown. These results have revealed completely unexpected levels of complexity and diversity, questioning the notion that aminoacyl-tRNA synthesis is one of the most conserved functions in gene expression. It has now become clear that the distribution of the various mechanisms of aminoacyl-tRNA synthesis in extant organisms has been determined by numerous gene transfer events, indicating that, while the process of protein biosynthesis is orthologous, its constituents are not.

scholarly journals Horizontal Gene Transfer Phylogenetics: A Random Walk Approach

2019 ◽  
Vol 37 (5) ◽  
pp. 1470-1479
Author(s):  
Gur Sevillya ◽  
Daniel Doerr ◽  
Yael Lerner ◽  
Jens Stoye ◽  
Mike Steel ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Order ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Gene Content ◽  
Genome Dynamics ◽  
Two Factors ◽  
History Of ◽  
Close Relatives

Abstract The dramatic decrease in time and cost for generating genetic sequence data has opened up vast opportunities in molecular systematics, one of which is the ability to decipher the evolutionary history of strains of a species. Under this fine systematic resolution, the standard markers are too crude to provide a phylogenetic signal. Nevertheless, among prokaryotes, genome dynamics in the form of horizontal gene transfer (HGT) between organisms and gene loss seem to provide far richer information by affecting both gene order and gene content. The “synteny index” (SI) between a pair of genomes combines these latter two factors, allowing comparison of genomes with unequal gene content, together with order considerations of their common genes. Although this approach is useful for classifying close relatives, no rigorous statistical modeling for it has been suggested. Such modeling is valuable, as it allows observed measures to be transformed into estimates of time periods during evolution, yielding the “additivity” of the measure. To the best of our knowledge, there is no other additivity proof for other gene order/content measures under HGT. Here, we provide a first statistical model and analysis for the SI measure. We model the “gene neighborhood” as a “birth–death–immigration” process affected by the HGT activity over the genome, and analytically relate the HGT rate and time to the expected SI. This model is asymptotic and thus provides accurate results, assuming infinite size genomes. Therefore, we also developed a heuristic model following an “exponential decay” function, accounting for biologically realistic values, which performed well in simulations. Applying this model to 1,133 prokaryotes partitioned to 39 clusters by the rank of genus yields that the average number of genome dynamics events per gene in the phylogenetic depth of genus is around half with significant variability between genera. This result extends and confirms similar results obtained for individual genera in different manners.

scholarly journals Staphylococcus epidermidis Phages Transduce Antimicrobial Resistance Plasmids and Mobilize Chromosomal Islands

mSphere ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Lenka Fišarová ◽  
Tibor Botka ◽  
Xin Du ◽  
Ivana Mašlaňová ◽  
Pavol Bárdy ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Resistance Genes ◽  
Staphylococcus Epidermidis ◽  
Content Type ◽  
Antimicrobial Resistance Genes ◽  
Evolutionary Relatedness ◽  
Resistance Plasmids

ABSTRACT Staphylococcus epidermidis is a leading opportunistic pathogen causing nosocomial infections that is notable for its ability to form a biofilm and for its high rates of antibiotic resistance. It serves as a reservoir of multiple antimicrobial resistance genes that spread among the staphylococcal population by horizontal gene transfer such as transduction. While phage-mediated transduction is well studied in Staphylococcus aureus, S. epidermidis transducing phages have not been described in detail yet. Here, we report the characteristics of four phages, 27, 48, 456, and 459, previously used for S. epidermidis phage typing, and the newly isolated phage E72, from a clinical S. epidermidis strain. The phages, classified in the family Siphoviridae and genus Phietavirus, exhibited an S. epidermidis-specific host range, and together they infected 49% of the 35 strains tested. A whole-genome comparison revealed evolutionary relatedness to transducing S. aureus phietaviruses. In accordance with this, all the tested phages were capable of transduction with high frequencies up to 10−4 among S. epidermidis strains from different clonal complexes. Plasmids with sizes from 4 to 19 kb encoding resistance to streptomycin, tetracycline, and chloramphenicol were transferred. We provide here the first evidence of a phage-inducible chromosomal island transfer in S. epidermidis. Similarly to S. aureus pathogenicity islands, the transfer was accompanied by phage capsid remodeling; however, the interfering protein encoded by the island was distinct. Our findings underline the role of S. epidermidis temperate phages in the evolution of S. epidermidis strains by horizontal gene transfer, which can also be utilized for S. epidermidis genetic studies. IMPORTANCE Multidrug-resistant strains of S. epidermidis emerge in both nosocomial and livestock environments as the most important pathogens among coagulase-negative staphylococcal species. The study of transduction by phages is essential to understanding how virulence and antimicrobial resistance genes spread in originally commensal bacterial populations. In this work, we provide a detailed description of transducing S. epidermidis phages. The high transduction frequencies of antimicrobial resistance plasmids and the first evidence of chromosomal island transfer emphasize the decisive role of S. epidermidis phages in attaining a higher pathogenic potential of host strains. To date, such importance has been attributed only to S. aureus phages, not to those of coagulase-negative staphylococci. This study also proved that the described transducing bacteriophages represent valuable genetic modification tools in S. epidermidis strains where other methods for gene transfer fail.

scholarly journals Evolutionary Dynamics of Vibrio cholerae O1 following a Single-Source Introduction to Haiti

mBio ◽  
2013 ◽  
Vol 4 (4) ◽  
Author(s):  
Lee S. Katz ◽  
Aaron Petkau ◽  
John Beaulaurier ◽  
Shaun Tyler ◽  
Elena S. Antonova ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Vibrio Cholerae ◽  
Evolutionary Dynamics ◽  
Sequence Data ◽  
Time Frame ◽  
Single Source ◽  
Content Type ◽  
Gene Acquisition

ABSTRACTPrior to the epidemic that emerged in Haiti in October of 2010, cholera had not been documented in this country. After its introduction, a strain ofVibrio choleraeO1 spread rapidly throughout Haiti, where it caused over 600,000 cases of disease and >7,500 deaths in the first two years of the epidemic. We applied whole-genome sequencing to a temporal series ofV. choleraeisolates from Haiti to gain insight into the mode and tempo of evolution in this isolated population ofV. choleraeO1. Phylogenetic and Bayesian analyses supported the hypothesis that all isolates in the sample set diverged from a common ancestor within a time frame that is consistent with epidemiological observations. A pangenome analysis showed nearly homogeneous genomic content, with no evidence of gene acquisition among Haiti isolates. Nine nearly closed genomes assembled from continuous-long-read data showed evidence of genome rearrangements and supported the observation of no gene acquisition among isolates. Thus, intrinsic mutational processes can account for virtually all of the observed genetic polymorphism, with no demonstrable contribution from horizontal gene transfer (HGT). Consistent with this, the 12 Haiti isolates tested by laboratory HGT assays were severely impaired for transformation, although unlike previously characterized noncompetentV. choleraeisolates, each expressedhapRand possessed a functional quorum-sensing system. Continued monitoring ofV. choleraein Haiti will illuminate the processes influencing the origin and fate of genome variants, which will facilitate interpretation of genetic variation in future epidemics.IMPORTANCEVibrio choleraeis the cause of substantial morbidity and mortality worldwide, with over three million cases of disease each year. An understanding of the mode and rate of evolutionary change is critical for proper interpretation of genome sequence data and attribution of outbreak sources. The Haiti epidemic provides an unprecedented opportunity to study an isolated, single-source outbreak ofVibrio choleraeO1 over an established time frame. By using multiple approaches to assay genetic variation, we found no evidence that the Haiti strain has acquired any genes by horizontal gene transfer, an observation that led us to discover that it is also poorly transformable. We have found no evidence that environmental strains have played a role in the evolution of the outbreak strain.

scholarly journals Duplication of leucyl-tRNA synthetase in an archaeal extremophile may play a role in adaptation to variable environmental conditions

2020 ◽  
Vol 295 (14) ◽  
pp. 4563-4576 ◽  
Author(s):  
Christopher S. Weitzel ◽  
Li Li ◽  
Changyi Zhang ◽  
Kristen K. Eilts ◽  
Nicholas M. Bretz ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Environmental Conditions ◽  
Active Sites ◽  
Hot Springs ◽  
Protein Translation ◽  
Selective Advantage ◽  
Trna Synthetase ◽  
Bioinformatics Analyses ◽  
Trna Synthetases ◽  
Editing Domain

Aminoacyl-tRNA synthetases (aaRSs) are ancient enzymes that play a fundamental role in protein synthesis. They catalyze the esterification of specific amino acids to the 3′-end of their cognate tRNAs and therefore play a pivotal role in protein synthesis. Although previous studies suggest that aaRS-dependent errors in protein synthesis can be beneficial to some microbial species, evidence that reduced aaRS fidelity can be adaptive is limited. Using bioinformatics analyses, we identified two distinct leucyl-tRNA synthetase (LeuRS) genes within all genomes of the archaeal family Sulfolobaceae. Remarkably, one copy, designated LeuRS-I, had key amino acid substitutions within its editing domain that would be expected to disrupt hydrolytic editing of mischarged tRNALeu and to result in variation within the proteome of these extremophiles. We found that another copy, LeuRS-F, contains canonical active sites for aminoacylation and editing. Biochemical and genetic analyses of the paralogs within Sulfolobus islandicus supported the hypothesis that LeuRS-F, but not LeuRS-I, functions as an essential tRNA synthetase that accurately charges leucine to tRNALeu for protein translation. Although LeuRS-I was not essential, its expression clearly supported optimal S. islandicus growth. We conclude that LeuRS-I may have evolved to confer a selective advantage under the extreme and fluctuating environmental conditions characteristic of the volcanic hot springs in which these archaeal extremophiles reside.

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