scholarly journals Parallel Evolution and Horizontal Gene Transfer of the pst Operon in Firmicutes from Oligotrophic Environments

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Alejandra Moreno-Letelier ◽  
Gabriela Olmedo ◽  
Luis E. Eguiarte ◽  
Leon Martinez-Castilla ◽  
Valeria Souza
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Parallel Evolution ◽  
3D Structure ◽  
Sequence Divergence ◽  
Housekeeping Genes ◽  
Phosphate Transport ◽  
Phosphate Binding ◽  
Maximum Likelihood Methods ◽  
Cuatro Ciénegas Basin

The high affinity phosphate transport system (pst) is crucial for phosphate uptake in oligotrophic environments. Cuatro Cienegas Basin (CCB) has extremely low P levels and its endemic Bacillus are closely related to oligotrophic marine Firmicutes. Thus, we expected the pst operon of CCB to share the same evolutionary history and protein similarity to marine Firmicutes. Orthologs of the pst operon were searched in 55 genomes of Firmicutes and 13 outgroups. Phylogenetic reconstructions were performed for the pst operon and 14 concatenated housekeeping genes using maximum likelihood methods. Conserved domains and 3D structures of the phosphate-binding protein (PstS) were also analyzed. The pst operon of Firmicutes shows two highly divergent clades with no correlation to the type of habitat nor a phylogenetic congruence, suggesting horizontal gene transfer. Despite sequence divergence, the PstS protein had a similar 3D structure, which could be due to parallel evolution after horizontal gene transfer events.

scholarly journals Adaptive evolution of hybrid bacteria by horizontal gene transfer

2021 ◽  
Vol 118 (10) ◽  
pp. e2007873118
Author(s):  
Jeffrey J. Power ◽  
Fernanda Pinheiro ◽  
Simone Pompei ◽  
Viera Kovacova ◽  
Melih Yüksel ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Adaptive Evolution ◽  
Gene Networks ◽  
Fitness Landscape ◽  
Parallel Evolution ◽  
Rapid Evolution ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Stationary Growth Phase

Horizontal gene transfer (HGT) is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer and about its effects on the recipient organism's physiology and fitness. Here, we address these questions in a parallel evolution experiment with two Bacillus subtilis lineages of 7% sequence divergence. We observe rapid evolution of hybrid organisms: gene transfer swaps ∼12% of the core genome in just 200 generations, and 60% of core genes are replaced in at least one population. By genomics, transcriptomics, fitness assays, and statistical modeling, we show that transfer generates adaptive evolution and functional alterations in hybrids. Specifically, our experiments reveal a strong, repeatable fitness increase of evolved populations in the stationary growth phase. By genomic analysis of the transfer statistics across replicate populations, we infer that selection on HGT has a broad genetic basis: 40% of the observed transfers are adaptive. At the level of functional gene networks, we find signatures of negative, positive, and epistatic selection, consistent with hybrid incompatibilities and adaptive evolution of network functions. Our results suggest that gene transfer navigates a complex cross-lineage fitness landscape, bridging epistatic barriers along multiple high-fitness paths.

scholarly journals Evolution and Molecular Phylogeny of Listeria monocytogenes Isolated from Human and Animal Listeriosis Cases and Foods

2005 ◽  
Vol 187 (16) ◽  
pp. 5537-5551 ◽  
Author(s):  
K. K. Nightingale ◽  
K. Windham ◽  
M. Wiedmann
Keyword(s):  
New York ◽  
Listeria Monocytogenes ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Positive Selection ◽  
New York State ◽  
Housekeeping Genes ◽  
Acid Sites ◽  
Food Samples ◽  
Phylogenetic Lineages

ABSTRACT To probe the evolution and phylogeny of Listeria monocytogenes from defined host species and environments, L. monocytogenes isolates from human (n = 60) and animal (n = 30) listeriosis cases and food samples (n = 30) were randomly selected from a larger collection of isolates (n = 354) obtained in New York State between 1999 and 2001. Partial sequencing of four housekeeping genes (gap, prs, purM, and ribC), one stress response gene (sigB), and two virulence genes (actA and inlA) revealed between 11 (gap) and 33 (inlA) allelic types as well as 52 sequence types (unique combination of allelic types). actA, ribC, and purM demonstrated the highest levels of nucleotide diversity (π > 0.05). actA and inlA as well as prs and the hypervariable housekeeping genes ribC and purM showed evidence of horizontal gene transfer and recombination. actA and inlA also showed evidence of positive selection at specific amino acid sites. Maximum likelihood phylogenies for all seven genes confirmed that L. monocytogenes contains two deeply separated evolutionary lineages. Lineage I was found to be highly clonal, while lineage II showed greater diversity and evidence of horizontal gene transfer. Allelic types were exclusive to lineages, except for a single gap allele, and nucleotide distance within lineages was much lower than that between lineages, suggesting that genetic exchange between lineages is rare. Our data show that (i) L. monocytogenes is a highly diverse species with at least two distinct phylogenetic lineages differing in their evolutionary history and population structure and (ii) horizontal gene transfer as well as positive selection contributed to the evolution of L. monocytogenes.

scholarly journals Evidence of Extensive Intraspecific Noncoding Reshuffling in a 169-kb Mitochondrial Genome of a Basidiomycetous Fungus

2019 ◽  
Vol 11 (10) ◽  
pp. 2774-2788 ◽  
Author(s):  
Hsin-Han Lee ◽  
Huei-Mien Ke ◽  
Chan-Yi Ivy Lin ◽  
Tracy J Lee ◽  
Chia-Lin Chung ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Size Variation ◽  
Sequence Divergence ◽  
Intergenic Sequence ◽  
Protein Coding ◽  
Genetic Lineages ◽  
Basidiomycetous Fungus ◽  
Mitochondrial Dnas ◽  
Phellinus Noxius

Abstract Comparative genomics of fungal mitochondrial genomes (mitogenomes) have revealed a remarkable pattern of rearrangement between and within major phyla owing to horizontal gene transfer and recombination. The role of recombination was exemplified at a finer evolutionary time scale in basidiomycetes group of fungi as they display a diversity of mitochondrial DNA inheritance patterns. Here, we assembled mitogenomes of six species from the Hymenochaetales order of basidiomycetes and examined 59 mitogenomes from 2 genetic lineages of Phellinus noxius. Gene order is largely collinear, while intergene regions are major determinants of mitogenome size variation. Substantial sequence divergence was found in shared introns consistent with high horizontal gene transfer frequency observed in yeasts, but we also identified a rare case where an intron was retained in five species since speciation. In contrast to the hyperdiversity observed in nuclear genomes of Phellinus noxius, mitogenomes’ intraspecific polymorphisms at protein-coding sequences are extremely low. Phylogeny network based on introns revealed turnover as well as exchange of introns between two lineages. Strikingly, some strains harbor a mosaic origin of introns from both lineages. Analysis of intergenic sequence indicated substantial differences between and within lineages, and an expansion may be ongoing as a result of exchange between distal intergenes. These findings suggest that the evolution in mitochondrial DNAs is usually lineage specific but chimeric mitotypes are frequently observed, thus capturing the possible evolutionary processes shaping mitogenomes in a basidiomycete. The large mitogenome sizes reported in various basidiomycetes appear to be a result of interspecific reshuffling of intergenes.

scholarly journals Diversification of OmpA and OmpF of Yersinia ruckeri is independent of the underlying species phylogeny and evidence of virulence-related selection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Michael J. Ormsby ◽  
Robert L. Davies
Keyword(s):  
Rainbow Trout ◽  
Amino Acid ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Atlantic Salmon ◽  
Sequence Variation ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Yersinia Ruckeri ◽  
Amino Acid Sequence Variation

AbstractYersinia ruckeri is the causative agent of enteric redmouth disease (ERM) which causes economically significant losses in farmed salmonids, especially Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss, Walbaum). However, very little is known about the genetic relationships of disease-causing isolates in these two host species or about factors responsible for disease. Phylogenetic analyses of 16 representative isolates based on the nucleotide sequences of 19 housekeeping genes suggests that pathogenic Atlantic salmon and rainbow trout isolates represent distinct host-specific lineages. However, the apparent phylogenies of certain isolates has been influenced by horizontal gene transfer and recombinational exchange. Splits decomposition analysis demonstrated a net-like phylogeny based on the housekeeping genes, characteristic of recombination. Comparative analysis of the distribution of individual housekeeping gene alleles across the isolates demonstrated evidence of genomic mosaicism and recombinational exchange involving certain Atlantic salmon and rainbow trout isolates. Comparative nucleotide sequence analysis of the key outer membrane protein genes ompA and ompF revealed that the corresponding gene trees were both non-congruent with respect to the housekeeping gene phylogenies providing evidence that horizontal gene transfer has influenced the evolution of both these surface protein-encoding genes. Analysis of inferred amino acid sequence variation in OmpA identified a single variant, OmpA.1, that was present in serotype O1 and O8 isolates representing typical pathogenic strains in rainbow trout and Atlantic salmon, respectively. In particular, the sequence of surface-exposed loop 3 differed by seven amino acids to that of other Y. ruckeri isolates. These findings suggest that positive selection has likely influenced the presence of OmpA.1 in these isolates and that loop 3 may play an important role in virulence. Amino acid sequence variation of OmpF was greater than that of OmpA and was similarly restricted mainly to the surface-exposed loops. Two OmpF variants, OmpF.1 and OmpF.2, were associated with pathogenic rainbow trout and Atlantic salmon isolates, respectively. These OmpF proteins had very similar amino acid sequences suggesting that positive evolutionary pressure has also favoured the selection of these variants in pathogenic strains infecting both species.

scholarly journals Exploring Genetic Diversity and Signatures of Horizontal Gene Transfer in Nodule Bacteria Associated with Lotus japonicus in Natural Environments

2019 ◽  
Vol 32 (9) ◽  
pp. 1110-1120 ◽  
Author(s):  
Masaru Bamba ◽  
Seishiro Aoki ◽  
Tadashi Kajita ◽  
Hiroaki Setoguchi ◽  
Yasuyuki Watano ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Lotus Japonicus ◽  
Population Expansion ◽  
Housekeeping Genes ◽  
Natural Environments ◽  
Symbiotic Genes ◽  
Nodule Bacteria ◽  
Wide Range

To investigate the genetic diversity and understand the process of horizontal gene transfer (HGT) in nodule bacteria associated with Lotus japonicus, we analyzed sequences of three housekeeping and five symbiotic genes using samples from a geographically wide range in Japan. A phylogenetic analysis of the housekeeping genes indicated that L. japonicus in natural environments was associated with diverse lineages of Mesorhizobium spp., whereas the sequences of symbiotic genes were highly similar between strains, resulting in remarkably low nucleotide diversity at both synonymous and nonsynonymous sites. Guanine-cytosine content values were lower in symbiotic genes, and relative frequencies of recombination between symbiotic genes were also lower than those between housekeeping genes. An analysis of molecular variance showed significant genetic differentiation among populations in both symbiotic and housekeeping genes. These results confirm that the Mesorhizobium genes required for symbiosis with L. japonicus behave as a genomic island (i.e., a symbiosis island) and suggest that this island has spread into diverse genomic backgrounds of Mesorhizobium via HGT events in natural environments. Furthermore, our data compilation revealed that the genetic diversity of symbiotic genes in L. japonicus-associated symbionts was among the lowest compared with reports of other species, which may be related to the recent population expansion proposed in Japanese populations of L. japonicus.

scholarly journals Protein citrullination was introduced into animals by horizontal gene transfer from cyanobacteria

2020 ◽  
Author(s):  
Thomas F. M. Cummings ◽  
Kevin Gori ◽  
Luis Sanchez-Pulido ◽  
Gabriel Gavriilidis ◽  
David Moi ◽  
...  
Keyword(s):  
Human Physiology ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Protein Modification ◽  
Sequence Divergence ◽  
Time Frame ◽  
Last Common Ancestor ◽  
Evolutionary Trajectory ◽  
Post Translational Modifications ◽  
Evolutionary Context

AbstractProtein post-translational modifications (PTMs) add an enormous amount of sophistication to biological systems but their origins are largely unexplored. Citrullination, a key regulatory mechanism in human physiology and pathophysiology, is particularly enigmatic in an evolutionary context. The citrullinating enzymes peptidylarginine deiminases (PADIs) are ubiquitous across vertebrates but absent from yeast, worms and flies. Here, we map the surprising evolutionary trajectory of PADIs into the animal lineage. We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologues. The animal and cyanobacterial PADIs share unique, functionally relevant synapomorphies that are absent from all other homologues. Molecular clock calculations and sequence divergence analyses using the fossil record estimate the last common ancestor of the cyanobacterial and animal PADIs to be approximately 1 billion years old, far younger than the 3.35-4.52 billion years known to separate bacterial and eukaryotic lineages. Under an assumption of vertical descent, PADI sequence change is anachronistically slow during this evolutionary time frame, even when compared to mitochondrial proteins, products of likely endosymbiont gene transfer and some of the most highly conserved proteins in life. The consilience of evidence indicates that PADIs were introduced from cyanobacteria into animals by horizontal gene transfer (HGT). The ancestral cyanobacterial protein is enzymatically active and can citrullinate eukaryotic proteins, suggesting that the PADI HGT event introduced a new catalytic capability into the regulatory repertoire of animals. This study reveals the unusual evolution of a pleiotropic protein modification with clear relevance in human physiology and disease.

scholarly journals The Phylogenomics of CRISPR-Cas System in Salmonella: an evolutionary race with housekeeping genes

2020 ◽  
Author(s):  
Simran Krishnakant Kushwaha ◽  
Chandrajit Lahiri ◽  
Bahaa Abdella ◽  
Sandhya Amol Marathe
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Virulence Factors ◽  
Horizontal Gene Transfer Event ◽  
Housekeeping Genes ◽  
Broad Host Range ◽  
Evolutionary Patterns ◽  
Transfer Event ◽  
Serovar Typhimurium ◽  
Cas Genes

AbstractSalmonellae display intricate evolutionary patterns comprising over 2500 serovars having diverse pathogenic profiles. The acquisition/exchange of various virulence factors influence the evolutionary framework. To gain insights into evolution of Salmonella as a pathogen in association with the CRISPR-Cas genes we performed phylogenetic surveillance across strains of 22 Salmonella serovars. The strains assorted into two main clades, pertaining to the differences in their CRISPR1-leader and cas operon. Considering Salmonella enterica subsp. enterica serovar Typhimurium and serovar Typhi as signature serovars, we classified the clades as CRISPR1-STM/cas-STM and CRISPR1-STY/cas-STY, respectively. Serovars of the two clades displayed better relatedness, concerning CRISPR-1 leader and cas operon, across genera than between themselves. This signifies the acquisition of CRISPR1/Cas region a horizontal gene transfer event owing to the presence of mobile genetic elements flanking CRISPR1 array. The CRISPR2 tree does not show such relation. Spacer mapping of the two CRISPR arrays suggests the construct to be canonical, with only 8.8% spacer conservation among the serovars. As opposed to broad-host-range serovars, the host-specific serovars harbor fewer spacers. All typhoidal serovars have CRISPR1-STY/cas-STY system. Comparison of CRISPR and cas phenograms with that of multilocus sequence typing (MLST) suggests differential evolution of CRISPR/Cas system implying supplementary roles beyond immunity.

scholarly journals Adaptive evolution of hybrid bacteria by horizontal gene transfer

2020 ◽  
Author(s):  
Jeffrey J. Power ◽  
Fernanda Pinheiro ◽  
Simone Pompei ◽  
Viera Kovacova ◽  
Melih Yüksel ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Statistical Modeling ◽  
Adaptive Evolution ◽  
Gene Networks ◽  
Evolutionary Dynamics ◽  
Fitness Landscape ◽  
Parallel Evolution ◽  
Evolution Experiment

AbstractHorizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient organism’s physiology and fitness. Here, we address these questions in a parallel evolution experiment with two Bacillus subtilis lineages of 7% sequence divergence. We observe rapid evolution of hybrid organisms: gene transfer swaps ~12% of the core genome in just 200 generations, and 60% of core genes are replaced in at least one population. By genomics, transcriptomics, fitness assays, and statistical modeling, we show that transfer generates adaptive evolution and functional alterations in hybrids. Specifically, our experiments reveal a strong, repeatable fitness increase of evolved populations in the stationary growth phase. By genomic analysis of the transfer statistics across replicate populations, we infer that selection on HGT has a broad genetic basis: 40% of the observed transfers are adaptive. At the level of functional gene networks, we find signatures of negative and positive selection, consistent with hybrid incompatibilities and adaptive evolution of network functions. Our results suggest that gene transfer navigates a complex cross-lineage fitness landscape, bridging epistatic barriers along multiple high-fitness paths.Significance statementIn a parallel evolution experiment, we probe lateral gene transfer between two Bacillus subtilis lineages close to the species boundary. We show that laboratory evolution by horizontal gene transfer can rapidly generate hybrid organisms with broad genomic and functional alterations. By combining genomics, transcriptomics, fitness assays and statistical modeling, we map the selective effects underlying gene transfer. We show that transfer takes place under genome-wide positive and negative selection, generating a net fitness increase in hybrids. The evolutionary dynamics efficiently navigates this fitness landscape, finding viable paths with increasing fraction of transferred genes.

scholarly journals Citrullination was introduced into animals by horizontal gene transfer from cyanobacteria

2021 ◽  
Author(s):  
Thomas F M Cummings ◽  
Kevin Gori ◽  
Luis Sanchez-Pulido ◽  
Gavriil Gavriilidis ◽  
David Moi ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Protein Modification ◽  
Sequence Divergence ◽  
Time Frame ◽  
Last Common Ancestor ◽  
Evolutionary Time ◽  
Evolutionary Trajectory ◽  
Post Translational Modifications ◽  
Eukaryotic Proteins

Abstract Protein post-translational modifications (PTMs) add great sophistication to biological systems. Citrullination, a key regulatory mechanism in human physiology and pathophysiology, is enigmatic from an evolutionary perspective. Although the citrullinating enzymes peptidylarginine deiminases (PADIs) are ubiquitous across vertebrates, they are absent from yeast, worms and flies. Based on this distribution PADIs were proposed to have been horizontally transferred, but this has been contested. Here, we map the evolutionary trajectory of PADIs into the animal lineage. We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologues. The animal and cyanobacterial PADI proteins share functionally relevant primary and tertiary synapomorphic sequences that are distinct from a second PADI type present in fungi and actinobacteria. Molecular clock calculations and sequence divergence analyses using the fossil record estimate the last common ancestor of the cyanobacterial and animal PADIs to be less than one billion years old. Additionally, under an assumption of vertical descent, PADI sequence change during this evolutionary time frame is anachronistically low, even when compared to products of likely endosymbiont gene transfer, mitochondrial proteins and some of the most highly conserved sequences in life. The consilience of evidence indicates that PADIs were introduced from cyanobacteria into animals by horizontal gene transfer (HGT). The ancestral cyanobacterial PADI is enzymatically active and can citrullinate eukaryotic proteins, suggesting that the PADI HGT event introduced a new catalytic capability into the regulatory repertoire of animals. This study reveals the unusual evolution of a pleiotropic protein modification.

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