Evolution of land plant genes encoding L-Ala-D/L-Glu epimerases (AEEs) via horizontal gene transfer and positive selection

ABSTRACT Arthrobacter chlorophenolicus A6, a previously described 4-chlorophenol-degrading strain, was found to degrade 4-chlorophenol via hydroxyquinol, which is a novel route for aerobic microbial degradation of this compound. In addition, 10 open reading frames exhibiting sequence similarity to genes encoding enzymes involved in chlorophenol degradation were cloned and designated part of a chlorophenol degradation gene cluster (cph genes). Several of the open reading frames appeared to encode enzymes with similar functions; these open reading frames included two genes, cphA-I and cphA-II, which were shown to encode functional hydroxyquinol 1,2-dioxygenases. Disruption of the cphA-I gene yielded a mutant that exhibited negligible growth on 4-chlorophenol, thereby linking the cph gene cluster to functional catabolism of 4-chlorophenol in A. chlorophenolicus A6. The presence of a resolvase pseudogene in the cph gene cluster together with analyses of the G+C content and codon bias of flanking genes suggested that horizontal gene transfer was involved in assembly of the gene cluster during evolution of the ability of the strain to grow on 4-chlorophenol.

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

Journal of Bacteriology ◽

10.1128/jb.187.16.5537-5551.2005 ◽

2005 ◽

Vol 187 (16) ◽

pp. 5537-5551 ◽

Cited By ~ 137

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.

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Horizontal Transfer of Bacterial Cytolethal Distending Toxin B Genes to Insects

Molecular Biology and Evolution ◽

10.1093/molbev/msz146 ◽

2019 ◽

Vol 36 (10) ◽

pp. 2105-2110 ◽

Cited By ~ 2

Author(s):

Kirsten I Verster ◽

Jennifer H Wisecaver ◽

Marianthi Karageorgi ◽

Rebecca P Duncan ◽

Andrew D Gloss ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Natural Enemies ◽

Larval Stage ◽

Horizontal Transfer ◽

Parasitoid Wasps ◽

Cytolethal Distending Toxin ◽

Toxin B ◽

Genes Encoding ◽

Hamiltonella Defensa

Abstract Horizontal gene transfer events have played a major role in the evolution of microbial species, but their importance in animals is less clear. Here, we report horizontal gene transfer of cytolethal distending toxin B (cdtB), prokaryotic genes encoding eukaryote-targeting DNase I toxins, into the genomes of vinegar flies (Diptera: Drosophilidae) and aphids (Hemiptera: Aphididae). We found insect-encoded cdtB genes are most closely related to orthologs from bacteriophage that infect Candidatus Hamiltonella defensa, a bacterial mutualistic symbiont of aphids that confers resistance to parasitoid wasps. In drosophilids, cdtB orthologs are highly expressed during the parasitoid-prone larval stage and encode a protein with ancestral DNase activity. We show that cdtB has been domesticated by diverse insects and hypothesize that it functions in defense against their natural enemies.

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The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2013.1021 ◽

2013 ◽

Vol 280 (1763) ◽

pp. 20131021 ◽

Cited By ~ 52

Author(s):

Yannick Pauchet ◽

David G. Heckel

Keyword(s):

Cell Wall ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Plant Cell ◽

Plant Cell Wall ◽

Genetic Material ◽

Leaf Beetle ◽

Glycoside Hydrolase Family ◽

Cell Wall Degrading Enzymes ◽

Genes Encoding

The primary plant cell wall comprises the most abundant polysaccharides on the Earth and represents a rich source of energy for organisms which have evolved the ability to digest them. Enzymes able to degrade plant cell wall polysaccharides are widely distributed in micro-organisms but are generally absent in animals, although their presence in insects, especially phytophagous beetles from the superfamilies Chrysomeloidea and Curculionoidea, has recently begun to be appreciated. The observed patchy distribution of endogenous genes encoding these enzymes in animals has raised questions about their evolutionary origins. Recent evidence suggests that endogenous plant cell wall degrading enzymes-encoding genes have been acquired by animals through a mechanism known as horizontal gene transfer (HGT). HGT describes how genetic material is moved by means other than vertical inheritance from a parent to an offspring. Here, we provide evidence that the mustard leaf beetle, Phaedon cochleariae , possesses in its genome genes encoding active xylanases from the glycoside hydrolase family 11 (GH11). We also provide evidence that these genes were originally acquired by P. cochleariae from a species of gammaproteobacteria through HGT. This represents the first example of the presence of genes from the GH11 family in animals.

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Horizontally transferred genes in the ctenophore Mnemiopsis leidyi

10.7287/peerj.preprints.3462 ◽

2018 ◽

Author(s):

Alexandra M Hernandez ◽

Joseph F Ryan

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genetic Information ◽

Mnemiopsis Leidyi ◽

Uncharacterized Protein ◽

Phylogenetic Incongruence ◽

Wide Range ◽

Growing Body ◽

Genes Encoding

Horizontal gene transfer has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that horizontal gene transfer (HGT) between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.

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Horizontally transferred genes in the ctenophore Mnemiopsis leidyi

10.7287/peerj.preprints.3462v3 ◽

2018 ◽

Author(s):

Alexandra M Hernandez ◽

Joseph F Ryan

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genetic Information ◽

Mnemiopsis Leidyi ◽

Uncharacterized Protein ◽

Phylogenetic Incongruence ◽

Wide Range ◽

Growing Body ◽

Genes Encoding

Horizontal gene transfer has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that horizontal gene transfer (HGT) between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.

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Deep sequencing revealed molecular signature of horizontal gene transfer of plant like transcripts in the mosquito Anopheles culicifacies: an evolutionary puzzle

F1000Research ◽

10.12688/f1000research.7534.1 ◽

2015 ◽

Vol 4 ◽

pp. 1523 ◽

Cited By ~ 3

Author(s):

Punita Sharma ◽

Tanwee Das De ◽

Swati Sharma ◽

Ashwani Kumar Mishra ◽

Tina Thomas ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Functional Role ◽

Underlying Mechanism ◽

Molecular Signature ◽

Anopheles Culicifacies ◽

Genomic Tools ◽

Plant Genes ◽

Experimental Validations

In prokaryotes, horizontal gene transfer (HGT) has been regarded as an important evolutionary drive to acquire and retain beneficial genes for their survival in diverse ecologies. However, in eukaryotes, the functional role of HGTs remains questionable, although current genomic tools are providing increased evidence of acquisition of novel traits within non-mating metazoan species. Here, we provide another transcriptomic evidence for the acquisition of massive plant genes in the mosquito,Anopheles culicifacies. Our multiple experimental validations including genomic PCR, RT-PCR, real-time PCR, immuno-blotting and immuno-florescence microscopy, confirmed that plant like transcripts (PLTs) are of mosquito origin and may encode functional proteins. A comprehensive molecular analysis of the PLTs and ongoing metagenomic analysis of salivary microbiome provide initial clues that mosquitoes may have survival benefits through the acquisition of nuclear as well as chloroplast encoded plant genes. Our findings of PLTs further support the similar questionable observation of HGTs in other higher organisms, which is still a controversial and debatable issue in the community of evolutionists. We believe future understanding of the underlying mechanism of the feeding associated molecular responses may shed new insights in the functional role of PLTs in the mosquito.

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Horizontally transferred genes in the ctenophore Mnemiopsis leidyi

PeerJ ◽

10.7717/peerj.5067 ◽

2018 ◽

Vol 6 ◽

pp. e5067 ◽

Cited By ~ 2

Author(s):

Alexandra M. Hernandez ◽

Joseph F. Ryan

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genetic Information ◽

Mnemiopsis Leidyi ◽

Uncharacterized Protein ◽

Phylogenetic Incongruence ◽

Wide Range ◽

Growing Body ◽

Genes Encoding

Horizontal gene transfer (HGT) has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that HGT between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.

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