scholarly journals Recombination and gene loss occur simultaneously during bacterial horizontal gene transfer

PLoS ONE ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. e0227987 ◽  
Author(s):  
Bert Ely
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Loss

scholarly journals Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile “Ferrovum”

2016 ◽  
Vol 7 ◽  
Author(s):  
Sophie R. Ullrich ◽  
Carolina González ◽  
Anja Poehlein ◽  
Judith S. Tischler ◽  
Rolf Daniel ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Evolution ◽  
Gene Loss

scholarly journals Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

2017 ◽  
Vol 83 (7) ◽  
Author(s):  
Xian Zhang ◽  
Xueduan Liu ◽  
Yili Liang ◽  
Xue Guo ◽  
Yunhua Xiao ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Adaptive Evolution ◽  
Gene Loss ◽  
Environmental Changes ◽  
Driving Forces ◽  
Critical Force ◽  
Phylogenomic Analysis ◽  
Content Type ◽  
Microbial Genomes

ABSTRACT Recent phylogenomic analysis has suggested that three strains isolated from different copper mine tailings around the world were taxonomically affiliated with Sulfobacillus thermosulfidooxidans. Here, we present a detailed investigation of their genomic features, particularly with respect to metabolic potentials and stress tolerance mechanisms. Comprehensive analysis of the Sulfobacillus genomes identified a core set of essential genes with specialized biological functions in the survival of acidophiles in their habitats, despite differences in their metabolic pathways. The Sulfobacillus strains also showed evidence for stress management, thereby enabling them to efficiently respond to harsh environments. Further analysis of metabolic profiles provided novel insights into the presence of genomic streamlining, highlighting the importance of gene loss as a main mechanism that potentially contributes to cellular economization. Another important evolutionary force, especially in larger genomes, is gene acquisition via horizontal gene transfer (HGT), which might play a crucial role in the recruitment of novel functionalities. Also, a successful integration of genes acquired from archaeal donors appears to be an effective way of enhancing the adaptive capacity to cope with environmental changes. Taken together, the findings of this study significantly expand the spectrum of HGT and genome reduction in shaping the evolutionary history of Sulfobacillus strains. IMPORTANCE Horizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional novel functionalities to increase the capacity of acidophiles to adapt to changing environments. Evidence also reveals a fascinating phenomenon of potential cross-kingdom HGT. Furthermore, genome streamlining may be a critical force in driving the evolution of microbial genomes. Taken together, this study provides insights into the importance of both HGT and gene loss in the evolution and diversification of bacterial genomes.

scholarly journals Evolution of plasmid mobility: origin and fate of non-conjugative plasmids

2021 ◽  
Author(s):  
Charles Coluzzi ◽  
Maria del Pilar Garcillán-Barcia ◽  
Fernando de la Cruz ◽  
Eduardo P.C. Rocha
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Transposable Elements ◽  
Gene Deletion ◽  
Gene Loss ◽  
Adaptive Traits ◽  
Plasmid Evolution ◽  
Conjugative Plasmids ◽  
Rate Of Evolution ◽  
Source Sink

AbstractConjugation drives horizontal gene transfer of many adaptive traits across prokaryotes. Yet, only a fourth of the plasmids encode the functions necessary to conjugate autonomously, others being non-mobile or mobilizable by other elements. How these different plasmids evolve is poorly understood. Here, we studied plasmid evolution in terms of their gene repertoires and relaxases. We observed that gene content in plasmid varies rapidly in relation to the rate of evolution of relaxases, such that plasmids with 95% identical relaxases have on average fewer than 50% of homologs. The identification of 249 recent transitions in terms of mobility types revealed that they are associated with even greater changes in gene repertoires, possibly mediated by transposable elements that are more abundant in such plasmids. These changes include pseudogenization of the conjugation locus, exchange of replication initiators, and extensive gene loss. In some instances, the transition between mobility types also leads to the genesis of novel plasmid taxonomic units. Most of these transitions are short-lived, suggesting a source-sink dynamic, where conjugative plasmids constantly generate mobilizable and putatively non-mobilizable plasmids by gene deletion. Yet, in few cases such transitions resulted in the emergence of large clades of relaxases present only in mobilizable plasmids, suggesting successful specialization of these families in the hijacking of diverse conjugative systems. Our results shed further light on the huge plasticity of plasmids, suggest that many non-conjugative plasmids emerged recently from conjugative elements and allowed to quantify how changes in plasmid mobility shape the variation of their gene repertoires.

scholarly journals Horizontal gene transfer drives the evolution of dependencies in bacteria

2019 ◽  
Author(s):  
Akshit Goyal
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Metabolic Networks ◽  
Gene Loss ◽  
Bacterial Species ◽  
Gene Gain ◽  
Metabolic Interactions ◽  
Gain Loss ◽  
Gains And Losses ◽  
The Impact

Many naturally-occurring bacteria lead a lifestyle of metabolic dependency, i.e., they depend on others for crucial resources. We do not understand what factors drive bacteria towards this lifestyle, and how. Here, we systematically show that horizontal gene transfer (HGT) plays a crucial role in the evolution of dependencies in bacteria. Across 835 bacterial species, we map gene gain-loss dynamics on a deep evolutionary tree, and assess the impact of HGT and gene loss on bacterial metabolic networks. Our analyses suggest that genes acquired by HGT can affect which genes are later lost. Dependency evolution is contingent on earlier HGT because of two reasons. First, we find that HGT typically adds new catabolic routes to bacterial metabolic networks. This increases the chance of new metabolic interactions between bacteria, which is a prerequisite for dependency evolution. Second, we show that gaining new routes can promote the loss of specific ancestral routes (a mechanism we call “coupled gains and losses”, CGLs). Phylogenetic patterns indicate that both types of dependencies — those mediated by CGLs and those purely by gene loss — are equally likely. Our results highlight HGT as an important driver of metabolic dependency evolution in bacteria.

scholarly journals HOW DOES THE HORIZONTAL GENE TRANSFER IN BACTERIA OCCUR AND THAN IS IT TIED UP

2007 ◽  
Vol 5 (2) ◽  
pp. 12-24
Author(s):  
Sergey V Shestakov
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Loss ◽  
Driving Forces ◽  
Decisive Role ◽  
Mobile Elements ◽  
Ecological Diversification ◽  
Population Processes ◽  
Definition Of

Horizontal gene transfer as well as mutations, ge- nomic reorganization and gene loss is one of major driving forces of speciation and evolution of bacteria. A notion of definition of "species genome" is presented. The role of various types of mobile elements in distant gene transfer is considered. The nature of barriers for suc- cessful gene transfer on the level of molecular, cell and population processes is uncovered. A special attention is paid to the contribution of different systems of recombination. Hypothesis on the decisive role of horizontal gene transfer in genetic and ecological diversification of bacteria is discussed.

scholarly journals Chemoreceptor Gene Loss and Acquisition via Horizontal Gene Transfer in Escherichia coli

2013 ◽  
Vol 195 (16) ◽  
pp. 3596-3602 ◽  
Author(s):  
K. Borziak ◽  
A. D. Fleetwood ◽  
I. B. Zhulin
Keyword(s):  
Escherichia Coli ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Loss

scholarly journals Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
David Moreira ◽  
Yvan Zivanovic ◽  
Ana I. López-Archilla ◽  
Miguel Iniesto ◽  
Purificación López-García
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Loss ◽  
De Novo ◽  
Small Cell ◽  
Bacterial Populations ◽  
Gene Acquisition ◽  
Cytoplasmic Content ◽  
New Hosts ◽  
Candidate Phyla Radiation

AbstractThe Candidate Phyla Radiation (CPR) constitutes a large group of mostly uncultured bacterial lineages with small cell sizes and limited biosynthetic capabilities. They are thought to be symbionts of other organisms, but the nature of this symbiosis has been ascertained only for cultured Saccharibacteria, which are epibiotic parasites of other bacteria. Here, we study the biology and the genome of Vampirococcus lugosii, which becomes the first described species of Vampirococcus, a genus of epibiotic bacteria morphologically identified decades ago. Vampirococcus belongs to the CPR phylum Absconditabacteria. It feeds on anoxygenic photosynthetic gammaproteobacteria, fully absorbing their cytoplasmic content. The cells divide epibiotically, forming multicellular stalks whose apical cells can reach new hosts. The genome is small (1.3 Mbp) and highly reduced in biosynthetic metabolism genes, but is enriched in genes possibly related to a fibrous cell surface likely involved in interactions with the host. Gene loss has been continuous during the evolution of Absconditabacteria, and generally most CPR bacteria, but this has been compensated by gene acquisition by horizontal gene transfer and de novo evolution. Our findings support parasitism as a widespread lifestyle of CPR bacteria, which probably contribute to the control of bacterial populations in diverse ecosystems.

Sign in / Sign up

Export Citation Format

Share Document