scholarly journals Roles of Horizontal Gene Transfer and Gene Integration in Evolution of 1,3-Dichloropropene- and 1,2-Dibromoethane-Degradative Pathways

2000 ◽  
Vol 182 (8) ◽  
pp. 2191-2199 ◽  
Author(s):  
Gerrit J. Poelarends ◽  
Leonid A. Kulakov ◽  
Michael J. Larkin ◽  
Johan E. T. van Hylckama Vlieg ◽  
Dick B. Janssen
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Regulatory Protein ◽  
Constitutive Expression ◽  
Haloalkane Dehalogenase ◽  
Coding Region ◽  
Integrase Gene ◽  
Gene Acquisition ◽  
Degrading Bacteria ◽  
Flanking Sequences

ABSTRACT The haloalkane-degrading bacteria Rhodococcus rhodochrous NCIMB13064, Pseudomonas pavonaceae 170, and Mycobacterium sp. strain GP1 share a highly conserved haloalkane dehalogenase gene (dhaA). Here, we describe the extent of the conserved dhaA segments in these three phylogenetically distinct bacteria and an analysis of their flanking sequences. The dhaA gene of the 1-chlorobutane-degrading strain NCIMB13064 was found to reside within a 1-chlorobutane catabolic gene cluster, which also encodes a putative invertase (invA), a regulatory protein (dhaR), an alcohol dehydrogenase (adhA), and an aldehyde dehydrogenase (aldA). The latter two enzymes may catalyze the oxidative conversion of n-butanol, the hydrolytic product of 1-chlorobutane, to n-butyric acid, a growth substrate for many bacteria. The activity of the dhaR gene product was analyzed in Pseudomonas sp. strain GJ1, in which it appeared to function as a repressor of dhaA expression. The 1,2-dibromoethane-degrading strain GP1 contained a conserved DNA segment of 2.7 kb, which included dhaR, dhaA, and part of invA. A 12-nucleotide deletion indhaR led to constitutive expression of dhaA in strain GP1, in contrast to the inducible expression of dhaAin strain NCIMB13064. The 1,3-dichloropropene-degrading strain 170 possessed a conserved DNA segment of 1.3 kb harboring little more than the coding region of the dhaA gene. In strains 170 and GP1, a putative integrase gene was found next to the conserveddhaA segment, which suggests that integration events were responsible for the acquisition of these DNA segments. The data indicate that horizontal gene transfer and integrase-dependent gene acquisition were the key mechanisms for the evolution of catabolic pathways for the man-made chemicals 1,3-dichloropropene and 1,2-dibromoethane.

scholarly journals Homologues of Genetic Transformation DNA Import Genes Are Required for Rhodobacter capsulatus Gene Transfer Agent Recipient Capability Regulated by the Response Regulator CtrA

2015 ◽  
Vol 197 (16) ◽  
pp. 2653-2663 ◽  
Author(s):  
Cedric A. Brimacombe ◽  
Hao Ding ◽  
Jeanette A. Johnson ◽  
J. Thomas Beatty
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Rhodobacter Capsulatus ◽  
Natural Transformation ◽  
Response Regulator ◽  
Content Type ◽  
Gene Acquisition ◽  
Metabolic Properties ◽  
Cell Genome ◽  
Key Aspects

ABSTRACTGene transfer agents (GTAs) morphologically resemble small, double-stranded DNA (dsDNA) bacteriophages; however, their only known role is to package and transfer random pieces of the producing cell genome to recipient cells. The best understood GTA is that ofRhodobacter capsulatus, termed RcGTA. We discovered that homologues of three genes involved in natural transformation in other bacteria,comEC,comF, andcomM, are essential for RcGTA-mediated gene acquisition. This paper gives genetic and biochemical evidence that RcGTA-borne DNA entry into cells requires the ComEC and ComF putative DNA transport proteins and genetic evidence that putative cytoplasmic ComM protein of unknown function is required for recipient capability. Furthermore, the master regulator of RcGTA production in <1% of a cell population, CtrA, which is also required for gene acquisition in recipient cells, is expressed in the vast majority of the population. Our results indicate that RcGTA-mediated gene transfer combines key aspects of two bacterial horizontal gene transfer mechanisms, where donor DNA is packaged in transducing phage-like particles and recipient cells take up DNA using natural transformation-related machinery. Both of these differentiated subsets of a culture population, donors and recipients, are dependent on the same response regulator, CtrA.IMPORTANCEHorizontal gene transfer (HGT) is a major driver of bacterial evolution and adaptation to environmental stresses. Traits such as antibiotic resistance or metabolic properties can be transferred between bacteria via HGT; thus, HGT can have a tremendous effect on the fitness of a bacterial population. The three classically described HGT mechanisms are conjugation, transformation, and phage-mediated transduction. More recently, the HGT factor GTA was described, where random pieces of producing cell genome are packaged into phage-like particles that deliver DNA to recipient cells. In this report, we show that transport of DNA borne by theR. capsulatusRcGTA into recipient cells requires key genes previously thought to be specific to natural transformation pathways. These findings indicate that RcGTA combines central aspects of phage-mediated transduction and natural transformation in an efficient, regulated mode of HGT.

Archaeal integrases and mechanisms of gene capture

2004 ◽  
Vol 32 (2) ◽  
pp. 222-226 ◽  
Author(s):  
Q. She ◽  
B. Shen ◽  
L. Chen
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Evolution ◽  
Trna Genes ◽  
Gene Fragment ◽  
Integrase Gene ◽  
Site Specific ◽  
Conjugative Plasmids ◽  
Site Specific Integration ◽  
Target Sites

Archaeal integrases facilitate the formation of two distinctive types of integrated element within archaeal chromosomes: the SSV type and pNOB8 type. The former carries a smaller N-terminal and a larger C-terminal integrase gene fragment, and the latter an intact integrase gene. All integrated elements overlap tRNA genes that were target sites for integration. It has been demonstrated that SSV (Sulfolobus spindle virus) viruses, carrying an SSV-type integrase gene, and conjugative plasmids, carrying a pNOB8-type integrase, are integrative elements. Two mechanisms have been proposed for stably maintaining an integrated element within archaeal chromosomes. There is also evidence for changes having occurred in the captured integrated elements present in archaeal genomes. Thus we infer that site-specific integration constitutes an important mechanism for horizontal gene transfer and genome evolution.

scholarly journals Interspecies transfer of syntenic RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture

2022 ◽  
Author(s):  
Josh Strable ◽  
Erica Unger-Wallace ◽  
Alejandro Aragón-Raygoza ◽  
Sarah Briggs ◽  
Erik Vollbrecht
Keyword(s):  
Gene Transfer ◽  
Upstream Region ◽  
Coding Region ◽  
Inflorescence Architecture ◽  
Inflorescence Development ◽  
Temporal Regulation ◽  
Functional Conservation ◽  
Inflorescence Morphology ◽  
Key Factor ◽  
Flanking Sequences

Grass inflorescences support floral structures that each bear a single grain, where variation in branch architecture directly impacts yield. The maize RAMOSA1 (ZmRA1) transcription factor acts as a key regulator of inflorescence development by imposing branch meristem determinacy. Here, we show RA1 transcripts accumulate in boundary domains adjacent to spikelet meristems in Sorghum bicolor (Sb) and Setaria viridis (Sv) inflorescences similar as in the developing maize tassel and ear. To evaluate functional conservation of syntenic RA1 orthologs and promoter cis sequences in maize, sorghum and setaria, we utilized interspecies gene transfer and assayed genetic complementation in a common inbred background by quantifying recovery of normal branching in highly ramified ra1-R mutants. A ZmRA1 transgene that includes endogenous upstream and downstream flanking sequences recovered normal tassel and ear branching in ra1-R. Interspecies expression of two transgene variants of the SbRA1 locus, modeled as the entire endogenous tandem duplication or just the non-frameshifted downstream copy, complemented ra1-R branching defects and induced novel fasciation and branch patterns. The SvRA1 locus lacks conserved, upstream noncoding cis sequences found in maize and sorghum; interspecies expression of an SvRA1 transgene did not or only partially recovered normal inflorescence forms. Driving expression of the SvRA1 coding region by the ZmRA1 upstream region, however, recovered normal inflorescence morphology in ra1-R. These data leveraging interspecies gene transfer suggest that cis-encoded temporal regulation of RA1 expression is a key factor in modulating branch meristem determinacy that ultimately impacts grass inflorescence architecture.

scholarly journals Environment-dependent fitness gains can be driven by horizontal gene transfer of transporter-encoding genes

2019 ◽  
Vol 116 (12) ◽  
pp. 5613-5622 ◽  
Author(s):  
David S. Milner ◽  
Victoria Attah ◽  
Emily Cook ◽  
Finlay Maguire ◽  
Fiona R. Savory ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Fitness Landscape ◽  
Single Gene ◽  
Transporter Gene ◽  
Metabolic Potential ◽  
Gene Acquisition ◽  
A Genome ◽  
Complex Polymers ◽  
Encoding Genes

Many microbes acquire metabolites in a “feeding” process where complex polymers are broken down in the environment to their subunits. The subsequent uptake of soluble metabolites by a cell, sometimes called osmotrophy, is facilitated by transporter proteins. As such, the diversification of osmotrophic microorganisms is closely tied to the diversification of transporter functions. Horizontal gene transfer (HGT) has been suggested to produce genetic variation that can lead to adaptation, allowing lineages to acquire traits and expand niche ranges. Transporter genes often encode single-gene phenotypes and tend to have low protein–protein interaction complexity and, as such, are potential candidates for HGT. Here we test the idea that HGT has underpinned the expansion of metabolic potential and substrate utilization via transfer of transporter-encoding genes. Using phylogenomics, we identify seven cases of transporter-gene HGT between fungal phyla, and investigate compatibility, localization, function, and fitness consequences when these genes are expressed inSaccharomyces cerevisiae. Using this approach, we demonstrate that the transporters identified can alter how fungi utilize a range of metabolites, including peptides, polyols, and sugars. We then show, for one model gene, that transporter gene acquisition by HGT can significantly alter the fitness landscape ofS. cerevisiae. We therefore provide evidence that transporter HGT occurs between fungi, alters how fungi can acquire metabolites, and can drive gain in fitness. We propose a “transporter-gene acquisition ratchet,” where transporter repertoires are continually augmented by duplication, HGT, and differential loss, collectively acting to overwrite, fine-tune, and diversify the complement of transporters present in a genome.

scholarly journals Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

2016 ◽  
Vol 113 (45) ◽  
pp. E7010-E7019 ◽  
Author(s):  
Zhenzhen Yang ◽  
Yeting Zhang ◽  
Eric K. Wafula ◽  
Loren A. Honaas ◽  
Paula E. Ralph ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genetic Material ◽  
Purifying Selection ◽  
Parasitic Plants ◽  
Rna Sequences ◽  
Full Spectrum ◽  
Gene Acquisition ◽  
Feeding Structure ◽  
Validation Procedure

Horizontal gene transfer (HGT) is the transfer of genetic material across species boundaries and has been a driving force in prokaryotic evolution. HGT involving eukaryotes appears to be much less frequent, and the functional implications of HGT in eukaryotes are poorly understood. We test the hypothesis that parasitic plants, because of their intimate feeding contacts with host plant tissues, are especially prone to horizontal gene acquisition. We sought evidence of HGTs in transcriptomes of three parasitic members of Orobanchaceae, a plant family containing species spanning the full spectrum of parasitic capabilities, plus the free-livingLindenbergia. Following initial phylogenetic detection and an extensive validation procedure, 52 high-confidence horizontal transfer events were detected, often from lineages of known host plants and with an increasing number of HGT events in species with the greatest parasitic dependence. Analyses of intron sequences in putative donor and recipient lineages provide evidence for integration of genomic fragments far more often than retro-processed RNA sequences. Purifying selection predominates in functionally transferred sequences, with a small fraction of adaptively evolving sites. HGT-acquired genes are preferentially expressed in the haustorium—the organ of parasitic plants—and are strongly biased in predicted gene functions, suggesting that expression products of horizontally acquired genes are contributing to the unique adaptive feeding structure of parasitic plants.

scholarly journals Plant nodulation inducers enhance horizontal gene transfer ofAzorhizobium caulinodanssymbiosis island

2016 ◽  
Vol 113 (48) ◽  
pp. 13875-13880 ◽  
Author(s):  
Jun Ling ◽  
Hui Wang ◽  
Ping Wu ◽  
Tao Li ◽  
Yu Tang ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Host Range ◽  
Regulatory Protein ◽  
Genomic Islands ◽  
Mutualistic Symbiosis ◽  
Transcriptional Regulatory ◽  
Lysr Family ◽  
Integrative And Conjugative Element

Horizontal gene transfer (HGT) of genomic islands is a driving force of bacterial evolution. Many pathogens and symbionts use this mechanism to spread mobile genetic elements that carry genes important for interaction with their eukaryotic hosts. However, the role of the host in this process remains unclear. Here, we show that plant compounds inducing the nodulation process in the rhizobium-legume mutualistic symbiosis also enhance the transfer of symbiosis islands. We demonstrate that the symbiosis island of theSesbania rostratasymbiont,Azorhizobium caulinodans, is an 87.6-kb integrative and conjugative element (ICEAc) that is able to excise, form a circular DNA, and conjugatively transfer to a specific site of gly-tRNA gene of other rhizobial genera, expanding their host range. The HGT frequency was significantly increased in the rhizosphere. An ICEAc-located LysR-family transcriptional regulatory protein AhaR triggered the HGT process in response to plant flavonoids that induce the expression of nodulation genes through another LysR-type protein, NodD. Our study suggests that rhizobia may sense rhizosphere environments and transfer their symbiosis gene contents to other genera of rhizobia, thereby broadening rhizobial host-range specificity.

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 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.

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