scholarly journals How sequence populations persist inside a genome

2020 ◽  
Author(s):  
Hye Jin Park ◽  
Chaitanya S. Gokhale ◽  
Frederic Bertels
Keyword(s):  
Simple Model ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Repetitive Sequences ◽  
Relevant Parameter ◽  
Bacterial Genomes ◽  
Bacterial Host ◽  
Biologically Relevant ◽  
A Genome ◽  
Model Sequence

AbstractCompared to their eukaryotic counterparts, bacterial genomes are small and contain extremely tightly packed genes. Therefore, discovering a large number of short repetitive sequences in the genomes of Pseudomonads and Enterobacteria is unexpected. These sequences can independently replicate in the host genome and form populations that persist for millions of years. Here we model the interactions of intragenomic sequence populations with the bacterial host. In a simple model, sequence populations either expand until they drive the host to extinction or the sequence population gets purged from the genome. Including horizontal gene transfer does not change the qualitative outcome of the model and leads to the extinction of the sequence population. However, a sequence population can be stably maintained, if each sequence provides a benefit that decreases with increasing sequence population size. But concurrently, the replication of the sequence population needs to be costly to the host. Surprisingly, in regimes where horizontal gene transfer plays a role, the benefit conferred by the sequence population does not have to exceed the damage it causes. Together, our analyses provide a plausible scenario for the persistence of sequence populations in bacterial genomes. More importantly, we hypothesize a limited biologically relevant parameter range, which can be tested in future experiments.

scholarly journals How sequence populations persist inside bacterial genomes

Genetics ◽  
2021 ◽  
Vol 217 (4) ◽  
Author(s):  
Hye Jin Park ◽  
Chaitanya S Gokhale ◽  
Frederic Bertels
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Population Size ◽  
Repetitive Sequences ◽  
Host Genome ◽  
Parameter Range ◽  
Relevant Parameter ◽  
Bacterial Genomes ◽  
Bacterial Host ◽  
Biologically Relevant

AbstractCompared to their eukaryotic counterparts, bacterial genomes are small and contain extremely tightly packed genes. Repetitive sequences are rare but not completely absent. One of the most common repeat families is REPINs. REPINs can replicate in the host genome and form populations that persist for millions of years. Here, we model the interactions of these intragenomic sequence populations with the bacterial host. We first confirm well-established results, in the presence and absence of horizontal gene transfer (hgt) sequence populations either expand until they drive the host to extinction or the sequence population gets purged from the genome. We then show that a sequence population can be stably maintained, when each individual sequence provides a benefit that decreases with increasing sequence population size. Maintaining a sequence population of stable size also requires the replication of the sequence population to be costly to the host, otherwise the sequence population size will increase indefinitely. Surprisingly, in regimes with high hgt rates, the benefit conferred by the sequence population does not have to exceed the damage it causes to its host. Our analyses provide a plausible scenario for the persistence of sequence populations in bacterial genomes. We also hypothesize a limited biologically relevant parameter range for the provided benefit, which can be tested in future experiments.

scholarly journals Complete Sequences of Two Plasmids Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain

2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Fabrício S. Campos ◽  
Fernando B. Cerqueira ◽  
Gil R. Santos ◽  
Eliseu J. G. Pereira ◽  
Roberto F. T. Corrêia ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Crucial Role ◽  
Bacterial Genomes ◽  
Content Type ◽  
Complete Sequences

Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. In this work, we sequenced two plasmids found in a Brazilian Bacillus thuringiensis serovar israelensis strain which showed 100% nucleotide identities with Bacillus thuringiensis serovar kurstaki plasmids.

scholarly journals A mobile genetic element increases bacterial host fitness by manipulating development

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Joshua M Jones ◽  
Ilana Grinberg ◽  
Avigdor Eldar ◽  
Alan D Grossman
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Mobile Genetic Elements ◽  
Selective Advantage ◽  
Host Cells ◽  
Bacterial Host ◽  
Host Fitness ◽  
Genetic Elements ◽  
Necessary And Sufficient ◽  
Integrative And Conjugative Element

Horizontal gene transfer is a major force in bacterial evolution. Mobile genetic elements are responsible for much of horizontal gene transfer and also carry beneficial cargo genes. Uncovering strategies used by mobile genetic elements to benefit host cells is crucial for understanding their stability and spread in populations. We describe a benefit that ICEBs1, an integrative and conjugative element of Bacillus subtilis, provides to its host cells. Activation of ICEBs1 conferred a frequency-dependent selective advantage to host cells during two different developmental processes: biofilm formation and sporulation. These benefits were due to inhibition of biofilm-associated gene expression and delayed sporulation by ICEBs1-containing cells, enabling them to exploit their neighbors and grow more prior to development. A single ICEBs1 gene, devI (formerly ydcO), was both necessary and sufficient for inhibition of development. Manipulation of host developmental programs allows ICEBs1 to increase host fitness, thereby increasing propagation of the element.

scholarly journals Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post–transfer refinement

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Joshua K Michener ◽  
Aline A Camargo Neves ◽  
Stéphane Vuilleumier ◽  
Françoise Bringel ◽  
Christopher J Marx
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Recombinant Strain ◽  
Mobile Genetic Element ◽  
Degradation Pathway ◽  
Environmental Isolates ◽  
Bacterial Host ◽  
Adaptive Process ◽  
Potential Applications ◽  
Effective Use

When microbes acquire new abilities through horizontal gene transfer, the genes and pathways must function under conditions with which they did not coevolve. If newly-acquired genes burden the host, their utility will depend on further evolutionary refinement of the recombinant strain. We used laboratory evolution to recapitulate this process of transfer and refinement, demonstrating that effective use of an introduced dichloromethane degradation pathway required one of several mutations to the bacterial host that are predicted to increase chloride efflux. We then used this knowledge to identify parallel, beneficial mutations that independently evolved in two natural dichloromethane-degrading strains. Finally, we constructed a synthetic mobile genetic element carrying both the degradation pathway and a chloride exporter, which preempted the adaptive process and directly enabled effective dichloromethane degradation across diverse Methylobacterium environmental isolates. Our results demonstrate the importance of post–transfer refinement in horizontal gene transfer, with potential applications in bioremediation and synthetic biology.

scholarly journals Many defense systems in microbial genomes, but which is defending whom from what?

2021 ◽  
Author(s):  
Eduardo P. C. Rocha ◽  
David Bikard
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Arms Race ◽  
Significant Fraction ◽  
Bacterial Genomes ◽  
Microbial Genomes ◽  
Genetic Elements ◽  
Cellular Defense ◽  
Defense Systems ◽  
Intragenomic Conflict

Prokaryotes have numerous mobile genetic elements (MGE) that mediate horizontal gene transfer between cells. These elements can be costly, even deadly, and cells use numerous defense systems to filter, control or inactivate them. Surprisingly, many phages, conjugative plasmids, and their parasites, phage satellites or mobilizable plasmids, encode defense systems homologous to those of bacteria. They constitute a significant fraction of the systems found in bacterial genomes. As components of MGEs, they have presumably evolved to provide them, not the cell, adaptive functions that may be defensive, offensive, or both. This sheds new light on the role, effect, and fate of the so called “cellular defense systems”, whereby they are not merely microbial defensive weapons in a two-partner arms race, but tools of intragenomic conflict between multiple genetic elements with divergent interests. It also raises many intriguing questions.

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 and the Evolution of Microvirid Coliphage Genomes

2006 ◽  
Vol 188 (3) ◽  
pp. 1134-1142 ◽  
Author(s):  
D. R. Rokyta ◽  
C. L. Burch ◽  
S. B. Caudle ◽  
H. A. Wichman
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Sparse Sampling ◽  
Apparent Difference ◽  
Genomic Evolution ◽  
Single Family ◽  
Bacterial Host ◽  
Double Stranded Dna ◽  
The Family

ABSTRACT Bacteriophage genomic evolution has been largely characterized by rampant, promiscuous horizontal gene transfer involving both homologous and nonhomologous source DNA. This pattern has emerged through study of the tailed double-stranded DNA (dsDNA) phages and is based upon a sparse sampling of the enormous diversity of these phages. The single-stranded DNA phages of the family Microviridae, including φX174, appear to evolve through qualitatively different mechanisms, possibly as result of their strictly lytic lifestyle and small genome size. However, this apparent difference could reflect merely a dearth of relevant data. We sought to characterize the forces that contributed to the molecular evolution of the Microviridae and to examine the genetic structure of this single family of bacteriophage by sequencing the genomes of microvirid phage isolated on a single bacterial host. Microvirids comprised 3.5% of the detectable phage in our environmental samples, and sequencing yielded 42 new microvirid genomes. Phylogenetic analysis of the genes contained in these and five previously described microvirid phages identified three distinct clades and revealed at least two horizontal transfer events between clades. All members of one clade have a block of five putative genes that are not present in any member of the other two clades. Our data indicate that horizontal transfer does contribute to the evolution of the microvirids but is both quantitatively and qualitatively different from what has been observed for the dsDNA phages.

scholarly journals Traffic at the tmRNA Gene

2003 ◽  
Vol 185 (3) ◽  
pp. 1059-1070 ◽  
Author(s):  
Kelly P. Williams
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Trna Gene ◽  
Attachment Site ◽  
Trna Genes ◽  
Site Specificity ◽  
Bacterial Genomes ◽  
Transcriptional Terminator ◽  
Significant Bias ◽  
Attachment Sites

ABSTRACT A partial screen for genetic elements integrated into completely sequenced bacterial genomes shows more significant bias in specificity for the tmRNA gene (ssrA) than for any type of tRNA gene. Horizontal gene transfer, a major avenue of bacterial evolution, was assessed by focusing on elements using this single attachment locus. Diverse elements use ssrA; among enterobacteria alone, at least four different integrase subfamilies have independently evolved specificity for ssrA, and almost every strain analyzed presents a unique set of integrated elements. Even elements using essentially the same integrase can be very diverse, as is a group with an ssrA-specific integrase of the P4 subfamily. This same integrase appears to promote damage routinely at attachment sites, which may be adaptive. Elements in arrays can recombine; one such event mediated by invertible DNA segments within neighboring elements likely explains the monophasic nature of Salmonella enterica serovar Typhi. One of a limited set of conserved sequences occurs at the attachment site of each enterobacterial element, apparently serving as a transcriptional terminator for ssrA. Elements were usually found integrated into tRNA-like sequence at the 3′ end of ssrA, at subsites corresponding to those used in tRNA genes; an exception was found at the non-tRNA-like 3′ end produced by ssrA gene permutation in cyanobacteria, suggesting that, during the evolution of new site specificity by integrases, tropism toward a conserved 3′ end of an RNA gene may be as strong as toward a tRNA-like sequence. The proximity of ssrA and smpB, which act in concert, was also surveyed.

scholarly journals Horizontal gene transfer barrier shapes the evolution of prokaryotic pangenomes

2020 ◽  
Author(s):  
Itamar Sela ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Evolution ◽  
Genome Size ◽  
Bacterial Genomes ◽  
Prokaryotic Genomes ◽  
Simplifying Assumptions ◽  
Specific Shape ◽  
Foreign Genes ◽  
The Cost

AbstractThe genomes of bacteria and archaea evolve by extensive loss and gain of genes which, for any group of related prokaryotic genomes, result in the formation of a pangenome with the universal, asymmetrical U-shaped distribution of gene commonality. To elucidate the evolutionary factors that define the specific shape of this distribution, we investigate the fit of simple models of genome evolution to the empirically observed gene commonality distributions and genomes intersections for 33 groups of closely related bacterial genomes. The combined analysis of genome intersections and gene commonality shows that at least one of the two simplifying assumptions that are usually adopted for modeling the evolution of the U-shaped distribution, those of infinitely many genes and constant genome size, is invalid. The violation of both these assumptions stems from the horizontal gene transfer barrier, i.e. the cost of accommodation of foreign genes by prokaryotes.

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