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 Exploring tRNA gene cluster in archaea

2018 ◽  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Cluster ◽  
Trna Gene ◽  
Gene Clusters ◽  
Gene Organization ◽  
Trna Genes ◽  
Genomic Analyses ◽  
Living Organisms

AbstractShared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organization of tRNA genes as clusters, but this trait has not been explored in archaea domain. Here, based on analyses of complete and draft archaeal genomes, we demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene cluster was identified at least in three Archaea class, Halobacteria, Methanobacteria and Methanomicrobia from Euryarchaeota supergroup. Genomic analyses also revealed evidence of tRNA gene cluster associated with mobile genetic elements and horizontal gene transfer inter/intra-domain. The presence of tRNA gene clusters in the three domain of life suggests a role of this type of tRNA gene organization in the biology of the living organisms.

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.

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 Tn7-CRISPR-Cas12K elements manage pathway choice using truncated repeat-spacer units to target tRNA attachment sites

2021 ◽  
Author(s):  
Shan-Chi Hsieh ◽  
Joseph E. Peters
Keyword(s):  
Attachment Site ◽  
Mobile Elements ◽  
Information Support ◽  
Trna Genes ◽  
Type I ◽  
Guide Rna ◽  
Guide Rnas ◽  
Attachment Sites ◽  
Type V ◽  
Future Work

AbstractCRISPR-Cas systems provide a defense against mobile elements. These defense systems have been naturally coopted multiple times for guide RNA-directed transposition by Tn7-like transposons. Elements associated with a type I-F CRISPR-Cas system categorize guide RNAs, maintaining a standard CRISPR array capable of acquiring new spacers targeting other mobile elements while maintaining a special guide RNA allowing integration into a conserved site in the chromosome called an attachment site. We show here that Tn7-like elements associated with a type V-K (Cas12K-based) system use a similar strategy to target diverse tRNA genes as attachment sites. These guides are encoded as truncated minimal repeat-spacer units and are found in distinct locations. Multiple pieces of information support that V-K guide RNAs are acquired using a type I-D adaptation system, but remain private to the V-K transposition process. This catalog of Cas12K elements and naturally occurring insertions will help future work engineering precision integration systems.

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 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.

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 Novel integrative elements and genomic plasticity in ocean ecosystems

2020 ◽  
Author(s):  
Thomas Hackl ◽  
Raphaël Laurenceau ◽  
Markus J. Ankenbrand ◽  
Christina Bliem ◽  
Zev Cariani ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Niche Differentiation ◽  
Mobile Genetic Elements ◽  
Microbial Evolution ◽  
Genomic Islands ◽  
Trna Genes ◽  
Marine Microbes ◽  
Genomic Plasticity ◽  
Genetic Elements

Horizontal gene transfer accelerates microbial evolution, promoting diversification and adaptation. The globally abundant marine cyanobacterium Prochlorococcus has a highly streamlined genome with frequent gene exchange reflected in its extensive pangenome. The source of its genomic variability, however, remains elusive since most cells lack the common mechanisms that enable horizontal gene transfer, including conjugation, transformation, plasmids and prophages. Examining 623 genomes, we reveal a diverse system of mobile genetic elements – cargo-carrying transposons we named tycheposons – that shape Prochlorococcus’ genomic plasticity. The excision and integration of tycheposons at seven tRNA genes drive the remodeling of larger genomic islands containing most of Prochlorococcus’ flexible genes. Most tycheposons carry genes important for niche differentiation through nutrient acquisition; others appear similar to phage parasites. Tycheposons are highly enriched in extracellular vesicles and phage particles in ocean samples, suggesting efficient routes for their dispersal, transmission and propagation. Supported by evidence for similar elements in other marine microbes, our work underpins the role of vesicle- and virus-mediated transfer of mobile genetic elements in the diversification and adaptation of microbes in dilute aquatic environments – adding a significant piece to the puzzle of what governs microbial evolution in the planet’s largest habitat.

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.

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