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Current Opinion in Genetics &... Dec 1999A restriction enzyme gene is often linked to a modification methylase gene the role of which is to protect a recognition site on DNA from breakage by the former. Loss of... (Review)
Review
A restriction enzyme gene is often linked to a modification methylase gene the role of which is to protect a recognition site on DNA from breakage by the former. Loss of some restriction-modification gene complexes leads to cell death through restriction breakage in the genome. Their behavior as genomic parasites/symbionts may explain the distribution of restriction sites and clarify certain aspects of bacterial recombination repair and mutagenesis. A comparison of bacterial genomes supports the hypothesis that restriction-modification gene complexes are mobile elements involved in various genome rearrangements and evolution.
Topics: Bacteria; DNA Restriction Enzymes; Evolution, Molecular; Genes, Bacterial; Genome, Bacterial; Host-Parasite Interactions; Interspersed Repetitive Sequences; Mutagenesis; Recombination, Genetic
PubMed: 10607611
DOI: 10.1016/s0959-437x(99)00026-x -
Trends in Genetics : TIG Mar 2006Dynamic shifts between open reading frames and the redefinition of codon meaning at specific sites, programmed by signals in mRNA, permits versatility of gene... (Review)
Review
Dynamic shifts between open reading frames and the redefinition of codon meaning at specific sites, programmed by signals in mRNA, permits versatility of gene expression. Such alterations are characteristic of organisms in all domains of life and serve a variety of functional purposes. In this article, we concentrate on programmed ribosomal frameshifting, stop codon read-through and transcriptional slippage in the decoding of phage genes and bacterial mobile elements. Together with their eukaryotic counterparts, the genes encoding these elements are the richest known source of nonstandard decoding. Recent analyses revealed several novel sequences encoding programmed alterations in gene decoding and provide a glimpse of the emerging picture.
Topics: Bacteriophages; Codon; Databases, Factual; Frameshift Mutation; Frameshifting, Ribosomal; Gene Expression Regulation; Interspersed Repetitive Sequences
PubMed: 16460832
DOI: 10.1016/j.tig.2006.01.005 -
Proceedings of the National Academy of... Jun 2011Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful... (Review)
Review
Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible "evolutionary functions" of SGEs.
Topics: Animals; DNA Transposable Elements; Evolution, Molecular; Genome; Humans; Interspersed Repetitive Sequences; Reproduction; Selection, Genetic
PubMed: 21690392
DOI: 10.1073/pnas.1102343108 -
The Journal of Eukaryotic Microbiology 1998Hypotrichs have evolved extraordinary ways of organizing, manipulating, and replicating the DNA in their micronuclear and macronuclear genomes. Short macronuclear DNA... (Review)
Review
Hypotrichs have evolved extraordinary ways of organizing, manipulating, and replicating the DNA in their micronuclear and macronuclear genomes. Short macronuclear DNA molecules containing single genes are created by excision from chromosomes, accompanied by massive elimination of the germline DNA sequences between genes. Germline genes themselves are interrupted by multiple noncoding segments called internal eliminated segments, or IESs, that divide genes into multiple macronuclear-destined segments, or MDSs. The functional significance of this organization is unknown. Over evolutionary time IESs accumulate mutations rapidly, are inserted into or excised from genes, and shift position along DNA molecules. MDSs are ligated to create functional genes when IESs are spliced out of micronuclear DNA during macronuclear development. MDSs in some germline genes are in scrambled disorder and become unscrambled in association with IES elimination. Replication of DNA in the macronucleus is accomplished by organization of replication enzymes and factors into a structure that sweeps through the macronucleus to replicate the many millions of gene-sized DNA molecules. The significance of many of the bizarre DNA phenomena in the evolutionary/functional success of hypotrichs is still unclear.
Topics: Animals; DNA, Protozoan; Genes, Protozoan; Genome, Protozoan; Hypotrichida; Interspersed Repetitive Sequences
PubMed: 9864847
DOI: 10.1111/j.1550-7408.1998.tb04552.x -
PLoS Biology Mar 2016The diversification of prokaryotes is accelerated by their ability to acquire DNA from other genomes. However, the underlying processes also facilitate genome infection...
The diversification of prokaryotes is accelerated by their ability to acquire DNA from other genomes. However, the underlying processes also facilitate genome infection by costly mobile genetic elements. The discovery that cells can uptake DNA by natural transformation was instrumental to the birth of molecular biology nearly a century ago. Surprisingly, a new study shows that this mechanism could efficiently cure the genome of mobile elements acquired through previous sexual exchanges.
Topics: Gene Transfer, Horizontal; Genome, Microbial; Interspersed Repetitive Sequences; Transformation, Bacterial
PubMed: 26987049
DOI: 10.1371/journal.pbio.1002417 -
Methods in Molecular Biology (Clifton,... 2009This chapter defines the agents that provide for the movement of genetic material which fuels the adaptive potential of life on our planet. The chapter has been... (Review)
Review
This chapter defines the agents that provide for the movement of genetic material which fuels the adaptive potential of life on our planet. The chapter has been structured to be broadly comprehensive, arbitrarily categorizing the mobilome into four classes: (1) transposons, (2) plasmids, (3) bacteriophage, and (4) self-splicing molecular parasites.Our increasing understanding of the mobilome is as dynamic as the mobilome itself. With continuing discovery, it is clear that nature has not confined these genomic agents of change to neat categories, but rather the classification categories overlap and intertwine. Massive sequencing efforts and their published analyses are continuing to refine our understanding of the extent of the mobilome. This chapter provides a framework to describe our current understanding of the mobilome and a foundation on which appreciation of its impact on genome evolution can be understood.
Topics: Bacteriophages; DNA Transposable Elements; Gene Transfer, Horizontal; Genome; Inteins; Interspersed Repetitive Sequences; Introns; Phylogeny; Plasmids
PubMed: 19271177
DOI: 10.1007/978-1-60327-853-9_2 -
Nature Communications Mar 2022The mobile resistance gene bla encodes the NDM enzyme which hydrolyses carbapenems, a class of antibiotics used to treat some of the most severe bacterial infections....
The mobile resistance gene bla encodes the NDM enzyme which hydrolyses carbapenems, a class of antibiotics used to treat some of the most severe bacterial infections. The bla gene is globally distributed across a variety of Gram-negative bacteria on multiple plasmids, typically located within highly recombining and transposon-rich genomic regions, which leads to the dynamics underlying the global dissemination of bla to remain poorly resolved. Here, we compile a dataset of over 6000 bacterial genomes harbouring the bla gene, including 104 newly generated PacBio hybrid assemblies from clinical and livestock-associated isolates across China. We develop a computational approach to track structural variants surrounding bla, which allows us to identify prevalent genomic contexts, mobile genetic elements, and likely events in the gene's global spread. We estimate that bla emerged on a Tn125 transposon before 1985, but only reached global prevalence around a decade after its first recorded observation in 2005. The Tn125 transposon seems to have played an important role in early plasmid-mediated jumps of bla, but was overtaken in recent years by other elements including IS26-flanked pseudo-composite transposons and Tn3000. We found a strong association between bla-carrying plasmid backbones and the sampling location of isolates. This observation suggests that the global dissemination of the bla gene was primarily driven by successive between-plasmid transposon jumps, with far more restricted subsequent plasmid exchange, possibly due to adaptation of plasmids to their specific bacterial hosts.
Topics: Anti-Bacterial Agents; Carbapenems; Interspersed Repetitive Sequences; Microbial Sensitivity Tests; Plasmids; beta-Lactamases
PubMed: 35241674
DOI: 10.1038/s41467-022-28819-2 -
Extremophiles : Life Under Extreme... Sep 2012Non-coding RNAs are key players in many cellular processes within organisms from all three domains of life. The range and diversity of small RNA functions beyond their... (Review)
Review
Non-coding RNAs are key players in many cellular processes within organisms from all three domains of life. The range and diversity of small RNA functions beyond their involvement in translation and RNA processing was first recognized for eukaryotes and bacteria. Since then, small RNAs were also found to be abundant in archaea. Their functions include the regulation of gene expression and the establishment of immunity against invading mobile genetic elements. This review summarizes our current knowledge about small RNAs used for regulation and defence in archaea.
Topics: Archaea; Gene Expression Regulation, Archaeal; Interspersed Repetitive Sequences; Protein Biosynthesis; RNA, Archaeal; RNA, Small Untranslated
PubMed: 22763819
DOI: 10.1007/s00792-012-0469-5 -
Trends in Genetics : TIG Oct 2009Duplicated sequences are substrates for the emergence of new genes and are an important source of genetic instability associated with rare and common diseases. Analyses... (Review)
Review
Duplicated sequences are substrates for the emergence of new genes and are an important source of genetic instability associated with rare and common diseases. Analyses of primate genomes have shown an increase in the proportion of interspersed segmental duplications (SDs) within the genomes of humans and great apes. This contrasts with other mammalian genomes that seem to have their recently duplicated sequences organized in a tandem configuration. In this review, we focus on the mechanistic origin and impact of this difference with respect to evolution, genetic diversity and primate phenotype. Although many genomes will be sequenced in the future, resolution of this aspect of genomic architecture still requires high quality sequences and detailed analyses.
Topics: Animals; Evolution, Molecular; Gene Duplication; Genetic Variation; Genome; Humans; Interspersed Repetitive Sequences; Models, Genetic; Phylogeny; Primates
PubMed: 19796838
DOI: 10.1016/j.tig.2009.08.002 -
Nature Reviews. Genetics Feb 2020All cellular life forms are afflicted by diverse genetic parasites, including viruses and other types of mobile genetic elements (MGEs), and have evolved multiple,... (Review)
Review
All cellular life forms are afflicted by diverse genetic parasites, including viruses and other types of mobile genetic elements (MGEs), and have evolved multiple, diverse defence systems that protect them from MGE assault via different mechanisms. Here, we provide our perspectives on how recent evidence points to tight evolutionary connections between MGEs and defence systems that reach far beyond the proverbial arms race. Defence systems incur a fitness cost for the hosts; therefore, at least in prokaryotes, horizontal mobility of defence systems, mediated primarily by MGEs, is essential for their persistence. Moreover, defence systems themselves possess certain features of selfish elements. Common components of MGEs, such as site-specific nucleases, are 'guns for hire' that can also function as parts of defence mechanisms and are often shuttled between MGEs and defence systems. Thus, evolutionary and molecular factors converge to mould the multifaceted, inextricable connection between MGEs and anti-MGE defence systems.
Topics: Biological Evolution; Evolution, Molecular; Gene Transfer, Horizontal; Host-Pathogen Interactions; Interspersed Repetitive Sequences
PubMed: 31611667
DOI: 10.1038/s41576-019-0172-9