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  • 1
    Publication Date: 2007-10-20
    Description: Horizontal gene transfer, in which genetic material is transferred from the genome of one organism to that of another, has been investigated in microbial species mainly through computational sequence analyses. To address the lack of experimental data, we studied the attempted movement of 246,045 genes from 79 prokaryotic genomes into Escherichia coli and identified genes that consistently fail to transfer. We studied the mechanisms underlying transfer inhibition by placing coding regions from different species under the control of inducible promoters. Our data suggest that toxicity to the host inhibited transfer regardless of the species of origin and that increased gene dosage and associated increased expression may be a predominant cause for transfer failure. Although these experimental studies examined transfer solely into E. coli, a computational analysis of gene-transfer rates across available bacterial and archaeal genomes supports that the barriers observed in our study are general across the tree of life.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sorek, Rotem -- Zhu, Yiwen -- Creevey, Christopher J -- Francino, M Pilar -- Bork, Peer -- Rubin, Edward M -- New York, N.Y. -- Science. 2007 Nov 30;318(5855):1449-52. Epub 2007 Oct 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17947550" target="_blank"〉PubMed〈/a〉
    Keywords: Archaea/classification/genetics ; Bacteria/classification/genetics ; Cloning, Molecular ; Computational Biology ; Escherichia coli/*genetics ; Gene Dosage ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Genetic Speciation ; Genome, Archaeal ; Genome, Bacterial ; Phylogeny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2009-01-20
    Description: Among cellular organisms, symbiotic bacteria provide the extreme examples of genome degradation and reduction. However, only isolated snapshots of eroding symbiont genomes have previously been available. We documented the dynamics of symbiont genome evolution by sequencing seven strains of Buchnera aphidicola from pea aphid hosts. We estimated a spontaneous mutation rate of at least 4 x 10(-9) substitutions per site per replication, which is more than 10 times as high as the rates previously estimated for any bacteria. We observed a high rate of small insertions and deletions associated with abundant DNA homopolymers, and occasional larger deletions. Although purifying selection eliminates many mutations, some persist, resulting in ongoing loss of genes and DNA from this already tiny genome. Our results provide a general model for the stepwise process leading to genome reduction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moran, Nancy A -- McLaughlin, Heather J -- Sorek, Rotem -- New York, N.Y. -- Science. 2009 Jan 16;323(5912):379-82. doi: 10.1126/science.1167140.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA. nmoran@email.arizona.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19150844" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aphids/*microbiology/physiology ; Base Composition ; Buchnera/*genetics/*physiology ; Evolution, Molecular ; *Gene Silencing ; *Genome, Bacterial ; INDEL Mutation ; Models, Genetic ; Molecular Sequence Data ; *Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Sequence Analysis, DNA ; Sequence Deletion ; *Symbiosis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2014-08-26
    Description: Riboswitches are ligand-binding elements contained within the 5' untranslated regions of bacterial transcripts, which generally regulate expression of downstream open reading frames. Here, we show that in Listeria monocytogenes, a riboswitch that binds vitamin B12 controls expression of a noncoding regulatory RNA, Rli55. Rli55, in turn, controls expression of the eut genes, whose products enable ethanolamine utilization and require B12 as a cofactor. Defects in ethanolamine utilization, or in its regulation by Rli55, significantly attenuate Listeria virulence in mice. Rli55 functions by sequestering the two-component response regulator EutV by means of a EutV-binding site contained within the RNA. Thus, Rli55 is a riboswitch-regulated member of the small group of regulatory RNAs that function by sequestering a protein and reveals a distinctive mechanism of signal integration in bacterial gene regulation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mellin, J R -- Koutero, Mikael -- Dar, Daniel -- Nahori, Marie-Anne -- Sorek, Rotem -- Cossart, Pascale -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Aug 22;345(6199):940-3. doi: 10.1126/science.1255083.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Unite des Interactions Bacteries-Cellules, Institut Pasteur, F-75015 Paris, France. INSERM, U604, Paris, F-75015 France. INRA, USC2020, F-75015 Paris, France. ; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. ; Unite des Interactions Bacteries-Cellules, Institut Pasteur, F-75015 Paris, France. INSERM, U604, Paris, F-75015 France. INRA, USC2020, F-75015 Paris, France. pcossart@pasteur.fr.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25146292" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions ; Animals ; Ethanolamine/*metabolism ; *Gene Expression Regulation, Bacterial ; Listeria monocytogenes/*genetics/metabolism/virology ; Mice ; Mice, Inbred BALB C ; Operon ; RNA, Untranslated/*metabolism ; Response Elements ; *Riboswitch ; Vitamin B 12/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2003-05-24
    Description: Alu repetitive elements can be inserted into mature messenger RNAs via a splicing-mediated process termed exonization. To understand the molecular basis and the regulation of the process of turning intronic Alus into new exons, we compiled and analyzed a data set of human exonized Alus. We revealed a mechanism that governs 3' splice-site selection in these exons during alternative splicing. On the basis of these findings, we identified mutations that activated the exonization of a silent intronic Alu.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lev-Maor, Galit -- Sorek, Rotem -- Shomron, Noam -- Ast, Gil -- New York, N.Y. -- Science. 2003 May 23;300(5623):1288-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12764196" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Deaminase/genetics ; *Alternative Splicing ; Alu Elements/*genetics ; Cell Line ; Cloning, Molecular ; DNA, Antisense ; Dinucleoside Phosphates/genetics ; *Exons ; Genome, Human ; Glucosyltransferases/genetics ; Humans ; Introns ; Mutagenesis, Site-Directed ; Point Mutation ; Polymerase Chain Reaction ; RNA-Binding Proteins ; Ribonucleoproteins, Small Nuclear/genetics/physiology ; Spliceosomes/metabolism ; Transfection ; Tumor Cells, Cultured
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2012-05-12
    Description: An extensive repertoire of modifications is known to underlie the versatile coding, structural and catalytic functions of RNA, but it remains largely uncharted territory. Although biochemical studies indicate that N(6)-methyladenosine (m(6)A) is the most prevalent internal modification in messenger RNA, an in-depth study of its distribution and functions has been impeded by a lack of robust analytical methods. Here we present the human and mouse m(6)A modification landscape in a transcriptome-wide manner, using a novel approach, m(6)A-seq, based on antibody-mediated capture and massively parallel sequencing. We identify over 12,000 m(6)A sites characterized by a typical consensus in the transcripts of more than 7,000 human genes. Sites preferentially appear in two distinct landmarks--around stop codons and within long internal exons--and are highly conserved between human and mouse. Although most sites are well preserved across normal and cancerous tissues and in response to various stimuli, a subset of stimulus-dependent, dynamically modulated sites is identified. Silencing the m(6)A methyltransferase significantly affects gene expression and alternative splicing patterns, resulting in modulation of the p53 (also known as TP53) signalling pathway and apoptosis. Our findings therefore suggest that RNA decoration by m(6)A has a fundamental role in regulation of gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dominissini, Dan -- Moshitch-Moshkovitz, Sharon -- Schwartz, Schraga -- Salmon-Divon, Mali -- Ungar, Lior -- Osenberg, Sivan -- Cesarkas, Karen -- Jacob-Hirsch, Jasmine -- Amariglio, Ninette -- Kupiec, Martin -- Sorek, Rotem -- Rechavi, Gideon -- England -- Nature. 2012 Apr 29;485(7397):201-6. doi: 10.1038/nature11112.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22575960" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/*analogs & derivatives/*genetics ; Alternative Splicing ; Animals ; Base Sequence ; Cell Line, Tumor ; Conserved Sequence ; Evolution, Molecular ; Hep G2 Cells ; Humans ; *Metabolome/genetics ; Methylation ; Methyltransferases/deficiency/genetics/metabolism ; Mice ; RNA/genetics/*metabolism ; RNA, Ribosomal/genetics/metabolism ; RNA, Transfer/genetics/metabolism ; RNA-Binding Proteins/metabolism ; Transcriptome/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2015-04-16
    Description: CRISPR-Cas (clustered, regularly interspaced short palindromic repeats coupled with CRISPR-associated proteins) is a bacterial immunity system that protects against invading phages or plasmids. In the process of CRISPR adaptation, short pieces of DNA ('spacers') are acquired from foreign elements and integrated into the CRISPR array. So far, it has remained a mystery how spacers are preferentially acquired from the foreign DNA while the self chromosome is avoided. Here we show that spacer acquisition is replication-dependent, and that DNA breaks formed at stalled replication forks promote spacer acquisition. Chromosomal hotspots of spacer acquisition were confined by Chi sites, which are sequence octamers highly enriched on the bacterial chromosome, suggesting that these sites limit spacer acquisition from self DNA. We further show that the avoidance of self is mediated by the RecBCD double-stranded DNA break repair complex. Our results suggest that, in Escherichia coli, acquisition of new spacers largely depends on RecBCD-mediated processing of double-stranded DNA breaks occurring primarily at replication forks, and that the preference for foreign DNA is achieved through the higher density of Chi sites on the self chromosome, in combination with the higher number of forks on the foreign DNA. This model explains the strong preference to acquire spacers both from high copy plasmids and from phages.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561520/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561520/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Levy, Asaf -- Goren, Moran G -- Yosef, Ido -- Auster, Oren -- Manor, Miriam -- Amitai, Gil -- Edgar, Rotem -- Qimron, Udi -- Sorek, Rotem -- 260432/European Research Council/International -- 336079/European Research Council/International -- England -- Nature. 2015 Apr 23;520(7548):505-10. doi: 10.1038/nature14302. Epub 2015 Apr 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel. ; Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25874675" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Bacteriophages/*genetics ; CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Consensus Sequence/genetics ; DNA Breaks, Double-Stranded ; DNA Repair ; DNA Replication/genetics ; DNA, Bacterial/*genetics ; DNA, Viral/*genetics ; Escherichia coli/*genetics ; Exodeoxyribonuclease V/metabolism ; Models, Biological ; Plasmids/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2011-07-02
    Description: Prochlorococcus cyanobacteria are extremely abundant in the oceans, as are the viruses that infect them. How hosts and viruses coexist in nature remains unclear, although the presence of both susceptible and resistant cells may allow this coexistence. Combined whole-genome sequencing and PCR screening technology now enables us to investigate the effect of resistance on genome evolution and the genomic mechanisms behind the long-term coexistence of Prochlorococcus and their viruses. Here we present a genome analysis of 77 substrains selected for resistance to ten viruses, revealing mutations primarily in non-conserved, horizontally transferred genes that localize to a single hypervariable genomic island. Mutations affected viral attachment to the cell surface and imposed a fitness cost to the host, manifested by significantly lower growth rates or a previously unknown mechanism of more rapid infection by other viruses. The mutant genes are generally uncommon in nature yet some carry polymorphisms matching those found experimentally. These data are empirical evidence indicating that viral-attachment genes are preferentially located in genomic islands and that viruses are a selective pressure enhancing the diversity of both island genes and island gene content. This diversity emerges as a genomic mechanism that reduces the effective host population size for infection by a given virus, thus facilitating long-term coexistence between viruses and their hosts in nature.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Avrani, Sarit -- Wurtzel, Omri -- Sharon, Itai -- Sorek, Rotem -- Lindell, Debbie -- England -- Nature. 2011 Jun 29;474(7353):604-8. doi: 10.1038/nature10172.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21720364" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Evolution, Molecular ; Genes, Bacterial/genetics ; *Genetic Variation ; Genome, Bacterial ; Genomic Islands/*genetics ; Genotype ; Molecular Sequence Data ; Mutation ; Phylogeny ; Podoviridae/*physiology ; Prochlorococcus/classification/*genetics/*virology ; Virus Attachment
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2015-08-01
    Description: Metagenomic sequencing increased our understanding of the role of the microbiome in health and disease, yet it only provides a snapshot of a highly dynamic ecosystem. Here, we show that the pattern of metagenomic sequencing read coverage for different microbial genomes contains a single trough and a single peak, the latter coinciding with the bacterial origin of replication. Furthermore, the ratio of sequencing coverage between the peak and trough provides a quantitative measure of a species' growth rate. We demonstrate this in vitro and in vivo, under different growth conditions, and in complex bacterial communities. For several bacterial species, peak-to-trough coverage ratios, but not relative abundances, correlated with the manifestation of inflammatory bowel disease and type II diabetes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korem, Tal -- Zeevi, David -- Suez, Jotham -- Weinberger, Adina -- Avnit-Sagi, Tali -- Pompan-Lotan, Maya -- Matot, Elad -- Jona, Ghil -- Harmelin, Alon -- Cohen, Nadav -- Sirota-Madi, Alexandra -- Thaiss, Christoph A -- Pevsner-Fischer, Meirav -- Sorek, Rotem -- Xavier, Ramnik J -- Elinav, Eran -- Segal, Eran -- New York, N.Y. -- Science. 2015 Sep 4;349(6252):1101-6. doi: 10.1126/science.aac4812. Epub 2015 Jul 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel. Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. ; Immunology Department, Weizmann Institute of Science, Rehovot, Israel. ; Department of Biological services, Weizmann Institute of Science, Rehovot, Israel. ; Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel. ; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School and Broad Institute, Cambridge, MA, USA. ; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. ; Immunology Department, Weizmann Institute of Science, Rehovot, Israel. eran.elinav@weizmann.ac.il eran.segal@weizmann.ac.il. ; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel. Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. eran.elinav@weizmann.ac.il eran.segal@weizmann.ac.il.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26229116" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/classification/genetics/*growth & development ; Diabetes Mellitus, Type 2/*microbiology ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Metagenome ; Metagenomics ; Microbiota/genetics/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2016-04-28
    Description: Riboswitches and attenuators are cis-regulatory RNA elements, most of which control bacterial gene expression via metabolite-mediated, premature transcription termination. We developed an unbiased experimental approach for genome-wide discovery of such ribo-regulators in bacteria. We also devised an experimental platform that quantitatively measures the in vivo activity of all such regulators in parallel and enables rapid screening for ribo-regulators that respond to metabolites of choice. Using this approach, we detected numerous antibiotic-responsive ribo-regulators that control antibiotic resistance genes in pathogens and in the human microbiome. Studying one such regulator in Listeria monocytogenes revealed an attenuation mechanism mediated by antibiotic-stalled ribosomes. Our results expose broad roles for conditional termination in regulating antibiotic resistance and provide a tool for discovering riboswitches and attenuators that respond to previously unknown ligands.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dar, Daniel -- Shamir, Maya -- Mellin, J R -- Koutero, Mikael -- Stern-Ginossar, Noam -- Cossart, Pascale -- Sorek, Rotem -- New York, N.Y. -- Science. 2016 Apr 8;352(6282):aad9822. doi: 10.1126/science.aad9822.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel. ; Institut Pasteur, Unite des Interactions Bacteries-Cellules, Paris, F-75015 France. INSERM, U604, Paris, F-75015 France. Institut National de la Recherche Agronomique, USC2020, Paris, F-75015 France. ; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel. rotem.sorek@weizmann.ac.il.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27120414" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/genetics ; Anti-Bacterial Agents/pharmacology ; Bacillus subtilis/drug effects/genetics ; Drug Resistance, Bacterial/*genetics ; Enterococcus faecalis/drug effects ; Gastrointestinal Microbiome/drug effects/genetics ; *Gene Expression Regulation, Bacterial ; Genome, Bacterial/genetics ; Genome-Wide Association Study/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Listeria monocytogenes/drug effects/genetics ; Ribosomes/metabolism ; Riboswitch/*genetics ; Sequence Analysis, RNA/methods ; *Transcription Termination, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2009-02-20
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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