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Wonseok Yoo, Dongbin Lim, Sangsoo Kim
A retron is a bacterial retroelement that encodes an RNA gene and a reverse transcriptase (RT). The former, once transcribed, works as a template primer for reverse transcription by the latter. The resulting DNA is covalently linked to the upstream part of the RNA; this chimera is called multicopy single-stranded DNA (msDNA), which is extrachromosomal DNA found in many bacterial species. Based on the conserved features in the eight known msDNA sequences, we developed a detection method and applied it to scan National Center for Biotechnology Information (NCBI) RefSeq bacterial genome sequences...
March 2016: Genomics & Informatics
Yide He, Diego Esteban-Fernández, Boris Neumann, Ulf Bergmann, Frank Bierkandt, Michael W Linscheid
UNLABELLED: In a proof of concept study, metal-coded affinity tags based on click chemistry (MeCAT-Click) were used to analyze the proteome of Escherichia coli (E. coli) in response to heat stress. This allows high labeling efficiency, high detection sensitivity, and multiplex capabilities, which are pivotal for its application to protein quantification. Two approaches are presented for relative quantification of differentially lanthanide-labeled proteins. The first approach uses isotope-labeling, where ESI-MS was utilized to quantify the differentially labeled proteins from different states of E...
March 16, 2016: Journal of Proteomics
Johanna R Elfenbein, Leigh A Knodler, Ernesto S Nakayasu, Charles Ansong, Heather M Brewer, Lydia Bogomolnaya, L Garry Adams, Michael McClelland, Joshua N Adkins, Helene L Andrews-Polymenis
Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine...
September 2015: PLoS Genetics
Steven Zimmerly, Li Wu
Reverse transcriptases (RTs) are usually thought of as eukaryotic enzymes, but they are also present in bacteria and likely originated in bacteria and migrated to eukaryotes. Only three types of bacterial retroelements have been substantially characterized: group II introns, diversity-generating retroelements, and retrons. Recent work, however, has identified a myriad of uncharacterized RTs and RT-related sequences in bacterial genomes, which exhibit great sequence diversity and a range of domain structures...
April 2015: Microbiology Spectrum
Jessica M Labonté, Erin K Field, Maggie Lau, Dylan Chivian, Esta Van Heerden, K Eric Wommack, Thomas L Kieft, Tullis C Onstott, Ramunas Stepanauskas
A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT) and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a 3 km-deep fracture water in the 2...
2015: Frontiers in Microbiology
Nicolás Toro, Rafael Nisa-Martínez
Much less is known about reverse transcriptases (RTs) in prokaryotes than in eukaryotes, with most prokaryotic enzymes still uncharacterized. Two surveys involving BLAST searches for RT genes in prokaryotic genomes revealed the presence of large numbers of diverse, uncharacterized RTs and RT-like sequences. Here, using consistent annotation across all sequenced bacterial species from GenBank and other sources via RAST, available from the PATRIC (Pathogenic Resource Integration Center) platform, we have compiled the data for currently annotated reverse transcriptases from completely sequenced bacterial genomes...
2014: PloS One
Anna Maj, Lukasz Dziewit, Jakub Czarnecki, Miroslawa Wlodarczyk, Jadwiga Baj, Grazyna Skrzypczyk, Dorota Giersz, Dariusz Bartosik
Plasmids are components of many bacterial genomes. They enable the spread of a large pool of genetic information via lateral gene transfer. Many bacterial strains contain mega-sized replicons and these are particularly common in Alphaproteobacteria. Considerably less is known about smaller alphaproteobacterial plasmids. We analyzed the genomes of 14 such plasmids residing in 4 multireplicon carotenoid-producing strains of the genus Paracoccus (Alphaproteobacteria): P. aestuarii DSM 19484, P. haeundaensis LG P-21903, P...
2013: PloS One
Johanna R Elfenbein, Tiana Endicott-Yazdani, Steffen Porwollik, Lydia M Bogomolnaya, Pui Cheng, Jinbai Guo, Yi Zheng, Hee-Jeong Yang, Marissa Talamantes, Christine Shields, Aimee Maple, Yury Ragoza, Kimberly DeAtley, Tyler Tatsch, Ping Cui, Katharine D Andrews, Michael McClelland, Sara D Lawhon, Helene Andrews-Polymenis
Cattle are naturally infected with Salmonella enterica serotype Typhimurium and exhibit pathological features of enteric salmonellosis that closely resemble those in humans. Cattle are the most relevant model of gastrointestinal disease resulting from nontyphoidal Salmonella infection in an animal with an intact microbiota. We utilized this model to screen a library of targeted single-gene deletion mutants to identify novel genes of Salmonella Typhimurium required for survival during enteric infection. Fifty-four candidate mutants were strongly selected, including numerous mutations in genes known to be important for gastrointestinal survival of salmonellae...
November 2013: Infection and Immunity
Toshi Shimamoto, Ashraf M Ahmed, Tadashi Shimamoto
Some bacteria produce a satellite RNA-DNA complex termed msDNA, multicopy single-stranded DNA. In this report, msDNA from Vibrio parahaemolyticus, a cause of acute gastroenteritis, was identified and named msDNA-Vp96. The retron element containing the ret gene, encoding the reverse transcriptase (RT) that is responsible for msDNA production, was cloned and characterized. Comparison of msDNA-Vp96 and msDNA-Vc95, from Vibrio cholerae, showed a high level of sequence similarity. We exchanged the two ret genes to examine whether msDNA was produced by the RT from different sources...
June 2013: Journal of Microbiology / the Microbiological Society of Korea
Rasel Das, Tadashi Shimamoto, Md Arifuzzaman
Retron is a retroelement that encodes msDNA (multicopy single-stranded DNA) which was significantly found mainly in Gram-negative pathogenic bacteria. We screened Yersinia frederiksenii ATCC 33641 contig01029 for the presence of retroelement by using bioinformatics tools and characterized a novel retron-Yf79 on the chromosome that encodes msDNA-Yf79. In this study, we perceived that, the codon usage of retron-Yf79 were noteworthy different from those of the Y. frederiksenii genome. It demonstrates that, the retron-Yf79 was a foreign DNA element and integrated into this organism genome during their evolution...
2011: Journal of Pathogens
Rasel Das, Tadashi Shimamoto, Sultan Mohammad Zahid Hosen, Mohammad Arifuzzaman
The multi-copy single-stranded DNA (msDNA) is yielded by the action of reverse transcriptase of retro-element in a wide range of pathogenic bacteria. Upon this phenomenon, it has been shown that msDNA is only produced by Eubacteria because many Eubacteria species contained reverse transcriptase in their special retro-element. We have screened around 111 Archaea at KEGG (Kyoto Encyclopedia of Genes and Genomes) database available at genome net server and observed three Methanosarcina species (M.acetivorans, M...
2011: Bioinformation
Sven-Oliver Dietz, Frank Hartmann, Thomas Schwarz, Tobias E Nowak, Annalisa Enders, Sebastian Kuhn, Alexander Hofmann, Pol Maria Rommens
BACKGROUND: In locking plate osteosynthesis of proximal humeral fractures, secondary varus malalignment is a specific complication. Retron nails (Tantum AG, Neumunster, Germany), among others, have been designed to improve medial support of the calcar humeri. The aim of our biomechanical study was to examine whether Retron nails provide increased stiffness for axial loads and adequate stiffness for torsional loads when compared with Philos plates (Synthes AG, Umkirch, Germany). MATERIALS AND METHODS: Twenty-two fresh-frozen paired humeri were collected...
May 2012: Journal of Shoulder and Elbow Surgery
Kumiko Inouye, Saori Tanimoto, Maki Kamimoto, Toshi Shimamoto, Tadashi Shimamoto
Bacterial reverse transcriptase (RT) is responsible for the production of an RNA-DNA complex called multicopy single-stranded DNA (msDNA). The genetic element required for the sysnthesis of msDNA is named a retron. Here, we characterize two novel retrons named retron-Vc81 and retron-Vc137 in Vibrio cholerae. Interestingly, retron-Vc81 and retron-Vc137 are replaced by retron-Vc95 at the same location on the chromosome.
July 2011: Microbiology and Immunology
Lenka Pilousova, Ivan Rychlik
Unlike all of the other retrons, the bacterial retron reverse transcriptase RrtE is capable of synthesizing small double-stranded DNA (sdsDNA) from template RNA. In this study, we analyzed the biosynthesis of the sdsDNA by RrtE in detail. We found out that the initiation of reverse transcription was dependent on a novel self-priming mechanism utilizing a free 3'OH of RNA that is reverse-transcribed into sdsDNA. The priming of the sdsDNA synthesis was not dependent on any particular nucleotide being used as a donor of 3'OH (unlike all of the other retrons, which prime from 2'OH of a particular guanosine) or any particular nucleotide being introduced into the sdsDNA first...
November 2011: Cellular and Molecular Life Sciences: CMLS
Devon A Mundal, Christopher T Avetta, Regan J Thomson
The recognition of structural elements (that is, retrons) that signal the application of specific chemical transformations is a key cognitive event in the design of synthetic routes to complex molecules. Reactions that produce compounds without an easily identifiable retron, by way of either substantial structural rearrangement or loss of the atoms required for the reaction to proceed, are significantly more difficult to apply during retrosynthetic planning, yet allow for non-traditional pathways that may facilitate efficient acquisition of the target molecule...
April 2010: Nature Chemistry
Dawn M Simon, Steven Zimmerly
Retroelements are usually considered to be eukaryotic elements because of the large number and variety in eukaryotic genomes. By comparison, reverse transcriptases (RTs) are rare in bacteria, with only three characterized classes: retrons, group II introns and diversity-generating retroelements (DGRs). Here, we present the results of a bioinformatic survey that aims to define the landscape of RTs across eubacterial, archaeal and phage genomes. We identify and categorize 1021 RTs, of which the majority are group II introns (73%)...
December 2008: Nucleic Acids Research
Timothy E Mattes, Anne K Alexander, Paul M Richardson, A Christine Munk, Cliff S Han, Paul Stothard, Nicholas V Coleman
Polaromonas sp. strain JS666 can grow on cis-1,2-dichloroethene (cDCE) as a sole carbon and energy source and may be useful for bioremediation of chlorinated solvent-contaminated sites. Analysis of the genome sequence of JS666 (5.9 Mb) shows a bacterium well adapted to pollution that carries many genes likely to be involved in hydrocarbon and xenobiotic catabolism and metal resistance. Clusters of genes coding for haloalkane, haloalkanoate, n-alkane, alicyclic acid, cyclic alcohol, and aromatic catabolism were analyzed in detail, and growth on acetate, catechol, chloroacetate, cyclohexane carboxylate, cyclohexanol, ferulate, heptane, 3-hydroxybenzoate, hydroxyquinol, gentisate, octane, protocatechuate, and salicylate was confirmed experimentally...
October 2008: Applied and Environmental Microbiology
Elisa García Garayoa, Dominique Rüegg, Peter Bläuenstein, Martin Zwimpfer, Irfan Ullah Khan, Veronique Maes, Alain Blanc, Annette G Beck-Sickinger, Dirk A Tourwé, P August Schubiger
INTRODUCTION: Bombesin, a neuropeptide with potential for breast and prostate tumor targeting, is rapidly metabolized in vivo, and as a result, uptake in tumor xenografts in mice is poor. An improvement can be expected from the introduction of nonnatural amino acids and spacers. Leu13 was replaced by cyclohexylalanine and Met14 by norleucine. Two spacers, -betaAla-betaAla- and 3,6-dioxa-8-aminooctanoic acid, were inserted between the receptor-binding amino acid sequence (7-14) of bombesin (BBS) and the retroN(alpha)-carboxymethyl histidine chelator used for labeling with the [99mTc](CO)3 core and the rhenium (Re) congener...
January 2007: Nuclear Medicine and Biology
Lenka Pilousova, Jitka Matiasovicova, Frantisek Sisak, Hana Havlickova, Ivan Rychlik
In Salmonella enterica serovar Typhimurium, retron reverse transcriptase (rrtT), which is part of St 85 retron, is quite ubiquitous and is located in the thdF -yidY intergenic region. In this study, we showed that rrtT is relatively unstable in multidrug resistant, Salmonella genomic island 1 (SGI 1) positive strains. Out of 365 field strains, 55 were free of retron. In 54 of the rrtT negative strains, the excision must have occurred by the same mechanism in which the rrtT together with five other genes was excised...
December 20, 2005: Veterinary Microbiology
B C Lampson, M Inouye, S Inouye
Retrons are distinct DNA sequences that code for a reverse transcriptase (RT) similar to the RTs produced by retroviruses and other types of retroelements. Retron DNAs are commonly associated with prophage DNA and are found in the genomes of a wide variety of different bacteria. The retron RT is used to synthesize a strange satellite DNA known as msDNA. msDNA is actually a complex of DNA, RNA, and probably protein. It is composed of a small, single-stranded DNA, linked to a small, single-stranded RNA molecule...
2005: Cytogenetic and Genome Research
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