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  1. Article ; Online: Bacterial antisense RNAs: how many are there, and what are they doing?

    Thomason, Maureen Kiley / Storz, Gisela

    Annual review of genetics

    2010  Volume 44, Page(s) 167–188

    Abstract: Antisense RNAs encoded on the DNA strand opposite another gene have the potential to form extensive base-pairing interactions with the corresponding sense RNA. Unlike other smaller regulatory RNAs in bacteria, antisense RNAs range in size from tens to ... ...

    Abstract Antisense RNAs encoded on the DNA strand opposite another gene have the potential to form extensive base-pairing interactions with the corresponding sense RNA. Unlike other smaller regulatory RNAs in bacteria, antisense RNAs range in size from tens to thousands of nucleotides. The numbers of antisense RNAs reported for different bacteria vary extensively, but hundreds have been suggested in some species. If all of these reported antisense RNAs are expressed at levels sufficient to regulate the genes encoded opposite them, antisense RNAs could significantly impact gene expression in bacteria. Here, we review the evidence for these RNA regulators and describe what is known about the functions and mechanisms of action for some of these RNAs. Important considerations for future research as well as potential applications are also discussed.
    MeSH term(s) Bacteria/genetics ; Gene Expression Regulation, Bacterial ; RNA, Antisense/chemistry ; RNA, Antisense/metabolism ; RNA, Bacterial/chemistry ; RNA, Bacterial/metabolism
    Chemical Substances RNA, Antisense ; RNA, Bacterial
    Language English
    Publishing date 2010-08-13
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 207928-8
    ISSN 1545-2948 ; 0066-4170 ; 0066-4197
    ISSN (online) 1545-2948
    ISSN 0066-4170 ; 0066-4197
    DOI 10.1146/annurev-genet-102209-163523
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Genetic variation and linkage disequilibrium in Bacillus anthracis.

    Zwick, Michael E / Thomason, Maureen Kiley / Chen, Peter E / Johnson, Henry R / Sozhamannan, Shanmuga / Mateczun, Alfred / Read, Timothy D

    Scientific reports

    2011  Volume 1, Page(s) 169

    Abstract: We performed whole-genome amplification followed by hybridization of custom-designed resequencing arrays to resequence 303 kb of genomic sequence from a worldwide panel of 39 Bacillus anthracis strains. We used an efficient algorithm contained within a ... ...

    Abstract We performed whole-genome amplification followed by hybridization of custom-designed resequencing arrays to resequence 303 kb of genomic sequence from a worldwide panel of 39 Bacillus anthracis strains. We used an efficient algorithm contained within a custom software program, UniqueMER, to identify and mask repetitive sequences on the resequencing array to reduce false-positive identification of genetic variation, which can arise from cross-hybridization. We discovered a total of 240 single nucleotide variants (SNVs) and showed that B. anthracis strains have an average of 2.25 differences per 10,000 bases in the region we resequenced. Common SNVs in this region are found to be in complete linkage disequilibrium. These patterns of variation suggest there has been little if any historical recombination among B. anthracis strains since the origin of the pathogen. This pattern of common genetic variation suggests a framework for recognizing new or genetically engineered strains.
    MeSH term(s) Alleles ; Animals ; Bacillus anthracis/classification ; Bacillus anthracis/genetics ; Bacillus anthracis/isolation & purification ; Bacillus anthracis/pathogenicity ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Evolution, Molecular ; Genetic Variation ; Genome, Bacterial ; Humans ; Linkage Disequilibrium ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Polymorphism, Single Nucleotide ; Recombination, Genetic
    Chemical Substances DNA, Bacterial
    Language English
    Publishing date 2011-11-24
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/srep00169
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Genomic characterization of the Yersinia genus.

    Chen, Peter E / Cook, Christopher / Stewart, Andrew C / Nagarajan, Niranjan / Sommer, Dan D / Pop, Mihai / Thomason, Brendan / Thomason, Maureen P Kiley / Lentz, Shannon / Nolan, Nichole / Sozhamannan, Shanmuga / Sulakvelidze, Alexander / Mateczun, Alfred / Du, Lei / Zwick, Michael E / Read, Timothy D

    Genome biology

    2010  Volume 11, Issue 1, Page(s) R1

    Abstract: Background: New DNA sequencing technologies have enabled detailed comparative genomic analyses of entire genera of bacterial pathogens. Prior to this study, three species of the enterobacterial genus Yersinia that cause invasive human diseases (Yersinia ...

    Abstract Background: New DNA sequencing technologies have enabled detailed comparative genomic analyses of entire genera of bacterial pathogens. Prior to this study, three species of the enterobacterial genus Yersinia that cause invasive human diseases (Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia enterocolitica) had been sequenced. However, there were no genomic data on the Yersinia species with more limited virulence potential, frequently found in soil and water environments.
    Results: We used high-throughput sequencing-by-synthesis instruments to obtain 25- to 42-fold average redundancy, whole-genome shotgun data from the type strains of eight species: Y. aldovae, Y. bercovieri, Y. frederiksenii, Y. kristensenii, Y. intermedia, Y. mollaretii, Y. rohdei, and Y. ruckeri. The deepest branching species in the genus, Y. ruckeri, causative agent of red mouth disease in fish, has the smallest genome (3.7 Mb), although it shares the same core set of approximately 2,500 genes as the other members of the species, whose genomes range in size from 4.3 to 4.8 Mb. Yersinia genomes had a similar global partition of protein functions, as measured by the distribution of Cluster of Orthologous Groups families. Genome to genome variation in islands with genes encoding functions such as ureases, hydrogenases and B-12 cofactor metabolite reactions may reflect adaptations to colonizing specific host habitats.
    Conclusions: Rapid high-quality draft sequencing was used successfully to compare pathogenic and non-pathogenic members of the Yersinia genus. This work underscores the importance of the acquisition of horizontally transferred genes in the evolution of Y. pestis and points to virulence determinants that have been gained and lost on multiple occasions in the history of the genus.
    MeSH term(s) Chromosome Mapping/methods ; Cluster Analysis ; Genetic Techniques ; Genetic Variation ; Genome, Bacterial ; Multigene Family ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Virulence ; Yersinia/genetics ; Yersinia enterocolitica/genetics ; Yersinia pestis/genetics
    Language English
    Publishing date 2010-01-04
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/gb-2010-11-1-r1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Genomic characterization of the Yersinia genus

    Chen, Peter E / Alexander Sulakvelidze / Alfred Mateczun / Andrew C Stewart / Brendan Thomason / Christopher Cook / Dan D Sommer / Lei Du / Maureen P Kiley Thomason / Michael E Zwick / Mihai Pop / Nichole Nolan / Niranjan Nagarajan / Shanmuga Sozhamannan / Shannon Lentz / Timothy D Read

    Genome biology. 2010 Jan., v. 11, no. 1

    2010  

    Abstract: BACKGROUND: New DNA sequencing technologies have enabled detailed comparative genomic analyses of entire genera of bacterial pathogens. Prior to this study, three species of the enterobacterial genus Yersinia that cause invasive human diseases (Yersinia ... ...

    Abstract BACKGROUND: New DNA sequencing technologies have enabled detailed comparative genomic analyses of entire genera of bacterial pathogens. Prior to this study, three species of the enterobacterial genus Yersinia that cause invasive human diseases (Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia enterocolitica) had been sequenced. However, there were no genomic data on the Yersinia species with more limited virulence potential, frequently found in soil and water environments. RESULTS: We used high-throughput sequencing-by-synthesis instruments to obtain 25- to 42-fold average redundancy, whole-genome shotgun data from the type strains of eight species: Y. aldovae, Y. bercovieri, Y. frederiksenii, Y. kristensenii, Y. intermedia, Y. mollaretii, Y. rohdei, and Y. ruckeri. The deepest branching species in the genus, Y. ruckeri, causative agent of red mouth disease in fish, has the smallest genome (3.7 Mb), although it shares the same core set of approximately 2,500 genes as the other members of the species, whose genomes range in size from 4.3 to 4.8 Mb. Yersinia genomes had a similar global partition of protein functions, as measured by the distribution of Cluster of Orthologous Groups families. Genome to genome variation in islands with genes encoding functions such as ureases, hydrogeneases and B-12 cofactor metabolite reactions may reflect adaptations to colonizing specific host habitats. CONCLUSIONS: Rapid high-quality draft sequencing was used successfully to compare pathogenic and non-pathogenic members of the Yersinia genus. This work underscores the importance of the acquisition of horizontally transferred genes in the evolution of Y. pestis and points to virulence determinants that have been gained and lost on multiple occasions in the history of the genus.
    Keywords evolution ; fish diseases ; genes ; habitats ; human diseases ; metabolites ; mouth ; pathogens ; sequence analysis ; virulence ; Yersinia enterocolitica ; Yersinia pestis ; Yersinia pseudotuberculosis
    Language English
    Dates of publication 2010-01
    Size p. 2294.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/gb-2010-11-1-r1
    Database NAL-Catalogue (AGRICOLA)

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