RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes

RASTA-Bacteria is an automated method that allows quick and reliable identification of toxin/antitoxin loci in sequenced prokaryotic genomes, whether they are annotated Open Reading Frames or not

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021

<p>Abstract</p> <p>Background</p> <p>Small untranslated RNAs (sRNAs) seem to be far more abundant than previously believed. The number of sRNAs confirmed in <it>E. coli </it>through various approaches is above 70, with several hundred more sRNA candidate genes under biological validation. Although the total number of sRNAs in any one species is still unclear, their importance in cellular processes has been established. However, unlike protein genes, no simple feature enables the prediction of the location of the corresponding sequences in genomes. Several approaches, of variable usefulness, to identify genomic sequences encoding sRNA have been described in recent years.</p> <p>Results</p> <p>We used a combination of <it>in silico </it>comparative genomics and microarray-based transcriptional profiling. This approach to screening identified ~60 intergenic regions conserved between <it>Sinorhizobium meliloti </it>and related members of the alpha-proteobacteria sub-group 2. Of these, 14 appear to correspond to novel non-coding sRNAs and three are putative peptide-coding or 5' UTR RNAs (ORF smaller than 100 aa). The expression of each of these new small RNA genes was confirmed by Northern blot hybridization.</p> <p>Conclusion</p> <p>Small non coding RNA (<it>sra</it>) genes can be found in the intergenic regions of alpha-proteobacteria genomes. Some of these <it>sra </it>genes are only present in <it>S. meliloti</it>, sometimes in genomic islands; homologues of others are present in related genomes including those of the pathogens <it>Brucella </it>and <it>Agrobacterium</it>.</p

Nessun Dorma, a novel centralspindlin partner, is required for cytokinesis in Drosophila spermatocytes

Nessun Dorma is a component of the ring canal with a polysaccharide-binding domain, which is important for cytokinesis during male meiosis

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021-4

<p><b>Copyright information:</b></p><p>Taken from "Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021"</p><p>http://www.biomedcentral.com/1471-2164/8/467</p><p>BMC Genomics 2007;8():467-467.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2245857.</p><p></p> of 1000 replicates. B. In northern blots, a signal for the predicted was detected corresponding to lengths of 144 and 106 nucleotides in total RNA from 1021 and to 140 and 132 nt in that from and , respectively

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021-1

<p><b>Copyright information:</b></p><p>Taken from "Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021"</p><p>http://www.biomedcentral.com/1471-2164/8/467</p><p>BMC Genomics 2007;8():467-467.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2245857.</p><p></p>e minimal, maximal and mean values of the percentage of GC

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021-0

<p><b>Copyright information:</b></p><p>Taken from "Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021"</p><p>http://www.biomedcentral.com/1471-2164/8/467</p><p>BMC Genomics 2007;8():467-467.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2245857.</p><p></p>f total RNA from strain 1021 was analyzed by Northern blotting hybridization with specific oligonucleotides [see Additional file ]; the molecular sizes were calculated in nucleotides (nt): > rnpB (372 nt), > tmRNA 3' end (204 nt), > 5S (120 nt), > 4.5S (95 nt), and > tmRNA 5' end (82 nt) [39]. Band > was not hybridized but its size is consistent with it being a tRNA. Exposure times were optimized for each panel and signal intensity does not indicate relative abundance of ncRNAs

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021-5

<p><b>Copyright information:</b></p><p>Taken from "Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021"</p><p>http://www.biomedcentral.com/1471-2164/8/467</p><p>BMC Genomics 2007;8():467-467.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2245857.</p><p></p>f total RNA from strain 1021 was analyzed by Northern blotting hybridization with specific oligonucleotides [see Additional file ]; the molecular sizes were calculated in nucleotides (nt): > rnpB (372 nt), > tmRNA 3' end (204 nt), > 5S (120 nt), > 4.5S (95 nt), and > tmRNA 5' end (82 nt) [39]. Band > was not hybridized but its size is consistent with it being a tRNA. Exposure times were optimized for each panel and signal intensity does not indicate relative abundance of ncRNAs

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021-3

<p><b>Copyright information:</b></p><p>Taken from "Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021"</p><p>http://www.biomedcentral.com/1471-2164/8/467</p><p>BMC Genomics 2007;8():467-467.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2245857.</p><p></p>ted DNA oligonucleotide probes [see Additional file ] and exposed for various times (therefore the intensities of the signals do not correspond to the relative abundance of each sRNA). The positions of RNA size standards are shown on the left. B. Distribution of the genes along the chromosome. The origin of replication (= sra01) and positions of , and are also indicated. Blue and red arrows represent genes on the reverse or forward strands, respectively. Genomic islands are indicated with grey boxes (Sme21T, Sme19T and Sme80S)

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021-2

<p><b>Copyright information:</b></p><p>Taken from "Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in strain 1021"</p><p>http://www.biomedcentral.com/1471-2164/8/467</p><p>BMC Genomics 2007;8():467-467.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2245857.</p><p></p> indicated as signal-to-noise SNR values (log2 scale), represented by a red panel. The position of each gene in the heat map is determined by its intensity. For the complementary Northern dot analysis, 10 μg of RNA, isolated from the most favourable expression condition, was spotted (in duplicate) onto a nylon membrane and hybridized with a radiolabelled specific probe [see Additional file ]