A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Voß, Björn ^a   Gierga, Gregor ^a   Axmann, Ilka M ^b   Hess, Wolfgang R ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b HUMBOLDT UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; UNTRANSLATED RNA; MICRORNA; RNA;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIOPLANKTON; BACTERIUM DETECTION; CELL LINEAGE; CHLOROBIACEAE; CYANOBACTERIUM; ESCHERICHIA COLI; GENOME ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SPIROCHETE; STRUCTURE ANALYSIS; CHEMISTRY; CONFORMATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; PHYLOGENY; SEQUENCE HOMOLOGY;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); CHLOROBIACEAE; CYANOBACTERIA; PROCHLOROCOCCUS; SPIROCHAETA;

BASE SEQUENCE; CELL LINEAGE; CYANOBACTERIA; GENOME, BACTERIAL; MICRORNAS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

EID: 38049182828     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-375     Document Type: Article

References (24)

1. Gottesman S The small RNA regulators of Escherichia coli: Roles and mechanisms Annu Rev Microbiol 2004, 58:303-328. 10.1146/ annurev.micro.58.030603.123841 15487940
2. Gottesman S Micros for microbes: Non-coding regulatory RNAs in bacteria Trends Genet 2005, 21(7):399-404. 10.1016/j.tig.2005.05.008 15913835
3. Vogel J Sharma CM How to find small non-coding RNAs in bacteria Biol Chem 2005, 386:1219-1238. 10.1515/BC.2005.140 16336117
4. Csiszar K Houmard J Damerval T Tandeau de Marsac N Transcriptional analysis of the cyanobacterial gvpABC operon in differentiated cells: occurrence of an antisense RNA complementary to three overlapping transcripts Gene 1987, 60(1):29-37. 10.1016/0378-1119(87)90210-1 2450053
5. Dühring U Axmann IM Hess WR Wilde A An internal antisense RNA regulates expression of the photosynthesis gene isiA Proc Natl Acad Sci USA 2006, 103:7054-7058. 1459017 16636284 10.1073/pnas.0600927103
6. Hernandez JA Muro-Pastor AM Flores E Bes MT Peleato ML Fillat MF Identification of a furA cis antisense RNA in the cyanobacterium Anabaena sp. PCC 7120 J Mol Biol 2005, 355:325-334. 10.1016/ j.jmb.2005.10.079 16324715
7. Axmann IM Kensche P Vogel J Kohl S Herzel H Hess WR Identification of cyanobacterial non-coding RNAs by comparative genome analysis Genome Biol 2005, 6(9):R73. 1242208 16168080 10.1186/gb-2005-6-9-r73
8. Barrick JE Sudarsan N Weinberg Z Ruzzo WL Breaker RR 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter RNA 2005, 11(5):774-784. 1370762 15811922 10.1261/ rna.7286705
9. Axmann IM Holtzendorff J Voss B Kensche P Hess WR Two distinct types of 6S RNA in Prochlorococcus Gene 2007. epub ahead of print: Doi:10.1016/ j.gene.2007.06.011
10. Tolonen AC Liszt GB Hess WR Genetic manipulation of Prochlorococcus MIT9313: GFP expression on an RSF1010 plasmid and Tn5 transposition Appl Environ Microbiol 2006, 72:7607-7613. 1694220 17041154 10.1128/ AEM.02034-06
11. Yao Z Barrick J Weinberg Z Neph S Breaker R Tompa M Ruzzo WL A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes PLoS Comput Biol 2007, 3(7):e126. 1913097 17616982 10.1371/journal.pcbi.0030126
12. Rippka R Deruelles J Waterbury JB Herdmann M Stanier RY Generic assignments, strain histories and properties of pure cultures of cyanobacteria J Gen Microbiol 1979, 111:1-61.
13. Moore LR Rocap G Chisholm SW Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes Nature 1998, 393(6684):464-467. 10.1038/30861 9624000
14. Urbach E Scanlan DJ Distel DL Waterbury JB Chisholm SW Rapid diversification of marine picophytoplankton with dissimilar light-harvesting structures inferred from sequences of Prochlorococcus and Synechococcus (Cyanobacteria) J Mol Evol 1998, 46(2):188-201. 10.1007/PL00006294 9452521
15. West NJ Scanlan DJ Niche-partitioning of Prochlorococcus populations in a stratified water column in the eastern north Atlantic ocean Appl Environ Microbiol 1999, 65(6):2585-2591. 91382 10347047
16. JGI website http://genome.jgi-psf.org/finished_microbes/nospu/ nospu.home.html
17. Genoscope http://www.genoscope.cns.fr/
18. Genbank http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi
19. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994, 22(22):4673-4680. 308517 7984417 10.1093/nar/22.22.4673
20. Voss B Structural analysis of aligned RNAs Nucleic Acids Res 2006, 34(19):5471-5481. 1636479 17020924 10.1093/nar/gkl692
21. Griffiths-Jones S RALEE - RNA ALignment editor in Emacs Bioinformatics 2005, 21(2):257-259. 10.1093/bioinformatics/bth489 15377506
22. Macke TJ Ecker DJ Gutell RR Gautheret D Case DA Sampath R RNAMotif, an RNA secondary structure definition and search algorithm Nucleic Acids Res 2001, 29(22):4724-4735. 92549 11713323 10.1093/nar/29.22.4724
23. Crooks GE Hon G Chandonia JM Brenner SE WebLogo: A sequence logo generator Genome Res 2004, 14(6):1188-1190. 419797 15173120 10.1101/ gr.849004
24. Kumar S Tamura K Nei M MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers Comput Appl Biosci 1994, 10(2):189-191. 8019868