The amazing world of bacterial structured RNAs

Genome Biology

Volumn 11, Issue 3, 2010, Pages

  Westhof, Eric ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RNA 23S; RNA 5S; SELENOCYSTEINE; UNTRANSLATED RNA;

ARCHAEAL GENOME; ARTICLE; DNA SEQUENCE; INTRON; METAGENOME; NONHUMAN; PROTEIN FUNCTION; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE; RNA BINDING; RNA SEQUENCE; RNA STRUCTURE; STRUCTURE ANALYSIS; ARCHAEBACTERIUM; BACTERIAL GENOME; BACTERIUM; BASE PAIRING; BIOLOGY; CHEMICAL STRUCTURE; CONFORMATION; GENETICS; GENOMICS; METHODOLOGY; PROTEIN MOTIF; REVIEW;

ARCHAEA; BACTERIA (MICROORGANISMS);

AMINO ACID MOTIFS; ARCHAEA; BACTERIA; BASE PAIRING; COMPUTATIONAL BIOLOGY; GENOME, ARCHAEAL; GENOME, BACTERIAL; GENOMICS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA, UNTRANSLATED;

EID: 77956932251     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2010-11-3-108     Document Type: Article

References (10)

1. Barrick JE, Breaker RR. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 2007, 8:R239. 10.1186/gb-2007-8-11-r239, 2258182, 17997835.
2. Benito Y, Kolb FA, Romby P, Lina G, Etienne J, Vandenesch F. Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression. RNA 2000, 6:668-679. 10.1017/S1355838200992550, 1369947, 10836788.
3. Weinberg Z, Perreault J, Meyer MM, Breaker RR. Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature 2009, 462:656-659. 10.1038/nature08586, 19956260.
4. Weinberg Z, Wang JX, Bogue J, Yang J, Corbino KA, Moy RH, Breaker RM. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes. Genome Biol 2010, 11:R31.
5. Menzel P, Gorodkin J, Stadler PF. The tedious task of finding homologous noncoding RNA genes. RNA 2009, 15:2075-2082. 10.1261/rna.1556009, 19861422.
6. Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL. De novo prediction of structured RNAs from genomic sequences. Trends Biotechnol 2009, 28:9-19. 10.1016/j.tibtech.2009.09.006, 19942311.
7. Yao Z, Weinberg Z, Ruzzo WL. CMfinder - -a covariance model based RNA motif finding algorithm. Bioinformatics 2006, 22:445-452. 10.1093/bioinformatics/btk008, 16357030.
8. Rivas E, Eddy SR. Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics 2000, 16:583-605. 10.1093/bioinformatics/16.7.583, 11038329.
9. Leontis NB, Stombaugh J, Westhof E. Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules. Biochimie 2002, 84:961-973. 10.1016/S0300-9084(02)01463-3, 12458088.
10. Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH. Structures of the bacterial ribosome at 3.5 A resolution. Science 2005, 310:827-834. 10.1126/science.1117230, 16272117.