The Yfr2 ncRNA family, a group of abundant RNA molecules widely conserved in cyanobacteria

被引：20

作者：

Gierga, Gregor

Voss, Bjoern

Hess, Wolfgang R. ^{[1
]}

机构：

[1] Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany

来源：

RNA BIOLOGY | 2009年 / 6卷 / 03期

关键词：

anabaena; cyanobacteria; non-coding RNA; prochlorococcus; RFAM; synechococcus; GENOME; PREDICTION; CORE;

D O I：

10.4161/rna.6.3.8921

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Sequence signatures, predicted secondary structures and experimental data suggest the Yfr2 family of non-coding RNAs (ncRNAs) to be present in nearly all cyanobacteria sequenced to date. The common features of the family members include a central consensus element (CCE), 5'-RKT SGA AAC WHG GHM ASA M-3', predicted to form a 12 nt single stranded region plus a short helical region consisting of three base pairs and one unpaired nucleotide that is either bulging or the begin of a short internal loop. Yfr2 family members are 63 to 100 nucleotides in size and they share a conserved region at the 5' end, starting with 5'-GUGAGGA-3' or a closely related motif. The genes for ncRNAs of this family are suggested to exist in highly variable copy numbers in the individual genomes, with up to nine copies in some marine Synechococcus.

引用

收藏

页码：222 / 227

页数：6

相关论文

共 18 条

[1] Identification of cyanobacterial non-coding RNAs by comparative genome analysis [J].

Axmann, IM ;

Kensche, P ;

Vogel, J ;

Kohl, S ;

Herzel, H ;

Hess, WR .

GENOME BIOLOGY, 2005, 6 (09)

[2] RNAalifold: improved consensus structure prediction for RNA alignments [J].

Bernhart, Stephan H. ;

Hofacker, Ivo L. ;

Will, Sebastian ;

Gruber, Andreas R. ;

Stadler, Peter F. .

BMC BIOINFORMATICS, 2008, 9 (1)

[3] A genetic manipulation system for oceanic cyanobacteria of the genus Synechococcus [J].

Brahamsha, B .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 1996, 62 (05) :1747-1751

[4] Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria [J].

Dufresne, Alexis ;

Ostrowski, Martin ;

Scanlan, David J. ;

Garczarek, Laurence ;

Mazard, Sophie ;

Palenik, Brian P. ;

Paulsen, Ian T. ;

de Marsac, Nicole Tandeau ;

Wincker, Patrick ;

Dossat, Carole ;

Ferriera, Steve ;

Johnson, Justin ;

Post, Anton F. ;

Hess, Wolfgang R. ;

Partensky, Frederic .

GENOME BIOLOGY, 2008, 9 (05)

[5] Characterization of true-branching cyanobacteria from geothermal sites and hot springs of Costa Rica [J].

Finsinger, Karin ;

Scholz, Ingeborg ;

Serrano, Aurelio ;

Morales, Saylen ;

Uribe-Lorio, Lorena ;

Mora, Marielos ;

Sittenfeld, Ana ;

Weckesser, Juergen ;

Hess, Wolfgang R. .

ENVIRONMENTAL MICROBIOLOGY, 2008, 10 (02) :460-473

[6]

Hess Wolfgang R., 2008, P89

[7] Detection of seven major evolutionary lineages in cyanobacteria based on the 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strains [J].

Honda, D ;

Yokota, A ;

Sugiyama, J .

JOURNAL OF MOLECULAR EVOLUTION, 1999, 48 (06) :723-739

[8] Patterns and implications of gene gain and loss in the evolution of Prochlorococcus [J].

Kettler, Gregory C. ;

Martiny, Adam C. ;

Huang, Katherine ;

Zucker, Jeremy ;

Coleman, Maureen L. ;

Rodrigue, Sebastien ;

Chen, Feng ;

Lapidus, Alla ;

Ferriera, Steven ;

Johnson, Justin ;

Steglich, Claudia ;

Church, George M. ;

Richardson, Paul ;

Chisholm, Sallie W. .

PLOS GENETICS, 2007, 3 (12) :2515-2528

[9] Clustal W and clustal X version 2.0 [J].

Larkin, M. A. ;

Blackshields, G. ;

Brown, N. P. ;

Chenna, R. ;

McGettigan, P. A. ;

McWilliam, H. ;

Valentin, F. ;

Wallace, I. M. ;

Wilm, A. ;

Lopez, R. ;

Thompson, J. D. ;

Gibson, T. J. ;

Higgins, D. G. .

BIOINFORMATICS, 2007, 23 (21) :2947-2948

[10] The cyanobacterial genome core and the origin of photosynthesis [J].

Mulkidjanian, Armen Y. ;

Koonin, Eugene V. ;

Makarova, Kira S. ;

Mekhedov, Sergey L. ;

Sorokin, Alexander ;

Wolf, Yuri I. ;

Dufresne, Alexis ;

Partensky, Frederic ;

Burd, Henry ;

Kaznadzey, Denis ;

Haselkorn, Robert ;

Galperin, Michael Y. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (35) :13126-13131