Rfam: updates to the RNA families database

Gardner, Paul P.; Daub, Jennifer; Tate, John; Nawrocki, Eric P.; Kolbe, Diana L.; Lindgreen, Stinus; Wilkinson, Adam C.; Finn, Robert D.; Griffiths-Jones, Sam; Eddy, Sean R.

doi:10.1093/nar/gkn766

Cited by 814 publications

(728 citation statements)

References 28 publications

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“…Small RNAs were analyzed using the Rfam (version 10.0) website (http://rfam.sanger.ac.uk/). Rfam is a collection of non-coding RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models, including 1446 families in January 2010 (Gardner et al, 2009). Finally, in order to identify MED134-specific small RNA that might not be represented in Rfam, we assembled a database of intergenic regions in the genome of MED134 longer than 100 bp (total 992 sequences), which might encode putative small RNAs.…”

Section: Methodsmentioning

confidence: 99%

Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium

et al. 2011

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Proteorhodopsin (PR) is a photoprotein that functions as a light-driven proton pump in diverse marine Bacteria and Archaea. Recent studies have suggested that PR may enhance both growth rate and yield in some flavobacteria when grown under nutrient-limiting conditions in the light. The direct involvement of PR, and the metabolic details enabling light-stimulated growth, however, remain uncertain. Here, we surveyed transcriptional and growth responses of a PR-containing marine flavobacterium during carbon-limited growth in the light and the dark. As previously reported (Gómez-Consarnau et al., 2007), Dokdonia strain MED134 exhibited light-enhanced growth rates and cell yields under low carbon growth conditions. Inhibition of retinal biosynthesis abolished the light-stimulated growth response, supporting a direct role for retinal-bound PR in light-enhanced growth. Among protein-coding transcripts, both PR and retinal biosynthetic enzymes showed significant upregulation in the light. Other light-associated proteins, including bacterial cryptochrome and DNA photolyase, were also expressed at significantly higher levels in the light. Membrane transporters for Na+/phosphate and Na+/alanine symporters, and the Na+-translocating NADH-quinone oxidoreductase (NQR) linked electron transport chain, were also significantly upregulated in the light. Culture experiments using a specific inhibitor of Na+-translocating NQR indicated that sodium pumping via NQR is a critical metabolic process in the light-stimulated growth of MED134. In total, the results suggested the importance of both the PR-enabled, light-driven proton gradient, as well as the generation of a Na+ ion gradient, as essential components for light-enhanced growth in these flavobacteria.

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Section: Methodsmentioning

confidence: 99%

Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium

et al. 2011

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“…However, only a portion of the canonical AdoCbl-sensing riboswitch could be initially recognized, suggesting that the E. faecalis eutT-G RNA element may be significantly different. Indeed, this putative RNA element was not identified by prior bioinformatics-based searches for AdoCbl-sensing riboswitches (28,29,31). Closer inspection of the eutT-G intergenic region yielded 2 key observations.…”

Section: Adocbl-sensing Riboswitches Are Found Within the Eut Locusmentioning

confidence: 99%

Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis

Fox¹,

Ramesh

Stearns

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

142

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Ethanolamine, a product of the breakdown of phosphatidylethanolamine from cell membranes, is abundant in the human intestinal tract and in processed foods. Effective utilization of ethanolamine as a carbon and nitrogen source may provide a survival advantage to bacteria that inhabit the gastrointestinal tract and may influence the virulence of pathogens. In this work, we describe a unique series of posttranscriptional regulatory strategies that influence expression of ethanolamine utilization genes (eut) in Enterococcus, Clostridium, and Listeria species. One of these mechanisms requires an unusual 2-component regulatory system. Regulation involves specific sensing of ethanolamine by a sensor histidine kinase (EutW), resulting in autophosphorylation and subsequent phosphoryl transfer to a response regulator (EutV) containing a RNA-binding domain. Our data suggests that EutV is likely to affect downstream gene expression by interacting with conserved transcription termination signals located within the eut locus. Breakdown of ethanolamine requires adenosylcobalamin (AdoCbl) as a cofactor, and, intriguingly, we also identify an intercistronic AdoCbl riboswitch that has a predicted structure different from previously established AdoCbl riboswitches. We demonstrate that association of AdoCbl to this riboswitch prevents formation of an intrinsic transcription terminator element located within the intercistronic region. Together, these results suggest an intricate and carefully coordinated interplay of multiple regulatory strategies for control of ethanolamine utilization genes. Gene expression appears to be directed by overlapping posttranscriptional regulatory mechanisms, each responding to a particular metabolic signal, conceptually akin to regulation by multiple DNAbinding transcription factors.riboswitch ͉ 2-component system

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“…The ITS2 region was assumed to end after the 9th nucleotide preceding the TCGGATCA pattern at the beginning of the large subunit of the nuclear ribosomal RNA gene region. Borders between ITS1 and 5.8S and between 5.8S and ITS2 were defined using the Rfam 5.8S seed alignment (Gardner et al 2009). A preliminary alignment was created using the G-INS-I algorithm of MAFFT version 6.820 (Katoh & Toh 2008).…”

Section: Alignment Of Itsmentioning

confidence: 99%

Extended phylogeny and a revised generic classification of thePannariaceae(Peltigerales, Ascomycota)

et al. 2014

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We estimated phylogeny in the lichen-forming ascomycete family Pannariaceae. We specifically modelled spatial (across-site) heterogeneity in nucleotide frequencies, as models not incorporating this heterogeneity were found to be inadequate for our data. Model adequacy was measured here as the ability of the model to reconstruct nucleotide diversity per site in the original sequence data. A potential non-orthologue in the internal transcribed spacer region (ITS) of Degelia plumbea was observed. We propose a revised generic classification for the Pannariaceae, accepting 30 genera, based on our phylogeny, previously published phylogenies, as well as available morphological and chemical data. Four genera are established as new: Austroparmeliella (for the 'Parmeliella' lacerata group), Nebularia (for the 'Parmeliella' incrassata group), Nevesia (for 'Fuscopannaria' sampaiana), and Pectenia (for the 'Degelia' plumbea group). Two genera are reduced to synonymy, Moelleropsis (included in Fuscopannaria) and Santessoniella (non-monophyletic; type included in Psoroma). Lepidocollema, described as monotypic, is expanded to include 23 species, most of which have been treated in the 'Parmeliella' mariana group. Homothecium and Leightoniella, previously treated in the Collemataceae, are here referred to the Pannariaceae. We propose 41 new species-level combinations in the newly described and re-circumscribed genera mentioned above, as well as in Leciophysma and Psoroma.

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Rfam: updates to the RNA families database

Cited by 814 publications

References 28 publications

Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium

Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium

Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis

Extended phylogeny and a revised generic classification of thePannariaceae(Peltigerales, Ascomycota)

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