Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA

Smith, Cameron; Heyne, Steffen; Richter, Andreas S.; Will, Sebastian; Backofen, Rolf

doi:10.1093/nar/gkq316

Cited by 200 publications

(180 citation statements)

References 30 publications

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“…Formation of photosynthetic complexes is induced by decreasing oxygen tension and is inhibited by light at intermediate oxygen tension. The regulation of photosynthesis genes in Rhodobacter has been intensively studied in the past and a regulatory network involving several regulatory proteins and parts of the electron transport chain emerged (10, *Genes with RSP numbers in boldface type are a possible PcrZ target as predicted by IntaRNA (27). RSP_0273-0275, RSP_0285-0291, RSP_0314-0315, and RSP_6108-0258 respectively belong to same operons.…”

Section: Discussionmentioning

confidence: 99%

“…We assumed that PcrZ may directly target mRNAs for photosynthesis genes. An IntaRNA search (27,28) suggested a base pairing between PcrZ and several mRNAs that showed altered expression levels in the microarray analysis (Table S1). When only putative targets with predicted energy values of less than −16 kcal/mol were considered, the predicted interacting nucleotides mapped preferentially to the three stem-loop structures in the 5′ part of PcrZ.…”

Section: Full-length Pcrz But Not a Smaller Processing Product Affectmentioning

confidence: 99%

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Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ

Mank

Berghoff

Hermanns

et al. 2012

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

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The small RNA PcrZ (photosynthesis control RNA Z) of the facultative phototrophic bacterium Rhodobacter sphaeroides is induced upon a drop of oxygen tension with similar kinetics to those of genes for components of photosynthetic complexes. High expression of PcrZ depends on PrrA, the response regulator of the PrrB/ PrrA two-component system with a central role in redox regulation in R. sphaeroides. In addition the FnrL protein, an activator of some photosynthesis genes at low oxygen tension, is involved in redox-dependent expression of this small (s)RNA. Overexpression of full-length PcrZ in R. sphaeroides affects expression of a small subset of genes, most of them with a function in photosynthesis. Some mRNAs from the photosynthetic gene cluster were predicted to be putative PcrZ targets and results from an in vivo reporter system support these predictions. Our data reveal a negative effect of PcrZ on expression of its target mRNAs. Thus, PcrZ counteracts the redox-dependent induction of photosynthesis genes, which is mediated by protein regulators. Because PrrA directly activates photosynthesis genes and at the same time PcrZ, which negatively affects photosynthesis gene expression, this is one of the rare cases of an incoherent feed-forward loop including an sRNA. Our data identified PcrZ as a trans acting sRNA with a direct regulatory function in formation of photosynthetic complexes and provide a model for the control of photosynthesis gene expression by a regulatory network consisting of proteins and a small noncoding RNA.α-proteobacteria | protochlorophyllide reductase

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Section: Discussionmentioning

confidence: 99%

Section: Full-length Pcrz But Not a Smaller Processing Product Affectmentioning

confidence: 99%

Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ

Mank

Berghoff

Hermanns

et al. 2012

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

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“…The ITS2 sequences of Fusarium occurring as endophytes, saprobes and pathogens (plant pathogenic and human pathogenic) were used to generate consensus RNA secondary structures using LocARNA version 1.5.2 (Smith et al 2010). It performed multiple alignments and generated consensus secondary structures of each category using realistic energy model for RNAs.…”

Section: Consensus Rna Secondary Structures Predictionmentioning

confidence: 99%

Molecular phylogeny and RNA secondary structure of Fusarium species with different lifestyles

Barik¹

2011

PPQ

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The definition of endophytes ranges from symbiotic to balanced antagonism and/or latent plant pathogens. This indicates a close affiliation between endophytes and pathogens but molecular evidence confirming these relationships are still to be elucidated. We investigated the relationship of endophytic, saprobic and pathogenic Fusarium species as a model genus based on ITS sequences and ITS2 secondary structure analysis. Altogether 212 Fusarium species mostly named in GenBank with ranging lifestyles were used in this study. Species deposited in GenBank were found to be often wrongly named based on sequence comparison as species with the same names were polyphyletic, while differently named species often had the same sequences. Phylogenetic analysis by three different methods (UPGMA, NJ and MP) revealed that similar named species clustered together, but did not form well distinct clades reflective of their lifestyles. Several species were polyphyletic, while several other unrelated species appear to share the same ITS sequences. Since ITS rDNA sequence based phylogeny did not showed distinct relationships, ITS2 consensus secondary structures were used. Endophytes showed close molecular structural affinity with pathogens but structural features of saprobes was very different. Although care must be taken when using sequences from named Fusarium species in GenBank this study provides molecular evidence that endophytes share a close relationship with pathogens and agrees with the assumption that endophytes are latent pathogens.

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“…29 The potential interaction-sites predicted by IntaRNA were all located in the coding region of the target-genes. The interaction energies ranged from -14.3 kcal/mol (aroF) to -9.8 kcal/mol (aroL).…”

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confidence: 99%