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Small RNAs, 5′ UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence.

Small RNAs, 5′ UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence.

FEMS Microbiol Rev. 2015 May;39(3):331-349

Authors: Oliva G, Sahr T, Buchrieser C

Abstract
Sequencing-based studies have illuminated increased transcriptional complexity within the genome structure of bacteria and have resulted in the identification of many small regulatory RNAs (sRNA) and a large amount of antisense transcription. It remains an open question whether these sRNAs all indeed play regulatory roles, but their identification led to an exponential increase in studies searching for their function. This allowed to show that sRNAs may modulate virulence gene expression, cellular differentiation, metabolic functions, adaptation to environmental conditions and pathogenesis. In this review we will provide mechanistic insights into how sRNAs bind mRNAs and/or proteins. Furthermore, the important roles of the RNA chaperone Hfq, the CsrA system and the CRISPR RNA will be discussed. We will then focus on sRNAs and 5(‘) untranslated region (UTR) elements of intracellular bacteria like Chlamydia, Listeria, Legionella, or Salmonella, and place emphasis on those that are expressed during replication in host cells and are implicated in virulence and metabolism. In addition, sRNAs that regulate motility, iron homeostasis, and differentiation or stress responses will be highlighted. Taken together sRNAs constitute key elements in many major regulatory networks governing the intracellular life and virulence of pathogenic bacteria.

PMID: 26009640 [PubMed – as supplied by publisher]

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SNORD76, a box C/D snoRNA, acts as a tumor suppressor in glioblastoma.

SNORD76, a box C/D snoRNA, acts as a tumor suppressor in glioblastoma.

Sci Rep. 2015;5:8588

Authors: Chen L, Han L, Wei J, Zhang K, Shi Z, Duan R, Li S, Zhou X, Pu P, Zhang J, Kang C

Abstract
Glioblastoma (GBM) is associated with disproportionately high morbidity and mortality, reflecting the need to develop new diagnostic and therapeutic targets for this disease. Recently, accumulating evidence has suggested that small nucleolar RNAs (snoRNAs) are gaining prominence and are more actively involved in tumorigenesis than previously thought. However, no report concerning the implication of snoRNAs in glioma has been published to date. In our study, SNORD76 was first found to be inversely associated with Hox Transcript Antisense Intergenic RNA (HOTAIR) knockdown, and surprisingly, forcibly expressed SNORD76 inhibited proliferation and growth of glioma cells. Moreover, downregulation of SNORD76 led to a more malignant phenotype. The pleiotropy of SNORD76 overexpression could be achieved at least partially through inducing cell cycle arrest at S phase by affecting the Rb-associated cell cycle regulation. Enforced SNORD76 expression in orthotopic tumors resulted in decreased tumor growth and the reduction of tumor volume. Additionally, in surgically resected glioma tissues, SNORD76, not its host gene, was associated with the WHO classification and was selectively downregulated in GBM (WHO grade IV). Collectively, our study adds to a growing body of evidence for the participation of snoRNAs in gliomagenesis and is the first to implicate a snoRNA in glioblastoma.

PMID: 25715874 [PubMed – in process]

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Forget the Selfish Gene: Evolution of Life Is Driven by the Selfish Ribosome, Research Suggests

Since the discovery of how DNA encodes genetic information, most research on the evolution of life has focused on genes. According to the ‘selfish gene’ theory, cells and organisms exist … Jan. 7, 2015 

— Delivered by Feed43 service http://bit.ly/1HNmGIG #scidaily

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The functional role of long non-coding RNAs and epigenetics

Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. The post-transcriptional regulation is influenced by these lncRNAs by interfering with the microRNA pathways, involving in diverse cellular processes. The regulation of gene expression by lncRNAs at the epigenetic level, transcriptional and post-transcriptional level have been well known and widely studied. Recent recognition

The functional role of long non-coding RNAs and epigenetics is a post from: lncRNA Blog

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RCas9: A Programmable RNA Editing Tool

newscenter.lbl.gov
– lcyarris
A powerful scientific tool for editing the DNA instructions in a genome can now also be applied to RNA, the molecule that translates DNA’s genetic instructions into the production of proteins. A team of researchers with Berkeley Lab and the University of California (UC) Berkeley has demonstrated a means by which the CRISPR/Cas9 protein complex can be programmed to recognize and cleave RNA at sequence-specific target sites. This finding has the potential to transform the study of RNA function by…  show all text
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@NIGMS on Twitter
@NIGMS: Boost for Synthetic #Biology: Powerful #DNA editing tool can now be programmed to edit RNA. bit.ly/cas9r http://ift.tt/1tnrJ9j
@SeqComplete on Twitter
@SeqComplete: mt #igem #synbio RCas9: A Programmable RNA Editing Tool http://ift.tt/1vInd7S, see more http://ift.tt/1s6DmVA
@anamika13 on Twitter
@anamika13: A powerful scientific tool for editing the DNA instructions in a genome can be applied to RNA: http://ift.tt/1vInd7S http://ift.tt/1vD8083
@idtdna on Twitter
@idtdna: Boost for Synthetic #Biology: Powerful #DNA editing tool can now be programmed to edit RNA. bit.ly/cas9r http://ift.tt/1tnrJ9j
@GeneRef on Twitter
@GeneRef: RCas9: A programmable RNA editing tool ow.ly/2OAc4k
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Prediction of uridine modifications in tRNA sequences

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Rfam 12.0 is out | Xfam Blog

We are pleased to announce the release of Rfam 12.0!
This release contains some major changes when compared with previous releases of Rfam, so please take a minute to read our release notes. Rfam 12.0 is the first version of Rfam which is based on Infernal 1.1, and as such contains many significant changes. In particular, the curator-defined thresholds have all been manually altered to ensure compatability with Infernal 1.1. This means that many families have seen significant increases or decre…  show all text
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@emblebi on Twitter
@emblebi: Some huge changes in @Xfam_EBI‘s new Rfam release: no BLAST, no full alns, no genomes, motifs, … Congrats folks! http://ift.tt/1rbv7by
@ppgardne on Twitter
@ppgardne: Some huge changes in @Xfam_EBI‘s new Rfam release: no BLAST, no full alns, no genomes, motifs, … Congrats folks! http://ift.tt/1rbv7by
@ppgardne on Twitter
@ppgardne: Rfam 12 released today. No more BLAST filters – Infernal’s now fast enough for complete database searches for RNAs.
http://ift.tt/1rbv7by
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XXI International Round Table on Nucleosides, Nucleotides and Nucleic Acids

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EMD-2660 — Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine — Wong W, Bai XC, Brown A, Fernandez IS, Hanssen E, Condron M, Tan YH, Baum J, Schere…

EMD-2660 — Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine — Wong W, Bai XC, Brown A, Fernandez IS, Hanssen E, Condron M, Tan YH, Baum J, Scheres SHW — The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. …
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@PDBeurope on Twitter
@PDBeurope: News from @elife on cryo-em for anti-malarials. #EMDB entry pdbe.org/emd-2660 et al. http://ift.tt/1pDUXAj http://ift.tt/1rrA12y
@PDBeurope on Twitter
@PDBeurope: .@elife Here’s the cryoEM map archived in #EMDB. pdbe.org/EMD-2660 http://ift.tt/1rrA9Py
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The Ribosome: A Record of Evolution – Space Ref (press release)

The Ribosome: A Record of Evolution
Space Ref (press release)
In a new study co-funded by the NASA Astrobiology Institute, scientists compared three-dimensional structures of ribosomes from a variety of species of varying biological complexity, including humans, yeast, bacteria and archaea. The team found

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