Acknowledgements requested in publications
« This work of the Interdisciplinary Thematic Institute IMCBio, as part of the ITI 2021-2028 program of the University of Strasbourg, CNRS and Inserm, was supported by IdEx Unistra (ANR-10-IDEX-0002), and by SFRI-STRAT’US project (ANR 20-SFRI-0012) and EUR IMCBio (ANR-17-EURE-0023) under the framework of the French Investments for the Future Program. »
2015
Durand, S; Tomasini, A; Braun, F; Condon, C; Romby, P
sRNA and mRNA turnover in Gram-positive bacteria Article de journal
Dans: FEMS Microbiol Rev, vol. 39, no. 3, p. 316-330, 2015, ISBN: 25934118, (1574-6976 (Electronic) 0168-6445 (Linking) Journal Article Review).
@article{nokey,
title = {sRNA and mRNA turnover in Gram-positive bacteria},
author = {S Durand and A Tomasini and F Braun and C Condon and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=25934118},
doi = {10.1093/femsre/fuv007},
isbn = {25934118},
year = {2015},
date = {2015-01-01},
journal = {FEMS Microbiol Rev},
volume = {39},
number = {3},
pages = {316-330},
abstract = {It is widely recognized that RNA degradation plays a critical role in gene regulation when fast adaptation of cell growth is required to respond to stress and changing environmental conditions. Bacterial ribonucleases acting alone or in concert with various trans-acting regulatory factors are important mediators of RNA degradation. Here, we will give an overview of what is known about ribonucleases in several Gram-positive bacteria, their specificities and mechanisms of action. In addition, we will illustrate how sRNAs act in a coordinated manner with ribonucleases to regulate the turnover of particular mRNA targets, and the complex interplay existing between the ribosome, the ribonucleases and RNAs.},
note = {1574-6976 (Electronic)
0168-6445 (Linking)
Journal Article
Review},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Durand, S; Braun, F; Lioliou, E; Romilly, C; Helfer, A C; Kuhn, L; Quittot, N; Nicolas, P; Romby, P; Condon, C
A nitric oxide regulated small RNA controls expression of genes involved in redox homeostasis in Bacillus subtilis Article de journal
Dans: PLoS Genet, vol. 11, no. 2, p. e1004957, 2015, ISBN: 25643072, (1553-7404 (Electronic) 1553-7390 (Linking) Journal Article Research Support, Non-U.S. Gov't).
@article{nokey,
title = {A nitric oxide regulated small RNA controls expression of genes involved in redox homeostasis in Bacillus subtilis},
author = {S Durand and F Braun and E Lioliou and C Romilly and A C Helfer and L Kuhn and N Quittot and P Nicolas and P Romby and C Condon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=25643072},
doi = {10.1371/journal.pgen.1004957},
isbn = {25643072},
year = {2015},
date = {2015-01-01},
journal = {PLoS Genet},
volume = {11},
number = {2},
pages = {e1004957},
abstract = {RsaE is the only known trans-acting small regulatory RNA (sRNA) besides the ubiquitous 6S RNA that is conserved between the human pathogen Staphylococcus aureus and the soil-dwelling Firmicute Bacillus subtilis. Although a number of RsaE targets are known in S. aureus, neither the environmental signals that lead to its expression nor its physiological role are known. Here we show that expression of the B. subtilis homolog of RsaE is regulated by the presence of nitric oxide (NO) in the cellular milieu. Control of expression by NO is dependent on the ResDE two-component system in B. subtilis and we determined that the same is true in S. aureus. Transcriptome and proteome analyses revealed that many genes with functions related to oxidative stress and oxidation-reduction reactions were up-regulated in a B. subtilis strain lacking this sRNA. We have thus renamed it RoxS. The prediction of RoxS-dependent mRNA targets also suggested a significant enrichment for mRNAs related to respiration and electron transfer. Among the potential direct mRNA targets, we have validated the ppnKB mRNA, encoding an NAD+/NADH kinase, both in vivo and in vitro. RoxS controls both translation initiation and the stability of this transcript, in the latter case via two independent pathways implicating RNase Y and RNase III. Furthermore, RNase Y intervenes at an additional level by processing the 5' end of the RoxS sRNA removing about 20 nucleotides. Processing of RoxS allows it to interact more efficiently with a second target, the sucCD mRNA, encoding succinyl-CoA synthase, thus expanding the repertoire of targets recognized by this sRNA.},
note = {1553-7404 (Electronic)
1553-7390 (Linking)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Georges, A; Dhote, V; Kuhn, L; Hellen, C U; Pestova, T V; Frank, J; Hashem, Y
Structure of mammalian eIF3 in the context of the 43S preinitiation complex Article de journal
Dans: Nature, vol. 525, no. 7570, p. 491-495, 2015, ISBN: 26344199, (1476-4687 (Electronic) 0028-0836 (Linking) Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't).
@article{nokey,
title = {Structure of mammalian eIF3 in the context of the 43S preinitiation complex},
author = {A Georges and V Dhote and L Kuhn and C U Hellen and T V Pestova and J Frank and Y Hashem},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=26344199},
doi = {10.1038/nature14891},
isbn = {26344199},
year = {2015},
date = {2015-01-01},
journal = {Nature},
volume = {525},
number = {7570},
pages = {491-495},
abstract = {During eukaryotic translation initiation, 43S complexes, comprising a 40S ribosomal subunit, initiator transfer RNA and initiation factors (eIF) 2, 3, 1 and 1A, attach to the 5'-terminal region of messenger RNA and scan along it to the initiation codon. Scanning on structured mRNAs also requires the DExH-box protein DHX29. Mammalian eIF3 contains 13 subunits and participates in nearly all steps of translation initiation. Eight subunits having PCI (proteasome, COP9 signalosome, eIF3) or MPN (Mpr1, Pad1, amino-terminal) domains constitute the structural core of eIF3, to which five peripheral subunits are flexibly linked. Here we present a cryo-electron microscopy structure of eIF3 in the context of the DHX29-bound 43S complex, showing the PCI/MPN core at approximately 6 A resolution. It reveals the organization of the individual subunits and their interactions with components of the 43S complex. We were able to build near-complete polyalanine-level models of the eIF3 PCI/MPN core and of two peripheral subunits. The implications for understanding mRNA ribosomal attachment and scanning are discussed.},
note = {1476-4687 (Electronic)
0028-0836 (Linking)
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Branscheid, A; Marchais, A; Schott, G; Lange, H; Gagliardi, D; Andersen, S U; Voinnet, O; Brodersen, P
SKI2 mediates degradation of RISC 5'-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis Article de journal
Dans: Nucleic Acids Res, vol. 43, no. 22, p. 10975-10988, 2015, ISBN: 26464441, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article Research Support, Non-U.S. Gov't).
@article{nokey,
title = {SKI2 mediates degradation of RISC 5'-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis},
author = {A Branscheid and A Marchais and G Schott and H Lange and D Gagliardi and S U Andersen and O Voinnet and P Brodersen},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=26464441},
doi = {10.1093/nar/gkv1014},
isbn = {26464441},
year = {2015},
date = {2015-01-01},
journal = {Nucleic Acids Res},
volume = {43},
number = {22},
pages = {10975-10988},
abstract = {Small regulatory RNAs are fundamental in eukaryotic and prokaryotic gene regulation. In plants, an important element of post-transcriptional control is effected by 20-24 nt microRNAs (miRNAs) and short interfering RNAs (siRNAs) bound to the ARGONAUTE1 (AGO1) protein in an RNA induced silencing complex (RISC). AGO1 may cleave target mRNAs with small RNA complementarity, but the fate of the resulting cleavage fragments remains incompletely understood. Here, we show that SKI2, SKI3 and SKI8, subunits of a cytoplasmic cofactor of the RNA exosome, are required for degradation of RISC 5', but not 3'-cleavage fragments in Arabidopsis. In the absence of SKI2 activity, many miRNA targets produce siRNAs via the RNA-dependent RNA polymerase 6 (RDR6) pathway. These siRNAs are low-abundant, and map close to the cleavage site. In most cases, siRNAs were produced 5' to the cleavage site, but several examples of 3'-spreading were also identified. These observations suggest that siRNAs do not simply derive from RDR6 action on stable 5'-cleavage fragments and hence that SKI2 has a direct role in limiting secondary siRNA production in addition to its function in mediating degradation of 5'-cleavage fragments.},
note = {1362-4962 (Electronic)
0305-1048 (Linking)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Blevins, T; Podicheti, R; Mishra, V; Marasco, M; Wang, J; Rusch, D; Tang, H; Pikaard, C S
Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis Article de journal
Dans: Elife, vol. 4, p. e09591, 2015, ISBN: 26430765, (2050-084X (Electronic) 2050-084X (Linking) Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't).
@article{nokey,
title = {Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis},
author = {T Blevins and R Podicheti and V Mishra and M Marasco and J Wang and D Rusch and H Tang and C S Pikaard},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=26430765},
doi = {10.7554/eLife.09591},
isbn = {26430765},
year = {2015},
date = {2015-01-01},
journal = {Elife},
volume = {4},
pages = {e09591},
abstract = {In Arabidopsis thaliana, abundant 24 nucleotide small interfering RNAs (24 nt siRNA) guide the cytosine methylation and silencing of transposons and a subset of genes. 24 nt siRNA biogenesis requires nuclear RNA polymerase IV (Pol IV), RNA-dependent RNA polymerase 2 (RDR2) and DICER-like 3 (DCL3). However, siRNA precursors are mostly undefined. We identified Pol IV and RDR2-dependent RNAs (P4R2 RNAs) that accumulate in dcl3 mutants and are diced into 24 nt RNAs by DCL3 in vitro. P4R2 RNAs are mostly 26-45 nt and initiate with a purine adjacent to a pyrimidine, characteristics shared by Pol IV transcripts generated in vitro. RDR2 terminal transferase activity, also demonstrated in vitro, may account for occasional non-templated nucleotides at P4R2 RNA 3' termini. The 24 nt siRNAs primarily correspond to the 5' or 3' ends of P4R2 RNAs, suggesting a model whereby siRNAs are generated from either end of P4R2 duplexes by single dicing events.},
note = {2050-084X (Electronic)
2050-084X (Linking)
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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