The RNA helicase CrhR as a regulatory factor
Ontology highlight
ABSTRACT:
ORGANISM(S): Synechocystis sp. PCC 6803
PROVIDER: GSE58544 | GEO | 2014/06/17
SECONDARY ACCESSION(S): PRJNA252851
REPOSITORIES: GEO
Similar Datasets
Project description:DEAD-box RNA-helicases catalyze the correct folding of structured RNAs and the formation of RNP complexes. The cyanobacterium Synechocystis sp. PCC 6803 encodes a single DEAD-box RNA helicase, CrhR (Slr0083) whose inactivation has severe effects on cellular physiology and morphology, particularly under cold stress. In order to identify potential RNA targets of CrhR, custom microarrays containing sequences corresponding to non-coding small RNAs (UTRs, ncRNAs, asRNAs, iRNAs) and all mRNAs were constructed. The RNAs exhibiting CrhR-dependent alteration of expression constitute both mRNA and small RNA transcripts. CrhR therefore is not a global regulator of RNA metabolism but instead interacts with a specific subset of the total RNA repertoire in Synechocystis, a CrhR-specific RNA regulon that functions predominately at low temperature. RNA half-life analyses indicated that expression of regulon members is controlled by a mechanism that does not involve CrhR-dependent RNA turnover. Biochemically, CrhR is able to anneal but not unwind an asRNA-mRNA target in vitro, providing evidence that regulation occurs through an RNA duplex intermediate. The data reveal a novel mechanism regulating the differential expression of operon members, crhR mutation disrupts a negative regulatory feedback loop involving CrhR regulation at an early stage of transcription in affected operons. We propose that CrhR is functioning as a RNA chaperone, similar to Hfq in enterobacteria, but regulating both post-transcriptional events and transcription termination, by altering sRNA metabolism. We monitored gene expression of an Synechocystis PCC6083 WT and a partial crhR knockout at 30M-BM-0C and after 3h of culturing at 20M-BM-0C. Each sample was done in biological triplicates.
2014-06-17 | E-GEOD-58544 | biostudies-arrayexpress
Project description:The model cyanobacterium Synechocystis sp. PCC 6803 was used for a systematic survey on the number and types of antisense (as)RNAs. A tiled microarray was constructed with probes for both strands of the genes or intergenic spacers with candidate transcripts predicted by an algorithm and an equally sized and distributed control set. The resulting 102,739 individual probes cover an accumulated length of 1,441,146 nt or about 40% of the total chromosome sequence of Synechocystis 6803. Hybridization of this array with total RNA isolated from cultures raised under different growth conditions identified a high number of transcripts from intergenic spacers and in antisense orientation to known genes (natural cis-asRNAs). Extrapolated to the whole genome, around 10% of all open reading frames in Synechocystis 6803 may have a corresponding asRNA, suggesting a much more important role of chromosomally encoded asRNAs in bacteria then anticipated so far. Keywords: stress response
2009-01-14 | GSE14410 | GEO
Project description:The model cyanobacterium Synechocystis sp. PCC 6803 was used for a systematic survey on the number and types of antisense (as)RNAs. A tiled microarray was constructed with probes for both strands of the genes or intergenic spacers with candidate transcripts predicted by an algorithm and an equally sized and distributed control set. The resulting 102,739 individual probes cover an accumulated length of 1,441,146 nt or about 40% of the total chromosome sequence of Synechocystis 6803. Hybridization of this array with total RNA isolated from cultures raised under different growth conditions identified a high number of transcripts from intergenic spacers and in antisense orientation to known genes (natural cis-asRNAs). Extrapolated to the whole genome, around 10% of all open reading frames in Synechocystis 6803 may have a corresponding asRNA, suggesting a much more important role of chromosomally encoded asRNAs in bacteria then anticipated so far. Keywords: stress response 4 RNA hybridizations, 2 DNA controls. The raw data from the DNA hybridizations are in the GSE14410_DNA_1.txt and GSE14410_DNA_2.txt files.
2010-05-14 | E-GEOD-14410 | biostudies-arrayexpress
Project description:cis-antisense RNAs (cis-asRNAs) in prokaryotes are more pervasive than originally thought. However, little is known about their expression patterns and functions. Here we determined transcriptomes and proteomes of E. coli at multiple time points in five culture conditions using directional RNA-seq and tandem mass spectrometry. We found that a highly varying portion (27.2%~90.8%) of transcribed genes had cis-asRNAs dependent on growth phases and culture conditions, and that almost all transcribed genes changed their cis-asRNA levels relative to the mRNA level at different growth phases and culture conditions. Intriguingly, the correlation between the protein and mRNA levels of genes is abolished the increasing cis-asRNA levels relative to the mRNA levels, suggesting that cis-asRNAs might directly or indirectly inhibit translation by forming duplexes with mRNAs. All data sets are available for data mining from a unified resource to support further biological discoveries and insights into cis-asRNA-mediated gene expressional regulation.
2022-02-28 | PXD001640 | Pride
Project description:Cis-encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of the vast majority of these RNAs remains unknown, and there is an ongoing discussion as to what extent these transcripts are the result of transcriptional noise. We show, by comparative transcriptomics of 20 bacterial species and one chloroplast, that the number of asRNAs is exponentially dependent on the genomic AT content, and that expression of asRNA at low levels exerts little impact in terms of energy consumption. A transcription model simulating mRNA and asRNA production indicates that the asRNA regulatory effect is only observed above certain expression thresholds, substantially higher than physiological transcript levels. These predictions were verified experimentally by overexpressing 9 different asRNAs in M. pneumoniae. Our results suggest that most of the antisense transcripts found in bacteria are the consequence of transcriptional noise, arising at spurious promoters throughout the genome.
2018-10-25 | PXD003231 | Pride
Project description:Cis-encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of the vast majority of these RNAs remains unknown, and there is an ongoing discussion as to what extent these transcripts are the result of transcriptional noise. We show, by comparative transcriptomics of 20 bacterial species and one chloroplast, that the number of asRNAs is exponentially dependent on the genomic AT content, and that expression of asRNA at low levels exerts little impact in terms of energy consumption. A transcription model simulating mRNA and asRNA production indicates that the asRNA regulatory effect is only observed above certain expression thresholds, substantially higher than physiological transcript levels. These predictions were verified experimentally by overexpressing 9 different asRNAs in M. pneumoniae. Our results suggest that most of the antisense transcripts found in bacteria are the consequence of transcriptional noise, arising at spurious promoters throughout the genome.
2016-01-18 | E-MTAB-4081 | biostudies-arrayexpress
Project description:LlorénsRico2016 - Effects of cis-Encoded
antisense RNAs (asRNAs) - Case3
Three putative
effects of the asRNAs were considered in this study: in case 1,
the binding of the asRNA to the corresponding mRNA induces
degradation of the duplex. In case 2, the binding of the asRNA
to the mRNA induces degradation of the mRNA, but not of the
asRNA. In case 3 (this model), the mRNA and the asRNA bind
reversibly to form a stable duplex, preventing translation of
the mRNA. In all the three cases, binding to the ribosome
protects the mRNA from the effect of the asRNA.
This model is described in the article:
Bacterial antisense RNAs are
mainly the product of transcriptional noise.
Lloréns-Rico V, Cano J,
Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano
L, Lluch-Senar M.
Sci Adv 2016 Mar; 2(3): e1501363
Abstract:
cis-Encoded antisense RNAs (asRNAs) are widespread along
bacterial transcriptomes. However, the role of most of these
RNAs remains unknown, and there is an ongoing discussion as to
what extent these transcripts are the result of transcriptional
noise. We show, by comparative transcriptomics of 20 bacterial
species and one chloroplast, that the number of asRNAs is
exponentially dependent on the genomic AT content and that
expression of asRNA at low levels exerts little impact in terms
of energy consumption. A transcription model simulating mRNA
and asRNA production indicates that the asRNA regulatory effect
is only observed above certain expression thresholds,
substantially higher than physiological transcript levels.
These predictions were verified experimentally by
overexpressing nine different asRNAs in Mycoplasma pneumoniae.
Our results suggest that most of the antisense transcripts
found in bacteria are the consequence of transcriptional noise,
arising at spurious promoters throughout the genome.
This model is hosted on
BioModels Database
and identified by:
MODEL1511170002.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-05-18 | MODEL1511170002 | BioModels
Project description:LlorénsRico2016 - Effects of cis-Encoded antisense RNAs (asRNAs) - Case1
Three
putative effects of the asRNAs were considered in this study: in
case 1
(this
model)
,
the binding of the asRNA to the corresponding mRNA induces
degradation of the duplex. In case 2, the binding of the asRNA to
the mRNA induces degradation of the mRNA, but not of the asRNA.
In case 3, the mRNA and the asRNA bind reversibly to form a
stable duplex, preventing translation of the mRNA. In all the
three cases, binding to the ribosome protects the mRNA from the
effect of the asRNA.
This model is described in the article:
Bacterial antisense RNAs are
mainly the product of transcriptional noise.
Lloréns-Rico V, Cano J,
Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano
L, Lluch-Senar M.
Sci Adv 2016 Mar; 2(3): e1501363
Abstract:
cis-Encoded antisense RNAs (asRNAs) are widespread along
bacterial transcriptomes. However, the role of most of these
RNAs remains unknown, and there is an ongoing discussion as to
what extent these transcripts are the result of transcriptional
noise. We show, by comparative transcriptomics of 20 bacterial
species and one chloroplast, that the number of asRNAs is
exponentially dependent on the genomic AT content and that
expression of asRNA at low levels exerts little impact in terms
of energy consumption. A transcription model simulating mRNA
and asRNA production indicates that the asRNA regulatory effect
is only observed above certain expression thresholds,
substantially higher than physiological transcript levels.
These predictions were verified experimentally by
overexpressing nine different asRNAs in Mycoplasma pneumoniae.
Our results suggest that most of the antisense transcripts
found in bacteria are the consequence of transcriptional noise,
arising at spurious promoters throughout the genome.
This model is hosted on
BioModels Database
and identified by:
MODEL1511170000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-05-18 | MODEL1511170000 | BioModels
Project description:LlorénsRico2016 - Effects of cis-Encoded
antisense RNAs (asRNAs) - Case1
Three
putative effects of the asRNAs were considered in this study: in
case 1
,
the binding of the asRNA to the corresponding mRNA induces
degradation of the duplex. In case 2
(this
model)
the binding of the asRNA to the mRNA induces degradation of the
mRNA, but not of the asRNA. In case 3, the mRNA and the asRNA
bind reversibly to form a stable duplex, preventing translation
of the mRNA. In all the three cases, binding to the ribosome
protects the mRNA from the effect of the asRNA.
This model is described in the article:
Bacterial antisense RNAs are
mainly the product of transcriptional noise.
Lloréns-Rico V, Cano J,
Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano
L, Lluch-Senar M.
Sci Adv 2016 Mar; 2(3): e1501363
Abstract:
cis-Encoded antisense RNAs (asRNAs) are widespread along
bacterial transcriptomes. However, the role of most of these
RNAs remains unknown, and there is an ongoing discussion as to
what extent these transcripts are the result of transcriptional
noise. We show, by comparative transcriptomics of 20 bacterial
species and one chloroplast, that the number of asRNAs is
exponentially dependent on the genomic AT content and that
expression of asRNA at low levels exerts little impact in terms
of energy consumption. A transcription model simulating mRNA
and asRNA production indicates that the asRNA regulatory effect
is only observed above certain expression thresholds,
substantially higher than physiological transcript levels.
These predictions were verified experimentally by
overexpressing nine different asRNAs in Mycoplasma pneumoniae.
Our results suggest that most of the antisense transcripts
found in bacteria are the consequence of transcriptional noise,
arising at spurious promoters throughout the genome.
This model is hosted on
BioModels Database
and identified by:
MODEL1511170001.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-05-18 | MODEL1511170001 | BioModels
Project description:Antisense RNAs (asRNAs) have diverse functions across three superkingdoms of life. However, their physiological roles for photosynthesis, the most efficient conversion system of solar energy and carbon dioxide into desirable biofuel, are elusive. To understand asRNA-mediated photosynthetic response, we systematically identified non-coding asRNAs and analyzed their differential regulation upon high light and/or low temperature. We found that large fractions of antisense regions are pervasively transcribed and differentially induced upon the change of light and/or temperature. Particularly, photosynthesis and ribosome related genes are mostly regulated by asRNA. Futhermore, we found that 93 long non-coding asRNAs spanning more than half of the cognate open reading frames (ORFs), unexpectedly. Intriguingly, many of them are associated with photosynthetic genes and they have positive role to the expression level of their cognate ORFs. Thus, our systematic transcriptome analysis of photosynthetic response indicates that asRNAs may finetune transcriptional response to enable efficient photosynthetic energy conversion.
2020-07-25 | GSE60109 | GEO