当前位置： SCI文献检索 > RNA Biology期刊下所有文献 > In vivo and in vitro analysis of 6S RNA-templated short transcripts in Bacillus subtilis.

In vivo and in vitro analysis of 6S RNA-templated short transcripts in Bacillus subtilis.

Abstract：

:By differential high-throughput RNA sequencing (dRNA-seq) we have identified "product RNAs" (pRNAs) as short as 8-12 nucleotides that are synthesized by Bacillus subtilis RNA polymerase (RNAP) in vivo using the regulatory 6S-1 RNA as template. The dRNA-seq data were confirmed by in vitro transcription experiments and Northern blotting. In our libraries, we were unable to detect statistically meaningful numbers of reads potentially representing pRNAs derived from 6S-2 RNA. However, pRNAs could be synthesized in vitro from 6S-2 RNA as template by the B. subtilis σ(A) RNAP. 6S-1 pRNA levels are low during exponential, increase in stationary, and burst during outgrowth from stationary phase, demonstrating that pRNA synthesis is a conserved regulatory mechanism, but a more dynamic and fine-tuning process than previously thought. Most pRNAs have a length of 8-15 nt, very few up to 24 nt. The average length of pRNAs tended to increase from stationary to outgrowth conditions. Synthesis of pRNA is initiated at C40 of 6S-1 RNA and U41 of 6S-2 RNA, yielding pRNAs with a 5'-terminal G or A residue, respectively. A B. subtilis 6S-1 RNA mutant strain encoding a pRNA with a 5'-terminal A residue showed the same relative distribution of ~14-nt pRNAs between the different growth states, but generally displayed lower pRNA levels than the reference strain encoding wild-type 6S-1 RNA. A ~two-fold lower affinity of the C40U mutant 6S-1 RNA towards σ(A) RNAP may have contributed to this reduction in pRNA levels. We infer that 6S-1 pRNA synthesis, although evolutionarily optimized for initiation with a +1G residue, is not primarily regulated at the transcription initiation level via growth phase-dependent variations in the cellular GTP pool.

journal_name

RNA Biol

journal_title

RNA biology

authors

Beckmann BM,Burenina OY,Hoch PG,Kubareva EA,Sharma CM,Hartmann RK

doi

10.4161/rna.8.5.16151

subject

Has Abstract

pub_date

2011-09-01 00:00:00

pages

839-49

issue

5

eissn

1547-6286

issn

1555-8584

pii

16151

journal_volume

8

pub_type

杂志文章

相关文献

RNA Biology文献大全
  • Antisense-mediated modulation of splicing: therapeutic implications for Duchenne muscular dystrophy.

    abstract：:While disruption of alternative splicing underlies many diseases, modulation of splicing using antisense oligonucleotides (AONs) can have therapeutic implications. The most notable example is Duchenne muscular dystrophy (DMD), where antisense-mediated exon skipping can restore the open reading frame and allow the synt...

    journal_title：RNA biology

    pub_type： 杂志文章,评审

    doi：10.4161/rna.7.4.12264

    authors： Aartsma-Rus A

    更新日期：2010-07-01 00:00:00

  • A comprehensive expression landscape of RNA-binding proteins (RBPs) across 16 human cancer types.

    abstract：:RNA-binding proteins (RBPs) are key regulators of posttranscriptional processes such as RNA maturation, localization, turnover and translation. Despite their dysregulation in various diseases including cancer, the landscape of RBP expression in human cancer has not been well elucidated. Here, we built a comprehensive ...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.1080/15476286.2019.1673657

    authors： Zhang B,Babu KR,Lim CY,Kwok ZH,Li J,Zhou S,Yang H,Tay Y

    更新日期：2020-02-01 00:00:00

  • RNase II: the finer details of the Modus operandi of a molecular killer.

    abstract：:The RNase II family of enzymes is ubiquitous and has crucial roles in the processing, degradation and quality control of all types of RNA. These exoribonucleases processively degrade RNA from the 3'-end releasing 5'-nucleotide monophosphates. In prokaryotes, RNase II and RNase R have two N-terminal CSD and one C-termi...

    journal_title：RNA biology

    pub_type： 杂志文章,评审

    doi：10.4161/rna.7.3.11490

    authors： Arraiano CM,Matos RG,Barbas A

    更新日期：2010-05-01 00:00:00

  • Casting a long shadow in the classroom: an educator's perspective of the contributions of Carl Woese.

    abstract：:"What does one do when the giants pass away?" remarked a very famous microbiologist to me, soon after the death of Carl Woese in late 2012. I teach microbiology and introductory cell and molecular biology at a small undergraduate institution; Woese's example and contributions have long been part of every class I teach...

    journal_title：RNA biology

    pub_type： 杂志文章,评审

    doi：10.4161/rna.28002

    authors： Martin M

    更新日期：2014-01-01 00:00:00

  • xRRM: a new class of RRM found in the telomerase La family protein p65.

    abstract：:Genuine La and La-related proteins group 7 (LARP7) bind to the non-coding RNAs transcribed by RNA polymerase III (RNAPIII), which end in UUU-3'OH. The La motif and RRM1 of these proteins (the La module) cooperate to bind the UUU-3'OH, protecting the RNA from degradation, while other domains may be important for RNA fo...

    journal_title：RNA biology

    pub_type： 杂志文章,评审

    doi：10.4161/rna.23608

    authors： Singh M,Choi CP,Feigon J

    更新日期：2013-03-01 00:00:00

  • Nonsense mediated decay induced by tethered human UPF3B is restricted to the cytoplasm.

    abstract：:The subcellular localization of the nonsense mediated decay (NMD) of mRNA transcripts bearing premature termination codons has been controversial. Recently, it has been demonstrated that RNA tethering of key mediators of NMD, including human UPF3B, accurately recreates NMD. Here, we have used tethered UPF3B, combined ...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：

    authors： Lu S,Cullen BR

    更新日期：2004-05-01 00:00:00

  • Modeling SNP mediated differential targeting of homologous 3'UTR by microRNA.

    abstract：:We had previously proposed that the post-transcriptional regulation through microRNA as a mechanism for incomplete penetrance and variable expressivity, leads to lack of correlation between genotype and phenotype. Here we report the validation of miRNA-target interactions we predicted earlier and demonstrate the regul...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.4161/rna.19318

    authors： Ahluwalia JK,Soni K,Sivasubbu S,Brahmachari V

    更新日期：2012-03-01 00:00:00

  • The interaction between RNA polymerase and the elongation factor NusA.

    abstract：:The synthesis of RNA is highly regulated at all stages by transcription factors. As an essential transcription elongation factor, NusA has been studied biochemically for more than 30 years. However, until now no structural information has been available on NusA-RNAP complexes and the NusA interaction site on RNAP was ...

    journal_title：RNA biology

    pub_type： 杂志文章,评审

    doi：10.4161/rna.7.3.12021

    authors： Yang X,Lewis PJ

    更新日期：2010-05-01 00:00:00

  • Regulation of gene expression through inefficient splicing of U12-type introns.

    abstract：:U12-type introns are a rare class of nuclear introns that are removed by a dedicated U12-dependent spliceosome and are thought to regulate the expression of their target genes owing through their slower splicing reaction. Recent genome-wide studies on the splicing of U12-type introns are now providing new insights on ...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.1080/15476286.2014.996454

    authors： Niemelä EH,Frilander MJ

    更新日期：2014-01-01 00:00:00

  • Identification and epigenetic analysis of divergent long non-coding RNAs in multilineage differentiation of human Neural Progenitor Cells.

    abstract：:Long non-coding RNAs have emerged as an important regulatory layer in biological systems. Of the various types of lncRNAs, one class (designated as divergent RNAs/XH), which is in head-to-head overlap with the coding genes, has emerged as a critical biotype that regulates development and cellular differentiation. This...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.1080/15476286.2018.1553482

    authors： Prajapati B,Fatma M,Maddhesiya P,Sodhi MK,Fatima M,Dargar T,Bhagat R,Seth P,Sinha S

    更新日期：2019-01-01 00:00:00

  • Tandem RNA isolation reveals functional rearrangement of RNA-binding proteins on CDKN1B/p27Kip1 3'UTRs in cisplatin treated cells.

    abstract：:Post-transcriptional control of gene expression is mediated via RNA-binding proteins (RBPs) that interact with mRNAs in a combinatorial fashion. While recent global RNA interactome capture experiments expanded the repertoire of cellular RBPs quiet dramatically, little is known about the assembly of RBPs on particular ...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.1080/15476286.2019.1662268

    authors： Iadevaia V,Wouters MD,Kanitz A,Matia-González AM,Laing EE,Gerber AP

    更新日期：2020-01-01 00:00:00

  • Modeling the Thermoproteaceae RNase P RNA.

    abstract：:The RNA component of the RNase P complex is found throughout most branches of the tree of life and is principally responsible for removing the 5' leader sequence from pre-tRNA transcripts during tRNA maturation. RNase P RNA has a number of universal core features, however variations in sequence and structure found in ...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.4161/rna.21502

    authors： Chan PP,Brown JW,Lowe TM

    更新日期：2012-09-01 00:00:00

  • Kinship in the SRP RNA family.

    abstract：:The signal recognition particle (SRP) is a ribonucleoprotein complex which participates in the targeting of protein to cellular membranes. The RNA component of the SRP has been found in all domains of life, but the size of the molecule and the number of RNA secondary structure elements vary considerably between the di...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.4161/rna.6.5.9753

    authors： Rosenblad MA,Larsen N,Samuelsson T,Zwieb C

    更新日期：2009-11-01 00:00:00

  • A family of non-classical pseudoknots in influenza A and B viruses.

    abstract：:A very conserved pseudoknot structure has been shown to fold in influenza virus RNA. The pseudoknot encompasses the 3' splice site of segment 8 RNA in both influenza A and B viruses. By sequence comparison of influenza virus strains, we derive a consensus motif that defines a novel RNA pseudoknot family. The orientati...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.4161/rna.7.2.11287

    authors： Gultyaev AP,Olsthoorn RC

    更新日期：2010-03-01 00:00:00

  • Toward a crystal-clear view of the viral RNA sensing and response by RIG-I-like receptors.

    abstract：:The RIG-I-like receptors (RLRs)--RIG-I, MDA5, and LGP2--detect intracellular pathogenic RNA and elicit an antiviral immune response during viral infection. The protein architecture of the RLR family consists of multiple functional domains, including N-terminal Caspase Activation and Recruitment Domains (CARDs) for sig...

    journal_title：RNA biology

    pub_type： 杂志文章,评审

    doi：10.4161/rna.27717

    authors： Luo D

    更新日期：2014-01-01 00:00:00

  • A novel antisense RNA ASPACT confers multi-level suppression of PACT and associated signalling.

    abstract：:The innate immune system is the frontline host protection against pathogens. Effective antiviral immunity is elicited upon recognition of viral RNAs by the host pattern recognition receptors. One of the major viral RNA sensors is retinoic acid inducible gene-1, which triggers the production of interferons (IFNs). In t...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.1080/15476286.2019.1624471

    authors： Kuo YP,Ma CP,Chen HW,Chen YT,Lai YH,Liu H,Kuo RL,Chin-Ming Tan B

    更新日期：2019-09-01 00:00:00

  • The many ways Epstein-Barr virus takes advantage of the RNA tool kit.

    abstract：:Epstein-Barr virus (EBV) was the first human cancer-causing virus to be discovered over fifty years ago. Given its relatively large genome size for a virus and hence the capacity to store more than mere protein-coding information, EBV also harbours genetic material for producing an array of distinct noncoding (nc)RNAs...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.1080/15476286.2021.1875184

    authors： Lee N

    更新日期：2021-01-30 00:00:00

  • Identification of a region of hantavirus nucleocapsid protein required for RNA chaperone activity.

    abstract：:Sin Nombre hantavirus (SNV) is a New World hantavirus and causes hantavirus cardiopulmonary syndrome. The viral nucleocapsid protein (N) is an RNA chaperone and has multiple functions important in virus replication. The three negative sense RNA segments of hantaviruses form panhandle structures through imperfect hydro...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.4161/rna.7.6.13862

    authors： Brown BA,Panganiban AT

    更新日期：2010-11-01 00:00:00

  • Riboswitch RNAs: regulation of gene expression by direct monitoring of a physiological signal.

    abstract：:Riboswitches are cis-encoded, cis-acting RNA elements that directly sense a physiological signal. Signal response results in a change in RNA structure that impacts gene expression. Elements of this type play an important role in bacteria, where they regulate a variety of fundamental cellular pathways. Riboswitch-media...

    journal_title：RNA biology

    pub_type： 杂志文章,评审

    doi：10.4161/rna.7.1.10757

    authors： Smith AM,Fuchs RT,Grundy FJ,Henkin TM

    更新日期：2010-01-01 00:00:00

  • Suppression of microRNAs by dual-targeting and clustered Tough Decoy inhibitors.

    abstract：:MicroRNAs (miRNAs) are ubiquitous regulators of gene expression that contribute to almost any cellular process. Methods for managing of miRNA activity are attracting increasing attention in relation to diverse experimental and therapeutic applications. DNA-encoded miRNA inhibitors expressed from plasmid or virus-based...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.4161/rna.23543

    authors： Hollensen AK,Bak RO,Haslund D,Mikkelsen JG

    更新日期：2013-03-01 00:00:00

  • TINCR, staufen1, and cellular differentiation.

    abstract：:The human genome encodes several thousand long non-protein coding transcripts>200 nucleotides in length, a subset of which were shown to play important roles in regulation of gene expression. We recently identified TINCR, a lncRNA required for induction of key differentiation genes in epidermal tissue, including genes...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.4161/rna.26249

    authors： Kretz M

    更新日期：2013-10-01 00:00:00

  • Genome-wide gene expression analysis of amphioxus (Branchiostoma belcheri) following lipopolysaccharide challenge using strand-specific RNA-seq.

    abstract：:Amphioxus is the closest living proxy for exploring the evolutionary origin of the immune system in vertebrates. To understand the immune responses of amphioxus to lipopolysaccharide (LPS), 5 ribosomal RNA (rRNA)-depleted libraries of amphioxus were constructed, including one control (0 h) library and 4 treatment libr...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.1080/15476286.2017.1367890

    authors： Zhang QL,Zhu QH,Xie ZQ,Xu B,Wang XQ,Chen JY

    更新日期：2017-12-02 00:00:00

  • Linking the association between circRNAs and Alzheimer's disease progression by multi-tissue circular RNA characterization.

    abstract：:Alzheimer's disease (AD) has devastating consequences for patients during its slow, progressive course. It is important to understand the pathology of AD onset. Recently, circular RNAs (circRNAs) have been found to participate in many human diseases including cancers and neurodegenerative conditions. In this study, we...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.1080/15476286.2020.1783487

    authors： Lo I,Hill J,Vilhjálmsson BJ,Kjems J

    更新日期：2020-12-01 00:00:00

  • Wobble uridine modifications-a reason to live, a reason to die?!

    abstract：:Wobble uridines (U34) are generally modified in all species. U34 modifications can be essential in metazoans but are not required for viability in fungi. In this review, we provide an overview on the types of modifications and how they affect the physico-chemical properties of wobble uridines. We describe the molecula...

    journal_title：RNA biology

    pub_type： 杂志文章,评审

    doi：10.1080/15476286.2017.1295204

    authors： Schaffrath R,Leidel SA

    更新日期：2017-09-02 00:00:00

  • Over-represented sequences located on 3' UTRs are potentially involved in regulatory functions.

    abstract：:Eukaryotic gene expression must be coordinated for the proper functioning of biological processes. This coordination can be achieved both at the transcriptional and post-transcriptional levels. In both cases, regulatory sequences placed at either promoter regions or on UTRs function as markers recognized by regulators...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.4161/rna.7116

    authors： Yoon K,Ko D,Doderer M,Livi CB,Penalva LO

    更新日期：2008-10-01 00:00:00

  • The isolated La-module of LARP1 mediates 3' poly(A) protection and mRNA stabilization, dependent on its intrinsic PAM2 binding to PABPC1.

    abstract：:The protein domain arrangement known as the La-module, comprised of a La motif (LaM) followed by a linker and RNA recognition motif (RRM), is found in seven La-related proteins: LARP1, LARP1B, LARP3 (La protein), LARP4, LARP4B, LARP6, and LARP7 in humans. Several LARPs have been characterized for their distinct activi...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.1080/15476286.2020.1860376

    authors： Mattijssen S,Kozlov G,Gaidamakov S,Ranjan A,Fonseca BD,Gehring K,Maraia RJ

    更新日期：2020-12-23 00:00:00

  • Replicating Potato spindle tuber viroid mediates de novo methylation of an intronic viroid sequence but no cleavage of the corresponding pre-mRNA.

    abstract：:In plants, Potato spindle tuber viroid (PSTVd) replication triggers post-transcriptional gene silencing (PTGS) and RNA-directed DNA methylation (RdDM) of homologous RNA and DNA sequences, respectively. PTGS predominantly occurs in the cytoplasm, but nuclear PTGS has been also reported. In this study, we investigated w...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.1080/15476286.2015.1017216

    authors： Dalakouras A,Dadami E,Bassler A,Zwiebel M,Krczal G,Wassenegger M

    更新日期：2015-01-01 00:00:00

  • Critical roles of RNA-binding proteins in miRNA biogenesis in Arabidopsis.

    abstract：:MicroRNAs (miRNAs) are key regulators of gene expression and play critical roles in modulating metabolism, development and physiology in animals and plants. miRNA levels are transcriptionally and post-transcriptionally controlled for their proper function. Recent studies have shown that RNA-binding proteins play impor...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.4161/rna.22740

    authors： Ren G,Yu B

    更新日期：2012-12-01 00:00:00

  • Synthesis of cysteinyl-tRNACys by a prolyl-tRNA synthetase.

    abstract：:The question of how cysteinyl-tRNA(Cys) is synthesized in organisms that lack a canonical cysteinyl-tRNA synthetase (CysRS) is an important open question in understanding protein synthesis. The prolyl-tRNA synthetase (ProRS) of wide ranging organisms has the ability to mis-activate cysteine without editing. This raise...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：

    authors： Zhang CM,Hou YM

    更新日期：2004-05-01 00:00:00

  • Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii.

    abstract：:Seryl-tRNA synthetase (SerRS) catalyzes the ligation of serine to the 3'-end of serine tRNA (tRNA(Ser)), which is typical of the type-2 tRNAs characterized by a long extra arm. The SerRSs are divided into two types, the archaeal/eukaryal and bacterial types. In this study, we solved the crystal structures of the SerRS...

    journal_title：RNA biology

    pub_type： 杂志文章

    doi：10.4161/rna.5.3.6876

    authors： Itoh Y,Sekine S,Kuroishi C,Terada T,Shirouzu M,Kuramitsu S,Yokoyama S

    更新日期：2008-07-01 00:00:00