Transcription-Austin最新文献_第5页

m⁶A RNA modification in transcription regulation. 转录调控中的m6A RNA修饰。

IF 3.6

Transcription-Austin Pub Date : 2021-10-01 DOI: 10.1080/21541264.2022.2057177

Junaid Akhtar, Margot Lugoboni, Guillaume Junion

引用次数: 9

Emerging insights into the function and structure of the Integrator complex. 对整合者复合体功能和结构的新认识。

IF 3.6

Transcription-Austin Pub Date : 2021-10-01 Epub Date: 2022-03-20 DOI: 10.1080/21541264.2022.2047583

Moritz M Pfleiderer, Wojciech P Galej

引用次数: 0

Macromolecular assemblies supporting transcription-translation coupling. 支持转录-翻译耦合的大分子组装。

IF 3.6

Transcription-Austin Pub Date : 2021-08-01 Epub Date: 2021-09-27 DOI: 10.1080/21541264.2021.1981713

Michael W Webster, Albert Weixlbaumer

引用次数: 6

RNA polymerases from low G+C gram-positive bacteria. 低G+C革兰氏阳性细菌的RNA聚合酶。

IF 3.6

Transcription-Austin Pub Date : 2021-08-01 Epub Date: 2021-08-17 DOI: 10.1080/21541264.2021.1964328

Michael Miller, Aaron J Oakley, Peter J Lewis

引用次数: 4

Single-molecule insights into torsion and roadblocks in bacterial transcript elongation. 单分子洞察扭转和障碍在细菌转录延伸。

IF 3.6

Transcription-Austin Pub Date : 2021-08-01 Epub Date: 2021-11-01 DOI: 10.1080/21541264.2021.1997315

Jin Qian, Wenxuan Xu, David Dunlap, Laura Finzi

{"title":"Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.","authors":"Jin Qian, Wenxuan Xu, David Dunlap, Laura Finzi","doi":"10.1080/21541264.2021.1997315","DOIUrl":"10.1080/21541264.2021.1997315","url":null,"abstract":"During transcription, RNA polymerase (RNAP) translocates along the helical template DNA while maintaining high transcriptional fidelity. However, all genomes are dynamically twisted, writhed, and decorated by bound proteins and motor enzymes. In prokaryotes, proteins bound to DNA, specifically or not, frequently compact DNA into conformations that may silence genes by obstructing RNAP. Collision of RNAPs with these architectural proteins, may result in RNAP stalling and/or displacement of the protein roadblock. It is important to understand how rapidly transcribing RNAPs operate under different levels of supercoiling or in the presence of roadblocks. Given the broad range of asynchronous dynamics exhibited by transcriptional complexes, single-molecule assays, such as atomic force microscopy, fluorescence detection, optical and magnetic tweezers, etc. are well suited for detecting and quantifying activity with adequate spatial and temporal resolution. Here, we summarize current understanding of the effects of torsion and roadblocks on prokaryotic transcription, with a focus on single-molecule assays that provide real-time detection and readout.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"12 4","pages":"219-231"},"PeriodicalIF":3.6,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8632135/pdf/KTRN_12_1997315.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39830211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. 核糖体相关蛋白塑造了整个细菌王国的染色质结构和转录调控。

IF 3.6

Transcription-Austin Pub Date : 2021-08-01 Epub Date: 2021-09-09 DOI: 10.1080/21541264.2021.1973865

Haley M Amemiya, Jeremy Schroeder, Peter L Freddolino

{"title":"Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom.","authors":"Haley M Amemiya, Jeremy Schroeder, Peter L Freddolino","doi":"10.1080/21541264.2021.1973865","DOIUrl":"10.1080/21541264.2021.1973865","url":null,"abstract":"Genome architecture has proven to be critical in determining gene regulation across almost all domains of life. While many of the key components and mechanisms of eukaryotic genome organization have been described, the interplay between bacterial DNA organization and gene regulation is only now being fully appreciated. An increasing pool of evidence has demonstrated that the bacterial chromosome can reasonably be thought of as chromatin, and that bacterial chromosomes contain transcriptionally silent and transcriptionally active regions analogous to heterochromatin and euchromatin, respectively. The roles played by histones in eukaryotic systems appear to be shared across a range of nucleoid-associated proteins (NAPs) in bacteria, which function to compact, structure, and regulate large portions of bacterial chromosomes. The broad range of extant NAPs, and the extent to which they differ from species to species, has raised additional challenges in identifying and characterizing their roles in all but a handful of model bacteria. Here we review the regulatory roles played by NAPs in several well-studied bacteria and use the resulting state of knowledge to provide a working definition for NAPs, based on their function, binding pattern, and expression levels. We present a screening procedure which can be applied to any species for which transcriptomic data are available. Finally, we note that NAPs tend to play two major regulatory roles - xenogeneic silencers and developmental regulators - and that many unrecognized potential NAPs exist in each bacterial species examined.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"12 4","pages":"182-218"},"PeriodicalIF":3.6,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8632127/pdf/KTRN_12_1973865.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39398135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mfd - at the crossroads of bacterial DNA repair, transcriptional regulation and molecular evolvability. Mfd--处于细菌 DNA 修复、转录调控和分子可进化性的十字路口。

IF 3.6

Transcription-Austin Pub Date : 2021-08-01 Epub Date: 2021-10-21 DOI: 10.1080/21541264.2021.1982628

Alexandra M Deaconescu

{"title":"Mfd - at the crossroads of bacterial DNA repair, transcriptional regulation and molecular evolvability.","authors":"Alexandra M Deaconescu","doi":"10.1080/21541264.2021.1982628","DOIUrl":"10.1080/21541264.2021.1982628","url":null,"abstract":"For survival, bacteria need to continuously evolve and adapt to complex environments, including those that may impact the integrity of the DNA, the repository of genetic information to be passed on to future generations. The multiple factors of DNA repair share the substrate on which they operate with other key cellular machineries, principally those of replication and transcription, implying a high degree of coordination of DNA-based activities. In this review, I focus on progress made in the understanding of the protein factors operating at the crossroads of these three fundamental processes, with emphasis on the mutation frequency decline protein (Mfd, aka TRCF). Although Mfd research has a rich history that goes back in time for more than half a century, recent reports hint that much remains to be uncovered. I argue that besides being a transcription-repair coupling factor (TRCF), Mfd is also a global regulator of transcription and a pro-mutagenic factor, and that the way it interfaces with transcription, replication and nucleotide excision repair makes it an attractive candidate for the development of strategies to curb molecular evolution, hence, antibiotic resistance.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"12 4","pages":"156-170"},"PeriodicalIF":3.6,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8632110/pdf/KTRN_12_1982628.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39537604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rho-dependent transcription termination: a revisionist view. rho依赖性转录终止:修正主义观点。

IF 3.6

Transcription-Austin Pub Date : 2021-08-01 Epub Date: 2021-10-27 DOI: 10.1080/21541264.2021.1991773

Zhitai Hao, Vladimir Svetlov, Evgeny Nudler

{"title":"Rho-dependent transcription termination: a revisionist view.","authors":"Zhitai Hao, Vladimir Svetlov, Evgeny Nudler","doi":"10.1080/21541264.2021.1991773","DOIUrl":"https://doi.org/10.1080/21541264.2021.1991773","url":null,"abstract":"Rho is a hexameric bacterial RNA helicase, which became a paradigm of factor-dependent transcription termination. The broadly accepted (\"textbook\") model posits a series of steps, wherein Rho first binds C-rich Rho utilization (rut) sites on nascent RNA, uses its ATP-dependent translocase activity to catch up with RNA polymerase (RNAP), and either pulls the transcript from the elongation complex or pushes RNAP forward, thus terminating transcription. However, this appealingly simple mechano-chemical model lacks a biological realism and is increasingly at odds with genetic and biochemical data. Here, we summarize recent structural and biochemical studies that have advanced our understanding of molecular details of RNA recognition, termination signaling, and RNAP inactivation in Rho-dependent transcription termination, rebalancing the view in favor of an alternative \"allosteric\" mechanism. In the revised model, Rho binds RNAP early in elongation assisted by the cofactors NusA and NusG, forming a pre-termination complex (PTC). The formation of PTC allows Rho to continuously sample nascent transcripts for a termination signal, which subsequently traps the elongation complex in an inactive state prior to its dissociation.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"12 4","pages":"171-181"},"PeriodicalIF":3.6,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8632121/pdf/KTRN_12_1991773.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39570205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 19

Transcription complexes as RNA chaperones. 作为RNA伴侣的转录复合物。

IF 3.6

Transcription-Austin Pub Date : 2021-08-01 Epub Date: 2021-11-01 DOI: 10.1080/21541264.2021.1985931

Nelly Said, Markus C Wahl

{"title":"Transcription complexes as RNA chaperones.","authors":"Nelly Said, Markus C Wahl","doi":"10.1080/21541264.2021.1985931","DOIUrl":"https://doi.org/10.1080/21541264.2021.1985931","url":null,"abstract":"To exert their functions, RNAs adopt diverse structures, ranging from simple secondary to complex tertiary and quaternary folds. In vivo, RNA folding starts with RNA transcription, and a wide variety of processes are coupled to co-transcriptional RNA folding events, including the regulation of fundamental transcription dynamics, gene regulation by mechanisms like attenuation, RNA processing or ribonucleoprotein particle formation. While co-transcriptional RNA folding and associated co-transcriptional processes are by now well accepted as pervasive regulatory principles in all organisms, investigations into the role of the transcription machinery in co-transcriptional folding processes have so far largely focused on effects of the order in which RNA regions are produced and of transcription kinetics. Recent structural and structure-guided functional analyses of bacterial transcription complexes increasingly point to an additional role of RNA polymerase and associated transcription factors in supporting co-transcriptional RNA folding by fostering or preventing strategic contacts to the nascent transcripts. In general, the results support the view that transcription complexes can act as RNA chaperones, a function that has been suggested over 30 years ago. Here, we discuss transcription complexes as RNA chaperones based on recent examples from bacterial transcription.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"12 4","pages":"126-155"},"PeriodicalIF":3.6,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/80/f0/KTRN_12_1985931.PMC8632103.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39830209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Bacterial transcription during growth arrest. 生长停滞期间的细菌转录

IF 3.6

Transcription-Austin Pub Date : 2021-08-01 Epub Date: 2021-09-06 DOI: 10.1080/21541264.2021.1968761

Megan Bergkessel

{"title":"Bacterial transcription during growth arrest.","authors":"Megan Bergkessel","doi":"10.1080/21541264.2021.1968761","DOIUrl":"10.1080/21541264.2021.1968761","url":null,"abstract":"Bacteria in most natural environments spend substantial periods of time limited for essential nutrients and not actively dividing. While transcriptional activity under these conditions is substantially reduced compared to that occurring during active growth, observations from diverse organisms and experimental approaches have shown that new transcription still occurs and is important for survival. Much of our understanding of transcription regulation has come from measuring transcripts in exponentially growing cells, or from in vitro experiments focused on transcription from highly active promoters by the housekeeping RNA polymerase holoenzyme. The fact that transcription during growth arrest occurs at low levels and is highly heterogeneous has posed challenges for its study. However, new methods of measuring low levels of gene expression activity, even in single cells, offer exciting opportunities for directly investigating transcriptional activity and its regulation during growth arrest. Furthermore, much of the rich structural and biochemical data from decades of work on the bacterial transcriptional machinery is also relevant to growth arrest. In this review, the physiological changes likely affecting transcription during growth arrest are first considered. Next, possible adaptations to help facilitate ongoing transcription during growth arrest are discussed. Finally, new insights from several recently published datasets investigating mRNA transcripts in single bacterial cells at various growth phases will be explored. Keywords: Growth arrest, stationary phase, RNA polymerase, nucleoid condensation, population heterogeneity.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"12 4","pages":"232-249"},"PeriodicalIF":3.6,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8632087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39390586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0