Critical Reviews in Biochemistry and Molecular Biology最新文献_第8页

Mammalian mitochondrial DNA replication and mechanisms of deletion formation. 哺乳动物线粒体DNA复制及缺失形成机制。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2020-12-01 Epub Date: 2020-09-24 DOI: 10.1080/10409238.2020.1818684

Maria Falkenberg, Claes M Gustafsson

引用次数: 30

NusG-dependent RNA polymerase pausing is a frequent function of this universally conserved transcription elongation factor. nusg依赖性RNA聚合酶暂停是这种普遍保守的转录延伸因子的常见功能。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2020-12-01 Epub Date: 2020-10-02 DOI: 10.1080/10409238.2020.1828261

Alexander V Yakhnin, Mikhail Kashlev, Paul Babitzke

{"title":"NusG-dependent RNA polymerase pausing is a frequent function of this universally conserved transcription elongation factor.","authors":"Alexander V Yakhnin, Mikhail Kashlev, Paul Babitzke","doi":"10.1080/10409238.2020.1828261","DOIUrl":"https://doi.org/10.1080/10409238.2020.1828261","url":null,"abstract":"Although transcription by RNA polymerase (RNAP) is highly processive, elongation can be transiently halted by RNAP pausing. Pausing provides time for diverse regulatory events to occur such as RNA folding and regulatory factor binding. The transcription elongation factors NusA and NusG dramatically affect the frequency and duration of RNAP pausing, and hence regulation of transcription. NusG is the only transcription factor conserved in all three domains of life; its homolog in archaea and eukaryotes is Spt5. This review focuses on NusG-dependent pausing, which is a common occurrence in Bacillus subtilis. B. NusG induces pausing about once per 3 kb at a consensus TTNTTT motif in the non-template DNA strand within the paused transcription bubble. A conserved region of NusG contacts the TTNTTT motif to stabilize the paused transcription elongation complex (TEC) in multiple catalytically inactive RNAP conformations. The density of NusG-dependent pause sites is 3-fold higher in untranslated regions, suggesting that pausing could regulate the expression of hundreds of genes in B. subtilis. We describe how pausing in 5' leader regions contributes to regulating the expression of B. subtilis genes by transcription attenuation and translation control mechanisms. As opposed to the broadly accepted view that NusG is an anti-pausing factor, phylogenetic analyses suggest that NusG-dependent pausing is a widespread mechanism in bacteria. This function of NusG is consistent with the well-established role of its eukaryotic homolog Spt5 in promoter-proximal pausing. Since NusG is present in all domains of life, NusG-dependent pausing could be a conserved mechanism in all organisms.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"55 6","pages":"716-728"},"PeriodicalIF":6.5,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2020.1828261","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38544445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

The molecular structure of long non-coding RNAs: emerging patterns and functional implications. 长链非编码rna的分子结构:新出现的模式和功能意义。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2020-12-01 Epub Date: 2020-10-12 DOI: 10.1080/10409238.2020.1828259

Isabel Chillón, Marco Marcia

引用次数: 44

From canonical to modified nucleotides: balancing translation and metabolism. 从标准核苷酸到修饰核苷酸:平衡翻译和代谢。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2020-12-01 Epub Date: 2020-09-16 DOI: 10.1080/10409238.2020.1818685

Federica Accornero, Robert L Ross, Juan D Alfonzo

{"title":"From canonical to modified nucleotides: balancing translation and metabolism.","authors":"Federica Accornero, Robert L Ross, Juan D Alfonzo","doi":"10.1080/10409238.2020.1818685","DOIUrl":"https://doi.org/10.1080/10409238.2020.1818685","url":null,"abstract":"Abstract Every type of nucleic acid in cells may undergo some kind of post-replicative or post-transcriptional chemical modification. Recent evidence has highlighted their importance in biology and their chemical complexity. In the following pages, we will describe new discoveries of modifications, with a focus on tRNA and mRNA. We will highlight current challenges and advances in modification detection and we will discuss how changes in nucleotide post-transcriptional modifications may affect cell homeostasis leading to malfunction. Although, RNA modifications prevail in all forms of life, the present review will focus on eukaryotic systems, where the great degree of intracellular compartmentalization provides barriers and filters for the level at which a given RNA is modified and will of course affect its fate and function. Additionally, although we will mention rRNA modification and modifications of the mRNA 5’-CAP structure, this will only be discussed in passing, as many substantive reviews have been written on these subjects. Here we will not spend much time describing all the possible modifications that have been observed; truly a daunting task. For reference, Bujnicki and coworkers have created MODOMICS, a useful repository for all types of modifications and their associated enzymes. Instead we will discuss a few examples, which illustrate our arguments on the connection of modifications, metabolism and ultimately translation. The fact remains, a full understanding of the long reach of nucleic acid modifications in cells requires both a global and targeted study of unprecedented scale, which at the moment may well be limited only by technology.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"55 6","pages":"525-540"},"PeriodicalIF":6.5,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2020.1818685","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38383196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Aromatase inhibitors. 芳香化酶抑制剂。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2020-11-25 DOI: 10.1007/978-3-7643-8693-1

J. Johnston

引用次数: 82

19-Noraldosterone. 19去羟甾酮。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2020-11-25 DOI: 10.1201/9781003068754-7

Y. Takeda

引用次数: 0

An updated perspective on the polymerase division of labor during eukaryotic DNA replication. 真核生物DNA复制过程中聚合酶分工的最新研究进展。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2020-10-01 Epub Date: 2020-09-03 DOI: 10.1080/10409238.2020.1811630

Thomas A Guilliam, Joseph T P Yeeles

引用次数: 28

Control of electron transfer by protein dynamics in photosynthetic reaction centers. 光合反应中心蛋白质动力学对电子转移的控制。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2020-10-01 Epub Date: 2020-09-03 DOI: 10.1080/10409238.2020.1810623

Michael Gorka, Dmitry A Cherepanov, Alexey Yu Semenov, John H Golbeck

{"title":"Control of electron transfer by protein dynamics in photosynthetic reaction centers.","authors":"Michael Gorka, Dmitry A Cherepanov, Alexey Yu Semenov, John H Golbeck","doi":"10.1080/10409238.2020.1810623","DOIUrl":"https://doi.org/10.1080/10409238.2020.1810623","url":null,"abstract":"Trehalose and glycerol are low molecular mass sugars/polyols that have found widespread use in the protection of native protein states, in both short- and long-term storage of biological materials, and as a means of understanding protein dynamics. These myriad uses are often attributed to their ability to form an amorphous glassy matrix. In glycerol, the glass is formed only at cryogenic temperatures, while in trehalose, the glass is formed at room temperature, but only upon dehydration of the sample. While much work has been carried out to elucidate a mechanistic view of how each of these matrices interact with proteins to provide stability, rarely have the effects of these two independent systems been directly compared to each other. This review aims to compile decades of research on how different glassy matrices affect two types of photosynthetic proteins: (i) the Type II bacterial reaction center from Rhodobacter sphaeroides and (ii) the Type I Photosystem I reaction center from cyanobacteria. By comparing aggregate data on electron transfer, protein structure, and protein dynamics, it appears that the effects of these two distinct matrices are remarkably similar. Both seem to cause a \"tightening\" of the solvation shell when in a glassy state, resulting in severely restricted conformational mobility of the protein and associated water molecules. Thus, trehalose appears to be able to mimic, at room temperature, nearly all of the effects on protein dynamics observed in low temperature glycerol glasses.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"55 5","pages":"425-468"},"PeriodicalIF":6.5,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2020.1810623","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38343482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Dynamic elements of replication protein A at the crossroads of DNA replication, recombination, and repair. 处于 DNA 复制、重组和修复十字路口的复制蛋白 A 的动态元素。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2020-10-01 Epub Date: 2020-08-28 DOI: 10.1080/10409238.2020.1813070

Colleen C Caldwell, Maria Spies

{"title":"Dynamic elements of replication protein A at the crossroads of DNA replication, recombination, and repair.","authors":"Colleen C Caldwell, Maria Spies","doi":"10.1080/10409238.2020.1813070","DOIUrl":"10.1080/10409238.2020.1813070","url":null,"abstract":"The heterotrimeric eukaryotic Replication protein A (RPA) is a master regulator of numerous DNA metabolic processes. For a long time, it has been viewed as an inert protector of ssDNA and a platform for assembly of various genome maintenance and signaling machines. Later, the modular organization of the RPA DNA binding domains suggested a possibility for dynamic interaction with ssDNA. This modular organization has inspired several models for the RPA-ssDNA interaction that aimed to explain how RPA, the high-affinity ssDNA binding protein, is replaced by the downstream players in DNA replication, recombination, and repair that bind ssDNA with much lower affinity. Recent studies, and in particular single-molecule observations of RPA-ssDNA interactions, led to the development of a new model for the ssDNA handoff from RPA to a specific downstream factor where not only stability and structural rearrangements but also RPA conformational dynamics guide the ssDNA handoff. Here we will review the current knowledge of the RPA structure, its dynamic interaction with ssDNA, and how RPA conformational dynamics may be influenced by posttranslational modification and proteins that interact with RPA, as well as how RPA dynamics may be harnessed in cellular decision making.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"55 5","pages":"482-507"},"PeriodicalIF":6.5,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821911/pdf/nihms-1648328.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38318859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2020-10-01 Epub Date: 2020-09-02 DOI: 10.1080/10409238.2020.1810621

Mrinmoyee Majumder, Roger H Johnson, Viswanathan Palanisamy

{"title":"Fragile X-related protein family: a double-edged sword in neurodevelopmental disorders and cancer.","authors":"Mrinmoyee Majumder, Roger H Johnson, Viswanathan Palanisamy","doi":"10.1080/10409238.2020.1810621","DOIUrl":"https://doi.org/10.1080/10409238.2020.1810621","url":null,"abstract":"The fragile X-related (FXR) family proteins FMRP, FXR1, and FXR2 are RNA binding proteins that play a critical role in RNA metabolism, neuronal plasticity, and muscle development. These proteins share significant homology in their protein domains, which are functionally and structurally similar to each other. FXR family members are known to play an essential role in causing fragile X mental retardation syndrome (FXS), the most common genetic form of autism spectrum disorder. Recent advances in our understanding of this family of proteins have occurred in tandem with discoveries of great importance to neurological disorders and cancer biology via the identification of their novel RNA and protein targets. Herein, we review the FXR family of proteins as they pertain to FXS, other mental illnesses, and cancer. We emphasize recent findings and analyses that suggest contrasting functions of this protein family in FXS and tumorigenesis based on their expression patterns in human tissues. Finally, we discuss current gaps in our knowledge regarding the FXR protein family and their role in FXS and cancer and suggest future studies to facilitate bench to bedside translation of the findings.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"55 5","pages":"409-424"},"PeriodicalIF":6.5,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2020.1810621","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38338204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 17