Critical Reviews in Biochemistry and Molecular Biology最新文献

The general transcription factors (GTFs) of RNA polymerase II and their roles in plant development and stress responses. RNA 聚合酶 II 的一般转录因子 (GTFs) 及其在植物发育和胁迫反应中的作用。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-10-01 Epub Date: 2024-10-03 DOI: 10.1080/10409238.2024.2408562

Shivam Sharma, Sanjay Kapoor, Athar Ansari, Akhilesh Kumar Tyagi

{"title":"The general transcription factors (GTFs) of RNA polymerase II and their roles in plant development and stress responses.","authors":"Shivam Sharma, Sanjay Kapoor, Athar Ansari, Akhilesh Kumar Tyagi","doi":"10.1080/10409238.2024.2408562","DOIUrl":"10.1080/10409238.2024.2408562","url":null,"abstract":"In eukaryotes, general transcription factors (GTFs) enable recruitment of RNA polymerase II (RNA Pol II) to core promoters to facilitate initiation of transcription. Extensive research in mammals and yeast has unveiled their significance in basal transcription as well as in diverse biological processes. Unlike mammals and yeast, plant GTFs exhibit remarkable degree of variability and flexibility. This is because plant GTFs and GTF subunits are often encoded by multigene families, introducing complexity to transcriptional regulation at both cellular and biological levels. This review provides insights into the general transcription mechanism, GTF composition, and their cellular functions. It further highlights the involvement of RNA Pol II-related GTFs in plant development and stress responses. Studies reveal that GTFs act as important regulators of gene expression in specific developmental processes and help equip plants with resilience against adverse environmental conditions. Their functions may be direct or mediated through their cofactor nature. The versatility of GTFs in controlling gene expression, and thereby influencing specific traits, adds to the intricate complexity inherent in the plant system.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"267-309"},"PeriodicalIF":6.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371200","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: 0

Methanogens and what they tell us about how life might survive on Mars. 甲烷菌及其对火星生命生存方式的启示。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-10-01 Epub Date: 2024-11-03 DOI: 10.1080/10409238.2024.2418639

Chellapandi Paulchamy, Sreekutty Vakkattuthundi Premji, Saranya Shanmugam

{"title":"Methanogens and what they tell us about how life might survive on Mars.","authors":"Chellapandi Paulchamy, Sreekutty Vakkattuthundi Premji, Saranya Shanmugam","doi":"10.1080/10409238.2024.2418639","DOIUrl":"10.1080/10409238.2024.2418639","url":null,"abstract":"Space exploration and research are uncovering the potential for terrestrial life to survive in outer space, as well as the environmental factors that affect life during interplanetary transfer. The presence of methane in the Martian atmosphere suggests the possibility of methanogens, either extant or extinct, on Mars. Understanding how methanogens survive and adapt under space-exposed conditions is crucial for understanding the implications of extraterrestrial life. In this article, we discuss methanogens as model organisms for obtaining energy transducers and producing methane in a simulated Martian environment. We also explore the chemical evolution of cellular composition and growth maintenance to support survival in extraterrestrial environments. Neutral selective pressure is imposed on the chemical composition of cellular components to increase cell survival and reduce growth under physiological conditions. Energy limitation is an evolutionary driver of macromolecular polymerization, growth maintenance, and survival fitness of methanogens. Methanogens grown in a Martian environment may exhibit global alterations in their metabolic function and gene expression at the system scale. A space systems biology approach would further elucidate molecular survival mechanisms and adaptation to a drastic outer space environment. Therefore, identifying a genetically stable methanogenic community is essential for biomethane production from waste recycling to achieve sustainable space-life support functions.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"337-362"},"PeriodicalIF":6.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142564136","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: 0

Mechanisms of immune evasion by Mycobacterium tuberculosis: the impact of T7SS and cell wall lipids on host defenses. 结核分枝杆菌逃避免疫的机制：T7SS 和细胞壁脂质对宿主防御的影响。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-10-01 Epub Date: 2024-10-08 DOI: 10.1080/10409238.2024.2411264

Asrar Ahmad Malik, Mohd Shariq, Javaid Ahmad Sheikh, Udyeshita Jaiswal, Haleema Fayaz, Gauri Shrivastava, Nasreen Z Ehtesham, Seyed E Hasnain

{"title":"Mechanisms of immune evasion by Mycobacterium tuberculosis: the impact of T7SS and cell wall lipids on host defenses.","authors":"Asrar Ahmad Malik, Mohd Shariq, Javaid Ahmad Sheikh, Udyeshita Jaiswal, Haleema Fayaz, Gauri Shrivastava, Nasreen Z Ehtesham, Seyed E Hasnain","doi":"10.1080/10409238.2024.2411264","DOIUrl":"10.1080/10409238.2024.2411264","url":null,"abstract":"Mycobacterium tuberculosis (M. tb) is one of the most successful human pathogens, causing a severe and widespread infectious disease. The frequent emergence of multidrug-resistant (MDR) strains has exacerbated this public health crisis, particularly in underdeveloped regions. M. tb employs a sophisticated array of virulence factors to subvert host immune responses, both innate and adaptive. It utilizes the early secretory antigenic target (ESAT6) secretion system 1 (ESX-1) type VII secretion system (T7SS) and cell wall lipids to disrupt phagosomal integrity, inhibiting phagosome maturation, and fusion with lysosomes. Although host cells activate mechanisms such as ubiquitin (Ub), Ub-ligase, and cyclic GMP-AMP synthase-stimulator of interferon genes 1 (CGAS-STING1)-mediated autophagy to inhibit M. tb survival within macrophages, the pathogen counteracts these defenses with its own virulence factors, thereby inhibiting autophagy and dampening host-directed responses. T7SSs are critical for transporting proteins across the complex mycobacterial cell envelope, performing essential functions, including metabolite uptake, immune evasion, and conjugation. T7SS substrates fall into two main families: ESAT-6 system proteins, which are found in both Firmicutes and Actinobacteria, and proline-glutamic acid (PE) and proline-proline-glutamic acid (PPE) proteins, which are unique to mycobacteria. Recent studies have highlighted the significance of T7SSs in mycobacterial growth, virulence, and pathogenesis. Understanding the mechanisms governing T7SSs could pave the way for novel therapeutic strategies to combat mycobacterial diseases, including tuberculosis (TB).","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"310-336"},"PeriodicalIF":6.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142388737","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: 0

Evolution, classification, and mechanisms of transport, activity regulation, and substrate specificity of ZIP metal transporters. ZIP 金属转运体的进化、分类和转运机制、活性调节和底物特异性。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-10-01 Epub Date: 2024-10-21 DOI: 10.1080/10409238.2024.2405476

Jian Hu, Yuhan Jiang

引用次数: 0

Exercise training and changes in skeletal muscle mitochondrial proteins: from blots to "omics". 运动训练与骨骼肌线粒体蛋白质的变化：从印迹到 "omics"。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-09-17 DOI: 10.1080/10409238.2024.2383408

Elizabeth G Reisman,Nikeisha J Caruana,David J Bishop

{"title":"Exercise training and changes in skeletal muscle mitochondrial proteins: from blots to \"omics\".","authors":"Elizabeth G Reisman,Nikeisha J Caruana,David J Bishop","doi":"10.1080/10409238.2024.2383408","DOIUrl":"https://doi.org/10.1080/10409238.2024.2383408","url":null,"abstract":"Mitochondria are essential, membrane-enclosed organelles that consist of ∼1100 different proteins, which allow for many diverse functions critical to maintaining metabolism. Highly metabolic tissues, such as skeletal muscle, have a high mitochondrial content that increases with exercise training. The classic western blot technique has revealed training-induced increases in the relatively small number of individual mitochondrial proteins studied (∼5% of the >1100 proteins in MitoCarta), with some of these changes dependent on the training stimulus. Proteomic approaches have identified hundreds of additional mitochondrial proteins that respond to exercise training. There is, however, surprisingly little crossover in the mitochondrial proteins identified in the published human training studies. This suggests that to better understand the link between training-induced changes in mitochondrial proteins and metabolism, future studies need to move beyond maximizing protein detection to adopting methods that will increase the reliability of the changes in protein abundance observed.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"17 1","pages":"1-23"},"PeriodicalIF":6.5,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142256280","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: 0

The biogenesis of potassium transporters: implications of disease-associated mutations. 钾转运体的生物生成：疾病相关突变的影响。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-06-01 Epub Date: 2024-07-01 DOI: 10.1080/10409238.2024.2369986

Morgan Kok, Jeffrey L Brodsky

{"title":"The biogenesis of potassium transporters: implications of disease-associated mutations.","authors":"Morgan Kok, Jeffrey L Brodsky","doi":"10.1080/10409238.2024.2369986","DOIUrl":"10.1080/10409238.2024.2369986","url":null,"abstract":"The concentration of intracellular and extracellular potassium is tightly regulated due to the action of various ion transporters, channels, and pumps, which reside primarily in the kidney. Yet, potassium transporters and cotransporters play vital roles in all organs and cell types. Perhaps not surprisingly, defects in the biogenesis, function, and/or regulation of these proteins are linked to range of catastrophic human diseases, but to date, few drugs have been approved to treat these maladies. In this review, we discuss the structure, function, and activity of a group of potassium-chloride cotransporters, the KCCs, as well as the related sodium-potassium-chloride cotransporters, the NKCCs. Diseases associated with each of the four KCCs and two NKCCs are also discussed. Particular emphasis is placed on how these complex membrane proteins fold and mature in the endoplasmic reticulum, how non-native forms of the cotransporters are destroyed in the cell, and which cellular factors oversee their maturation and transport to the cell surface. When known, we also outline how the levels and activities of each cotransporter are regulated. Open questions in the field and avenues for future investigations are further outlined.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"154-198"},"PeriodicalIF":6.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11444911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141466780","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

Pioneer factors: nature or nurture? 先驱因素：天性还是后天培养？

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-06-01 Epub Date: 2024-05-22 DOI: 10.1080/10409238.2024.2355885

Shane Stoeber, Holly Godin, Cheng Xu, Lu Bai

引用次数: 0

Mitochondrial sirtuin 3 and role of natural compounds: the effect of post-translational modifications on cellular metabolism. 线粒体 sirtuin 3 和天然化合物的作用：翻译后修饰对细胞代谢的影响。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-06-01 Epub Date: 2024-07-11 DOI: 10.1080/10409238.2024.2377094

Francesca Oppedisano, Salvatore Nesci, Anna Spagnoletta

{"title":"Mitochondrial sirtuin 3 and role of natural compounds: the effect of post-translational modifications on cellular metabolism.","authors":"Francesca Oppedisano, Salvatore Nesci, Anna Spagnoletta","doi":"10.1080/10409238.2024.2377094","DOIUrl":"10.1080/10409238.2024.2377094","url":null,"abstract":"Sirtuins (SIRTs) are a family of proteins with enzymatic activity. In particular, they are a family of class III NAD+-dependent histone deacetylases and ADP-ribosyltransferases. NAD+-dependent deac(et)ylase activities catalyzed by sirtuin include ac(et)ylation, propionylation, butyrylation, crotonylation, manylation, and succinylation. Specifically, human SIRT3 is a 399 amino acid protein with two functional domains: a large Rossmann folding motif and NAD+ binding, and a small complex helix and zinc-binding motif. SIRT3 is widely expressed in mitochondria-rich tissues and is involved in maintaining mitochondrial integrity, homeostasis, and function. Moreover, SIRT3 regulates related diseases, such as aging, hepatic, kidney, neurodegenerative and cardiovascular disease, metabolic diseases, and cancer development. In particular, one of the most significant and damaging post-translational modifications is irreversible protein oxidation, i.e. carbonylation. This process is induced explicitly by increased ROS production due to mitochondrial dysfunction. SIRT3 is carbonylated by 4-hydroxynonenal at the level of Cys280. The carbonylation induces conformational changes in the active site, resulting in allosteric inhibition of SIRT3 activity and loss of the ability to deacetylate and regulate antioxidant enzyme activity. Phytochemicals and, in particular, polyphenols, thanks to their strong antioxidant activity, are natural compounds with a positive regulatory action on SIRT3 in various pathologies. Indeed, the enzymatic SIRT3 activity is modulated, for example, by different natural polyphenol classes, including resveratrol and the bergamot polyphenolic fraction. Thus, this review aims to elucidate the mechanisms by which phytochemicals can interact with SIRT3, resulting in post-translational modifications that regulate cellular metabolism.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"199-220"},"PeriodicalIF":6.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589869","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: 0

Molecular insights into the prototypical single-stranded DNA-binding protein from E. coli. 大肠杆菌单链 DNA 结合蛋白原型的分子研究。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-02-01 Epub Date: 2024-05-21 DOI: 10.1080/10409238.2024.2330372

Nina J Bonde, Alexander G Kozlov, Michael M Cox, Timothy M Lohman, James L Keck

引用次数: 0

Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques. 利用生化和模拟技术探究蛋白质赖氨酸甲基转移酶的催化机理。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-02-01 Epub Date: 2024-03-07 DOI: 10.1080/10409238.2024.2318547

Philipp Schnee, Jürgen Pleiss, Albert Jeltsch

{"title":"Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques.","authors":"Philipp Schnee, Jürgen Pleiss, Albert Jeltsch","doi":"10.1080/10409238.2024.2318547","DOIUrl":"10.1080/10409238.2024.2318547","url":null,"abstract":"Protein lysine methyltransferases (PKMTs) transfer up to three methyl groups to the side chains of lysine residues in proteins and fulfill important regulatory functions by controlling protein stability, localization and protein/protein interactions. The methylation reactions are highly regulated, and aberrant methylation of proteins is associated with several types of diseases including neurologic disorders, cardiovascular diseases, and various types of cancer. This review describes novel insights into the catalytic machinery of various PKMTs achieved by the combined application of biochemical experiments and simulation approaches during the last years, focusing on clinically relevant and well-studied enzymes of this group like DOT1L, SMYD1-3, SET7/9, G9a/GLP, SETD2, SUV420H2, NSD1/2, different MLLs and EZH2. Biochemical experiments have unraveled many mechanistic features of PKMTs concerning their substrate and product specificity, processivity and the effects of somatic mutations observed in PKMTs in cancer cells. Structural data additionally provided information about the substrate recognition, enzyme-substrate complex formation, and allowed for simulations of the substrate peptide interaction and mechanism of PKMTs with atomistic resolution by molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. These simulation technologies uncovered important mechanistic details of the PKMT reaction mechanism including the processes responsible for the deprotonation of the target lysine residue, essential conformational changes of the PKMT upon substrate binding, but also rationalized regulatory principles like PKMT autoinhibition. Further developments are discussed that could bring us closer to a mechanistic understanding of catalysis of this important class of enzymes in the near future. The results described here illustrate the power of the investigation of enzyme mechanisms by the combined application of biochemical experiments and simulation technologies.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"20-68"},"PeriodicalIF":6.2,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140048996","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: 0