Critical Reviews in Biochemistry and Molecular Biology最新文献

Catalase-peroxidase (KatG): a potential frontier in tuberculosis drug development.

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-12-01 Epub Date: 2025-02-27 DOI: 10.1080/10409238.2025.2470630

Aimin Liu

{"title":"Catalase-peroxidase (KatG): a potential frontier in tuberculosis drug development.","authors":"Aimin Liu","doi":"10.1080/10409238.2025.2470630","DOIUrl":"10.1080/10409238.2025.2470630","url":null,"abstract":"Mycobacterium tuberculosis (Mtb) depends on the bifunctional enzyme catalase-peroxidase (KatG) for survival within the host. KatG exhibits both catalase and peroxidase activities, serving distinct yet critical roles. While its peroxidase activity is essential for activating the frontline tuberculosis drug isoniazid, its catalase activity protects Mtb from oxidative stress. This bifunctional enzyme is equipped with a unique, protein-derived cofactor, methionine-tyrosine-tryptophan (MYW), which enables catalase activity to efficiently disproportionate hydrogen peroxide in phagocytes. Recent studies reveal that the MYW cofactor naturally exists in a hydroperoxylated form (MYW-OOH) when cell cultures are grown under ambient conditions. New findings highlight a dynamic regulation of KatG activity, wherein the modification of the protein cofactor is removable-from MYW-OOH to MYW-at body temperature or in the presence of micromolar concentrations of hydrogen peroxide. This reversible modification modulates KatG's dual activities: MYW-OOH inhibits catalase activity while enhancing peroxidase activity, demonstrating the chemical accessibility of the cofactor. Such duality positions KatG as a unique target for tuberculosis drug development. Therapeutic strategies that exploit cofactor modification could hold promise, particularly against drug-resistant strains with impaired peroxidase activity. By selectively inhibiting catalase activity, these approaches would render Mtb more vulnerable to oxidative stress while enhancing isoniazid activation-a double-edged strategy for combating tuberculosis.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"434-446"},"PeriodicalIF":6.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11935562/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514882","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

A structural view of nickel-pincer nucleotide cofactor-related biochemistry. 钳镍核苷酸辅因子相关生物化学的结构观点。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-12-01 Epub Date: 2025-01-19 DOI: 10.1080/10409238.2025.2451443

Santhosh Gatreddi, Shramana Chatterjee, Aiko Turmo, Jian Hu, Robert P Hausinger

引用次数: 0

The common chemical logic of 'bridged' peroxo species in mononuclear non-heme iron systems.

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-12-01 Epub Date: 2025-01-29 DOI: 10.1080/10409238.2025.2455084

Kirklin L McWhorter, Vatsal Purohit, Joseph A Ambarian, Riddhi Jhunjhunwala, Katherine M Davis

{"title":"The common chemical logic of 'bridged' peroxo species in mononuclear non-heme iron systems.","authors":"Kirklin L McWhorter, Vatsal Purohit, Joseph A Ambarian, Riddhi Jhunjhunwala, Katherine M Davis","doi":"10.1080/10409238.2025.2455084","DOIUrl":"10.1080/10409238.2025.2455084","url":null,"abstract":"Mononuclear non-heme iron enzymes catalyze a wide array of important oxidative transformations. They are correspondingly diverse in both structure and mechanism. Despite significant evolutionary distance, it is becoming increasingly apparent that these enzymes nonetheless illustrate a compelling case of mechanistic convergence via the formation of peroxo species bridging metal and substrate. Aromatic amino acid hydroxylases and 2-oxoglutarate (2OG)-dependent enzymes, for example, form bridged acyl- or alkylperoxo intermediates en route to highly oxidizing ferryl species, while catechol dioxygenases utilize such 'bridged' peroxos directly. Analogous acylperoxoiron intermediates have also been demonstrated to precede a perferryl oxidant in biomimetic systems. Herein, we synthesize the results of structural, spectroscopic and computational studies on these systems to gain insight into the shared chemical logic that drives iron-peracid formation and reactivity. In all cases, reactions are tuned via the electron-donating properties of coordinating ligands. Second-sphere residues have also been demonstrated to modulate the orientation of the bridge, thereby influencing reaction outcomes. The effect of carboxylic acid addition to relevant biomimetic catalyst reactions further underscores these fundamental chemical principles. Altogether, we provide a comprehensive analysis of the cross-cutting mechanisms that guide peroxo formation and subsequent oxidative chemistry performed by non-heme mononuclear iron catalysts.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"418-433"},"PeriodicalIF":6.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058274","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

Discovery, functional characterization, and structural studies of the NRPS-independent siderophore synthetases.

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-12-01 Epub Date: 2025-03-14 DOI: 10.1080/10409238.2025.2476476

Ketan D Patel, Mercedes B Fisk, Andrew M Gulick

{"title":"Discovery, functional characterization, and structural studies of the NRPS-independent siderophore synthetases.","authors":"Ketan D Patel, Mercedes B Fisk, Andrew M Gulick","doi":"10.1080/10409238.2025.2476476","DOIUrl":"10.1080/10409238.2025.2476476","url":null,"abstract":"To adapt to low-iron environments, many bacteria produce siderophores, low molecular weight iron chelators that are secreted into the environment where they bind ferric iron. The production of siderophore uptake systems then allows retrieval of the iron-complexed siderophore into the cell, where the metal ion can be used for structural and catalytic roles in many proteins. While many siderophores are produced by the activity of a family of large modular nonribosomal peptide synthetase (NRPS) enzymes, a second class of siderophores are produced by an alternate pathway. These so-called NRPS-independent siderophores (NIS) are biosynthesized through a shared catalytic step that is performed by an NIS synthetase. These enzymes catalyze the formation of an amide linkage between a carboxylate and an amine or, more rarely, form an ester with a hydroxyl substrate. Here we describe the discovery and biochemical studies of diverse NIS synthetases from different siderophore pathways to provide insight into their substrate specificity and catalytic mechanism. The structures of a small number of family members are additionally described that correlates the functional work with the enzyme structure. While the field has come a long way since it was described as a \"long-overlooked\" family in 2009, there remains much to discover in this large and important enzyme family.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"447-471"},"PeriodicalIF":6.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623528","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

Structures, mechanisms, and kinetic advantages of the SgrAI filament forming mechanism. SgrAI长丝成形机理的结构、机理及动力学优势。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-12-01 Epub Date: 2024-12-19 DOI: 10.1080/10409238.2024.2440315

Nancy C Horton, Dmitry Lyumkis

{"title":"Structures, mechanisms, and kinetic advantages of the SgrAI filament forming mechanism.","authors":"Nancy C Horton, Dmitry Lyumkis","doi":"10.1080/10409238.2024.2440315","DOIUrl":"10.1080/10409238.2024.2440315","url":null,"abstract":"This review documents investigations leading to the unprecedented discovery of filamentation as a mode of enzyme regulation in the type II restriction endonuclease SgrAI. Filamentation is defined here as linear or helical polymerization of a single enzyme as occurs for SgrAI, and has now been shown to occur in many other enzyme systems, including conserved metabolic enzymes. In the case of SgrAI, filamentation activates the DNA cleavage rate by up to 1000-fold and also alters the enzyme's DNA sequence specificity. The investigations began with the observation that SgrAI cleaves two types of recognition sequences, primary and secondary, but cleaves the secondary sequences only when present on the same DNA as at least one primary. DNA cleavage rate measurements showed how the primary sequence is both a substrate and an allosteric effector of SgrAI. Biophysical measurements indicated that the activated form of SgrAI, stimulated by binding to the primary sequence, consisted of varied numbers of the SgrAI bound to DNA. Structural studies revealed the activated state of SgrAI as a left-handed helical filament which stabilizes an altered enzyme conformation, which binds a second divalent cation in the active site. Efforts to determine the mechanism of DNA sequence specificity alteration are ongoing and current models are discussed. Finally, global kinetic modeling of the filament mediated DNA cleavage reaction and simulations of in vivo activity suggest that the filament mechanism evolved to rapidly cleave invading DNA while protecting the Streptomyces host genome.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"363-401"},"PeriodicalIF":6.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142851922","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 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