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Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2024-03-07 Philipp Schnee, Jürgen Pleiss, Albert Jeltsch
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 stab...
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Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2024-03-05 Karishma Seem, Simardeep Kaur, Suresh Kumar, Trilochan Mohapatra
Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the conte...
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Collaborators or competitors: the communication between RNA polymerase II and the nucleosome during eukaryotic transcription Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2024-01-30 Haley A. Hardtke, Y. Jessie Zhang
Decades of scientific research have been devoted to unraveling the intricacies of eukaryotic transcription since the groundbreaking discovery of eukaryotic RNA polymerases in the late 1960s. RNA po...
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Insights into the metabolism, signaling, and physiological effects of 2’,3’-cyclic nucleotide monophosphates in bacteria Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2024-02-02 Nick J. Marotta, Emily E. Weinert
2’,3’-cyclic nucleotide monophosphates (2’,3’-cNMPs) have been discovered within both prokaryotes and eukaryotes in the past decade and a half, raising questions about their conserved existence in ...
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Hemoglobin wonders: a fascinating gas transporter dive into molluscs Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2024-01-08 Weifeng Zhang, Yang Zhang, Xizhi Shi, Shi Wang, Yongbo Bao
Hemoglobin (Hb) has been identified in at least 14 molluscan taxa so far. Research spanning over 130 years on molluscan Hbs focuses on their genes, protein structures, functions, and evolution. Mol...
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Platelet protein synthesis, regulation, and post-translational modifications: mechanics and function Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2023-06-22 Gerald Soslau
Dogma had been firmly entrenched in the minds of the scientific community that the anucleate mammalian platelet was incapable of protein biosynthesis since their identification in the late 1880s. T...
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Protein aggregation-inhibition: a therapeutic route from Parkinson’s disease to sickle cell anemia Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2023-05-09 Gabriel F. Martins, N. Galamba
Abstract Protein aggregation is implicated in multiple diseases, so-called proteinopathies, ranging from neurodegenerative disorders such as Alzheimer’s disease and Parkinson’s disease (PD) to type 2 diabetes mellitus and sickle cell disease (SCD). The structure of the protein aggregates and the kinetics and mechanisms of aggregation have been the object of intense research over the years toward the
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The tricarboxylic acid (TCA) cycle: a malleable metabolic network to counter cellular stress Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2023-04-26 Alex MacLean, Felix Legendre, Vasu D. Appanna
Abstract The tricarboxylic acid (TCA) cycle is a primordial metabolic pathway that is conserved from bacteria to humans. Although this network is often viewed primarily as an energy producing engine fueling ATP synthesis via oxidative phosphorylation, mounting evidence reveals that this metabolic hub orchestrates a wide variety of pivotal biological processes. It plays an important part in combatting
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Distinct enzymatic strategies for de novo generation of disulfide bonds in membranes Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2023-04-25 Weikai Li
Abstract Disulfide bond formation is a catalyzed reaction essential for the folding and stability of proteins in the secretory pathway. In prokaryotes, disulfide bonds are generated by DsbB or VKOR homologs that couple the oxidation of a cysteine pair to quinone reduction. Vertebrate VKOR and VKOR-like enzymes have gained the epoxide reductase activity to support blood coagulation. The core structures
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G-quadruplexes in bacteria: insights into the regulatory roles and interacting proteins of non-canonical nucleic acid structures Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2023-03-31 Rachel R. Cueny, Sarah D. McMillan, James L. Keck
Abstract G-quadruplexes (G4s) are highly stable, non-canonical DNA or RNA structures that can form in guanine-rich stretches of nucleic acids. G4-forming sequences have been found in all domains of life, and proteins that bind and/or resolve G4s have been discovered in both bacterial and eukaryotic organisms. G4s regulate a variety of cellular processes through inhibitory or stimulatory roles that
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2-5A-Mediated decay (2-5AMD): from antiviral defense to control of host RNA Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2023-03-20 Eliza Prangley, Alexei Korennykh
Abstract Mammalian cells are exquisitely sensitive to the presence of double-stranded RNA (dsRNA), a molecule that they interpret as a signal of viral presence requiring immediate attention. Upon sensing dsRNA cells activate the innate immune response, which involves transcriptional mechanisms driving inflammation and secretion of interferons (IFNs) and interferon-stimulated genes (ISGs), as well as
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Regulation of loop extrusion on the interphase genome Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2023-03-15 Hyogyung Shin, Yoori Kim
Abstract In the human cell nucleus, dynamically organized chromatin is the substrate for gene regulation, DNA replication, and repair. A central mechanism of DNA loop formation is an ATPase motor cohesin-mediated loop extrusion. The cohesin complexes load and unload onto the chromosome under the control of other regulators that physically interact and affect motor activity. Regulation of the dynamic
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Challenges and opportunities for circRNA identification and delivery Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2023-03-14 Jiani Dong, Zhuoer Zeng, Ying Huang, Chuanpin Chen, Zeneng Cheng, Qubo Zhu
Abstract Circular RNAs (circRNAs) are evolutionarily conserved noncoding RNAs with tissue-specific expression patterns, and exert unique cellular functions that have the potential to become biomarkers in therapeutic applications. Therefore, accurate and sensitive detection of circRNA with facile platforms is essential for better understanding of circRNA biological processes and circRNA-related disease
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Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2023-03-06 Julia S. Martin del Campo, Jack Rigsbee, Marcelo Bueno Batista, Florence Mus, Luis M. Rubio, Oliver Einsle, John W. Peters, Ray Dixon, Dennis R. Dean, Patricia C. Dos Santos
Abstract Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic
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Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2023-03-03 Aleksandr A. Arzamasov, Andrei L. Osterman
Abstract Bifidobacteria are early colonizers of the human neonatal gut and provide multiple health benefits to the infant, including inhibiting the growth of enteropathogens and modulating the immune system. Certain Bifidobacterium species prevail in the gut of breastfed infants due to the ability of these microorganisms to selectively forage glycans present in human milk, specifically human milk oligosaccharides
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Sulfur incorporation into biomolecules: recent advances Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2022-11-20 Shramana Chatterjee, Robert P. Hausinger
Abstract Sulfur is an essential element for a variety of cellular constituents in all living organisms and adds considerable functionality to a wide range of biomolecules. The pathways for incorporating sulfur into central metabolites of the cell such as cysteine, methionine, cystathionine, and homocysteine have long been established. Furthermore, the importance of persulfide intermediates during the
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Creation and resolution of non-B-DNA structural impediments during replication Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2022-09-28 Christopher Mellor, Consuelo Perez, Julian E. Sale
Abstract During replication, folding of the DNA template into non-B-form secondary structures provides one of the most abundant impediments to the smooth progression of the replisome. The core replisome collaborates with multiple accessory factors to ensure timely and accurate duplication of the genome and epigenome. Here, we discuss the forces that drive non-B structure formation and the evidence
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Energetics, kinetics, and pathways of SNARE assembly in membrane fusion Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2022-09-24 Yongli Zhang, Lu Ma, Huan Bao
Abstract Fusion of transmitter-containing vesicles with plasma membranes at the synaptic and neuromuscular junctions mediates neurotransmission and muscle contractions, respectively, thereby underlying all thoughts and actions. The fusion process is driven by the coupled folding and assembly of three synaptic SNARE proteins––syntaxin-1 and SNAP-25 on the target plasma membrane (t-SNAREs) and VAMP2
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Reversible and bidirectional signaling of notch ligands Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2022-09-01 Elenaé Vázquez-Ulloa, Kai-Lan Lin, Marcela Lizano, Cecilia Sahlgren
Abstract The Notch signaling pathway is a direct cell-cell communication system involved in a wide variety of biological processes, and its disruption is observed in several pathologies. The pathway is comprised of a ligand-expressing (sender) cell and a receptor-expressing (receiver) cell. The canonical ligands are members of the Delta/Serrate/Lag-1 (DSL) family of proteins. Their binding to a Notch
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What makes functional amyloids work? Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2022-08-23 Ansgar B. Siemer
Abstract Although first described in the context of disease, cross-β (amyloid) fibrils have also been found as functional entities in all kingdoms of life. However, what are the specific properties of the cross-β fibril motif that convey biological function, make them especially suited for their particular purpose, and distinguish them from other fibrils found in biology? This review approaches these
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Hypoxia-regulated microRNAs: the molecular drivers of tumor progression Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2022-07-28 Sakunie Sawai, Pooi-Fong Wong, Thamil Selvee Ramasamy
Abstract Hypoxia is a common feature of the tumor microenvironment (TME) of nearly all solid tumors, leading to therapeutic failure. The changes in stiffness of the extracellular matrix (ECM), pH gradients, and chemical balance that contribute to multiple cancer hallmarks are closely regulated by intratumoral oxygen tension via its primary mediators, hypoxia-inducible factors (HIFs). HIFs, especially
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Cohesin in DNA damage response and double-strand break repair Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2022-02-03 Wenya Hou, Yan Li, Jiaxin Zhang, Yisui Xia, Xueting Wang, Hongxiang Chen, Huiqiang Lou
Abstract Cohesin, a four-subunit ring comprising SMC1, SMC3, RAD21 and SA1/2, tethers sister chromatids by DNA replication-coupled cohesion (RC-cohesion) to guarantee correct chromosome segregation during cell proliferation. Postreplicative cohesion, also called damage-induced cohesion (DI-cohesion), is an emerging critical player in DNA damage response (DDR). In this review, we sum up recent progress
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Unraveling the complex regulatory networks in biofilm formation in bacteria and relevance of biofilms in environmental remediation Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-12-22 Kumari Uma Mahto, Swetambari Kumari, Surajit Das
Abstract Biofilms are assemblages of bacteria embedded within a matrix of extracellular polymeric substances (EPS) attached to a substratum. The process of biofilm formation is a complex phenomenon regulated by the intracellular and intercellular signaling systems. Various secondary messenger molecules such as cyclic dimeric guanosine 3′,5′-monophosphate (c-di-GMP), cyclic adenosine 3′,5′-monophosphate
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Structure and function of ClpXP, a AAA+ proteolytic machine powered by probabilistic ATP hydrolysis Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-12-19 Robert T. Sauer, Xue Fei, Tristan A. Bell, Tania A. Baker
Abstract ClpXP is an archetypical AAA+ protease, consisting of ClpX and ClpP. ClpX is an ATP-dependent protein unfoldase and polypeptide translocase, whereas ClpP is a self-compartmentalized peptidase. ClpXP is currently the only AAA+ protease for which high-resolution structures exist, the molecular basis of recognition for a protein substrate is understood, extensive biochemical and genetic analysis
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Emerging biological functions of ribonuclease 1 and angiogenin Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-12-09 Emily R. Garnett, Ronald T. Raines
Abstract Pancreatic-type ribonucleases (ptRNases) are a large family of vertebrate-specific secretory endoribonucleases. These enzymes catalyze the degradation of many RNA substrates and thereby mediate a variety of biological functions. Though the homology of ptRNases has informed biochemical characterization and evolutionary analyses, the understanding of their biological roles is incomplete. Here
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The mechanisms of human lymphoid chromosomal translocations and their medical relevance Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-12-07 Di Liu, Michael R. Lieber
Abstract The most common human lymphoid chromosomal translocations involve concurrent failures of the recombination activating gene (RAG) complex and Activation-Induced Deaminase (AID). These are two enzymes that are normally expressed for purposes of the two site-specific DNA recombination processes: V(D)J recombination and class switch recombination (CSR). First, though it is rare, a low level of
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Mitochondrial acute oxygen sensing and signaling Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-12-01 José López-Barneo, Patricia Ortega-Sáenz
Abstract Oxygen (O2) is essential for life and therefore the supply of sufficient O2 to the tissues is a major physiological challenge. In mammals, a deficit of O2 (hypoxia) triggers rapid cardiorespiratory reflexes (e.g. hyperventilation and increased heart output) that within a few seconds increase the uptake of O2 by the lungs and its distribution throughout the body. The prototypical acute O2-sensing
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Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-12-01 Nikolay E. Shirokikh
Abstract During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5′ and 3′ untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and
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Mechanisms of hexameric helicases Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-08-17 Amy J. Fernandez, James M. Berger
Abstract Ring-shaped hexameric helicases are essential motor proteins that separate duplex nucleic acid strands for DNA replication, recombination, and transcriptional regulation. Two evolutionarily distinct lineages of these enzymes, predicated on RecA and AAA+ ATPase folds, have been identified and characterized to date. Hexameric helicases couple NTP hydrolysis with conformational changes that move
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Biosynthesis and trafficking of heme o and heme a: new structural insights and their implications for reaction mechanisms and prenylated heme transfer Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-08-25 Elise D. Rivett, Lim Heo, Michael Feig, Eric L. Hegg
Abstract Aerobic respiration is a key energy-producing pathway in many prokaryotes and virtually all eukaryotes. The final step of aerobic respiration is most commonly catalyzed by heme-copper oxidases embedded in the cytoplasmic or mitochondrial membrane. The majority of these terminal oxidases contain a prenylated heme (typically heme a or occasionally heme o) in the active site. In addition, many
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The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-10-11 Yousuf A. Khan, K. Ian White, Axel T. Brunger
Abstract ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of proteins found throughout all domains of life. The hallmark of this family is a conserved AAA+ domain responsible for a diverse range of cellular activities. Typically, AAA+ proteins transduce chemical energy from the hydrolysis of ATP into mechanical energy through conformational change, which can drive
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Causes and consequences of impaired methionine synthase activity in acquired and inherited disorders of vitamin B12 metabolism Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-10-05 Jean-Louis Guéant, Rosa-Maria Guéant-Rodriguez, Viola J. Kosgei, David Coelho
Abstract Methyl-Cobalamin (Cbl) derives from dietary vitamin B12 and acts as a cofactor of methionine synthase (MS) in mammals. MS encoded by MTR catalyzes the remethylation of homocysteine to generate methionine and tetrahydrofolate, which fuel methionine and cytoplasmic folate cycles, respectively. Methionine is the precursor of S-adenosyl methionine (SAM), the universal methyl donor of transmethylation
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Diverse triterpene skeletons are derived from the expansion and divergent evolution of 2,3-oxidosqualene cyclases in plants Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-10-02 Jing Wang, Yanhong Guo, Xue Yin, Xiaoning Wang, Xiaoquan Qi, Zheyong Xue
Abstract Triterpenoids are one of the largest groups of secondary metabolites and exhibit diverse structures, which are derived from C30 skeletons that are biosynthesized via the isoprenoid pathway by cyclization of 2,3-oxidosqualene. Triterpenoids have a wide range of biological activities, and are used in functional foods, drugs, and as industrial materials. Due to the low content levels in their
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Reprogramming of the epigenome in neurodevelopmental disorders Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-10-02 Khadija D. Wilson, Elizabeth G. Porter, Benjamin A. Garcia
Abstract The etiology of neurodevelopmental disorders (NDDs) remains a challenge for researchers. Human brain development is tightly regulated and sensitive to cellular alterations caused by endogenous or exogenous factors. Intriguingly, the surge of clinical sequencing studies has revealed that many of these disorders are monogenic and monoallelic. Notably, chromatin regulation has emerged as highly
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Regulation of mRNA decay in E. coli Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-09-21 Bijoy K. Mohanty, Sidney R. Kushner
Abstract Detailed studies of the Gram-negative model bacterium, Escherichia coli, have demonstrated that post-transcriptional events exert important and possibly greater control over gene regulation than transcription initiation or effective translation. Thus, over the past 30 years, considerable effort has been invested in understanding the pathways of mRNA turnover in E. coli. Although it is assumed
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Regulation of protein function and degradation by heme, heme responsive motifs, and CO Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-09-13 Angela S. Fleischhacker, Anindita Sarkar, Liu Liu, Stephen W. Ragsdale
Abstract Heme is an essential biomolecule and cofactor involved in a myriad of biological processes. In this review, we focus on how heme binding to heme regulatory motifs (HRMs), catalytic sites, and gas signaling molecules as well as how changes in the heme redox state regulate protein structure, function, and degradation. We also relate these heme-dependent changes to the affected metabolic processes
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Novel insights into the mechanism of cell cycle kinases Mec1(ATR) and Tel1(ATM) Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-06-20 Elias A. Tannous, Peter M. Burgers
Abstract DNA replication is a highly precise process which usually functions in a perfect rhythm with cell cycle progression. However, cells are constantly faced with various kinds of obstacles such as blocks in DNA replication, lack of availability of precursors and improper chromosome alignment. When these problems are not addressed, they may lead to chromosome instability and the accumulation of
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Mechanisms linking endoplasmic reticulum (ER) stress and microRNAs to adipose tissue dysfunction in obesity Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-06-28 Kalhara R. Menikdiwela, João Pedro Tôrres Guimarães, Latha Ramalingam, Nishan S. Kalupahana, Jannette M. Dufour, Rachel L. Washburn, Naima Moustaid-Moussa
Abstract Over accumulation of lipids in adipose tissue disrupts metabolic homeostasis by affecting cellular processes. Endoplasmic reticulum (ER) stress is one such process affected by obesity. Biochemical and physiological alterations in adipose tissue due to obesity interfere with adipose ER functions causing ER stress. This is in line with increased irregularities in other cellular processes such
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Guanine quadruplexes and their roles in molecular processes Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-06-23 Shruti Mishra, Swathi Kota, Reema Chaudhary, H. S. Misra
Abstract The role of guanine quadruplexes (G4) in fundamental biological processes like DNA replication, transcription, translation and telomere maintenance is recognized. G4 structure dynamics is regulated by G4 structure binding proteins and is thought to be crucial for the maintenance of genome integrity in both prokaryotic and eukaryotic cells. Growing research over the last decade has expanded
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The amyloid proteome: a systematic review and proposal of a protein classification system Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-07-27
Abstract Amyloidosis is a disease caused by pathological fibril aggregation and deposition of proteins in different tissues and organs. Thirty-six fibril-forming proteins have been identified. So far, proteomic evaluation of amyloid focused on the detection and characterization of fibril proteins mainly for diagnostic purposes or to find novel fibril-forming proteins. However, amyloid deposits are
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The evolutionary history of the HUP domain Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-08-12 Ita Gruic-Sovulj, Liam M. Longo, Jagoda Jabłońska, Dan S. Tawfik
Abstract Among the enzyme lineages that undoubtedly emerged prior to the last universal common ancestor is the so-called HUP, which includes Class I aminoacyl tRNA synthetases (AARSs) as well as enzymes mediating NAD, FAD, and CoA biosynthesis. Here, we provide a detailed analysis of HUP evolution, from emergence to structural and functional diversification. The HUP is a nucleotide binding domain that
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Isothermal amplifications – a comprehensive review on current methods Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-07-15 Jörn Glökler, Theam Soon Lim, Jeunice Ida, Marcus Frohme
Abstract The introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has
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Ribosome-associated quality control and CAT tailing Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-07-07 Conor J. Howard, Adam Frost
Abstract Translation is the set of mechanisms by which ribosomes decode genetic messages as they synthesize polypeptides of a defined amino acid sequence. While the ribosome has been honed by evolution for high-fidelity translation, errors are inevitable. Aberrant mRNAs, mRNA structure, defective ribosomes, interactions between nascent proteins and the ribosomal exit tunnel, and insufficient cellular
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The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-06-20 Christine A. Ziegler, Peter L. Freddolino
Abstract Since the discovery of the Escherichia coli leucine-responsive regulatory protein (Lrp) almost 50 years ago, hundreds of Lrp homologs have been discovered, occurring in 45% of sequenced bacteria and almost all sequenced archaea. Lrp-like proteins are often referred to as the feast/famine regulatory proteins (FFRPs), reflecting their common regulatory roles. Acting as either global or local
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Miro proteins connect mitochondrial function and intercellular transport Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-06-17 Zuzana Nahacka, Renata Zobalova, Maria Dubisova, Jakub Rohlena, Jiri Neuzil
Abstract Mitochondria are organelles present in most eukaryotic cells, where they play major and multifaceted roles. The classical notion of the main mitochondrial function as the powerhouse of the cell per se has been complemented by recent discoveries pointing to mitochondria as organelles affecting a number of other auxiliary processes. They go beyond the classical energy provision via acting as
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Cholesterol efflux pathways, inflammation, and atherosclerosis Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-06-28 Anouk G. Groenen, Benedek Halmos, Alan R. Tall, Marit Westerterp
Abstract Plasma levels of high-density lipoprotein (HDL) inversely correlate with the incidence of cardiovascular diseases (CVD). The causal relationship between plasma HDL-cholesterol levels and CVD has been called into question by Mendelian randomization studies and the majority of clinical trials not showing any benefit of plasma HDL-cholesterol raising drugs on CVD. Nonetheless, recent Mendelian
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Modular optimization in metabolic engineering Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-06-27 Matthew Wong, Abinaya Badri, Christopher Gasparis, Georges Belfort, Mattheos Koffas
Abstract There is an increasing demand for bioproducts produced by metabolically engineered microbes, such as pharmaceuticals, biofuels, biochemicals and other high value compounds. In order to meet this demand, modular optimization, the optimizing of subsections instead of the whole system, has been adopted to engineer cells to overproduce products. Research into modularity has focused on traditional
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Cancer cells dysregulate PI3K/AKT/mTOR pathway activation to ensure their survival and proliferation: mimicking them is a smart strategy of gammaherpesviruses Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-06-15 Mara Cirone
Abstract The serine/threonine kinase mammalian target of rapamycin (mTOR) is the catalytic subunit of two complexes, mTORC1 and mTORC2, which have common and distinct subunits that mediate separate and overlapping functions. mTORC1 is activated by plenty of nutrients, and the two complexes can be activated by PI3K signaling. mTORC2 acts as an upstream regulator of AKT, and mTORC1 acts as a downstream
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Cellular mechanisms of mtDNA heteroplasmy dynamics Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-06-13 Claudia V. Pereira, Bryan L. Gitschlag, Maulik R. Patel
Abstract Heteroplasmy refers to the coexistence of more than one variant of the mitochondrial genome (mtDNA). Mutated or partially deleted mtDNAs can induce chronic metabolic impairment and cause mitochondrial diseases when their heteroplasmy levels exceed a critical threshold. These mutant mtDNAs can be maternally inherited or can arise de novo. Compelling evidence has emerged showing that mutant
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Regulation of the redox metabolome and thiol proteome by hydrogen sulfide Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-03-15 Roshan Kumar, Ruma Banerjee
Abstract Overproduction of reactive oxygen species and compromised antioxidant defenses perturb intracellular redox homeostasis and is associated with a myriad of human diseases as well as with the natural process of aging. Hydrogen sulfide (H2S), which is biosynthesized by organisms ranging from bacteria to man, influences a broad range of physiological functions. A highly touted molecular mechanism
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A local regulatory network in the testis mediated by laminin and collagen fragments that supports spermatogenesis Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-03-25 Linxi Li, Huitao Li, Lingling Wang, Tiao Bu, Shiwen Liu, Baiping Mao, C. Yan Cheng
Abstract It is almost five decades since the discovery of the hypothalamic-pituitary-testicular axis. This refers to the hormonal axis that connects the hypothalamus, pituitary gland and testes, which in turn, regulates the production of spermatozoa through spermatogenesis in the seminiferous tubules, and testosterone through steroidogenesis by Leydig cells in the interstitium, of the testes. Emerging
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The role of non-genetic information in evolutionary frameworks Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-05-10 Katherine L. Moran, Yelyzaveta Shlyakhtina, Maximiliano M. Portal
Abstract The evolution of organisms has been a subject of paramount debate for hundreds of years and though major advances in the field have been made, the precise mechanisms underlying evolutionary processes remain fragmentary. Strikingly, the majority of the core principles accepted across the many fields of biology only consider genetic information as the major - if not exclusive - biological information
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SMART approaches for genome-wide analyses of skeletal muscle stem and niche cells Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-04-07 Darren M. Blackburn, Felicia Lazure, Vahab D. Soleimani
Abstract Muscle stem cells (MuSCs) also called satellite cells are the building blocks of skeletal muscle, the largest tissue in the human body which is formed primarily of myofibers. While MuSCs are the principal cells that directly contribute to the formation of the muscle fibers, their ability to do so depends on critical interactions with a vast array of nonmyogenic cells within their niche environment
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Sweet systems: technologies for glycomic analysis and their integration into systems biology Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-04-05 Shuhui Chen, Rui Qin, Lara K. Mahal
Abstract Found in virtually every organism, glycans are essential molecules that play important roles in almost every aspect of biology. The composition of glycome, the repertoire of glycans in an organism or a biological sample, is often found altered in many diseases, including cancer, infectious diseases, metabolic and developmental disorders. Understanding how glycosylation and glycomic changes
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How can a traffic light properly work if it is always green? The paradox of CK2 signaling Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-04-11 Christian Borgo, Claudio D’Amore, Luca Cesaro, Stefania Sarno, Lorenzo A. Pinna, Maria Ruzzene, Mauro Salvi
Abstract CK2 is a constitutively active protein kinase that assuring a constant level of phosphorylation to its numerous substrates supports many of the most important biological functions. Nevertheless, its activity has to be controlled and adjusted in order to cope with the varying needs of a cell, and several examples of a fine-tune regulation of its activity have been described. More importantly
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ETF dehydrogenase advances in molecular genetics and impact on treatment Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-04-07 Sara Missaglia, Daniela Tavian, Corrado Angelini
Abstract Electron transfer flavoprotein dehydrogenase, also called ETF-ubiquinone oxidoreductase (ETF-QO), is a protein localized in the inner membrane of mitochondria, playing a central role in the electron-transfer system. Indeed, ETF-QO mediates electron transport from flavoprotein dehydrogenases to the ubiquinone pool. ETF-QO mutations are often associated with riboflavin-responsive multiple acyl-CoA
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The complexity and regulation of repair of alkylation damage to nucleic acids Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-01-12 Ning Tsao, Orlando D. Schärer, Nima Mosammaparast
Abstract DNA damaging agents have been a cornerstone of cancer therapy for nearly a century. The discovery of many of these chemicals, particularly the alkylating agents, are deeply entwined with the development of poisonous materials originally intended for use in warfare. Over the last decades, their anti-proliferative effects have focused on the specific mechanisms by which they damage DNA, and
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Multifaceted regulation of translation by the epitranscriptomic modification N6-methyladenosine Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-01-08 Xiao-Min Liu, Jun Zhou
Abstract Translation occurring on cytoplasmic mRNA is precisely governed at three consecutive stages, including initiation, elongation and termination. A growing body of evidence has revealed that an emerging epitranscriptomic code N6-methyladenosine (m6A), asymmetrically present in a large subset of coding and non-coding transcripts, is crucially required for mediating the translatomic stability.
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Mobility and disorder in antibody and antigen binding sites do not prevent immunochemical recognition Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-01-18 Vladimir N. Uversky, Marc H. V. Van Regenmortel
Abstract The known polyspecificity of antibodies, which is crucial for efficient immune response, is determined by the conformational flexibility and intrinsic disorder encoded in local peculiarities of the amino acid sequence of antibodies within or in the vicinity of their complementarity determining regions. Similarly, epitopes represent fuzzy binding sites, which are also characterized by local
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Coordinated roles of SLX4 and MutSβ in DNA repair and the maintenance of genome stability Crit. Rev. Biochem. Mol. Biol. (IF 6.5) Pub Date : 2021-02-17 Sarah J. Young, Stephen C. West
Abstract SLX4 provides a molecular scaffold for the assembly of multiple protein complexes required for the maintenance of genome stability. It is involved in the repair of DNA crosslinks, the resolution of recombination intermediates, the response to replication stress and the maintenance of telomere length. To carry out these diverse functions, SLX4 interacts with three structure-selective endonucleases