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Critical Reviews in Biochemistry and Molecular Biology

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https://www.readbyqxmd.com/read/29108429/sources-of-spontaneous-mutagenesis-in-bacteria
#1
Jeremy W Schroeder, Ponlkrit Yeesin, Lyle A Simmons, Jue D Wang
Mutations in an organism's genome can arise spontaneously, that is, in the absence of exogenous stress and prior to selection. Mutations are often neutral or deleterious to individual fitness but can also provide genetic diversity driving evolution. Mutagenesis in bacteria contributes to the already serious and growing problem of antibiotic resistance. However, the negative impacts of spontaneous mutagenesis on human health are not limited to bacterial antibiotic resistance. Spontaneous mutations also underlie tumorigenesis and evolution of drug resistance...
November 6, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29108427/what-is-all-this-fuss-about-tus-comparison-of-recent-findings-from-biophysical-and-biochemical-experiments
#2
Bojk A Berghuis, Vlad-Stefan Raducanu, Mohamed M Elshenawy, Slobodan Jergic, Martin Depken, Nicholas E Dixon, Samir M Hamdan, Nynke H Dekker
Synchronizing the convergence of the two-oppositely moving DNA replication machineries at specific termination sites is a tightly coordinated process in bacteria. In Escherichia coli, a "replication fork trap" - found within a chromosomal region where forks are allowed to enter but not leave - is set by the protein-DNA roadblock Tus-Ter. The exact sequence of events by which Tus-Ter blocks replisomes approaching from one direction but not the other has been the subject of controversy for many decades. Specific protein-protein interactions between the nonpermissive face of Tus and the approaching helicase were challenged by biochemical and structural studies...
November 6, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29098880/specificity-of-reversible-adp-ribosylation-and-regulation-of-cellular-processes
#3
Kerryanne Crawford, Juan José Bonfiglio, Andreja Mikoč, Ivan Matic, Ivan Ahel
Proper and timely regulation of cellular processes is fundamental to the overall health and viability of organisms across all kingdoms of life. Thus, organisms have evolved multiple highly dynamic and complex biochemical signaling cascades in order to adapt and survive diverse challenges. One such method of conferring rapid adaptation is the addition or removal of reversible modifications of different chemical groups onto macromolecules which in turn induce the appropriate downstream outcome. ADP-ribosylation, the addition of ADP-ribose (ADPr) groups, represents one of these highly conserved signaling chemicals...
November 3, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28976219/finding-the-needle-in-the-haystack-towards-solving-the-protein-folding-problem-computationally
#4
Bian Li, Michaela Fooksa, Sten Heinze, Jens Meiler
Prediction of protein tertiary structures from amino acid sequence and understanding the mechanisms of how proteins fold, collectively known as "the protein folding problem," has been a grand challenge in molecular biology for over half a century. Theories have been developed that provide us with an unprecedented understanding of protein folding mechanisms. However, computational simulation of protein folding is still difficult, and prediction of protein tertiary structure from amino acid sequence is an unsolved problem...
October 4, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28954549/functions-of-smarcal1-zranb3-and-hltf-in-maintaining-genome-stability
#5
Lisa A Poole, David Cortez
A large number of SNF2 family, DNA and ATP-dependent motor proteins are needed during transcription, DNA replication, and DNA repair to manipulate protein-DNA interactions and change DNA structure. SMARCAL1, ZRANB3, and HLTF are three related members of this family with specialized functions that maintain genome stability during DNA replication. These proteins are recruited to replication forks through protein-protein interactions and bind DNA using both their motor and substrate recognition domains (SRDs)...
September 28, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28901199/new-tricks-for-the-glycyl-radical-enzyme-family
#6
Lindsey R F Backman, Michael A Funk, Christopher D Dawson, Catherine L Drennan
Glycyl radical enzymes (GREs) are important biological catalysts in both strict and facultative anaerobes, playing key roles both in the human microbiota and in the environment. GREs contain a backbone glycyl radical that is post-translationally installed, enabling radical-based mechanisms. GREs function in several metabolic pathways including mixed acid fermentation, ribonucleotide reduction and the anaerobic breakdown of the nutrient choline and the pollutant toluene. By generating a substrate-based radical species within the active site, GREs enable C-C, C-O and C-N bond breaking and formation steps that are otherwise challenging for nonradical enzymes...
September 13, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28644060/lytic-transglycosylases-concinnity-in-concision-of-the-bacterial-cell-wall
#7
REVIEW
David A Dik, Daniel R Marous, Jed F Fisher, Shahriar Mobashery
The lytic transglycosylases (LTs) are bacterial enzymes that catalyze the non-hydrolytic cleavage of the peptidoglycan structures of the bacterial cell wall. They are not catalysts of glycan synthesis as might be surmised from their name. Notwithstanding the seemingly mundane reaction catalyzed by the LTs, their lytic reactions serve bacteria for a series of astonishingly diverse purposes. These purposes include cell-wall synthesis, remodeling, and degradation; for the detection of cell-wall-acting antibiotics; for the expression of the mechanism of cell-wall-acting antibiotics; for the insertion of secretion systems and flagellar assemblies into the cell wall; as a virulence mechanism during infection by certain Gram-negative bacteria; and in the sporulation and germination of Gram-positive spores...
October 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28635330/multiple-functions-of-insulin-degrading-enzyme-a-metabolic-crosslight
#8
REVIEW
Grazia R Tundo, Diego Sbardella, Chiara Ciaccio, Giuseppe Grasso, Magda Gioia, Andrea Coletta, Fabio Polticelli, Donato Di Pierro, Danilo Milardi, Peter Van Endert, Stefano Marini, Massimo Coletta
Insulin-degrading enzyme (IDE) is a ubiquitous zinc peptidase of the inverzincin family, which has been initially discovered as the enzyme responsible for insulin catabolism; therefore, its involvement in the onset of diabetes has been largely investigated. However, further studies on IDE unraveled its ability to degrade several other polypeptides, such as β-amyloid, amylin, and glucagon, envisaging the possible implication of IDE dys-regulation in the "aggregopathies" and, in particular, in neurodegenerative diseases...
October 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28635326/encapsulins-molecular-biology-of-the-shell
#9
REVIEW
Robert J Nichols, Caleb Cassidy-Amstutz, Thawatchai Chaijarasphong, David F Savage
Compartmentalization is both a fundamental principle of cellular organization and an emerging theme in prokaryotic biology. Work in the past few decades has shown that protein-based organelles called microcompartments enhance the function of encapsulated cargo proteins. More recently, the repertoire of known prokaryotic organelles has expanded beyond microcompartments to include a new class of smaller proteinaceous compartments, termed nanocompartments (also known as encapsulins). Nanocompartments are icosahedral capsids that are smaller and less complex than microcompartments...
October 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28618839/sphingosine-kinase-and-sphingosine-1-phosphate-in-liver-pathobiology
#10
REVIEW
Timothy Rohrbach, Michael Maceyka, Sarah Spiegel
Over 20 years ago, sphingosine-1-phosphate (S1P) was discovered to be a bioactive signaling molecule. Subsequent studies later identified two related kinases, sphingosine kinase 1 and 2, which are responsible for the phosphorylation of sphingosine to S1P. Many stimuli increase sphingosine kinase activity and S1P production and secretion. Outside the cell, S1P can bind to and activate five S1P-specific G protein-coupled receptors (S1PR1-5) to regulate many important cellular and physiological processes in an autocrine or paracrine manner...
October 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28524697/emerging-functions-of-multi-protein-complex-mediator-with-special-emphasis-on-plants
#11
REVIEW
Naveen Malik, Pinky Agarwal, Akhilesh Tyagi
Mediator is a multi-subunit protein complex which is involved in transcriptional regulation in yeast and other eukaryotes. As a co-activator, it connects information from transcriptional activators/repressors to transcriptional machinery including RNA polymerase II and general transcription factors. It is not only involved in transcription initiation but also has important roles to play in transcription elongation and termination. Functional attributes of different Mediator subunits have been largely defined in yeast and mammalian systems earlier, while such studies in plants have gained momentum recently...
October 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28814116/the-dark-side-of-the-ring-role-of-the-dna-sliding-surface-of-pcna
#12
Matteo De March, Alfredo De Biasio
The proliferating cell nuclear antigen (PCNA) sliding clamp lies at the heart of the accurate duplication of eukaryotic genomes. While the outer surface of the PCNA ring interacts with polymerases and other factors, the role of the inner wall facing the DNA is elusive. Recent evidence shows that conserved basic residues in the PCNA central channel create a specific surface that recognizes the DNA backbone and enables the clamp to slide by rotationally tracking the DNA helix. The sliding surface can be modulated (i) through lysine acetylation, which triggers PCNA degradation during nucleotide excision repair (NER) and stimulates repair by homologous recombination (HR) or (ii) through binding of the protein factor p15(PAF), which turns off DNA lesion bypass...
August 17, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28799433/cell-cycle-transcription-control-dream-muvb-and-rb-e2f-complexes
#13
Martin Fischer, Gerd A Müller
The precise timing of cell cycle gene expression is critical for the control of cell proliferation; de-regulation of this timing promotes the formation of cancer and leads to defects during differentiation and development. Entry into and progression through S phase requires expression of genes coding for proteins that function in DNA replication. Expression of a distinct set of genes is essential to pass through mitosis and cytokinesis. Expression of these groups of cell cycle-dependent genes is regulated by the RB pocket protein family, the E2F transcription factor family, and MuvB complexes together with B-MYB and FOXM1...
August 11, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28545305/clostridium-difficile-toxins-a-and-b-receptors-pores-and-translocation-into-cells
#14
REVIEW
Kathleen E Orrell, Zhifen Zhang, Seiji N Sugiman-Marangos, Roman A Melnyk
The most potent toxins secreted by pathogenic bacteria contain enzymatic moieties that must reach the cytosol of target cells to exert their full toxicity. Toxins such as anthrax, diphtheria, and botulinum toxin all use three well-defined functional domains to intoxicate cells: a receptor-binding moiety that triggers endocytosis into acidified vesicles by binding to a specific host-cell receptor, a translocation domain that forms pores across the endosomal membrane in response to acidic pH, and an enzyme that translocates through these pores to catalytically inactivate an essential host cytosolic substrate...
August 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28524749/ubiquitin-enzymes-in-the-regulation-of-immune-responses
#15
REVIEW
Petra Ebner, Gijs A Versteeg, Fumiyo Ikeda
Ubiquitination plays a central role in the regulation of various biological functions including immune responses. Ubiquitination is induced by a cascade of enzymatic reactions by E1 ubiquitin activating enzyme, E2 ubiquitin conjugating enzyme, and E3 ubiquitin ligase, and reversed by deubiquitinases. Depending on the enzymes, specific linkage types of ubiquitin chains are generated or hydrolyzed. Because different linkage types of ubiquitin chains control the fate of the substrate, understanding the regulatory mechanisms of ubiquitin enzymes is central...
August 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28427283/break-induced-replication-in-eukaryotes-mechanisms-functions-and-consequences
#16
REVIEW
Cynthia J Sakofsky, Anna Malkova
Break-induced replication (BIR) is an important pathway specializing in repair of one-ended double-strand DNA breaks (DSBs). This type of DSB break typically arises at collapsed replication forks or at eroded telomeres. BIR initiates by invasion of a broken DNA end into a homologous template followed by initiation of DNA synthesis that can proceed for hundreds of kilobases. This synthesis is drastically different from S-phase replication in that instead of a replication fork, BIR proceeds via a migrating bubble and is associated with conservative inheritance of newly synthesized DNA...
August 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28402189/going-non-viral-the-sleeping-beauty-transposon-system-breaks-on-through-to-the-clinical-side
#17
REVIEW
Michael Hudecek, Zsuzsanna Izsvák, Sandra Johnen, Matthias Renner, Gabriele Thumann, Zoltán Ivics
Molecular medicine has entered a high-tech age that provides curative treatments of complex genetic diseases through genetically engineered cellular medicinal products. Their clinical implementation requires the ability to stably integrate genetic information through gene transfer vectors in a safe, effective and economically viable manner. The latest generation of Sleeping Beauty (SB) transposon vectors fulfills these requirements, and may overcome limitations associated with viral gene transfer vectors and transient non-viral gene delivery approaches that are prevalent in ongoing pre-clinical and translational research...
August 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28325102/building-up-and-breaking-down-mechanisms-controlling-recombination-during-replication
#18
REVIEW
Dana Branzei, Barnabas Szakal
The complete and faithful duplication of the genome is an essential prerequisite for proliferating cells to maintain genome integrity. This objective is greatly challenged by DNA damage encountered during replication, which causes fork stalling and in certain cases, fork breakage. DNA damage tolerance (DDT) pathways mitigate the effects on fork stability induced by replication fork stalling by mediating damage-bypass and replication fork restart. These DDT mechanisms, largely relying on homologous recombination (HR) and specialized polymerases, can however contribute to genome rearrangements and mutagenesis...
August 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28741966/the-connections-of-wnt-pathway-components-with-cell-cycle-and-centrosome-side-effects-or-a-hidden-logic
#19
Vítězslav Bryja, Igor Červenka, Lukáš Čajánek
Wnt signaling cascade has developed together with multicellularity to orchestrate the development and homeostasis of complex structures. Wnt pathway components - such as β-catenin, Dishevelled (DVL), Lrp6, and Axin-- are often dedicated proteins that emerged in evolution together with the Wnt signaling cascade and are believed to function primarily in the Wnt cascade. It is interesting to see that in recent literature many of these proteins are connected with cellular functions that are more ancient and not limited to multicellular organisms - such as cell cycle regulation, centrosome biology, or cell division...
July 25, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28670937/marr-family-transcription-factors-dynamic-variations-on-a-common-scaffold
#20
Dinesh K Deochand, Anne Grove
Members of the multiple antibiotic resistance regulator (MarR) family of transcription factors are critical for bacterial cells to respond to chemical signals and to convert such signals into changes in gene activity. Obligate dimers belonging to the winged helix-turn-helix protein family, they are critical for regulation of a variety of functions, including degradation of organic compounds and control of virulence gene expression. The conventional regulatory paradigm is based on a genomic locus in which the gene encoding the MarR protein is divergently oriented from a gene under its control; MarR binding to the intergenic region controls expression of both genes by changing the interaction of RNA polymerase with gene promoters...
July 3, 2017: Critical Reviews in Biochemistry and Molecular Biology
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