Stationary phase mutagenesis in B. subtilis: a paradigm to study genetic diversity programs in cells under stress.

Abstract:

:One of the experimental platforms to study programs increasing genetic diversity in cells under stressful or nondividing conditions is adaptive mutagenesis, also called stationary phase mutagenesis or stress-induced mutagenesis. In some model systems, there is evidence that mutagenesis occurs in genes that are actively transcribed. Some of those genes may be actively transcribed as a result of environmental stress giving the appearance of directed mutation. That is, cells under conditions of starvation or other stresses accumulate mutations in transcribed genes, including those transcribed because of the selective pressure. An important question concerns how, within the context of stochastic processes, a cell biases mutation to genes under selection pressure? Because the mechanisms underlying DNA transactions in prokaryotic cells are well conserved among the three domains of life, these studies are likely to apply to the examination of genetic programs in eukaryotes. In eukaryotes, increasing genetic diversity in differentiated cells has been implicated in neoplasia and cell aging. Historically, Escherichia coli has been the paradigm used to discern the cellular processes driving the generation of adaptive mutations; however, examining adaptive mutation in Bacillus subtilis has contributed new insights. One noteworthy contribution is that the B. subtilis' ability to accumulate chromosomal mutations under conditions of starvation is influenced by cell differentiation and transcriptional derepression, as well as by proteins homologous to transcription and repair factors. Here we revise and discuss concepts pertaining to genetic programs that increase diversity in B. subtilis cells under nutritional stress.

authors

Robleto EA,Yasbin R,Ross C,Pedraza-Reyes M

doi

10.1080/10409230701597717

subject

Has Abstract

pub_date

2007-09-01 00:00:00

pages

327-39

issue

5

eissn

1040-9238

issn

1549-7798

pii

782795575

journal_volume

42

pub_type

杂志文章,评审
  • A beta amyloidogenesis: unique, or variation on a systemic theme?

    abstract::For more than a century amyloid was considered to be an interesting, unique, but inconsequential pathologic entity that rarely caused significant clinical problems. We now recognize that amyloid is not one entity. In vivo it is a uniform organization of a disease, or process, specific protein co-deposited with a set o...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409239709082674

    authors: Kisilevsky R,Fraser PE

    更新日期:1997-01-01 00:00:00

  • Bacterial ribonucleases and their roles in RNA metabolism.

    abstract::Ribonucleases (RNases) are mediators in most reactions of RNA metabolism. In recent years, there has been a surge of new information about RNases and the roles they play in cell physiology. In this review, a detailed description of bacterial RNases is presented, focusing primarily on those from Escherichia coli and Ba...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.1080/10409238.2019.1651816

    authors: Bechhofer DH,Deutscher MP

    更新日期:2019-06-01 00:00:00

  • HEPN RNases - an emerging class of functionally distinct RNA processing and degradation enzymes.

    abstract::HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding) RNases are an emerging class of functionally diverse RNA processing and degradation enzymes. Members are defined by a small α-helical bundle encompassing a short consensus RNase motif. HEPN dimerization is a universal requirement for RNase activation as the c...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章

    doi:10.1080/10409238.2020.1856769

    authors: Pillon MC,Gordon J,Frazier MN,Stanley RE

    更新日期:2021-02-01 00:00:00

  • Iron acquisition through the bacterial transferrin receptor.

    abstract::Transferrin is one of the sources of iron that is most readily available to colonizing and invading pathogens. In this review, we look at iron uptake by the bacterial transferrin receptor that is found in the families Neisseriaceae, Pasteurellaceae and Moraxellaceae. This bipartite receptor consists of the TonB-depend...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.1080/10409238.2017.1293606

    authors: Pogoutse AK,Moraes TF

    更新日期:2017-06-01 00:00:00

  • Actin filament nucleation and elongation factors--structure-function relationships.

    abstract::The spontaneous and unregulated polymerization of actin filaments is inhibited in cells by actin monomer-binding proteins such as profilin and Tbeta4. Eukaryotic cells and certain pathogens use filament nucleators to stabilize actin polymerization nuclei, whose formation is rate-limiting. Known filament nucleators inc...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409230903277340

    authors: Dominguez R

    更新日期:2009-11-01 00:00:00

  • Translational control of eukaryotic gene expression.

    abstract::Translational control mechanisms are, besides transcriptional control and mRNA stability, the most determining for final protein levels. A large number of accessory factors that assist the ribosome during initiation, elongation, and termination of translation are required for protein synthesis. Cap-dependent translati...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.1080/10409230902882090

    authors: Van Der Kelen K,Beyaert R,Inzé D,De Veylder L

    更新日期:2009-07-01 00:00:00

  • How it all starts: Initiation of the clotting cascade.

    abstract::The plasma coagulation system in mammalian blood consists of a cascade of enzyme activation events in which serine proteases activate the proteins (proenzymes and procofactors) in the next step of the cascade via limited proteolysis. The ultimate outcome is the polymerization of fibrin and the activation of platelets,...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409238.2015.1050550

    authors: Smith SA,Travers RJ,Morrissey JH

    更新日期:2015-01-01 00:00:00

  • From canonical to modified nucleotides: balancing translation and metabolism.

    abstract::Every type of nucleic acid in cells may undergo some kind of post-replicative or post-transcriptional chemical modification. Recent evidence has highlighted their importance in biology and their chemical complexity. In the following pages, we will describe new discoveries of modifications, with a focus on tRNA and mRN...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章

    doi:10.1080/10409238.2020.1818685

    authors: Accornero F,Ross RL,Alfonzo JD

    更新日期:2020-12-01 00:00:00

  • FeII/alpha-ketoglutarate-dependent hydroxylases and related enzymes.

    abstract::FeII/alpha-ketoglutarate (alphaKG)-dependent hydroxylases catalyze an amazing diversity of reactions that result in protein side-chain modifications, repair of alkylated DNA/RNA, biosynthesis of antibiotics and plant products, metabolism related to lipids, and biodegradation of a variety of compounds. These enzymes po...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.1080/10409230490440541

    authors: Hausinger RP

    更新日期:2004-01-01 00:00:00

  • AMPK inhibition in health and disease.

    abstract::All living organisms depend on dynamic mechanisms that repeatedly reassess the status of amassed energy, in order to adapt energy supply to demand. The AMP-activated protein kinase (AMPK) alphabetagamma heterotrimer has emerged as an important integrator of signals managing energy balance. Control of AMPK activity inv...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409238.2010.488215

    authors: Viollet B,Horman S,Leclerc J,Lantier L,Foretz M,Billaud M,Giri S,Andreelli F

    更新日期:2010-08-01 00:00:00

  • Specificity of reversible ADP-ribosylation and regulation of cellular processes.

    abstract::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...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.1080/10409238.2017.1394265

    authors: Crawford K,Bonfiglio JJ,Mikoč A,Matic I,Ahel I

    更新日期:2018-02-01 00:00:00

  • Adaptive mutation in Saccharomyces cerevisiae.

    abstract::Adaptive mutation is a generic term for processes that allow individual cells of nonproliferating cell populations to acquire advantageous mutations and thereby to overcome the strong selective pressure of proliferation-limiting environmental conditions. Prerequisites for an occurrence of adaptive mutation are that th...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.1080/10409230701507773

    authors: Heidenreich E

    更新日期:2007-07-01 00:00:00

  • Comparative modeling of proteins in the design of novel renin inhibitors.

    abstract::Renin, the first enzyme in the renin-angiotensin system, is critically important for the maintenance of blood pressure, and, therefore, as a target for antihypertensive therapy. The three-dimensional structure of renin would be an invaluable aid in understanding the functional properties of renin as well as in the des...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409239109081721

    authors: Hutchins C,Greer J

    更新日期:1991-01-01 00:00:00

  • Chimeric aptamers in cancer cell-targeted drug delivery.

    abstract::Aptamers are single-stranded structured oligonucleotides (DNA or RNA) that can bind to a wide range of targets ("apatopes") with high affinity and specificity. These nucleic acid ligands, generated from pools of random-sequence by an in vitro selection process referred to as systematic evolution of ligands by exponent...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409238.2011.614592

    authors: Kanwar JR,Roy K,Kanwar RK

    更新日期:2011-12-01 00:00:00

  • Nonenzymatic deamidation of asparaginyl and glutaminyl residues in proteins.

    abstract::Some asparagine and glutamine residues in proteins undergo deamidation to aspartate and glutamate with rates that depend upon the sequence and higher-order structure of the protein. Functional groups within the protein can catalyze this reaction, acting as general acids, bases, or stabilizers of the transition state. ...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409239109081719

    authors: Wright HT

    更新日期:1991-01-01 00:00:00

  • Torsins: not your typical AAA+ ATPases.

    abstract::Torsin ATPases (Torsins) belong to the widespread AAA+ (ATPases associated with a variety of cellular activities) family of ATPases, which share structural similarity but have diverse cellular functions. Torsins are outliers in this family because they lack many characteristics of typical AAA+ proteins, and they are t...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409238.2015.1091804

    authors: Rose AE,Brown RS,Schlieker C

    更新日期:2015-01-01 00:00:00

  • Serotonin receptor signaling and regulation via β-arrestins.

    abstract::Serotonin receptors are the product of 15 distinct genes, 14 of which are G protein-coupled receptors. These receptors are expressed in a wide range of cell types, including distinct neuronal populations, and promote diverse functional responses in multiple organ systems. These receptors are important for mediating th...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409238.2010.516741

    authors: Bohn LM,Schmid CL

    更新日期:2010-12-01 00:00:00

  • Rab-dependent cellular trafficking and amyotrophic lateral sclerosis.

    abstract::Rab GTPases are becoming increasingly implicated in neurodegenerative disorders, although their role in amyotrophic lateral sclerosis (ALS) has been somewhat overlooked. However, dysfunction of intracellular transport is gaining increasing attention as a pathogenic mechanism in ALS. Many previous studies have focused ...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.1080/10409238.2018.1553926

    authors: Parakh S,Perri ER,Jagaraj CJ,Ragagnin AMG,Atkin JD

    更新日期:2018-12-01 00:00:00

  • Cold denaturation of proteins.

    abstract::This article summarizes all experimental facts concerning the cold denaturation of single-domain, multi-domain, and multimeric globular proteins in aqueous solutions with and without urea and guanidine hydrochloride. The facts obtained by various experimental techniques are analyzed thermodynamically and it is shown t...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409239009090612

    authors: Privalov PL

    更新日期:1990-01-01 00:00:00

  • RAGE and its ligands: from pathogenesis to therapeutics.

    abstract::Receptor for advanced glycation end products (RAGE) is an immunoglobulin-like receptor present on cell surface. RAGE binds to an array of structurally diverse ligands, acts as a pattern recognition receptor (PRR) and is expressed on cells of different origin performing different functions. RAGE ligation leads to the i...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章

    doi:10.1080/10409238.2020.1819194

    authors: Jangde N,Ray R,Rai V

    更新日期:2020-12-01 00:00:00

  • Dynamic structure of plasma fibronectin.

    abstract::Fibronectin is a large vertebrate glycoprotein that is found in soluble and insoluble forms and involved in diverse processes. Protomeric fibronectin is a dimer of subunits, each of which comprises 29-31 modules - 12 type I, two type II and 15-17 type III. Plasma fibronectin is secreted by hepatocytes and circulates i...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.1080/10409238.2016.1184224

    authors: Maurer LM,Ma W,Mosher DF

    更新日期:2015-07-01 00:00:00

  • Leukocytic oxygen activation and microbicidal oxidative toxins.

    abstract::Following a brief introduction of cellular response to stimulation comprising leukocyte activation, three major areas are discussed: (1) the neutrophil oxidase; (2) myeloperoxidase (MPO)-dependent oxidative microbicidal reactions; and (3) MPO-independent oxidative reactions. Topics included in section (A) are current ...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409238909082555

    authors: Hurst JK,Barrette WC Jr

    更新日期:1989-01-01 00:00:00

  • Lytic transglycosylases: concinnity in concision of the bacterial cell wall.

    abstract::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...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.1080/10409238.2017.1337705

    authors: Dik DA,Marous DR,Fisher JF,Mobashery S

    更新日期:2017-10-01 00:00:00

  • Enzymology of the acetyl-CoA pathway of CO2 fixation.

    abstract::We know of three routes that organisms have evolved to synthesize complex organic molecules from CO2: the Calvin cycle, the reverse tricarboxylic acid cycle, and the reductive acetyl-CoA pathway. This review describes the enzymatic steps involved in the acetyl-CoA pathway, also called the Wood pathway, which is the ma...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409239109114070

    authors: Ragsdale SW

    更新日期:1991-01-01 00:00:00

  • Molecular paleontology and complexity in the last eukaryotic common ancestor.

    abstract::Eukaryogenesis, the origin of the eukaryotic cell, represents one of the fundamental evolutionary transitions in the history of life on earth. This event, which is estimated to have occurred over one billion years ago, remains rather poorly understood. While some well-validated examples of fossil microbial eukaryotes ...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409238.2013.821444

    authors: Koumandou VL,Wickstead B,Ginger ML,van der Giezen M,Dacks JB,Field MC

    更新日期:2013-07-01 00:00:00

  • PTP1B: a simple enzyme for a complex world.

    abstract::Our understanding of the fundamental regulatory roles that tyrosine phosphatases play within cells has advanced significantly in the last two decades. Out-dated ideas that tyrosine phosphatases acts solely as the "off" switch counterbalancing the action of tyrosine kinases has proved to be flawed. PTP1B is the most ch...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409238.2013.819830

    authors: Feldhammer M,Uetani N,Miranda-Saavedra D,Tremblay ML

    更新日期:2013-09-01 00:00:00

  • SRA and its binding partners: an expanding role for RNA-binding coregulators in nuclear receptor-mediated gene regulation.

    abstract::The discovery that SRA RNA can function as a nuclear receptor (NR) coactivator resulted in a fundamental change in the perception of how NRs and their coregulators may regulate hormone signaling pathways. The subsequent identification of molecules capable of binding SRA, including SHARP, p68, and more recently SLIRP, ...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.1080/10409230802661719

    authors: Colley SM,Leedman PJ

    更新日期:2009-01-01 00:00:00

  • The role of RecQ helicases in non-homologous end-joining.

    abstract::DNA double-strand breaks are highly toxic DNA lesions that cause genomic instability, if not efficiently repaired. RecQ helicases are a family of highly conserved proteins that maintain genomic stability through their important roles in several DNA repair pathways, including DNA double-strand break repair. Double-stra...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409238.2014.942450

    authors: Keijzers G,Maynard S,Shamanna RA,Rasmussen LJ,Croteau DL,Bohr VA

    更新日期:2014-11-01 00:00:00

  • The structure, role, and regulation of type 1 protein phosphatases.

    abstract::Type 1 protein phosphatases (PP-1) comprise a group of widely distributed enzymes that specifically dephosphorylate serine and threonine residues of certain phosphoproteins. They all contain an isoform of the same catalytic subunit, which has an extremely conserved primary structure. One of the properties of PP-1 that...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章,评审

    doi:10.3109/10409239209082564

    authors: Bollen M,Stalmans W

    更新日期:1992-01-01 00:00:00

  • The complexity and regulation of repair of alkylation damage to nucleic acids.

    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 effec...

    journal_title:Critical reviews in biochemistry and molecular biology

    pub_type: 杂志文章

    doi:10.1080/10409238.2020.1869173

    authors: Tsao N,Schärer OD,Mosammaparast N

    更新日期:2021-01-12 00:00:00