bluuebunny/crossref_metadata_2025 huggingface dataset:
Two-Carbon Compounds and Fatty Acids as Carbon Sources
Authors: Clark David P. , Cronan John E.
Published: May 2014

This review concerns the uptake and degradation of those molecules that are wholly or largely converted to acetyl-coenzyme A (CoA) in the first stage of metabolism in
Escherichia coli
and
Salmonella enterica
. These include acetate, acetoacetate, butyrate and longer fatty acids in wild type cells plus ethanol and some longer alcohols in certain mutant strains. Entering metabolism as acetyl-CoA has two important general consequences. First, generation of energy from acetyl-CoA requires operation of both the citric acid cycle and the respiratory chain to oxidize the NADH produced. Hence, acetyl-CoA serves as an energy source only during aerobic growth or during anaerobic respiration with such alternative electron acceptors as nitrate or trimethylamine oxide. In the absence of a suitable oxidant, acetyl-CoA is converted to a mixture of acetic acid and ethanol by the pathways of anaerobic fermentation. Catabolism of acetyl-CoA via the citric acid cycle releases both carbon atoms of the acetyl moiety as carbon dioxide and growth on these substrates as sole carbon source therefore requires the operation of the glyoxylate bypass to generate cell material. The pair of related two-carbon compounds, glycolate and glyoxylate are also discussed. However, despite having two carbons, these are metabolized via malate and glycerate, not via acetyl-CoA. In addition, mutants of
E. coli
capable of growth on ethylene glycol metabolize it via the glycolate pathway, rather than via acetyl- CoA. Propionate metabolism is also discussed because in many respects its pathway is analogous to that of acetate. The transcriptional regulation of these pathways is discussed in detail.
Tricarboxylic Acid Cycle and Glyoxylate Bypass
Authors: Cronan, John E. , Laporte David
Published: May 2014

The tricarboxylic acid (TCA) cycle plays two essential roles in metabolism. First, under aerobic conditions the cycle is responsible for the total oxidation of acetyl-CoA that is derived mainly from the pyruvate produced by glycolysis. Second, TCA cycle intermediates are required in the biosynthesis of several amino acids. Although the TCA cycle has long been considered a “housekeeping” pathway in
Escherichia coli
and
Salmonella enterica
, the pathway is highly regulated at the transcriptional level. Much of this control is exerted in response to respiratory conditions. The TCA cycle gene-protein relationship and mutant phenotypes have been well studied, although a few loose ends remain. The realization that a “shadow” TCA cycle exists that proceeds through methylcitrate has cleared up prior ambiguities. The glyoxylate bypass has long been known to be essential for growth on carbon sources such as acetate or fatty acids because this pathway allowsnet conversion of acetyl-CoA to metabolic intermediates. Strains lacking this pathway fail to grow on these carbon sources, since acetate carbon entering the TCA cycle is quantitatively lost as CO
2
resulting in the lack of a means to replenish the dicarboxylic acids consumed in amino acid biosynthesis. The TCA cycle gene-protein relationship and mutant phenotypes have been well studied, although the identity of the small molecule ligand that modulates transcriptional control of the glyoxylate cycle genes by binding to the IclR repressor remains unknown. The activity of the cycle is also exerted at the enzyme level by the reversible phosphorylation of the TCA cycle enzyme isocitrate dehydrogenase catalyzed by a specific kinase/phosphatase to allow isocitratelyase to compete for isocitrate and cleave this intermediate to glyoxylate and succinate.
Biosynthesis of Cysteine
Authors: Kredich Nicholas M.
Published: May 2014

The synthesis of L-cysteine from inorganic sulfur is the predominant mechanism by which reduced sulfur is incorporated into organic compounds. L-cysteineis used for protein and glutathione synthesis and serves as the primary source of reduced sulfur in L-methionine, lipoic acid, thiamin, coenzyme A (CoA), molybdopterin, and other organic molecules. Sulfate and thiosulfate uptake in
E. coli
and serovar Typhimurium are achieved through a single periplasmic transport system that utilizes two different but similar periplasmic binding proteins. Kinetic studies indicate that selenate and selenite share a single transporter with sulfate, but molybdate also has a separate transport system. During aerobic growth, the reduction of sulfite to sulfide is catalyzed by NADPH-sulfite reductase (SiR), and serovar Typhimurium mutants lacking this enzyme accumulate sulfite from sulfate, implying that sulfite is a normal intermediate in assimilatory sulfate reduction. L-Cysteine biosynthesis in serovar Typhimurium and
E. coli
ceases almost entirely when cells are grown on L-cysteine or L-cystine, owing to a combination of end product inhibition of serine transacetylase by L-cysteine and a gene regulatory system known as the cysteine regulon, wherein genes for sulfate assimilation and alkanesulfonate utilization are expressed only when sulfur is limiting. In vitro studies with the
cysJIH
,
cysK
, and
cysP
promoters have confirmed that they are inefficient at forming transcription initiation complexes without CysB and N-acetyl-L-serine. Activation of the
tauA
and
ssuE
promoters requires Cbl. It has been proposed that the three serovar Typhimurium anaerobic reductases for sulfite, thiosulfate, and tetrathionate may function primarily in anaerobic respiration.
Regulation of Serine, Glycine, and One-Carbon Biosynthesis
Authors: Stauffer George V.
Published: May 2014

The biosynthesis of serine, glycine, and one-carbon (C
1
) units constitutes a major metabolic pathway in
Escherichia coli
and
Salmonella enterica
serovar Typhimurium. C
1
units derived from serine and glycine are used in the synthesis of purines, histidine, thymine, pantothenate, and methionine and in the formylation of the aminoacylated initiator fMet-TRNA
fMet
used to start translation in
E. coli
and serovar Typhimurium. The need for serine, glycine, and C
1
units in many cellular functions makes it necessary for the genes encoding enzymes for their synthesis to be carefully regulated to meet the changing demands of the cell for these intermediates. This review discusses the regulation of the following genes:
serA
,
serB
, and
serC
;
gly
gene;
gcvTHP
operon;
lpdA
;
gcvA
and
gcvR
; and
gcvB
genes. Threonine utilization (the Tut cycle) constitutes a secondary pathway for serine and glycine biosynthesis. L-Serine inhibits the growth of
E. coli
cells in GM medium, and isoleucine releases this growth inhibition. The
E. coli
glycine transport system (Cyc) has been shown to transport glycine, D-alanine, D-serine, and the antibiotic D-cycloserine. Transport systems often play roles in the regulation of gene expression, by transporting effector molecules into the cell, where they are sensed by soluble or membrane-bound regulatory proteins.
Methionine
Authors: Hondorp Elise R. , Matthews Rowena G.
Published: May 2014

This review focuses on the steps unique to methionine biosynthesis, namely the conversion of homoserine to methionine. The past decade has provided a wealth of information concerning the details of methionine metabolism and the review focuses on providing a comprehensive overview of the field, emphasizing more recent findings. Details of methionine biosynthesis are addressed along with key cellular aspects, including regulation, uptake, utilization, AdoMet, the methyl cycle, and growing evidence that inhibition of methionine biosynthesis occurs under stressful cellular conditions. The first unique step in methionine biosynthesis is catalyzed by the
metA
gene product, homoserine transsuccinylase (HTS, or homoserine O-succinyltransferase). Recent experiments suggest that transcription of these genes is indeed regulated by MetJ, although the repressor-binding sites have not yet been verified. Methionine also serves as the precursor of
S
-adenosylmethionine, which is an essential molecule employed in numerous biological processes.
S
-adenosylhomocysteine is produced as a consequence of the numerous AdoMet-dependent methyl transfer reactions that occur within the cell. In
E. coli
and
Salmonella
, this molecule is recycled in two discrete steps to complete the methyl cycle. Cultures challenged by oxidative stress appear to experience a growth limitation that depends on methionine levels.
E. coli
that are deficient for the manganese and iron superoxide dismutases (the sodA and sodB gene products, respectively) require the addition of methionine or cysteine for aerobic growth. Modulation of methionine levels in response to stressful conditions further increases the complexity of its regulation.
Biosynthesis of Histidine
Authors: Winkler Malcolm E. , Ramos-Montañez Smirla
Published: May 2014

The biosynthesis of histidine in
Escherichia coli
and
Salmonella typhimurium
has been an important model system for the study of relationships between the flow of intermediates through a biosynthetic pathway and the control of the genes encoding the enzymes that catalyze the steps in a pathway. This article provides a comprehensive review of the histidine biosynthetic pathway and enzymes, including regulation of the flow of intermediates through the pathway and mechanisms that regulate the amounts of the histidine biosynthetic enzymes. In addition, this article reviews the structure and regulation of the histidine (
his
) biosynthetic operon, including transcript processing, Rho-factor-dependent “classical” polarity, and the current model of
his
operon attenuation control. Emphasis is placed on areas of recent progress. Notably, most of the enzymes that catalyze histidine biosynthesis have recently been crystallized, and their structures have been determined. Many of the histidine biosynthetic intermediates are unstable, and the histidine biosynthetic enzymes catalyze some chemically unusual reactions. Therefore, these studies have led to considerable mechanistic insight into the pathway itself and have provided deep biochemical understanding of several fundamental processes, such as feedback control, allosteric interactions, and metabolite channeling. Considerable recent progress has also been made on aspects of
his
operon regulation, including the mechanism of pp(p)Gpp stimulation of
his
operon transcription, the molecular basis for transcriptional pausing by RNA polymerase, and pathway evolution. The progress in these areas will continue as sophisticated new genomic, metabolomic, proteomic, and structural approaches converge in studies of the histidine biosynthetic pathway and mechanisms of control of
his
biosynthetic genes in other bacterial species.
Nucleotides, Nucleosides, and Nucleobases
Authors: Jensen Kaj Frank , Dandanell Gert , Hove-Jensen Bjarne , WillemoËs Martin
Published: May 2014

We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in
Escherichia coli
and
Salmonella
,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the
N
-glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the
de novo
pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.
Biogenesis and Homeostasis of Nicotinamide Adenine Dinucleotide Cofactor
Authors: Osterman Andrei
Published: May 2014

Universal and ubiquitous redox cofactors, nicotinamide adenine dinucleotide (NAD) and its phosphorylated analog (NADP), collectively contribute to approximately 12% of all biochemical reactions included in the metabolic model of
Escherichia coli
K-12. A homeostasis of the NAD pool faithfully maintained by the cells results from a dynamic balance in a network of NAD biosynthesis, utilization, decomposition, and recycling pathways that is subject to tight regulation at various levels. A brief overview of NAD utilization processes is provided in this review, including some examples of nonredox utilization. The review focuses mostly on those aspects of NAD biogenesis and utilization in
E. coli
and
Salmonella
that emerged within the past 12 years. The first pyridine nucleotide cycle (PNC) originally identified in mammalian systems and termed the Preiss-Handler pathway includes a single-step conversion of niacin (Na) to NaMN by nicotinic acid phosphoribosyltransferase (PncB). In
E. coli
and many other prokaryotes, this enzyme, together with nicotinamide deamidase (PncA), compose the major pathway for utilization of the pyridine ring in the form of amidated (Nm) or deamidated (Na) precursors. The existence of various regulatory mechanisms and checkpoints that control the NAD biosynthetic machinery reflects the importance of maintaining NAD homeostasis in a variety of growth conditions. Among the most important regulatory mechanisms at the level of individual enzymes are a classic feedback inhibition of NadB, the first enzyme of NAD de novo biosynthesis, by NAD and a metabolic regulation of NadK by reduced cofactors.
Cytochrome
c
Biogenesis
Authors: Stevens Julie M. , Ferguson Stuart J.
Published: May 2014

Escherichia coli
employs several
c
-type cytochromes, which are found in the periplasm or on the periplasmic side of the cytoplasmic membrane; they are used for respiration under different growth conditions. All
E. coli
c
-type cytochromes are multiheme cytochromes;
E. coli
does not have a monoheme cytochrome
c
of the kind found in mitochondria. The attachment of heme to cytochromes
c
occurs in the periplasm, and so the apoprotein must be transported across the cytoplasmic membrane; this step is mediated by the Sec system, which transports unfolded proteins across the membrane. The protein CcmE has been found to bind heme covalently via a single bond and then transfer the heme to apocytochromes. It should be mentioned that far less complex systems for cytochrome
c
biogenesis exist in other organisms and that enterobacteria do not function as a representative model system for the process in general, although plant mitochondria use the Ccm system found in
E. coli
. The variety and distribution of cytochromes and their biogenesis systems reflect their significance and centrality in cellular bioenergetics, though the necessity for and origin of the diverse biogenesis systems are enigmatic.
Biosynthesis and Insertion of the Molybdenum Cofactor
Authors: Magalon Axel , Mendel Ralf R.
Published: May 2014

The transition element molybdenum (Mo) is of primordial importance for biological systems as it is required by enzymes catalyzing key reactions in global carbon, sulfur, and nitrogen metabolism. In order to gain biological activity, Mo has to be complexed by a special cofactor. With the exception of bacterial nitrogenase, all Mo-dependent enzymes contain a unique pyranopterin-based cofactor coordinating a Mo atom at their catalytic site. Various types of reactions are catalyzed by Mo enzymes in prokaryotes, including oxygen atom transfer, sulfur or proton transfer, hydroxylation, or even nonredox ones. Mo enzymes are widespread in prokaryotes, and many of them were likely present in LUCA. To date, more than 50–mostly bacterial–Mo enzymes are described in nature. In a few eubacteria and in many archaea, Mo is replaced by tungsten bound to the same unique pyranopterin. How Moco is synthesized in bacteria is reviewed as well as the way until its insertion into apo-Mo-enzymes.
Biosynthesis of Pantothenic Acid and Coenzyme A
Authors: Leonardi Roberta , Jackowski Suzanne
Published: May 2014

Pantothenate is vitamin B5 and is the key precursor for the biosynthesis of coenzyme A (CoA), a universal and essential cofactor involved in a myriad of metabolic reactions, including the synthesis of phospholipids, the synthesis and degradation of fatty acids, and the operation of the tricarboxylic acid cycle. CoA is also the only source of the phosphopantetheine prosthetic group for enzymes that shuttle intermediates between the active sites of enzymes involved in fatty acid, nonribosomal peptide, and polyketide synthesis. Pantothenate can be synthesized de novo and/or transported into the cell through a pantothenatepermease. Pantothenate uptake is essential for those organisms that lack the genes to synthesize this vitamin. The intracellular levels of CoA are controlled by the balance between synthesis and degradation. In particular, CoA is assembled in five enzymatic steps, starting from the phosphorylation of pantothenate to phosphopantothenatecatalyzed by pantothenate kinase, the product of the coaA gene. In some bacteria, the production of phosphopantothenate by pantothenate kinase is the rate limiting and most regulated step in the biosynthetic pathway. CoA synthesis additionally networks with other vitamin-associated pathways, such as thiamine and folic acid.
Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation
Authors: Cronan John E.
Published: May 2014

Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid was discovered 60 years ago, it was not known how either coenzyme is made until recently. In
Escherichia coli
the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway, in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin, were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise and the BioH esterase for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl-ACP of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyl transferase, followed by sulfur insertion at carbons C6 and C8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and thus there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate protein.
Assembly of Outer Membrane β-Barrel Proteins: the Bam Complex
Authors: Malinverni Juliana C. , Silhavy Thomas J.
Published: May 2014

The major class of integral proteins found in the outer membrane (OM) of
E. coli
and
Salmonella
adopt a β-barrel conformation (OMPs). OMPs are synthesized in the cytoplasm with a typical signal sequence at the amino terminus, which directs them to the secretion machinery (SecYEG) located in the inner membrane for translocation to the periplasm. Chaperones such as SurA, or DegP and Skp, escort these proteins across the aqueous periplasm protecting them from aggregation. The chaperones then deliver OMPs to a highly conserved outer membrane assembly site termed the Bam complex. In
E. coli
, the Bam complex is composed of an essential OMP, BamA, and four associated OM lipoproteins, BamBCDE, one of which, BamD, is also essential. Here we provide an overview of what we know about the process of OMP assembly and outline the various hypotheses that have been proposed to explain how proteins might be integrated into the asymmetric OM lipid bilayer in an environment that lacks obvious energy sources. In addition, we describe the envelope stress responses that ensure the fidelity of OM biogenesis and how factors, such as phage and certain toxins, have coopted this essential machine to gain entry into the cell.
The DNA Exonucleases of
Escherichia coli
Authors: Lovett Susan T.
Published: May 2014

DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry, and biological functions of the 17 exonucleases currently identified in the bacterium
Escherichia coli
. These include the exonucleases associated with DNA polymerases I (
polA
), II (
polB
), and III (
dnaQ/mutD
); Exonucleases I (
xonA/sbcB
), III (
xthA
), IV, VII (
xseAB
), IX (
xni/xgdG
), and X (
exoX
); the RecBCD, RecJ, and RecE exonucleases; SbcCD endo/exonucleases; the DNA exonuclease activities of RNase T (
rnt
) and Endonuclease IV (
nfo
); and TatD. These enzymes are diverse in terms of substrate specificity and biochemical properties and have specialized biological roles. Most of these enzymes fall into structural families with characteristic sequence motifs, and members of many of these families can be found in all domains of life.
DNA Topoisomerases
Authors: Evans-Roberts Katherine , Maxwell Anthony
Published: May 2014

DNA topoisomerases are enzymes that control the topological state of DNA in all cells; they have central roles in DNA replication and transcription. They are classified into two types, I and II, depending on whether they catalyze reactions involving the breakage of one or both strands of DNA. Structural and mechanistic distinctions have led to further classifications: IA, IB, IC, IIA, and IIB. The essence of the topoisomerase reaction is the ability of the enzymes to stabilize transient breaks in DNA, via the formation of tyrosyl-phosphate covalent intermediates. The essential nature of topoisomerases and their ability to stabilize DNA breaks has led to them being key targets for antibacterial and anticancer agents. This chapter reviews the basic features of topoisomerases focussing mainly on the prokaryotic enzymes. We highlight recent structural advances that have given new insight into topoisomerase mechanisms and into the molecular basis of the action of topoisomerase-specific drugs.
Undecaprenyl Phosphate Synthesis
Authors: TouzÉ Thierry , Mengin-Lecreulx Dominique
Published: May 2014

Undecaprenyl phosphate (C55-P) is an essential 55-carbon long-chain isoprene lipidinvolved in the biogenesis of bacterial cell wall carbohydrate polymers: peptidoglycan, O antigen, teichoic acids, and other cell surface polymers. It functions as a lipid carrier that allows the traffic of sugar intermediates across the plasma membrane, towards the periplasm,where the polymerization of the different cellwall components occurs. At the end of these processes, the lipid is released in a pyrophosphate form (C55-PP). C55-P arises from the dephosphorylation of C55-PP, which itself originates from either a recycling event or a
de novo
synthesis. In
Escherichia coli
, the formation of C55-PP is catalyzed by the essential UppS synthase, a soluble cis-prenyltransferase, whichadds eight isoprene units ontofarnesyl pyrophosphate. Severalapo- and halo-UppSthree-dimensional structures have provided a high level of understanding of this enzymatic step. The following dephosphorylationstep is required before the lipid carrier can accept a sugar unit at the cytoplasmic face of the membrane. Four integralmembrane proteins have been shown to catalyzethis reaction in E. coli:BacA and three members of the PAP2 super-family:YbjG, LpxT, and PgpB. None of these enzymes is essential,but the simultaneous inactivation of
bacA
,
ybjG
, and
pgpB
genes gave rise to a lethal phenotype, raising the question of the relevance of such a redundancy of activity. It was alsorecently shown that LpxTcatalyzes the specific transfer of the phosphate group arising from C55-PP to the lipidA moiety of lipopolysaccharides, leading to a lipid-A 1-diphosphate form whichaccounts for one-third of the total lipidA in wild-type
E. coli
cells. The active sites of LpxT, PgpB,andYbjG were shown to face the periplasm, suggesting that PAP2 enzymes arerather involved in C55-PP recycling. These recent discoveries have opened the way to the elucidation of the functional and structural characterization of these different phosphatases.
Structure and Assembly of
Escherichia coli
Capsules
Authors: Whitfield Chris
Published: May 2014

The capsule is a cell surface structure composed of long-chain polysaccharides that envelops many isolates of
Escherichia coli
. It protects the cell against host defenses or physical environmental stresses, such as desiccation. The component capsular polysaccharides (CPSs) are major surface antigens in
E. coli
. They are named K antigens (after the German word

K
apsel

). Due to variations in CPS structures, more than 80 serologically unique K antigens exist in
E. coli
. Despite the hypervariability in CPS structures, only two capsule-assembly strategies exist in
E. coli
. These have led to the assignment of group 1 and group 2 capsules, and many of the key elements of the corresponding assembly pathways have been resolved. Structural features, as well as genetic and regulatory variations, give rise to additional groups 3 and 4. These employ the same biosynthesis processes described in groups 2 and 1, respectively. Each isolate possesses a distinctive set of cytosolic and inner-membrane enzymes, which generate a precise CPS structure, defining a given K serotype. Once synthesized, a multiprotein complex is needed to translocate the nascent CPS across the Gram-negative cell envelope to the outer surface of the outer membrane, where the capsule structure is assembled. While the translocation machineries for group 1 and group 2 CPSs are fundamentally different from one another, they possess no specificity for a given CPS structure. Each is conserved in all isolates producing capsules belonging to a particular group.
Glycogen: Biosynthesis and Regulation
Authors: Preiss Jack
Published: May 2014

The accumulation of glycogen occurs in
Escherichia coli
and
Salmonella enterica
serovar Typhimurium as well as in many other bacteria. Glycogen will be formed when there is an excess of carbon under conditions in which growth is limited due to the lack of a growth nutrient, e.g., a nitrogen source. The structural genes of the glycogen biosynthetic enzymes of
E. coli
and
S. serovar
Typhimurium have been cloned previously, and that has provided insights in the genetic regulation of glycogen synthesis. An important aspect of the regulation of glycogen synthesis is the allosteric regulation of the ADP-Glc PPase. The current information, views, and concepts regarding the regulation of enzyme activity and the expression of the glycogen biosynthetic enzymes are presented in this review. The recent information on the amino acid residues critical for the activity of both glycogen synthase and branching enzyme (BE) is also presented. The residue involved in catalysis in the
E. coli
ADP-Glc PPase was determined by comparing a predicted structure of the enzyme with the known three-dimensional structures of sugar-nucleotide PPase domains. The molecular cloning of the
E. coli
glg
K-12 structural genes greatly facilitated the subsequent study of the genetic regulation of bacterial glycogen biosynthesis. Results from studies of glycogen excess
E. coli
B mutants SG3 and AC70R1, which exhibit enhanced levels of the enzymes in the glycogen synthesis pathway (i.e., they are derepressed mutants), suggested that glycogen synthesis is under negative genetic regulation.
Cell-to-Cell Signaling in
Escherichia coli
and
Salmonella
Authors: Kendall Melissa M. , Sperandio Vanessa
Published: May 2014

Bacteria must be able to respond rapidly to changes in the environment in order to survive. One means of coordinating gene expression relies on tightly regulated and complex signaling systems. One of the first signaling systems that was described in detail is quorum sensing (QS). During QS, a bacterial cell produces and secretes a signaling molecule called an autoinducer (AI). As the density of the bacterial population increases, so does the concentration of secreted AI molecules, thereby allowing a bacterial species to coordinate gene expression based on population density. Subsequent studies have demonstrated that bacteria are also able to detect signal molecules produced by other species of bacteria as well as hormones produced by their mammalian hosts. These types of signaling interactions have been termed cell-to-cell signaling because the interaction does not rely on a threshold concentration of bacterial cells. This review discusses the three main types of cell-to-cell signaling mechanisms used by
E. coli
and
Salmonella
, including the LuxR process, in which
E. coli
and
Salmonella
detect signals produced by other species of bacteria; the LuxS/AI-2 system, in which
E. coli
and
Salmonella
participate in intra- and interspecies signaling; and the AI-3/ epinephrine/norepinephrine system, in which
E. coli
and
Salmonella
recognize self-produced AI, signal produced by other microbes, and/or the human stress hormones epinephrine or norepinephrine.
Stationary-Phase Gene Regulation in
Escherichia coli
§
Authors: Hengge Regine
Published: May 2014

In their stressful natural environments, bacteria often are in stationary phase and use their limited resources for maintenance and stress survival. Underlying this activity is the general stress response, which in
Escherichia coli
depends on the σ
S
(RpoS) subunit of RNA polymerase. σ
S
is closely related to the vegetative sigma factor σ
70
(RpoD), and these two sigmas recognize similar but not identical promoter sequences. During the postexponential phase and entry into stationary phase, σ
S
is induced by a fine-tuned combination of transcriptional, translational, and proteolytic control. In addition, regulatory "short-cuts" to high cellular σ
S
levels, which mainly rely on the rapid inhibition of σ
S
proteolysis, are triggered by sudden starvation for various nutrients and other stressful shift conditons. σ
S
directly or indirectly activates more than 500 genes. Additional signal input is integrated by σ
S
cooperating with various transcription factors in complex cascades and feedforward loops. Target gene products have stress-protective functions, redirect metabolism, affect cell envelope and cell shape, are involved in biofilm formation or pathogenesis, or can increased stationary phase and stress-induced mutagenesis. This review summarizes these diverse functions and the amazingly complex regulation of σ
S
. At the molecular level, these processes are integrated with the partitioning of global transcription space by sigma factor competition for RNA polymerase core enzyme and signaling by nucleotide second messengers that include cAMP, (p)ppGpp, and c-di-GMP. Physiologically, σ
S
is the key player in choosing between a lifestyle associated with postexponential growth based on nutrient scavenging and motility and a lifestyle focused on maintenance, strong stress resistance, and increased adhesiveness. Finally, research with other proteobacteria is beginning to reveal how evolution has further adapted function and regulation of σ
S
to specific environmental niches.
The Origin of Mutants under Selection: Interactions of Mutation, Growth, and Selection
Authors: Andersson Dan I. , Hughes Diarmaid , Roth John R.
Published: May 2014

The classical experiments of Luria and Delbrück showed convincingly that mutations exist before selection and do not contribute to the creation of mutations when selection is lethal. In contrast, when nonlethal selections are used,measuring mutation rates and separating the effects of mutation and selection are difficult and require methods to fully exclude growth after selection has been applied. Although many claims of stress-induced mutagenesis have been made, it is difficult to exclude the influence of growth under nonlethal selection conditions in accounting for the observed increases in mutant frequency. Instead, for many of the studied experimental systems the increase in mutant frequency can be explainedbetter by the ability of selection to detect small differences in growth rate caused by common small effect mutations. A verycommon mutant class,found in response to many different types of selective regimensin which increased gene dosage can resolve the problem, is gene amplification. In the well-studied
lac
system of Cairns and Foster, the apparent increase in Lac+revertants can be explained by high-level amplification of the
lac
operon and the increased probability for a reversion mutation to occur in any one of the amplified copies. The associated increase in general mutation rate observed in revertant cells in that system is an artifact caused by the coincidental co-amplification of the nearby
dinB
gene (encoding the error-prone DNA polymerase IV) on the particular plasmid used for these experiments. Apart from the
lac
system, similar gene amplification processes have been described for adaptation to toxic drugs, growth in host cells, and various nutrient limitations.
Evolution and Ecology of
Salmonella
Authors: Winfield Mollie D. , Groisman Eduardo A.
Published: May 2014

Over the past 120 to 160 million years, the genus
Salmonella
has evolved into a complex group of more than 2,300 genetically and phenotypically diverse serovars. Members of this genus are able to infect a wide diversity of vertebrate and invertebrate hosts; disease manifestations in humans range from gastroenteritis to typhoid fever. The evolution of the genus
Salmonella
and the divergence and radiation of particular lineages within this group have resulted from selection acting on new genetic variation generated by events such as the gain, loss, and/or rearrangement of genetic material. These types of genetic events have contributed to the speciation of
Salmonella
from its ancestral association with cold-blood animals to a pathogen of warm-blooded hosts. Moreover, adaptive radiation due to changes in gene content within
S. enterica
subspecies I has impacted host specificity and aided in the selection of host-restricted, host-adapted, and non-host-adapted serovars. In addition to the genetic diversity important for the wide phenotypic heterogeneity within the genus, a subset of core
Salmonella
-specific genes present in all
Salmonella
species and serovars has been identified that may contribute to the conserved aspects of the lifestyle of this microorganism, including the ability to survive in nutrient-poor nonhost environments such as soil and water. Whole-genome comparisons of isolates differing in host range and virulence will continue to elucidate the genetic mechanisms that have contributed to the evolution and diverse ecology of the genus
Salmonella
.
Stress-Induced Mutagenesis
Authors: Williams Ashley B. , Foster Patricia L.
Published: May 2014

Early research on the origins and mechanisms of mutation led to the establishment of the dogma that, in the absence of external forces, spontaneous mutation rates are constant. However, recent results from a variety of experimental systems suggest that mutation rates can increase in response to selective pressures. This chapter summarizes data demonstrating that,under stressful conditions,
Escherichia coli
and
Salmonella
can increase the likelihood of beneficial mutations by modulating their potential for genetic change.Several experimental systems used to study stress-induced mutagenesis are discussed, with special emphasison the Foster-Cairns system for "adaptive mutation" in
E. coli
and
Salmonella
. Examples from other model systems are given to illustrate that stress-induced mutagenesis is a natural and general phenomenon that is not confined to enteric bacteria. Finally, some of the controversy in the field of stress-induced mutagenesis is summarized and discussed, and a perspective on the current state of the field is provided.
Direct DNA Lesion Reversal and Excision Repair in
Escherichia coli
Authors: Couvé Sophie , Ishchenko Alexander A. , Fedorova Olga S. , Ramanculov Erlan M. , Laval Jacques , Saparbaev Murat
Published: May 2014

Cellular DNA is constantly challenged by various endogenous and exogenous genotoxic factors that inevitably lead to DNA damage: structural and chemical modifications of primary DNA sequence. These DNA lesions are either cytotoxic, because they block DNA replication and transcription, or mutagenic due to the miscoding nature of the DNA modifications, or both, and are believed to contribute to cell lethality and mutagenesis. Studies on DNA repair in
Escherichia coli
spearheaded formulation of principal strategies to counteract DNA damage and mutagenesis, such as: direct lesion reversal, DNA excision repair, mismatch and recombinational repair and genotoxic stress signalling pathways. These DNA repair pathways are universal among cellular organisms. Mechanistic principles used for each repair strategies are fundamentally different. Direct lesion reversal removes DNA damage without need for excision and de novo DNA synthesis, whereas DNA excision repair that includes pathways such as base excision, nucleotide excision, alternative excision and mismatch repair, proceeds through phosphodiester bond breakage, de novo DNA synthesis and ligation. Cell signalling systems, such as adaptive and oxidative stress responses, although not DNA repair pathways
per se,
are nevertheless essential to counteract DNA damage and mutagenesis. The present review focuses on the nature of DNA damage, direct lesion reversal, DNA excision repair pathways and adaptive and oxidative stress responses in
E. coli
.
DNA Mismatch Repair
Authors: Marinus M. G.
Published: May 2014

DNA mismatch repair (MMR) corrects replication errors in newly synthesized DNA. It also has an antirecombination action on heteroduplexes that contain similar but not identical sequences. This review focuses on the genetics and development of MMR and not on the latest biochemical mechanisms. The main focus is on MMR in
Escherichia coli
, but examples from
Streptococcuspneumoniae
and
Bacillussubtilis
have also been included. In most organisms, only MutS (detects mismatches) and MutL (an endonuclease) and a single exonucleaseare present. How this system discriminates between newlysynthesized and parental DNA strands is not clear. In
E. coli
and its relatives, however, Dam methylation is an integral part of MMR and is the basis for strand discrimination. A dedicated site-specific endonuclease, MutH, is present, andMutL has no endonuclease activity; four exonucleases can participate in MMR. Although it might seem that the accumulated wealth of genetic and biochemical data has given us a detailed picture of the mechanism of MMR in
E. coli
, the existence of three competing models to explain the initiation phase indicates the complexity of the system. The mechanism of the antirecombination action of MMR is largely unknown, but only MutS and MutL appear to be necessary. A primary site of action appears to be on RecA, although subsequent steps of the recombination process can also be inhibited. In this review, the genetics of Very Short Patch (VSP) repair of T/G mismatches arising from deamination of 5-methylcytosineresidues is also discussed.
Homologous Recombination—Enzymes and Pathways
Authors: Michel Bénédicte , Leach David
Published: May 2014

Homologous recombination is an ubiquitous process that shapes genomes and repairs DNA damage. The reaction is classically divided into three phases: presynaptic, synaptic, and postsynaptic. In
Escherichia coli
, the presynaptic phase involves either RecBCD or RecFOR proteins, which act on DNA double-stranded ends and DNA single-stranded gaps, respectively; the central synaptic steps are catalyzed by the ubiquitous DNA-binding protein RecA; and the postsynaptic phase involves either RuvABC or RecG proteins, which catalyze branch-migration and, in the case of RuvABC, the cleavage of Holliday junctions. Here, we review the biochemical properties of these molecular machines and analyze how, in light of these properties, the phenotypes of null mutants allow us to define their biological function(s). The consequences of point mutations on the biochemical properties of recombination enzymes and on cell phenotypes help refine the molecular mechanisms of action and the biological roles of recombination proteins. Given the high level of conservation of key proteins like RecA and the conservation of the principles of action of all recombination proteins, the deep knowledge acquired during decades of studies of homologous recombination in bacteria is the foundation of our present understanding of the processes that govern genome stability and evolution in all living organisms.
Adhesins of Enterotoxigenic
Escherichia coli
Strains That Infect Animals
Authors: Schifferli Dieter M.
Published: May 2014

The first described adhesive antigen of
Escherichia coli
strains isolated from animals was the K88 antigen, expressed by strains from diarrheic pigs. The K88 antigen was visible by electron microscopy as a surface-exposed filament that was thin and flexible and had hemagglutinating properties. Many different fimbriae have been identified in animal enterotoxigenic
E. coli
(ETEC) and have been discussed in this article. The role of these fimbriae in the pathogenesis of ETEC has been best studied with K88, K99, 987P, and F41. Each fimbrial type carries at least one adhesive moiety that is specific for a certain host receptor, determining host species, age, and tissue specificities. ETEC are the most frequently diagnosed pathogens among neonatal and post-weaning piglets that die of diarrhea. Immune electron microscopy of animal ETEC fimbriae usually shows that the minor subunits are located at the fimbrial tips and at discrete sites along the fimbrial threads. Since fimbriae most frequently act like lectins by binding to the carbohydrate moieties of glycoproteins or glycolipids, fimbrial receptors have frequently been studied with red blood cells of various animal species. Identification and characterization of the binding moieties of ETEC fimbrial adhesins should be useful for the design of new prophylactic or therapeutic strategies. Some studies describing potential receptor or adhesin analogues that interfere with fimbria-mediated colonization have been described in the article.
Adhesins of Diffusely Adherent and Enteroaggregative
Escherichia coli
Authors: Le Bouguénec Chantal , Nataro James P.
Published: May 2014

Epidemiological studies have implicated enteroaggregative
Escherichia coli
(EAEC) strains in acute and persistent diarrhea in children, in food-borne diarrhea outbreaks, and in traveler's diarrhea, and this group is recognized as an emerging pathotype of enteric disease. Diffusely adherent
E. coli
(DAEC) have been implicated as a cause of diarrhea, especially in children more than 2 years old, in both developing and developed countries. Although EAEC and DAEC strains appear to have different molecular equipment for attachment to host cell surfaces, identification and characterization of the gene clusters encoding adherence evidenced close relatedness between those determinants most frequently detected in isolates belonging to these two pathotypes of diarrheagenic
E. coli
. DAEC strains are a heterogeneous group of
E. coli
isolates, many of which express the related so-called Dr adhesins. The single designation is based on the identification of one similar cellular receptor for all these proteins. Although structurally different, they all recognize the Dr human blood group antigen on the decay-accelerating factor (DAF or CD55). These adhesins are encoded by a family of closely related operons, the first characterized and sequenced being the
afa
operon. Consequently, it has been suggested that this group of DAEC strains producing such adhesins be named the Afa/Dr DAEC family. Three distinct but closely related gene clusters coding for phenotypically and morphologically distinct aggregative adherence fimbriae (AAF) have been characterized. In each case, electron microscopy revealed that bacterial surfaces were surrounded by long, relatively flexible fimbrial structures.
Adhesins of Enteropathogenic
Escherichia coli
Authors: Torres Alfredo G.
Published: May 2014

Enteropathogenic
Escherichia coli
(EPEC) strains induce morphological changes in infected epithelial cells. The resulting attaching and effacing (A/E) lesion is characterized by intimate bacterial adherence to epithelial cells, with microvillus destruction, cytoskeletal rearrangement, and aggregation of host cytoskeletal proteins. This review presents an overview of the adhesion mechanisms used for the colonization of the human gastrointestinal tract by EPEC. The mechanisms underlying EPEC adhesion, prior to and during the formation of the A/E lesion, and the host cytosolic responses to bacterial infection leading to diarrheal disease are discussed.
Type 1 Fimbriae, Curli, and Antigen 43: Adhesion, Colonization, and Biofilm Formation
Authors: Klemm Per , Schembri Mark
Published: May 2014

This review is primarily concerned with the first step in biofilm formation, namely, bacterial attachment to surfaces. It describes three examples of bacterial adhesins, each of which belongs to a different subgroup and follows different strategies for surface presentation and adhesin exposure. These are type 1 fimbriae, very long stiff rodlike organelles; curli, amorphous fluffy coat structures; and finally antigen 43, short outer membrane structures with a simple assembly system. Their role as adhesins, their structure and biosynthesis, and their role in biofilm formation are described in detail in the review. The FimH protein presented by type 1 fimbriae seems to be a highly versatile adhesin fulfilling a diverse spectrum of roles ranging from pellicle and biofilm formation to being a bona fide virulence factor in uropathogenic
E. coli
(UPEC) strains, where it plays important roles in the manifestation of cystitis. Curli formation promotes two fundamental processes associated with biofilm formation: initial adhesion and cell-to-cell aggregation. A role for curli in the colonization of inert surfaces has been demonstrated. Severe sepsis and septic shock are frequently caused by gram-negative bacteria, and several factors suggest a significant role for curli during
E. coli
sepsis. The protection provided by Ag43-mediated aggregation was underlined in a series of experiments addressing the role of Ag43 in protection against oxidizing agents. Type 1 fimbriae, curli, and Ag43 are structurally different bacterial surface structures and follow completely different strategies for surface display and assembly.