bluuebunny/crossref_metadata_2025 huggingface dataset:
Biosynthesis of Proline
Authors: Csonka Laszlo N. , Leisinger Thomas
Published: May 2014

Proline was among the last biosynthetic precursors to have its biosynthetic pathway unraveled. This review recapitulates the findings on the biosynthesis and transport of proline. Glutamyl kinase (GK) catalyzes the ATP-dependent phosphorylation of L-glutamic acid. Purification of γ-GK from
Escherichia coli
was facilitated by the expression of the
proB
and
proA
genes from a high-copy-number plasmid and the development of a specific coupled assay based on the NADPH-dependent reduction of GP by γ-glutamyl phosphate reductase (GPR). GPR catalyzes the NADPH-dependent reduction of GP to GSA. Site directed mutagenesis was used to identify residues that constitute the active site of
E. coli
GK. This analysis indicated that there is an overlap between the binding sites for glutamate and the allosteric inhibitor proline, suggesting that proline competes with the binding of glutamate. The review also summarizes the genes involved in the metabolism of proline in
E. coli
and
Salmonella
. Among the completed genomic sequences of
Enterobacteriaceae
, genes specifying all three proline biosynthetic enzymes can be discerned in
E. coli
,
Shigella
,
Salmonella enterica
,
Serratia marcescens
,
Erwinia carotovora
,
Yersinia
,
Photorhabdus luminescens
, and
Sodalis glossinidius
strain morsitans. The intracellular proline concentration increases with increasing external osmolality in proline-overproducing mutants. This apparent osmotic regulation of proline accumulation in the overproducing strains may be the result of increased retention or recapture of proline, achieved by osmotic stimulation of the ProP or ProU proline transport systems. A number of proline analogs can be incorporated into proteins in vivo or in vitro.
Biosynthesis and Regulation of the Branched-Chain Amino Acids†
Authors: Salmon Kirsty A. , Yang Chin-Rang , Hatfield G. Wesley
Published: May 2014

This review focuses on more recent studies concerning the systems biology of branched-chain amino acid biosynthesis, that is, the pathway-specific and global metabolic and genetic regulatory networks that enable the cell to adjust branched-chain amino acid synthesis rates to changing nutritional and environmental conditions. It begins with an overview of the enzymatic steps and metabolic regulatory mechanisms of the pathways and descriptions of the genetic regulatory mechanisms of the individual operons of the isoleucine-leucine-valine (
ilv
) regulon. This is followed by more-detailed discussions of recent evidence that global control mechanisms that coordinate the expression of the operons of this regulon with one another and the growth conditions of the cell are mediated by changes in DNA supercoiling that occur in response to changes in cellular energy charge levels that, in turn, are modulated by nutrient and environmental signals. Since the parallel pathways for isoleucine and valine biosynthesis are catalyzed by a single set of enzymes, and because the AHAS-catalyzed reaction is the first step specific for valine biosynthesis but the second step of isoleucine biosynthesis, valine inhibition of a single enzyme for this enzymatic step might compromise the cell for isoleucine or result in the accumulation of toxic intermediates. The operon-specific regulatory mechanisms of the operons of the
ilv
regulon are discussed in the review followed by a consideration and brief review of global regulatory proteins such as integration host factor (IHF), Lrp, and CAP (CRP) that affect the expression of these operons.
From Iron and Cysteine to Iron-Sulfur Clusters: the Biogenesis Protein Machineries
Authors: Fontecave Marc , Py Béatrice , Ollagnier de Choudens Sandrine , Barras FréDéric
Published: May 2014

This review describes the two main systems, namely the
Isc
(iron-sulfur cluster) and
Suf
(sulfur assimilation) systems, utilized by
Escherichia coli
and
Salmonella
for the biosynthesis of iron-sulfur (Fe-S) clusters, as well as other proteins presumably participating in this process. In the case of Fe-S cluster biosynthesis, it is assumed that the sulfur atoms from the cysteine desulfurase end up at cysteine residues of the scaffold protein, presumably waiting for iron atoms for cluster assembly. The review discusses the various potential iron donor proteins. For in vitro experiments, in general, ferrous salts are used during the assembly of Fe-S clusters, even though this approach is unlikely to reflect the physiological conditions. The fact that sulfur atoms can be directly transferred from cysteine desulfurases to scaffold proteins supports a mechanism in which the latter bind sulfur atoms first and iron atoms afterwards. In
E. coli
,
fdx
gene inactivation results in a reduced growth rate and reduced Fe-S enzyme activities. Interestingly, the SufE structure resembles that of IscU, strengthening the notion that the two proteins share the property of acting as acceptors of sulfur atoms provided by cysteine desulfurases. Several other factors have been suggested to participate in cluster assembly and repair in
E. coli
and
Salmonella
. Most of them were identified by their abilities to act as extragenic and/or multicopy suppressors of mutations in Fe-S cluster metabolism, while others possess biochemical properties that are consistent with a role in Fe-S cluster biogenesis.
Biosynthesis of Riboflavin
Authors: Fischer Markus , Bacher Adelbert
Published: May 2014

The biosynthesis of riboflavin requires 1 equivalent of GTP and 2 equivalents of ribulose phosphate. The first committed reactions of the convergent pathway are catalyzed by GTP hydrolase II and 3,4-dihydroxy-2-butanone 4-phosphate synthase. The initial reaction steps afford 5-amino-6-ribitylaminopyrimidine 5′-phosphate, which needs to be dephosphorylated by a hitherto elusive hydrolase. The dephosphorylated pyrimidine is condensed with the carbohydrate precursor, 3,4-dihydroxy-2-butanone 4-phosphate. The resulting 6,7-dimethyl-8-ribityllumazine affords riboflavin by a mechanistically unique dismutation, i.e., by formation of a pentacyclic dimer that is subsequently fragmented.
Folate Biosynthesis, Reduction, and Polyglutamylation and the Interconversion of Folate Derivatives
Authors: Green Jacalyn M. , Matthews Rowena G.
Published: May 2014

Many microorganisms and plants possess the ability to synthesize folic acid derivatives de novo, initially forming dihydrofolate. All the folic acid derivatives that serve as recipients and donors of one-carbon units are derivatives of tetrahydrofolate, which is formed from dihydrofolate by an NADPH-dependent reduction catalyzed by dihydrofolate reductase (FolA). This review discusses the biosynthesis of dihydrofolate monoglutamate, its reduction to tetrahydrofolate monoglutamate, and the addition of glutamyl residues to form folylpolyglutamates.
Escherichia coli
and
Salmonella
, like many microorganisms that can synthesize folate de novo, appear to lack the ability to transport folate into the cell and are thus highly susceptible to inhibitors of folate biosynthesis. The review includes a brief discussion of the inhibition of folate biosynthesis by sulfa drugs. The folate biosynthetic pathway can be divided into two sections. First, the aromatic precursor chorismate is converted to paminobenzoic acid (PABA) by the action of three proteins. Second, the pteridine portion of folate is made from GTP and coupled to PABA to generate dihydropteroate, and the bifunctional protein specified by
folC
, dihydrofolate synthetase, or folylpolyglutamate synthetase, adds the initial glutamate molecule to form dihydrofolate (H
2
PteGlu
1
, or dihydropteroylmonoglutamate). Bacteriophage T4 infection of
E. coli
has been shown to cause alterations in the metabolism of folate derivatives. Infection is associated with an increase in the chain lengths in folylpolyglutamates and particularly the accumulation of hexaglutamate derivatives.
Biosynthesis and Use of Cobalamin (B
12
)
Authors: Escalante-Semerena Jorge C. , Warren Martin J.
Published: May 2014

This review summarizes research performed over the last 23 years on the genetics, enzyme structures and functions, and regulation of the expression of the genes encoding functions involved in adenosylcobalamin (AdoCbl, or coenzyme B
12
) biosynthesis. It also discusses the role of coenzyme B
12
in the physiology of
Salmonella enterica
serovar Typhimurium LT2 and
Escherichia coli
. John Roth's seminal contributions to the field of coenzyme B
12
biosynthesis research brought the power of classical and molecular genetic, biochemical, and structural approaches to bear on the extremely challenging problem of dissecting the steps of what has turned out to be one of the most complex biosynthetic pathways known. In
E. coli
and serovar Typhimurium, uro’gen III represents the first branch point in the pathway, where the routes for cobalamin and siroheme synthesis diverge from that for heme synthesis. The cobalamin biosynthetic pathway in
P. denitrificans
was the first to be elucidated, but it was soon realized that there are at least two routes for cobalamin biosynthesis, representing aerobic and anaerobic variations. The expression of the AdoCbl biosynthetic operon is complex and is modulated at different levels. At the transcriptional level, a sensor response regulator protein activates the transcription of the operon in response to 1,2-Pdl in the environment. Serovar Typhimurium and
E. coli
use ethanolamine as a source of carbon, nitrogen, and energy. In addition, and unlike
E. coli
, serovar Typhimurium can also grow on 1,2-Pdl as the sole source of carbon and energy.
Biosynthesis of Membrane Lipids
Authors: Cronan, John E. , Rock Charles O.
Published: May 2014

The pathways in
Escherichia coli
and (largely by analogy)
S. enterica
remain the paradigm of bacterial lipid synthetic pathways, although recently considerable diversity among bacteria in the specific areas of lipid synthesis has been demonstrated. The structural biology of the fatty acid synthetic proteins is essentially complete. However, the membrane-bound enzymes of phospholipid synthesis remain recalcitrant to structural analyses. Recent advances in genetic technology have allowed the essentialgenes of lipid synthesis to be tested with rigor, and as expected most genes are essential under standard growth conditions. Conditionally lethal mutants are available in numerous genes, which facilitates physiological analyses. The array of genetic constructs facilitates analysis of the functions of genes from other organisms. Advances in mass spectroscopy have allowed very accurate and detailed analyses of lipid compositions as well as detection of the interactions of lipid biosynthetic proteins with one another and with proteins outside the lipid pathway. The combination of these advances has resulted in use of
E. coli
and
S. enterica
for discovery of new antimicrobials targeted to lipid synthesis and in deciphering the molecular actions of known antimicrobials. Finally,roles for bacterial fatty acids other than as membrane lipid structural components have been uncovered. For example, fatty acid synthesis plays major roles in the synthesis of the essential enzyme cofactors, biotin and lipoic acid. Although other roles for bacterial fatty acids, such as synthesis of acyl-homoserine quorum-sensing molecules, are not native to
E. coli
introduction of the relevant gene(s) synthesis of these foreign molecules readily proceeds and the sophisticated tools available can used to decipher the mechanisms of synthesis of these molecules.
Type V Secretion: the Autotransporter and Two-Partner Secretion Pathways
Authors: Bernstein Harris D.
Published: May 2014

The autotransporter and two-partner secretion (TPS) pathways are used by
E. coli
and many other Gram-negative bacteria to delivervirulence factors into the extracellular milieu.Autotransporters arecomprised of an N-terminal extracellular ("passenger") domain and a C-terminal β barrel domain ("β domain") that anchors the protein to the outer membrane and facilitates passenger domain secretion. In the TPS pathway, a secreted polypeptide ("exoprotein") is coordinately expressed with an outer membrane protein that serves as a dedicated transporter. Bothpathways are often grouped together under the heading "type V secretion" because they have many features in common and are used for the secretion of structurally related polypeptides, but it is likely that theyhave distinct evolutionary origins. Although it was proposed many years ago that autotransporterpassenger domains are transported across the outer membrane through a channel formed by the covalently linked β domain, there is increasing evidence that additional factors are involved in the translocation reaction. Furthermore, details of the mechanism of protein secretion through the TPS pathway are only beginning to emerge. In this chapter I discussour current understanding ofboth early and late steps in the biogenesis of polypeptides secreted through type V pathways and current modelsofthe mechanism of secretion.
Biogenesis and Membrane Targeting of Lipoproteins
Authors: Narita Shin-Ichiro , Tokuda Hajime
Published: May 2014

Bacterial lipoproteins represent a unique class of membrane proteins, which are anchored to membranes through triacyl chains attached to the amino-terminal cysteine. They are involved in various functions localized in cell envelope.
Escherichia coli
possesses more than 90 species of lipoproteins, most of which are localized in the outer membrane, with others being in the inner membrane. All lipoproteins are synthesized in the cytoplasm with an N-terminal signal peptide, translocated across the inner membrane by the Sec translocon to the periplasmic surface of the inner membrane, and converted to mature lipoproteins through sequential reactions catalyzed by three lipoprotein-processing enzymes: Lgt, LspA, and Lnt. The sorting of lipoproteins to the outer membrane requires a system comprising five Lol proteins. An ATP-binding cassette transporter, LolCDE, initiates the sorting by mediating the detachment of lipoproteins from the inner membrane. Formation of the LolA-lipoprotein complex is coupled to this LolCDE-dependent release reaction. LolA accommodates the amino-terminal acyl chain of lipoproteins in its hydrophobic cavity, thereby generating a hydrophilic complex that can traverse the periplasmic space by diffusion. Lipoproteins are then transferred to LolB on the outer membrane and anchored to the inner leaflet of the outer membrane by the action of LolB. In contrast, since LolCDE does not recognize lipoproteins possessing Asp at position +2, these lipoproteins remain anchored to the inner membrane. Genes for Lol proteins are widely conserved among gram-negative bacteria, and Lol-mediated outer membrane targeting of lipoproteins is considered to be the general lipoprotein localization mechanism.
Initiation of DNA Replication
Authors: Leonard Alan C. , Grimwade Julia E.
Published: May 2014

In recent years it has become clear that complex regulatory circuits control the initiation step of DNA replication by directing the assembly of a multicomponent molecular machine (the orisome) that separates DNA strands and loads replicative helicase at
oriC
, the unique chromosomal origin of replication. This chapter discusses recent efforts to understand the regulated protein-DNA interactions that are responsible for properly timed initiation of chromosome replication. It reviews information about newly identified nucleotide sequence features within
Escherichia coli oriC
and the new structural and biochemical attributes of the bacterial initiator protein DnaA. It also discusses the coordinated mechanisms that prevent improperly timed DNA replication. Identification of the genes that encoded the initiators came from studies on temperature-sensitive, conditional-lethal mutants of
E. coli
, in which two DNA replication-defective phenotypes, "immediate stop" mutants and "delayed stop" mutants, were identified. The kinetics of the delayed stop mutants suggested that the defective gene products were required specifically for the initiation step of DNA synthesis, and subsequently, two genes,
dnaA
and
dnaC
, were identified. The DnaA protein is the bacterial initiator, and in
E. coli
, the DnaC protein is required to load replicative helicase. Regulation of DnaA accessibility to
oriC
, the ordered assembly and disassembly of a multi-DnaA complex at
oriC
, and the means by which DnaA unwinds
oriC
remain important questions to be answered and the chapter discusses the current state of knowledge on these topics.
Promoter Escape by
Escherichia coli
RNA Polymerase
Authors: Hsu Lilian M.
Published: May 2014

Promoter escape is the process that an initiated RNA polymerase (RNAP) molecule undergoes to achieve the initiation-elongation transition. Having made this transition, an RNAP molecule would be relinquished from its promoter hold to perform productive (full-length) transcription. Prior to the transition, this process is accompanied by abortive RNA formation—the amount and pattern of which is controlled by the promoter sequence information. Qualitative and quantitative analysis of abortive/productive transcription from several
Escherichia coli
promoters and their sequence variants led to the understanding that a strong (RNAP-binding) promoter is more likely to be rate limited (during transcription initiation) at the escape step and produce abortive transcripts. Of the two subelements in a promoter, the PRR (the core Promoter Recognition Region) was found to set the initiation frequency and the rate-limiting step, while the ITS (the Initial Transcribed Sequence region) modulated the ratio of abortive versus productive transcription. The highly abortive behavior of
E. coli
RNAP could be ameliorated by the presence of Gre (transcript cleavage stimulatory) factor(s), linking the first step in abortive RNA formation by the initial transcribing complexes (ITC) to RNAP backtracking. The discovery that translocation during the initiation stage occurs via DNA scrunching provided the source of energy that converts each ITC into a highly unstable "stressed intermediate." Mapping all of the biochemical information onto an X-ray crystallographic structural model of an open complex gave rise to a plausible mechanism of transcription initiation. The chapter concludes with contemplations of the kinetics and thermodynamics of abortive initiation-promoter escape.
Modified Nucleosides of
Escherichia coli
Ribosomal RNA
Authors: Ofengand James , Del Campo Mark
Published: May 2014

The modified nucleosides of RNA are chemically altered versions of the standard A, G, U, and C nucleosides. This review reviews the nature and location of the modified nucleosides of
Escherichia coli
rRNA, the enzymes that form them, and their known and/or putative functional role. There are seven Ψ (pseudouridines) synthases to make the 11 pseudouridines in rRNA. There is disparity in numbers because RluC and RluD each make 3 pseudouridines. Crystal structures have shown that the Ψ synthase domain is a conserved fold found only in all five families of Ψ synthases. The conversion of uridine to Ψ has no precedent in known metabolic reactions. Other enzymes are known to cleave the glycosyl bond but none carry out rotation of the base and rejoining to the ribose while still enzyme bound. Ten methyltransferases (MTs) are needed to make all the methylated nucleosides in 16S RNA, and 14 are needed for 23S RNA. Biochemical studies indicate that the modes of substrate recognition are idiosyncratic for each Ψ synthase since no common mode of recognition has been detected in studies of the seven synthases. Eight of the 24 expected MTs have been identified, and six crystal structures have been determined. Seven of the MTs and five of the structures are class I MTs with the appropriate protein fold plus unique appendages for the Ψ synthases. The remaining MT, RlmB, has the class IV trefoil knot fold.
Transfer RNA Modification
Authors: Björk Glenn R. , Hagervall Tord G.
Published: May 2014

Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from
Escherichia coli/Salmonella enterica
contains 31 different modified nucleosides, which are all, except for one (Queuosine[Q]), synthesized on an oligonucleotide precursor, which through specific enzymes later matures into tRNA. The corresponding structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The syntheses of some of them (e.g.,several methylated derivatives) are catalyzed by one enzyme, which is position and base specific, but synthesis of some have a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N
6
-threonyladenosine [t6A],and Q). Several of the modified nucleosides are essential for viability (e.g.,lysidin, t
6
A, 1-methylguanosine), whereas deficiency in others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those, which are present in the body of the tRNA, have a primarily stabilizing effect on the tRNA. Thus, the ubiquitouspresence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
Messenger RNA Decay
Authors: Kushner Sidney R.
Published: May 2014

This chapter discusses several topics relating to the mechanisms of mRNA decay. These topics include the following: important physical properties of mRNA molecules that can alter their stability; methods for determining mRNA half-lives; the genetics and biochemistry of proteins and enzymes involved in mRNA decay; posttranscriptional modification of mRNAs; the cellular location of the mRNA decay apparatus; regulation of mRNA decay; the relationships among mRNA decay, tRNA maturation, and ribosomal RNA processing; and biochemical models for mRNA decay.
Escherichia coli
has multiple pathways for ensuring the effective decay of mRNAs and mRNA decay is closely linked to the cell's overall RNA metabolism. Finally, the chapter highlights important unanswered questions regarding both the mechanism and importance of mRNA decay.
Peptidoglycan Recycling
Authors: Uehara Tsuyoshi , Park James T.
Published: May 2014

Peptidoglycan (PG) recycling allows
Escherichia coli
to reuse the massive amounts of sacculus components that are released during elongation. Goodell and Schwarz, in 1985, labeled
E. coli
cells with 3H-diaminopimelic acid (DAP) and chased. During the chase, the DAP pool dropped dramatically, whereas the precursor pool dropped only slightly. This could only occur if DAP from the sacculi was being used to produce more precursor. They calculated that the cells were recycling about 45% of their wall DAP (actually, 60% of the side walls, since the poles are stable). Thus, recycling was discovered. Goodell went on to show that the tripeptide,
L
-Ala-
D
-Glu-DAP, could be taken up via opp and used directly to form PG. It was subsequently shown that uptake was predominantly via a permease, AmpG, that was specific for GlcNAc-anhMurNAc with attached peptides. Eleven genes have been identified which appear to have as their sole function the recovery of degradation products from PG. PG represents only 2.5% of the cell mass, so the reason for this investment in recycling is obscure. Recycling enzymes exist that are specific for every bond in the principal product taken up by AmpG, namely, GlcNAc-anh-MurNAc-tetrapeptide. However, most of the tripeptide,
L
-Ala-
D
-Glu-DAP, is used by murein peptide ligase (Mpl) to form the precursor intermediate UDP-MurNAc-tripeptide. anh-MurNAc can be converted to GlcNAc by a two-step process and thus is available for use. Surprisingly, in the absence of AmpD, an enzyme that cleaves the anh-MurNAc-
L
-Ala bond, anh-MurNAc-tripeptide accumulates, resulting in induction of beta-lactamase. However, this has nothing to do with the induction of beta-lactamase by beta-lactam antibiotics. Uehara, Suefuji, and Park (unpublished data) have some evidence suggesting that murein pentapeptide may be involved. The presence of orthologs suggests that recycling also exists in many Gram-negative bacteria. Surprisingly, the ortholog search also revealed that all mammals may have an AmpG ortholog! Hence, mammalian AmpG may be involved in the process of innate immunity.
The Cold Shock Response
Authors: Phadtare Sangita , Inouye Masayori
Published: May 2014

This review focuses on the cold shock response of
Escherichia coli
. Change in temperature is one of the most common stresses that an organism encounters in nature. Temperature downshift affects the cell on various levels: (i) decrease in the membrane fluidity; (ii) stabilization of the secondary structures of RNA and DNA; (iii) slow or inefficient protein folding; (iv) reduced ribosome function, affecting translation of non-cold shock proteins; (v) increased negative supercoiling of DNA; and (vi) accumulation of various sugars. Cold shock proteins and certain sugars play a key role in dealing with the initial detrimental effect of cold shock and maintaining the continued growth of the organism at low temperature. CspA is the major cold shock protein of
E. coli
, and its homologues are found to be widespread among bacteria, including psychrophilic, psychrotrophic, mesophilic, and thermophilic bacteria, but are not found in archaea or cyanobacteria. Significant, albeit transient, stabilization of the cspA mRNA immediately following temperature downshift is mainly responsible for its cold shock induction. Various approaches were used in studies to detect cold shock induction of cspA mRNA. Sugars are shown to confer protection to cells undergoing cold shock. The study of the cold shock response has implications in basic and health-related research as well as in commercial applications. The cold shock response is elicited by all types of bacteria and affects these bacteria at various levels, such as cell membrane, transcription, translation, and metabolism.
Osmotic Stress
Authors: Altendorf Karlheinz , Booth Ian R. , Gralla Jay , Greie Jörg-Christian , Rosenthal Adam Z. , Wood Janet M.
Published: May 2014

Escherichia coli
and
Salmonella
encounter osmotic pressure variations in natural environments that include host tissues, food, soil, and water. Osmotic stress causes water to flow into or out of cells, changing their structure, physics, and chemistry in ways that perturb cell functions.
E. coli
and
Salmonella
limit osmotically induced water fluxes by accumulating and releasing electrolytes and small organic solutes, some denoted compatible solutes because they accumulate to high levels without disturbing cell functions. Osmotic upshifts inhibit membrane-based energy transduction and macromolecule synthesis while activating existing osmoregulatory systems and specifically inducing osmoregulatory genes. The osmoregulatory response depends on the availability of osmoprotectants (exogenous organic compounds that can be taken up to become compatible solutes). Without osmoprotectants, K
+
accumulates with counterion glutamate, and compatible solute trehalose is synthesized. Available osmoprotectants are taken up via transporters ProP, ProU, BetT, and BetU. The resulting compatible solute accumulation attenuates the K
+
glutamate response and more effectively restores cell hydration and growth. Osmotic downshifts abruptly increase turgor pressure and strain the cytoplasmic membrane. Mechanosensitive channels like MscS and MscL open to allow nonspecific solute efflux and forestall cell lysis. Research frontiers include (i) the osmoadaptive remodeling of cell structure, (ii) the mechanisms by which osmotic stress alters gene expression, (iii) the mechanisms by which transporters and channels detect and respond to osmotic pressure changes, (iv) the coordination of osmoregulatory programs and selection of available osmoprotectants, and (v) the roles played by osmoregulatory mechanisms as
E. coli
and
Salmonella
survive or thrive in their natural environments.
The Influence of Ecological Factors on the Distribution and the Genetic Structure of
Escherichia coli
Authors: Gordon David M.
Published: May 2014

This review focuses on recent data concerning the ecological factors that determine the distribution of
Escherichia coli
and the genetic structures of naturally occurring
E. coli
populations. It summarizes some of the older literature concerning the dynamics of
E. coli
populations within a host and poses some questions that arise from our more recently acquired understanding of the factors affecting the genetic structures of
E. coli
populations. Multilocus enzyme electrophoresis (MLEE) studies indicate that
E. coli
, relative to other members of the family
Enterobacteriaceae
, exhibits a moderate degree of genetic diversity. The existence of subspecific structure in
E. coli
has for the most part been determined by largely neutral in its effects on the fitness of a strain. The consequences for
E. coli
of the transition between its primary and secondary habitats are of considerable practical significance for water quality assessment and disease transmission.
E. coli
causes a significant fraction of human bacterial disease and is responsible for two main types of disease in humans and domestic animals: diarrheal disease and extraintestinal infections. The observed distribution of strains from the different
E. coli
genetic groups indicates that they have different life history tactics and ecological niches. A and B1 strains appear to be generalists, as they can be recovered from any vertebrate group. Group B2 and D strains appear to be more specialized, as they are largely restricted to endothermic vertebrates.
Translesion DNA Synthesis
Authors: Vaisman Alexandra , McDonald John P. , Woodgate Roger
Published: May 2014

All living organisms are continually exposed to agents that damage their DNA, which threatens the integrity of their genome. As a consequence, cells are equipped with a plethora of DNA repair enzymes to remove the damaged DNA. Unfortunately, situations nevertheless arise where lesions persist, and these lesions block the progression of the cell's replicase. In these situations, cells are forced to choose between recombination-mediated "damage avoidance" pathways or a specialized DNA polymerase (pol) to traverse the blocking lesion. The latter process is referred to as Translesion DNA Synthesis (TLS). As inferred by its name, TLS not only results in bases being (mis)incorporated opposite DNA lesions but also bases being (mis)incorporated downstream of the replicase-blocking lesion, so as to ensure continued genome duplication and cell survival.
Escherichia coli
and
Salmonella typhimurium
possess five DNA polymerases, and while all have been shown to facilitate TLS under certain experimental conditions, it is clear that the LexA-regulated and damage-inducible pols II, IV, and V perform the vast majority of TLS under physiological conditions. Pol V can traverse a wide range of DNA lesions and performs the bulk of mutagenic TLS, whereas pol II and pol IV appear to be more specialized TLS polymerases.
Homologous Recombination—Experimental Systems, Analysis, and Significance
Authors: Kuzminov Andrei
Published: May 2014

Homologous recombination is the most complex of all recombination events that shape genomes and produce material for evolution. Homologous recombination events are exchanges between DNA molecules in the lengthy regions of shared identity, catalyzed by a group of dedicated enzymes. There is a variety of experimental systems in
Escherichia coli
and
Salmonella
to detect homologous recombination events of several different kinds. Genetic analysis of homologous recombination reveals three separate phases of this process: pre-synapsis (the early phase), synapsis (homologous strand exchange), and post-synapsis (the late phase). In
E. coli
, there are at least two independent pathway of the early phase and at least two independent pathways of the late phase. All this complexity is incongruent with the originally ascribed role of homologous recombination as accelerator of genome evolution: there is simply not enough duplication and repetition in enterobacterial genomes for homologous recombination to have a detectable evolutionary role and therefore not enough selection to maintain such a complexity. At the same time, the mechanisms of homologous recombination are uniquely suited for repair of complex DNA lesions called chromosomal lesions. In fact, the two major classes of chromosomal lesions are recognized and processed by the two individual pathways at the early phase of homologous recombination. It follows, therefore, that homologous recombination events are occasional reflections of the continual recombinational repair, made possible in cases of natural or artificial genome redundancy.
The Life of Commensal
Escherichia coli
in the Mammalian Intestine
Authors: Conway Tyrell , Krogfelt Karen A. , Cohen Paul S.
Published: May 2014

In this chapter we review the literature with respect to what is known about how
Escherichia coli
colonizesthe mammalian intestine. We begin with a brief discussion of the mammalian large intestine, the major site that commensal strains of
E. coli
colonize. Next, evidence is discussed showing that, in order to colonize,
E. coli
must be able to penetrate and grow in the mucus layer of the large intestine. This is followed by discussions of colonization resistance, i.e., factors that are involved in the ability of a complete microbiota (microflora) to resist colonization by an invading bacterium, the advantages and disadvantages of the in vivo colonization models used in colonization research, the initiation and maintenance stages of
E. coli
colonization, and the rate of
E. coli
growth in the intestine. The next two sections of the chapter discuss the role of motility in colonization and how adhesion to mucosal receptors aids or inhibits penetration of the intestinal mucus layer and thereby either promotes or prevents
E. coli
colonization. Finally, the contribution of nutrition to the ability of
E. coli
to colonize is discussed based on the surprising finding that different nutrients are used by
E. coli
MG1655, a commensal strain, and by
E. coli
EDL933, an enterohemorrhagic strain, to colonize the intestine.
Colonization of Abiotic Surfaces
Authors: Beloin Christophe , Da Re Sandra , Ghigo Jean-Marc
Published: May 2014

E. coli
is a relevant model organism for the study of the molecular mechanisms underlying surface colonization. This process requires two essential steps: adhesion to a surface, followed by cell-cell adhesion counteracting the shear forces of the environment, with both steps contributing to the formation of a biofilm. This review provides an overview of the current knowledge of the genetic analyses aiming at identifying factors involved in both of these two highly related biological processes, with a particular emphasis on studies performed in
Escherichia coli
K-12. Bacterial adhesion to abiotic surfaces is likely to be highly dependent on the physicochemical and electrostatic interactions between the bacterial envelope and the substrate, which is itself often conditioned by the fluids to which it is exposed. Genetic analyses have revealed the diversity of genetic factors in
E. coli
that participate in colonization and biofilm formation on abiotic surfaces. The study of surface colonization and biofilm formation represents a rapidly expanding field of investigation. The use of
E. coli
K-12 to investigate the genetic basis of bacterial interactions with surfaces has led to the identification of a large repertoire of adhesins whose expression is subject to a complex interplay between regulatory networks. Understanding how
E. coli
K-12 behaves in complex biofilm communities will certainly contribute to an understanding of how natural commensal and pathogenic
E. coli
isolates develop.
Autotransporter Proteins
Authors: Henderson Ian R. , Nataro James P.
Published: May 2014

This review focuses on the function of the
Escherichia coli
and
Salmonella
autotransporters for which a considerable amount of literature is available. Members of the serine protease autotransporters of the
Enterobacteriaceae
(SPATEs) family are proteins from
E. coli
and
Shigella
spp., which, like the
Neisseria
and
Haemophilus influenzae
IgA1 proteases and Hap, possess a consensus serine protease motif. The largest subfamily of autotransporters is defined by the AidA conserved domain COG3468 and consists of members from a diverse range of animal and plant pathogens including
E. coli
,
S. enterica
,
Yersinia pestis
. This subfamily, which is composed of more than 55 proteins, possesses some of the best-characterized autotransporter proteins including the
S. flexneri
mediator of motility IcsA, the major phase-variable
E. coli
outer membrane protein antigen 43 (Ag43) and the diffuse adhering
E. coli
(DAEC) adhesin AIDA-I, from which this subfamily derives its name. Another member of the AIDA-I family, and one of the most studied autotransporter proteins, is IcsA. The autotransporter pathway is emerging as the most common mechanism of protein translocation across the gram-negative outer membrane.
Shiga Toxins: Potent Poisons, Pathogenicity Determinants, and Pharmacological Agents
Authors: Melton-Celsa A. R. , Smith M. J. , O’Brien A. D.
Published: May 2014

The Shiga toxins (Stxs), also known as Vero toxins and previously called Shiga-like toxins, are a family of potent protein synthesis inhibitors made by
Shigella dysenteriae
type 1 and some serogroups of
Escherichia coli
that cause bloody diarrhea in humans. Stxs act as virulence factors for both
S. dysenteriae
and
E. coli
and contribute to the disease process initiated by those organisms both directly and indirectly. A handful of methods exist for toxin purification, and the toxins can now even be purchased commercially. However, the Stxs are now classified as select agents, and specific rules govern the distribution of both the toxin and clones of the toxin. Toxin delivery into the host in
S. dysenteriae
type 1 is most likely aided by the invasiveness of that organism. Although the Stxs are made and produced by bacteria, they do not appear to act against either their host organism or other bacteria under normal circumstances, most likely because the A subunit is secreted from the cytoplasm as soon as it is synthesized and because the holotoxin cannot enter intact bacterial cells. The effectiveness of antibiotic therapy in patients infected with Stx-producing
E. coli
(STEC) such as O157:H7 as well as the potential risks of such treatment are areas of controversy. Several studies indicate that the course of the diarrhea stage of the disease is unaltered by antibiotic treatment. Several groups anticipate that a therapy that targets the Stxs is an important component of trying to alleviate disease caused by Stx-producing bacteria.
Modulation of Iron Availability at the Host-Pathogen Interface in Phagocytic Cells
Authors: Forbes John , Lam-Yuk-Tseung Steven , Gros Philippe
Published: May 2014

This review summarizes recent data on iron metabolism in macrophages, with a special emphasis on possible bacteriostatic and bactericidal consequences for intracellular pathogens. It includes the role of biological chelators and transporters in normal macrophage physiology and antimicrobial defense. Iron is an essential metal cofactor for many biochemical pathways in mammals. However, excess iron promotes the formation of cytotoxic oxygen derivatives so that systemic iron levels must be tightly regulated. The mechanism of iron recycling by macrophages including iron efflux from erythrocyte-containing phagosomes, iron release from macrophages, and entry into the transferrin (Tf) cycle remain poorly understood. Ferroportin expression in the liver, spleen, and bone marrow cells appears to be restricted to macrophages. Mutant mice bearing a conditional deletion of the ferroportin gene in macrophages show retention of iron by hepatic Kupffer cells and splenic macrophages. Hepcidin is induced by lipopolysaccharide (LPS) in mouse spleens and splenic macrophage in vitro and appears to mediate the LPS-induced down-regulation of ferroportin in the intestine and in splenic macrophages, suggesting that inflammatory agents may regulate iron metabolism through modulation of ferroportin expression. The host transporter Nramp1 may compete directly with bacterial divalent-metal transport systems for the acquisition of divalent metals within the phagosomal space. The ultimate outcome of these competing interactions influences the ability of pathogens to survive and replicate intracellularly. This seems particularly relevant to the
Salmonella
,
Leishmania
, and
Mycobacterium
spp., in which inactivating mutations in Nramp1 abrogate the natural resistance of macrophages to these pathogens.
Salmonella
as an Inducer of Autoimmunity
Authors: Soloski Mark J. , Metcalf Eleanor S.
Published: May 2014

A clear etiological link has been established between infection with several gram-negative enteric pathogens, including
Salmonella
spp., and the incidence of reactive arthritis (ReA), an autoimmune disease that largely affects the joints. ReA is sometimes referred to as Reiter's syndrome, particularly when accompanied by uveitis and urethritis. This review reviews the evidence etiologically linking
Salmonella
infection with autoimmune disease and addresses the roles that bacterial and host elements play in controlling disease outcome. ReA is an autoimmune disease that largely consists of painful joint inflammation but also can include inflammation of the eye, gastrointestinal tract, and skin. ReA is a member of a broad spectrum of chronic inflammatory disorders termed the seronegative spondyloarthropathies (SNSpAs) that includes ankylosing spondylitis (AS), psoriatic arthritis, and enteropathic arthritis.
Salmonella
species, as well as other enteric pathogens associated with postgastroenteritis ReA, are facultative intracellular gram-negative bacteria. Many studies have analyzed the association of the HLA class I molecule, HLA-B27, with SNSpAs. Whereas B27 has been shown to be present in 90 to 95% of cases of AS, the association of the B27 haplotype with other SNSpAs is more tenuous. The clear association between ReA and infection with
Salmonella
or other gram-negative enteric pathogens has led to the suggestion that the adaptive immune response to infection has an autoimmune component. In addition to various
Salmonella
species, other gram-negative enteric pathogens have been linked to the development of ReA. Given their close relationship to
Salmonella
, this review considers the involvement of
Shigella
species in ReA.
Vaccines against Infections Caused bySalmonella,Shigella, and PathogenicEscherichia coli
Authors: Guzman Carlos A. , Borsutzky Stefan , Favre Didier , Dietrich Guido
Published: May 2014

Infectious diseases represent one of the most common causes of death worldwide, with the enteropathogenic bacteriaSalmonellaandShigellaand pathogenicEscherichia colibeing among the most detrimental. Currently, vaccination represents the preferred method of preventing such infections. For stimulating the adaptive immune response, immunizations are frequently based on formulations which include inactivated whole-cell vaccines, live attenuated vaccines, or subunit vaccines. These can be administered via a parenteral or mucosal route, the latter having the advantage that it most closely mimics the actual course of infection. In addition to the type of vaccine and method of application, important consideration needs to be paid to safety, efficacy, and cost, which are often major bottlenecks in the successful implementation of vaccines. In this chapter we take a limited look at the history surrounding vaccinations involvingSalmonella,Shigella, and pathogenicE. coli.Salmonellainfections, which can lead to typhoid fever, are becoming increasing difficult to treat with antibiotics due to multi-drug-resistant strains. At present, the parenteral Vi-based subunit vaccines and the live attenuated oral vaccine Ty21a have proven to be the vaccines of choice, with high levels of protective efficacy and limited side effects.Shigellainfections are responsible for the diarrheal disease shigellosis. Various live and nonliving mucosal and parenteral vaccines have been tested, with the most promising candidates evolving around those that stimulate the production of O-antigen-specific antibodies. PathogenicEscherichia coliinfections can lead to severe diseases due to the bacterium's production of several specific toxins. Vaccines against this bacterium target its toxins, as well as surface-exposed antigens, all of which have been found to be effective as immunogens.
Cytokines in Salmonellosis
Authors: Mastroeni Pietro , Bryant Clare
Published: May 2014

The recruitment and activation of phagocytic cells in infected tissues and the induction of T-cell- and B-cell-dependent acquired immunity are crucial for the control and resolution of
Salmonella
infections. These complex processes require the interaction of bacteria with a multitude of cell surface receptors and the controlled production of soluble mediators. The mechanisms of cytokine induction in response to
Salmonella
and the role of cytokine networks in
Salmonella
infections are the main foci of this review. Pathogen-associated molecular pattern receptors play an important role in recognition of bacteria by the host. Effective immunity against the bacterium therefore relies on the ability of the host to recruit phagocytes in the tissues and to enhance the antibacterial functions of these inflammatory cells. TNF-a, IFN-?, IL12, IL15, and IL18 are needed for the full expression of innate host resistance to
Salmonella
. The genes for mammalian cytokines can be cloned into suitable vectors and expressed in
Salmonella
as functional proteins. The in vivo production of cytokines by
Salmonella
carriers can have therapeutic applications and can modulate immune functions in the host. The possibility to modulate antigen-specific immune responses by expressing cytokines in
Salmonella
is illustrated by the increase in
Salmonella
-specific IgA responses induced by administration of IL-5-expressing bacteria. The same cytokines that are responsible for endotoxic shock are elevated in the late stages of lethal
Salmonella
infections, indicating that the toxicity of
Salmonella
lipopolysaccharide (LPS) may actually be contributing to the death of the host.
Nitric Oxide in
Salmonella
and
Escherichia coli
Infections
Authors: VÁzquez-Torres AndrÉs , Fang Ferric C.
Published: May 2014

This review discusses the role that nitric oxide (NO) and its congeners play on various stages in the pathophysiology of
Escherichia coli
and
Salmonella
infections, with special emphasis on the regulatory pathways that lead to high NO synthesis, the role of reactive nitrogen species (RNS) in host resistance, and the bacterial molecular targets and defense mechanisms that protect enteric bacteria against the nitrosative stress encountered in diverse host anatomical sites. In general, NO can react directly with prosthetic groups containing transition metal centers, with other radicals, or with sulfhydryl groups in the presence of an electron acceptor. Binding to iron complexes is probably the best characterized direct reaction of NO in biological systems. The targets of RNS are numerous. RNS can facilitate oxidative modifications including lipid peroxidation, hydroxylation, and DNA base and protein oxidation. In addition, RNS can inflict nitrosative stress through the nitrosation of amines and sulfhydryls. Numerous vital bacterial molecules can be targeted by NO. It is therefore not surprising that enteropathogenic bacteria are armed with a number of sensors to coordinate the protective response to nitrosative stress, along with an assortment of antinitrosative defenses that detoxify, repair, or avoid the deleterious effects of RNS encountered within the host. NO and NO-derived RNS play important roles in innate immunity to
Salmonella
and
E. coli
. Enzymatic NO production by NO synthases can be enhanced by microbial and other inflammatory stimuli and it exerts direct antimicrobial actions as well as immunomodulatory and vasoregulatory effects.