Molecular Microbiology

Imlay, James A.

doi: 10.1111/j.1365-2958.2008.06213.xpmid: 18363793

Historically many bacteria have been classified as obligate anaerobes. They have been construed as wholly intolerant of oxygen, a feature that was originally ascribed to their lack of superoxide dismutases and catalases. Clostridial species were regarded as classic examples. We now know that this view is quite wrong: enzymes that scavenge superoxide, hydrogen peroxide and even oxygen itself abound in anaerobes. In the current issue of Molecular Microbiology, Hillmann et al. demonstrate that full production of these proteins can allow Clostridium acetobutylicum to survive and even grow in oxygenated culture medium. Evidently, oxidative defences in anaerobes can be robust. In all likelihood, they are critical for the movement of bacteria through aerobic environments to new anaerobic habitats.

Newton, Gerald L.; Fahey, Robert C.

doi: 10.1111/j.1365-2958.2008.06222.xpmid: 18430078

Mycothiol (MSH) is the major thiol in Actinobacteria and plays a role analogous to that of glutathione. The biosynthetic pathway has been established in mycobacteria and is initiated by the glycosyltransferase MshA. A key mycothiol‐dependent detoxification pathway utilizes the amidase (Mca) to cleave mycothiol S‐conjugates to produce GlcN‐Ins and a mercapturic acid excreted from the cell. How expression of mycothiol genes is regulated in mycobacteria has been unclear so the report in this issue by Park and Roe showing that in Streptomyces coelicolor the redox controlled anti‐sigma factor RsrA that binds the regulator σR controls key elements of mycothiol metabolism is a major advance. Conditions that deplete thiols are shown to induce directly expression of sigR, rsrA, mshA and mca, as well as the thioredoxin reductase–thioredoxin system, generating an autoregulatory cycle that persists until the thiol‐depleting condition is alleviated. Evidence for indirect induction of mshB–D to support mycothiol biosynthesis is also presented. It was shown in vitro that mycothiol, like reduced thioredoxin and dithiothreitol, can reduce oxidized RsrA to activate its binding to σR. These studies establish for the first time how mycothiol metabolism is regulated to cope with stress from thiol reactive toxins.

Cornelis, Pierre

doi: 10.1111/j.1365-2958.2008.06223.xpmid: 18430079

Pyoverdine is a fluorescent, high‐affinity peptide siderophore produced by different Pseudomonas species. The genes for pyoverdine biosynthesis depend on PvdS, an extracytoplasmic sigma factor. In this issue of Molecular Microbiology, Swingle et al. demonstrate that in the plant pathogen Pseudomonas syringae PvdS not only regulates the production of pyoverdine (core regulon), but also controls expression of other genes likely to be involved in the adaptation to the environment (accessory regulon). This accessory regulon is variable, as different sets of genes seem to be recruited according to the Pseudomonas species and its specific ecological niche.

Fischer, Reinhard; Zekert, Nadine; Takeshita, Norio

doi: 10.1111/j.1365-2958.2008.06193.xpmid: 18399939

One kind of the most extremely polarized cells in nature are the indefinitely growing hyphae of filamentous fungi. A continuous flow of secretion vesicles from the hyphal cell body to the growing hyphal tip is essential for cell wall and membrane extension. Because microtubules (MT) and actin, together with their corresponding motor proteins, are involved in the process, the arrangement of the cytoskeleton is a crucial step to establish and maintain polarity. In Saccharomyces cerevisiae and Schizosaccharomyces pombe, actin‐mediated vesicle transportation is sufficient for polar cell extension, but in S. pombe, MTs are in addition required for the establishment of polarity. The MT cytoskeleton delivers the so‐called cell‐end marker proteins to the cell pole, which in turn polarize the actin cytoskeleton. Latest results suggest that this scenario may principally be conserved from S. pombe to filamentous fungi. In addition, in filamentous fungi, MTs could provide the tracks for long‐distance vesicle movement. In this review, we will compare the interaction of the MT and the actin cytoskeleton and their relation to the cortex between yeasts and filamentous fungi. In addition, we will discuss the role of sterol‐rich membrane domains in combination with cell‐end marker proteins for polarity establishment.

Pelicic, Vladimir

doi: 10.1111/j.1365-2958.2008.06197.xpmid: 18399938

The widespread role of pili as colonization factors in pathogens has long been recognized in Gram‐negative bacteria and more recently in Gram‐positive bacteria, making the study of these hair‐like filaments a perennial hot topic for research. No other pili are found in as many or as diverse bacteria as type IV pili. This is likely a consequence of their ancient origin and unique ability to promote multiple and strikingly different phenotypes such as attachment to surfaces, aggregation, uptake of DNA during transformation, motility, etc. Two decades of investigations in several model species have shed some light on the structure of these filaments and the molecular basis of some of the properties they confer. Moreover, recent discoveries have led to a better knowledge of the genetic basis and molecular mechanisms of type IV pili biogenesis. This brings us a few steps closer to understanding how these filaments are produced, but leaves us wondering whether (as in the famous motto that inspired the title) out of the many models studied will emerge one unifying mechanism.

Buist, Girbe; Steen, Anton; Kok, Jan; Kuipers, Oscar P.

doi: 10.1111/j.1365-2958.2008.06211.xpmid: 18430080

Bacteria retain certain proteins at their cell envelopes by attaching them in a non‐covalent manner to peptidoglycan, using specific protein domains, such as the prominent LysM (Lysin Motif) domain. More than 4000 (Pfam PF01476) proteins of both prokaryotes and eukaryotes have been found to contain one or more Lysin Motifs. Notably, this collection contains not only truly secreted proteins, but also (outer‐)membrane proteins, lipoproteins or proteins bound to the cell wall in a (non‐)covalent manner. The motif typically ranges in length from 44 to 65 amino acid residues and binds to various types of peptidoglycan and chitin, most likely recognizing the N‐acetylglucosamine moiety. Most bacterial LysM‐containing proteins are peptidoglycan hydrolases with various cleavage specificities. Binding of certain LysM proteins to cells of Gram‐positive bacteria has been shown to occur at specific sites, as binding elsewhere is hindered by the presence of other cell wall components such as lipoteichoic acids. Interestingly, LysM domains of certain plant kinases enable the plant to recognize its symbiotic bacteria or sense and induce resistance against fungi. This interaction is triggered by chitin‐like compounds that are secreted by the symbiotic bacteria or released from fungi, demonstrating an important sensing function of LysMs.

Hillmann, Falk; Fischer, Ralf‐Jörg; Saint‐Prix, Florence; Girbal, Laurence; Bahl, Hubert

doi: 10.1111/j.1365-2958.2008.06192.xpmid: 18430081

Clostridia belong to those bacteria which are considered as obligate anaerobe, e.g. oxygen is harmful or lethal to these bacteria. Nevertheless, it is known that they can survive limited exposure to air, and often eliminate oxygen or reactive derivatives via NAD(P)H‐dependent reduction. This system does apparently contribute to survival after oxidative stress, but is insufficient to establish long‐term tolerance of aerobic conditions. Here we show that manipulation of the regulatory mechanism of this defence mechanism can trigger aerotolerance in the obligate anaerobe Clostridium acetobutylicum. Deletion of a peroxide repressor (PerR)‐homologous protein resulted in prolonged aerotolerance, limited growth under aerobic conditions and rapid consumption of oxygen from an aerobic environment. The mutant strain also revealed higher resistance to H2O2 and activities of NADH‐dependent scavenging of H2O2 and organic peroxides in cell‐free extracts increased by at least one order of magnitude. Several genes encoding the putative enzymes were upregulated and identified as members of the clostridial PerR regulon, including the heat shock protein Hsp21, a reverse rubrerythrin which was massively produced and became the most abundant protein in the absence of PerR. This multifunctional protein is proposed to play the crucial role in the oxidative stress defence.

Park, Joo‐Hong; Roe, Jung‐Hye

doi: 10.1111/j.1365-2958.2008.06191.xpmid: 18430082

Mycothiol (MSH) is a small thiol molecule with a cysteine‐ligated disaccharide structure found in actinomycetes that include streptomycetes and mycobacteria. In Streptomyces coelicolor, a model organism for antibiotic production and differentiation, the amount of MSH is under the control of a sigma factor σR, which is regulated by an antisigma factor RsrA with a thiol‐disulphide redox switch. We found that the first gene (mshA) in the biosynthetic pathway for MSH and the gene for amidase (mca) that participates in detoxifying mycothiol‐reactive drugs are under direct control of σR. The σR target genes are induced not only by a thiol oxidant diamide, but also by alkylating agents that cause a rapid decrease in MSH. Expression of the σR regulon was also elevated in MSH‐deficient mutants, suggesting that a decrease in the level of MSH is a natural intracellular trigger for σR activation. We found that MSH was capable of reducing RsrA to bind σR, whereas glutathione was not. These results support a proposal that the RsrA‐σR system senses the intracellular level of reduced MSH, and that MSH serves as a natural modulator of the transcription system for its own replenishment in addition to being a redox buffer and drug detoxifier.

Swingle, Bryan; Thete, Deepti; Moll, Monica; Myers, Christopher R.; Schneider, David J.; Cartinhour, Samuel

doi: 10.1111/j.1365-2958.2008.06209.xpmid: 18363796

Bacteria that survive under variable conditions possess an assortment of genetic regulators to meet these challenges. The group IV or extracytoplasmic function (ECF) sigma factors regulate gene expression in response to specific environmental signals by altering the promoter specificity of RNA polymerase. We have undertaken a study of PvdS, a group IV sigma factor encoded by Pseudomonas syringae pv. tomato DC3000 (DC3000), a plant pathogen that is likely to encounter variations in nutrient availability as well as plant host defences. The gene encoding PvdS was previously identified by sequence similarity to the Pseudomonas aeruginosa orthologue, which directs transcription of genes encoding the biosynthesis of pyoverdine, a siderophore involved in iron acquisition, and is responsible for the characteristic fluorescence of the pseudomonads. We identified 15 promoters regulated by PvdS in DC3000 and characterized the promoter motif using computational analysis. Mutagenesis of conserved nucleotides within the motif interfered with promoter function and the degree of the effect was different depending on which region of the motif was mutated. Hidden Markov models constructed from alignments of sequence motifs extracted from DC3000 and PAO1 were used to query genomes of DC3000 and other fluorescent pseudomonads for similar motifs. We conclude that the role of PvdS as a regulator of pyoverdine synthesis is conserved among the fluorescent pseudomonads, but the promoters recognized by PvdS orthologues may differ subtly from species to species.

Papenfort, Kai; Pfeiffer, Verena; Lucchini, Sacha; Sonawane, Avinash; Hinton, Jay C. D.; Vogel, Jörg

doi: 10.1111/j.1365-2958.2008.06189.xpmid: 18399940

Post‐transcriptional repression of porin synthesis has emerged as a major function of Hfq‐dependent, small non‐coding RNAs (sRNAs). Many enterobacteria express OmpX‐like porins, a family of outer membrane proteins whose physiological roles and structural properties have been studied intensively. While regulatory sRNAs have been identified for most major and many minor porins of Salmonella and Escherichia coli, a post‐transcriptional regulator of OmpX levels has never been found. Here, we have taken a ‘reverse target search’ approach by systematic inactivation of Salmonella sRNA genes, and screening 35 sRNA deletion strains for effects on OmpX synthesis. We have identified the Hfq‐dependent CyaR (formerly RyeE) sRNA as an ompX repressor. Global transcriptomic profiling following induction of CyaR expression suggests that ompX mRNA is the primary target of this sRNA under standard growth conditions. The results of phylogenetic and mutational analyses suggest that a conserved RNA hairpin of CyaR, featuring a C‐rich apical loop, acts to sequester the Shine–Dalgarno sequence of ompX mRNA and to inhibit translational initiation. We have also discovered that cyaR expression is tightly controlled by the cyclic AMP receptor protein, CRP. This represents a new link between porin repression and nutrient availability that is likely to be widely conserved among enterobacteria.