authoritative, comprehensive and systematic

Recent progress in vaccines against fungal diseases

The genome biology of phytoplasma: modulators of plants and insects

Molecular mechanisms of probiotic action: a proteomic perspective

Anopheles gambiae pathogen susceptibility: the intersection of genetics, immunity and ecology

Antigenic variation and the generation of diversity in malaria parasites

Making (good) use of Wolbachia: what the models say

The control of death and lysis in staphylococcal biofilms: a coordination of physiological signals

Coordinate regulation of Gram-positive cell surface components

Recent advances in pneumococcal peptidoglycan biosynthesis suggest new vaccine and antimicrobial targets

Making a beta-barrel: assembly of outer membrane proteins in Gram-negative bacteria

Hfq structure, function and ligand binding

Recent studies on Hfq have provided a deeper understanding of the multiple functions of this pleiotropic post-transcriptional regulator. Insights into the mechanism of Hfq action have come from a variety of approaches. A key finding was the characterization of two RNA binding sites: the Proximal Site, which binds sRNA and mRNA; and the Distal Site, which binds poly(A) tails. Hfq was shown to interact with PAP I, PNP and RNase E, proteins that are involved in mRNA decay and in vitro, was shown…

Volume 10, Issue 2, 01 April 2007, Pp 125-133
Brennan, R.G. | Link, T.M.

Mechanism of RNA silencing by Hfq-binding small RNAs

The stress-induced small RNAs SgrS and RyhB in Escherichia coli form a specific ribonucleoprotein complex with RNAse E and Hfq resulting in translation inhibition, RNAse E-dependent degradation of target mRNAs. Translation inhibition is the primary event for gene silencing and degradation of these small RNAs is coupled with the degradation of target mRNAs. The crucial base-pairs for action of SgrS are confined to the 6 nt region overlapping the Shine-Dalgarno sequence of the target mRNA. Hfq…

Volume 10, Issue 2, 01 April 2007, Pp 134-139
Aiba, H.

Type VI secretion: a beginner's guide

Type VI secretion is a newly described mechanism for protein transport across the cell envelope of Gram-negative bacteria. Components that have been partially characterised include an IcmF homologue, the ATPase ClpV, a regulatory FHA domain protein and the secreted VgrG and Hcp proteins. Type VI secretion is clearly a key virulence factor for some important pathogenic bacteria and has been implicated in the translocation of a potential effector protein into eukaryotic cells by at least one…

Volume 11, Issue 1, 01 February 2008, Pp 3-8
Bingle, L.E. | Bailey, C.M. | Pallen, M.J.

CsrB sRNA family: sequestration of RNA-binding regulatory proteins

Noncoding regulatory RNA molecules, also known as small RNAs, participate in several bacterial regulatory networks. The central component of the carbon storage regulator (Csr) and the homologous repressor of secondary metabolites (Rsm) systems is an RNA binding protein (CsrA or RsmA) that regulates gene expression post-transcriptionally by affecting ribosome binding and/or mRNA stability. Members of the CsrB family of noncoding regulatory RNA molecules contain multiple CsrA binding sites and…

Volume 10, Issue 2, 01 April 2007, Pp 156-163
Babitzke, P. | Romeo, T.

The mechanisms of carbon catabolite repression in bacteria

Carbon catabolite repression (CCR) is the paradigm of cellular regulation. CCR happens when bacteria are exposed to two or more carbon sources and one of them is preferentially utilised (frequently glucose). CCR is often mediated by several mechanisms, which can either affect the synthesis of catabolic enzymes via global or specific regulators or inhibit the uptake of a carbon source and thus the formation of the corresponding inducer. The major CCR mechanisms operative in Enterobacteriaceae…

Volume 11, Issue 2, 01 April 2008, Pp 87-93
Deutscher, J.

Small noncoding RNAs controlling pathogenesis

Infectious diseases are a leading cause of mortality worldwide. A major challenge in achieving their eradication is a better understanding of bacterial pathogenesis processes. The recent discovery of small noncoding RNAs (sRNAs) as modulators of gene expression in response to environmental cues has brought a new insight into bacterial regulation. sRNAs coordinate complex networks of stress adaptation and virulence gene expression. sRNAs generally ensure such a regulation by pairing to mRNAs of…

Volume 10, Issue 2, 01 April 2007, Pp 182-188
Toledo-Arana, A. | Repoila, F. | Cossart, P.

Small RNAs controlling iron metabolism

Iron is one of the most important metals in the metabolism of many organisms, including bacteria, in which it serves as a cofactor in multiple enzymatic reactions. Most of the earlier research on iron regulation in bacteria has focused on the transcriptional regulator Fur and its effect on the many genes involved in iron uptake. More recent work demonstrates the essential role of a small regulatory RNA, RyhB, in iron metabolism. RyhB downregulates a large number of transcripts encoding…

Volume 10, Issue 2, 01 April 2007, Pp 140-145
Massé, E. | Salvail, H. | Desnoyers, G. | Arguin, M.

c-di-GMP-mediated regulation of virulence and biofilm formation

It is now apparent that the signaling molecule 3′,5′-cyclic diguanylic acid (c-di-GMP) is a central regulator of the prokaryote biofilm lifestyle and recent evidence also links this molecule to virulence. Environmentally responsive signal transduction systems that control expression and/or activity of the enzymes (GGDEF and EAL domain containing proteins) that are responsible for synthesis and degradation of c-di-GMP have recently been identified. Members of the phosphorelay family feature…

Volume 10, Issue 1, 01 February 2007, Pp 17-23
Cotter, P.A. | Stibitz, S.

Regulatory mechanisms employed by cis-encoded antisense RNAs

Bacterial small regulatory RNAs that act by base-pairing can be divided into two classes: cis-encoded and trans-encoded antisense RNAs. The former - mainly discovered in plasmids, phages and transposons - are encoded in the same DNA locus and are therefore completely complementary to their targets over a long sequence stretch. Regulatory mechanisms employed by these RNAs encompass inhibition of primer maturation or RNA pseudoknot formation, transcriptional attenuation, inhibition of translation…

Volume 10, Issue 2, 01 April 2007, Pp 102-109
Brantl, S.

Quorum sensing and environmental adaptation in Pseudomonas aeruginosa: a tale of regulatory networks and multifunctional signal molecules

Bacteria employ sophisticated cell-to-cell communication or 'quorum sensing' (QS) systems for promoting collective behaviours that depend on the actions of one or more chemically distinct diffusible signal molecules. As determinants of cell population density, multiple QS systems are often integrated with each other and within global regulatory networks and subject to the prevailing environmental conditions as well as the presence and activities of other organisms. QS signal molecules, although…

Volume 12, Issue 2, 01 April 2009, Pp 182-191
Williams, P. | Cámara, M.

Pulling together: an integrated model of Toxoplasma cell invasion

The protozoan Toxoplasma gondii invades a wide array of animal cells using an actin/myosin-based motor complex to drive active penetration. This broad specificity implies that the parasite has developed a means of using a widely expressed receptor, many different receptors, or perhaps a receptor produced by T. gondii itself. Recently, there has been an explosion in identification of the molecules involved, including those that comprise the 'moving junction' that slides over the parasite as it…

Volume 10, Issue 1, 01 February 2007, Pp 83-89
Carruthers, V. | Boothroyd, J.C.

Role of polysaccharides in Pseudomonas aeruginosa biofilm development

During the past decade, there has been a renewed interest in using Pseudomonas aeruginosa as a model system for biofilm development and pathogenesis. Since the biofilm matrix represents a crucial interface between the bacterium and the host or its environment, considerable effort has been expended to acquire a more complete understanding of the matrix composition. Here, we focus on recent developments regarding the roles of alginate, Psl, and Pel polysaccharides in the biofilm matrix. © 2007…

Volume 10, Issue 6, 01 December 2007, Pp 644-648
Ryder, C. | Byrd, M. | Wozniak, D.J.

The type VI secretion system: translocation of effectors and effector-domains

A number of prominent Gram-negative bacteria use the type VI secretion system (T6SS) to transport proteins across the bacterial envelope. Rapid progress is being made in elucidating the structural components of the T6SS apparatus, and a few effectors have been reported to pass through it. However, this is not the complete story: a family of T6SS proteins, the VgrGs, share structural features with the cell-puncturing device of the T4 bacteriophage, and may be used in a similar fashion by…

Volume 12, Issue 1, 01 February 2009, Pp 11-17
Pukatzki, S. | McAuley, S.B. | Miyata, S.T.

Adaptation to the host environment: regulation of the SPI1 type III secretion system in Salmonella enterica serovar Typhimurium

Salmonella enterica invades the intestinal epithelium of the host using a type III secretion system encoded on Salmonella pathogenicity island 1 (SPI1). The bacteria integrate environmental signals from a variety of global regulatory systems to precisely induce transcription of SPI1. The regulatory circuit converges on expression of HilA, which directly regulates transcription of the SPI1 apparatus genes. Transcription of hilA is controlled by a complex feed-forward loop. Regulatory signals…

Volume 10, Issue 1, 01 February 2007, Pp 24-29
Ellermeier, J.R. | Slauch, J.M.

Control of bacterial transcription, translation and replication by (p)ppGpp

The small nucleotides pppGpp and ppGpp (or (p)ppGpp) are rapidly synthesized in response to nutritional stress. In Escherichia coli, the enzymes RelA and SpoT are triggered by different starvation signals to produce (p)ppGpp. In many Gram-positive bacteria this is carried out by RelA and two small homologs. (p)ppGpp, along with the transcription factor DksA, has profound effects on transcription initiation in E. coli. (p)ppGpp/DksA exert differential effects on promoters by playing upon their…

Volume 11, Issue 2, 01 April 2008, Pp 100-105
Srivatsan, A. | Wang, J.D.

Maturation and degradation of RNA in bacteria

RNA decay plays an important role, not only in recycling nucleotides but also in determining the rapidity with which cells can react to changing growth conditions. The degradation process can be regulated, thus providing an often-underestimated means of controlling gene expression. Recent developments in the field of RNA maturation and decay in two key model organisms, Escherichia coli and Bacillus subtilis, include the resolution of the structures of many of the participants in these processes…

Volume 10, Issue 3, 01 June 2007, Pp 271-278
Condon, C.

Comparative genomics: the bacterial pan-genome

Bacterial genome sequencing has become so easy and accessible that the genomes of multiple strains of more and more individual species have been and will be generated. These data sets provide for in depth analysis of intra-species diversity from various aspects. The pan-genome analysis, whereby the size of the gene repertoire accessible to any given species is characterized together with an estimate of the number of whole genome sequences required for proper analysis, is being increasingly…

Volume 11, Issue 5, 01 October 2008, Pp 472-477
Tettelin, H. | Riley, D. | Cattuto, C. | Medini, D.

A renaissance for the pioneering 16S rRNA gene

Culture-independent molecular surveys using the 16S rRNA gene have become a mainstay for characterizing microbial community structure over the past quarter century. More recently this approach has been overshadowed by metagenomics, which provides a global overview of a community's functional potential rather than just an inventory of its inhabitants. However, the pioneering 16S rRNA gene is making a comeback in its own right thanks to a number of methodological advancements including higher…

Volume 11, Issue 5, 01 October 2008, Pp 442-446
Tringe, S.G. | Hugenholtz, P.

Salmonella takes control: effector-driven manipulation of the host

Salmonella pathogenesis relies upon the delivery of over thirty specialised effector proteins into the host cell via two distinct type III secretion systems. These effectors act in concert to subvert the host cell cytoskeleton, signal transduction pathways, membrane trafficking and pro-inflammatory responses. This allows Salmonella to invade non-phagocytic epithelial cells, establish and maintain an intracellular replicative niche and, in some cases, disseminate to cause systemic disease. This…

Volume 12, Issue 1, 01 February 2009, Pp 117-124
McGhie, E.J. | Brawn, L.C. | Hume, P.J. | Humphreys, D. | Koronakis, V.

Antibiotic resistant Staphylococcus aureus: a paradigm of adaptive power

Nothing documents better the spectacular adaptive capacity of Staphylococcus aureus than the response of this important human and animal pathogen to the introduction of antimicrobial agents into the clinical environment. The effectiveness of penicillin introduced in the early 1940s was virtually annulled within a decade because of the plasmid epidemics that spread the ß-lactamase gene through the entire species of S. aureus. In 1960 within one to two years of the introduction of penicillinase…

Volume 10, Issue 5, 01 October 2007, Pp 428-435
de Lencastre, H. | Oliveira, D. | Tomasz, A.

RNA antitoxins

Recent genomic analyses revealed a surprisingly large number of toxin-antitoxin loci in free-living prokaryotes. The antitoxins are proteins or antisense RNAs that counteract the toxins. Two antisense RNA-regulated toxin-antitoxin gene families, hok/sok and ldr, are unrelated sequence-wise but have strikingly similar properties at the level of gene and RNA organization. Recently, two SOS-induced toxins were found to be regulated by RNA antitoxins. One such toxin, SymE, exhibits similarity with…

Volume 10, Issue 2, 01 April 2007, Pp 117-124
Gerdes, K. | Wagner, E.G.H.

Pseudomonas syringae type III secretion system effectors: repertoires in search of functions

The ability of Pseudomonas syringae to grow and cause diseases in plants is dependent on the injection of multiple effector proteins into plant cells via the type III secretion system (T3SS). Genome-enabled bioinformatic/experimental methods have comprehensively identified the repertoires of effectors and related T3SS substrates for P. syringae pv. tomato DC3000 and three other sequenced strains. The effector repertoires are diverse and internally redundant. Insights into effector functions are…

Volume 12, Issue 1, 01 February 2009, Pp 53-60
Cunnac, S. | Lindeberg, M. | Collmer, A.

Microbial phenotypic heterogeneity and antibiotic tolerance

Phenotypic heterogeneity, defined as metastable variation in cellular parameters generated by epigenetic mechanisms, is crucial for the persistence of bacterial populations under fluctuating selective pressures. Diversity ensures that some individuals will survive a potentially lethal stress, such as an antibiotic, that would otherwise obliterate the entire population. The refractoriness of bacterial infections to antibiotic therapy has been ascribed to antibiotic-tolerant variants known as…

Volume 10, Issue 1, 01 February 2007, Pp 30-38
Dhar, N. | McKinney, J.D.

Target identification of small noncoding RNAs in bacteria

Small noncoding RNAs have been discovered at a staggering rate in Escherichia coli and many other bacteria. Most of the sRNAs of known function regulate gene expression by binding to specific mRNAs or proteins. Given the scores of sRNAs of unknown function, the identification of their cellular targets has become urgent. Here, we review the diverse strategies that have been used to identify and validate bacterial sRNA targets. These include the pulse-expression of sRNAs followed by global…

Volume 10, Issue 3, 01 June 2007, Pp 262-270
Vogel, J. | Wagner, E.G.H.

Plant pathogenic bacterial type III effectors subdue host responses

Like animals, plants sense bacterial pathogens through surface-localized pattern recognition receptors (PRRs) and intracellular nucleotide-binding leucine-rich repeat proteins (NB-LRR) and trigger defense responses. Many plant-pathogenic bacteria secrete a large repertoire of effector proteins into host cells to modulate host responses, enabling successful infection and multiplication in plants. A number of these effector proteins target plant innate immunity signaling pathways, while others…

Volume 11, Issue 2, 01 April 2008, Pp 179-185
Zhou, J.-M. | Chai, J.

Silencing of foreign DNA in bacteria

Antibiotic resistance in the environment: a link to the clinic?

Extracellular signaling and multicellularity in Bacillus subtilis

The role of Dectin-1 in the host defence against fungal infections

Studying bacterial transcriptomes using RNA-seq

Recurrent infections and immune evasion strategies of Staphylococcus aureus

Escherichia coli physiology and metabolism dictates adaptation to diverse host microenvironments

Salmonella persistence and transmission strategies

Exploitation of cellular pathways by Dengue virus

TAL effectors are remote controls for gene activation