Reviews & Analysis

The rise of antibiotic resistance, together with collateral damage to the human microbiota as a result of antibiotic use, means that new antimicrobials need to be developed. Here, Cotter, Ross and Hill discuss the potential of bacteriocins, which are active against a range of bacteria, have low toxicity towards the host, are easily modifiable and can even be producedin situ.

In this Progress article, Cossart and colleagues discuss the unique features of unusually long antisense RNAs and discuss the excludon paradigm, which describes a genomic locus that encodes a long antisense RNA which inhibits the expression of one operon while simultaneously driving the expression of the adjacent operon.

The endoribonuclease RNase E is widespread in bacteria and is crucial for the control of RNA metabolism in the cell. In this Review, George Mackie discusses the role of RNase E in stable RNA processing and mRNA decay, and proposes a new model to reconcile the dynamics of RNA metabolism with the cellular localization of this enzyme.

Repair of double-strand DNA breaks by homologous recombination can be carried out in bacteria by RecBCD, AddAB and AdnAB. Here, Dale Wigley discusses recent insights into how these complexes mediate repair, as well as their evolution.

Sporulation inBacillus subtilisresults in the formation of an endospore surrounded by a multilayered protective structure, known as the coat. In this Review, Patrick Eichenberger and colleagues describe recent studies that have illuminated the architecture of the coat and the dynamics of coat assembly.

Regulated cell death is a key process in plant and animal development, but does it occur in parasitic protozoa? Jeremy Mottram and colleagues assess the evidence of regulated cell death in these organisms and propose that protozoan cell death should be classified as either necrotic or incidental.

Fungi produce a diverse array of secondary metabolites that have a range of functions and great pharmacological potential. In this Review, Axel Brakhage describes the regulatory pathways governing the production of these secondary metabolites and discusses how this knowledge provides a new avenue for drug discovery.

Mucosal-associated invariant T (MAIT) cells have an intrinsic capacity to recognize a broad microbial repertoire through their invariant T cell receptor, which interacts with antigen presented by MHC class I-related protein 1 (MR1). Here, Marielle Gold and David Lewinsohn highlight recent insights suggesting that this unique, 'innate' T cell subset plays an important part in the early recognition and containment of infection.

Compared with our understanding of the microbial ecology of the rhizosphere (the below-ground parts of plants), our understanding of the microbial ecology of the phyllosphere (the aerial parts of plants) has lagged behind, but this has begun to change in recent years. Here, Julia Vorholt reviews the latest research into the composition of microbial phyllosphere communities, the factors that drive this composition and the adaptation of these communities to the plant environment.

Although it may never be possible for a single animal model to recapitulate all of the features of HIV-1 infection of humans, there have been great advances in the development of small-animal and non-human primate models, as well as in the development of recombinant challenge viruses. Here, the authors review the advantages and disadvantages of the different animal models of HIV/AIDS with respect to their use in the preclinical development of vaccines and antiretroviral therapies.

The throughput of protein structure determination has increased greatly over the past decade, thanks to advances in X-ray crystallography and NMR spectroscopy. Protein structure information is now routinely used in vaccine design, and here, Rappuoli and colleagues describe some of the most recent developments in this new field of structural vaccinology.

Invertebrates lack conventional antibody-based immunity but have the capacity to distinguish between symbionts and pathogens. In this Review, Nyholm and Graf describe how the innate immune system of four model invertebrates functions in the establishment and maintenance of bacterial symbioses.

Pseudomonas aeruginosainfection of the airways is a major cause of mortality and morbidity for patients with cystic fibrosis (CF). Here, Molin and colleagues discuss howP. aeruginosa infection evolves from a state of early, intermittent colonization to a state of chronic infection. Studying the in vivo adaptation of P. aeruginosawill enhance our understanding of bacterial evolution, and could also be important for the development of new therapeutic strategies for CF-associated and other chronic infections.

It has recently emerged that environmental factors such as ambient temperature can strongly influence insect immunity and, thus, shape the outcome of host–parasite interactions. Here, Murdock, Thomas and colleagues argue that, to get more accurate insights into vector resistance, we need to incorporate temperature variation into studies.

Predicting the virulence of a particular bacterial strain is a complex task that currently cannot be achieved from genome sequence data alone. In this Opinion article, Massey and colleagues present a framework for the construction of a systems biology-based tool that they think could be used to predict virulence phenotypes fromStaphylococcus aureusgenomic sequences using existing technologies.

RepABC family plasmids are found exclusively in alphaproteobacteria. The replication and partitioning proteins of these plasmids are encoded by a single operon, therepABCcassette. Here, Pinto, Pappas and Winans review the regulation of RepABC plasmid replication and partitioning, including the mechanisms that allow plasmid copynumber to be increased in response to external cues.

The intracellular parasiteToxoplasma gondiican infect a range of hosts and occasionally causes serious disease in humans. In this Review, Hunter and Sibley summarize recent studies that implicate rhoptry kinases and a dense-granule protein as mediators of acute virulence in the mouse model. They also describe the complex interplay between these parasite effector proteins and the innate immune system.

Proteus mirabilisis one of the leading causes of catheter-associated urinary tract infections. Here, Armbruster and Mobley review the many recent advances in our understanding ofP. mirabilispathogenicity, including the elucidation of the intricate connections between metabolism, swarming motility and urease activity.

Most protein export in bacteria occurs through the Sec pathway and relies on the essential ATPase SecA to push substrates through the SecYEG translocon. Here, Braunstein and Feltcher describe how mycobacteria and some Gram-positive bacteria secrete certain substrates using additional versions of SecA and other Sec components.

A bidirectional neurohumoral communication system known as the gut–brain axis integrates the activities of the intestine and the brain. In this Progress article, Collins, Surette and Bercik describe recent evidence suggesting that the intestinal microbiota is intimately connected with the gut–brain axis and can influence animal behaviour, development and health.