Review Articles in 2012

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.

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.

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.

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.

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.

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.

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.

Fungal heat shock protein 90 (Hsp90) is an essential chaperone that regulates a range of cellular processes by ensuring the correct folding of a specific group of client proteins. In this Review, Brown and colleagues describe the roles and regulation of Hsp90 and discuss how it acts as a biological transistor to modulate fungal signalling networks.

The two commercially available prophylactic vaccines that target human papilloma virus type 16 (HPV16) and HPV18 have proved extremely effective. Here, Schiller and Lowy summarize the characteristics of both the vaccines and HPV that have contributed to this success and speculate on whether or not this information could be used to direct the development of vaccines against other sexually transmitted viruses.

Many bacteria and archaea synthesize intracellular gas-filled proteinaceous structures known as gas vesicles to act as flotation devices in aqueous environments. Here, Felicitas Pfeifer describes the basic properties of these interesting structures, the proteins that form them, the gene clusters that encode them and the regulation of their production.

In recent years, thanks to the development of whole-genome amplification methods, it has become possible to sequence the genome of a single bacterial cell. Here, Roger Lasken reviews the development of single-cell sequencing techniques and their most recent applications.

The infection process is accompanied by widespread changes in gene expression in both host and pathogen. Here, Vogel and colleagues explore the feasibility of simultaneously analysing the transcriptomes of both host and pathogen using RNA deep-sequencing approaches.

Even when receiving antiretroviral therapy, HIV-infected individuals have an increased risk of mortality owing to systemic immune activation. Sandler and Douek review evidence showing that the translocation of microbial products from the intestine into the circulation may contribute to this risk and discuss potential therapeutic strategies.

Viruses are the most diverse and uncharacterized components of all the major ecosystems on Earth, including that within the mammalian gut. Here, Gordon and colleagues review our current understanding of the diversity and ecology of the bacteriophages present in the human gut and discuss how an improved understanding of phage dynamics could revitalize phage therapy.

Marine sponges can contain dense and diverse microbial communities that can constitute up to 35% of the sponge biomass. In this Review, Hentschel and colleagues describe how genomic insights into both sponges and their associated microbiota are beginning to illuminate the functional and evolutionary roles of each partner in this association.