Reviews & Analysis

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 this Opinion article, Hajishengallis and colleagues propose that certain low-abundance microorganisms, termed 'keystone pathogens', can disrupt a normally benign commensal microbiota, leading to a microbial community structure that is associated with the development of disease.

SAMHD1 has emerged as a novel HIV restriction factor that inhibits viral replication by limiting dNTP availability. Here, Schwartz and colleagues discuss the studies that led to the identification and characterization of SAMHD1, and speculate on why HIV-1 does not encode the SAMHD1-targeting protein, Vpx.

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.

In this Progress article, Pallen, Loman and colleagues present a snapshot of the high-throughput sequencing platforms available to microbiologists today, together with the relevant analytical tools, and evaluate their strengths and weaknesses in obtaining bacterial genome sequences.

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.

Correlation and co-occurrence patterns found in metagenomic and phylogenetic data sets are increasingly being used to predict species interactions in the environment. Here, Faust and Raes describe the range of approaches for predicting microbial network models, the pitfalls that are associated with each approach and the future for developing ecosystem-wide models.

Vertebrates protect against infection through the sequestration of nutrient metals, and bacterial pathogens have evolved sophisticated acquisition strategies to circumvent this host defence. In this Review, Hood and Skaar describe this molecular arms race for nutrients.

Although more than one-third of the Earth's continental surface is permanently or seasonally arid, microbial communities have evolved to cope with the extreme stresses that are imposed by such environments. Here, Pointing and Belnap describe the microbial communities that are found in desert environments and the biogeological processes that they carry out.

Viroporins belong to a growing family of virally encoded proteins that form aqueous channels in the membranes of host cells. Here, Carrasco and colleagues review the structure and diverse biological functions of these proteins during the viral life cycle, as well as their potential as antiviral therapeutic targets.

Recent high-throughput sequencing studies have provided a first glimpse of the microbiome associated with late-stage colorectal cancer. In this Opinion article, Tjalsma and colleagues present a driver–passenger model to account for the distinct temporal associations of particular bacteria with the diseased tissue during oncogenesis.

Gene transfer agents (GTAs) have been identified in four bacterial and archaeal lineages. These genetic entities resemble phages, but the genes encoding the phage-like structure of the GTA particle are encoded within the genome of the producing cell, and GTAs instead package random pieces of the producing cell's genome. Here, the defining characteristics, potential functions and possible origins of GTAs are reviewed.

The twin-arginine translocation (Tat) protein export system is present in the membranes of most bacteria and archaea and transports folded proteins while maintaining the permeability barrier of the membrane. Here, Palmer and Berks summarize the recent advances in our understanding of how this remarkable system functions.

Did the cenancestor have a phospholipid membrane? In this Opinion article, Lombard, López-García and Moreira discuss how recent top-down phylogenomic analyses have provided new information to address this question.

Encounters between the replication and transcription machineries occur frequently in bacterial cells and are detrimental to fitness. Here, Grossman, Wang and colleagues review the two different types of replication–transcription conflict and describe the mechanisms that bacteria use to prevent and resolve these conflicts.