Review Articles in 2012

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.

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.

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.

Asthma is a heterogeneous, complex disease, and its causes have environmental, immunological, genetic and microbial components. In this Review, Edwardset al. describe how microorganisms can influence the risk, severity and pathogenesis of asthma, and protection against the disease.

The public health community worldwide has struggled with tuberculosis (TB) control for many years. Here, Christian Leinhardt and colleagues review the evolution of global TB control policies, including the Stop TB Strategy, and discuss the challenges and obstacles associated with control of this ancient disease.

Dissolved oxygen concentration is a crucial organizing principle in marine ecosystems. In this Review, Hallam and colleagues describe recent advances in our understanding of the ecological and microbial features of oxygen-starved regions of the ocean, known as oxygen minimum zones.

With the advent of high-throughput sequencing, the genomes of many economically important filamentous fungal and oomycete plant pathogens have been sequenced, revealing a trend in several lineages for repeat driven expansion. Sylvain Raffaele and Sophien Kamoun review the genomic features of these pathogens, with a particular focus on genome structure and plasticity.

Retroviral integration into the genome of a germ cell can lead to colonization of the germ line, giving rise to an endogenous retrovirus (ERV). This Review describes the intimate evolutionary relationship between these viruses and their vertebrate hosts.

In this Review, Martens and colleagues describe how dietary and endogenous glycans shape the composition of the gut microbiota and how individual microorganisms degrade these glycans. They also highlight the potential to influence this ecosystem for better health and nutrition.

Many Gram-negative bacteria use type II secretion systems (T2SSs) to translocate a range of proteins across the outer membrane from the periplasm. In this Review, Hol and colleagues describe how recent structural and biochemical studies have provided insights into the biogenesis and architecture of T2SSs and the mechanism by which they function.

Over the past 30 years researchers have developed a global picture of bacterial evolution by using both laboratory-basedin vivo evolution experiments and in silicoevolution of digital organisms. Schneider and colleagues review the advantages and disadvantages of both approaches and synthesize the contributions of both methods to our understanding of bacterial adaptation.

Given the rise of antibiotic resistance and the decreasing rate of discovery of new antimicrobials, exploring new paradigms for antimicrobial therapy is essential. Here, Hancock, Nijnik and Philpott describe the promise of one such alternative approach: host-directed immunomodulatory therapies for enhancing protective antimicrobial immunity.

HIV-1 has been subjected to more structural analyses than any other virus. Here, Engelman and Cherepanov review recent advances in HIV-1 structural biology, focusing on the impact that these results have had on our understanding of viral replication and on the development of new therapeutics.

Arias and Murray discuss the factors that may have contributed to the rise of enterococci as nosocomial pathogens, with an emphasis on the epidemiology and pathogenesis of these species and their mechanisms of resistance to the most relevant anti-enterococcal agents used in clinical practice.

RNA thermometers allow bacteria to respond quickly to temperature changes by controlling the translation of existing or nascent mRNAs. Here, Kortmann and Narberhaus discuss zipper-like thermometers, which control the translation of heat shock and virulence genes, and switch-like thermometers, which control the translation of cold shock and phage genes.

Modelling of metabolic networks has facilitated genome-scale analysis of microbial metabolism for both basic and applied uses. Here, Palsson and colleagues describe the ever-growing 'phylogeny' of constraint-based reconstruction and analysis (COBRA) approaches used for modelling numerous aspects of microbial life.