Review Articles

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.

Autotransporters are a superfamily of proteins that were thought to contain all of the functional elements required for their delivery, via the type V secretion pathway, to the outer membrane of Gram-negative bacteria. In this Review, Leyton, Rossiter and Henderson describe how recent studies have challenged the perceived simplicity of this secretion pathway.

The bacterial signalling nucleotide ppGpp is known to regulate promoter selection by RNA polymerase to direct the response to stress. Here, Dalebroux and Swanson look at other ways in which ppGpp helps bacteria to alter their physiology in order to accommodate fluctuating nutrient supplies and environmental stresses.

Interactions between the pathogenic neisseriae (Neisseria gonorrhoeae and Neisseria meningitidis) and neutrophils are central to the progression of both gonorrhoea and meningococcal meningitis. Here, Criss and Seifert review these interactions and propose a model in which this relationship promotes, rather than blocks, the infection cycle.

Production of viral progeny requires the coordination of a series of events. In this Review, Patton and colleagues examine structural insights into how regulation of the life cycle of rotaviruses and otherReoviridaefamily members is coupled with the assembly and disassembly of the viral particle.

Synthetic biology approaches for thede novodesign of biosynthetic pathways have developed rapidly in recent years. Takano and colleagues describe the latest computational tools available and discuss how they can be applied now and further developed for future synthetic biology efforts.

Justin Radolf and colleagues summarize our accumulated knowledge of the molecular biology and virulence ofBorrelia burgdorferi, and its interactions with the arthropod vector and mammalian hosts.

The peptidoglycan sacculus maintains bacterial cell shape and provides mechanical strength to resist osmotic challenge. In this Review, Vollmer and colleagues describe recent insights into the mechanisms of peptidoglycan synthesis in Gram-negative bacteria and how this process is regulated by cytoskeletal and outer-membrane components.

The replication of positive-sense RNA ((+)RNA) viruses involves numerous interactions between the RNA and proteins of the virus and proteins, membranes and lipids of the host. Host factors are thus key determinants of viral pathology as well as viral evolution. In this Review, Nagy and Pogany outline our current understanding of the host factors that facilitate the replication of (+)RNA viruses.

Proteasomes exist in all domains of life and serve to degrade proteins. In eukaryotes, proteins are primarily targeted for proteasomal degradation through the addition of ubiquitin. Similarly, archaea and bacteria modify proteins with Pup and Samps, respectively, and this may also serve as a signal for proteasomal degradation.

Candida albicanscan grow as unicellular budding yeast cells and as filamentous hyphae. Mihai Netea and colleagues discuss the molecular mechanisms that drive this dimorphism, the changes that lead to differential interaction with the host, and the immunological mechanisms that discriminate between tissue colonization and invasion.