Reviews & Analysis

Interactions between insects and microorganisms are important in insect disease, dissemination of pathogens to animals and plants, and as models for host–pathogen interactions. Here, the interactions between bacteria and insects, and the strategies that both use to influence these interactions, are reviewed.

In this Opinion article, the authors consider the classification of viruses, and propose a new classification system that divides all biological entities into two groups of organisms: ribosome-encoding organisms (eukaryotes, archaea and bacteria) and capsid-encoding organisms (viruses). Unclassified selfish nucleic acids are grouped as 'orphan replicons'.

The successful replication of mammalian DNA viruses requires that they gain control of key cellular signalling pathways, including the phosphatidylinositol 3′-kinase–Akt–mammalian target of rapamycin (PI3K–Akt–mTOR) pathway. This Review discusses the range of mechanisms that mammalian DNA viruses use to activate this pathway, as well as the multiple mechanisms these viruses have evolved to circumvent inhibitory stress signalling.

Knipe and Cliffe review the mechanisms that underlie the switch from a lytic to a latent infection in the widespread pathogen herpes simplex virus (HSV). They propose a new model in which an epigenetic switch determines whether a lytic or a latent infection occurs and discuss viral functions that might regulate chromatin assembly on the HSV genome and effect this epigenetic switch.

Stewart and Franklin discuss the processes that generate chemical gradients in biofilms, the genetic and physiological responses of the bacteria as they adapt to these gradients and the techniques that can be used to visualize and measure microscale physiological heterogeneities of bacteria in biofilms.

The insertion of proteins into the bacterial cytoplasmic membrane is a complex and dynamic process. Sophisticated translocases are responsible for decoding the topogenic sequences within membrane proteins that direct membrane protein insertion and orientation. Here, Xie and Dalbey highlight what is known about the role of the Sec and YidC translocases in the folding and insertion of bacterial membrane proteins.

CRISPR systems, which are composed of direct repeats that are separated by similarly sized non-repetitive spacers, confer resistance to phages in many bacteria and most archaea. This new antiviral tactic is thought to involve an RNA-interference-like mechanism, and is reviewed in this Progress article.

Leah Cowen reviews the mechanisms that potentiate the evolution of fungal drug resistance, with an emphasis on the central role of the molecular chaperone heat shock protein 90 (Hsp90) in altering the relationship between genotype and phenotype in an environmentally contingent manner, which thereby 'sculpts' the course of evolution.

Bacteria can precisely adjust their membrane lipid compositions to control the biophysical properties of their membranes, which allows them to thrive in various physical environments. Here, Charles Rock and Yong-Mei Zhang review the biochemical processes that are responsible for bacterial membrane lipid homeostasis.

Filamentation has been implicated in bacterial survival of exposure to environmental stresses, but in this Opinion, Sheryl S. Justice and colleagues propose that the morphological plasticity of pathogenic bacteria is a direct and adaptive response to the sensing of environmental changes.

The complement system is an essential and efficient component of the immune system's antimicrobial machinery, but many pathogens have developed parallel routes of escape. Understanding complement processes and interactions on a molecular level is essential for the development of novel therapies, and this Review provides a comprehensive overview and update of recent developments in this field.

Mutually beneficial relationships between prokaryotes and eukaryotes are possible because of the ability of microorganisms and their hosts to communicate with each other. In this Review, David Hughes and Vanessa Sperandio discuss how inter-kingdom communication can be 'hijacked' by bacterial pathogens, and how hosts can fight back.

Dietary plant polysaccharides are a major energy source for the anaerobic microbiota that inhabit the mammalian large intestine and rumen. Flint and colleagues discuss polysaccharide utilization by gut anaerobes, focusing on two examples, the use of insoluble structural polysaccharides byRuminococcus flavefaciens and the use of starch by Bacteroides thetaiotaomicron.

The exit of intracellular bacteria from host cells is a crucial stage in microbial pathogenesis that is driven by an evolutionary requirement for efficient dissemination to neighbouring cells and transmission to new hosts. In this comprehensive Review, the authors discuss the diverse repertoire of strategies that is used by intracellular pathogens to escape their host cells.

Most viral vaccines protect against disease by generating neutralizing antibodies. This Review examines the problem of eliciting broad HIV-1 neutralization through vaccination by drawing parallels with the successful subunit influenza virus vaccine and with efforts to develop a pandemic influenza vaccine.

For the full potential of microbial genomics to be realized, a complete understanding of the metabolic capacities of microbial life is required. In this Innovation, the authors discuss new system-biology technologies that enable the identification of novel metabolites and their biochemical connections within metabolic networks.

Shigellause a type III secretion system to deliver effector proteins into the host-cell cytoplasm, where they can usurp host-cell functions and signalling pathways. In this Progress article, Chihiro Sasakawa and colleagues highlight the most recent advances in our understanding of the exact functions of the manyShigellatype III-secreted effectors.

Why do we seem to be losing the fight against tuberculosis? In this Review, James Sacchettini, Eric Rubin and Joel Freundlich review the recent and ongoing efforts to produce new antitubercular drugs and the properties of current investigational agents.

Targeting bacterial virulence is an alternative approach to antimicrobial therapy. This Review considers recent efforts towards antivirulence-based drug discovery in the framework of marketable drugs, and discusses what challenges remain and the factors that are crucial to developing the antivirulence therapeutic approach.

Salmonellae cause systemic diseases by invading and replicating inside epithelial cells and macrophages. Two functionally distinct type III secretion systems that are encoded onSalmonella pathogenicity islands 1 and 2 transfer Salmonellaspp. effector proteins into host cells. The dynamic molecular interplay between these bacterial effectors and host responses is discussed in this Review.