Review Articles in 2014

Recent studies have indicated that the recognition of microorganism-associated molecular patterns (MAMPs) by G protein-coupled receptors (GPCRs) involves a larger set of chemotactic MAMPs and corresponding GPCRs than was previously thought. Peschel and colleagues review bacterial leukocyte-attracting molecules, the corresponding human receptors, and their roles in antibacterial host defence.

Some bacteria interact with the endoplasmic reticulum (ER) to generate intracellular compartments that promote bacterial replication. However, conditions of physiological stress in the ER elicit the unfolded protein response (UPR), which is a cytoprotective response that is also involved in innate immune sensing. Here, Celli and Tsolis discuss how bacteria and the ER interact, including how bacteria induce the UPR, how subversion of the UPR promotes bacterial proliferation and how the UPR participates in innate immune responses against intracellular bacteria.

Antibiotic-resistant bacteria are causing a global health crisis. Here, the authors review recent advances in our understanding of the mechanisms by which bacteria are either intrinsically resistant or acquire resistance to antibiotics. This information should aid the discovery and development of new compounds that can circumvent or neutralize existing resistance mechanisms.

The marine cyanobacteriumProchlorococcusis the most abundant photosynthetic organism on earth. In this Review, Chisholm and colleagues highlight the enormous genomic diversity of this phototroph, discuss the factors that contribute to this diversity and consider its ecological consequences.

Influenza A virus has only eight genes, so it is dependent on host proteins and pathways to mediate viral ribonucleoprotein (vRNP) trafficking and to promote vRNP functions at all stages of the virus life cycle. Here, Kawaoka and colleagues describe the trafficking and functions of influenza A vRNPs in host cells, emphasizing how vRNPs interact with and depend on host factors and pathways, how vRNP structure contributes to its function and the key open questions that still need to be answered.

Acetogenic bacteria rely on the reduction of CO₂ to acetate by the Wood–Ljungdahl pathway to couple energy conservation and biomass production. However, how energy is conserved in acetogens has been an enigma. Here, Schuchmann and Müller describe recent insights into the biochemistry and genetics of the energy metabolism of model acetogens, highlight how these bacteria link CO₂fixation to energy conservation and propose a new bioenergetic classification for acetogens.

The shift in the receptor-binding specificity of influenza A viruses is mostly determined by mutations in viral haemagglutinin. In this Review, Gao and colleagues discuss recent crystallographic studies that provide molecular insights into haemagglutinin–host receptor interactions that have enabled several influenza A virus subtypes to 'jump' from avian to human hosts.

To understand the network of reactions within the biogeochemical (iron) Fe cycle, it is necessary to determine which abiotic or microbially mediated reactions are dominant under various environmental conditions. Kappler and colleagues review the major biotic and abiotic reactions in the biogeochemical Fe cycle.

Recent efforts have focused on the development of therapies that could eradicate HIV-1 infection or achieve a durable remission of viraemia in the absence of antiretroviral therapy; however, targeting viral quiescence within specific cellular reservoirs so that residual infection can be cleared remains a challenge. In this Review, Margolis and colleagues explore new approaches to eradicate established HIV-1 infection.

Viral infection is induced by binding of the virus to host sialylated glycans on the cell surface. Glycan array studies and structure determination provide new insights into the virus–silaic acid interaction and its functional role in viral disease. This Review highlights principles of glycan binding that are used by influenza virus, reovirus, adenovirus and rotavirus.

Orthobunyaviruses are transmitted by arthropod vectors and can infect humans, animals and crops. In this Review, Elliott describes recent genetic and structural advances that have revealed important insights into the composition of orthobunyavirus virions, viral transcription and replication, and viral interactions with the host innate immune response.

Accumulating evidence suggests that the gut microbiota has a role in the aetiology of colorectal cancer (CRC). In this Review, Flint and colleagues discuss the complex interplay between diet, the microbiota and microbial metabolites and argue that the combined metabolome of the microbiota has both protective and detrimental effects on inflammation and the progression of CRC.

The Hawaii Ocean Time-series programme recently completed 25 years of continuous operation. Matthew Church and David Karl look back on some of the major discoveries that have come from this long-term programme and its contribution to our evolving understanding of microbial oceanography.

Marine phytoplankton blooms are annual spring events that are accompanied by a surge in heterotrophic bacteria, primarily roseobacters, flavobacteria and members of the Gammaproteobacteria, which recycle most of the carbon that is fixed by the primary producers. In this Review, Buchanet al. describe the emerging physiological features and functions of these bacterial communities and their interactions with phytoplankton.

Pathogens block or subvert host cellular processes to promote successful infection. One host protein that is targeted by invading pathogens is the small GTPase RAB11, which functions in vesicular trafficking. Bier and colleagues discuss the various mechanisms that pathogens have evolved to disrupt or subvert RAB11-dependent pathways as part of their infection strategy.

The mouse pathogenCitrobacter rodentium has long been used as a model for investigating the pathogenesis of the important enteric human pathogens, enterohaemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli(EPEC). In this Review, Frankel and colleagues discuss the infection cycle of this pathogen, the mucosal immune response that is elicited and the role of the gut microbiota in preventing colonization.

Although studies in 2D cell culture systems have provided great insights into the biology and pathogenesis of HIV-1 infection, such studies cannot account for many aspects of host physiology that affect HIV-1in vivo. Fackler et al. discuss the development and application of more integrative studies, including organotypic 3D culture systems, small-animal models and advanced live-cell imaging, and the impact of such studies on our understanding of the mechanisms of HIV-1 spread.

Bacterial ADP-ribosyltransferase toxins (bARTTs) transfer ADP-ribose to a range of eukaryotic proteins to promote bacterial pathogenesis. In this Review, the authors discuss the structural and functional properties of the most recently identified novel bARTTs, which are produced by various human, insect and plant pathogens and were identified using bioinformatic analyses.

Compared with traditional model bacteria, the processes of growth and division are unusual in mycobacteria. In this Review, Rubin and Kieser discuss polar growth, asymmetric division and cell wall remodelling in mycobacteria and consider how these processes might contribute to the population heterogeneity and pathogenesis ofMycobacterium tuberculosis.

Humans can resist infection by African trypanosomes, owing to the trypanolytic activity of apolipoprotein L1 (APOL1), which is associated with two serum complexes, trypanosome lytic factor 1 (TLF1) and TFL2.Trypanosoma brucei rhodesiense and Trypanosoma brucei gambiense evade this defence mechanism by expressing resistance proteins and in turn, populations in western Africa can restore resistance to T. b. rhodesiense via sequence variation in APOL1. Pays et. al. review this complex relationship and its evolutionary importance.