Reviews & Analysis

Polintons are large DNA transposons that are widespread in the genomes of eukaryotes. Here, Krupovic and Koonin propose that Polintons were the first group of eukaryotic double-stranded DNA viruses to evolve from bacteriophages and that they gave rise to most large DNA viruses of eukaryotes and various other selfish elements.

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.

In this Opinion article, Baquero and colleagues propose a hierarchical system for estimating the risks associated with genes present in environmental resistomes, by evaluating the likelihood of their introduction into human pathogens, and the consequences of such introduction events for the treatment of bacterial infections.

The debate on whether to allow experiments that increase the transmission and/or pathogenicity of potential pandemic pathogens has recently gained renewed attention, particularly as a result of studies on influenza viruses. Here, five experts discuss the benefits and risks associated with these gain-of-function experiments, and how the ongoing debate affects the scientific community and the general public.

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.

In addition to their role in inhibiting apoptosis, viral anti-apoptotic proteins function in multiple immune and metabolic pathways to promote fitness and pathogenesis. In this Progress article, Jung and colleagues review novel functions of these viral proteins in the regulation of autophagy, as well as in the nuclear factor-κB (NF-κB) pathway and in interferon signalling.

Recent studies have shown that submicroscopicPlasmodium falciparuminfections are an important, but often undetected, reservoir of malaria and are major contributors to transmission. In this Opinion article, Bousema and colleagues discuss the epidemiology of these infections and the prospects for intervention strategies, and they argue for the wider deployment of molecular diagnostic tools to understand and quantify infection dynamics.

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.

In this Opinion article, Dan Barouch and Louis Picker discuss recent data regarding the clinical development of novel serotype adenovirus and cytomegalovirus vaccine vectors for use in HIV-1 vaccines.

Combination antiretroviral therapy (cART) has revolutionized the treatment of HIV-1 infection, but the mechanistic basis of successful treatment is poorly understood. In this Opinion article, Siliciano and Laskey present a model to assess the efficacy of antiretroviral drugs and argue that this is a more accurate metric to predict the success of cART than current metrics.

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.

The crosstalk between the metabolic pathways of intracellular pathogens and host cells can have important consequences for infection. In this Progress article, Neyrolles and colleagues describe recent insights into nitrogen acquisition and assimilation inMycobacterium tuberculosisand highlight potential links to bacterial virulence.

The extensive genome reduction that is observed in bacterial endosymbionts is expected for species with small effective population sizes; however, similar reduction is observed in some free-living marine cyanobacteria that have extremely large effective population sizes. In this Opinion article, the authors discuss the different hypotheses that have been proposed to account for this reductive genome evolution at both ends of the bacterial population size spectrum.

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.