Progress

Previously, Zika virus was thought to cause mild infection, and serious complications only recently emerged. Liu, Shi and Qin discuss how the virus has evolved during its recent global spread and consider how these changes might be linked to pathogenesis.

Marine oxygen minimum zones are expanding globally as a result of rising temperatures. In this Progress article, Bertagnolli and Stewart describe the ecological and functional diversity of the microbial communities that inhabit these zones and their contribution to biogeochemical cycles.

In this Progress article, McGinn and Marraffini review recent studies that have advanced our understanding of the molecular mechanisms of spacer integration, protospacer capture and primed spacer acquisition, and discuss the future of the field.

Canonical two-component systems catalyse autophosphorylation of the histidine kinase, transfer of the phosphoryl group to the regulator and dephosphorylation of the phosphoregulator. In this Progress article, Jacob-Dubuisson and colleagues highlight recent structural insights into the signalling and catalytic mechanisms of sensor histidine kinases.

The recent epidemic of Zika virus (ZIKV) in the Americas has revealed the devastating consequences of ZIKV infection, particularly in pregnant women. In this Progress article, Barouch and colleagues discuss recent preclinical studies and lessons learned from first-in-human clinical trials with ZIKV vaccines.

In this Progress article, Collins and colleagues discuss how CRISPR-based analyses in genetically intractable microorganisms, including mycobacteria, fungi and parasites, have enabled the discovery of novel gene functions, the investigation of genetic interaction networks and the identification of virulence factors.

CRISPR–Cas adaptive immune systems are widespread in prokaryotes. In this Progress article, Maxwell and colleagues highlight how phages and other mobile genetic elements inactivate CRISPR–Cas systems using anti-CRISPR proteins and outline evolutionary and biotechnological implications of anti-CRISPR protein activity.

Prokaryotic Argonaute proteins, homologues of eukaryotic Argonaute proteins involved in RNA interference, have recently been demonstrated to mediate host defence in archaea and bacteria. In this Progress article, van der Oost and colleagues explore the structures and biological functions of the prokaryotic Argonaute proteins, and discuss their potential applications in genome editing.

In this Progress article, Buchanan and colleagues discuss recent studies that have advanced our understanding of the structure of the fully assembled β-barrel assembly machinery (BAM) complex and the interactions between the individual components. They also detail the mechanistic insights that have been gained and explore two emerging models for BAM-mediated outer membrane protein biogenesis in bacteria.

Protozoan parasites produce extracellular vesicles to communicate with the host and within the parasite population. In this Progress article, Hajduk and colleagues review the production and effects of extracellular vesicles from parasites, includingPlasmodium spp., Trichomonas vaginalisand kinetoplastids.

In this Progress article, Stephanie Karst describes how the gut microbiota promotes intestinal infection by enteric viruses. She discusses direct mechanisms by which bacteria stabilize viral particles and facilitate viral attachment to host cells, and indirect mechanisms by which the microbiota suppresses antiviral immune responses.

Although the mechanisms of CRISPR–Cas interference have largely been elucidated, how new sequence memories are stored had remained unknown. In this Progress article, Amitai and Sorek discuss recent advances in the study of this adaptation stage of CRISPR immunity.

It has recently been suggested that p53, which regulates the survival and metabolism of host cells, is commonly manipulated by intracellular bacterial pathogens. In this Progress article, Siegl and Rudel discuss mechanisms of p53 manipulation and consider the consequences for pathogenesis.

Viral apoptotic mimicry, defined by the exposure of phosphatidylserine on the pathogen surface, is emerging as a common theme used by enveloped viruses to promote infection. In this Progress article, Amara and Mercer discuss how viruses acquire phosphatidylserine and how this mimicry might facilitate cell entry and evasion of the immune response.

The archaeal genome is organized by either eukaryotic-like histone proteins or bacterial-like architectural proteins. Dame and colleagues discuss the interplay between chromatin proteins and components of the basal and regulatory transcription machinery, and describe how these factors cooperate in nucleoid structuring and gene regulation.

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.

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.

Although the CRISPR–Cas system of prokaryotes has an established role in defence, recent studies suggest that this system has other functional roles. Here, Westra and colleagues explore the more unconventional roles of CRISPR–Cas, such as endogenous gene regulation and genome remodelling, and consider their evolutionary implications.

Understanding the pharmacokinetic and pharmacodynamic properties of anti-tuberculosis drugs is crucial for designing more effective dosing regimens. In this Progress article, Véronique Dartois describes the methods that are available to monitor the distribution of drugs as they travel from the blood compartment to granulomatous lesions and penetrate infected immune cells to finally reach their intended targets inside mycobacterial cells.

Energy-coupling factor transporters mediate the uptake of essential micronutrients in prokaryotes. On the basis of recent structural studies, Dirk Slotboom discusses a testable model for the unusual mechanism of transport that is involved and considers the implications for our understanding of membrane transporters.