Review Articles in 2015

Phenotypic heterogeneity is a ubiquitous feature of microbial communities, even within groups of genetically identical cells. In this Review, Martin Ackermann describes the molecular mechanisms that lead to phenotypic heterogeneity and discusses how heterogeneity can increase survival and productivity of microbial populations.

Microorganisms produce a wealth of structurally diverse specialized metabolites with great potential for use in medicine and agriculture. In this Review, Rutledge and Challis provide an overview of the approaches that are available to identify and activate cryptic microbial biosynthetic gene clusters, which represent an untapped reservoir of useful metabolites.

In this article, Eric Freed reviews recent progress in elucidating the steps involved in HIV-1 assembly, release and maturation, highlighting how these events are orchestrated by the viral Gag precursor protein and how this information is being used to develop novel anti-HIV-1 therapeutics.

In this Review, Lee and colleagues describe the mechanism of fusion between virus and host cell membranes that occurs during enveloped virus entry and discuss how broad-spectrum antivirals can target this process to prevent viral infection.

HIV-1 infection typically results from the transmission of a single viral variant, the transmitted/founder (T/F) virus. In this Review, Joseph and colleagues discuss how studying these T/F viruses contributes to a better understanding of HIV-1 transmission and affects prevention strategies.

Crabb and colleagues discuss the molecular genetics systems that are currently available forPlasmodium falciparum and Plasmodium berghei, including conditional systems and gene editing tools, and examine the insights that have been gained into the function of genes that are important during the blood stages of the parasites.

In this Review, Waksman and colleagues describe the structural and mechanistic details of the six secretion systems (types I–VI) of Gram-negative bacteria, the unique mycobacterial type VII secretion system, the chaperone–usher pathway and the curli biogenesis machinery. They discuss both conserved and divergent properties of these systems and their potential as targets of novel antibacterial compounds.

In this Review, Huttenhower and colleagues discuss how integrating multi-omic data types — including genomics, transcriptomics, proteomics and metabolomics — enables a better characterization of the composition and function of human-associated and environmental microbial communities.

In this Review, Malim and colleagues discuss the evidence that type I interferons (IFNs) can control HIV-1 replicationin vivoand debate the controversial role of IFNs in promoting the pathological sequelae of chronic HIV-1 infection.

Bacteria form biofilms as a strategy for survival and persistence. In this Review, Yildiz and colleagues discussVibrio cholerae surface attachment and the biofilm matrix components. They also review the regulatory network that governs V. choleraebiofilm formation, including the transcriptional regulators of key genes involved in this process, as well as the roles of small nucleotides and small RNAs.

In bacteria, ribosome stalling is a frequent event that threatens viability. In this Review, Kenneth Keiler discusses the triggers of ribosome stalling, the physiological consequences of stalling and the mechanisms used by bacteria to rescue stalled ribosomes, includingtrans-translation and the alternative pathways mediated by alternative ribosome-rescue factor A (ArfA) and ArfB.

Urinary tract infections (UTIs) pose a severe public health problem and are caused by a range of pathogens. In this Review, Hultgren and colleagues discuss how basic science studies are elucidating the molecular mechanisms of UTI pathogenesis and how this knowledge is being used for the development of novel clinical treatments for UTIs.

In this Review, Gerdes and colleagues discuss the multifaceted alarmones guanosine tetraphosphate and guanosine pentaphosphate (collectively referred to as (p)ppGpp) and their functions in the regulation of bacterial physiology, including their synthesis and degradation, as well as their role in transcriptional regulation, in GTP biosynthesis and in the formation of bacterial persisters.

Salmonella entericaserovars are human pathogens that are commonly used to study host–bacterium interaction mechanisms. In this Review, Bäumler and colleagues discuss how the innate immune system recognizes non-typhoidal and typhoidal serovars, and how specific virulence factors and changes in virulence gene regulation alter innate immune responses.

In this Review, Miller and colleagues discuss the arsenal of effector proteins that salmonellae use to manipulate their animal hosts, in addition to the host response to these infections. The authors also discuss the challenges ahead for unravelling the mechanistic details of effector function.

Predicting the future global distribution of vector-borne diseases is a complex task that depends on the generation of accurate mathematical models. Here, Messina and colleagues compare and contrast the main approaches that have been used to predict the future distribution of dengue and propose a set of minimum criteria for future projections that, by analogy, are applicable to other vector-borne diseases.

The detection and subsequent analysis of low-abundance microbial populations — the 'rare biosphere' — have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. Lynch and Neufeld discuss the ecology of rare microbial populations and highlight molecular and computational methods for targeting taxonomic 'blind spots' in the rare biosphere of complex microbial communities.

B cells are essential components of the immune response against infection. However, several bacteria, viruses and parasites are able to infect B cells and manipulate B cell functions and survival. Here, the authors review how pathogens use B cells as reservoirs, manipulate B cell differentiation and interfere with B cell survival, and they discuss the implications for ongoing immune responses.

In this Review, Fuhrman and colleagues summarize our current understanding of marine microbial community dynamics at various scales — from hours to decades — and consider how long-term time series illustrate important ecological concepts such as community resilience and seasonality, as well as interactions among microorganisms in the global oceans.

Plasmodium falciparum, the malaria parasite, relies on post-translational modifications of proteins to regulate several fundamental aspects of its life cycle and pathogenesis. Here, Doerig and colleagues focus on the roles of protein phosphorylation, acetylation, methylation and lipidation inP. falciparumbiology, and they discuss how the enzymes that mediate these modifications can be targeted by novel antimalarial drugs.