Review Articles in 2013

Vaheri and colleagues discuss the molecular and cell biology of hantavirus infection and provide an overview of the virus-induced and immune-mediated pathology caused by this virus family in humans.

Raoult and colleagues review recent developments in clinical microbiology, including the development of mass spectrometry-based diagnostics and point-of-care tests, which might change clinical practice.

Clathrin-mediated endocytosis is exploited by bacterial and viral pathogens during internalization. Humphries and Way review recent studies which highlight the fact that, in addition to a structural role, clathrin can function as a signalling platform during pathogen entry, and other studies revealing that, in conjunction with actin, clathrin is involved in pathogen cell–cell spread and release.

Many mobile genetic elements, such as transposons, plasmids and viruses, must cleave their own DNA to effect transposition, replication or conjugation. Here, Chandler and colleagues describe the HUH endonucleases, which use a unique mechanism to cleave and rejoin single-stranded DNA in order to mobilize and disseminate such elements.

Cyclic di-AMP is one of the latest cyclic nucleotide second messengers to be discovered in bacteria. Here, Corrigan and Gründling provide an overview of the enzymes involved in its synthesis and degradation, the currently known receptor proteins and the cellular pathways that are known to be directly or indirectly controlled by this newly identified second messenger.

The obligate intracellular bacteriumCoxiella burnetii causes both acute and chronic zoonotic infections. Here, Samuel and colleagues discuss the recent technological advances that have facilitated a deeper understanding of the molecular mechanisms of C. burnetiipathogenesis, including host cell invasion and modulation by virulence factors exported through the type IV Dot/Icm secretion system.

Lipid A is the bioactive component of the Gram-negative outer membrane and is extensively remodelled to enable the bacterium to subvert the immune system of the host. Here, Needham and Trent describe the regulation of lipid A-modifying enzymes, the host defences that target lipid A and the strategies that bacterial pathogens use to avoid immune detection.

Hepatitis C virus infection is a major cause of liver cirrhosis and cancer, and current therapies are often ineffective or have severe side effects. Here, Bartenschlager and colleagues review how structural and functional insights into the viral life cycle have allowed the development of novel direct-acting antiviral agents.

Katze and colleagues provide an overview of the evolution of systems virology and the insights obtained from using such methodologies to study virus–host interactions. Combining systems, mathematical and computational approaches with traditional virology research will offer a better understanding of how viruses cause disease and will help in the development of therapeutics.

To survive in oxic environments, all organisms require mechanisms to degrade toxic reactive oxygen species (ROS). In this Review, James Imlay describes the oxidative stress response ofEscherichia coliand considers the damage caused by ROS and the adaptive strategies used by this bacterium to minimize intracellular ROS accumulation.

The global rise of antibiotic resistance and the paucity of novel antimicrobial compounds in the pipeline have revived interest in the use of metals as antimicrobial agents. Here, Lemire, Harrison and Turner describe the principles of metal toxicity, the uptake of metals by microbial cells and the distinct types of cellular damage that they cause. They also discuss the use of metal-based agents as antimicrobials.

Helicobacter pyloriresides exclusively in the hostile environment of the stomach in approximately 50% of the human population and is a strong risk factor for cancer. Here, Salama, Hartung and Müller describe how this bacterium establishes persistent colonization through the interplay of virulence determinants and the subversion and manipulation of the host's immune response.

Organophosphonates contain the chemically stable C–P bond and are the most abundant form of P in the biosphere. McGrath and colleagues review recent advances in our understanding of microbial phosphonate metabolism and the role of these compounds in the global P cycle.

Small ubiquitin-like modifier (SUMO) modifications have emerged as key regulators of many intracellular pathways. Here, Everett and colleagues review the interplay between viruses and the SUMO pathway in infected cells, and the consequences of these interactions for the viral life cycle and for intrinsic and innate immunity.

Microorganisms can form complex, spatially organized communities that are coordinated by both physical and chemical intercellular interactions, as well as by other molecules present in the surrounding environment. Here, Whiteley and colleagues describe a number of microscale techniques for reproducing small bacterial communities in the laboratory. They also discuss the analytical tools available to monitor the impact of spatial organization on both bacterial behaviour and the generation of phenotypic heterogeneity.

Many bacterial species have evolved specialized secretion systems that deliver effector proteins into host cells in order to promote bacterial survival and replication. To exert their functions in a spatially coordinated manner, effector proteins must be accurately targeted to specific subcellular compartments. Here, Hicks and Galán review how bacterial effectors exploit the host cell machinery involved in processes such as lipidation and ubiquitylation to accurately target the biochemical activities of these effectors within the host cell.

In vitrosingle-molecule technologies have emerged as powerful tools for the study of complex biological phenomena. Here, Robinson and van Oijen summarize the latest insights that fluorescence-based single-molecule studies have provided for DNA replication, transcription and translation in bacterial cells.

RNA viruses have extremely high mutation rates, which are crucial for the ability of these viruses to adapt but can also lead to population extinction. Here, Andino and colleagues describe the mechanisms that RNA viruses use to cope with the high mutational load and discuss the impact of mutational robustness on population dynamics, pathogenicity and antiviral therapies.

Many plants engage in symbiotic associations with microorganisms, in which the interactions are beneficial to both partners. Two of the best studied partnerships are rhizobial and mycorrhizal colonization. Giles Oldroyd highlights the commonalities in the symbiosis signalling pathways involved in these associations and how, despite these commonalities, sufficient specificity is maintained to ensure appropriate responses to each symbiont.

The ability of human papillomaviruses (HPVs) to cause disease is strongly dependent on the strict coordination of viral gene expression with the differentiation state of the infected cell. Here, Johansson and Schwartz summarize the role of splicing and polyadenylation in the regulation of HPV gene expression and discuss the viral and cellular factors that control these processes.