Review Articles in 2008

What makes the human body a good growth medium for bacterial pathogens? In this Review, Brown, Palmer and Whiteley outline how the host growth environment affects disease and discuss the potential for targeting host metabolic pathways for therapeutic development.

Using the process of carbon catabolite repression (CCR), bacteria control gene expression and protein activity to preferentially metabolize the carbon sources that are most easily accessible and allow fastest growth. Recent findings have provided new insight into the mechanisms that different bacteria use to control CCR.

The nanoscale analysis of microbial cells using atomic force microscopy (AFM) is emerging as an exciting, rapidly evolving research field. Specifically, AFM allows us to address fundamental microbiological questions by observing membrane proteins and live cells at high resolution.

Central nervous system infections are an important cause of morbidity and mortality. Here, Kwang Sik Kim summarizes our current understanding of the mechanisms that are involved in traversal of the blood–brain barrier by selected meningitis-causing microorganisms.

The shewanellae are masters of metabolism and can catabolize numerous carbon sources either aerobically or anaerobically using a range of electron acceptors. Ubiquitous among microbial communities from marine to soil environments, this genus is important in carbon cycling and bioremediation. Systems-biology approaches could shed new light on the ecophysiology of these bacteria.

In recent years, the interactions between viruses and cellular metabolism have become a topic of great interest. Viral infections that disrupt liver function can be accompanied by changes in iron homeostasis, and iron loading of the liver can exacerbate chronic viral disease. Here, Hal Drakesmith and Andrew Prentice consider some examples of how viruses such as HIV-1, hepatitis C virus and arenaviruses manipulate cellular iron metabolism.

Oncolytic viruses can be reprogrammed into vectors for use in cancer therapy by combining three types of modification: targeting, arming and shielding. Roberto Cattaneo and colleagues discuss the principles of virus reprogramming using adenovirus, a DNA virus with a naked icosahedral capsid, and measles virus, an enveloped RNA virus with a helical capsid, as the main examples.

Methanogenic archaea with and without cytochromes have been identified. This Review focuses on differences in energy conservation during the reduction of CO₂ with H₂ to CH₄. In methanogens with cytochromes, the first and last steps are coupled chemiosmotically, and the authors propose that in methanogens without cytochromes, these steps are coupled by a cytoplasmic enzyme complex that mediates flavin-based electron bifurcation.

In the first of a series of articles that focus on systems biology in microorganisms, Douglas Young and colleagues describe how systems biology provides a new and integrative tool that can be used to probe host–pathogen interactions during persistent infection, usingMycobacterium tuberculosisas an example.

Structures of RNA polymerase enzymes have advanced our understanding of transcription initiation in all kingdoms of life. This Review discusses bacterial promoter structure, recent advances in our understanding of the successive promoter–RNA polymerase complexes that contribute to the kinetics of transcription initiation and unconventional regulators that target RNA polymerase, but not DNA, for the control of transcription initiation in bacteria.

The flagellum is a beautiful structure and a fascinating model system for understanding how genes are regulated to ensure the correct assembly of a complex structure. Chevance and Hughes discuss the regulation of flagellar gene transcription and how it is intimately coupled to the assembly of this exquisite bacterial nanomachine.

Thirteen years after the first bacterial genome was sequenced, Rino Rappuoli, Stanley Falkow and colleagues review what has changed in microbiology research as a consequence of genomics and address the implications of the genomic era for the future of microbiology.

The dynamics of infectious diseases are complex, so developing models that can capture key features of the spread of infection is important. Grassly and Fraser provide an introduction to the mathematical analysis and modelling of disease transmission, which, in addition to informing public health disease control measures, is also important for understanding pathogen evolution and ecology.

Sulphate-reducing bacteria (SRB) are anaerobic microorganisms that can use sulphate as a terminal electron acceptor. These organisms are ubiquitous in anoxic habitats, where they have an important role in both the sulphur and carbon cycles. Muyzer and Stams provide an overview of the diversity, physiology and distribution of SRB and their applications to environmental biotechnology.

Bacteria and archaea have found many solutions to the problem of how to move in liquids and on solid surfaces. Although the use of a rotary flagellum in bacteria is the best-studied mode of bacterial movement, spirochaetes constrain their flagella in the periplasm, some bacteria move using type IV pili, cyanobacteria use surface spicules and others glide on surfaces without using appendages.

This Review summarizes contemporary approaches for defining species in Bacteria and Archaea and contrasts these approaches with various reports on microbial population genetic patterns. The authors conclude that contemporary method-based approaches lack a theoretical definition and new approaches are needed that should be guided by a method-free species concept that is based on cohesive evolutionary forces.

Many viruses induce the formation of altered membrane structures upon replication in host cells. This Review examines how viruses modify intracellular membranes, highlights similarities between the structures that are induced by viruses from different families and discusses how these structures could be formed.

Amann and Fuchs provide an update on recent methodological improvements to fluorescencein situhybridization protocols, with a particular focus on whether the original group-specific probes, which were mostly developed more than 10 years ago, are still valid.

The development of lactic acid bacteria as delivery vehicles for therapeutics, anti-infectives and vaccines at mucosa is discussed in this Review. Engineered LAB could be deployed to treat conditions such as allergy and inflammatory bowel disease, and might also be adopted in the fight against pathogens, including HIV-1 infection.

Rickettsiae are obligate parasites that cause sometimes deadly human infections, including epidemic typhus and Rocky Mountain spotted fever. David Walker and Nahed Ismail review the early and late events in pathogenesis and immunity, including virulence mechanisms and rickettsial manipulation of host cells.