Opinion in 2008

Similarities between the intracellular pathogenic strategies of the bacteriumYersinia pestis and the fungus Cryptococcus neoformansare used to illustrate the author's proposal that these pathogens acquired their intracellular survival strategies by a process of convergent evolution, possibly in response to interactions with other hosts in the environment, such as amoebae.

Affordable, high-throughput sequencing technology has led to a flood of publicly available bacterial genome sequence data, presenting both an opportunity and a challenge for the microbiologist. New computational approaches, such as e-Science and Grid-based technologies, can help to analyse genomic data and address these challenges.

The realization that there is structural similarity between viruses that infect all three domains of life has led to calls for additions to the way in which the virosphere is classified. In this Opinion, the vertical β-barrel viral lineage is used as an example to support reclassification of viruses into superlineages.

The functions of dendritic cells during malaria have been the subject of intensive investigations, the results of which have been controversial. Here, Michelle Wykes and Michael Good propose that the species and strain ofPlasmodiumare some of the key factors that affect dendritic cell function.

Microbial bioenergy could be used to generate large amounts of carbon-neutral alternatives to fossil fuels. This article discusses the contribution of genomic resources to the generation of bioenergy by bacteria and archaea.

The authors discuss a new hypothesis, based on a body of evidence that has accumulated over the past 10 years, that non-structural proteins of RNA viruses, such as hepatitis C and dengue, have roles in virion maturation and assembly.

Autoinducer 2 (AI2) is the only quorum-sensing signal that is shared by Gram-negative and Gram-positive bacteria. Because AI2 biosynthesis, specified by theluxS gene, is linked to S-adenosyl homocysteine recycling, determining whether luxSbiofilm phenotypes are due to signalling or effects on bacterial metabolism is not straightforward, and is discussed here.

Using examples from the Cuatro Ciénegas basin in Mexico, Souzaet al. argue that the occurrence of strong ecosystem nutrient limitation, especially by phosphorus, encourages local microbial endemism because it reduces horizontal gene transfer among locally adapting microbial lineages.

The discovery of proteorhodopsin genes during metagenomic analyses of marine bacteria and archaea challenged the notion that all solar energy is captured by microbial chlorophyll molecules in these environments. But have subsequent studies confirmed the energy-transducing roles of microbial proteorhodopsins? Here, the authors suggest that energy transduction might be one of many roles for these fascinating proteins.

Although Kawasaki disease (KD) is the most common cause of acquired heart disease in children in the developed world, its aetiology remains unknown. In this Opinion, Anne Rowley and colleagues discuss evidence, including recently identified cytoplasmic inclusion bodies, which suggests that KD is caused by an infectious agent.

DNA acquisition and loss have important roles in bacterial genome evolution. Jörg Hacker and colleagues look at how this genomic fluidity can be harnessed in the development of new diagnostics and molecular epidemiological methods.

In this Opinion article, the authors consider the classification of viruses, and propose a new classification system that divides all biological entities into two groups of organisms: ribosome-encoding organisms (eukaryotes, archaea and bacteria) and capsid-encoding organisms (viruses). Unclassified selfish nucleic acids are grouped as 'orphan replicons'.

Filamentation has been implicated in bacterial survival of exposure to environmental stresses, but in this Opinion, Sheryl S. Justice and colleagues propose that the morphological plasticity of pathogenic bacteria is a direct and adaptive response to the sensing of environmental changes.