Hot off the presses! Mar 01

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Latest Articles Include:

• In this issue
  - Nature Reviews Microbiology 8(3):155 (2010)
  The study of the molecular biology of bacteria goes back nearly a century, but some fundamental processes, such as DNA replication and compaction, remain poorly understood. On page 163, Katayama and colleagues describe recent progress in our understanding of the initiation of DNA replication, focusing on the control of the regulatory protein DnaA and the replication origin.
• Editorial: A birthday gift for GAVI
  - Nature Reviews Microbiology 8(3):156 (2010)
  The GAVI Alliance was established in 2000 in response to the need to dramatically increase vaccine coverage for children in developing countries. Initially called the Global Alliance for Vaccination and Immunization, it is a coalition of partners, including national governments, international organizations, bilateral donors (donors that deal directly with one government), the vaccine production industry and non-governmental organizations.
• Symbiosis: Breaking the rhizobial barrier
  - Nature Reviews Microbiology 8(3):157 (2010)
  Rhizobial bacteria form mutualistic endosymbioses with legumes, in which they induce the formation of root nodules and fix nitrogen. The rhizobia constitute a phylogenetically diverse range of soil bacteria, and it is thought that repeated and independent horizontal gene transfer events led to the spread of symbiotic capabilities to previously non-symbiotic bacteria.
• Viral infection: miRNAs help KSHV lay low
  - Nature Reviews Microbiology 8(3):158 (2010)
  Kaposi's sarcoma-associated herpesvirus (KSHV) establishes a long-term, latent infection in its target cells, during which a limited repertoire of viral genes is expressed. Among these are 17 microRNAs (miRNAs), which have an unclear role in the viral life cycle.
• In brief: Virology, Systems biology, Bacterial physiology
  - Nature Reviews Microbiology 8(3):158 (2010)
  Repulsion of superinfecting virions: a mechanism for rapid virus spread Doceul, V.et al. Science21 Jan 2010 (doi:10.1126/science.1183173)
• Industrial microbiology: Fuelling the renewable revolution
  - Nature Reviews Microbiology 8(3):158 (2010)
  The production of fuels and other high-value chemicals through microbial fermentation has the potential to provide a sustainable alternative to petrochemicals. Publishing in Nature, Jay Keasling and colleagues now describe the engineering of Escherichia coli to produce structurally tailored fatty acids and their derivatives from simple sugars and plant-derived biomass.
• In brief: Bacterial pathogenicity, Environmental microbiology, Innate immunity
  - Nature Reviews Microbiology 8(3):159 (2010)
  A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria Hood, R. D.et al. Cell Host Microbe 7, 25–37 (2010)
• Archaea: Singled out from the crowd
  - Nature Reviews Microbiology 8(3):160 (2010)
  Ubiquitin is a small eukaryotic protein with a characteristic β-grasp fold that can be conjugated to other proteins. In many cases, the conjugated protein is then targeted for degradation by the proteasome, and ubiquitin is recycled for further rounds of conjugation.
• Parasitology: Epigenetic regulation of VSG expression
  - Nature Reviews Microbiology 8(3):160 (2010)
  The controversial issue of the chromatin structure at VSG expression site loci in African trypanosomes seems to have been resolved with the publication of two papers in Eukaryotic Cell showing that nucleosomes are depleted at active VSG expression sites.In the bloodstream of the mammalian host, Trypanosoma brucei avoids immune detection by periodically switching its variant surface glycoprotein (VSG) 'coat' by a process known as antigenic variation.
• Taming the next-gen beast
  - Nature Reviews Microbiology 8(3):161 (2010)
  This month's Genome Watch discusses how alternative approaches to using second-generation sequencing technologies are powerful tools for the analysis of common pathogenic bacteria.
• In the news
  - Nature Reviews Microbiology 8(3):162 (2010)
  Experts warn that a patient's weight should be taken into account when prescribing antibiotics, as body weight can affect the distribution and metabolism of a drug. With obesity levels rising in many parts of the world, Matthew Falagas and Drosos Karageorgopoulos, in an article published in The Lancet, advise doctors to tailor antibiotic doses to a patient's weight and body composition to achieve maximal benefit from treatment.
• Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC
  - Nature Reviews Microbiology 8(3):163 (2010)
  Chromosomal replication must be limited to once and only once per cell cycle. This is accomplished by multiple regulatory pathways that govern initiator proteins and replication origins. A principal feature of DNA replication is the coupling of the replication reaction to negative-feedback regulation. Some of the factors that are important in this process have been discovered, including the clamp (DNA polymerase III subunit-β (DnaN)), the datA locus, SeqA, DnaA homologue protein (Hda) and YabA, as well as factors that are involved at other stages of the regulatory mechanism, such as DnaA initiator-associating protein (DiaA), the DnaA-reactivating sequence (DARS) loci and Soj. Here, we describe the regulation of DnaA, one of the central proteins involved in bacterial DNA replication, by these factors in Escherichia coli, Bacillus subtilis and Caulobacter crescentus.
• Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens
  - Nature Reviews Microbiology 8(3):171 (2010)
  How can probiotic bacteria transduce their health benefits to the host? Bacterial cell surface macromolecules are key factors in this beneficial microorganism–host crosstalk, as they can interact with host pattern recognition receptors (PRRs) of the gastrointestinal mucosa. In this Review, we highlight the documented signalling interactions of the surface molecules of probiotic bacteria (such as long surface appendages, polysaccharides and lipoteichoic acids) with PRRs. Research on host–probiotic interactions can benefit from well-documented host–microorganism studies that span the spectrum from pathogenicity to mutualism. Distinctions and parallels are therefore drawn with the interactions of similar molecules that are presented by gastrointestinal commensals and pathogens.
• Bacterial nucleoid-associated proteins, nucleoid structure and gene expression
  Dillon SC Dorman CJ - Nature Reviews Microbiology 8(3):185 (2010)
  Emerging models of the bacterial nucleoid show that nucleoid-associated proteins (NAPs) and transcription contribute in combination to the dynamic nature of nucleoid structure. NAPs and other DNA-binding proteins that display gene-silencing and anti-silencing activities are emerging as key antagonistic regulators of nucleoid structure. Furthermore, it is becoming clear that the boundary between NAPs and conventional transcriptional regulators is quite blurred and that NAPs facilitate the evolution of novel gene regulatory circuits. Here, NAP biology is considered from the standpoints of both gene regulation and nucleoid structure.
• The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes
  Srikhanta YN Fox KL Jennings MP - Nature Reviews Microbiology 8(3):196 (2010)
  In several host-adapted pathogens, phase variation has been found to occur in genes that encode methyltransferases associated with type III restriction–modification systems. It was recently shown that in the human pathogens Haemophilus influenzae, Neisseria gonorrhoeae and Neisseria meningitidis phase variation of a type III DNA methyltransferase, encoded by members of the mod gene family, regulates the expression of multiple genes. This novel genetic system has been termed the 'phasevarion' (phase-variable regulon). The wide distribution of phase-variable mod family genes indicates that this may be a common strategy used by host-adapted bacterial pathogens to randomly switch between distinct cell types.
• The population genetics of commensal Escherichia coli
  - Nature Reviews Microbiology 8(3):207 (2010)
  The primary habitat of Escherichia coli is the vertebrate gut, where it is the predominant aerobic organism, living in symbiosis with its host. Despite the occurrence of recombination events, the population structure is predominantly clonal, allowing the delineation of major phylogenetic groups. The genetic structure of commensal E. coli is shaped by multiple host and environmental factors, and the determinants involved in the virulence of the bacteria may in fact reflect adaptation to commensal habitats. A better characterization of the commensal niche is necessary to understand how a useful commensal can become a harmful pathogen. In this Review we describe the population structure of commensal E. coli, the factors involved in the spread of different strains, how the bacteria can adapt to different niches and how a commensal lifestyle can evolve into a pathogenic one.
• A complex journey: transmission of microbial symbionts
  - Nature Reviews Microbiology 8(3):218 (2010)
  The perpetuation of symbioses through host generations relies on symbiont transmission. Horizontally transmitted symbionts are taken up from the environment anew by each host generation, and vertically transmitted symbionts are most often transferred through the female germ line. Mixed modes also exist. In this Review we describe the journey of symbionts from the initial contact to their final residence. We provide an overview of the molecular mechanisms that mediate symbiont attraction and accumulation, interpartner recognition and selection, as well as symbiont confrontation with the host immune system. We also discuss how the two main transmission modes shape the evolution of the symbiotic partners.
• Viral shape-shifting: norovirus evasion of the human immune system
  - Nature Reviews Microbiology 8(3):231 (2010)
  Noroviruses are the most common cause of food-borne gastroenteritis worldwide, and explosive outbreaks frequently occur in community settings, where the virus can immobilize large numbers of infected individuals for 24–48 hours, making the development of effective vaccines and antiviral therapies a priority. However, several challenges have hampered therapeutic design, including: the limitations of cell culture and small-animal model systems; the complex effects of host pre-exposure histories; differential host susceptibility, which is correlated with blood group and secretor status; and the evolution of novel immune escape variants. In this Review, we discuss the molecular and structural mechanisms that facilitate the persistence of noroviruses in human populations.
• Correspondence: Spectrum of latent tuberculosis — existing tests cannot resolve the underlying phenotypes
  - Nature Reviews Microbiology 8(3):242 (2010)
  In their recent Review (The spectrum of latent tuberculosis: rethinking the biology and intervention strategies. Nature Rev. Microbiol. 7, 845–855 (2009)
• Author Reply: Spectrum of latent tuberculosis — existing tests cannot resolve the underlying phenotypes: author's reply
  - Nature Reviews Microbiology 8(3):242 (2010)
  We agree with the comments in response to our Review (The spectrum of latent tuberculosis: rethinking the biology and intervention strategies. Nature Rev. Microbiol. 7, 845–855 (2009)