Hot off the presses! Oct 01 Nat Rev Micro

The Oct 01 issue of the Nat Rev Micro is now up on Pubget (About Nat Rev Micro): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

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  - Nat Rev Micro 8(10):675 (2010)
  
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  - Nat Rev Micro 8(10):676 (2010)
  
• Innate immunity: TRIM5α: the tie that binds | PDF (187 KB)
  - Nat Rev Micro 8(10):677 (2010)
  Cross-species transmission of simian immunodeficiency virus (SIV) has resulted in the spread of the virus among monkey species and has given rise to HIV-1 and HIV-2 in humans. However, before becoming established in a new species, retroviruses must overcome any immune barriers to cross-species transmission.
• Bacterial physiology: Life on the ropes | PDF (195 KB)
  - Nat Rev Micro 8(10):678 (2010)
  Enterohaemorrhagic and enteropathogenic strains of Escherichia coli (EHEC and EPEC, respectively), both major causes of diarrhoeal illness in developed countries, secrete a range of effector proteins and toxins during colonization of the gut. Writing in the Journal of Biological Chemistry, Girón and colleagues now report that the effector proteins EspC and EspP oligomerize to form large macromolecular structures that exhibit adhesive and cytopathic properties and might act as a substratum for biofilm formation.
• HIV: Crucial crossing | PDF (220 KB)
  - Nat Rev Micro 8(10):678 (2010)
  A new paper in PLoS Pathogens provides the first direct immunohistochemical evidence of the translocation of microbial products from the intestinal lumen during chronic simian immunodeficiency virus (SIV) infection.Persistent systemic immune activation is a defining characteristic of pathogenic HIV-1 and SIV infections.
• Bacterial pathogenicity: Vitamin B6 hits H. pylori sweet spot | PDF (298 KB)
  - Nat Rev Micro 8(10):678 (2010)
  The vitamin B6-dependent glycosylation of flagella is required for full Helicobacter pylori motility and virulence, according to a new paper from Richard Ferrero and colleagues in mBio.Prolonged in vitro passage of H. pylori
• Antimicrobials | Microbial ecology | Symbiosis | PDF (177 KB)
  - Nat Rev Micro 8(10):679 (2010)
  Bacterial charity work leads to population-wide resistance Lee, H. H.et al. Nature 467, 82–85 (2010)
• Bacterial pathogenesis: Messing up the membrane | PDF (162 KB)
  - Nat Rev Micro 8(10):680 (2010)
  The marine bacterium Vibrio parahaemolyticus induces cell death by injecting effectors into host cells through its type III secretion system 1 (T3SS1). The T3SS1-secreted effector VPA0450 contributes to host cell death, and Orth and colleagues now find that it achieves this by disrupting the interaction between the host cell membrane and the actin cortex.
• Bacterial physiology: Bacillus takes the temperature | PDF (158 KB)
  - Nat Rev Micro 8(10):680 (2010)
  At low temperatures, the fatty acyl chains of the lipids in cell membranes shift from a fluid to a non-fluid arrangement, making the membrane thicker and more rigid. In Bacillus subtilis, autophosphorylation of the histidine kinase thermosensor DesK at low temperatures triggers expression of the acyl lipid desaturase Î"5-Des (encoded by des), which promotes membrane fluidity to overcome the cold-induced rigidity.
• Seeking perfection | PDF (204 KB)
  - Nat Rev Micro 8(10):681 (2010)
  This month's Genome Watch discusses ways to automatically produce 'base-perfect' genome sequences.
• In the news | PDF (217 KB)
  - Nat Rev Micro 8(10):682 (2010)
  The carbapenem family of antibiotics is often used as a last resort to treat individuals infected with multidrug-resistant strains of bacteria. The threat posed by the emergence of bacterial strains that are resistant to carbapenems is demonstrated by the recent death of a Belgian man who became infected with a New Delhi metallo-β-lactamase 1 (NDM1)-positive bacterial strain following hospitalization during a trip to Pakistan.
• The ParMRC system: molecular mechanisms of plasmid segregation by actin-like filaments
  - Nat Rev Micro 8(10):683 (2010)
  The ParMRC plasmid partitioning apparatus is one of the best characterized systems for bacterial DNA segregation. Bundles of actin-like filaments are used to push plasmids to opposite poles of the cell, whereupon they are stably inherited on cell division. This plasmid-encoded system comprises just three components: an actin-like protein, ParM, a DNA-binding adaptor protein, ParR, and a centromere-like region, parC. The properties and interactions of these components have been finely tuned to enable ParM filaments to search the cell space for plasmids and then move ParR–parC-bound DNA molecules apart. In this Review, we look at some of the most exciting questions in the field concerning the exact molecular mechanisms by which the components of this self-contained system modulate one another's activity to achieve bipolar DNA segregation.
• Interactions between bacterial pathogens and mitochondrial cell death pathways
  Rudel T Kepp O Kozjak-Pavlovic V - Nat Rev Micro 8(10):693 (2010)
  The modulation of host cell death pathways by bacteria has been recognized as a major pathogenicity mechanism. Among other strategies, bacterial pathogens can hijack the cell death machinery of host cells by influencing the signalling pathways that converge on the mitochondria. In particular, many bacterial proteins have evolved to interact in a highly specific manner with host mitochondria, thereby modulating the decision between cell life and death. In this Review, we explore the intimate interactions between bacterial pathogens and mitochondrial cell death pathways.
• Microbial electrosynthesis â€" revisiting the electrical route for microbial production
  - Nat Rev Micro 8(10):706 (2010)
  Microbial electrocatalysis relies on microorganisms as catalysts for reactions occurring at electrodes. Microbial fuel cells and microbial electrolysis cells are well known in this context; both use microorganisms to oxidize organic or inorganic matter at an anode to generate electrical power or H2, respectively. The discovery that electrical current can also drive microbial metabolism has recently lead to a plethora of other applications in bioremediation and in the production of fuels and chemicals. Notably, the microbial production of chemicals, called microbial electrosynthesis, provides a highly attractive, novel route for the generation of valuable products from electricity or even wastewater. This Review addresses the principles, challenges and opportunities of microbial electrosynthesis, an exciting new discipline at the nexus of microbiology and electrochemistry.
• Advantages and limitations of current network inference methods
  De Smet R Marchal K - Nat Rev Micro 8(10):717 (2010)
  Network inference, which is the reconstruction of biological networks from high-throughput data, can provide valuable information about the regulation of gene expression in cells. However, it is an underdetermined problem, as the number of interactions that can be inferred exceeds the number of independent measurements. Different state-of-the-art tools for network inference use specific assumptions and simplifications to deal with underdetermination, and these influence the inferences. The outcome of network inference therefore varies between tools and can be highly complementary. Here we categorize the available tools according to the strategies that they use to deal with the problem of underdetermination. Such categorization allows an insight into why a certain tool is more appropriate for the specific research question or data set at hand.
• Evolution of diverse cell division and vesicle formation systems in Archaea
  Makarova KS Yutin N Bell SD Koonin EV - Nat Rev Micro 8(10):731 (2010)
  Recently a novel cell division system comprised of homologues of eukaryotic ESCRT-III (endosomal sorting complex required for transport III) proteins was discovered in the hyperthermophilic crenarchaeote Sulfolobus acidocaldarius. On the basis of this discovery, we undertook a comparative genomic analysis of the machineries for cell division and vesicle formation in Archaea. Archaea possess at least three distinct membrane remodelling systems: the FtsZ-based bacterial-type system, the ESCRT-III-based eukaryote-like system and a putative novel system that uses an archaeal actin-related protein. Many archaeal genomes encode assortments of components from different systems. Evolutionary reconstruction from these findings suggests that the last common ancestor of the extant Archaea possessed a complex membrane remodelling apparatus, different components of which were lost during subsequent evolution of archaeal lineages. By contrast, eukaryotes seem to have inherited all t! hree ancestral systems.
• The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?
  - Nat Rev Micro 8(10):743 (2010)
  The origin of eukaryotes and their evolutionary relationship with the Archaea is a major biological question and the subject of intense debate. In the context of the classical view of the universal tree of life, the Archaea and the Eukarya have a common ancestor, the nature of which remains undetermined. Alternative views propose instead that the Eukarya evolved directly from a bona fide archaeal lineage. Several recent large-scale phylogenomic studies using an array of approaches are divided in supporting either one or the other scenario, despite analysing largely overlapping data sets of universal genes. We examine the reasons for such a lack of consensus and consider how alternative approaches may enable progress in answering this fascinating and as-yet-unresolved question.
• Correspondence: History of science is good for you
  - Nat Rev Micro 8(10):752 (2010)
  We note with considerable interest the recent editorial in Nature Reviews Microbiology(Raiders of the lost articles. Nature Rev. Microbiol.8, 610 (2010)