Hot off the presses! Jul 01 Nat Rev Micro

The Jul 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 9(7):479 (2011)
  
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  - Nat Rev Micro 9(7):480 (2011)
  
• Immunology: NLRP6 keeps the bad bacteria at bay | PDF (194 KB)
  - Nat Rev Micro 9(7):481 (2011)
  The mammalian host needs to control the composition of its associated microbiota very carefully, as microbiota alterations (dysbiosis) have been associated with various diseases. Flavell and colleagues now show that an inflammasome built around NLRP6 (NOD-, LRR- and pyrin domain-containing 6) is important in maintaining a 'healthy' gut flora and that NLRP6-deficient animals have an altered gut microbiota that predisposes them to suffer from severe colitis.
• Plant virology: Sign turns yellow for Y-sat-infected tobacco | PDF (169 KB)
  - Nat Rev Micro 9(7):482 (2011)
  Two reports in a recent PLoS Pathogens issue provide the first demonstration that small interfering RNAs (siRNAs) that are derived from viral satellite RNAs cause disease symptoms in plants by downregulating host genes. Smith and colleagues, and Shimura and colleagues show that the yellowing symptoms resulting from infection of tobacco plants with the Y-satellite (Y-sat) RNA are caused by the downregulation of CHLI — which is important in chlorophyll synthesis — by Y-sat-derived siRNA.
• Antimicrobials: Killing persisters while they sleep | PDF (174 KB)
  - Nat Rev Micro 9(7):482 (2011)
  Bacterial persisters are a subpopulation of dormant cells that have been implicated in a range of chronic and recurrent infections through their ability to survive antibiotic treatments. Although most cellular processes are completely shut down in persisters, translation still occurs, albeit at a reduced rate, making the use of aminoglycoside antibiotics (which target the ribosome) an attractive option.
• Applied microbiology | Parasitology | PDF (99 KB)
  - Nat Rev Micro 9(7):482 (2011)
  Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol Yim, H.et al. Nature Chem. Biol.22 May 2011 (doi:10.1038/nchembio.580)
• Microbial ecology: Bacteria reinforce plant defences | PDF (379 KB)
  - Nat Rev Micro 9(7):483 (2011)
  Plants growing in soils with disease-suppressive qualities resist infection by specific soil-borne pathogens much better than plants growing in similar soils that lack these qualities. This protection seems to be provided by the resident soil microbiota, but little is known about the precise microorganisms and mechanisms involved.
• Parasitology: Adding insult to injury | PDF (168 KB)
  - Nat Rev Micro 9(7):484 (2011)
  Eukaryotic cells can repair plasma membrane damage through a mechanism that relies on the influx of extracellular Ca2+; this triggers the fusion of lysosomes with the plasma membrane, resulting in the secretion of acid sphingomyelinase. In turn, this enzyme cleaves sphingomyelin in the outer leaflet of the membrane, generating ceramide, which creates increased inward curvature of the membrane, thereby supporting endocytosis of the damaged membrane.
• Parasitology: The malaria food channel | PDF (196 KB)
  - Nat Rev Micro 9(7):484 (2011)
  To survive within erythrocytes, malaria parasites modify the permeability of the host membrane to increase nutrient uptake. Although one or more ion channels were thought to be involved, the precise uptake mechanism and its genetic basis were unknown.
• Genome watch: Singled out | PDF (281 KB)
  - Nat Rev Micro 9(7):485 (2011)
  This month's Genome Watch reviews a recent article that demonstrates the use of single-cell genomics as a means of characterizing uncultivated microorganisms.
• In the news | PDF (264 KB)
  - Nat Rev Micro 9(7):486 (2011)
  Scientists in the United States have identified a homologue of hepatitis C virus (HCV) that infects dogs, the first time that HCV has been detected in animals other than human and primates. The virus was identified during a study of an outbreak of viral respiratory infections in dog shelters.
• Motor helps gliders to gain traction
  - Nat Rev Micro 9(7):482 (2011)
  Nature Reviews Microbiology9 398 (2011); doi:10.1038/nrmicro2579 In this Research highlight, we omitted to mention an earlier publication that had shown similar results to the article discussed. We have now added the following reference to alert readers to this: We apologize to the authors of the earlier study for this omission.
• Rulers and sensors in Chlamydomonas
  - Nat Rev Micro 9(7):482 (2011)
  In this Research highlight, our statement that this article revealed that "CALK phosphorylation ... is the first example of flagellar length being linked to a post-translational modification" was vague and possibly misleading. What we intended to convey was that this article revealed the first example of absolute flagellar length directly promoting changes in a post-translational modification; the role of post-translational modifications in the regulation of flagella has been described previously in many publications. The text now reads: "CALK phosphorylation ... is the first example showing that absolute flagellar length may be translated into a post-translational modification". We apologize for any potential confusion.
• Bacterial protein toxins that modify host regulatory GTPases
  - Nat Rev Micro 9(7):487 (2011)
  Many bacterial pathogens produce protein toxins to outmanoeuvre the immune system of the host. Some of these proteins target regulatory GTPases such as those belonging to the RHO family, which control the actin cytoskeleton of the host cell. In this Review, I discuss a diversity of mechanisms that are used by bacterial effectors and toxins to modulate the activity of host GTPases, with a focus on covalent modifications such as ADP-ribosylation, glucosylation, adenylylation, proteolysis, deamidation and transglutamination.
• Emerging patterns of marine nitrogen fixation
  - Nat Rev Micro 9(7):499 (2011)
  Biological N2 fixation is an important part of the marine nitrogen cycle as it provides a source of new nitrogen that can support biological carbon export and sequestration. Research in the past decade has focused on determining the patterns of distribution and abundance of diazotrophs, defining the environmental features leading to these patterns and characterizing the factors that constrain marine N2 fixation overall. In this Review, we describe how variations in the deposition of iron from dust to different ocean basins affects the limiting nutrient for N2 fixation and the distribution of different diazotrophic species. However, many questions remain about marine N2 fixation, including the role of temperature, fixed nitrogen species, CO2 and physical forcing in controlling N2 fixation, as well as the potential for heterotrophic N2 fixation.
• How does a hypha grow? The biophysics of pressurized growth in fungi
  - Nat Rev Micro 9(7):509 (2011)
  The mechanisms underlying the growth of fungal hyphae are rooted in the physical property of cell pressure. Internal hydrostatic pressure (turgor) is one of the major forces driving the localized expansion at the hyphal tip which causes the characteristic filamentous shape of the hypha. Calcium gradients regulate tip growth, and secretory vesicles that contribute to this process are actively transported to the growing tip by molecular motors that move along cytoskeletal structures. Turgor is controlled by an osmotic mitogen-activated protein kinase cascade that causes de novo synthesis of osmolytes and uptake of ions from the external medium. However, as discussed in this Review, turgor and pressure have additional roles in hyphal growth, such as causing the mass flow of cytoplasm from the basal mycelial network towards the expanding hyphal tips at the colony edge.
• Host factors involved in retroviral budding and release
  - Nat Rev Micro 9(7):519 (2011)
  The plasma membrane is the final barrier that enveloped viruses must cross during their egress from the infected cell. Here, we review recent insights into the cell biology of retroviral assembly and release; these insights have driven a new understanding of the host proteins, such as the ESCRT machinery, that are used by retroviruses to promote their final separation from the host cell. We also review antiviral host factors such as tetherin, which can directly inhibit the release of retroviral particles. These studies have illuminated the role of the lipid bilayer as the unexpected target for virus restriction by the innate immune response.
• Fever from the forest: prospects for the continued emergence of sylvatic dengue virus and its impact on public health
  - Nat Rev Micro 9(7):532 (2011)
  The four dengue virus (DENV) serotypes that circulate among humans emerged independently from ancestral sylvatic progenitors that were present in non-human primates, following the establishment of human populations that were large and dense enough to support continuous inter-human transmission by mosquitoes. This ancestral sylvatic-DENV transmission cycle still exists and is maintained in non-human primates and Aedes mosquitoes in the forests of Southeast Asia and West Africa. Here, we provide an overview of the ecology and molecular evolution of sylvatic DENV and its potential for adaptation to human transmission. We also emphasize how the study of sylvatic DENV will improve our ability to understand, predict and, ideally, avert further DENV emergence.
• Biased gene transfer in microbial evolution
  - Nat Rev Micro 9(7):543 (2011)
  Horizontal gene transfer (HGT) is an important evolutionary process that allows the spread of innovations between distantly related organisms. We present evidence that prokaryotes (bacteria and archaea) are more likely to transfer genetic material with their close relatives than with distantly related lineages. This bias in transfer partners can create phylogenetic signals that are difficult to distinguish from the signal created through shared ancestry. Preferences for transfer partners can be revealed by studying the distribution patterns of divergent genes with identical functions. In many respects, these genes are similar to alleles in a population, except that they coexist only in higher taxonomic groupings and are acquired by a species through HGT. We also discuss the role of biased gene transfer in the formation of taxonomically recognizable natural groups in the tree or net of life.
• Correspondence: Microbial carbon pump: additional considerations
  - Nat Rev Micro 9(7):555 (2011)
  The framework concept of the microbial carbon pump (MCP) and the idea that it stores recalcitrant dissolved organic matter (RDOM) in deep oceans for millennia was first proposed by Jiao et al. (Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean.Nature Rev. Microbiol.8, 593–599 (2010)