Hot off the presses! Dec 01 Nat Rev Microbiol

The Dec 01 issue of the Nat Rev Microbiol is now up on Pubget (About Nat Rev Microbiol): 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 Microbiol 9(12):829 (2011)
  
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  - Nat Rev Microbiol 9(12):830 (2011)
  
• Viral infection: The gut microbiota: friend or foe? | PDF (155 KB)
  - Nat Rev Microbiol 9(12):831 (2011)
  We normally think of the gut microbiota as the 'friendly' bacteria that carry out many beneficial functions, including protecting us from infection. But two studies now identify a different side to the gut microbiota, showing that it can actually facilitate viral infection and promote transmission.
• Fungal physiology: Ustilago takes control | PDF (234 KB)
  - Nat Rev Microbiol 9(12):832 (2011)
  In a recent Nature paper, a group of researchers from Germany demonstrate that the Ustilago maydis effector protein Cmu1 is a virulence factor that can move through plant cells, redirecting plant metabolic pathways to favour fungal infection.
• Antiviral immunity: Viral restriction goes nuclear | PDF (226 KB)
  - Nat Rev Microbiol 9(12):832 (2011)
  Promyelocytic leukaemia (PML) protein is the key organizer of nuclear bodies and has been implicated in defence against viral infection. Writing in the Journal of Virology, Maroui et al.
• Bacterial physiology: Seeing Caulobacter in 3D | PDF (220 KB)
  - Nat Rev Microbiol 9(12):834 (2011)
  What are the factors that determine the global conformation and architecture of a bacterial genome? In a recent Molecular Cell paper, a comprehensive three-dimensional analysis of the Caulobacter crescentus genome provides some answers to this fundamental question.
• Bacterial physiology: Stressed bacteria aren't lost without a leader | PDF (234 KB)
  - Nat Rev Microbiol 9(12):834 (2011)
  Toxin–antitoxin (TA) modules consist of a stable toxin and a labile antitoxin and are used to regulate growth and death in bacteria in response to a variety of signals. Vesper et al.
• Molecular biology: Nature of the genetic code finally revealed! | PDF (160 KB)
  - Nat Rev Microbiol 9(12):835 (2011)
  This December marks the fiftieth anniversary of the publication of the landmark article by Francis Crick et al., describing the nature of the genetic code.
• Archaea: Thaumarchaeota go it alone | PDF (108 KB)
  - Nat Rev Microbiol 9(12):832 (2011)
  The proposal that the Thaumarchaeota should be considered as a separate phylum within the Archaea, rather than a branch of the Crenarchaeota, has gained further support from the first analysis of the thaumarchaeal cell cycle. Pelve et al.Nitrosopumilus maritimus and found that it differs substantially from that of crenarchaea, with a much longer pre-replication phase (G1) and a shorter post-replication phase (G2, mitosis and cell division).
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  - Nat Rev Microbiol 9(12):832 (2011)
  
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  - Nat Rev Microbiol 9(12):832 (2011)
  
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  - Nat Rev Microbiol 9(12):833 (2011)
  
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  - Nat Rev Microbiol 9(12):833 (2011)
  
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  - Nat Rev Microbiol 9(12):833 (2011)
  
• Animals learn new tricks from microorganisms | PDF (195 KB)
  - Nat Rev Microbiol 9(12):836 (2011)
  This month's Genome Watch reviews a series of recent papers that describes horizontal gene transfer from microorganisms to nematodes.
• In the news | PDF (192 KB)
  - Nat Rev Microbiol 9(12):837 (2011)
  Potential trachoma vaccine A potential vaccine has been developed against trachoma, an ocular Chlamydia trachomatis infection that is responsible for about 8 million cases of blindness worldwide (3% of all cases). The researchers tested this live attenuated vaccine on six cynomolgus macaques, which were subsequently challenged with C. trachomatis. In contrast to unvaccinated animals, which became infected and shed infectious bacteria, three of the six vaccinated animals did not develop any symptoms and did not shed infectious bacteria. The three other vaccinated animals developed symptoms similar to those of the naive animals, but had lower levels of infectious bacteria. This led the researchers to remark that "preventing disease requires complete or near complete inhibition of bacterial growth". The vaccine consists of a C. trachomatis strain that has been cured of a plasmid. The resulting strain has a growth rate similar to that of wild-type bacteria, but does not induce the strong innate immune response that is induced by wild-type bacteria. In the future, this vaccine may also be useful against sexually transmitted C. trachomatis infections. J. Exp. Med./ScienceNews Tenofovir: killing two birds with one stone A new study has revealed how the anti-HIV compound tenofovir can also protect against infection with human herpesvirus 1 (HHV-1) and HHV-2. Tenofovir was previously shown to decrease the transmission of HIV by 39%, and in the same report it was noted that tenofovir also decreased the risk of acquiring HHV-2 by 51%, even though tenofovir had previously been shown to have no effect on herpesviruses. This new study now shows that tenofovir inhibits the replication of HHV-1 and HHV-2 only at the high levels that are obtained with a 1% topical gel; no effect was detected at the levels achieved by oral tenofovir administration. Inhibition of herpesviral replication was detected in various cells lines, including keratinocytes, in which HHVs replicate in infected hosts. Uninfected host cells were unaffected by tenofovir, even at levels several times higher than those obtained with the 1% gel. Biochemical analysis revealed that the compound is converted to tenofovir diphosphate and t! hat this metabolite inhibits the activity of the herpesviral polymerase. Cell Host Microbe/New York Times Filovirus's European cousin A recent die-off of bats in caves in Spain has been linked to infection with a previously unknown filovirus, marking the first time that filoviruses have been found to circulate in a population outside of sub-Saharan Africa and the Philippines. The virus, named Lloviu virus after the cave in which the dead bats were found, was detected in several organs, with the highest levels of virus in the lung, spleen and liver. Similar to other filoviral infections, the pathology of the dead bats' lungs was consistent with viral pneumonia, and no filovirus could be detected in healthy bats from the same area, indicating that the filoviral infection was the likely cause of death. Enough DNA to cover the entire viral genome could be amplified, and this DNA revealed that the virus is most closely related to the ebolaviruses. Further phylogenetic analyses placed the time of divergence with Ebolavirus at around 68,400 years ago and the most recent common ancestor of filoviruses at around 15! 5,500 years ago. PLoS Pathog. Infectious agent for colon cancer? Two reports have linked colorectal cancer to the bacterium Fusobacterium nucleatum, which is a constituent of the oral microbiota that has previously been linked to periodontitis and appendicitis. To identify changes in the microbiota that are associated with the cancer, both studies used large-scale sequencing; the first study matched RNA extracted from 11 colorectal carcinomas to RNA from healthy tissue, and the second study investigated DNA from colorectal cancers. These analyses revealed that F. nucleatum was over-represented in colon cancer tissue compared with levels in colonic tissue from healthy controls. In one of the studies, the bacterium was also shown to be associated with the tumour by fluorescence microscopy. Although these studies did not show causation, the results provide intriguing insights into a possible role for a member of the gut microbiota in the induction of cancer. Genome Res./ScienceDaily A new toxin in MRSA's core Researchers have identified a superantigen encoded in the genome of methicillin-resistant Staphylococcus aureus (MRSA). Superantigens are toxins that hyperactivate a large number of T cells and thereby induce systemic disease. The previously identified S. aureus superantigens are encoded on mobile genetic elements, such as plasmids, transposons and bacteriophages. As a result, most strains of MRSA carry only a subset of the toxins, and the most common toxins are present in only about half of MRSA strains. By contrast, this newly discovered chromosomally encoded toxin, staphylococcal enterotoxin-like toxin X (SElX), was detected in 95% of the 114 strains tested, and further analysis of six strains showed that it was present in the same chromosomal location in these strains. SElX is produced during infection of humans, cows and sheep; antibodies against the toxin were detected in the serum of 20 out of 23 individuals who had been infected with MRSA, and in only one out of 47 individuals who were not known to have been infected. Further biochemical analysis showed that the toxin is mitogenic for human T cells, indicating that it does indeed act as a superantigen, and deletion of the gene that encodes the toxin produced a strain that had reduced lethality in a rabbit model. PLoS Pathog.
• Regulated proteolysis in Gram-negative bacteria — how and when?
  - Nat Rev Microbiol 9(12):839 (2011)
  Most bacteria live in a dynamic environment where temperature, availability of nutrients and the presence of various chemicals vary, which requires rapid adaptation. Many of the adaptive changes are determined by changes in the transcription of global regulatory networks, but this response is slow because most bacterial proteins are stable and their concentration remains high even after transcription slows down. To respond rapidly, an additional level of regulation has evolved: the degradation of key proteins. However, as proteolysis is an irreversible process, it is subject to tight regulation of substrate binding and degradation. Here we review the roles of the proteolytic enzymes in Gram-negative bacteria and how these enzymes can be regulated to target only a subset of proteins.
• Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes
  - Nat Rev Microbiol 9(12):849 (2011)
  The compatible solute dimethylsulphoniopropionate (DMSP) has important roles in marine environments. It is an anti-stress compound made by many single-celled plankton, some seaweeds and a few land plants that live by the shore. Furthermore, in the oceans it is a major source of carbon and sulphur for marine bacteria that break it down to products such as dimethyl sulphide, which are important in their own right and have wide-ranging effects, from altering animal behaviour to seeding cloud formation. In this Review, we describe how recent genetic and genomic work on the ways in which several different bacteria, and some fungi, catabolize DMSP has provided new and surprising insights into the mechanisms, regulation and possible evolution of DMSP catabolism in microorganisms.
• Viral subversion of the host protein synthesis machinery
  - Nat Rev Microbiol 9(12):860 (2011)
  Viruses are fully reliant on the translation machinery of their host cells to produce the polypeptides that are essential for viral replication. Consequently, viruses recruit host ribosomes to translate viral mRNAs, typically using virally encoded functions to seize control of cellular translation factors and the host signalling pathways that regulate their activity. This not only ensures that viral proteins will be produced, but also stifles innate host defences that are aimed at inhibiting the capacity of infected cells for protein synthesis. Remarkably, nearly every step of the translation process can be targeted by virally encoded functions. This Review discusses the diverse strategies that viruses use to subvert host protein synthesis functions and regulate mRNA translation in infected cells.
• Actin organization and dynamics in filamentous fungi
  - Nat Rev Microbiol 9(12):876 (2011)
  Growth and morphogenesis of filamentous fungi is underpinned by dynamic reorganization and polarization of the actin cytoskeleton. Actin has crucial roles in exocytosis, endocytosis, organelle movement and cytokinesis in fungi, and these processes are coupled to the production of distinct higher-order structures (actin patches, cables and rings) that generate forces or serve as tracks for intracellular transport. New approaches for imaging actin in living cells are revealing important similarities and differences in actin architecture and organization within the fungal kingdom, and have yielded key insights into cell polarity, tip growth and long-distance intracellular transport. In this Review, we discuss the contribution that recent live-cell imaging and mutational studies have made to our understanding of the dynamics and regulation of actin in filamentous fungi.
• The development of vaccines: how the past led to the future
  - Nat Rev Microbiol 9(12):889 (2011)
  The history of vaccine development has seen many accomplishments, but there are still many diseases that are difficult to target, and new technologies are being brought to bear on them. Past successes have been largely due to elicitation of protective antibodies based on predictions made from the study of animal models, natural infections and seroepidemiology. Those predictions have often been correct, as indicated by the decline of many infections for which vaccines have been made over the past 200 years.
• Tackling antibiotic resistance
  - Nat Rev Microbiol 9(12):894 (2011)
  The development and spread of antibiotic resistance in bacteria is a universal threat to both humans and animals that is generally not preventable but can nevertheless be controlled, and it must be tackled in the most effective ways possible. To explore how the problem of antibiotic resistance might best be addressed, a group of 30 scientists from academia and industry gathered at the Banbury Conference Centre in Cold Spring Harbor, New York, USA, from 16 to 18 May 2011. From these discussions there emerged a priority list of steps that need to be taken to resolve this global crisis.
• Trichoderma: the genomics of opportunistic success
  - Nat Rev Microbiol 9(12):896 (2011)
  Nature Reviews Microbiology9, 749–759 (2011) The authors wish to acknowledge that the work of B.A.H., C.M.K. and P.K.M. was supported in part by grant TB-8031-08 from the Texas Department of Agriculture, USA, and the US–Israel Binational Agricultural Research and Development Fund. The authors apologize for this oversight.