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New insights into other importantPublisher: NPG; Journal: Nature: Nature; Article Type: Biology letter DOI: 10.1038/nature06269Page 2 of 33 symbiotic functions including H 2 metabolism, CO 2 -reductive acetogenesis and N 2 fixation are also provided by this first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Our results underscore how complex even a 1-μl environment can be.All known termite species form obligate, nutritional mutualisms with diverse gut microbial species found nowhere else in nature 3 . Despite nearly a century of study, however, science still has only a meagre understanding of the exact roles of the host and symbiotic microbiota in the complex processes of lignocellulose degradation and conversion. Especially conspicuous is our poor understanding of the hindgut communities of wood-feeding 'higher'termites, the most species-rich and abundant of all termite lineages 4 . Higher termites do not contain hindgut flagellate protozoa, which have long been known to be sources of cellulases and hemicellulases in the 'lower' termites. The host tissue of all wood-feeding termites is known to be the source of one cellulase, a single-domain glycohydrolase family 9 enzyme that is secreted and active in the anterior compartments of the gut tract 5 . Only in recent years has research provided support for a role of termite gut bacteria in the production of relevant hydrolytic enzymes. That evidence includes the observed tight attachment of bacteria to wood particles, the antibacterial sensitivity of particle-bound cellulase activity 2 , and the discovery of a gene encoding a novel endoxylanase (glycohydrolase family 11) from bacterial DNA harvested from the gut tract of a Nasutitermes species 6 . Here, in an effort to learn about gene-centred details relevant to the diverse roles of bacterial symbionts in these successful wood-degrading insects,we initiated a metagenomic analysis of a wood-feeding 'higher' termite hindgut community, performed a proteomic analysis with clarified gut fluid from the same sample, and examined a set of candidate enzymes identified during the course of the study for demonstrable cellulase activity.A nest of an arboreal species closely related to Nasutitermes ephratae and N. corniger ( Supplementary Fig. 1) was collected near Guápiles, Costa Rica. From worker specimens, luminal contents were sampled specifically from the largest hindgut compartment, the microbedense, microlitre-sized region alternatively known as the paunch or the third proctodeal segment (P3; Fig. 1a). In the interest of interpretive clarity, we specifically excluded sampling from and analysis of the microbiota attached to the P3 epithelium and the other distinct microbial communities associated with the other hindgut compartments.Publisher: NPG; Journal: Nature: Nature; Article Type: Biology letter DOI: 10.1038/nature06269Page 3 of 33Total community DNA from pooled P3 luminal contents was purified, cloned and sequenced. About 71 million base pairs of Sang...

The activity of the DAF-2 insulin-like receptor is required for Caenorhabditis elegans reproductive growth and normal adult life span. Informatic analysis identified 37 C. elegans genes predicted to encode insulin-like peptides. Many of these genes are divergent insulin superfamily members, and many are clustered, indicating recent diversification of the family. The ins genes are primarily expressed in neurons, including sensory neurons, a subset of which are required for reproductive development. Structural predictions and likely C-peptide cleavage sites typical of mammalian insulins suggest that ins-1 is most closely related to insulin. Overexpression of ins-1, or expression of human insulin under the control of ins-1 regulatory sequences, causes partially penetrant arrest at the dauer stage and enhances dauer arrest in weak daf-2 mutants, suggesting that INS-1 and human insulin antagonize DAF-2 insulin-like signaling. A deletion of the ins-1 coding region does not enhance or suppress dauer arrest, indicating a functional redundancy among the 37 ins genes. Of five other ins genes tested, the only other one bearing a predicted C peptide also antagonizes daf-2 signaling, whereas four ins genes without a C peptide do not, indicating functional diversity within the ins family. Insulin and its related proteins define a superfamily of secreted proteins that share a structural motif stabilized by a set of stereotypical disulfide bonds (Blundell and Humbel 1980;Murray-Rust et al. 1992). Insulin superfamily genes are ubiquitous in vertebrates, and have been identified in invertebrates, including insects, molluscs, and the nematode Caenorhabditis elegans (Duret et al. 1998;Gregoire et al. 1998;Smit et al. 1998;Kawano et al. 2000). Seven members of the insulin superfamily have been identified in humans, including insulin (Brown et al. 1955), insulin-like growth factors (IGFs) I and II (Rinderknecht and Humbel 1978a,b), relaxins HI and HII (Bedarkar et al. 1977;Schwabe and McDonald 1977), early placenta insulin-like peptide (EPIL) (Chassin et al. 1995;Koman et al. 1996), and relaxin-like factor (Bullesbach and Schwabe 1995). These hormones mediate diverse functions. Insulin is a metabolic hormone that acts on target tissues to increase glucose uptake and energy storage, IGFs are mitogenic stimulators that control cell survival and proliferation, and relaxin causes dilation of the symphysis pubis before parturition and vasodilation. No function is yet known for either EPIL or relaxin-like factor. Bombyxin in silk moths (Satake et al. 1997), and the neurons that secrete locust and molluscan insulin-related proteins (Smit et al. 1988;Lagueux et al. 1990) regulate metabolism, implicating insulin-like proteins in metabolic control broadly in animal phylogeny. The insulin-like proteins that regulate metabolism, insulin in vertebrates, bombyxin from silk moths, molluscan MIP, and locust LIRP, appear to be processed proteolytically to remove an internal C peptide (Smit et al. 1988;Lagueux et al. 1990;Kondo et al. 1996). This proc...

We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial ecosystems without the need for culture. This device was used to perform a directed survey of the human subgingival crevice and to isolate bacteria having rod-like morphology. Several isolated microbes had a 16S rRNA sequence that placed them in candidate phylum TM7, which has no cultivated or sequenced members. Genome amplification from individual TM7 cells allowed us to sequence and assemble >1,000 genes, providing insight into the physiology of members of this phylum. This approach enables single-cell genetic analysis of any uncultivated minority member of a microbial community.environmental microbiology ͉ metagenomics ͉ microfluidics ͉ single-cell analysis

A bio-based economy has the potential to provide sustainable substitutes for petroleum-based products and new chemical building blocks for advanced materials. We previously engineered Saccharomyces cerevisiae for industrial production of the isoprenoid artemisinic acid for use in antimalarial treatments. Adapting these strains for biosynthesis of other isoprenoids such as β-farnesene (CH), a plant sesquiterpene with versatile industrial applications, is straightforward. However, S. cerevisiae uses a chemically inefficient pathway for isoprenoid biosynthesis, resulting in yield and productivity limitations incompatible with commodity-scale production. Here we use four non-native metabolic reactions to rewire central carbon metabolism in S. cerevisiae, enabling biosynthesis of cytosolic acetyl coenzyme A (acetyl-CoA, the two-carbon isoprenoid precursor) with a reduced ATP requirement, reduced loss of carbon to CO-emitting reactions, and improved pathway redox balance. We show that strains with rewired central metabolism can devote an identical quantity of sugar to farnesene production as control strains, yet produce 25% more farnesene with that sugar while requiring 75% less oxygen. These changes lower feedstock costs and dramatically increase productivity in industrial fermentations which are by necessity oxygen-constrained. Despite altering key regulatory nodes, engineered strains grow robustly under taxing industrial conditions, maintaining stable yield for two weeks in broth that reaches >15% farnesene by volume. This illustrates that rewiring yeast central metabolism is a viable strategy for cost-effective, large-scale production of acetyl-CoA-derived molecules.