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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
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    Genome Insider podcast: THE Bioenergy Tree
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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
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Home › CSP Plans › Why Sequence the Oyster Mushroom?

Approved Proposals FY07

Why Sequence the Oyster Mushroom?

pleurotusPleurotus ostreatus, the oyster mushroom, is an active lignin degrader in the forests. Lignin is the second most abundant biopolymer on Earth and its breakdown is a necessary step for making cellulose (the most abundant carbon biopolymer) accessible to further enzymatic processes. The understanding of the whole-genome regulation of P. ostreatus lignocellulolytic enzymes would facilitate its use in in-situ bioremediation processes and other biotechnological processes.

P. ostreatus is a saprophyte in the wild (i.e., it lives on dead or decaying matter). The comparison of its genome with that of other saprophytic, ectomycorrhizal (having filaments that grow between root cells), and pathogenic basidiomycetes would help in identifying specific gene sets for these different lifestyles. P. ostreatus occupies the third position in the worldwide market of industrially produced mushrooms. This fungus can grow easily on a variety of organic substrates, including agricultural wastes that P. ostreatus is able to recycle for animal foodstuff. The identification of the genetic basis of substrate colonization by P. ostreatus and of the induction of fruiting will facilitate the expansion of the range of agricultural wastes amenable to conversion using this fungus.

P. ostreatus also produces various secondary metabolites of medical interest. Knowledge of the genomics of P. ostreatus secondary metabolism will help to improve the production of these compounds. A number of quantitative trait loci controlling growth rate and industrial quality and productivity have been identified in P. ostreatus. The complete genome sequence will allow the analysis of the structure and mechanism of function of these quantitative genes.

Principal Investigators: Antonio Pisabarro, Lucia Ramirez (Public Univ. of Navarre), Allan C. Gathman (Southeast Missouri State Univ.), Francis Martin (INRA, France), Ursel Kues (Univ. of Göttingen), Yitzhak Hadar (Hebrew Univ. of Jerusalem), Christian Kubicek (Tech. Univ. of Vienna), Dan Cullen (Univ. of Wisconsin-Madison), Bernard Henrissat (Univ. Aix-Marseille I & II), Rytas Vlgalys (Duke Univ.), Juan Francisco Martin (Instituto de Biotecnologia de Leon).

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