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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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    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)
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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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    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 Biogeochemically Important Bacteria?

Approved Proposals FY08

Why Sequence Biogeochemically Important Bacteria?

DOE JGI will be sequencing three biogeochemically important bacteria, Diaphorobacter sp. strain TPSY, Ferrutens nitratireducens strain 2002 and Azospira suillum strain PS. These organisms represent diverse genera capable of anaerobically oxidizing both iron(II) and humic acids by using nitrate as the electron acceptor. Two of these organisms, strain 2002 and strain TPSY, are also capable of the anaerobic nitrate-dependent oxidation of uranium(IV) to uranium(VI).

Left to right, Azospira suillum PS, Ferrutens nitratireducens 2002, and Diaphorobacter TPSY.

Left to right, Azospira suillum PS, Ferrutens nitratireducens 2002, and Diaphorobacter TPSY.

Nitrate-dependent microbial metal oxidation is of critical importance because of its potential effect on the fate and transport of radioactive contaminants. Nitrate-dependent Iron(II) oxidation by organisms such as these offers a unique and robust alternative for the immobilization of toxic heavy metals and radionuclides in contaminated sites. Furthermore, recent studies investigating biological oxidation of immobilized tetravalent uranium have demonstrated that anaerobic uranium(IV) bio-oxidation coupled to the reduction of nitrate presents a microbial metabolism that can potentially reverse and/or inhibit any reductive uranium remediation strategy via the subsequent remobilization of uranium. The ability of Diaphorobacter sp. strain TPSY and Ferrutens nitratireducens to oxidize uranium(IV) to uranium(VI) and resolubilize the immobilized uranium raise important questions regarding the long-term stability of immobilized uranium in the environment. Although each of these metabolisms represent significant controls on the fate and transport of uranium in the environment, nothing is yet known of the proteomic or genomic processes involved. The sequencing of the genomes of these three model nitrate-dependent metal-oxidizing organisms will allow a significant advancement in our understanding of these critical biogeochemical processes.

Principal Investigators: John Coates (Univ. of California, Berkeley)

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