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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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    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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Home › CSP Plans › Why Sequence Six Archaea?

Approved Proposals FY06

Why Sequence Six Archaea?

Archaea are the least well characterized of the three domains of life, and yet they share many important features with eukaryotes and are the key to understanding both the development of the eukaryotic cell and the origins and nature of the last universal common ancestor. In addition, many archaeal organisms are of interest in their own right because of their extremophilic properties (i.e., living at high temperature, low pH, or high salt concentration) and the uniqueness of their cellular organization.

JGI plans to sequence six archaeal genomes selected for their phylogenetic diversity and their ability to complement the genomes already published, thereby providing a fuller understanding of the major archaeal phyla. Three of the choices are methanogens, two from the order Methanomicrobiales, the only order of methanogens for which no representatives have yet been sequenced. The remaining methanogen, Methanothermus fervidus, is a hyperthermophilic representative of the Methanobacteriales and will be only the second genome characterized from this major taxon. JGI will also sequence a psychrophilic, phylogenetically distant halophile to complement the two published mesophilic halophile genomes. Two genomes from the kingdom Crenarchaeota will widen the extremely narrow phylogenetic scope of sequenced crenarchaeal genomes. The genome sequences will enable researchers to determine the set of genes common to all archaea and the gene sets defining the major subdivisions of the archaea, leading to a greater understanding of the biology and evolution of this domain.

This work will be of immense importance to evolutionary biologists and will further promote comparative genome analysis across the full biological spectrum. It will also help the community to refine and extend ongoing evolutionary debates addressing horizontal gene transfer. The genome sequences will greatly improve our understanding of the general nature of the amino acid changes in adaptation to high- or low-temperature environments. The genomes will also help the protein structure community to determine the structural features that allow proteins to operate at extremes of temperature, pH, and salinity. The genomes of the methanogens will give more insight into the metabolic and bioenergetic pathways required for the production of methane from waste material.

CSP project participants: Carl R. Woese (proposer), Gary Olsen, and Claudia Reich (Univ. of Illinois at Urbana-Champaign); Iain Anderson (JGI); Rick Cavicchioli (Univ. of New South Wales); Shil DasSarma (Univ. of Maryland Biotechnology Inst.); Harald Huber (Univ. Regensburg); Nikos Kyrpides (JGI), William Whitman (Univ. of Georgia).

Genome Portal Sites: Methanoculleus marisnigri JR1 , Thermofilum pendens Hrk 5

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