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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)
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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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    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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Home › CSP Plans › Why Sequence Three Acidovorax Species?

Approved Proposals FY06

Why Sequence Three Acidovorax Species?

Intimate interactions between bacteria and eukaryotes have influenced the course of organismal evolution and ecological distribution. While ubiquitous, there is generally little understanding of the physiological basis of such associations, particularly when they are nonpathogenic in nature (symbiotic). Earthworms of the family Lumbricidae harbor novel symbiotic betaproteobacteria within their nephridia (excretory organ). Few symbiotic betaprotebacteria have been reported, and no other beneficial bacteria are described that specifically colonize the excretory organs of animals. To better understand the physiological and evolutionary dimensions of this symbiosis, JGI will sequence the genome of the isolated Acidovorax symbiont, and the genomes of two additional species within the genus: the plant pathogen A. avenae subsp. citrulli, and the nitroaromatic compound-degrader Acidovorax sp. JS42. Comparison of genomes from representatives of this single phylogenetic group will provide a genomic perspective on genetic and metabolic features that characterize these very divergent lifestyles–symbiotic, pathogenic, and free living. In addition to contributing to our understanding of the earthworm symbiosis, this information should extend general understanding of the adaptive radiation of microorganisms and be of benefit to several scientific fields of economic and environmental importance.

The availability of genomes from three Acidovorax species will provide an important comparative framework. The sequence of A. avenae subsp. citrulli should provide information about the character of the division between closely related symbiotic and pathogenic bacteria. The sequencing of Acidovorax sp. JS42 will provide information about the gene content of a free-living species with a catabolic capacity relevant to bioremediation of nitroaromatic-contaminated soils. Thus, the genome sequence data will be of interest to a broad group of investigators, immediately drawing together a diverse and interdisciplinary group of researchers that have explored different physiological and ecological dimensions of this genus, as well as those interested in the features of host/microbe interactions in general.

CSP project participants: David A. Stahl (proposer), Seana K. Davidson, and Nicolás Pinel (Univ. of Washington).

Genome Portal Sites: Acidovorax avenae subsp. citrulli, Acidovorax JS42 and Acidovorax symbiont (Verminephrobacter eiseniae EF01-2)

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