Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis

Kim, Jay W.; Brawley, Susan H.; Prochnik, Simon; Chovatia, Mansi; Grimwood, Jane; Jenkins, Jerry; LaButti, Kurt; Mavromatis, Konstantinos; Nolan, Matt; Zane, Matthew; Schmutz, Jeremy; Stiller, John W.; Grossman, Arthur R.

doi:10.1371/journal.pone.0151883

Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis

Journal Article · Fri Mar 25 00:00:00 EDT 2016 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0151883· OSTI ID:1615260

Kim, Jay W. ^[1]; Brawley, Susan H. ^[2]; Prochnik, Simon ^[3]; Chovatia, Mansi ^[3]; Grimwood, Jane ^[4]; Jenkins, Jerry ^[4]; LaButti, Kurt ^[3]; Mavromatis, Konstantinos ^[3]; Nolan, Matt ^[3]; Zane, Matthew ^[3]; Schmutz, Jeremy ^[4]; Stiller, John W. ^[5]; Grossman, Arthur R. ^[6]

Univ. of California, Santa Cruz, CA (United States)
Univ. of Maine, Orono, ME (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
East Carolina Univ., Greenville, NC (United States)
Carnegie Inst. for Science, Stanford, CA (United States)

Porphyra is a macrophytic red alga of the Bangiales that is important ecologically and economically. We describe the genomes of three bacteria in the phylum Planctomycetes (designated P1, P2 and P3) that were isolated from blades of Porphyra umbilicalis (P.um.1). These three Operational Taxonomic Units (OTUs) belong to distinct genera; P2 belongs to the genus Rhodopirellula, while P1 and P3 represent undescribed genera within the Planctomycetes. Comparative analyses of the P1, P2 and P3 genomes show large expansions of distinct gene families, which can be widespread throughout the Planctomycetes (e.g., protein kinases, sensors/response regulators) and may relate to specific habitat (e.g., sulfatase gene expansions in marine Planctomycetes) or phylogenetic position. Notably, there are major differences among the Planctomycetes in the numbers and sub-functional diversity of enzymes (e.g., sulfatases, glycoside hydrolases, polysaccharide lyases) that allow these bacteria to access a range of sulfated polysaccharides in macroalgal cell walls. These differences suggest that the microbes have varied capacities for feeding on fixed carbon in the cell walls of P.um.1 and other macrophytic algae, although the activities among the various bacteria might be functionally complementary in situ. Additionally, phylogenetic analyses indicate augmentation of gene functions through expansions arising from gene duplications and horizontal gene transfers; examples include genes involved in cell wall degradation (e.g., κ-carrageenase, alginate lyase, fucosidase) and stress responses (e.g., efflux pump, amino acid transporter). Finally P1 and P2 contain various genes encoding selenoproteins, many of which are enzymes that ameliorate the impact of environmental stresses that occur in the intertidal habitat.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1615260

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 3 Vol. 11; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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