Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga
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.
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.
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.. (March 2016). Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga. PLoS ONE, 11(3), 1- 22. Retrieved from http://hdl.handle.net/10342/5467
Kim, Jay W., and Brawley, Susan H., and Prochnik, Simon, and Chovatia, Mansi, and Grimwood, Jane, and Jenkins, Jerry, and LaButti, Kurt, and Mavromatis, Konstantinos, and Nolan, Matt, and Zane, Matthew, and Schmutz, Jeremy, and Stiller, John W., and Grossman, Arthur R.. "Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga". PLoS ONE. 11:3. (1-22), March 2016. April 24, 2019. http://hdl.handle.net/10342/5467.
Kim, Jay W. and Brawley, Susan H. and Prochnik, Simon and Chovatia, Mansi and Grimwood, Jane and Jenkins, Jerry and LaButti, Kurt and Mavromatis, Konstantinos and Nolan, Matt and Zane, Matthew and Schmutz, Jeremy and Stiller, John W. and Grossman, Arthur R., "Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga," PLoS ONE 11, no. 3 (March 2016), http://hdl.handle.net/10342/5467 (accessed April 24, 2019).
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.. Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga. PLoS ONE. March 2016; 11(3): 1-22. http://hdl.handle.net/10342/5467. Accessed April 24, 2019.