The Ravel Laboratory for Microbial Genomics
Genome Sequence of Prochloron didemni: an obligate cyanobacterial symbiont of the marine ascidian Lissoclinum patella.
Collaborators: Eric Schmidt, University of Utah and Margo Haygood, Scripps Oceanographic Institute. Jonathan Eisen, University of California Davis and TIGR. Frédéric Partensky, Station Biologique, Roscoff, France.
Funding: NSF
Prochloron didemni, an obligate cyanobacterial symbiont of coral reef ascidian Lissoclinum patella, shares many characteristics with free-living cyanobacteria, the genomes of which have been previously sequenced. Phylogenetically, P. didemni is more closely related to Synechocystis spp., major players in global carbon fixation with biotechnological importance. P. didemni is a prochlorophyte and thus shares photosynthetic features with free-living cyanobacterial prochlorophytes and with plant chloroplasts. Prochlorophytes and relatives have been estimated to contribute one-third of global fixed carbon, making an understanding of their unusual photosynthesis especially important. In this project, the genome of P. didemni is being sequenced and annotated, providing the first genome sequence of an obligate cyanobacterial symbiont. The genome sequence is of value in its own right in the elucidation of genes responsible for symbioses between chordates and bacteria. In addition, comparative genomics is being employed to further define the unique photosynthetic characteristics of prochlorophytes and plant chloroplasts, as well as to determine which factors are important in the conversion of free-living cyanobacteria (Synechocystis) into obligate symbiotic cyanobacteria (Prochloron).
Figure 1. A phylogenetic tree constructed from 16S rDNA sequences depicts the close relationship between Prochloron didemni and Synechocystis PCC6308. The other two chl a/b containing cyanobacteria, Prochlorococcus and Prochlorothrix hollandica, form a separate lineage and are not closely related to P. didemni. None of the three chl a/b containing prochlorophytes are specifically related to the chloroplasts of higher plants. *: organism for which genome sequence is available.
Figure 2. Left: Prochloron didemni cells. Center: A single L. patella colony (approx 3 cm in length). Green sections of the tunic contain P. didemni. Right: A cross-section of L. patella, showing green Prochloron cells.
Many secondary metabolites are found in Prochloron-bearing ascidians, and genomic studies has provided insight on the role and evolutionary origins of these compounds.
Over the last 30 years, marine sponges and ascidians have been widely studied for their unique secondary metabolic content. Many compounds from these organisms have been used to study basic cellular processes, and a few have been introduced into human clinical trials. It has been proposed that the cyclic peptides of the patellamide class found in didemnid extracts are synthesized by Prochloron spp., but studies in which host and symbiont cells are separated and chemically analyzed to identify the biosynthetic source have yielded inconclusive results. As part of the Prochloron didemni sequencing project, we identified patellamide biosynthetic genes and confirmed their function by heterologous expression of the whole pathway in Escherichia coli. The primary sequence of patellamides A and C is encoded on a single ORF that resembles a precursor peptide. We propose that this prepatellamide is heterocyclized to form thiazole and oxazoline rings, and the peptide is cleaved to yield the two cyclic patellamides, A and C. This work represents the full sequencing and functional expression of a marine natural-product pathway from an obligate symbiont. In addition, a related cluster was identified in Trichodesmium erythraeum IMS101, an important bloom-forming cyanobacterium.
PROJECTS
