Marine Microbiology Group - College of Marine Science - University of South Florida
Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South FloridaMarine Microbiology Group - College of Marine Science - University of South Florida
Marine Microbiology Group - College of Marine Science - University of South Florida
Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida
Marine Microbiology Group - College of Marine Science - University of South Florida

RESEARCH - REGULATION OF CARBON FIXATION

Metagenomic Analysis of Oceanic Picoplankton Communities - The Search for rbcL

The gene for the major carbon fixation enzyme in picocyanobacteria (rbcL) has been shown to be contained in a conserved operon, which we have termed the rbcL genomic environment. To understand genomic arrangements of carbon fixation genes we have made large insert libraries from the Gulf of Mexico and the LEO-15 site off Tuckerton, NJ. These were BAC libraries made from concentration of 200 L seawater and suspending the cells in agar plugs. After proteinase K and lysozyme treatment, the DNA-containing plugs were partially digested with HindIII, the desired mw bands excised and cloned into Epicentre's pIndigoBAC vectors.

The resulting 3200 clone library from the Gulf of Mexico was screened for rbcL-containing inserts using form I, form II, and formIII/IV probes. Ten clones hybridized (dots are in duplicate, the two circled ones were identical). Eight were sequenced by DOE JGI (Paul Richardson). All clones were derived from naturally occurring marine Synechococcus.


The sequences compared to Synechococcus WH8102 appear below.


Partial chromosome alignment of Synechococcus sp. WH 8102 and Gulf of Mexico BACs 3M9 and 5B2, showing areas of similarity shaded blue. Presumptive genes on 5B2 are color coded showing organisms to which they have closest homology. Green: Synechococcus 8102; blue: Prochlorococcus; orange: Synechocystis; purple: other cyanobacteria including Nostoc and Trichodesmium. The rbcL gene is colored red as a point of reference. Click here to see a full-size version.


Synteny of genes near the rbcL operon for 2 BAC sequences, Synechococcus 8102, and two Prochlorococcus genomes. Genes are color-coded based on related functions. Red: CO2 fixation; blue: carboxysome; yellow: NADH dehydrogenase; green: protochloro-phyllide reductase-related. Click here to see a full-size version.

These results show that there is tremendous conservation of synteny in the immediate rbcL genomic environment, and that insertion of genes that expand the metabolic capacity can occur outside these areas of high conservation.


  • To find out more about Rubisco genes in the environment, click here.

  • To learn more about carbon and nitrogen dynamics in the Mississippi, click here.

  • To learn more about the metagenomic analysis of oceanic picoplankton communities click here.

  • To learn more about the relationship between CO2 drawdown and phytoplankton gene expression click here.

Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida
Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida
Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida
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Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida Marine Microbiology Group - College of Marine Science - University of South Florida