Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) has been described as the most abundant protein on earth (Ellis, 1979). On a global scale, the great majority of autotrophic processes that drive microbial ecosystems use this enzyme for the conversion of dissolved inorganic carbon (DIC) into organic carbon. Although the primary intracellular carbon fixation pathway operating in phytoplankton is the Calvin-Benson-Bassham (CBB) cycle, which employs Rubisco, the molecular inefficiency of this enzyme makes it a very poor CO2-trapping mechanism. In addition to the enzyme's very low turnover number, a competing oxygenase function further reduces its efficiency. The Rubisco-based carbon fixation pathway evolved early in evolutionary history, when CO2 levels were high and oxygen levels were very low.Rubisco (form I) is found as a hexadecamer of 8 large and small subunits (L8S8) with a native molecular weight of ~550 kD. As expected, there is considerable conservation of mechanistically significant active site residues of this enzyme throughout evolution. Regions containing such residues make for ideal PCR primers to retrieve rbcL/cbbL sequences from uncultivated photoautotrophs. The autotrophic phytoplankton in the oceans cluster primarily in the form I group. This group has been further subdivided into form IA (phycoerythrin-containing) cyanobacteria including Synechococcus and Trichodesmium, as well as Prochlorococcus and many sulfur oxidizing bacteria, form IB (other cyanobacteria, chlorophytes such as prasinophytes), and form ID (the chromophytic algae such as diatoms, prymnesiophytes, pelagophytes, bolidophytes, etc.) (Tabita, 1995; 1999). A few dinoflagellates (peridinin-containing forms such as Symbodinium and Gonyaulax) contain a form II enzyme, which is a dimer of large subunits (L2; Morse et al., 1995).
In most eukaryotic phytoplankton, the rbcL gene is contained on the plastid (chloroplast) genome, is intronless, and behaves like a prokaryotic gene (no poly A tail to the mRNA). In form IB-containing eukaryotes, the rbcS gene is nuclear-encoded, and the holoenzyme is assembled in the chloroplast. In the form ID algae, the rbcL and rbcS genes are adjacent and are chloroplast-encoded; both genes are co-transcribed. In form IA picocyanobacteria, the rbcL/rbcS genes are surrounded by genes that encode carbon concentrating mechanism and carboxysome proteins. In form II Rubisco-containing dinoflagellates, the rbcL gene is nuclear-encoded.
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