Description of carbon fixation pathway based on <italic>Skeletonema marinoi</italic> transcriptome

Abstract

Diatoms can fix approximately 1016 g CO2 into organic carbon every year, equivalent to roughly 20% of global primary production. They are the basis for important food webs, having considerable impacts on carbon cycle and biological carbon pump that draws down CO2 from the atmosphere to the ocean interior. Nevertheless, the K 1/2 of their ribulose- 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is 40~60 μ mol L - 1, higher than the apparent photosynthetic K 1/2 (CO2) for ambient CO2. Growth and kinetic studies have shown that diatoms can avoid CO2 limitation through CO2 concentrating mechanisms. Recently the carbon fixation metabolism pathway in diatoms is further elucidated by the presence of a complete set of genes essential for this metabolic route in Thalassiosira pseudonana and Phaeodactylum tricornutum because of their entire availablegenome information. In this study, we used RNA-Seq technology to confirm the existence of necessary genes for plant-like C4 activity in Skeletonema marinoi , which is a complex biological trait that enables S. marinoi to either has high water-use efficiency or accumulate biomass at a fast rate. The carbon fixation metabolism pathway of S. marinoi involves 20 enzymes and 34 coding genes, including the complete key enzymes especially for C4 pathway, which are phosphoenolpyruvate carboxylase (PEPC), phosphoenolpyruvate carboxykinase (PEPCK) and pyruvate orthophosphate dikinase (PPDK). Comparing with the homologous genes of carbon fixation metabolism pathway in T. pseudonana and P. tricornutum , these genes showed little divergence. Besides, the gene differential expression of S. marinoi in carbon fixation metabolism pathway was identified at growth stages using digital gene expression profiling. The results indicated the number of differential expression genes was 7 and 3 in C3 and C4 pathway, respectively. As for the differential expression of coding genes in growth stages, there were 8 and 10 coding genes in the stationary and decline phase, respectively versus to those in the exponential phase. The gene expression of fructose-1,6-bisphosphatase (FBP), fructose-bisphosphate aldolase (ALDO) and PPDK was changed significantly after the exponential phase. The FBP and ALDO are not only responsible for the carbon fixation metabolism pathway, but also as the key enzymes in the glycolytic metabolism pathway, which links closely with the flow direction of carbon and the synthesis of carbohydrates. The PPDK, a cardinal enzyme of the C4 pathway, catalyzing the regeneration of phosphoenol pyruvate(PEP), evolved as an adaptation to high light intensity, high temperature, low concentration of CO2 and dryness. Therefore, the formation of PEP through PPDK is considered to be very important in the C4 pathway. This study will contribute to analyze the gene regulation of key enzymes involved in the carbon metabolism of S. marinoi , explain the reason for huge amounts of primary production by diatom, and enhance our knowledge on the carbon fixation mechanism, which provides a new insight into understanding carbon biogeochemical cycle.