Nitrogen assimilation in cassava: implications for carbon metabolism and biomass synthesis

Abstract

The nitrogen assimilation pathway in cassava was reconstructed by comparative genomics approach to understand the underlying metabolism as well as the interaction between carbon and nitrogen assimilation towards the synthesis of metabolic phenotype. First, theproteins of cassava were annotated via sequence similarity search against genes of 11 template plants obtained from KEGG and PMN databases, employing reciprocal BLASTp(E-value ≤ 1x10−10, identity percentage ≥ 60, and coverage percentage ≥ 80). The template plants comprised well-known plant, starchy crops, nitrogen-fixing crops and crops that are evolutionarily related to cassava and includedArabidopsis thaliana, Oryzasativa, Zea mays, Ricinuscommunis, Solanumtuberosum, Brassica rapa, Cicerarietinum, Jatrophacurcas, Medicagotruncatula, Phaseolus vulgaris and Glycine max.The pathway was then curatedwith reactions obtained from the CassavaCyc database to ensure full pathway connectivity.It was subsequently validated with cloned sequence of cassava from the GenBank and cassava transcriptome data from literature. The resulting N-assimilation pathway, covering the conversion of nitrate to amino acids (glutamine and glutamate),consists of 14 biochemical reactions corresponding to 59 genes, 73 proteins and 2 transport reactions. At least 92 percent of the identified proteins in the pathway were supported by the transcriptome data. In addition, the proposed N-assimilation pathway contains four additional enzymes, including glutamate synthase, nitrilase, formamidase and carbamoyl phosphate synthasecompared to the existing N-assimilation pathway in CassavaCyc database. Taken together, the N-assimilation pathway herein proposed identified reactions involved in N-assimilation and represents a forward step towards understanding metabolic basis for cassava yield as well as its phenotypic plasticity and adaptation to stress.