Identification and functional analysis of LCI15, a suppressor of the air dier phenotype of LCIB mutants in Chlamydomonas reinhardtii
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The eukaryotic alga, Chlamydomonas reinhardtii, acclimates to limiting CO2 conditions by the induction of the CO2-concentrating mechanism (CCM) – a complex system of changes in its metabolism, gene expression patterns, and physiology – to compensate for the reduction in the amount of available CO2 and counter the hindrance to its ability to photosynthesize and grow. LCIB, a gene upregulated in such conditions, encodes a protein potentially involved in uptake of CO2 into the cell and in preventing the leakage of CO2 out of the cell. This protein is indispensable for growth in air-level CO2 (~350-400 ppm), since mutants in this gene are unable to grow (hence they are called air dier mutants). Several mutants that have second-site alterations that restore growth in air-level CO2 (i.e., suppress the air dier phenotype) have been isolated. Identifying the genes that are mutated in these suppressors and the functions of the encoded proteins will help us better discern the role of LCIB and comprehend the workings of the entire mechanism.
To identify the locus of the mutated gene in one suppressor mutant, crosses were performed between the mutant strain and a non-mutant, polymorphic wild-type strain, and a large population of recombinant progeny that segregated against the mutation of interest was amassed. Using a strain that has unique single nucleotide polymorphisms (SNPs) as the non-mutant parent allowed us to seek a particular characteristic (the polymorphisms) in the region of interest in the genome of the progeny. With a sequenced genome, a library of SNPs in the polymorphic strain, and a pool of the genomic DNA from the entire population, we mapped the mutation to a specific region of the genome and narrowed potential candidates down to a small number of genes. By cosegregation analysis, we were able to confirm one of the candidates, LCI15, as the implicated gene. Preliminary functional analyses with semi-quantitative RT-PCR and Western immunoblots reveal the LCI15 protein as possibly playing an overarching role in regulation in the CCM and offer terms for discussing potential methods by which the lack of LCI15 might potentially mask the deleterious effects of the absence of LCIB.