Utilization of a chloroplast membrane sulfolipid as a major internal sulfur source for protein synthesis in the early phase of sulfur starvation inChlamydomonas reinhardtii

RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival

The Chlamydomonas reinhardtii transcriptome was characterized from nutrient-replete and sulfur-depleted wild-type and snrk2.1 mutant cells. This mutant is null for the regulatory Ser-Thr kinase SNRK2.1, which is required for acclimation of the alga to sulfur deprivation. The transcriptome analyses used microarray hybridization and RNA-seq technology. Quantitative RT-PCR evaluation of the results obtained by these techniques showed that RNA-seq reports a larger dynamic range of expression levels than do microarray hybridizations. Transcripts responsive to sulfur deprivation included those encoding proteins involved in sulfur acquisition and assimilation, synthesis of sulfur-containing metabolites, Cys degradation, and sulfur recycling. Furthermore, we noted potential modifications of cellular structures during sulfur deprivation, including the cell wall and complexes associated with the photosynthetic apparatus. Moreover, the data suggest that sulfur-deprived cells accumulate proteins with fewer sulfur-containing amino acids. Most of the sulfur deprivation responses are controlled by the SNRK2.1 protein kinase. The snrk2.1 mutant exhibits a set of unique responses during both sulfur-replete and sulfur-depleted conditions that are not observed in wild-type cells; the inability of this mutant to acclimate to S deprivation probably leads to elevated levels of singlet oxygen and severe oxidative stress, which ultimately causes cell death. The transcriptome results for wild-type and mutant cells strongly suggest the occurrence of massive changes in cellular physiology and metabolism as cells become depleted for sulfur and reveal aspects of acclimation that are likely critical for cell survival.

Regulation of synthesis and degradation of a sulfolipid under sulfur-starved conditions and its physiological significance in Chlamydomonas reinhardtii

Regulation of synthesis and degradation of sulfoquinovosyl diacylglycerol (SQDG), one of the membrane lipids that construct thylakoids, under sulfur (S)-starved conditions and its physiological significance were explored in a green alga, Chlamydomonas reinhardtii. Here, we used sac1 and sac3 mutants defective in response to ambient S-status to characterize the system of known induction of SQDG degradation by S starvation that ensures a major S source for protein synthesis. The SQDG synthesis system was monitored in the wild type during S starvation. An SQDG-deficient mutant, hf-2, was utilized to discover functions where SQDG metabolism participates during S starvation. The induction of SQDG degradation was largely repressed in both sac1 and sac3 mutants. The SQDG synthesis capacity was increased by 40% after S starvation, with a sixfold elevation in the mRNA level of the SQD1 gene for SQDG synthesis. Compared with the wild type, hf-2 had decreased protein accumulation, photosystem (PS) I stability and growth rate. A role of SQDG as an S storage lipid is fulfilled under the control of both SAC1 and SAC3 genes, and it is essential for proper protein synthesis in acclimatization of cells to S starvation. The enhancement in SQDG synthesis may reflect the importance of SQDG as the membrane lipid that stabilizes the PSI complex.

A chloroplastic UDP-glucose pyrophosphorylase from Arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis

Plants synthesize a sulfur-containing lipid, sulfoquinovosyldiacylglycerol, which is one of three nonphosphorus glycerolipids that provide the bulk of the structural lipids in photosynthetic membranes. Here, the identification of a novel gene, UDP-glucose pyrophosphorylase3 (UGP3), required for sulfolipid biosynthesis is described. Transcriptome coexpression analysis demonstrated highly correlated expression of UGP3 with known genes for sulfolipid biosynthesis in Arabidopsis thaliana. Liquid chromatography-mass spectrometry analysis of leaf lipids in two Arabidopsis ugp3 mutants revealed that no sulfolipid was accumulated in these mutants, indicating the participation of UGP3 in sulfolipid biosynthesis. From the deduced amino acid sequence, UGP3 was presumed to be a UDP-glucose pyrophosphorylase (UGPase) involved in the generation of UDP-glucose, serving as the precursor of the polar head of sulfolipid. Recombinant UGP3 was able to catalyze the formation of UDP-glucose from glucose-1-phosphate and UTP. A transient assay using fluorescence fusion proteins and UGPase activity in isolated chloroplasts indicated chloroplastic localization of UGP3. The transcription level of UGP3 was increased by phosphate starvation. A comparative genomics study on UGP3 homologs across different plant species suggested the structural and functional conservation of the proteins and, thus, a committing role for UGP3 in sulfolipid synthesis.

Genetic interactions between regulators of Chlamydomonas phosphorus and sulfur deprivation responses

The Chlamydomonas reinhardtii PSR1 gene is required for proper acclimation of the cells to phosphorus (P) deficiency. P-starved psr1 mutants show signs of secondary sulfur (S) starvation, exemplified by the synthesis of extracellular arylsulfatase and the accumulation of transcripts encoding proteins involved in S scavenging and assimilation. Epistasis analysis reveals that induction of the S-starvation responses in P-limited psr1 cells requires the regulatory protein kinase SNRK2.1, but bypasses the membrane-targeted activator, SAC1. The inhibitory kinase SNRK2.2 is necessary for repression of S-starvation responses during both nutrient-replete growth and P limitation; arylsulfatase activity and S deficiency-responsive genes are partially induced in the P-deficient snrk2.2 mutants and become fully activated in the P-deficient psr1snrk2.2 double mutant. During P starvation, the sac1snrk2.2 double mutants or the psr1sac1snrk2.2 triple mutants exhibit reduced arylsulfatase activity compared to snrk2.2 or psr1snrk2.2, respectively, but the sac1 mutation has little effect on the abundance of S deficiency-responsive transcripts in these strains, suggesting a post-transcriptional role for SAC1 in elicitation of S-starvation responses. Interestingly, P-starved psr1snrk2.2 cells bleach and die more rapidly than wild-type or psr1 strains, suggesting that activation of S-starvation responses during P deprivation is deleterious to the cell. From these results we infer that (i) P-deficient growth causes some internal S limitation, but the S-deficiency responses are normally inhibited during acclimation to P deprivation; (ii) the S-deficiency responses are not completely suppressed in P-deficient psr1 cells and consequently these cells synthesize some arylsulfatase and exhibit elevated levels of transcripts for S-deprivation genes; and (iii) this increased expression is controlled by regulators that modulate transcription of S-responsive genes during S-deprivation conditions. Overall, the work strongly suggests integration of the different circuits that control nutrient-deprivation responses in Chlamydomonas.

Upregulation of PG synthesis on sulfur-starvation for PS I in Chlamydomonas

Sulfur(S)-starvation was previously shown to induce the degradation of an acidic lipid in chloroplasts, sulfoquinovosyl diacylglycerol (SQDG), to yield a major internal S-source in a green alga, Chlamydomonas reinhardtii. We here found that the synthesis of phosphatidylglycerol (PG), the other acidic lipid in chloroplasts, is activated to elevate its content up to a level that just compensates for the loss of SQDG. Similar activation of PG synthesis was also observed in an SQDG-deficient mutant under S-replete conditions, which led us to propose that upregulation of PG synthesis under S-starved conditions occurs through direct sensing of SQDG-loss, but not of S-starvation. Moreover, thylakoid membranes isolated from S-starved cells were reduced in photosystem I activity on treatment with phospholipase A(2) that specifically broke down PG, which suggested a critical role of PG that is increased under S-starved conditions in the maintenance of the photosystem I activity.