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Global Changes in Chlamydomonas Gene Expression Regulated by Carbon Dioxide and CIA5/CCM1

ABSTRACT: We used RNA-Seq to query the Chlamydomonas reinhardtii transcriptome for regulation by CO2 concentration and by the transcription regulator CIA5(CCM1). Both CO2 concentration and CIA5 are known to play roles in induction of an essential CO2-concentrating mechanism (CCM), but the degree of interaction and the extent of global regulation beyond the CCM were not previously understood. We compared the transcriptome of a wild type strain vs. a cia5 strain under 3 CO2 supply conditions: high CO2 (H-CO2; 5%); low CO2 (L-CO2; 0.03 to 0.05%); and very-low CO2 (VL-CO2; <0.02%). Our goals were to: 1) reveal candidate genes that, through changes in their expression, distinguish multiple acclimation states induced by H-CO2, L-CO2, and VL-CO2; 2) reveal genes regulated directly or indirectly by CIA5; and 3) reveal genes responding to the interaction between CIA5 and changes in CO2 concentration. Our results revealed a small group of genes as encoding putative Ci transporters based on their expression patterns. The results also showed a massive and much broader impact on global gene regulation by CIA5/CCM1, which directly or indirectly affected 15% of the Chlamydomonas genome. The transcriptomes under L-CO2 and VL-CO2 conditions were not significantly different, suggesting that these two acclimation states must be controlled by mechanisms operating beyond transcript abundance.

ORGANISM(S): Chlamydomonas reinhardtii

PROVIDER: GSE33927 | GEO | 2012/08/10

SECONDARY ACCESSION(S): PRJNA148227

REPOSITORIES: GEO

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Project description:Zinc is an essential nutrient because of its role in catalysis and in stabilizing protein structure, but excess zinc can also be deleterious. Four nutritional zinc states have been identified in the alga Chlamydomonas reinhardtii: zinc toxic, zinc replete, zinc deficient and zinc limited. Growth is inhibited in zinc-limited and zinc toxic cells relative to zinc-replete cells, while zinc-deficiency is visually asymptomatic but distinguished by the accumulation of transcripts encoding ZIP family transporters. To identify targets of zinc deficiency and mechanisms of zinc acclimation, we used RNA-seq to probe zinc nutrition responsive changes in gene expression. We identified a subset of genes encoding zinc-handling components, including ZIP family transporters and candidate zinc chaperones. In addition, we noted an impact on two other regulatory pathways, the carbon concentrating mechanism (CCM) and the nutritional copper regulon. Targets of transcription factor Ccm1 and various CAH genes are up-regulated in zinc-deficiency, as a likely consequence of reduced carbonic anhydrase activity, which is validated by mass spectrometry and immunoblot analysis of Cah1, Cah3 and Cah4. Chlamydomonas is therefore not able to grow photoautotrophically in air in zinc limiting conditions, but supplementation with 1% CO2 restores growth to wild-type rates, suggesting that the inability to maintain CCM is a major consequence of zinc limitation. Surprisingly, we noted also that the Crr1 regulon, which responds to Cu limitation, is also turned on in zinc deficiency, and in fact, Crr1 is required for growth in zinc-limiting conditions. Zinc deficient cells are functionally copper deficient, as evidenced by reduced plastocyanin abundance, even though they hyperaccumulate copper up to 50-fold over normal levels. We suggest that zinc-deficient cells sequester Cu in a bio-unavailable form, perhaps to prevent mis-metallation of critical zinc sites. Zn-limited wild-type cells were generated by transfer of cells from the first round of growth in medium with no supplemental Zn into TAP medium supplemented or not with 2.5 ÂµM Zn-EDTA The control samples for this study are represented in GSE25622

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Global Changes in Chlamydomonas Gene Expression Regulated by Carbon Dioxide and CIA5/CCM1

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