1 3 Plant Mol Biol DOI 10.1007/s11103-014-0183-z Regulation of CCM genes in Chlamydomonas reinhardtii during conditions of light–dark cycles in synchronous cultures Srikanth Tirumani · Mallikarjuna Kokkanti · Vishal Chaudhari · Manish Shukla · Basuthkar J. Rao Received: 8 July 2013 / Accepted: 19 February 2014 © Springer Science+Business Media Dordrecht 2014 not to positively correlate with that of CCM, the protein regulation matched with CCM status: in spite of high tran- script levels in dark, CAH3 protein reached peak level only in light and localized entirely to pyrenoid, a site function- ally relevant for CCM. Moreover, in dark, CAH3 protein level not only reduced but also the protein localized as a diffused pattern in chloroplast. We propose that transcrip- tion of most CCM genes, followed by protein level changes including their intracellular localization of a subset is sub- ject to light–dark cycles. Keywords Air-level CO 2 · Bicarbonate transporter · Carbonic anhydrase · CO 2 -concentrating mechanism · Light–dark cycles · Transcriptional regulation Abbreviations CAs Carbonic anhydrases CO 2 Carbon dioxide CCM CO 2 -concentrating mechanism Ci Inorganic carbon DIC Dissolved inorganic carbon L:D Light:dark ML 6 h of incubation in light (mid-light) CL 12 h of incubation in light (complete-light) MD 6 h of incubation in dark (mid-dark) CD 12 h of incubation in dark (complete-dark) qRT-PCR Quantitative real time PCR RT-PCR Reverse transcription PCR Introduction CO 2 undergoes reduction in photosynthetic reactions to form carbohydrates that supplies food and energy to the bio- sphere. Hence any change in the CO 2 availability in local Abstract We have investigated transcript level changes of CO 2 -concentrating mechanism (CCM) genes during light– dark (12 h:12 h) cycles in synchronized Chlamydomonas reinhardtii at air-level CO 2 . CCM gene transcript levels vary at various times of light–dark cycles, even at same air- level CO 2 . Transcripts of inorganic carbon transporter genes (HLA3, LCI1, CCP1, CCP2 and LCIA) and mitochondrial carbonic anhydrase genes (CAH4 and CAH5) are up regu- lated in light, following which their levels decline in dark. Contrastingly, transcripts of chloroplast carbonic anhy- drases namely CAH6, CAH3 and LCIB are up regulated in dark. CAH3 and LCIB transcript levels reached maximum by the end of dark, followed by high expression into early light period. In contrast, CAH6 transcript level stayed high in dark, followed by high level even in light. Moreover, the up regulation of transcripts in dark was undone by high CO 2 , suggesting that the dark induced CCM transcripts were regulated by CO 2 even in dark when CCM is absent. Thus while the CAH3 transcript level modulations appear Srikanth Tirumani and Mallikarjuna Kokkanti share co-first- authorship in this work. Electronic supplementary material The online version of this article (doi:10.1007/s11103-014-0183-z) contains supplementary material, which is available to authorized users. S. Tirumani · V. Chaudhari · M. Shukla · B. J. Rao (*) B-202, Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India e-mail: bjrao@tifr.res.in URL: http://www.tifr.res.in/~dbs/faculty/bjr/Mission.html S. Tirumani · M. Kokkanti Department of Botany and Microbiology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522510, Andhra Pradesh, India