Structural model, physiology and regulation of Slr0006 in Synechocystis PCC 6803
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Original Paper
Structural model, physiology and regulation of Slr0006 in Synechocystis PCC 6803 Dalton Carmel · Käthe M. Dahlström · Maija Holmström · Yagut Allahverdiyeva · Natalia Battchikova · Eva‑Mari Aro · Tiina A. Salminen · Paula Mulo
Received: 14 January 2013 / Revised: 27 August 2013 / Accepted: 2 September 2013 / Published online: 17 September 2013 © Springer-Verlag Berlin Heidelberg 2013
Abstract The slr0006 gene of Synechocystis sp. PCC 6803 is upregulated at mRNA and protein level under carbon limitation. The T(N11)A motif in the upstream region of slr0006 is a binding site for transcriptional regulator NdhR, and accumulation of the Slr0006 protein in ndhR deletion mutant grown in high CO2 suggests that NdhR may be a negative regulator of slr0006. Accumulation requires photosynthetic electron transfer, because no Slr0006 was detected in darkness or in the presence of electron transfer inhibitors DCMU and DBMIB. Structural modeling of the Slr0006 protein suggests that it adopts Sua5/YciO/YrdC family fold, which is an α/β twisted open-sheet structure. Similar to the structurally known members of this protein family, the surface of Slr0006 contains positively charged cavity indicating a possible binding site for RNA or nucleotides. Moreover, Slr0006 was co-localized with 30S ribosomal proteins and rRNA, suggesting involvement in processes linked to protein synthesis.
Communicated by Erko Stackebrandt. Dalton Carmel and Käthe M. Dahlström have contributed equally to this work. D. Carmel · M. Holmström · Y. Allahverdiyeva · N. Battchikova · E.-M. Aro · P. Mulo (*) Department of Biochemistry, Molecular Plant Biology, University of Turku, 20014 Turku, Finland e-mail: [email protected] K. M. Dahlström · T. A. Salminen (*) Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, Biocity A 3rd Floor, Tykistökatu 6, 20520 Turku, Finland e-mail: [email protected]
Keywords Carbon concentrating mechanisms · NdhR · Ribosome · Sua5/YciO/YrdC
Introduction Inorganic carbon (Ci) limitation causes significant upregulation of the carbon concentrating mechanisms (CCMs) in Synechocystis sp. PCC 6803 (hereafter referred as Synechocystis), being evident both at mRNA (Wang et al. 2004; Eisenhut et al. 2007) and protein level (Battchikova et al. 2010). A shift of the cells from high (3 %) to air level (0.039 %) CO2 significantly enhances the expression of the NDH-1MS complex located in the thylakoid membrane, SbtA and BCT-1 bicarbonate transporters present at the plasma membrane, as well as RuBisCO and components of the carboxysomes located in the cytosol (Battchikova et al. 2010). Moreover, several genes in Synechocystis, which encode proteins with unknown function, are upregulated upon Ci limitation and, hence, might be involved in the low CO2 acclimation process (Battchikova et al. 2010). Expression of various genes encoding the CCM components is controlled by a number of regulatory proteins, such as sigma factors (Tuominen et al. 2008), NdhR (Woodger et al. 2007), CmpR (Omata et al. 200
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