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Structural model, physiology and regulation of Slr0006 in Synechocystis PCC 6803

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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.

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Acknowledgments

We thank Prof. Ogawa for providing the mutants ∆ndhD1/D2, ∆ndhD3/D4 and ∆ndhB, and Dr. Burnap for providing the ∆ndhR strain. Drs. T. Tyystjärvi, M. Eisenhut, S. Järvi and S. Kangasjärvi are gratefully acknowledged for fruitful discussions. Prof. M. Johnson is acknowledged for the excellent facilities at the Structural Bioinformatics Laboratory at the Department of Biochemistry and Pharmacy at Åbo Akademi University. Use of Biocenter Finland infrastructure at Åbo Akademi (bioinformatics, structural biology, and translational activities) and the National Doctoral Programme in Informational and Structural Biology is also acknowledged. This study was financially supported by the Academy of Finland (Grants Number: 118637 and 263667), Maj and Tor Nessling Foundation, the Finnish Graduate School of Plant Biology, Åbo Akademi Graduate School, Sigrid Juselius Foundation, and the Tor, Joe and Pentti Borgs Foundation.

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Department of Biochemistry, Molecular Plant Biology, University of Turku, 20014, Turku, Finland

    Dalton Carmel, Maija Holmström, Yagut Allahverdiyeva, Natalia Battchikova, Eva-Mari Aro & Paula Mulo

  2. Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, Biocity A 3rd Floor, Tykistökatu 6, 20520, Turku, Finland

    Käthe M. Dahlström & Tiina A. Salminen

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  1. Dalton Carmel
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  2. Käthe M. Dahlström
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Correspondence to Tiina A. Salminen or Paula Mulo.

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Communicated by Erko Stackebrandt.

Dalton Carmel and Käthe M. Dahlström have contributed equally to this work.

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Carmel, D., Dahlström, K.M., Holmström, M. et al. Structural model, physiology and regulation of Slr0006 in Synechocystis PCC 6803. Arch Microbiol 195, 727–736 (2013). https://doi.org/10.1007/s00203-013-0924-4

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  • DOI: https://doi.org/10.1007/s00203-013-0924-4

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