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Genomic analysis of parallel-evolved cyanobacterium Synechocystis sp. PCC 6803 under acid stress

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Abstract

Experimental evolution is a powerful tool for clarifying phenotypic and genotypic changes responsible for adaptive evolution. In this study, we isolated acid-adapted Synechocystis sp. PCC 6803 (Synechocystis 6803) strains to identify genes involved in acid tolerance. Synechocystis 6803 is rarely found in habitants with pH < 5.75. The parent (P) strain was cultured in BG-11 at pH 6.0. We gradually lowered the pH of the medium from pH 6.0 to pH 5.5 over 3 months. Our adapted cells could grow in acid stress conditions at pH 5.5, whereas the parent cells could not. We performed whole-genome sequencing and compared the acid-adapted and P strains, thereby identifying 11 SNPs in the acid-adapted strains, including in Fo F1-ATPase. To determine whether the SNP genes responded to acid stress, we examined gene expression in the adapted strains using quantitative reverse-transcription polymerase chain reaction. sll0914, sll1496, sll0528, and sll1144 expressions increased under acid stress in the P strain, whereas sll0162, sll0163, slr0623, and slr0529 expressions decreased. There were no differences in the SNP genes expression levels between the P strain and two adapted strains, except for sll0528. These results suggest that SNPs in certain genes are involved in acid stress tolerance in Synechocystis 6803.

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Abbreviations

QRT-PCR:

Real-time quantitative reverse-transcription polymerase chain reaction

Synechocystis 6803:

Synechocystis sp. PCC 6803

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Acknowledgments

This study was supported by the Program for Development of Strategic Research Center in Private Universities, which was supported by MEXT (S1001020). This study was supported by MEXT-Supported Program for the Strategic Research Foundation at Private Universities, 2013–2017 (S1311017). The authors would like to thank Enago (www.enago.jp) for the English language review.

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Authors and Affiliations

  1. Research Center for RNA Science, Research Institute for Science and Technology, Tokyo University of Science, 2641, Yamasaki, Noda, Chiba, 278-8510, Japan

    Junji Uchiyama & Hisataka Ohta

  2. Genome Research Center, Nodai Research Institute, Tokyo University of Agriculture, Setagaya-ku, Tokyo, 156-8502, Japan

    Yu Kanesaki

  3. Department of Biology, Faculty of Science, Tokyo University of Science, Shinjuku-ku, Tokyo, 162-8601, Japan

    Naoya Iwata, Ryousuke Asakura, Kento Funamizu, Rizumu Tasaki, Mina Agatsuma, Hiroko Tahara, Ayumi Matsuhashi & Hisataka Ohta

  4. Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, 156-8502, Japan

    Hirofumi Yoshikawa

  5. Laboratory of Electron Microscopy, School of Medicine, Mie University, Tsu, 514-8507, Japan

    Satoru Ogawa

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  1. Junji Uchiyama
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  2. Yu Kanesaki
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Correspondence to Junji Uchiyama.

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Uchiyama, J., Kanesaki, Y., Iwata, N. et al. Genomic analysis of parallel-evolved cyanobacterium Synechocystis sp. PCC 6803 under acid stress. Photosynth Res 125, 243–254 (2015). https://doi.org/10.1007/s11120-015-0111-3

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