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Functional Analysis of the Synechococcus elongatus PCC 7942 Genome

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Functional Genomics and Evolution of Photosynthetic Systems

Part of the book series: Advances in Photosynthesis and Respiration ((AIPH,volume 33))

Summary

Many genes related to the circadian clock have been discovered and studied in Synechococcus elongatus PCC 7942, the model organism for cyanobacterial circadian rhythms. However, the partners of some known clock components are still unidentified, and undiscovered pathways are predicted to exist that connect the central clock to other cellular functions. Identification of all clock components in S. elongatus is necessary for fully elucidating molecular mechanisms of the cyanobacterial circadian clock, as well as the relationship of the circadian clock to metabolism and other essential cellular activities. We adopted a transposon-mediated in vitro mutagenesis and sequencing strategy to disrupt essentially every locus in the genome and screen each insertional mutant for altered circadian phenotypes in S. elongatus. The completion of the genome sequence by the Department of Energy Joint Genome Institute greatly facilitated our functional genomics project, which is very close to the finish line with 88% of the genome mutagenized and more than 75% of loci screened for circadian function. Among the first 700 genes surveyed, 70 new clock loci were discovered that represent an array of functional categories.

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Abbreviations

S. elongatus :

Synechococcus elongatus PCC 7942

Cm:

chloramphenicol

Km:

kanamycin

ORF:

open reading frame

PCR:

polymerase chain reaction

RFLP:

restriction fragment length polymorphism

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Acknowledgments

We thank the following undergraduate students who contributed to the S. elongatus functional genomics project: Kimberly Baker, Carla Blumentritt, Audra Boettcher-Herring, Zack Bussey, Krista Cole, Priyanka Desai, Robert Dover, Ramiro Fernandez, Randall Gil, Judith Kwarteng-Amaning, Shaun McMurtry, Minh Nguyen, Ogonna (Kinney) Nwawka, Victoria Omishakin, Cassie Reyna, Nancy Reyes, Johnathan Siefert, Lindsay Stautzenberger, Ola Tokunbo. Alejandra Gonzales, Brandi Mohler, Isabel Salinas, and Pamela Sandoval contributed as technicians to the early stages of this work and Drs. Lisa Campbell and Sunil Pabbi participated as sabbatical visitors. Dr. Phil Beremand of the Laboratory for Functional Genomics and Larry Harris-Haller of the Gene Technologies Laboratory provided technical advice and support. JGI provided the complete S. elongatus PCC 7942 sequence. This project was initiated with grants to Philip A Youderian and SSG by the National Science Foundation (MCB-0196144 to PY and MCB-9818031 to SSG) and continued with support by the US Department of Energy (DE-FG03-00ER15055 to SSG) and the National Institutes of Health (R01 GM59336 and P01 NS39546 to SSG). AT and development of CyanoBIKE were supported by NSF grant DBI- DBI-0516378 to Jeff Elhai.

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Authors and Affiliations

  1. Synthetic Genomics Inc, 11149 North Torrey Pines Road, La Jolla, CA, 92037, USA

    You Chen

  2. Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843-3258, USA

    C. Kay Holtman

  3. Center for the Study of Biological Complexity, Virginia Commonwealth University, 1000 W. Cary Street, Richmond, VA, 23284, USA

    Arnaud Taton

  4. Division of Biological Sciences, Center for Chronobiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA

    Susan S. Golden

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  1. You Chen
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  2. C. Kay Holtman
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  3. Arnaud Taton
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  4. Susan S. Golden
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Correspondence to Susan S. Golden .

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Editors and Affiliations

  1. Dept. Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, 74075, Oklahoma, USA

    Robert Burnap

  2. School of Life Sciences &, Center for Bioenergy & Photosynthesis, Arizona State University, Tempe, 85287-4501, Arizona, USA

    Wim Vermaas

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Chen, Y., Holtman, C.K., Taton, A., Golden, S.S. (2012). Functional Analysis of the Synechococcus elongatus PCC 7942 Genome. In: Burnap, R., Vermaas, W. (eds) Functional Genomics and Evolution of Photosynthetic Systems. Advances in Photosynthesis and Respiration, vol 33. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-1533-2_5

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