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Analysis of the evolution of the family of the Sig genes encoding plant sigma factors

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Abstract

Within the latter decade, sigma subunits of bacterial-type RNA polymerases were found in eukaryote cells. In the higher plants and algae, these subunits determine the promoter specificity of the chloroplast multisubunit RNA polymerase. In the higher plants, sigma subunits are encoded by the family of nuclear Sig genes comprising 5–6 genes. Several conclusions as to the evolution of this gene family were deduced from the comparison of the deduced amino acid sequences and the sites of intron location.

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References

  1. Shematorova, E.K. and Shpakovski, G.V., Structure and Functions of Eukaryotic Nuclear DNA-Dependent RNA Polymerase I, Mol. Biol. (Moscow), 2002, vol. 36, pp. 1–17.

    Article  CAS  Google Scholar 

  2. Helmann, J.D. and Chamberlin, M.J., Structure and Function of Bacterial Sigma Factors, Annu. Rev. Biochem., 1988, vol. 57, pp. 839–872.

    Article  PubMed  CAS  Google Scholar 

  3. Allison, L.A., The Role of Sigma Factors in Plastid Transcription, Biochimie, 2000, vol. 82, pp. 537–548.

    Article  PubMed  CAS  Google Scholar 

  4. Lysenko, E.A. and Kusnetsov, V.V., Plastid RNA Polymerases, Mol. Biol. (Moscow), 2005, vol. 39, pp. 661–674.

    Article  CAS  Google Scholar 

  5. Dyall, S.D., Brown, M.T., and Johnson, P.J., Ancient Invasions: From Endosymbionts to Organelles, Science, 2004, vol. 304, pp. 253–257.

    Article  PubMed  CAS  Google Scholar 

  6. Martin, W., Rujan, T., Richly, E., Hansen, A., Cornelsen, S., Lins, T., Leister, D., Stoebe, B., Hasegawa, M., and Penny, D., Evolutionary Analysis of Arabidopsis, Cyanobacterial, and Chloroplast Genomes Reveals Plastid Phylogeny and Thousands of Cyanobacterial Genes in the Nucleus, Proc. Natl. Acad. Sci. USA, 2002, vol. 99, pp. 12 246–12 251.

    CAS  Google Scholar 

  7. Imamura, S., Yoshihara, S., Nakano, S., Shiozaki, N., Yamada, A., Tanaka, K., Takahashi, H., Asayama, M., and Shirai, M., Purification, Characterization, and Gene Expression of All Sigma Factors of RNA Polymerase in a Cyanobacterium, J. Mol. Biol., 2003, vol. 325, pp. 857–872.

    Article  PubMed  CAS  Google Scholar 

  8. Kaneko, T., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y., Miyajima, N., Hirosawa, M., Sugiura, M., Sasamoto, S., Kimura, T., Hosouchi, T., Matsuno, A., Muraki, A., Nakazaki, N., Naruo, K., Okumura, S., Shimpo, S., Takeuchi, C., Wada, T., Watanabe, A., Yamada, M., Yasuda, M., and Tabata, S., Sequence Analysis of the Genome of the Unicellular Cyanobacterium synechocystis sp. Strain PCC6803: 2. Sequence Determination of the Entire Genome and Assignment of Potential Protein-Coding Regions, DNA Res., 1996, vol. 3, pp. 109–136.

    Article  PubMed  CAS  Google Scholar 

  9. Kaneko, T., Nakamura, Y., Wolk, C.P., Kuritz, T., Sasamoto, S., Watanabe, A., Iriguchi, M., Ishikawa, A., Kawashima, K., Kimura, T., Kishida, Y., Kohara, M., Matsumoto, M., Matsuno, A., Muraki, A., Nakazaki, N., Shimpo, S., Sugimoto, M., Takazawa, M., Yamada, M., Yasuda, M., and Tabata, S., Complete Genomic Sequence of the Filamentous Nitrogen-Fixing Cyanobacterium Anabaena sp. Strain PCC 7120, DNA Res., 2001, vol. 8, pp. 205–213, suppl., pp. 227–253.

    Article  PubMed  CAS  Google Scholar 

  10. Odintsova, M.S. and Yurina, N.P., Plastid Genomes of Higher Plants and Algae: Structure and Functions, Mol. Biol. (Moscow), 2003, vol. 37, pp. 649–662.

    Article  CAS  Google Scholar 

  11. Kanamaru, K., Nagashima, A., Fujiwara, M., Shimada, H., Shirano, Y., Nakabayashi, K., Shibata, D., Tanaka, K., and Takahashi, H., An Arabidopsis Sigma Factor (SIG2)-Dependent Expression of Plastid Encoded tRNAs in Chloroplasts, Plant Cell Physiol., 2001, vol. 42, pp. 1034–1043.

    Article  PubMed  CAS  Google Scholar 

  12. Nagashima, A., Hanaoka, M., Shikanai, T., Fujiwara, M., Kanamaru, K., Takahashi, H., and Tanaka, K., The Multiple-Stress Responsive Plastid Sigma Factor, SIG5, Directs Activation of the psbD Blue Light-Responsive Promoter (BLRP) in Arabidopsis thaliana, Plant Cell Physiol., 2004, vol. 45, pp. 357–368.

    Article  PubMed  CAS  Google Scholar 

  13. Ishizaki, Y., Tsunoyama, Y., Hatano, K., Ando, K., Kato, K., Shinmyo, A., Kobori, M., Takeba, G., Nakahira, Y., and Shiina, T., A Nuclear Encoded Sigma Factor, Arabidopsis SIG6, Recognizes Sigma-70 Type Chloroplast Promoters and Regulates Early Chloroplast Development in Cotyledons, Plant J., 2005, vol. 42, pp. 133–144.

    Article  PubMed  CAS  Google Scholar 

  14. Tan, S. and Troxler, R.F., Characterization of Two Chloroplast RNA Polymerase Sigma Factors from Zea mays: Photoregulation and Differential Expression, Proc. Natl. Acad. Sci. USA, 1999, vol. 96, pp. 5316–5321.

    Article  PubMed  CAS  Google Scholar 

  15. Tanaka, K., Tozawa, Y., Mochizuki, N., Shinozaki, K., Nagatani, A., Wakasa, K., and Takahashi, H., Characterization of Three cDNA Species Encoding Plastid RNA Polymerase Sigma Factors in Arabidopsis thaliana: Evidence for the Sigma Factor Heterogeneity in Higher Plant Plastids, FEBS Lett., 1997, vol. 413, pp. 309–313.

    Article  PubMed  CAS  Google Scholar 

  16. Oikawa, K., Tanaka, K., and Takahashi, H., Two Types of Differently Photo-Regulated Nuclear Genes That Encode Sigma Factors for a Chloroplast RNA Polymerase in the Red Alga Cyanidium caldarium Strain RK-1, Gene, 1998, vol. 210, pp. 277–285.

    Article  PubMed  CAS  Google Scholar 

  17. Fujiwara, M., Nagashima, A., Kanamaru, K., Tanaka, K., and Takahashi, H., Three New Nuclear Genes, SigD, SigE, SigF, Encoding Putative Plastid RNA Polymerase Sigma Factors in Arabidopsis thaliana, FEBS Lett., 2000, vol. 481, pp. 47–52.

    Article  PubMed  CAS  Google Scholar 

  18. Huckauf, J., Nomura, C., Forchhammer, K., and Hagemann, M., Stress Responses of Synechocystis sp. Strain PCC 6803 Mutants Impaired in Genes Encoding Putative Alternative Sigma Factors, Microbiology, 2000, vol. 146, pp. 2877–2889.

    PubMed  CAS  Google Scholar 

  19. Khudyakov, I.Y. and Golden, J.W., Identification and Inactivation of Three Group 2 Sigma Factor Genes in Anabaena sp. Strain PCC 7120, J. Bacteriol., 2001, vol. 183, pp. 6667–6675.

    Article  PubMed  CAS  Google Scholar 

  20. Nair, U., Ditty, J.L., Min, H., and Golden, S.S., Roles for Sigma Factors in Global Circadian Regulation of the Cynobacterial Genome, J. Bacteriol., 2002, vol. 184, pp. 3530–3538.

    Article  PubMed  CAS  Google Scholar 

  21. Liu, B. and Troxler, R.F., Molecular Characterization of a Positively Photoregulated Nuclear Gene for a Chloroplast RNA Polymerase Sigma Factor in Cyanidium caldarium, Proc. Natl. Acad. Sci. USA, 1996, vol. 93, pp. 3313–3318.

    Article  PubMed  CAS  Google Scholar 

  22. Lu, G. and Moriyama, E.N., Vector NTI, a Balanced All-in-One Sequence Analysis Suite, Brief. Bioinform., 2004, vol. 5, pp. 378–388.

    Article  PubMed  CAS  Google Scholar 

  23. Thompson, J.D., Higgins, D.G., and Gibson, T.J., CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice, Nucleic Acids Res., 1994, vol. 22, pp. 4673–4680.

    PubMed  CAS  Google Scholar 

  24. Saitou, N. and Nei, M., The Neighbour-Joining Method: A New Method for Reconstructing Phylogenetic Trees, Mol. Biol. Evol., 1987, vol. 4, pp. 406–425.

    PubMed  CAS  Google Scholar 

  25. Carter, M.L., Smith, A.C., Kobayashi, H., Purton, S., and Herrin, D., Structure, Circadian Regulation and Bioinformatics Analysis of the Unique Sigma Factor Gene in Chlamydomonas reinhardtii, Photosynth. Res., 2004, vol. 82, pp. 339–349.

    Article  PubMed  CAS  Google Scholar 

  26. Ichikawa, K., Sugita, M., Imaizumi, T., Wada, M., and Aoki, S., Differential Expression on a Daily Basis of Plastid Sigma Factor Genes from the Moss Physcomitrella patens, Regulatory Interactions among PpSig5, the Circadian Clock, and Blue Light Signaling Mediated by Cryptochromes, Plant Physiol., 2004, vol. 136, pp. 4285–4298.

    Article  PubMed  CAS  Google Scholar 

  27. Deutsch, M. and Long, M., Intron-Exon Structures of Eukaryotic Model Organisms, Nucleic Acids Res., 1999, vol. 27, pp. 3219–3228.

    Article  PubMed  CAS  Google Scholar 

  28. Kanamaru, K., Fujiwara, M., Seki, M., Katagiri, T., Nakamura, M., Mochizuki, N., Nagatani, A., Shinozaki, A., Tanaka, K., and Takahashi, H., Plastidic RNA Polymerase Sigma Factors in Arabidopsis, Plant Cell Physiol., 1999, vol. 40, pp. 832–842.

    PubMed  CAS  Google Scholar 

  29. Turmel, M., Otis, C., and Lemieux, C., The Chloroplast and Mitochondrial Genome Sequences of the Charophyte Chaetosphaeridium globosum: Insights into the Timing of the Events That Restructured Organelle DNAs within the Green Algal Lineage That Led to Land Plants, Proc. Natl. Acad. Sci. USA, 2002, vol. 99, pp. 11275–11280.

    Article  PubMed  CAS  Google Scholar 

  30. Stegemann, S., Hartmann, S., Ruf, S., and Bock, R., High-Frequency Gene Transfer from the Chloroplast Genome to the Nucleus, Proc. Natl. Acad. Sci. USA, 2003, vol. 100, pp. 8828–8833.

    Article  PubMed  CAS  Google Scholar 

  31. Matsuo, M., Ito, Y., Yamauchi, R., and Obokata, J., The Rice Nuclear Genome Continuously Integrates, Shuffles, and Eliminates the Chloroplast Genome to Cause Chloroplast-Nuclear DNA Flux, Plant Cell, 2005, vol. 17, pp. 665–675.

    Article  PubMed  CAS  Google Scholar 

  32. Hecker, M. and Völker, U., Non-Specific, General and Multiple Stress Resistance of Growth-Restricted Bacillus subtilis Cells by the Expression of the SigmaB Regulon, Mol. Microbiol., 1998, vol. 29, pp. 1129–1136.

    Article  PubMed  CAS  Google Scholar 

  33. Schopf, J.W., The Fossil Record: Tracing the Roots of the Cyanobacterium Lineage, The Ecology of Cyanobacteria, Witton, B.A. and Potts, M., Eds., Dordrecht: Kluwer, 2000, pp. 13–35.

    Google Scholar 

  34. Hartung, F., Blattner, F.R., and Puchta, H., Intron Gain and Loss in the Evolution of the Conserved Eukaryotic Recombination Machinery, Nucleic Acids Res., 2002, vol. 30, pp. 5175–5181.

    Article  PubMed  CAS  Google Scholar 

  35. Oikawa, K., Fujiwara, M., Nakazato, E., Tanaka, K., and Takahashi, H., Characterization of Two Plastid Sigma Factor, SigA1 and SigA2, That Mainly Function in Mature Chloroplasts in Nicotiana tabacum, Gene, 2000, vol. 261, pp. 221–228.

    Article  PubMed  CAS  Google Scholar 

  36. Tozawa, Y., Tanaka, K., Takahashi, H., and Wakasa, K., Nuclear Encoding of a Plastid Sigma Factor in Rice and Its Tissue-and Light-Dependent Expression, Nucleic Acids Res., 1998, vol. 26, pp. 415–419.

    Article  PubMed  CAS  Google Scholar 

  37. Kasai, K., Kawagishi-Kobayashi, M., Teraishi, M., Ito, Y., Ochi, K., Wakasa, K., and Tozawa, Y., Differential Expression of Three Plastidial Sigma Factors, OsSIG1, OsSIG2A, and OsSIG2B, during Leaf Development in Rice, BioSci. Biotech. Biochem., 2004, vol. 68, pp. 973–977.

    Article  CAS  Google Scholar 

  38. Privat, I., Hakimi, M.A., Buhot, L., Favory, J.J., and Lerbs-Mache, S., Characterization of Arabidopsis Plastid Sigma-Like Transcription Factors SIG1, SIG2 and SIG3, Plant Mol. Biol., 2003, vol. 51, pp. 385–399.

    Article  PubMed  CAS  Google Scholar 

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  1. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya ul. 35, Moscow, 127276, Russia

    E. A. Lysenko

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Original Russian Text © E.A. Lysneko, 2006, published in Fiziologiya Rastenii, 2006, Vol. 53, No. 5, pp. 684–694.

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Lysenko, E.A. Analysis of the evolution of the family of the Sig genes encoding plant sigma factors. Russ J Plant Physiol 53, 605–614 (2006). https://doi.org/10.1134/S1021443706050037

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  • DOI: https://doi.org/10.1134/S1021443706050037

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