Unusual features in the photosynthetic machinery of Halorhodospira halochloris DSM 1059 revealed by complete genome sequencing

  • Yusuke TsukataniEmail author
  • Yuu HiroseEmail author
  • Jiro Harada
  • Chinatsu Yonekawa
  • Hitoshi Tamiaki
Original Article


Halorhodospira halochloris is an anaerobic, halophilic, purple photosynthetic bacterium belonging to γ-Proteobacteria. H. halochloris is also characteristic as a thermophilic phototrophic isolate producing bacteriochlorophyll (BChl) b. Here, we report the complete genome sequence of H. halochloris DSM 1059. The genetic arrangement for this bacterium’s photosynthetic apparatus is of particular interest; its genome contains two sets of puf operons encoding the reaction center and core light-harvesting 1 (LH1) complexes having almost identical nucleotide sequences (e.g., 98.8–99.9% of nucleotide identities between two sets of pufLM genes, but 100% of deduced amino acid sequence identities). This duplication of photosynthetic genes may provide a glimpse at natural selection in action. The β-polypeptides of the LH1 complex in purple bacteria usually contain two histidine residues to bind BChl a; however, those of H. halochloris were revealed to have four histidine residues, indicating unusual pigment organization in the LH1 complex of this species. Like in other BChl b-producing phototrophs, the genome of H. halochloris lacks the divinyl reductase genes bciA and bciB. The phylogeny of chlorophyllide a oxidoreductase, which catalyzes committed steps in the synthesis of BChl a and BChl b, indicates that evolution toward BChl b production is convergent. Geranylgeranyl reductase (BchP) of H. halochloris has an insertion region in its primary structure, which could be important for its unusual sequential reduction reactions.


Bacteriochlorophyll Chlorophyllide a oxidoreductase Geranylgeranyl reductase Photosynthetic gene cluster Puf operon Reaction center 





Chlorophyllide a oxidoreductase


Light harvesting 1


Photosynthetic gene cluster


Reaction center



We thank Mr. Keita Mori for the help in preparing the genomic DNA. This work was partially supported by JSPS KAKENHI [Grant Numbers: JP26840099 and JP17H05231 (to Y.T.), JP15H05578 (to Y.H.), and JP17H06436 (to H.T.)].


  1. Alberti M, Burke DH, Hearst JE (1995) Structure and sequence of the photosynthesis gene cluster. In: Blankenship RE, Madigan MT, Bauer CE (eds) Anoxygenic photosynthetic bacteria. Kluwer Publishers, Dordrecht, pp 1083–1106Google Scholar
  2. Bauer CE, Marrs BL (1988) Rhodobacter capsulatus puf operon encodes a regulatory protein (PufQ) for bacteriochlorophyll biosynthesis. Proc Natl Acad Sci USA 85:7074–7078CrossRefGoogle Scholar
  3. Chidgey J, Jackson P, Dickman M, Hunter N (2017) PufQ regulates porphyrin flux at the haem/bacteriochlorophyll branchpoint of tetrapyrrole biosynthesis via interactions with ferrochelatase. Mol Microbiol 106:961–975CrossRefGoogle Scholar
  4. Deisenhofer J, Epp O, Miki K, Huber R, Michel H (1985) Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3 Å resolution. Nature 318:618–624CrossRefGoogle Scholar
  5. Ethirajan M, Chen Y, Joshi P, Pandey RK (2011) The role of porphyrin chemistry in tumor imaging and photodynamic therapy. Chem Soc Rev 40:340–362CrossRefGoogle Scholar
  6. Galinsky E, Truper HG (1982) Betaine, a compatible solute in the extremely halophilic phototrophic bacterium Ectothiorhodospira halochloris. FEMS Lett 13:357–360CrossRefGoogle Scholar
  7. Harada J, Mizoguchi T, Tsukatani Y, Yokono M, Tanaka A, Tamiaki H (2014) Chlorophyllide a oxidoreductase works as one of the divinyl reductases specifically involved in bacteriochlorophyll a biosynthesis. J Biol Chem 289:12716–12726CrossRefGoogle Scholar
  8. Imhoff JF, Suling J (1996) The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA analyses. Arch Microbiol 165:106–113CrossRefGoogle Scholar
  9. Imhoff JF, Truper HG (1977) Ectothiorhodospira halochloris sp. nov., a new extremely halophilic phototrophic bacterium containing bacteriochlorophyll b. Arch Microbiol 114:115–121CrossRefGoogle Scholar
  10. Jiao N, Zhang R, Zheng Q (2010) Coexistence of two different photosynthetic operons in Citromicrobium bathyomarinum JL354 as revealed by whole-genome sequencing. J Bacteriol 192:1169–1170CrossRefGoogle Scholar
  11. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  12. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760CrossRefGoogle Scholar
  13. Maresca JA, Graham JE, Bryant DA (2008) The biochemical basis for structural diversity in the carotenoids of chlorophototrophic bacteria. Photosynth Res 97:121–140CrossRefGoogle Scholar
  14. Masuda S, Yoshida M, Nagashima KVP, Shimada K, Matsuura K (1999) A new cytochrome subunit bound to the photosynthetic reaction center in the purple bacterium, Rhodovulum sulfidophilum. J Biol Chem 274:10795–10801CrossRefGoogle Scholar
  15. Mizoguchi T, Isaji M, Harada J, Watabe K, Tamiaki H (2009) Structural determination of the ∆2,10-phytadienyl substituent in the 17-propionate of bacteriochlorophyll-b from Halorhodospira halochloris. J Porphyrins Phthalocyanines 13:41–50CrossRefGoogle Scholar
  16. Mizoguchi T, Isaji M, Harada J, Tsukatani Y, Tamiaki H (2015) The 17-propionate esterifying variants of bacteriochlorophyll-a and bacteriopheophytin-a in purple photosynthetic bacteria. J Photochem Photobiol B: Biol 142:244–249CrossRefGoogle Scholar
  17. Nagashima S, Nagashima KVP (2013) Comparison of photosynthesis gene clusters retrieved from total genome sequences of purple bacteria. In: Beatty TJ (ed) Genome evolution of photosynthetic bacteria. Academic Press, Cambridge, pp 151–178CrossRefGoogle Scholar
  18. Nagashima KVP, Sakuragi Y, Shimada K, Matsuura K (1998) Comparative analysis of the primary structure of the reaction center-bound cytochrome subunit in purple bacteria. Photosynth Res 55:349–355CrossRefGoogle Scholar
  19. Niwa S, Yu LJ, Takeda K, Hirano Y, Kawakami T, Wang-Otomo ZY, Miki K (2014) Structure of the LH1-RC complex from Thermochromatium tepidum at 3.0 Å. Nature 508:228–232CrossRefGoogle Scholar
  20. Nomata J, Mizoguchi T, Tamiaki H, Fujita Y (2006) A second nitrogenase-like enzyme for bacteriochlorophyll biosynthesis. Reconstitution of chlorophyllide a reducatase with purified X-protein (BchX) and YZ-protein (BchY-BchZ) from Rhodobacter capsulatus. J Biol Chem 281:15021–15028CrossRefGoogle Scholar
  21. Qian P, Siebert CA, Wang P, Canniffe DP, Hunter CN (2018) Cryo-EM structure of the Blastochloris viridis LH1-RC complex at 2.9 Å. Nature 556:203–208CrossRefGoogle Scholar
  22. Roszak AW, Howard TD, Southall J, Gardiner AT, Law CJ, Isaacs NW, Cogdell RJ (2003) Crystal structure of the RC-LH1 core complex from Rhodopseudomonas palustris. Science 302:1969–1972CrossRefGoogle Scholar
  23. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
  24. Singh KS, Kirksey J, Hoff WD, Deole R (2014) Draft genome sequence of the extremely halophilic phototrophic purple sulfur bacterium Halorhodospira halochloris. J Genomics 6:118–120CrossRefGoogle Scholar
  25. Steiner R, Schäfer W, Blos I, Wieschhoff H, Scheer H (1981) ∆2,10-Phytadienol as esterifying alcohol of bacteriochlorophyll b from Ectothiorhodospira halochloris. Z Naturforsch C 36:417–420CrossRefGoogle Scholar
  26. Takaichi S, Maoka T, Hanada S, Imhoff JF (2001) Dihydroxylycopene diglucoside diesters: a novel class of carotenoids from the phototrophic purple sulfur bacteria Halorhodospira abdelmalekii and Halorhodospira halochloris. Arch Microbiol 175:161–167CrossRefGoogle Scholar
  27. Tamiaki H, Teramura M, Tsukatani Y (2016) Reduction processes in biosynthesis of chlorophyll molecules: chemical implication of enzymatically regio- and stereoselective hydrogenations in the late stages of their biosynthetic pathway. Bull Chem Soc Jpn 89:161–173CrossRefGoogle Scholar
  28. Tamiaki H, Nomura K, Mizoguchi T (2017) Preparation of regio- and stereoisomeric di- and tetrahydrogeranylgeraniols and identification of esterifying groups in natural (bacterio)chlorophylls. Bioorg Med Chem 25:6361–6370CrossRefGoogle Scholar
  29. Tanizawa Y, Fujisawa T, Nakamura Y (2017) DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 34:1037–1039CrossRefGoogle Scholar
  30. Tsukatani Y, Matsuura K, Masuda S, Shimada K, Hiraishi A, Nagashima KVP (2004) Phylogenetic distribution of unusual triheme to tetraheme cytochrome subunit in the reaction center complex of purple photosynthetic bacteria. Photosynth Res 79:83–91CrossRefGoogle Scholar
  31. Tsukatani Y, Yamamoto H, Harada J, Yoshitomi T, Nomata J, Kasahara M, Mizoguchi T, Fujita Y, Tamiaki H (2013a) An unexpectedly branched biosynthetic pathway for bacteriochlorophyll b capable of absorbing nearinfrared light. Sci Rep 3:1217CrossRefGoogle Scholar
  32. Tsukatani Y, Yamamoto H, Mizoguchi T, Fujita Y, Tamiaki H (2013b) Completion of biosynthetic pathways for bacteriochlorophyll g in Heliobacterium modesticaldum: The C8-ethylidene group formation. Biochim Biophys Acta 1827:1200–1204CrossRefGoogle Scholar
  33. Tsukatani Y, Harada J, Nomata J, Yamamoto H, Fujita Y, Mizoguchi T, Tamiaki H (2015a) Rhodobacter sphaeroides mutants overexpressing chlorophyllide a oxidoreductase of Blastochloris viridis elucidate functions of enzymes in late bacteriochlorophyll biosynthetic pathways. Sci Rep 5:9741CrossRefGoogle Scholar
  34. Tsukatani Y, Hirose Y, Harada J, Misawa N, Mori K, Inoue K, Tamiaki H (2015b) Complete genome sequence of the bacteriochlorophyll b-producing photosynthetic bacterium Blastochloris viridis. Genome Announc 3:e01006–e01015CrossRefGoogle Scholar
  35. Wagner-Hubert R, Brunisholz RA, Bissig I, Frank G, Zuber H (1988) A new possible binding site for bacteriochlorophyll b in a light-harvesting polypeptide of the bacterium Ectothiorhodospira halochloris. FEBS Lett 233:7–11CrossRefGoogle Scholar
  36. Wagner-Hubert R, Brunisholz RA, Bissig I, Frank G, Suter F, Zuber H (1992) The primary structure of the antenna polypeptides of Ectothiorhodospira halochloris and Ectothiorhodospira halophila: four core-type antenna polypeptides in E. halochloris and E. halophila. Euro J Biochem 205:917–925CrossRefGoogle Scholar
  37. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9:e112963CrossRefGoogle Scholar
  38. Wang XF, Tamiaki H (2010) Cyclic tetrapyrrole based molecules for dye-sensitized solar cells. Energy Environ Sci 3:94–106CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Research and Development Center for Marine BiosciencesJapan Agency for Marine-Earth Science and Technology (JAMSTEC)KanagawaJapan
  2. 2.Department of Environmental and Life SciencesToyohashi University of TechnologyAichiJapan
  3. 3.Department of Medical BiochemistryKurume University School of MedicineFukuokaJapan
  4. 4.Graduate School of Life SciencesRitsumeikan UniversityShigaJapan

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