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. 1989 Jan;171(1):473–482. doi: 10.1128/jb.171.1.473-482.1989

Structural and functional analysis of transcriptional control of the Rhodobacter capsulatus puf operon.

C W Adams 1, M E Forrest 1, S N Cohen 1, J T Beatty 1
PMCID: PMC209611  PMID: 2492501

Abstract

We report data indicating that the Rhodobacter capsulatus puf operon promoter and the site for its oxygen regulation are located more than 700 base pairs upstream from the previously identified puf genes and have identified the nucleotide sequences that constitute these control signals. A model is proposed in which a polycistronic transcript at least 3.4 kilobases in length is initiated near the O2-regulated promoter and is processed posttranscriptionally by endonucleolytic cleavage at multiple sites, yielding discrete mRNA segments that are degraded at different rates. A newly identified gene (pufQ), which includes a hydrophobic domain having some similarity to domains of the products of the pufL and pufM genes, begins 313 nucleotides into the puf transcript and is located entirely within the most rapidly degraded segment of the transcript. A previously identified puf transcript segment encoding structural proteins for photosynthetic membrane complexes persists after degradation of the most 5' region of the transcript and is itself subject to segmentally specific degradation. Our results suggest a model in which differential expression of the multiple genes encoded by the puf operon is at least in part attributable to major differences in the rates of decay of the various segments of puf mRNA.

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Selected References

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  1. Aliabadi Z., Warren F., Mya S., Foster J. W. Oxygen-regulated stimulons of Salmonella typhimurium identified by Mu d(Ap lac) operon fusions. J Bacteriol. 1986 Mar;165(3):780–786. doi: 10.1128/jb.165.3.780-786.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Allen J. P., Feher G., Yeates T. O., Rees D. C., Deisenhofer J., Michel H., Huber R. Structural homology of reaction centers from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis as determined by x-ray diffraction. Proc Natl Acad Sci U S A. 1986 Nov;83(22):8589–8593. doi: 10.1073/pnas.83.22.8589. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bauer C. E., Marrs B. L. Rhodobacter capsulatus puf operon encodes a regulatory protein (PufQ) for bacteriochlorophyll biosynthesis. Proc Natl Acad Sci U S A. 1988 Oct;85(19):7074–7078. doi: 10.1073/pnas.85.19.7074. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bauer C. E., Young D. A., Marrs B. L. Analysis of the Rhodobacter capsulatus puf operon. Location of the oxygen-regulated promoter region and the identification of an additional puf-encoded gene. J Biol Chem. 1988 Apr 5;263(10):4820–4827. [PubMed] [Google Scholar]
  5. Beck E., Bremer E. Nucleotide sequence of the gene ompA coding the outer membrane protein II of Escherichia coli K-12. Nucleic Acids Res. 1980 Jul 11;8(13):3011–3027. doi: 10.1093/nar/8.13.3011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Belasco J. G., Beatty J. T., Adams C. W., von Gabain A., Cohen S. N. Differential expression of photosynthesis genes in R. capsulata results from segmental differences in stability within the polycistronic rxcA transcript. Cell. 1985 Jan;40(1):171–181. doi: 10.1016/0092-8674(85)90320-4. [DOI] [PubMed] [Google Scholar]
  7. Berk A. J., Sharp P. A. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell. 1977 Nov;12(3):721–732. doi: 10.1016/0092-8674(77)90272-0. [DOI] [PubMed] [Google Scholar]
  8. COHEN-BAZIRE G., SISTROM W. R., STANIER R. Y. Kinetic studies of pigment synthesis by non-sulfur purple bacteria. J Cell Physiol. 1957 Feb;49(1):25–68. doi: 10.1002/jcp.1030490104. [DOI] [PubMed] [Google Scholar]
  9. Cannon M., Hill S., Kavanaugh E., Cannon F. A molecular genetic study of nif expression in Klebsiella pneumoniae at the level of transcription, translation and nitrogenase activity. Mol Gen Genet. 1985;198(2):198–206. doi: 10.1007/BF00382996. [DOI] [PubMed] [Google Scholar]
  10. Chen C. Y., Beatty J. T., Cohen S. N., Belasco J. G. An intercistronic stem-loop structure functions as an mRNA decay terminator necessary but insufficient for puf mRNA stability. Cell. 1988 Feb 26;52(4):609–619. doi: 10.1016/0092-8674(88)90473-4. [DOI] [PubMed] [Google Scholar]
  11. Clark W. G., Davidson E., Marrs B. L. Variation of levels of mRNA coding for antenna and reaction center polypeptides in Rhodopseudomonas capsulata in response to changes in oxygen concentration. J Bacteriol. 1984 Mar;157(3):945–948. doi: 10.1128/jb.157.3.945-948.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Davidson E., Daldal F. Primary structure of the bc1 complex of Rhodopseudomonas capsulata. Nucleotide sequence of the pet operon encoding the Rieske cytochrome b, and cytochrome c1 apoproteins. J Mol Biol. 1987 May 5;195(1):13–24. doi: 10.1016/0022-2836(87)90323-8. [DOI] [PubMed] [Google Scholar]
  13. Drews G., Oelze J. Organization and differentiation of membranes of phototrophic bacteria. Adv Microb Physiol. 1981;22:1–92. doi: 10.1016/s0065-2911(08)60325-2. [DOI] [PubMed] [Google Scholar]
  14. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene. 1984 Jun;28(3):351–359. doi: 10.1016/0378-1119(84)90153-7. [DOI] [PubMed] [Google Scholar]
  16. Hui A., Hayflick J., Dinkelspiel K., de Boer H. A. Mutagenesis of the three bases preceding the start codon of the beta-galactosidase mRNA and its effect on translation in Escherichia coli. EMBO J. 1984 Mar;3(3):623–629. doi: 10.1002/j.1460-2075.1984.tb01858.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Johnson J. A., Wong W. K., Beatty J. T. Expression of cellulase genes in Rhodobacter capsulatus by use of plasmid expression vectors. J Bacteriol. 1986 Aug;167(2):604–610. doi: 10.1128/jb.167.2.604-610.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Klug G., Adams C. W., Belasco J., Doerge B., Cohen S. N. Biological consequences of segmental alterations in mRNA stability: effects of deletion of the intercistronic hairpin loop region of the Rhodobacter capsulatus puf operon. EMBO J. 1987 Nov;6(11):3515–3520. doi: 10.1002/j.1460-2075.1987.tb02677.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kranz R. G., Haselkorn R. Anaerobic regulation of nitrogen-fixation genes in Rhodopseudomonas capsulata. Proc Natl Acad Sci U S A. 1986 Sep;83(18):6805–6809. doi: 10.1073/pnas.83.18.6805. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Marrs B. Genetic recombination in Rhodopseudomonas capsulata. Proc Natl Acad Sci U S A. 1974 Mar;71(3):971–973. doi: 10.1073/pnas.71.3.971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  23. Messing J. New M13 vectors for cloning. Methods Enzymol. 1983;101:20–78. doi: 10.1016/0076-6879(83)01005-8. [DOI] [PubMed] [Google Scholar]
  24. Moss B. 5' end labeling of RNA with capping and methylating enzymes. Gene Amplif Anal. 1981;2:253–266. [PubMed] [Google Scholar]
  25. Prentki P., Krisch H. M. In vitro insertional mutagenesis with a selectable DNA fragment. Gene. 1984 Sep;29(3):303–313. doi: 10.1016/0378-1119(84)90059-3. [DOI] [PubMed] [Google Scholar]
  26. Schmidhauser T. J., Helinski D. R. Regions of broad-host-range plasmid RK2 involved in replication and stable maintenance in nine species of gram-negative bacteria. J Bacteriol. 1985 Oct;164(1):446–455. doi: 10.1128/jb.164.1.446-455.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Shaw D. J., Rice D. W., Guest J. R. Homology between CAP and Fnr, a regulator of anaerobic respiration in Escherichia coli. J Mol Biol. 1983 May 15;166(2):241–247. doi: 10.1016/s0022-2836(83)80011-4. [DOI] [PubMed] [Google Scholar]
  28. Smith A. J. DNA sequence analysis by primed synthesis. Methods Enzymol. 1980;65(1):560–580. doi: 10.1016/s0076-6879(80)65060-5. [DOI] [PubMed] [Google Scholar]
  29. Weaver P. F., Wall J. D., Gest H. Characterization of Rhodopseudomonas capsulata. Arch Microbiol. 1975 Nov 7;105(3):207–216. doi: 10.1007/BF00447139. [DOI] [PubMed] [Google Scholar]
  30. Wilbur W. J., Lipman D. J. Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci U S A. 1983 Feb;80(3):726–730. doi: 10.1073/pnas.80.3.726. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Williams J. C., Steiner L. A., Feher G. Primary structure of the reaction center from Rhodopseudomonas sphaeroides. Proteins. 1986 Dec;1(4):312–325. doi: 10.1002/prot.340010405. [DOI] [PubMed] [Google Scholar]
  32. Wilson H. R., Chan P. T., Turnbough C. L., Jr Nucleotide sequence and expression of the pyrC gene of Escherichia coli K-12. J Bacteriol. 1987 Jul;169(7):3051–3058. doi: 10.1128/jb.169.7.3051-3058.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Winkelman J. W., Clark D. P. Anaerobically induced genes of Escherichia coli. J Bacteriol. 1986 Jul;167(1):362–367. doi: 10.1128/jb.167.1.362-367.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Youvan D. C., Bylina E. J., Alberti M., Begusch H., Hearst J. E. Nucleotide and deduced polypeptide sequences of the photosynthetic reaction-center, B870 antenna, and flanking polypeptides from R. capsulata. Cell. 1984 Jul;37(3):949–957. doi: 10.1016/0092-8674(84)90429-x. [DOI] [PubMed] [Google Scholar]
  35. Youvan D. C., Ismail S. Light-harvesting II (B800-B850 complex) structural genes from Rhodopseudomonas capsulata. Proc Natl Acad Sci U S A. 1985 Jan;82(1):58–62. doi: 10.1073/pnas.82.1.58. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Zhu Y. S., Hearst J. E. Regulation of expression of genes for light-harvesting antenna proteins LH-I and LH-II; reaction center polypeptides RC-L, RC-M, and RC-H; and enzymes of bacteriochlorophyll and carotenoid biosynthesis in Rhodobacter capsulatus by light and oxygen. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7613–7617. doi: 10.1073/pnas.83.20.7613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Zoller M. J., Smith M. Oligonucleotide-directed mutagenesis of DNA fragments cloned into M13 vectors. Methods Enzymol. 1983;100:468–500. doi: 10.1016/0076-6879(83)00074-9. [DOI] [PubMed] [Google Scholar]
  38. Zucconi A. P., Beatty J. T. Posttranscriptional regulation by light of the steady-state levels of mature B800-850 light-harvesting complexes in Rhodobacter capsulatus. J Bacteriol. 1988 Feb;170(2):877–882. doi: 10.1128/jb.170.2.877-882.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. von Gabain A., Belasco J. G., Schottel J. L., Chang A. C., Cohen S. N. Decay of mRNA in Escherichia coli: investigation of the fate of specific segments of transcripts. Proc Natl Acad Sci U S A. 1983 Feb;80(3):653–657. doi: 10.1073/pnas.80.3.653. [DOI] [PMC free article] [PubMed] [Google Scholar]

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