1887

Chapter 17 : Molecular Biology of the Model Piezophile, DSS12

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

Molecular Biology of the Model Piezophile, DSS12, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815646/9781555814236_Chap17-1.gif /docserver/preview/fulltext/10.1128/9781555815646/9781555814236_Chap17-2.gif

Abstract:

This chapter focuses on the molecular characteristics of pressure adaptation in DSS12 and recent advances in developing genetics and utilizing genomics. Sigma 54 plays an important role in pressure-regulated transcription in , although it should be noted that the expression of sigma 54 is not itself regulated by pressure. Any of these trans-acting factors (sigma 54, NtrC, or NtrB) could play an important role in pressure-regulated transcription in this piezophilic bacterium. Downstream from the pressure-regulated operon described is an open reading frame (ORF) homologous to the cydD gene of . Another aspect of transcription in piezophiles is the stability of the quaternary structure of RNA polymerase. It is likely that the sigma subunit stabilizes the core enzyme through alteration of the quaternary structure of RNA polymerase, resulting in piezotolerance. One possible explanation for the low conjugation frequency is that the optimal mating temperature for DSS12R is 20°C, which is much lower than the optimal temperature for . This study provided the first demonstration of gene transfer in the piezophilic bacterium DSS12. The study of the mechanisms for adaptation to high-pressure environments, including gene regulatory systems, may now also proceed in vivo using genetic approaches in this piezophile. Therefore, genomic analysis of marine extremophiles may lead to the discovery of new functions for genes.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17

Key Concept Ranking

Gene Expression and Regulation
0.7933199
Transcription Start Site
0.57412547
RNA Polymerase
0.56521744
Bacterial Proteins
0.5261884
0.7933199
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1.
Figure 1.

Diagrammatic representation of the pressure-regulated genes in strain DSS12. (A) Pressure-regulated operon; (B) glutamine synthetase operon. Bold numbers (#2 in panel A and #1 in panel B) show the transcription start sites controlled by the sigma 54 factor.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2.
Figure 2.

Autophosphorylation of the NtrB protein, -phosphorylation of NtrB-P to the NtrC protein in vitro, and Western blot analysis of expression of the NtrC under different pressure conditions. (A) Autophosphorylation of NtrB incubated in the presence of [γ-P]ATP at several temperature conditions. Lane 1, 0°C; lane 2, 10°C; lane 3, 24°C; lane 4, 37°C. (B) -Phosphorylation to NtrC incubated with the phosphorylated NtrB-P at 10°C for 1 min. Lane 5, phosphorylated NtrB; lane 6, phosphorylated NtrC. (C) Lysates prepared from cells cultured at 0.1 or 50 MPa were fractionated by SDS–10% PAGE and then blotted onto a polyvinylidene fluoride membrane. The membrane was treated with antiserum against NtrC.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3.
Figure 3.

Model for pressure regulation of gene expression in the piezophilic strain DSS12.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4.
Figure 4.

Reduced minus oxidized difference spectra of membrane fractions from Each fraction was obtained from the cells grown under a pressure of 0.1 MPa with shaking (A), grown under a pressure of 0.1 MPa under microaerobic conditions (B), and grown under a pressure of 50 MPa with microaerobic conditions (C). An absorption peak at 629 nm and a trough at 649 nm are specifically detected in the membrane fraction of cells grown under a pressure of 50 MPa. These spectral properties are typical of -type cytochromes ( ).

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5.
Figure 5.

Diagram of the HPEA. (A) High-pressure electrophoresis chamber for HPEA.(a) Connection to the power supply (anode); (b) connection to the power supply (cathode); (c) buffers; (d) silicone oil KF-96-1.5CS; (e) glass microcapillary tube; (f) O-ring to partition a space into the upper and lower spaces; (g) connection to a high-pressure pump. (B) Photograph of the HPEA. 1, high-pressure electrophoresis chamber; 2, high-pressure hand pump; 3, pressure gauge.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6.
Figure 6.

Effects of high hydrostatic pressure on subunit association in RNA polymerase in (A), (B), and without sigma factor (C). Native PAGE was performed at 0.1 MPa (upper panels) or 140 MPa (lower panels), followed by SDS-PAGE at 0.1 MPa. Proteins were visualized by silver staining. Each subunit of RNA polymerase is shown by an open circle. M, molecular mass markers; 1st dim, one-dimensional separation; 2nd dim, two-dimensional separation.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 7.
Figure 7.

Images of 1% agarose electrophoresis of plasmid extracted from DSS12R transconjugants.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 8.
Figure 8.

Annotation of ORFs in the genome. The total genome size is 4.9 Mbp, and approximately 4,600 ORFs are predicted.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555815646.ch17
1. Cook, G. M.,, J. Membrillo-Hernandez, and, R. K. Poole.1997. Transcriptional regulation of the cydDC operon, encoding a heterodimeric ABC transporter required for assembly of cytochromes c and bd in Escherichia coli K-12: regulation by oxygen and alternative electron acceptors. J. Bacteriol. 179:6525 6530.
2. Cotter, P. A.,, S. B. Melville,, J. A. Albrecht, and, R. P. Gunsalus. 1997. Aerobic regulation of cytochrome d oxidase (cydAB) operon expression in Escherichia coli: roles of Fnr and ArcA in repression and activation. Mol. Microbiol. 25:605–615.
3. Erijman, L., and, R. M. Clegg. 1995. Heterogeneity of E. coli RNA polymerase revealed by high pressure. J. Mol. Biol. 253:259265.
4. Fukuchi, J.,, T. Sato,, C. Kato,, M. Ito, and, K. Horikoshi. 2002. The host-vector system for deep-sea piezophilic bacteria, Shewanella violacea DSS12 and Moritella japonica DSK1. JAMSTECR 46:157161. (In Japanese.)
5. Georgiou, C. D.,, H. Fang, and, R. B. Gennis. 1987. Identification of the cydC locus required for expression of the functional form of the cytochrome d terminal oxidase complex in Escherichia coli. J. Bacteriol. 169:21072112.
6. Govantes, F.,, J. A. Albrecht, and, R. P. Gunsalus. 2000. Oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon: roles of multiple promoters and the Fnr-1 and Fnr-2 binding sites. Mol. Microbiol. 37:14561469.
7. Greiner, D. P.,, K. A. Hughes,, A. H. Gunasekera, and, C. F. Meares.1996. Binding of the σ70 protein to the core subunits of Escherichia coli RNA polymerase, studied by iron-EDTA protein footprinting. Proc. Natl. Acad. Sci. USA 93:7175.
8. Heidelberg, J. F.,, I. T. Paulsen,, K. E. Nelson,, E. J. Gaidos,, W. C. Nelson,, T. D. Read,, J. A. Eisen,, R. Seshadri,, N. Ward,, B. Methe,, R. Clayton,, T. Meyer,, A. Tsapin,, J. Scott,, M. Beanan,, L. Brinkac,, S. Daugherty,, R. T. DeBoy,, R. J. Dodson,, A. S. Durkin,, D. H. Haft,, J. F. Kolonay,, R. Madupu,, J. D. Peterson,, L. A. Umayam,, O. White,, A. M. Wolf,, J. Vamathevan,, J. Weidman,, M. Impraim,, K. Lee,, K. Berry,, C. Lee,, J. Mueller,, H. Khouri,, J. Gill,, T. R. Utterback,, L. A. McDonald,, T. V. Feldblyum,, H. O. Smith,, J. C. Venter,, K. H. Nealson, and, C. M. Fraser. 2003. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol. 20:11181123.
9. Ikegami, A.,, K. Nakasone,, M. Fujita,, S. Fujii,, C. Kato,, R. Usami, and, K. Horikoshi. 2000. Cloning and characterization of the gene encoding RNA polymerase sigma factor σ54 of deep-sea piezophilic Shewanella violacea. Biochim. Biophys. Acta 1491:315320.
10. Ikegami, A.,, K. Nakasone,, C. Kato,, Y. Nakamura,, I. Yoshikawa,, R. Usami, and, K. Horikoshi. 2000. Glutamine synthetase gene expression at elevated hydrostatic pressure in a deep-sea piezophilic Shewanella violacea. FEMS Microbiol. Lett. 192:9195.
11. Ikegami, A.,, K. Nakasone,, C. Kato,, R. Usami, and, K. Horikoshi. 2000. Structural analysis of ntrBC genes of deep-sea piezophilic Shewanella violacea. Biosci. Biotechnol. Biochem. 64:915918.
12. Kato, C.,, T. Sato, and, K. Horikoshi. 1995. Isolation and properties of barophilic and barotolerant bacteria from deep-sea mud samples. Biodivers. Conserv. 4:19.
13. Kato, C.,, H. Tamegai,, A. Ikegami,, R. Usami, and, K. Horikoshi. 1996. Open reading frame 3 of the barotolerant bacterium strain DSS12 is complementary with cydD in Escherichia coli: cydD functions are required for cell stability at high pressure. J. Biochem. 120:301305.
14. Kawano, H.,, K. Nakasone,, M. Matsumoto,, R. Usami,, C. Kato, and, F. Abe. 2004. Differential pressure resistance in the activity of RNA polymerase isolated from Shewanella violacea and Escherichia coli. Extremophiles 8:367375.
15. Kita, K.,, K. Konishi, and, Y. Anraku. 1984. Terminal oxidases of Escherichia coli aerobic respiratory chain. I. Purification and properties of cytochrome b562-o complex from cells in the early exponential phase of aerobic growth. J. Biol. Chem. 259:33683374.
16. Kita, K.,, K. Konishi, and, Y. Anraku. 1984. Terminal oxidases of Escherichia coli aerobic respiratory chain. II. Purification and properties of cytochrome b558-d complex from cells grown with limited oxygen and evidence of branched electron-carrying systems. J. Biol. Chem. 259:33753381.
17. Merrick, M. J., and, R. A. Edwards. 1995. Nitrogen control in bacteria. Microbiol. Rev. 59:604622.
18. Nakasone, K.,, A. Ikegami,, C. Kato,, R. Usami, and, K. Horikoshi. 1998. Mechanisms of gene expression controlled by pressure in deep-sea microorganisms. Extremophiles 2:149154.
19. Nakasone, K.,, A. Ikegami,, C. Kato,, R. Usami, and, K. Horikoshi. 1999. Analysis of cis-elements upstream of the pressure-regulated operon in the deep-sea barophilic bacterium Shewanella violacea strain DSS12. FEMS Microbiol. Lett. 176:351356.
20. Nakasone, K.,, A. Ikegami,, H. Kawano,, R. Usami,, C. Kato, and, K. Horikoshi. 2002. Transcriptional regulation under pressure conditions by the RNA polymerase σ54 factor with a two component regulatory system in Shewanella violacea. Extremophiles 6:8995.
21. Nakasone, K.,, H. Mori,, T. Baba, and, C. Kato. 2003. Whole-genome analysis of piezophilic and psychrophilic microorganism. Kagaku to Seibutsu 41:3239. (In Japanese.)
22. Nakasone, K.,, M. Yamada,, M. H. Qureshi,, C. Kato, and, K. Horikoshi. 2001. Piezoresponse of the cyooperon coding for quinol oxidase subunits in a deep-sea piezophilic bacterium, Shewanella violacea. Biosci. Biotechnol. Biochem. 65:690693.
23. Ninfa, A. J.,, L. J. Reitzer, and, B. Magasanik. 1987. Initiation of transcription at the bacterial glnAp2 promoter by purified E. coli components is facilitated by enhancers. Cell 50:10391046.
24. Nogi, Y.,, C. Kato, and, K. Horikoshi. 1998. Taxonomic studies of deep-sea barophilic Shewanella species, and Shewanella violacea sp. nov., a new barophilic bacterial species. Arch. Microbiol. 170:331338.
25. Poole, R. K.,, F. Gibson, and, G. Wu. 1994. The cydD gene product, component of a heterodimeric ABC transporter, is required for assembly of periplasmic cytochrome c and of cytochrome bd in Escherichia coli. FEMS Microbiol. Lett. 117:217224.
26. Poole, R. K.,, L. Hatch,, M. W. J. Cleeter,, F. Gibson,, G. B. Cox, and, G. Wu. 1993. Cytochrome bd biosynthesis in Escherichia coli: the sequences of the cydC and cydD genes suggest that they encode the components of an ABC membrane transporter. Mol. Microbiol. 10:421430.
27. Poole, R. K.,, H. D. Williams,, A. Downie, and, F. Gibson. 1989. Mutations affecting the cytochrome d-containing oxidase complex of Escherichia coli K12: identification and mapping of a fourth locus, cydD. J. Gen. Microbiol. 135:18651874.
28. Qureshi, M. H.,, C. Kato, and, K. Horikoshi. 1998. Purification of a ccb type quinol oxidase specifically induced in a deep-sea barophilic bacterium, Shewanella sp. strain DB-172F. Extremophiles 2:9399.
29. Qureshi, M. H.,, C. Kato, and, K. Horikoshi. 1998. Purification of two pressure-regulated c-type cytochromes from a deep-sea bacterium, Shewanella sp. strain DB-172F. FEMS Microbiol. Lett. 161:301 309.
30. Sato, T.,, C. Kato, and, K. Horikoshi. 1995. Effect of high pressure on gene expression by lac and tac promoters in Escherichia coli. J. Mar. Biotechnol. 3:8992.
31. Simon, R.,, U. Priefer, and, A. Puhler. 1983. A broad host range mobilization system for in vivo genetic engineering. Bio/Technology 1:784791.
32. Tamegai, H.,, C. Kato, and, K. Horikoshi. 1998. Pressure-regulated respiratory system in barotolerant bacterium, Shewanella sp. strain DSS12. J. Biochem. Mol. Biol. Biophys. 1:213220.
33. Tamegai, H.,, H. Kawano,, A. Ishii,, S. Chikuma,, K. Nakasone, and, C. Kato. 2005. Pressure-regulated biosynthesis of cytochrome bd in piezo- and psychrophilic deep-sea bacterium Shewanella violacea DSS12. Extremophiles 9:247253.
34. Wu, F. Y.,, L. R. Yarbrough, and, C. W. Wu. 1976. Conformational transition of Escherichia coli RNA polymerase induced by the interaction of sigma subunit with core enzyme. Biochemistry 15:3254 3258.
35. Yamada, M.,, K. Nakasone,, H. Tamegai,, C. Kato,, R. Usami, and, K. Horikoshi. 2000. Pressure-regulation of soluble cytochromes c in a deep-sea piezophilic bacterium, Shewanella violacea. J. Bacteriol. 182:2945 2952.

Tables

Generic image for table
TABLE 1.

Composition of cytochromes in

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
Generic image for table
TABLE 2.

Comparison of DSS12 conjugation efficiencies with different plasmids

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error