1887

Chapter 4 : Global Approaches to the Bacterial Cell as an Integrated System

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

Global Approaches to the Bacterial Cell as an Integrated System, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817640/9781555812324_Chap04-1.gif /docserver/preview/fulltext/10.1128/9781555817640/9781555812324_Chap04-2.gif

Abstract:

New technologies made possible by this sequence data, such as DNA microarrays, in combination with the small size and ease of genetic manipulation of bacteria, now make it possible to identify the complete genetic regulatory circuitry that controls the bacterial cell. Analysis of the global gene expression profile of the bacterial cell during its cell cycle, under conditions of environmental challenge, and during pathogen invasion of host organisms will provide an unprecedented understanding of the bacterial cell as an integrated system. This chapter addresses the use of microarrays for study of a wide range of microbiological problems with emphasis on the profoundly different results that this genome-wide technique provides relative to the analysis of single genes and conventional forward genetics. By assaying the response of all genes to a given genetic or environmental perturbation in parallel and simultaneously, the microarray results identify whole pathways or subroutines of the organism’s genetic regulatory circuitry. The immobilized arrays, or spots, of DNA are typically the products of PCR that generate amplicons ranging from a few hundred base pairs to several kilobases in length. Application of microarray-based genomic analysis to study the cell cycle of , has recently led to a dramatic increase in one's understanding of regulation of the bacterial cell cycle. Although microarrays were initially developed to analyze RNA levels, they can also be used to examine DNA samples.

Citation: Laub M, Shapiro L, McAdams H. 2005. Global Approaches to the Bacterial Cell as an Integrated System, p 53-64. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch4

Key Concept Ranking

Aromatic Amino Acid Biosynthesis
0.44918796
Transcription Start Site
0.41547287
0.44918796
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1.
Figure 1.

Overview of the microarray technique. (A) With arrays made by robotically spotting PCR amplicons, either RNA or DNA levels in a reference culture sample can be compared with RNA or DNA levels in a sample culture. The RNA or DNA samples are converted to fluorescently labeled cDNA samples which are competitively hybridized on a spotted microarray. The reference and sample are labeled with different colors. Comparison of the relative fluorescent levels from each label in a spot indicates relative ratios of the corresponding gene in the genome. (B) Oligonucleotide arrays are made by direct synthesis of short probes on a solid substrate. A population of cDNAs, derived from either RNA or DNA, is biotinylated and hybridized to an oligonucleotide array. Staining with streptavidin-phycoerythrin then provides a quantitative fluorescent signal with the signal strength (shaded spots) for each oligonucleotide probe, indicating the level of the cRNA or cDNA in the sample culture.

Citation: Laub M, Shapiro L, McAdams H. 2005. Global Approaches to the Bacterial Cell as an Integrated System, p 53-64. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2.
Figure 2.

Temporally coordinated events of the cell cycle. Cells in the G phase have a single polar flagellum and several polar pili. These motile “swarmer” cells are unable to initiate replication of their single, circular chromosome. In response to signals that are not yet understood, swarmer cells differentiate by shedding their polar flagellum and pili and subsequently synthesizing a stalk at that same pole. This sessile “stalked” cell has a tubular extension of the cell envelope, the stalk, with a holdfast substance at the tip allowing the cell to adhere to various surfaces. Coincident with the morphological transition of swarmer to stalked cell, DNA replication is initiated (G-to-S transition). As the stalked cell proceeds through S phase, it establishes a cell division site by constructing a FtsZ ring and appears pinched. Soon thereafter, these pinched predivisional cells begin constructing a new polar flagellum at the pole opposite the stalk. Upon completion of DNA replication, the daughter cell chromosomes segregate to opposite ends of the cell followed by an asymmetric cell division at a site slightly closer to the new flagellar pole. This asymmetric (in both size and morphology) division produces daughter cells with different morphologies and distinct cell fates. The smaller progeny swarmer cells are equivalent to G-phase cells and cannot replicate their DNA until after the obligate swarmer-to-stalked cell transition. The progeny stalked cell, on the other hand, immediately reinitiates replication of its chromosome without an intervening G phase. Progeny stalked cells thus function as “stem cells” that produce new swarmer cells at each division. Black bars indicate the approximate time of execution of cell cycle events. Gray shading indicates the cell types in which the master regulator CtrA is present and activated (by phosphorylation). CtrA is present in swarmer cells where it can repress DNA replication initiation by binding to the origin of replication. During the swarmer-to-stalked cell transition, CtrA protein is rapidly degraded so that chromosome replication can initiate ( ). After replication is initiated, synthesis of CtrA is restarted in the stalked cell.

Citation: Laub M, Shapiro L, McAdams H. 2005. Global Approaches to the Bacterial Cell as an Integrated System, p 53-64. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3.
Figure 3.

Regulatory network governing cell cycle progression in . Phosphorylated CtrA acts as a transcription factor to control a wide range of cell cycle-dependent events, as described in the text. Gene expression microarrays now provide a critical tool for identification of such large-scale regulons. (Modified from reference with permission of the publisher.)

Citation: Laub M, Shapiro L, McAdams H. 2005. Global Approaches to the Bacterial Cell as an Integrated System, p 53-64. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817640.chap4
1. Behr, M. A.,, M. A. Wilson,, W. P. Gill,, H. Salamon,, G. K. Schoolnik,, S. Rane,, and P. M. Small. 1999. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284:15201523.
2. Domian, I. J.,, K. C. Quon,, and L. Shapiro. 1997. Cell type-specific phosphorylation and proteolysis of a transcriptional regulator controls the G1-to-S transition in a bacterial cell cycle. Cell 90:415424.
3. Domian, I. J.,, A. Reisenauer,, and L. Shapiro. 1999. Feedback control of a master bacterial cell-cycle regulator. Proc. Natl. Acad. Sci. USA 96:66486653.
4. Eisen, M. B.,, and P. O. Brown. 1999. DNA arrays for analysis of gene expression. Methods Enzymol. 303:179205.
5. Fraser, C. M.,, J. A. Eisen,, and S. L. Salzberg. 2000. Microbial genome sequencing. Nature 406:799803.
6. Gmuender, H.,, K. Kuratli,, K. Di Padova,, C. P. Gray,, W. Keck,, and S. Evers. 2001. Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis. Genome Res. 11:2842.
7. Gober, J. W.,, and J. C. England,. 2000. Regulation of flagellum biosynthesis and motility in Caulobacter, p. 319339. In Y. V. Brun, and L. J. Shimkets (ed.), Prokaryotic Development. ASM Press, Washington, D.C.
8. Hegde, P.,, R. Qi,, K. Abernathy,, C. Gay,, S. Dharap,, R. Gaspard,, J. E. Hughes,, E. Snesrud,, N. Lee,, and J. Quackenbush. 2000. A concise guide to cDNA microarray analysis. BioTechniques 29:548550, 552554, 556 passim.
9. Israel, D. A.,, N. Salama,, C. N. Arnold,, S. F. Moss,, T. Ando,, H. P. Wirth,, K. T. Tham,, M. Camorlinga,, M. J. Blaser,, S. Falkow,, and R. M. Peek, Jr. 2001. Helicobacter pylori strain-specific differences in genetic content, identified by microarray, influence host inflammatory responses. J. Clin. Investig. 107:611620.
10. Ivanov, I.,, C. Schaab,, S. Planitzer,, U. Teichmann,, A. Machl,, S. Theml,, S. Meier-Ewert,, B. Seizinger,, and H. Loferer. 2000. DNA microarray technology and antimicrobial drug discovery. Pharmacogenomics 1:169178.
11. Iyer, V. R.,, C. E. Horak,, C. S. Scafe,, D. Botstein,, M. Snyder,, and P. O. Brown. 2001. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409:533538.
12. Khodursky, A. B.,, B. J. Peter,, N. R. Cozzarelli,, D. Botstein,, P. O. Brown,, and C. Yanofsky. 2000. DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc. Natl. Acad. Sci. USA 97:1217012175.
13. Khodursky, A. B.,, B. J. Peter,, M. B. Schmid,, J. DeRisi,, D. Botstein,, P. O. Brown,, and N. R. Cozzarelli. 2000. Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. Proc. Natl. Acad. Sci. USA 97:94199424.
14. Laub, M. T.,, H. H. McAdams,, T. Feldblyum,, C. M. Fraser,, and L. Shapiro. 2000. Global analysis of the genetic network controlling a bacterial cell cycle. Science 290:21442148.
15. Lockhart, D. J.,, H. Dong,, M. C. Byrne,, M. T. Follettie,, M. V. Gallo,, M. S. Chee,, M. Mittmann,, C. Wang,, M. Kobayashi,, H. Horton,, and E. L. Brown. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14:16751680.
16. Ouimet, M. C.,, and G. T. Marczynski. 2000. Analysis of a cell-cycle promoter bound by a response regulator. J. Mol. Biol. 302:761775.
17. Quackenbush, J. 2001. Computational analysis of microarray data. Nat. Rev. Genet. 2:418427.
18. Quon, K. C.,, G. T. Marczynski,, and L. Shapiro. 1996. Cell cycle control by an essential bacterial two-component signal transduction protein. Cell 84:8393.
19. Ren, B.,, F. Robert,, J. J. Wyrick,, O. Aparicio,, E. G. Jennings,, I. Simon,, J. Zeitlinger,, J. Schreiber,, N. Hannett,, E. Kanin,, T. L. Volkert,, C. J. Wilson,, S. P. Bell,, and R. A. Young. 2000. Genome-wide location and function of DNA binding proteins. Science 290:23062309.
20. Salama, N.,, K. Guillemin,, T. K. McDaniel,, G. Sherlock,, L. Tompkins,, and S. Falkow. 2000. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc. Natl. Acad. Sci. USA 97:1466814673.
21. Selinger, D. W.,, K. J. Cheung,, R. Mei,, E. M. Johansson,, C. S. Richmond,, F. R. Blattner,, D. J. Lockhart,, and G. M. Church. 2000. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat. Biotechnol. 18:12621268.
22. Tao, H.,, C. Bausch,, C. Richmond,, F. R. Blattner,, and T. Conway. 1999. Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J. Bacteriol. 181:64256440.
23. Troesch, A.,, H. Nguyen,, C. G. Miyada,, S. Desvarenne,, T. R. Gingeras,, P. M. Kaplan,, P. Cros,, and C. Mabilat. 1999. Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. J. Clin. Microbiol. 37:4955.
24. Wilson, M.,, J. DeRisi,, H. H. Kristensen,, P. Imboden,, S. Rane,, P. O. Brown,, and G. K. Schoolnik. 1999. Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. Proc. Natl. Acad. Sci. USA 96:1283312838.
25. Ye, R. W.,, W. Tao,, L. Bedzyk,, T. Young,, M. Chen,, and L. Li. 2000. Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions. J. Bacteriol. 182:44584465.
26. Zimmer, D. P.,, E. Soupene,, H. L. Lee,, V. F. Wendisch,, A. B. Khodursky,, B. J. Peter,, R. A. Bender,, and S. Kustu. 2000. Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. Proc. Natl. Acad. Sci. USA 97:1467414679.

Tables

Generic image for table
Table 1.

Applications of microarrays for analysis of bacterial systems

Citation: Laub M, Shapiro L, McAdams H. 2005. Global Approaches to the Bacterial Cell as an Integrated System, p 53-64. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch4
Generic image for table
Table 2.

Comparison of microarray technologies

Citation: Laub M, Shapiro L, McAdams H. 2005. Global Approaches to the Bacterial Cell as an Integrated System, p 53-64. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch4
Generic image for table
Table 3.

Information categories for documenting microarray experiments

Citation: Laub M, Shapiro L, McAdams H. 2005. Global Approaches to the Bacterial Cell as an Integrated System, p 53-64. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch4

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