A computational study of bacterial gene regulation and adaptation ...

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Chapter 1: Global regulators of bacterial transcription initiationof this percentage with those for Fis (33%) and IHF (37%) illustrates the predominance ofrepressive interactions involving H-NS. Moreover, H-NS is present at high levels throughoutthe bacterial life cycle (Azam et al. 1999); this would ensure stable repression of H genes inthe absence of other relieving factors, which could include other protein factors as well aschanges in environmental conditions - such as temperature and Mg 2+ concentration - whichinfluence DNA curvature (Dieckmann 1987; Ussery et al. 1999) and consequently H-NSbinding (Yamada et al. 1990).1.4.5. Functional implications of extremely high upstream AT-content genes:supercoiling and horizontal transferThe above results point to a role of global transcription factors in ensuring that genes withextremely high upstream AT-content show lower maximal expression levels than others.However, it leads us to ask further questions:What is the nature of these genes which have extremely high upstream AT-content, but berepressed by a global transcription factor? Is the AT-content simply an evolutionarymechanism that achieves efficient binding of these factors to the DNA? Is there any otherfunctional basis underlying this extreme AT-content?First, we used gene expression data for two critical points of the bacterial growth phase,namely mid-log and stationary phases in order to see whether H genes show any pattern(Brokx et al. 2004; Faith et al. 2007). Interestingly, H genes show greater differential upregulationin stationary phase over mid-log phase than L and C genes (Figure 1.5A; PW = 1.0x 10 -5 ; comparing the distributions of FDR-adjusted p-values for differential expression for Hagainst L and C combined). At a standard adjusted p-value cutoff of 0.05, 183 (41%) H genesare up-regulated in stationary phase, compared against 75 (17%) that are down-regulated.This preference for up-regulating H genes in stationary phase represents a strong enrichmentover C and L genes (PF = 1.7 x 10 -8 ; F for Fisher exact test). Since stationary phase representsa condition in which DNA is less-negatively supercoiled, an extremely high AT-content mightbe necessary to counteract this effect and permit formation of the open complex.40
Chapter 1: Global regulators of bacterial transcription initiation(A)fis coexpression(B)ihfAB coexpressionPearson correlation coefficientwith fis!1.0 !0.5 0.0 0.5 1.0Pearson correlation coefficientwith ihfA and ihfB!1.0 !0.5 0.0 0.5 1.0H/stat H/other All leadH/stat H/other All lead(C)(D)FIS ChIP!chip intensity ratio0 2 4 6 8 10IHF ChIP!chip intensity ratio0 2 4 6 8 100 1 2 3 4H!NS ChIP!chip intensity ratio0 1 2 3 4H!NS ChIP!chip intensity ratioFigure 1.6. Anti-silencing of H-NS-repressed genes. Co-expression of various groups of lead and H-lead genes with (A) Fis and (B) ihfA and ihfB. H/stat stands for lead genes with extremely high ATcontentthat are upregulated in stationary phase; H/other for all other H-group lead genes. Thehorizontal dashed line is drawn at zero. (C) ChIP-chip intensity correlation between H-NS and Fis. (D)ChIP-chip intensity correlation between H-NS and IHFIn order to test whether supercoiling plays a role in the up-regulation of H genes in stationaryphase, we first employed microarray data. We find that H genes show a poor correlation, incomparison to L and C genes, with the expression of gyrA and gyrB (PW < 2.2 x 10 -16 ; Figure1.5B) that form gyrase, the enzyme that induces negative supercoils in the DNA. Anotherprotein that generates negative supercoiling in-vitro is HU (Guo and Adhya 2007). H genesonce again show a clearly reduced correlation with hupA and hupB which comprise HU (PW
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two-domain architectures wherethese
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(A)60% of genomes from class4530150
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Discussion and conclusionsDiscussio
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Discussion and conclusionsD1.1.3. C
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Discussion and conclusionsD2. Futur
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BibliographyAmikam, D., Steinberger
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BibliographyBlattner, F.R., Plunket
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BibliographyChen, S.L., Hung, C.S.,
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BibliographyEchols, N., Harrison, P
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Bibliographysystem level analysis o
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BibliographyHerring, C.D., Raghunat
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BibliographyJenal, U., and Malone,
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BibliographyKeseler, I.M., Collado-
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BibliographyLee, S.H., Angelichio,
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BibliographyMcClelland, M., Sanders
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BibliographyO Croinin, T., Carroll,
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BibliographyPrice, M.N., Dehal, P.S
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BibliographySatriano, J., and Schlo
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BibliographySteinberger, O., Lapido
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BibliographyUssery, D.W., Wassenaar
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BibliographyYanofsky, C. 1981. Atte
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Appendix 1Appendix 1.1: Differences
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Appendix 1Appendix 1.5: Gene expres
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Appendix 2Appendix 2.1: Differences
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Appendix 2Appendix 2.3: Co-regulati
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Appendix 2Appendix 2.5: Flux coupli
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Appendix 2Appendix 2.7: Co-regulati
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Appendix 2Appendix 2.8B: Connectivi
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Appendix 2Appendix 2.10: Correlatio
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Appendix 2Appendix 2.12A: Robustnes
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Appendix 3Appendix 3Supplementary m
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Reaction ID Regulatory metabolite I
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Appendix 3Appendix 3.3B: Direct reg
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Appendix 3Appendix 3.4B: Direct reg
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Appendix 4Appendix 4Supplementary m
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Appendix 4Motile organisms are rich
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Appendix 4We can expand the analysi
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Appendix 5Appendix 5.1A: PFAMs for
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Appendix 5Appendix 5.1C: PFAMs for
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Appendix 5Appendix 5.2B: Small-mole
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Appendix 5Appendix 5.3: Organisms s
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Appendix 5Appendix 5.5: Partner dom
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Appendix 5fraction of SDRRs would a
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Appendix 5Appendix 5.6C: Non-hybrid
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Appendix 5Appendix 5.8: List of org
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Appendix 6Appendix 6List of genomes
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Appendix 648. Mycobacterium tubercu
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Appendix 6144. Bacillus cereus ATCC
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Appendix 6240. Nitrobacter winograd
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Appendix 6336. Cytophaga hutchinson
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Appendix 6432. Acinetobacter bauman
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Appendix 6528. Enterobacter sakazak
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Appendix 6624. Polynucleobacter nec
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Appendix 7Appendix 7List of genomes
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Appendix 748. Bordetella parapertus
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Appendix 7144. Haemophilus somnus14
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Appendix 7240. Prochlorococcus mari
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Appendix 7336. Synechococcus sp. CC
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Downloaded from genome.cshlp.org on
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JOURNAL OF BACTERIOLOGY, June 2008,
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VOL. 190, 2008 P. MIRABILIS GENOME
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2 Nucleic Acids Research, 2008PCR a
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4 Nucleic Acids Research, 2008Table
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8 Nucleic Acids Research, 2008solve
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An Assessment of the Role of DNA Ad
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DAM and Transcriptionpotential of s
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