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

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Chapter 1: Global regulators of bacterial transcription initiation1.4. Results1.4.1. High AT-content in regions of transcription initiation is a conservedpropertyWe classified all genes in the E. coli K12 MG1655 into ‘lead’ and ‘non-lead’ genes. The firstgene of a multi-gene operon was defined as the operon’s lead gene; all single-gene operonswere also classified as lead genes. All other genes in multi-gene operons were defined as nonleadgenes. Note that upstream of lead genes is a transcription initiation site; this is not truefor non-lead genes. For this study, DNA region upto -100 immediately 5’ of the ORF wasdefined as the upstream region.We compared the AT content of upstream sequences of lead genes to that of non-lead genes inthe E. coli K12 MG1655 genome. We confirm earlier results (Mitchison 2005; Ussery et al.2004) which showed that upstream sequences of lead genes have significantly higher ATcontentthan those of non-lead genes (Figure 1.2A). In order to prove that such high ATcontent is not an artifact of genome base composition we compared the AT-content ofupstream regions with that of the corresponding ORFs (Figure 1.2B). Clearly, regions(A)(B)AT content (%) in -1 to -100 region30 40 50 60 70 80Q3+1.5 x IQRQ3= 75th percentileMedianQ1= 25th percentileQ1-1.5 x IQRdifference between AT content (%)of upstream region and gene body!20 !10 0 10 20 30leadnonlead32leadnonleadFigure 1.2. AT content and transcription initiation in E. coli. (A) Distribution of AT contents of the-100 regions of lead and non-lead genes. (B) Difference between the AT contents of the -100 regionand the gene body for lead and non-lead genes. In these box plots, which are used extensively in thisthesis, the thick horizontal line represents the median of a distribution; the light horizontal linesenclosing the box at the top and the bottom represent the 75th and the 25 percentiles of thedistribution, respectively; the thin horizontal lines above and below the box mark the outlier limits,defined by 1.5 times IQR (difference between the values representing the 75th and the 25thpercentiles) above or below the 75th or the 25th percentile repectively. Points shown as dots areoutliers. These are labelled in (A).
Chapter 1: Global regulators of bacterial transcription initiationupstream of lead genes have an AT content which is, on average, 8 percentage points higherthan that of the immediately downstream ORF. The corresponding value for non-lead genes isonly 2 percentage points. The difference between these two sets of genes is significant (PW
Page 3 and 4: Statement of lengthThis thesis does
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Chapter 4: Comparative genomics of
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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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JOURNAL OF BACTERIOLOGY, June 2008,
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VOL. 190, 2008 P. MIRABILIS GENOME
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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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