A historical account of RegulonDB“Swiss-Prot 20 years meeting”, Fortaleza Brazil,

August 3rd, 2006Julio Collado-Vides

Center for Genomic Sciences, UNAM, México

Campus Morelos U N A M

S1, S2, S3, Sn… T1, T2, T3…Tn

Specific interactions map (i,j) dependency relationships

Collado-Vides (1991) Comput. Applic. Biosci.

Long distance dependencies:(i,j)works, (i, m) does not work, (k, m) works

Collado-Vides J., Magasanik B. and Gralla J.D. (1991) "Control site location and transcriptional regulation in Escherichia coli" Microbiol. Reviews. 55:371-394

The collection of sigma 54 promoters

Universals of regulation or stamp collection?

Pr'''

Pr''

Pr'

Op'

D-Op

Op(r)Op(p)

Op(R)

Pr

I'

I(R)D - I

I(p)I(r)Op(r)

D-Op

Op

di = -93

I

cj2= -62.5

CRP

Pr

lac

Op

ci = +9

LacI

Op

di= +402

A final derivation for a transcription unit

Collado-Vides J. (1992) "Grammatical model of the regulation of gene expression" Proc.Natl.Acad.Sci.USA 89:9405-9409

Predictions. A Linear set of combinations

Rosenblueth D.A., Thieffry D., Huerta A.M., Salgado H., and Collado-Vides J. (1996) "Syntactic recognition of regulatory regions in Escherichia coli" CABIOS   12: 415-422.

Map of the complete E.coli sequence.

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AllActivatorRepressorDualUnknown

Pérez-Rueda E., and Collado-Vides J. (2000) " Nucleic Acids Research 28: 1838-1847

HTH Position and Function of Regulators

Distances:between genes inside operons between transcription units

Prediction of operons

Salgado et al., (2000) Proc.Natl.Acad.Sci.USA 97: 6652-6657

Prediction of operons

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-1.5 -1 -0.5 0 0.5 1 1.5

Escherichia coli

SensitivitySpecificityAccuracy

Threshold

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0.8

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-1.5 -1 -0.5 0 0.5 1 1.5

Bacillus subtilis

SensitivitySpecificityAccuracy

ThresholdMoreno-Hagelsieb (2001) Trends in Genetics)

Prediction of operons

Promoter prediction. Dense Regions of Promoter-like Signals

Huerta A.M. and Collado-Vides J. (2003) Transcription in Dense Regions of Promoter-like SignalsJ.Mol.Biol. 333:261-278

http://www.ccg.unam.mx/Computational_Genomics/regulondb/ http://www.ecocyc.org/

Annotation (Regulation, operon organization)

Summary of RegulonDB information by year.Object 1997 1998 1999 2000 2001 2002 2003 2004 2005 20064

Regulons 99 83 83 165 166 172 179 183 266

Regulatory Interactions 533 433 433 642 935 990 1119 1303 1811 1930

TFs Binding Sites 406 469 750 812 950 1129 1230 1326

Products:

RNAs 11 5 115 115 115 116 117 117 117

polypeptides 4207 4290 4290 4290 4292 4290 4290 4290

Transcriptional Factors 80 83 83 165 166 172 179 1831 139 150

Genes 542 456 4405 4405 4405 4405 4408 4408 4408 4408

Transcription units 292 230 374 528 657 694 747 803 1230 1304

Promoters 200 239 432 624 746 783 860 939 1160 1285

Effectors 35 36 36 36 66 66 67 68 73 73

External References 2050 2011 4394 4704 4943 5053 5224 19522 27872 29912

Synonyms 681 3525 3525 3525 3544 3578 3612 11945 16430

Terminators 40 86 106 108 118 122 128 130

RBSs 59 98 133 134 153 158 179 179

Conformation of Transcriptional Regulators

83 201 203 221 234 1503 160

Evidences 39 39

External DataBases 11 14

Operons 770 899

1. There is a total of 322 transcriptional DNA-binding regulators, from which 183 have experimental evidence and the rest have been predicted based on their helix-turn-helix DNA binding motif.

2. Only MedLine References.3. Only de active conformations.4. RegulonDB Relase 5.1

Summary of RegulonDB information by year.

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1997 1998 1999 2000 2001 2002 2003 2004 2005

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Total

Transcription Unit

Promoter

Terminator

Regulon

TF

Conformation

RI

Site

Effector

RBS

TRN and the Global and Local TFs

Martínez-Antonio A. Current Opinion in Microbiology, 2003

Classifying Tfs based on their signal metabolite

• TFs were classified on the basis of the cellular location of the signal sensed:

• (a) External sensing - signals are localized outside the periplasm,– two-components systems (E-TC) and those using metabolites

transported into the cell (E-TM).

• (b) Internal sensing: f the signal is inside the periplasmic region (synthesized by the cell or redox)

– - synthesized by the cell or redox state (I-SM) – - DNA-bending (I-DB).

• (c) Hybrid TFs: The signal is synthesized in the cell, and can be also transported into the cell

Internal sensing regulators govern regulation of regulators

• (a) Venn diagram showing the overlap in the transcriptional regulation of regulated genes affected by Internal (32 TFs, 27%), External (62 TFs, 52%) and Hybrid (26TFs, 22%) classes.

• (d) Regulation of regulators. Continuous lines -regulation, Dashed lines autoregulation.

Active annotation in Regulon DB

*Transcription start site*Promoter assignation*Sigma factor assignation

Resultsand

data analysis

Experimental mapping procedure:5’ RACE (rapid amplification cDNA ends)

modificated for high-throughput

Magallanes Project (with Enrique Morett at IBT): Global Transcription Initiation Mapping and Active Promoter Annotation

Transcriptionalunits database

Microarraydatabase

Primerdesign

First genomic project of global transcriptional mapping start site for a prokariotic organisms

Magallanes Project. Examples: Hypothetical genes.

Transcriptional units experimentally explored: 421

Transcriptional units experimentally resolved: 164 (145 new data)

Experimental growth conditions tested: 3

Data up to date

b0119 (yeaL)

Genomic sequence

AACGACACAATGCCCGGTGAATGAGATTCCCGGGCATTTTTTTATTTCTAAACCATCGCCGTTCCGCTGTTTTTCTCCG

GTAAGGCTGCGATAATTACATCAATGGCGCAATGCGATTTCGGTGCATTGCCGGGAGCAGAGGAACACACTATGGATTAP1 70

-10 +1

-35

b0391 (yaiE)

TACTGCAAAAACAGCTCGATGTTCCTGTCTTGCTGTCTAACGTATTGATTGCACGGCTGGCTGCGGAATTACTGGTGTA

ATTTTGCGTGACAGCCAGCGCCTCTGGCCCCTATAGTGAAGTAGATGTTCAACTACCAAACAGGGCCAGTTTATGCTTCP1 70

-10 +1-35

Genomic sequence

Computational Genomics Group

Araceli HuertaErnesto Pérez RuedaDavid RosenbluethDenis ThieffryGabriel MorenoEnrique Morett

The Lord of The Rings: Lessons for Genomics and Bioinformatics

1. Achievement of communities of diversity of beings

2. Ambitious projects

GETools

GETools

Full genome prediction of regulatory binding sites

Full genome prediction of regulatory binding sites