Seminar Presentation

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Discovery of New Regulatory Motifs of Purine
Biosynthetic Genes in Escherichia Coli and
Bacillus Subtilis Indiana University School of
Informatics Haifeng Zhao
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Outline of Presentation

• Project Goals
• Introduction
• PlatCom
• Discovery of DNA Regulatory Motifs
• Results
• Discussion

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Project Goals

• Develop a Platform for Comparative Study of
  Predicted Proteins and Genomic Sequences
• Analyze the Transcription Regulatory Motifs of De
  Novo Purine Biosynthetic Pathway of Escherichia
  Coli and Bacillus Subtilis.

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Purine de novo synthesis
http//gtcw3.aist-nara.ac.jp/mori/research/dbservi
ce/operon/fig17.htm
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Genbank Data
A_thaliana Bacteria C_elegans Plasmodium_falciparu
m P_falciparum S_cerevisiae D_melanogaster Anophe
les_gambiae H_sapiens R_norvegicus MITOCH
ONDRIA M_musculus
Escherichia_coli Bacillus_subtilis
Completely Sequenced Genomes
Genomes
Incompletely Sequenced Genomes
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PlatCom

• A Platform for Computational
• Comparative Genomics
• 1. Building databases of all pairwise
  comparisons.
• 2. A toolkit for multiple genome comparisons.

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PlatCom
Genbank Data
BlastZ Gapped BLAST algorithm designed for
aligning two long genomic sequences
.fna.cmp
.faa.cmp
FASTA
.est.cmp
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PlatCorm
Browser
NCBI FTP Server
IBM Super Computer
Server
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PlatCom

• Dynamically Update the Databases
• Update Genome Data
• Add New Genome Data
• Automatically Detect Missing Data

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Discovery of DNA Regulatory Motifs
Genome Sequences
Predict Coregulated Set of Genes
Use Motif-Finding Aglorithm on Upstream Regions
DNA Regulatory Motifs
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Identify De Novo Purine (PurR) Biosynthetic Genes
of E. coli
http//biocyc.org
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Identify Orthologs of Bacteria in COG Database
547 Genes
COG0015 COG0026 COG0034 COG0041 COG0046 COG0047
COG0138 COG0150 COG0151 COG0152 COG0299 COG0516
COG0517 COG0518 COG0519

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Identify Upstream Regulatory Regions
A
B
C
Operon Head
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Convert Gene Names of COG Database to Gene Names
of GenBank Database
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Extract upstream regions
GenBank .gbk
DataBases of Upstream Regions
Parser
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Motif-Finding Algorithms

• Gibbs Sampler Algorithm
• AlignACE ( Based on Gibbs Sampler )
• MEME
• MACAW

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Run AlignACE and MEME
100, 300 bp Upstream Databases
AlignACE
MEME
Motifs
ScanACE
MAST
Escherichia Coli Bacillus Subtilis
Sites
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DPInteract (E. coli)
gtguaBA 48-gt74 ggtagatgcaatcggttacgctctgt gtpurB
-205-gt-179 TGCCGACGCAATCGGTTACCTTGATG gtpurC
148-gt174 atgatacgcaaacgtgtgcgtctgca gtpurEK
66-gt92 GAGCAAGGAAAACGGTTGCGTGGCTG gtpurF
tccctacgcaaacgttttctttttct gtpurH
102-gt128 GCGTTGCGCAAACGTTTTCGTTACAA gtpurL
71-gt97 tttccacgcaaacggtttcgtcagcg gtpurMN
59-gt85 cagtctcgcaaacgtttgctttccct
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pur Operon of Bacillus subtilis
The Bacillus subtilis purEKBCQLFMNHD operon,
called the pur operon, encodes 10 enzymes
required for de novo purine tynthesis. The
Dnase I footprinting of the pur operon covered
from -179 to -30 upstream region. The common
DNA recognition element for binding of PurR to
pur operon is not known.
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Results AlignACE (Escherichia Coli)
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Results AlignACE (Bacillus Subtilis)
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Results MEME (Escherichia Coli)
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Results MEME (Bacillus Subtilis)
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Results Locations of Mapped Genes of Escherichia
coli and Bacillus subtilis
AlignACE
MEME
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Discussion

• PlatCom A Platform for Comparative Study of
• Multiple Genomes

Multiple Tools
Multiple Genomes
Escherichia Coli Bacillus Subtilis
AlignACE MEME
Many Significant new motifs are found
Performance
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Acknowledgement
Sun Kim, Advisor
Zhiping Wang, Classmate