Reconstruction of Amino Acid Biosynthesis Pathways from the Complete Genome Sequence Hidemasa Bono e

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Reconstruction of Amino Acid Biosynthesis
Pathways from the Complete Genome
SequenceHidemasa Bono et al.Genome Res. 1998 8
203-210.

• Chun-Yu Chen
• Institute of HIDM, NYMU
• June 2003

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Basic Molecular Biology
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Introduction to Metabolic Pathway Reconstruction

• Genome annotation
• The three layers of genome annotation where,
  what and how?

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Gene annotation
Pathway reconstruction
Nature Reviews GENETICS Vol 2 July 2001
493-503.
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Introduction to Metabolic Pathway Reconstruction
Annotated genome
Enzyme-gene relation
enzymes
Reaction-enzyme relation
reactions
Reaction-connection relation
Metabolic Pathway for specific function
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Past Studies and Motivation

• The weak points of current gene annotation
  methods.
• Global features?A set of enzymes that performs a
  cellular function.
• If we can computerize such biological knowledge
  in a proper way, the functional prediction can be
  improved and better automated.

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• 145 Published Complete Genomes
• Archaeal 16 species
• Bacterial 110 species
• Eukaryal 19 (Homo sapiens, plants, insects,
  nematodes, protozoa, fungi, )
• 345 Prokaryotic Ongoing Genomes
• Archaeal 23 species
• Bacterial 322 species

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Methods

• Orthologous Gene Table
• Definition of orthologous in KEGG
• gene A in org1 is most similar to gene B in org2
  and gene B in org2 is most similar to gene A in
  org1.
• GFIT Program
• A is similar to B and
• B belongs to group C
• ? A belongs to group C

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Results

• Reference Pathways
• EC Number Assignment
• Missing Enzymes
• Reconstruction of Amino Acid Biosynthetic Pathways

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Results Reference Pathways

• Primary organized from the compilations of
• the Japanese Biochemical Society(Nishizuka 1980,
  1997)
• the wall chart of Boehringer Mannheim(Gerhard
  1992)
• Has been verified with a number of printed and
  on-line sources.

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The wall chart of Boehringer Mannheim.
http//us.expasy.org/cgi-
bin/show_thumbnails.pl
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Results Reference Pathways

• The current metabolic knowledge is represented by
  117 pathway diagrams. (June 2003)
• Manually drawn and continuously updated.

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KEGG Kyoto Encyclopedia of Genes and Genomes
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Reference Pathway
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Results Reference Pathways

• Represent a network of interacting molecules.
• An enzyme or a compound is clickable to retrieve
  related information from the LIGAND
  database.(Suyama et al. 1993 Goto et al. 1998)
• KEGG is linked to detailed molecular information
  through the DBGET/LinkDB system.(Fujibuchi et
  al. 1997 Kanehisa 1997b)

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DBGET Database Links _at_ GenomeNet
http//www.genome.ad.jp/dbget/dbget.links.html
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Results Reference Pathways

• What is gene catalog?
• Orthologous gene table
• An organism-specific pathway are reconstructed by
  comparing the gene catalog against the reference
  pathway.

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Escherichia coli K-12 MG1655
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Results

• Reference Pathways
• EC Number Assignment
• Missing Enzymes
• Reconstruction of Amino Acid Biosynthetic Pathways

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Results EC Number Assignment

• Whats the problem?
• Gene Function Identification Tool (GFIT) has been
  utilized for automatically identifying enzyme
  genes and assigning EC numbers.
• Enzyme genes
• 20 in bacteria
• 14 in yeast
• 75 80 of the enzyme genes in each organism
  have been mapped.

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Results

• Reference Pathways
• EC Number Assignment
• Missing Enzymes
• Reconstruction of Amino Acid Biosynthetic Pathways

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Results Missing Enzymes

• When the metabolic pathway is incomplete
  reconstructed?

The lysine biosynthesis pathway taken from KEGG.
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Results Missing Enzymes

• When the metabolic pathway is incomplete
  reconstructed?
• Gene function identification has not been done
  extensively enough.
• GFIT using an extensive search of homologs and
  alternative assignments to resolve this problem.

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Results Missing Enzymes

• When the metabolic pathway is incomplete
  reconstructed?
• Our knowledge is not sufficient.
• There may be an alternative enzyme or a set of
  enzymes that can fill the missing reactions.
• PATHCOMP is useful for searching alternative
  reaction paths(Goto et al. 1996)

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Pyruvate
L-Alanine
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Results

• Reference Pathways
• EC Number Assignment
• Missing Enzymes
• Reconstruction of Amino Acid Biosynthetic Pathways

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Discussion

• It is possible that a different organism has a
  different set of functionally related enzymes,
  that perform, as a group, its biological
  function.

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Discussion

• 16 genes is assigned to the aminotransferase
  class (2.6.1) for E. coli.
• 7 genes for H. influenzae.
• Seems to have all the amino acid biosynthesis
  pathways as shown by Tatusov et al. (1996) as
  well.
• An enzyme in H. influenzae plays multiple
  functional roles that are taken by different
  enzymes in E. coli?

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Discussion

• 3 genes for H. pylori.
• Wide variations in the degree of annotation in
  different complete genome sequences.
• E. coli.
• Synechocystis

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Discussion

• Danger!!
• It is possible that an erroneous description is
  propagated to a number of entries without knowing
  where the error actually originated.
• KEGG can be utilized to check the validity of
  assignments made by sequence similarities.

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Discussion

• The enzymes represent 20 of the genes in
  bacterial genomes.
• The proportion becomes smaller in higher
  organisms.
• Started to computerize a number of regulatory
  pathways, such as
• Membrane transport
• Signal transduction
• Cell cycle
• Developmental pathways

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Thank you

• Please give me any suggestions or comments.

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References

• http//www.genome.org/cgi/content/full/8/3/203
• http//www.genome.ad.jp/kegg/pathway/map/map01150.
  html
• http//www.genome.ad.jp/kegg/pathway/map/map00300.
  html
• http//www.google.com/search?hlenieUTF-8oeUTF
  -8qGenome-scaleFunctionIdentificationTool22
  GFIT22
• http//www.genome.ad.jp/kegg/java/org_list.html
• http//www1.linkclub.or.jp/bonohu/kuicr/research/
  1998/

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References

• Systematic Prediction of Orthologous Units of
  Genes in the Complete Genomehttp//www1.linkclub.
  or.jp/bonohu/kuicr/research/1998/GIW98/