Comparing the Complete S. cerevisiae and C. elegans Proteomes: Orthology and Divergence

Stephen A. Chervitz

Saccharomces Genome Database

NCBI

Boston University

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Goals of this study Explore protein sequence and domain

conservation between S. cerevisiae and C. elegans. Unicellular vs. multicellular lifestyles

Classify yeast and worm similarity groups using functional annotation of yeast genes.

Enhance the SGD website and add value to the worm genomic sequence.

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Organization of this study

Shared core biology Whole protein sequence comparisons

Divergence Protein domain comparisions

No gene predictions No mitochondrial sequence

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Definitions

Orthologs: Genes from different species that perform the same biological function and are likely to be evolved from a common ancestral gene.

Paralogs: Genes that perform different biological functions in the same species that likely arose by duplication and divergence from a common ancestral gene.

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Genome Scorecards

Saccharomyces cerevisiae Caenorhabditis elegansx200X20,000

No. of cells: 1 ~1000Size (Mbp): 12 97Chromosomes: 16 6Predicted ORFs: 6,217 19,099Percent coding: 72% 27%ORFs with gene names: 3,344 (53%) 688 (4%)

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Core biology is carried out by similar numbers of proteins

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Building a Biological Rosetta Stone

P-ValueYeast ORFs with

functional descriptionWorm orthologs with functional description

1e-10 86% 64%1e-20 89% 69%1e-40 93% 61%1e-60 96% 74%1e-80 96% 74%1e-100 98% 77%1e-200 98% 88%

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Distribution of core biological functions conserved in both yeast and worm

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Core Biological Functions Signal Transduction: kinases, phosphatases, Ras

superfamily and other GTP-binding proteins,GDP/GTP exchange factors, ADP-ribosylation factors, adenylyl/guanylyl cyclases, phosphatidylinositol kinases, EF-hand proteins

DNA/RNA Metabolism: polymerases, helicases, topoisomerases, repair/recombination-related, nucleases, primases, splicing factors, initiation/elongation factors (transcription & translation), tRNA synthetases, histone acetylases/deacetylases

Transport & Secretion: ABC transporters, permeases, vesicle coat & fusion proteins, clatherin-accociated, protein targeting, signal recognition particle, nuclear pore-associated

Cytoskeletal: Actin, myosin, tubulin, actin-related proteins, actin-interacting proteins, septins, cytokinesis-related proteins

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Core Biological Functions (cont’d) Ribosomal:ribosomal proteins (small & large subunit),

ribosome processing proteins Protein Folding and Degradation: heat shock

proteins, chaperonins, proteasome subunits, ubiquitin-related, peptidyl prolyl cis-trans isomerase, protein disulfide isomerases, aminopeptidases, post-translational modifying enzymes (farnesyltransferase, myristoyltransferase, glycosylation, GPI-anchoring)

Intermediary Metabolism: dehydrogenases, reductases, mutases, lyases, isomerases, carboxylases, decarboxylases, nucleotide biosynthetic enzymes, transaminases, deaminases, epimerases, oxygenases, cytochromes, flavoproteins

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Constructing Sequence Similarity Groups

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Similarity Groups: MCM DNA replication initiator complex

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Similarity Groups: Tubulin

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Multiple Sequence Alignments

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Domain Analysis

122 common eukaryotic protein domains. Associated with regulation of gene expression

and signal transduction. Compare occurrence and domain architectures

in yeast and worm protein sequences. Position-dependent weight matrices (profiles)

to detect domains (PSI-BLAST). Classify worm-only, yeast-only, and shared

domains.

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Worm-Only Domains Nuclear hormone receptors Epidermal growth factor Degenerins FMRFamides (neuropeptides) Cadherin PTB (phosphotyrosine binding) T-box, SMAD (transcription factor domains) Insulin-like peptides Laminin NT

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Yeast-Only Domains

C6 (Zn-binding cluster) ASPES (DNA-binding)

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Shared Domains (Yeast & Worm) Protein kinase catalytic C2H2 Finger AAA ATPase DAG Kinase Arrestin Ankyrin SWI/SNF helicase RING-finger bHLH RHO GAP/GEF Plecstrin homology SH3 Ubiquitin

SH2 cNMP-signaling domains CaM EF-hands Homeodomains Potassium channels 7TM receptors HINT Immunoglobulin LRR vWA MATH POZ LIM

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Frequency of occurrence of common domains

Domain counts are normalized to the number of proteins with a given domain per 1000 genes.

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Conclusions Core biological functions are carried out by

orthologous proteins occurring in comparable numbers in yeast and worm.

These represent approx. 40% of the predicted yeast ORFs and 20% of the predicted worm ORFs.

Regulatory and signaling proteins in worm do not have orthologs in yeast but often share domains.

Complete results are available online at SGD at http://genome-www.stanford.edu/Saccharomyces/worm

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Future Directions

Incorporate more sensitive sequence search results. More sophisticated clustering scheme.

Multi-domain proteins and weak similarities.

Up-to-date with to changes in the genomic datasets. Add/remove protein coding regions Correction of errors in the genomic sequence Sequence name changes

Extended annotation support. Controlled vocabularies, gene function ontologies.

Comparative genomics framework for additional genomes. More flexible browsing of genome-wide similarities.

Prototype yeast genome protein similarity Java viewer

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Genome-wide protein similarity view Explore protein sequence similarities within or

between genomes Graphical user interface Available at SGD for the yeast genome

Sequence Resources, Protein Similarity View

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Acknowledgements

Saccharomyces Genome Database (Stanford) Gavin Sherlock Cathy Ball Selina Dwight Midori Harris Kara Dolinski Shuai Weng Eric Hester Mike Cherry David Botstein

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Acknowledgements (cont’d)

NCBI (Nat’l Library of Medicine) L. Aravind Eugene Koonin

Boston University Scott Mohr James Freeman Temple Smith

Neomorphic Software (Berkeley) www.neomorphic.com

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Extra slides

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Single-linkage clustering and multi-domain proteins

“Chaining”

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3.

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Whole genomic DNA microarrayDeRisi et al.(1997) Science 278: 680

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Building a Biological Rosetta Stone