Low molecular weight proteins: a challenge for post-genomic research

Area of Science:

• Genomics
• Proteomics
• Bioinformatics

Background:

• The EcoGene project aims to improve the representation and prediction of protein sequences encoded by the Escherichia coli K-12 genome.
• Recent completion of E. coli genome sequencing has led to the deposition of results in the SWISSPROT database.

Purpose of the Study:

• To refine the prediction of the entire set of E. coli K-12 chromosomally encoded protein sequences.
• To specifically address the challenges in predicting low molecular weight (small) proteins.

Main Methods:

• Examination of E. coli K-12 DNA sequences and public database annotations.
• Derivation of a small protein subset (< or = 150 amino acids) from the complete genome.
• Utilizing database searches and multiple alignments to identify conserved residues (motifs).

Main Results:

• Discovery that predicting small proteins (< or = 150 aa) is problematic and requires special attention.
• Identification of new small genes and conserved motifs in other organisms using E. coli small proteins.
• Two-thirds of E. coli small proteins remain uncharacterized experimentally.

Conclusions:

• Accurate prediction and characterization of small proteins necessitate careful application of computational and laboratory methods.
• Challenges in protein sequence identification extend beyond small proteins and E. coli to all sequence databases.
• Further research is needed to improve the analysis and understanding of small proteins in genomics.