Evaluating Evolutionary Constraint on the Rapidly Evolving Gene matK Using Protein Composition

• Published in: Journal of molecular evolution Vol. 66; no. 2; pp. 85 - 97
• Main Authors: Barthet, Michelle M, Hilu, Khidir W
• Format: Journal Article
• Language: English
• Published: New York New York : Springer-Verlag 01.02.2008; Springer-Verlag; Springer Nature B.V
• Subjects: Amino Acid Sequence; Amino acids; Amino Acids - analysis; Animal Genetics and Genomics; Biomedical and Life Sciences; Cell Biology; Chemical properties; DNA, Chloroplast - genetics; Evolution, Molecular; Evolutionary Biology; Genes; Genes, Mitochondrial - genetics; Genes, Plant; Genetic Variation; INDEL Mutation - genetics; Life Sciences; Microbiology; Molecular Sequence Data; Open Reading Frames - genetics; Plant biology; Plant Cells; Plant Genetics and Genomics; Plant Proteins - chemistry; Plant Proteins - genetics; Plant Sciences; Plants - genetics; Protein Structure, Tertiary - genetics; Proteins; Pseudogenes - genetics; Sequence Alignment; Amino acid composition; Phylogenetics; Functional constraint; Rapidly evolving gene
• ISSN: 0022-2844; 1432-1432
• DOI: 10.1007/s00239-007-9060-6

The rapidly evolving chloroplast matK gene has nucleotide and amino acid substitution rates suggestive of progression toward a pseudogene state. However, molecular evidence has demonstrated that matK is expressed and functional. We explore in this paper the underlying factors behind the mode and tempo of matK evolution that allow this protein coding gene to accommodate such elevated rates of substitution and yet maintain functionality. Conservative amino acid replacement may reconcile the fast evolutionary rate in matK with conservation in protein function. Based on this premise, we have examined putative amino acid sequences for MATK from across green plants to determine constraint on this protein as indicated by variation in composition of amino acid side chain category. Amino acids in the MATK ORF were divided into six categories based on chemical properties of their side chains: nonpolar, uncharged (pH 7), basic, acidic, aromatic, and “special” (amino acids that specifically affect protein structure, i.e., proline, glycine, and cysteine). The amount of standard deviation (SD) in side chain composition was used as a measure of variation and constraint, where a low SD implied high evolutionary constraint and a high SD implied low constraint. Further, we used secondary structure prediction to evaluate if conservation observed in side chain composition was reflected in stable predicted structure. The results of this study demonstrate evolutionary constraint on MATK, identify three regions of functional importance, show highly conserved secondary structure, and support the putative function of MATK as a group II intron maturase.