Intrinsic Nature of Evolution to Erase Molecular Imprint at The Sequence Level Meant That The Same Sequence Motif Could not Be Dated Over Time in The Same Gene Without Comparisons With Homologs

Abstract

Biologists trace the evolutionary provenance and ancestry of proteins and genes through multiple sequence alignment in search of molecular fingerprints that chronicle the evolutionary story of a particular type of gene such as 16S rRNA. Such molecular fingerprints could be conserved sequence motifs that are capable to also chronicle some sequence diversity to accommodate the different species partaking in the evolutionary dance. But, this approach is limited to obtaining provenance and evolutionary relatedness information for a particular class of gene or protein. It could not be translated into revealing the evolutionary story of a particular stretch of DNA in the same gene of a specific species. Such limitations come about due to the nature in which evolutionary process erases the prior molecular imprint (such as a dinucleotide motif) during evolution. Specifically, evolutionary processes are helped by occurrence of mutations, insertions or deletions. All of the above processes change the DNA with replacement of the original nucleotide or amino acid motif. Hence, important evidence that chronicle the evolutionary story such as TA dinucleotide evolving to GA, and then to GC are lost as the sequence changes in the same sequence region of the gene or protein. Applicable also to insertion and deletion mediated evolutionary processes, such limitations preclude the assignment of time-point in the evolutionary story of a particular gene in a specific species. To garner an initial understanding of the evolutionary trajectory that has been transversed by the gene or protein, one has to compare its overall sequence with those of the same gene in other species in a process known as multiple sequence alignment that could yield a phylogenetic tree. Collectively, understanding the origins of particular function or sequence motifs in proteins afford biologist a glimpse into how specific functionalities evolve in a protein, and the circumstances that underpin its evolution. But, the intrinsic nature of evolutionary processes to erase the prior sequence motif in the gene or protein at the same loci through mutation, insertion or deletion meant that it is impossible to chronicle the evolutionary story of a gene in a specific species. To ameliorate the problem, biologists developed the approach of multiple sequence alignment that help reveal the sequence regions that align between the same gene or protein in different species that tells a collective evolutionary story at the sequence level.

Keywords: evolutionary provenance, multiple sequence alignment, insertion, deletion, mutation, sequence motif, biochemistry, bioinformatics, evolutionary biology, molecular biology, microbiology