The set of genes corresponding to the ‘core functions for life’ has been an elusive topic in molecular biology since its beginnings, more than 70 years ago. Early on, it was assumed that there is a set of core protein sequences, which encode a core set of functions, that are found in all of life, and that these could be easily identified from their sequences. However, now that thousands (and soon millions) of genomes have been sequenced, no full-length protein-coding genes are conserved. One commonly used explanation for this observation is that this might be due to incomplete, poorer quality of genomes. To put this in perspective, according to GenBank, 20 years ago, 100% of the prokaryotic genomes available were complete (28 out of 28 genomes by December, 2000); today less than 10% are complete (20,571 out of 283,857 genomes, in November, 2020). Even if only the high-quality genomes are used, there is still no conservation of proteins.
A protein functional domain can be thought of as a discrete, somewhat conserved structural unit, that can convey a particular function in a protein sequence. Thus, a protein can be abstracted as a set of functional domains, with scaffolding or ‘spacer’ sequences between. Analysis at this more abstract functional level can potentially overcome the limitations of protein sequence variability. In Chapter 1, we demonstrate the method to assess genome quality, using a basic set of genome features. This can help filter out the low-quality genomes. The study in Chapter 2 shows the use of a compressed sparse matrix algorithm to reduce computational resources and time to perform the matrix manipulation during the functional domain analysis. In Chapter 3, by analysis of nearly a billion of proteins, we estimate that there are 171 universal functions across bacteria, archaea, and eukaryotes.
The general features of life appear to maintain basic metabolism and heredity processes (replication, transcription, translation) and deal with damage due to environmental assaults. Overall, these studies advance general knowledge of conserved protein functions and can potentially shed light on the evolution of life forms.
|Advisor:||Ussery, David W.|
|Commitee:||Nookaew, Intawat, Robeson, Michael S., II, Jun, Se-Ran, Leuze, Michael R.|
|School:||University of Arkansas for Medical Sciences|
|School Location:||United States -- Arkansas|
|Source:||DAI-B 82/7(E), Dissertation Abstracts International|
|Subjects:||Bioinformatics, Genetics, Molecular biology|
|Keywords:||Comparative genomics, Core functions, Evolution, Functional domain, Genome quality, Protein|
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