Modeling Information Systems In Prokaryotic Genomes

Michigan State University, East Lansing MI

Investigators

Abstract

The expressed purpose of this project is to understand the relationship of base periodicity to the overall structure of information in prokaryotic genomes. The longer-term goal of the research is to use an understanding of the total information in chromosomes to construct and test mathematical models that simulate the dynamics of information evolution and exchange in prokaryotes. The objectives are to characterize the origins, organization and fate of genomic information in prokaryotes by developing and applying methods for system identification to track genes and the integrity of their information over time. A longer term goal is to model the content, structure, and behavior of information in prokaryotic chromosomes by characterizing signals from the frequency and organization of sequence and genes over multiple scales of measure. The scales of measure will vary from a few nucleotides to an entire chromosome. Protein-coding nucleotide sequences characteristically tend to repeat bases at three-step intervals, thereby producing short-range periodicity. Prior work from our lab established that Fourier analysis of signals from nucleotide periodicity revealed a tendency for genes from the same prokaryotic chromosome to exhibit similar patterns of short-range nucleotide periodicity. At the same time, long-range base periodicity and models of gene clustering patterns suggest that prokaryotic chromosomes have a fractal structure of base-repeat and gene clustering information. A fractal information structure for a chromosome is one in which the pattern of information for a large segment is similar to the pattern for a smaller unit used to build the larger structure. This research seeks to determine whether and to what extent a common information infrastructure exists in a genome and methods to measure it. New and established pattern recognition methods are being developed to study the structure of periodic information by analyzing the records of base periodicity in a set of prokaryotic genomes to compare with the signals from four other parameters of total information that influence periodicity. Other parameters will include measures of: ii) relative nucleotide frequency; iii) relative nucleotide arrangement; iv) relative codon frequency; and v) relative codon arrangement. Overall research objectives are designed to study: 1) signal variation in chromosomal gene and ORF (Open Reading Frame) populations; and 2) fractal structures of information in chromosomes. This study will probe the history and structure(s) of information in bacterial genomes. Potentially, the expected results could be used to build a theoretical framework to explain the early history of bacterial chromosome formation.