symmetry in the language of gene expression a survey of gene promoter networks in multiple bacterial species and non-σ regulons对称的语言基因表达基因启动子网络的调查在多个细菌物种和non-σ调节子.pdf

Symmetry 2011, 3, 750-766; doi:10.3390/sym3040750 OPEN ACCESS symmetry ISSN 2073-8994 /journal/symmetry Article Symmetry in the Language of Gene Expression: A Survey of Gene Promoter Networks in Multiple Bacterial Species and Non-σ Regulons Preston R. Aldrich *, Robert K. Horsley and Stefan M. Turcic Department of Biological Sciences, Benedictine University, Lisle, IL 60532, USA; E-Mails: Robert_Horsley@ (R.K.H.); Stefan_Turcic@ (S.M.T.) * Author to whom correspondence should be addressed; E-Mail: paldrich@; Tel.: +630-829-6519; Fax: +630-829-6547. Received: 5 September 2011; in revised form: 8 October 2011 / Accepted: 11 November 2011 / Published: 18 November 2011 Abstract: The language of gene expression displays topological symmetry. An important step during gene expression is the binding of transcriptional proteins to DNA promoters adjacent to a gene. Some proteins bind to many promoters in a genome, defining a regulon of genes wherein each promoter might vary in DNA sequence relative to the average consensus. Here we examine the linguistic organization of gene promoter networks, wherein each node in the network represents a promoter and links between nodes represent the extent of base pair-sharing. Prior work revealed a fractal nucleus in several σ-factor regulons from Escherichia coli . We extend these findings to show fractal nuclei in gene promoter networks from three bacterial species, E. coli, Bacillus subtilis, and Pseudomonas aerugi