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Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks
Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism
Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655
A genetic footprinting technique is used for a genome-wide assessment of genes required for robust aerobic growth of Escherichia coli in rich media to identify 620 genes as essential and 3,126 genes as dispensable for growth under these conditions.
Comparative genomics of bacterial zinc regulons: Enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins
Zinc regulons were predicted to contain a candidate component of the ATP binding cassette, zinT, and candidate AdcR-binding sites were identified upstream of genes encoding pneumococcal histidine triad proteins from a number of pathogenic streptococci, suggesting that PHT proteins are involved in the invasion process.
Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes*
A highly conserved RNA secondary structure, the regulatory B12 element, is found in the upstream regions of cobalamin biosynthetic/transport genes in eubacteria, and B12 regulons of various bacteria are thought to include enzymes from known B12-dependent or alternative pathways.
Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation.
A model for regulation based on formation of alternative RNA structures involving the RFN elements is suggested and several new candidate riboflavin transporters were identified.
Computational Reconstruction of Iron- and Manganese-Responsive Transcriptional Networks in α-Proteobacteria
The detailed comparative and phylogenetic analyses of the regulatory systems allowed us to propose a theory about the possible evolution of Fe and Mn regulons in alpha-proteobacteria, and expand the range of genes involved in iron homeostasis and demonstrates considerable interconnection between iron-responsive regulatory systems.
Comparative genomic analysis of T-box regulatory systems in bacteria.
A new structural class of T-boxes containing duplicated terminator-antiterminator elements and unusual reduced T- boxes regulating initiation of translation in the Actinobacteria is described.
Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria
This study for the first time demonstrates the adaptability of the comparative genomic approach to de novo reconstruction of a regulatory network in a poorly studied taxonomic group of bacteria.
Comparative Genomics of Thiamin Biosynthesis in Procaryotes
Thiamin-mediated regulation based on formation of alternative RNA structures involving the THI element is suggested, which is widely distributed in eubacteria and also occurs in some archaea.
Gene recognition via spliced sequence alignment.
A spliced alignment algorithm and software tool that explores all possible exon assemblies in polynomial time and finds the multiexon structure with the best fit to a related protein.