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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. Expand
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Experimental determination and system level analysis of essential genes in Escherichia coli MG1655.
Defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. We used a genetic footprintingExpand
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Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes*
Using comparative analysis of genes, operons, and regulatory elements, we describe the cobalamin (vitamin B12) biosynthetic pathway in available prokaryotic genomes. Here we found a highly conservedExpand
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Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation.
The riboflavin biosynthesis in bacteria was analyzed using comparative analysis of genes, operons and regulatory elements. A model for regulation based on formation of alternative RNA structuresExpand
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Comparative genomics of bacterial zinc regulons: Enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins
Zinc is an important component of many proteins, but in large concentrations it is poisonous to the cell. Thus its transport is regulated by zinc repressors ZUR of proteobacteria and Gram-positiveExpand
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Computational Reconstruction of Iron- and Manganese-Responsive Transcriptional Networks in α-Proteobacteria
We used comparative genomics to investigate the distribution of conserved DNA-binding motifs in the regulatory regions of genes involved in iron and manganese homeostasis in alpha-proteobacteria. Expand
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Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains.
Recent advances enabled by the Hi-C technique have unraveled many principles of chromosomal folding that were subsequently linked to disease and gene regulation. In particular, Hi-C revealed thatExpand
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Comparative genomic analysis of T-box regulatory systems in bacteria.
T-box antitermination is one of the main mechanisms of regulation of genes involved in amino acid metabolism in Gram-positive bacteria. T-box regulatory sites consist of conserved sequence and RNAExpand
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Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization
BackgroundNickel (Ni) and cobalt (Co) are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of vitaminExpand
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Comparative Genomics of Thiamin Biosynthesis in Procaryotes
Vitamin B1 in its active form thiamin pyrophosphate is an essential coenzyme that is synthesized by coupling of pyrimidine (hydroxymethylpyrimidine; HMP) and thiazole (hydroxyethylthiazole) moietiesExpand
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