Haas, Crysten E, Rodionov, Dmitry A, Kropat, Janette, Malasarn, Davin, Merchant, Sabeeha S
Abstract Background COG0523 proteins are, like the nickel chaperones of the UreG family, part of the G3E family of GTPases linking them to metallocenter biosynthesis. Even though the first...
Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization (2009)
Zhang, Yan, Rodionov, Dmitry A, Gelfand, Mikhail S, Gladyshev, Vadim N
Abstract Background Nickel (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...
Sorci, Leonardo, Martynowski, Dariusz, Rodionov, Dmitry A., Eyobo, Yvonne, Zogaj, Xhavit, Klose, Karl E., ...
Enzymes involved in the last 2 steps of nicotinamide adenine dinucleotide (NAD) cofactor biosynthesis, which catalyze the adenylylation of the nicotinic acid mononucleotide (NaMN) precursor to...
A Novel Class of Modular Transporters for Vitamins in Prokaryotes (2009)
Rodionov, Dmitry A., Hebbeln, Peter, Eudes, Aymerick, Beek, Josy Ter, Rodionova, Irina A., Erkens, Guus B., ...
The specific and tightly controlled transport of numerous nutrients and metabolites across cellular membranes is crucial to all forms of life. However, many of the transporter proteins involved have...
Desai, Tasha A., Rodionov, Dmitry A., Gelfand, Mikhail S., Alm, Eric J., Rao, Christopher V.
The transcriptional program for a gene consists of the promoter necessary for recruiting RNA polymerase along with neighboring operator sites that bind different activators and repressors. From a...
Eudes, Aymerick, Erkens, Guus B., Slotboom, Dirk J., Rodionov, Dmitry A., Naponelli, Valeria, Hanson, Andrew D.
Genes encoding high-affinity folate- and thiamine-binding proteins (FolT, ThiT) were identified in the Lactobacillus casei genome, expressed in Lactococcus lactis, and functionally characterized....
Rodionov, Dmitry A., Li, Xiaoqing, Rodionova, Irina A., Yang, Chen, Sorci, Leonardo, Dervyn, Etienne, ...
A comparative genomic approach was used to reconstruct transcriptional regulation of NAD biosynthesis in bacteria containing orthologs of Bacillus subtilis gene yrxA, a previously identified...
Rodionov, Dmitry A., De Ingeniis, Jessica, Mancini, Chiara, Cimadamore, Flavio, Zhang, Hong, Osterman, Andrei L., ...
A novel family of transcription factors responsible for regulation of various aspects of NAD synthesis in a broad range of bacteria was identified by comparative genomics approach. Regulators of this...
McNeil, Leslie Klis, Reich, Claudia, Aziz, Ramy K., Bartels, Daniela, Cohoon, Matthew, Disz, Terry, ...
The National Microbial Pathogen Data Resource (NMPDR) (http://www.nmpdr.org) is a National Institute of Allergy and Infections Disease (NIAID)-funded Bioinformatics Resource Center that supports...
Dmitry A. Rodionov, Mikhail S. Gelfand, Jonathan D. Todd
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....
Dmitry A Rodionov, Mikhail S Gelfand, Jonathan D. Todd
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....
McNeil, Leslie Klis, Reich, Claudia, Aziz, Ramy K., Bartels, Daniela, Cohoon, Matthew, Disz, Terry, ...
The National Microbial Pathogen Data Resource (NMPDR) (http://www.nmpdr.org) is a National Institute of Allergy and Infections Disease (NIAID)-funded Bioinformatics Resource Center that supports...
McNeil, Leslie Klis, Reich, Claudia, Aziz, Ramy K., Bartels, Daniela, Cohoon, Matthew, Disz, Terry, ...
The National Microbial Pathogen Data Resource (NMPDR) (http://www.nmpdr.org) is a National Institute of Allergy and Infections Disease (NIAID)-funded Bioinformatics Resource Center that supports...
Dmitry A. Rodionov, Inna L. Dubchak, Adam P. Arkin, Eric J. Alm, Mikhail S. Gelfand
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...
Rodionov, Dmitry A., Dubchak, Inna L., Arkin, Adam P., Alm, Eric J., Gelfand, Mikhail S.
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...
Dmitry A Rodionov, Inna L Dubchak, Adam P Arkin, Eric J Alm, Mikhail S Gelfand
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...
Ross Overbeek, Tadhg Begley, Ralph M. Butler, Jomuna V. Choudhuri, Terry Disz, Elizabeth M. Glass, ...
Overbeek, Ross, Begley, Tadhg, Butler, Ralph M., Choudhuri, Jomuna V., Chuang, Han-Yu, Cohoon, Matthew, ...
The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the...
Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria (2004)
Rodionov, Dmitry A, Dubchak, Inna, Arkin, Adam, Alm, Eric, Gelfand, Mikhail S
Abstract Background Relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. The recent availability of...
Reconstruction Of Regulatory And Metabolic Pathways In Metal-Reducing delta-Proteobacteria (2004)
Rodionov, Dmitry A., Dubchak, Inna, Arkin, Adam, Alm, Eric, Gelfand, Mikhail S.
Relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. The recent availability of complete finished or...
Rodionov, Dmitry A., Vitreschak, Alexey G., Mironov, Andrey A., Gelfand, Mikhail S.
Regulation of the methionine biosynthesis and transport genes in bacteria is rather diverse and involves two RNA-level regulatory systems and at least three DNA-level systems. In particular, the...
Rodionov, Dmitry A., Vitreschak, Alexey G., Mironov, Andrey A., Gelfand, Mikhail S.
Comparative analysis of genes, operons and regulatory elements was applied to the lysine biosynthetic pathway in available bacterial genomes. We report identification of a lysine‐specific RNA...
VITRESCHAK, ALEXEY G., RODIONOV, DMITRY A., MIRONOV, ANDREY A., GELFAND, MIKHAIL S.
Cobalamin in the form of adenosylcobalamin (Ado-CBL) is known to repress expression of genes for vitamin B12 biosynthesis and be transported by a posttranscriptional regulatory mechanism, which...
Vitreschak, Alexey G., Rodionov, Dmitry A., Mironov, Andrey A., Gelfand, Mikhail S.
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 structures...
Conservation of the Biotin Regulon and the BirA Regulatory Signal in Eubacteria and Archaea (2002)
Rodionov, Dmitry A., Mironov, Andrei A., Gelfand, Mikhail S.
Vitreschak, Alexey G., Rodionov, Dmitry A., Mironov, Andrey A., Gelfand, Mikhail S.
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 structures...
Conservation of the Biotin Regulon and the BirA Regulatory Signal in Eubacteria and Archaea
Rodionov, Dmitry A., Mironov, Andrei A., Gelfand, Mikhail S.
Biotin is a necessary cofactor of numerous biotin-dependent carboxylases in a variety of microorganisms. The strict control of biotin biosynthesis in Escherichia coli is mediated by the bifunctional...
Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?
Rodionov, Dmitry A., Vitreschak, Alexey G., Mironov, Andrey A., Gelfand, Mikhail S.
Comparative analysis of genes, operons and regulatory elements was applied to the lysine biosynthetic pathway in available bacterial genomes. We report identification of a lysine-specific RNA...
Rodionov, Dmitry A., Vitreschak, Alexey G., Mironov, Andrey A., Gelfand, Mikhail S.
Regulation of the methionine biosynthesis and transport genes in bacteria is rather diverse and involves two RNA-level regulatory systems and at least three DNA-level systems. In particular, the...
Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria
Rodionov, Dmitry A, Dubchak, Inna, Arkin, Adam, Alm, Eric, Gelfand, Mikhail S
A study of the genetic and regulatory factors in several biosynthesis, metal ion homeostasis, stress response, and energy metabolism pathways suggests that phylogenetically diverse δ-proteobacteria...
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
Overbeek, Ross, Begley, Tadhg, Butler, Ralph M., Choudhuri, Jomuna V., Chuang, Han-Yu, Cohoon, Matthew, ...
The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the...
Rodionov, Dmitry A, Dubchak, Inna L, Arkin, Adam P, Alm, Eric J, Gelfand, Mikhail S
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...
Rodionov, Dmitry A., Hebbeln, Peter, Gelfand, Mikhail S., Eitinger, Thomas
The transition metals nickel and cobalt, essential components of many enzymes, are taken up by specific transport systems of several different types. We integrated in silico and in vivo methods for...
VITRESCHAK, ALEXEY G., RODIONOV, DMITRY A., MIRONOV, ANDREY A., GELFAND, MIKHAIL S.
Cobalamin in the form of adenosylcobalamin (Ado-CBL) is known to repress expression of genes for vitamin B12 biosynthesis and be transported by a posttranscriptional regulatory mechanism, which...
Vitreschak, Alexey G., Rodionov, Dmitry A., Mironov, Andrey A., Gelfand, Mikhail S.
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 structures...
Conservation of the Biotin Regulon and the BirA Regulatory Signal in Eubacteria and Archaea
Rodionov, Dmitry A., Mironov, Andrei A., Gelfand, Mikhail S.
Biotin is a necessary cofactor of numerous biotin-dependent carboxylases in a variety of microorganisms. The strict control of biotin biosynthesis in Escherichia coli is mediated by the bifunctional...
Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?
Rodionov, Dmitry A., Vitreschak, Alexey G., Mironov, Andrey A., Gelfand, Mikhail S.
Comparative analysis of genes, operons and regulatory elements was applied to the lysine biosynthetic pathway in available bacterial genomes. We report identification of a lysine-specific RNA...
Rodionov, Dmitry A., Vitreschak, Alexey G., Mironov, Andrey A., Gelfand, Mikhail S.
Regulation of the methionine biosynthesis and transport genes in bacteria is rather diverse and involves two RNA-level regulatory systems and at least three DNA-level systems. In particular, the...
Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria
Rodionov, Dmitry A, Dubchak, Inna, Arkin, Adam, Alm, Eric, Gelfand, Mikhail S
A study of the genetic and regulatory factors in several biosynthesis, metal ion homeostasis, stress response, and energy metabolism pathways suggests that phylogenetically diverse δ-proteobacteria...
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
Overbeek, Ross, Begley, Tadhg, Butler, Ralph M., Choudhuri, Jomuna V., Chuang, Han-Yu, Cohoon, Matthew, ...
The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the...
Rodionov, Dmitry A, Dubchak, Inna L, Arkin, Adam P, Alm, Eric J, Gelfand, Mikhail S
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...
Rodionov, Dmitry A., Hebbeln, Peter, Gelfand, Mikhail S., Eitinger, Thomas
The transition metals nickel and cobalt, essential components of many enzymes, are taken up by specific transport systems of several different types. We integrated in silico and in vivo methods for...
VITRESCHAK, ALEXEY G., RODIONOV, DMITRY A., MIRONOV, ANDREY A., GELFAND, MIKHAIL S.
Cobalamin in the form of adenosylcobalamin (Ado-CBL) is known to repress expression of genes for vitamin B12 biosynthesis and be transported by a posttranscriptional regulatory mechanism, which...
Rodionov, Dmitry A, Gelfand, Mikhail S, Todd, Jonathan D, Curson, Andrew R. J, Johnston, Andrew W. B
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....
McNeil, Leslie Klis, Reich, Claudia, Aziz, Ramy K., Bartels, Daniela, Cohoon, Matthew, Disz, Terry, ...
The National Microbial Pathogen Data Resource (NMPDR) () is a National Institute of Allergy and Infections Disease (NIAID)-funded Bioinformatics Resource Center that supports research in selected...
Hebbeln, Peter, Rodionov, Dmitry A., Alfandega, Anja, Eitinger, Thomas
BioMNY proteins are considered to constitute tripartite biotin transporters in prokaryotes. Recent comparative genomic and experimental analyses pointed to the similarity of BioMN to homologous...
Rodionov, Dmitry A., Kurnasov, Oleg V., Stec, Boguslaw, Wang, Yan, Roberts, Mary F., Osterman, Andrei L.
Di-myo-inositol 1,1′-phosphate (DIP) is a major osmoprotecting metabolite in a number of hyperthermophilic species of archaea and bacteria. Although the DIP biosynthesis pathway was previously...
Rodionov, Dmitry A., Li, Xiaoqing, Rodionova, Irina A., Yang, Chen, Sorci, Leonardo, Dervyn, Etienne, ...
A comparative genomic approach was used to reconstruct transcriptional regulation of NAD biosynthesis in bacteria containing orthologs of Bacillus subtilis gene yrxA, a previously identified...
Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators
Rodionov, Dmitry A., De Ingeniis, Jessica, Mancini, Chiara, Cimadamore, Flavio, Zhang, Hong, Osterman, Andrei L., ...
A novel family of transcription factors responsible for regulation of various aspects of NAD synthesis in a broad range of bacteria was identified by comparative genomics approach. Regulators of this...
Yang, Chen, Rodionov, Dmitry A., Rodionova, Irina A., Li, Xiaoqing, Osterman, Andrei L.
Members of a novel glycerate-2-kinase (GK-II) family were tentatively identified in a broad range of species, including eukaryotes and archaea and many bacteria that lack a canonical enzyme of the...
Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization
Zhang, Yan, Rodionov, Dmitry A, Gelfand, Mikhail S, Gladyshev, Vadim N
Identification of Genes Encoding the Folate- and Thiamine-Binding Membrane Proteins in Firmicutes▿ ‡
Eudes, Aymerick, Erkens, Guus B., Slotboom, Dirk J., Rodionov, Dmitry A., Naponelli, Valeria, Hanson, Andrew D.
Genes encoding high-affinity folate- and thiamine-binding proteins (FolT, ThiT) were identified in the Lactobacillus casei genome, expressed in Lactococcus lactis, and functionally characterized....
Engineering transcription factors with novel DNA-binding specificity using comparative genomics
Desai, Tasha A., Rodionov, Dmitry A., Gelfand, Mikhail S., Alm, Eric J., Rao, Christopher V.
The transcriptional program for a gene consists of the promoter necessary for recruiting RNA polymerase along with neighboring operator sites that bind different activators and repressors. From a...
Pinchuk, Grigory E., Rodionov, Dmitry A., Yang, Chen, Li, Xiaoqing, Osterman, Andrei L., Dervyn, Etienne, ...
The ability to use lactate as a sole source of carbon and energy is one of the key metabolic signatures of Shewanellae, a diverse group of dissimilatory metal-reducing bacteria commonly found in...
A Novel Class of Modular Transporters for Vitamins in Prokaryotes ▿ †
Rodionov, Dmitry A., Hebbeln, Peter, Eudes, Aymerick, Ter Beek, Josy, Rodionova, Irina A., Erkens, Guus B., ...
The specific and tightly controlled transport of numerous nutrients and metabolites across cellular membranes is crucial to all forms of life. However, many of the transporter proteins involved have...
Kazakov, Alexey E., Rodionov, Dmitry A., Alm, Eric, Arkin, Adam Paul, Dubchak, Inna, Gelfand, Mikhail S.
Bacteria can use branched-chain amino acids (ILV, i.e., isoleucine, leucine, valine) and fatty acids (FAs) as sole carbon and energy sources converting ILV into acetyl-coenzyme A (CoA),...
Sorci, Leonardo, Martynowski, Dariusz, Rodionov, Dmitry A., Eyobo, Yvonne, Zogaj, Xhavit, Klose, Karl E., ...
Enzymes involved in the last 2 steps of nicotinamide adenine dinucleotide (NAD) cofactor biosynthesis, which catalyze the adenylylation of the nicotinic acid mononucleotide (NaMN) precursor to...