Regulation of biosynthesis and transport of aromatic amino acids in low-GC Gram-positive bacteria. 2003

Ekaterina M Panina, and Alexey G Vitreschak, and Andrey A Mironov, and Mikhail S Gelfand
Graduate Program in Molecular, Cellular and Integrative Life Sciences, 172 Molecular Science Building, University of California at Los Angeles, Los Angeles, CA 90095-1570, USA.

Computational comparative techniques were applied to analysis of the aromatic amino acid regulon in Gram-positive bacteria. A new candidate transcription regulation signal of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase and shikimate kinase genes was identified in Streptococcus and Lactococcus species. New T-boxes were found upstream of aromatic amino acid biosynthesis and transport genes in the Bacillus/Clostridium group. The substrate specificity of proteins from the PabA/TrpG family was assigned based on metabolic reconstruction and analysis of regulatory signals and phylogenetic patterns. New candidate tryptophan transporters were identified; their specificity was predicted by analysis of T-box regulatory sites. Comparison of all available genomes shows that regulation of genes of the aromatic amino acid biosynthesis pathway is quite labile and involves at least four regulatory systems, two at the DNA level and two more involving competition of alternative RNA secondary structures for transcription and/or translation regulation at the RNA level.

UI MeSH Term Description Entries
D008969 Molecular Sequence Data Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D009876 Operon In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION. Operons
D010723 3-Deoxy-7-Phosphoheptulonate Synthase An enzyme that catalyzes the formation of 7-phospho-2-keto-3-deoxy-D-arabinoheptonate from phosphoenolpyruvate and D-erythrose-4-phosphate. It is one of the first enzymes in the biosynthesis of TYROSINE and PHENYLALANINE. This enzyme was formerly listed as EC 4.1.2.15. 2-Dehydro-3-Deoxyphosphoheptonate Aldolase,3-Deoxyarabinoheptulosonate-7-Phosphate Synthetase,DAHP Synthase,Phospho-2-Keto-3-Deoxyheptonate Aldolase,3-Deoxy-Arabino-Heptulosonate-7-Phosphate Synthase,3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase,DAH7-P,2 Dehydro 3 Deoxyphosphoheptonate Aldolase,3 Deoxy 7 Phosphoheptulonate Synthase,3 Deoxy Arabino Heptulosonate 7 Phosphate Synthase,3 Deoxy D Arabino Heptulosonate 7 Phosphate Synthase,3 Deoxyarabinoheptulosonate 7 Phosphate Synthetase,Aldolase, 2-Dehydro-3-Deoxyphosphoheptonate,Aldolase, Phospho-2-Keto-3-Deoxyheptonate,Phospho 2 Keto 3 Deoxyheptonate Aldolase,Synthase, 3-Deoxy-7-Phosphoheptulonate,Synthase, 3-Deoxy-Arabino-Heptulosonate-7-Phosphate,Synthase, 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate,Synthase, DAHP,Synthetase, 3-Deoxyarabinoheptulosonate-7-Phosphate
D010802 Phylogeny The relationships of groups of organisms as reflected by their genetic makeup. Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D002352 Carrier Proteins Proteins that bind or transport specific substances in the blood, within the cell, or across cell membranes. Binding Proteins,Carrier Protein,Transport Protein,Transport Proteins,Binding Protein,Protein, Carrier,Proteins, Carrier
D004269 DNA, Bacterial Deoxyribonucleic acid that makes up the genetic material of bacteria. Bacterial DNA
D006094 Gram-Positive Bacteria Bacteria which retain the crystal violet stain when treated by Gram's method. Gram Positive Bacteria
D000637 Transaminases A subclass of enzymes of the transferase class that catalyze the transfer of an amino group from a donor (generally an amino acid) to an acceptor (generally a 2-keto acid). Most of these enzymes are pyridoxyl phosphate proteins. (Dorland, 28th ed) EC 2.6.1. Aminotransferase,Aminotransferases,Transaminase
D000878 Anthranilate Synthase An enzyme that catalyzes the formation of anthranilate (o-aminobenzoate) and pyruvic acid from chorismate and glutamine. Anthranilate is the biosynthetic precursor of tryptophan and numerous secondary metabolites, including inducible plant defense compounds. EC 4.1.3.27. Anthranilate Synthetase,Anthranilate Synthase Component I,Synthase, Anthranilate,Synthetase, Anthranilate
D001421 Bacteria, Anaerobic Bacteria that can survive and grow in the complete, or nearly complete absence of oxygen. Anaerobic Bacteria

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