Biomaterial Database

Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. 2006

Mike Withers, and Lorenz Wernisch, and Mario dos Reis

School of Crystallography, Birkbeck College, University of London, UK.

Transfer RNA genes tend to be presented in multiple copies in the genomes of most organisms, from bacteria to eukaryotes. The evolution and genomic structure of tRNA genes has been a somewhat neglected area of molecular evolution. Escherichia coli, the first phylogenetic species for which more than two different strains have been sequenced, provides an invaluable framework to study the evolution of tRNA genes. In this work, a detailed analysis of the tRNA structure of the genomes of Escherichia coli strains K12, CFT073, and O157:H7, Shigella flexneri 2a 301, and Salmonella typhimurium LT2 was carried out. A phylogenetic analysis of these organisms was completed, and an archaeological map depicting the main events in the evolution of tRNA genes was drawn. It is shown that duplications, deletions, and horizontal gene transfers are the main factors driving tRNA evolution in these genomes. On average, 0.64 tRNA insertions/duplications occur every million years (Myr) per genome per lineage, while deletions occur at the slower rate of 0.30 per million years per genome per lineage. This work provides a first genomic glance at the problem of tRNA evolution as a repetitive process, and the relationship of this mechanism to genome evolution and codon usage is discussed.

UI	MeSH Term	Description	Entries
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
D003062	Codon	A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).	Codon, Sense,Sense Codon,Codons,Codons, Sense,Sense Codons
D004926	Escherichia coli	A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.	Alkalescens-Dispar Group,Bacillus coli,Bacterium coli,Bacterium coli commune,Diffusely Adherent Escherichia coli,E coli,EAggEC,Enteroaggregative Escherichia coli,Enterococcus coli,Diffusely Adherent E. coli,Enteroaggregative E. coli,Enteroinvasive E. coli,Enteroinvasive Escherichia coli
D012343	RNA, Transfer	The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.	Suppressor Transfer RNA,Transfer RNA,tRNA,RNA, Transfer, Suppressor,Transfer RNA, Suppressor,RNA, Suppressor Transfer
D014644	Genetic Variation	Genotypic differences observed among individuals in a population.	Genetic Diversity,Variation, Genetic,Diversity, Genetic,Diversities, Genetic,Genetic Diversities,Genetic Variations,Variations, Genetic
D016680	Genome, Bacterial	The genetic complement of a BACTERIA as represented in its DNA.	Bacterial Genome,Bacterial Genomes,Genomes, Bacterial
D017353	Gene Deletion	A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.	Deletion, Gene,Deletions, Gene,Gene Deletions
D018628	Gene Dosage	The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.	Gene Copy Number,Copy Number, Gene,Copy Numbers, Gene,Dosage, Gene,Dosages, Gene,Gene Copy Numbers,Gene Dosages,Number, Gene Copy,Numbers, Gene Copy
D019143	Evolution, Molecular	The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.	Molecular Evolution,Genetic Evolution,Evolution, Genetic
D020440	Gene Duplication	Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.	Duplication, Gene,Duplications, Gene,Gene Duplications