ReviewMicrobiology and molecular biology reviews : MMBR2008
Cohesion group approach for evolutionary analysis of TyrA, a protein family with wide-ranging substrate specificities.
Review in Microbiology and molecular biology reviews : MMBR, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
17 citing papers in PubMed, 33 citations in OpenAlex.
- An Efficient Prephenate Dehydrogenase Gene for the Biosynthesis of L-tyrosine: Gene Mining, Sequence Analysis, and Expression Optimization.Foods (Basel, Switzerland) · 2023Article
- Production of Hydroxycarboxylic Acid Receptor 3 (HCAMicroorganisms · 2021Article
- Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain.The FEBS journal · 2020Article
- Harnessing evolutionary diversification of primary metabolism for plant synthetic biology.The Journal of biological chemistry · 2019Review
- Evolutionary Diversification of Primary Metabolism and Its Contribution to Plant Chemical Diversity.Frontiers in plant science · 2019Review
- Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants.Nature chemical biology · 2017Article
- Conserved Molecular Mechanism of TyrA Dehydrogenase Substrate Specificity Underlying Alternative Tyrosine Biosynthetic Pathways in Plants and Microbes.Frontiers in molecular biosciences · 2017Article
- Characterization of two key enzymes for aromatic amino acid biosynthesis in symbiotic archaea.Extremophiles : life under extreme conditions · 2016Article
- Three different classes of aminotransferases evolved prephenate aminotransferase functionality in arogenate-competent microorganisms.The Journal of biological chemistry · 2014Article
- Diversity and versatility of the Thermotoga maritima sugar kinome.Journal of bacteriology · 2012Article
- The alternative translational profile that underlies the immune-evasive state of persistence in Chlamydiaceae exploits differential tryptophan contents of the protein repertoire.Microbiology and molecular biology reviews : MMBR · 2012Review
- The FGGY carbohydrate kinase family: insights into the evolution of functional specificities.PLoS computational biology · 2011Article
- Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.Microbiology and molecular biology reviews : MMBR · 2009Review
- Innovations in host and microbial sialic acid biosynthesis revealed by phylogenomic prediction of nonulosonic acid structure.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- The crystal structure of Aquifex aeolicus prephenate dehydrogenase reveals the mode of tyrosine inhibition.The Journal of biological chemistry · 2009Article
- Unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analyses and genome context.BMC evolutionary biology · 2008Article
- Metabolic engineering of Escherichia coli for L-tyrosine production by expression of genes coding for the chorismate mutase domain of the native chorismate mutase-prephenate dehydratase and a cyclohexadienyl dehydrogenase from Zymomonas mobilis.Applied and environmental microbiology · 2008Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
Many enzymes and other proteins are difficult subjects for bioinformatic analysis because they exhibit variant catalytic, structural, regulatory, and fusion mode features within a protein family whose sequences are not highly conserved. However, such features reflect dynamic and interesting scenarios of evolutionary importance. The value of experimental data obtained from individual organisms is instantly magnified to the extent that given features of the experimental organism can be projected upon related organisms. But how can one decide how far along the similarity scale it is reasonable to go before such inferences become doubtful? How can a credible picture of evolutionary events be deduced within the vertical trace of inheritance in combination with intervening events of lateral gene transfer (LGT)? We present a comprehensive analysis of a dehydrogenase protein family (TyrA) as a prototype example of how these goals can be accomplished through the use of cohesion group analysis. With this approach, the full collection of homologs is sorted into groups by a method that eliminates bias caused by an uneven representation of sequences from organisms whose phylogenetic spacing is not optimal. Each sufficiently populated cohesion group is phylogenetically coherent and defined by an overall congruence with a distinct section of the 16S rRNA gene tree. Exceptions that occasionally are found implicate a clearly defined LGT scenario whereby the recipient lineage is apparent and the donor lineage of the gene transferred is localized to those organisms that define the cohesion group. Systematic procedures to manage and organize otherwise overwhelming amounts of data are demonstrated.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.