ArticleGenome biology2003
Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria.
Article in Genome biology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 30 citations in OpenAlex.
- Genetic Context Significantly Influences the Maintenance and Evolution of Degenerate Pathways.Genome biology and evolution · 2021Article
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- Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean.BMC genomics · 2018Article
- Evolutionary diversification of protein-protein interactions by interface add-ons.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone.Applied and environmental microbiology · 2016Article
- Evolution of tryptophan biosynthetic pathway in microbial genomes: a comparative genetic study.Systems and synthetic biology · 2014Article
- A general model of codon bias due to GC mutational bias.PloS one · 2010Article
- A comparative genomics approach to understanding the biosynthesis of the sunscreen scytonemin in cyanobacteria.BMC genomics · 2009Article
- Organization, evolution, and expression analysis of the biosynthetic gene cluster for scytonemin, a cyanobacterial UV-absorbing pigment.Applied and environmental microbiology · 2009Article
- Evolution of prokaryotic SPFH proteins.BMC evolutionary biology · 2009Article
- Evolution of bacterial trp operons and their regulation.Current opinion in microbiology · 2008Review
- Cohesion group approach for evolutionary analysis of TyrA, a protein family with wide-ranging substrate specificities.Microbiology and molecular biology reviews : MMBR · 2008Review
- Phylogenomic analysis of natural selection pressure in Streptococcus genomes.BMC evolutionary biology · 2007Article
- Molecular genetics and genomic analysis of scytonemin biosynthesis in Nostoc punctiforme ATCC 29133.Journal of bacteriology · 2007Article
- Molecular mechanism of tryptophan-dependent transcriptional regulation in Chlamydia trachomatis.Journal of bacteriology · 2006Article
- Article
- Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori.BMC genomics · 2005Article
- A core catalytic domain of the TyrA protein family: arogenate dehydrogenase from Synechocystis.The Biochemical journal · 2004Article
- Inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy.BMC biology · 2004Article
- Conservation of adjacency as evidence of paralogous operons.Nucleic acids research · 2004Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundTryptophan-pathway genes that exist within an apparent operon-like organization were evaluated as examples of multi-genic genomic regions that contain phylogenetically incongruous genes and coexist with genes outside the operon that are congruous. A seven-gene cluster in Xylella fastidiosa includes genes encoding the two subunits of anthranilate synthase, an aryl-CoA synthetase, and trpR. A second gene block, present in the Anabaena/Nostoc lineage, but not in other cyanobacteria, contains a near-complete tryptophan operon nested within an apparent supraoperon containing other aromatic-pathway genes.
resultsThe gene block in X. fastidiosa exhibits a sharply delineated low-GC content. This, as well as bias of codon usage and 3:1 dinucleotide analysis, strongly implicates lateral gene transfer (LGT). In contrast, parametric studies and protein tree phylogenies did not support the origination of the Anabaena/Nostoc gene block by LGT.
conclusionsJudging from the apparent minimal amelioration, the low-GC gene block in X. fastidiosa probably originated by LGT at a relatively recent time. The surprising inability to pinpoint a donor lineage still leaves room for alternative, albeit less likely, explanations other than LGT. On the other hand, the large Anabaena/Nostoc gene block does not seem to have arisen by LGT. We suggest that the contemporary Anabaena/Nostoc array of divergent paralogs represents an ancient ancestral state of paralog divergence, with extensive streamlining by gene loss occurring in the lineage of descent representing other (unicellular) cyanobacteria.
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