title: Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria.
abstract: BACKGROUND
  Tryptophan-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.
  
  
  RESULTS
  The 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.
  
  
  CONCLUSIONS
  Judging 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.
authors.affiliation: Department of Microbiology and Cell Science, University of Florida, PO Box 110700, Gainesville, FL 32611, USA.
authors.forename: Gary
authors.initials: G
authors.lastname: Xie
authors.forename: Carol A
authors.initials: CA
authors.lastname: Bonner
authors.forename: Tom
authors.initials: T
authors.lastname: Brettin
authors.forename: Raphael
authors.initials: R
authors.lastname: Gottardo
authors.forename: Nemat O
authors.initials: NO
authors.lastname: Keyhani
authors.forename: Roy A
authors.initials: RA
authors.lastname: Jensen
mesh_terms: D000595:Amino Acid Sequence; D017033:Anabaena / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D000458:Cyanobacteria / Q000235:genetics* / Q000378:metabolism; D020563:Gammaproteobacteria / Q000235:genetics* / Q000378:metabolism; D022761:Gene Transfer, Horizontal; D008969:Molecular Sequence Data; D009876:Operon / Q000235:genetics*; D010802:Phylogeny; D012097:Repressor Proteins / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D014364:Tryptophan / Q000096:biosynthesis*; D029968:Escherichia coli Proteins
chemical_list: D001426:Bacterial Proteins; D003062:Codon; D012097:Repressor Proteins; D014364:Tryptophan; C027190:TRPR protein, E coli; D029968:Escherichia coli Proteins