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The emerging periplasm-localized subclass of AroQ chorismate mutases, exemplified by those from Salmonella typhimurium and Pseudomonas aeruginosa

David H Calhoun, Carol A Bonner, Wei Gu, Gary Xie and Roy A Jensen*

Genome Biology 2001, 2:research0030-research0030.16 doi:10.1186/gb-2001-2-8-research0030

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In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection

Kathleen Marchal, Sigrid De Keersmaecker, Pieter Monsieurs, Nadja van Boxel, Karen Lemmens, Gert Thijs, Jos Vanderleyden, Bart De Moor Genome Biology 2004, 5:R9 (29 January 2004)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A genome-wide computational screen for targets of the PmrA transcription factor in Salmonella typhimurium has identified novel target genes.

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Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria

Gary Xie, Carol A Bonner, Tom Brettin, Raphael Gottardo, Nemat O Keyhani, Roy A Jensen Genome Biology 2003, 4:R14 (29 January 2003)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated. A seven-gene cluster in Xylella fastidiosa exhibits a sharply delineated low-GC content. This strongly implicates lateral gene transfer. In contrast, parametric studies and protein tree phylogenies did not support the origination of a gene block in the Anabaena/Nostoc lineage by lateral gene transfer.

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Significance of two distinct types of tryptophan synthase beta chain in Bacteria, Archaea and higher plants

Gary Xie, Christian Forst, Carol Bonner, Roy A Jensen Genome Biology 2001, 3:research0004-research0004.13 (14 December 2001)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Tryptophan synthase consists of two subunits, α and β. Two subgroups of β chain exist; the major group TrpEb_1 and the minor group, TrpEb_2. Conserved amino-acid residues of TrpEb_1 that make allosteric contact with the TrpEa subunit (the α chain) are absent in TrpEb_2. Representatives of Archaea, Bacteria and higher plants all exist that possess both TrpEb_1 and TrpEb_2. at least six lineages of the Archaea are likely to use TrpEb_2 as the functional β chain.

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