Horizontally acquired DAP pathway as a unit of self-regulation
Article first published online: 16 DEC 2010
© 2010 The Authors. Journal of Evolutionary Biology © 2010 European Society For Evolutionary Biology
Journal of Evolutionary Biology
Volume 24, Issue 3, pages 587–595, March 2011
How to Cite
SUN, G. and HUANG, J. (2011), Horizontally acquired DAP pathway as a unit of self-regulation. Journal of Evolutionary Biology, 24: 587–595. doi: 10.1111/j.1420-9101.2010.02192.x
- Issue published online: 21 FEB 2011
- Article first published online: 16 DEC 2010
- Received 10 September 2010; revised 29 October 2010; accepted 9 November 2010
- 1999. Mutations that cause threonine sensitivity identify catalytic and regulatory regions of the aspartate kinase of Saccharomyces cerevisiae. Yeast 15: 1331–1345. , &
- 2002. Extensive feature detection of N-terminal protein sorting signals. Bioinformatics 18: 298–305. , , , &
- 2010. The dynamic genome of Hydra. Nature 464: 592–596. , , , , , et al.
- 2009. Homology modeling and molecular dynamics study on N-acetylneuraminate lyase. J. Mol. Model. 15: 323–328. , , &
- 2008. Analysis of a horizontally transferred pathway involved in vitamin B-6 biosynthesis from the soybean cyst nematode Heterodera glycines. Mol. Biol. Evol. 25: 2085–2098. , , , , &
- 1969. Regulation of branched biosynthetic pathways in bacteria. Science 165: 556–562.
- 2005. Functional metabolism: regulation and adaptation. Am. J. Hum. Biol. 17: 524–525.
- 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113.
- 1999. ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci. 8: 978–984. , &
- 2007. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2: 953–971. , , &
- 2005. PHYLIP (Phylogeny Inference Package) version 3.61. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
- 2008. Ancient recruitment by chromists of green algal genes encoding enzymes for carotenoid biosynthesis. Mol. Biol. Evol. 25: 2653–2667. , , , , , et al.
- 1995. Regulation of lysine and threonine synthesis. Plant Cell 7: 899–906.
- 2000. Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 10: 1719–1725. , &
- 2002. Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19: 2226–2238. , &
- 2009. Estimating maximum likelihood phylogenies with PhyML. Methods Mol. Biol. 537: 113–137. , , &
- 2008. Concerted gene recruitment in early plant evolution. Genome Biol. 9: R109. &
- 2004. A first glimpse into the pattern and scale of gene transfer in the Apicomplexa. Int. J. Parasitol. 34: 265–274. , , &
- 2005. The evolution of microbial phosphonate degradative pathways. J. Mol. Evol. 61: 682–690. , &
- 2005. Biosynthesis of lysine in plants: evidence for a variant of the known bacterial pathways. Biochim. Biophys. Acta 1721: 27–36. , , , , , et al.
- 2006. An LL-diaminopimelate aminotransferase defines a novel variant of the lysine biosynthesis pathway in plants. Plant Physiol. 140: 292–301. , , &
- 2007. Inhibition of lysine biosynthesis: an evolving antibiotic strategy. Mol. Biosyst. 3: 458–465. , &
- 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. USA 96: 3801–3806. , &
- 2010. Recent progress in deciphering the biosynthesis of aspartate-derived amino acids in plants. Mol. Plant. 3: 54–65. &
- 2004. Regulatory analysis of amino acid synthesis pathway in Escherichia coli: aspartate family. Enzyme Microb. Technol. 35: 694–706. , , , , &
- 2003. Mimicking natural evolution in vitro: an N-acetylneuraminate lyase mutant with an increased dihydrodipicolinate synthase activity. Proc. Natl. Acad. Sci. USA 100: 5694–5699. , &
- 2006. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34: D354–D357. , , , , , et al.
- 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 6: 29. , , , &
- 2008. Horizontal gene transfer in eukaryotic evolution. Nat. Rev. Genet. 9: 605–618. &
- 1999. Mutational analysis of the feedback sites of lysine-sensitive aspartokinase of Escherichia coli. FEMS Microbiol. Lett. 173: 211–215. , &
- 2002. The closest unicellular relatives of animals. Curr. Biol. 12: 1773–1778. , , , &
- 2008. Marks’ Basic Medical Biochemistry: A Clinical Approach, 3rd edn. Lippincott Williams & Wilkins, Philadelphia. &
- 2009. NAD biosynthesis evolution in bacteria: lateral gene transfer of kynurenine pathway in Xanthomonadales and Flavobacteriales. Mol. Biol. Evol. 26: 399–406. , &
- 2009. Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. Microbiol. Mol. Biol. Rev. 73: 594–651. , , , &
- 2010. Phylogenetically-based variation in the regulation of the Calvin cycle enzymes, phosphoribulokinase and glyceraldehyde-3-phosphate dehydrogenase, in algae. J. Exp. Bot. 61: 735–745. , , &
- 2002. Predicting functional linkages from gene fusions with confidence. Appl. Bioinformatics 1: 93–100. &
- 1993. Regulation of aspartate-derived amino-acid biosynthesis in the yeast Saccharomyces cerevisiae. Current Microbiology 26: 313–322. &
- 1993. Isolation of a mutant allele that deregulates the threonine biosynthesis in Saccharomyces cerevisiae. Curr. Genet. 24: 465–471. , , &
- 2009. Multiple horizontal gene transfer events and domain fusions have created novel regulatory and metabolic networks in the oomycete genome. PLoS ONE 4: e6133. , , , , &
- 2000. Evolutionary implications of the mosaic pyrimidine-biosynthetic pathway in eukaryotes. Gene 257: 209–222. , &
- 2009. Functional replacement of a primary metabolic pathway via multiple independent eukaryote-to-eukaryote gene transfers and selective retention. J. Evol. Biol. 22: 1882–1894. , &
- 2007. TBestDB: a taxonomically broad database of expressed sequence tags (ESTs). Nucleic Acids Res. 35: D445–D451. , , , , , et al.
- 2001. Mutation analysis of the feedback inhibition site of aspartokinase III of Escherichia coli K-12 and its use in L-threonine production. Biosci. Biotechnol. Biochem. 65: 1149–1154. , &
- 2006. Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences. Eukaryot. Cell 5: 272–276. &
- 2000. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16: 276–277. , &
- 2006. Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements. Eukaryot. Cell 5: 1517–1531. , , , , , et al.
- 2008. Enzymes of the shikimic acid pathway encoded in the genome of a basal metazoan, Nematostella vectensis, have microbial origins. Proc. Natl. Acad. Sci. USA 105: 2533–2537. , , , , , et al.
- 2004. Gene transfer in the evolution of parasite nucleotide biosynthesis. Proc. Natl. Acad. Sci. USA 101: 3154–3159. , , , , , et al.
- 2010. Algal genes in the closest relatives of animals. Mol. Biol. Evol. 27: 2879–2889. , , &
- 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876–4882. , , , &
- 2009. The evolutionary history of lysine biosynthesis pathways within eukaryotes. J. Mol. Evol. 69: 240–248. , , , &
- 2000. Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nat. Genet. 26: 141–142. &
- 2002. Molecular evolution of the lysine biosynthetic pathways. J. Mol. Evol. 55: 445–459. , &
- 2005. A new mutation in the yeast aspartate kinase induces threonine accumulation in a temperature-regulated way. Yeast 22: 99–110. , , &
- 1964. Distribution of lysine pathways among fungi – evolutionary implications. Am. Nat. 98: 435–446.
- 2005. A novel splice variant of human gene NPL, mainly expressed in human liver, kidney and peripheral blood leukocyte. DNA Seq. 16: 137–142. , , , , , et al.
- 2006. The alpha-aminoadipate pathway for lysine biosynthesis in fungi. Cell Biochem. Biophys. 46: 43–64. , , , &
- 2006. Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res. 16: 1099–1108. , , , &