Koonin E (2009) Evolution of genome architecture. Int J Biochem Cell Biol 41:298–306
PubMed
Article
CAS
Google Scholar
Hurst LD, Pal C, Lercher MJ (2004) The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 5:299–310
PubMed
Article
CAS
Google Scholar
Jacob F, Perrin D, Sanchez C, Monod J (1960) L’operon: Groupe de genes a l’expression coordonne par un operateur. C R Acad Sci 245: 1727–729
Google Scholar
Jacob F, Monod J (1961) On the regulation of gene activity. In: Cold Spring Harbor Symposium Quantitative Biology 26, pp 193–211
Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318–356
PubMed
CAS
Article
Google Scholar
Warren PB, ten Wolde PR (2004) Statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli. J Mol Biol 342:1379–1390
PubMed
Article
CAS
Google Scholar
Korbel JO, Jensen LJ, von Mering C, Bork P (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol 22:911–917
PubMed
Article
CAS
Google Scholar
Kepes F (2004) Periodic transcriptional organization of the E. coli genome. J Mol Biol 340:957–964
PubMed
Article
CAS
Google Scholar
Price MN, Arkin AP, Alm EJ (2006) The life-cycle of operons. PLoS Genet 2:0859–0873
CAS
Google Scholar
Lawrence JG, Roth JR (1996) Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143:1843–1860
PubMed
CAS
Google Scholar
Lawrence JG (2002) Shared strategies in gene organization among prokaryotes and eukaryotes. Cell 110:407–413
PubMed
Article
CAS
Google Scholar
Price MN, Huang KH, Alm EJ, Arkin AP (2005) Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Res 15:809–819
PubMed
Article
CAS
Google Scholar
Omelchenko MV, Makarova KS, Wolf YI, Rogozin IB, Koonin EV (2003) Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol 4:R55
PubMed
Article
Google Scholar
Pal C, Hurst JD (2004) Evidence against the selfish operon theory. Trends Genet 20:232–234
PubMed
Article
CAS
Google Scholar
Rocha EPC (2008) The organization of the bacterial genome. Annu Rev Genet 42:211–233
PubMed
Article
CAS
Google Scholar
Hazkani-Covo E, Graur D (2005) Evolutionary conservation of bacterial operons: does transcriptional connectivity matter? Genetica 124:145–166
PubMed
Article
CAS
Google Scholar
Dekel E, Alon U (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 436:588–592
PubMed
Article
CAS
Google Scholar
Dandekar T, Snel B, Huynen M, Bork P (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 23:324–328
PubMed
Article
CAS
Google Scholar
Swain PS (2004) Efficient attenuation of stochasticity in gene expression through post-transcriptional control. J Mol Biol 344:965–976
PubMed
Article
CAS
Google Scholar
Butland G, Peregrine-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433:531–537
PubMed
Article
CAS
Google Scholar
Kolesov G, Wunderlich Z, Laikova ON, Gelfand MS, Mirny LA (2007) How gene order is influenced by the biophysics of transcription regulation. Proc Natl Acad Sci USA 104:13948–13953
PubMed
Article
CAS
Google Scholar
Hershberg R, Yeger-Lotem E, Margalit H (2005) Chromosomal organization is shaped by the transcription regulatory network. Trends Genet 21:138–142
PubMed
Article
CAS
Google Scholar
McFall E (1986) cis-Acting proteins. J Bacteriol 167:429–432
PubMed
CAS
Google Scholar
Golding I, Cox EC (2006) Physical nature of bacterial cytoplasm. Phys Rev Lett 96:98102–98104
Article
CAS
Google Scholar
Thanaraj TA, Argos P (1996) Ribosome-mediated translational pause and protein domain organization. Protein Sci 5:1594–1612
PubMed
Article
CAS
Google Scholar
Danchin A, Guerdoux-Jamet P, Moszer I, Nitschke P (2000) Mapping the bacterial cell architecture into the chromosome. Philos Trans R Soc Lond B 355:179–190
Article
CAS
Google Scholar
Daubin V, Ochman H (2004) Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res 14:1036–1042
PubMed
Article
CAS
Google Scholar
de Daruvar A, Collado-Vides J, Valencia A (2009) Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus subtilis. J Mol Evol 55:211–221
Article
Google Scholar
Ermolaeva MD, White O, Salzberg SL (2001) Prediction of operons in microbial genomes. Nucleic Acids Res 29:1216–1221
PubMed
Article
CAS
Google Scholar
Lathe WC, Snel B, Bork P (2000) Gene context conservation of a higher order than operons. Trends Biochem 25:474–479
Article
CAS
Google Scholar
Rogozin IB, Makarova KS, Murvai J, Czabarka E, Wolf YI, Tatusov RL, Szekely LA, Koonin EV (2002) Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res 30:2212–2223
PubMed
Article
CAS
Google Scholar
Keller NP, Turner G, Bennett JW (2005) Fungal secondary metabolism—from biochemistry to genomics. Nat Rev Microbiol 3:937–947
PubMed
Article
CAS
Google Scholar
Fox EM, Howlett BJ (2008) Secondary metabolism: regulation and role in fungal biology. Curr Opin Microbiol 11:481–487
PubMed
Article
CAS
Google Scholar
Turgeon BG, Bushley KE (2009) Secondary metabolism. In: Borkovich K, Ebbole D (eds) Cellular and molecular biology of filamentous fungi. American Society of Microbiology, Washington D.C. (in press)
Bohnert HU, Fudal I, Dioh W, Tharreau D, Notteghem JL, Lebrun MH (2004) A putative polyketide synthase/peptide synthetase from Magnaporthe grisea signals pathogen attack to resistant rice. Plant Cell 16:2499–2513
PubMed
Article
Google Scholar
Collemare J, Pianfetti M, Houlle AE, Morin D, Camborde L, Gagey MJ, Barbisan C, Fudal I, Lebrun MH, Bohnert HU (2008) Magnaporthe grisea avirulence gene ACE1 belongs to an infection-specific gene cluster involved in secondary metabolism. New Phytol 179:196–208
PubMed
Article
CAS
Google Scholar
Brosch G, Ransom R, Lechner T, Walton JD, Loidl P (1995) Inhibition of maize histone deacetylases by HC toxin, the host-selective toxin of Cochliobolus carbonum. Plant Cell 7:1941–1950
PubMed
Article
CAS
Google Scholar
Pedley KF, Walton JD (2001) Regulation of cyclic peptide biosynthesis in a plant pathogenic fungus by a novel transcription factor. Proc Natl Acad Sci USA 98:14174–14179
PubMed
Article
CAS
Google Scholar
Walton JD (2006) HC-toxin. Phytochem Anal 67:1406–1413
Article
CAS
Google Scholar
Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, Bennett J, Bowyer P, Chen D, Collins M, Coulsen R, Davies R, Dyer P, Farman M, Fedorova N, Fedorova N, Feldblyum TV, Fischer G, Fosker N, Fraser A, Garcia JL, Garcia MJ, Goble A, Goldman GH, Gomi K, Griffith-Jones S, Gwilliam R, Haas B, Haas H, Harris D, Horiuchi H, Huang J, Humphray S, Jimenez J, Keller N, Khouri H, Kitamoto K, Kobayashi T, Konzack S, Kulkarni R, Kumagai T, Lafton A, Latge JP, Li W, Lord A, Lu C, Majoros WH, May GS, Miller B, Mohamoud Y, Molina M, Monod M, Mouyna I, Mulligan S, Murphy L, O’Neil S, Paulsen I, Penalva MA, Pertea M, Price C, Pritchard BL, Quail MA, Rabbinowitsch E, Rawlins N, Rajandream MA, Reichard U, Renauld H, Robson GD, de Cordoba SR, Rodriguez-Pena JM, Ronning CM, Rutter S, Salzberg SL, Sanchez M, Saunders D, Seeger K, Squares R, Squares S, Takeuchi M, Tekaia F, Turner G, Carlos Weidman J, White O, Woodward J, Yu JH, Fraser C, Galagan JE, Asai K, Machida M, Hall C, Barrell B, Denning DW (2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438:1151–1156
PubMed
Article
CAS
Google Scholar
Pelaez F (2005) Biological activities of fungal metabolites. In: An Z (ed) Handbook of industrial mycology. Marcel Dekker, New York, pp 49–92
Google Scholar
Oide S, Moeder W, Krasnoff S, Gibson D, Haas H, Yoshioka K, Turgeon BG (2006) NPS6, encoding a nonribosomal peptide synthetase involved in siderophore-mediated iron metabolism, is a conserved virulence determinant of plant pathogenic ascomycetes. Plant Cell 18:2836–2853
PubMed
Article
CAS
Google Scholar
Elliott CE, Gardiner DM, Thomas G, Cozijnsen A, Van de Wouw A, Howlett BJ (2007) Production of the toxin sirodesmin PL by Leptosphaeria maculans during infection of Brassica napus. Mol Plant Pathol 8:791–802
Article
CAS
PubMed
Google Scholar
Rohlfs M, Albert M, Keller NP, Kempken F (2007) Secondary chemicals protect mould from fungivory. Biol Lett 3:523–525
PubMed
Article
Google Scholar
Tanaka A, Tapper BA, Popay A, Parker EJ, Scott B, Scott B (2005) A symbiosis expressed non-ribosomal peptide synthetase from a mutualistic fungal endophyte of perennial ryegrass confers protection to the symbiotum from insect herbivory. Mol Microbiol 57:1036–1050
PubMed
Article
CAS
Google Scholar
Woloshuk CP, Foutz KR, Brewer JF, Bhatnagar D, Cleveland TE, Payne GA (1994) Molecular characterization of aflR, a regulatory locus for aflatoxin biosynthesis. Appl Environ Microbiol 60:2408–2414
PubMed
CAS
Google Scholar
Georgianna DR, Payne GA (2009) Genetic regulation of aflatoxin biosynthesis: from gene to genome. Fungal Genet Biol 46:113–125
PubMed
Article
CAS
Google Scholar
Proctor R, Hohn T, McCormick S, Desjardins A (1995) Tri6 encodes an unusual zinc finger protein involved in regulation of trichothecene biosynthesis in Fusarium sporotrichiodes. Appl Environ Microbiol 61:1923–1930
PubMed
CAS
Google Scholar
Young C, Bryant M, Christensen M, Tapper B, Bryan G, Scott B (2005) Molecular cloning and genetic analysis of a symbiosis-expressed gene cluster for lolitrem biosynthesis from a mutualistic endophyte of perennial ryegrass. Mol Genet Genomics 274:13–29
PubMed
Article
CAS
Google Scholar
Young CA, Felitti S, Shields K, Spangenberg G, Johnson RD, Bryan GT, Saikia S, Scott B (2006) A complex gene cluster for indole-diterpene biosynthesis in the grass endophyte Neotyphodium lolii. Fungal Genet Biol 43:679–693
PubMed
Article
CAS
Google Scholar
Young CA, Tapper BA, May K, Moon CD, Schardl CL, Scott B (2009) Indole-diterpene biosynthetic capability of Epichloe endophytes as predicted by ltm gene analysis. Appl Environ Microbiol 75(7):2200–2211
PubMed
Article
CAS
Google Scholar
Fleetwood DJ, Scott B, Lane GA, Tanaka A, Johnson RD (2007) A complex ergovaline gene cluster in Epichloe endophytes of grasses. Appl Environ Microbiol 73:2571–2579
PubMed
Article
CAS
Google Scholar
Bok JW, Keller NP (2004) LaeA, a regulator of secondary metabolism in Aspergillus spp. Eukaryot Cell 3:527–535
PubMed
Article
CAS
Google Scholar
Yu JH, Keller N (2005) Regulation of secondary metabolism in filamentous fungi. Annu Rev Phytopathol 43:437–458
PubMed
Article
CAS
Google Scholar
Bok JW, Hoffmeister D, Maggio-Hall LA, Murillo R, Glasner JD, Keller NP (2006) Genomic mining for Aspergillus natural products. Chem Biol 13:31–37
PubMed
Article
CAS
Google Scholar
Hoffmeister D, Keller NP (2007) Natural products of filamentous fungi: enzymes, genes, and their regulation. Nat Prod Rep 24:393–416
PubMed
Article
CAS
Google Scholar
Keller NP, Bok JW, Chung D, Perrin RM, Shwab EK (2006) LaeA, a global regulator of Aspergillus toxins. Med Mycol 44:83–85
Article
CAS
Google Scholar
Perrin RM, Fedorova ND, Bok JW, Cramer RA, Wortman JR, Kim HS, Nierman WC, Keller NP (2007) Transcriptional regulation of chemical diversity in Aspergillus fumigatus by LaeA. PLoS Pathog 3:e50
PubMed
Article
CAS
Google Scholar
Shwab EK, Bok JW, Tribus M, Galehr J, Graessle S, Keller NP (2007) Histone deacetylase activity regulates chemical diversity in Aspergillus. Eukaryot Cell 6:1656–1664
PubMed
Article
CAS
Google Scholar
Williams RB, Henrikson JC, Hoover AR, Lee AE, Cichewicz RH (2008) Epigenetic remodeling of the fungal secondary metabolome. Org Biomol Chem 6:1895–1897
PubMed
Article
CAS
Google Scholar
Henrikson JC, Hoover AR, Joyner PM, Cichewicz RH (2009) A chemical epigenetics approach for engineering the in situ biosynthesis of a cryptic natural product from Aspergillus niger. Org Biomol Chem 7:435–438
PubMed
Article
CAS
Google Scholar
Bergmann S, Schumann J, Scherlach K, Lange C, Brakhage AA, Hertweck C (2007) Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. Nat Chem Biol 3:213–217
PubMed
Article
CAS
Google Scholar
Bayram O, Krappmann S, Ni M, Bok JW, Helmstaedt K, Valerius O, Braus-Stromeyer S, Kwon NJ, Keller NP, Yu JH (2008) VelB/VeA/LaeA complex coordinates light signal with fungal development and secondary metabolism. Science 320:1504–1506
PubMed
Article
CAS
Google Scholar
Kosalková K, Garcia-Estrada C, Ullán RV, Godio RP, Feltrer R, Teijeira F, Mauriz E, Martin JF (2009) The global regulator LaeA controls penicillin biosynthesis, pigmentation and sporulation, but not roquefortine C synthesis in Penicillium chrysogenum. Biochimie 91:214–225
PubMed
Article
CAS
Google Scholar
Rosewich U, Kistler H (2000) Role of horizonal gene transfer in the evolution of fungi. Annu Rev Phytopathol 38:325–363
PubMed
Article
CAS
Google Scholar
Walton JD (2000) Horizontal gene transfer and the evolution of secondary metabolite gene clusters in fungi: an hypothesis. Fungal Genet Biol 30:167–171
PubMed
Article
CAS
Google Scholar
Smith MW, Feng DF, Doolittle RF (1992) Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem Sci 17:489–493
PubMed
Article
CAS
Google Scholar
Patron NJ, Waller RF, Cozijnsen AJ, Straney DC, Gardiner DM, Nierman WC, Howlett BJ (2007) Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes. BMC Evol Biol 7:174
PubMed
Article
CAS
Google Scholar
Khaldi N, Collemare J, Lebrun MH, Wolfe K (2008) Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi. Genome Biol 9:R18
PubMed
Article
CAS
Google Scholar
Carbone I, Ramirez-Prado J, Jakobek J, Horn B (2007) Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster. BMC Evol Biol 7:111
PubMed
Article
CAS
Google Scholar
Ehrlich KC, Yu J, Cotty PJ (2005) Aflatoxin biosynthesis gene clusters and flanking regions. J Appl Microbiol 99:518–527
PubMed
Article
CAS
Google Scholar
Kusumoto K, Nogata Y, Ohta H (2000) Directed deletions in the aflatoxin biosynthesis gene homolog cluster of Aspergillus oryzae. Curr Genet 37:104–111
PubMed
Article
CAS
Google Scholar
Chang PK, Horn BW, Dorner JW (2005) Sequence breakpoints in the aflatoxin biosynthesis gene cluster and flanking regions in nonaflatoxigenic Aspergillus flavus isolates. Fungal Genet Biol 42:914–923
PubMed
Article
CAS
Google Scholar
Kämper J, Kahmann R, Böller M, Ma L-J, Brefort T, Saville BJ, Banuett F, Kronstad JW, Müller O (2006) Insights from the genome of the biotrophic funal plant pathogen Ustilago maydis. Nature 444:97–101
PubMed
Article
CAS
Google Scholar
Hittinger CT, Rokas A, Carroll SB (2004) Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc Natl Acad Sci USA 101:14144–14149
PubMed
Article
CAS
Google Scholar
Wong S, Wolfe KH (2005) Birth of a metabolic gene cluster in yeast by adaptive gene relocation. Nat Genet 37:777–782
PubMed
Article
CAS
Google Scholar
Hall C, Dietrich FS (2007) The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering. Genetics 177:2293–2307
PubMed
Article
CAS
Google Scholar
Cooper TG (1996) Regulation of allantoin catabolism in Saccharomyces cerevisiae. In: Marzluf GA (ed) The mycota III: biochemistry and molecular biology. Springer, Berlin, pp 139–169
Google Scholar
Peoples MB, Gifford RM (1997) Regulation of the transport of nitrogen and carbon in higher plants. In: Dennis DT, Layzell DB, Lefebvre DD, Turpin DH (eds) Plant metabolism. Longman, Singapore, pp 525–538
Google Scholar
Bursell E (1967) The excretion of nitrogen in insects. Adv Insect Physiol 4:33–67
Article
CAS
Google Scholar
Pal C, Hurst LD (2003) Evidence for co-evolution of gene order and recombination rate. Nat Genet 33:392–395
PubMed
Article
CAS
Google Scholar
Hartig A, Simon MM, Schuster T, Gaugherty JR, Yoo HS, Cooper TG (1992) Differentially regulated malate synthase genes participate in carbon and nitrogen metabolism of S.cerevisiae. Nucleic Acids Res 20:5677–5686
PubMed
Article
CAS
Google Scholar
Meneghini MD, Wu M, Madhani HD (2003) Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of heterochromatin. Cell 112:725–736
PubMed
Article
CAS
Google Scholar
Guillemette B, Bataille AR, Gévry N, Adam M, Blanchette M, Robert F, Gaudreau L (2005) Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol 3:2100–2110
Article
CAS
Google Scholar
Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, de Montigny J, Marck C, Neuveglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisrame A, Boyer J, Cattolico L, Confanioleri F, de Daruvar A, Despons L, Fabre E, Fairhed C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequink C, Jaunizux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur IMLMH, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richrd GF, Straub ML, Suleau A, Swennen D, Kekaia F, Wesolowski LM, Westhof E, Wikrth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Boucher C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL (2004) Genome evolution in yeasts. Nature 430:35–44
PubMed
Article
Google Scholar
Andersson SG, Kurland CG (1998) Reductive evolution of resident genomes. Trends Microbiol 6:263–268
PubMed
Article
CAS
Google Scholar
Lawrence JG, Hendrix RW, Casjens S (2001) Where are the pseudogenes in bacterial genomes? Trends Microbiol 9:535–540
PubMed
Article
CAS
Google Scholar
Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honore N, Garnier T, Churcher C, Harris D, Mungall K, Basham D, Brown D, Chillingworth T, Connor R, Davies RM, Devlin K, Duthoy S, Feltwell T, Fraser A, Hamlin N, Holroyd S, Hornsby S, Hornsby T, Jagels K, Lacroix C, Maclean J, Moule S, Murphy L, Oliver K, Quail MA, Rajandream MA, Rutherford KM, Rutter S, Seeger K, Simon S, Simmonds M, Skelton J, Squares R, Squares S, Stevens K, Taylor K, Whitehead S, Woodward JR, Barrell BG (2001) Massive gene decay in the leprosy bacillus. Nature 409:1007–1011
PubMed
Article
CAS
Google Scholar
Xie G, Bonner CA, Jensen RA (2002) Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution and a novel operon for tryptophan recapture. Genome Biol 3
Harrison PM, Gerstein M (2002) Studying genomes through the aeons: protein families, pseudogenes and proteome evolution. J Mol Biol 318:1155–1174
PubMed
Article
CAS
Google Scholar
Moran NA (2003) Tracing the evolution of gene loss in obligate bacterial symbionts. Curr Opin Microbiol 6:512–518
PubMed
Article
CAS
Google Scholar
Bungard RA (2004) Photosynthetic evolution in parasitic plants: insight from the chloroplast genome. BioEssays 26:235–247
PubMed
Article
CAS
Google Scholar
Bell G (1997) The basics of selection. Chapman & Hall, New York
Google Scholar
Kassen R (2002) The experimental evolution of specialists, generalists, and the maintenance of diversity. J Evol Biol 15:173–190
Article
Google Scholar
MacLean RG, Bell G (2002) Experimental adaptive radiation in Pseudomonas. Am Nat 160:569–581
PubMed
Article
Google Scholar
Frey M, Kliem R, Saedler H, Gierl A (1995) Expression of a cytochrome P450 gene family in maize. Mol Gen Genet 246:100–109
PubMed
Article
CAS
Google Scholar
Frey M, Chomet P, Glawischnig E, Stettner C, Grun S, Winklmair A, Eisenreich W, Bacher A, Meeley RB, Briggs SP, Simcox K, Gierl A (1997) Analysis of a chemical plant defense mechanism in grasses. Science 277:696–699
PubMed
Article
CAS
Google Scholar
Gierl A, Frey M (2001) Evolution of benzoxazinone biosynthesis and indole production in maize. Planta 213:493–498
PubMed
Article
CAS
Google Scholar
Qi X, Bakht S, Leggett M, Maxwell C, Melton R, Osbourn A (2004) A gene cluster for secondary metabolism in oat: implications for the evolution of metabolic diversity in plants. Proc Natl Acad Sci USA 101:8233–8238
PubMed
Article
CAS
Google Scholar
Qi X, Bakht S, Qin B, Leggett M, Hemmings A, Mellon F, Eagles J, Werck-Reichart D, Schaller H, Lesot A, Melton R, Osbourn A (2006) A different function for a member of an ancient and highly conserved cytochrome P450 family: from essential sterol to plant defense. Proc Natl Acad Sci USA 103:18848–18853
PubMed
Article
CAS
Google Scholar
Field B, Osbourn AE (2008) Metabolic diversification—independent assembly of operon-like gene clusters in different plants. Science 320:543–547
PubMed
Article
CAS
Google Scholar
Wilderman PR, Xu M, Jin Y, Coates RM, Peters RJ (2004) Identification of syn-imara-7,15-diene synthase reveals functional clustering of terpene synthases involved in rice phytoalexin/allelochemical biosynthesis. Plant Physiol 135:2098–2105
PubMed
Article
CAS
Google Scholar
Shimura K, Okada A, Okada K, Jikumaru Y, Ko KW, Toyomasu T, Sassa T, Hasegawa M, Kodama O, Shibuya N, Koga J, Nojiri H, Yamane H (2007) Identification of a biosynthetic gene cluster in rice for momilactones. J Biol Chem 282:34013–34018
PubMed
Article
CAS
Google Scholar
Papadopoulou K, Melton RE, Leggett M, Daniels MJ, Osbourn AE (1999) Compromised disease resistance in saponin-deficient plants. Proc Natl Acad Sci USA 96:12923–12928
PubMed
Article
CAS
Google Scholar
Barnes JP, Putnam AR (1987) Role of benzoxazinones in allelopathy by rye (Secale cereale L.). J Chem Ecol 13:889–906
Article
CAS
Google Scholar
Niemeyer HM (1988) Hydroxamic acids (4-hydroxy-1, 4-benzoxazin-3-ones), defense chemicals in the Gramineae. Phytochem Anal 27:3349–3358
Article
CAS
Google Scholar
Wu H, Haig T, Pratley J, Deidre L, An M (2001) Allelochemicals in wheat (Triticum aestivum L.): production and exudation of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one. J Chem Ecol 27:1691–1700
PubMed
Article
CAS
Google Scholar
Sicker D, Frey M, Schulz M, Gierl A (2000) Role of natural benzoxazinones in the survival strategy of plants. Int Rev Cytol 198:319–346
PubMed
Article
CAS
Google Scholar
Moraes MCB, Birkett MA, Gordon-Weeks R, Smart LB, Martin JL, Pye BJ, Bromilow R, Pickett JA (2008) cis-Jasmone induces accumulation of defence compounds in wheat, Triticum aestivum. Phytochem Anal 69:9–17
Article
CAS
Google Scholar
Frey M, Stettner C, Paré PW, Schmelz EA, Tumlinson JH, Gierl A (2000) An herbivore elicitor activates the gene for indole emission in maize. Proc Natl Acad Sci USA 26:14801–14806
Article
Google Scholar
von Rad U, Hüttl R, Lottspeich F, Gierl A, Frey M (2001) Two glucosyltransferases are involved in detoxification of benzoxazinoids in maize. Plant J 28:633–642
Article
Google Scholar
Frey M, Huber K, Woong JP, Sicker D, Lindberg P, Meeley RB, Simmons CR, Yalpani N, Gierl A (2003) A 2-oxoglutarate-dependent dioxygenase is integrated in DIMBOA-biosynthesis. Phytochem Anal 62:371–376
Article
CAS
Google Scholar
Jonczyk R, Schmidt H, Osterrieder A, Fiesselmann A, Schullehner K, Haslbeck M, Sicker D, Hofmann D, Yalprani N, Simmons C, Frey M, Gierl A (2008) Elucidation of the final reactions of DIMBOA-glucoside biosynthesis in maize: characterization of Bx6 and Bx7. Plant Physiol 146:1053–1063
PubMed
Article
CAS
Google Scholar
Nomura T, Ishihara A, Imaishi H, Endo T, Ohkawa H, Iwamura H (2002) Molecular characterization and chromosomal localization of cytochrome P450 genes involved in the biosynthesis of cyclic hydroxamic acids in hexaploid wheat. Mol Genet Genomics 267:210–217
PubMed
Article
CAS
Google Scholar
Nomura T, Ishihara A, Imaishi H, Ohkawa H, Endo T, Iwamura H (2003) Rearrangement of the genes for the biosynthesis of benzoxazinones in the evolution of Triticeae species. Planta 77:6–782
Google Scholar
Nomura T, Ishihara A, Iwamura H, Endo T (2007) Molecular characterization of benzoxazinone-deficient mutation in diploid wheat. Phytochem Anal 68:1008–1016
Article
CAS
Google Scholar
Grün S, Frey M, Gierl A (2005) Evolution of the indole alkaloid biosynthesis in the genus Hordeum: distribution of gramine and DIBOA and isolation of the benzoxazinoid biosynthesis genes from Hordeum lechleri. Phytochem Anal 66:1264–1272
Article
CAS
Google Scholar
Sandhu D, Gill KS (2002) Gene-containing regions of wheat and the other grass genomes. Plant Physiol 128:803–811
PubMed
Article
CAS
Google Scholar
Nomura T, Nasuda S, Kawaura K, Ogihara Y, Kato N, Sato F, Kojima T, Toyoda A, Iwamura H, Endo T (2008) Structures of the three homoeologous loci of wheat benzoxazinone biosynthetic genes TaBx3 and TaBx4 and characterization of their promoter sequences. Theor Appl Genet 116:373–381
PubMed
Article
CAS
Google Scholar
Schullehner K, Dick R, Vitzthum F, Schwab W, Brandt W, Frey M, Gierl A (2008) Benzoxazinoid biosynthesis in dicot plants. Phytochem Anal 69:2668–2677
Article
CAS
Google Scholar
Hostettmann KA, Marston A (1995) Saponins. Chemistry and pharmacology of natural products. Cambridge University Press, Cambridge
Google Scholar
Haralampidis K, Bryan G, Qi X, Papadopoulou K, Bakht S, Melton R, Osbourn AE (2001) A new class of oxidosqualene cyclases directs synthesis of antimicrobial phytoprotectants in monocots. Proc Natl Acad Sci USA 98:13431–13436
PubMed
Article
CAS
Google Scholar
Mylona P, Owatworakit A, Papadopoulou K, Jenner H, Qin B, Findlay K, Hill L, Qi X, Bakht S, Melton R, Osbourn A (2008) Sad3 and Sad4 are required for saponin biosynthesis and root development in oat. Plant Cell 20:201–212
PubMed
Article
CAS
Google Scholar
Chappell J (2002) The genetics and molecular genetics of terpene and sterol origami. Curr Opin Plant Biol 5:151–157
PubMed
Article
CAS
Google Scholar
Amoutzias G, Van de Peer Y (2008) Together we stand: genes cluster to coordinate regulation. Dev Cell 14:640–642
PubMed
Article
CAS
Google Scholar
Sproul D, Gilbert N, Bickmore WA (2005) The role of chromatin structure in regulating the expression of clustered genes. Nat Rev Genet 6:775–781
PubMed
Article
CAS
Google Scholar
Michalak P (2008) Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 91:243–248
PubMed
Article
CAS
Google Scholar
Horton R, Wilming L, Rand V, Lovering RC, Bruford EA, Khodiyar VK, Lush MJ, Povey S, Talbot CC, Wright MW, Wain HM, Trowsdale J, Ziegler A, Beck S (2004) Gene map of the extended human MHC. Nat Rev Genet 5:889–899
PubMed
Article
CAS
Google Scholar
Kosak ST, Groudine M (2004) Gene order and dynamic domains. Science 306:644–647
PubMed
Article
CAS
Google Scholar
Singer DS, Mozes E, Kirshner S, Kohn LD (1997) Role of MHC class I molecules in autoimmune disease. Crit Rev Immunol 17:463–468
PubMed
CAS
Google Scholar
Drozina G, Kohoutek J, Jabrane-Ferrat N, Peterlin BM (2005) Expression of MHC II genes. Curr Top Microbiol Immunol 290:147–170
PubMed
Article
CAS
Google Scholar
Dean A (2006) On a chromosome far, far away: LCRs and gene expression. Trends Genet 22:38–45
PubMed
Article
CAS
Google Scholar
Krawczyk M, Seguin-Estevez Q, Leimgruber E, Sperisen P, Schmid C, Bucher P, Reith W (2008) Identification of CIITA regulated genetic module dedicated for antigen presentation. PLoS Genet 4:e1000058
PubMed
Article
CAS
Google Scholar
Galande S, Purbey PK, Notani D, Kumar PP (2007) The third dimension of gene regulation: organization of dynamic chromatin loopscape by SATB1. Curr Opin Genet Dev 17:408–414
PubMed
Article
CAS
Google Scholar
Ottaviani D, Lever E, Mitter R, Jones T, Forshew T, Christova R, Tomazou EM, Rakyan VK, Krawetz SA, Platts AE, Segarane B, Beck S, Sheer D (2008) Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex. Genome Res 18:1778–1786
PubMed
Article
CAS
Google Scholar
Kumar P, Bischof O, Purbey PK, Notani D, Urlaub H, Dejean A, Galande S (2007) Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus. Nat Cell Biol 9:U45–U57
Article
CAS
Google Scholar
Wang J, Shiels C, Sasieni P, Wu PJ, Islam SA, Freemont PS, Sheer D (2004) Promyelocytic leukemia nuclear bodies associate with transcriptionally active genomic regions. J Cell Biol 164:515–526
PubMed
Article
CAS
Google Scholar
Kelley J, Walter L, Trowsdale J (2005) Comparative genomics of major histocompatibility complexes. Immunogenetics 56:683–695
PubMed
Article
CAS
Google Scholar
Yunis EJ, Larsen CE, Fernandez-Vina M, Awdeh ZL, Romero T, Hansen JA, Alper CA (2003) Inheritable variable sizes of DNA stretches in the human MHC: conserved extended haplotypes and their fragments or blocks. Tissue Antigens 62:1–20
PubMed
Article
CAS
Google Scholar
Kasahara M (2007) The 2R hypothesis: an update. Curr Opin Immunol 19:547–552
PubMed
Article
CAS
Google Scholar
Kaufman TC, Lewis R, Wakimoto B (1980) Cytogenetic analysis of chromosome 3 in Drosophila melanogaster: the homoeotic gene complex in polytene chromosome interval 84a-B. Genetics 94:115–133
PubMed
CAS
Google Scholar
Lewis EB (1978) A gene complex controlling segmentation in Drosophila. Nature 276:565–570
PubMed
Article
CAS
Google Scholar
McGinnis W, Garber RL, Wirz J, Kuroiwa A, Gehring WJ (1984) A homologous protein-coding sequence in Drosophila homeotic genes and its conservation in other metazoans. Cell 37:403–408
PubMed
Article
CAS
Google Scholar
Scott MP, Weiner AJ (1984) Structural relationships among genes that control development: sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila. Proc Natl Acad Sci USA 411:5–4119
Google Scholar
Chourrout D, Delsuc F, Chourrout P, Edvardsen RB, Rentzsch F, Renfer E, Jensen MF, Zhu B, de Jong P, Steele RE, Technau U (2006) Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements. Nature 442:684–687
PubMed
Article
CAS
Google Scholar
Seo HC, Edvardsen RB, Maeland AD, Bjordal M, Jensen MF, Hansen A, Flaat M, Weissenbach J, Lehrach H, Wincker P, Reinhardt R, Chourrout D (2004) Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica. Nature 431:67–71
PubMed
Article
CAS
Google Scholar
Deschamps J (2007) Ancestral and recently recruited global control of the Hox genes in development. Curr Opin Genet Dev 17:422–427
PubMed
Article
CAS
Google Scholar
Marletaz F, Holland LZ, Laudet V, Schubert M (2006) Retinoic acid signaling and the evolution of chordates. Int J Biol Sci 2:38–47
PubMed
CAS
Google Scholar
Yekta S, Tabin CJ, Bartel DP (2008) MicroRNAs in the Hox network: an apparent link to posterior prevalence. Nat Rev Genet 9:789–796
PubMed
Article
CAS
Google Scholar
Li Q, Peterson KR, Fang X, Stamatoyannopoulos G (2002) Locus control regions. Blood 100:3077–3086
PubMed
Article
CAS
Google Scholar
Wozniak RJ, Bresnick EH (2008) Epigenetic control of complex loci during erythropoiesis. Curr Top Dev Biol 82:55–83
PubMed
Article
CAS
Google Scholar
Gross DS, Garrard WT (1988) Nuclease hypersensitive sites in chromatin. Annu Rev Biochem 57:159–197
PubMed
Article
CAS
Google Scholar
Spieth J, Brooke G, Kuersten S, Lea K, Blumenthal T (1993) Operons in C. elegans: polycistronic mRNA precursors are processed by trans-splicing of SL2 to downstream coding regions. Cell 73:521–532
PubMed
Article
CAS
Google Scholar
Zorio DAR, Cheng NSN, Blumenthal T, Spieth J (1994) Operons as a common form of chromosomal organization in C. elegans. Nature 372:270–272
PubMed
Article
CAS
Google Scholar
Blumenthal T, Evans D, Link CD, Guffanti A, Lawson D, Thierry-Mieg J, Thierry-Mieg D, Chiu WL, Duke K, Kiraly M, Kim SK (2002) A global analysis of Caenorhabditis elegans operons. Nature 417:851–854
PubMed
Article
CAS
Google Scholar
Blumenthal T, Gleason KS (2003) Caenorhabditis elegans operons: form and function. Nat Rev Genet 4:110–118
Article
CAS
Google Scholar
Lercher MJ, Blumenthal T, Hurst LD (2003) Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res 13:238–243
PubMed
Article
CAS
Google Scholar
Lawrence J (1999) Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr Opin Genet Dev 9:642–648
PubMed
Article
CAS
Google Scholar
Blumenthal T (2005) Trans-splicing and operons. In: The C. elegans Research Community (eds) WormBook, pp 1–9. http://www.wormbook.org
Qian WF, Zhang JZ (2008) Evolutionary dynamics of nematode operons: easy come, slow go. Genome Res 18:412–421
PubMed
Article
CAS
Google Scholar
Ganot P, Kallesoe T, Reinhardt R, Chourrout D, Thompson EM (2004) Spliced-leader RNA trans splicing in a chordate, Oikopleura dioica, with a compact genome. Mol Cell Biol 24:7795–7805
PubMed
Article
CAS
Google Scholar
Satou Y, Hamaguchi M, Takeuchi K, Hastings KEM, Satoh N (2006) Genomic overview of mRNA 5′-leader trans-splicing in the ascidian Ciona intestinalis. Nucleic Acids Res 34:3378–3388
PubMed
Article
CAS
Google Scholar
Satou Y, Mineta K, Ogasawara M, Sasakura Y, Shoguchi E, Ueno K, Yamada L, Matsumoto J, Wasserscheid J, Dewar K, Wiley GB, Macmil SL, Roe BA, Zeller RW, Hastings KE, Lemaire P, Lindquist E, Endo T, Hotta K, Inaba K (2008) Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations. Genome Biol 9:R152
PubMed
Article
CAS
Google Scholar
Marletaz F, Gilles A, Caubit X, Perez Y, Dossat C, Samain S, Gyapay G, Wincker P, Le Parco Y (2008) Chaetognath transcriptome reveals ancestral and unique features among bilaterians. Genome Biol 9:R152
Article
CAS
Google Scholar
Blumenthal T (2004) Operons in eukaryotes. Brief Funct Genomic Proteomic 3:199–211
PubMed
Article
CAS
Google Scholar
Pouchkina-Stantcheva NN, Tunnacliffe A (2005) Spliced leader RNA-mediated trans-splicing in phylum Rotifera. Mol Biol Evol 22:1482–1489
PubMed
Article
CAS
Google Scholar
Andrews J, Smith M, Merakovsky J, Coulson M, Hannan F, Kelly LE (1996) The stoned locus of Drosophila melanogaster produces a dicistronic transcript and encodes two distinct polypeptides. Genetics 143:1699–1711
PubMed
CAS
Google Scholar
Ramanathan P, Guo J, Whitehead RN, Brogna S (2008) The intergenic spacer of the Drosophila Adh-Adhr dicistronic mRNA stimulates internal translation initiation. RNA Biol 5:149–156
PubMed
CAS
Google Scholar
Brogna S, Ashburner M (1997) The Adh-related gene of Drosophila melanogaster is expressed as a functional dicistronic messenger RNA: multigenic transcription in higher organisms. EMBO J 16:2023–2031
PubMed
Article
CAS
Google Scholar
Ben-Shahar Y, Nannapaneni K, Casavant TL, Scheetz TE, Welsh MJ (2007) Eukaryotic operon-like transcription of functionally related genes in Drosophila. Proc Natl Acad Sci USA 104:222–227
PubMed
Article
CAS
Google Scholar
Lee SJ (1991) Expression of growth/differentiation factor 1 in the nervous system: conservation of a bicistronic structure. Proc Natl Acad Sci USA 88:4250–4254
PubMed
Article
CAS
Google Scholar
Eiden LE (1998) The cholinergic gene locus. J Neurochem 70:2227–2240
PubMed
CAS
Article
Google Scholar
Reiss J, Cohen N, Dorche C, Mandel H, Mendel RR, Stallmeyer B, Zabot MT, Dierks T (1998) Mutations in a polycistronic nuclear gene associated with molybdenum cofactor deficiency. Nat Genet 20:51–53
PubMed
Article
CAS
Google Scholar
Wang BH, Shi GZ, Fu YC, Xu XH (2007) Cloning and characterization of a LASS1-GDF1 transcript in rat cerebral cortex: conservation of a bicistronic structure. DNA Seq 18:92–103
PubMed
Article
CAS
Google Scholar
Garcia-Rios M, Fujita T, LaRosa PC, Locy RD, Clithero JM, Bressan RA, Csonka LN (1997) Cloning of a polycistronic cDNA from tomato encoding gamma-glutamyl kinase and gamma-glutamyl phosphate reductase. Proc Natl Acad Sci USA 94:8249–8254
PubMed
Article
CAS
Google Scholar
Muralla R, Chen E, Sweeney C, Gray JA, Dickerman A, Nikolau BJ, Meinke D (2008) A bifunctional locus (BIO3-BIO1) required for biotin biosynthesis in Arabidopsis. Plant Physiol 146:60–73
PubMed
Article
CAS
Google Scholar
Thimmapuram J, Duan H, Liu L, Schuler MA (2005) Bicistronic and fused monocistronic transcripts are derived from adjacent loci in the Arabidopsis genome. RNA 11:128–138
PubMed
Article
CAS
Google Scholar
Chung KR, Daub ME, Ehrenshaft M (2003) Expression of the cercosporin toxin resistance gene (CRG1) as a dicistronic mRNA in the filamentous fungus Cercospora nicotianae. Curr Genet 43:415–424
PubMed
Article
CAS
Google Scholar
Stahl FW, Murray NE (1966) The evolution of gene clusters and genetic circularity in microorganisms. Genetics 53:569–576
PubMed
CAS
Google Scholar
Nei M (1967) Modification of linkage intensity by natural selection. Genetics 57:625–641
PubMed
CAS
Google Scholar
Nei M (2003) Let’s stick together. Heredity 90:411–412
PubMed
Article
CAS
Google Scholar
Krogan NJ (2003) A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Cell 12:1565–1576
CAS
Google Scholar
Lemons D, McGinnis W (2006) Genomic evolution of Hox gene clusters. Science 313:1918–1922
PubMed
Article
CAS
Google Scholar
Kim SI, Bultman SJ, Kiefer CM, Dean A, Bresnick EH (2009) BRG1 requirement for long-range interaction of a locus control region with a downstream promoter. Proc Natl Acad Sci USA 106:2259–2264
PubMed
Article
CAS
Google Scholar
Usdin TB, Eiden LE, Bonner TI, Erickson JD (1995) Molecular biology of the vesicular ACh transporter. Trends Neurosci 18:218–222
PubMed
Article
CAS
Google Scholar
Mugford ST, Qi X, Bakht S, Hill L, Wegel E, Hughes RK, Papadopoulou K, Melton R, Philo M, Sainsbury F, Lomonossoff GP, Deb Roy A, Goss RJM, Osbourn A (2009) A serine carboxypeptidase-like acyltransferase is required for synthesis of antimicrobial compounds and disease resistance in oats. Plant Cell. http://www.plantcell.org/cgi/doi/10.1105/tpc.109.065870