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Volumn 213, Issue , 2015, Pages 88-98

A genomic and transcriptomic approach to investigate the blue pigment phenotype in Pseudomonas fluorescens

Author keywords

Blue mozzarella; Comparative genomics and transcriptomics; Pseudomonas fluorescens

Indexed keywords

INDOLE DERIVATIVE; PIGMENT; TRANSCRIPTOME; TRYPTOPHAN; OXIDOREDUCTASE;

EID: 84943663843     PISSN: 01681605     EISSN: 18793460     Source Type: Journal    
DOI: 10.1016/j.ijfoodmicro.2015.05.024     Document Type: Article
Times cited : (47)

References (62)
  • 1
    • 85015531669 scopus 로고    scopus 로고
    • Extraction of indigo dye (powdered, form) from the leaf of Indigofera tinctoria
    • Adeyanju O., Emmanuel S.E., Akomolafe S.F. Extraction of indigo dye (powdered, form) from the leaf of Indigofera tinctoria. Int. J. Phys. Sci. 2011, 6:137-143.
    • (2011) Int. J. Phys. Sci. , vol.6 , pp. 137-143
    • Adeyanju, O.1    Emmanuel, S.E.2    Akomolafe, S.F.3
  • 2
    • 84862503656 scopus 로고    scopus 로고
    • Gegenees: fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups
    • Agren J., Sundström A., Håfström T., Segerman B. Gegenees: fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups. PLoS ONE 2012, 7:e39107.
    • (2012) PLoS ONE , vol.7 , pp. e39107
    • Agren, J.1    Sundström, A.2    Håfström, T.3    Segerman, B.4
  • 5
    • 2542454687 scopus 로고    scopus 로고
    • Genetic analysis of violacein biosynthesis by Chromobacterium violaceum
    • Antônio R.V., Creczynski-Pasa T.B. Genetic analysis of violacein biosynthesis by Chromobacterium violaceum. Genet. Mol. Res. 2004, 3:85-91.
    • (2004) Genet. Mol. Res. , vol.3 , pp. 85-91
    • Antônio, R.V.1    Creczynski-Pasa, T.B.2
  • 8
    • 0024996111 scopus 로고
    • Biosynthesis of anthraquinones by interspecies cloning of actinorhodin biosynthesis genes in Streptomycetes: clarification of actinorhodin gene functions
    • Bartel P.L., Zhu C.B., Lampel J.S., Dosch D.C., Connors N.C., Strohl W.R., Beale J.M., Floss H.G. Biosynthesis of anthraquinones by interspecies cloning of actinorhodin biosynthesis genes in Streptomycetes: clarification of actinorhodin gene functions. J. Bacteriol. 1990, 172:4816-4826.
    • (1990) J. Bacteriol. , vol.172 , pp. 4816-4826
    • Bartel, P.L.1    Zhu, C.B.2    Lampel, J.S.3    Dosch, D.C.4    Connors, N.C.5    Strohl, W.R.6    Beale, J.M.7    Floss, H.G.8
  • 9
    • 0025581736 scopus 로고
    • The shikimate pathway-a metabolic tree with many branches
    • Bentley R. The shikimate pathway-a metabolic tree with many branches. CRC Crit. Rev. Biochem. Mol. Biol. 1990, 25:307-384.
    • (1990) CRC Crit. Rev. Biochem. Mol. Biol. , vol.25 , pp. 307-384
    • Bentley, R.1
  • 10
    • 0036207217 scopus 로고    scopus 로고
    • Application of metabolic engineering to improve both the production and use of biotech indigo
    • Berry A., Dodge T.C., Pepsin M., Weyler W. Application of metabolic engineering to improve both the production and use of biotech indigo. J. Ind. Microbiol. Biotechnol. 2002, 28:127-133.
    • (2002) J. Ind. Microbiol. Biotechnol. , vol.28 , pp. 127-133
    • Berry, A.1    Dodge, T.C.2    Pepsin, M.3    Weyler, W.4
  • 12
    • 9344269395 scopus 로고    scopus 로고
    • Self-generated diversity produces "insurance effects" in biofilm communities
    • Boles B.R., Thoendel M., Singh P.K. Self-generated diversity produces "insurance effects" in biofilm communities. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:16630-16635.
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 16630-16635
    • Boles, B.R.1    Thoendel, M.2    Singh, P.K.3
  • 13
    • 84855236038 scopus 로고    scopus 로고
    • Triggering the production of the cryptic blue pigment indigoidine from Photorhabdus luminescens
    • Brachmann A.O., Kirchner F., Kegler C., Kinski S.C., Schmitt I., Bode H.B. Triggering the production of the cryptic blue pigment indigoidine from Photorhabdus luminescens. J. Biotechnol. 2012, 157:96-99.
    • (2012) J. Biotechnol. , vol.157 , pp. 96-99
    • Brachmann, A.O.1    Kirchner, F.2    Kegler, C.3    Kinski, S.C.4    Schmitt, I.5    Bode, H.B.6
  • 14
    • 84899053239 scopus 로고    scopus 로고
    • Effect of storage temperature on the microbial composition of ready-to-use vegetables
    • Caldera L., Franzetti L. Effect of storage temperature on the microbial composition of ready-to-use vegetables. Curr. Microbiol. 2014, 68:133-139.
    • (2014) Curr. Microbiol. , vol.68 , pp. 133-139
    • Caldera, L.1    Franzetti, L.2
  • 15
    • 84904877652 scopus 로고    scopus 로고
    • Pepsin-digested bovine lactoferrin prevents Mozzarella cheese blue discoloration caused by Pseudomonas fluorescens
    • Caputo L., Quintieri L., Bianchi D.M., Decastelli L., Monaci L., Visconti A., Baruzzi F. Pepsin-digested bovine lactoferrin prevents Mozzarella cheese blue discoloration caused by Pseudomonas fluorescens. Food Microbiol. 2015, 46:15-24.
    • (2015) Food Microbiol. , vol.46 , pp. 15-24
    • Caputo, L.1    Quintieri, L.2    Bianchi, D.M.3    Decastelli, L.4    Monaci, L.5    Visconti, A.6    Baruzzi, F.7
  • 17
    • 84857188863 scopus 로고    scopus 로고
    • Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data
    • Carver T., Harris S.R., Berriman M., Parkhill J., McQuillan J.A. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 2012, 28:464-469.
    • (2012) Bioinformatics , vol.28 , pp. 464-469
    • Carver, T.1    Harris, S.R.2    Berriman, M.3    Parkhill, J.4    McQuillan, J.A.5
  • 18
    • 77956181142 scopus 로고    scopus 로고
    • Unique features of Erwinia chrysanthemi (Dickeya dadantii) RA3B genes involved in the blue indigoidine production
    • Chu M.K., Lin L.F., Twu C.S., Lin R.H., Lin Y.C., Hsu S.T., Tzeng K.C., Huang H.C. Unique features of Erwinia chrysanthemi (Dickeya dadantii) RA3B genes involved in the blue indigoidine production. Microbiol. Res. 2010, 165:483-495.
    • (2010) Microbiol. Res. , vol.165 , pp. 483-495
    • Chu, M.K.1    Lin, L.F.2    Twu, C.S.3    Lin, R.H.4    Lin, Y.C.5    Hsu, S.T.6    Tzeng, K.C.7    Huang, H.C.8
  • 19
    • 24644503098 scopus 로고    scopus 로고
    • Blast2go: a universal tool for annotation, visualization and analysis in functional genomics research
    • Conesa A., Götz S., García-Gómez J.M., Terol J., Talón M., Robles M. Blast2go: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21:3674-3676.
    • (2005) Bioinformatics , vol.21 , pp. 3674-3676
    • Conesa, A.1    Götz, S.2    García-Gómez, J.M.3    Terol, J.4    Talón, M.5    Robles, M.6
  • 20
    • 77952883471 scopus 로고    scopus 로고
    • Iron uptake and metabolism in pseudomonads
    • Cornelis P. Iron uptake and metabolism in pseudomonads. Appl. Microbiol. Biotechnol. 2010, 86:1637-1645.
    • (2010) Appl. Microbiol. Biotechnol. , vol.86 , pp. 1637-1645
    • Cornelis, P.1
  • 21
    • 77957151956 scopus 로고    scopus 로고
    • SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data
    • Cox M.P., Peterson D.A., Biggs P.J. SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinf. 2010, 11:485.
    • (2010) BMC Bioinf. , vol.11 , pp. 485
    • Cox, M.P.1    Peterson, D.A.2    Biggs, P.J.3
  • 22
    • 84863772202 scopus 로고    scopus 로고
    • Production of the antimicrobial secondary metabolite indigoidine -contributes to competitive surface colonization by the marine roseobacter Phaeobacter sp. strain Y4I
    • Cude W.N., Mooney J., Tavanaei A.A., Hadden M.K., Frank A.M., Gulvik C.A., May A.L., Buchan A. Production of the antimicrobial secondary metabolite indigoidine -contributes to competitive surface colonization by the marine roseobacter Phaeobacter sp. strain Y4I. Appl. Environ. Microbiol. 2012, 78:4771-4780.
    • (2012) Appl. Environ. Microbiol. , vol.78 , pp. 4771-4780
    • Cude, W.N.1    Mooney, J.2    Tavanaei, A.A.3    Hadden, M.K.4    Frank, A.M.5    Gulvik, C.A.6    May, A.L.7    Buchan, A.8
  • 23
    • 0031016611 scopus 로고    scopus 로고
    • Isolation and characterization of the Azospirillum brasilense trpE(G) gene, encoding anthranilate synthase
    • De Troch P., Dosselaere F., Keijers V., de Wilde P., Vanderleyden J. Isolation and characterization of the Azospirillum brasilense trpE(G) gene, encoding anthranilate synthase. Curr. Microbiol. 1997, 34:27-32.
    • (1997) Curr. Microbiol. , vol.34 , pp. 27-32
    • De Troch, P.1    Dosselaere, F.2    Keijers, V.3    de Wilde, P.4    Vanderleyden, J.5
  • 24
    • 84907956140 scopus 로고    scopus 로고
    • Characterization of Gram-negative psychrotrophic bacteria isolated from Italian bulk tank milk
    • Decimo M., Morandi S., Silvetti T., Brasca M. Characterization of Gram-negative psychrotrophic bacteria isolated from Italian bulk tank milk. J. Food Sci. 2014, 79:M2081-M2090.
    • (2014) J. Food Sci. , vol.79 , pp. M2081-M2090
    • Decimo, M.1    Morandi, S.2    Silvetti, T.3    Brasca, M.4
  • 25
    • 84872336795 scopus 로고    scopus 로고
    • Next-generation sequencing: the future of molecular genetics in poultry production and food safety
    • Diaz-Sanchez S., Hanning I., Pendleton S., D'Souza D. Next-generation sequencing: the future of molecular genetics in poultry production and food safety. Poult. Sci. 2012, 92:562-572.
    • (2012) Poult. Sci. , vol.92 , pp. 562-572
    • Diaz-Sanchez, S.1    Hanning, I.2    Pendleton, S.3    D'Souza, D.4
  • 26
    • 0028801011 scopus 로고
    • Formation of indigo and related compounds from indolecarboxylic acids by aromatic acid-degrading bacteria: chromogenic reactions for cloning genes encoding dioxygenases that act on aromatic acids
    • Eaton R.W., Chapman P.J. Formation of indigo and related compounds from indolecarboxylic acids by aromatic acid-degrading bacteria: chromogenic reactions for cloning genes encoding dioxygenases that act on aromatic acids. J. Bacteriol. 1995, 177:6983-6988.
    • (1995) J. Bacteriol. , vol.177 , pp. 6983-6988
    • Eaton, R.W.1    Chapman, P.J.2
  • 27
    • 0017772177 scopus 로고
    • The van urk-Salkowski reagent-a sensitive and specific chromogenic reagent for silica gel thin-layer chromatographic detection and identification of indole-derivatives
    • Ehmann A. The van urk-Salkowski reagent-a sensitive and specific chromogenic reagent for silica gel thin-layer chromatographic detection and identification of indole-derivatives. J. Chromatogr. 1977, 132:267-276.
    • (1977) J. Chromatogr. , vol.132 , pp. 267-276
    • Ehmann, A.1
  • 28
    • 0020612907 scopus 로고
    • Expression of naphthalene oxidation genes in Escherichia coli results in the biosynthesis of indigo
    • Ensley B.D., Ratzkin B., Osslund T.D., Simon M.J., Wackett L.P., Gibson D.T. Expression of naphthalene oxidation genes in Escherichia coli results in the biosynthesis of indigo. Science 1983, 222:167-169.
    • (1983) Science , vol.222 , pp. 167-169
    • Ensley, B.D.1    Ratzkin, B.2    Osslund, T.D.3    Simon, M.J.4    Wackett, L.P.5    Gibson, D.T.6
  • 30
    • 34147139531 scopus 로고    scopus 로고
    • Characterisation of Pseudomonas spp. isolated from foods
    • Franzetti L., Scarpellini M. Characterisation of Pseudomonas spp. isolated from foods. Ann. Microbiol. 2007, 57:39-47.
    • (2007) Ann. Microbiol. , vol.57 , pp. 39-47
    • Franzetti, L.1    Scarpellini, M.2
  • 31
    • 34447296239 scopus 로고    scopus 로고
    • Multilocus sequence analysis of biocontrol fluorescent Pseudomonas spp. producing the antifungal compound 2,4-diacetylphloroglucinol
    • Frapolli M., Défago G., Moënne-Loccoz Y. Multilocus sequence analysis of biocontrol fluorescent Pseudomonas spp. producing the antifungal compound 2,4-diacetylphloroglucinol. Environ. Microbiol. 2007, 9:1939-1955.
    • (2007) Environ. Microbiol. , vol.9 , pp. 1939-1955
    • Frapolli, M.1    Défago, G.2    Moënne-Loccoz, Y.3
  • 32
    • 79959240236 scopus 로고    scopus 로고
    • CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes
    • Galardini M., Biondi E.G., Bazzicalupo M., Mengoni A. CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol. Med. 2011, 21:6-11.
    • (2011) Source Code Biol. Med. , vol.21 , pp. 6-11
    • Galardini, M.1    Biondi, E.G.2    Bazzicalupo, M.3    Mengoni, A.4
  • 33
    • 0026538084 scopus 로고    scopus 로고
    • A study of the incidence of different fluorescent Pseudomonas species and biovars in the microflora of fresh and spoiled meat and fish, raw milk, cheese, soil and water
    • Gennari M., Dragotto F. A study of the incidence of different fluorescent Pseudomonas species and biovars in the microflora of fresh and spoiled meat and fish, raw milk, cheese, soil and water. J. Appl. Bacteriol. 2012, 72:281-288.
    • (2012) J. Appl. Bacteriol. , vol.72 , pp. 281-288
    • Gennari, M.1    Dragotto, F.2
  • 36
    • 84875483479 scopus 로고    scopus 로고
    • Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools
    • Kisand V., Lettieri T. Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools. BMC Genomics 2013, 14:211.
    • (2013) BMC Genomics , vol.14 , pp. 211
    • Kisand, V.1    Lettieri, T.2
  • 38
    • 84911805738 scopus 로고    scopus 로고
    • Differential contributions of two SARP family regulatory genes to indigoidine biosynthesis in Streptomyces lavendulae FRI-5
    • Kurniawan Y.N., Kitani S., Maeda A., Nihira T. Differential contributions of two SARP family regulatory genes to indigoidine biosynthesis in Streptomyces lavendulae FRI-5. Appl. Microbiol. Biotechnol. 2014, 98:9713-9721.
    • (2014) Appl. Microbiol. Biotechnol. , vol.98 , pp. 9713-9721
    • Kurniawan, Y.N.1    Kitani, S.2    Maeda, A.3    Nihira, T.4
  • 39
    • 84862496171 scopus 로고    scopus 로고
    • The effect of iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5
    • Lim C.K., Hassan K.A., Tetu S.G., Loper J.E., Paulsen I.T. The effect of iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5. PLoS ONE 2012, 7:e39139.
    • (2012) PLoS ONE , vol.7 , pp. e39139
    • Lim, C.K.1    Hassan, K.A.2    Tetu, S.G.3    Loper, J.E.4    Paulsen, I.T.5
  • 43
    • 0027478744 scopus 로고
    • Construction of metabolic operons catalyzing the de novo biosynthesis of indigo in Escherichia coli
    • Murdock D., Ensley B.D., Serdar C., Thalen M. Construction of metabolic operons catalyzing the de novo biosynthesis of indigo in Escherichia coli. Biotechnology 1993, 11:381-386.
    • (1993) Biotechnology , vol.11 , pp. 381-386
    • Murdock, D.1    Ensley, B.D.2    Serdar, C.3    Thalen, M.4
  • 44
    • 0031937237 scopus 로고    scopus 로고
    • Indigo formation by aromatic hydrocarbon-degrading bacteria
    • O'Connor K.E., Hartmans S. Indigo formation by aromatic hydrocarbon-degrading bacteria. Biotechnol. Lett. 1998, 20:219-223.
    • (1998) Biotechnol. Lett. , vol.20 , pp. 219-223
    • O'Connor, K.E.1    Hartmans, S.2
  • 45
    • 0030678622 scopus 로고    scopus 로고
    • Indigo formation by microorganisms expressing styrene monooxygenase activity
    • O'Connor K.E., Dobson A.D., Hartmans S. Indigo formation by microorganisms expressing styrene monooxygenase activity. Appl. Environ. Microbiol. 1997, 63:4287-4291.
    • (1997) Appl. Environ. Microbiol. , vol.63 , pp. 4287-4291
    • O'Connor, K.E.1    Dobson, A.D.2    Hartmans, S.3
  • 46
    • 77957948829 scopus 로고    scopus 로고
    • The Pseudomonas story
    • Palleroni N.J. The Pseudomonas story. Environ. Microbiol. 2010, 12:1377-1383.
    • (2010) Environ. Microbiol. , vol.12 , pp. 1377-1383
    • Palleroni, N.J.1
  • 47
    • 77949302729 scopus 로고    scopus 로고
    • Biosynthesis of indigo dye by newly isolated naphthalene-degrading strain Pseudomonas sp. HOB1 and its application in dyeing cotton fabric
    • Pathak H., Madamwar D. Biosynthesis of indigo dye by newly isolated naphthalene-degrading strain Pseudomonas sp. HOB1 and its application in dyeing cotton fabric. Appl. Biochem. Biotechnol. 2010, 160:1616-1626.
    • (2010) Appl. Biochem. Biotechnol. , vol.160 , pp. 1616-1626
    • Pathak, H.1    Madamwar, D.2
  • 48
    • 1542476187 scopus 로고    scopus 로고
    • Rapid Alert System for Food and Feed (RASFF) Annual Report 2010.
    • (2010) Annual Report
  • 49
    • 0036168701 scopus 로고    scopus 로고
    • Characterization of indigoidine biosynthetic genes in Erwinia chrysanthemi and role of this blue pigment in pathogenicity
    • Reverchon S., Rouanet C., Expert D., Nasser W. Characterization of indigoidine biosynthetic genes in Erwinia chrysanthemi and role of this blue pigment in pathogenicity. J. Bacteriol. 2002, 184:654-665.
    • (2002) J. Bacteriol. , vol.184 , pp. 654-665
    • Reverchon, S.1    Rouanet, C.2    Expert, D.3    Nasser, W.4
  • 50
    • 84863510698 scopus 로고    scopus 로고
    • Psychrotrophic bacteria and milk and dairy products quality
    • Samaržija D., Zamberlin Š., Pogačić T. Psychrotrophic bacteria and milk and dairy products quality. Mljekarstvo 2012, 62:77-95.
    • (2012) Mljekarstvo , vol.62 , pp. 77-95
    • Samaržija, D.1    Zamberlin, Š.2    Pogačić, T.3
  • 52
    • 84901417347 scopus 로고    scopus 로고
    • Prokka: rapid prokaryotic genome annotation
    • Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014, 30:2068-2069.
    • (2014) Bioinformatics , vol.30 , pp. 2068-2069
    • Seemann, T.1
  • 55
    • 84873743076 scopus 로고    scopus 로고
    • Next-generation sequencing and its potential impact on food microbial genomics
    • Solieri L., Dakal T.C., Giudici P. Next-generation sequencing and its potential impact on food microbial genomics. Ann. Microbiol. 2012, 63:21-37.
    • (2012) Ann. Microbiol. , vol.63 , pp. 21-37
    • Solieri, L.1    Dakal, T.C.2    Giudici, P.3
  • 56
    • 0014161713 scopus 로고
    • The intracellular blue pigment of Pseudomonas lemonnieri
    • Starr M.P., Knackmuss H.J., Cosens G. The intracellular blue pigment of Pseudomonas lemonnieri. Arch. Mikrobiol. 1967, 59:287-294.
    • (1967) Arch. Mikrobiol. , vol.59 , pp. 287-294
    • Starr, M.P.1    Knackmuss, H.J.2    Cosens, G.3
  • 58
    • 84943663476 scopus 로고    scopus 로고
    • Structural and regulatory genes controlling indigoidine production in Vogesella indigofera: involvement of a peptide synthetase homolog
    • Unpublished.
    • van de Loo, F.J., Keese, P., Llewellyn, D., 1998. Structural and regulatory genes controlling indigoidine production in Vogesella indigofera: involvement of a peptide synthetase homolog. Unpublished. http://getentry.ddbj.nig.ac.jp/getentry/na/AF088856/?filetype=html#cds3.
    • (1998)
    • van de Loo, F.J.1    Keese, P.2    Llewellyn, D.3
  • 60
    • 84884352806 scopus 로고    scopus 로고
    • Use of Pseudomonas spp. for the bioremediation of environmental pollutants: a review
    • Wasi S., Tabrez S., Ahmad M. Use of Pseudomonas spp. for the bioremediation of environmental pollutants: a review. Environ. Monit. Assess. 2013, 185:8147-8155.
    • (2013) Environ. Monit. Assess. , vol.185 , pp. 8147-8155
    • Wasi, S.1    Tabrez, S.2    Ahmad, M.3
  • 61
    • 0141454823 scopus 로고    scopus 로고
    • Ancient origin of the tryptophan operon and the dynamics of evolutionary change
    • Xie G., Keyhani N.O., Bonner C.A., Jensen R.A. Ancient origin of the tryptophan operon and the dynamics of evolutionary change. Microbiol. Mol. Biol. Rev. 2003, 67:303-342.
    • (2003) Microbiol. Mol. Biol. Rev. , vol.67 , pp. 303-342
    • Xie, G.1    Keyhani, N.O.2    Bonner, C.A.3    Jensen, R.A.4
  • 62
    • 84873742882 scopus 로고    scopus 로고
    • An indigoidine biosynthetic gene cluster from Streptomyces chromofuscus ATCC 49982 contains an unusual IndB homologue
    • Yu D., Xu F., Valiente J., Wang S., Zhan J. An indigoidine biosynthetic gene cluster from Streptomyces chromofuscus ATCC 49982 contains an unusual IndB homologue. J. Ind. Microbiol. Biotechnol. 2013, 40:159-168.
    • (2013) J. Ind. Microbiol. Biotechnol. , vol.40 , pp. 159-168
    • Yu, D.1    Xu, F.2    Valiente, J.3    Wang, S.4    Zhan, J.5


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