메뉴 건너뛰기




Volumn 169, Issue 3, 2017, Pages 547-558.e15

Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut

Author keywords

anhydrotetracycline; Bacteroides; gene regulation; gut; inducible promoter; microbiome; sialic acid; synthetic biology

Indexed keywords

DRINKING WATER; SIALIDASE;

EID: 85018499853     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2017.03.045     Document Type: Article
Times cited : (143)

References (58)
  • 1
    • 80051616646 scopus 로고    scopus 로고
    • Inability of Prevotella bryantii to form a functional Shine-Dalgarno interaction reflects unique evolution of ribosome binding sites in Bacteroidetes
    • Accetto, T., Avguštin, G., Inability of Prevotella bryantii to form a functional Shine-Dalgarno interaction reflects unique evolution of ribosome binding sites in Bacteroidetes. PLoS ONE 6 (2011), e22914–e22919.
    • (2011) PLoS ONE , vol.6 , pp. e22914-e22919
    • Accetto, T.1    Avguštin, G.2
  • 3
    • 0034559920 scopus 로고    scopus 로고
    • Analysis of cepA and other Bacteroides fragilis genes reveals a unique promoter structure
    • Bayley, D.P., Rocha, E.R., Smith, C.J., Analysis of cepA and other Bacteroides fragilis genes reveals a unique promoter structure. FEMS Microbiol. Lett. 193 (2000), 149–154.
    • (2000) FEMS Microbiol. Lett. , vol.193 , pp. 149-154
    • Bayley, D.P.1    Rocha, E.R.2    Smith, C.J.3
  • 4
    • 51249093061 scopus 로고    scopus 로고
    • The application of Tet repressor in prokaryotic gene regulation and expression
    • Bertram, R., Hillen, W., The application of Tet repressor in prokaryotic gene regulation and expression. Microb. Biotechnol. 1 (2008), 2–16.
    • (2008) Microb. Biotechnol. , vol.1 , pp. 2-16
    • Bertram, R.1    Hillen, W.2
  • 5
    • 0032170592 scopus 로고    scopus 로고
    • Control of erythropoietin delivery by doxycycline in mice after intramuscular injection of adeno-associated vector
    • Bohl, D., Salvetti, A., Moullier, P., Heard, J.M., Control of erythropoietin delivery by doxycycline in mice after intramuscular injection of adeno-associated vector. Blood 92 (1998), 1512–1517.
    • (1998) Blood , vol.92 , pp. 1512-1517
    • Bohl, D.1    Salvetti, A.2    Moullier, P.3    Heard, J.M.4
  • 6
    • 84913559202 scopus 로고    scopus 로고
    • Modulation of chemical composition and other parameters of the cell at different exponential growth rates
    • Bremer, H., Dennis, P.P., Modulation of chemical composition and other parameters of the cell at different exponential growth rates. Ecosal Plus 3 (2008), 1–49.
    • (2008) Ecosal Plus , vol.3 , pp. 1-49
    • Bremer, H.1    Dennis, P.P.2
  • 7
    • 77954129578 scopus 로고    scopus 로고
    • Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids
    • Bryksin, A.V., Matsumura, I., Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids. Biotechniques 48 (2010), 463–465.
    • (2010) Biotechniques , vol.48 , pp. 463-465
    • Bryksin, A.V.1    Matsumura, I.2
  • 9
    • 84891644827 scopus 로고    scopus 로고
    • Preparation and characterization of metformin hydrochloride loaded-Eudragit®RSPO and Eudragit®RSPO/PLGA nanoparticles
    • Cetin, M., Atila, A., Sahin, S., Vural, I., Preparation and characterization of metformin hydrochloride loaded-Eudragit®RSPO and Eudragit®RSPO/PLGA nanoparticles. Pharm. Dev. Technol. 18 (2013), 570–576.
    • (2013) Pharm. Dev. Technol. , vol.18 , pp. 570-576
    • Cetin, M.1    Atila, A.2    Sahin, S.3    Vural, I.4
  • 10
    • 84962124787 scopus 로고    scopus 로고
    • Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species
    • Chatzidaki-Livanis, M., Geva-Zatorsky, N., Comstock, L.E., Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species. Proc. Natl. Acad. Sci. USA 113 (2016), 3627–3632.
    • (2016) Proc. Natl. Acad. Sci. USA , vol.113 , pp. 3627-3632
    • Chatzidaki-Livanis, M.1    Geva-Zatorsky, N.2    Comstock, L.E.3
  • 14
    • 76749119387 scopus 로고    scopus 로고
    • BLAST-EXPLORER helps you building datasets for phylogenetic analysis
    • Dereeper, A., Audic, S., Claverie, J.M., Blanc, G., BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol. Biol., 10, 2010, 8.
    • (2010) BMC Evol. Biol. , vol.10 , pp. 8
    • Dereeper, A.1    Audic, S.2    Claverie, J.M.3    Blanc, G.4
  • 15
    • 28544451327 scopus 로고    scopus 로고
    • Foundations for engineering biology
    • Endy, D., Foundations for engineering biology. Nature 438 (2005), 449–453.
    • (2005) Nature , vol.438 , pp. 449-453
    • Endy, D.1
  • 17
    • 79955025122 scopus 로고    scopus 로고
    • Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice
    • Goodman, A.L., Kallstrom, G., Faith, J.J., Reyes, A., Moore, A., Dantas, G., Gordon, J.I., Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc. Natl. Acad. Sci. USA 108 (2011), 6252–6257.
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 6252-6257
    • Goodman, A.L.1    Kallstrom, G.2    Faith, J.J.3    Reyes, A.4    Moore, A.5    Dantas, G.6    Gordon, J.I.7
  • 19
    • 84860541398 scopus 로고    scopus 로고
    • Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries
    • Goodman, A.L., Wu, M., Gordon, J.I., Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries. Nat. Protoc. 6 (2011), 1969–1980.
    • (2011) Nat. Protoc. , vol.6 , pp. 1969-1980
    • Goodman, A.L.1    Wu, M.2    Gordon, J.I.3
  • 20
    • 0033852409 scopus 로고    scopus 로고
    • UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition
    • Gourse, R.L., Ross, W., Gaal, T., UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol. Microbiol. 37 (2000), 687–695.
    • (2000) Mol. Microbiol. , vol.37 , pp. 687-695
    • Gourse, R.L.1    Ross, W.2    Gaal, T.3
  • 22
    • 55549088221 scopus 로고    scopus 로고
    • Identification and use of the putative Bacteroides ovatus xylanase promoter for the inducible production of recombinant human proteins
    • Hamady, Z.Z.R., Farrar, M.D., Whitehead, T.R., Holland, K.T., Lodge, J.P.A., Carding, S.R., Identification and use of the putative Bacteroides ovatus xylanase promoter for the inducible production of recombinant human proteins. Microbiology 154 (2008), 3165–3174.
    • (2008) Microbiology , vol.154 , pp. 3165-3174
    • Hamady, Z.Z.R.1    Farrar, M.D.2    Whitehead, T.R.3    Holland, K.T.4    Lodge, J.P.A.5    Carding, S.R.6
  • 23
    • 0032548818 scopus 로고    scopus 로고
    • Stepwise selection of TetR variants recognizing tet operator 4C with high affinity and specificity
    • Helbl, V., Hillen, W., Stepwise selection of TetR variants recognizing tet operator 4C with high affinity and specificity. J. Mol. Biol. 276 (1998), 313–318.
    • (1998) J. Mol. Biol. , vol.276 , pp. 313-318
    • Helbl, V.1    Hillen, W.2
  • 24
    • 0032548989 scopus 로고    scopus 로고
    • Stepwise selection of TetR variants recognizing tet operator 6C with high affinity and specificity
    • Helbl, V., Tiebel, B., Hillen, W., Stepwise selection of TetR variants recognizing tet operator 6C with high affinity and specificity. J. Mol. Biol. 276 (1998), 319–324.
    • (1998) J. Mol. Biol. , vol.276 , pp. 319-324
    • Helbl, V.1    Tiebel, B.2    Hillen, W.3
  • 25
    • 3242701306 scopus 로고    scopus 로고
    • Structure-based design of Tet repressor to optimize a new inducer specificity
    • Henssler, E.M., Scholz, O., Lochner, S., Gmeiner, P., Hillen, W., Structure-based design of Tet repressor to optimize a new inducer specificity. Biochemistry 43 (2004), 9512–9518.
    • (2004) Biochemistry , vol.43 , pp. 9512-9518
    • Henssler, E.M.1    Scholz, O.2    Lochner, S.3    Gmeiner, P.4    Hillen, W.5
  • 26
    • 0028030082 scopus 로고
    • Mechanisms underlying expression of Tn10 encoded tetracycline resistance
    • Hillen, W., Berens, C., Mechanisms underlying expression of Tn10 encoded tetracycline resistance. Annu. Rev. Microbiol. 48 (1994), 345–369.
    • (1994) Annu. Rev. Microbiol. , vol.48 , pp. 345-369
    • Hillen, W.1    Berens, C.2
  • 27
    • 84982272821 scopus 로고    scopus 로고
    • A novel tightly regulated gene expression system for the human intestinal symbiont Bacteroides thetaiotaomicron
    • Horn, N., Carvalho, A.L., Overweg, K., Wegmann, U., Carding, S.R., Stentz, R., A novel tightly regulated gene expression system for the human intestinal symbiont Bacteroides thetaiotaomicron. Front. Microbiol., 7, 2016, 1080.
    • (2016) Front. Microbiol. , vol.7 , pp. 1080
    • Horn, N.1    Carvalho, A.L.2    Overweg, K.3    Wegmann, U.4    Carding, S.R.5    Stentz, R.6
  • 29
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486 (2012), 207–214.
    • (2012) Nature , vol.486 , pp. 207-214
  • 30
    • 1342285086 scopus 로고    scopus 로고
    • Two mutations in the tetracycline repressor change the inducer anhydrotetracycline to a corepressor
    • Kamionka, A., Bogdanska-Urbaniak, J., Scholz, O., Hillen, W., Two mutations in the tetracycline repressor change the inducer anhydrotetracycline to a corepressor. Nucleic Acids Res. 32 (2004), 842–847.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 842-847
    • Kamionka, A.1    Bogdanska-Urbaniak, J.2    Scholz, O.3    Hillen, W.4
  • 31
    • 46049115447 scopus 로고    scopus 로고
    • Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices
    • Koropatkin, N.M., Martens, E.C., Gordon, J.I., Smith, T.J., Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure 16 (2008), 1105–1115.
    • (2008) Structure , vol.16 , pp. 1105-1115
    • Koropatkin, N.M.1    Martens, E.C.2    Gordon, J.I.3    Smith, T.J.4
  • 33
    • 35248894483 scopus 로고    scopus 로고
    • Engineered Tet repressors with recognition specificity for the tetO-4C5G operator variant
    • Krueger, M., Scholz, O., Wisshak, S., Hillen, W., Engineered Tet repressors with recognition specificity for the tetO-4C5G operator variant. Gene 404 (2007), 93–100.
    • (2007) Gene , vol.404 , pp. 93-100
    • Krueger, M.1    Scholz, O.2    Wisshak, S.3    Hillen, W.4
  • 35
    • 0029593631 scopus 로고
    • Thermodynamic analysis of tetracycline-mediated induction of Tet repressor by a quantitative methylation protection assay
    • Lederer, T., Takahashi, M., Hillen, W., Thermodynamic analysis of tetracycline-mediated induction of Tet repressor by a quantitative methylation protection assay. Anal. Biochem. 232 (1995), 190–196.
    • (1995) Anal. Biochem. , vol.232 , pp. 190-196
    • Lederer, T.1    Takahashi, M.2    Hillen, W.3
  • 36
    • 84884411052 scopus 로고    scopus 로고
    • Bacterial colonization factors control specificity and stability of the gut microbiota
    • Lee, S.M., Donaldson, G.P., Mikulski, Z., Boyajian, S., Ley, K., Mazmanian, S.K., Bacterial colonization factors control specificity and stability of the gut microbiota. Nature 501 (2013), 426–429.
    • (2013) Nature , vol.501 , pp. 426-429
    • Lee, S.M.1    Donaldson, G.P.2    Mikulski, Z.3    Boyajian, S.4    Ley, K.5    Mazmanian, S.K.6
  • 39
    • 55249108031 scopus 로고    scopus 로고
    • Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont
    • Martens, E.C., Chiang, H.C., Gordon, J.I., Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 4 (2008), 447–457.
    • (2008) Cell Host Microbe , vol.4 , pp. 447-457
    • Martens, E.C.1    Chiang, H.C.2    Gordon, J.I.3
  • 40
    • 69949168816 scopus 로고    scopus 로고
    • Comparison of Bacteroides thetaiotaomicron and Escherichia coli 16S rRNA gene expression signals
    • Mastropaolo, M.D., Thorson, M.L., Stevens, A.M., Comparison of Bacteroides thetaiotaomicron and Escherichia coli 16S rRNA gene expression signals. Microbiology 155 (2009), 2683–2693.
    • (2009) Microbiology , vol.155 , pp. 2683-2693
    • Mastropaolo, M.D.1    Thorson, M.L.2    Stevens, A.M.3
  • 41
    • 84965042706 scopus 로고    scopus 로고
    • Host-derived sialic acids are an important nutrient source required for optimal bacterial fitness in vivo
    • e02237–e15
    • McDonald, N.D., Lubin, J.B., Chowdhury, N., Boyd, E.F., Host-derived sialic acids are an important nutrient source required for optimal bacterial fitness in vivo. MBio, 7, 2016 e02237–e15.
    • (2016) MBio , vol.7
    • McDonald, N.D.1    Lubin, J.B.2    Chowdhury, N.3    Boyd, E.F.4
  • 42
    • 84938323503 scopus 로고    scopus 로고
    • Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota
    • Mimee, M., Tucker, A.C., Voigt, C.A., Lu, T.K., Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota. Cell Syst. 1 (2015), 62–71.
    • (2015) Cell Syst. , vol.1 , pp. 62-71
    • Mimee, M.1    Tucker, A.C.2    Voigt, C.A.3    Lu, T.K.4
  • 44
    • 0034087676 scopus 로고    scopus 로고
    • Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system
    • Orth, P., Schnappinger, D., Hillen, W., Saenger, W., Hinrichs, W., Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nat. Struct. Biol. 7 (2000), 215–219.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 215-219
    • Orth, P.1    Schnappinger, D.2    Hillen, W.3    Saenger, W.4    Hinrichs, W.5
  • 45
    • 84882267201 scopus 로고    scopus 로고
    • Structural and biochemical characterization of the broad substrate specificity of Bacteroides thetaiotaomicron commensal sialidase
    • Park, K.H., Kim, M.G., Ahn, H.J., Lee, D.H., Kim, J.H., Kim, Y.W., Woo, E.J., Structural and biochemical characterization of the broad substrate specificity of Bacteroides thetaiotaomicron commensal sialidase. Biochim. Biophys. Acta. 1834 (2013), 1510–1519.
    • (2013) Biochim. Biophys. Acta. , vol.1834 , pp. 1510-1519
    • Park, K.H.1    Kim, M.G.2    Ahn, H.J.3    Lee, D.H.4    Kim, J.H.5    Kim, Y.W.6    Woo, E.J.7
  • 46
    • 84862987256 scopus 로고    scopus 로고
    • Development of an IPTG inducible expression vector adapted for Bacteroides fragilis
    • Parker, A.C., Smith, J.C., Development of an IPTG inducible expression vector adapted for Bacteroides fragilis. Plasmid 68 (2012), 86–92.
    • (2012) Plasmid , vol.68 , pp. 86-92
    • Parker, A.C.1    Smith, J.C.2
  • 47
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: discriminating signal peptides from transmembrane regions
    • Petersen, T.N., Brunak, S., von Heijne, G., Nielsen, H., SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8 (2011), 785–786.
    • (2011) Nat. Methods , vol.8 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    von Heijne, G.3    Nielsen, H.4
  • 49
  • 53
    • 84946069451 scopus 로고    scopus 로고
    • UniProt: a hub for protein information
    • UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 43 (2015), D204–D212.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D204-D212
  • 54
    • 84997207176 scopus 로고    scopus 로고
    • Effects of sialic acid modifications on virus binding and infection
    • Wasik, B.R., Barnard, K.N., Parrish, C.R., Effects of sialic acid modifications on virus binding and infection. Trends Microbiol. 24 (2016), 991–1001.
    • (2016) Trends Microbiol. , vol.24 , pp. 991-1001
    • Wasik, B.R.1    Barnard, K.N.2    Parrish, C.R.3
  • 55
    • 84874805852 scopus 로고    scopus 로고
    • Defining the bacteroides ribosomal binding site
    • Wegmann, U., Horn, N., Carding, S.R., Defining the bacteroides ribosomal binding site. Appl. Environ. Microbiol. 79 (2013), 1980–1989.
    • (2013) Appl. Environ. Microbiol. , vol.79 , pp. 1980-1989
    • Wegmann, U.1    Horn, N.2    Carding, S.R.3
  • 57
    • 35448985445 scopus 로고    scopus 로고
    • Bacteroides: the good, the bad, and the nitty-gritty
    • Wexler, H.M., Bacteroides: the good, the bad, and the nitty-gritty. Clin. Microbiol. Rev. 20 (2007), 593–621.
    • (2007) Clin. Microbiol. Rev. , vol.20 , pp. 593-621
    • Wexler, H.M.1
  • 58
    • 40649129275 scopus 로고    scopus 로고
    • Preparation of genomic DNA from bacteria
    • 00:1:2.4:2.4.1–2.4.5
    • Wilson, K., Preparation of genomic DNA from bacteria. Curr. Protoc. Mol. Biol., 2001 00:1:2.4:2.4.1–2.4.5.
    • (2001) Curr. Protoc. Mol. Biol.
    • Wilson, K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.