-
1
-
-
84938860309
-
Transcription factor-based biosensors enlightened by the analyte
-
1 Fernandez-López, R., Ruiz, R., de la Cruz, F., Moncalián, G., Transcription factor-based biosensors enlightened by the analyte. Front Microbiol, 6, 2015, 648.
-
(2015)
Front Microbiol
, vol.6
, pp. 648
-
-
Fernandez-López, R.1
Ruiz, R.2
de la Cruz, F.3
Moncalián, G.4
-
2
-
-
84889260345
-
A closed-loop synthetic gene circuit for the treatment of diet-induced obesity in mice
-
2 Rössger, K., Charpin-El-Hamri, G., Fussenegger, M., A closed-loop synthetic gene circuit for the treatment of diet-induced obesity in mice. Nat Commun, 2013, 4.
-
(2013)
Nat Commun
, pp. 4
-
-
Rössger, K.1
Charpin-El-Hamri, G.2
Fussenegger, M.3
-
3
-
-
77950676224
-
Self-sufficient control of urate homeostasis in mice by a synthetic circuit
-
3 Kemmer, C., Gitzinger, M., Daoud-El Baba, M., Djonov, V., Stelling, J., Fussenegger, M., Self-sufficient control of urate homeostasis in mice by a synthetic circuit. Nat Biotechnol 28 (2010), 355–360.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 355-360
-
-
Kemmer, C.1
Gitzinger, M.2
Daoud-El Baba, M.3
Djonov, V.4
Stelling, J.5
Fussenegger, M.6
-
4
-
-
84875515904
-
Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis
-
4 Dietrich, J.a., Shis, D.L., Alikhani, A., Keasling, J.D., Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis. ACS Synth Biol 2 (2013), 47–58.
-
(2013)
ACS Synth Biol
, vol.2
, pp. 47-58
-
-
Dietrich, J.A.1
Shis, D.L.2
Alikhani, A.3
Keasling, J.D.4
-
5
-
-
84919359797
-
Evolution-guided optimization of biosynthetic pathways
-
5 Raman, S., Rogers, J.K., Taylor, N.D., Church, G.M., Evolution-guided optimization of biosynthetic pathways. Proc Natl Acad Sci USA, 2014, 10.1073/pnas.1409523111.
-
(2014)
Proc Natl Acad Sci USA
-
-
Raman, S.1
Rogers, J.K.2
Taylor, N.D.3
Church, G.M.4
-
6
-
-
84905668376
-
Improving fatty acids production by engineering dynamic pathway regulation and metabolic control
-
6 Xu, P., Li, L., Zhang, F., Stephanopoulos, G., Koffas, M., Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. Proc Natl Acad Sci USA, 2014, 10.1073/pnas.1406401111.
-
(2014)
Proc Natl Acad Sci USA
-
-
Xu, P.1
Li, L.2
Zhang, F.3
Stephanopoulos, G.4
Koffas, M.5
-
7
-
-
84963568291
-
Genetic circuit design automation
-
aac7341-aac7341
-
7 Nielsen, A.A.K., Der, B.S., Shin, J., Vaidyanathan, P., Paralanov, V., Strychalski, E.A., Ross, D., Densmore, D., Voigt, C.A., Genetic circuit design automation. Science (80), 352, 2016 aac7341-aac7341.
-
(2016)
Science (80)
, vol.352
-
-
Nielsen, A.A.K.1
Der, B.S.2
Shin, J.3
Vaidyanathan, P.4
Paralanov, V.5
Strychalski, E.A.6
Ross, D.7
Densmore, D.8
Voigt, C.A.9
-
8
-
-
84941242926
-
Synthetic biosensors for precise gene control and real-time monitoring of metabolites
-
8 Rogers, J.K., Guzman, C.D., Taylor, N.D., Raman, S., Anderson, K., Church, G.M., Synthetic biosensors for precise gene control and real-time monitoring of metabolites. Nucleic Acids Res, 2015, 10.1093/nar/gkv616.
-
(2015)
Nucleic Acids Res
-
-
Rogers, J.K.1
Guzman, C.D.2
Taylor, N.D.3
Raman, S.4
Anderson, K.5
Church, G.M.6
-
9
-
-
84952978551
-
Transcription factor-based biosensors in biotechnology: current state and future prospects
-
9 Mahr, R., Frunzke, J., Transcription factor-based biosensors in biotechnology: current state and future prospects. Appl Microbiol Biotechnol, 2015, 10.1007/s00253-015-7090-3.
-
(2015)
Appl Microbiol Biotechnol
-
-
Mahr, R.1
Frunzke, J.2
-
10
-
-
84986247556
-
Applications and advances of metabolite biosensors for metabolic engineering
-
10 Liu, D., Evans, T., Zhang, F., Applications and advances of metabolite biosensors for metabolic engineering. Metab Eng 31 (2015), 15–22.
-
(2015)
Metab Eng
, vol.31
, pp. 15-22
-
-
Liu, D.1
Evans, T.2
Zhang, F.3
-
11
-
-
84875521674
-
RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes
-
11 Cipriano, M.J., Novichkov, P.N., Kazakov, A.E., Rodionov, D.A., Arkin, A.P., Gelfand, M.S., Dubchak, I., RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BMC Genom, 14, 2013, 213.
-
(2013)
BMC Genom
, vol.14
, pp. 213
-
-
Cipriano, M.J.1
Novichkov, P.N.2
Kazakov, A.E.3
Rodionov, D.A.4
Arkin, A.P.5
Gelfand, M.S.6
Dubchak, I.7
-
12
-
-
84886739636
-
RegPrecise 3.0 – a resource for genome-scale exploration of transcriptional regulation in bacteria
-
12 Novichkov, P.S., Kazakov, A.E., Ravcheev, D.A., Leyn, S.A., Kovaleva, G.Y., Sutormin, R.A., Kazanov, M.D., Riehl, W., Arkin, A.P., Dubchak, I., et al. RegPrecise 3.0 – a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genom, 14, 2013, 745.
-
(2013)
BMC Genom
, vol.14
, pp. 745
-
-
Novichkov, P.S.1
Kazakov, A.E.2
Ravcheev, D.A.3
Leyn, S.A.4
Kovaleva, G.Y.5
Sutormin, R.A.6
Kazanov, M.D.7
Riehl, W.8
Arkin, A.P.9
Dubchak, I.10
-
13
-
-
84976874666
-
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
-
gkv1156
-
13 Gama-Castro, S., Salgado, H., Santos-Zavaleta, A., Ledezma-Tejeida, D., Muñiz-Rascado, L., García-Sotelo, J.S., Alquicira-Hernández, K., Martínez-Flores, I., Pannier, L., Castro-Mondragón, J.A., et al. RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. Nucleic Acids Res, 44, 2015 gkv1156.
-
(2015)
Nucleic Acids Res
, vol.44
-
-
Gama-Castro, S.1
Salgado, H.2
Santos-Zavaleta, A.3
Ledezma-Tejeida, D.4
Muñiz-Rascado, L.5
García-Sotelo, J.S.6
Alquicira-Hernández, K.7
Martínez-Flores, I.8
Pannier, L.9
Castro-Mondragón, J.A.10
-
14
-
-
58149193224
-
Bionemo: molecular information on biodegradation metabolism
-
14 Carbajosa, G., Trigo, A., Valencia, A., Cases, I., Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Res 37 (2009), D598–D602.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. D598-D602
-
-
Carbajosa, G.1
Trigo, A.2
Valencia, A.3
Cases, I.4
-
15
-
-
84856604046
-
Sensing xenobiotic compounds: lessons from bacteria that face pollutants in the environment
-
Horizon Scientific Press
-
15 de Lorenzo, V., Silva-Rocha, R., Carbajosa, G., Galvão, T.C.C.I., Sensing xenobiotic compounds: lessons from bacteria that face pollutants in the environment. Sensory Mechanisms in Bacteria, 2010, Horizon Scientific Press, 81–105.
-
(2010)
Sensory Mechanisms in Bacteria
, pp. 81-105
-
-
de Lorenzo, V.1
Silva-Rocha, R.2
Carbajosa, G.3
Galvão, T.C.C.I.4
-
16
-
-
84905163367
-
Comparative genomics and evolution of regulons of the LacI-family transcription factors
-
An example of the use of comparative genomic methods and in silico prediction of transcription factor binding sites to reconstruct regulons. Functional information of the genes in the regulon was used to propose effectors for allosteric transcription factors of the LacI family.
-
16• Ravcheev, D.A., Khoroshkin, M.S., Laikova, O.N., Tsoy, O.V., Sernova, N.V., Petrova, S.A., Rakhmaninova, A.B., Novichkov, P.S., Gelfand, M.S., Rodionov, D.A., Comparative genomics and evolution of regulons of the LacI-family transcription factors. Front Microbiol, 5, 2014, 294 An example of the use of comparative genomic methods and in silico prediction of transcription factor binding sites to reconstruct regulons. Functional information of the genes in the regulon was used to propose effectors for allosteric transcription factors of the LacI family.
-
(2014)
Front Microbiol
, vol.5
, pp. 294
-
-
Ravcheev, D.A.1
Khoroshkin, M.S.2
Laikova, O.N.3
Tsoy, O.V.4
Sernova, N.V.5
Petrova, S.A.6
Rakhmaninova, A.B.7
Novichkov, P.S.8
Gelfand, M.S.9
Rodionov, D.A.10
-
17
-
-
84875463123
-
Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum
-
17 Kazanov, M.D., Li, X., Gelfand, M.S., Osterman, A.L., Rodionov, D.A., Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. Nucleic Acids Res 41 (2013), 790–803.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 790-803
-
-
Kazanov, M.D.1
Li, X.2
Gelfand, M.S.3
Osterman, A.L.4
Rodionov, D.A.5
-
18
-
-
84870604440
-
Genome context as a predictive tool for identifying regulatory targets of the TetR family transcriptional regulators
-
18 Ahn, S.K., Cuthbertson, L., Nodwell, J.R., Genome context as a predictive tool for identifying regulatory targets of the TetR family transcriptional regulators. PLoS One, 7, 2012, e50562.
-
(2012)
PLoS One
, vol.7
, pp. e50562
-
-
Ahn, S.K.1
Cuthbertson, L.2
Nodwell, J.R.3
-
19
-
-
84874341859
-
Deglycosylation as a mechanism of inducible antibiotic resistance revealed using a global relational tree for one-component regulators
-
Demonstration of the benefit of using predictions from genetic context coupled with phylogenomics to identify new couples of aTF-effectors. After unravelling one such couple, the author ended up characterizing a new antibiotic resistance mechanism.
-
19• Cuthbertson, L., Ahn, S.K., Nodwell, J.R., Deglycosylation as a mechanism of inducible antibiotic resistance revealed using a global relational tree for one-component regulators. Chem Biol 20 (2013), 232–240 Demonstration of the benefit of using predictions from genetic context coupled with phylogenomics to identify new couples of aTF-effectors. After unravelling one such couple, the author ended up characterizing a new antibiotic resistance mechanism.
-
(2013)
Chem Biol
, vol.20
, pp. 232-240
-
-
Cuthbertson, L.1
Ahn, S.K.2
Nodwell, J.R.3
-
20
-
-
84884753046
-
Metagenomic screening for aromatic compound-responsive transcriptional regulators
-
20 Uchiyama, T., Miyazaki, K., Metagenomic screening for aromatic compound-responsive transcriptional regulators. PLoS ONE, 8, 2013, e75795.
-
(2013)
PLoS ONE
, vol.8
, pp. e75795
-
-
Uchiyama, T.1
Miyazaki, K.2
-
21
-
-
79251580632
-
Design and application of a mevalonate-responsive regulatory protein
-
21 Tang, S.-Y., Cirino, P.C., Design and application of a mevalonate-responsive regulatory protein. Angew Chem Int Ed Engl 50 (2011), 1084–1086.
-
(2011)
Angew Chem Int Ed Engl
, vol.50
, pp. 1084-1086
-
-
Tang, S.-Y.1
Cirino, P.C.2
-
22
-
-
84879999713
-
Screening for enhanced triacetic acid lactone production by recombinant Escherichia coli expressing a designed triacetic acid lactone reporter
-
22 Tang, S.-Y., Qian, S., Akinterinwa, O., Frei, C.S., Gredell, J.A., Cirino, P.C., Screening for enhanced triacetic acid lactone production by recombinant Escherichia coli expressing a designed triacetic acid lactone reporter. J Am Chem Soc 135 (2013), 10099–10103.
-
(2013)
J Am Chem Soc
, vol.135
, pp. 10099-10103
-
-
Tang, S.-Y.1
Qian, S.2
Akinterinwa, O.3
Frei, C.S.4
Gredell, J.A.5
Cirino, P.C.6
-
23
-
-
84935854110
-
Design of an ectoine-responsive AraC mutant and its application in metabolic engineering of ectoine biosynthesis
-
23 Chen, W., Zhang, S., Jiang, P., Yao, J., He, Y., Chen, L., Gui, X., Dong, Z., Tang, S.-Y., Design of an ectoine-responsive AraC mutant and its application in metabolic engineering of ectoine biosynthesis. Metab Eng 30 (2015), 149–155.
-
(2015)
Metab Eng
, vol.30
, pp. 149-155
-
-
Chen, W.1
Zhang, S.2
Jiang, P.3
Yao, J.4
He, Y.5
Chen, L.6
Gui, X.7
Dong, Z.8
Tang, S.-Y.9
-
24
-
-
84916207914
-
Engineering allostery
-
24 Raman, S., Taylor, N., Genuth, N., Fields, S., Church, G.M., Engineering allostery. Trends Genet 30 (2014), 521–528.
-
(2014)
Trends Genet
, vol.30
, pp. 521-528
-
-
Raman, S.1
Taylor, N.2
Genuth, N.3
Fields, S.4
Church, G.M.5
-
25
-
-
84927591028
-
Modular, multi-input transcriptional logic gating with orthogonal LacI/GalR family chimeras
-
25 Shis, D.L., Hussain, F., Meinhardt, S., Swint-Kruse, L., Bennett, M.R., Modular, multi-input transcriptional logic gating with orthogonal LacI/GalR family chimeras. ACS Synth Biol 3 (2014), 645–651.
-
(2014)
ACS Synth Biol
, vol.3
, pp. 645-651
-
-
Shis, D.L.1
Hussain, F.2
Meinhardt, S.3
Swint-Kruse, L.4
Bennett, M.R.5
-
26
-
-
84870607623
-
Novel insights from hybrid LacI/GalR proteins: family-wide functional attributes and biologically significant variation in transcription repression
-
26 Meinhardt, S., Manley, M.W., Becker, N.A., Hessman, J.A., Maher, L.J., Swint-Kruse, L., Novel insights from hybrid LacI/GalR proteins: family-wide functional attributes and biologically significant variation in transcription repression. Nucleic Acids Res 40 (2012), 11139–11154.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 11139-11154
-
-
Meinhardt, S.1
Manley, M.W.2
Becker, N.A.3
Hessman, J.A.4
Maher, L.J.5
Swint-Kruse, L.6
-
27
-
-
84959338997
-
AlloRep. A repository of sequence, structural and mutagenesis data for the LacI/GalR transcription regulators
-
27 Sousa, F.L., Parente, D.J., Shis, D.L., Hessman, J.A., Chazelle, A., Bennett, M.R., Teichmann, S.A., Swint-Kruse, L., AlloRep. A repository of sequence, structural and mutagenesis data for the LacI/GalR transcription regulators. J Mol Biol 428 (2016), 671–678.
-
(2016)
J Mol Biol
, vol.428
, pp. 671-678
-
-
Sousa, F.L.1
Parente, D.J.2
Shis, D.L.3
Hessman, J.A.4
Chazelle, A.5
Bennett, M.R.6
Teichmann, S.A.7
Swint-Kruse, L.8
-
28
-
-
84930999631
-
Rosetta comparative modeling for library design: engineering alternative inducer specificity in a transcription factor
-
28 Jha, R.K., Chakraborti, S., Kern, T.L., Fox, D.T., Strauss, C.E.M., Rosetta comparative modeling for library design: engineering alternative inducer specificity in a transcription factor. Proteins 83 (2015), 1327–1340.
-
(2015)
Proteins
, vol.83
, pp. 1327-1340
-
-
Jha, R.K.1
Chakraborti, S.2
Kern, T.L.3
Fox, D.T.4
Strauss, C.E.M.5
-
29
-
-
84956609810
-
Engineering an allosteric transcription factor to respond to new ligands
-
This project made use and compared libraries obtained through three different strategies to drive LacI specificity toward new chemicals. In addition to computational design with Rosetta, protein-wide single-amino-acid saturation mutagenesis and error-prone PCR, they used a final shuffling step to gather together the best mutations from all strategies.
-
29•• Taylor, N.D., Garruss, A.S., Moretti, R., Chan, S., Arbing, M.A., Cascio, D., Rogers, J.K., Isaacs, F.J., Kosuri, S., Baker, D., et al. Engineering an allosteric transcription factor to respond to new ligands. Nat Methods 13 (2015), 177–183 This project made use and compared libraries obtained through three different strategies to drive LacI specificity toward new chemicals. In addition to computational design with Rosetta, protein-wide single-amino-acid saturation mutagenesis and error-prone PCR, they used a final shuffling step to gather together the best mutations from all strategies.
-
(2015)
Nat Methods
, vol.13
, pp. 177-183
-
-
Taylor, N.D.1
Garruss, A.S.2
Moretti, R.3
Chan, S.4
Arbing, M.A.5
Cascio, D.6
Rogers, J.K.7
Isaacs, F.J.8
Kosuri, S.9
Baker, D.10
-
30
-
-
84942279910
-
Rational protein engineering guided by deep mutational scanning
-
30 Shin, H., Cho, B.-K., Rational protein engineering guided by deep mutational scanning. Int J Mol Sci 16 (2015), 23094–23110.
-
(2015)
Int J Mol Sci
, vol.16
, pp. 23094-23110
-
-
Shin, H.1
Cho, B.-K.2
-
31
-
-
84905217368
-
Deep mutational scanning: a new style of protein science
-
31 Fowler, D.M., Fields, S., Deep mutational scanning: a new style of protein science. Nat Methods 11 (2014), 801–807.
-
(2014)
Nat Methods
, vol.11
, pp. 801-807
-
-
Fowler, D.M.1
Fields, S.2
-
32
-
-
84966298459
-
Engineering transcriptional regulator effector specificity using computational design and in vitro rapid prototyping: developing a vanillin sensor
-
Demonstration of the power of combining structural bioinformatic tools, expert knowledge and cell free transcription-translation assay to develop a biosensor. After screening only 27 variants, the authors identified two aTF exhibiting a specific response to vanillin.
-
32• de los Santos, E.L.C., Meyerowitz, J.T., Mayo, S.L., Murray, R.M., Engineering transcriptional regulator effector specificity using computational design and in vitro rapid prototyping: developing a vanillin sensor. ACS Synth. Biol. 5 (2016), 287–295, 10.1021/acssynbio.5b00090 Demonstration of the power of combining structural bioinformatic tools, expert knowledge and cell free transcription-translation assay to develop a biosensor. After screening only 27 variants, the authors identified two aTF exhibiting a specific response to vanillin.
-
(2016)
ACS Synth. Biol.
, vol.5
, pp. 287-295
-
-
de los Santos, E.L.C.1
Meyerowitz, J.T.2
Mayo, S.L.3
Murray, R.M.4
-
33
-
-
33644956913
-
Surveying biotransformations with à la carte genetic traps: translating dehydrochlorination of lindane (gamma-hexachlorocyclohexane) into lacZ-based phenotypes
-
33 Mohn, W.W., Garmendia, J., Galvao, T.C., de Lorenzo, V., Surveying biotransformations with à la carte genetic traps: translating dehydrochlorination of lindane (gamma-hexachlorocyclohexane) into lacZ-based phenotypes. Environ Microbiol 8 (2006), 546–555.
-
(2006)
Environ Microbiol
, vol.8
, pp. 546-555
-
-
Mohn, W.W.1
Garmendia, J.2
Galvao, T.C.3
de Lorenzo, V.4
-
34
-
-
84919650083
-
Design, construction, and characterization of a set of biosensors for aromatic compounds
-
34 Xue, H., Shi, H., Yu, Z., He, S., Liu, S., Hou, Y., Pan, X., Wang, H., Zheng, P., Cui, C., et al. Design, construction, and characterization of a set of biosensors for aromatic compounds. ACS Synth Biol 3 (2014), 1011–1014.
-
(2014)
ACS Synth Biol
, vol.3
, pp. 1011-1014
-
-
Xue, H.1
Shi, H.2
Yu, Z.3
He, S.4
Liu, S.5
Hou, Y.6
Pan, X.7
Wang, H.8
Zheng, P.9
Cui, C.10
-
35
-
-
84994000776
-
Expanding biosensing abilities through computer-aided design of metabolic pathways
-
This article demonstrates the systematization of both in silico design and in vivo implementation of SEMP to detect new chemicals. Five new biosensors are characterized as example.
-
35•• Libis, V., Delépine, B., Faulon, J.-L., Expanding biosensing abilities through computer-aided design of metabolic pathways. ACS Synth Biol, 2016, 10.1021/acssynbio.5b00225 This article demonstrates the systematization of both in silico design and in vivo implementation of SEMP to detect new chemicals. Five new biosensors are characterized as example.
-
(2016)
ACS Synth Biol
-
-
Libis, V.1
Delépine, B.2
Faulon, J.-L.3
-
36
-
-
84959519771
-
Genetically encoded sensors enable real-time observation of metabolite production
-
This metabolic engineering project took advantage of a SEMP approach to enable real-time monitoring of high value added product formation in E. coli.
-
36•• Rogers, J.K., Church, G.M., Genetically encoded sensors enable real-time observation of metabolite production. Proc Natl Acad Sci USA 113 (2016), 2388–2393 This metabolic engineering project took advantage of a SEMP approach to enable real-time monitoring of high value added product formation in E. coli.
-
(2016)
Proc Natl Acad Sci USA
, vol.113
, pp. 2388-2393
-
-
Rogers, J.K.1
Church, G.M.2
-
37
-
-
84979588132
-
SensiPath: computer-aided design of sensing-enabling metabolic pathways
-
37 Delépine, B., Libis, V., Carbonell, P., Faulon, J.-L., SensiPath: computer-aided design of sensing-enabling metabolic pathways. Nucleic Acids Res, 2016, 10.1093/nar/gkw305.
-
(2016)
Nucleic Acids Res
-
-
Delépine, B.1
Libis, V.2
Carbonell, P.3
Faulon, J.-L.4
-
38
-
-
84877143100
-
Structural explanation for allolactose (lac operon inducer) synthesis by lacZ β-galactosidase and the evolutionary relationship between allolactose synthesis and the lac repressor
-
38 Wheatley, R.W., Lo, S., Jancewicz, L.J., Dugdale, M.L., Huber, R.E., Structural explanation for allolactose (lac operon inducer) synthesis by lacZ β-galactosidase and the evolutionary relationship between allolactose synthesis and the lac repressor. J Biol Chem 288 (2013), 12993–13005.
-
(2013)
J Biol Chem
, vol.288
, pp. 12993-13005
-
-
Wheatley, R.W.1
Lo, S.2
Jancewicz, L.J.3
Dugdale, M.L.4
Huber, R.E.5
-
39
-
-
84962455146
-
Unraveling the specific regulation of the central pathway for anaerobic degradation of 3-methylbenzoate
-
An example of natural SEMP thoroughly characterized in its host and also reproduced in E. coli.
-
39• Juárez, J.F., Liu, H., Zamarro, M.T., McMahon, S., Liu, H., Naismith, J.H., Eberlein, C., Boll, M., Carmona, M., Díaz, E., Unraveling the specific regulation of the central pathway for anaerobic degradation of 3-methylbenzoate. J Biol Chem 290 (2015), 12165–12183 An example of natural SEMP thoroughly characterized in its host and also reproduced in E. coli.
-
(2015)
J Biol Chem
, vol.290
, pp. 12165-12183
-
-
Juárez, J.F.1
Liu, H.2
Zamarro, M.T.3
McMahon, S.4
Liu, H.5
Naismith, J.H.6
Eberlein, C.7
Boll, M.8
Carmona, M.9
Díaz, E.10
-
40
-
-
84904816444
-
From the phosphoenolpyruvate phosphotransferase system to selfish metabolism: a story retraced in Pseudomonas putida
-
40 Pflüger-Grau, K., de Lorenzo, V., From the phosphoenolpyruvate phosphotransferase system to selfish metabolism: a story retraced in Pseudomonas putida. FEMS Microbiol Lett 356 (2014), 144–153.
-
(2014)
FEMS Microbiol Lett
, vol.356
, pp. 144-153
-
-
Pflüger-Grau, K.1
de Lorenzo, V.2
-
41
-
-
84942256331
-
Competitive inhibition can linearize dose-response and generate a linear rectifier
-
41 Savir, Y., Tu, B.P., Springer, M., Competitive inhibition can linearize dose-response and generate a linear rectifier. Cell Syst 1 (2015), 238–245.
-
(2015)
Cell Syst
, vol.1
, pp. 238-245
-
-
Savir, Y.1
Tu, B.P.2
Springer, M.3
-
42
-
-
84965164284
-
The structure of the transcriptional repressor KstR in complex with CoA thioester cholesterol metabolites sheds light on the regulation of cholesterol catabolism in Mycobacterium tuberculosis
-
42 Ho, N.A.T., Dawes, S.S., Crowe, A.M., Casabon, I., Gao, C., Kendall, S.L., Baker, E.N., Eltis, L.D., Lott, J.S., The structure of the transcriptional repressor KstR in complex with CoA thioester cholesterol metabolites sheds light on the regulation of cholesterol catabolism in Mycobacterium tuberculosis. J Biol Chem 291 (2016), 7256–7266.
-
(2016)
J Biol Chem
, vol.291
, pp. 7256-7266
-
-
Ho, N.A.T.1
Dawes, S.S.2
Crowe, A.M.3
Casabon, I.4
Gao, C.5
Kendall, S.L.6
Baker, E.N.7
Eltis, L.D.8
Lott, J.S.9
-
43
-
-
84903485867
-
Deciphering the transcriptional regulation of cholesterol catabolic pathway in mycobacteria: identification of the inducer of KstR repressor
-
43 García-Fernández, E., Medrano, F.J., Galán, B., García, J.L., Deciphering the transcriptional regulation of cholesterol catabolic pathway in mycobacteria: identification of the inducer of KstR repressor. J Biol Chem 289 (2014), 17576–17588.
-
(2014)
J Biol Chem
, vol.289
, pp. 17576-17588
-
-
García-Fernández, E.1
Medrano, F.J.2
Galán, B.3
García, J.L.4
-
44
-
-
84896954234
-
Toward a generalized and high-throughput enzyme screening system based on artificial genetic circuits
-
44 Choi, S., Rha, E., Lee, S.J., Kim, H., Kwon, K., Jeong, Y., Rhee, Y.H., Song, J.J., Kim, H., Lee, S., Toward a generalized and high-throughput enzyme screening system based on artificial genetic circuits. ACS Synth. Biol. 3 (2014), 163–171, 10.1021/sb400112u.
-
(2014)
ACS Synth. Biol.
, vol.3
, pp. 163-171
-
-
Choi, S.1
Rha, E.2
Lee, S.J.3
Kim, H.4
Kwon, K.5
Jeong, Y.6
Rhee, Y.H.7
Song, J.J.8
Kim, H.9
Lee, S.10
-
45
-
-
84868579851
-
High-throughput screening system based on phenolics-responsive transcription activator for directed evolution of organophosphate-degrading enzymes
-
45 Jeong, Y.S., Choi, S.L., Kyeong, H.H., Kim, J.H., Kim, E.J., Pan, J.G., Rha, E., Song, J.J., Lee, S.G., Kim, H.S., High-throughput screening system based on phenolics-responsive transcription activator for directed evolution of organophosphate-degrading enzymes. Protein Eng Des Sel 25 (2012), 725–731.
-
(2012)
Protein Eng Des Sel
, vol.25
, pp. 725-731
-
-
Jeong, Y.S.1
Choi, S.L.2
Kyeong, H.H.3
Kim, J.H.4
Kim, E.J.5
Pan, J.G.6
Rha, E.7
Song, J.J.8
Lee, S.G.9
Kim, H.S.10
-
46
-
-
78149437429
-
Product-induced gene expression, a product-responsive reporter assay used to screen metagenomic libraries for enzyme-encoding genes
-
46 Uchiyama, T., Miyazaki, K., Product-induced gene expression, a product-responsive reporter assay used to screen metagenomic libraries for enzyme-encoding genes. Appl Environ Microbiol 76 (2010), 7029–7035.
-
(2010)
Appl Environ Microbiol
, vol.76
, pp. 7029-7035
-
-
Uchiyama, T.1
Miyazaki, K.2
-
47
-
-
84887778351
-
Novel biosensors based on flavonoid-responsive transcriptional regulators introduced into Escherichia coli
-
47 Siedler, S., Stahlhut, S.G., Malla, S., Maury, J., Neves, A.R., Novel biosensors based on flavonoid-responsive transcriptional regulators introduced into Escherichia coli. Metab Eng 21 (2014), 2–8.
-
(2014)
Metab Eng
, vol.21
, pp. 2-8
-
-
Siedler, S.1
Stahlhut, S.G.2
Malla, S.3
Maury, J.4
Neves, A.R.5
-
48
-
-
0015527295
-
lac Repressor–operator interaction. VI. The natural inducer of the lac operon
-
48 Jobe, A., Bourgeois, S., lac Repressor–operator interaction. VI. The natural inducer of the lac operon. J Mol Biol 69 (1972), 397–408.
-
(1972)
J Mol Biol
, vol.69
, pp. 397-408
-
-
Jobe, A.1
Bourgeois, S.2
-
49
-
-
1342343002
-
Role of benzylsuccinate in the induction of the tutE tutFDGH gene complex of T. aromatica strain T1
-
49 Coschigano, P.W., Bishop, B.J., Role of benzylsuccinate in the induction of the tutE tutFDGH gene complex of T. aromatica strain T1. FEMS Microbiol Lett 231 (2004), 261–266.
-
(2004)
FEMS Microbiol Lett
, vol.231
, pp. 261-266
-
-
Coschigano, P.W.1
Bishop, B.J.2
-
50
-
-
84896817067
-
Characterization of LgnR, an IclR family transcriptional regulator involved in the regulation of L-gluconate catabolic genes in Paracoccus sp. 43P
-
50 Shimizu, T., Nakamura, A., Characterization of LgnR, an IclR family transcriptional regulator involved in the regulation of L-gluconate catabolic genes in Paracoccus sp. 43P. Microbiology 160 (2014), 623–634.
-
(2014)
Microbiology
, vol.160
, pp. 623-634
-
-
Shimizu, T.1
Nakamura, A.2
-
51
-
-
84862249243
-
Characterization of FerC, a MarR-type transcriptional regulator, involved in transcriptional regulation of the ferulate catabolic operon in Sphingobium sp. strain SYK-6
-
51 Kasai, D., Kamimura, N., Tani, K., Umeda, S., Abe, T., Fukuda, M., Masai, E., Characterization of FerC, a MarR-type transcriptional regulator, involved in transcriptional regulation of the ferulate catabolic operon in Sphingobium sp. strain SYK-6. FEMS Microbiol Lett 332 (2012), 68–75.
-
(2012)
FEMS Microbiol Lett
, vol.332
, pp. 68-75
-
-
Kasai, D.1
Kamimura, N.2
Tani, K.3
Umeda, S.4
Abe, T.5
Fukuda, M.6
Masai, E.7
-
52
-
-
84861203670
-
Anaerobic p-coumarate degradation by Rhodopseudomonas palustris and identification of CouR, a MarR repressor protein that binds p-coumaroyl coenzyme A
-
52 Hirakawa, H., Schaefer, A.L., Greenberg, E.P., Harwood, C.S., Anaerobic p-coumarate degradation by Rhodopseudomonas palustris and identification of CouR, a MarR repressor protein that binds p-coumaroyl coenzyme A. J Bacteriol 194 (2012), 1960–1967.
-
(2012)
J Bacteriol
, vol.194
, pp. 1960-1967
-
-
Hirakawa, H.1
Schaefer, A.L.2
Greenberg, E.P.3
Harwood, C.S.4
-
53
-
-
84902180011
-
Benzoate metabolism intermediate benzoyl coenzyme A affects gentisate pathway regulation in Comamonas testosteroni
-
53 Chen, D.-W., Zhang, Y., Jiang, C.-Y., Liu, S.-J., Benzoate metabolism intermediate benzoyl coenzyme A affects gentisate pathway regulation in Comamonas testosteroni. Appl Environ Microbiol 80 (2014), 4051–4062.
-
(2014)
Appl Environ Microbiol
, vol.80
, pp. 4051-4062
-
-
Chen, D.-W.1
Zhang, Y.2
Jiang, C.-Y.3
Liu, S.-J.4
-
54
-
-
80052322974
-
Phenylacetyl coenzyme A is an effector molecule of the TetR family transcriptional repressor PaaR from Thermus thermophilus HB8
-
54 Sakamoto, K., Agari, Y., Kuramitsu, S., Shinkai, A., Phenylacetyl coenzyme A is an effector molecule of the TetR family transcriptional repressor PaaR from Thermus thermophilus HB8. J Bacteriol 193 (2011), 4388–4395.
-
(2011)
J Bacteriol
, vol.193
, pp. 4388-4395
-
-
Sakamoto, K.1
Agari, Y.2
Kuramitsu, S.3
Shinkai, A.4
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