Engineered microbial biosensors based on bacterial two-component systems as synthetic biotechnology platforms in bioremediation and biorefinery

Microbial Cell Factories

Volumn 16, Issue 1, 2017, Pages

  Ravikumar, Sambandam ^a   Baylon, Mary Grace ^b   Park, Si Jae ^b   Choi, Jong il ^a  

^a Chonnam National University   (South Korea)

^b Ewha Womans University   (South Korea)

Author keywords

Biorefinery; Bioremediation; Biosensor; Genetic circuit; Two component regulatory system

Indexed keywords

CHEMICAL COMPOUND; HEAVY METAL; PROTEIN HISTIDINE KINASE; TRANSCRIPTION FACTOR;

ADSORPTION KINETICS; BACTERIAL PHENOMENA AND FUNCTIONS; BIOENGINEERING; BIOMASS; BIOREFINERY; BIOREMEDIATION; BIOSENSOR; BIOTECHNOLOGICAL PROCEDURES; METABOLIC ENGINEERING; NONHUMAN; POLLUTANT; REGULATORY MECHANISM; REVIEW; SCREENING; TWO COMPONENT REGULATORY SYSTEM; BIOTECHNOLOGY; GENE EXPRESSION REGULATION; GENETIC PROCEDURES; GENETICS; METABOLISM; SIGNAL TRANSDUCTION;

BIODEGRADATION, ENVIRONMENTAL; BIOMASS; BIOSENSING TECHNIQUES; BIOTECHNOLOGY; GENE EXPRESSION REGULATION; HISTIDINE KINASE; METABOLIC ENGINEERING; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

EID: 85018521136     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/s12934-017-0675-z     Document Type: Review

References (68)

1. Wanekaya AK, Chen W, Mulchandani A. Recent biosensing developments in environmental security. J Environ Monit. 2008;10:703-12.
2. Liu X, Germaine KJ, Ryan D, Dowling DN. Development of a GFP-based biosensor for detecting the bioavailability and biodegradation of polychlorinated biphenyls (PCBs). J Environ Eng Landsc. 2007;15:261-8.
3. Lovley DR, Coates JD. Bioremediation of metal contamination. Curr Opin Biotechnol. 1997;8:285-9.
4. Bae W, Wu CH, Kostal J, Mulchandani A, Chen W. Enhanced mercury biosorption by bacterial cells with surface-displayed MerR. Appl Environ Microbiol. 2003;69:3176-80.
5. Harvey BR, Georgiou G, Hayhurst A, Jeong KJ, Iverson BL, Rogers GK. Anchored periplasmic expression, a versatile technology for the isolation of high-affinity antibodies from Escherichia coli-expressed libraries. Proc Natl Acad Sci U S A. 2004;101:9193-8.
6. Lee JS, Shin KS, Pan JG, Kim CJ. Surface-displayed viral antigens on Salmonella carrier vaccine. Nat Biotechnol. 2000;18:645-8.
7. Taschner S, Meinke A, Gabain AV, Boyd AP. Selection of peptide entry motifs by bacterial surface display. Biochem J. 2002;367:393-402.
8. Casino P, Rubio V, Marina A. The mechanism of signal transduction by two-component systems. Curr Opin Struct Biol. 2010;20:763-71.
9. Tropel D, Van Der Meer JR. Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol Mol Biol Rev. 2004;68:474-500.
10. Leonhartsberger S, Huber A, Lottspeich F, Böck A. The hydH/G genes from Escherichia coli code for a zinc and lead responsive two-component regulatory system. J Mol Biol. 2001;307:93-105.
11. Munson GP, Lam DL, Outten FW, O'Halloran TV. Identification of a copper-responsive two-component system on the chromosome of Escherichia coli K-12. J Bacteriol. 2000;182:5864-71.
12. Gupta A, Matsui K, Lo JF, Silver S. Molecular basis for resistance to silver cations in Salmonella. Nat Med. 1999;5:183-8.
13. López-Maury L, García-Domínguez M, Florencio FJ, Reyes JC. A two-component signal transduction system involved in nickel sensing in the cyanobacterium Synechocystis sp. PCC 6803. Mol Microbiol. 2002;43:247-56.
14. Dean CR, Poole K. Expression of the ferric enterobactin receptor (PfeA) of Pseudomonas aeruginosa: involvement of a two-component regulatory system. Mol Microbiol. 1993;8:1095-103.
15. Díaz E, Prieto MA. Bacterial promoters triggering biodegradation of aromatic pollutants. Curr Opin Biotechnol. 2000;11:467-75.
16. Velasco A, Alonso S, Garcia JL, Perera J, Díaz E. Genetic and functional analysis of the styrene catabolic cluster of Pseudomonas sp. strain Y2. J Bacteriol. 1998;180:1063-71.
17. Sagi E, Hever N, Rosen R, Bartolome AJ, Premkumar JR, Ulber R, Lev O, Scheper T, Belkin S. Fluorescence and bioluminescence reporter functions in genetically modified bacterial sensor strains. Sens Actuators B Chem. 2003;90:2-8.
18. Yong YC, Zhong JJ. A genetically engineered whole-cell pigment-based bacterial biosensing system for quantification of N-butyryl homoserine lactone quorum sensing signal. Biosens Bioelectron. 2009;25:41-7.
19. Biran I, Babai R, Levcov K, Rishpon J, Ron EZ. Online and in situ monitoring of environmental pollutants: electrochemical biosensing of cadmium. Environ Microbiol. 2000;2:285-90.
20. Corbisier P, Ji G, Nuyts G, Mergeay M, Silver S. luxAB gene fusions with the arsenic and cadmium resistance operons of Staphylococcus aureus plasmid pI258. FEMS Microbiol Lett. 1993;110:231-8.
21. Ivask A, Hakkila K, Virta M. Detection of organomercurials with sensor bacteria. Anal Chem. 2001;73:5168-71.
22. Selifonova O, Burlage R, Barkay T. Bioluminescent sensors for detection of bioavailable Hg(II) in the environment. Appl Environ Microbiol. 1993;59:3083-90.
23. Tauriainen S, Karp M, Chang W, Virta M. Luminescent bacterial sensor for cadmium and lead. Biosens Bioelectron. 1998;13:931-8.
24. Ravikumar S, Yoo IK, Lee SY, Hong SH. A study on the dynamics of the zraP gene expression profile and its application to the construction of zinc adsorption bacteria. Bioprocess Biosyst Eng. 2011;34:1119-26.
25. Ravikumar S, Yoo IK, Lee SY, Hong SH. Construction of copper removing bacteria through the integration of two-component system and cell surface display. Appl Biochem Biotechnol. 2011;165:1674-81.
26. Grebe TW, Stock J. Bacterial chemotaxis: the five sensors of a bacterium. Curr Biol. 1998;8:R154-7.
27. Skerker JM, Prasol MS, Perchuk BS, Biondi EG, Laub MT. Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis. PLoS Biol. 2005;3:e334.
28. Utsumi R, Brissette RE, Rampersaud A, Forst SA, Oosawa K, Inouye M. Activation of bacterial porin gene expression by a chimeric signal transducer in response to aspartate. Science. 1989;245:1246-9.
29. Baumgartner JW, Kim C, Brissette RE, Inouye M, Park C, Hazelbauer GL. Transmembrane signalling by a hybrid protein: communication from the domain of chemoreceptor Trg that recognizes sugar-binding proteins to the kinase/phosphatase domain of osmosensor EnvZ. J Bacteriol. 1994;176:1157-63.
30. Oh YH, Eom IY, Joo JC, Yu JH, Song BK, Lee SH, Hong SH, Park SJ. Recent advances in development of biomass pretreatment technologies used in biorefinery for the production of bio-based fuels, chemicals and polymers. Korean J Chem Eng. 2015;32:1945-59.
31. Oh YH, Eom GT, Kang KH, Joo JC, Jang YA, Choi JW, Song BK, Lee SH, Park SJ. Construction of heterologous gene expression cassettes for the development of recombinant Clostridium beijerinckii. Bioprocess Biosyst Eng. 2016;39:555-63.
32. Kim S, Jang YS, Ha SC, Ahn JW, Kim EJ, Lim JH, Cho C, Ryu YS, Lee SK, Lee SY, Kim KJ. Redox-switch regulatory mechanism of thiolase from Clostridium acetobutylicum. Nat Commun. 2015;6:8410.
33. Jang YS, Malaviya A, Cho C, Lee J, Lee SY. Butanol production from renewable biomass by Clostridia. Bioresour Technol. 2012;123:653-63.
34. Jojima T, Noburyu R, Sasaki M, Tajima T, Suda M, Yukawa H, Inui M. Metabolic engineering for improved production of ethanol by Corynebacterium glutamicum. Appl Microbiol Biotechnol. 2015;99:1165-72.
35. Gaida SM, Liedtke A, Jentges AH, Engels B, Jennewein S. Metabolic engineering of Clostridium cellulolyticum for the production of n-butanol from crystalline cellulose. Microb Cell Fact. 2016;15:6.
36. Shin JH, Park SH, Oh YH, Choi JW, Lee MH, Cho JS, Jeong KJ, Joo JC, Yu J, Park SJ, Lee SY. Metabolic engineering of Corynebacterium glutamicum for enhanced production of 5-aminovaleric acid. Microb Cell Fact. 2016;15:174.
37. Oh YH, Choi JW, Kim EY, Song BK, Jeong KJ, Park K, Kim IK, Woo HM, Lee SH, Park SJ. Construction of synthetic promoter-based expression cassettes for the production of cadaverine in recombinant Corynebacterium glutamicum. Appl Biochem Biotechnol. 2015;176:2065-75.
38. Choi JW, Yim SS, Lee SH, Kang TJ, Park SJ, Jeong KJ. Enhanced production of gamma-aminobutyrate (GABA) in recombinant Corynebacterium glutamicum by expressing glutamate decarboxylase active in expanded pH range. Microb Cell Fact. 2015;14:21.
39. Park SJ, Kim EY, Noh W, Park HM, Oh YH, Lee SH, Song BK, Jegal J, Lee SY. Metabolic engineering of Escherichia coli for the production of 5-aminovalerate and glutarate as C5 platform chemicals. Metab Eng. 2013;16:42-7.
40. Abdel-Rahman MA, Xiao Y, Tashiro Y, Wang Y, Zendo T, Sakai K, Sonomoto K. Fed-batch fermentation for enhanced lactic acid production from glucose/xylose mixture without carbon catabolite repression. J Biosci Bioeng. 2015;119:153-8.
41. Li Y, Wang X, Ge X, Tian P. High production of 3-hydroxypropionic acid in Klebsiella pneumoniae by systematic optimization of glycerol metabolism. Sci Rep. 2016;6:26932.
42. Choi SY, Park SJ, Kim WJ, Yang JE, Lee H, Shin J, Lee SY. One-step fermentative production of poly(lactate-co-glycolate) from carbohydrates in Escherichia coli. Nat Biotechnol. 2016;34:435-40.
43. Yang JE, Kim JW, Oh YH, Choi SY, Lee H, Park AR, Shin J, Park SJ, Lee SY. Biosynthesis of poly(2-hydroxyisovalerate-co-lactate) by metabolically engineered Escherichia coli. Biotechnol J. 2016;11:1572-85.
44. Chae CG, Kim YJ, Lee SJ, Oh YH, Yang JE, Joo JC, Kang KH, Jang YA, Lee H, Park AR, Song BK, Lee SY, Park SJ. Biosynthesis of poly(2-hydroxybutyrate-co-lactate) in metabolically engineered Escherichia coli. Biotechnol Bioproc Eng. 2016;21:169-74.
45. Park SJ, Jang YA, Noh W, Oh YH, Lee H, David Y, Baylon MG, Shin J, Yang JE, Choi SY, Lee SH, Lee SY. Metabolic engineering of Ralstonia eutropha for the production of polyhydroxyalkanoates from sucrose. Biotechnol Bioeng. 2015;112:638-43.
46. Meng DC, Wang Y, Wu LP, Shen R, Chen JC, Wu Q, Chen GQ. Production of poly(3-hydroxypropionate) and poly(3-hydroxybutyrate-co-3-hydroxypropionate) from glucose by engineering Escherichia coli. Metab Eng. 2015;29:189-95.
47. Zhang S, Liu Y, Bryant DA. Metabolic engineering of Synechococcus sp. PCC 7002 to produce poly-3-hydroxybutyrate and poly-3-hydroxybutyrate-co-4-hydroxybutyrate. Metab Eng. 2015;32:174-83.
48. Kim HS, Oh YH, Jang YA, Kang KH, David Y, Yu JH, Song BK, Choi JI, Chang YK, Joo JC, Park SJ. Recombinant Ralstonia eutropha engineered to utilize xylose and its use for the production of poly(3-hydroxybutyrate) from sunflower stalk hydrolysate solution. Microb Cell Fact. 2016;15:95.
49. Oh YH, Lee SH, Jang YA, Choi JW, Hong KS, Yu JH, Shin J, Song BK, Mastan SG, David Y, Baylon MG, Lee SY, Park SJ. Development of rice bran treatment process and its use for the synthesis of polyhydroxyalkanoates from rice bran hydrolysate solution. Bioresour Technol. 2015;181:283-90.
50. Park SJ, Park JP, Lee SY. Production of poly(3-hydroxybutyrate) from whey by fed-batch culture of recombinant Escherichia coli in a pilot-scale fermenter. Biotechnol Lett. 2002;24:185-9.
51. Kim DY, Yim SC, Lee PC, Lee WG, Lee SY, Chang HN. Batch and continuous fermentation of succinic acid from wood hydrolysate by Mannheimia succiniciproducens MBEL55E. Enzyme Microb Technol. 2004;35:648-53.
52. Saha BC, Nichols NN, Qureshi N, Kennedy GJ, Iten LB, Cotta MA. Pilot scale conversion of wheat straw to ethanol via simultaneous saccharification and fermentation. Bioresour Technol. 2015;175:17-22.
53. Zhang Y, Kumar A, Hardwidge PR, Tanaka T, Kondo A, Vadlani PV. d-lactic acid production from renewable lignocellulosic biomass via genetically modified Lactobacillus plantarum. Biotechnol Prog. 2016;32:271-8.
54. Yang J, Seo SW, Jang S, Shin SI, Lim CH, Roh TY, Jung GY. Synthetic RNA devices to expedite the evolution of metabolite-producing microbes. Nat Commun. 2013;4:1413.
55. Ganesh I, Ravikumar S, Lee SH, Park SJ, Hong SH. Engineered fumarate sensing Escherichia coli based on novel chimeric two-component system. J. Biotechnol. 2013;168:560-6.
56. Ganesh I, Ravikumar S, Yoo IK, Hong SH. Construction of malate-sensing Escherichia coli by introduction of a novel chimeric two-component system. Bioprocess Biosyst Eng. 2015;38:797-804.
57. Ravikumar S, Ganesh I, Maruthamuthu MK, Hong SH. Engineering Escherichia coli to sense acidic amino acids by introduction of a chimeric two-component system. Korean J Chem Eng. 2015;32:2073-7.
58. Ham TS, Lee SK, Keasling JD, Arkin AP. A tightly regulated inducible expression system utilizing the fim inversion recombination switch. Biotechnol Bioeng. 2006;94:1-4.
59. Voigt CA. Genetic parts to program bacteria. Curr Opin Biotechnol. 2006;17:548-57.
60. Yokobayashi Y, Weiss R, Arnold FH. Directed evolution of a genetic circuit. Proc Natl Acad Sci U S A. 2002;99:16587-91.
61. Isaacs FJ, Hasty J, Cantor CR, Collins JJ. Prediction and measurement of an autoregulatory genetic module. Proc Natl Acad Sci USA. 2003;100:7714-9.
62. Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature. 2000;403:339-42.
63. Mandal M, Breaker RR. Gene regulation by riboswitches. Nat Rev Mol Cell Biol. 2004;5:451-63.
64. Guet CC, Elowitz MB, Hsing W, Leibler S. Combinatorial synthesis of genetic networks. Science. 2002;296:1466-70.
65. Zhang F, Keasling J. Biosensors and their applications in microbial metabolic engineering. Trends Microbiol. 2011;19:323-9.
66. Pham VD, Ravikumar S, Lee SH, Hong SH, Yoo IK. Modification of response behavior of zinc sensing HydHG two-component system using a self-activation loop and genomic integration. Bioprocess Biosyst Eng. 2013;36:1185-90.
67. Ravikumar S, Ganesh I, Yoo IK, Hong SH. Construction of a bacterial biosensor for zinc and copper and its application to the development of multifunctional heavy metal adsorption bacteria. Process Biochem. 2012;47:758-65.
68. Maruthamuthu MK, Ganesh I, Ravikumar S, Hong SH. Evaluation of zraP gene expression characteristics and construction of a lead (Pb) sensing and removal system in a recombinant Escherichia coli. Biotechnol Lett. 2015;37:659-64.