615
Views
12
CrossRef citations to date
0
Altmetric
Review Articles

Conventional genetic manipulation of desulfurizing bacteria and prospects of using CRISPR-Cas systems for enhanced desulfurization activity

, , &
Pages 300-320 | Received 24 Dec 2019, Accepted 15 May 2020, Published online: 12 Jun 2020

References

  • Abbasian F, Lockington R, Mallavarapu M, Naidu R. 2015. A comprehensive review of aliphatic hydrocarbon biodegradation by bacteria. Appl Biochem Biotechnol. 176(3):670–699.
  • Abin-Fuentes A, Mohamed ME-S, Wang DI, Prather KL. 2013. Exploring the mechanism of biocatalyst inhibition in microbial desulfurization. Appl Environ Microbiol. 79(24):7807–7817.
  • Adlakha J, Singh P, Ram SK, Kumar M, Singh MP, Singh D, Sahai V, Srivastava P. 2016. Optimization of conditions for deep desulfurization of heavy crude oil and hydrodesulfurized diesel by Gordonia sp. IITR100. Fuel. 184:761–769.
  • Adli M. 2018. The CRISPR tool kit for genome editing and beyond. Nat Commun. 9(1):1911.
  • Aggarwal S, Karimi I, Kilbane Ii JJ, Lee DY. 2012. Roles of sulfite oxidoreductase and sulfite reductase in improving desulfurization by Rhodococcus erythropolis. Mol Biosyst. 8(10):2724–2732.
  • Akhtar N, Akhtar K, Ghauri MA. 2018. Biodesulfurization of thiophenic compounds by a 2-hydroxybiphenyl-resistant Gordonia sp. HS126-4N carrying dszABC genes. Curr Microbiol. 75(5):597–597.
  • Akhtar N, Ghauri MA, Akhtar K. 2016a. Dibenzothiophene desulfurization capability and evolutionary divergence of newly isolated bacteria. Arch Microbiol. 198(6):509–519.
  • Akhtar N, Ghauri MA, Akhtar K. 2016b. Exploring coal biodesulfurization potential of a novel organic sulfur metabolizing Rhodococcus spp.(Eu-32)–a case study. Geomicrobiol J. 33(6):468–472.
  • Alves L, Paixão SM, Pacheco R, Ferreira AF, Silva CM. 2015. Biodesulfurization of fossil fuels: energy, emissions and cost analysis. RSC Adv. 5(43):34047–34057.
  • Aparicio T, de Lorenzo V, Martinez-Garcia E. 2018. CRISPR/Cas9-based counterselection boosts recombineering efficiency in Pseudomonas putida. Biotechnol J. 13(5):e1700161
  • Bachmann RT, Johnson AC, Edyvean RGJ. 2014. Biotechnology in the petroleum industry: An overview. Int Biodeterior Biodegradation. 86:225–237.
  • Barbosa ACC, Neves RPP, Sousa SF, Ramos MJ, Fernandes PA. 2018. Mechanistic studies of a flavin monooxygenase: sulfur oxidation of dibenzothiophenes by DszC. ACS Catal. 8(10):9298–9311.
  • Bhanjadeo MM, Rath K, Gupta D, Pradhan N, Biswal SK, Mishra BK, Subudhi U. 2018. Differential desulfurization of dibenzothiophene by newly identified MTCC strains: Influence of operon array. PLoS One. 13(3):e0192536.
  • Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, Marraffini LA. 2013. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 41(15):7429–7437.
  • Boniek D, Figueiredo D, dos Santos AFB, de Resende Stoianoff MA. 2015. Biodesulfurization: a mini review about the immediate search for the future technology. Clean Techn Environ Policy. 17(1):29–37.
  • Borgne SL, Quintero R. 2003. Biotechnological processes for the refining of petroleum. Fuel Process Technol. 81(2):155–169.
  • Chen S, Zhao C, Liu Q, Zang M, Liu C, Zhang Y. 2018. Thermophilic biodesulfurization and its application in oil desulfurization. Appl Microbiol Biotechnol. 102(21):9015–9089.
  • Cho S, Shin J, Cho BK. 2018. Applications of CRISPR/Cas system to bacterial metabolic engineering. IJMS. 19(4):1089.
  • Coco WM, Levinson WE, Crist MJ, Hektor HJ, Darzins A, Pienkos PT, Squires CH, Monticello DJ. 2001. DNA shuffling method for generating highly recombined genes and evolved enzymes. Nat Biotechnol. 19(4):354–359.
  • da Gama Ferreira R, Azzoni AR, Freitas S. 2018. Techno-economic analysis of the industrial production of a low-cost enzyme using E. coli: the case of recombinant β-glucosidase. Biotechnol Biofuels. 11:81.
  • Debabov VG. 2010. Microbial desulfurization of motor fuel. Appl Biochem Microbiol. 46(8):733–738.
  • Dejaloud A, Habibi A. 2019. Bioenergetic aspects of dibenzothiophene desulfurization by growing cells of Ralstonia eutropha. Pollution. 5:709–719.
  • Dejaloud A, Vahabzadeh F, Habibi A. 2017. Ralstonia eutropha as a biocatalyst for desulfurization of dibenzothiophene. Bioprocess Biosyst Eng. 40(7):969–980.
  • Delorenzo DM, Rottinghaus AG, Henson WR, Moon TS. 2018. Molecular toolkit for gene expression control and genome modification in Rhodococcus opacus PD630. ACS Synth Biol. 7(2):727–738.
  • Ding W, Weng H, Du G, Chen J, Kang Z. 2017. 5-Aminolevulinic acid production from inexpensive glucose by engineering the C4 pathway in Escherichia coli. J Ind Microbiol Biotechnol. 44(8):1127–1135.
  • Dong C, Fontana J, Patel A, Carothers JM, Zalatan JG. 2018. Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria. Nat Commun. 9(1):2489.
  • Eberhardt F, Aguirre A, Paoletti L, Hails G, Braia M, Ravasi P, Peiru S, Menzella HG. 2018. Pilot-scale process development for low-cost production of a thermostable biodiesel refining enzyme in Escherichia coli. Bioprocess Biosyst Eng. 41(4):555–564.
  • Ferreira P, Sousa SF, Fernandes PA, Ramos MJ. 2017. Improving the catalytic power of the DszD enzyme for the biodesulfurization of crude oil and derivatives. Chemistry. 23(68):17231–17241.
  • Fokum E, Zabed HM, Guo Q, Yun J, Yang M, Pang H, An Y, Li W, Qi X. 2019. Metabolic engineering of bacterial strains using CRISPR/Cas9 systems for biosynthesis of value-added products. Food Biosci. 28:125–132.
  • Furuya T, Takahashi S, Ishii Y, Kino K, Kirimura K. 2004. Cloning of a gene encoding flavin reductase coupling with dibenzothiophene monooxygenase through coexpression screening using indigo production as selective indication. Biochem Biophys Res Commun. 313(3):570–575.
  • Galán B, Díaz E, García JL. 2000. Enhancing desulfurization by engineering a flavin reductase‐encoding gene cassette in recombinant biocatalysts. Environ Microbiol. 2:687–694.
  • Gallagher JR, Olson ES, Stanley DC. 1993. Microbial desulfurization of dibenzothiophene: a sulfur-specific pathway. FEMS Microbiol Lett. 107(1):31–35.
  • Gallardo ME, Ferrández A, De Lorenzo V, García JL, Diaz E. 1997. Designing recombinant Pseudomonas strains to enhance biodesulfurization. J Bacteriol. 179(22):7156–7160.
  • Gray KA, Mrachko GT, Squires CH. 2003. Biodesulfurization of fossil fuels. Curr Opin Microbiol. 6(3):229–235.
  • Gray KA, Pogrebinsky OS, Mrachko GT, Xi L, Monticello DJ, Squires CH. 1996. Molecular mechanisms of biocatalytic desulfurization of fossil fuels. Nat Biotechnol. 14(13):1705–1709.
  • Gunther NW, Nunez A, Fett W, Solaiman DK. 2005. Production of rhamnolipids by Pseudomonas chlororaphis, a nonpathogenic bacterium. Appl Environ Microbiol. 71(5):2288–2293.
  • Guo D, Kong S, Zhang L, Pan H, Wang C, Liu Z. 2018. Biosynthesis of advanced biofuel farnesyl acetate using engineered Escherichia coli. Bioresour Technol. 269:577–580.
  • Hasan Z, Jeon J, Jhung SH. 2012. Oxidative desulfurization of benzothiophene and thiophene with WOx/ZrO2 catalysts: effect of calcination temperature of catalysts. J Hazard Mater. 205–206:216–221.
  • Heo MJ, Jung HM, Um J, Lee SW, Oh MK. 2017. Controlling citrate synthase expression by CRISPR/Cas9 genome editing for n-butanol production in Escherichia coli. ACS Synth Biol. 6(2):182–189.
  • Hirasawa K, Ishii Y, Kobayashi M, Koizumi K, Maruhashi K. 2001. Improvement of desulfurization activity in Rhodococcus erythropolis KA2-5-1 by genetic engineering. Biosci Biotechnol Biochem. 65(2):239–246.
  • Hullahalli K, Rodrigues M, Nguyen UT, Palmer K. 2018. An attenuated CRISPR-Cas system in Enterococcus faecalis permits DNA acquisition. MBio. 9(3):e 00414–e 00418.
  • Ibrahim E, Jones KD, Taylor KE, Hosseney EN, Mills PL, Escudero JM. 2018. Recombinant E. coli cellulases, β-glucosidase, and polygalacturonase convert a citrus processing waste into biofuel precursors. ACS Sustainable Chem Eng. 6(6):7304–7312.
  • Ishii Y, Ohshiro T, Aoi Y, Suzuki M, Izumi Y. 2000. Identification of the gene encoding a NAD(P)H-flavin oxidoreductase coupling with dibenzothiophene (DBT)-desulfurizing enzymes from the DBT-nondesulfurizing bacterium Paenibacillus polymyxa A-1. J Biosci Bioeng. 90(2):220–222.
  • Izumi Y, Ohshiro T. 2001. Purification and characterization of enzymes involved in desulfurization of dibezothiophene in fossil fuels. J Mol Catal B Enzym. 11(4–6):1061–1064.
  • Javadli R, de Klerk A. 2012. Desulfurization of heavy oil. Appl Petrochem Res. 1(1–4):3–19.
  • Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA. 2013. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol. 31(3):233–239.
  • Jiang Y, Chen B, Duan C, Sun B, Yang J, Yang S. 2015. Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl Environ Microbiol. 81(7):2506–2514.
  • Jiang C, Li L, Yang Y, Xing J, Liu H, Cheng J. 2002. Effect of surfactants on microbial removal of organic sulfur in diesel oil. Chin J Proc Eng. 2:122–126.
  • Kamali N, Tavallaie M, Bambai B, Karkhane AA, Miri M. 2010. Site-directed mutagenesis enhances the activity of NADH-FMN oxidoreductase (DszD) activity of Rhodococcus erythropolis. Biotechnol Lett. 32(7):921–927.
  • Kayser K, Cleveland L, Park H-S, Kwak J-H, Kolhatkar A, Kilbane J. 2002. Isolation and characterization of a moderate thermophile, Mycobacterium phlei GTIS10, capable of dibenzothiophene desulfurization. Appl Microbiol Biotechnol. 59(6):737–746.
  • Khosravinia S, Mahdavi MA, Gheshlaghi R, Dehghani H. 2018. Characterization of truncated dsz operon responsible for dibenzothiophene biodesulfurization in Rhodococcus sp. FUM94. Appl Biochem Biotechnol. 184(3):885–896.
  • Khosravinia S, Mahdavi MA, Gheshlaghi R, Dehghani H, Rasekh B. 2018. Construction and characterization of a new recombinant vector to remove sulfate repression of dsz promoter transcription in biodesulfurization of dibenzothiophene. Front Microbiol. 9:1578–1578.
  • Kilbane JJ. 2006. Microbial biocatalyst developments to upgrade fossil fuels. Curr Opin Biotechnol. 17(3):305–314.
  • Kim SK, Han GH, Seong W, Kim H, Kim SW, Lee DH, Lee SG. 2016. CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production. Metab Eng. 38:228–240.
  • Kirimura K, Harada K, Iwasawa H, Tanaka T, Iwasaki Y, Furuya T, Ishii Y, Kino K. 2004. Identification and functional analysis of the genes encoding dibenzothiophene-desulfurizing enzymes from thermophilic bacteria. Appl Microbiol Biotechnol. 65(6):703–713.
  • Knott GJ, Doudna JA. 2018. CRISPR-Cas guides the future of genetic engineering. Science. 361(6405):866–869.
  • Konishi M, Kishimoto M, Omasa T, Katakura Y, Shioya S, Ohtake H. 2005. Effect of sulfur sources on specific desulfurization activity of Rhodococcus erythropolis KA2-5-1 in exponential fed-batch culture. J Biosci Bioeng. 99(3):259–263.
  • Langner T, Kamoun S, Belhaj K. 2018. CRISPR crops: plant genome editing toward disease resistance. Annu Rev Phytopathol. 56:479–512.
  • Liang L, Liu R, Garst AD, Lee T, Nogue VSI, Beckham GT, Gill RT. 2017. CRISPR enabled trackable genome engineering for isopropanol production in Escherichia coli. Metab Eng. 41:1–10.
  • Li L, Liao Y, Luo Y, Zhang G, Liao X, Zhang W, Zheng S, Han S, Lin Y, Liang S. 2019. Improved efficiency of the desulfurization of oil sulfur compounds in Escherichia coli using a combination of desensitization engineering and DszC overexpression. ACS Synth Biol. 8(6):1441–1451.
  • Li G-q, Li S-s, Zhang M-l, Wang J, Zhu L, Liang F-l, Liu R-l, Ma T. 2008. Genetic rearrangement strategy for optimizing the dibenzothiophene biodesulfurization pathway in Rhodococcus erythropolis. Appl Environ Microbiol. 74(4):971–976.
  • Li G-Q, Ma T, Li S-S, Li H, Liang F-L, Liu R-L. 2007. Improvement of dibenzothiophene desulfurization activity by removing the gene overlap in the dsz operon. Biosci Biotechnol Biochem. 71(4):849–854.
  • Li GQ, Ma T, Li JH, Li H, Liu RL. 2006. Co-expression of Rhodococcus sp. DS-3 dszABC and dszD gene with incompatible plasmids in Escherichia coli. Acta Microbiol Sin. 46:275–279.
  • Li Y, Peng N. 2019. Endogenous CRISPR-Cas system-based genome editing and antimicrobials: review and prospects. Front Microbiol. 10:2247–2471.
  • Li H, Shen CR, Huang CH, Sung LY, Wu MY, Hu YC. 2016. CRISPR-Cas9 for the genome engineering of cyanobacteria and succinate production. Metab Eng. 38:293–302.
  • Liu JL, Goldman ER, Zabetakis D, Walper SA, Turner KB, Shriver-Lake LC, Anderson GP. 2015. Enhanced production of a single domain antibody with an engineered stabilizing extra disulfide bond. Microb Cell Fact. 14:158.
  • Ma T. 2010. The desulfurization pathway in Rhodococcus. In: Alvarez HM, editor. Biology of Rhodococcus. Springer-Verlag Berlin and Heidelberg GmbH & Co; p. 207–230.
  • Maass D, Todescato D, Moritz D, Oliveira JV, Oliveira D, De Souza AU, Souza SG. 2015. Desulfurization and denitrogenation of heavy gas oil by Rhodococcus erythropolis ATCC 4277. Bioprocess Biosyst Eng. 38(8):1447–1453.
  • Maghsoudi S, Kheirolomoom A, Vossoughi M, Tanaka E, Katoh S. 2000. Selective desulfurization of dibenzothiophene by newly isolated Corynebacterium sp. strain P32C1. Biochem Eng J. 5(1):11–16.
  • Ma T, Li G, Li J, Liang F, Liu R. 2006. Desulfurization of dibenzothiophene by Bacillus subtilis recombinants carrying dszABC and dszD genes. Biotechnol Lett. 28(14):1095–1100.
  • Marella ER, Holkenbrink C, Siewers V, Borodina I. 2018. Engineering microbial fatty acid metabolism for biofuels and biochemicals. Curr Opin Biotechnol. 50:39–46.
  • Marisch K, Bayer K, Cserjan-Puschmann M, Luchner M, Striedner G. 2013. Evaluation of three industrial Escherichia coli strains in fed-batch cultivations during high-level SOD protein production. Microb Cell Fact. 12:58.
  • Marshall R, Maxwell CS, Collins SP, Jacobsen T, Luo ML, Begemann MB, Gray BN, January E, Singer A, He Y, et al. 2018. Rapid and scalable characterization of CRISPR technologies using an E. coli cell-free transcription-translation system . Mol Cell. 69(1):146–157.
  • Martínez I, El-Said Mohamed M, Santos VE, García JL, García-Ochoa F, Díaz E. 2017. Metabolic and process engineering for biodesulfurization in Gram-negative bacteria. J Biotechnol. 262:47–55.
  • Martínez I, García JL, Díaz E. 2017. Genetic engineering for removal of sulfur from fuel aromatic heterocycles. In: Lee SY, editor. Consequences of microbial interactions with hydrocarbons, oils, and lipids: production of fuels and chemicals. Cham: Springer International Publishing; p. 183–204.
  • Martínez I, Mohamed ME-S, Rozas D, García JL, Díaz E. 2016. Engineering synthetic bacterial consortia for enhanced desulfurization and revalorization of oil sulfur compounds. Metab Eng. 35:46–54.
  • Martinez I, Gao H, Bennett GN, San K-Y. 2018. High yield production of four-carbon dicarboxylic acids by metabolically engineered Escherichia coli. J Ind Microbiol Biotechnol. 45(1):53–60.
  • Matsui T, Hirasawa K, Koizumi K-i, Maruhashi K, Kurane R. 2001. Effect of dszD gene expression on benzothiophene degradation of Rhodococcus sp. strain T09. Process Biochem. 37(1):31–34.
  • Matsui T, Hirasawa K, Koizumi K-i, Maruhashi K, Kurane R. 2001. Optimization of the copy number of dibenzothiophene desulfurizing genes to increase the desulfurization activity of recombinant Rhodococcus sp. Biotechnol Lett. 23(20):1715–1718.
  • Matsui T, Hirasawa K, Konishi J, Tanaka Y, Maruhashi K, Kurane R. 2001. Microbial desulfurization of alkylated dibenzothiophene and alkylated benzothiophene by recombinant Rhodococcus sp. strain T09. Appl Microbiol Biotechnol. 56(1–2):196–200.
  • Matsui T, Noda K-I, Tanaka Y, Maruhashi K, Kurane R. 2002. Recombinant Rhodococcus sp. strain T09 Can desulfurize DBT in the presence of inorganic sulfate. Curr Microbiol. 45(4):240–244.
  • Meesala L, Balomajumder C, Chatterjee S, Roy P. 2008. Biodesulfurization of dibenzothiophene using recombinant Pseudomonas strain. J Chem Technol Biotechnol. 83(3):294–298.
  • Mohebali G, Ball AS. 2008. Biocatalytic desulfurization (BDS) of petrodiesel fuels. Microbiol (Reading, Engl). 154(Pt 8):2169–2183.
  • Monticello DJ. 2000. Biodesulfurization and the upgrading of petroleum distillates. Curr Opin Biotechnol. 11(6):540–546.
  • Mougiakos I, Bosma EF, Ganguly J, van der Oost J, van Kranenburg R. 2018. Hijacking CRISPR-Cas for high-throughput bacterial metabolic engineering: advances and prospects. Curr Opin Biotechnol. 50:146–157.
  • Mougiakos I, Mohanraju P, Bosma EF, Vrouwe V, Finger Bou M, Naduthodi MIS, Gussak A, Brinkman RBL, van Kranenburg R, van der Oost J. 2017. Characterizing a thermostable Cas9 for bacterial genome editing and silencing. Nat Commun. 8(1):1647.
  • Nakade S, Yamamoto T, Sakuma T. 2017. Cas9, Cpf1 and C2c1/2/3-What's next? Bioengineered. 8(3):265–273.
  • Nazari F, Kefayati M-E, Raheb J. 2017. Isolation, identification, and characterization of a novel chemolithoautotrophic bacterium with high potential in biodesulfurization of natural or industrial gasses and biogas. Energ Source Part A. 39(10):971–977.
  • Noda K, Watanabe K, Maruhashi K. 2003. Recombinant Pseudomonas putida carrying both the dsz and hcu genes can desulfurize dibenzothiophene in n-tetradecane. Biotechnol Lett. 25(14):1147–1150.
  • Noda K-i, Watanabe K, Maruhashi K. 2002. Cloning of a rhodococcal promoter using a transposon for dibenzothiophene biodesulfurization. Biotechnol Lett. 24(22):1875–1882.
  • Nuhu AA. 2013. Bio-catalytic desulfurization of fossil fuels: a mini review. Rev Environ Sci Biotechnol. 12(1):9–23.
  • Ohshiro T, Ishii Y, Matsubara T, Ueda K, Izumi Y, Kino K, Kirimura K. 2005. Dibenzothiophene desulfurizing enzymes from moderately thermophilic bacterium Bacillus subtilis WU-S2B: purification, characterization and overexpression. J Biosci Bioeng. 100(3):266–273.
  • Ohshiro T, Ohkita R, Takikawa T, Manabe M, Lee WC, Tanokura M, Izumi Y. 2007. Improvement of 2'-hydroxybiphenyl-2-sulfinate desulfinase, an enzyme involved in the dibenzothiophene desulfurization pathway, from Rhodococcus erythropolis KA2-5-1 by site-directed mutagenesis . Biosci Biotechnol Biochem. 71(11):2815–2821.
  • Omori T, Monna L, Saiki Y, Kodama T. 1992. Desulfurization of dibenzothiophene by Corynebacterium sp. strain SY1. Appl Environ Microbiol. 58(3):911–915.
  • Onaka T, Konishi J, Ishii Y, Maruhashi K. 2001. Desulfurization characteristics of thermophilic Paenibacillus sp. strain A11-2 against asymmetrically alkylated dibenzothiophenes. J Biosci Bioeng. 92(2):193–196.
  • Pan J, Wu F, Wang J, Yu L, Khayyat NH, Stark BC, Kilbane JJ. 2013. Enhancement of desulfurization activity by enzymes of the Rhodococcus dsz operon through coexpression of a high sulfur peptide and directed evolution. Fuel. 112:385–390.
  • Papizadeh M, Roayaei Ardakani M, Motamedi H. 2017. Growth-phase dependent biodesulfurization of dibenzothiophene by Enterobacter sp. strain NISOC-03. Pollution. 3:101–111.
  • Park H-S, Kayser KJ, Kwak J-H, Kilbane JJ. 2004. Heterologous gene expression in Thermus thermophilus: beta-galactosidase, dibenzothiophene monooxygenase, PNB carboxy esterase, 2-aminobiphenyl-2,3-diol dioxygenase, and chloramphenicol acetyl transferase . J Ind Microbiol Biotechnol. 31(4):189–197.
  • Porgar S, Rahmanian N. 2015. Hydrodesulfurization of crude oil over Co-Mo catalysts in a slurry reactor. J Multidiscip Eng Sci Technol. 2:1205–1211.
  • Porto B, Maass D, Oliveira JV, de Oliveira D, Yamamoto CI, Ulson de Souza AA, Ulson de Souza SMAG. 2018. Heavy gas oil biodesulfurization using a low-cost bacterial consortium. J Chem Technol Biotechnol. 93(8):2359–2363.
  • Raheb J, Hajipour MJ. 2011. The stable rhamnolipid biosurfactant production in genetically engineered Pseudomonas strain reduced energy consumption in biodesulfurization. Energy Sourc A Recovery Util Environ Eff. 33(22):2113–2121.
  • Raheb J, Hajipour MJ, Saadati M, Rasekh B, Memari B. 2009. The Enhancement of biodesulfurization activity in a novel indigenous engineered Pseudomonas putida. Iran Biomed J. 13:207–213.
  • Raheb JH, Javad M, Memari B. 2010. Increasing of biodesulfurization activity of newly recombinant Pseudomonas aeruginosa ATCC 9027 by cloning the flavin reductase gene. Int J Biotechnol Biochem. 6:219–229.
  • Raheb SNJ, Karkhane AA, Yakhchali B, Flint K. 2005. Designing a new recombinant strain with additional copy number of dsz cluster to enhance biodesulfurization activity in Pseudomonas aeruginosa ATCC 9027. Iran J Sci Technol. 29:195–199.
  • Raheb J, Memari B, Hajipour MJ. 2011. Gene-manipulated desulfurizing strain Pseudomonas putida reduced energy consuming in the biodesulfurization process. Energy Sourc A Recovery Util Environ Eff. 33(21):2018–2026.
  • Rangra S, Kabra M, Gupta V, Srivastava P. 2018. Improved conversion of dibenzothiophene into sulfone by surface display of dibenzothiophene monooxygenase (DszC) in recombinant Escherichia coli. J Biotechnol. 287:59–67.
  • Rashidi L, Dariani JT, Khosravi-Darani K. 2009. Biodesulfurization: biochemical and genetic engineering aspects, dynamic biochemistry. Dyn Biochem Process Biotechnol Mol Biol. 1:24–31.
  • Reichmuth DS, Blanch HW, Keasling JD. 2004. Dibenzothiophene biodesulfurization pathway improvement using diagnostic GFP fusions. Biotechnol Bioeng. 88(1):94–99.
  • Reichmuth DS, Hittle JL, Blanch HW, Keasling JD. 2000. Biodesulfurization of dibenzothiophene in Escherichia coli is enhanced by expression of a Vibrio harveyi oxidoreductase gene. Biotechnol Bioeng. 67(1):72–79.
  • Rousset F, Cui L, Siouve E, Depardieu F, Bikard D. 2018. Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. BioRxiv. 308916.
  • Rude MA, Schirmer A. 2009. New microbial fuels: a biotech perspective. Curr Opin Microbiol. 12(3):274–281.
  • Rütering M, Cress BF, Schilling M, Rühmann B, Koffas MAG, Sieber V, Schmid J. 2017. Tailor-made exopolysaccharides—CRISPR-Cas9 mediated genome editing in Paenibacillus polymyxa. Synthetic Biol. 2(1):ysx007.
  • Sadare O, Obazu F, Daramola M. 2017. Biodesulfurization of petroleum distillates—current status, opportunities and future challenges. Environments. 4:85.
  • Santos SCC, Alviano DS, Alviano CS, Pádula M, Leitão AC, Martins OB, Ribeiro CMS, Sassaki MYM, Matta CPS, Bevilaqua J, et al. 2006. Characterization of Gordonia sp. strain F.5.25.8 capable of dibenzothiophene desulfurization and carbazole utilization. Appl Microbiol Biotechnol. 71(3):355–362.
  • Schwartz C, Curtis N, Löbs AK, Wheeldon I. 2018. Multiplexed CRISPR activation of cryptic sugar metabolism enables Yarrowia lipolytica growth on cellobiose. Biotechnol J. 13(9):e1700584.
  • Shapiro RS, Chavez A, Collins JJ. 2018. CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms. Nat Rev Microbiol. 16(6):333–339.
  • Shavandi M, Sadeghizadeh M, Zomorodipour A, Khajeh K. 2009. Biodesulfurization of dibenzothiophene by recombinant Gordonia alkanivorans RIPI90A. Bioresour Technol. 100(1):475–479.
  • Shavandi M, Soheili M, Zareian S, Akbari N, Khajeh K. 2013. The gene cloning, overexpression, purification, and characterization of dibenzothiophene monooxygenase and desulfinase from Gordonia alkanivorans RIPI90A. J Pet Sci Technol. 3:57–64.
  • Soleimani M, Bassi A, Margaritis A. 2007. Biodesulfurization of refractory organic sulfur compounds in fossil fuels. Biotechnol Adv. 25(6):570–596.
  • Soriano BG, Ng JW, Cui L, Becavin C, Bikard D. 2018. Genome-wide CRISPR-Cas9 screen in E. coli identifies design rules for efficient targeting. BioRxiv. 308148.
  • Stanislaus A, Marafi A, Rana MS. 2010. Recent advances in the science and technology of ultra low sulfur diesel (ULSD) production. Catal Today. 153(1–2):1–68.
  • Su T, Su J, Liu S, Zhang C, He J, Huang Y, Xu S, Gu L. 2018. Structural and biochemical characterization of bdsA from Bacillus subtilis WU-S2B, a key enzyme in the “4S” desulfurization Pathway. Front Microbiol. 9:231.
  • Takada M, Nomura N, Okada H, Nakajima-Kambe T, Nakahara T, Uchiyama H. 2005. De-repression and comparison of oil-water separation activity of the dibenzothiophene desulfurizing bacterium, Mycobacterium sp. G3. Biotechnol Lett. 27(12):871–874.
  • Tan SZ, Reisch CR, Prather KLJ. 2018. A robust CRISPR interference gene repression system in Pseudomonas. J Bacteriol. 200(7):e00575–17.
  • Tao F, Liu Y, Luo Q, Su F, Xu Y, Li F, Yu B, Ma C, Xu P. 2011. Novel organic solvent-responsive expression vectors for biocatalysis: application for development of an organic solvent-tolerant biodesulfurizing strain. Bioresour Technol. 102(20):9380–9387.
  • Tao F, Yu B, Xu P, Ma CQ. 2006. Biodesulfurization in biphasic systems containing organic solvents. Appl Environ Microbiol. 72(7):4604–4609.
  • Tong Y, Robertsen HL, Blin K, Weber T, Lee SY. 2018. CRISPR-Cas9 toolkit for Actinomycete genome editing. In: Jensen MK, Keasling JD, editors. Synthetic metabolic pathways. New York (NY): Humana Press; p. 163–184.
  • Wang J, Butler RR, III,Wu F, Pombert J-F, Kilbane JJ, II, Stark BC. 2017. Enhancement of microbial biodesulfurization via genetic engineering and adaptive evolution. PLoS One. 12(1):e0168833.
  • Wang X, Cheng W, Yang Q, Niu H, Liu Q, Liu Y, Gao M, Xu M, Xu A, Liu S, et al. 2018. Contribution of the Kodama and 4S pathways to the dibenzothiophene biodegradation in different coastal wetlands under different C/N ratios. J Environ Sci. 69:217–226.
  • Wang J, Davaadelger B, Salazar JK, Butler RR, Pombert J-F, Kilbane JJ, Stark BC. 2015. Isolation and characterization of an interactive culture of two Paenibacillus species with moderately thermophilic desulfurization ability. Biotechnol Lett. 37(11):2201–2211.
  • Wang B, Hu Q, Zhang Y, Shi R, Chai X, Liu Z, Shang X, Zhang Y, Wen T. 2018. A RecET-assisted CRISPR-Cas9 genome editing in Corynebacterium glutamicum. Microb Cell Fact. 17(1):63.
  • Wang MD, Li W, Wang DH, Shi Y. 2004. Desulfurization of dibenzothiophene by a newly isolated Corynebacterium sp. ZD-1 in aqueous phase. J Environ Sci (China). 16:1011–1015.
  • Wang W, Ma T, Lian K, Zhang Y, Tian H, Ji K, Li G. 2013. Genetic analysis of benzothiophene biodesulfurization pathway of Gordonia terrae strain C-6. PLoS One. 8(12):e84386.
  • Wang J, Zhang C, Feng B. 2020. The rapidly advancing Class 2 CRISPR-Cas technologies: A customizable toolbox for molecular manipulations. J Cell Mol Med. 24(6):3256–3270.
  • Wu J, Du G, Chen J, Zhou J. 2015. Enhancing flavonoid production by systematically tuning the central metabolic pathways based on a CRISPR interference system in Escherichia coli. Sci Rep. 5:13477.
  • Wu MY, Sung LY, Li H, Huang CH, Hu YC. 2017. Combining CRISPR and CRISPRi systems for metabolic engineering of E. coli and 1,4-BDO biosynthesis. ACS Synth Biol. 6(12):2350–2361.
  • Wu T, Ye L, Zhao D, Li S, Li Q, Zhang B, Bi C, Zhang X. 2017. Membrane engineering - a novel strategy to enhance the production and accumulation of β-carotene in Escherichia coli . Metab Eng. 43(Pt A):85–91.
  • Xia J, Wang L, Zhu JB, Sun CJ, Zheng MG, Zheng L, Lou YH, Shi L. 2016. Expression of Shewanella frigidimarina fatty acid metabolic genes in E. coli by CRISPR/cas9-coupled lambda red recombineering. Biotechnol Lett. 38(1):117–122.
  • Xiong B, Li Z, Liu L, Zhao D, Zhang X, Bi C. 2018. Genome editing of Ralstonia eutropha using an electroporation-based CRISPR-Cas9 technique. Biotechnol Biofuels. 11:172.
  • Xu P, Gu Q, Wang W, Wong L, Bower AG, Collins CH, Koffas MA. 2013. Modular optimization of multi-gene pathways for fatty acids production in E. coli. Nat Commun. 4:1409.
  • Xu P, Ranganathan S, Fowler ZL, Maranas CD, Koffas MA. 2011. Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. Metab Eng. 13(5):578–587.
  • Yan H, Kishimoto M, Omasa T, Katakura Y, Suga K-I, Okumura K, Yoshikawa O. 2000. Increase in desulfurization activity of Rhodococcus erythropolis KA2-5-1 using ethanol feeding. J Biosci Bioeng. 89(4):361–366.
  • Yang JE, Park SJ, Kim WJ, Kim HJ, Kim BJ, Lee H, Shin J, Lee SY. 2018. One-step fermentative production of aromatic polyesters from glucose by metabolically engineered Escherichia coli strains. Nat Commun. 9(1):79.
  • Zerbini F, Zanella I, Fraccascia D, Konig E, Irene C, Frattini LF, Tomasi M, Fantappie L, Ganfini L, Caproni E, et al. 2017. Large scale validation of an efficient CRISPR/Cas-based multi gene editing protocol in Escherichia coli. Microb Cell Fact. 16(1):68.
  • Zhou Y, Liu P, Gan Y, Sandoval W, Katakam AK, Reichelt M, Rangell L, Reilly D. 2016. Enhancing full-length antibody production by signal peptide engineering. Microb Cell Fact. 15:47.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.