Research Article | Volume 13, Supplement 1, July, 2025
Whole genome sequencing of pollution thriving E. coli and its fermentation ability of biomass for bioethanol production
An attempt was made to isolate Escherichia coli strains from a polluted environment to explore the potentiality of the production of bioethanol. The whole genome sequencing (WGS) confirmed the strain as E. coli. The whole genome provided insight into structural and function annotations and mined into their potent enzymes for ethanol production. The WGS of the E. coli strain contributed nearly 23% of total genes involved in carbohydrate metabolism, and the highest Clusters of Orthologous Genes (COGs) were recorded around 447 Carbohydrate transport and metabolism genes. Additionally, E. coli enzymes, namely protease, alcohol dehydrogenase, and lyase enzymes, were observed, and each could potentially play a crucial role in ethanol production. Despite their importance in ethanol production, structural information for these enzymes from the microorganism remains unavailable. In the current investigation, genomic data of E. coli genome from three sequences were selected. Subsequently, the 3D structure of protease, alcohol dehydrogenase, and lyase enzymes were modeled and validated using structural bioinformatics methodologies. The gas chromatography of the fermented byproducts using this strain was analyzed, and it was seen that 2-butanol had the highest quantification of 31.055%, while ethanol resulted in 7.907%. This study provides the real-world applicability of the wild E. coli strain in bioethanol production.
Subramanian K, Suresh K, Yadav N, Kaur N, Thakur SS. Whole genome sequencing of pollution thriving E. coli and its fermentation ability of biomass for bioethanol production. J Appl Biol Biotech. 2025;13(Suppl 1): 97–104. http://doi.org/10.7324/JABB.2025.227583
1. Holechek JL, Geli HM, Sawalhah MN, Valdez R. A global assessment: can renewable energy replace fossil fuels by 2050? Sustainability 2022;14(8):4792; doi: https://doi.org/10.3390/su14084792
2. Aditiya HB, Mahlia TMI, Chong WT, Nur H, Sebayang AH. Second generation bioethanol production: a critical review. Renew Sust Energ Rev 2016;66:631–53; doi: https://doi.org/10.1016/j.rser.2016.07.015
3. McMillan JD. Bioethanol production: status and prospects. Renew Ener 1997;10(2–3):295–302; doi: https://doi.org/10.1016/0960-1481(96)00081-X
4. Koppolu V, Vasigala VKR. Role of Escherichia coli in biofuel production. Microbiol Insights 2016;9:MBI-S10878; doi: https://doi.org/10.4137/MBI.S108
5. Ingram LO, Conway T, Clark DP, Sewell GW, Preston J. Genetic engineering of ethanol production in Escherichia coli. Appl Environ Microbiol 1987;53(10):2420–5; doi: https://doi.org/10.1128/aem.53.10.2420-2425.1987
6. Yomano LP, York SW, Ingram LO. Isolation and characterization of ethanol-tolerant mutants of Escherichia coli KO11 for fuel ethanol production. J Ind Microbiol Biotechnol 1998;20(2):132–8; doi: https://doi.org/10.1038/sj.jim.2900496
7. Yomano LP, York SW, Zhou S, Shanmugam KT, Ingram LO. Re-engineering Escherichia coli for ethanol production. Biotechnol Lett 2008;30:2097–103; doi: https://doi.org/10.1007/s10529-008-9821-3
8. Chang D, Islam ZU, Zheng J, Zhao J, Cui X, Yu Z. Inhibitor tolerance and bioethanol fermentability of levoglucosan-utilizing Escherichia coli were enhanced by overexpression of stress-responsive gene ycfR: the proteomics-guided metabolic engineering. Synth Syst Biotechnol 2021;6(4):384–95; doi: https://doi.org/10.1016/j.synbio.2021.11.003
9. Horinouchi T, Tamaoka K, Furusawa C, Ono N, Suzuki S, Hirasawa T, et al. Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress. BMC Genomics 2010;11:1–11; doi: https://doi.org/10.1186/1471-2164-11-579
10. Munjal N, Mattam A, Pramanik D, Srivastava P, Yazdani SS. Modulation of endogenous pathways enhances bioethanol yield and productivity in Escherichia coli. Microb Cell Fact 2012;11:1–12; doi: https://doi.org/10.1186/1475-2859-11-145
11. Adnan NAA, Suhaimi SN, Abd-Aziz S, Hassan MA, Phang LY. Optimization of bioethanol production from glycerol by Escherichia coli SS1. Renew Energ 2014;66:625–33; doi: https://doi.org/10.1016/j.renene.2013.12.032
12. Bautista VM, Hernández SC, González LR, Jiménez LD. Saccharomyces cerevisiae vs Escherichia coli in the valorization of crude glycerol to produce ethanol. Bioresour Technol Rep 2023;24:101634; doi: https://doi.org/10.1016/j.biteb.2023.101634
13. Atsumi S, Hanai T, Liao JC. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008;451(7174):86–9; doi: https://doi.org/10.1038/nature06450
14. Ohmiya K, Sakka K, Kimura T. Anaerobic bacterial degradation for the effective utilization of biomass. Biotechnol Bioprocess Eng 2005;10:482–93; doi: https://doi.org/10.1007/BF02932282
15. Wang J, Chen L, Tian X, Gao L, Niu X, Shi M, et al. Global metabolomic and network analysis of Escherichia coli responses to exogenous biofuels. J Proteome Res 2013;12(11):5302–12; doi: https://doi.org/10.1021/pr400640u
16. Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al. Highly accurate protein structure prediction with AlphaFold. Nature 2021;596(7873):583–9; doi: https://doi.org/10.1038/s41586-021-03819-2
17. Lerminiaux NA, Cameron ADS. Horizontal transfer of antibiotic resistance genes in clinical environments. Can J Microbiol 2019;65(1):34–44; doi: https://doi.org/10.1139/cjm-2018-0275
18. Levy SB. Antibiotic resistance-the problem intensifies. Adv Drug Deliv Rev 2005;57(10):1446–50; doi: https://doi.org/10.1016/j.addr.2005.04.001
19. Askari-khorasgani O, Pessarakli M. Safety assessment of genetically modified crops for yield increase and resistance to both biotic and abiotic stresses and their impact on human and environment. Adv Plants Agric Res 2018;8(2):109–12; doi: https://doi.org/10.15406/apar.2018.08.00300
20. Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci 2021;30(1):70–82; doi: https://doi.org/10.1002/pro.3943
21. Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci 2018;27(1):14–25; doi: https://doi.org/10.1002/pro.3235
22. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26(2):283–91; doi: https://doi.org/10.1107/S0021889892009944
23. Jendele L, Krivak R, Skoda P, Novotny M, Hoksza D. PrankWeb: a web server for ligand binding site prediction and visualization. Nucleic Acids Res 2019;47(W1):W345–9; doi: https://doi.org/10.1093/nar/gkz424
24. Lawford HG, Rousseau JD. Ethanol production by recombinant Escherichia coli carrying genes from Zymomonas mobilis. Appl Biochem Biotechnol 1991;28:221–36; doi: https://doi.org/10.1007/BF02922603
25. Rao K, Chaudhari V, Varanasi S, Kim DS. Enhanced ethanol fermentation of brewery wastewater using the genetically modified strain E. coli KO11. Appl Microbiol Biotechnol 2007;74:50–60; doi: https://doi.org/10.1007/s00253-006-0643-8
26. Lindsay SE, Bothast RJ, Ingram LO. Improved strains of recombinant Escherichia coli for ethanol production from sugar mixtures. Appl Microbiol Biotechnol 1995;43:70–5; doi: https://doi.org/10.1007/BF00170625
27. Dombek KM, Ingram LO. Determination of the intracellular concentration of ethanol in Saccharomyces cerevisiae during fermentation. Appl Environ Microbiol 1986;51(1):197–200; doi:
28. Blattner FR, Plunkett III G, Bloch CA, Perna NT, Burland V, Riley M, et al. The complete genome sequence of Escherichia coli K-12. Science 1997;277(5331):1453–62; doi: https://doi.org/10.1126/science.277.5331.1453
29. Clark D, Cronan Jr JE. Escherichia coli mutants with altered control of alcohol dehydrogenase and nitrate reductase. J Bacteriol 1980;141(1):177–83; doi: https://doi.org/10.1128/jb.141.1.177-183.1980
30. Wang KY, Zhang J, Hsu YC, Lin H, Han Z, Pang J, et al. Bioinspired framework catalysts: from enzyme immobilization to biomimetic catalysis. Chem Rev 2023;123(9):5347–420; doi: https://doi.org/10.1021/acs.chemrev.2c00879
31. Buijs NA, Siewers V, Nielsen J. Advanced biofuel production by the yeast Saccharomyces cerevisiae. Curr Opin Chem Biol 2013;17(3):480–8; doi: https://doi.org/10.1016/j.cbpa.2013.03.036
32. Lawford HG, Rousseau JD. Loss of ethanologenicity in Escherichia coli B recombinants pLOI297 and KO11 during growth in the absence of antibiotics. Biotechnol Lett 1995;17:751–6; doi: https://doi.org/10.1007/BF00130363
33. Lawford HG, Rousseau JD. Mannose fermentation by an ethanologenic recombinant Escherichia coli. Biotechnol Lett 1993;15:615–20; doi: https://doi.org/10.1007/BF00138551
34. Okuda N, Ninomiya K, Takao M, Katakura Y, Shioya S. Microaeration enhances productivity of bioethanol from hydrolysate of waste house wood using ethanologenic Escherichia coli KO11. J Biosci Bioeng 2007;103(4):350–7; doi: https://doi.org/10.1263/jbb.103.350
35. Raina N, Slathia PS, Sharma P. Response surface methodology (RSM) for optimization of thermochemical pretreatment method and enzymatic hydrolysis of deodar sawdust (DS) for bioethanol production using separate hydrolysis and co-fermentation (SHCF). Biomass Convers Biorefin 2020;12: 5175–95; doi: https://doi.org/10.1007/s13399-020-00970-0
36. Domínguez E, del Río PG, Romaní A, Garrote G, Domingues L. Hemicellulosic bioethanol production from fast-growing Paulownia biomass. Processes 2021;9(1):173; doi: https://doi.org/10.3390/pr9010173
37. Vargas-Bautista C, Rahlwes K, Straight P. Bacterial competition reveals differential regulation of the pks genes by Bacillus subtilis. J Bacteriol 2014;196(4):717–28; doi: https://doi.org/10.1128/jb.01022-1
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