FOOD MICROBIOLOGY AND GENETICS: ESCHERICHIA COLI

Abstract

Food microbiology focuses on examining microorganisms that impact the production, quality and safety of food, while microbial genetics is concerned with investigating the genetic information mechanisms of microorganisms. Microbial genetics is a field within the pioneering discipline of microbiology and genetic engineering. Microbial genetics analyzes microorganisms to understand how genes function and how they are regulated. It also identifies gene products that operate through various mechanisms. This study provides an introductory examination by investigating a significant model microorganism such as Escherichia coli, which helps us to understand food microbiology and genetics.

Keywords

• Food microbiology
• Bacterial genetics
• Escherichia coli

GIDA MİKROBİYOLOJİSİ VE GENETİK: ESCHERICHIA COLI

Abstract

Gıda mikrobiyolojisi, gıdaların üretimi, kalitesi ve güvenliği üzerinde etkisi olan mikroorganizmaların incelenmesine odaklanırken, mikrobiyel genetik, mikroorganizmaların kalıtsal bilgi mekanizmalarının araştırılmasıyla ilgilenir. Mikrobiyel genetik, öncü bir disiplin olan mikrobiyoloji ve genetik mühendisliği içinde bir alandır. Bu alan, genlerin nasıl çalıştığını ve nasıl kontrol edildiğini anlamak, farklı mekanizmalarla çalışan gen ürünlerini belirlemek gibi amaçlarla mikroorganizmaları analiz eder. Bu çalışmada gıda mikrobiyolojisi ve genetik başlığını anlamamıza yardımcı olan Escherichia coli gibi önemli bir model mikroorganizma üzerinden giriş niteliğinde bir inceleme yapılmıştır.

Keywords

• Gıda mikrobiyolojisi
• Bakteriyel genetik
• Escherichia coli

References

1. Alberini, C. M. (2009). Transcription factors in long-term memory and synaptic plasticity. Physiological reviews, 89(1): 121-145, doi:10.1152/physrev.00017.2008.
2. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P. (2002). Isolating, cloning, and sequencing DNA. In: Molecular Biology of the Cell, Garland Science, NewYork.
3. Arroyo-Olarte, R. D., Bravo Rodríguez, R., Morales-Ríos, E. (2021). Genome Editing in Bacteria: CRISPR-Cas and Beyond. Microorganisms, 9(4), doi:10.3390/ microorganisms9040844.
4. ATCC. (2024). Escherichia coli (ATCC® 29055™). ATCC. https://genomes.atcc.org/ genomes/ac6f0af3fb53407f?tab=overview-tab (Erişim Tarihi: 11.01.2024).
5. Beal, M. A., Meier, M. J., Dykes, A., Yauk, C. L., Lambert, I. B., Marchetti, F. (2023). The functional mutational landscape of the lacZ gene. iScience, 26(12): 108407, doi:10.1016/ j.isci.2023.108407.
6. Bigler, A. (2023). Propelling Rare Disease Research for More Than 50 Years. National Institute of General Medical Sciences. https://biobeat.nigms.nih.gov/category/genes/ (Erişim Tarihi: 04.05.2023).
7. Blattner, F. R., Plunkett, G., 3rd, Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B., Shao, Y. (1997). The complete genome sequence of Escherichia coli K-12. Science, 277(5331): 1453-1462, doi:10.1126/science.277.5331.1453.
8. Blount, Z. D. (2015). The unexhausted potential of E. coli. Elife, 4: e05826.

9. CDC. (2022a). Escherichia coli https://www.cdc.gov/ecoli/index.html (Erişim Tarihi: 05.05.2023).
10. CDC. (2022b). Whole Genome Sequencing. https://www.cdc.gov/pulsenet/pathogens/wgs.html (Erişim Tarihi: 06.06.2023).
11. De La Cruz, F., Frost, L. S., Meyer, R. J., Zechner, E. L. (2010). Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiology Reviews, 34(1): 18-40, doi:10.1111/j.1574-6976.2009.00195.x.
12. Denamur, E., Clermont, O., Bonacorsi, S., Gordon, D. (2021). The population genetics of pathogenic Escherichia coli. Nature Reviews Microbiology, 19(1): 37-54, doi:10.1038/s41579-020-0416-x.
13. Dion, M. B., Shah, S. A., Deng, L., Thorsen, J., Stokholm, J., Krogfelt, K. A., Schjørring, S., Horvath, P., Allard, A., Nielsen, D. S., Petit, M.-A., Moineau, S. (2024). Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages. The ISME Journal, doi:10.1093/ismejo/wrae005.
14. Dobrin, R., Beg, Q. K., Barabási, A.-L., Oltvai, Z. N. (2004). Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. BMC bioinformatics, 5(1): 1-8, doi:10.1186/1471-2105-5-10.
15. Dong, H., Cui, Y., Zhang, D. (2021). CRISPR/Cas Technologies and Their Applications in Escherichia coli. Front Bioeng Biotechnol, 9: 762676, doi:10.3389/ fbioe.2021.762676.
16. EcoCyc. (2024). Escherichia coli K-12 substr. MG1655 reference genome (EcoCyc) EcoCyc. https://ecocyc.org/cgweb (Erişim Tarihi: 11.01.2024).
17. Fakruddin, M., Mohammad Mazumdar, R., Bin Mannan, K. S., Chowdhury, A., Hossain, M. (2013). Critical factors affecting the success of cloning, expression, and mass production of enzymes by recombinant E. coli. International Scholarly Research Notices, 2013, doi:10.5402/2013/ 590587.
18. Fillol-Salom, A., Alsaadi, A., Sousa, J. A. M. d., Zhong, L., Foster, K. R., Rocha, E. P., Penades, J. R., Ingmer, H., Haaber, J. (2019). Bacteriophages benefit from generalized transduction. PLoS pathogens, 15(7): e1007888, doi:10.1371/ journal.ppat.1007888.
19. Foster-Nyarko, E., Pallen, M. J. (2022). The microbial ecology of Escherichia coli in the vertebrate gut. FEMS Microbiology Reviews, 46(3): fuac008, doi:10.1093/femsre/fuac008.
20. Ghatak, S., King, Z. A., Sastry, A., Palsson, B. O. (2019). The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function. Nucleic acids research, 47(5): 2446-2454, doi:10.1093/nar/gkz030.
21. Griswold, A. (2008). Genome Packaging in Prokaryotes: The Circular Chromosomes of E. coli. Nature Education, 1(57).
22. Grohmann, E., Muth, G. n., Espinosa, M. (2003). Conjugative plasmid transfer in gram-positive bacteria. Microbiology and molecular biology reviews, 67(2): 277-301, doi:10.1128/mmbr.67.2.277-301.2003.
23. Headd, B., Bradford, S. A. (2020). The Conjugation Window in an Escherichia coli K-12 Strain with an IncFII Plasmid. Applied and environmental microbiology, 86(17): e00948-00920, doi:10.1128/AEM.00948-20.
24. Henderson, H. (2020). New Study Shows Huge Phages Are Everywhere. https://innovativegenomics.org/news/huge-phages-are-everywhere/ (Erişim Tarihi: 16.02.2024).
25. Holmes, R. K., Jobling, M. G. (1996). Genetics. In: Medical microbiology S. Baron (ed.), 4th Edition, University of Texas Medical Branch at Galveston, Galveston (TX).
26. Horvath, P., Barrangou, R. (2010). CRISPR/Cas, the immune system of bacteria and archaea. Science, 327(5962): 167-170, doi:10.1126/ science.117955.
27. Huang, C.-J., Lin, H., Yang, X. (2012). Industrial production of recombinant therapeutics in Escherichia coli and its recent advancements. Journal of Industrial Microbiology and Biotechnology, 39(3): 383-399, doi:10.1007/s10295-011-1082-9.
28. Idalia, V.-M. N., Bernardo, F. (2017). Escherichia coli as a model organism and its application in biotechnology. Recent Advances on Physiology, Pathogenesis and Biotechnological Applications, 13: 253-274.
29. Ingle, D. J., Valcanis, M., Kuzevski, A., Tauschek, M., Inouye, M., Stinear, T., Levine, M. M., Robins-Browne, R. M., Holt, K. E. (2016). In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages. Microbial Genomics, 2(7): e000064, doi:10.1099/ mgen.0.000064.
30. Iranzadeh, A., Mulder, N. J. (2019). Bacterial Pan-Genomics. In: Microbial Genomics in Sustainable Agroecosystems: Volume 1, V. Tripathi, P. Kumar, P. Tripathi, A. Kishore (ed.), Springer, Singapore, pp. 21-38.
31. Ishino, Y., Shinagawa, H., Makino, K., Amemura, M., Nakata, A. (1987). Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of bacteriology, 169(12): 5429-5433.
32. 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. Applied and environmental microbiology, 81(7): 2506-2514, doi:10.1128/AEM.04023-14.
33. Joseph, A., Cointe, A., Mariani Kurkdjian, P., Rafat, C., Hertig, A. (2020). Shiga toxin-associated hemolytic uremic syndrome: A narrative review. Toxins, 12(2): 67, doi:10.3390/toxins12020067.
34. Kadner, R. J., Rogers, K. (2023). Exchange of genetic information. Britannica. https://www.britannica.com/science/bacteria/The-importance-of-bacteria-to-humans (Erişim Tarihi: 16.05.2023).
35. Kalnins, A., Otto, K., Rüther, U., Müller-Hill, B. (1983). Sequence of the lacZ gene of Escherichia coli. Embo Journal, 2(4): 593-597, doi:10.1002/j.1460-2075.1983.tb01468.x.
36. Kaper, J. B., Nataro, J. P., Mobley, H. L. (2004). Pathogenic escherichia coli. Nature Reviews Microbiology, 2(2): 123-140, doi:10.1038/ nrmicro818.
37. Karp, P. D., Kothari, A., Paley, S., Krummenacker, M., Paulsen, I., Mackie, A., Moore, L., Collado-Vides, J., Bonavides-Martinez, C., Gama-Castro, S., Santos-Zavaleta, A., Tierrafria, V. H., Figueroa, P. L. (2021). Summary of Escherichia coli K-12 substr. MG1655, version 27.5 Tier 1 Highly Curated Database. EcoCyc. https://ecocyc.org/ECOLI/ organism-summary (Erişim Tarihi: 15.01.2024).
38. Kasman, L. M., Porter, L. D. (2021). Bacteriophages. Treasure Island (FL).
39. Keseler, I. M., Gama-Castro, S., Mackie, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Kothari, A., Krummenacker, M., Midford, P. E., Muñiz-Rascado, L. (2021). The EcoCyc database in 2021. Frontiers in Microbiology, 12: 711077, doi:10.3389/fmicb.2021.711077.
40. KhanAcademy. (2023). DNA sequencing. https://www.khanacademy.org/science/ap-biology/gene-expression-and-regulation/biotechnology/a/dna-sequencing (Erişim Tarihi: 06.06.2023).
41. Kukurba, K. R., Montgomery, S. B. (2015). RNA sequencing and analysis. Cold Spring Harbor Protocols, 2015(11), doi:10.1101/pdb.top084970.
42. Lee, S. Y., Nielsen, J., Stephanopoulos, G. (2017). Emerging areas in bioengineering. John Wiley & Sons, Republic of Korea, ISBN:3527803289.
43. Lewis, T. (2013). Human genome project marks 10th anniversary. https://www.livescience.com/ 28708-human-genome-project-anniversary.html (Erişim Tarihi: 06.06.2023).
44. Li, H., Shen, C. R., Huang, C.-H., Sung, L.-Y., Wu, M.-Y., Hu, Y.-C. (2016). CRISPR-Cas9 for the genome engineering of cyanobacteria and succinate production. Metabolic engineering, 38: 293-302, doi:10.1016/j.ymben.2016.09.006.
45. Liang, L., Liu, R., Garst, A. D., Lee, T., Beckham, G. T., Gill, R. T. (2017). CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli. Metabolic engineering, 41: 1-10, doi:10.1016/ j.ymben.2017.02.009.
46. Lorenzo, J. M., Munekata, P. E., Dominguez, R., Pateiro, M., Saraiva, J. A., Franco, D. (2018). Main Groups of Microorganisms of Relevance for Food Safety and Stability: General Aspects and Overall Description. In: Innovative Technologies for Food Preservation, F. J. Barba, A. S. Sant'Ana, V. Orlien, M. Koubaa (ed.), Academic Press, pp. 53-107.
47. Ma, H.-W., Kumar, B., Ditges, U., Gunzer, F., Buer, J., Zeng, A.-P. (2004). An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic acids research, 32(22): 6643-6649, doi:10.1093/nar/gkh1009.
48. Mackie, A. (2015). Summary of Regulatory Influences on lacZ. EcoCyc. https://ecocyc.org/ gene?orgid=ECOLI&id=EG10527 (Erişim Tarihi: 11.01.2024).
49. Maeder, M. L., Gersbach, C. A. (2016). Genome-editing technologies for gene and cell therapy. Molecular Therapy, 24(3): 430-446, doi:10.1038/ mt.2016.10.
50. Makałowski, W. (2001). The human genome structure and organization. Acta Biochimica Polonica, 48(3): 587-598.
51. Maloy, S. (2001). Bacterial Genetics. In: Encyclopedia of Genetics, S. Brenner J. H. Miller (ed.), Academic Press, New York, pp. 156-163.
52. Maloy, S. (2013). Bacterial Genetics. In: Encyclopedia of Biodiversity (Second Edition), S. A. Levin (ed.), Academic Press, Waltham, pp. 317-325.
53. Martínez-Antonio, A., Janga, S. C., Thieffry, D. (2008). Functional organisation of Escherichia coli transcriptional regulatory network. Journal of Molecular Biology, 381(1): 238-247, doi:10.1016/ j.jmb.2008.05.054.
54. Martinson, J. N., Walk, S. T. (2020). Escherichia coli residency in the gut of healthy human adults. EcoSal Plus, 9(1), doi:10.1128/ecosalplus.esp-0003-2020.
55. Najafi, M. B. H., Pezeshki, P. (2013). Bacterial mutation; types, mechanisms and mutant detection methods: a review. European Scientific Journal.
56. NCBI. (2024). Genome Information by Organism:Escherichia coli. https://www.ncbi.nlm.nih.gov/genome/browse#!/prokaryotes/167/ (Erişim Tarihi: 11.01.2024). NHGRI. (2023). Plasmid. https://www.genome.gov/genetics-glossary/Plasmid (Erişim Tarihi: 21.05.2023).
57. Nichols, R. J., Sen, S., Choo, Y. J., Beltrao, P., Zietek, M., Chaba, R., Lee, S., Kazmierczak, K. M., Lee, K. J., Wong, A. (2011). Phenotypic landscape of a bacterial cell. Cell, 144(1): 143-156, doi:10.1016/j.cell.2010.11.052.
58. NIGMS. (2023). What is genetics? https://nigms.nih.gov/education/fact-sheets/Pages/genetics.aspx#:~:text=%E2%80%8B%E2%80%8B%E2%80%8BWhat%20is,that%20help%20the%20body%20work (Erişim Tarihi: 04.05.2023).
59. O'Donnell, M., Langston, L., Stillman, B. (2013). Principles and concepts of DNA replication in bacteria, archaea, and eukarya. Cold Spring Harbor Perspectives in Biology, 5(7), doi:10.1101/cshperspect.a010108.
60. Okuda, S., Kawashima, S., Kobayashi, K., Ogasawara, N., Kanehisa, M., Goto, S. (2007). Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC genomics, 8: 1-12, doi:10.1186/1471-2164-8-48.
61. Petreaca, R. (2013). Yeast Genetics. In: Brenner's Encyclopedia of Genetics: Second Edition, Elsevier Inc., pp. 385-387.
62. Pitout, J. D., Finn, T. J. (2020). The evolutionary puzzle of Escherichia coli ST131. Infection, Genetics and Evolution, 81: 104265.
63. Raleigh, E. A., Low, K. B. (2013). Conjugation. In: Brenner's Encyclopedia of Genetics (Second Edition), S. Maloy K. Hughes (ed.), Academic Press, San Diego, pp. 144-151.
64. Roach, J. C., Boysen, C., Wang, K., Hood, L. (1995). Pairwise end sequencing: a unified approach to genomic mapping and sequencing. Genomics, 26(2): 345-353, doi:10.1016/0888-7543(95)80219-C.
65. Roach, J. C., Glusman, G., Smit, A. F., Huff, C. D., Hubley, R., Shannon, P. T., Rowen, L., Pant, K. P., Goodman, N., Bamshad, M. (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science, 328(5978): 636-639.
66. Robins-Browne, R. M., Holt, K. E., Ingle, D. J., Hocking, D. M., Yang, J., Tauschek, M. (2016). Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing? Front Cell Infect Microbiology, 6: 141, doi:10.3389/fcimb.2016.00141.
67. Rosano, G. L., Ceccarelli, E. A. (2014). Recombinant protein expression in Escherichia coli: advances and challenges. Frontiers in Microbiology, 5: 172, doi:10.3389/fmicb.2014.00172.
68. Ruiz, N., Silhavy, T. J. (2022). How Escherichia coli Became the Flagship Bacterium of Molecular Biology. Journal of bacteriology, 204(9): e00230-00222, doi:10.1128/jb.00230-22.
69. Salgado, H., Gama-Castro, S., Peralta-Gil, M., Diaz-Peredo, E., Sánchez-Solano, F., Santos-Zavaleta, A., Martinez-Flores, I., Jiménez-Jacinto, V., Bonavides-Martinez, C., Segura-Salazar, J. (2006). RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic acids research, 34(suppl_1): 394-397, doi:10.1093/nar/gkj156.
70. Shao, Q., Hawkins, A., Zeng, L. (2015). Phage DNA dynamics in cells with different fates. Biophysical journal, 108(8): 2048-2060, doi:10.1016/j.bpj.2015.03.027.
71. Shen-Orr, S. S., Milo, R., Mangan, S., Alon, U. (2002). Network motifs in the transcriptional regulation network of Escherichia coli. Nature genetics, 31(1): 64-68, doi:10.1038/ng881.
72. Siegler, R. L. (1994). Spectrum of extrarenal involvement in postdiarrheal hemolytic-uremic syndrome. The Journal of pediatrics, 125(4): 511-518.
73. Sorek, R., Kunin, V., Hugenholtz, P. (2008). CRISPR—a widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Reviews Microbiology, 6(3): 181-186, doi:10.1038/nrmicro1793.
74. Taj, M. K., Samreen, Z., Ling, J. X., Taj, I., Hassan, T., Yunlin, W. (2014). Escherichia coli as a model organism. International Journal of Engineering Research and Science and Technology, 3(2): 1-8.
75. Trevors, J. (1999). Evolution of gene transfer in bacteria. World Journal of Microbiology and Biotechnology, 15: 1-6.
76. USDA. (2011). Overview of Food Microbiology. https://www.fsis.usda.gov/sites/default/files/media_file/2020-08/PHVt-Food_Microbiology.pdf (Erişim Tarihi: 04.05.2023).
77. Vasilyev, N., Liu, M. M., Epshtein, V., Shamovsky, I., Nudler, E. (2024). General transcription factor from Escherichia coli with a distinct mechanism of action. Nature Structural & Molecular Biology: 1-9, doi:10.1038/s41594-023-01154-w.
78. Virolle, C., Goldlust, K., Djermoun, S., Bigot, S., Lesterlin, C. (2020). Plasmid transfer by conjugation in Gram-negative bacteria: from the cellular to the community level. Genes, 11(11): 1239, doi:10.3390/genes11111239.
79. Wang, D., Farhana, A. (2023). Biochemistry, RNA Structure. StatPearls Publishing, Treasure Island (FL). Weinstock, G. M. (2013). Microbial Genetics. In: Brenner's Encyclopedia of Genetics (Second Edition), S. Maloy K. Hughes (ed.), Academic Press, San Diego, pp. 392-395.
80. Wu, M. Y., Sung, L. Y., Li, H., Huang, C. H., Hu, Y. C. (2017). Combining CRISPR and CRISPRi Systems for Metabolic Engineering of E. coli and 1,4-BDO Biosynthesis. ACS Synthetic Biology, 6(12): 2350-2361, doi:10.1021/acssynbio.7b00251.
81. Xu, W., Klumbys, E., Ang, E. L., Zhao, H. (2020). Emerging molecular biology tools and strategies for engineering natural product biosynthesis. Metabolic Engineering Communications, 10: e00108, doi:10.1016/j.mec.2019.e00108.
82. Yang, D., Prabowo, C. P. S., Eun, H., Park, S. Y., Cho, I. J., Jiao, S., Lee, S. Y. (2021). Escherichia coli as a platform microbial host for systems metabolic engineering. Essays in biochemistry, 65(2): 225-246, doi:10.1042/EBC20200172.
83. Yano, B., Taniguchi, I., Gotoh, Y., Hayashi, T., Nakamura, K. (2023). Dynamic changes in Shiga toxin (Stx) 1 transducing phage throughout the evolution of O26:H11 Stx-producing Escherichia coli. Scientific reports, 13(1): 4935, doi:10.1038/s41598-023-32111-8.