MinGenome: An in Silico Top-Down Approach for the Synthesis of Minimized Genomes

ACS Synthetic Biology

Volumn 7, Issue 2, 2018, Pages 462-473

  Wang, Lin ^a   Maranas, Costas D ^a  

^a The Pennsylvania State University   (United States)

Author keywords

E. coli; genome scale model; MILP; minimal genome; top down

Indexed keywords

DNA; TRANSCRIPTION FACTOR; BACTERIAL DNA; ESCHERICHIA COLI PROTEIN;

ALGORITHM; ARTICLE; COMPUTER MODEL; ESCHERICHIA COLI; ESSENTIAL GENE; GENE DELETION; GENE SEQUENCE; GENETIC TRANSCRIPTION; GENOME SIZE; LETHAL GENE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; SYSTEM ANALYSIS; BACTERIAL GENOME; GENE EDITING; GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES;

BASE SEQUENCE; DNA, BACTERIAL; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EDITING; GENOME, BACTERIAL; PROMOTER REGIONS, GENETIC; SEQUENCE DELETION; TRANSCRIPTION FACTORS;

EID: 85042201864     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.7b00296     Document Type: Article

References (49)

1. Choi, K. R., Cho, J. S., Shin, J. H., Yang, D., and Lee, S. Y. (2016) Systems Metabolic Engineering of Escherichia coli EcoSal Plus 10.1128/ecosalplus.ESP-0010-2015
2. Shlomi, T., Eisenberg, Y., Sharan, R., and Ruppin, E. (2007) A genome-scale computational study of the interplay between transcriptional regulation and metabolism Mol. Syst. Biol. 3, 101 10.1038/msb4100141
3. Chan, L. Y., Kosuri, S., and Endy, D. (2005) Refactoring bacteriophage T7 Mol. Syst. Biol. 1, E10 10.1038/msb4100025
4. Smanski, M. J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L. B. A., Giannoukos, G., Ciulla, D., Busby, M., Calderon, J., Nicol, R., Gordon, D. B., Densmore, D., and Voigt, C. A. (2014) Functional optimization of gene clusters by combinatorial design and assembly Nat. Biotechnol. 32, 1241-U104 10.1038/nbt.3063
5. Hutchison, C. A., Chuang, R.-Y., Noskov, V. N., Assad-Garcia, N., Deerinck, T. J., Ellisman, M. H., Gill, J., Kannan, K., Karas, B. J., Ma, L., Pelletier, J. F., Qi, Z.-Q., Richter, R. A., Strychalski, E. A., Sun, L., Suzuki, Y., Tsvetanova, B., Wise, K. S., Smith, H. O., Glass, J. I., Merryman, C., Gibson, D. G., and Venter, J. C. (2016) Design and synthesis of a minimal bacterial genome Science 351, aad6253-aad6253 10.1126/science.aad6253
6. Richardson, S. M., Mitchell, L. A., Stracquadanio, G., Yang, K., Dymond, J. S., DiCarlo, J. E., Lee, D., Huang, C. L. V., Chandrasegaran, S., Cai, Y., Boeke, J. D., and Bader, J. S. (2017) Design of a synthetic yeast genome Science 355, 1040-1044 10.1126/science.aaf4557
7. Vickers, C. E., Blank, L. M., and Kroemer, J. O. (2010) Chassis cells for industrial biochemical production Nat. Chem. Biol. 6, 875-877 10.1038/nchembio.484
8. Kolisnychenko, V., Plunkett, G., Herring, C. D., Fehér, T., Pósfai, J., Blattner, F. R., and Pósfai, G. (2002) Engineering a reduced Escherichia coli genome Genome Res. 12, 640-647 10.1101/gr.217202
9. Hashimoto, M., Ichimura, T., Mizoguchi, H., Tanaka, K., Fujimitsu, K., Keyamura, K., Ote, T., Yamakawa, T., Yamazaki, Y., Mori, H., Katayama, T., and Kato, J. I. (2005) Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome Mol. Microbiol. 55, 137-149 10.1111/j.1365-2958.2004.04386.x
10. Pósfai, G., Plunkett, G., Fehér, T., Frisch, D., Keil, G. M., Umenhoffer, K., Kolisnychenko, V., Stahl, B., Sharma, S. S., de Arruda, M., Burland, V., Harcum, S. W., and Blattner, F. R. (2006) Emergent Properties of Reduced-Genome Escherichia coli Science 312, 1044-1046 10.1126/science.1126439
11. Mizoguchi, H., Mori, H., and Fujio, T. (2007) Escherichia coli minimum genome factory Biotechnol. Appl. Biochem. 46, 157-167 10.1042/BA20060107
12. Mizoguchi, H., Sawano, Y., Kato, J., and Mori, H. (2008) Superpositioning of deletions promotes growth of Escherichia coli with a reduced genome DNA Res. 15, 277 10.1093/dnares/dsn019
13. Kato, J. I. and Hashimoto, M. (2008) Construction of Long Chromosomal Deletion Mutants of Escherichia coli and Minimization of the Genome, in Microbial Gene Essentiality: Protocols and Bioinformatics, pp 279-293, Humana Press, Totowa, NJ.
14. Hirokawa, Y., Kawano, H., Tanaka-Masuda, K., Nakamura, N., Nakagawa, A., Ito, M., Mori, H., Oshima, T., and Ogasawara, N. (2013) Genetic manipulations restored the growth fitness of reduced-genome Escherichia coli J. Biosci. Bioeng. 116, 52-58 10.1016/j.jbiosc.2013.01.010
15. Tsoy, O., Yurieva, M., Kucharavy, A., O'Reilly, M., and Mushegian, A. (2013) Minimal genome encoding proteins with constrained amino acid repertoire Nucleic Acids Res. 41, 8444-8451 10.1093/nar/gkt610
16. Le Cong Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., and Zhang, F. (2013) Multiplex Genome Engineering Using CRISPR/Cas Systems Science 339, 819-823 10.1126/science.1231143
17. Pal, C., Papp, B., Lercher, M. J., Csermely, P., Oliver, S. G., and Hurst, L. D. (2006) Chance and necessity in the evolution of minimal metabolic networks Nature 440, 667-670 10.1038/nature04568
18. Yizhak, K., Tuller, T., Papp, B., and Ruppin, E. (2011) Metabolic modeling of endosymbiont genome reduction on a temporal scale Mol. Syst. Biol. 7, 479-479 10.1038/msb.2011.11
19. Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Sayers, E. W. (2013) GenBank Nucleic Acids Res. 41, D36-D42 10.1093/nar/gks1195
20. Keseler, I. M., Mackie, A., and Peralta-Gil, M. (2013) EcoCyc: fusing model organism databases with systems biology Nucleic Acids Res. 33, D334 10.1093/nar/gki108
21. 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., Medina-Rivera, A., Solano-Lira, H., Bonavides-Martínez, C., Pérez-Rueda, E., Alquicira-Hernández, S., Porrón-Sotelo, L., López-Fuentes, A., Hernández-Koutoucheva, A., Moral-Chávez, V. D., Rinaldi, F., and Collado-Vides, J. (2016) RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond Nucleic Acids Res. 44, D133-D143 10.1093/nar/gkv1156
22. Reuß, D. R., Altenbuchner, J., Mäder, U., Rath, H., Ischebeck, T., Sappa, P. K., Thürmer, A., Guérin, C., Nicolas, P., Steil, L., Zhu, B., Feussner, I., Klumpp, S., Daniel, R., Commichau, F. M., Völker, U., and Stülke, J. (2017) Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism Genome Res. 27, 289-299 10.1101/gr.215293.116
23. Orth, J. D., Conrad, T. M., Na, J., Lerman, J. A., Nam, H., Feist, A. M., and Palsson, B. O. (2011) A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011 Mol. Syst. Biol. 7, 535-535 10.1038/msb.2011.65
24. Kato, J. I. and Hashimoto, M. (2007) Construction of consecutive deletions of the Escherichia coli chromosome Mol. Syst. Biol. 3, 132 10.1038/msb4100174
25. Bubunenko, M., Baker, T., and Court, D. L. (2007) Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli J. Bacteriol. 189, 2844-2853 10.1128/JB.01713-06
26. Gerdes, S. Y., Scholle, M. D., Campbell, J. W., Balázsi, G., Ravasz, E., Daugherty, M. D., Somera, A. L., Kyrpides, N. C., Anderson, I., Gelfand, M. S., Bhattacharya, A., Kapatral, V., D'Souza, M., Baev, M. V., Grechkin, Y., Mseeh, F., Fonstein, M. Y., Overbeek, R., Barabási, A. L., Oltvai, Z. N., and Osterman, A. L. (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG1655 J. Bacteriol. 185, 5673-5684 10.1128/JB.185.19.5673-5684.2003
27. Helling, R. B. (1994) Why does Escherichia coli have two primary pathways for synthesis of glutamate? J. Bacteriol. 176, 4664-4668 10.1128/jb.176.15.4664-4668.1994
28. Suthers, P. F., Zomorrodi, A., and Maranas, C. D. (2009) Genome-scale gene/reaction essentiality and synthetic lethality analysis Mol. Syst. Biol. 5, 301 10.1038/msb.2009.56
29. Von Kamp, A., Klamt, S., and Maranas, C. D. (2014) Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks PLoS Comput. Biol. 10, e1003378 10.1371/journal.pcbi.1003378
30. Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (1997) A Genomic Perspective on Protein Families Science 278, 631-637 10.1126/science.278.5338.631
31. McCutcheon, J. P. and Moran, N. A. (2012) Extreme genome reduction in symbiotic bacteria Nat. Rev. Microbiol. 10, 13-26 10.1038/nrmicro2670
32. Covert, M. W., Knight, E. M., Reed, J. L., and Herrgard, M. J. (2004) Integrating high-throughput and computational data elucidates bacterial networks Nature 429, 92 10.1038/nature02456
33. Chandrasekaran, S. and Price, N. D. (2010) Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis Proc. Natl. Acad. Sci. U. S. A. 107, 17845-17850 10.1073/pnas.1005139107
34. Song, Y., Lai, L., and Li, Z. (2017) Large-scale genomic deletions mediated by CRISPR/Cas9 system Oncotarget 8, 5647 10.18632/oncotarget.14543
35. van der Rest, M. E., Frank, C., and Molenaar, D. (2000) Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Escherichia coli J. Bacteriol. 182, 6892-6899 10.1128/JB.182.24.6892-6899.2000
36. Lerman, J. A., Hyduke, D. R., Latif, H., Portnoy, V. A., Lewis, N. E., Orth, J. D., Schrimpe-Rutledge, A. C., Smith, R. D., Adkins, J. N., Zengler, K., and Palsson, B. O. (2012) In silico method for modelling metabolism and gene product expression at genome scale Nat. Commun. 3, 929 10.1038/ncomms1928
37. Klumpp, S. and Hwa, T. (2008) Growth-rate-dependent partitioning of RNA polymerases in bacteria Proc. Natl. Acad. Sci. U. S. A. 105, 20245-20250 10.1073/pnas.0804953105
38. Hui, S., Silverman, J. M., Chen, S. S., Erickson, D. W., Basan, M., Wang, J., Hwa, T., and Williamson, J. R. (2015) Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria Mol. Syst. Biol. 11, 784-e784 10.15252/msb.20145697
39. Zetsche, B., Gootenberg, J. S., Abudayyeh, O. O., Slaymaker, I. M., Makarova, K. S., Essletzbichler, P., Volz, S. E., Joung, J., van der Oost, J., Regev, A., Koonin, E. V., and Zhang, F. (2015) Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System Cell 163, 759-771 10.1016/j.cell.2015.09.038
40. Li, Y., Lin, Z., Huang, C., Zhang, Y., Wang, Z., Tang, Y.-J., Chen, T., and Zhao, X. (2015) Metabolic engineering of Escherichia coli using CRISPR?Cas9 meditated genome editing Metab. Eng. 31, 13-21 10.1016/j.ymben.2015.06.006
41. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., and Mori, H. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection Mol. Syst. Biol. 10.1038/msb4100050
42. Aziz, R. K., Khaw, V. L., Monk, J. M., Brunk, E., Lewis, R., Loh, S. I., Mishra, A., Nagle, A. A., Satyanarayana, C., Dhakshinamoorthy, S., Luche, M., Kitchen, D. B., Andrews, K. A., Palsson, B. O., and Charusanti, P. (2015) Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC Front. Microbiol. 6, 5144 10.3389/fmicb.2015.00958
43. Thamm, A. M., Li, G., Taja-Moreno, M., Gerdes, S. Y., de Crécy-Lagard, V., Bruner, S. D., and Hanson, A. D. (2017) A strictly monofunctional bacterial hydroxymethylpyrimidine phosphate kinase precludes damaging errors in thiamin biosynthesis Biochem. J. 474, 2887 10.1042/BCJ20170437
44. Saha, R., Verseput, A. T., Berla, B. M., Mueller, T. J., Pakrasi, H. B., Maranas, C. D., and Parkinson, J. (2012) Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803 PLoS One 7, e48285 10.1371/journal.pone.0048285
45. Khodayari, A., Zomorrodi, A. R., Liao, J. C., and Maranas, C. D. (2014) A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data Metab. Eng. 25, 50-62 10.1016/j.ymben.2014.05.014
46. Khodayari, A. and Maranas, C. D. (2016) A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains Nat. Commun. 7, 13806 10.1038/ncomms13806
47. Danchin, A. and Fang, G. (2016) Unknown unknowns: essential genes in quest for function Microb. Biotechnol. 9, 530-540 10.1111/1751-7915.12384
48. Luo, H., Lin, Y., Gao, F., and Zhang, C. T. (2014) DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements Nucleic Acids Res. 42, D574 10.1093/nar/gkt1131
49. Juhas, M., Reuß, D. R., Zhu, B., and Commichau, F. M. (2014) Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering Microbiology 160, 2341-2351 10.1099/mic.0.079376-0