دورية أكاديمية
أعرض في EDS

Development of both type I-B and type II CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum .

التفاصيل البيبلوغرافية
العنوان: Development of both type I-B and type II CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum .
المؤلفون: Walker JE; Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80303, USA.; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA., Lanahan AA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.; Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA., Zheng T; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.; Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA., Toruno C; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.; Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA., Lynd LR; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.; Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA., Cameron JC; Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80303, USA.; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.; Department of Biochemistry, University of Colorado, Boulder, CO, 80303, USA.; National Renewable Energy Laboratory, Biosciences Center, Golden, USA., Olson DG; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.; Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA., Eckert CA; Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80303, USA.; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.; National Renewable Energy Laboratory, Biosciences Center, Golden, USA.
المصدر: Metabolic engineering communications [Metab Eng Commun] 2019 Nov 28; Vol. 10, pp. e00116. Date of Electronic Publication: 2019 Nov 28 (Print Publication: 2020).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Elsevier B.V Country of Publication: Netherlands NLM ID: 101642117 Publication Model: eCollection Cited Medium: Internet ISSN: 2214-0301 (Electronic) Linking ISSN: 22140301 NLM ISO Abbreviation: Metab Eng Commun Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: [Amsterdam] : Elsevier B.V., [2014]-
مستخلص: The robust lignocellulose-solubilizing activity of C. thermocellum makes it a top candidate for consolidated bioprocessing for biofuel production. Genetic techniques for C. thermocellum have lagged behind model organisms thus limiting attempts to improve biofuel production. To improve our ability to engineer C. thermocellum , we characterized a native Type I-B and heterologous Type II Clustered Regularly-Interspaced Short Palindromic Repeat (CRISPR)/cas (CRISPR associated) systems. We repurposed the native Type I-B system for genome editing. We tested three thermophilic Cas9 variants (Type II) and found that GeoCas9, isolated from Geobacillus stearothermophilus , is active in C. thermocellum . We employed CRISPR-mediated homology directed repair to introduce a nonsense mutation into pyrF . For both editing systems, homologous recombination between the repair template and the genome appeared to be the limiting step. To overcome this limitation, we tested three novel thermophilic recombinases and demonstrated that exo / beta homologs, isolated from Acidithiobacillus caldus , are functional in C. thermocellum . For the Type I-B system an engineered strain, termed LL1586, yielded 40% genome editing efficiency at the pyrF locus and when recombineering machinery was expressed this increased to 71%. For the Type II GeoCas9 system, 12.5% genome editing efficiency was observed and when recombineering machinery was expressed, this increased to 94%. By combining the thermophilic CRISPR system (either Type I-B or Type II) with the recombinases, we developed a new tool that allows for efficient CRISPR editing. We are now poised to enable CRISPR technologies to better engineer C. thermocellum for both increased lignocellulose degradation and biofuel production.
Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Lee Lynd is a co-founder of the Enchi Corporation, which has a financial interest in C. thermocellum. Work within was filed as a provisional patent, Provisional Patent Application No. 62/896,555 titled Novel Recombineering Machinery to Increase Homology Directed Genome Editing in Thermophilic Microbes.
References: J Genet Genomics. 2017 Nov 20;44(11):541-548. (PMID: 29169919)
Front Microbiol. 2017 Sep 07;8:1744. (PMID: 28936208)
Proc Natl Acad Sci U S A. 2012 Sep 25;109(39):E2579-86. (PMID: 22949671)
J Biotechnol. 2015 Apr 20;200:1-5. (PMID: 25680931)
mBio. 2018 Feb 20;9(1):. (PMID: 29463653)
Trends Biotechnol. 2016 Jul;34(7):575-587. (PMID: 26944793)
Nucleic Acids Res. 2012 Oct;40(19):9887-96. (PMID: 22879377)
Metab Eng Commun. 2015 Mar 30;2:23-29. (PMID: 34150505)
Nat Biotechnol. 2013 Mar;31(3):227-9. (PMID: 23360964)
Emerg Microbes Infect. 2018 Aug 6;7(1):141. (PMID: 30082713)
Clin Microbiol Infect. 2018 Oct;24(10):1095-1099. (PMID: 29604353)
Methods Enzymol. 2012;510:317-30. (PMID: 22608734)
Science. 2018 Jul 6;361(6397):. (PMID: 29880725)
Appl Environ Microbiol. 2019 Oct 1;85(20):. (PMID: 31399410)
Biotechnol Biofuels. 2016 Oct 18;9:219. (PMID: 27777621)
Microbiology (Reading). 2009 Mar;155(Pt 3):733-740. (PMID: 19246744)
Genome Biol. 2015 Nov 10;16:231. (PMID: 26553065)
PLoS One. 2013 Jul 09;8(7):e69032. (PMID: 23874856)
ACS Synth Biol. 2017 Jun 16;6(6):1103-1113. (PMID: 28277645)
Nat Biotechnol. 2013 Mar;31(3):233-9. (PMID: 23360965)
Metab Eng. 2017 Jul;42:157-167. (PMID: 28649005)
Cell. 2013 May 9;153(4):910-8. (PMID: 23643243)
Sci Rep. 2016 May 09;6:25666. (PMID: 27157668)
Nat Commun. 2014 Oct 29;5:5344. (PMID: 25352017)
Appl Environ Microbiol. 2017 May 1;83(10):. (PMID: 28258147)
Metab Eng Commun. 2016 Jan 29;3:30-38. (PMID: 29468112)
ACS Synth Biol. 2016 Jul 15;5(7):721-32. (PMID: 27115041)
Microbiol Mol Biol Rev. 2002 Sep;66(3):506-77, table of contents. (PMID: 12209002)
Nat Struct Mol Biol. 2014 Jun;21(6):528-34. (PMID: 24793649)
Nat Commun. 2016 Sep 30;7:12800. (PMID: 27687501)
J Bacteriol. 2002 Jul;184(13):3586-97. (PMID: 12057953)
EMBO J. 2011 Apr 6;30(7):1335-42. (PMID: 21343909)
Appl Environ Microbiol. 2015 Jul;81(13):4423-31. (PMID: 25911483)
Annu Rev Microbiol. 2007;61:259-82. (PMID: 17506672)
Nat Commun. 2018 May 15;9(1):1911. (PMID: 29765029)
J Bacteriol. 2019 Jul 24;201(16):. (PMID: 31085694)
Cell. 2013 Feb 28;152(5):1173-83. (PMID: 23452860)
Nat Commun. 2017 Nov 21;8(1):1647. (PMID: 29162801)
Sci Adv. 2016 Feb 05;2(2):e1501254. (PMID: 26989779)
Nat Commun. 2017 Nov 10;8(1):1424. (PMID: 29127284)
Microb Cell Fact. 2017 Nov 16;16(1):205. (PMID: 29145843)
J Biotechnol. 2014 Mar 10;173:65-7. (PMID: 24384234)
Curr Opin Biotechnol. 2012 Jun;23(3):396-405. (PMID: 22176748)
Biochim Biophys Acta Gen Subj. 2017 Nov;1861(11 Pt B):2993-3000. (PMID: 28238733)
Science. 2008 Aug 15;321(5891):960-4. (PMID: 18703739)
Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8931-6. (PMID: 24889625)
ACS Synth Biol. 2018 Apr 20;7(4):1085-1094. (PMID: 29544049)
Biotechnol Biofuels. 2019 Jul 23;12:186. (PMID: 31367231)
Nucleic Acids Res. 2016 Mar 18;44(5):2462-73. (PMID: 26837577)
J Microbiol Methods. 2017 Sep;140:5-11. (PMID: 28610973)
Sci Rep. 2017 Nov 7;7(1):14672. (PMID: 29116155)
Nucleic Acids Res. 2016 Feb 29;44(4):e34. (PMID: 26467477)
Science. 2012 Aug 17;337(6096):816-21. (PMID: 22745249)
Biotechnol Biofuels. 2015 Sep 15;8:138. (PMID: 26379770)
Sci Rep. 2016 Jan 11;6:19044. (PMID: 26750307)
Georgian Med News. 2018 Feb;(Issue):172-176. (PMID: 29578445)
ACS Synth Biol. 2019 Apr 19;8(4):633-640. (PMID: 30943368)
Genes Dev. 2008 Dec 15;22(24):3489-96. (PMID: 19141480)
J Biol Eng. 2012 May 11;6(1):5. (PMID: 22578246)
Sci Rep. 2019 May 31;9(1):8123. (PMID: 31148548)
Metab Eng. 2018 May;47:49-59. (PMID: 29530750)
Biotechnol Biofuels. 2014 Mar 21;7:40. (PMID: 24655715)
Appl Environ Microbiol. 2010 Oct;76(19):6591-9. (PMID: 20693441)
Science. 2013 Feb 15;339(6121):823-6. (PMID: 23287722)
Nature. 2011 Mar 31;471(7340):602-7. (PMID: 21455174)
Biotechnol J. 2016 Jul;11(7):961-72. (PMID: 27213844)
Trends Biochem Sci. 2015 Jan;40(1):58-66. (PMID: 25468820)
Biotechnol Bioeng. 2019 Jun;116(6):1475-1483. (PMID: 30739328)
ACS Synth Biol. 2016 Dec 16;5(12):1355-1361. (PMID: 27276212)
Science. 2013 Feb 15;339(6121):819-23. (PMID: 23287718)
Curr Opin Biotechnol. 2005 Oct;16(5):577-83. (PMID: 16154338)
J Mol Biol. 1990 Oct 5;215(3):403-10. (PMID: 2231712)
Elife. 2013 Jan 29;2:e00471. (PMID: 23386978)
فهرسة مساهمة: Keywords: 5-FOA, 5-fluoroorotic acid; CFU, colony forming unit; CRISPR; CRISPR/Cas, Clustered Regularly-Interspaced Short Palindromic Repeat/CRISPR associated; Cas9; Cas9n, nickase Cas9; Clostridium thermocellum; HDR, homology-directed repair; HR, homologous recombination; PAM, protospacer adjacent motif; RNP, Cas9-sgRNA ribonucleoprotein; Thermophilic recombineering; Tm, thiamphenicol; Type I–B; sgRNA, single guide RNA
تواريخ الأحداث: Date Created: 20200101 Latest Revision: 20231027
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC6926293
DOI: 10.1016/j.mec.2019.e00116
PMID: 31890588
قاعدة البيانات: MEDLINE
الوصف
تدمد:2214-0301
DOI:10.1016/j.mec.2019.e00116