دورية أكاديمية
Modular (de)construction of complex bacterial phenotypes by CRISPR/nCas9-assisted, multiplex cytidine base-editing.
العنوان: | Modular (de)construction of complex bacterial phenotypes by CRISPR/nCas9-assisted, multiplex cytidine base-editing. |
---|---|
المؤلفون: | Volke DC; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark., Martino RA; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina., Kozaeva E; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark., Smania AM; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina., Nikel PI; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark. pabnik@biosustain.dtu.dk. |
المصدر: | Nature communications [Nat Commun] 2022 May 31; Vol. 13 (1), pp. 3026. Date of Electronic Publication: 2022 May 31. |
نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
اللغة: | English |
بيانات الدورية: | Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE |
أسماء مطبوعة: | Original Publication: [London] : Nature Pub. Group |
مواضيع طبية MeSH: | CRISPR-Cas Systems*/genetics , Gene Editing*/methods, Bacteria/genetics ; Cytidine/genetics ; Phenotype |
مستخلص: | CRISPR/Cas technologies constitute a powerful tool for genome engineering, yet their use in non-traditional bacteria depends on host factors or exogenous recombinases, which limits both efficiency and throughput. Here we mitigate these practical constraints by developing a widely-applicable genome engineering toolset for Gram-negative bacteria. The challenge is addressed by tailoring a CRISPR base editor that enables single-nucleotide resolution manipulations (C·G → T·A) with >90% efficiency. Furthermore, incorporating Cas6-mediated processing of guide RNAs in a streamlined protocol for plasmid assembly supports multiplex base editing with >85% efficiency. The toolset is adopted to construct and deconstruct complex phenotypes in the soil bacterium Pseudomonas putida. Single-step engineering of an aromatic-compound production phenotype and multi-step deconstruction of the intricate redox metabolism illustrate the versatility of multiplex base editing afforded by our toolbox. Hence, this approach overcomes typical limitations of previous technologies and empowers engineering programs in Gram-negative bacteria that were out of reach thus far. (© 2022. The Author(s).) |
References: | mSystems. 2021 Mar 16;6(2):. (PMID: 33727391) Biotechnol J. 2020 Jul;15(7):e1900404. (PMID: 32558098) Biotechnol Bioeng. 2004 Aug 20;87(4):516-24. (PMID: 15286989) Sci Rep. 2019 Nov 28;9(1):17822. (PMID: 31780717) Environ Microbiol. 2002 Dec;4(12):824-41. (PMID: 12534466) ACS Synth Biol. 2018 Nov 16;7(11):2665-2674. (PMID: 30335370) Bioinformatics. 2009 Jul 15;25(14):1754-60. (PMID: 19451168) Metab Eng. 2001 Oct;3(4):289-300. (PMID: 11676565) Arch Microbiol. 2010 Aug;192(8):639-50. (PMID: 20549192) Curr Opin Biotechnol. 2017 Aug;46:134-140. (PMID: 28365497) J Microbiol. 2006 Dec;44(6):671-3. (PMID: 17205047) Biochem J. 2001 Mar 15;354(Pt 3):707-15. (PMID: 11237876) Microb Cell Fact. 2020 Sep 3;19(1):172. (PMID: 32883277) mBio. 2018 Aug 28;9(4):. (PMID: 30154264) Microbiol Mol Biol Rev. 2000 Sep;64(3):624-53. (PMID: 10974129) iScience. 2018 Aug 31;6:222-231. (PMID: 30240613) Adv Microb Physiol. 2021;79:25-88. (PMID: 34836612) RNA. 2012 Apr;18(4):661-72. (PMID: 22345129) J Biotechnol. 2017 Sep 10;257:211-221. (PMID: 27871872) Data Brief. 2016 Jan 22;6:738-44. (PMID: 26870759) Curr Opin Biotechnol. 2017 Oct;47:120-132. (PMID: 28738232) Trends Biotechnol. 2019 Oct;37(10):1121-1142. (PMID: 30995964) Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2833-8. (PMID: 16477005) Proc Natl Acad Sci U S A. 2019 Oct 8;116(41):20366-20375. (PMID: 31548381) Synth Syst Biotechnol. 2016 Feb 12;1(2):118-121. (PMID: 29062934) Bio Protoc. 2021 Feb 20;11(4):e3917. (PMID: 33732804) PLoS One. 2020 Sep 2;15(9):e0238592. (PMID: 32877448) Nat Commun. 2021 Apr 15;12(1):2261. (PMID: 33859194) J Biol Chem. 2015 Oct 23;290(43):25920-32. (PMID: 26350459) Nat Biotechnol. 2014 Jun;32(6):569-76. (PMID: 24770325) Biotechnol J. 2021 Mar;16(3):e2000165. (PMID: 33085217) Nat Rev Mol Cell Biol. 2015 Sep;16(9):568-76. (PMID: 26081612) Metab Eng. 2020 Nov;62:62-71. (PMID: 32828991) Curr Opin Microbiol. 2020 Oct;57:22-30. (PMID: 32599531) Nat Biotechnol. 2020 Jul;38(7):824-844. (PMID: 32572269) Biotechnol J. 2016 Oct;11(10):1309-1319. (PMID: 27367544) Metab Eng. 2021 Jan;63:141-147. (PMID: 33307189) Metab Eng. 2021 Sep;67:373-386. (PMID: 34343699) J Bacteriol. 2009 May;191(10):3367-74. (PMID: 19304846) Gene. 1983 Dec;26(2-3):273-82. (PMID: 6323265) Nature. 2015 Jul 23;523(7561):481-5. (PMID: 26098369) Trends Biotechnol. 2018 Feb;36(2):134-146. (PMID: 28778606) Appl Environ Microbiol. 1997 Feb;63(2):761-2. (PMID: 9023954) Gigascience. 2021 Feb 16;10(2):. (PMID: 33590861) Trends Biotechnol. 2022 Apr 8;:. (PMID: 35410817) Nucleic Acids Res. 2010 Sep;38(16):e164. (PMID: 20601685) Trends Microbiol. 2020 Jun;28(6):512-513. (PMID: 32396829) J Bacteriol. 1990 Jun;172(6):3496-9. (PMID: 2111810) Front Bioeng Biotechnol. 2020 Jul 31;8:905. (PMID: 32850749) ACS Synth Biol. 2021 May 21;10(5):1214-1226. (PMID: 33843192) Metab Eng Commun. 2020 Mar 19;10:e00126. (PMID: 32215253) J Mol Biol. 1993 Dec 20;234(4):1270-3. (PMID: 8263929) Biotechnol Bioeng. 1996 Oct 5;52(1):129-40. (PMID: 18629859) Environ Microbiol. 2020 Jan;22(1):45-58. (PMID: 31599106) Biochemistry. 2019 Sep 10;58(36):3727-3734. (PMID: 31433621) J Basic Microbiol. 2003;43(5):399-406. (PMID: 12964183) ISME J. 2021 Jun;15(6):1751-1766. (PMID: 33432138) Nat Commun. 2018 May 15;9(1):1911. (PMID: 29765029) Nature. 2017 Nov 23;551(7681):464-471. (PMID: 29160308) Environ Microbiol. 2016 Oct;18(10):3565-3582. (PMID: 27348295) Nat Commun. 2017 Nov 21;8(1):1647. (PMID: 29162801) Antimicrob Agents Chemother. 2016 Jan 04;60(3):1767-78. (PMID: 26729493) Appl Microbiol Biotechnol. 2020 Sep;104(18):7745-7766. (PMID: 32789744) Nat Commun. 2020 Oct 7;11(1):5045. (PMID: 33028813) J Bacteriol. 2009 Apr;191(7):2112-21. (PMID: 19181802) J Microbiol Methods. 2006 Mar;64(3):391-7. (PMID: 15987659) Nat Commun. 2020 Nov 27;11(1):6073. (PMID: 33247095) J Gen Microbiol. 1986 Feb;132(2):565-8. (PMID: 3086500) Bioresour Technol. 2021 Jan;319:124239. (PMID: 33254462) ACS Catal. 2020 Jul 17;10(14):7512-7525. (PMID: 32733773) Nature. 2016 Apr 20;533(7603):420-4. (PMID: 27096365) Microb Biotechnol. 2020 Jan;13(1):233-249. (PMID: 30861315) J Bacteriol. 1985 Nov;164(2):918-21. (PMID: 2997137) Science. 2016 Sep 16;353(6305):. (PMID: 27492474) Nat Rev Genet. 2018 Dec;19(12):770-788. (PMID: 30323312) Cell Res. 2017 Oct;27(10):1289-1292. (PMID: 28849781) Mol Microbiol. 2014 Jul;93(1):98-112. (PMID: 24811454) Bioresour Technol. 2021 Jan;320(Pt B):124412. (PMID: 33249259) Nat Chem Biol. 2021 Dec;17(12):1262-1270. (PMID: 34663942) Science. 2012 Aug 17;337(6096):816-21. (PMID: 22745249) Nucleic Acids Res. 2013 Jan;41(Database issue):D666-75. (PMID: 23180763) Nat Commun. 2021 Nov 25;12(1):6872. (PMID: 34824225) Nat Microbiol. 2018 Apr;3(4):423-429. (PMID: 29403014) Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11329-34. (PMID: 18678916) Microb Biotechnol. 2020 Jul;13(4):1145-1161. (PMID: 32267616) Environ Microbiol. 2016 Oct;18(10):3403-3424. (PMID: 26913973) Nucleic Acids Res. 2018 Jul 2;46(W1):W205-W208. (PMID: 29722870) Nat Biotechnol. 2020 Jul;38(7):892-900. (PMID: 32284586) Synth Syst Biotechnol. 2020 Sep 02;5(4):277-292. (PMID: 32954022) Microb Cell Fact. 2015 Dec 21;14:201. (PMID: 26691337) BMB Rep. 2021 Feb;54(2):98-105. (PMID: 33298245) Appl Environ Microbiol. 1989 Nov;55(11):2850-5. (PMID: 16348047) Sci Rep. 2017 Oct 26;7(1):14134. (PMID: 29074996) Microb Cell Fact. 2016 Apr 11;15:61. (PMID: 27067813) Nature. 2009 Aug 13;460(7257):894-898. (PMID: 19633652) ACS Synth Biol. 2015 Dec 18;4(12):1341-51. (PMID: 26133359) Cell Syst. 2018 May 23;6(5):569-578.e7. (PMID: 29753645) Front Microbiol. 2019 Feb 22;10:208. (PMID: 30853946) ACS Synth Biol. 2018 Jan 19;7(1):10-15. (PMID: 29161506) iScience. 2020 Mar 27;23(3):100946. (PMID: 32179472) |
المشرفين على المادة: | 5CSZ8459RP (Cytidine) |
تواريخ الأحداث: | Date Created: 20220531 Date Completed: 20220602 Latest Revision: 20220716 |
رمز التحديث: | 20221213 |
مُعرف محوري في PubMed: | PMC9156665 |
DOI: | 10.1038/s41467-022-30780-z |
PMID: | 35641501 |
قاعدة البيانات: | MEDLINE |
تدمد: | 2041-1723 |
---|---|
DOI: | 10.1038/s41467-022-30780-z |