Single and multiplexed gene repression in solventogenic Clostridium via Cas12a-based CRISPR interference

Jones, 2016, CO2 fixation by anaerobic non-photosynthetic mixotrophy for improved carbon conversion, Nat Commun, 7, 10.1038/ncomms12800 Poehlein, 2017, Microbial solvent formation revisited by comparative genome analysis, Biotechnol Biofuels, 10, 58, 10.1186/s13068-017-0742-z Baral, 2016, Techno-economic analysis of cellulosic butanol production from corn stover through acetone–butanol–ethanol fermentation, Energy Fuels, 30, 5779, 10.1021/acs.energyfuels.6b00819 Wen, 2019, Improved n-butanol production from Clostridium cellulovorans by integrated metabolic and evolutionary engineering, Appl Environ Microbiol, 85, 10.1128/AEM.02560-18 Qi, 2018, Improvement of butanol production in Clostridium acetobutylicum through enhancement of NAD(P)H availability, J Ind Microbiol Biotechnol, 45, 993, 10.1007/s10295-018-2068-7 Wen, 2020, Metabolic engineering of Clostridium cellulovorans to improve butanol production by consolidated bioprocessing, ACS Synth Biol, 9, 304, 10.1021/acssynbio.9b00331 Rotta, 2015, Closed genome sequence of Clostridium pasteurianum ATCC 6013, Genome Announc, 3, 10.1128/genomeA.01596-14 Enany, 2014, Structural and functional analysis of hypothetical and conserved proteins of Clostridium tetani, J Infect Public Health, 7, 296, 10.1016/j.jiph.2014.02.002 Lacey, 2018, Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens, BMC Genom, 19, 379, 10.1186/s12864-018-4771-1 Patakova, 2019, Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level, Sci Rep, 9, 1371, 10.1038/s41598-018-37679-0 Joseph, 2018, Recent developments of the synthetic biology toolkit for Clostridium, Front Microbiol, 9, 10.3389/fmicb.2018.00154 Kim, 2020, Transcription factor-based biosensors and inducible systems in non-model bacteria: current progress and future directions, Curr Opin Biotechnol, 64, 39, 10.1016/j.copbio.2019.09.009 Al-Hinai, 2012, Novel system for efficient isolation of Clostridium double-crossover allelic exchange mutants enabling markerless chromosomal gene deletions and DNA integration, Appl Environ Microbiol, 78, 8112, 10.1128/AEM.02214-12 Ehsaan, 2016, Mutant generation by allelic exchange and genome resequencing of the biobutanol organism Clostridium acetobutylicum ATCC 824, Biotechnol Biofuels, 9, 4, 10.1186/s13068-015-0410-0 Heap, 2007, The ClosTron: a universal gene knock-out system for the genus Clostridium, J Microbiol Methods, 70, 452, 10.1016/j.mimet.2007.05.021 Xu, 2017, Cas9 nickase-assisted RNA repression enables stable and efficient manipulation of essential metabolic genes in Clostridium cellulolyticum, Front Microbiol, 8, 1744, 10.3389/fmicb.2017.01744 Nakayama, 2008, Metabolic engineering for solvent productivity by downregulation of the hydrogenase gene cluster hupCBA in Clostridium saccharoperbutylacetonicum strain N1-4, Appl Microbiol Biotechnol, 78, 483, 10.1007/s00253-007-1323-z Pyne, 2015, Antisense-RNA-mediated gene downregulation in Clostridium pasteurianum, Fermentation, 1, 10.3390/fermentation1010113 Jinek, 2012, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, 337, 816, 10.1126/science.1225829 Zetsche, 2015, Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system, Cell, 163, 759, 10.1016/j.cell.2015.09.038 Zetsche, 2016, Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array, Nat Biotechnol, 35, 31, 10.1038/nbt.3737 Zhang, 2019, Optimizing a CRISPR-Cpf1-based genome engineering system for Corynebacterium glutamicum, Microb Cell Factories, 18, 60, 10.1186/s12934-019-1109-x Marshall, 2018, Rapid and scalable characterization of CRISPR Technologies using an E. coli cell-free transcription-translation system, Mol Cell, 69, 146, 10.1016/j.molcel.2017.12.007 Tu, 2017, A 'new lease of life': FnCpf1 possesses DNA cleavage activity for genome editing in human cells, Nucleic Acids Res, 45, 11295, 10.1093/nar/gkx783 Zhong, 2018, Plant genome editing using FnCpf1 and LbCpf1 nucleases at redefined and altered PAM sites, Mol Plant, 11, 999, 10.1016/j.molp.2018.03.008 Swiat, 2017, FnCpf1: a novel and efficient genome editing tool for Saccharomyces cerevisiae, Nucleic Acids Res, 45, 12585, 10.1093/nar/gkx1007 Tóth, 2018, Mb- and FnCpf1 nucleases are active in mammalian cells: activities and PAM preferences of four wild-type Cpf1 nucleases and of their altered PAM specificity variants, Nucleic Acids Res, 46, 10272 Joseph, 2021, 611 Qi, 2013, Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression, Cell, 152, 1173, 10.1016/j.cell.2013.02.022 Zhao, 2019, CRISPR-Cas12a-Mediated gene deletion and regulation in Clostridium ljungdahlii and its application in carbon flux redirection in synthesis gas fermentation, ACS Synth Biol, 8, 2270, 10.1021/acssynbio.9b00033 Gao, 2017, Engineered Cpf1 variants with altered PAM specificities, Nat Biotechnol, 35, 789, 10.1038/nbt.3900 Ran, 2015, In vivo genome editing using Staphylococcus aureus Cas9, Nature, 520, 186, 10.1038/nature14299 Zhang, 2013, Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis, Mol Cell, 50, 488, 10.1016/j.molcel.2013.05.001 Garneau, 2010, The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA, Nature, 468, 67, 10.1038/nature09523 Esvelt, 2013, Orthogonal Cas9 proteins for RNA-guided gene regulation and editing, Nat Methods, 10, 1116, 10.1038/nmeth.2681 Heap, 2009, A modular system for Clostridium shuttle plasmids, J Microbiol Methods, 78, 79, 10.1016/j.mimet.2009.05.004 Cobb, 2015, High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system, ACS Synth Biol, 4, 723, 10.1021/sb500351f Mermelstein, 1992, Expression of cloned homologous fermentative genes in Clostridium acetobutylicum ATCC 824, Biotechnology (N Y), 10, 190 Mermelstein, 1993, In vivo methylation in Escherichia coli by the Bacillus subtilis phage phi 3T I methyltransferase to protect plasmids from restriction upon transformation of Clostridium acetobutylicum ATCC 824, Appl Environ Microbiol, 59, 1077, 10.1128/aem.59.4.1077-1081.1993 Pyne, 2013, Development of an electro transformation protocol for genetic manipulation of Clostridium pasteurianum, Biotechnol Biofuels, 6, 50, 10.1186/1754-6834-6-50 Sandoval, 2015, Whole-genome sequence of an evolved Clostridium pasteurianum strain reveals Spo0A deficiency responsible for increased butanol production and superior growth, Biotechnol Biofuels, 8, 227, 10.1186/s13068-015-0408-7 Bustin, 2009, The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments, Clin Chem, 55, 611, 10.1373/clinchem.2008.112797 Jones, 2008, The transcriptional program underlying the physiology of clostridial sporulation, Genome Biol, 9, R114, 10.1186/gb-2008-9-7-r114 Specht, 2020, Massively parallel CRISPRi assays reveal concealed thermodynamic determinants of dCas12a binding, Proc Natl Acad Sci U S A, 117, 11274, 10.1073/pnas.1918685117 Zhang, 2022, The off-target effect of CRISPR-Cas12a system toward insertions and deletions between target DNA and crRNA sequences, Anal Chem, 94, 8596, 10.1021/acs.analchem.1c05499 Kim, 2020, Enhancement of target specificity of CRISPR-Cas12a by using a chimeric DNA-RNA guide, Nucleic Acids Res, 48, 8601, 10.1093/nar/gkaa605 Cui, 2018, A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9, Nat Commun, 9, 1912, 10.1038/s41467-018-04209-5 Zhou, 2020, CRISPR-Cas12a-Assisted genome editing in amycolatopsis mediterranei, Front Bioeng Biotechnol, 8, 698, 10.3389/fbioe.2020.00698 Zhang, 2020, Efficient multiplex genome editing in streptomyces via engineered CRISPR-Cas12a systems, Front Bioeng Biotechnol, 8, 726, 10.3389/fbioe.2020.00726 Harris, 2002, Northern, morphological, and fermentation analysis of spo0A inactivation and overexpression in Clostridium acetobutylicum ATCC 824, J Bacteriol, 184, 3586, 10.1128/JB.184.13.3586-3597.2002 Al-Hinai, 2014, σK of Clostridium acetobutylicum is the first known sporulation-specific sigma factor with two developmentally separated roles, one early and one late in sporulation, J Bacteriol, 196, 287, 10.1128/JB.01103-13 Fackler, 2021, Transcriptional control of Clostridium autoethanogenum using CRISPRi, Synth Biol, 6, ysab008, 10.1093/synbio/ysab008 Silvis, 2021, Morphological and transcriptional responses to CRISPRi knockdown of essential genes in Escherichia coli, mBio, 12, 10.1128/mBio.02561-21 Jiang, 2009, Disruption of the acetoacetate decarboxylase gene in solvent-producing Clostridium acetobutylicum increases the butanol ratio, Metab Eng, 11, 284, 10.1016/j.ymben.2009.06.002 Buddrus, 2016, Crystal structure of pyruvate decarboxylase from Zymobacter palmae, Acta Crystallogr. Sect. F Struct. Biol. Commun., 72, 700, 10.1107/S2053230X16012012 Hossain, 1996, Characterization of pyruvate decarboxylase genes from rice, Plant Mol Biol, 31, 761, 10.1007/BF00019464 Mücke, 1996, Pyruvate decarboxylase from Pisum sativum, Eur J Biochem, 237, 373, 10.1111/j.1432-1033.1996.0373k.x Ishchuk, 2008, Overexpression of pyruvate decarboxylase in the yeast Hansenula polymorpha results in increased ethanol yield in high-temperature fermentation of xylose, FEMS Yeast Res, 8, 1164, 10.1111/j.1567-1364.2008.00429.x Grimmler, 2011, Genome-wide gene expression analysis of the switch between acidogenesis and solventogenesis in continuous cultures of Clostridium acetobutylicum, J Mol Microbiol Biotechnol, 20, 1 Dharani, 2021, Engineering Clostridium acetobutylicum for enhanced solvent production by overexpression of pyruvate decarboxylase from Zymomonas mobilis, Appl Biochem Microbiol, 57, 611, 10.1134/S0003683821050045 Ventura, 2013, Enhanced butanol production in Clostridium acetobutylicum ATCC 824 by double overexpression of 6-phosphofructokinase and pyruvate kinase genes, Appl Microbiol Biotechnol, 97, 7505, 10.1007/s00253-013-5075-7 Schwarz, 2017, Towards improved butanol production through targeted genetic modification of Clostridium pasteurianum, Metab Eng, 40, 124, 10.1016/j.ymben.2017.01.009 Li, 2016, CRISPR-based genome editing and expression control systems in Clostridium acetobutylicum and Clostridium beijerinckii, Biotechnol J, 11, 961, 10.1002/biot.201600053 Bruder, 2016, Extending CRISPR-Cas9 technology from genome editing to transcriptional engineering in genus Clostridium, Appl Environ Microbiol, 82, 6109, 10.1128/AEM.02128-16 Pyne, 2016, Disruption of the Reductive 1,3-Propanediol Pathway Triggers Production of 1,2-Propanediol for Sustained Glycerol Fermentation by <span class="named-content genus-species" id="named-content-1">Clostridium pasteurianum</span>, Appl Environ Microbiol, 82, 5375, 10.1128/AEM.01354-16 Johnson, 2016, The role of 1,3-propanediol production in fermentation of glycerol by Clostridium pasteurianum, Bioresour Technol, 209, 1, 10.1016/j.biortech.2016.02.088 Hartman, 2011, Construction and characterization of a lactose-inducible promoter system for controlled gene expression in Clostridium perfringens, Appl Environ Microbiol, 77, 471, 10.1128/AEM.01536-10 Andersch, 1983, Level of enzymes involved in acetate, butyrate, acetone and butanol formation by Clostridium acetobutylicum, Eur J Appl Microbiol Biotechnol, 18, 327, 10.1007/BF00504740