Construction of Strong Promoters by Assembling Sigma Factor Binding Motifs.


Journal

Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969

Informations de publication

Date de publication:
2022
Historique:
entrez: 21 6 2022
pubmed: 22 6 2022
medline: 24 6 2022
Statut: ppublish

Résumé

Development of strong promoters is of growing interest in the field of biotechnology and synthetic biology. Here we present a protocol for the construction of strong prokaryotic promoters that can be recognized by designated multiple sigma factors by interlocking their cognate binding motifs on DNA strands. Strong and stress responsive promoters for Escherichia coli and Bacillus subtilis have been created following the presented protocol. Customized promoters could be easily developed for fine-tuning gene expression or overproducing enzymes with prokaryotic cell factories.

Identifiants

pubmed: 35727448
doi: 10.1007/978-1-0716-2152-3_9
doi:

Substances chimiques

Sigma Factor 0
DNA-Directed RNA Polymerases EC 2.7.7.6

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

137-147

Informations de copyright

© 2022. Springer Science+Business Media, LLC, part of Springer Nature.

Références

Zhang N, Darbari VC, Glyde R, Zhang XD, Buck M (2016) The bacterial enhancer-dependent RNA polymerase. Biochem J 473:3741–3753
doi: 10.1042/BCJ20160741C pubmed: 27789741
Barnard A, Wolfe A, Busby S (2004) Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes. Curr Opin Microbiol 7:102–108
doi: 10.1016/j.mib.2004.02.011 pubmed: 15063844
Block DHS, Hussein R, Liang LW, Lim HN (2012) Regulatory consequences of gene translocation in bacteria. Nucleic Acids Res 40:8979–8992
doi: 10.1093/nar/gks694 pubmed: 22833608 pmcid: 3467084
Browning DF, Busby SJW (2016) Local and global regulation of transcription initiation in bacteria. Nat Rev Microbiol 14:638–650
doi: 10.1038/nrmicro.2016.103 pubmed: 27498839
Browning DF, Butala M, Busby SJW (2019) Bacterial transcription factors: regulation by pick “N” mix. J Mol Biol 431:4067–4077
doi: 10.1016/j.jmb.2019.04.011 pubmed: 30998934
Feklistov A (2013) RNA polymerase: in search of promoters. Ann N Y Acad Sci 1293:25
doi: 10.1111/nyas.12197 pubmed: 23855603
Kazmierczak MJ, Wiedmann M, Boor KJ (2005) Alternative sigma factors and their roles in bacterial virulence. Microbiol Mol Biol Rev 69(4):527–543
doi: 10.1128/MMBR.69.4.527-543.2005 pubmed: 16339734 pmcid: 1306804
Yuzenkova Y, Tadigotla VR, Severinov K, Zenkin N (2011) A new basal promoter element recognized by RNA polymerase core enzyme. EMBO J 30(18):3766–3775
doi: 10.1038/emboj.2011.252 pubmed: 21792175 pmcid: 3173786
Feklistov A, Sharon BD, Darst SA, Gross CA (2014) Bacterial sigma factors: a historical, structural, and genomic perspective. In: Gottesman S (ed) Annual review of microbiology. Annual Reviews, New York, NY
Paget MS (2015) Bacterial sigma factors and anti-sigma factors: structure, function and distribution. Biomolecules 5(3):1245–1265
doi: 10.3390/biom5031245 pubmed: 26131973 pmcid: 4598750
Dall’Alba G, Casa PL, Notari DL, Adami AG, Echeverrigaray S, Silva SDE (2019) Analysis of the nucleotide content of Escherichia coli promoter sequences related to the alternative sigma factors. J Mol Recognit 32:e2770. https://doi.org/10.1002/jmr.2770
doi: 10.1002/jmr.2770 pubmed: 30458580
Osterberg S, del Peso-Santos T, Shingler V (2011) Regulation of alternative sigma factor use. In: Gottesman S, Harwood CS (eds) Annual review of microbiology, vol 65. Annual Reviews, New York, NY
Kandavalli VK, Huy T, Ribeiro AS (2016) Effects of sigma factor competition are promoter initiation kinetics dependent. Biochim Biophys Acta Gene Regul Mech 1859(10):1281–1288
doi: 10.1016/j.bbagrm.2016.07.011
Barker MM, Gaal T, Gourse RL (2001) Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP. J Mol Biol 305:689–702
doi: 10.1006/jmbi.2000.4328 pubmed: 11162085
Mauri M, Klumpp S (2014) A model for sigma factor competition in bacterial cells. PLoS Comp Biol 10:e1003845. https://doi.org/10.1371/journal.pcbi.1003845
doi: 10.1371/journal.pcbi.1003845
Klaholz BP (2017) The ribosome holds the RNA polymerase on track in bacteria. Trends Biochem Sci 42:686–689
doi: 10.1016/j.tibs.2017.07.003 pubmed: 28801047
Seo SW, Yang J, Min BE, Jang S, Lim JH, Lim HG, Kim SC, Kim SY, Jeong JH, Jung GY (2013) Synthetic biology: tools to design microbes for the production of chemicals and fuels. Biotechnol Adv 31:811–817
doi: 10.1016/j.biotechadv.2013.03.012 pubmed: 23578899
Wang Y, Liu QT, Weng HJ, Shi YA, Chen J, Du GC, Kang Z (2019) Construction of synthetic promoters by assembling the sigma factor binding -35 and -10 boxes. Biotechnol J 14:e1800298. https://doi.org/10.1002/biot.201800298
doi: 10.1002/biot.201800298 pubmed: 30457214
Wang Y, Shi YN, Hu LT, Du GC, Chen J, Kang Z (2019) Engineering strong and stress-responsive promoters in Bacillus subtilis by interlocking sigma factor binding motifs. Synth Syst Biotechnol 4:197–203
doi: 10.1016/j.synbio.2019.10.004 pubmed: 31750410 pmcid: 6849360
Campagne S, Marsh ME, Capitani G, Vorholt JA, Allain FHT (2014) Structural basis for -10 promoter element melting by environmentally induced sigma factors. Nat Struct Mol Biol 21(3):269–276
doi: 10.1038/nsmb.2777 pubmed: 24531660
Aghaabdollahian S, Rabbani M, Ghaedi K, Sadeghi HMM (2014) Molecular cloning of reteplase and its expression in E. coli using tac promoter. Adv Biomed Res 3:190
doi: 10.4103/2277-9175.140622 pubmed: 25298959 pmcid: 4189210
Marbach A, Bettenbrock K (2012) Lac operon induction in Escherichia coli: systematic comparison of IPTG and TMG induction and influence of the transacetylase LacA. J Biotechnol 157:82–88
doi: 10.1016/j.jbiotec.2011.10.009 pubmed: 22079752
Cho H, Winans SC (2007) TraA, TraC and TraD autorepress two divergent quorum-regulated promoters near the transfer origin of the Ti plasmid of Agrobacterium tumefaciens. Mol Microbiol 63:1769–1782
doi: 10.1111/j.1365-2958.2007.05624.x pubmed: 17367394
Helmann JD (2019) Where to begin? Sigma factors and the selectivity of transcription initiation in bacteria. Mol Microbiol 112(2):335–347
doi: 10.1111/mmi.14309 pubmed: 31119812 pmcid: 7046172
Xia YZ, Li K, Li JJ, Wang TQ, Gu LC, Xun LY (2019) T5 exonuclease-dependent assembly offers a low-cost method for efficient cloning and site-directed mutagenesis. Nucleic Acids Res 47:e15. https://doi.org/10.1093/nar/gky1169
doi: 10.1093/nar/gky1169 pubmed: 30462336
Mekler V, Pavlova O, Severinov K (2011) Interaction of Escherichia coli RNA polymerase sigma (70) subunit with promoter elements in the context of free sigma (70), rna polymerase holoenzyme, and the beta’-sigma (70) complex. J Biol Chem 286:270–279
doi: 10.1074/jbc.M110.174102 pubmed: 20952386
Koo BM, Rhodius VA, Campbell EA, Gross CA (2009) Dissection of recognition determinants of Escherichia coli sigma(32) suggests a composite -10 region with an extended -10 motif and a core -10 element. Mol Microbiol 72:815–829
doi: 10.1111/j.1365-2958.2009.06690.x pubmed: 19400791 pmcid: 4412615
Burgess RR (2013) Sigma factors. In: Maloy S, Hughes K (eds) Brenner’s encyclopedia of genetics, 2nd edn. Academic Press, San Diego, CA
Das S, Noe JC, Paik S, Kitten T (2005) An improved arbitrary primed PCR method for rapid characterization of transposon insertion sites. J Microbiol Methods 63(1):89–94
doi: 10.1016/j.mimet.2005.02.011 pubmed: 16157212
Saez NJ, Vincentelli R (2014) High-throughput expression screening and purification of recombinant proteins in E. coli. Methods Mol Biol 1091:33–53
doi: 10.1007/978-1-62703-691-7_3 pubmed: 24203323

Auteurs

Yonglin Zhang (Y)

The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.

Yang Wang (Y)

The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.

Jianghua Li (J)

The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.
The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Wuxi, China.

Chao Wang (C)

The Science Center for Future Foods, Jiangnan University, Wuxi, China.

Guocheng Du (G)

The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.
The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Wuxi, China.

Zhen Kang (Z)

The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China. zkang@jiangnan.edu.cn.
The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Wuxi, China. zkang@jiangnan.edu.cn.
The Science Center for Future Foods, Jiangnan University, Wuxi, China. zkang@jiangnan.edu.cn.

Articles similaires

Female Biofilms Animals Lactobacillus Mice

A computational model for bacteriophage ϕX174 gene expression.

Alexis M Hill, Tanvi A Ingle, Claus O Wilke
1.00
Gene Expression Regulation, Viral Promoter Regions, Genetic Bacteriophage phi X 174 Computer Simulation Models, Genetic
Host Specificity Bacteriophages Genomics Algorithms Escherichia coli
Arabidopsis Amorphophallus Plants, Genetically Modified Phylogeny Droughts

Classifications MeSH