An Easy-to-Use Plasmid Toolset for Efficient Generation and Benchmarking of Synthetic Small RNAs in Bacteria.
Anti-Bacterial Agents
/ metabolism
Bacteria
/ genetics
Benchmarking
Escherichia coli
/ genetics
Gene Expression Regulation, Bacterial
/ genetics
Oxacillin
/ metabolism
Plasmids
/ genetics
RNA, Bacterial
/ genetics
RNA, Messenger
/ genetics
RNA, Small Untranslated
/ genetics
beta-Lactams
/ metabolism
antibiotic resistance
gene regulation
sRNA scaffold
seed region
synthetic biology
synthetic sRNA
Journal
ACS synthetic biology
ISSN: 2161-5063
Titre abrégé: ACS Synth Biol
Pays: United States
ID NLM: 101575075
Informations de publication
Date de publication:
16 09 2022
16 09 2022
Historique:
pubmed:
1
9
2022
medline:
20
9
2022
entrez:
31
8
2022
Statut:
ppublish
Résumé
Synthetic biology approaches life from the perspective of an engineer. Standardized and de novo design of genetic parts to subsequently build reproducible and controllable modules, for example, for circuit design, is a key element. To achieve this, natural systems and elements often serve as a blueprint for researchers. Regulation of protein abundance is controlled at DNA, mRNA, and protein levels. Many tools for the activation or repression of transcription or the destabilization of proteins are available, but easy-to-handle minimal regulatory elements on the mRNA level are preferable when translation needs to be modulated. Regulatory RNAs contribute considerably to regulatory networks in all domains of life. In particular, bacteria use small regulatory RNAs (sRNAs) to regulate mRNA translation. Slowly, sRNAs are attracting the interest of using them for broad applications in synthetic biology. Here, we promote a "plug and play" plasmid toolset to quickly and efficiently create synthetic sRNAs to study sRNA biology or their application in bacteria. We propose a simple benchmarking assay by targeting the
Identifiants
pubmed: 36044590
doi: 10.1021/acssynbio.2c00164
pmc: PMC9486967
doi:
Substances chimiques
Anti-Bacterial Agents
0
RNA, Bacterial
0
RNA, Messenger
0
RNA, Small Untranslated
0
beta-Lactams
0
Oxacillin
UH95VD7V76
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2989-3003Références
BioData Min. 2017 Sep 5;10:30
pubmed: 28878825
Algorithms Mol Biol. 2011 Nov 24;6:26
pubmed: 22115189
Nucleic Acids Res. 2018 Jul 27;46(13):e79
pubmed: 29741723
Biochimie. 2015 Jul;114:18-29
pubmed: 25792421
ACS Synth Biol. 2012 Jan 20;1(1):6-13
pubmed: 23651005
Genes Dev. 2007 Nov 1;21(21):2804-17
pubmed: 17974919
Nat Struct Mol Biol. 2009 Aug;16(8):840-6
pubmed: 19620966
EMBO J. 2019 Aug 15;38(16):e101650
pubmed: 31313835
Cell Syst. 2017 Oct 25;5(4):418-426.e4
pubmed: 28964700
Gene. 1991 Apr;100:13-26
pubmed: 2055464
J Biol Chem. 1999 Apr 16;274(16):10936-44
pubmed: 10196173
Mol Microbiol. 2016 Jul;101(1):136-51
pubmed: 26992034
Mol Microbiol. 1990 Jul;4(7):1063-7
pubmed: 1700254
ACS Synth Biol. 2018 Nov 16;7(11):2665-2674
pubmed: 30335370
J Mol Biol. 1992 Aug 5;226(3):735-45
pubmed: 1324324
Proc Natl Acad Sci U S A. 2010 Nov 23;107(47):20435-40
pubmed: 21059903
Nucleic Acids Res. 2011 Apr;39(8):e50
pubmed: 21296758
Appl Microbiol Biotechnol. 2022 Apr;106(7):2517-2527
pubmed: 35291022
Nucleic Acids Res. 2009 Nov;37(20):e133
pubmed: 19726584
Science. 2016 Aug 5;353(6299):aaf5573
pubmed: 27256883
Science. 2021 Sep 17;373(6561):1349-1353
pubmed: 34446442
Science. 1997 Sep 5;277(5331):1453-62
pubmed: 9278503
PLoS One. 2011 Feb 18;6(2):e16765
pubmed: 21364738
J Bacteriol. 1993 Oct;175(19):6299-313
pubmed: 8407802
PLoS One. 2020 Sep 2;15(9):e0238592
pubmed: 32877448
Wiley Interdiscip Rev RNA. 2021 Jul;12(4):e1640
pubmed: 33386705
BMC Bioinformatics. 2016 Apr 19;17:172
pubmed: 27094401
Mol Cell. 2021 Nov 4;81(21):4354-4356
pubmed: 34739827
Mol Microbiol. 2008 Oct;70(1):258-70
pubmed: 18761622
Adv Genet. 2015;90:133-208
pubmed: 26296935
PLoS Biol. 2016 Sep 15;14(9):e1002552
pubmed: 27631336
Gene. 2006 Sep 1;379:109-15
pubmed: 16750601
ACS Synth Biol. 2016 Dec 16;5(12):1362-1368
pubmed: 27306697
Nat Rev Microbiol. 2018 Oct;16(10):601-615
pubmed: 29995832
Nucleic Acids Res. 2017 Jul 27;45(13):8116-8127
pubmed: 28609783
Science. 1990 Aug 3;249(4968):505-10
pubmed: 2200121
Nat Rev Microbiol. 2011 Aug 15;9(8):578-89
pubmed: 21760622
Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9396-401
pubmed: 22645344
Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
pubmed: 12824337
Microbiol Spectr. 2018 May;6(3):
pubmed: 29932045
FEMS Microbiol Rev. 2019 May 1;43(3):304-339
pubmed: 30721976
Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6640-5
pubmed: 10829079
Nucleic Acids Res. 2017 Jul 3;45(W1):W435-W439
pubmed: 28472523
Mol Microbiol. 2017 Mar;103(6):1020-1033
pubmed: 27997707
Curr Biol. 2004 Dec 29;14(24):2271-6
pubmed: 15620655
BMC Microbiol. 2015 Nov 04;15:255
pubmed: 26531808
Nature. 2017 Oct 12;550(7675):280-284
pubmed: 28976959
J Mol Biol. 1983 Jun 5;166(4):557-80
pubmed: 6345791
Nature. 2021 Sep;597(7878):720-725
pubmed: 34489594
Nature. 1990 Aug 30;346(6287):818-22
pubmed: 1697402
Virology. 1955 Jul;1(2):190-206
pubmed: 13267987
PLoS One. 2008;3(11):e3647
pubmed: 18985154
Mol Cell. 2008 Dec 26;32(6):827-37
pubmed: 19111662
Science. 2017 Nov 24;358(6366):1019-1027
pubmed: 29070703
Mol Cell. 2007 May 11;26(3):381-92
pubmed: 17499044
Sci Rep. 2019 Oct 3;9(1):14256
pubmed: 31582786
Mol Cell. 2011 Sep 16;43(6):880-91
pubmed: 21925377
EMBO J. 2015 Oct 14;34(20):2557-73
pubmed: 26373314
Methods Enzymol. 1991;204:63-113
pubmed: 1943786
Biochemistry. 2017 Mar 7;56(9):1181-1198
pubmed: 28206750
Nat Methods. 2020 Jan;17(1):41-44
pubmed: 31768060
Nat Biotechnol. 2013 Feb;31(2):170-4
pubmed: 23334451
Antimicrob Agents Chemother. 2000 May;44(5):1387-90
pubmed: 10770787
J Biotechnol. 2006 May 29;123(3):273-80
pubmed: 16388869
Proc Natl Acad Sci U S A. 1989 Apr;86(7):2172-5
pubmed: 2648393
PLoS Biol. 2019 Jan 10;17(1):e3000107
pubmed: 30629605
BMB Rep. 2014 Nov;47(11):619-24
pubmed: 24411463
Nat Methods. 2009 May;6(5):343-5
pubmed: 19363495
Nucleic Acids Res. 2019 Jan 8;47(D1):D221-D229
pubmed: 30395267
J Proteome Res. 2012 Nov 2;11(11):5145-56
pubmed: 23017020
Biotechnol J. 2013 Dec;8(12):1379-95
pubmed: 24124015
Nat Protoc. 2013 Sep;8(9):1694-707
pubmed: 23928502
Nucleic Acids Res. 2022 Feb 22;50(3):1783-1793
pubmed: 35061908
J Bacteriol. 1995 Jul;177(14):4121-30
pubmed: 7608087
ACS Synth Biol. 2016 Dec 16;5(12):1441-1454
pubmed: 27434774