Development of two compatible plasmids to assess sRNA-mediated post-transcriptional regulation in Acinetobacter baumannii

References

1. Papenfort K, Melamed S. Small RNAs, large networks: posttranscriptional regulons in Gram-negative bacteria. Annu Rev Microbiol 2023; 77:23–43 [View Article] [PubMed]
   [Google Scholar]
2. Papenfort K, Storz G. Insights into bacterial metabolism from small RNAs. Cell Chem Biol 2024; 31:1571–1577 [View Article] [PubMed]
   [Google Scholar]
3. Barquist L, Vogel J. Accelerating discovery and functional analysis of small RNAs with new technologies. Annu Rev Genet 2015; 49:367–394 [View Article] [PubMed]
   [Google Scholar]
4. Georg J, Lalaouna D, Hou S, Lott SC, Caldelari I et al. The power of cooperation: experimental and computational approaches in the functional characterization of bacterial sRNAs. Mol Microbiol 2020; 113:603–612 [View Article] [PubMed]
   [Google Scholar]
5. Hör J, Gorski SA, Vogel J. Bacterial RNA biology on a genome scale. Mol Cell 2018; 70:785–799 [View Article] [PubMed]
   [Google Scholar]
6. Liu F, Chen Z, Zhang S, Wu K, Bei C et al. In vivo RNA interactome profiling reveals 3’UTR-processed small RNA targeting a central regulatory hub. Nat Commun 2023; 14:8106 [View Article]
   [Google Scholar]
7. Urban JH, Vogel J. Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic Acids Res 2007; 35:1018–1037 [View Article] [PubMed]
   [Google Scholar]
8. Vogel J, Wagner EGH. Target identification of small noncoding RNAs in bacteria. Curr Opin Microbiol 2007; 10:262–270 [View Article] [PubMed]
   [Google Scholar]
9. Sharma CM, Vogel J. Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol 2009; 12:536–546 [View Article] [PubMed]
   [Google Scholar]
10. Urban JH, Vogel J. A green fluorescent protein (GFP)-based plasmid system to study post-transcriptional control of gene expression in vivo. In Serganov A. ed Riboswitches: Methods and Protocols Totowa, NJ: Humana Press; pp 301–319 [View Article]
    [Google Scholar]
11. Corcoran CP, Podkaminski D, Papenfort K, Urban JH, Hinton JCD et al. Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA. Mol Microbiol 2012; 84:428–445 [View Article] [PubMed]
    [Google Scholar]
12. Kröger C, Kary SC, Schauer K, Cameron ADS. Genetic regulation of virulence and antibiotic resistance in Acinetobacter baumannii. Genes 2016; 8:12 [View Article] [PubMed]
    [Google Scholar]
13. Jie J, Chu X, Li D, Luo Z. A set of shuttle plasmids for gene expression in Acinetobacter baumannii. PLoS One 2021; 16:e0246918 [View Article] [PubMed]
    [Google Scholar]
14. Intorcia V, Sava RL, Schroeder GP, Gebhardt MJ. A series of vectors for inducible gene expression in multidrug-resistant Acinetobacter baumannii. Appl Environ Microbiol 2024; 90:e0047424 [View Article] [PubMed]
    [Google Scholar]
15. Hunger M, Schmucker R, Kishan V, Hillen W. Analysis and nucleotide sequence of an origin of DNA replication in Acinetobacter calcoaceticus and its use for Escherichia coli shuttle plasmids. Gene 1990; 87:45–51 [View Article] [PubMed]
    [Google Scholar]
16. Lucidi M, Runci F, Rampioni G, Frangipani E, Leoni L et al. New shuttle vectors for gene cloning and expression in multidrug-resistant Acinetobacter species. Antimicrob Agents Chemother 2018; 62:e02480-17 [View Article] [PubMed]
    [Google Scholar]
17. Ducas-Mowchun K, De Silva PM, Crisostomo L, Fernando DM, Chao T-C et al. Next generation of Tn7-based single-copy insertion elements for use in multi- and pan-drug-resistant strains of Acinetobacter baumannii. Appl Environ Microbiol 2019; 85:e00066-19 [View Article] [PubMed]
    [Google Scholar]
18. Lucidi M, Visaggio D, Prencipe E, Imperi F, Rampioni G et al. New shuttle vectors for real-time gene expression analysis in multidrug-resistant Acinetobacter species: in vitro and in vivo responses to environmental stressors. Appl Environ Microbiol 2019; 85:e01334-19 [View Article] [PubMed]
    [Google Scholar]
19. Bacon EE, Tran JS, Nadig N, Peters JM. Modular, inducible, and titratable expression systems for Escherichia coli and Acinetobacter baumannii. Microbiol Spectr 2024; 12:e01306–24 [View Article]
    [Google Scholar]
20. Singer JT, van Tuijl JJ, Finnerty WR. Transformation and mobilization of cloning vectors in Acinetobacter spp. J Bacteriol 1986; 165:301–303 [View Article] [PubMed]
    [Google Scholar]
21. Chung CT, Niemela SL, Miller RH. One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc Natl Acad Sci USA 1989; 86:2172–2175 [View Article]
    [Google Scholar]
22. Xia Y, Li K, Li J, Wang T, Gu L et al. T5 exonuclease-dependent assembly offers a low-cost method for efficient cloning and site-directed mutagenesis. Nucleic Acids Res 2019; 47:e15 [View Article] [PubMed]
    [Google Scholar]
23. Zhang Y, Werling U, Edelmann W. SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res 2012; 40:e55–e55 [View Article] [PubMed]
    [Google Scholar]
24. Kröger C, Dillon SC, Cameron ADS, Papenfort K, Sivasankaran SK et al. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci USA 2012; 109:E1277–86 [View Article] [PubMed]
    [Google Scholar]
25. Kröger C, MacKenzie KD, Alshabib EY, Kirzinger MWB, Suchan DM et al. The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978. Nucleic Acids Res 2018; 46:9684–9698 [View Article] [PubMed]
    [Google Scholar]
26. Jacobs AC, Thompson MG, Black CC, Kessler JL, Clark LP et al. AB5075, a highly virulent isolate of Acinetobacter baumannii, as a model strain for the evaluation of pathogenesis and antimicrobial treatments. mBio 2014; 5:e01076–14 [View Article]
    [Google Scholar]
27. Godeux A-S, Svedholm E, Lupo A, Haenni M, Venner S et al. Scarless removal of large resistance island AbaR results in antibiotic susceptibility and increased natural transformability in Acinetobacter baumannii. Antimicrob Agents Chemother 2020; 64:00951–20 [View Article]
    [Google Scholar]
28. Hamrock FJ, Ryan D, Shaibah A, Ershova AS, Mogre A et al. Global analysis of the RNA-RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO. Nucleic Acids Res 2024; 52:11283–11300 [View Article] [PubMed]
    [Google Scholar]
29. Loehfelm TW, Luke NR, Campagnari AA. Identification and characterization of an Acinetobacter baumannii biofilm-associated protein. J Bacteriol 2008; 190:1036–1044 [View Article] [PubMed]
    [Google Scholar]
30. De Gregorio E, Del Franco M, Martinucci M, Roscetto E, Zarrilli R et al. Biofilm-associated proteins: news from Acinetobacter. BMC Genomics 2015; 16:933 [View Article] [PubMed]
    [Google Scholar]
31. Busch A, Richter AS, Backofen R. IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 2008; 24:2849–2856 [View Article] [PubMed]
    [Google Scholar]
32. Diesh C, Stevens GJ, Xie P, De Jesus Martinez T, Hershberg EA et al. JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biol 2023; 24:74 [View Article] [PubMed]
    [Google Scholar]
33. Sharma CM, Darfeuille F, Plantinga TH, Vogel J. A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev 2007; 21:2804–2817 [View Article]
    [Google Scholar]
34. Papenfort K, Bouvier M, Mika F, Sharma CM, Vogel J. Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNA. Proc Natl Acad Sci USA 2010; 107:20435–20440 [View Article]
    [Google Scholar]
35. Sharma CM, Papenfort K, Pernitzsch SR, Mollenkopf H, Hinton JCD et al. Pervasive post‐transcriptional control of genes involved in amino acid metabolism by the Hfq‐dependent GcvB small RNA. Molecular Microbiology 2011; 81:1144–1165 [View Article]
    [Google Scholar]
36. Papenfort K, Podkaminski D, Hinton JCD, Vogel J. The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair. Proc Natl Acad Sci USA 2012; 109:E757–64 [View Article] [PubMed]
    [Google Scholar]
37. Fröhlich KS, Papenfort K, Berger AA, Vogel J. A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD. Nucleic Acids Res 2012; 40:3623–3640 [View Article] [PubMed]
    [Google Scholar]
38. Chao Y, Papenfort K, Reinhardt R, Sharma CM, Vogel J. An atlas of Hfq-bound transcripts reveals 3’ UTRs as a genomic reservoir of regulatory small RNAs. EMBO J 2012; 31:4005–4019 [View Article] [PubMed]
    [Google Scholar]
39. Fröhlich KS, Haneke K, Papenfort K, Vogel J. The target spectrum of SdsR small RNA in Salmonella. Nucleic Acids Res 2016; 44:10406–10422 [View Article] [PubMed]
    [Google Scholar]
40. Smirnov A, Wang C, Drewry LL, Vogel J. Molecular mechanism of mRNA repression in trans by a ProQ-dependent small RNA. EMBO J 2017; 36:1029–1045 [View Article] [PubMed]
    [Google Scholar]
41. Miyakoshi M, Matera G, Maki K, Sone Y, Vogel J. Functional expansion of a TCA cycle operon mRNA by a 3’ end-derived small RNA. Nucleic Acids Res 2019; 47:2075–2088 [View Article] [PubMed]
    [Google Scholar]
42. Melamed S, Adams PP, Zhang A, Zhang H, Storz G. RNA-RNA interactomes of ProQ and Hfq reveal overlapping and competing roles. Mol Cell 2020; 77:411–425 [View Article] [PubMed]
    [Google Scholar]
43. Faigenbaum-Romm R, Reich A, Gatt YE, Barsheshet M, Argaman L et al. Hierarchy in Hfq chaperon occupancy of small RNA targets plays a major role in their regulation. Cell Rep 2020; 30:3127–3138 [View Article] [PubMed]
    [Google Scholar]
44. Herzog R, Peschek N, Fröhlich KS, Schumacher K, Papenfort K. Three autoinducer molecules act in concert to control virulence gene expression in Vibrio cholerae. Nucleic Acids Res 2019; 47:3171–3183 [View Article] [PubMed]
    [Google Scholar]
45. Peschek N, Herzog R, Singh PK, Sprenger M, Meyer F et al. RNA-mediated control of cell shape modulates antibiotic resistance in Vibrio cholerae. Nat Commun 2020; 11:6067 [View Article] [PubMed]
    [Google Scholar]
46. Wu K, Lin X, Lu Y, Dong R, Jiang H et al. RNA interactome of hypervirulent Klebsiella pneumoniae reveals a small RNA inhibitor of capsular mucoviscosity and virulence. Nat Commun 2024; 15:6946 [View Article]
    [Google Scholar]
47. Ghandour R, Devlitsarov D, Popp P, Melamed S, Huber M et al. ProQ-associated small RNAs control motility in Vibrio cholerae. Nucleic Acids Res 2025; 53:gkae1283 [View Article] [PubMed]
    [Google Scholar]
48. Ryan D, Bornet E, Prezza G, Alampalli SV, Franco de Carvalho T et al. An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity. Nat Microbiol 2024; 9:1130–1144 [View Article] [PubMed]
    [Google Scholar]
49. Schilling D, Gerischer U. The Acinetobacter baylyi Hfq gene encodes a large protein with an unusual C terminus. J Bacteriol 2009; 191:5553–5562 [View Article] [PubMed]
    [Google Scholar]
50. Sharma A, Dubey V, Sharma R, Devnath K, Gupta VK et al. The unusual glycine-rich C terminus of the Acinetobacter baumannii RNA chaperone Hfq plays an important role in bacterial physiology. J Biol Chem 2018; 293:13377–13388 [View Article] [PubMed]
    [Google Scholar]
51. Sett A, Maiti PK, Garg K, Hussain A, Saini S et al. “GGFGGQ” repeats in Hfq of Acinetobacter baumannii are essential for nutrient utilization and virulence. J Biol Chem 2024; 300:107895 [View Article] [PubMed]
    [Google Scholar]
52. Köbel TS, Melo Palhares R, Fromm C, Szymanski W, Angelidou G et al. An easy-to-use plasmid toolset for efficient generation and benchmarking of synthetic small RNAs in bacteria. ACS Synth Biol 2022; 11:2989–3003 [View Article] [PubMed]
    [Google Scholar]
53. Brück M, Köbel TS, Dittmar S, Ramírez Rojas AA, Georg J et al. A library-based approach allows systematic and rapid evaluation of seed region length and reveals design rules for synthetic bacterial small RNAs. iScience 2024; 27:110774 [View Article]
    [Google Scholar]
54. Chang PH, Juhrend B, Olson TM, Marrs CF, Wigginton KR. Degradation of extracellular antibiotic resistance genes with UV₂₅₄ treatment. Environ Sci Technol 2017; 51:6185–6192 [View Article] [PubMed]
    [Google Scholar]
55. D’Souza R, Pinto NA, Higgins PG, Hwang I, Yong D et al. First report of the carbapenemase gene blaOXA-499 in Acinetobacter pittii. Antimicrob Agents Chemother 2017; 61:02676–16 [View Article]
    [Google Scholar]
56. Nagahari K, Sakaguchi K. RSF1010 plasmid as a potentially useful vector in Pseudomonas species. J Bacteriol 1978; 133:1527–1529 [View Article] [PubMed]
    [Google Scholar]
57. Lee MD, Henk AD. RSF1010-based shuttle vectors for cloning and expression in Pasteurella multocida. Vet Microbiol 1997; 54:369–374 [View Article] [PubMed]
    [Google Scholar]
58. Bishé B, Taton A, Golden JW. Modification of RSF1010-based broad-host-range plasmids for improved conjugation and cyanobacterial bioprospecting. iScience 2019; 20:216–228 [View Article] [PubMed]
    [Google Scholar]
59. Mann M, Wright PR, Backofen R. IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions. Nucleic Acids Res 2017; 45:W435–W439 [View Article] [PubMed]
    [Google Scholar]