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Nowak KP, Sobolewska-Ruta A, Jagiełło A, Bierczyńska-Krzysik A, Kierył P, Wawrzyniak P. Molecular and Functional Characterization of MobK Protein-A Novel-Type Relaxase Involved in Mobilization for Conjugational Transfer of Klebsiella pneumoniae Plasmid pIGRK. Int J Mol Sci 2021; 22:5152. [PMID: 34068033 PMCID: PMC8152469 DOI: 10.3390/ijms22105152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 02/01/2023] Open
Abstract
Conjugation, besides transformation and transduction, is one of the main mechanisms of horizontal transmission of genetic information among bacteria. Conjugational transfer, due to its essential role in shaping bacterial genomes and spreading of antibiotics resistance genes, has been widely studied for more than 70 years. However, new and intriguing facts concerning the molecular basis of this process are still being revealed. Most recently, a novel family of conjugative relaxases (Mob proteins) was distinguished. The characteristic feature of these proteins is that they are not related to any of Mobs described so far. Instead of this, they share significant similarity to tyrosine recombinases. In this study MobK-a tyrosine recombinase-like Mob protein, encoded by pIGRK cryptic plasmid from the Klebsiella pneumoniae clinical strain, was characterized. This study revealed that MobK is a site-specific nuclease and its relaxase activity is dependent on both a conserved catalytic tyrosine residue (Y179) that is characteristic of tyrosine recombinases and the presence of Mg2+ divalent cations. The pIGRK minimal origin of transfer sequence (oriT) was also characterized. This is one of the first reports presenting tyrosine recombinase-like conjugative relaxase protein. It also demonstrates that MobK is a convenient model for studying this new protein family.
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Affiliation(s)
- Katarzyna Paulina Nowak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland;
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
| | - Agnieszka Sobolewska-Ruta
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
| | - Agata Jagiełło
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
- Central Forensic Laboratory of the Police, Biology Department, Iwicka 14, 00-735 Warsaw, Poland
| | - Anna Bierczyńska-Krzysik
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
- Curiosity Diagnostics Sp. z o.o., Duchnicka 3, Building 16, Entrance A, 01-796 Warsaw, Poland
| | - Piotr Kierył
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
| | - Paweł Wawrzyniak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland;
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
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Wawrzyniak P, Sobolewska-Ruta A, Zaleski P, Łukasiewicz N, Kabaj P, Kierył P, Gościk A, Bierczyńska-Krzysik A, Baran P, Mazurkiewicz-Pisarek A, Płucienniczak A, Bartosik D. Molecular dissection of the replication system of plasmid pIGRK encoding two in-frame Rep proteins with antagonistic functions. BMC Microbiol 2019; 19:254. [PMID: 31722681 PMCID: PMC6854812 DOI: 10.1186/s12866-019-1595-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 09/10/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Gene overlapping is a frequent phenomenon in microbial genomes. Excluding so-called "trivial overlapping", there are significant implications of such genetic arrangements, including regulation of gene expression and modification of protein activity. It is also postulated that, besides gene duplication, the appearance of overlapping genes (OGs) is one of the most important factors promoting a genome's novelty and evolution. OGs coding for in-frame proteins with different functions are a particularly interesting case. In this study we identified and characterized two in-frame proteins encoded by OGs on plasmid pIGRK from Klebsiella pneumoniae, a representative of the newly distinguished pHW126 plasmid family. RESULTS A single repR locus located within the replication system of plasmid pIGRK encodes, in the same frame, two functional polypeptides: a full-length RepR protein and a RepR' protein (with N-terminal truncation) translated from an internal START codon. Both proteins form homodimers, and interact with diverse DNA regions within the plasmid replication origin and repR promoter operator. Interestingly, RepR and RepR' have opposing functions - RepR is crucial for initiation of pIGRK replication, while RepR' is a negative regulator of this process. Nevertheless, both proteins act cooperatively as negative transcriptional regulators of their own expression. CONCLUSIONS Regulation of the initiation of pIGRK replication is a complex process in which a major role is played by two in-frame proteins with antagonistic functions. In-frame encoded Rep proteins are uncommon, having been described in only a few plasmids. This is the first description of such proteins in a plasmid of the pHW126 family.
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Affiliation(s)
- Paweł Wawrzyniak
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096 Warsaw, Poland
| | - Agnieszka Sobolewska-Ruta
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Piotr Zaleski
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Natalia Łukasiewicz
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Paulina Kabaj
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096 Warsaw, Poland
| | - Piotr Kierył
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Agata Gościk
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096 Warsaw, Poland
| | - Anna Bierczyńska-Krzysik
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Piotr Baran
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Anna Mazurkiewicz-Pisarek
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Andrzej Płucienniczak
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096 Warsaw, Poland
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Yuan L, Li L, Zheng F, Shi Y, Xie X, Chai A, Li B. The complete genome sequence of Rahnella aquatilis ZF7 reveals potential beneficial properties and stress tolerance capabilities. Arch Microbiol 2019; 202:483-499. [PMID: 31707426 DOI: 10.1007/s00203-019-01758-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 10/08/2019] [Accepted: 10/25/2019] [Indexed: 01/28/2023]
Abstract
Rahnella aquatilis ZF7 is a plant beneficial strain isolated from Sakura tree soil with potential for biocontrol. Here, we present the complete genome sequence of R. aquatilis ZF7, which consists of one 4.49 Mb circular chromosome and a 54-kb plasmid named pRAZF7. Phylogenetic analyses revealed that R. aquatilis ZF7 is much similar to the strains Rahnella sp. Y9602 and R. aquatilis HX2 than others evaluated. In this study, multiple genes encoding functions that likely contribute to plant growth promotion, biocontrol and stress tolerance were identified by comparative genome analyses, including IAA production, phosphate solubilization, antibiotic resistance and formation of Se nanoparticles (SeNPs). In addition, these functions were also confirmed by in vitro experiments. Considering its ability to form SeNPs, strain R. aquatilis ZF7 will contribute to nano-agriculture. Overall, the features of R. aquatilis ZF7 make it a high potential and competitive strain in biocontrol, and the genome data will help further studies on the mechanisms of plant growth promotion and biocontrol.
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Affiliation(s)
- Lifang Yuan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Lei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fei Zheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Horticulture and Landscape Architecture, Tianjin Agricultural University, Tianjin, 300384, China
| | - Yanxia Shi
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xuewen Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ali Chai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Baoju Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Rozhon W. The replication protein of pHW126 auto-controls its expression. Plasmid 2017; 90:38-43. [PMID: 28300545 DOI: 10.1016/j.plasmid.2017.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 10/20/2022]
Abstract
pHW126 belongs to a small group of rolling circle plasmids. So far, the region mediating autonomous replication has been identified and it was shown that the rep gene is required for replication. However, the regulation of rep expression remained elusive. Here evidence is presented that expression of the replication gene rep is auto-regulated. Sequence analysis revealed a conserved stretch in the rep promoter consisting of three imperfect direct repeats (DR2.1, DR2.2 and DR2.3). Assays for promoter activity showed that these direct repeats act as an enhancer of transcriptional activity. Interestingly, the activating effect was reduced in the presence of Rep protein. Electrophoretic mobility shift assays demonstrated that the Rep protein can directly bind to direct repeats DR2.1 and DR2.3 while DR2.2 is not bound but places DR2.1 and DR2.3 in an appropriate distance. These results show that the synthesis of Rep protein is auto-regulated. In the absence of Rep protein the promoter is, due to the presence of the direct repeats acting as a transcriptional enhancer, highly active. Binding of Rep to the direct repeats reduces the transcription rate significantly. Since this regulation mechanism is independent of a specialised regulator protein it is presumably a very economic strategy.
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Affiliation(s)
- Wilfried Rozhon
- Biotechnology of Horticultural Crops, TUM School for Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Straße 1, 85354 Freising-Weihenstephan, Germany.
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Zaleski P, Wawrzyniak P, Sobolewska A, Łukasiewicz N, Baran P, Romańczuk K, Daniszewska K, Kierył P, Płucienniczak G, Płucienniczak A. pIGWZ12 – A cryptic plasmid with a modular structure. Plasmid 2015; 79:37-47. [DOI: 10.1016/j.plasmid.2015.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/07/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
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Unterholzner SJ, Hailer B, Poppenberger B, Rozhon W. Characterisation of the stbD/E toxin-antitoxin system of pEP36, a plasmid of the plant pathogen Erwinia pyrifoliae. Plasmid 2013; 70:216-25. [PMID: 23632277 DOI: 10.1016/j.plasmid.2013.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/15/2013] [Accepted: 04/17/2013] [Indexed: 11/29/2022]
Abstract
pEP36 is a plasmid ubiquitously present in Erwinia pyrifoliae, a pathogen which causes black stem blight of Asian pear. pEP36 is highly stable in its host, even in the absence of selective pressure. The plasmid is closely related to pEA29, which is widespread in E. amylovora, the causative agent of fire blight of apple and pear trees. Here we report that pEP36 possesses a functional hybrid toxin-antitoxin module, stbD/E(pEP36), with the toxin showing homology to the RelE/ParE proteins and the antidote belonging to the Phd/YefM antitoxin family. Bacteria expressing the StbE(pEP36) toxin arrest cell growth and enter a viable but non-culturable stage. However, they maintain their typical cell length and do not show filamentation. Pulse-chase experiments revealed that StbE(pEP36) acts as a global inhibitor of protein synthesis while it does not interfere with DNA and RNA synthesis. The StbD(pEP36) antitoxin is capable of neutralising StbE(pEP36) toxicity. Additional experiments show that the stbD/E(pEP36) module can stabilise plasmids at least 20-fold. Thus the toxin-antitoxin system may contribute to the remarkable stability of pEP36.
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Affiliation(s)
- Simon J Unterholzner
- Biotechnology of Horticultural Crops, Technische Universität München, Liesel-Beckmann-Straße 1, 85354 Freising, Germany.
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Rozhon W, Khan M, Poppenberger B. Identification of the region required for maintaining pHW126 in its monomeric form. FEMS Microbiol Lett 2012; 331:89-96. [PMID: 22448845 DOI: 10.1111/j.1574-6968.2012.02557.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 03/22/2012] [Indexed: 11/29/2022] Open
Abstract
The pHW126-like plasmids are a recently discovered small group of cryptic plasmids replicating by the rolling circle mode. The replication origin of pHW126 consists of a conserved stretch, four perfect direct repeats and a so-called accessory region. The latter increases plasmid stability but is not absolutely necessary for replication. Here, we report that deletion of the accessory region causes rapid multimerization of pHW126. While the number of pHW126-units per cell remains constant, the number of physically independent plasmid molecules is reduced by approximately 40%, rendering random distribution to daughter cells less effective. A conserved inverted repeat within the accessory region could be identified as a sequence necessary for maintaining pHW126 in its monomeric form. A mutant version of pHW126 lacking this inverted repeat could be rescued by placing the single-strand initiation site (ssi) of pHW15 on the plus strand, while including the ssi in the opposite direction had no effect. Thus, our data provide evidence that multimer formation is, besides copy number reduction and ssDNA accumulation, an additional means how loss of a mechanism ensuring efficient lagging strand synthesis may cause destabilization of rolling circle plasmids.
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Affiliation(s)
- Wilfried Rozhon
- Biotechnology of Horticultural Crops, Technische Universität München, Freising, Germany.
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