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Bi D, Xie Y, Tai C, Jiang X, Zhang J, Harrison EM, Jia S, Deng Z, Rajakumar K, Ou HY. A Site-Specific Integrative Plasmid Found in Pseudomonas aeruginosa Clinical Isolate HS87 along with A Plasmid Carrying an Aminoglycoside-Resistant Gene. PLoS One 2016; 11:e0148367. [PMID: 26841043 PMCID: PMC4739549 DOI: 10.1371/journal.pone.0148367] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/19/2016] [Indexed: 12/30/2022] Open
Abstract
Plasmids play critical roles in bacterial fitness and evolution of Pseudomonas aeruginosa. Here two plasmids found in a drug-resistant P. aeruginosa clinical isolate HS87 were completely sequenced. The pHS87b plasmid (11.2 kb) carries phage-related genes and function-unknown genes. Notably, pHS87b encodes an integrase and has an adjacent tRNAThr-associated attachment site. A corresponding integrated form of pHS87b at the tRNAThr locus was identified on the chromosome of P. aeruginosa, showing that pHS87b is able to site-specifically integrate into the 3’-end of the tRNAThr gene. The pHS87a plasmid (26.8 kb) displays a plastic structure containing a putative replication module, stability factors and a variable region. The RepA of pHS87a shows significant similarity to the replication proteins of pPT23A-family plasmids. pHS87a carries a transposon Tn6049, a truncated insertion sequence ΔIS1071 and a Tn402-like class 1 integron which contains an aacA4 cassette that may confer aminoglycoside resistance. Thus, pHS87b is a site-specific integrative plasmid whereas pHS87a is a plastic antibiotic resistance plasmid. The two native plasmids may promote the fitness and evolution of P. aeruginosa.
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Affiliation(s)
- Dexi Bi
- State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Yingzhou Xie
- State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Cui Tai
- State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Xiaofei Jiang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jie Zhang
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
| | - Ewan M. Harrison
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | - Shiru Jia
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
| | - Zixin Deng
- State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Kumar Rajakumar
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | - Hong-Yu Ou
- State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai, China
- * E-mail:
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Cheng L, House MW, Weiss WJ, Banks MK. Monitoring sulfide-oxidizing biofilm activity on cement surfaces using non-invasive self-referencing microsensors. WATER RESEARCH 2016; 89:321-329. [PMID: 26707733 DOI: 10.1016/j.watres.2015.11.066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/15/2015] [Accepted: 11/28/2015] [Indexed: 06/05/2023]
Abstract
Microbially influenced corrosion (MIC) in concrete results in significant cost for infrastructure maintenance. Prior studies have employed molecular techniques to identify microbial community species in corroded concrete, but failed to explore bacterial activity and functionality during deterioration. In this study, biofilms of different sulfur-oxidizing bacteria compositions were developed on the surface of cement paste samples to simulate the natural ecological succession of microbial communities during MIC processes. Noninvasive, self-referencing (SR) microsensors were used to quantify real time changes of oxygen, hydrogen ion and calcium ion flux for the biofilm to provide more information about bacterial behavior during deterioration. Results showed higher transport rates in oxygen consumption, and hydrogen ion at 4 weeks than 2 weeks, indicating increased bacterial activity over time. Samples with five species biofilm had the highest hydrogen ion and calcium ion transport rates, confirming attribution of acidophilic sulfur-oxidizing microorganisms (ASOM). Differences in transport rates between three species samples and two species samples confirmed the diversity between Thiomonas intermedia and Starkeya novella. The limitations of SR sensors in corrosion application could be improved in future studies when combined with molecular techniques to identify the roles of major bacterial species in the deterioration process.
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Affiliation(s)
- Liqiu Cheng
- Zachry Department of Civil Engineering, Texas A&M University, 3136 TAMU, College Station, TX 77843-3136, USA.
| | - Mitch W House
- Lyles School of Civil Engineering, Purdue University, 550 Stadium Mall Drive, West Lafayette, IN 47907-2051, USA
| | - W Jason Weiss
- Lyles School of Civil Engineering, Purdue University, 550 Stadium Mall Drive, West Lafayette, IN 47907-2051, USA; Bindley Bioscience Center, Physiological Sensing Facility, Discovery Park, Purdue University, 1203 W. State Street, West Lafayette, IN 47907-2057, USA
| | - M Katherine Banks
- Zachry Department of Civil Engineering, Texas A&M University, 3136 TAMU, College Station, TX 77843-3136, USA
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Sundin GW. Genomic insights into the contribution of phytopathogenic bacterial plasmids to the evolutionary history of their hosts. ANNUAL REVIEW OF PHYTOPATHOLOGY 2007; 45:129-51. [PMID: 17367270 DOI: 10.1146/annurev.phyto.45.062806.094317] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Plasmids are common residents of phytopathogenic bacteria and contribute significantly to host evolution in a multi-faceted manner. Plasmids tend to encode determinants of virulence and ecological fitness that can enhance adaptation to a specific niche or can influence niche expansion. Many of these determinants appear to have been acquired from other bacteria via horizontal transfer, illustrating an important function of plasmids in the acquisition of sequences that enable rapid evolution. These genes can ultimately be delivered to the host chromosome through plasmid integration events, thus stabilizing important acquired determinants within the genome. Most plasmids characterized in phytopathogenic bacteria are self-transmissible and possess suites of genes encoding type IV secretion systems. In addition, the phytopathogenic bacterial plasmid "mobilome" includes insertion sequence and other transposable elements that contribute to the movement of sequences within and between genomes. Possession of mosaic and ever-changing plasmids allows phytopathogenic bacteria to maintain a dynamic, flexible genome and possible advantage in host-pathogen and other environmental interactions that belies the concept of plasmids as apparently selfish genetic elements.
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Affiliation(s)
- George W Sundin
- Department of Plant Pathology and Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA.
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Yagura M, Nishio SY, Kurozumi H, Wang CF, Itoh T. Anatomy of the replication origin of plasmid ColE2-P9. J Bacteriol 2006; 188:999-1010. [PMID: 16428404 PMCID: PMC1347323 DOI: 10.1128/jb.188.3.999-1010.2006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plasmid ColE2-P9 origin is a 32-bp region which is specifically recognized by the plasmid-specified Rep protein to initiate DNA replication. We analyzed the structural and functional organization of the ColE2 origin by using various derivatives carrying deletions and single-base-pair substitutions. The origin may be divided into three subregions: subregion I, which is important for stable binding of the Rep protein; subregion II, which is important for binding of the Rep protein and for initiation of DNA replication; and subregion III, which is important for DNA replication but apparently not for binding of the Rep protein. The Rep protein might recognize three specific DNA elements in subregions I and II. The relative transformation frequency of the autonomously replicating plasmids carrying deletions in subregion I is lower, and nevertheless the copy numbers of these plasmids in host bacteria are higher than those of the wild-type plasmid. Efficient and stable binding of the Rep protein to the origin might be important for the replication efficiency to be at the normal (low) level. Subregion II might be essential for interaction with the catalytic domain of the Rep protein for primer RNA synthesis. The 8-bp sequence across the border of subregions II and III, including the primer sequence, is conserved in the (putative) origins of many plasmids, the putative Rep proteins of which are related to the ColE2-P9 Rep protein. Subregion III might be required for a step that is necessary after Rep protein binding has taken place.
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Affiliation(s)
- Masaru Yagura
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto, Nagano 390-8621, Japan.
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Kalyaeva E, Bass I, Kholodii G, Nikiforov V. A broad host range plasmid vector that does not encode replication proteins. FEMS Microbiol Lett 2002; 211:91-5. [PMID: 12052556 DOI: 10.1111/j.1574-6968.2002.tb11208.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The 640-bp minimal replication region derived from a plasmid DNA preparation from an Acidothiobacillus ferrooxidans strain capable of autonomous replication in a range of Gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa, Acinetobacter calcoaceticus and Alcaligenes faecalis) was identified. This DNA fragment (named TFK replicon) does not encode Rep proteins and appears to be unrelated to other known replicons.
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Affiliation(s)
- Eza Kalyaeva
- Institute of Molecular Genetics, Russian Academy of Sciences, 123182, Moscow, Russia
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Abstract
The whole nucleotide sequence of pT3.2I, the smallest plasmid of the acidophilic bacterium Thiobacillus T3.2, has been determined. pT3.2I is 15,390 bp long with a 53.7% GC content. Different regions can be defined in it: one 2569-bp putative insertion sequence similar to other insertion sequences of some Agrobacterium Ti plasmids; and a longer sequence, which occurs in two almost identical copies, differing only in a 1-bp deletion (6406 and 6405 bp). Several open reading frames and some smaller sequences were found in this duplicated region: ORFA and ORFG, encoding a putative polyol dehydrogenase and a putative RepA replication protein, respectively, an 83-bp sequence which could code for an antisense RNA, and a 36-bp region highly homologous to ori sequences of ColE2- and ColE3-related plasmids. Another putative gene, ORFH, is only present in the longer copy of this region (it is deleted in the short copy) and might encode a 90-amino-acid polypeptide which could act as a second replication protein, RepB. Based on sequence comparisons, pT3. 2I can be related to plasmids in the pColE2-CA42 incB incompatibility group.
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Affiliation(s)
- T Aparicio
- Department of Biochemistry and Molecular Biology, Complutense University of Madrid, Madrid, 28040, Spain
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Huang TC, Burr TJ. Characterization of plasmids that encode streptomycin-resistance in bacterial epiphytes of apple. J Appl Microbiol 1999; 86:741-51. [PMID: 10347868 DOI: 10.1046/j.1365-2672.1999.00719.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Streptomycin resistance in strains of Pseudomonas syringae pv. papulans, Pantoea agglomerans and a yellow-pigmented, non-fluorescent Pseudomonas sp. (Py), isolated from apple orchards in New York and Washington states, is predominantly associated with strA-strB genes carried on conjugal plasmids (R plasmids). None of 128 resistant Erwinia amylovora strains from the eastern and western USA hybridized with a strA-strB probe, SMP3. Resistant Py strains transfered R plasmids to Ps. syringae pv. papulans and to Py in vitro at frequencies of 10(-1)-10(-2) per recipient cell whereas Ps. syringae pv. papulans transferred its plasmids at frequencies of 10(-2) to below detectable levels. Transfer of R plasmids to P. agglomerans was not detected and resistant P. agglomerans did not transfer their R plasmids to any recipients. R plasmids were found to be highly diverse as measured by DNA fingerprint analysis. Transfer-deficient transposon mutants of R plasmid pCPP519 were generated, and 3.9 kb EcoRI and 3.0 kb SmaI fragments that hybridized with a Tn5 probe were cloned and sequenced. The deduced amino acid sequences of the 3.9 kb fragment were similar to proteins involved in replication, nicking at oriT, and piliation in other bacteria.
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Affiliation(s)
- T C Huang
- Department of Plant Pathology, Cornell University, New York State Agricultural Experiment Station, Geneva 14456, USA
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Leret V, Trautwetter A, Rind A, Blanco C. pBLA8, from Brevibacterium linens, belongs to a gram-positive subfamily of ColE2-related plasmids. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 10):2827-2836. [PMID: 9802024 DOI: 10.1099/00221287-144-10-2827] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A 3.1 kb DNA fragment from pBLA8, a Brevibacterium linens cryptic plasmid, containing all the information required for autonomous replication was cloned and sequenced. Using deletion analysis, the fragment essential and sufficient for autonomous replication was delimited to 1.5 kb. This fragment is characterized by the presence of an ori site located upstream of an operon encoding two proteins, RepA and RepB, both essential for replication. Based on structural similarities and a strong conservation of ori, RepA and RepB, pBLA8 was assigned to a new subfamily of the ColE2 plasmid family. This subfamily is distinguished by the requirement for two Rep proteins and the location of an ori site upstream of the repAB operon. RepA is thought to encode primase activity, whereas RepB could be a DNA-binding protein. An Escherichia coli-B. linens shuttle vector, derived from pBLA8, was constructed. Its host spectrum was extended to Arthrobacter species.
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De Mot R, Nagy I, De Schrijver A, Pattanapipitpaisal P, Schoofs G, Vanderleyden J. Structural analysis of the 6 kb cryptic plasmid pFAJ2600 from Rhodococcus erythropolis NI86/21 and construction of Escherichia coli-Rhodococcus shuttle vectors. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 10):3137-3147. [PMID: 9353918 DOI: 10.1099/00221287-143-10-3137] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The complete nucleotide sequence of the 5936 bp cryptic plasmid pFAJ2600 from Rhodococcus erythropolis NI86/21 was determined. Based on the characteristics of its putative replication genes, repA and repB, pFAJ2600 was assigned to the family of pAL5000-related small replicons identified in Mycobacterium (pAL5000), Corynebacterium (pXZ10142), Brevibacterium (pRBL1), Bifidobacterium (pMB1) and Neisseria (pJD1). The replication systems of these plasmids show striking similarities to the ones used by the ColE2 family of plasmids from Enterobacteria with respect to both trans-acting factors and ori sequences. Two possible plasmid stabilization systems are encoded on pFAJ2600: a site-specific recombinase (PmrA) related to the Escherichia coli Xer proteins for plasmid multimer resolution and an ATPase (ParA) related to the A-type of proteins in sop/par partitioning systems. The proposed replication termination region of pFAJ2600 has features in common with the Ter loci of Bacillus subtilis. Chimeras composed of a pUC18-Cmr derivative inserted in the parA-repA intergenic region of vector pFAJ2600 produced vectors that could be shuttled between Escherichia coli and several Rhodococcus species (R. erythropolis, R. fascians, R. rhodochrous, R. ruber). The pFAJ2600-based shuttle vector pFAJ2574 was stably maintained in R. erythropolis and R. fascians growing under non-selective conditions.
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Affiliation(s)
- René De Mot
- F. A. Janssens Laboratory of Genetics, Department of Applied Plant Sciences, Catholic University of Leuven, Willem de Croylaan 42, B-3001 Heverlee, Belgium
| | - István Nagy
- F. A. Janssens Laboratory of Genetics, Department of Applied Plant Sciences, Catholic University of Leuven, Willem de Croylaan 42, B-3001 Heverlee, Belgium
| | - Adinda De Schrijver
- F. A. Janssens Laboratory of Genetics, Department of Applied Plant Sciences, Catholic University of Leuven, Willem de Croylaan 42, B-3001 Heverlee, Belgium
| | - Pranee Pattanapipitpaisal
- F. A. Janssens Laboratory of Genetics, Department of Applied Plant Sciences, Catholic University of Leuven, Willem de Croylaan 42, B-3001 Heverlee, Belgium
| | - Geert Schoofs
- F. A. Janssens Laboratory of Genetics, Department of Applied Plant Sciences, Catholic University of Leuven, Willem de Croylaan 42, B-3001 Heverlee, Belgium
| | - Jos Vanderleyden
- F. A. Janssens Laboratory of Genetics, Department of Applied Plant Sciences, Catholic University of Leuven, Willem de Croylaan 42, B-3001 Heverlee, Belgium
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English RS, Jin S, Shively JM. Use of Electroporation To Generate a Thiobacillus neapolitanus Carboxysome Mutant. Appl Environ Microbiol 1995; 61:3256-60. [PMID: 16535117 PMCID: PMC1388571 DOI: 10.1128/aem.61.9.3256-3260.1995] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two cloning vectors designed for use in Escherichia coli and the thiobacilli were constructed by combining a Thiobacillus intermedius plasmid replicon with a multicloning site, lacZ(prm1), and either a kanamycin or a streptomycin resistance gene. Conditions necessary for the introduction of DNA into T. intermedius and T. neapolitanus via electroporation were examined and optimized. By using optimal electroporation conditions, the gene encoding a carboxysome shell protein, csoS1A, was insertionally inactivated in T. neapolitanus. The mutant showed a reduced number of carboxysomes and an increased level of CO(inf2) necessary for growth.
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