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Ulloa-Muñoz R, Olivera-Gonzales P, Castañeda-Barreto A, Villena GK, Tamariz-Angeles C. Diversity of endophytic plant-growth microorganisms from Gentianella weberbaueri and Valeriana pycnantha, highland Peruvian medicinal plants. Microbiol Res 2020; 233:126413. [PMID: 31981904 DOI: 10.1016/j.micres.2020.126413] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/19/2019] [Accepted: 01/10/2020] [Indexed: 10/25/2022]
Abstract
Microbial diversity in Peruvian mountain areas is poorly know, specially endophytic microorganisms of medicinal native plants from the Cordillera Blanca. So, nine bacterial and six fungal species were isolated from Gentianella weberbaueri and Valeriana pycnantha. According to 16S rDNA analysis, bacterial strains belong to genera Rahnella, Pseudomonas, Serratia, Rouxiella, and Bacillus; while ITS analysis showed that fungi belong to Pyrenochaeta, Scleroconidioma, Cryptococcus, and Plenodomus genera. Rahnella sp. GT24B and P. trivialis VT20B solubilized tricalcium phosphate and produced siderophores at 10 and 24 °C. Five bacteria strains produced indol-3-acetic acid (IAA) at 10 and 24 °C, where Rahnella sp. VT19B showed more production at 10 °C than 24 °C. Rahnella sp. GT24B, Serratia sp. VT28B, and Rahnella sp. GT25B inhibited Fusarium oxysporum growth up to 100, 78 and 74 %, respectively. R. inusitata VT25B and B. licheniformis GT10B showed high cellulolytic and proteolytic activities. On the other hand, only a few fungi moderately inhibited growth of F. oxysporum, and produced siderophores and cellulases. Most of bacteria inoculated on Medicago sativa "alfalfa" and Triticum aestivum "wheat" seeds got better root development, especially Rahnella sp. GT24B, Rouxiella sp.VT24B, Serratia sp. VT28B, and Rahnella sp. VT34B. Finally, this study is the first report of endophytic microorganisms associated to wild medicinal high-mountain Peruvian plants and it show a valuable microbial diversity and its possible role in promoting growth of crops and wild medicinal plants.
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Affiliation(s)
- Rocío Ulloa-Muñoz
- Facultad de Ciencias Agrarias, Universidad Nacional Santiago Antúnez de Mayolo, Av. Centenario 200, 02002 Independencia, Ancash Huaraz, Peru
| | - Percy Olivera-Gonzales
- Centro de Investigación de la Biodiversidad y Recursos Genéticos, Facultad de Ciencias, Universidad Nacional Santiago Antúnez de Mayolo, Av. Centenario 200, 02002 Independencia, Ancash, Huaraz, Peru
| | - Alberto Castañeda-Barreto
- Centro de Investigación de la Biodiversidad y Recursos Genéticos, Facultad de Ciencias, Universidad Nacional Santiago Antúnez de Mayolo, Av. Centenario 200, 02002 Independencia, Ancash, Huaraz, Peru
| | - Gretty K Villena
- Laboratorio de Micología y Biotecnología, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima 12, Peru
| | - Carmen Tamariz-Angeles
- Centro de Investigación de la Biodiversidad y Recursos Genéticos, Facultad de Ciencias, Universidad Nacional Santiago Antúnez de Mayolo, Av. Centenario 200, 02002 Independencia, Ancash, Huaraz, Peru.
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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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Zharikova NV, Iasakov TR, Bumazhkin BK, Patutina EO, Zhurenko EI, Korobov VV, Sagitova AI, Kuznetsov BB, Markusheva TV. Isolation and sequence analysis of pCS36-4CPA, a small plasmid from Citrobacter sp. 36-4CPA. Saudi J Biol Sci 2018; 25:660-671. [PMID: 29736141 PMCID: PMC5935869 DOI: 10.1016/j.sjbs.2016.02.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/07/2015] [Accepted: 02/08/2016] [Indexed: 11/22/2022] Open
Abstract
A small plasmid designated pCS36-4CPA with a size of 5217 base pairs and G-C content of 50.74% was isolated from Citrobacter sp. 36-4CPA. The origin of replication (ori) of the plasmid was identified as a region of about 800 bp in length with an identity of 67.1% to the ColE1 plasmid at the nucleotide level. The replication region contained typical elements of ColE1-like plasmids: RNA I and RNA II with their corresponding -10 and -35 boxes, a single-strand initiation site (ssi), and a lagging-strand termination site (terH). As seen in other ColE1-like plasmids, pCS36-4CPA carried mobilisation machinery that include mobABCD genes but it did not possess the rom gene. Analysis of the multimer resolution site (mrs) was performed and XerC and XerD binding sites were identified. Also, the 70-nt transcript Rcd of pCS36-4CPA was predicted and similarity of the transcript's secondary structure with those of the ColE1-family was shown. The cargo module of pCS36-4CPA contained three open reading frames (ORFs). Two of them (ORF5 and ORF6) showed no significant homology to any known gene sequences but contained putative THAP DNA-binding (DBD) and type II restriction endonuclease EcoO109I domains. The seventh open reading frame (ORF7) encodes YhdJ-like DNA modification methylase. The region highly homologous to pCS36-4CPA was found in the Salmonella phage SE2 genome.
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Ares-Arroyo M, Bernabe-Balas C, Santos-Lopez A, Baquero MR, Prasad KN, Cid D, Martin-Espada C, San Millan A, Gonzalez-Zorn B. PCR-Based Analysis of ColE1 Plasmids in Clinical Isolates and Metagenomic Samples Reveals Their Importance as Gene Capture Platforms. Front Microbiol 2018; 9:469. [PMID: 29615998 PMCID: PMC5864857 DOI: 10.3389/fmicb.2018.00469] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/28/2018] [Indexed: 02/04/2023] Open
Abstract
ColE1 plasmids are important vehicles for the spread of antibiotic resistance in the Enterobacteriaceae and Pasteurellaceae families of bacteria. Their monitoring is essential, as they harbor important resistant determinants in humans, animals and the environment. In this work, we have analyzed ColE1 replicons using bioinformatic and experimental approaches. First, we carried out a computational study examining the structure of different ColE1 plasmids deposited in databases. Bioinformatic analysis of these ColE1 replicons revealed a mosaic genetic structure consisting of a host-adapted conserved region responsible for the housekeeping functions of the plasmid, and a variable region encoding a wide variety of genes, including multiple antibiotic resistance determinants. From this exhaustive computational analysis we developed a new PCR-based technique, targeting a specific sequence in the conserved region, for the screening, capture and sequencing of these small plasmids, either specific for Enterobacteriaceae or specific for Pasteurellaceae. To validate this PCR-based system, we tested various collections of isolates from both bacterial families, finding that ColE1 replicons were not only highly prevalent in antibiotic-resistant isolates, but also present in susceptible bacteria. In Pasteurellaceae, ColE1 plasmids carried almost exclusively antibiotic resistance genes. In Enterobacteriaceae, these plasmids encoded a large range of traits, including not only antibiotic resistance determinants, but also a wide variety of genes, showing the huge genetic plasticity of these small replicons. Finally, we also used a metagenomic approach in order to validate this technique, performing this PCR system using total DNA extractions from fecal samples from poultry, turkeys, pigs and humans. Using Illumina sequencing of the PCR products we identified a great diversity of genes encoded by ColE1 replicons, including different antibiotic resistance determinants, supporting the previous results achieved with the collections of bacterial isolates. In addition, we detected cryptic ColE1 plasmids in both families with no known genes in their variable region, which we have named sentinel plasmids. In conclusion, in this work we present a useful genetic tool for the detection and analysis of ColE1 plasmids, and confirm their important role in the dissemination of antibiotic resistance, especially in the Pasteurellaceae family of bacteria.
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Affiliation(s)
- Manuel Ares-Arroyo
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Cristina Bernabe-Balas
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Alfonso Santos-Lopez
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Maria R Baquero
- Departamento de Microbiología, Facultad de Veterinaria, Universidad Alfonso X el Sabio, Madrid, Spain
| | - Kashi N Prasad
- Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Dolores Cid
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Carmen Martin-Espada
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Alvaro San Millan
- Servicio de Microbiología Hospital Universitario Ramón y Cajal, Instituto de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Bruno Gonzalez-Zorn
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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Rozhon W, Kammermeier L, Schramm S, Towfique N, Adebimpe Adedeji N, Adesola Ajayi S, Poppenberger B. Quantification of the Pyrrolizidine Alkaloid Jacobine in Crassocephalum crepidioides by Cation Exchange High-Performance Liquid Chromatography. PHYTOCHEMICAL ANALYSIS : PCA 2018; 29:48-58. [PMID: 28836707 DOI: 10.1002/pca.2713] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 06/07/2023]
Abstract
INTRODUCTION Pyrrolizidine alkaloids (PAs) are secondary plant metabolites with considerable hepatoxic, tumorigenic and genotoxic potential. For separation, reversed phase chromatography is commonly used because of its excellent compatibility with detection by mass spectrometry. However, reversed phase chromatography has a low selectivity for PAs. OBJECTIVE The objective of this work was to investigate the suitability of cation exchange chromatography for separation of PAs and to develop a rapid method for quantification of jacobine in Crassocephalum crepidioides that is suitable for analysis of huge sample numbers as required for mutant screening procedures. RESULTS We demonstrate that cation exchange chromatography offers excellent selectivity for PAs allowing their separation from most other plant metabolites. Due to the high selectivity, plant extracts can be directly analysed after simple sample preparation. Detection with UV at 200 nm instead of mass spectrometry can be applied, which makes the method very simple and cost-effective. The recovery rate of the method exceeded 95%, the intra-day and inter-day standard deviations were below 7% and the limit of detection and quantification were 1 mg/kg and 3 mg/kg, respectively. CONCLUSION The developed method is sufficiently sensitive for reproducible detection of jacobine in C. crepidioides. Simple sample preparation and rapid separation allows for quantification of jacobine in plant material in a high-throughput manner. Thus, the method is suitable for genetic screenings and may be applicable for other plant species, for instance Jacobaea maritima. In addition, our results show that C. crepidioides cannot be considered safe for human consumption. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Wilfried Rozhon
- Biotechnology of Horticultural Crops, Technische Universität München, Liesel-Beckmann-Straße 1, 85354, Freising-Weihenstephan, Germany
| | - Lukas Kammermeier
- Biotechnology of Horticultural Crops, Technische Universität München, Liesel-Beckmann-Straße 1, 85354, Freising-Weihenstephan, Germany
| | - Sebastian Schramm
- Biotechnology of Horticultural Crops, Technische Universität München, Liesel-Beckmann-Straße 1, 85354, Freising-Weihenstephan, Germany
| | - Nayeem Towfique
- Biotechnology of Horticultural Crops, Technische Universität München, Liesel-Beckmann-Straße 1, 85354, Freising-Weihenstephan, Germany
| | - N Adebimpe Adedeji
- Department of Crop Production and Protection, Obafemi Awolowo University, PMB 013, Ilé-Ifè, 220005, Nigeria
| | - S Adesola Ajayi
- Department of Crop Production and Protection, Obafemi Awolowo University, PMB 013, Ilé-Ifè, 220005, Nigeria
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, Technische Universität München, Liesel-Beckmann-Straße 1, 85354, Freising-Weihenstephan, Germany
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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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8
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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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Fathallh Eida M, Nagaoka T, Wasaki J, Kouno K. Phytate degradation by fungi and bacteria that inhabit sawdust and coffee residue composts. Microbes Environ 2012; 28:71-80. [PMID: 23100024 PMCID: PMC4070677 DOI: 10.1264/jsme2.me12083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Phytate is the primary source of organic phosphorus, but it cannot be directly utilized by plants and is strongly adsorbed by the soil, reducing bioavailability. Composting is a process used to improve the bioavailability of phytate in organic wastes through degradation by microorganisms. In this study, we aimed to investigate the phytate-degrading ability of fungi and bacteria that inhabit sawdust compost and coffee residue compost, and their contribution to the composting process. In the plate assay, the fungi that formed clear zones around their colonies belonged to the genera Mucor, Penicillium, Galactomyces, Coniochaeta, Aspergillus, and Fusarium, while the bacteria belonged to the genera Pseudomonas, Enterobacter, Chitinophaga, and Rahnella. Eight fungal isolates (genera Mucor, Penicillium, Galactomyces, and Coniochaeta) and four bacterial isolates (genera Pseudomonas, Enterobacter, and Rahnella) were selected to evaluate phytase activity in their liquid culture and their ability to degrade phytate in organic materials composed of mushroom media residue and rice bran. The selected fungi degraded phytate in organic materials to varying degrees. Penicillium isolates showed the highest degradation ability and Coniochaeta isolate exhibited relatively high degradation ability. The clear zone diameters of these fungal isolates displayed significantly positive and negative correlations with inorganic and phytate phosphorus contents in the organic materials after incubation, respectively; however, none of the selected bacteria reduced phytate phosphorus in organic materials. It is therefore possible that fungi are major contributors to phytate degradation during composting.
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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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Rozhon W, Khan M, Petutschnig E, Poppenberger B. Identification of cis- and trans-acting elements in pHW126, a representative of a novel group of rolling circle plasmids. Plasmid 2010; 65:70-6. [PMID: 20854841 DOI: 10.1016/j.plasmid.2010.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 09/13/2010] [Accepted: 09/14/2010] [Indexed: 10/19/2022]
Abstract
pHW126, pIGRK, pIGMS31 and pRAO1 are the only known members of a novel and as yet uncharacterised family of rolling circle plasmids. pHW126 contains only two open reading frames, of which one shows homology to pMV158-family mobilisation proteins. Here we provide evidence that the second open reading frame encodes a replication protein (Rep). Mutation or deletion of this gene resulted in replication deficient constructs, but providing functional Rep from a compatible vector rescued these constructs, indicating that Rep acts in trans. An approximately 300 bp cis-acting region representing the origin of replication was identified upstream of the rep gene. The origin was identified to be composed of three parts: an accessory region, a conserved stretch and four perfect tandem repeats. The two latter elements were essential for replication. Constructs with a deletion of the accessory region could still replicate, but their loss rate was high, indicating that the accessory region is necessary for plasmid maintenance under non-selective conditions. Interestingly, pHW126 could replicate in all Enterobacteriaceae tested while Agrobacterium tumefaciens and Pseudomonas syringae were inappropriate hosts. Thus, pHW126 seems to have a rather limited host range.
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Affiliation(s)
- Wilfried Rozhon
- Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria.
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Abstract
Pantoea stewartii SW2 contains 13 plasmids. One of these plasmids, pSW200, has a replicon that resembles that of ColE1. This study demonstrates that pSW200 contains a 9-bp UP element, 5'-AAGATCTTC, which is located immediately upstream of the -35 box in the RNAII promoter. A transcriptional fusion study reveals that substituting this 9-bp sequence reduces the activity of the RNAII promoter by 78%. The same mutation also reduced the number of plasmid copies from 13 to 5, as well as the plasmid stability. When a similar sequence in a ColE1 derivative, pYCW301, is mutated, the copy number of the plasmid also declines from 34 to 16 per cell. Additionally, inserting this 9-bp sequence stabilizes an unstable pSW100 derivative, pSW142K, which also contains a replicon resembling that of ColE1, indicating the importance of this sequence in maintaining the stability of the plasmid. In conclusion, the 9-bp sequence upstream of the -35 box in the RNAII promoter is required for the efficient synthesis of RNAII and maintenance of the stability of the plasmids in the ColE1 family.
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Rozhon W, Petutschnig E, Khan M, Summers DK, Poppenberger B. Frequency and diversity of small cryptic plasmids in the genus Rahnella. BMC Microbiol 2010; 10:56. [PMID: 20170524 PMCID: PMC2831885 DOI: 10.1186/1471-2180-10-56] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 02/19/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rahnella is a widely distributed genus belonging to the Enterobacteriaceae and frequently present on vegetables. Although Rahnella has interesting agro-economical and industrial properties and several strains possess antibiotic resistances and toxin genes which might spread within microbial communities, little is known about plasmids of this genus. Thus, we isolated a number of Rahnella strains and investigated their complements of small plasmids. RESULTS In total 53 strains were investigated and 11 plasmids observed. Seven belonged to the ColE1 family; one was ColE2-like and three shared homology to rolling circle plasmids. One of them belonged to the pC194/pUB110 family and two showed similarity to poorly characterised plasmid groups. The G+C content of two rolling circle plasmids deviated considerably from that of Rahnella, indicating that their usual hosts might belong to other genera. Most ColE1-like plasmids formed a subgroup within the ColE1 family that seems to be fairly specific for Rahnella. Intriguingly, the multimer resolution sites of all ColE1-like plasmids had the same orientation with respect to the origin of replication. This arrangement might be necessary to prevent inappropriate synthesis of a small regulatory RNA that regulates cell division. Although the ColE1-like plasmids did not possess any mobilisation system, they shared large parts with high sequence identity in coding and non-coding regions. In addition, highly homologous regions of plasmids isolated from Rahnella and the chromosomes of Erwinia tasmaniensis and Photorhabdus luminescens could be identified. CONCLUSIONS For the genus Rahnella we observed plasmid-containing isolates at a frequency of 19%, which is in the average range for Enterobacteriaceae. These plasmids belonged to different groups with members of the ColE1-family most frequently found. Regions of striking sequence homology of plasmids and bacterial chromosomes highlight the importance of plasmids for lateral gene transfer (including chromosomal sequences) to distinct genera.
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Affiliation(s)
- Wilfried Rozhon
- Max F Perutz Laboratories, University of Vienna, Dr Bohrgasse 9, Vienna, Austria.
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14
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Rozhon W, Baubec T, Mayerhofer J, Mittelsten Scheid O, Jonak C. Rapid quantification of global DNA methylation by isocratic cation exchange high-performance liquid chromatography. Anal Biochem 2008; 375:354-60. [PMID: 18249178 DOI: 10.1016/j.ab.2008.01.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 01/03/2008] [Indexed: 10/22/2022]
Abstract
The DNA of many eukaryotes is methylated at specific cytosine residues in connection with gene regulation. Here we report a method for the quantification of global cytosine methylation based on enzymatic hydrolysis of DNA, dephosphorylation, and subsequent high-performance cation exchange chromatography. Nucleosides are separated in less than 3 min under isocratic conditions on a benzenesulfonic acid-modified silica phase and detected by UV absorption. As little as 1 microg of DNA is sufficient to measure 5-methyldeoxycytosine levels with a typical relative standard deviation of less than 3%. As a proof of concept, the method was applied for analysis of DNA from several Arabidopsis thaliana mutants affected in DNA methylation and from Medicago sativa seedlings treated with the environmental pollutant chromium(VI).
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Affiliation(s)
- Wilfried Rozhon
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria.
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15
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Beazley MJ, Martinez RJ, Sobecky PA, Webb SM, Taillefert M. Uranium biomineralization as a result of bacterial phosphatase activity: insights from bacterial isolates from a contaminated subsurface. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2007; 41:5701-7. [PMID: 17874776 DOI: 10.1021/es070567g] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Uranium contamination is an environmental concern at the Department of Energy's Field Research Center in Oak Ridge, Tennessee. In this study, we investigated whether phosphate biomineralization, or the aerobic precipitation of U(VI)-phosphate phases facilitated by the enzymatic activities of microorganisms, offers an alternative to the more extensively studied anaerobic U(VI) bioreduction. Three heterotrophic bacteria isolated from FRC soils were studied for their ability to grow and liberate phosphate in the presence of U(VI) and an organophosphate between pH 4.5 and 7.0. The objectives were to determine whether the strains hydrolyzed sufficient phosphate to precipitate uranium, to determine whether low pH might have an effect on U(VI) precipitation, and to identify the uranium solid phase formed during biomineralization. Two bacterial strains hydrolyzed sufficient organophosphate to precipitate 7395% total uranium after 120 h of incubation in simulated groundwater. The highest rates of uranium precipitation and phosphatase activity were observed between pH 5.0 and 7.0. EXAFS spectra identified the uranyl phosphate precipitate as an autunite/meta-autunite group mineral. The results of this study indicate that aerobic heterotrophic bacteria within a uranium-contaminated environment that can hydrolyze organophosphate, especially in low pH conditions, may play an important role in the bioremediation of uranium.
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Affiliation(s)
- Melanie J Beazley
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0340, USA
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