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Biological characteristics and genome analysis of a novel phage vB_KpnP_IME279 infecting Klebsiella pneumoniae. Folia Microbiol (Praha) 2020; 65:925-936. [PMID: 33064268 DOI: 10.1007/s12223-020-00775-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/19/2020] [Indexed: 10/23/2022]
Abstract
Klebsiella pneumoniae (family Enterobacteriaceae) is a gram-negative bacterium that has strong pathogenicity to humans and can cause sepsis, pneumonia, and urinary tract infection. In recent years, the unreasonable use of antibacterial drugs has led to an increase in drug-resistant strains of K. pneumoniae, a serious threat to public health. Bacteriophages, viruses that infect bacteria, are ubiquitous in the natural environment. They are considered to be the most promising substitute for antibiotics because of their high specificity, high efficiency, high safety, low cost, and short development cycle. In this study, a novel phage designated vB_KpnP_IME279 was successfully isolated from hospital sewage using a multidrug-resistant strain of K. pneumoniae as an indicator. A one-step growth curve showed that vB_KpnP_IME279 has a burst size of 140 plaque-forming units/cell and a latent period of 20 min at its optimal multiplicity of infection (MOI = 0.1). Phage vB_KpnP_IME279 survives in a wide pH range between 3 and 11 and is stable at temperatures ranging from 40 to 60 °C. Ten of the 20 strains of K. pneumoniae including the host bacteria were lysed by the phage vB_KpnP_IME279, and the multilocus sequence typing and wzi typing of the 10 strains were ST11, ST37, ST375, wzi209, wzi52, and wzi72, respectively. The genome of vB_KpnP_IME279 is 42,518 bp long with a G + C content of 59.3%. Electron microscopic observation showed that the phage belongs to the family Podoviridae. BLASTN alignment showed that the genome of the phage has low similarity with currently known phages. The evolutionary relationship between phage vB_KpnP_IME279 and other Podoviridae was analyzed using a phylogenetic tree based on sequences of phage major capsid protein and indicates that the phage vB_KpnP_IME279 belongs to the Podoviridae subfamily. These data enhance understanding of K. pneumoniae phages and will help in development of treatments for multidrug-resistant bacteria using phages.
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Peng X, Deng X, Tang X, Tan T, Zhang D, Liu B, Lin H. Involvement of Lhcb6 and Lhcb5 in Photosynthesis Regulation in Physcomitrella patens Response to Abiotic Stress. Int J Mol Sci 2019; 20:ijms20153665. [PMID: 31357454 PMCID: PMC6695650 DOI: 10.3390/ijms20153665] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/20/2019] [Accepted: 07/22/2019] [Indexed: 11/16/2022] Open
Abstract
There are a number of highly conserved photosystem II light-harvesting antenna proteins in moss whose functions are unclear. Here, we investigated the involvement of chlorophyll-binding proteins, Lhcb6 and Lhcb5, in light-harvesting and photosynthesis regulation in Physcomitrella patens. Lhcb6 or Lhcb5 knock-out resulted in a disordered thylakoid arrangement, a decrease in the number of grana membranes, and an increase in the number of starch granule. The absence of Lhcb6 or Lhcb5 did not noticeably alter the electron transport rates. However, the non-photochemical quenching activity in the lhcb5 mutant was dramatically reduced when compared to wild-type or lhcb6 plants under abiotic stress. Lhcb5 plants were more sensitive to photo-inhibition, while lhcb6 plants showed little difference compared to the wild-type plants under high-light stress. Moreover, both mutants showed a growth malformation phenotype with reduced chlorophyll content in the gametophyte. These results suggested that Lhcb6 or Lhcb5 played a unique role in plant development, thylakoid organization, and photoprotection of PSII in Physcomitrella, especially when exposed to high light or osmotic environments.
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Affiliation(s)
- Xingji Peng
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Xingguang Deng
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Xiaoya Tang
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Tinghong Tan
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Dawei Zhang
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Baohui Liu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Honghui Lin
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China.
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Liang WW, Huang JH, Li CP, Yang LT, Ye X, Lin D, Chen LS. MicroRNA-mediated responses to long-term magnesium-deficiency in Citrus sinensis roots revealed by Illumina sequencing. BMC Genomics 2017; 18:657. [PMID: 28836935 PMCID: PMC5571589 DOI: 10.1186/s12864-017-3999-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 08/01/2017] [Indexed: 01/17/2023] Open
Abstract
Background Magnesium (Mg)-deficiency occurs most frequently in strongly acidic, sandy soils. Citrus are grown mainly on acidic and strong acidic soils. Mg-deficiency causes poor fruit quality and low fruit yield in some Citrus orchards. For the first time, we investigated Mg-deficiency-responsive miRNAs in ‘Xuegan’ (Citrus sinensis) roots using Illumina sequencing in order to obtain some miRNAs presumably responsible for Citrus Mg-deficiency tolerance. Results We obtained 101 (69) miRNAs with increased (decreased) expression from Mg-starved roots. Our results suggested that the adaptation of Citrus roots to Mg-deficiency was related to the several aspects: (a) inhibiting root respiration and related gene expression via inducing miR158 and miR2919; (b) enhancing antioxidant system by down-regulating related miRNAs (miR780, miR6190, miR1044, miR5261 and miR1151) and the adaptation to low-phosphorus (miR6190); (c) activating transport-related genes by altering the expression of miR6190, miR6485, miR1044, miR5029 and miR3437; (d) elevating protein ubiquitination due to decreased expression levels of miR1044, miR5261, miR1151 and miR5029; (e) maintaining root growth by regulating miR5261, miR6485 and miR158 expression; and (f) triggering DNA repair (transcription regulation) by regulating miR5176 and miR6485 (miR6028, miR6190, miR6485, miR5621, miR160 and miR7708) expression. Mg-deficiency-responsive miRNAs involved in root signal transduction also had functions in Citrus Mg-deficiency tolerance. Conclusions We obtained several novel Mg-deficiency-responsive miRNAs (i.e., miR5261, miR158, miR6190, miR6485, miR1151 and miR1044) possibly contributing to Mg-deficiency tolerance. These results revealed some novel clues on the miRNA-mediated adaptation to nutrient deficiencies in higher plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3999-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei-Wei Liang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jing-Hao Huang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Pomological Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China
| | - Chun-Ping Li
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lin-Tong Yang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xin Ye
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dan Lin
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Li-Song Chen
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Beike AK, Lang D, Zimmer AD, Wüst F, Trautmann D, Wiedemann G, Beyer P, Decker EL, Reski R. Insights from the cold transcriptome of Physcomitrella patens: global specialization pattern of conserved transcriptional regulators and identification of orphan genes involved in cold acclimation. THE NEW PHYTOLOGIST 2015; 205:869-81. [PMID: 25209349 PMCID: PMC4301180 DOI: 10.1111/nph.13004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/17/2014] [Indexed: 05/21/2023]
Abstract
The whole-genome transcriptomic cold stress response of the moss Physcomitrella patens was analyzed and correlated with phenotypic and metabolic changes. Based on time-series microarray experiments and quantitative real-time polymerase chain reaction, we characterized the transcriptomic changes related to early stress signaling and the initiation of cold acclimation. Transcription-associated protein (TAP)-encoding genes of P. patens and Arabidopsis thaliana were classified using generalized linear models. Physiological responses were monitored with pulse-amplitude-modulated fluorometry, high-performance liquid chromatography and targeted high-performance mass spectrometry. The transcript levels of 3220 genes were significantly affected by cold. Comparative classification revealed a global specialization of TAP families, a transcript accumulation of transcriptional regulators of the stimulus/stress response and a transcript decline of developmental regulators. Although transcripts of the intermediate to later response are from evolutionarily conserved genes, the early response is dominated by species-specific genes. These orphan genes may encode as yet unknown acclimation processes.
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Affiliation(s)
- Anna K Beike
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
| | - Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
- Institut für Humangenetik, Universitätsklinikum FreiburgBreisacherstr. 33, D-79106, Freiburg, Germany
| | - Florian Wüst
- Cell Biology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
| | - Danika Trautmann
- Cell Biology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
- Institut National de la Recherche Agronomique28 rue de Herrlisheim, F-68021, Colmar, France
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
| | - Peter Beyer
- Cell Biology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
- FRISYS - Freiburg Initiative for Systems Biology79104, Freiburg, Germany
- BIOSS–Centre for Biological Signaling Studies79104, Freiburg, Germany
- FRIAS– Freiburg Institute for Advanced Studies79104, Freiburg, Germany
- TIP–Trinational Institute for Plant Research79104, Freiburg, Germany
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