scholarly journals Identification and Characterization of a Novel Robigovirus Species from Sweet Cherry in Turkey

Pathogens ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 57 ◽  
Author(s):  
Kadriye Çağlayan ◽  
Vahid Roumi ◽  
Mona Gazel ◽  
Eminur Elçi ◽  
Mehtap Acioğlu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Open Reading Frames ◽  
Cherry Tree ◽  
Coding Regions ◽  
Sweet Cherries ◽  
Identification And Characterization ◽  
Reading Frames

High throughput sequencing of total RNA isolated from symptomatic leaves of a sweet cherry tree (Prunus avium cv. 0900 Ziraat) from Turkey identified a new member of the genus Robigovirus designated cherry virus Turkey (CVTR). The presence of the virus was confirmed by electron microscopy and overlapping RT-PCR for sequencing its whole-genome. The virus has a ssRNA genome of 8464 nucleotides which encodes five open reading frames (ORFs) and comprises two non-coding regions, 5′ UTR and 3′ UTR of 97 and 296 nt, respectively. Compared to the five most closely related robigoviruses, RdRp, TGB1, TGB2, TGB3 and CP share amino acid identities ranging from 43–53%, 44–60%, 39–43%, 38–44% and 45–50%, respectively. Unlike the four cherry robigoviruses, CVTR lacks ORFs 2a and 5a. Its genome organization is therefore more similar to African oil palm ringspot virus (AOPRV). Using specific primers, the presence of CVTR was confirmed in 15 sweet cherries and two sour cherries out of 156 tested samples collected from three regions in Turkey. Among them, five samples were showing slight chlorotic symptoms on the leaves. It seems that CVTR infects cherry trees with or without eliciting obvious symptoms, but these data should be confirmed by bioassays in woody and possible herbaceous hosts in future studies.

scholarly journals Functional-Genomics-Based Identification and Characterization of Open Reading Frames Encoding α-Glucoside-Processing Enzymes in the Hyperthermophilic Archaeon Pyrococcus furiosus

2007 ◽  
Vol 74 (4) ◽  
pp. 1281-1283 ◽  
Author(s):  
Donald A. Comfort ◽  
Chung-Jung Chou ◽  
Shannon B. Conners ◽  
Amy L. VanFossen ◽  
Robert M. Kelly
Keyword(s):  
Glycoside Hydrolase ◽  
Bioinformatics Analysis ◽  
Pyrococcus Furiosus ◽  
Transcriptional Response ◽  
Open Reading Frames ◽  
Processing Enzymes ◽  
Response Information ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT Bioinformatics analysis and transcriptional response information for Pyrococcus furiosus grown on α-glucans led to the identification of a novel isomaltase (PF0132) representing a new glycoside hydrolase (GH) family, a novel GH57 β-amylase (PF0870), and an extracellular starch-binding protein (1,141 amino acids; PF1109-PF1110), in addition to several other putative α-glucan-processing enzymes.

scholarly journals Multilocus Characterization, Gene Expression Analysis of Putative Immunodominant Protein Coding Regions, and Development of Recombinase Polymerase Amplification Assay for Detection of ‘Candidatus Phytoplasma Pruni’ in Prunus avium

2019 ◽  
Vol 109 (6) ◽  
pp. 983-992 ◽  
Author(s):  
Dan Edward V. Villamor ◽  
Kenneth C. Eastwell
Keyword(s):  
High Throughput Sequencing ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Protein A ◽  
Recombinase Polymerase Amplification ◽  
Sequencing Data ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Regions ◽  
Reverse Transcription Pcr

Western X (WX) disease, caused by ‘Candidatus Phytoplasma pruni’, is a devastating disease of sweet cherry resulting in the production of small, bitter-flavored fruits that are unmarketable. Escalation of WX disease in Washington State prompted the development of a rapid detection assay based on recombinase polymerase amplification (RPA) to facilitate timely removal and replacement of diseased trees. Here, we report on a reliable RPA assay targeting putative immunodominant protein coding regions that showed comparable sensitivity to polymerase chain reaction (PCR) in detecting ‘Ca. Phytoplasma pruni’ from crude sap of sweet cherry tissues. Apart from the predominant strain of ‘Ca. Phytoplasma pruni’, the RPA assay also detected a novel strain of phytoplasma from several WX-affected trees. Multilocus sequence analyses using the immunodominant protein A (idpA), imp, rpoE, secY, and 16S ribosomal RNA regions from several ‘Ca. Phytoplasma pruni’ isolates from WX-affected trees showed that this novel phytoplasma strain represents a new subgroup within the 16SrIII group. Examination of high-throughput sequencing data from total RNA of WX-affected trees revealed that the imp coding region is highly expressed, and as supported by quantitative reverse transcription PCR data, it showed higher RNA transcript levels than the previously proposed idpA coding region of ‘Ca. Phytoplasma pruni’.

scholarly journals Identification and Characterization of a Gene Cluster for Synthesis of the Polyketide Antibiotic 2,4-Diacetylphloroglucinol from Pseudomonas fluorescens Q2-87

1999 ◽  
Vol 181 (10) ◽  
pp. 3155-3163 ◽  
Author(s):  
M. Gita Bangera ◽  
Linda S. Thomashow
Keyword(s):  
Genomic Dna ◽  
Plant Pathogens ◽  
Polyketide Synthase ◽  
Open Reading Frames ◽  
Fungal Plant Pathogens ◽  
Repressor Proteins ◽  
Flanking Regions ◽  
Identification And Characterization ◽  
Reading Frames

The polyketide metabolite 2,4-diacetylphloroglucinol (2,4-DAPG) is produced by many strains of fluorescent Pseudomonas spp. with biocontrol activity against soilborne fungal plant pathogens. Genes required for 2,4-DAPG synthesis by P. fluorescensQ2-87 are encoded by a 6.5-kb fragment of genomic DNA that can transfer production of 2,4-DAPG to 2,4-DAPG-nonproducing recipientPseudomonas strains. In this study the nucleotide sequence was determined for the 6.5-kb fragment and flanking regions of genomic DNA from strain Q2-87. Six open reading frames were identified, four of which (phlACBD) comprise an operon that includes a set of three genes (phlACB) conserved between eubacteria and archaebacteria and a gene (phlD) encoding a polyketide synthase with homology to chalcone and stilbene synthases from plants. The biosynthetic operon is flanked on either side by phlEand phlF, which code respectively for putative efflux and regulatory (repressor) proteins. Expression in Escherichia coli of phlA, phlC, phlB, andphlD, individually or in combination, identified a novel polyketide biosynthetic pathway in which PhlD is responsible for the production of monoacetylphloroglucinol (MAPG). PhlA, PhlC, and PhlB are necessary to convert MAPG to 2,4-DAPG, and they also may function in the synthesis of MAPG.

scholarly journals Identification and Characterization of Phytoplasmal Genes, Employing a Novel Method of Isolating Phytoplasmal Genomic DNA

2003 ◽  
Vol 185 (22) ◽  
pp. 6513-6521 ◽  
Author(s):  
Sharon Melamed ◽  
Edna Tanne ◽  
Raz Ben-Haim ◽  
Orit Edelbaum ◽  
David Yogev ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Plant Pathogens ◽  
Open Reading Frames ◽  
Rrna Genes ◽  
Unique Method ◽  
Novel Method ◽  
Identification And Characterization ◽  
Reading Frames ◽  
Large Background

ABSTRACT Phytoplasmas are unculturable, insect-transmissible plant pathogens belonging to the class Mollicutes. To be transmitted, the phytoplasmas replicate in the insect body and are delivered to the insect's salivary glands, from where they are injected into the recipient plant. Because phytoplasmas cannot be cultured, any attempt to recover phytoplasmal DNA from infected plants or insects has resulted in preparations with a large background of host DNA. Thus, studies of the phytoplasmal genome have been greatly hampered, and aside from the rRNA genes, only a few genes have hitherto been isolated and characterized. We developed a unique method to obtain host-free phytoplasmal genomic DNA from the insect vector's saliva, and we demonstrated the feasibility of this method by isolating and characterizing 78 new putative phytoplasmal open reading frames and their deduced proteins. Based on the newly accumulated information on phytoplasmal genes, preliminary characteristics of the phytoplasmal genome are discussed.

scholarly journals Optimization and characterization of Royal Dawn cherry (Prunus avium) phenolics extraction

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Lisard Iglesias-Carres ◽  
Anna Mas-Capdevila ◽  
Francisca Isabel Bravo ◽  
Miquel Mulero ◽  
Begoña Muguerza ◽  
...  
Keyword(s):  
Food Industry ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Specific Method ◽  
Phenolic Composition ◽  
Phenolic Profile ◽  
Beneficial Effects ◽  
Sweet Cherries ◽  
Precise Characterization

AbstractTo correlate the beneficial effects of cherry consumption with their phenolic composition, a full and precise characterization is required. However, there is not a specific method to fully extract all phenolic compounds from sweet cherries. Thus, this study aimed to optimize the extraction of sweet cherry phenolics by response surface methodology and fully characterize the phenolic profile of Royal Dawn sweet cherries by HPLC-ESI-MS/MS. Extraction conditions were evaluated and optimized to 55 °C, MeOH 72%, 12 mL/g in two extraction steps. Royal Dawn sweet cherries presented rutin as the predominant phenolic compound, unlike most sweet cherry varieties. Additionally, ethanol was evaluated as a replacement solvent, obtaining lower extraction rates, especially for anthocyanins. However, in terms of total amounts, non-anthocyanin compounds were similarly extracted. The developed methodology was fast and can be routinely used in the evaluation of the phenolic profile of sweet cherries and to produce phenolic-rich extracts for the food industry.

scholarly journals Fruit Quality Characterization of New Sweet Cherry Cultivars as a Good Source of Bioactive Phenolic Compounds with Antioxidant and Neuroprotective Potential

Antioxidants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 677
Author(s):  
Fabiana Antognoni ◽  
Giulia Potente ◽  
Roberto Mandrioli ◽  
Cristina Angeloni ◽  
Michela Freschi ◽  
...  
Keyword(s):  
Phenolic Compounds ◽  
High Performance ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Total Anthocyanin ◽  
Sweet Cherries ◽  
Array Detection ◽  
Sweet Cherry Cultivars ◽  
New Cultivars

Sweet cherries (Prunus avium L.) are highly appreciated fruits for their taste, color, nutritional value, and beneficial health effects. In this work, seven new cultivars of sweet cherry were investigated for their main quality traits and nutraceutical value. The phytochemical profile of three classes of phenolic compounds and the antioxidant activity of the new cultivars were investigated through high-performance liquid chromatography with diode array detection (HPLC-DAD) and spectrophotometric assays, respectively, and compared with those of commonly commercialized cultivars. Cyanidine-3-O-rutinoside was the main anthocyanin in all genotypes, and its levels in some new cultivars were about three-fold higher than in commercial ones. The ORAC-assayed antioxidant capacity was positively correlated with the total anthocyanin index. The nutraceutical value of the new cultivars was investigated in terms of antioxidant/neuroprotective capacity in neuron-like SH-SY5Y cells. Results demonstrated that the new cultivars were more effective in counteracting oxidative stress and were also able to upregulate brain-derived neurotrophic factor (BDNF), a pro-survival neurotrophin, suggesting their potential pleiotropic role in counteracting neurodegenerations.

scholarly journals Transcriptomic analysis reveals insights into the response to Hop stunt viroid (HSVd) in sweet cherry (Prunus avium L.) fruits

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10005
Author(s):  
Li Xu ◽  
Xiaojuan Zong ◽  
Jiawei Wang ◽  
Hairong Wei ◽  
Xin Chen ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Mapk Signaling ◽  
Cherry Tree ◽  
Stunt Viroid ◽  
Hop Stunt Viroid ◽  
Wide Range ◽  
Plant Pathogen Interactions

Hop stunt viroid (HSVd) is a member of the genus Hostuviroid of the family Pospiviroidae and has been found in a wide range of herbaceous and woody hosts. It causes serious dapple fruit symptoms on infected sweet cherry, notably inducing cherry tree decay. In order to better understand the molecular mechanisms of HSVd infection in sweet cherry fruit, transcriptome analysis of HSVd-infected and healthy sweet cherry fruits was carried out. A total of 1,572 differentially expressed genes (DEGs) were identified, involving 961 upregulated DEGs and 611 downregulated DEGs. Functional analysis indicated that the DEGs were mainly involved in plant hormone signal transduction, plant–pathogen interactions, secondary metabolism, and the MAPK signaling pathway. In addition, C2H2 zinc finger, MYB, bHLH, AP2/ERF, C2C2-dof, NAC and WRKY transcription factors can respond to HSVd infection. In order to confirm the high-throughput sequencing results, 16 DEGs were verified by RT-qPCR analysis. The results provided insight into the pathways and genes of sweet cherry fruit in response to HSVd infection.

scholarly journals A Gene Encoding l-Methionine γ-Lyase Is Present in Enterobacteriaceae Family Genomes: Identification and Characterization of Citrobacter freundiil-Methionine γ-Lyase

2005 ◽  
Vol 187 (11) ◽  
pp. 3889-3893 ◽  
Author(s):  
Ilya V. Manukhov ◽  
Daria V. Mamaeva ◽  
Sergei M. Rastorguev ◽  
Nicolai G. Faleev ◽  
Elena A. Morozova ◽  
...  
Keyword(s):  
Shigella Flexneri ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
High Sequence Identity ◽  
E Coli ◽  
The Family ◽  
Serovar Typhimurium ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT Citrobacter freundii cells produce l-methionine γ-lyase when grown on a medium containing l-methionine. The nucleotide sequence of the hybrid plasmid with a C. freundii EcoRI insert of about 3.0 kbp contained two open reading frames, consisting of 1,194 nucleotides and 1,296 nucleotides, respectively. The first one (denoted megL) encoded l-methionine γ-lyase. The enzyme was overexpressed in Escherichia coli and purified. The second frame encoded a protein belonging to the family of permeases. Regions of high sequence identity with the 3′-terminal part of the C. freundii megL gene located in the same regions of Salmonella enterica serovar Typhimurium, Shigella flexneri, E. coli, and Citrobacter rodentium genomes were found.

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