scholarly journals Identification of bacterial virulence factors based on an integration of experimental and in silico transcription factor target discovery

2020 ◽  
Author(s):  
P. V. Vychyk ◽  
Y. A. Nikolaichik
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Sites ◽  
In Silico ◽  
Soft Rot ◽  
Bacterial Virulence ◽  
Dickeya Dadantii ◽  
Soft Rot Disease ◽  
Transcription Factor Target ◽  
Rot Disease

In silico transcription factors binding sites analysis in Dickeya dadantii genome matches published experimental results and predicts new regulators for genes inducing soft-rot disease in plants.

scholarly journals First Report of Soft Rot Disease on Pak Choi (Brassica chinensis) Caused by Dickeya dadantii subsp. dieffenbachiae in Malaysia

Plant Disease ◽  
2016 ◽  
Vol 100 (1) ◽  
pp. 209-209 ◽  
Author(s):  
E. Golkhandan ◽  
S. Kamaruzaman ◽  
M. A. Zainalabidin ◽  
A. Nasehi
Keyword(s):  
Soft Rot ◽  
Dickeya Dadantii ◽  
Pak Choi ◽  
Brassica Chinensis ◽  
First Report ◽  
Soft Rot Disease ◽  
Rot Disease

scholarly journals The Virulence of a Dickeya dadantii 3937 Mutant Devoid of Osmoregulated Periplasmic Glucans Is Restored by Inactivation of the RcsCD-RcsB Phosphorelay

2010 ◽  
Vol 192 (13) ◽  
pp. 3484-3490 ◽  
Author(s):  
Franck Bouchart ◽  
Gilles Boussemart ◽  
Anne-France Prouvost ◽  
Virginie Cogez ◽  
Edwige Madec ◽  
...  
Keyword(s):  
Plant Species ◽  
Soft Rot ◽  
Dickeya Dadantii ◽  
Soft Rot Disease ◽  
Low Level ◽  
Pleiotropic Phenotype ◽  
Wide Range ◽  
Induced Mutagenesis ◽  
Rot Disease ◽  
High Level

ABSTRACT Dickeya dadantii is a pectinolytic phytopathogen enterobacterium that causes soft rot disease on a wide range of plant species. The virulence of D. dadantii involves several factors, including the osmoregulated periplasmic glucans (OPGs) that are general constituents of the envelope of proteobacteria. In addition to the loss of virulence, opg-negative mutants display a pleiotropic phenotype, including decreased motility and increased exopolysaccharide synthesis. A nitrosoguanidine-induced mutagenesis was performed on the opgG strain, and restoration of motility was used as a screen. The phenotype of the opg mutant echoes that of the Rcs system: high level activation of the RcsCD-RcsB phosphorelay is needed to activate exopolysaccharide synthesis and to repress motility, while low level activation is required for virulence in enterobacteria. Here, we show that mutations in the RcsCDB phosphorelay system restored virulence and motility in a D. dadantii opg-negative strain, indicating a relationship between the Rcs phosphorelay and OPGs.

scholarly journals Relationship of Resistance-Related Enzyme activity and Salicylic Acid content in Phalaenopsis Species with different levels of resistance to DIckeya Dadantii

2022 ◽  
Vol 0 (0) ◽  
Author(s):  
I Putu Wahyu SANJAYA ◽  
Dewi SUKMA ◽  
Sudarsono SUDARSONO ◽  
Ming-Tsair CHAN
Keyword(s):  
Salicylic Acid ◽  
Lignin Content ◽  
Soft Rot ◽  
Disease Assessment ◽  
Post Inoculation ◽  
Necrotrophic Pathogen ◽  
Dickeya Dadantii ◽  
Soft Rot Disease ◽  
Resistant Species ◽  
Rot Disease

ABSTRACT Orchids (Phalaenopsis) are ornamental plants that are cultivated commercially and in great demand in the market. Soft-rot disease (SRD) caused by the necrotrophic pathogen Dickeya dadantii is a cause of considerable economic loss to cultivators of many orchid species. Our previous experiment identified a limited number of species that were resistant to D. dadantii. This study aimed to validate the resistance level of four Phalaenopsis species in a detached leaf inoculation protocol to identify the resistance mechanism(s) involved. Soft-rot symptom diameter was measured from 6 to 18 hours post-inoculation (HPI) with D. dadantii. Disease assessment confirmed that P. amboinensis is a resistant species, P. pantherina is a susceptible species, and P. amabilis and P. schilleriana are very susceptible species. There was no difference in the lignin content between the resistant and very susceptible species. Detailed observation of resistant and very susceptible species, P. amboinensis vs. P. amabilis, revealed higher phenylalanine ammonia-lyase (PAL) and peroxidase (POD) in P. amabilis than in P. amboinensis. In contrast, there was higher salicylic acid (SA) content in P. amboinensis than in P. amabilis. These results suggest that POD and PAL activities may not be effective in defense against soft-rot disease, while SA plays an important role in the resistance of P. amboinensis to D. dadantii. Low PAL activity in P. amboinensis implies that the SA contents from the isochorismate pathway may be involved in the mechanism of P. amboinensis resistance to D. dadantii. Therefore, endogenous SA content may be a good indicator for screening resistant species in Phalaenopsis.

scholarly journals Persistent Interactions of Core Histone Tails with Nucleosomal DNA following Acetylation and Transcription Factor Binding

1998 ◽  
Vol 18 (11) ◽  
pp. 6293-6304 ◽  
Author(s):  
Vesco Mutskov ◽  
Delphine Gerber ◽  
Dimitri Angelov ◽  
Juan Ausio ◽  
Jerry Workman ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Molecular Biology ◽  
Binding Sites ◽  
Cross Linking ◽  
Uv Laser ◽  
Histone Tail ◽  
Histone Tails ◽  
Nucleosomal Dna ◽  
Core Histones

ABSTRACT In this study, we examined the effect of acetylation of the NH2 tails of core histones on their binding to nucleosomal DNA in the absence or presence of bound transcription factors. To do this, we used a novel UV laser-induced protein-DNA cross-linking technique, combined with immunochemical and molecular biology approaches. Nucleosomes containing one or five GAL4 binding sites were reconstituted with hypoacetylated or hyperacetylated core histones. Within these reconstituted particles, UV laser-induced histone-DNA cross-linking was found to occur only via the nonstructured histone tails and thus presented a unique tool for studying histone tail interactions with nucleosomal DNA. Importantly, these studies demonstrated that the NH2 tails were not released from nucleosomal DNA upon histone acetylation, although some weakening of their interactions was observed at elevated ionic strengths. Moreover, the binding of up to five GAL4-AH dimers to nucleosomes occupying the central 90 bp occurred without displacement of the histone NH2 tails from DNA. GAL4-AH binding perturbed the interaction of each histone tail with nucleosomal DNA to different degrees. However, in all cases, greater than 50% of the interactions between the histone tails and DNA was retained upon GAL4-AH binding, even if the tails were highly acetylated. These data illustrate an interaction of acetylated or nonacetylated histone tails with DNA that persists in the presence of simultaneously bound transcription factors.

Specific transcription factors stimulate simian virus 40 and polyomavirus origins of DNA replication

1992 ◽  
Vol 12 (6) ◽  
pp. 2514-2524 ◽  
Author(s):  
Z S Guo ◽  
M L DePamphilis
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Replication ◽  
Binding Sites ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
T Antigen ◽  
Activation Domains ◽  
Auxiliary Component ◽  
Cell Extracts

The origins of DNA replication (ori) in simian virus 40 (SV40) and polyomavirus (Py) contain an auxiliary component (aux-2) composed of multiple transcription factor binding sites. To determine whether this component stimulated replication by binding specific transcription factors, aux-2 was replaced by synthetic oligonucleotides that bound a single transcription factor. Sp1 and T-antigen (T-ag) sites, which exist in the natural SV40 aux-2 sequence, provided approximately 75 and approximately 20%, respectively, of aux-2 activity when transfected into monkey cells. In cell extracts, only T-ag sites were active. AP1 binding sites could replace completely either SV40 or Py aux-2. Mutations that eliminated AP1 binding also eliminated AP1 stimulation of replication. Yeast GAL4 binding sites that strongly stimulated transcription in the presence of GAL4 proteins failed to stimulate SV40 DNA replication, although they did partially replace Py aux-2. Stimulation required the presence of proteins consisting of the GAL4 DNA binding domain fused to specific activation domains such as VP16 or c-Jun. These data demonstrate a clear role for transcription factors with specific activation domains in activating both SV40 and Py ori. However, no correlation was observed between the ability of specific proteins to stimulate promoter activity and their ability to stimulate origin activity. We propose that only transcription factors whose specific activation domains can interact with the T-ag initiation complex can stimulate SV40 and Py ori-core activity.

scholarly journals Kemampuan Bakteri Endofit Akar dan Ubi Kentang untuk Menekan Penyakit Busuk Lunak (Erwinia carotovora pv. carotovora) pada Ubi

Agrikultura ◽  
2016 ◽  
Vol 27 (3) ◽  
Author(s):  
Noor Istifadah ◽  
Muhamad Salman Umar ◽  
Sudarjat Sudarjat ◽  
Luciana Djaya
Keyword(s):  
Biological Control ◽  
Potato Tuber ◽  
Endophytic Bacteria ◽  
Erwinia Carotovora ◽  
Soft Rot ◽  
Soft Rot Disease ◽  
Post Harvest ◽  
Rot Disease

ABSTRACTThe abilities of endophytic bacteria from potato roots and tubers to suppress soft rot disease (Erwinia carotovora pv. carotovora) in potato tuberSoft rot disease caused by Erwinia carotovora pv. carotovora is one of limiting factors in cultivation and post harvest of potato. The eco-friendly control measure that can be developed for controlling the diseases is biological control. Microbes that are potential as biological control agents include endophytic bacteria. This paper discussed the results of study examining the potential of endophytic bacteria isolated from roots and tubers of potato to inhibit the growth of E. carotovora pv. carotovora in vitro and suppress soft rot disease in potato tuber. The results showed that among 24 isolates examined, four isolates of endophytic bacteria (one isolate from potato tuber and three isolates from potato roots) inhibited the growth of E. carotovora pv. carotovora in vitro with inhibition zone 3.5-6.8 mm. In the in vivo test, the isolates inhibited the soft rot disease in potato tuber by 71.5-86.4%. The isolate that tended to show relatively better inhibition in vitro and in vivo was isolate from potato tuber which is CK U3 (Lysinibacillus sp.)Keywords: Biological control, Endophytic bacteria, Post-harvest, Potato, Soft rot diseaseABSTRAKPenyakit busuk lunak yang disebabkan bakteri Erwinia carotovora pv. carotovora, merupakan salah satu kendala dalam budidaya dan pascapanen kentang. Cara pengendalian ramah lingkungan yang dapat dikembangkan untuk menekan penyakit tersebut adalah pengendalian biologi. Kelompok mikroba yang berpotensi sebagi agens pengendali biologi adalah bakteri endofit. Artikel ini mendiskusikan potensi isolat bakteri endofit yang berasal dari ubi dan akar kentang untuk menghambat pertumbuhan bakteri E. carotovora pv. carotovora secara in vitro dan menekan perkembangan penyakit busuk lunak pada ubi kentang. Hasil percobaan menunjukkan bahwa diantara 24 isolat bakteri yang diuji, terdapat empat isolat bakteri endofit (satu isolat dari ubi kentang dan tiga isolat dari akar kentang) yang dapat menghambat pertumbuhan bakteri E. carotovora pv. carotovora secara in vitro dengan zona penghambatan sebesar 3,5-6,8 mm. Pada pengujian secara in vivo, isolat-isolat tersebut dapat menekan perkembangan penyakit busuk lunak pada ubi kentang sebesar 71,5-86,4%. Isolat yang cenderung menunjukkan penghambatan relatif lebih baik secara in vitro dan in vivo adalah isolat bakteri endofit asal ubi kentang yaitu isolat CK U3 (Lysinibacillus sp.).Kata Kunci: Pengendalian biologi, Bakteri endofit, Pascapanen, Kentang, Penyakit busuk basah

scholarly journals HOT or not: examining the basis of high-occupancy target regions

2017 ◽  
Author(s):  
Katarzyna Wreczycka ◽  
Vedran Franke ◽  
Bora Uyar ◽  
Ricardo Wurmus ◽  
Altuna Akalin
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Sites ◽  
Cell Types ◽  
Data Sets ◽  
Gene Promoters ◽  
Quadruplex Dna ◽  
Golden Standard ◽  
Multiple Cell ◽  
Multiple Species

AbstractHigh-occupancy target (HOT) regions are the segments of the genome with unusually high number of transcription factor binding sites. These regions are observed in multiple species and thought to have biological importance due to high transcription factor occupancy. Furthermore, they coincide with house-keeping gene promoters and the associated genes are stably expressed across multiple cell types. Despite these features, HOT regions are solemnly defined using ChIP-seq experiments and shown to lack canonical motifs for transcription factors that are thought to be bound there. Although, ChIP-seq experiments are the golden standard for finding genome-wide binding sites of a protein, they are not noise free. Here, we show that HOT regions are likely to be ChIP-seq artifacts and they are similar to previously proposed “hyper-ChIPable” regions. Using ChIP-seq data sets for knocked-out transcription factors, we demonstrate presence of false positive signals on HOT regions. We observe sequence characteristics and genomic features that are discriminatory of HOT regions, such as GC/CpG-rich k-mers and enrichment of RNA-DNA hybrids (R-loops) and DNA tertiary structures (G-quadruplex DNA). The artificial ChIP-seq enrichment on HOT regions could be associated to these discriminatory features. Furthermore, we propose strategies to deal with such artifacts for the future ChIP-seq studies.

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