scholarly journals Selection of target genes for pcr diagnostics of Xanthomonas arboricola virulent for cereals and brassicas

2021 ◽  
Vol 104 (2) ◽  
pp. 87-96
Author(s):  
E. I. Kyrova* ◽  
A. N. Ignatov
Keyword(s):  
Target Genes ◽  
Detection System ◽  
Draft Genome ◽  
Pcr Analysis ◽  
Specific Pcr ◽  
Xanthomonas Species ◽  
Type 3 Secretion System ◽  
Xanthomonas Arboricola ◽  
Physiological Tests ◽  
Type 3

Plant pathogenic xanthomonads virulent to wheat, rye, barley, tomato, sunflower, and brassicas were isolated in Russia in 2001–2008. Physiological tests and multilocus sequence typing analysis confirmed their position within the Xanthomonas arboricola species. The obtained draft genome sequence of representative strain 3004 from barley plants, which is also virulent to sunflower, brassicas, and chestnut, demonstrated an absence of the Type 3 Secretion System T3SS and an evidence for the lateral gene transfer of some other virulence genes from distantly related bacteria. It was concluded that T4SS genes can be used as the target for group-specific PCR analysis of the emerging pathogen. It was proposed to use virD4, virB3, virB4, and virB9 genes to design a detection system. After preliminary experiments with classic PCR for the chosen genes, primers and TaqMan(R) probe were designed to specifically amplify a 121 bp fragment of the VirD4 gene. Amplification products were obtained for all target Xanthomonas arboricola strains and were not detected in other Xanthomonas species, or in other pathogenic or epiphytic bacteria occurring on these host plants. The assay readily detected Xanthomonas arboricola infection in diseased plants and from bacterial colonies isolated on semi-selective media, and was more sensitive and specific than traditional plating methods.

scholarly journals Species of the genus Xanthomonas infecting cereals and oilseeds in the Russian Federation and its diagnostics

2020 ◽  
Vol 18 ◽  
pp. 00017
Author(s):  
Elena Kyrova ◽  
Maria Egorova ◽  
Alexander Ignatov
Keyword(s):  
Host Plants ◽  
Pathogenic Bacteria ◽  
Detection System ◽  
Draft Genome ◽  
Pcr Analysis ◽  
Specific Pcr ◽  
Novel Host ◽  
The Russian Federation ◽  
Xanthomonas Arboricola ◽  
Physiological Tests

Plant pathogenic bacteria of the genus Xanthomonas display high levels of genetic diversity and cause remarkable damage to about 400 plant species. In 2001–2008, a new group of strains of Xanthomonas arboricola has been found as pathogens on novel host plants such as wheat, rye, barley, tomato, sunflower, and brassicas in Russia. Physiological tests and multilocus sequence typing (MLST) analysis confirmed their position within the Xanthomonas arboricola species. The obtained draft genome sequence of Xanthomonas arboricola strain 3004 from barley plants, also virulent to sunflower, brassicas, and chestnut, has demonstrated an evidence for the lateral gene transfer (LGT) of the virulence genes. It can be suggested that the virE and other genes of T4SS, obtained due to LGT, may contribute to the host range extension. Thus, T4SS genes can be used as the target for group-specific PCR analysis of this emerging pathogen of cereals and oilseeds. We propose to use virB3, virB4, and virB9 genes to design a detection system.

scholarly journals Comparative Genomics of Xanthomonaseuroxanthea and Xanthomonas arboricola pv. juglandis Strains Isolated from a Single Walnut Host Tree

2021 ◽  
Vol 9 (3) ◽  
pp. 624
Author(s):  
Camila Fernandes ◽  
Leonor Martins ◽  
Miguel Teixeira ◽  
Jochen Blom ◽  
Joël F. Pothier ◽  
...  
Keyword(s):  
Extracellular Enzymes ◽  
Walnut Tree ◽  
Size Number ◽  
A Genome ◽  
Type 3 Secretion System ◽  
Xanthomonas Arboricola ◽  
Chromosomal Sequences ◽  
Related Proteins ◽  
Type 3 ◽  
Genome Comparisons

The recent report of distinct Xanthomonas lineages of Xanthomonas arboricola pv. juglandis and Xanthomonas euroxanthea within the same walnut tree revealed that this consortium of walnut-associated Xanthomonas includes both pathogenic and nonpathogenic strains. As the implications of this co-colonization are still poorly understood, in order to unveil niche-specific adaptations, the genomes of three X. euroxanthea strains (CPBF 367, CPBF 424T, and CPBF 426) and of an X. arboricola pv. juglandis strain (CPBF 427) isolated from a single walnut tree in Loures (Portugal) were sequenced with two different technologies, Illumina and Nanopore, to provide consistent single scaffold chromosomal sequences. General genomic features showed that CPBF 427 has a genome similar to other X. arboricola pv. juglandis strains, regarding its size, number, and content of CDSs, while X. euroxanthea strains show a reduction regarding these features comparatively to X. arboricola pv. juglandis strains. Whole genome comparisons revealed remarkable genomic differences between X. arboricola pv. juglandis and X. euroxanthea strains, which translates into different pathogenicity and virulence features, namely regarding type 3 secretion system and its effectors and other secretory systems, chemotaxis-related proteins, and extracellular enzymes. Altogether, the distinct genomic repertoire of X. euroxanthea may be particularly useful to address pathogenicity emergence and evolution in walnut-associated Xanthomonas.

scholarly journals Functional Analysis of p53 Binding under Differential Stresses

2006 ◽  
Vol 26 (19) ◽  
pp. 7030-7045 ◽  
Author(s):  
Adam J. Krieg ◽  
Ester M. Hammond ◽  
Amato J. Giaccia
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Target Genes ◽  
Cpg Island ◽  
P53 Protein ◽  
Pcr Analysis ◽  
Glutathione Peroxidase 1 ◽  
Specific Pcr ◽  
Subsequent Effect ◽  
P53 Target Genes ◽  
Hct116 Cells

ABSTRACT Hypoxia and DNA damage stabilize the p53 protein, but the subsequent effect that each stress has on transcriptional regulation of known p53 target genes is variable. We have used chromatin immunoprecipitation followed by CpG island (CGI) microarray hybridization to identify promoters bound by p53 under both DNA-damaging and non-DNA-damaging conditions in HCT116 cells. Using gene-specific PCR analysis, we have verified an association with CGIs of the highest enrichment (>2.5-fold) (REV3L, XPMC2H, HNRPUL1, TOR1AIP1, glutathione peroxidase 1, and SCFD2), with CGIs of intermediate enrichment (>2.2-fold) (COX7A2L, SYVN1, and JAG2), and with CGIs of low enrichment (>2.0-fold) (MYC and PCNA). We found little difference in promoter binding when p53 is stabilized by these two distinctly different stresses. However, expression of these genes varies a great deal: while a few genes exhibit classical induction with adriamycin, the majority of the genes are unchanged or are mildly repressed by either hypoxia or adriamycin. Further analysis using p53 mutated in the core DNA binding domain revealed that the interaction of p53 with CGIs may be occurring through both sequence-dependent and -independent mechanisms. Taken together, these experiments describe the identification of novel p53 target genes and the subsequent discovery of distinctly different expression phenomena for p53 target genes under different stress scenarios.

scholarly journals Control of the Type 3 Secretion System in Vibrio harveyi by Quorum Sensing through Repression of ExsA

2010 ◽  
Vol 76 (15) ◽  
pp. 4996-5004 ◽  
Author(s):  
Christopher M. Waters ◽  
Julie T. Wu ◽  
Meghan E. Ramsey ◽  
Rebecca C. Harris ◽  
Bonnie L. Bassler
Keyword(s):  
Quorum Sensing ◽  
Cell Density ◽  
Target Genes ◽  
High Cell Density ◽  
Vibrio Harveyi ◽  
Secretion System ◽  
High Cell ◽  
Type 3 Secretion System ◽  
Type 3 ◽  
Low Cell Density

ABSTRACT The type 3 secretion system (T3SS) genes of Vibrio harveyi are activated at low cell density and repressed at high cell density by quorum sensing (QS). Repression requires LuxR, the master transcriptional regulator of QS-controlled genes. Here, we determine the mechanism underlying the LuxR repression of the T3SS system. Using a fluorescence-based cell sorting approach, we isolated V. harveyi mutants that are unable to express T3SS genes at low cell density and identified two mutations in the V. harveyi exsBA operon. While LuxR directly represses the expression of exsBA, complementation and epistasis analyses reveal that it is the repression of exsA expression, but not exsB expression, that is responsible for the QS-mediated repression of T3SS genes at high cell density. The present work further defines the genes in the V. harveyi QS regulon and elucidates a mechanism demonstrating how multiple regulators can be linked in series to direct the expression of QS target genes specifically at low or high cell density.

scholarly journals YtxR Acts as an Overriding Transcriptional Off Switch for the Yersinia enterocolitica Ysc-Yop Type 3 Secretion System

2008 ◽  
Vol 191 (2) ◽  
pp. 514-524 ◽  
Author(s):  
Grace L. Axler-DiPerte ◽  
Stewart J. Hinchliffe ◽  
Brendan W. Wren ◽  
Andrew J. Darwin
Keyword(s):  
Yersinia Enterocolitica ◽  
Secretion System ◽  
Pcr Analysis ◽  
Virulence Plasmid ◽  
Reverse Transcription Pcr ◽  
Dnase I Footprinting ◽  
Type 3 Secretion System ◽  
Fusion Analysis ◽  
Type 3

ABSTRACT The Yersinia enterocolitica YtxR protein is a LysR-type transcriptional regulator that induces expression of the ytxAB locus, which encodes a putative ADP-ribosylating toxin. The ytxR and ytxAB genes are not closely linked in the Y. enterocolitica chromosome, and whereas ytxR is present in all sequenced Yersinia spp., the ytxAB locus is not. These observations suggested that there might be other YtxR-regulon members besides ytxAB and prompted us to investigate coregulated genes and gene products by using transcriptional and proteomic approaches. Microarray and reverse transcription-PCR analysis showed that YtxR strongly activates expression of the yts2 locus, which encodes a putative type 2 secretion system, as well as several uncharacterized genes predicted to encode extracytoplasmic proteins. Strikingly, we also discovered that under Ysc-Yop type 3 secretion system-inducing conditions, YtxR prevented the appearance of Yop proteins in the culture supernatant. Microarray and lacZ operon fusion analysis showed that this was due to specific repression of ysc-yop gene expression. YtxR was also able to repress VirF-dependent Φ(yopE-lacZ) and Φ(yopH-lacZ) expression in a strain lacking the virulence plasmid, which suggested a direct repression mechanism. This was supported by DNase I footprinting, which showed that YtxR interacted with the yopE and yopH control regions. Therefore, YtxR is a newly identified regulator of the ysc-yop genes that can act as an overriding off switch for this critical virulence system.

scholarly journals The HrpG/HrpX Regulon of Xanthomonads—An Insight to the Complexity of Regulation of Virulence Traits in Phytopathogenic Bacteria

2021 ◽  
Vol 9 (1) ◽  
pp. 187
Author(s):  
Doron Teper ◽  
Sheo Shankar Pandey ◽  
Nian Wang
Keyword(s):  
Regulatory Network ◽  
Regulatory Networks ◽  
Focal Point ◽  
Genetic Regulation ◽  
Transcriptional Regulators ◽  
Secretion System ◽  
In Planta ◽  
Type 3 Secretion System ◽  
Type 3 ◽  
Made In

Bacteria of the genus Xanthomonas cause a wide variety of economically important diseases in most crops. The virulence of the majority of Xanthomonas spp. is dependent on secretion and translocation of effectors by the type 3 secretion system (T3SS) that is controlled by two master transcriptional regulators HrpG and HrpX. Since their discovery in the 1990s, the two regulators were the focal point of many studies aiming to decipher the regulatory network that controls pathogenicity in Xanthomonas bacteria. HrpG controls the expression of HrpX, which subsequently controls the expression of T3SS apparatus genes and effectors. The HrpG/HrpX regulon is activated in planta and subjected to tight metabolic and genetic regulation. In this review, we cover the advances made in understanding the regulatory networks that control and are controlled by the HrpG/HrpX regulon and their conservation between different Xanthomonas spp.

scholarly journals Reproductive failure in mice lacking inter-alpha-trypsin inhibitor (ITI) – ITI target genes in mouse ovary identified by microarray analysis

2004 ◽  
Vol 183 (1) ◽  
pp. 29-38 ◽  
Author(s):  
Mika Suzuki ◽  
Hiroshi Kobayashi ◽  
Yoshiko Tanaka ◽  
Naohiro Kanayama ◽  
Toshihiko Terao
Keyword(s):  
Real Time ◽  
Trypsin Inhibitor ◽  
Target Genes ◽  
Reproductive Function ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Reproductive Process ◽  
Female Mice ◽  
Retinoid Metabolism ◽  
Regulatory Effects

Bikunin, a Kunitz-type protease inhibitor, is found in blood and urine. It has been established by two laboratories independently that the bikunin knockout female mice display a severe reduction in fertility: the cumulus oophorus has a defect in forming the extracellular hyaluronan-rich matrix during expansion. Proteins of the inter-alpha-trypsin inhibitor (ITI) family are eliminated in mice in which the bikunin gene has been inactivated, since bikunin is essential for their biosynthesis. Proteins of the ITI family may contribute to the microenvironment in which ovulation takes place. It is not clear, however, whether a single mechanism affects the reproductive function including ovulation. For identifying the full repertoire of the ITI deficiency-related genes, a cDNA microarray hybridization screening was conducted using mRNA from ovaries of wild-type or bik−/− female mice. A number of genes were identified and their regulation was confirmed by real-time RT-PCR analysis. Our screen identified that 29 (0.7%) and 5 genes (0.1%) of the genes assayed were, respectively, up- and down-regulated twofold or more. The identified genes can be classified into distinct subsets. These include stress-related, apoptosis-related, proteases, signaling molecules, aging-related, cytokines, hyaluronan metabolism and signaling, reactive oxygen species-related, and retinoid metabolism, which have previously been implicated in enhancing follicle development and/or ovulation. Real-time RT-PCR analysis confirmed that these genes were up- and down-regulated two- to tenfold by bikunin knockout. These studies demonstrate that proteins of the ITI family may exert potent regulatory effects on a major physiological reproductive process, ovulation.

scholarly journals Quantitative Multiplex Methylation-Specific PCR Analysis Doubles Detection of Tumor Cells in Breast Ductal Fluid

2006 ◽  
Vol 12 (11) ◽  
pp. 3306-3310 ◽  
Author(s):  
Mary Jo Fackler ◽  
Kara Malone ◽  
Zhe Zhang ◽  
Eric Schilling ◽  
Elizabeth Garrett-Mayer ◽  
...  
Keyword(s):  
Tumor Cells ◽  
Pcr Analysis ◽  
Methylation Specific Pcr ◽  
Specific Pcr ◽  
Ductal Fluid

Discovery and Characterization of Differentially Expressed Soybean MiRNAs and Their Targets During Soybean Mosaic Virus Infection Unveils Novel Insight Into Soybean-SMV Interaction

2021 ◽  
Author(s):  
Bowen Li ◽  
Adhimoolam Karthikeyan ◽  
Liqun Wang ◽  
Jinlong Yin ◽  
Tongtong Jin ◽  
...  
Keyword(s):  
Virus Infection ◽  
Mosaic Virus ◽  
Target Genes ◽  
Soybean Mosaic Virus ◽  
Expression Patterns ◽  
Defense Responses ◽  
Pcr Analysis ◽  
Functional Annotations ◽  
Additional Information ◽  
Insight Into

Abstract Background: Soybean mosaic virus (SMV) is the most devastating pathogen of soybean. MicroRNAs (miRNAs) are a class of non-coding RNAs (21-24 nucleotides) and play important roles in regulating defense responses against pathogens. However, miRNA's response to SMV in soybean is not as well documented. Result: In this study, we analyzed 18 miRNA libraries, including three biological replicates from two soybean lines (Resistant and susceptible lines to SMV strain SC3 selected from the near-isogenic lines of Qihuang No. 1× Nannong1138-2) after virus infection at three different time intervals (0 dpi, 7 dpi, and 14 dpi). A total of 1,092 miRNAs, including 608 known miRNAs and 484 novel miRNAs were detected. Differential expression analyses identified the miRNAs responded during soybean-SMV interaction. Then, miRNAs potential target genes were predicted via data mining, and functional annotation was done by Gene Ontology (GO) analysis. Eventually, the expression patterns of several miRNAs validated by quantitative real-time PCR analysis are consistent with sequencing results. Conclusion: We have identified a large number of miRNAs and their target genes and also functional annotations. Our study provides additional information on soybean miRNAs and an insight into the role of miRNAs during SMV-infection in soybean.

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