scholarly journals Agroinfiltration Is a Versatile Tool That Facilitates Comparative Analyses of Avr9/Cf-9-Induced and Avr4/Cf-4-Induced Necrosis

2000 ◽  
Vol 13 (4) ◽  
pp. 439-446 ◽  
Author(s):  
Renier A. L. Van der Hoorn ◽  
Franck Laurent ◽  
Ronelle Roth ◽  
Pierre J. G. M. De Wit
Keyword(s):  
Gene Expression ◽  
Resistance Genes ◽  
Signal Transduction Pathway ◽  
Potato Virus X ◽  
Extracellular Proteins ◽  
Induced Responses ◽  
Avirulence Genes ◽  
Versatile Tool ◽  
Tomato Pathogen ◽  
Avr Gene

The avirulence genes Avr9 and Avr4 from the fungal tomato pathogen Cladosporium fulvum encode extracellular proteins that elicit a hypersensitive response when injected into leaves of tomato plants carrying the matching resistance genes, Cf-9 and Cf-4, respectively. We successfully expressed both Avr9 and Avr4 genes in tobacco with the Agrobacterium tumefaciens transient transformation assay (agroinfiltration). In addition, we expressed the matching resistance genes, Cf-9 and Cf-4, through agroinfiltration. By combining transient Cf gene expression with either transgenic plants expressing one of the gene partners, Potato virus X (PVX)-mediated Avr gene expression, or elicitor injections, we demonstrated that agroinfiltration is a reliable and versatile tool to study Avr/Cf-mediated recognition. Significantly, agroinfiltration can be used to quantify and compare Avr/Cf-induced responses. Comparison of different Avr/Cf-interactions within one tobacco leaf showed that Avr9/Cf-9-induced necrosis developed slower than necrosis induced by Avr4/Cf-4. Quantitative analysis demonstrated that this temporal difference was due to a difference in Avr gene activities. Transient expression of matching Avr/Cf gene pairs in a number of plant families indicated that the signal transduction pathway required for Avr/Cf-induced responses is conserved within solana-ceous species. Most non-solanaceous species did not develop specific Avr/Cf-induced responses. However, co-expression of the Avr4/Cf-4 gene pair in lettuce resulted in necrosis, providing the first proof that a resistance (R) gene can function in a different plant family.

scholarly journals Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1107
Author(s):  
Long Song ◽  
Jing Qin Wu ◽  
Chong Mei Dong ◽  
Robert F. Park
Keyword(s):  
Gene Expression ◽  
Leaf Rust ◽  
De Novo ◽  
Puccinia Triticina ◽  
Integrated Analysis ◽  
Avirulence Genes ◽  
Integrated Framework ◽  
Rust Pathogen ◽  
Avr Gene ◽  
Avr Genes

The leaf rust pathogen, Puccinia triticina (Pt), threatens global wheat production. The deployment of leaf rust (Lr) resistance (R) genes in wheat varieties is often followed by the development of matching virulence in Pt due to presumed changes in avirulence (Avr) genes in Pt. Identifying such Avr genes is a crucial step to understand the mechanisms of wheat-rust interactions. This study is the first to develop and apply an integrated framework of gene expression, single nucleotide polymorphism (SNP), insertion/deletion (InDel), and copy number variation (CNV) analysis in a rust fungus and identify candidate avirulence genes. Using a long-read based de novo genome assembly of an isolate of Pt (‘Pt104’) as the reference, whole-genome resequencing data of 12 Pt pathotypes derived from three lineages Pt104, Pt53, and Pt76 were analyzed. Candidate avirulence genes were identified by correlating virulence profiles with small variants (SNP and InDel) and CNV, and RNA-seq data of an additional three Pt isolates to validate expression of genes encoding secreted proteins (SPs). Out of the annotated 29,043 genes, 2392 genes were selected as SP genes with detectable expression levels. Small variant comparisons between the isolates identified 27–40 candidates and CNV analysis identified 14–31 candidates for each Avr gene, which when combined, yielded the final 40, 64, and 69 candidates for AvrLr1, AvrLr15, and AvrLr24, respectively. Taken together, our results will facilitate future work on experimental validation and cloning of Avr genes. In addition, the integrated framework of data analysis that we have developed and reported provides a more comprehensive approach for Avr gene mining than is currently available.

Plant disease resistance genes: unravelling how they work

1995 ◽  
Vol 73 (S1) ◽  
pp. 495-505 ◽  
Author(s):  
Kim E. Hammond-Kosack ◽  
Jonathan D. G. Jones
Keyword(s):  
Resistance Genes ◽  
Plant Disease Resistance ◽  
Defense Responses ◽  
Host Responses ◽  
Cladosporium Fulvum ◽  
Avirulence Genes ◽  
In Planta ◽  
Molecular Events ◽  
Cf Resistance Genes ◽  
Avr Gene

Resistance (R) genes confer on a plant the ability to defend itself following microbial attack. Each R gene exhibits an extreme specificity of action and is only effective against a microbe that has the corresponding functional avirulence (Avr) gene. This article reviews the strategies and experimental approaches deployed to understand the molecular events underlying the specificity of action of various tomato Cf resistance genes that results in incompatibility to the fungal pathogen Cladosporium fulvum. Topics covered include the clustering of Cf genes, the biology of Cf-dependent incompatibility, the map-based and transposon tagging approaches used to clone the Cf-2 and Cf-9 genes, respectively, identification by mutagenesis of other plant loci required for full Cf-9 mediated resistance, the expression of a functional Avr9 gene in planta and its lethal consequences to Cf-9 containing plants, the physiological and molecular host responses to C. fulvum and AVR elicitor challenges and some genetic approaches to ascertain the crucial components of the defense response. Key words: Cladosporium fulvum, Lycopersicon esculentum, tomato leaf mold, Cf resistance genes, fungal avirulence genes, plant defense responses.

scholarly journals Insight into the bZIP Gene Family in Solanum tuberosum: Genome and Transcriptome Analysis to Understand the Roles of Gene Diversification in Spatiotemporal Gene Expression and Function

2020 ◽  
Vol 22 (1) ◽  
pp. 253
Author(s):  
Venura Herath ◽  
Jeanmarie Verchot
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Functional Groups ◽  
Leucine Zipper ◽  
Expression Profiles ◽  
Crop Improvement ◽  
Potato Virus X ◽  
Tissue Growth ◽  
Abiotic Stress Response ◽  
Sequence Alignments

The basic region-leucine zipper (bZIP) transcription factors (TFs) form homodimers and heterodimers via the coil–coil region. The bZIP dimerization network influences gene expression across plant development and in response to a range of environmental stresses. The recent release of the most comprehensive potato reference genome was used to identify 80 StbZIP genes and to characterize their gene structure, phylogenetic relationships, and gene expression profiles. The StbZIP genes have undergone 22 segmental and one tandem duplication events. Ka/Ks analysis suggested that most duplications experienced purifying selection. Amino acid sequence alignments and phylogenetic comparisons made with the Arabidopsis bZIP family were used to assign the StbZIP genes to functional groups based on the Arabidopsis orthologs. The patterns of introns and exons were conserved within the assigned functional groups which are supportive of the phylogeny and evidence of a common progenitor. Inspection of the leucine repeat heptads within the bZIP domains identified a pattern of attractive pairs favoring homodimerization, and repulsive pairs favoring heterodimerization. These patterns of attractive and repulsive heptads were similar within each functional group for Arabidopsis and S. tuberosum orthologs. High-throughput RNA-seq data indicated the most highly expressed and repressed genes that might play significant roles in tissue growth and development, abiotic stress response, and response to pathogens including Potato virus X. These data provide useful information for further functional analysis of the StbZIP gene family and their potential applications in crop improvement.

scholarly journals LncGSEA: a versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanan Ren ◽  
Ting-You Wang ◽  
Leah C. Anderton ◽  
Qi Cao ◽  
Rendong Yang
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Clinical Samples ◽  
Sequencing Data ◽  
Multiple Cancer ◽  
Regulatory Pathways ◽  
Cancer Transcriptome ◽  
Versatile Tool

Abstract Background Long non-coding RNAs (lncRNAs) are a growing focus in cancer research. Deciphering pathways influenced by lncRNAs is important to understand their role in cancer. Although knock-down or overexpression of lncRNAs followed by gene expression profiling in cancer cell lines are established approaches to address this problem, these experimental data are not available for a majority of the annotated lncRNAs. Results As a surrogate, we present lncGSEA, a convenient tool to predict the lncRNA associated pathways through Gene Set Enrichment Analysis of gene expression profiles from large-scale cancer patient samples. We demonstrate that lncGSEA is able to recapitulate lncRNA associated pathways supported by literature and experimental validations in multiple cancer types. Conclusions LncGSEA allows researchers to infer lncRNA regulatory pathways directly from clinical samples in oncology. LncGSEA is written in R, and is freely accessible at https://github.com/ylab-hi/lncGSEA.

scholarly journals Differential Expression of the CO2 Fixation Operons of Rhodobacter sphaeroides by the Prr/Reg Two-Component System during Chemoautotrophic Growth

2002 ◽  
Vol 184 (23) ◽  
pp. 6654-6664 ◽  
Author(s):  
Janet L. Gibson ◽  
James M. Dubbs ◽  
F. Robert Tabita
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Cytochrome Oxidase ◽  
Rhodobacter Sphaeroides ◽  
Rhodobacter Capsulatus ◽  
Response Regulator ◽  
Signal Transduction Pathway ◽  
Pentose Phosphate ◽  
Bisphosphate Carboxylase

ABSTRACT In Rhodobacter sphaeroides, the two cbb operons encoding duplicated Calvin-Benson Bassham (CBB) CO2 fixation reductive pentose phosphate cycle structural genes are differentially controlled. In attempts to define the molecular basis for the differential regulation, the effects of mutations in genes encoding a subunit of Cbb3 cytochrome oxidase, ccoP, and a global response regulator, prrA (regA), were characterized with respect to CO2 fixation (cbb) gene expression by using translational lac fusions to the R. sphaeroides cbb I and cbbII promoters. Inactivation of the ccoP gene resulted in derepression of both promoters during chemoheterotophic growth, where cbb expression is normally repressed; expression was also enhanced over normal levels during phototrophic growth. The prrA mutation effected reduced expression of cbbI and cbbII promoters during chemoheterotrophic growth, whereas intermediate levels of expression were observed in a double ccoP prrA mutant. PrrA and ccoP1 prrA strains cannot grow phototrophically, so it is impossible to examine cbb expression in these backgrounds under this growth mode. In this study, however, we found that PrrA mutants of R. sphaeroides were capable of chemoautotrophic growth, allowing, for the first time, an opportunity to directly examine the requirement of PrrA for cbb gene expression in vivo under growth conditions where the CBB cycle and CO2 fixation are required. Expression from the cbbII promoter was severely reduced in the PrrA mutants during chemoautotrophic growth, whereas cbbI expression was either unaffected or enhanced. Mutations in ccoQ had no effect on expression from either promoter. These observations suggest that the Prr signal transduction pathway is not always directly linked to Cbb3 cytochrome oxidase activity, at least with respect to cbb gene expression. In addition, lac fusions containing various lengths of the cbbI promoter demonstrated distinct sequences involved in positive regulation during photoautotrophic versus chemoautotrophic growth, suggesting that different regulatory proteins may be involved. In Rhodobacter capsulatus, ribulose 1,5-bisphosphate carboxylase-oxygenase (RubisCO) expression was not affected by cco mutations during photoheterotrophic growth, suggesting that differences exist in signal transduction pathways regulating cbb genes in the related organisms.

scholarly journals Multiple Evolutionary Trajectories Have Led to the Emergence of Races in Fusarium oxysporum f. sp. lycopersici

2016 ◽  
Vol 83 (4) ◽  
Author(s):  
V. Chellappan Biju ◽  
Like Fokkens ◽  
Petra M. Houterman ◽  
Martijn Rep ◽  
Ben J. C. Cornelissen
Keyword(s):  
Transposable Elements ◽  
Fusarium Oxysporum ◽  
Resistance Genes ◽  
Pcr Analysis ◽  
Genomic Fragment ◽  
Avirulence Genes ◽  
Content Type ◽  
Race 1 ◽  
Tomato Cultivars ◽  
Race 2

ABSTRACT Race 1 isolates of Fusarium oxysporum f. sp. lycopersici (FOL) are characterized by the presence of AVR1 in their genomes. The product of this gene, Avr1, triggers resistance in tomato cultivars carrying resistance gene I. In FOL race 2 and race 3 isolates, AVR1 is absent, and hence they are virulent on tomato cultivars carrying I. In this study, we analyzed an approximately 100-kb genomic fragment containing the AVR1 locus of FOL race 1 isolate 004 (FOL004) and compared it to the sequenced genome of FOL race 2 isolate 4287 (FOL4287). A genomic fragment of 31 kb containing AVR1 was found to be missing in FOL4287. Further analysis suggests that race 2 evolved from race 1 by deletion of this 31-kb fragment due to a recombination event between two transposable elements bordering the fragment. A worldwide collection of 71 FOL isolates representing races 1, 2, and 3, all known vegetative compatibility groups (VCGs), and five continents was subjected to PCR analysis of the AVR1 locus, including the two bordering transposable elements. Based on phylogenetic analysis using the EF1-α gene, five evolutionary lineages for FOL that correlate well with VCGs were identified. More importantly, we show that FOL races evolved in a stepwise manner within each VCG by the loss of function of avirulence genes in a number of alternative ways. IMPORTANCE Plant-pathogenic microorganisms frequently mutate to overcome disease resistance genes that have been introduced in crops. For the fungus Fusarium oxysporum f. sp. lycopersici, the causal agent of Fusarium wilt in tomato, we have identified the nature of the mutations that have led to the overcoming of the I and I-2 resistance genes in all five known clonal lineages, which include a newly discovered lineage. Five different deletion events, at least several of which are caused by recombination between transposable elements, have led to loss of AVR1 and overcoming of I. Two new events affecting AVR2 that led to overcoming of I-2 have been identified. We propose a reconstruction of the evolution of races in FOL, in which the same mutations in AVR2 and AVR3 have occurred in different lineages and the FOL pathogenicity chromosome has been transferred to new lineages several times.

scholarly journals Increased Resistance to Multiple Antimicrobials and Altered Resistance Gene Expression in CMY-2-Positive Salmonella enterica following a Simulated Patient Treatment with Ceftriaxone

2012 ◽  
Vol 78 (22) ◽  
pp. 8062-8066 ◽  
Author(s):  
Russell D. Hamilton ◽  
Holly J. Hulsebus ◽  
Samina Akbar ◽  
Jeffrey T. Gray
Keyword(s):  
Gene Expression ◽  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
The United States ◽  
Simulated Patient ◽  
Patient Treatment ◽  
Content Type

ABSTRACTSalmonellosis is one of the most common causes of food-borne disease in the United States. Increasing antimicrobial resistance and corresponding increases in virulence present serious challenges. Currently, empirical therapy for invasiveSalmonella entericainfection includes either ceftriaxone or ciprofloxacin (E. L. Hohmann, Clin. Infect. Dis. 32:263–269, 2001). TheblaCMY-2gene confers resistance to ceftriaxone, the antimicrobial of choice for pediatric patients with invasiveSalmonella entericainfections, making these infections especially dangerous (J. M. Whichard et al., Emerg. Infect. Dis. 11:1464–1466, 2005). We hypothesized thatblaCMY-2-positiveSalmonella entericawould exhibit increased MICs to multiple antimicrobial agents and increased resistance gene expression following exposure to ceftriaxone using a protocol that simulated a patient treatmentin vitro. SevenSalmonella entericastrains survived a simulated patient treatmentin vitroand, following treatment, exhibited a significantly increased ceftriaxone MIC. Not only would these isolates be less responsive to further ceftriaxone treatment, but because theblaCMY-2genes are commonly located on large, multidrug-resistant plasmids, increased expression of theblaCMY-2gene may be associated with increased expression of other drug resistance genes located on the plasmid (N. D. Hanson and C. C. Sanders, Curr. Pharm. Des. 5:881–894, 1999). The results of this study demonstrate that a simulated patient treatment with ceftriaxone can alter the expression of antimicrobial resistance genes, includingblaCMY-2andfloRinS. entericaserovar Typhimurium andS. entericaserovar Newport. Additionally, we have shown increased MICs following a simulated patient treatment with ceftriaxone for tetracycline, amikacin, ceftriaxone, and cefepime, all of which have resistance genes commonly located on CMY-2 plasmids. The increases in resistance observed are significant and may have a negative impact on both public health and antimicrobial resistance ofSalmonella enterica.

scholarly journals Genetic control of Pyrenophora teres virulence to three barley accessions

2017 ◽  
Vol 38 (SI 2 - 6th Conf EFPP 2002) ◽  
pp. 612-614
Author(s):  
N. Mironenko ◽  
O. Filatova ◽  
O. Afanasenko
Keyword(s):  
Genetic Control ◽  
Resistance Genes ◽  
Pyrenophora Teres ◽  
Avirulence Genes ◽  
Monogenic Inheritance ◽  
Barley Resistance ◽  
Barley Genotypes

Ascospore progeny of cross of Pyrenophora teres f. teres isolates was evaluated on virulence to three barley genotypes. Monogenic inheritance of virulence (26 a:17 v and 31 a:18 v) was shown to cultivar Harbin and accession c 21272 and supported by results of two fungal backcrosses. The existence of three unlinked avirulence genes to CI 4922 is suggested (37 a:7 v). The model of interaction between barley resistance genes and avirulence genes with postulated fungal genotypes is proposed.

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