scholarly journals RPW8/HR Repeats Predict NLR-dependent Hybrid Performance

2019 ◽  
Author(s):  
Cristina A. Barragan ◽  
Rui Wu ◽  
Sang-Tae Kim ◽  
Wanyan Xi ◽  
Anette Habring ◽  
...  
Keyword(s):  
Genetic Interaction ◽  
Gene Copy Number ◽  
Gene Clusters ◽  
Gene Copy ◽  
Hybrid Necrosis ◽  
Resistance Proteins ◽  
Broad Spectrum Resistance ◽  
Structural Differences ◽  
Allele Specific ◽  
Complex Manner

SummaryHybrid offspring can look very different from their parents, including having greatly increased or decreased fitness. In many plant species, conflicts between divergent elements of the immune system can cause hybrids to express autoimmunity, a generally deleterious syndrome known as hybrid necrosis. We are investigating multiple hybrid necrosis cases in Arabidopsis thaliana that are caused by allele-specific interactions between different variants at two unlinked resistance (R) gene clusters. One is the RESISTANCE TO PERONOSPORA PARASITICA 7 (RPP7) cluster, which encodes an intracellular nucleotide binding site-leucine rich repeat (NLR) immune receptors that confer strain-specific resistance to oomycetes. The other is the RESISTANCE TO POWDERY MILDEW 8 (RPW8)/HOMOLOG OF RPW8 (HR) locus, which encodes atypical resistance proteins that can confer broad-spectrum resistance to filamentous pathogens. There is extensive structural variation in the RPW8/HR cluster, both at the level of gene copy number and at the level of C-terminal protein repeats of unknown function. We demonstrate that the number of RPW8/HR repeats correlate, albeit in a complex manner, with the severity of hybrid necrosis when these alleles are combined with specific RPP7 variants. This observation suggests that gross structural differences, rather than individual amino acid polymorphisms, guide the genetic interaction between RPW8/HR and RPP7 alleles. We discuss these findings in light of the similarity of RPW8/HR proteins with pore-forming toxins, MLKL and HET-S, from mammals and fungi.

scholarly journals A giant chimeric NLR gene confers extreme broad-spectrum resistance to a plant pathogen

2021 ◽  
Author(s):  
Jianxin Ma ◽  
Weidong Wang ◽  
Liyang Chen ◽  
Kevin Fengler ◽  
Joy Bolar ◽  
...  
Keyword(s):  
Broad Spectrum ◽  
Gene Copy Number ◽  
Gene Clusters ◽  
Genomic Region ◽  
Phytophthora Sojae ◽  
Gene Copy ◽  
Gene Copy Number Variation ◽  
Promoter Fusion ◽  
Broad Spectrum Resistance ◽  
Number Variation

Abstract Phytophthora root and stem rot (PRSR) caused by Phytophthora sojae is the most destructive soybean soil-borne disease worldwide. Discovery of genes conferring broad-spectrum resistance to the pathogen is an urgent need to prevent the outbreak of the disease. Here we show that soybean Rps11 is a 27.7-kb nucleotide-binding site-leucine-rich repeat (NBS-LRR or NLR) gene conferring extreme broad-spectrum resistance to the pathogen. Rps11 is located in a genomic region harboring a cluster of unusually large NLR genes belonging to a single evolutionary lineage that is distinct from all other lineages in the soybean genome, and was derived from rounds of intergenic and intragenic unequal recombination. Such recombination events have resulted in promoter fusion and expansion of the LRR domain that presumably explains such broadness of the resistance spectrum. The NLR gene cluster exhibits drastic structural diversification among phylogenetically representative varieties, including gene copy number variation ranging from five to 23 copies, and absence of allelic copies of Rps11 (i.e., rps11) in any of the non-Rps11-donor varieties examined. Our study thus exemplifies innovative evolution of NLR genes and NLR gene clusters and will accelerate the deployment of Rps11 for soybean protection.

scholarly journals A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Weidong Wang ◽  
Liyang Chen ◽  
Kevin Fengler ◽  
Joy Bolar ◽  
Victor Llaca ◽  
...  
Keyword(s):  
Broad Spectrum ◽  
Gene Copy Number ◽  
Gene Clusters ◽  
Genomic Region ◽  
Phytophthora Sojae ◽  
Gene Copy ◽  
Gene Copy Number Variation ◽  
Promoter Fusion ◽  
Broad Spectrum Resistance ◽  
Number Variation

AbstractPhytophthora root and stem rot caused by P. sojae is a destructive soybean soil-borne disease found worldwide. Discovery of genes conferring broad-spectrum resistance to the pathogen is a need to prevent the outbreak of the disease. Here, we show that soybean Rps11 is a 27.7-kb nucleotide-binding site-leucine-rich repeat (NBS-LRR or NLR) gene conferring broad-spectrum resistance to the pathogen. Rps11 is located in a genomic region harboring a cluster of large NLR genes of a single origin in soybean, and is derived from rounds of unequal recombination. Such events result in promoter fusion and LRR expansion that may contribute to the broad resistance spectrum. The NLR gene cluster exhibits drastic structural diversification among phylogenetically representative varieties, including gene copy number variation ranging from five to 23 copies, and absence of allelic copies of Rps11 in any of the non-Rps11-donor varieties examined, exemplifying innovative evolution of NLR genes and NLR gene clusters.

scholarly journals A Novel Reductive Dehalogenase, Identified in a Contaminated Groundwater Enrichment Culture and in Desulfitobacterium dichloroeliminans Strain DCA1, Is Linked to Dehalogenation of 1,2-Dichloroethane

2007 ◽  
Vol 73 (9) ◽  
pp. 2990-2999 ◽  
Author(s):  
Massimo Marzorati ◽  
Francesca de Ferra ◽  
Hilde Van Raemdonck ◽  
Sara Borin ◽  
Elena Allifranchini ◽  
...  
Keyword(s):  
Amino Acid ◽  
Gene Cluster ◽  
Enrichment Culture ◽  
Gene Copy Number ◽  
Gene Clusters ◽  
Amino Acid Identity ◽  
Chlorinated Ethenes ◽  
Gene Copy ◽  
Direct Pcr ◽  
Reductive Dehalogenase

ABSTRACT A mixed culture dechlorinating 1,2-dichloroethane (1,2-DCA) to ethene was enriched from groundwater that had been subjected to long-term contamination. In the metagenome of the enrichment, a 7-kb reductive dehalogenase (RD) gene cluster sequence was detected by inverse and direct PCR. The RD gene cluster had four open reading frames (ORF) showing 99% nucleotide identity with pceB, pceC, pceT, and orf1 of Dehalobacter restrictus strain DSMZ 9455T, a bacterium able to dechlorinate chlorinated ethenes. However, dcaA, the ORF encoding the catalytic subunit, showed only 94% nucleotide and 90% amino acid identity with pceA of strain DSMZ 9455T. Fifty-three percent of the amino acid differences were localized in two defined regions of the predicted protein. Exposure of the culture to 1,2-DCA and lactate increased the dcaA gene copy number by 2 log units, and under these conditions the dcaA and dcaB genes were actively transcribed. A very similar RD gene cluster with 98% identity in the dcaA gene sequence was identified in Desulfitobacterium dichloroeliminans strain DCA1, the only known isolate that selectively dechlorinates 1,2-DCA but not chlorinated ethenes. The dcaA gene of strain DCA1 possesses the same amino acid motifs as the new dcaA gene. Southern hybridization using total genomic DNA of strain DCA1 with dcaA gene-specific and dcaB- and pceB-targeting probes indicated the presence of two identical or highly similar dehalogenase gene clusters. In conclusion, these data suggest that the newly described RDs are specifically adapted to 1,2-DCA dechlorination.

scholarly journals Dietary adaptation in Neandertal, Denisovan and Sapiens revealed by gene copy number variation

2021 ◽  
Author(s):  
Riccardo Vicedomini ◽  
Lelia Polit ◽  
Silvana Condemi ◽  
Laura Longo ◽  
Alessandra Carbone
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Homo Sapiens ◽  
Gene Copy Number ◽  
Gene Clusters ◽  
Genomic Variation ◽  
Gene Copy ◽  
Efficient System ◽  
Dietary Adaptation ◽  
Number Variation

Dietary adaptation is the acquisition of an efficient system to digest food available in an ecosystem. To find the genetic basis for human dietary adaptation, we searched 16 genomes from Neandertal, Denisovan and Early Sapiens for food digestion genes that tend to have more or fewer copies than the modern human reference genome. Here, we identify 11 genes, including three gene clusters, with discernible copy number variation trends at the population level. The genomic variation shows how metabolic pathways for lipid, brown fat, protein or carbohydrate metabolism adapt to metabolize food from animal or plant sources. Interpreting the copy number profiles in relation to fossil evidence shows that Homo sapiens had an evolutionary advantage compared to Neandertal and Denisovan in adapting to cold and temperate ecosystems.

scholarly journals Analysis of CYP2D6 Allele Frequencies and Identification of Novel SNPs and Sequence Variations in Sardinians

ISRN Genetics ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Matteo Falzoi ◽  
Luigi Pira ◽  
Paolo Lazzari ◽  
Luca Pani
Keyword(s):  
Enzyme Level ◽  
Gene Copy Number ◽  
Drug Level ◽  
Caucasian Population ◽  
Allele Frequencies ◽  
Gene Copy ◽  
Sequencing Analysis ◽  
Gene Deletions ◽  
Allele Specific ◽  
Dna Sequencing Analysis

The CYP2D6 enzyme is involved in the metabolism of many commonly prescribed drugs. The presence of polymorphisms in the CYP2D6 gene may modulate the enzyme level and activity affecting individual responses, to pharmacological treatment in drug level, response and adverse reactions. Aims. This study aimed to analyze the determination of allele frequencies in Sardinians and the comparison to frequencies found in the Caucasian Population. Methods and Materials. We used a Long PCR strategy coupled to direct genomic DNA sequencing analysis. An amplification allele-specific was carried out to infer the correct allelic phase. The TaqMan Gene Copy Number Assay (Applied Biosystems) was used to verify the presence of gene deletions/multiplications. Results and Conclusions. Our results indicated that CYP2D6 allele frequencies in Sardinians differed from those previously detected in the Caucasian Population. Moreover, three new SNPs and four novel haplotypes were identified.

Epidermal Growth Factor Receptor (EGFr) status detection in correlation to objective response on cetuximab-based therapy in patients (pts) with advanced colorectal cancer (ACC)

2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 21070-21070
Author(s):  
A. Gevorgyan ◽  
M. Di Bartolomeo ◽  
S. Andreola ◽  
M. Orsenigo ◽  
P. Casieri ◽  
...  
Keyword(s):  
Protein Expression ◽  
Clinical Benefit ◽  
Statistical Significance ◽  
Objective Response ◽  
Gene Copy Number ◽  
Growth Factor Receptor ◽  
Gene Clusters ◽  
Gene Copy ◽  
Dual Colour ◽  
Cetuximab Therapy

21070 Background: In current clinical practice Cetuximab represents a standard therapy for Irinotecan resistant pts with ACC, where EGFR-immunohistochemistry (IHC) evaluation is positive. In absence of reliable molecular predictors of the clinical benefit to anti-EGFR therapy, we have studied EGFR protein expression and gene status in order to correlate them to the clinical response. Methods: We investigated 40 primary colorectal carcinoma specimens. EGFR-protein expression was evaluated by Immunohistochemistry (IHC) using PharmDX-Kit DAKO Cytomation. IHC evaluation was performed using combined score based on the sum of percentage of positive cells and the staining of each sample. We identified three EGFR-score categories: 0–2, 3–5, 6–7 corresponding to low, intermediate and high expression respectively. EGFR-genetic status was conducted by Dual-Colour FISH (LSI EGFR-probe Vysis Inc).Gene and chromosome 7 copy numbers were identified by fluorescence in situ hybridization (FISH-LSI EGFR-Dual-colour-probe Vysis-Inc) as follows: tumor samples had a high EGFR-gene copy number if there was high polysomy ( 4-copies 40% of cells) or gene amplification (gene-clusters, gene/chromosome ratio per cell of 2, 15 copies of EGFR/ cell in 10% of cells) . The analysis of clinical data from all patients treated with Cetuximab (400–250mg/m2/w) and Irinotecan (300mg/m2/d1q21) was then performed. Results: EGFR-(IHC) high score was observed in 7pts from which only 2 had an objective response (OR). Intermediate (13pts) with 3 OR, low (12pts) with 1 OR and negative (8pts) with 2OR. Main FISH patterns were: high polisomy/amplification in 8pts with no response on cetuximab therapy. Low polisomy described in 19pts with 3 cases of disease remission. Disomy in 13pts with 5OR. No relationship was detected between IHC-score evaluation and FISH pattern. The clinical benefit (OR+stable disease =6months) was 65% in score-group 0–2; whereas 46% and 57% in groups 3–5/6–7 respectively, without statistical significance. Conclusion: According to our experience, IHC and FISH are unable to provide adequate selection criteria for the patients with different EGFR-status expression, who can benefit from Cetuximab therapy. No significant financial relationships to disclose.

scholarly journals Functional interactions between unlinked muscle genes within haploinsufficient regions of the Drosophila genome.

Genetics ◽  
1988 ◽  
Vol 119 (1) ◽  
pp. 105-121
Author(s):  
T Homyk ◽  
C P Emerson
Keyword(s):  
Muscle Development ◽  
Gene Copy Number ◽  
Large Family ◽  
Mutant Gene ◽  
Genetic Interactions ◽  
Gene Copy ◽  
Drosophila Genome ◽  
Gene Products ◽  
New Genes ◽  
Allele Specific

Abstract Mutations in 13 genes affecting muscle development in Drosophila have been examined in pairwise combinations for evidence of genetic interactions. Heterozygous combinations of mutations in five genes, including the gene coding for myosin heavy chain, result in more severe phenotypes than respective single heterozygous mutant controls. The various mutant interactions include examples showing allele-specific intergenic interactions, gene specific interactions, and allele-specific intragenic complementations, suggesting that some interactions result from the manner in which mutant gene products associate. Interactions that result from alterations in "+" gene copy number were also uncovered, suggesting that normal myofibril development requires that the relative amounts of respective gene products produced be tightly regulated. The importance of the latter parameter is substantiated by the finding that all five interacting loci map to disperse haploinsufficient or haplolethal regions of the genome. The implications of the present findings are discussed in relation to pursuing the phenomena involving genetic interactions to identify new genes encoding interacting myofibrillar proteins, to examine the nature of intermolecular interactions in mutant and normal development and to decipher the quantitative and temporal regulation of a large family of functionally related gene products.

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