scholarly journals Analysis of intraspecies diversity reveals a subset of highly variable plant immune receptors and predicts their binding sites

2021 ◽  
Author(s):  
Daniil M Prigozhin ◽  
Ksenia V Krasileva
Keyword(s):  
Binding Sites ◽  
Plant Immunity ◽  
Brachypodium Distachyon ◽  
Allelic Diversity ◽  
Antigen Binding ◽  
Leucine Rich Repeat ◽  
Downstream Signaling ◽  
High Allelic Diversity ◽  
Intraspecies Diversity ◽  
Receptor Family

Abstract The evolution of recognition specificities by the immune system depends on the generation of receptor diversity and on connecting the binding of new antigens with the initiation of downstream signaling. In plant immunity, the innate Nucleotide-Binding Leucine Rich Repeat (NLR) receptor family enables antigen binding and immune signaling. In this study, we surveyed the NLR complements of 62 ecotypes of Arabidopsis thaliana and 54 lines of Brachypodium distachyon and identified a limited number of NLR subfamilies that show high allelic diversity. We show that the predicted specificity-determining residues cluster on the surfaces of Leucine Rich Repeat domains, but the locations of the clusters vary among NLR subfamilies. By comparing NLR phylogeny, allelic diversity, and known functions of the Arabidopsis NLRs, we formulate a hypothesis for the emergence of direct and indirect pathogen-sensing receptors and of the autoimmune NLRs. These findings reveal the recurring patterns of evolution of innate immunity and can inform NLR engineering efforts.

scholarly journals Intraspecies diversity reveals a subset of highly variable plant immune receptors and predicts their binding sites

2020 ◽  
Author(s):  
Daniil M Prigozhin ◽  
Ksenia V Krasileva
Keyword(s):  
Innate Immunity ◽  
Arabidopsis Thaliana ◽  
Immune System ◽  
Binding Sites ◽  
Plant Immunity ◽  
Brachypodium Distachyon ◽  
Allelic Diversity ◽  
Leucine Rich Repeat ◽  
The Family ◽  
Intraspecies Diversity

AbstractEvolution of recognition specificities by the immune system depends on the generation of receptor diversity, and connecting binding of new antigens with initiation of downstream signalling. In plant immunity, these functions are enabled by the family of innate Nucleotide-Binding Leucine Rich Repeat (NLR) receptors. In this paper we surveyed the NLR complements of 62 ecotypes of Arabidopsis thaliana and 54 lines of Brachypodium distachyon and identified a limited number of NLR subfamilies responsible for generation of new receptor specificities. We show that the predicted specificity-determining residues cluster on the surfaces of Leucine Rich Repeat domains, but the location of the clusters varies between NLR subfamilies. By comparing NLR phylogeny, allelic diversity, and known functions of the Arabidopsis NLRs, we formulate a hypothesis for emergence of direct and indirect pathogen sensing receptors, and of the autoimmune NLRs. These findings reveal the recurring patterns of evolution of innate immunity and inform NLR engineering efforts.

Aggregation prone regions in antibody sequences raised against Vibrio cholerae: A bioinformatic approach

2020 ◽  
Vol 15 ◽  
Author(s):  
Zakia Akter ◽  
Anamul Haque ◽  
Md. Sabir Hossain ◽  
Firoz Ahmed ◽  
Md Asiful Islam
Keyword(s):  
Vibrio Cholerae ◽  
Binding Sites ◽  
Bioinformatic Analysis ◽  
Antigen Binding ◽  
Short Term ◽  
Protein Database ◽  
The Stability ◽  
Bioinformatic Approach ◽  
Self Aggregation ◽  
Complementarity Determining Region

Background: Cholera, a diarrheal illness causes millions of deaths worldwide due to large outbreaks. Monoclonal antibody used as therapeutic purposes of cholera are prone to be unstable due to various factors including self-aggregation. Objectives: In this bioinformatic analysis, we identified the aggregation prone regions (APRs) of different immunogens of antibody sequences (i.e., CTB, ZnM-CTB, ZnP-CTB, TcpA-CT-CTB, ZnM-TcpA-CT-CTB, ZnP-TcpA-CT-CTB, ZnM-TcpA, ZnP-TcpA, TcpA-CT-TcpA, ZnM-TcpA-CT-TcpA, ZnP-TcpA-CT-TcpA, Ogawa, Inaba and ZnM-Inaba) raised against Vibrio cholerae. Methods: To determine APRs in antibody sequences that were generated after immunizing Vibrio cholerae immunogens on Mus musculus, a total of 94 sequences were downloaded as FASTA format from a protein database and the algorithms such as Tango, Waltz, PASTA 2.0, and AGGRESCAN were followed to analyze probable APRs in all of the sequences. Results: A remarkably high number of regions in the monoclonal antibodies were identified to be APRs which could explain a cause of instability/short term protection of anticholera vaccine. Conclusion: To increase the stability, it would be interesting to eliminate the APR residues from the therapeutic antibodies in a such way that the antigen binding sites or the complementarity determining region loops involved in antigen recognition are not disrupted.

scholarly journals Unexpectedly High Allelic Diversity at the KIT Locus Causing Dominant White Color in the Domestic Pig

Genetics ◽  
2002 ◽  
Vol 160 (1) ◽  
pp. 305-311
Author(s):  
G Pielberg ◽  
C Olsson ◽  
A-C Syvänen ◽  
L Andersson
Keyword(s):  
Coat Color ◽  
Allelic Diversity ◽  
Growth Factor Receptor ◽  
Small Sample ◽  
Color Variation ◽  
Large White ◽  
High Genetic Diversity ◽  
High Allelic Diversity ◽  
Stem Cell Growth Factor ◽  
New Alleles

Abstract Mutations in KIT encoding the mast/stem cell growth factor receptor (MGF) are responsible for coat color variation in domestic pigs. The dominant white phenotype is caused by two mutations, a gene duplication and a splice mutation in one of the copies leading to skipping of exon 17. Here we applied minisequencing and pyrosequencing for quantitative analysis of the number of copies with the splice form. An unexpectedly high genetic diversity was revealed in white pigs. We found four different KIT alleles in a small sample of eight Large White females used as founder animals in a wild boar intercross. A similar number of KIT alleles was found in commercial populations of white Landrace and Large White pigs. We provide evidence for at least two new KIT alleles in pigs, both with a triplication of the gene. The results imply that KIT alleles with the duplication are genetically unstable and new alleles are most likely generated by unequal crossing over. This study provides an improved method for genotyping the complicated Dominant white/KIT locus in pigs. The results also suggest that some alleles may be associated with negative pleiotropic effects on other traits.

scholarly journals Mutant glucocorticoid receptor binding elements on the interleukin-6 promoter regulate dexamethasone effects

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wen-Teng Chang ◽  
Ming-Yuan Hong ◽  
Chien-Liang Chen ◽  
Chi-Yuan Hwang ◽  
Cheng-Chieh Tsai ◽  
...  
Keyword(s):  
Binding Sites ◽  
Inflammatory Diseases ◽  
Inducible Promoter ◽  
Transcriptional Factor ◽  
Factor Binding ◽  
Inflammatory Processes ◽  
Nuclear Receptor Family ◽  
Specificity Protein ◽  
Receptor Family ◽  
Pro Inflammatory Cytokines

Abstract Background Glucocorticoids (GCs) have been extensively used as essential modulators in clinical infectious and inflammatory diseases. The GC receptor (GR) is a transcription factor belonging to the nuclear receptor family that regulates anti-inflammatory processes and releases pro-inflammatory cytokines, such as interleukin (IL)-6. Results Five putative GR binding sites and other transcriptional factor binding sites were identified on theIL-6 promoter, and dexamethasone (DEX) was noted to reduce the lipopolysaccharide (LPS)-induced IL-6 production. Among mutant transcriptional factor binding sites, nuclear factor-kappa B (NF-κB), activator protein (AP)-1, and specificity protein (Sp)1–2 sites reduced basal and LPS-induced IL-6 promoter activities through various responses. The second GR binding site (GR2) was noted to play a crucial role in both basal and inducible promoter activities in LPS-induced inflammation. Conclusions We concluded that selective GR2 modulator might exert agonistic and antagonistic effects and could activate crucial signaling pathways during the LPS-stimulated inflammatory process.

scholarly journals Predominant VH genes expressed in innate antibodies are associated with distinctive antigen-binding sites

1999 ◽  
Vol 96 (5) ◽  
pp. 2262-2267 ◽  
Author(s):  
K. J. Seidl ◽  
J. A. Wilshire ◽  
J. D. MacKenzie ◽  
A. B. Kantor ◽  
L. A. Herzenberg ◽  
...  
Keyword(s):  
Binding Sites ◽  
Antigen Binding ◽  
Vh Genes ◽  
Innate Antibodies

scholarly journals The Hypersensitive Induced Reaction and Leucine-Rich Repeat Proteins Regulate Plant Cell Death Associated with Disease and Plant Immunity

2011 ◽  
Vol 24 (1) ◽  
pp. 68-78 ◽  
Author(s):  
Hyong Woo Choi ◽  
Young Jin Kim ◽  
Byung Kook Hwang
Keyword(s):  
Cell Death ◽  
Xanthomonas Campestris ◽  
Plant Immunity ◽  
Yeast Cells ◽  
Leucine Rich Repeat ◽  
Virus Induced Gene Silencing ◽  
Susceptible Cell ◽  
Gene Transcripts ◽  
Induced Reaction ◽  
Pepper Plants

Pathogen-induced programmed cell death (PCD) is intimately linked with disease resistance and susceptibility. However, the molecular components regulating PCD, including hypersensitive and susceptible cell death, are largely unknown in plants. In this study, we show that pathogen-induced Capsicum annuum hypersensitive induced reaction 1 (CaHIR1) and leucine-rich repeat 1 (CaLRR1) function as distinct plant PCD regulators in pepper plants during Xanthomonas campestris pv. vesicatoria infection. Confocal microscopy and protein gel blot analyses revealed that CaLRR1 and CaHIR1 localize to the extracellular matrix and plasma membrane (PM), respectively. Bimolecular fluorescent complementation and coimmunoprecipitation assays showed that the extracellular CaLRR1 specifically binds to the PM-located CaHIR1 in pepper leaves. Overexpression of CaHIR1 triggered pathogen-independent cell death in pepper and Nicotiana benthamiana plants but not in yeast cells. Virus-induced gene silencing (VIGS) of CaLRR1 and CaHIR1 distinctly strengthened and compromised hypersensitive and susceptible cell death in pepper plants, respectively. Endogenous salicylic acid levels and pathogenesis-related gene transcripts were elevated in CaHIR1-silenced plants. VIGS of NbLRR1 and NbHIR1, the N. benthamiana orthologs of CaLRR1 and CaHIR1, regulated Bax- and avrPto-/Pto-induced PCD. Taken together, these results suggest that leucine-rich repeat and hypersensitive induced reaction proteins may act as cell-death regulators associated with plant immunity and disease.

NLRP6 Induces Pyroptosis by Activation of Caspase-1 in Gingival Fibroblasts

2018 ◽  
Vol 97 (12) ◽  
pp. 1391-1398 ◽  
Author(s):  
W. Liu ◽  
J. Liu ◽  
W. Wang ◽  
Y. Wang ◽  
X. Ouyang
Keyword(s):  
Innate Immune ◽  
Gingival Tissue ◽  
Gingival Fibroblasts ◽  
Leucine Rich Repeat ◽  
Nucleotide Binding Domain ◽  
Commensal Bacterium ◽  
Caspase 1 ◽  
Proinflammatory Mediators ◽  
First Time ◽  
Receptor Family

NLRP6, a member of the nucleotide-binding domain, leucine-rich repeat-containing (NLR) innate immune receptor family, has been reported to participate in inflammasome formation. Activation of inflammasome triggers a caspase-1–dependent programming cell death called pyroptosis. However, whether NLRP6 induces pyroptosis has not been investigated. In this study, we showed that NLRP6 overexpression activated caspase-1 and gasdermin-D and then induced pyroptosis of human gingival fibroblasts, resulting in release of proinflammatory mediators interleukin (IL)–1β and IL-18. Moreover, NLRP6 was highly expressed in gingival tissue of periodontitis compared with healthy controls. Porphyromonas gingivalis, which is a commensal bacterium and has periodontopathic potential, induced pyroptosis of gingival fibroblasts by activation of NLRP6. Together, we, for the first time, identified that NLRP6 could induce pyroptosis of gingival fibroblasts by activation of caspase-1 and may play a role in periodontitis.

scholarly journals Regulation and Functions of ROP GTPases in Plant–Microbe Interactions

Cells ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 2016
Author(s):  
Stefan Engelhardt ◽  
Adriana Trutzenberg ◽  
Ralph Hückelhoven
Keyword(s):  
Cell Invasion ◽  
Rho Gtpases ◽  
Fungal Pathogens ◽  
Plant Immunity ◽  
Pathogen Resistance ◽  
Research Field ◽  
Rho Proteins ◽  
Downstream Signaling ◽  
Microbe Interactions ◽  
Developmental Reprogramming

Rho proteins of plants (ROPs) form a specific clade of Rho GTPases, which are involved in either plant immunity or susceptibility to diseases. They are intensively studied in grass host plants, in which ROPs are signaling hubs downstream of both cell surface immune receptor kinases and intracellular nucleotide-binding leucine-rich repeat receptors, which activate major branches of plant immune signaling. Additionally, invasive fungal pathogens may co-opt the function of ROPs for manipulation of the cytoskeleton, cell invasion and host cell developmental reprogramming, which promote pathogenic colonization. Strikingly, mammalian bacterial pathogens also initiate both effector-triggered susceptibility for cell invasion and effector-triggered immunity via Rho GTPases. In this review, we summarize central concepts of Rho signaling in disease and immunity of plants and briefly compare them to important findings in the mammalian research field. We focus on Rho activation, downstream signaling and cellular reorganization under control of Rho proteins involved in disease progression and pathogen resistance.

Sign in / Sign up

Export Citation Format

Share Document