Identification of Immune Related LRR-Containing Genes in Maize (Zea maysL.) by Genome-Wide Sequence Analysis

A large number of immune receptors consist of nucleotide binding site-leucine rich repeat (NBS-LRR) proteins and leucine rich repeat-receptor-like kinases (LRR-RLK) that play a crucial role in plant disease resistance. Although many NBS-LRR genes have been previously identified inZea mays, there are no reports on identifying NBS-LRR genes encoded in the N-terminal Toll/interleukin-1 receptor (TIR) motif and identifying genome-wide LRR-RLK genes. In the present study, 151 NBS-LRR genes and 226 LRR-RLK genes were identified after performing bioinformatics analysis of the entire maize genome. Of these identified genes, 64 NBS-LRR genes and four TIR-NBS-LRR genes were identified for the first time. The NBS-LRR genes are unevenly distributed on each chromosome with gene clusters located at the distal end of each chromosome, while LRR-RLK genes have a random chromosomal distribution with more paired genes. Additionally, six LRR-RLK/RLPs including FLS2, PSY1R, PSKR1, BIR1, SERK3, and Cf5 were characterized inZea maysfor the first time. Their predicted amino acid sequences have similar protein structures with their respective homologues in other plants, indicating that these maize LRR-RLK/RLPs have the same functions as their homologues act as immune receptors. The identified gene sequences would assist in the study of their functions in maize.

Download Full-text

Genome-wide identification and comparative analysis of NBS-LRR resistance genes in Brassica napus

Crop and Pasture Science ◽

10.1071/cp17214 ◽

2018 ◽

Vol 69 (1) ◽

pp. 72 ◽

Cited By ~ 24

Author(s):

Salman Alamery ◽

Soodeh Tirnaz ◽

Philipp Bayer ◽

Reece Tollenaere ◽

Boulos Chaloub ◽

...

Keyword(s):

Comparative Analysis ◽

Brassica Napus ◽

Resistance Genes ◽

Plant Disease Resistance ◽

Interleukin 1 ◽

Critical Role ◽

Coiled Coil ◽

Genome Wide ◽

High Level ◽

Plant Disease Resistance Genes

Plant disease-resistance genes play a critical role in providing resistance against pathogens. The largest family of resistance genes are the nucleotide-binding site (NBS) and leucine-rich repeat (LRR) genes. They are classified into two major subfamilies, toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) and coiled-coil (CC)-NBS-LRR (CNL) proteins. We have identified and characterised 641 NBS-LRR genes in Brassica napus, 249 in B. rapa and 443 in B. oleracea. A ratio of 1 : 2 of CNL : TNL genes was found in the three species. Domain structure analysis revealed that 57% of the NBS-LRR genes are typical resistance genes and contain all three domains (TIR/CC, NBS, LRR), whereas the remaining genes are partially deleted or truncated. Of the NBS-LRR genes, 59% were found to be physically clustered, and individual genes involved in clusters were more polymorphic than those not clustered. Of the NBS-LRR genes in B. napus, 50% were identified as duplicates, reflecting a high level of genomic duplication and rearrangement. Comparative analysis between B. napus and its progenitor species indicated that >60% of NBS-LRR genes are conserved in B. napus. This study provides a valuable resource for the identification and characterisation of candidate NBS-LRR genes.

Download Full-text

Genome-wide Identification of Disease Resistance Genes (R Genes) in Wheat

10.1101/2020.07.18.210286 ◽

2020 ◽

Author(s):

Ethan J. Andersen ◽

Lauren E. Lindsey ◽

Madhav P. Nepal

Keyword(s):

Resistance Genes ◽

Functional Divergence ◽

Interleukin 1 ◽

Crop Improvement ◽

Aegilops Tauschii ◽

Gene Clusters ◽

R Genes ◽

Genome Wide ◽

Large Expansion ◽

Encoding Genes

ABSTRACTProteins encoded by plant resistance genes (R genes) detect pathogenic effectors and initiate immune responses. Although R genes in many plant genomes are identified, they are yet to be identified in wheat. The major objectives of this project were to conduct genome-wide identification of the NB-ARC-encoding R genes in wheat (Triticum aestivum L.) and assess their genomic architecture and potential functional divergence. Wheat protein sequences were obtained from the Ensembl Genomes database, and genes were identified using interpro program. Chromosomal locations of the R genes were determined and syntenic analyses were performed. Altogether, 2151 wheat NB-ARC-encoding genes were identified, among which 1298 genes formed 547 gene clusters. Many of these gene clusters included highly similar genes likely formed by tandem duplications. Among the NB-ARC-encoding genes, 1552 (∼72%) encode Leucine-Rich Repeats (LRRs), 802 are Coiled-Coil (CC) domain-encoding CC-NBS-LRR (CNL) genes and three are Resistance to Powdery mildew 8 (RPW8) domain-encoding RPW8-NBS-LRR (RNL) genes. Surprisingly, five of the NB-ARC-encoding genes encoded a Toll/Interleukin-1 Receptor (TIR), with no LRR, known as TN genes. CNL clades formed similar nesting patterns with a large expansion of CNL-C group like previously reported findings in wheat relatives. Comparisons of the wheat genome with barley (Hordeum vulgare L.) and Tausch’s goatgrass (Aegilops tauschii Coss.), showed similar locations for homologous NB-ARC-encoding genes. These results showed that R genes in wheat have diversified through duplication to encode receptors that recognize rapidly evolving pathogenic effectors. Identified R genes in this study have implications in plant breeding, as a source of resistance for crop improvement.

Download Full-text

Identification, characterization, and expression profiles of the GASA genes in cotton

Journal of Cotton Research ◽

10.1186/s42397-021-00081-9 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Kaikai QIAO ◽

Changkai MA ◽

Jiaoyan LV ◽

Chaojun ZHANG ◽

Qifeng MA ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Expression Profiles ◽

Protein Structures ◽

Genome Wide ◽

Giberellic Acid ◽

Hormone Responses ◽

Key Driver ◽

Polymerase Chain ◽

First Time

Abstract Background GASA (Giberellic Acid Stimulated in Arabidopsis) gene family plays a crucial role in the phytohormone signaling pathway, growth and development, and stress responses in plants. Many GASA homologs have been identified in various plants. Nevertheless, little is known about these proteins in cotton. Results In the current study, we identified 19, 17, 25, 33, and 38 GASA genes via genome-wide analyses of Gossypium herbaceum, G. arboreum, G. raimondii, G. barbadense, and G. hirsutum, respectively, and performed comprehensive bioinformatics and expression analyses. According to our results, 132 GASA proteins shared similar protein structures and were classified into four groups based on the phylogenetic tree. A synteny analysis suggested that segmental duplication was a key driver in the expansion of the GASA gene family. Meanwhile, the cis-element and protein interaction analyses indicated that GhGASA proteins play a significant role in the hormone responses. Transcriptomic and qRT-PCR (Quantitative real time-polymerase chain reaction) analyses revealed diverse expression profiles of the GhGASA genes in different organs under abiotic stresses, indicating that some GhGASA genes possibly participate in fiber development and abiotic-stress responses. Conclusions The GASA genes in cotton were systematically identified and analyzed for the first time in this paper, and it suggested that the GASA genes are important to the development and growth of cotton. These results will support future exploration of the functions of GASA genes in cotton.

Download Full-text

A Truncated TIR-NBS Protein TN10 Pairs with Two Clustered TIR-NBS-LRR Immune Receptors and Contributes to Plant Immunity in Arabidopsis

International Journal of Molecular Sciences ◽

10.3390/ijms22084004 ◽

2021 ◽

Vol 22 (8) ◽

pp. 4004

Author(s):

Yongming Chen ◽

Guitao Zhong ◽

Huiren Cai ◽

Renjie Chen ◽

Na Liu ◽

...

Keyword(s):

Gene Cluster ◽

Plant Disease Resistance ◽

Plant Immunity ◽

Interleukin 1 ◽

Chromosome 1 ◽

Immune Receptors ◽

Arabidopsis Ecotype ◽

Genomic Arrangement ◽

Tir Domains ◽

Encoding Genes

The encoding genes of plant intracellular nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain receptors (NLRs) often exist in the form of a gene cluster. Several recent studies demonstrated that the truncated Toll/interleukin-1 receptor-NBS (TIR-NBS) proteins play important roles in immunity. In this study, we identified a large TN gene cluster on Arabidopsis ecotype Col-0 chromosome 1, which included nine TN genes, TN4 to TN12. Interestingly, this cluster also contained two typical TIR-NBS-LRR genes: At1g72840 and At1g72860 (hereinafter referred to as TNL40 and TNL60, respectively), which formed head-to-head genomic arrangement with TN4 to TN12. However, the functions of these TN and TNL genes in this cluster are still unknown. Here, we showed that the TIR domains of both TNL40 and TNL60 associated with TN10 specifically. Furthermore, both TNL40TIR and TNL60TIR induced cell death in Nicotiana tabacum leaves. Subcellular localization showed that TNL40 mainly localized in the cytoplasm, whereas TNL60 and TN10 localized in both the cytoplasm and nucleus. Additionally, the expression of TNL40, TNL60, and TN10 were co-regulated after inoculated with bacterial pathogens. Taken together, our study indicates that the truncated TIR-NBS protein TN10 associates with two clustered TNL immune receptors, and may work together in plant disease resistance

Download Full-text

Genome-wide functional analysis of hot pepper immune receptors reveals an autonomous NLR cluster in seed plants

10.1101/2019.12.16.878959 ◽

2019 ◽

Author(s):

Hye-Young Lee ◽

Hyunggon Mang ◽

Eun-Hye Choi ◽

Ye-Eun Seo ◽

Myung-Shin Kim ◽

...

Keyword(s):

Cell Death ◽

Coiled Coil ◽

Seed Plants ◽

Hot Pepper ◽

R Gene ◽

Leucine Rich Repeat ◽

Nucleotide Binding Domain ◽

Immune Receptors ◽

Genome Wide ◽

Hr Cell Death

AbstractPlants possess hundreds of intracellular immune receptors encoding nucleotide-binding domain and leucine-rich repeat (NLR) proteins. Autoactive NLRs, in some cases a specific NLR domain, induce plant cell death in the absence of pathogen infection. In this study, we identified a group of NLRs (G10) carrying autoactive coiled-coil (CC) domains in pepper (Capsicum annuum L. cv. CM334) by genome-wide transient expression analysis. The G10-CC-mediated cell death mimics hypersensitive response (HR) cell death triggered by interaction between NLR and effectors derived from pathogens. Sequence alignment and mutagenesis analyses revealed that the intact α1 helix of G10-CCs is critical for both G10-CC- and R gene-mediated HR cell death. The cell death induced by G10-CCs does not require known helper NLRs, suggesting G10-NLRs are novel singleton NLRs. We also found that G10-CCs localize in the plasma membrane as Arabidopsis singleton NLR ZAR1. Extended studies revealed that autoactive G10-CCs are well conserved in other Solanaceae plants, including tomato, potato, and tobacco, as well as a monocot plant, rice. Furthermore, G10-NLR is an ancient form of NLR that present in all tested seed plants (spermatophytes). Our studies not only uncover the autonomous NLR cluster in plants but also provide powerful resources for dissecting the underlying molecular mechanism of NLR-mediated cell death in plants.

Download Full-text

TIR domains of plant immune receptors are 2',3'-cAMP/cGMP synthetases mediating cell death

10.1101/2021.11.09.467869 ◽

2021 ◽

Author(s):

Dongli Yu ◽

Wen Song ◽

Eddie Yong Jun Tan ◽

Li Liu ◽

Yu Cao ◽

...

Keyword(s):

Cell Death ◽

Immune Responses ◽

Interleukin 1 ◽

Structural Data ◽

Negative Regulator ◽

Synthetase Activity ◽

Leucine Rich Repeat ◽

Tir Domain ◽

Immune Receptors ◽

Tir Domains

2′,3′-cAMP is a positional isomer of the well-established second messenger 3′,5′-cAMP, but little is known on the biology of this noncanonical cyclic nucleotide monophosphate (cNMP). Toll/interleukin-1 receptor (TIR) domains of nucleotide-binding leucine-rich repeat (NLR) immune receptors have NADase function necessary but insufficient to activate plant immune responses. Here we show that plant TIR proteins, besides being NADases, act as 2′,3′-cAMP/cGMP synthetases by hydrolyzing RNA/DNA. Structural data shows that a TIR domain adopts distinct oligomers with dual and exclusive enzymatic activity. Mutations specifically disrupting the synthetase activity abrogate TIR-mediated cell death in Nicotiana benthamiana, supporting an important role for these cNMPs in TIR signaling. Furthermore, the Arabidopsis negative regulator of TIR-NLR signaling, NUDT7 displays 2′,3′-cAMP/cGMP but not 3′,5′-cAMP/cGMP phosphodiesterase activity and suppresses cell death activity of TIRs in N. benthamiana. Our study identifies a novel family of 2′,3′-cAMP/cGMP synthetase and establishes a role for the noncanonical cNMPs in plant immune responses.

Download Full-text

Biosynthetic strategies for tetramic acid formation

Natural Product Reports ◽

10.1039/d0np00099j ◽

2021 ◽

Author(s):

Xuhua Mo ◽

Tobias A. M. Gulder

Keyword(s):

Molecular Mechanism ◽

Gene Clusters ◽

Acid Formation ◽

Biosynthetic Gene ◽

Tetramic Acid ◽

Biosynthetic Gene Clusters ◽

The Individual ◽

First Time ◽

Acid Unit

Over 30 biosynthetic gene clusters for natural tetramate have been identified. This highlight reviews the biosynthetic strategies for formation of tetramic acid unit for the first time, discussing the individual molecular mechanism in detail.

Download Full-text

Variation in VKORC1 Is Associated with Vascular Dementia

Journal of Alzheimer s Disease ◽

10.3233/jad-201256 ◽

2021 ◽

Vol 80 (3) ◽

pp. 1329-1337

Author(s):

Jure Mur ◽

Daniel L. McCartney ◽

Daniel I. Chasman ◽

Peter M. Visscher ◽

Graciela Muniz-Terrera ◽

...

Keyword(s):

Atrial Fibrillation ◽

Vascular Dementia ◽

Genetic Variant ◽

Warfarin Dose ◽

Uk Biobank ◽

Parental History ◽

Genome Wide ◽

History Of ◽

First Time ◽

The Relationship

Background: The genetic variant rs9923231 (VKORC1) is associated with differences in the coagulation of blood and consequentially with sensitivity to the drug warfarin. Variation in VKORC1 has been linked in a gene-based test to dementia/Alzheimer’s disease in the parents of participants, with suggestive evidence for an association for rs9923231 (p = 1.8×10–7), which was included in the genome-wide significant KAT8 locus. Objective: Our study aimed to investigate whether the relationship between rs9923231 and dementia persists only for certain dementia sub-types, and if those taking warfarin are at greater risk. Methods: We used logistic regression and data from 238,195 participants from UK Biobank to examine the relationship between VKORC1, risk of dementia, and the interplay with warfarin use. Results: Parental history of dementia, APOE variant, atrial fibrillation, diabetes, hypertension, and hypercholesterolemia all had strong associations with vascular dementia (p < 4.6×10–6). The T-allele in rs9923231 was linked to a lower warfarin dose (βperT - allele = –0.29, p < 2×10–16) and risk of vascular dementia (OR = 1.17, p = 0.010), but not other dementia sub-types. However, the risk of vascular dementia was not affected by warfarin use in carriers of the T-allele. Conclusion: Our study reports for the first time an association between rs9923231 and vascular dementia, but further research is warranted to explore potential mechanisms and specify the relationship between rs9923231 and features of vascular dementia.

Download Full-text

Genome-Wide Identification and Analysis of CC-NBS-LRR Family in Response to Downy Mildew and Black Rot in Chinese Cabbage

International Journal of Molecular Sciences ◽

10.3390/ijms22084266 ◽

2021 ◽

Vol 22 (8) ◽

pp. 4266

Author(s):

Yan Liu ◽

Dalong Li ◽

Na Yang ◽

Xiaolong Zhu ◽

Kexin Han ◽

...

Keyword(s):

Downy Mildew ◽

Chinese Cabbage ◽

Plant Disease Resistance ◽

Expression Profiles ◽

Black Rot ◽

Genome Wide ◽

Pathogenesis Related ◽

Effector Triggered Immunity ◽

Gene Structures ◽

Bacteria And Fungi

The nucleotide-binding site–leucine-rich repeat (NBS–LRR) gene family is the largest group of plant disease resistance (R) genes widespread in response to viruses, bacteria, and fungi usually involved in effector triggered immunity (ETI). Forty members of the Chinese cabbage CC type NBS–LRR family were investigated in this study. Gene and protein characteristics, such as distributed locations on chromosomes and gene structures, were explored through comprehensive analysis. CC–NBS–LRR proteins were classified according to their conserved domains, and the phylogenetic relationships of CC–NBS–LRR proteins in Brassica rapa, Arabidopsis thaliana, and Oryza sativa were compared. Moreover, the roles of BrCC–NBS–LRR genes involved in pathogenesis-related defense were studied and analyzed. First, the expression profiles of BrCC–NBS–LRR genes were detected by inoculating with downy mildew and black rot pathogens. Second, sensitive and resistant Chinese cabbage inbred lines were screened by downy mildew and black rot. Finally, the differential expression levels of BrCC–NBS–LRR genes were monitored at 0, 1, 3, 6, 12 and 24 h for short and 0, 3, 5, 7, 10 and 14 days for long inoculation time. Our study provides information on BrCC–NBS–LRR genes for the investigation of the functions and mechanisms of CC-NBS-LRR genes in Chinese cabbage.

Download Full-text

The Leucine-Rich Repeat Domain Can Determine Effective Interaction Between RPS2 and Other Host Factors in Arabidopsis RPS2-Mediated Disease Resistance

Genetics ◽

10.1093/genetics/158.1.439 ◽

2001 ◽

Vol 158 (1) ◽

pp. 439-450 ◽

Cited By ~ 4

Author(s):

Diya Banerjee ◽

Xiaochun Zhang ◽

Andrew F Bent

Keyword(s):

Disease Resistance ◽

Pseudomonas Syringae ◽

Plant Disease Resistance ◽

Effective Interaction ◽

Molecular Genetic ◽

Defense Responses ◽

Host Factors ◽

Leucine Rich Repeat ◽

Domain Swap ◽

Allele Specific

Abstract Like many other plant disease resistance genes, Arabidopsis thaliana RPS2 encodes a product with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. This study explored the hypothesized interaction of RPS2 with other host factors that may be required for perception of Pseudomonas syringae pathogens that express avrRpt2 and/or for the subsequent induction of plant defense responses. Crosses between Arabidopsis ecotypes Col-0 (resistant) and Po-1 (susceptible) revealed segregation of more than one gene that controls resistance to P. syringae that express avrRpt2. Many F2 and F3 progeny exhibited intermediate resistance phenotypes. In addition to RPS2, at least one additional genetic interval associated with this defense response was identified and mapped using quantitative genetic methods. Further genetic and molecular genetic complementation experiments with cloned RPS2 alleles revealed that the Po-1 allele of RPS2 can function in a Col-0 genetic background, but not in a Po-1 background. The other resistance-determining genes of Po-1 can function, however, as they successfully conferred resistance in combination with the Col-0 allele of RPS2. Domain-swap experiments revealed that in RPS2, a polymorphism at six amino acids in the LRR region is responsible for this allele-specific ability to function with other host factors.

Download Full-text