scholarly journals Concerted expansion and contraction of immune receptor gene repertoires in plant genomes

2022 ◽  
Author(s):  
Bruno Pok Man Ngou ◽  
Robert Heal ◽  
Michele Wyler ◽  
Marc W Schmid ◽  
Jonathan DG Jones
Keyword(s):  
Cell Surface ◽  
Plant Species ◽  
Receptor Gene ◽  
Gene Families ◽  
Immune Receptor ◽  
Plant Genomes ◽  
Immune Receptors ◽  
Copy Numbers

Recent reports suggest that cell-surface and intracellular immune receptors function synergistically to activate robust defence against pathogens, but whether or not they co-evolve is unclear. Here we determined the copy numbers of cell-surface and intracellular immune receptors in 208 species. Surprisingly, these receptor gene families contract and/or expand together in plant genomes, suggesting the mutual potentiation of immunity initiated by cell-surface and intracellular receptors is reflected in the concerted co-evolution of the size of their repertoires across plant species.

scholarly journals Scripting Analyses of Genomes in Ensembl Plants

2022 ◽  
pp. 27-55
Author(s):  
Bruno Contreras-Moreira ◽  
Guy Naamati ◽  
Marc Rosello ◽  
James E. Allen ◽  
Sarah E. Hunt ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Species ◽  
Genome Sequence ◽  
Functional Annotation ◽  
Plant Pathogens ◽  
Gene Families ◽  
Ensembl Genome Browser ◽  
Plant Genomes ◽  
History Of ◽  
Genome Scale

AbstractEnsembl Plants (http://plants.ensembl.org) offers genome-scale information for plants, with four releases per year. As of release 47 (April 2020) it features 79 species and includes genome sequence, gene models, and functional annotation. Comparative analyses help reconstruct the evolutionary history of gene families, genomes, and components of polyploid genomes. Some species have gene expression baseline reports or variation across genotypes. While the data can be accessed through the Ensembl genome browser, here we review specifically how our plant genomes can be interrogated programmatically and the data downloaded in bulk. These access routes are generally consistent across Ensembl for other non-plant species, including plant pathogens, pests, and pollinators.

scholarly journals Isopentenyl Phosphate Kinases are Ubiquitous and Copy Numbers are Conserved in Plant Genomes

2019 ◽  
Author(s):  
Ben Hu ◽  
Heng Yao ◽  
Feng Li ◽  
Ran Wang ◽  
Yalong Xu ◽  
...  
Keyword(s):  
Plant Species ◽  
Mevalonate Pathway ◽  
Isoprenoid Biosynthesis ◽  
Plant Genome ◽  
Peptide Sequence ◽  
Plant Genomes ◽  
Copy Numbers ◽  
Key Enzyme ◽  
Domains Of Life ◽  
Isopentenyl Phosphate

Abstract Key message: Isopentenyl phosphate kinase (IPK) is a key enzyme in mevalonate pathway in isoprenoid biosynthesis. We analyzed 37 presumptive IPK sequences from 35 plants. An specific evolution model was found in plant IPKs, which can be used as an new target in studying the plant isoprenoids metabilte. Abstract: Isopentenyl phosphate kinase (IPK) is a recently discovered enzyme played key role in mevalonate pathway in isoprenoid biosynthesis. Here, we showed that IPKs are ubiquitously present in plant genomes. All IPKs previously identified had AAK domain. From 35 plant species with genome assembly data available, we extracted all AAK family members. Using OrthoMCL, we identified a group of 37 sequences in which Arabidopsis IPK was included. Further analysis showed that each peptide sequence in this group has a His residue which is a signature of IPK enzyme, indicating that the genes in this group were IPKs. Not like these in other domains of life which showed spotty distribution over the tree of life, virtually all plant genomes we analyzed here had IPK genes. Further, copy numbers of IPKs were very conserved in that no higher than 2 copies remained in each plant genome. Plant IPKs formed a distinctive clade in phylogenetic tree of plant AAK gene family, and had a phylogenetic topology conformed to that of plant species. The IPKs we identified here would provide new molecular targets for characterization of plant mevalonate pathway, and shed light on biochemistry of plant isoprenoids biosynthesis.

scholarly journals Divergent Traits and Ligand-Binding Properties of the Cytomegalovirus CD48 Gene Family

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 813
Author(s):  
Pablo Martínez-Vicente ◽  
Domènec Farré ◽  
Pablo Engel ◽  
Ana Angulo
Keyword(s):  
Cell Surface ◽  
Cell Function ◽  
Nk Cell ◽  
Receptor Gene ◽  
Costimulatory Molecule ◽  
Gene Families ◽  
Biochemical Properties ◽  
Cell Surface Receptor ◽  
Binding Properties ◽  
Cell Surface Molecule

The genesis of gene families by the capture of host genes and their subsequent duplication is a crucial process in the evolution of large DNA viruses. CD48 is a cell surface molecule that interacts via its N-terminal immunoglobulin (Ig) domain with the cell surface receptor 2B4 (CD244), regulating leukocyte cytotoxicity. We previously reported the presence of five CD48 homologs (vCD48s) in two related cytomegaloviruses, and demonstrated that one of them, A43, binds 2B4 and acts as a soluble CD48 decoy receptor impairing NK cell function. Here, we have characterized the rest of these vCD48s. We show that they are highly glycosylated proteins that display remarkably distinct features: divergent biochemical properties, cellular locations, and temporal expression kinetics. In contrast to A43, none of them interacts with 2B4. Consistent with this, molecular modeling of the N-terminal Ig domains of these vCD48s evidences notable changes as compared to CD48, suggesting that they interact with alternative targets. Accordingly, we demonstrate that one of them, S30, tightly binds CD2, a crucial T- and NK-cell adhesion and costimulatory molecule. Thus, our findings show how a key host immune receptor gene captured by a virus can be subsequently remodeled to evolve new immunoevasins with altered binding properties.

Plant cell surface immune receptor complex signaling

2019 ◽  
Vol 50 ◽  
pp. 18-28 ◽  
Author(s):  
Wei-Lin Wan ◽  
Katja Fröhlich ◽  
Rory N Pruitt ◽  
Thorsten Nürnberger ◽  
Lisha Zhang
Keyword(s):  
Cell Surface ◽  
Plant Cell ◽  
Receptor Complex ◽  
Immune Receptor ◽  
Complex Signaling

scholarly journals Loss of CD4 membrane expression and CD4 mRNA during acute human immunodeficiency virus replication.

1988 ◽  
Vol 168 (6) ◽  
pp. 1953-1969 ◽  
Author(s):  
P Salmon ◽  
R Olivier ◽  
Y Riviere ◽  
E Brisson ◽  
J C Gluckman ◽  
...  
Keyword(s):  
Cell Surface ◽  
Virus Replication ◽  
Receptor Gene ◽  
Human Immunodeficiency Virus Replication ◽  
Hiv Replication ◽  
Membrane Expression ◽  
Receptor Modulation ◽  
Immunodeficiency Virus ◽  
Vaccinia Viruses ◽  
Hiv Envelope

Using mAbs and genomic probe to the CD4 molecule, the HIV receptor, we demonstrated that HIV replication induces the disappearance of its functional receptor from the cell surface by two distinct mechanisms. First, after being expressed onto the cell surface, HIV envelope gp110 will complex CD4, efficiently masking the CD4 epitope used by the virus to bind its receptor. This phenomenon occurs on the surface of each infected cell and is not due to the release of soluble gp110; infection with recombinant HIV/vaccinia viruses expressing a mutated HIV env gene designed to prevent gp110 release from the cell surface induces a similar gp/CD4 complexes formation. Second, virus replication induces a dramatic and rapid loss of CD4 mRNA transcripts, preventing new CD4 molecules from being synthesized. These two mechanisms of receptor modulation could have been developed to avoid reinfection of cells replicating the virus as well as to produce more infectious particles. These results suggest that the classical virus interference documented for other retroviruses might not only be due to receptor/envelope interaction, but might also depend on receptor gene expression.

scholarly journals Divergent Traits and Ligand-Binding Features of the Cytomegalovirus CD48 Gene Family

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 23
Author(s):  
Pablo Martinez-Vicente ◽  
Domènec Farré ◽  
Elena Gracia-Latorre ◽  
Pablo Engel ◽  
Ana Angulo
Keyword(s):  
Cell Surface ◽  
Nk Cell ◽  
Viral Evolution ◽  
Costimulatory Molecule ◽  
Surface Protein ◽  
Gene Families ◽  
Biochemical Properties ◽  
Cell Surface Receptor ◽  
Type I ◽  
Independent Functions

The genesis of gene families through the capture of host genes and their subsequent duplication is a crucial process in the evolution of large DNA viruses. CD48 is a cell surface protein with an ectodomain composed of two immunoglobulin (Ig) domains. Via its N-terminal Ig domain, CD48 interacts with the cell surface receptor 2B4, triggering signal transduction events that regulate leukocyte cytotoxicity. We previously reported the presence of five CD48 homologs (vCD48s) in two related cytomegaloviruses, derived from a common host CD48 ancestor gene acquired by retrotranscription. Recently, we examined one member of this family, A43, showing that it acts as a functional viral decoy receptor, binding with high affinity and stability to 2B4 and impairing NK-cell cytotoxicity. Here, we have characterized the rest of the vCD48s. We show that they are highly glycosylated type I transmembrane proteins that display remarkably distinct features: dissimilar structures (e.g., different size stalks and cytoplasmic tails), biochemical properties, locations (cell surface/soluble), and temporal kinetic classes. We found that, in contrast to A43, none of them interacts with 2B4. Consistent with this, the molecular modeling of the N-terminal Ig domains of these vCD48s evidences significant changes in the numbers and lengths of their β-strands and inter-sheet loops that participate in the interaction of CD48 with 2B4. This suggests that these vCD48s have diverged to perform new 2B4-independent functions. Interestingly, we determined that one of them, S30, tightly binds CD2, a T- and NK-cell adhesion and costimulatory molecule whose primary ligand is CD58. Thus, altogether, our results show how a key host immune receptor captured by a virus can be subsequently remodeled during viral evolution to yield new molecules with improved affinities to their cognate receptors or with shifted binding specificities to additional immune targets, expanding the repertoire of viral immunoevasins.

scholarly journals Molecular Characterization of the Aphis gossypii Olfactory Receptor Gene Families

PLoS ONE ◽  
2014 ◽  
Vol 9 (6) ◽  
pp. e101187 ◽  
Author(s):  
Depan Cao ◽  
Yang Liu ◽  
William B. Walker ◽  
Jianhong Li ◽  
Guirong Wang
Keyword(s):  
Molecular Characterization ◽  
Olfactory Receptor ◽  
Receptor Gene ◽  
Aphis Gossypii ◽  
Gene Families ◽  
Olfactory Receptor Gene

scholarly journals Tomato I2 Immune Receptor Can Be Engineered to Confer Partial Resistance to the Oomycete Phytophthora infestans in Addition to the Fungus Fusarium oxysporum

2015 ◽  
Vol 28 (12) ◽  
pp. 1316-1329 ◽  
Author(s):  
Artemis Giannakopoulou ◽  
John F. C. Steele ◽  
Maria Eugenia Segretin ◽  
Tolga O. Bozkurt ◽  
Ji Zhou ◽  
...  
Keyword(s):  
Phytophthora Infestans ◽  
Fusarium Oxysporum ◽  
Partial Resistance ◽  
Response Spectrum ◽  
Coiled Coil ◽  
Wild Type ◽  
Immune Receptor ◽  
Immune Receptors ◽  
Oomycete Pathogen ◽  
Altered Response

Plants and animals rely on immune receptors, known as nucleotide-binding domain and leucine-rich repeat (NLR)-containing proteins, to defend against invading pathogens and activate immune responses. How NLR receptors respond to pathogens is inadequately understood. We previously reported single-residue mutations that expand the response of the potato immune receptor R3a to AVR3aEM, a stealthy effector from the late blight oomycete pathogen Phytophthora infestans. I2, another NLR that mediates resistance to the wilt-causing fungus Fusarium oxysporum f. sp. lycopersici, is the tomato ortholog of R3a. We transferred previously identified R3a mutations to I2 to assess the degree to which the resulting I2 mutants have an altered response. We discovered that wild-type I2 protein responds weakly to AVR3a. One mutant in the N-terminal coiled-coil domain, I2I141N, appeared sensitized and displayed markedly increased response to AVR3a. Remarkably, I2I141N conferred partial resistance to P. infestans. Further, I2I141N has an expanded response spectrum to F. oxysporum f. sp. lycopersici effectors compared with the wild-type I2 protein. Our results suggest that synthetic immune receptors can be engineered to confer resistance to phylogenetically divergent pathogens and indicate that knowledge gathered for one NLR could be exploited to improve NLR from other plant species.

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