Biology subjects

Jones, J. D.

Publications and source records attributed to Jones, J. D..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Conserved 5-methyluridine tRNA modification modulates ribosome translocation

While the centrality of post-transcriptional modifications to RNA biology has long been acknowledged, the function of the vast majority of modified sites remains to be discovered. Illustrative of this, there is not yet a discrete biological role assigned for one the most highly conserved modifications, 5-methyluridine at position 54 in tRNAs (m5U54). Here, we uncover contributions of m5U54 to both tRNA maturation and protein synthesis. Our mass spectrometry analyses demonstrate that cells lacking the enzyme that installs m5U in the T-loop (TrmA in E. coli, Trm2 in S. cerevisiae) exhibit altered tRNA modifications patterns. Furthermore, m5U54 deficient tRNAs are desensitized to small molecules that prevent translocation in vitro. This finding is consistent with our observations that, relative to wild-type cells, trm2{Delta} cell growth and transcriptome-wide gene expression are less perturbed by translocation inhibitors. Together our data suggest a model in which m5U54 acts as an important modulator of tRNA maturation and translocation of the ribosome during protein synthesis.

biochemistry↗

bioRxiv2023

ATR2Cala2 from Arabidopsis-infecting downy mildew requires 4 TIR-NLR immune receptors for full recognition

O_LIArabidopsis Col-0 RPP2A and RPP2B confer recognition of Arabidopsis downy mildew (Hyaloperonospora arabidopsidis [Hpa]) isolate Cala2, but the identity of the recognized ATR2Cala2 effector was unknown. C_LIO_LITo reveal ATR2Cala2, an F2 population was generated from a cross between Hpa-Cala2 and Hpa-Noks1. We identified ATR2Cala2 as a non-canonical RxLR-type effector that carries a signal peptide, a dEER motif, and WY domains but no RxLR motif. Recognition of ATR2Cala2and its effector function were verified by biolistic bombardment, ectopic expression and Hpa infection. C_LIO_LIATR2Cala2 is recognized in accession Col-0 but not in Ler-0 in which RPP2A and RPP2B are absent. In ATR2Emoy2 and ATR2Noks1 alleles, a frameshift results in an early stop codon. RPP2A and RPP2B are essential for the recognition of ATR2Cala2. Stable and transient expression of ATR2Cala2 under 35S promoter in Arabidopsis and Nicotiana benthamiana enhances disease susceptibility. C_LIO_LITwo additional Col-0 TIR-NLR (TNL) genes (RPP2C and RPP2D) adjacent to RPP2A and RPP2B are quantitatively required for full resistance to Hpa-Cala2. C_LIO_LIWe compared RPP2 haplotypes in multiple Arabidopsis accessions and showed that all 4 genes are present in all ATR2Cala2-recognizing accessions. C_LI

plant biology↗

bioRxiv2023

The immune receptor SNC1 monitors helper NLRs targeted by a bacterial effector

Plants deploy intracellular receptors to counteract pathogen effectors that suppress cell-surface receptor-mediated immunity. To what extent pathogens manipulate also immunity mediated by intracellular receptors, and how plants tackle such manipulation, remains unknown. Arabidopsis thaliana encodes three very similar ADR1 class helper NLRs (ADR1, ADR1-L1 and ADR1-L2), which play key roles in plant immunity initiated by intracellular receptors. Here, we report that Pseudomonas syringae AvrPtoB, an effector with E3 ligase activity, can suppress ADR1-L1- and ADR1-L2-mediated cell death. ADR1, however, evades such suppression by diversification of two ubiquitination sites targeted by AvrPtoB. The intracellular sensor NLR SNC1 interacts with and guards the CCR domains of ADR1-L1 and ADR-L2. Removal of ADR1-L1 and ADR1-L2 or delivery of AvrPtoB activates SNC1, which then signals through ADR1 to trigger immunity. Our work not only uncovers the long sought-after physiological function of SNC1 in pathogen defense, but also that reveals how plants can use dual strategies, sequence diversification and a multiple layered guard-guardee system, to counteract pathogen attack on core immunity functions.

plant biology↗

bioRxiv2023

Seed Longevity is Controlled by Metacaspases

To survive extreme desiccation, seeds enter dormancy that can last millennia. This dormancy involves the accumulation of protective but structurally disordered storage proteins through unknown adjustments of proteolytic surveillance mechanisms. Mutation of all six types II metacaspases (MCAs)-II in the model plant Arabidopsis revealed their essential role in modulating these proteolytic mechanisms. MCA-II mutant seeds fail to properly target at the endoplasmic reticulum (ER) the AAA ATPase Cell Division Cycle 48 (CDC48) to dispose of misfolded proteins. MCA-IIs cleave a CDC48 adaptor, the ubiquitination regulatory X domain-containing (PUX) responsible for localizing CDC48 to the lipid droplets. When cleaved, CDC48-PUX is inactivated and allows a lipid droplet-to-ER shuttling of CDC48, an important step in the regulation of seeds lifespan. In sum, we uncover antagonism between proteolytic pathways bestowing longevity. One-Sentence SummaryMetacaspase proteases confer seed longevity by antagonizing CDC48 activity.

plant biology↗

bioRxiv2022

Extensive immune receptor repertoire diversity in disease-resistant rice landraces

Plants have powerful defence mechanisms, and extensive immune receptor repertoires, yet crop monocultures are prone to epidemic diseases. Rice is susceptible to many diseases, such as rice blast caused by Magnaporthe oryzae. Varietal resistance of rice to blast relies on intracellular nucleotide binding, leucine-rich repeat (NLR) receptors that recognize specific pathogen molecules and trigger immune responses. In the Yuanyang terraces in south-west China, rice landraces rarely show severe losses to disease whereas commercial inbred lines show pronounced field susceptibility. Here, we investigate within-landrace NLR sequence diversity of nine rice landraces and eleven modern varieties of indica, japonica and aus using complexity reduction techniques. We find that NLRs display high sequence diversity in landraces, consistent with balancing selection, and that balancing selection at NLRs is more pervasive in landraces than modern varieties. Notably, modern varieties lack many ancient NLR haplotypes that are retained in some landraces. Our study emphasises the value of standing genetic variation that is maintained in farmer landraces as resource to make modern crops and agroecosystems less prone to disease.

evolutionary biology↗

bioRxiv2022

The Solanum americanum pangenome and effectoromics reveal new resistance genes against potato late blight

Late blight caused by the oomycete pathogen Phytophthora infestans continues to cause major worldwide losses in potato and tomato. Most accessions of Solanum americanum, a globally distributed, wild Solanaceae plant, are highly resistant to late blight. We generated high-quality reference genomes of four S. americanum accessions, re-sequenced 52 accessions, and we defined variation in the NLR immune receptor genes (the S. americanum NLRome). We further screened for variation in recognition of [~]315 P. infestans RXLR effectors in 52 S. americanum accessions. Using these genotypic and phenotypic data, we cloned three novel NLR-encoding genes Rpi-amr4, Rpi-amr16 and Rpi-amr17, and determined their corresponding RXLR effector genes Avramr4 (PITG_22825), Avramr16 (PITG_02860) and Avramr17 (PITG_04373) from P. infestans. These genomic resources and methodology will support efforts to convert potato into a "nonhost" of late blight and can be applied to diseases of other crops.

plant biology↗

bioRxiv2022

Oligomerisation of a plant helper NLR requires cell-surface and intracellular immune receptor activation

Plant disease resistance involves both detection of microbial molecular patterns by cell-surface pattern recognition receptors and detection of pathogen effectors by intracellular NLR immune receptors. NLRs are classified as sensor NLRs, involved in effector detection, or helper NLRs required for sensor NLR signalling. TIR-domain-containing sensor NLRs (TNLs) require helper NLRs NRG1 and ADR1 for resistance, and their activation of defense also requires the lipase-domain proteins EDS1, SAG101 and PAD4. We investigated how the helper NLR NRG1 supports TNL-initiated immunity with EDS1 and SAG101. We find that NRG1 associates with EDS1 and SAG101 at the plasma membrane and in the nucleus, but only self-associates at the plasma membrane. Activation of TNLs is sufficient to trigger NRG1-EDS1-SAG101 interaction, but cell-surface receptor-initiated defense is also required to form an oligomeric Resistosome. The data point to formation of NRG1-EDS1-SAG101 heterotrimers in the nucleus upon intracellular receptor activation alone and indicate formation of NRG1-EDS1-SAG101 Resistosomes at the plasma membrane upon co-activation of intracellular and cell surface-receptor pathways.

plant biology↗

bioRxiv2022

Methylated guanosine and uridine modifications in S. cerevisiae mRNAs modulate translation elongation

Chemical modifications to protein encoding messenger RNA (mRNA) can modulate their localization, translation and stability within cells. Over 15 different types of mRNA modifications have been identified by sequencing and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) technologies. While LC-MS/MS is arguably the most essential tool available for studying analogous protein post-translational modifications, the high-throughput discovery and quantitative characterization of mRNA modifications by LC-MS/MS has been hampered by the difficulty of obtaining sufficient quantities of pure mRNA and limited sensitivities for modified nucleosides. To overcome these challenges, we improved the mRNA purification and LC-MS/MS pipelines to identify new S. cerevisiae mRNA modifications and quantify 50 ribonucleosides in a single analysis. The methodologies we developed result in no detectable non-coding RNA modifications signals in our purified mRNA samples and provide the lowest limit of detection reported for ribonucleoside modification LC-MS/MS analyses. These advancements enabled the detection and quantification of 13 S. cerevisiae mRNA ribonucleoside modifications and revealed four new S. cerevisiae mRNA modifications at low to moderate levels (1-methyguanosine, N2-methylguanosine, N2, N2-dimethylguanosine, and 5-methyluridine). We identified four enzymes that incorporate these modifications into S. cerevisiae mRNAs (Trm10, Trm11, Trm1, and Trm2), though our results suggest that guanosine and uridine nucleobases are also non-enzymatically methylated at low levels. Regardless of whether they are incorporated in a programmed manner or as the result of RNA damage, we reasoned that the ribosome will encounter the modifications that we detect in cells and used a reconstituted translation system to discern the consequences of modifications on translation elongation. Our findings demonstrate that the introduction of 1-methyguanosine, N2-methylguanosine and 5-methyluridine into mRNA codons impedes amino acid addition in a position dependent manner. This work expands the repertoire of nucleoside modifications that the ribosome must decode in S. cerevisiae. Additionally, it highlights the challenge of predicting the effect of discrete modified mRNA sites on translation de novo because individual modifications influence translation differently depending on mRNA sequence context.

biochemistry↗

bioRxiv2022

Effector-dependent activation and oligomerization of NRC helper NLRs by Rpi-amr3 and Rpi-amr1

Plant pathogens compromise crop yields. Plants have evolved robust innate immunity that depends in part on intracellular Nucleotide-binding, Leucine Rich-Repeat (NLR) immune receptors that activate defense responses upon detection of pathogen-derived effectors. Most "sensor" NLRs that detect effectors require the activity of "helper" NLRs, but how helper NLRs support sensor NLR function is poorly understood. Many Solanaceae NLRs require the NRC (NLR-Required for Cell death) class of helper NLRs. We show here that Rpi-amr3, a sensor NLR from Solanum americanum, detects AVRamr3 from the potato late blight pathogen, Phytophthora infestans, and activates oligomerization of the helper NLR NRC2 into a high-molecular weight resistosome. The NRC2 resistosome also forms upon recognition of P. infestans effector AVRamr1 by another sensor NLR, Rpi-amr1. The ATP-binding motif of Rpi-amr3 is required for NRC2 resistosome formation, but not for interaction with the cognate effector. The NRC2 resistosome can be activated by AVRamr3 homologs from other Phytophthora species. Mechanistic understanding of NRC resistosome formation will underpin engineering crops with durable disease resistance.

plant biology↗

bioRxiv2022

A hierarchical genotyping framework using DNA melting temperatures applied to adenovirus species typing

Known genetic variation for a pathogen, in conjunction with post-PCR melting curve analysis, can be leveraged to provide increased taxonomic detail for pathogen identification in commercial molecular diagnostic tests. The increased taxonomic detail may be used by clinicians and public health decision makers to observe circulation patterns, monitor for outbreaks, and inform local testing practices. We propose a method for expanding the taxonomic resolution of PCR diagnostic systems by incorporating a priori knowledge of the assay design and publicly available sequence information into a genotyping classification model. For multiplexed PCR systems, this framework is generalized to incorporate information from multiple assays that react with different gene targets of the same pathogen to increase classification accuracy. To illustrate the method, a hierarchical classification model is developed for the BioFire(R) Respiratory 2.1 Panel and the BioFire(R) Respiratory 2 Panel (collectively the BioFire Respiratory Panels - highly multiplexed PCR diagnostic tests) to predict the species of human adenovirus (HAdV) from Adenovirus Detected test results. Performance of the classification model was characterized via a 10-fold cross-validation on a labeled dataset and exhibited 95% {+/-} 4% accuracy. The model was then applied to the BioFire(R) Syndromic Trends dataset, which contains deidentified patient test data from BioFire Respiratory Panels collected at over 100 sites across the globe since 2015. Adenovirus Detected test results in BioFire Syndromic Trends were classified to produce predicted prevalence of each HAdV species within the United States from 2018 through 2021. These results show a marked change in both the predicted prevalence for HAdV and the species makeup with the onset of the COVID-19 pandemic. In particular, HAdV-B decreased from a pre-pandemic predicted prevalence of up to 40% to less than 5% in 2021, while HAdV-A and HAdV-F species both increased in predicted prevalence. Author SummaryIn the diagnosis of infectious disease there is often a trade-off between time to result, cost, and the amount of information gained about the pathogen. We develop a method that can provide increased genotypic information about a pathogen in a test result, with no additional time or cost. Our method is applied to the BioFire Respiratory(R) 2.1 Panel and the BioFire Respiratory(R) 2 Panel to speciate positive test results for adenovirus. The method shows robust performance in correctly identifying the adenovirus species from the test results. We estimate the prevalence of each adenovirus species in the United States by applying this method to adenovirus positive test results in the BioFire Syndromic Trends network. This information can be used in near real-time to augment the Centers for Disease Control and Prevention efforts to monitor adenovirus species circulation. Our mathematical framework can be generalized to other genotyping applications.

molecular biology↗

bioRxiv2022

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

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.

plant biology↗

bioRxiv2021

Novel effector recognition capacity engineered into a paired NLR complex

The Arabidopsis RRS1-R Resistance gene confers recognition of the bacterial acetyltransferase PopP2 and another bacterial effector, AvrRps4. The RRS1-S allele recognizes AvrRps4 but not PopP2. RRS1- R/RRS1-S heterozygotes cannot recognize PopP2. RRS1-R and RRS1-S also suppress the constitutive RPS4-dependent autoactivity of RRS1-Rslh1. Phytoplasmas cause important plant diseases, and their effectors can cause degradation of specific host proteins. We tested whether attaching a pathogen effector-dependent degron to RRS1-R, enabling its degradation by phytoplasma effector SAP05, could derepress RRS1-Rslh1 autoactivity, resulting in SAP05-dependent resistance. In transient assays in tobacco, RRS1-R-derived constructs can confer a hypersensitive response (HR) to SAP05. However, phytoplasma infection assays in transgenic Arabidopsis resulted in delayed disease symptoms but not full resistance. We provide a proof-of-concept strategy utilizing the recessiveness of a plant immune receptor gene to engineer recognition of a pathogen effector that promotes degradation of a specific host protein.

plant biology↗

bioRxiv2021

Perception of structurally distinct effectors by the integrated WRKY domain of a plant immune receptor.

Plants use intracellular immune receptors (NLRs) to detect pathogen-derived effector proteins. The Arabidopsis NLR pair RRS1-R/RPS4 confers disease resistance to different bacterial pathogens by perceiving structurally distinct effectors AvrRps4 from Pseudomonas syringae pv. pisi and PopP2 from Ralstonia solanacearum via an integrated WRKY domain in RRS1-R. How the WRKY domain of RRS1 (RRS1WRKY) perceives distinct classes of effector to initiate an immune response is unknown. We report here the crystal structure of the in planta processed C-terminal domain of AvrRps4 (AvrRps4C) in complex with RRS1WRKY. Perception of AvrRps4C by RRS1WRKY is mediated by the {beta}2-{beta}3 segment of RRS1WRKY that binds an electronegative patch on the surface of AvrRps4C. Structure-based mutations that disrupt AvrRps4C/RRS1WRKY interactions in vitro compromise RRS1/RPS4-dependent immune responses. We also show that AvrRps4C can associate with the WRKY domain of the related but distinct RRS1B/RPS4B NLR pair, and the DNA binding domain of AtWRKY41, with similar binding affinities. This work demonstrates how integrated domains in plant NLRs can directly bind structurally distinct effectors to initiate immunity. SignificanceThis study reveals a mechanism of effector recognition by a plant NLR immune receptor that carries an integrated domain (ID) which mimics an authentic pathogen effector target. An Arabidopsis immune receptor carrying RRS1 and RPS4 NLR proteins detects the Pseudomonas syringae pv. pisi secreted effector AvrRps4 via a WRKY ID in RRS1. We used structural biology to reveal the mechanisms of AvrRps4/WRKY interaction and demonstrated that this binding is essential for effector recognition in planta. Our analysis revealed distinctive features of the WRKY ID that mediate the recognition of structurally distinct effectors from different bacterial pathogens. These insights could enable engineering NLRs with novel recognition specificities, and enhances our understanding of how effectors interact with host proteins.

plant biology↗

bioRxiv2021

Rpi-amr3 confers resistance to multiple Phytophthora species by recognizing a conserved RXLR effector

Diverse pathogens from the genus Phytophthora cause disease and reduce yields in many crop plants. Although many Resistance to Phytophthora infestans (Rpi) genes effective against potato late blight have been cloned, few have been cloned against other Phytophthora species. Most Rpi genes encode nucleotide-binding domain, leucine-rich repeat-containing (NLR) proteins, that recognize RXLR effectors. However, whether NLR proteins can recognize RXLR effectors from multiple different Phytophthora pathogens has rarely been investigated. Here, we report the effector AVRamr3 from P. infestans that is recognized by Rpi-amr3 from S. americanum. We show here that AVRamr3 is broadly conserved in many different Phytophthora species, and that recognition of AVRamr3 homologs enables resistance against multiple Phytophthora pathogens, including P. parasitica and P. palmivora. Our findings suggest a novel path to identifying R genes against important plant pathogens.

plant biology↗

bioRxiv2021

The immune Rysto receptor recognizes a broadly conserved feature of potyviral coat proteins

Potyviruses are the largest group of plant RNA viruses, causing significant losses in many crops. Among them, potato virus Y (PVY) is particularly important, and enhances the severity of infections by other viruses. The Rysto gene confers PVY resistance and encodes a TIR-NLR intracellular immune receptors that recognizes PVY coat protein (CP). To define a minimal CP fragment sensed by Rysto, we created a series of truncated CP variants and expressed these CP derivatives in Rysto transgenic plants. Deletions that affect the 149 amino acid CP core region lose the ability to trigger Rysto-dependent defence activation. Furthermore, point mutations in the amino acid residues Ser126, Arg157, and Asp201 of the highly conserved RNA-binding pocket of potyviral CP, reduce or abolish Rysto-dependent responses, demonstrating that appropriate folding of the CP core is required for Rysto-mediated recognition. Consistent with these data, we found Rysto recognises CPs of various viruses that share a similar core region, but not those lacking it. Finally, we demonstrated that Rysto provides immunity to plum pox virus and turnip mosaic virus, demonstrating its wide range of applications in disease-resistant crop engineering. In parallel, we showed that CP triggered Rysto activation is SAG101- but not PAD4- or SA-level dependent. Our findings shed new light on how R proteins can detect viruses by sensing highly conserved structural patterns.

plant biology↗

bioRxiv2021

Evolutionary trade-offs at the Arabidopsis WRR4A resistance locus underpin alternate Albugo candida recognition specificities

The oomycete Albugo candida causes white rust of Brassicaceae, including vegetable and oilseed crops, and wild relatives such as Arabidopsis thaliana. Novel White Rust Resistance (WRR)-genes from Arabidopsis enable new insights into plant/parasite co-evolution. WRR4A from Arabidopsis accession Col-0 provides resistance to many but not all white rust races, and encodes a nucleotide-binding (NB), leucine-rich repeat (LRR) (NLR) immune receptor protein. Col-0 WRR4A resistance is broken by a Col-0-virulent isolate of A. candida race 4 (AcEx1). We identified an allele of WRR4A in Arabidopsis accession Oy-0 and other accessions that confers full resistance to AcEx1. WRR4AOy-0 carries a C-terminal extension required for recognition of AcEx1, but reduces recognition of several effectors recognized by the WRR4ACol-0 allele. WRR4AOy-0 confers full resistance to AcEx1 when expressed as a transgene in the oilseed crop Camelina sativa. SignificanceA C-terminal extension in an allele of the Arabidopsis resistance-protein WRR4A changes effector recognition specificity, enabling the WRR4AOy-0 allele to confer immunity to Albugo candida races that overcome the WRR4ACol-0 allele. This resistance can be transferred to the oil-producing crop Camelina sativa. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/437434v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@a68de6org.highwire.dtl.DTLVardef@ae0addorg.highwire.dtl.DTLVardef@4b3384org.highwire.dtl.DTLVardef@12330b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2020

Chromatin accessibility landscapes activated by cell surface and intracellular immune receptors

Activation of cell Surface and Intracellular Receptor-Mediated Immunity (SRMI and IRMI) results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which SRMI and IRMI lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility; both SRMI and IRMI increase chromatin accessibility at induced defense genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by SRMI and IRMI, and by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanism between the two immune systems.

plant biology↗

bioRxiv2020

A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector

Late blight caused by Phytophthora infestans greatly constrains potato production. Many Resistance (R) genes were cloned from wild Solanum species and/or introduced into potato cultivars by breeding. However, individual R genes have been overcome by P. infestans evolution; durable resistance remains elusive. We positionally cloned a new R gene, Rpi-amr1, from Solanum americanum, that encodes an NRC helper-dependent CC-NLR protein. Rpi-amr1 confers resistance in potato to all 19 P. infestans isolates tested. Using association genomics and long-read RenSeq, we defined eight additional Rpi-amr1 alleles from different S. americanum and related species. Despite only [~]90% identity between Rpi-amr1 proteins, all confer late blight resistance but differentially recognize Avramr1 orthologs and paralogs. We propose that Rpi-amr1 gene family diversity facilitates detection of diverse paralogs and alleles of the recognized effector, enabling broad-spectrum and durable resistance against P. infestans.

plant biology↗