Biology subjects

McKenzie, N.

Publications and source records attributed to McKenzie, N..

8 recordsLinked to original sources

bioRxiv2022

The integrated LIM-peptidase domain of the CSA1/CHS3 paired immune receptor detects changes in DA1 family peptidase inhibitors to confer Albugo candida resistance in Arabidopsis.

White blister rust, caused by the oomycete Albugo candida, is a widespread disease of Brassica crops. The Arabidopsis CSA1/DAR4 (also known as CSA1/CHS3) paired immune receptor carries an Integrated Domain (ID) with homology to the DA1 family of peptidases. Using domain swaps with DA1 family members, we show that the DAR4 ID acts as an integrated decoy for DAR3, which interacts with and inhibits the peptidase activities of DA1, DAR1 and DAR2 family members. Albugo infection rapidly lowered DAR3 levels and activates DA1 peptidase activity. This promotes endoreduplication of host tissues to support pathogen growth. We propose that DAR4/CSA1 senses the actions of a putative Albugo effector that reduces DAR3 levels and initiates defense.

plant biology↗

bioRxiv2020

The Receptor Kinase BRI1 promotes cell proliferation in Arabidopsis by phosphorylation- mediated inhibition of the growth repressing peptidase DA1.

Brassinosteroids (BR) have centrally important functions in plant growth by promoting cell proliferation and cell expansion through phosphorylation-mediated regulatory cascades that are initiated by perception of BR by receptor-like kinases of the BRI1 family. These BR-mediated growth responses have been explained by transcriptional controls mediated by phosphorylation of BES1/BZR1 transcription factors. Here we link BRI1-mediated phosphorylation to another growth regulatory network that directly mediates protein stability. BRI1 and its co-receptor BAK1 phosphorylate and inhibit the activities of the growth repressor DA1 by promoting the formation of high molecular weight complexes. Phospho-mimic forms of DA1 are less active while phospho-dead mutants have increased growth-repressive activity, while their regulatory monoubiquitylation is unaffected. BR inhibition of DA1 activity maintains higher levels of DA1 substrates such as UBP15 that sustain the potential for cell proliferation during leaf growth. Reduced BR levels lead to activation of DA1 peptidase activity and a transition from cell proliferation to cell growth and differentiation. This dual monoubiquitylation-phosphorylation regulation supports the key role of BR levels in maintaining the proliferative potential of cells during organ growth.

plant biology↗

bioRxiv2020

Variation in the expression of a transmembrane protein influences cell growth in Arabidopsis thaliana petals by altering auxin availability.

BackgroundThe same species of plant can exhibit highly diverse sizes and shapes of organs that are genetically determined. Defining genetic variation underlying this morphological diversity is an important objective in evolutionary studies and it also helps identify the functions of genes influencing plant growth and development. Extensive screens of mutagenised Arabidopsis populations have identified multiple genes and mechanisms affecting organ size and shape, but relatively few studies have exploited the rich diversity of natural populations to identify genes involved in growth control. ResultsWe screened a relatively well characterised collection of Arabidopsis thaliana ecotypes for variation in petal size. Association analyses identified sequence and gene expression variation on chromosome 4 that made a substantial contribution to differences in petal area. Variation in expression of At4g16850 (named as KSK), encoding a hypothetical protein, had a substantial role on variation in organ size by influencing cell size. Over-expression of KSK led to larger petals with larger cells and promoted the formation of stamenoid features. The expression of auxin-responsive genes known to limit cell growth was reduced in response to KSK over-expression. ANT expression was also reduced in KSK over-expression lines, consistent with altered floral identities. Auxin availability was reduced in KSK over-expressing cells, consistent with changes in auxin-responsive gene expression. KSK may therefore influence auxin availability during petal development. ConclusionsUnderstanding how genetic variation influences plant growth is important for both evolutionary and mechanistic studies. We used natural populations of Arabidopsis thaliana to identify sequence variation in a promoter region of Arabidopsis ecotypes that mediated differences in the expression of a previously uncharacterised membrane protein. This variation contributed to altered auxin availability and cell size during petal growth.

plant biology↗

bioRxiv2019

Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of hexaploid wheat and diploid Aegilops tauschii

Polyploidy has been centrally important in driving the evolution of plants, and leads to alterations in gene expression that are thought to underlie the emergence of new traits. Despite the common occurrence of these global patterns of altered gene expression in polyploids, the mechanisms involved are not well understood. Using a precise framework of highly conserved syntenic genes on hexaploid wheat chromosome 3DL and its progenitor 3L chromosome arm of diploid Aegilops tauschii, we show that 70% of these genes exhibited proportionally reduced gene expression, in which expression in the hexaploid context of the 3DL genes was approximately 40% of the levels observed in diploid Ae. tauschii. Many genes showing elevated expression during later stages of grain development in wheat compared to Ae. tauschii. Gene sequence and methylation differences accounted for only a few cases of differences in gene expression. In contrast, large scale patterns of reduced chromatin accessibility of genes in the hexaploid chromosome arm compared to its diploid progenitor were correlated with observed overall reduction in gene expression and differential gene expression. Therefore, that an overall reduction in accessible chromatin underlies the major differences in gene expression that results from polyploidization.

genomics↗

bioRxiv2018

Natural variation in expression of the HECT E3 ligase UPL3 influences seed size and crop yields in Brassica napus by altering regulatory gene expression.

Identifying genetic variation that increases crop yields is a primary objective in plant breeding. We have used association analyses of Brassica napus (oilseed rape/canola) accessions to identify variation in the expression of a HECT E3 ligase gene, BnaUPL3.C03, that influences seed size and final yield. We establish a mechanism in which UPL3 mediates the proteasomal degradation of LEC2, a master regulator of seed maturation. Reduced UPL3 expression increases LEC2 protein levels and prolongs expression of lipid biosynthetic genes and seed maturation. Natural variation in BnaUPL3.C03 expression has not yet been exploited in current Brassica napus breeding lines and can therefore be used as a new approach to maximize future yields in this important oil crop.

plant biology↗

bioRxiv2017

Independent assessment and improvement of wheat genome assemblies using Fosill jumping libraries

BackgroundThe accurate sequencing and assembly of very large, often polyploid, genomes remain a challenging task, limiting long range sequence information and phased sequence variation for applications such as plant breeding. The 15 Gb hexaploid bread wheat genome has been particularly challenging to sequence, and several contending approaches recently generated accurate long range assemblies. Understanding errors in these assemblies is important for optimising future sequencing and assembly approaches and for comparative genomics.\n\nResultsHere we use a Fosill 38 Kb jumping library to assess medium and longer range order of different publicly available wheat genome assemblies. Modifications to the Fosill protocol generated longer Illumina sequences and enabled comprehensive genome coverage. Analyses of two independent BAC based chromosome-scale assemblies, two independent Illumina whole genome shotgun assemblies, and a hybrid long read (PacBio) and short read (Illumina) assembly were carried out. We revealed a variety of discrepancies using Fosill mate-pair mapping and validated several of each class. In addition, Fosill mate-pairs were used to scaffold a whole genome Illumina assembly, leading to a three-fold increase in N50 values.\n\nConclusionsOur analyses, using an independent means to validate different wheat genome assemblies, show that whole genome shotgun assemblies are significantly more accurate by all measures compared to BAC-based chromosome scale assemblies. Although current whole genome assemblies are reasonably accurate and useful, additional steps will be needed for the rapid, cost effective and complete sequencing and assembly of wheat genomes.

genomics↗

bioRxiv2016

Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis

The characteristic shapes and sizes of organs are established by cell proliferation patterns and final cell sizes, but the underlying molecular mechanisms coordinating these are poorly understood. Here we characterize a ubiquitin-activated peptidase called DA1 that limits the duration of cell proliferation during organ growth in Arabidopsis thaliana. The peptidase is activated by two RING E3 ligases, BB and DA2, which are subsequently cleaved by the activated peptidase and destabilized. In the case of BB, cleavage leads to destabilization by the RING E3 ligase PRT1 of the N-end rule pathway. DA1 peptidase activity also cleaves the de-ubiquitylase UBP15, which promotes cell proliferation, and the transcription factors TCP15 and TCP22, which promote cell proliferation proliferation and repress endoreduplication. We propose that DA1 peptidase activity regulates the duration of cell proliferation and the transition to endoreduplication and differentiation during organ formation in plants by coordinating the destabilization of regulatory proteins.

plant biology↗

bioRxiv2016

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

Advances in genome sequencing and assembly technologies are generating many high quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimised data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents more than 78% of the genome with a scaffold N50 of 88.8kbp that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNAseq and PacBio full-length cDNAs to identify 104,091 high confidence protein-coding genes and 10,156 non-coding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop. [Supplemental material is available for this article.]

genomics↗