Broad-spectrum ubiquitin/ubiquitin-like deconjugation activity of the rhizobial effector NopD from Bradyrhizobium (sp. XS1150).

The post-translational modification of proteins by ubiquitin-like modifiers (UbLs), such as SUMO, ubiquitin, and Nedd8, regulates a vast array of cellular processes. Dedicated UbL deconjugating proteases families reverse these modifications. During bacterial infection, effector proteins, including deconjugating proteases, are released to disrupt host cell defenses and promote bacterial survival.

Non-foliar photosynthesis and nitrogen assimilation influence grain yield in durum wheat regardless of water conditions.

There is a need to generate improved crop varieties adapted to the ongoing changes in the climate. We studied durum wheat canopy and central metabolism of six different photosynthetic organs in two yield-contrasting varieties. The aim was to understand the mechanisms associated with the water stress response and yield performance.

GenoDrawing: An Autoencoder Framework for Image Prediction from SNP Markers.

Advancements in genome sequencing have facilitated whole-genome characterization of numerous plant species, providing an abundance of genotypic data for genomic analysis. Genomic selection and neural networks (NNs), particularly deep learning, have been developed to predict complex traits from dense genotypic data. Autoencoders, an NN model to extract features from images in an unsupervised manner, has proven to be useful for plant phenotyping.

LeTra: a leaf tracking workflow based on convolutional neural networks and intersection over union.

Background: The study of plant photosynthesis is essential for productivity and yield. Thanks to the development of high-throughput phenotyping (HTP) facilities, based on chlorophyll fluorescence imaging, photosynthetic traits can be measured in a reliable, reproducible and efficient manner. In most state-of-the-art HTP platforms, these traits are automatedly analyzed at individual plant level, but information at leaf level is often restricted by the use of manual annotation.

Thorough Characterization of , a QTL Involved in Melon Fruit Climacteric Behavior and Aroma Volatile Composition.

The effect of the QTL involved in climacteric ripening on the fruit VOC composition was studied using a set of Near-Isogenic Lines (NILs) containing overlapping introgressions from the Korean accession PI 16375 on the chromosome 3 in the climacteric 'Piel de Sapo' (PS) genetic background. was mapped in an interval of 1.24 Mb that contained a NAC transcription factor.

Transient Overexpression of E2Fb to Induce Cell Divisions in Nicotiana benthamiana Pavement Cells.

The availability of a fast and controlled mitotic model system that could simplify the generation of genetic material and reduce the experimental time from months to days would largely benefit research in plant cell division. In this protocol, we propose the use of pavement cells of Nicotiana benthamiana leaves to study cell division, which is artificially induced by Agrobacterium-mediated transient overexpression of the transcription factor E2Fb. The cell division-inducing overexpression of E2Fb can be combined with the expression of fluorescent protein-tagged proteins of interest or with dyes, which could be visualized throughout the cell cycle under the microscope.

The Sequential Action of MIDA9/PP2C.D1, PP2C.D2, and PP2C.D5 Is Necessary to Form and Maintain the Hook After Germination in the Dark.

During seedling etiolation after germination in the dark, seedlings have closed cotyledons and form an apical hook to protect the meristem as they break through the soil to reach the surface. Once in contact with light, the hook opens and cotyledons are oriented upward and separate. Hook development in the dark after seedling emergence from the seed follows three distinctly timed and sequential phases: formation, maintenance, and eventual opening.

Decreased Levels of Thioredoxin Influences Stomatal Development and Aperture but Not Photosynthesis under Non-Stress and Saline Conditions.

Salinity has a negative impact on plant growth, with photosynthesis being downregulated partially due to osmotic effect and enhanced cellular oxidation. Redox signaling contributes to the plant response playing thioredoxins (TRXs) a central role. In this work we explore the potential contribution of Arabidopsis TRX1 to the photosynthetic response under salinity analyzing Arabidopsis wild-type (WT) and two mutant lines in their growth under short photoperiod and higher light intensity than previous reported works.

New Role for LRR-Receptor Kinase in Sensing of Reactive Oxygen Species.

Understanding how reactive oxygen species (ROS) are sensed could help engineer plants with better stress responses that are relying on the production of ROS. Here, we summarize the latest research in ROS signaling with focus on the discovery by Wu et al. of a leucine-rich repeat receptor kinase (LRR-RK) as a hydrogen peroxide (HO) sensor.

Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.

Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture. Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation. Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.

High-depth African genomes inform human migration and health.

The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed. Here we performed whole-genome sequencing analyses of 426 individuals-comprising 50 ethnolinguistic groups, including previously unsampled populations-to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism.

Paternal Origins and Migratory Episodes of Domestic Sheep.

The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world.

The photoperiodic response of hypocotyl elongation involves regulation of CDF1 and CDF5 activity.

Hypocotyl elongation relies on directional cell expansion, a process under light and circadian clock control. Under short photoperiods (SD), hypocotyl elongation in Arabidopsis thaliana follows a rhythmic pattern, a process in which circadian morning-to-midnight waves of the transcriptional repressors PSEUDO-RESPONSE REGULATORS (PRRs) jointly gate PHYTOCHROME-INTERACTING FACTOR (PIF) activity to dawn. Previously, we described CYCLING DOF FACTOR 5 (CDF5) as a target of this antagonistic PRR/PIF dynamic interplay.

Bacterial Infection Disrupts Clock Gene Expression to Attenuate Immune Responses.

The circadian clock modulates immune responses in plants and animals; however, it is unclear how host-pathogen interactions affect the clock. Here we analyzed clock function in Arabidopsis thaliana mutants with defective immune responses and found that enhanced disease susceptibility 4 (eds4) displays alterations in several circadian rhythms. Mapping by sequencing revealed that EDS4 encodes the ortholog of NUCLEOPORIN 205, a core component of the inner ring of the nuclear pore complex (NPC).

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana.

Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear.

TIR domains of plant immune receptors are NAD-cleaving enzymes that promote cell death.

Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors activate cell death and confer disease resistance by unknown mechanisms. We demonstrate that plant Toll/interleukin-1 receptor (TIR) domains of NLRs are enzymes capable of degrading nicotinamide adenine dinucleotide in its oxidized form (NAD). Both cell death induction and NAD cleavage activity of plant TIR domains require known self-association interfaces and a putative catalytic glutamic acid that is conserved in both bacterial TIR NAD-cleaving enzymes (NADases) and the mammalian SARM1 (sterile alpha and TIR motif containing 1) NADase.

Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis.

Background: Circadian rhythms modulate growth and development in all organisms through interlocking transcriptional-translational feedback loops. The transcriptional loop involves chromatin modifications of central circadian oscillators in mammals and plants. However, the molecular basis for rhythmic epigenetic modifications and circadian regulation is poorly understood.

Emerging roles of vascular brassinosteroid receptors of the BRI1-like family.

Brassinosteroids (BRs) are essential hormones for plant growth and development that are perceived at the plasma membrane by a group of Leucine-Rich Repeat Receptor-Like Kinases (LRR-RLKs) of the BRASSINOSTEROID INSENSITIVE 1 (BRI1) family. The BRI1 receptor was first discovered by genetic screenings based on the dwarfism of BR-deficient plants. There are three BRI1 homologs, named BRI1-like 1, 2 and 3 (BRLs), yet only BRL1 and BRL3 behave as functional BR receptors.

Structural insights into SUMO E1-E2 interactions in Arabidopsis uncovers a distinctive platform for securing SUMO conjugation specificity across evolution.

SUMOylation of proteins involves the concerted action of the E1-activating enzyme, E2-conjugating enzyme and E3-ligases. An essential discrimination step in the SUMOylation pathway corresponds to the initial interaction between E1 ubiquitin-fold domain (UFD) and E2 enzymes. Although E2 orthologs possess high sequence identity, the E2 binding region of the UFD domains has diverged across evolution.