Targeting plant cysteine oxidase activity for improved submergence tolerance

Differential expression analysis of soybean pod tissue between Canadian environments identifies differences in sulfur-containing amino acid-related gene expression

Soybean seeds are rich in oil and protein; however, the seed composition is influenced by genotype and environment. For years, it has been observed that soybeans grown in western Canada have lower seed protein concentration (by ∼1%-5% total seed weight) than those grown in eastern Canada. In this study, soybean seeds harvested from five varieties were grown in four different locations in Canada (east and west growing regions) and analyzed using RNA-sequencing. Using gene ontology and biological pathway mapping, we identified a difference in cysteine and methionine metabolism between soybeans grown in eastern and western Canada that may attribute to the difference in seed protein concentration. Further, we identified differential gene expression within the oil biosynthesis pathway, specifically upregulation of lipoxygenases in western-grown soybeans, which may also influence seed composition and/or membrane fluidity. The information gained in this study is useful for marker assisted selection in soybean breeding programs across Canada and globally.

Measuring plant cysteine oxidase interactions with substrates using intrinsic tryptophan fluorescence

Plant Cysteine Oxidases (PCOs) are oxygen-sensing enyzmes that catalyse oxidation of cysteinyl residues at the N-termini of target proteins, triggering their degradation via the N-degron pathway. PCO oxygen sensitivity means that in low oxygen conditions (hypoxia), their activity reduces and target proteins are stabilised. PCO substrates include Group VII Ethylene Response Factors (ERFVIIs) involved in adaptive responses to the acute hypoxia experienced upon plant submergence, as well as Little Zipper 2 (ZPR2) and Vernalisation 2 (VRN2) which are involved in developmental processes in hypoxic niches. The PCOs are potential targets for improving submergence tolerance through enzyme engineering or chemical treatment. To achieve this, a detailed understanding of their biological function is required. Here, we report development of an assay that exploits the intrinsic fluorescence of Arabidopsis thaliana PCO tryptophan residues. By using Ni(II)-substitued enzymes and preparing the assay under anaerobic conditions, tryptophan fluorescence quenching is observed on enzyme:substrate complex formation, allowing quantification of binding affinities. Our assay revealed that, broadly, AtPCO4 and AtPCO5 have stronger interactions with ERFVII substrates than ZPR2 and VRN2, suggesting ERFVIIs are primary targets of these enzymes. It also revealed a positive cooperative binding effect for interactions between AtPCOs4/5 and ERFVIIs and ZPR2. The assay is experimentally straightforward and can be used to further interogate PCO interactions with substrates.

Designed to breathe: synthetic biology applications in plant hypoxia

Over the past years, plant hypoxia research has produced a considerable number of new resources to monitor low oxygen responses in model species, mainly Arabidopsis thaliana. Climate change urges the development of effective genetic strategies aimed at improving plant resilience during flooding events. This need pushes forward the search for optimized tools that can reveal the actual oxygen available to plant cells, in different organs or under various conditions, and elucidate the mechanisms underlying plant hypoxic responses, complementing the existing transcriptomics, proteomics, and metabolic analysis methods. Oxygen-responsive reporters, dyes, and nanoprobes are under continuous development, as well as novel synthetic strategies that make precision control of plant hypoxic responses realistic. In this review, we summarize the recent progress made in the definition of tools for oxygen response monitoring in plants, either adapted from bacterial and animal research or peculiar to plants. Moreover, we highlight how adoption of a synthetic biology perspective has enabled the design of novel genetic circuits for the control of oxygen-dependent responses in plants. Finally, we discuss the current limitations and challenges toward the implementation of synbio solutions in the plant low-oxygen biology field.

Destined for destruction: The role of methionine aminopeptidases and plant cysteine oxidases in N-degron formation

The cysteine/arginine (Cys/Arg) branch of the N-degron pathway controls the stability of certain proteins with methionine (Met)-Cys N-termini, initiated by Met cleavage and Cys oxidation. In seeding plants, target proteins include the Group VII Ethylene Response Factors, which initiate adaptive responses to low oxygen (hypoxic) stress, as well as Vernalization 2 (VRN2) and Little Zipper 2 (ZPR2), which are involved in responses to endogenous developmental hypoxia. It is essential that these target proteins are only degraded by the N-degron pathway under the appropriate physiological conditions. Modification of their N-termini is under enzymatic control by Met Aminopeptidases (MetAPs) and Plant Cysteine Oxidases (PCOs); therefore, the substrate-binding requirements and catalytic effectiveness of these enzymes are important for defining which Met-Cys-initiating proteins are degraded. Physiological conditions can also impact the activity of these enzymes, and the well-characterized oxygen sensitivity of the PCOs ensures target proteins are stabilized in hypoxia. In this review we compile the functional and structural properties of MetAPs and PCOs, including their interactions with substrates. We also consider the evolution of MetAPs and PCOs through the plant kingdom to highlight their important role in controlling the initial steps of this branch of the N-degron pathway.

Ubiquitin E3 ligases in the plant Arg/N-degron pathway

Regulation of protein longevity via the ubiquitin (Ub) - proteasome pathway is fundamental to eukaryotic biology. Ubiquitin E3 ligases (E3s) interact with substrate proteins and provide specificity to the pathway. A small subset of E3s bind to specific exposed N-termini (N-degrons) and promote the ubiquitination of the bound protein. Collectively these E3s, and other N-degron binding proteins, are known as N-recognins. There is considerable functional divergence between fungi, animal, and plant N-recognins. In plants, at least three proteins (PRT1, PRT6, and BIG) participate in the Arg/N-degron pathway. PRT1 has demonstrated E3 ligase activity, whereas PRT6 and BIG are candidate E3s. The Arg/N-degron pathway plays a central role in plant development, germination, and submersion tolerance. The pathway has been manipulated both to improve crop performance and for conditional protein degradation. A more detailed structural and biochemical understanding of the Arg/N-recognins and their substrates is required to fully realise the biotechnological potential of the pathway. This perspective focuses on the structural and molecular details of substrate recognition and ubiquitination in the plant Arg/N-degron pathway. While PRT1 appears to be plant specific, the PRT6 and BIG proteins are similar to UBR1 and UBR4, respectively. Analysis of the cryo-EM structures of Saccharomyces UBR1 suggests that the mode of ubiquitin conjugating enzyme (E2) and substrate recruitment is conserved in PRT6, but regulation of the two N-recognins may be significantly different. The structurally characterised domains from human UBR4 are also likely to be conserved in BIG, however, there are sizeable gaps in our understanding of both proteins.

The role of ethylene in the regulation of plant response mechanisms to waterlogging stress

Waterlogging stands as a common environmental challenge, significantly affecting plant growth, yield, and, in severe cases, survival. In response to waterlogging stress, plants exhibit a series of intricate physiologic, metabolic, and morphologic adaptations. Notably, the gaseous phytohormone ethylene is rapidly accumulated in the plant submerged tissues, assuming an important regulatory factor in plant-waterlogging tolerance. In this review, we summarize recent advances in research on the mechanisms of ethylene in the regulation of plant responses to waterlogging stress. Recent advances found that both ethylene biosynthesis and signal transduction make indispensable contributions to modulating plant adaptation mechanisms to waterlogged condition. Ethylene was also discovered to play an important role in plant physiologic metabolic responses to waterlogging stress, including the energy mechanism, morphologic adaptation, ROS regulation and interactions with other phytohormones. The comprehensive exploration of ethylene and its associated genes provides valuable insights into the precise strategies to leverage ethylene metabolism for enhancing plant resistance to waterlogging stress.

Elucidating the callus-to-shoot-forming mechanism in Capsicum annuum 'Dempsey' through comparative transcriptome analyses

BACKGROUND

The formation of shoots plays a pivotal role in plant organogenesis and productivity. Despite its significance, the underlying molecular mechanism of de novo regeneration has not been extensively elucidated in Capsicum annuum 'Dempsey', a bell pepper cultivar. To address this, we performed a comparative transcriptome analysis focusing on the differential expression in C. annuum 'Dempsey' shoot, callus, and leaf tissue. We further investigated phytohormone-related biological processes and their interacting genes in the C. annuum 'Dempsey' transcriptome based on comparative transcriptomic analysis across five species.

RESULTS

We provided a comprehensive view of the gene networks regulating shoot formation on the callus, revealing a strong involvement of hypoxia responses and oxidative stress. Our comparative transcriptome analysis revealed a significant conservation in the increase of gene expression patterns related to auxin and defense mechanisms in both callus and shoot tissues. Consequently, hypoxia response and defense mechanism emerged as critical regulators in callus and shoot formation in C. annuum 'Dempsey'. Current transcriptome data also indicated a substantial decline in gene expression linked to photosynthesis within regenerative tissues, implying a deactivation of the regulatory system governing photosynthesis in C. annuum 'Dempsey'.

CONCLUSION

Coupled with defense mechanisms, we thus considered spatial redistribution of auxin to play a critical role in the shoot morphogenesis via primordia outgrowth. Our findings shed light on shoot formation mechanisms in C. annuum 'Dempsey' explants, important information for regeneration programs, and have broader implications for precise molecular breeding in recalcitrant crops.

QTL Analysis for Rice Quality-Related Traits and Fine Mapping of qWCR3

The quality of rice, evaluated using multiple quality-related traits, is the main determinant of its market competitiveness. In this study, two japonica rice varieties with significant differences in quality-related traits were used as parents to construct two populations, BC3F2 and BC3F2:3, with Kongyu131 (KY131) as the recurrent parent. A genetic linkage map was constructed using the BC3F2 population based on 151 pairs of SSR/InDel polymorphic markers selected between the parents. Grain-shape-related traits (grain length GL, grain width GW, and length-to-width ratio LWR), chalkiness-related traits (white-core rate WCR, white-belly rate WBR, white-back rate BR, and chalkiness rate CR), and amylose content (AC) were investigated in the two populations in 2017 and 2018. Except for BR and CR, the traits showed similar characteristics with a normal distribution in both populations. Genetic linkage analysis was conducted for these quality-related traits, and a total of 37 QTLs were detected in the two populations. Further validation was performed on the newly identified QTLs with larger effects, and three grain shape QTLs and four chalkiness QTLs were successfully validated in different environments. One repeatedly validated QTL, qWCR3, was selected for fine mapping and was successfully narrowed down to a 100 kb region in which only two genes, LOC_0s03g45210 and LOC_0s03g45320, exhibited sequence variations between the parents. Furthermore, the variation of LOC_Os03g45210 leads to a frameshift mutation and premature protein termination. The results of this study provide a theoretical basis for positional cloning of the qWCR3 gene, thus offering new genetic resources for rice quality improvement.

Spatiotemporal oxygen dynamics in young leaves reveal cyclic hypoxia in plants

Oxygen is essential for plant growth and development. Hypoxia occurs in plants due to limited oxygen availability following adverse environmental conditions as well in hypoxic niches in otherwise normoxic environments. However, the existence and functional integration of spatiotemporal oxygen dynamics with plant development remains unknown. In animal systems dynamic fluctuations in oxygen availability are known as cyclic hypoxia. In this study, we demonstrate that cyclic fluctuations in internal oxygen levels occur in young emerging leaves of Arabidopsis plants. Cyclic hypoxia in plants is based on a mechanism requiring the ETHYLENE RESPONSE FACTORS type VII (ERFVII) that are central components of the oxygen-sensing machinery in plants. The ERFVII-dependent mechanism allows precise adjustment of leaf growth in response to carbon status and oxygen availability within plant cells. This study thus establishes a functional connection between internal spatiotemporal oxygen dynamics and developmental processes of plants.

Unraveling the genetic enigma of rice submergence tolerance: Shedding light on the role of ethylene response factor-encoding gene SUB1A-1

The world's low-lying rice (Oryza sativa) cultivation areas are under threat of submergence or flash flooding due to global warming. Rice plants manifest a variety of physiological and morphological changes to cope with submergence and hypoxia, including lowering carbohydrate consumption, inhibiting shoot elongation, and forming a thicker leaf gas film during submergence. Functional studies have revealed that submergence tolerance in rice is mainly determined by an ethylene response factor (ERF) transcription factor-encoding gene, namely SUBMERGENCE 1A-1 (SUB1A-1) located in the SUB1 quantitative trait locus. The SUB1A-1-dependent submergence tolerance is manifested through hormonal signaling involving ethylene, gibberellic acid, brassinosteroid, auxin and jasmonic acid. Considerable progress has been made toward the introduction of SUB1A-1 into rice varieties through a conventional marker-assisted backcrossing approach. Here, we review the recent advances in the physiological, biochemical and molecular dynamics of rice submergence tolerance mediated by the 'quiescence strategy'. Thus, the present review aims to provide researchers with insights into the genetics of rice submergence tolerance and future perspectives for designing submergence-resilient plants for sustainable agriculture under the uncertainties of climate change.

Genome-Wide Identification and Analysis of the Plant Cysteine Oxidase (PCO) Gene Family in Brassica napus and Its Role in Abiotic Stress Response

Plant Cysteine Oxidase (PCO) is a plant O₂-sensing enzyme catalyzing the oxidation of cysteine to Cys-sulfinic acid at the N-termini of target proteins. To better understand the Brassica napus PCO gene family, PCO genes in B. napus and related species were analyzed. In this study, 20, 7 and 8 PCO genes were identified in Brassica napus, Brassica rapa and Brassica oleracea, respectively. According to phylogenetic analysis, the PCOs were divided into five groups: PCO1, PCO2, PCO3, PCO4 and PCO5. Gene organization and motif distribution analysis suggested that the PCO gene family was relatively conserved during evolution. According to the public expression data, PCO genes were expressed in different tissues at different developmental stages. Moreover, qRT-PCR data showed that most of the Bna/Bra/BoPCO5 members were expressed in leaves, roots, flowers and siliques, suggesting an important role in both vegetative and reproductive development. Expression of BnaPCO was induced by various abiotic stress, especially waterlogging stress, which was consistent with the result of cis-element analysis. In this study, the PCO gene family of Brassicaceae was analyzed for the first time, which contributes to a comprehensive understanding of the origin and evolution of PCO genes in Brassicaceae and the function of BnaPCO in abiotic stress responses.

Transcriptomic and metabolomic analyses reveal the potential mechanism of waterlogging resistance in cotton (Gossypium hirsutum L.)

Introduction

Cotton (Gossypium hirsutum L.) is susceptible to long-term waterlogging stress; however, genomic information of cotton response mechanisms toward long days of waterlogging is quite elusive.

Methods

Here, we combined the transcriptome and metabolome expression level changes in cotton roots after 10 and 20 days of waterlogging stress treatment pertaining to potential resistance mechanisms in two cotton genotypes.

Results and discussion

Numerous adventitious roots and hypertrophic lenticels were induced in CJ1831056 and CJ1831072. Transcriptome analysis revealed 101,599 differentially expressed genes in cotton roots with higher gene expression after 20 days of stress. Reactive oxygen species (ROS) generating genes, antioxidant enzyme genes, and transcription factor genes (AP2, MYB, WRKY, and bZIP) were highly responsive to waterlogging stress among the two genotypes. Metabolomics results showed higher expressions of stress-resistant metabolites sinapyl alcohol, L-glutamic acid, galactaric acid, glucose 1-phosphate, L-valine, L-asparagine, and melibiose in CJ1831056 than CJ1831072. Differentially expressed metabolites (adenosine, galactaric acid, sinapyl alcohol, L-valine, L-asparagine, and melibiose) significantly correlated with the differentially expressed PRX52, PER1, PER64, and BGLU11 transcripts. This investigation reveals genes for targeted genetic engineering to improve waterlogging stress resistance to enhance abiotic stress regulatory mechanisms in cotton at the transcript and metabolic levels of study.

Integrated Transcriptomic and Metabolomics Analysis of the Root Responses of Orchardgrass to Submergence Stress

Submergence stress can severely affect plant growth. Orchardgrass (Dactylis glomerata L.) is an important forage grass, and the molecular mechanisms of orchardgrass to submergence stress are not well understood. The roots of the flood-tolerant cultivar "Dian Bei" were harvested at 0 h, 8 h and 24 h of submergence stress. The combined transcriptomic and metabolomic analyses showed that β-alanine metabolism, flavonoid biosynthesis, and biosynthesis of amino acid pathways were significantly enriched at 8 h and 24 h of submergence stress and were more pronounced at 24 h. Most of the flavonoid biosynthesis-related genes were down-regulated for the synthesis of metabolites such as naringenin, apigenin, naringin, neohesperidin, naringenin chalcone, and liquiritigenin in response to submergence stress. Metabolites such as phenylalanine, tyrosine, and tryptophan were up-regulated under stress. The predominant response of flavonoid and amino acids biosynthesis to submergence stress suggests an important role of these pathways in the submergence tolerance of orchardgrass.

Kinetic Measurements to Investigate the Oxygen-Sensing Properties of Plant Cysteine Oxidases

Enzymatic O₂ sensors transduce the availability of O₂ within the cell into a physiological, typically adaptive response. One such O₂-sensing enzymatic family is the N-terminal cysteine dioxygenases in plants (plant cysteine oxidases [PCOs]). In vitro kinetic studies have determined the O₂-sensing capacity of PCOs. Here we describe the rationale and experimental protocol for an assay with which the O₂ sensitivity of Arabidopsis thaliana PCOs (AtPCOs) can be measured. We explain each step from the recombinant protein synthesis of AtPCOs to the steady-state kinetic assays of AtPCOs for primary substrate and O₂ from which kinetic parameters can be derived. The same techniques can be applied to other N-terminal cysteine thiol dioxygenases, e.g. 2-aminoethanethiol dioxygenase (ADO), and similar principles can be applied to determine kinetic characteristics of other oxygenase enzymes towards O₂.

Plant proteostasis: a proven and promising target for crop improvement

The Green Revolution of the 1960s accomplished dramatic increases in crop yields through genetic improvement, chemical fertilisers, irrigation, and mechanisation. However, the current trajectory of population growth, against a backdrop of climate change and geopolitical unrest, predicts that agricultural production will be insufficient to ensure global food security in the next three decades. Improvements to crops that go beyond incremental gains are urgently needed. Plant biology has also undergone a revolution in recent years, through the development and application of powerful technologies including genome sequencing, a pantheon of 'omics techniques, precise genome editing, and step changes in structural biology and microscopy. Proteostasis - the collective processes that control the protein complement of the cell, comprising synthesis, modification, localisation, and degradation - is a field that has benefitted from these advances. This special issue presents a selection of the latest research in this vibrant field, with a particular focus on protein degradation. In the current article, we highlight the diverse and widespread contributions of plant proteostasis to agronomic traits, suggest opportunities and strategies to manipulate different elements of proteostatic mechanisms for crop improvement, and discuss the challenges involved in bringing these ideas into practice.