The impact of Arabidopsis on human health: diversifying our portfolio

Leaf Senescence Database v5.0: A Comprehensive Repository for Facilitating Plant Senescence Research

Through an extensive literature survey, we have upgraded the Leaf Senescence Database (LSD v5.0; https://ngdc.cncb.ac.cn/lsd/), a curated repository of comprehensive senescence-associated genes (SAGs) and their corresponding mutants. Since its inception in 2010, LSD undergoes frequent updates to encompass the latest advances in leaf senescence research and its current version comprises a high-quality collection of 31,740 SAGs and 1,209 mutants from 148 species, which were manually searched based on robust experimental evidence and further categorized according to their functions in leaf senescence. Furthermore, LSD was greatly enriched with comprehensive annotations for the SAGs through meticulous curation using both manual and computational methods. In addition, it was equipped with user-friendly web interfaces that facilitate text queries, BLAST searches, and convenient download of SAG sequences for localized analysis. Users can effortlessly navigate the database to access a plethora of information, including literature references, mutants, phenotypes, multi-omics data, miRNA interactions, homologs in other plants, and cross-links to various databases. Taken together, the upgraded version of LSD stands as the most comprehensive and informative plant senescence-related database to date, incorporating the largest collection of SAGs and thus bearing great utility for a wide range of studies related to plant senescence.

Arabidopsis as a model for translational research

Arabidopsis thaliana is currently the most-studied plant species on earth, with an unprecedented number of genetic, genomic, and molecular resources having been generated in this plant model. In the era of translating foundational discoveries to crops and beyond, we aimed to highlight the utility and challenges of using Arabidopsis as a reference for applied plant biology research, agricultural innovation, biotechnology, and medicine. We hope that this review will inspire the next generation of plant biologists to continue leveraging Arabidopsis as a robust and convenient experimental system to address fundamental and applied questions in biology. We aim to encourage lab and field scientists alike to take advantage of the vast Arabidopsis datasets, annotations, germplasm, constructs, methods, molecular and computational tools in our pursuit to advance understanding of plant biology and help feed the world's growing population. We envision that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability.

Arabidopsis thaliana: a powerful model organism to explore histone modifications and their upstream regulations

Histones are subjected to extensive covalent modifications that affect inter-nucleosomal interactions as well as alter chromatin structure and DNA accessibility. Through switching the corresponding histone modifications, the level of transcription and diverse downstream biological processes can be regulated. Although animal systems are widely used in studying histone modifications, the signalling processes that occur outside the nucleus prior to histone modifications have not been well understood due to the limitations including non viable mutants, partial lethality, and infertility of survivors. Here, we review the benefits of using Arabidopsis thaliana as the model organism to study histone modifications and their upstream regulations. Similarities among histones and key histone modifiers such as the Polycomb group (PcG) and Trithorax group (TrxG) in Drosophila, Human, and Arabidopsis are examined. Furthermore, prolonged cold-induced vernalization system has been well-studied and revealed the relationship between the controllable environment input (duration of vernalization), its chromatin modifications of FLOWERING LOCUS C (FLC), following gene expression, and the corresponding phenotypes. Such evidence suggests that research on Arabidopsis can bring insights into incomplete signalling pathways outside of the histone box, which can be achieved through viable reverse genetic screenings based on the phenotypes instead of direct monitoring of histone modifications among individual mutants. The potential upstream regulators in Arabidopsis can provide cues or directions for animal research based on the similarities between them.

DNA language models are powerful predictors of genome-wide variant effects

The expanding catalog of genome-wide association studies (GWAS) provides biological insights across a variety of species, but identifying the causal variants behind these associations remains a significant challenge. Experimental validation is both labor-intensive and costly, highlighting the need for accurate, scalable computational methods to predict the effects of genetic variants across the entire genome. Inspired by recent progress in natural language processing, unsupervised pretraining on large protein sequence databases has proven successful in extracting complex information related to proteins. These models showcase their ability to learn variant effects in coding regions using an unsupervised approach. Expanding on this idea, we here introduce the Genomic Pre-trained Network (GPN), a model designed to learn genome-wide variant effects through unsupervised pretraining on genomic DNA sequences. Our model also successfully learns gene structure and DNA motifs without any supervision. To demonstrate its utility, we train GPN on unaligned reference genomes of Arabidopsis thaliana and seven related species within the Brassicales order and evaluate its ability to predict the functional impact of genetic variants in A. thaliana by utilizing allele frequencies from the 1001 Genomes Project and a comprehensive database of GWAS. Notably, GPN outperforms predictors based on popular conservation scores such as phyloP and phastCons. Our predictions for A. thaliana can be visualized as sequence logos in the UCSC Genome Browser (https://genome.ucsc.edu/s/gbenegas/gpn-arabidopsis). We provide code (https://github.com/songlab-cal/gpn) to train GPN for any given species using its DNA sequence alone, enabling unsupervised prediction of variant effects across the entire genome.

Status of genome function annotation in model organisms and crops

Since the entry into genome-enabled biology several decades ago, much progress has been made in determining, describing, and disseminating the functions of genes and their products. Yet, this information is still difficult to access for many scientists and for most genomes. To provide easy access and a graphical summary of the status of genome function annotation for model organisms and bioenergy and food crop species, we created a web application (https://genomeannotation.rheelab.org) to visualize, search, and download genome annotation data for 28 species. The summary graphics and data tables will be updated semi-annually, and snapshots will be archived to provide a historical record of the progress of genome function annotation efforts. Clear and simple visualization of up-to-date genome function annotation status, including the extent of what is unknown, will help address the grand challenge of elucidating the functions of all genes in organisms.

Genomic and transcriptomic analysis of sacred fig (Ficus religiosa)

BACKGROUND

Peepal/Bodhi tree (Ficus religiosa L.) is an important, long-lived keystone ecological species. Communities on the Indian subcontinent have extensively employed the plant in Ayurveda, traditional medicine, and spiritual practices. The Peepal tree is often thought to produce oxygen both during the day and at night by Indian folks. The goal of our research was to produce molecular resources using whole-genome and transcriptome sequencing techniques.

RESULTS

The complete genome of the Peepal tree was sequenced using two next-generation sequencers Illumina HiSeq1000 and MGISEQ-2000. We assembled the draft genome of 406 Mb, using a hybrid assembly workflow. The genome annotation resulted in 35,093 protein-coding genes; 53% of its genome consists of repetitive sequences. To understand the physiological pathways in leaf tissues, we analyzed photosynthetically distinct conditions: bright sunny days and nights. The RNA-seq analysis supported the expression of 26,479 unigenes. The leaf transcriptomic analysis of the diurnal and nocturnal periods revealed the expression of the significant number of genes involved in the carbon-fixation pathway.

CONCLUSIONS

This study presents a draft hybrid genome assembly for F. religiosa and its functional annotated genes. The genomic and transcriptomic data-derived pathways have been analyzed for future studies on the Peepal tree.

Use of Arabidopsis thaliana as a model to understand specific carcinogenic events: Comparison of the molecular machinery associated with cancer-hallmarks in plants and humans

Model organisms are fundamental in cancer research given that they rise the possibility to characterize in a quantitative-objective fashion the organisms as a whole in ways that are infeasible in humans. From this perspective, model organisms with short generation times and established protocols for genetic manipulation allow the understanding of basic biology principles that might guide carcinogenic onset. The cancer-hallmarks (CHs) approach, a modular perspective for cancer understanding, stands that underlying the variability among different cancer types, critical events support the carcinogenic origin and progression. Thus, CHs as interconnected genetic circuitry, have a causal effect over cancer biogenesis and might represent a comparison scaffold among model organisms to identify and characterize evolutionarily conserved modules to understand cancer. Nevertheless, the identification of novel cancer regulators by comparative genomics approaches relies on selecting specific biological processes or related signaling cascades that limit the type of detected regulators, even more, holistic analysis from a systemic perspective is absent. Similarly, although the plant Arabidopsis thaliana has been used as a model organism to dissect specific disease-associated mechanisms, given the evolutionary distance between plants and humans, a general concern about the utility of using A. thaliana as a cancer model persists. In the present research, we take advantage of the CHs paradigm as a framework to establish a functional systemic comparison between plants and humans, that allowed the identification not only of specific novel key genetic regulators, but also, biological processes, metabolic systems, and genetic modules that might contribute to the neoplastic transformation. We propose five cancer-hallmarks that overlapped in conserved mechanisms and processes between Arabidopsis and human and thus, represent mechanisms which study can be prioritized in A. thaliana as an alternative model for cancer research. Additionally, derived from network analyses and machine learning strategies, a new set of potential candidate genes that might contribute to neoplastic transformation is described. These findings postulate A. thaliana as a suitable model to dissect, not all, but specific cancer properties, highlighting the importance of using alternative complementary models to understand carcinogenesis.

Genome survey sequencing-based SSR marker development and their validation in Dendrocalamus longispathus

Bamboo is an important genetic resource in India, supporting rural livelihood and industries. Unfortunately, most Indian bamboo taxa are devoid of basic genomic or marker information required to comprehend the genetic processes for further conservation and management. In this study, we perform genome survey sequencing for development of de novo genomic SSRs in Dendrocalamus longispathus, a socioeconomically important bamboo species of northeast India. Using Illumina platform, 69.49 million raw reads were generated and assembled into 1,145,321 contig with GC content 43% and N50 1228 bp. In total, 46,984 microsatellite repeats were mined-out wherein di-nucleotide repeats were most abundant (54.71%) followed by mono- (31.91%) and tri-repeats (9.85%). Overall, AT-rich repeats were predominant in the genome, but GC-rich motifs were more frequent in tri-repeats. Afterwards, 21,596 SSR loci were successfully tagged with the primer pairs, and a subset of 50 were validated through polymerase chain reaction amplification. Of these, 36 SSR loci were successfully amplified, and 16 demonstrated polymorphism. Using 13 polymorphic SSRs, a moderate level of gene diversity (He = 0.480; Ar = 3.52) was recorded in the analysed populations of D. longispathus. Despite the high gene flow (Nm = 4.928) and low genetic differentiation (F_ST = 0.119), severe inbreeding (F_IS = 0.407) was detected. Further, genetic clustering and STRUCTURE analysis revealed that the entire genetic variability is captured under two major gene pools. Conclusively, we present a comprehensive set of novel SSR markers in D. longispathus as well as other taxa of tropical woody bamboos.

Plant and microbial sciences as key drivers in the development of metabolomics research

This year marks the 25th anniversary of the coinage of the term metabolome [S. G. Oliver et al., Trends Biotech. 16, 373-378 (1998)]. As the field rapidly advances, it is important to take stock of the progress which has been made to best inform the disciplines future. While a medical-centric perspective on metabolomics has recently been published [M. Giera et al., Cell Metab. 34, 21-34 (2022)], this largely ignores the pioneering contributions made by the plant and microbial science communities. In this perspective, we provide a contemporary overview of all fields in which metabolomics is employed with particular emphasis on both methodological and application breakthroughs made in plant and microbial sciences that have shaped this evolving research discipline from the very early days of its establishment. This will not cover all types of metabolomics assays currently employed but will focus mainly on those utilizing mass spectrometry-based measurements since they are currently by far the most prominent. Having established the historical context of metabolomics, we will address the key challenges currently facing metabolomics and offer potential approaches by which these can be faced. Most salient among these is the fact that the vast majority of mass features are as yet not annotated with high confidence; what we may refer to as definitive identification. We discuss the potential of both standard compound libraries and artificial intelligence technologies to address this challenge and the use of natural variance-based approaches such as genome-wide association studies in attempt to assign specific functions to the myriad of structurally similar and complex specialized metabolites. We conclude by stating our contention that as these challenges are epic and that they will need far greater cooperative efforts from biologists, chemists, and computer scientists with an interest in all kingdoms of life than have been made to date. Ultimately, a better linkage of metabolome and genome data will likely also be needed particularly considering the Earth BioGenome Project.

A rich and bountiful harvest: Key discoveries in plant cell biology

The field of plant cell biology has a rich history of discovery, going back to Robert Hooke's discovery of cells themselves. The development of microscopes and preparation techniques has allowed for the visualization of subcellular structures, and the use of protein biochemistry, genetics, and molecular biology has enabled the identification of proteins and mechanisms that regulate key cellular processes. In this review, seven senior plant cell biologists reflect on the development of this research field in the past decades, including the foundational contributions that their teams have made to our rich, current insights into cell biology. Topics covered include signaling and cell morphogenesis, membrane trafficking, cytokinesis, cytoskeletal regulation, and cell wall biology. In addition, these scientists illustrate the pathways to discovery in this exciting research field.

Symmetric and Asymmetric Models for the Arabidopsis thaliana Plasma Membrane: A Simulation Study

Arabidopsis thaliana is an important model organism, which has attracted many biologists. While most research efforts have been on studying the genetics and proteins of this organism, a systematic study of its lipidomics is lacking. Here, we present a novel, asymmetric model of its cell membrane with its lipid composition consisting of five glycerophospholipids, two glycolipids, and sitosterol determined from multiple independent experiments. A typical lipid type in plant membranes is glycosyl inositol phosphoryl ceramide (GIPC), which accounts for about 10% of the total lipids in the outer leaflet in our model. Two symmetric models representing the inner and outer leaflets of the membrane were built and simulated until equilibrium was reached and then combined to form the asymmetric model. Our results indicate that the outer leaflet is more rigid and tightly packed compared to the inner leaflet. Pressure profiles for the two leaflets are overall similar though the outer leaflet exhibits larger oscillations. A special focus on lipid organization is discussed and the interplay between glycolipids and sitosterols is found to be important. The current model provides a baseline for future modeling of similar membranes and can be used to study partitioning of small molecules in the membrane or further developed to study the interaction between plant membrane proteins and lipids.

Into the weeds: new insights in plant stress

Weeds, plants that thrive in the face of disturbance, have eluded human's attempts at control for >12 000 years, positioning them as a unique group of extreme stress tolerators. The most successful weeds have a suite of traits that enable them to rapidly adapt to environments typified by stress, growing in hostile conditions or subject to massive destruction from agricultural practices. Through their ability to persist and adapt, weeds illuminate principles of evolution and provide insights into weed management and crop improvement. Here we highlight why the time is right to move beyond traditional model systems and leverage weeds to gain a deeper understanding of the mechanisms, adaptations, and genetic and physiological bases for stress tolerance.

Structure of the Arabidopsis thaliana glutamate receptor-like channel GLR3.4

Glutamate receptor-like channels (GLRs) play vital roles in various physiological processes in plants, such as wound response, stomatal aperture control, seed germination, root development, innate immune response, pollen tube growth, and morphogenesis. Despite the importance of GLRs, knowledge about their molecular organization is limited. Here we use X-ray crystallography and single-particle cryo-EM to solve structures of the Arabidopsis thaliana GLR3.4. Our structures reveal the tetrameric assembly of GLR3.4 subunits into a three-layer domain architecture, reminiscent of animal ionotropic glutamate receptors (iGluRs). However, the non-swapped arrangement between layers of GLR3.4 domains, binding of glutathione through S-glutathionylation of cysteine C205 inside the amino-terminal domain clamshell, unique symmetry, inter-domain interfaces, and ligand specificity distinguish GLR3.4 from representatives of the iGluR family and suggest distinct features of the GLR gating mechanism. Our work elaborates on the principles of GLR architecture and symmetry and provides a molecular template for deciphering GLR-dependent signaling mechanisms in plants.

Transcriptome analysis to identify key genes involved in terpenoid and rosmarinic acid biosynthesis in lemon balm (Melissa officinalis)

Melissa officinalis (lemon balm) is a well-known pharmaceutical plant in traditional medicine around the world because of the high-value secondary metabolites. Nowadays, advances in computational biology and bioinformatics have opened new avenues to plant-based natural product drug discovery. Despite the pharmacological importance, there is low information about the genes encoding the important biosynthetic pathways related to the secondary metabolite in M. officinalis. In this study, the main genes related to the rosmarinic acid (RA) and terpenoid biosynthesis pathways were detected using transcriptome analysis. Furthermore, we isolated and characterized a novel M. officinalis Hydroxyphenylpyruvate reductase (HPPR) gene involved in RA biosynthesis pathway. An effective pipeline was used to generate 37,055 unigenes by evaluating 42,837,601 Illumina paired-end reads. Functional annotation of the unigenes revealed that 27,363 (73.84%) and 35,822 (96.67%) unigenes had significant similarity to identified proteins in the SwissProt and NR databases, respectively. Also, 10,062 (36.83%) out of 37,055 unigenes were assigned to 399 KEGG pathways. Since terpenes and RA are two prominent metabolites in this plant, the attention of this study has been on the pathways related to them. A total of 149 unigenes were found that are related to the terpenoids biosynthesis, including 75 unigenes involved in the methyl-erythritol phosphate and mevalonate pathway, terpenoid backbone biosynthesis genes, and 74 unigenes related to the terpene synthase. We also identified 144 and 30 unigenes that were associated with the biosynthesis of phenylpropanoid and the rosmarinic acid pathway. Consequently, this investigation can be a comprehensive and accurate transcriptome basis for further investigation in the metabolic engineering and detection of new genes and pathways in M. officinalis.

Hispidulin: A novel natural compound with therapeutic potential against human cancers

Cancer is one of the most devastating disease and leading cause of death worldwide. The conventional anticancer drugs are monotarget, toxic, expensive and suffer from drug resistance. Development of multi-targeted drugs from natural products has emerged as a new paradigm to overcome aforementioned conventionally encountered obstacles. Hispidulin (HIS), is a biologically active natural flavone with versatile biological and pharmacological activities. The anticancer, antimutagenic, antioxidative and anti-inflammatory properties of HIS have been reported. The aim of this review is to summarize the findings of several studies over the last few decades on the anticancer activity of HIS published in various databases including PubMed, Google Scholar, and Scopus. HIS has been shown to reduce the growth of cancer cells by inducing apoptosis, arresting cell cycle, inhibiting angiogenesis, invasion and metastasis via modulating multiple signaling pathways implicated in cancer initiation and progression. Multitargeted anticancer activity of HIS remains the strongest point for developing it into potential anticancer drug. We also highlighted the natural sources, anticancer mechanism, cellular targets, and chemo-sensitizing potential of HIS. This review will provide bases for design and conduct of further pre-clinical and clinical trials to develop HIS into a lead structure for future anticancer therapy.

Beyond What Your Retina Can See: Similarities of Retinoblastoma Function between Plants and Animals, from Developmental Processes to Epigenetic Regulation

The Retinoblastoma protein (pRb) is a key cell cycle regulator conserved in a wide variety of organisms. Experimental analysis of pRb's functions in animals and plants has revealed that this protein participates in cell proliferation and differentiation processes. In addition, pRb in animals and its orthologs in plants (RBR), are part of highly conserved protein complexes which suggest the possibility that analogies exist not only between functions carried out by pRb orthologs themselves, but also in the structure and roles of the protein networks where these proteins are involved. Here, we present examples of pRb/RBR participation in cell cycle control, cell differentiation, and in the regulation of epigenetic changes and chromatin remodeling machinery, highlighting the similarities that exist between the composition of such networks in plants and animals.

Physiological, Metabolic, and Transcriptomic Analyses Reveal the Responses of Arabidopsis Seedlings to Carbon Nanohorns

Carbon-based nanomaterials have potential applications in nanoenabled agriculture. However, the physiological and molecular mechanisms underlying single-walled carbon nanohorn (SWCNH)-mediated plant growth remain unclear. Here, we investigated the effects of SWCNHs on Arabidopsis grown in ¹/₄-strength Murashige and Skoog medium via physiological, genetic, and molecular analyses. Treatment with 0.1 mg/L SWCNHs promoted primary root (PR) growth and lateral root (LR) formation; 50 and 100 mg/L SWCNHs inhibited PR growth. Treatment with 0.1 mg/L SWCNHs increased the lengths of the meristematic and elongation zones, and transcriptomic and genetic analyses confirmed the positive effects of SWCNHs on root tip stem cell niche activity and meristematic cell division potential. Increased expression of YUC3 and YUC5 and increased PIN2 abundance improved PR growth and LR development in 0.1 mg/L SWCNH-treated seedlings. Metabolomic analyses revealed that SWCNHs altered the levels of sugars, amino acids, and organic acids, suggesting that SWCNHs reprogrammed carbon/nitrogen metabolism in plants. SWCNHs also regulate plant growth and development by increasing the levels of several secondary metabolites; transcriptomic analyses further supported these results. The present results are valuable for continued use of SWCNHs in agri-nanotechnology, and these molecular approaches could serve as examples for studies on the effects of nanomaterials in plants.

Common Functions of Disordered Proteins across Evolutionary Distant Organisms

Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence–structure–function relationship. Hence, classic sequence- or structure-based bioinformatic approaches are often not well suited to identify homology or predict the function of unknown intrinsically disordered proteins. Here, we give selected examples of intrinsic disorder in plant proteins and present how protein function is shared, altered or distinct in evolutionary distant organisms. Furthermore, we explore how examining the specific role of disorder across different phyla can provide a better understanding of the common features that protein disorder contributes to the respective biological mechanism.

Arabidopsis proteome and the mass spectral assay library

Arabidopsis is an important model organism and the first plant with its genome completely sequenced. Knowledge from studying this species has either direct or indirect applications for agriculture and human health. Quantitative proteomics by data-independent acquisition mass spectrometry (SWATH/DIA-MS) was recently developed and is considered as a high-throughput, massively parallel targeted approach for accurate proteome quantification. In this approach, a high-quality and comprehensive spectral library is a prerequisite. Here, we generated an expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We applied DIA-MS using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups of which 1,787 were differentially expressed. MS data are available via ProteomeXchange with identifier PXD012708 and PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.

Arabidopsis proteome and the mass spectral assay library

Arabidopsis is an important model organism and the first plant with its genome completely sequenced. Knowledge from studying this species has either direct or indirect applications for agriculture and human health. Quantitative proteomics by data-independent acquisition mass spectrometry (SWATH/DIA-MS) was recently developed and is considered as a high-throughput, massively parallel targeted approach for accurate proteome quantification. In this approach, a high-quality and comprehensive spectral library is a prerequisite. Here, we generated an expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We applied DIA-MS using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups of which 1,787 were differentially expressed. MS data are available via ProteomeXchange with identifier PXD012708 and PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.

Arabidopsis proteome and the mass spectral assay library

Arabidopsis is an important model organism and the first plant with its genome completely sequenced. Knowledge from studying this species has either direct or indirect applications for agriculture and human health. Quantitative proteomics by data-independent acquisition mass spectrometry (SWATH/DIA-MS) was recently developed and is considered as a high-throughput, massively parallel targeted approach for accurate proteome quantification. In this approach, a high-quality and comprehensive spectral library is a prerequisite. Here, we generated an expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We applied DIA-MS using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups of which 1,787 were differentially expressed. MS data are available via ProteomeXchange with identifier PXD012708 and PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.

Measurement(s)	Proteome
Technology Type(s)	mass spectrometry assay • computational modeling technique
Sample Characteristic - Organism	Arabidopsis thaliana

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9959036

Making glue from seeds and gums: Working with plant-based polymers to introduce students to plant biochemistry

Plants and plant products are key to the survival of life on earth. Despite this fact, the significance of plant biochemistry is often underrepresented in science curricula. We designed an innovative laboratory activity to engage students in learning about the biochemical properties of natural polymers produced by plants. The focus of the hands-on activity is on mucilages and gums, which contain complex polysaccharides that have applications in industry. The 1.5-h activity is organized into three laboratory exercises. It begins with a demonstration of the water absorption property of seed coat mucilage upon hydration of seeds from psyllium, a plant that is grown commercially for mucilage production. The second exercise involves microscopy of a variety of plant seeds stained with ruthenium red dye to visualize pectin polysaccharides of the seed mucilage. Students learn about phenotypic variation among plant species and how the seed coat mucilage is beneficial to keep seeds hydrated during germination. The third exercise highlights an industrial application of plant gums as adhesives. The students prepare edible glue made with gum arabic, a type of plant polymer from the dried exudate of the Acacia plant. This three-part activity has been implemented in conjunction with a Girls Researching Our World (GROW) summer workshop for sixth to eighth graders over a 4-year period. It may be adapted as a laboratory activity for students of all ages, for example, to enhance biochemistry education for high-school students or undergraduate non-majors. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):468-475, 2019.

Towards Building a Plant Cell Atlas

Enormous societal challenges, such as feeding and providing energy for a growing population in a dramatically changing climate, necessitate technological advances in plant science. Plant cells are fundamental organizational units that mediate the production, transport, and storage of our primary food sources, and they sequester a significant proportion of the world's carbon. New technologies allow comprehensive descriptions of cells that could accelerate research across fields of plant science. Complementary to the efforts towards understanding the cellular diversity in human brain and immune systems, a Plant Cell Atlas (PCA) that maps molecular machineries to cellular and subcellular domains, follows their dynamic movements, and describes their interactions would accelerate discovery in plant science and help to solve imminent societal problems.

Phyto-miRNAs-based regulation of metabolites biosynthesis in medicinal plants

Medicinal plants, are known to produce a wide range of plant secondary metabolites (PSMs) applied as insecticides, drugs, dyes and toxins in agriculture, medicine, industry and bio-warfare plus bio-terrorism, respectively. However, production of PSMs is usually in small quantities, so we need to find novel ways to increase both quantity and quality of them. Fortunately, biotechnology suggests several options through which secondary metabolism in plants can be engineered in innovative ways to: 1) over-produce the useful metabolites, 2) down-produce the toxic metabolites, 3) produce the new metabolites. Among the ways, RNA interference (RNAi) technology which involves gene-specific regulation by small non-coding RNAs (sncRNAs) have been recently emerged as a promising tool for plant biotechnologist, not only to decipher the function of plant genes, but also for development of the plants with improved and novel traits through manipulation of both desirable and undesirable genes. Among sncRNAs, miRNAs have been recorded various regulatory roles in plants such as development, signal transduction, response to environmental stresses, metabolism. Certainly, the use of miRNAs in metabolic engineering requires identification of miRNAs involved in metabolites biosynthesis, understanding of the biosynthetic pathways, as well as the identification of key points of the pathways in which the miRNAs have their own effect. Thus, we firstly consider these three issues on metabolic engineering of medicinal plants. Our review shows, application of miRNAs can open a novel perspective to metabolic engineering of medicinal plants.

Genes involved in miRNA biogenesis affect meiosis and fertility

MicroRNAs (miRNAs) are a class of small (containing about 22 nucleotides) single-stranded non-coding RNAs that regulate gene expression at the post-transcriptional level in plants and animals, being absent from unicellular organisms. They act on diverse key physiological and cellular processes, such as development and tissue differentiation, cell identity, cell cycle progression, and programmed cell death. They are also likely to be involved in a broad spectrum of human diseases. Particularly, this review examines and summarizes work characterizing the function of miRNAs in gametogenesis and fertility. Although numerous studies have elucidated the involvement of reproductive-specific small interfering RNAs (siRNAs) in regulating germ cell development and meiosis, less is known about the role of miRNAs in these processes. We focus on the study of hypomorphic and null alleles of genes encoding components of miRNA biogenesis in both plants (Arabidopsis thaliana) and mammals (Mus musculus). We compare the consequences of the presence of these mutations on male meiosis in both species.

Indole-3-carbinol: a plant hormone combatting cancer

A diet rich in cruciferous vegetables such as cauliflower, broccoli, and cabbage has long been considered healthy, and various epidemiological studies suggest that the consumption of cruciferous vegetables contributes to a cancer-protecting diet. While these vegetables contain a vast array of phytochemicals, the mechanism by which these vegetables counteract cancer is still largely unresolved. Numerous in situ studies have implicated indole-3-carbinol, a breakdown product of the glucosinolate indole-3-ylmethylglucosinolate, as one of the phytochemicals with anti-cancer properties. Indole-3-carbinol influences a range of cellular processes, but the mechanisms by which it acts on cancer cells are slowly being revealed. Recent studies on the role of indole-3-carbinol in Arabidopsis opens the door for cross-kingdom comparisons that can help in understanding the roles of this important phytohormone in both plant biology and combatting cancer.

Inferring defense-related gene families in Arabidopsis and wheat

BACKGROUND

A large number of disease resistance genes or QTLs in crop plants are identified through conventional genetics and genomic tools, but their functional or molecular characterization remains costly, labor-intensive and inaccurate largely due to the lack of deep sequencing of large and complex genomes of many important crops such as allohexaploid wheat (Triticum aestivum L.). On the other hand, gene annotation and relevant genomic resources for disease resistance and other defense-related traits are more abundant in model plant Arabidopsis (Arabidopsis thaliana). The objectives of this study are (i) to infer homology of defense-related genes in Arabidopsis and wheat and (ii) to classify these homologous genes into different gene families.

RESULTS

We employed three bioinformatics and genomics approaches to identifying candidate genes known to affect plant defense and to classifying these protein-coding genes into different gene families in Arabidopsis. These approaches predicted up to 1790 candidate genes in 11 gene families for Arabidopsis defense to biotic stresses. The 11 gene families included ABC, NLR and START, the three families that are already known to confer rust resistance in wheat, and eight new families. The distributions of predicted SNPs for individual rust resistance genes were highly skewed towards specific gene families, including eight one-to-one uniquely matched pairs: Lr21-NLR, Lr34-ABC, Lr37-START, Sr2-Cupin, Yr24-Transcription factor, Yr26-Transporter, Yr36-Kinase and Yr53-Kinase. Two of these pairs, Lr21-NLR and Lr34-ABC, are expected because Lr21 and Lr34 are well known to confer race-specific and race-nonspecific resistance to leaf rust (Puccinia triticina) and they encode NLR and ABC proteins.

CONCLUSIONS

Our inference of 11 known and new gene families enhances current understanding of functional diversity with defense-related genes in genomes of model plant Arabidopsis and cereal crop wheat. Our comparative genomic analysis of Arabidopsis and wheat genomes is complementary to the conventional map-based or marker-based approaches for identification of genes or QTLs for rust resistance genes in wheat and other cereals. Race-specific and race-nonspecific candidate genes predicted by our study may be further tested and combined in breeding for durable resistance to wheat rusts and other pathogens.

Araport11: a complete reannotation of the Arabidopsis thaliana reference genome

The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, the various classes of non-coding RNA, and small RNA. The TAIR10 annotation update had a profound impact on Arabidopsis research but was released more than 5 years ago. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress. Using an integrative annotation pipeline, we assembled tissue-specific RNA-Seq libraries from 113 datasets and constructed 48 359 transcript models of protein-coding genes in eleven tissues. In addition, we annotated various classes of non-coding RNA including microRNA, long intergenic RNA, small nucleolar RNA, natural antisense transcript, small nuclear RNA, and small RNA using published datasets and in-house analytic results. Altogether, we identified 635 novel protein-coding genes, 508 novel transcribed regions, 5178 non-coding RNAs, and 35 846 small RNA loci that were formerly unannotated. Analysis of the splicing events and RNA-Seq based expression profiles revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. Furthermore, we present 692 uniformly expressed housekeeping genes, 43% of whose human orthologs are also housekeeping genes. This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species.

Field Guide to Plant Model Systems

For the past several decades, advances in plant development, physiology, cell biology, and genetics have relied heavily on the model (or reference) plant Arabidopsis thaliana. Arabidopsis resembles other plants, including crop plants, in many but by no means all respects. Study of Arabidopsis alone provides little information on the evolutionary history of plants, evolutionary differences between species, plants that survive in different environments, or plants that access nutrients and photosynthesize differently. Empowered by the availability of large-scale sequencing and new technologies for investigating gene function, many new plant models are being proposed and studied.

CSDB_GT: a new curated database on glycosyltransferases

Glycosyltransferases (GTs) are carbohydrate-active enzymes (CAZy) involved in the synthesis of natural glycan structures. The application of CAZy is highly demanded in biotechnology and pharmaceutics. However, it is being hindered by the lack of high-quality and comprehensive repositories of the research data accumulated so far. In this paper, we describe a new curated Carbohydrate Structure Glycosyltransferase Database (CSDB_GT). Currently, CSDB_GT provides ca. 780 activities exhibited by GTs, as well as several other CAZy, found in Arabidopsis thaliana and described in ca. 180 publications. It covers most published data on A. thaliana GTs with evidenced functions. CSDB_GT is linked to the Carbohydrate Structure Database (CSDB), which stores data on archaeal, bacterial, fungal and plant glycans. The CSDB_GT data are supported by experimental evidences and can be traced to original publications. CSDB_GT is freely available at http://csdb.glycoscience.ru/gt.html.

The Role of SWI/SNF Chromatin Remodeling Complexes in Hormone Crosstalk

SWI/SNF-type ATP-dependent chromatin remodeling complexes (CRCs) are evolutionarily conserved multiprotein machineries controlling DNA accessibility by regulating chromatin structure. We summarize here recent advances highlighting the role of SWI/SNF in the regulation of hormone signaling pathways and their crosstalk in Arabidopsis thaliana. We discuss the functional interdependences of SWI/SNF complexes and key elements regulating developmental and hormone signaling pathways by indicating intriguing similarities and differences in plants and humans, and summarize proposed mechanisms of SWI/SNF action on target loci. We postulate that, given their viability, several plant SWI/SNF mutants may serve as an attractive model for searching for conserved functions of SWI/SNF CRCs in hormone signaling, cell cycle control, and other regulatory pathways.

New strategy for drug discovery by large-scale association analysis of molecular networks of different species

The development of modern omics technology has not significantly improved the efficiency of drug development. Rather precise and targeted drug discovery remains unsolved. Here a large-scale cross-species molecular network association (CSMNA) approach for targeted drug screening from natural sources is presented. The algorithm integrates molecular network omics data from humans and 267 plants and microbes, establishing the biological relationships between them and extracting evolutionarily convergent chemicals. This technique allows the researcher to assess targeted drugs for specific human diseases based on specific plant or microbe pathways. In a perspective validation, connections between the plant Halliwell-Asada (HA) cycle and the human Nrf2-ARE pathway were verified and the manner by which the HA cycle molecules act on the human Nrf2-ARE pathway as antioxidants was determined. This shows the potential applicability of this approach in drug discovery. The current method integrates disparate evolutionary species into chemico-biologically coherent circuits, suggesting a new cross-species omics analysis strategy for rational drug development.

50 years of Arabidopsis research: highlights and future directions

922 I. 922 II. 922 III. 925 IV. 925 V. 926 VI. 927 VII. 928 VIII. 929 IX. 930 X. 931 XI. 932 XII. 933 XIII. Natural variation and genome-wide association studies 934 XIV. 934 XV. 935 XVI. 936 XVII. 937 937 References 937 SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.

Killing cancer with platycodin D through multiple mechanisms

Cancer is a multi-faceted disease comprised of a combination of genetic, epigenetic, metabolic and signalling aberrations which severely disrupt the normal homoeostasis of cell growth and death. Rational developments of highly selective drugs which specifically block only one of the signalling pathways have been associated with limited therapeutic success. Multi-targeted prevention of cancer has emerged as a new paradigm for effective anti-cancer treatment. Platycodin D, a triterpenoid saponin, is one the major active components of the roots of Platycodon grandiflorum and possesses multiple biological and pharmacological properties including, anti-nociceptive, anti-atherosclerosis, antiviral, anti-inflammatory, anti-obesity, immunoregulatory, hepatoprotective and anti-tumour activities. Recently, the anti-cancer activity of platycodin D has been extensively studied. The purpose of this review was to give our perspectives on the current status of platycodin D and discuss its anti-cancer activity and molecular mechanisms which may help the further design and conduct of pre-clinical and clinical trials to develop it successfully into a potential lead drug for oncological therapy. Platycodin D has been shown to fight cancer by inducing apoptosis, cell cycle arrest, and autophagy and inhibiting angiogenesis, invasion and metastasis by targeting multiple signalling pathways which are frequently deregulated in cancers suggesting that this multi-target activity rather than a single effect may play an important role in developing platycodin D into potential anti-cancer drug.

Evolution of TERT-interacting lncRNAs: expanding the regulatory landscape of telomerase

Long non-coding RNAs (lncRNAs) evolve rapidly and are functionally diverse. The emergence of new lncRNAs is driven by genome disturbance events, including whole genome duplication, and transposition. One of the few lncRNAs with a conserved role throughout eukaryotes is the telomerase RNA, TER. TER works in concert with the telomerase reverse transcriptase (TERT) to maintain telomeres. Here we discuss recent findings from Arabidopsis thaliana and its relatives illustrating the remarkable evolutionary flexibility within TER and the potential for non-canonical TERT-lncRNA interactions. We highlight the two TERs in A. thaliana. One is a conventional telomerase template. The other lncRNA negatively regulates telomerase activity in response to DNA damage, a function mediated by co-option of a transposable element. In addition, we discuss evidence for multiple independent TER loci throughout the plant family Brassicaceae, and how these loci not only reflect rapid convergent evolution, but also the flexibility of having a lncRNA at the core of telomerase. Lastly, we discuss the propensity for TERT to bind a suite of non-templating lncRNAs, and how such RNAs may facilitate telomerase regulation and off-telomere functions.

Transgenic plants as low-cost platform for chemotherapeutic drugs screening

In this work we explored the possibility of using genetically modified Arabidopsis thaliana plants as a rapid and low-cost screening tool for evaluating human anticancer drugs action and efficacy. Here, four different inhibitors with a validated anticancer effect in humans and distinct mechanism of action were screened in the plant model for their ability to interfere with the cytoskeletal and endomembrane networks. We used plants expressing a green fluorescent protein (GFP) tagged microtubule-protein (TUA6-GFP), and three soluble GFPs differently sorted to reside in the endoplasmic reticulum (GFPKDEL) or to accumulate in the vacuole through a COPII dependent (AleuGFP) or independent (GFPChi) mechanism. Our results demonstrated that drugs tested alone or in combination differentially influenced the monitored cellular processes including cytoskeletal organization and endomembrane trafficking. In conclusion, we demonstrated that A. thaliana plants are sensitive to the action of human chemotherapeutics and can be used for preliminary screening of drugs efficacy. The cost-effective subcellular imaging in plant cell may contribute to better clarify drugs subcellular targets and their anticancer effects.

Could FaRP-Like Peptides Participate in Regulation of Hyperosmotic Stress Responses in Plants?

The ability to respond to hyperosmotic stress is one of the numerous conserved cellular processes that most of the organisms have to face during their life. In metazoans, some peptides belonging to the FMRFamide-like peptide (FLP) family were shown to participate in osmoregulation via regulation of ion channels; this is, a well-known response to hyperosmotic stress in plants. Thus, we explored whether FLPs exist and regulate osmotic stress in plants. First, we demonstrated the response of Arabidopsis thaliana cultured cells to a metazoan FLP (FLRF). We found that A. thaliana express genes that display typical FLP repeated sequences, which end in RF and are surrounded by K or R, which is typical of cleavage sites and suggests bioactivity; however, the terminal G, allowing an amidation process in metazoan, seems to be replaced by W. Using synthetic peptides, we showed that amidation appears unnecessary to bioactivity in A. thaliana, and we provide evidence that these putative FLPs could be involved in physiological processes related to hyperosmotic stress responses in plants, urging further studies on this topic.

Circadian redox signaling in plant immunity and abiotic stress

SIGNIFICANCE

Plant crops are critically important to provide quality food and bio-energy to sustain a growing human population. Circadian clocks have been shown to deliver an adaptive advantage to plants, vastly increasing biomass production by efficient anticipation to the solar cycle. Plant stress, on the other hand, whether biotic or abiotic, prevents crops from reaching maximum productivity.

RECENT ADVANCES

Stress is associated with fluctuations in cellular redox and increased phytohormone signaling. Recently, direct links between circadian timekeeping, redox fluctuations, and hormone signaling have been identified. A direct implication is that circadian control of cellular redox homeostasis influences how plants negate stress to ensure growth and reproduction.

CRITICAL ISSUES

Complex cellular biochemistry leads from perception of stress via hormone signals and formation of reactive oxygen intermediates to a physiological response. Circadian clocks and metabolic pathways intertwine to form a confusing biochemical labyrinth. Here, we aim to find order in this complex matter by reviewing current advances in our understanding of the interface between these networks.

FUTURE DIRECTIONS

Although the link is now clearly defined, at present a key question remains as to what extent the circadian clock modulates redox, and vice versa. Furthermore, the mechanistic basis by which the circadian clock gates redox- and hormone-mediated stress responses remains largely elusive.

On the role of AtDMC1, AtRAD51 and its paralogs during Arabidopsis meiosis

Meiotic recombination plays a critical role in achieving accurate chromosome segregation and increasing genetic diversity. Many studies, mostly in yeast, have provided important insights into the coordination and interplay between the proteins involved in the homologous recombination pathway, especially the recombinase RAD51 and the meiosis-specific DMC1. Here we summarize the current progresses on the function of both recombinases and the CX3 complex encoded by AtRAD51 paralogs, in the plant model species Arabidopsis thaliana. Similarities and differences respect to the function of these proteins in other organisms are also indicated.

Assessing Pseudomonas virulence with the nonmammalian host model: Arabidopsis thaliana

The popular plant model, Arabidopsis thaliana, has been used to successfully identify novel Pseudomonas aeruginosa genes that are involved in virulence. These genes have also been shown to be important for mammalian infection, demonstrating that this bacterium has a conserved set of virulence factors with broad range. This chapter describes using A. thaliana as a plant model for P. aeruginosa infection and describes obtaining the plants, preparing the inoculum, infecting the leaves, and collecting and interpreting the data. This protocol allows for both a qualitative assessment of symptoms and a quantitative measurement of the bacterial growth inside the leaves.

A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues

Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.

Menthol-enhanced cytotoxicity of cigarette smoke demonstrated in two bioassay models

Background

Cigarette smoke is harmful to human health at both cellular and genetic levels. Recently, a unique bioassay for smoke cytotoxicity using air pollution-sensitive plant cells (tobacco) has been proposed.

Methods

Model plant cells (tobacco Bel-W3 cells) and human cells (alveolar epithelial A549 cells) suspended in fresh culture media were exposed to cigarette smoke sampled after lighting the tip of cigarettes (with vs. without menthol capsules) which were attached to a glass pipe connected to the cell-containing plastic tubes. Control cultures were also assessed.

Results

After exposing tobacco plant cells to cigarette smoke, cell death occurred in a dose-dependent manner. Cell death was significantly enhanced by mentholated smoke, while menthol alone was shown to be inert suggesting that menthol synergistically contributes to the enhancement of cell death, initiated by smoke-associated compounds. The enhanced toxicity of mentholated smoke was confirmed in human alveolar epithelial A549 cells.

Conclusions

Cigarette smoke cytotoxicity leading to cell death assessed in plant and human model cells was enhanced by menthol. Further research into these findings is encouraged.

ABA says NO to UV-B: a universal response?

Abscisic acid (ABA) signaling pathways have been widely characterized in plants, whereas the function of ABA in animals is less well understood. However, recent advances show ABA production by a wide range of lower animals and higher mammals. This enables a new evaluation of ABA signaling pathways in different organisms in response to common environmental stress, such as ultraviolet (UV)-B. In this opinion article, we propose that the induction of common signaling components, such as ABA, nitric oxide (NO) and Ca(2+), in plant and animal cells in response to high doses of UV-B, suggests that the evolution of a general mechanism activated by UV-B is conserved in divergent multicellular organisms challenged by a changing common environment.

Identification of putative cancer genes through data integration and comparative genomics between plants and humans

Coordination of cell division with growth and development is essential for the survival of organisms. Mistakes made during replication of genetic material can result in cell death, growth defects, or cancer. Because of the essential role of the molecular machinery that controls DNA replication and mitosis during development, its high degree of conservation among organisms is not surprising. Mammalian cell cycle genes have orthologues in plants, and vice versa. However, besides the many known and characterized proliferation genes, still undiscovered regulatory genes are expected to exist with conserved functions in plants and humans. Starting from genome-wide Arabidopsis thaliana microarray data, an integrative strategy based on coexpression, functional enrichment analysis, and cis-regulatory element annotation was combined with a comparative genomics approach between plants and humans to detect conserved cell cycle genes involved in DNA replication and/or DNA repair. With this systemic strategy, a set of 339 genes was identified as potentially conserved proliferation genes. Experimental analysis confirmed that 20 out of 40 selected genes had an impact on plant cell proliferation; likewise, an evolutionarily conserved role in cell division was corroborated for two human orthologues. Moreover, association analysis integrating Homo sapiens gene expression data with clinical information revealed that, for 45 genes, altered transcript levels and relapse risk clearly correlated. Our results illustrate how a systematic exploration of the A. thaliana genome can contribute to the experimental identification of new cell cycle regulators that might represent novel oncogenes or/and tumor suppressors.

Distant plant homologues: don't throw out the baby

Plants and metazoans share many similarities in terms of conserved proteins. Antibodies have been used extensively to detect remote homologues, many of which are yet to be identified conclusively. Genome sequencing and the creation of novel sequence or structure comparison programs have assisted greatly in the identification of distant protein homologues. The continuing development of new software algorithms and the combining of bioinformatics with proteomics offer hope that remaining homologues will be soon identified.