RNA-Seq and WGCNA Analyses Reveal Key Regulatory Modules and Genes for Salt Tolerance in Cotton

The problem of soil salinization has seriously hindered agricultural development. Cotton is a pioneering salinity-tolerant crop, so harvesting its key salinity-tolerant genes is important for improving crop salt tolerance. In this study, we analyzed changes in the transcriptome expression profiles of the salt-tolerant cultivar Lu Mian 28 (LM) and the salt-sensitive cultivar Zhong Mian Suo 12 (ZMS) after applying salt stress, and we constructed weighted gene co-expression networks (WGCNA). The results indicated that photosynthesis, amino acid biosynthesis, membrane lipid remodeling, autophagy, and ROS scavenging are key pathways in the salt stress response. Plant-pathogen interactions, plant hormone signal transduction, the mitogen-activated protein kinase (MAPK) signaling pathway, and carotenoid biosynthesis are the regulatory networks associated with these metabolic pathways that confer cotton salt tolerance. The gene-weighted co-expression network was used to screen four modules closely related to traits, identifying 114 transcription factors, including WRKYs, ERFs, NACs, bHLHs, bZIPs, and MYBs, and 11 hub genes. This study provides a reference for acquiring salt-tolerant cotton and abundant genetic resources for molecular breeding.

Rare earth elements perturb root architecture and ion homeostasis in Arabidopsis thaliana

Rare earth elements (REEs) are crucial elements for current high-technology and renewable energy advances. In addition to their increasing usage and their low recyclability leading to their release into the environment, REEs are also used as crop fertilizers. However, little is known regarding the cellular and molecular effects of REEs in plants, which is crucial for better risk assessment, crop safety and phytoremediation. Here, we analysed the ionome and transcriptomic response of Arabidopsis thaliana exposed to a light (lanthanum, La) and a heavy (ytterbium, Yb) REE. At the transcriptome level, we observed the contribution of ROS and auxin redistribution to the modified root architecture following REE exposure. We found indications for the perturbation of Fe homeostasis by REEs in both roots and leaves of Arabidopsis suggesting competition between REEs and Fe. Furthermore, we propose putative ways of entry of REEs inside cells through transporters of microelements. Finally, similar to REE accumulating species, organic acid homeostasis (e.g. malate and citrate) appears critical as a tolerance mechanism in response to REEs. By combining ionomics and transcriptomics, we elucidated essential patterns of REE uptake and toxicity response of Arabidopsis and provide new hypotheses for a better evaluation of the impact of REEs on plant homeostasis.

Arabidopsis root growth and development under metal exposure presented in an adverse outcome pathway framework

Due to human activities, soils become more and more polluted with metals, which imposes risks for human health and wildlife welfare. As most of the metals end up in the food chain through accumulation in plants, we need to establish science-based environmental criteria and risk management policies. To meet these necessities, a thorough understanding is required of how these metals accumulate in and affect plants. Many studies have been conducted towards this aim, but strikingly, only a few entries can be found in ecotoxicological databases, especially on Arabidopsis thaliana, which serves as a model species for plant (cell) physiology and genetic studies. As experimental conditions seem to vary considerably throughout literature, extrapolation or comparison of data is rather difficult or should be approached with caution. Furthermore, metal-polluted soils often contain more than one metal, yet limited studies investigated the impact of metal mixtures on plants. This review aims to compile all data concerning root system architecture under Cu, Cd and Zn stress, in single or multi-metal exposure in A. thaliana, and link it to metal-induced responses at different biological levels. Global incorporation into an adverse outcome pathway framework is presented.

Towards early-warning gene signature of Chlamydomonas reinhardtii exposed to Hg-containing complex media

The potential of using gene expression signature as a biomarker of toxicants exposure was explored in the microalga Chlamydomonas reinhardtii exposed 2 h to mercury (Hg) as inorganic mercury (IHg) and methyl mercury (MeHg) in presence of copper (Cu) and Suwannee River Humic Acid (SRHA). Total cellular Hg (THg = IHg + MeHg) decreased in presence of SRHA for 0.7 nM IHg and 0.4 nM MeHg, but increased for 70 nM IHg exposure. In mixtures of IHg + MeHg and (IHg or MeHg) + Cu, SRHA decreased THg uptake, except for 0.7 nM IHg + 0.4 nM MeHg which was unchanged (p-value>0.05). In the absence of SRHA, 0.5 μM Cu strongly decreased intracellular THg concentration for 70 nM IHg, while it had no effect for 0.7 nM IHg and 0.4 nM MeHg. The expression of single transcripts was not correlated with measured THg uptake, but a subset of 60 transcripts showed signatures specific to the exposed metal(s) and was congruent with exposure concentration. Notably, the range of fold change values of this subset correlated with THg bioaccumulation with a two-slope pattern in line with [THg]_intra/[THg]_med ratios. Gene expression signature seems a promising approach to complement chemical analyses to assess bioavailability of toxicants in presence of other metals and organic matter.

Translational Metabolomics: Current Challenges and Future Opportunities

Metabolomics is one of the latest omics technologies that has been applied successfully in many areas of life sciences. Despite being relatively new, a plethora of publications over the years have exploited the opportunities provided through this data and question driven approach. Most importantly, metabolomics studies have produced great breakthroughs in biomarker discovery, identification of novel metabolites and more detailed characterisation of biological pathways in many organisms. However, translation of the research outcomes into clinical tests and user-friendly interfaces has been hindered due to many factors, some of which have been outlined hereafter. This position paper is the summary of discussion on translational metabolomics undertaken during a peer session of the Australian and New Zealand Metabolomics Conference (ANZMET 2018) held in Auckland, New Zealand. Here, we discuss some of the key areas in translational metabolomics including existing challenges and suggested solutions, as well as how to expand the clinical and industrial application of metabolomics. In addition, we share our perspective on how full translational capability of metabolomics research can be explored.

Identification and comprehensive analysis of the characteristics and roles of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in Sedum alfredii Hance responding to cadmium stress

Sedum alfredii Hance is a Zn/Cd co-hyperaccumulator and its underlying molecular mechanism of Cd tolerance is worthy to be elucidated. Although numerous studies have reported the uptake, sequestration and detoxification of Cd in S. alfredii Hance, how it senses Cd-stress stimuli and transfers signals within tissues remains unclear. Leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are vital for plant growth, development, immunity and signal transduction. Till now, there is lack of comprehensive studies addressing their functions in S. alfredii Hance responding to Cd stress. In the present study, we identified 60 LRR-RLK genes in S. alfredii Hance based on transcriptome analysis under Cd stress. They were categorized into 11 subfamilies and most of them had highly conserved protein structures and motif compositions. The inter-family diversity provided evidence for their functional divergence, supported by their expression level and profile in tissues under Cd stress. Co-expression network analysis revealed that the most highly connected hubs, Sa0F.522, Sa0F.1036, Sa28F.115 and Sa1F.472, were closely related with other genes involved in metal transport, stimulus response and transcription regulations. Of the ten hub genes exhibiting differential expression dynamics under the short-term Cd stress (Sa0F.522, Sa0F.1036 and Sa28F.115) were dramatically induced in the whole plant. Among them, Sa0F.522 gene was heterologously expressed in a Cd-sensitive yeast cell line and its function in Cd signal perception was confirmed. For the first time, our findings performed a comprehensive analysis of LRR-RLKs in S. alfredii Hance, mapped their expression patterns under Cd stress, and identified the key roles of Sa0F.522, Sa0F.1036 and Sa28F.115 in Cd signal transduction.

Molecular Effects, Speciation, and Competition of Inorganic and Methyl Mercury in the Aquatic Plant Elodea nuttallii

Mercury (Hg) remains hazardous in aquatic environments because of its biomagnification in food webs. Nonetheless, Hg uptake and impact in primary producers is still poorly understood. Here, we compared the cellular toxicity of inorganic and methyl Hg (IHg and MeHg, respectively) in the aquatic plant Elodea nuttallii. IHg and MeHg regulated contigs involved in similar categories (e.g., energy metabolism, development, transport, secondary metabolism), but MeHg regulated more contigs, supporting a higher molecular impact than IHg. At the organism level, MeHg induced antioxidants, while IHg decreased chlorophyll content. The uptake of Hg and expression of a subset of contigs was subsequently studied in complex media. Measured uptake pointed to a contrasted impact of cell walls and copper (Cu) on IHg and MeHg. Using a speciation modeling, differences in uptake were attributed to the differences in affinities of IHg and MeHg to organic matter in relation to Cu speciation. We also identified a distinct gene expression signature for IHg, MeHg, and Cu, further supporting different molecular toxicity of these trace elements. Our data provided fundamental knowledge on IHg and MeHg uptake in a key aquatic primary producer and confirmed the potential of transcriptomics to assess Hg exposure in environmentally realistic systems.

The metabolic effects of mercury during the biological cycle of vines (Vitis vinifera)

Mercury (Hg) is a major environmental pollutant that can be disposed to the environment by human activities, reaching crops like vineyards during irrigation with contaminated waters. A 2-year study was performed to monitor Hg variations during reproductive and vegetative stages of vines after Hg supplementation. Variations were focused on total Hg concentration, the molecular weight of Hg fractions and Hg-proteins associations in roots, stems and leaves. Total Hg concentrations increased during reproductive stages and decreased during vegetative stages. Variations in length of these stages were observed, according to an extension of the vegetative period. Six months post Hg administration, in roots, stems and leaves, initial Hg proteic fractions of 200 kDa were catabolized to 66 kDa fractions according to a transition from reproductive to vegetative stages. However, 24 months after Hg supplementation, the 66 kDa Hg proteic fraction was continuously determined in a prolonged senescence. Accordingly, the identified proteins associated to Hg show catabolic functions such as endopeptidases, hydrolases, glucosidases and nucleosidases. Stress associated proteins, like peroxidase and chitinase were also found associated to Hg. During the reproductive periods of vines, Hg was associated to membrane proteins, such as ATPases and lipid transfer proteins, especially in roots where Hg is absorbed.

Transcriptomic Response of Arabidopsis thaliana Exposed to CuO Nanoparticles, Bulk Material, and Ionic Copper

Engineered nanoparticles (ENPs) exhibit unique properties advantageous in a number of applications, but they also represent potential health and environmental risks. In this study, we investigated the phytotoxic mechanism of CuO ENPs using transcriptomic analysis and compared this response with the response to CuO bulk particles and ionic Cu²⁺. Ionic Cu²⁺ at the concentration of 0.16 mg L^-1 changed transcription of 2692 genes (p value of <0.001, fold change of ≥2) after 7 days of exposure, whereas CuO ENPs and bulk particles (both in the concentration of 10 mg L^-1) altered the expression of 922 and 482 genes in Arabidopsis thaliana roots, respectively. The similarity between transcription profiles of plants exposed to ENPs and ionic Cu²⁺ indicated that the main factor in phytotoxicity was the release of Cu²⁺ ions from CuO ENPs after 7 days of exposure. The effect of Cu²⁺ ions was evident in all treatments, as indicated by the down-regulation of genes involved in metal homeostasis and transport and the up-regulation of oxidative stress response genes. ENPs were more soluble than bulk particles, resulting in the up-regulation of metallochaperone-like genes or the down-regulation of aquaporins and metal transmembrane transporters that was also characteristic for ionic Cu²⁺ exposure.

Skewing in Arabidopsis roots involves disparate environmental signaling pathways

BACKGROUND

Skewing root patterns provide key insights into root growth strategies and mechanisms that produce root architectures. Roots exhibit skewing and waving when grown on a tilted, impenetrable surface. The genetics guiding these morphologies have been examined, revealing that some Arabidopsis ecotypes skew and wave (e.g. WS), while others skew insignificantly but still wave (e.g. Col-0). The underlying molecular mechanisms of skewing and waving remain unclear. In this study, transcriptome data were derived from two Arabidopsis ecotypes, WS and Col-0, under three tilted growth conditions in order to identify candidate genes involved in skewing.

RESULTS

This work identifies a number of genes that are likely involved in skewing, using growth conditions that differentially affect skewing and waving. Comparing the gene expression profiles of WS and Col-0 in different tilted growth conditions identified 11 candidate genes as potentially involved in the control of skewing. These 11 genes are involved in several different cellular processes, including sugar transport, salt signaling, cell wall organization, and hormone signaling.

CONCLUSIONS

This study identified 11 genes whose change in expression level is associated with root skewing behavior. These genes are involved in signaling and perception, rather than the physical restructuring of root. Future work is needed to elucidate the potential role of these candidate genes during root skewing.