Integration of transcriptomic and proteomic analysis towards understanding the systems biology of root hairs

Comparative transcriptome analysis between inbred lines and hybrids provides molecular insights into K+ content heterosis of tobacco (Nicotiana tabacum L.)

Potassium (K⁺) is essential for crop growth. Increasing the K⁺ content can often directly promote the improvement of crop yield and quality. Heterosis plays an important role in genetic improvement and leads to genetic gains. We found that the K⁺ content of tobacco showed significant heterosis, which is highly significant for cultivating tobacco varieties with high K⁺ content. However, the mechanism by which K⁺ content heterosis occurs in tobacco leaves is not clear. In this study, a comprehensive comparative transcriptome sequencing analysis of root samples from the hybrid G70 × GDH11 and its parental inbred lines G70 and GDH11 was performed to elucidate the importance of the root uptake capacity of K⁺ in the formation of heterosis. The results showed that 29.53% and 60.49% of the differentially expressed genes (DEGs) exhibited dominant and over-dominant expression patterns, respectively. These non-additive upregulated DEGs were significantly enriched in GO terms, such as metal ion transport and reaction, ion balance and homeostasis, ion channel activity, root meristem growth, and regulation of root hairs. The KEGG annotation results indicated that these genes were mainly involved in the pathways such as energy metabolism, carbohydrate formation, amino acid metabolism, and signal transduction. Further analysis showed that probable potassium transporter 17 (NtKT17) and potassium transporter 5-like (NtKT5), associated with potassium ion absorption, glutamate receptor 2.2-like and glutamate receptor 2.8-like, associated with ion channel activity, LOC107782957, protein detoxification 42-like, and probable glutamate carboxypeptidase 2, associated with root configuration, showed a significantly higher expression in the hybrids. These results indicated that the over-dominant expression pattern of DEGs played a key role in the heterosis of K⁺ content in tobacco leaves, and the overexpression of the genes related to K⁺ uptake, transport, and root development in hybrids helped to improve the K⁺ content of plants, thus showing the phenomenon of heterosis.

Three-in-one method for high throughput plant multi-omics

Multi-omics has gained momentum over the past few years especially in plant single cell-type analysis as they aim to understand cellular molecular networks across different levels of genetic information flow. For multi-omics sample preparation, molecular extractions performed non-simultaneously create rooms for variation, inaccurate data, waste of limited samples, resources and labor. Here we optimized a protocol for 3-in-1 simultaneous extraction of RNA, metabolites, and proteins from the same single cell-type sample. We adapted a commercially available RNA kit with a few modifications to obtain high quality starting materials for sequencing and LC-MS/MS-based metabolomics and proteomics. RNAs are bound to the column, metabolites were extracted in a polar solvent and proteins are precipitated using acetone. This creates an all-in-one workflow using a standard RNA kit. Little training is required to carry out this protocol as it is simple and easy to use. It may be used with a wide range of plant species and different amounts of starting materials, including single cells.

PERK13 modulates phosphate deficiency-induced root hair elongation in Arabidopsis

Phosphate starvation (-Pi)-induced root hair is crucial for enhancing plants' Pi absorption. Proline-rich extensin-like receptor kinase 13 (PERK13) is transcriptionally induced by -Pi and co-expressed with genes associated with root hair growth. However, how PERK13 participates in -Pi-induced root hair growth remains unclear. Here, we found that PERK13 was transcriptionally responsive to Pi, nitrogen, and iron deficiencies. Loss of PERK13 function (perk13) enhanced root hair growth under Pi/nitrogen limitation. Similar phenotype was also observed in transgenic lines overexpressing PERK13 (PERK13ox). Under -Pi, both perk13 and PERK13ox showed prolonged root hair elongation and increased reactive oxygen species (ROS). Deletion analysis showed, in PERK13ox, the extracellular domain was indispensable for PERK13 in -Pi-induced root hair growth. Different transcription profiles were observed under -Pi between perk13 and PERK13ox with the jasmonate zim-domain genes being repressed in perk13 and genes involved in cell wall remodeling being increased in PERK13ox. Taken together, we demonstrated that PERK13 participates in -Pi-induced root hair growth probably via regulating root hair elongation and the generation of ROS. Our study also suggested PERK13 probably being a vital hub coupling the environmental cues and root hair growth, and might play dual roles in -Pi-induced root hair growth via different processes.

Plant Systems Biology at the Single-Cell Level

Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system.

Complexity and specificity of the maize (Zea mays L.) root hair transcriptome

Root hairs are tubular extensions of epidermis cells. Transcriptome profiling demonstrated that the single cell-type root hair transcriptome was less complex than the transcriptome of multiple cell-type primary roots without root hairs. In total, 831 genes were exclusively and 5585 genes were preferentially expressed in root hairs [false discovery rate (FDR) ≤1%]. Among those, the most significantly enriched Gene Ontology (GO) functional terms were related to energy metabolism, highlighting the high energy demand for the development and function of root hairs. Subsequently, the maize homologs for 138 Arabidopsis genes known to be involved in root hair development were identified and their phylogenetic relationship and expression in root hairs were determined. This study indicated that the genetic regulation of root hair development in Arabidopsis and maize is controlled by common genes, but also shows differences which need to be dissected in future genetic experiments. Finally, a maize root view of the eFP browser was implemented including the root hair transcriptome of the present study and several previously published maize root transcriptome data sets. The eFP browser provides color-coded expression levels for these root types and tissues for any gene of interest, thus providing a novel resource to study gene expression and function in maize roots.

The seed-borne Southern bean mosaic virus hinders the early events of nodulation and growth in Rhizobium-inoculated Phaseolus vulgaris L

To simulate seed-borne virus transmission, a noninvasive protocol was designed to infect the radicle of germinating seeds, with 100% effectiveness. Preinfection of 24-h-old black bean (Phaseolus vulgaris L.) radicles by Southern bean mosaic virus (SBMV) followed by Rhizobium inoculation 48h later caused a drastic reduction in root nodulation. Results were attributed to active virus replication within the elongating zone of the radicle at least 32h before Rhizobium inoculation, which elicited severe anatomical malformations; an abnormal accumulation of apoplastic reactive oxygen species in the rhizodermis, cortex, inner cortical and endodermic root cells; the formation of atypical root hair tips and the collapse of 94% of the root hairs in the SBMV-preinfected radicles. Adult SBMV-preinfected plants showed exacerbated virus symptoms and 80% growth reduction ascribed to major virus-induced ultrastructural alterations in the nodules. The accumulation of ureides, α-amino acids and total reducing sugars in the leaves and nodules of SBMV-preinfected plants are indicators of the hindering effects of SBMV infection on N2 fixation and ureide catabolism, causing N starvation. The exogenous addition of 1 or 4μM naringenin, genistein or daidzein did not counteract the deleterious effects of SBMV preinfection on nodulation.

Nod Factor Effects on Root Hair-Specific Transcriptome of Medicago truncatula: Focus on Plasma Membrane Transport Systems and Reactive Oxygen Species Networks

Root hairs are involved in water and nutrient uptake, and thereby in plant autotrophy. In legumes, they also play a crucial role in establishment of rhizobial symbiosis. To obtain a holistic view of Medicago truncatula genes expressed in root hairs and of their regulation during the first hours of the engagement in rhizobial symbiotic interaction, a high throughput RNA sequencing on isolated root hairs from roots challenged or not with lipochitooligosaccharides Nod factors (NF) for 4 or 20 h was carried out. This provided a repertoire of genes displaying expression in root hairs, responding or not to NF, and specific or not to legumes. In analyzing the transcriptome dataset, special attention was paid to pumps, transporters, or channels active at the plasma membrane, to other proteins likely to play a role in nutrient ion uptake, NF electrical and calcium signaling, control of the redox status or the dynamic reprogramming of root hair transcriptome induced by NF treatment, and to the identification of papilionoid legume-specific genes expressed in root hairs. About 10% of the root hair expressed genes were significantly up- or down-regulated by NF treatment, suggesting their involvement in remodeling plant functions to allow establishment of the symbiotic relationship. For instance, NF-induced changes in expression of genes encoding plasma membrane transport systems or disease response proteins indicate that root hairs reduce their involvement in nutrient ion absorption and adapt their immune system in order to engage in the symbiotic interaction. It also appears that the redox status of root hair cells is tuned in response to NF perception. In addition, 1176 genes that could be considered as "papilionoid legume-specific" were identified in the M. truncatula root hair transcriptome, from which 141 were found to possess an ortholog in every of the six legume genomes that we considered, suggesting their involvement in essential functions specific to legumes. This transcriptome provides a valuable resource to investigate root hair biology in legumes and the roles that these cells play in rhizobial symbiosis establishment. These results could also contribute to the long-term objective of transferring this symbiotic capacity to non-legume plants.