Root-knot nematode modulates plant CLE3-CLV1 signaling as a long-distance signal for successful infection.

Plants use many long-distance and systemic signals to modulate growth and development, as well as respond to biotic and abiotic stresses. Parasitic nematodes infect host plant roots and cause severe damage to crop plants. However, the molecular mechanisms that regulate parasitic nematode infections are still unknown. Here, we show that plant parasitic root-knot nematodes (RKNs), Meloidogyne incognita, modulate the host CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (CLE)-CLV1 signaling module to promote the infection progression. Plants deficient in the CLE signaling pathway show enhanced RKN resistance, whereas CLE overexpression leads to increased susceptibility toward RKN. Grafting analysis shows that CLV1 expression in the shoot alone is sufficient to positively regulate RKN infection. Together with results from the split-root culture system, infection assays, and CLE3-CLV1 binding assays, we conclude that mobile root-derived CLE signals are perceived by CLV1 in the shoot, which subsequently produce systemic signals to promote gall formation and RKN reproduction.

Collection of Xylem Exudates from the Model Plant Arabidopsis and the Crop Plant Soybean.

A number of molecules, such as secreted peptides, have been shown to mediate root-to-shoot signaling in response to various conditions. The xylem is a pathway for water and molecules that are translocated from roots to shoots. Therefore, collecting and analyzing xylem exudates is an efficient approach to study root-to-shoot long-distance signaling. Here, we describe a step-by-step protocol for the collection of xylem exudate from the model plant Arabidopsis and the crop plant soybean ( Glycine max ). In this protocol, we can collect xylem exudate from plants cultured under normal growth conditions without using special equipment. Graphical abstract: Xylem exudates on the cut surfaces of an Arabidopsis hypocotyl and a soybean internode.

Comparative transcriptome analysis during tuberous stem formation in Kohlrabi (B. oleracea var. gongylodes) at early growth periods (seedling stages).

Tuberous stem of kohlrabi is an important agronomic trait, however, the molecular basis of tuberization is poorly understood. To elucidate the tuberization mechanism, we conducted a comparative transcriptomic analysis between kohlrabi and broccoli at 10 and 20 days after germination (DAG) as tuberous stem initiated between these time points. A total of 5580 and 2866 differentially expressed transcripts (DETs) were identified between genotypes (kohlrabi vs. broccoli) and growth stages (10 DAG vs. 20 DAG), respectively, and most of the DETs were down-regulated in kohlrabi. Gene ontology (GO) and KEGG pathway enrichment analyses showed that the DETs between genotypes are involved in cell wall loosening and expansion, cell cycle and division, carbohydrate metabolism, hormone transport, hormone signal transduction and in several transcription factors. The DETs identified in those categories may directly/indirectly relate to the initiation and development of tuberous stem in kohlrabi. In addition, the expression pattern of the hormone synthesis related DETs coincided with the endogenous IAA, IAAsp, GA, ABA, and tZ profiles in kohlrabi and broccoli seedlings, that were revealed in our phytohormone analysis. This is the first report on comparative transcriptome analysis for tuberous stem formation in kohlrabi at early growth periods. The resulting data could provide significant insights into the molecular mechanism underlying tuberous stem development in kohlrabi as well as in other tuberous organ forming crops.

Altered carbon status in Glycine max hairy roots induced by Agrobacterium rhizogenes.

Plants fix CO2 into carbohydrates through photosynthesis, and various organisms interact with plants to obtain carbohydrates. Agrobacterium rhizogenes is a soil bacterium known as a plant pathogen that induces hairy root disease. Through A. rhizogenes-plant interactions, transfer-DNA (T-DNA) of the Ri plasmid is inserted into the host plant genome, leading to excessive formation of hairy roots and the synthesis of opines that are carbon and nitrogen sources for A. rhizogenes. In this study, we analyzed the carbohydrate contents in soybean (Glycine max) hairy roots. We found that the starch content was strongly increased in hairy roots, whereas the glucose was significantly decreased. On the other hand, no significant differences were observed in sucrose levels between the main roots and hairy roots of A. rhizogenes-inoculated plants. This result suggests that A. rhizogenes infection caused a change in primary carbon metabolism in the host plant cells.

Identification of a Male Sterile Candidate Gene in Lilium x formolongi and Transfer of the Gene to Easter Lily (L. longiflorum) via Hybridization.

Pollen-free varieties are advantageous in promoting cut-flower production. In this study, we identified a candidate mutation which is responsible for pollen sterility in a strain of Lilium × formolongi, which was originally identified as a naturally occurred male-sterile plant in a seedling population. The pollen sterility occurred due to the degradation of pollen mother cells (PMCs) before meiotic cell division. Genetic analysis suggested that the male-sterile phenotype is attributed to one recessive locus. Transcriptome comparison between anthers of sterile and fertile plants in a segregated population identified a transcript that was expressed only in pollen-fertile plants, which is homologous to TDF1 (DEFECTIVE in TAPETAL DEVELOPMENT and FUNCTION1) in Arabidopsis, a gene encoding a transcription factor AtMYB35 that is known as a key regulator of pollen development. Since tdf1 mutant shows male sterility, we assumed that the absence transcript of the TDF1-like gene, named as LflTDF1, is the reason for pollen sterility observed in the mutant. A 30 kbp-long nanopore sequence read containing LflTDF1 was obtained from a pollen-fertile accession. PCR analyses using primers designed from the sequence suggested that at least a 30kbp-long region containing LflTDF1 was deleted or replaced by unknown sequence in the pollen-sterile mutant. Since the cross between L. × formolongi and Easter lily (L. longiflorum) is compatible, we successfully introgressed the male-sterile allele, designated as lfltdf1, to Easter lily. To our knowledge, this is the first report of molecular identification of a pollen-sterile candidate gene in lily. The identification and marker development of LflTDF1 gene will assist pollen-free lily breeding of Easter lilies and other lilies.

Long-distance translocation of CLAVATA3/ESR-related 2 peptide and its positive effect on roots sucrose status.

In vascular plants, roots anchor themselves into the soil and take up water and nutrients to provide them to the shoots. Therefore, continuous growth and development of the roots are important for plant life. To achieve this, photosynthesizing leaves must be able to supply sufficient photoassimilates to the roots. However, the mechanisms by which plants maintain carbon levels in roots remain elusive. Here, we focused on the Arabidopsis (Arabidopsis thaliana) CLAVATA3/ESR-related 2 (CLE2) peptide, which was detected in Arabidopsis xylem exudate, and its homologs. CLE2 and CLE3 genes responded to carbon-deficient conditions. Loss- and gain-of-function mutant analyses showed that CLE genes positively affected root sucrose level. Mutations in the CLE genes resulted in a high shoot/root ratio under sucrose-free conditions. Grafting experiments demonstrated the systemic effect of CLE peptide genes. These findings provide insights into the molecular basis for the relationship between roots and leaves in maintenance of the root sucrose levels and growth.

Characterization of Oligopeptides in Solanum lycopersicum Xylem Exudates.

The xylem is the main pathway for the transport of water and molecules from roots to shoots. To date, it has been reported that secreted oligopeptides mediate root-to-shoot signaling, and some long-distance mobile oligopeptides have been detected in xylem exudates. However, the conservation of a number of oligopeptides and the overall features of peptide fragments contained in xylem exudates are poorly understood. Here, we conducted a comprehensive analysis of small proteins and peptides in tomato (Solanum lycopersicum) xylem exudates and characterized the identified peptide fragments. We found that putative secreted proteins were enriched in xylem exudates compared with all proteins in the tomato protein database. We identified seven oligopeptides that showed common features of bioactive oligopeptides, including homologs of CLV3/ESR-related (CLE), C-TERMINALLY ENCODED PEPTIDE (CEP), and CASPARIAN STRIP INTEGRITY FACTOR (CIF) peptides. Furthermore, five of the identified oligopeptides were homologs of the soybean xylem exudate-associated oligopeptides that we previously reported. Our results suggest that oligopeptides in xylem exudates are conserved across plant species and provide insights into not only root-to-shoot signaling but also the maintenance of the xylem conduit.

Regulation of ammonium acquisition and use in Oryza longistaminata ramets under nitrogen source heterogeneity.

Oryza longistaminata, a wild rice, vegetatively reproduces and forms a networked clonal colony consisting of ramets connected by rhizomes. Although water, nutrients, and other molecules can be transferred between ramets via the rhizomes, inter-ramet communication in response to spatially heterogeneous nitrogen availability is not well understood. We studied the response of ramet pairs to heterogeneous nitrogen availability using a split hydroponic system that allowed each ramet root to be exposed to different conditions. Ammonium uptake was compensatively enhanced in the sufficient-side root when roots of the ramet pairs were exposed to ammonium-sufficient and ammonium-deficient conditions. Comparative transcriptome analysis revealed that a gene regulatory network for effective ammonium assimilation and amino acid biosynthesis was activated in the sufficient-side roots. Allocation of absorbed nitrogen from the nitrogen-sufficient to the nitrogen-deficient ramets was rather limited. Nitrogen was preferentially used for newly growing axillary buds on the sufficient-side ramets. Biosynthesis of trans-zeatin (tZ), a cytokinin, was upregulated in response to the nitrogen supply, but tZ appeared not to target the compensatory regulation. Our results also implied that the O. longistaminata putative ortholog of rice (Oryza sativa) C-terminally encoded peptide1 plays a role as a nitrogen-deficient signal in inter-ramet communication, providing compensatory upregulation of nitrogen assimilatory genes. These results provide insights into the molecular basis for efficient growth strategies of asexually proliferating plants growing in areas where the distribution of ammonium ions is spatially heterogeneous.

Chest compressions become deeper when pushing with forward lean: A simulation study.

AIM: Chest compression depth (CCD) in cardiopulmonary resuscitation is important. However, lightweight rescuers have difficulty achieving an appropriate depth. Chest compression force (CCFORCE) can be increased by placing the arms at 100° to the patient's frontal plane. In a simulation manikin study, we compared the CCD at 90° and 100° among lightweight Asian females and hypothesized that the CCD would be greater when the arms were placed at 100°. METHODS: We included 35 lightweight female students from Shimane University who performed compressions 30 times each at 90° and 100°. The CCFORCE and CCD and the residual force on the chest wall during decompression for each chest compression were compared using CPRmeter-2. RESULTS: Of the 35 participants, 3 were excluded because their angles deviated from the prescribed angle. Thirty-two participants were categorized according to CCD at 90°: ≤40 mm (group 1), 41-49 mm (group 2), and ≥ 50 mm (group 3). The overall mean CCD increased from 90° to 100° (44.3 ± 8.2 mm vs. 48.1 ± 7.2 mm; p < 0.05). The mean CCD changes between 90° and 100° were 34.4 ± 4.7 mm vs. 42.9 ± 4.8 mm (p < 0.05) in group 1, 44.9 ± 2.5 mm vs. 47.0 ± 4.2 mm (p = 0.17) in group 2, and 53.0 ± 2.7 mm vs. 55.4 ± 5.6 mm (p < 0.05) in group 3. The residual force was greater when the chest compression angle was 100°. CONCLUSION: CCD can be increased for lightweight rescuers when using a forward leaning position of 100° to the frontal plane of the patient. Further research is required to obtain more realistic situations.

Long-distance peptide signaling essential for nutrient homeostasis in plants.

Organ-to-organ communication is indispensable for higher organisms to maintain homeostasis over their entire life. Recent findings have uncovered that plants, like animals, mediate organ-to-organ communication by long-distance signaling through the vascular system. In particular, xylem-mobile secreted peptides have attracted much attention as root-to-shoot long-distance signaling molecules in response to fluctuating environmental nutrient status. Several leguminous CLE peptides induced by rhizobial inoculation act as 'satiety' signals in long-distance negative feedback of nodule formation. By contrast, Arabidopsis CEP family peptides induced by local nitrogen (N)-starvation behave as systemic 'hunger' signals to promote compensatory N acquisition in other parts of the roots. Xylem sap peptidomics also implies the presence of still uncharacterized long-distance signaling peptides. This review highlights the current understanding of and new insights into the mechanisms and functions of root-to-shoot long-distance peptide signaling during environmental responses.

A comprehensive strategy for identifying long-distance mobile peptides in xylem sap.

There is a growing awareness that secreted pemediate organ-to-organ communication in higher plants. Xylem sap peptidomics is an effective but challenging approach for identifying long-distance mobile peptides. In this study we developed a simple, gel-free purification system that combines o-chlorophenol extraction with HPLC separation. Using this system, we successfully identified seven oligopeptides from soybean xylem sap exudate that had one or more post-transcriptional modifications: glycosylation, sulfation and/or hydroxylation. RNA sequencing and quantitative PCR analyses showed that the peptide-encoding genes are expressed in multiple tissues. We further analyzed the long-distance translocation of four of the seven peptides using gene-encoding peptides with single amino acid substitutions, and identified these four peptides as potential root-to-shoot mobile oligopeptides. Promoter-GUS analysis showed that all four peptide-encoding genes were expressed in the inner tissues of the root endodermis. Moreover, we found that some of these peptide-encoding genes responded to biotic and/or abiotic factors. These results indicate that our purification system provides a comprehensive approach for effectively identifying endogenous small peptides and reinforce the concept that higher plants employ various peptides in root-to-shoot signaling.

Shoot HAR1 mediates nitrate inhibition of nodulation in Lotus japonicus.

Nitrate is a major environmental factor in the inhibition of nodulation. In a model legume Lotus japonicus, a CLV1-like receptor kinase, HAR1, mediates nitrate inhibition and autoregulation of nodulation. Autoregulation of nodulation involves root-to-shoot-to-root long-distance communication, and HAR1 functions in shoots. However, it remains elusive where HAR1 functions in the nitrate inhibition of nodulation. We performed grafting experiments with the har1 mutant under various nitrate conditions, and found that shoot HAR1 is critical for the inhibition of nodulation at 10 mM nitrate. Combined with our recent finding that the nitrate-induced CLE-RS2 glycopeptide binds directly to the HAR1 receptor, this result suggests that CLE-RS2/HAR1 long-distance signaling plays an important role in the both nitrate inhibition and the autoregulation of nodulation.

Dynamics of long-distance signaling via plant vascular tissues.

Plant vascular systems are constructed by specific cell wall modifications through which cells are highly specialized to make conduits for water and nutrients. Xylem vessels are formed by thickened cell walls that remain after programmed cell death, and serve as water conduits from the root to the shoot. In contrast, phloem tissues consist of a complex of living cells, including sieve tube elements and their neighboring companion cells, and translocate photosynthetic assimilates from mature leaves to developing young tissues. Intensive studies on the content of vascular flow fluids have unveiled that plant vascular tissues transport various types of gene product, and the transport of some provides the molecular basis for the long-distance communications. Analysis of xylem sap has demonstrated the presence of proteins in the xylem transpiration stream. Recent studies have revealed that CLE and CEP peptides secreted in the roots are transported to above ground via the xylem in response to plant-microbe interaction and soil nitrogen starvation, respectively. Their leucine-rich repeat transmembrane receptors localized in the shoot phloem are required for relaying the signal from the shoot to the root. These findings well-fit to the current scenario of root-to-shoot-to-root feedback signaling, where peptide transport achieves the root-to-shoot signaling, the first half of the signaling process. Meanwhile, it is now well-evidenced that proteins and a range of RNAs are transported via the phloem translocation system, and some of those can exert their physiological functions at their destinations, including roots. Thus, plant vascular systems may serve not only as conduits for the translocation of essential substances but also as long-distance communication pathways that allow plants to adapt to changes in internal and external environments at the whole plant level.

Root-derived CLE glycopeptides control nodulation by direct binding to HAR1 receptor kinase.

Leguminous plants establish a symbiosis with rhizobia to enable nitrogen fixation in root nodules under the control of the presumed root-to-shoot-to-root negative feedback called autoregulation of nodulation. In Lotus japonicus, autoregulation is mediated by CLE-RS genes that are specifically expressed in the root, and the receptor kinase HAR1 that functions in the shoot. However, the mature functional structures of CLE-RS gene products and the molecular nature of CLE-RS/HAR1 signalling governed by these spatially distant components remain elusive. Here we show that CLE-RS2 is a post-translationally arabinosylated glycopeptide derived from the CLE domain. Chemically synthesized CLE-RS glycopeptides cause significant suppression of nodulation and directly bind to HAR1 in an arabinose-chain and sequence-dependent manner. In addition, CLE-RS2 glycopeptide specifically produced in the root is found in xylem sap collected from the shoot. We propose that CLE-RS glycopeptides are the long sought mobile signals responsible for the initial step of autoregulation of nodulation.

Too much love, a novel Kelch repeat-containing F-box protein, functions in the long-distance regulation of the legume-Rhizobium symbiosis.

The interaction of legumes with N2-fixing bacteria collectively called rhizobia results in root nodule development. The number of nodules formed is tightly restricted through the systemic negative feedback control by the host called autoregulation of nodulation (AON). Here, we report the characterization and gene identification of TOO MUCH LOVE (TML), a root factor that acts during AON in a model legume Lotus japonicus. In our genetic analyses using another root-regulated hypernodulation mutant, plenty, the tml-1 plenty double mutant showed additive effects on the nodule number, whereas the tml-1 har1-7 double mutant did not, suggesting that TML and PLENTY act in different genetic pathways and that TML and HAR1 act in the same genetic pathway. The systemic suppression of nodule formation by CLE-RS1/RS2 overexpression was not observed in the tml mutant background, indicating that TML acts downstream of CLE-RS1/RS2. The tml-1 Snf2 double mutant developed an excessive number of spontaneous nodules, indicating that TML inhibits nodule organogenesis. Together with the determination of the deleted regions in tml-1/-2/-3, the fine mapping of tml-4 and the next-generation sequencing analysis, we identified a nonsense mutation in the Kelch repeat-containing F-box protein. As the gene knockdown of the candidate drastically increased the number of nodules, we concluded that it should be the causative gene. An expression analysis revealed that TML is a root-specific gene. In addition, the activity of ProTML-GUS was constitutively detected in the root tip and in the nodules/nodule primordia upon rhizobial infection. In conclusion, TML is a root factor acting at the final stage of AON.

Use of organic solvents in large research institutions in Japan.

OBJECTIVES: Laboratories in research institutions use organic solvents in research and development. Nevertheless, the types of solvents in use have been seldom reported. This study was initiated to elucidate types of organic solvents used in large research institutions in Japan, with a focus on possible different use among research fields. METHODS: In 2010-2011, 4517 laboratories in seven large research institutions were visited. In accordance with legal stipulations, air in each laboratory was collected in polyvinyl fluoride bags and analyzed by direct injection into a gas-chromatograph for 47 types of organic solvents. In evaluation, the laboratories were grouped by 5 research fields, i.e., agriculture, biology, medicine, natural science, and technology and engineering. RESULTS: Types of organic solvents commonly used in research activities were not diverse. Those commonly used were chloroform and 1,2-dichloroethane out of 7 Group 1 organic solvents (with high toxicities); 6 organic solvents, i.e., acetone and methyl alcohol in general, ethyl acetate, hexane and toluene in technology and engineering laboratories; and xylenes in medical fields out of 40 Group 2 organic solvents (with relatively low toxicities). Judging from solvent vapor concentrations, work environments in more than 99 % of laboratories were considered adequate. Nevertheless, use of chloroform in high-performance liquid chromatography (HPLC) resulted in inadequate environments in 30 laboratories (0.7 %). CONCLUSIONS: Organic solvents commonly used were not very diverse. Work environments in research laboratories were generally good, but the environment with use of chloroform in HPLC analysis remained yet to be improved.

Organic solvent use in enterprises in Japan.

This study was initiated to elucidate possible changes in types of organic solvents (to be called solvents in short) used in enterprises in Japan through comparison of current solvent types with historical data since 1983. To investigate current situation in solvent use in enterprises, surveys were conducted during one year of 2009 to 2010. In total, workroom air samples in 1,497 unit workplaces with solvent use were analyzed in accordance with regulatory requirements. Typical use pattern of solvents was as mixtures, accounting for >70% of cases. Adhesives spreading (followed by adhesion) was relatively common in small-scale enterprises, whereas printing and painting work was more common in middle-scale ones, and solvent use for testing and research purpose was basically in large-scaled enterprises. Through-out printing, painting, surface coating and adhesive application, toluene was most common (being detected in 49 to 82% of workplaces depending on work types), whereas isopropyl alcohol was most common (49%) in degreasing, cleaning and wiping workplaces. Other commonly used solvents were methyl alcohol, ethyl acetate and acetone (33 to 37%). Comparison with historical data in Japan and literature-retrieved data outside of Japan all agreed with the observation that toluene is the most commonly used solvent. Application of trichloroethylene and 1,1,1-trichloroethane, once common in 1980s, has ceased to exist in recent years.

Organic solvent use in research institutions in Japan.

In 2008-2009, types of organic solvents used and air-borne vapor concentrations were surveyed in 1909 laboratories in four large research institutions in accordance with current regulations. The results were classified into 5 groups in terms of research fields (agriculture, biology, medicine, natural science, and technology and engineering) and evaluated after the regulatory rules. Laboratory air analyses by gas chromatography identified 5 and 20 solvents out of 7 Group 1 solvents and 40 Group 2 solvents, respectively; 10 solvents were used in more than 10% of the laboratories in each of the 5 research fields. The use of unmixed single solvent appeared to be unique in research laboratories in contrast to use of solvent mixtures in industrial facilities for production. Laboratories of technology and engineering fields used more various organic solvents more frequently, whereas use of xylenes appeared to be more specific to laboratories of bio-medical fields. Among the commonly used solvents, chloroform was the leading solvent to induce poorer results in regulatory classification (i.e., Class 3 in Administrative Control Classes) typically when applied in high pressure liquid chromatography which was too voluminous to be accommodated in a local exhaustion chamber.

Expression and functional analysis of a CLV3-like gene in the model legume Lotus japonicus.

Plant aerial parts are differentiated from stem cells that are located in the shoot apical meristem (SAM). CLAVATA3 (CLV3)-CLV1 is a well-known ligand-receptor pair, which functions in SAM maintenance. In Lotus japonicus, HYPERNODULATION ABERRANT ROOT FORMATION1 (HAR1) shows the highest similarity with CLV1 of all Arabidopsis receptor-like kinases (RLKs). However, HAR1 functions in the systemic regulation of root nodule development, but does not appear to function in SAM maintenance. Therefore, the gene that is responsible for SAM maintenance in L. japonicus is largely unknown. Here, we identified the L. japonicus CLV3-like (LjCLV3) gene as a counterpart of AtCLV3 and performed expression and functional analysis. LjCLV3 transcripts were detected in the central region of the shoot meristems. However, unlike AtCLV3, LjCLV3 expression was not detected in the epidermal layer, but in the inner layers of the shoot meristems. RNA interference (RNAi) of LjCLV3 caused enlargement of not only the SAM, but also the primary and secondary inflorescence meristems (IMs). Furthermore, LjCLV3-silenced plants exhibited fasciated stems and an increased number of flowers per peduncle. These results reveal that LjCLV3 is responsible for the maintenance of the SAM as well as the primary and secondary IMs.

The Clavata2 genes of pea and Lotus japonicus affect autoregulation of nodulation.

The number of root nodules developing on legume roots after rhizobial infection is controlled by the plant shoot through autoregulation and mutational inactivation of this mechanism leads to hypernodulation. We have characterised the Pisum sativum (pea) Sym28 locus involved in autoregulation and shown that it encodes a protein similar to the Arabidopsis CLAVATA2 (CLV2) protein. Inactivation of the PsClv2 gene in four independent sym28 mutant alleles, carrying premature stop codons, results in hypernodulation of the root and changes to the shoot architecture. In the reproductive phase sym28 shoots develops additional flowers, the stem fasciates, and the normal phyllotaxis is perturbed. Mutational substitution of an amino acid in one leucine rich repeat of the corresponding Lotus japonicus LjCLV2 protein results in increased nodulation. Similarly, down-regulation of the Lotus Clv2 gene by RNAi mediated reduction of the transcript level also resulted in increased nodulation. Gene expression analysis of LjClv2 and Lotus hypernodulation aberrant root formation Har1 (previously shown to regulate nodule numbers) indicated they have overlapping organ expression patterns. However, we were unable to demonstrate a direct protein-protein interaction between LjCLV2 and LjHAR1 proteins in contrast to the situation between equivalent proteins in Arabidopsis. LjHAR1 was localised to the plasma membrane using a YFP fusion whereas LjCLV2-YFP localised to the endoplasmic reticulum when transiently expressed in Nicotiana benthamiana leaves. This finding is the most likely explanation for the lack of interaction between these two proteins.