Lateral Root Formation In Response Research Articles

Early lateral root formation in response to calcium and nickel shows variation within disjunct populations of Arabidopsis lyrata spp. lyrata

Root architecture is important in nutrient uptake and avoidance of toxic compounds within the soil. Arabidopsis lyrata spp. lyrata has widespread distribution in disjunct environments that encounter unique stressors starting at germination. Five populations of A. lyrata spp. lyrata show local adaptation to Nickel (Ni) but cross-tolerance to variations in Calcium (Ca) concentration within the soil. Differentiation among the populations begins early in development and appears to impact timing of lateral root formation; therefore the purpose of the study was to understand changes in root architecture and root exploration in response to Ca and Ni within the first three weeks of growth. Lateral root formation was first characterized under one concentration of Ca and Ni. Lateral root formation and tap root length were reduced in all five populations in response to Ni compared to Ca, with the least reduction in the three serpentine populations. When the populations were exposed to a gradient (either Ca or Ni) there were differences in population response based on the nature of the gradient. Start side was the greatest determinant of root exploration and lateral root formation under a Ca gradient, while population was the greatest determinant of root exploration and lateral root formation under a Ni gradient. All populations exhibited about the same frequency of root exploration under a Ca gradient, while the serpentine populations exhibited much higher levels of root exploration under a Ni gradient compared to the two non-serpentine populations. Differences among populations in response to Ca and Ni demonstrate the importance of stress responses early in development, particularly in species that have widespread distribution among disparate habitats.

Transcriptomic and metabolomic analyses reveal that melatonin promotes melon root development under copper stress by inhibiting jasmonic acid biosynthesis

Melatonin has been shown to alleviate the effects of abiotic stress and to regulate plant development. Copper, a common heavy metal and soil pollutant, can suppress plant growth and development. In this work, we explored the protective effects of exogenous melatonin on lateral root formation in response to copper stress using melon seeds subjected to three germination treatments: CK1 (control), CK2 (300 μmol/L CuSO4), and MT3 (300 μmol/L melatonin + 300 μmol/L CuSO4). Melatonin pretreatment increased the antioxidant enzyme activities and root vigor, and decreased the proline and malondialdehyde (MDA) contents in the roots of copper-stressed melon seedlings. We then used transcriptomic and metabolomic analyses to explore the mechanisms by which exogenous melatonin protects against copper stress. There were 70 significant differentially expressed genes (DEGs) (28 upregulated, 42 downregulated) and 318 significantly differentially expressed metabolites (DEMs) (168 upregulated, 150 downregulated) between the MT3 and CK2 treatments. Melatonin pretreatment altered the expression of genes related to redox and cell wall formation processes. In addition, we found that members of the AP2/ERF, BBR/BPC, GRAS, and HD-ZIP transcription factor families may have vital roles in lateral root development. Melatonin also increased the level of Glutathione (GSH), which chelates excess Cu2+. The combined transcriptomic and metabolomic analysis revealed DEGs and DEMs involved in jasmonic acid (JA) biosynthesis, including four lipoxygenase-related genes and two metabolites (linoleic acid and lecithin) related to melatonin’s alleviation effect on copper toxicity. This research elucidated the molecular mechanisms of melatonin’s protective effects in copper-stressed melon.

Rhizotaxis Modulation in Arabidopsis Is Induced by Diffusible Compounds Produced during the Cocultivation of Arabidopsis and the Endophytic Fungus Serendipita indica.

Rhizotaxis is established under changing environmental conditions via periodic priming of lateral root (LR) initiation at the root tips and adaptive LR formation along the primary root (PR). In contrast to the adaptable LR formation in response to nutrient availability, there is little information on root development during interactions with beneficial microbes. The Arabidopsis root system is characteristically modified upon colonization by the root endophytic fungus Serendipita indica, accompanied by a marked stimulation of LR formation and the inhibition of PR growth. This root system modification has been attributed to endophyte-derived indole-3-acetic acid (IAA). However, it has yet to be clearly explained how fungal IAA affects the intrinsic LR formation process. In this study, we show that diffusible compounds (chemical signals) other than IAA are present in the coculture medium of Arabidopsis and S. indica and induce auxin-responsive DR5::GUS expression in specific sections within the pericycle layer. The DR5::GUS expression was independent of polar auxin transport and the major IAA biosynthetic pathways, implicating unidentified mechanisms responsible for the auxin response and LR formation. Detailed metabolite analysis revealed the presence of multiple compounds that induce local auxin responses and LR formation. We found that benzoic acid (BA) cooperatively acted with exogenous IAA to generate a local auxin response in the pericycle layer, suggesting that BA is one of the chemical signals involved in adaptable LR formation. Identification and characterization of the chemical signals will contribute to a greater understanding of the molecular mechanisms underlying adaptable root development and to unconventional technologies for sustainable agriculture.

Hydrogen peroxide is involved in methane-induced tomato lateral root formation.

Pharmacological and molecular evidence reveals a novel role of methane (CH4) gas in root organogenesis, the induction of lateral root (LR) formation, and this response might require hydrogen peroxide (H2O2) synthesis. Although plants can produce CH4 and release this to atmosphere, the beneficial role(s) of CH4 are not fully elucidated. In this study, the fumigation with CH4 not only increased NADPH oxidase activity and H2O2 production, but also induced tomato lateral root primordial formation and thereafter LR development. However, exogenously applied argon and nitrogen failed to influence LR formation. Above responses triggered by CH4 were sensitive to the removal of endogenous H2O2 with dimethylthiourea (DMTU; a membrane-permeable scavenger of H2O2), suggesting the hypothesis that CH4's effect on LR formation could be mediated by endogenous H2O2. Diphenylene iodonium (DPI) inhibition of the H2O2 generating enzyme NADPH oxidase attenuated H2O2 synthesis and impaired LR formation in response to CH4, confirming the requirement of NADPH oxidase-dependent H2O2. Meanwhile, the alterations of endogenous H2O2 concentrations failed to influence CH4 production in tomato seedlings. Molecular evidence revealed that CH4-induced SlCDKA1, SlCYCA2;1, and SlCYCA3;1 transcripts, and -decreased SlKRP2 mRNA were impaired by DMTU or DPI. Contrasting changes in LR formation-related miR390a and miR160 transcripts and their target genes, including SlARF4 and SlARF16, were observed. Together, our pharmacological and molecular evidence suggested the requirement of H2O2 synthesis in CH4-triggered tomato LR formation, partially via the regulation of cell cycle regulatory genes, miRNA-, and tasiRNA-modulated gene expression.

The ARF7 and ARF19 Transcription Factors Positively Regulate PHOSPHATE STARVATION RESPONSE1 in Arabidopsis Roots.

PHOSPHATE STARVATION RESPONSE1 (PHR1) is a key regulatory component of the response to phosphate (Pi) starvation. However, the regulation of PHR1 in this response remains poorly understood. Here, we report that PHR1 is a target of the transcription factors AUXIN RESPONSE FACTOR7 (ARF7) and ARF19 and is positively regulated by auxin signaling in Arabidopsis (Arabidopsis thaliana) roots. PHR1 expression was induced by exogenous auxin and suppressed by auxin transport inhibitors in Arabidopsis roots. In the PHR1 promoter, three auxin-response elements, which are bound directly by ARF7 and ARF19, were shown to be essential for PHR1 expression. The arf7, arf19, and arf7 arf19 mutants showed down-regulated expression of PHR1 and downstream Pi starvation-induced genes in roots; they also exhibited defective Pi uptake in roots and overaccumulation of anthocyanin in shoots. The induction of lateral root formation in response to low Pi and to exogenous auxin was decreased in the phr1 mutant, whereas the expression of LATERAL ORGAN BOUNDARIES-DOMAIN16 (LBD16) and LBD29 was not changed significantly. PHR1 acted independently of LBD16 and LBD29 in the regulation of lateral root formation in response to low Pi. Under low-Pi conditions, lateral root impairment in the arf7 arf19 mutant was partially rescued by constitutive expression of PHR1, demonstrating that reduced PHR1 expression contributed to the arf7 arf19 phenotype. In addition to PHR1, other genes encoding MYB-CC members also were targets of ARF7 and ARF19. Our work thus reveals a mechanism coordinating auxin signaling and the PHR1 regulon in Arabidopsis responses to Pi deficiency.

Genetic Control of Lateral Root Formation in Cereals.

Cereals form complex root systems composed of different root types. Lateral root formation is a major determinant of root architecture and is instrumental for the efficient uptake of water and nutrients. Positioning and patterning of lateral roots and cell types involved in their formation are unique in monocot cereals. Recent discoveries advanced the molecular understanding of the intrinsic genetic control of initiation and elongation of lateral roots in cereals by distinct, in part root-type-specific genetic programs. Moreover, molecular networks modulating the plasticity of lateral root formation in response to water and nutrient availability and arbuscular mycorrhizal fungal colonization have been identified. These novel discoveries provide a better mechanistic understanding of postembryonic lateral root development in cereals.

Interaction between HY1 and H2O2 in auxin-induced lateral root formation in Arabidopsis

Haem oxygenase-1 (HO-1) and hydrogen peroxide (H2O2) are two key downstream signals of auxin, a well-known phytohormone regulating plant growth and development. However, the inter-relationship between HO-1 and H2O2 in auxin-mediated lateral root (LR) formation is poorly understood. Herein, we revealed that exogenous auxin, 1-naphthylacetic acid (NAA), could simultaneously stimulate Arabidopsis HO-1 (HY1) gene expression and H2O2 generation. Subsequently, LR formation was induced. NAA-induced HY1 expression is dependent on H2O2. This conclusion was supported by analyzing the removal of H2O2 with ascorbic acid (AsA) and dimethylthiourea (DMTU), both of which could block NAA-induced HY1 expression and LR formation. H2O2-induced LR formation was inhibited by an HO-1 inhibitor zinc protoporphyrin IX (Znpp) in wild-type and severely impaired in HY1 mutant hy1-100. Simultaneously, HY1 is required for NAA-mediated H2O2 generation, since Znpp inhibition of HY1 blocked the NAA-induced H2O2 production and LR formation. Genetic data demonstrated that hy1-100 was significantly impaired in H2O2 production and LR formation in response to NAA, compared with wild-type plants. The addition of carbon monoxide-releasing molecule-2 (CORM-2), the carbon monoxide (CO) donor, induced H2O2 production and LR formation, both of which were decreased by DMTU. Moreover, H2O2 and CORM-2 mimicked the NAA responses in the regulation of cell cycle genes expression, all of which were blocked by Znpp or DMTU, respectively, confirming that both H2O2 and CO were important in the early LR initiation. In summary, our pharmacological, genetic and molecular evidence demonstrated a close inter-relationship between HY1 and H2O2 existing in auxin-induced LR formation in Arabidopsis.

The RNA‐seq approach to discriminate gene expression profiles in response to melatonin on cucumber lateral root formation

Cucumber is a model cucurbitaceous plant with a known genome sequence which is important for studying molecular mechanisms of root development. In this study, RNA sequencing was employed to explore the mechanism of melatonin-induced lateral root formation in cucumber under salt stress. Three groups of seeds were examined, that is, seeds primed without melatonin (CK), seeds primed in a solution containing 10 or 500 μmol/L melatonin (M10 and M500, respectively). These seeds were then germinated in NaCl solution. The RNA-seq analysis generated 16,866,670 sequence reads aligned with 17,920 genes, which provided abundant data for the analysis of lateral root formation. A total of 17,552, 17,450, and 17,393 genes were identified from roots of the three treatments (CK, M10 and M500, respectively). The expression of 121 genes was significantly up-regulated, and 196 genes were significantly down-regulated in M500 which showed an obvious increase on the number of lateral roots. These genes were significantly enriched in 57 KEGG pathways and 16 GO terms (M500 versus CK). Based on their expression pattern, peroxidase-related genes were selected as the candidates to be involved in the melatonin response. Several transcription factor families might play important roles in lateral root formation processes. A number of genes related to cell wall formation, carbohydrate metabolic processes, oxidation/reduction processes, and catalytic activity also showed different expression patterns as a result of melatonin treatments. This RNA-sequencing study will enable the scientific community to better define the molecular processes that affect lateral root formation in response to melatonin treatment.

Auxin distribution is differentially affected by nitrate in roots of two rice cultivars differing in responsiveness to nitrogen

Although ammonium (NH4(+)) is the preferred form of nitrogen over nitrate (NO3(-)) for rice (Oryza sativa), lateral root (LR) growth in roots is enhanced by partial NO3(-) nutrition (PNN). The roles of auxin distribution and polar transport in LR formation in response to localized NO3(-) availability are not known. Time-course studies in a split-root experimental system were used to investigate LR development patterns, auxin distribution, polar auxin transport and expression of auxin transporter genes in LR zones in response to localized PNN in 'Nanguang' and 'Elio' rice cultivars, which show high and low responsiveness to NO3(-), respectively. Patterns of auxin distribution and the effects of polar auxin transport inhibitors were also examined in DR5::GUS transgenic plants. Initiation of LRs was enhanced by PNN after 7 d cultivation in 'Nanguang' but not in 'Elio'. Auxin concentration in the roots of 'Nanguang' increased by approx. 24 % after 5 d cultivation with PNN compared with NH4(+) as the sole nitrogen source, but no difference was observed in 'Elio'. More auxin flux into the LR zone in 'Nanguang' roots was observed in response to NO3(-) compared with NH4(+) treatment. A greater number of auxin influx and efflux transporter genes showed increased expression in the LR zone in response to PNN in 'Nanguang' than in 'Elio'. The results indicate that higher NO3(-) responsiveness is associated with greater auxin accumulation in the LR zone and is strongly related to a higher rate of LR initiation in the cultivar 'Nanguang'.

Genetic screening and analysis of <I>suppressors of asa1-1</I> (soa) defective in jasmonate-mediated lateral root formation in <I>Arabidopsis</I>

It has been shown that jasmonate modulates the lateral root development through crosstalk with auxin in Arabidopsis thaliana. Exogenous application of jasmonate stimulates lateral root formation in wild type but inhibits lateral root formation in asa1-1. Our previous work has demonstrated that the lateral root formation defect of asa1-1 is co-related with jasmonte effect on PIN2 protein levels. To further elucidate the molecular mechanisms underlying jasmonate-mediated reduction of plasma membrane (PM)-resident PIN2 abundance, we have conducted a genetic screen to identify suppressors of asa1-1 (soa), which showed lateral root formation in the presence of jasmonate. Here, we described the basic characterization of soa563 and soa856. We showed that both soa563 and soa856 displayed restored lateral root formation in response to exogenous jasmonate. In addition, jasmonate-induced PIN2:GFP reduction was blocked in these two mutants. Our on-going effort to identify genes defined by these mutants promise to shed new light on the understanding of the molecular mechanisms controlling jasmonate-mediated regulation of PIN2 protein trafficking and turnover.

Characterization of drr1, an alkamide-resistant mutant of Arabidopsis, reveals an important role for small lipid amides in lateral root development and plant senescence.

Alkamides belong to a class of small lipid signals of wide distribution in plants, which are structurally related to the bacterial quorum-sensing signals N-acyl-l-homoserine lactones. Arabidopsis (Arabidopsis thaliana) seedlings display a number of root developmental responses to alkamides, including primary root growth inhibition and greater formation of lateral roots. To gain insight into the regulatory mechanisms by which these compounds alter plant development, we performed a mutant screen for identifying Arabidopsis mutants that fail to inhibit primary root growth when grown under a high concentration of N-isobutyl decanamide. A recessive N-isobutyl decanamide-resistant mutant (decanamide resistant root [drr1]) was isolated because of its continued primary root growth and reduced lateral root formation in response to this alkamide. Detailed characterization of lateral root primordia development in the wild type and drr1 mutants revealed that DRR1 is required at an early stage of pericycle cell activation to form lateral root primordia in response to both N-isobutyl decanamide and N-decanoyl-l-homoserine lactone, a highly active bacterial quorum-sensing signal. Exogenously supplied auxin similarly inhibited primary root growth and promoted lateral root formation in wild-type and drr1 seedlings, suggesting that alkamides and auxin act by different mechanisms to alter root system architecture. When grown both in vitro and in soil, drr1 mutants showed dramatically increased longevity and reduced hormone- and age-dependent senescence, which were related to reduced lateral root formation when exposed to stimulatory concentrations of jasmonic acid. Taken together, our results provide genetic evidence indicating that alkamides and N-acyl-l-homoserine lactones can be perceived by plants to modulate root architecture and senescence-related processes possibly by interacting with jasmonic acid signaling.

Response of root branching to abscisic acid is correlated with nodule formation both in legumes and nonlegumes

Legumes are unique among higher plants in forming a symbiosis with Rhizobium. Phylogenetic studies indicate this symbiosis may have evolved as many as three times within the Fabaceae; alternatively, a predisposition for nodulation evolved early in the history of the legume lineage. We have identified a physiological trait-increased lateral root formation in response to abscisic acid (ABA)- that marks all nodulating and non-nodulating legume species in our study set with the exception of Chamaecrista fasciculata and Cercis occidentalis. In contrast, nonlegume species tested decrease lateral root formation in response to ABA. Cercis is not a descendant of any common ancestor hypothesized to have evolved Rhizobium nodulation and has an intermediate response to ABA, partway between that of nonlegumes and legumes. We suggest that acquisition of altered responsiveness of roots to ABA is coincident with the appearance of a predisposition for nodulation within the legumes, followed by a loss in Chamaecrista. In addition, we demonstrate that altered ABA responsiveness of lateral root formation characterizes roots of the actinorhizal nodulator, Casuarina glauca, but not the closely related, nonactinorhizal species, Betula papyrifera. Thus our data provide evidence for a physiological root trait associated with nodulation both in legumes and in an actinorhizal plant.

Protein Geranylgeranyltransferase I Is Involved in Specific Aspects of Abscisic Acid and Auxin Signaling in Arabidopsis

Arabidopsis (Arabidopsis thaliana) mutants lacking a functional ERA1 gene, which encodes the beta-subunit of protein farnesyltransferase (PFT), exhibit pleiotropic effects that establish roles for protein prenylation in abscisic acid (ABA) signaling and meristem development. Here, we report the effects of T-DNA insertion mutations in the Arabidopsis GGB gene, which encodes the beta-subunit of protein geranylgeranyltransferase type I (PGGT I). Stomatal apertures of ggb plants were smaller than those of wild-type plants at all concentrations of ABA tested, suggesting that PGGT I negatively regulates ABA signaling in guard cells. However, germination of ggb seeds in response to ABA was similar to the wild type. Lateral root formation in response to exogenous auxin was increased in ggb seedlings compared to the wild type, but no change in auxin inhibition of primary root growth was observed, suggesting that PGGT I is specifically involved in negative regulation of auxin-induced lateral root initiation. Unlike era1 mutants, ggb mutants exhibited no obvious developmental phenotypes. However, era1 ggb double mutants exhibited more severe developmental phenotypes than era1 mutants and were indistinguishable from plp mutants lacking the shared alpha-subunit of PFT and PGGT I. Furthermore, overexpression of GGB in transgenic era1 plants partially suppressed the era1 phenotype, suggesting that the relatively weak phenotype of era1 plants is due to partial redundancy between PFT and PGGT I. These results are discussed in the context of Arabidopsis proteins that are putative substrates of PGGT I.

Nodulation ofPhaseolus vulgarisbyRhizobium etliis enhanced by the presence ofBacillus

The ability of Bacillus spp. to alter the nodulation of Phaseolus vulgaris by Rhizobium etli was assessed. The simultaneous presence of both Rhizobium etli TAL 182 and Bacillus megaterium S49 on plant roots during the early stages of plant growth was necessary for enhanced nodulation of Phaseolus vulgaris by the Rhizobium microsymbiont. Coinoculation with both bacterial species also facilitated heterologous nodulation of Rhizobium TAL 182 on Phaseolus acutifolius. These results are consistent with earlier reports of increased root hair proliferation and lateral root formation in response to coinoculation. Split-root experiments revealed that coinoculation partially suppressed host-controlled regulation of nodulation, implicating a plant interaction with the two bacterial species. Changes to the nodulation potential of R. etli due to coinoculation with Bacillus spp. demonstrate the potential for root-associated organisms other than rhizobia to alter the dynamics of the legume–Rhizobium symbiosis.Key words: Bacillus, nodulation enhancement, heterologous nodulation.