Identification and function of miRNA-mRNA interaction pairs during lateral root development of hemi-parasitic Santalum album L. seedlings

Sandalwood (Santalum album L.) is a hemi-parasitic tree species famous for its santalol and santalene, which are extracted from its heartwood and roots. The ability to understand root functionality within its branched root system would benefit the regulation of sandalwood growth and enhance the commercial value of sandalwood. Phenotypic and anatomical evidence in this study indicated that seed germination stage 4 (SG4) seemed pivotal for lateral root (LR) morphogenesis. Small RNA (sRNA) high-throughput sequencing of root tissues at three sub-stages of SG4 (lateral root primordia initiation (LRPI), lateral root primordia development (LRPD), and lateral root primordia emergence (LRPE)) was performed to identify microRNAs (miRNAs) associated with LR development. A total of 135 miRNAs, including 70 differentially expressed miRNAs (DEMs), were screened. Ten DEMs were selected to investigate transcript abundance in different organs or developmental stages. Among 100 negative DEM-mRNA interaction pairs, four targets (Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8) were selected for studying cleavage sites by 5' RLM-RACE validation. The expression mode of the four miRNA-mRNA pairs was investigated after indole-3-acetic acid (IAA) treatment. IAA enhanced the abundance of homeobox-leucine-zipper protein 32 (HOX32), laccase 12 (LAC12), myeloblastosis86 (MYB86), and pectin methylesterase inhibitor6 (PMEI6) target transcripts by reducing the expression of Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8 in the first 10 min. A schematic model of miRNA-regulated LR development is proposed for this hemi-parasitic species. This novel genetic information for improving sandalwood root growth and development may allow for the cultivation of fast-growing and high-yielding plantations.

OsAMT1;1 and OsAMT1;2 Coordinate Root Morphological and Physiological Responses to Ammonium for Efficient Nitrogen Foraging in Rice

Optimal plant growth and development rely on morphological and physiological adaptions of the root system to forage heterogeneously distributed nitrogen (N) in soils. Rice grows mainly in the paddy soil where ammonium (NH4+) is present as the major N source. Although root NH4+ foraging behaviors are expected to be agronomically relevant, the underlying mechanism remains largely unknown. Here, we showed that NH4+ supply transiently enhanced the high-affinity NH4+ uptake and stimulated lateral root (LR) branching and elongation. These synergistic physiological and morphological responses were closely related to NH4+-induced expression of NH4+ transporters OsAMT1;1 and OsAMT1;2 in roots. The two independent double mutants (dko) defective in OsAMT1;1 and OsAMT1;2 failed to induce NH4+ uptake and stimulate LR formation, suggesting that OsAMT1s conferred the substrate-dependent root NH4+ foraging. In dko plants, NH4+ was unable to activate the expression of OsPIN2, and the OsPIN2 mutant (lra1) exhibited a strong reduction in NH4+-triggered LR branching, suggesting that the auxin pathway was likely involved in OsAMT1s-dependent LR branching. Importantly, OsAMT1s-dependent root NH4+ foraging behaviors facilitated rice growth and N acquisition under fluctuating NH4+ supply. These results revealed an essential role of OsAMT1s in synergizing root morphological and physiological processes, allowing for efficient root NH4+ foraging to optimize N capture under fluctuating N availabilities.

Glutathione produced by γ-glutamyl cysteine synthetase acts downstream of hydrogen to positively influence lateral root branching

Hydrogen gas (H₂) mediation of lateral root (LR) branching was previously described. However, related signaling pathway is largely unexplored. In this study, we discovered that application with H₂ using hydrogen-rich water, mimicking the responses of exogenous glutathione (GSH), not only enhanced GSH synthesis, but also induced tomato LR development. The changes in the transcripts of auxin signaling-related genes and cell cycle regulatory genes were matched with above phenotypes. The addition of H₂ could trigger higher transcript levels of SlGSH1 and SlGSH2, encoding γ-glutamylcysteine synthetase (γ-ECS) and glutathione synthetase (GS), confirming the stimulation of GSH synthesis. These responses were greatly abolished when the inhibitor of γ-ECS was applied. The inhibition in lateral root primordium development, especially in emergence stage, was also observed. Genetic evidence revealed that the defects in GSH production and lateral rooting in Arabidopsis cad2-1, a γ-ECS defective mutant, were obviously abolished in the presence of GSH compared to those in the presence of H₂. Further evidence revealed that mRNA levels of target genes elicited by H₂ in wild-type, were differentially impaired in mutant plants. Together, above data clearly demonstrated that γ-ECS-dependent GSH production might be closely associated with H₂ control of LR branching.

TDIF peptides regulate root growth by affecting auxin homeostasis and PINs expression in Arabidopsis thaliana

TDIF and TDIF-like peptides in excess simultaneously facilitate primary root elongation and lateral root formation through regulating auxin distribution and transport. Tracheary element differentiation inhibitory factor (TDIF) plays key roles in mediating cell-cell communication and stem cell maintenance during vascular development. Recently, TDIF has also been linked to lateral root (LR) organogenesis through Brassinosteroid Insensitive 2 (BIN2) action. In this work, by comparing the in vitro and in vivo activities of AtCLE41-encoded TDIF and one poplar-derived TDIF-like peptide in Arabidopsis thaliana, we demonstrated that both TDIFs promoted primary root (PR) growth and stimulated LR formation. Without affecting auxin biosynthesis and catabolism, TDIFs suppressed the auxin maxima at PR apex but intensified the auxin accumulation at LR initiation sites along the longitudinal axis of PR. TDIF did not alter root sensitivity to exogenous auxin and mutants with varied endogenous auxin levels responded to TDIF peptides in a wild-type manner but to a lesser extent. Intriguingly, TDIF specifically upregulated the transcript abundance of PINs and multiple pin mutants displayed insensitivity to TDIF, demonstrating that PIN-mediated polar auxin transport (PAT) is indispensably required for the TDIF-induced root phenotypes. Taken together, our results revealed that TDIF might target PAT via mobilizing auxin efflux carriers to dynamically regulate the auxin signaling output and hence facilitate PR growth and LR formation.

Methane-induced lateral root formation requires the participation of nitric oxide signaling

Although methane (CH₄)-induced lateral root (LR) formation has been discovered, the identification of downstream signaling compounds has yet to be fully elucidated. Here, we report a unique mechanism for the involvement of nitric oxide (NO) in the above CH₄-mediated pathway in tomato (Solanum lycopersicum L.) and Arabidopsis thaliana. NO was produced rapidly in the root tissues of tomato seedlings when CH₄ was administrated exogenously. The scavenging of NO with its scavengers prevented lateral root primordia formation and thereafter lateral rooting triggered by CH₄. Gene expression analysis revealed that similar to the responses of sodium nitroprusside (SNP; a NO-releasing compound), CH₄-induced SlCYCA2;1, SlCYCA3;1, and SlCDKA1 transcripts, and -downregulated SlKRP2 mRNA, were differentially abolished when endogenous NO was removed by its scavengers. Changes in the lateral root-related miRNA genes (SlmiR160 and SlmiR390a) and their target genes (SlARF16 and SlARF4), exhibited similar tendencies. Similar to those results in tomato, the addition of CH₄ and SNP could obviously induce NO production and LR formation in Arabidopsis seedlings, which were correlated with the transcriptional profiles of representative LR-related genes. Combine with these findings in tomato and Arabidopsis thaliana, our results showed that NO might act, at least partially, as the downstream signaling molecule for CH₄ control of lateral rooting.

Brachypodium distachyon tar2lhypo mutant shows reduced root developmental response to symbiotic signal but increased arbuscular mycorrhiza

Auxin is a major phytohormone that controls root development. A role for auxin is also emerging in the control of plant-microbe interactions, including for the establishment of root endosymbiosis between plants and arbuscular mycorrhizal fungi (AMF). Auxin perception is important both for root colonization by AMF and for arbuscule formation. AMF produce symbiotic signals called lipo-chitooligosaccharides (LCOs) that can modify auxin homeostasis and promote lateral root formation (LRF). Since Brachypodium distachyon (Brachypodium) has a different auxin sensitivity compared to other plant species, we wondered whether this would interfere with the effect of auxin in arbuscular mycorrhizal (AM) symbiosis. Here we tested whether tar2l^hypo a Brachypodium mutant with an increase in endogenous auxin content is affected in LRF stimulation by LCOs and in AM symbiosis. We found that, in contrast to control plants, LCO treatment inhibited LRF of the tar2l^hypo mutant. However, the level of AMF colonization and the abundance of arbuscules were increased in tar2l^hypo compared to control plants, suggesting that auxin also plays a positive role in both AMF colonization and arbuscule formation in Brachypodium.

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.

L-Cysteine desulfhydrase-dependent hydrogen sulfide is required for methane-induced lateral root formation

Methane-triggered lateral root formation is not only a universal event, but also dependent on L-cysteine desulfhydrase-dependent hydrogen sulfide signaling. Whether or how methane (CH₄) triggers lateral root (LR) formation has not been elucidated. In this report, CH₄ induction of lateral rooting and the role of hydrogen sulfide (H₂S) were dissected in tomato and Arabidopsis by using physiological, anatomical, molecular, and genetic approaches. First, we discovered that CH₄ induction of lateral rooting is a universal event. Exogenously applied CH₄ not only triggered tomato lateral rooting, but also increased activities of L-cysteine desulfhydrase (DES; a major synthetic enzyme of H₂S) and induced endogenous H₂S production, and contrasting responses were observed in the presence of hypotaurine (HT; a scavenger of H₂S) or DL-propargylglycine (PAG; an inhibitor of DES) alone. CH₄-triggered lateral rooting were sensitive to the inhibition of endogenous H₂S with HT or PAG. The changes in the transcripts of representative cell cycle regulatory genes, miRNA and its target genes were matched with above phenotypes. In the presence of CH₄, Arabidopsis mutant Atdes1 exhibited defects in lateral rooting, compared with the wild-type. Molecular evidence showed that the transcriptional profiles of representative target genes modulated by CH₄ in wild-type plants were impaired in Atdes1 mutant. Overall, our data demonstrate the main branch of the DES-dependent H₂S signaling cascade in CH₄-triggered LR formation.

Rice Inositol Polyphosphate Kinase (OsIPK2) Directly Interacts with OsIAA11 to Regulate Lateral Root Formation

The plant hormone auxin controls many aspects of plant growth and development by promoting the degradation of Auxin/Indole-3-acetic acid (Aux/IAA) proteins. The domain II (DII) of Aux/IAA proteins is sufficient for eliciting the degradation by directly interacting with the auxin receptor F-box protein TIR1 to form a TIR1/AFBs-Aux/IAA complex in an auxin-dependent manner. However, the underlying mechanisms of fine-tuning Aux/IAA degradation by auxin stimuli remain to be elucidated. Here, we show that OsIPK2, a rice (Oryza sativa) inositol polyphosphate kinase, directly interacts with an Aux/IAA protein OsIAA11 to repress its degradation. In a rice protoplast transient expression system, the auxin-induced degradation of Myc-OsIAA11 fusion was delayed by co-expressed GFP-OsIPK2 proteins. Furthermore, expressing additional OsIPK2 or its N-terminal amino acid sequence enhanced the accumulation of OsIAA11 proteins in transgenic plants, which in turn caused defects in lateral root formation and auxin response. Taken together, we identify a novel co-factor of Aux/IAA in auxin signaling and demonstrate its role in regulating lateral root development.

Hydrogen peroxide is involved in hydrogen sulfide-induced lateral root formation in tomato seedlings

BACKGROUND

Both hydrogen sulfide (H₂S) and hydrogen peroxide (H₂O₂) are separately regarded as a highly reactive molecule involved in root morphogenesis. In this report, corresponding causal link governing lateral root formation was investigated.

METHODS

By using pharmacological, anatomic, and molecular approaches, evidence presented here revealed the molecular mechanism underlying tomato lateral root development triggered by H₂S.

RESULTS

A H₂S donor sodium hydrosulfide (NaHS) triggered the accumulation of H₂O₂, the up-regulation of RBOH1 transcript, and thereafter tomato lateral root formation. Above responses were sensitive to the H₂O₂ scavenger (dimethylthiourea; DMTU) and the inhibitor of NADPH oxidase (diphenylene idonium; DPI), showing that the accumulations of H₂O₂ and increased RBOH1 transcript were respectively prevented. Lateral root primordial and lateral root formation were also impaired. Further molecular evidence revealed that H₂S-modulated gene expression of cell cycle regulatory genes, including up-regulation of SlCYCA2;1, SlCYCA3;1, and SlCDKA1, and the down-regulation of SlKRP2, were prevented by the co-treatment with DMTU or DPI. Above mentioned inducing phenotypes were consistent with the changes of lateral root formation-related microRNA transcripts: up-regulation of miR390a and miR160, and with the opposite tendencies of their target genes (encoding auxin response factors). Contrasting tendencies were observed when DMTU or DPI was added together. The occurrence of H₂S-mediated S-sulfhydration during above responses was preliminarily discovered.

CONCLUSIONS

Overall, these results suggested an important role of RBOH1-mediated H₂O₂ in H₂S-elicited tomato lateral root development, and corresponding H₂S-target proteins regulated at transcriptional and post-translational levels.

Involvement of glutathione in β-cyclodextrin-hemin complex-induced lateral root formation in tomato seedlings

β-cyclodextrin-hemin complex (β-CDH) was shown to induce lateral root (LR) formation in tomato. However, the molecular mechanism is still elusive. In this report, the role of reduced glutathione (GSH) in the induction of lateral root triggered by β-CDH was investigated. Similar to the responses of β-CDH, exogenously applied with 0.1 mΜ GSH not only increased endogenous GSH content determined by spectrophotography and the monochlorobimane (MCB)-dependent fluorescent analysis, but also induced, thereafter, LR formation. Meanwhile, both β-CDH- and GSH-induced lateral root primordia (LRP) exhibited a similar accelerated anatomic structure. Above inducible responses were blocked significantly when the _L-buthionine-(S,R)-sulfoximine (BSO), a potent and specific inhibitor of the enzyme catalyzing the first step of GSH biosynthesis, was separately applied. Upon β-CDH treatment, the changes of endogenous GSH content determined by spectrophotography and fluorescent analysis were consistent with the transcripts of two GSH synthetic genes, GSH1 and GSH2 encoding γ-glutamyl cysteine synthetase and glutathione synthetase, respectively. Exogenously applied with β-CDH could rescue N-1-naphthylphthalamic acid (NPA; IAA depletion)-triggered inhibition of LR formation. Further molecular evidence revealed that both β-CDH and GSH modulated gene expression of cell cycle regulatory genes (CYCA2;1, CYCA3;1, CYCD3;1, and CDKA1) and auxin signaling genes (ARF7 and RSI-1), six marker genes responsible for LR formation. By contrast, above changes were sensitive to the co-treatment with BSO. All together, these results suggest a role for GSH in the regulation of tomato LR development triggered by β-CDH.

Auxin-induced hydrogen sulfide generation is involved in lateral root formation in tomato

Similar to auxin, hydrogen sulfide (H2S), mainly produced by l-cysteine desulfhydrase (DES; EC 4.4.1.1) in plants, could induce lateral root formation. The objective of this study was to test whether H2S is also involved in auxin-induced lateral root development in tomato (Solanum lycopersicum L.) seedlings. We observed that auxin depletion-induced down-regulation of transcripts of SlDES1, decreased DES activity and endogenous H2S contents, and the inhibition of lateral root formation were rescued by sodium hydrosulfide (NaHS, an H2S donor). However, No additive effects were observed when naphthalene acetic acid (NAA) was co-treated with NaHS (lower than 10 mM) in the induction of lateral root formation. Subsequent work revealed that a treatment with NAA or NaHS could simultaneously induce transcripts of SlDES1, DES activity and endogenous H2S contents, and thereafter the stimulation of lateral root formation. It was further confirmed that H2S or HS(-), not the other sulfur-containing components derived from NaHS, was attributed to the stimulative action. The inhibition of lateral root formation and decreased of H2S metabolism caused by an H2S scavenger hypotaurine (HT) were reversed by NaHS, but not NAA. Molecular evidence revealed that both NaHS- or NAA-induced modulation of some cell cycle regulatory genes, including the up-regulation of SlCDKA;1, SlCYCA2;1, together with simultaneous down-regulation of SlKRP2, were differentially reversed by HT pretreatment. To summarize, above results clearly suggested that H2S might, at least partially, act as a downstream component of auxin signaling to trigger lateral root formation.

Form matters: morphological aspects of lateral root development

BACKGROUND

The crucial role of roots in plant nutrition, and consequently in plant productivity, is a strong motivation to study the growth and functioning of various aspects of the root system. Numerous studies on lateral roots, as a major determinant of the root system architecture, mostly focus on the physiological and molecular bases of developmental processes. Unfortunately, little attention is paid either to the morphological changes accompanying the formation of a lateral root or to morphological defects occurring in lateral root primordia. The latter are observed in some mutants and occasionally in wild-type plants, but may also result from application of external factors.

SCOPE AND CONCLUSIONS

In this review various morphological aspects of lateral branching in roots are analysed. Morphological events occurring during the formation of a typical lateral root are described. This process involves dramatic changes in the geometry of the developing organ that at early stages are associated with oblique cell divisions, leading to breaking of the symmetry of the cell pattern. Several types of defects in the morphology of primordia are indicated and described. Computer simulations show that some of these defects may result from an unstable field of growth rates. Significant changes in both primary and lateral root morphology may also be a consequence of various mutations, some of which are auxin-related. Examples reported in the literature are considered. Finally, lateral root formation is discussed in terms of mechanics. In this approach the primordium is considered as a physical object undergoing deformation and is characterized by specific mechanical properties.

Ethylene-induced changes in lignification and cell wall-degrading enzymes in the roots of mungbean (Vigna radiata) sprouts

As an important regulator, ethylene inhibits root growth and development in plants. To determine the mechanism of ethylene on root elongation growth and lateral root formation, ethylene-induced lignification and cell wall-degrading enzymes in the roots of mungbean sprouts were tested. We initially observed that primary root elongation and lateral root numbers were inhibited, while lignin content was enhanced by ethephon (ETH). Cell wall remolding proteins, polygalacturonase (PG) and carboxymethyl cellulose (Cx) activities were reduced, but α-expansins and xyloglucan endotransglucosylases/hydrolases (XTH) were enhanced by ETH. The promotion in lignin production was correlated with changes in activities of key lignin biosynthesis enzymes and hydrogen peroxide (H2O2) content. These actions induced by ETH were altered via treatment with an ethylene perception antagonist (Ag+). We subsequently demonstrated that the role of endogenous ethylene in regulating root elongation growth and lateral root formation were correlated with lignification and cell wall-degrading enzymes, respectively. These results suggested that the ethylene-regulated inhibition of primary root elongation growth was caused by an increase in lignification that reinforced the cell wall and shortened root length, and the suppression of lateral root formation was linked to activities of PG, Cx, α-expansins and XTH.

EXPANSINA17 up-regulated by LBD18/ASL20 promotes lateral root formation during the auxin response

Expansins are non-hydrolytic cell wall-loosening proteins involved in a variety of plant developmental processes during which cell wall modification occurs. Cell wall remodeling proteins including expansins have been suggested to be involved in cell separation to facilitate the emergence of lateral roots (LRs) through the overlaying tissues of the primary root. LBD18/ASL20 activates EXPANSINA14 (EXPA14) expression by directly binding to the EXPA14 promoter to enhance LR emergence in Arabidopsis thaliana. Here we show that EXPA17 is another target gene regulated by LBD18 to promote LR formation in Arabidopsis. We showed that nuclear translocation of the LBD18:GR fusion protein expressed under the Cauliflower mosaic virus (CaMV) 35S promoter or under the LBD18 promoter by dexamethasone treatment results in an increase in EXPA17 transcript levels. β-Glucuronidase (GUS) expression under the EXPA17 promoter, which is detected only in the roots of the wild type, was reduced in the LR primordium and overlaying tissues in an lbd18 mutant background. The number of emerged LRs of the EXPA17 RNAi (RNA interference) Arabidopsis lines was significantly lower than that of the wild type. Overexpression of EXPA17 in Arabidopsis increased the density of emerged LRs in the presence of auxin compared with the wild type. LR induction experiments with a gravitropic stimulus showed that LR emergence is delayed in the EXPA17 RNAi plants compared with the wild type. In addition, EXPA4 expression was also detected in overlaying tissues of the LR primordium and was inducible by LBD18. Taken together, these results support the notion that LBD18 up-regulates a subset of EXP genes to enhance cell separation to promote LR emergence in Arabidopsis.