Small Auxin-up RNA Research Articles

Comparative Genomic Analysis of SAUR Gene Family, Cloning and Functional Characterization of Two Genes (PbrSAUR13 and PbrSAUR52) in Pyrus bretschneideri.

The SAUR (small auxin-up RNA) gene family is the biggest family of early auxin response genes in higher plants and has been associated with the control of a variety of biological processes. Although SAUR genes had been identified in several genomes, no systematic analysis of the SAUR gene family has been reported in Chinese white pear. In this study, comparative and systematic genomic analysis has been performed in the SAUR gene family and identified a total of 116 genes from the Chinese white pear. A phylogeny analysis revealed that the SAUR family could be classified into four groups. Further analysis of gene structure (introns/exons) and conserved motifs showed that they are diverse functions and SAUR-specific domains. The most frequent mechanisms are whole-genome duplication (WGD) and dispersed duplication (DSD), both of which may be important in the growth of the SAUR gene family in Chinese white pear. Moreover, cis-acting elements of the PbrSAUR genes were found in promoter regions associated with the auxin-responsive elements that existed in most of the upstream sequences. Remarkably, the qRT-PCR and transcriptomic data indicated that PbrSAUR13 and PbrSAUR52 were significantly expressed in fruit ripening. Subsequently, subcellular localization experiments revealed that PbrSAUR13 and PbrSAUR52 were localized in the nucleus. Moreover, PbrSAUR13 and PbrSAUR52 were screened for functional verification, and Dangshan pear and frandi strawberry were transiently transformed. Finally, the effects of these two genes on stone cells and lignin were analyzed by phloroglucinol staining, Fourier infrared spectroscopy, and qRT-PCR. It was found that PbrSAUR13 promoted the synthesis and accumulation of stone cells and lignin, PbrSAUR52 inhibited the synthesis and accumulation of stone cells and lignin. In conclusion, these results indicate that PbrSAUR13 and PbrSAUR52 are predominantly responsible for lignin inhibit synthesis, which provides a basic mechanism for further study of PbrSAUR gene functions.

SAUR8, a small auxin-up RNA gene in poplar, confers drought tolerance to transgenic Arabidopsis plants

SAUR (small auxin-up RNA) is an early auxin-responsive gene. In this study, a novel SAUR gene PtSAUR8 was cloned from poplar (Populus trichocarpa), and subcellular location analysis showed that it is targeted to the nuclear membrane. In addition, PtSAUR8 overexpression in Arabidopsis improved the plant resistance to drought stress. Meanwhile, the loss of function mutant saur53 showed more drought sensitivity compared to the WT. PtSAUR8 conferred drought tolerance in transgenic Arabidopsis, as determined through phenotypic and stress-associated physiological indicator analyses, namely, root length, germination rate, relative water content, proline content, CAT content, POD content, malondialdehyde content, hydrogen peroxide content, and relative conductivity. In addition, after the 1 μM abscisic acid (ABA) treatment, the PtSAUR8-OE lines promoted stomata closure. Quantitative fluorescence analysis of related genes induced by drought mutant stress further confirmed that overexpression of PtSAUR8 can improve drought resistance in transgenic Arabidopsis lines. Therefore, PtSAUR8 may play a role in plant drought resistance through ABA-mediated pathways; thus, providing new research materials for molecular breeding of poplar resistance.

Genome-wide characterization and expression analysis of SAUR gene family in Melon (Cucumis melo L.).

We identified 66 melon SAUR genes by bioinformatic analyses. CmSAUR19, 38, 58, 62 genes are specifically expressed in different stages of fruit growth, suggesting their participation in regulating fruit development. Auxin plays a crucial role in plant growth by regulating the multiple auxin response genes. However, in melon (Cucumis melo L.), the functions of the auxin early response gene family SAUR (Small auxin up RNA) genes in fruit development are still poorly understood. Through genome-wide characterization of CmSAUR family in melon, we identified a total of 66 CmSAUR genes. The open reading frames of the CmSAUR genes ranged from 234 to 525bp, containing only one exon and lacking introns. Chromosomal position and phylogenetic tree analyses found that the two gene clusters in the melon chromosome are highly homologous in the Cucurbitaceae plants. Among the four conserved motifs in CmSAUR proteins, motif 1, motif 2, and motif 3 located in most of the family protein sequences, and motif 4 showed a close correlation with the two gene clusters. The CmSAUR28 and CmSAUR58 genes have auxin response elements located in the promoters, suggesting they may be involved in the auxin signaling pathway to regulate fruit development. Through transcriptomic profiling in the four developmental stages of fruit and different lateral organs, we selected 16 differentially-expressed SAUR genes for performing further expression analyses. qRT-PCR results showed that five SAUR genes are specifically expressed in flower organs and ovaries. CmSAUR19 and CmSAUR58 were significantly accumulated in the early developmental stage of the fruit. CmSAUR38 and CmAUR62 showed high expression in the climacteric and post-climacteric stages, suggesting their specific role in controlling fruit ripening. This work provides a foundation for further exploring the function of the SAUR gene in fruit development.

Identification of a Major QTL and Validation of Related Genes for Tiller Angle in Rice Based on QTL Analysis.

An ideal plant architecture is an important condition to achieve high crop yields. The tiller angle is an important and complex polygenic trait of rice (Oryza sativa L.) plant architecture. Therefore, the discovery and identification of tiller angle-related genes can aid in the improvement of crop architecture and yield. In the present study, 222 SSR markers were used to establish a high-density genetic map of rice doubled haploid population, and a total of 8 quantitative trait loci (QTLs) were detected based on the phenotypic data of the tiller angle and tiller crown width over 2 years. Among them, four QTLs (qTA9, qCW9, qTA9-1, and qCW9-1) were overlapped at marker interval RM6235–RM24288 on chromosome 9 with a large effect value regarded as a stable major QTL. The selected promising related genes were further identified by relative gene expression analysis, which gives us a basis for the future cloning of these genes. Finally, OsSAURq9, which belongs to the SMALL AUXIN UP RNA (SAUR), an auxin-responsive protein family, was selected as a target gene. Overall, this work will help broaden our knowledge of the genetic control of tiller angle and tiller crown width, and this study provides both a good theoretical basis and a new genetic resource for the breeding of ideal-type rice.

SAUR15 interaction with BRI1 activates plasma membrane H+-ATPase to promote organ development of Arabidopsis.

Brassinosteroids (BRs) are an important group of plant steroid hormones that regulate growth and development. Several members of the SMALL AUXIN UP RNA (SAUR) family have roles in BR-regulated hypocotyl elongation and root growth. However, the mechanisms are unclear. Here, we show in Arabidopsis (Arabidopsis thaliana) that SAUR15 interacts with cell surface receptor-like kinase BRASSINOSTEROID-INSENSITIVE 1 (BRI1) in BR-treated plants, resulting in enhanced BRI1 phosphorylation status and recruitment of the co-receptor BRI1-ASSOCIATED RECEPTOR KINASE 1. Genetic and phenotypic assays indicated that the SAUR15 effect on BRI1 can be uncoupled from BRASSINOSTEROID INSENSITIVE 2 activity. Instead, we show that SAUR15 promotes BRI1 direct activation of plasma membrane H+-ATPase (PM H+-ATPase) via phosphorylation. Consequently, SAUR15–BRI1–PM H+-ATPase acts as a direct, PM-based mode of BR signaling that drives cell expansion to promote the growth and development of various organs. These data define an alternate mode of BR signaling in plants.

PpSAUR43, an Auxin-Responsive Gene, Is Involved in the Post-Ripening and Softening of Peaches

Auxin’s role in the post-ripening of peaches is widely recognized as important. However, little is known about the processes by which auxin regulates fruit post-ripening. As one of the early auxin-responsive genes, it is critical to understand the role of small auxin-up RNA (SAUR) genes in fruit post-ripening and softening. Herein, we identified 72 PpSAUR auxin-responsive factors in the peach genome and divided them into eight subfamilies based on phylogenetic analysis. Subsequently, the members related to peach post-ripening in the PpSAUR gene family were screened, and we targeted PpSAUR43. The expression of PpSAUR43 was decreased with fruit post-ripening in melting flesh (MF) fruit and was high in non-melting flesh (NMF) fruit. The overexpression of PpSAUR43 showed a slower rate of firmness decline, reduced ethylene production, and a delayed fruit post-ripening process. The MADS-box gene family plays an important regulatory role in fruit ripening. In this study, we showed with yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BIFC) experiments that PpSAUR43 can interact with the MADS-box transcription factor PpCMB1(PpMADS2), which indicates that PpSAUR43 may inhibit fruit ripening by suppressing the function of the PpCMB1 protein. Together, these results indicate that PpSAUR43 acts as a negative regulator involved in the peach post-ripening process.

The CCCH zinc finger protein C3H15 negatively regulates cell elongation by inhibiting brassinosteroid signaling.

Plant CCCH proteins participate in the control of multiple developmental and adaptive processes, but the regulatory mechanisms underlying these processes are not well known. In this study, we showed that the Arabidopsis (Arabidopsis thaliana) CCCH protein C3H15 negatively regulates cell elongation by inhibiting brassinosteroid (BR) signaling. Genetic and biochemical evidence showed that C3H15 functions downstream of the receptor BR INSENSITIVE 1 (BRI1) as a negative regulator in the BR pathway. C3H15 is phosphorylated by the GLYCOGEN SYNTHASE KINASE 3 -like kinase BR-INSENSITIVE 2 (BIN2) at Ser111 in the cytoplasm in the absence of BRs. Upon BR perception, C3H15 transcription is enhanced, and the phosphorylation of C3H15 by BIN2 is reduced. The dephosphorylated C3H15 protein accumulates in the nucleus, where C3H15 regulates transcription via G-rich elements (typically GGGAGA). C3H15 and BRASSINAZOLE RESISTANT 1 (BZR1)/BRI1-EMS-SUPPRESSOR 1 (BES1), two central transcriptional regulators of BR signaling, directly suppress each other and share a number of BR-responsive target genes. Moreover, C3H15 antagonizes BZR1 and BES1 to regulate the expression of their shared cell elongation-associated target gene, SMALL AUXIN-UP RNA 15 (SAUR15). This study demonstrates that C3H15-mediated BR signaling may be parallel to, or even attenuate, the dominant BZR1 and BES1 signaling pathways to control cell elongation. This finding expands our understanding of the regulatory mechanisms underlying BR-induced cell elongation in plants.

The SAUR gene family in coffee: genome-wide identification and gene expression analysis during somatic embryogenesis.

Small auxin-up RNA (SAUR) genes form a wide family supposedly involved in different physiological and developmental processes in plants such as leaf senescence, auxin signaling and transport, hypocotyl development and tolerance to abiotic stresses. The transcription of SAUR genes is quickly induced by auxins, a group of phytohormones of major importance on embryo development. To better understand the distribution and expression profile of such still not explored family in Coffea sp., especially during the development of somatic embryogenesis (SE), SAUR members were characterized in silico using the available Coffea canephora genome data and analyzed for gene expression by RT-qPCR in C. arabica embryogenic samples. Over C. canephora genome 31 CcSAURs were distributed by 11 chromosomes. Out of these 31 gene members, 5 SAURs were selected for gene expression analysis in C. arabica embryogenic materials. CaSAUR12 and CaSAUR18 were the members highly expressed through almost all plant materials. The other genes had more expression in at least one of the developing embryo stages or plantlets. The CaSAUR12 was the only member to exhibit an increased expression in both non-embryogenic calli and the developing embryo stages. The identification of SAUR family on C. canephora genome followed by the analysis of gene expression profile across coffee somatic embryogenesis process on C. arabica represents a further additional step towards a better comprehension of molecular components acting on SE. Along with new research about this gene family such knowledge may support studies about clonal propagation methods via somatic embryogenesis to help the scientific community towards improvements into coffee crop.

Transcriptome analysis of peach fruit under 1-MCP treatment provides insights into regulation network in melting peach softening

Abstract Peach (Prunus persica L.) displays distinguish texture phenotype during postharvest, which could be classified into three types, including melting flesh (MF), non-melting flesh, and stony-hard. MF peach would soften rapidly with an outbreak of ethylene production, which causes huge wastage during fruit transportation and storage. 1-Methylcyclopropene (1-MCP) was used to alleviate fruit softening. In this study, we performed RNA-sequencing on two MF peach cultivars (‘YuLu’ and ‘Yanhong’) after 1-MCP treatment to identify the candidate genes participating in peach fruit softening. A total of 167 genes were identified by weighted gene coexpression network analysis and correlation analysis that could respond to 1-MCP treatment and might be related to softening. Among them, 5 auxin-related genes including 2 indole-3-acetic acid, 1 auxin response transcription factor and 2 small auxin-up RNAs, and 4 cell wall modifying genes (PpPG1, PpPG2, PpPG24 and PpPMEI) were characterized as key genes participating in MF peach softening. Furthermore, 2 transcription factors, which belong to HD-ZIP and MYB, were predicted as candidates regulating softening process by constructing a transcriptional network of these 4 cell wall modifying genes combined with expression pattern analysis, of which HD-ZIP could trans-activate the promoter of PpPG1.

The Sequential Action of MIDA9/PP2C.D1, PP2C.D2, and PP2C.D5 Is Necessary to Form and Maintain the Hook After Germination in the Dark.

During seedling etiolation after germination in the dark, seedlings have closed cotyledons and form an apical hook to protect the meristem as they break through the soil to reach the surface. Once in contact with light, the hook opens and cotyledons are oriented upward and separate. Hook development in the dark after seedling emergence from the seed follows three distinctly timed and sequential phases: formation, maintenance, and eventual opening. We previously identified MISREGULATED IN DARK9 (MIDA9) as a phytochrome interacting factor (PIF)-repressed gene in the dark necessary for hook development during etiolated growth. MIDA9 encodes the type 2C phosphatase PP2C.D1, and pp2c-d1/mida9 mutants exhibit open hooks in the dark. Recent evidence has described that PP2C.D1 and other PP2C.D members negatively regulate SMALL AUXIN UP RNA (SAUR)-mediated cell elongation. However, the fundamental question of the timing of PP2C.D1 action (and possibly other members of the PP2C.D family) during hook development remains to be addressed. Here, we show that PP2C.D1 is required immediately after germination to form the hook. pp2c.d1/mida9 shows reduced cell expansion in the outer layer of the hook and, therefore, does not establish the differential cell growth necessary for hook formation, indicating that PP2C.D1 is necessary to promote cell elongation during this early stage. Additionally, genetic analyses of single and high order mutants in PP2C.D1, PP2C.D2, and PP2C.D5 demonstrate that the three PP2C.Ds act collectively and sequentially during etiolation: whereas PP2C.D1 dominates hook formation, PP2C.D2 is necessary during the maintenance phase, and PP2C.D5 acts to prevent opening during the third phase together with PP2C.D1 and PP2C.D2. Finally, we uncover a possible connection of PP2C.D1 levels with ethylene physiology, which could help optimize hook formation during post-germinative growth in the dark.

The Rice Small Auxin-Up RNA Gene OsSAUR33 Regulates Seed Vigor via Sugar Pathway during Early Seed Germination.

Seed vigor affects seed germination and seedling emergence, and therefore is an important agronomic trait in rice. Small auxin-up RNAs (SAURs) function in a range of developmental processes, but their role in seed vigor remains unclear. Here, we observed that disruption of OsSAUR33 resulted in reduced germination rates and low seed uniformity in early germination. Expression of OsSAUR33 was higher in mature grains and early germinating seeds. RNA-seq analysis revealed that OsSAUR33 modulated seed vigor by affecting the mobilization of stored reserves during germination. Disruption of OsSAUR33 increased the soluble sugar content in dry mature grains and seeds during early germination. OsSAUR33 interacted with the sucrose non-fermenting-1-related protein kinase OsSnRK1A, a regulator of the sugar signaling pathway, which influences the expression of sugar signaling-related genes during germination. Disruption of OsSAUR33 increased sugar-sensitive phenotypes in early germination, suggesting OsSAUR33 likely affects seed vigor through the sugar pathway. One elite haplotype of OsSAUR33 associated with higher seed vigor was identified mainly in indica accessions. This study provides insight into the effects of OsSAUR33 on seed vigor in rice.

Genome-wide identification and characterization of small auxin-up RNA (SAUR) gene family in plants: evolution and expression profiles during normal growth and stress response

BackgroundAuxin is critical to plant growth and development, as well as stress responses. Small auxin-up RNA (SAUR) is the largest family of early auxin responsive genes in higher plants. However, the function of few SAUR genes is known owing to functional redundancy among the many family members.ResultsIn this study, we conducted a phylogenetic analysis using protein sequences of 795 SAURs from Anthoceros angustus, Marchantia polymorpha, Physcomitrella patens, Selaginella moellendorffii, Ginkgo biloba, Gnetum montanum, Amborella trichopoda, Arabidopsis thaliana, Oryza sativa, Zea mays, Glycine max, Medicago truncatula and Setaria italica. The phylogenetic trees showed that the SAUR proteins could be divided into 10 clades and three subfamilies, and that SAUR proteins of three bryophyte species were only located in subfamily III, which suggested that they may be ancestral. From bryophyta to anthophyta, SAUR family have appeared very large expansion. The number of SAUR gene in Fabaceae species was considerably higher than that in other plants, which may be associated with independent whole genome duplication event in the Fabaceae lineages. The phylogenetic trees also showed that SAUR genes had expanded independently monocotyledons and dicotyledons in angiosperms. Conserved motif and protein structure prediction revealed that SAUR proteins were highly conserved among higher plants, and two leucine residues in motif I were observed in almost all SAUR proteins, which suggests the residues plays a critical role in the stability and function of SAUR proteins. Expression analysis of SAUR genes using publicly available RNA-seq data from rice and soybean indicated functional similarity of members in the same clade, which was also further confirmed by qRT-PCR. Summarization of SAUR functions also showed that SAUR functions were usually consistent within a subclade.ConclusionsThis study provides insights into the evolution and function of the SAUR gene family from bryophyta to anthophyta, particularly in Fabaceae plants. Future investigation to understand the functions of SAUR family members should employ a clade as the study unit.

SAUR proteins and PP2C.D phosphatases regulate H+-ATPases and K+ channels to control stomatal movements.

Activation of plasma membrane (PM) H+-ATPase activity is crucial in guard cells to promote light-stimulated stomatal opening, and in growing organs to promote cell expansion. In growing organs, SMALL AUXIN UP RNA (SAUR) proteins inhibit the PP2C.D2, PP2C.D5, and PP2C.D6 (PP2C.D2/5/6) phosphatases, thereby preventing dephosphorylation of the penultimate phosphothreonine of PM H+-ATPases and trapping them in the activated state to promote cell expansion. To elucidate whether SAUR-PP2C.D regulatory modules also affect reversible cell expansion, we examined stomatal apertures and conductances of Arabidopsis thaliana plants with altered SAUR or PP2C.D activity. Here, we report that the pp2c.d2/5/6 triple knockout mutant plants and plant lines overexpressing SAUR fusion proteins exhibit enhanced stomatal apertures and conductances. Reciprocally, saur56 saur60 double mutants, lacking two SAUR genes normally expressed in guard cells, displayed reduced apertures and conductances, as did plants overexpressing PP2C.D5. Although altered PM H+-ATPase activity contributes to these stomatal phenotypes, voltage clamp analysis showed significant changes also in K+ channel gating in lines with altered SAUR and PP2C.D function. Together, our findings demonstrate that SAUR and PP2C.D proteins act antagonistically to facilitate stomatal movements through a concerted targeting of both ATP-dependent H+ pumping and channel-mediated K+ transport.

The Crosstalk between Cytokinin and Auxin Signaling Pathways in the Control of Natural Senescence of Arabidopsis thaliana Leaves

Natural senescence of leaves is a regular physiological process subjected to a certain genetic program and controlled by various phytohormones. Cytokinins (CKs) play a crucial role in the leaf-senescence control being negative regulators of this process. We previously reported on the prolonged vegetative growth and the development of a double knockout ahk2ahk3 mutant of Arabidopsis thaliana Heynh. (L.) for the genes encoding CK receptors. According to the data of the transcriptomic analysis and real-time RT‑PCR of selected genes performed in this study, the delay of leaf senescence in ahk2ahk3 mutants is accompanied by enhanced (4–281-fold) expression of the group of SAUR (small auxin-up RNA) genes encoding auxin response proteins and by upregulation of the SSPP (senescence-suppressed protein phosphatase) gene, whose expression level significantly (137-fold) exceeded that in a wild-type transcriptome. Thus, it is quite possible that under significant inhibition of the CK signaling leaf senescence in Arabidopsis plants regulated via a compensatory mechanism connected with changes in the expression of the SAUR gene family and a certain pool of genes related to the auxin transport and signaling.

Class I TCP proteins TCP14 and TCP15 are required for elongation and gene expression responses to auxin

Two class I TCP transcription factors are required for an efficient elongation of hypocotyls in response to auxin and for the correct expression of a subset of auxin-inducible genes In this work, we analyzed the response to auxin of plants with altered function of the class I TEOSINTE BRANCHED 1, CYCLOIDEA, PCF (TCP) transcription factors TCP14 and TCP15. Several SMALL AUXIN UP RNA (SAUR) genes showed decreased expression in mutant plants defective in these TCPs after an increase in ambient temperature to 29°C, a condition that causes an increase in endogenous auxin levels. Overexpression of SAUR63 caused a more pronounced elongation response in the mutant than in the wild-type at 29°C, suggesting that the decreased expression of SAUR genes is partly responsible for the defective elongation at warm temperature. Notably, several SAUR genes and the auxin response gene IAA19 also showed reduced expression in the mutant after auxin treatment, while the expression of other SAUR genes and of IAA29 was not affected or was even higher. Expression of the auxin reporter DR5::GUS was also higher in a tcp15 mutant than in a wild-type background after auxin treatment. However, the elongation of hypocotyls in response to auxin was impaired in the mutant. Remarkably, a significant proportion of auxin inducible genes and of targets of the AUXIN RESPONSE FACTOR 6 are regulated by TCP15 and often contain putative TCP recognition motifs in their promoters. Furthermore, we demonstrated that several among them are recognized by TCP15 in vivo. Our results indicate that TCP14 and TCP15 are required for an efficient elongation response to auxin, most likely by regulating a subset of auxin inducible genes related to cell expansion.

Comparative analysis of the expression of sex candidate genes in flower of dioecious and hermaphrodite grapevine (Vitis vinifera L. ssp.)

Vitis vinifera L. can be divided into two subspecies, V. vinifera subsp. vinifera, the cultivated grapevine, and its wild ancestor, V. vinifera subsp. sylvestris. Three flower types have been described: hermaphrodite and female in some varieties of vinifera, and male or female flowers in sylvestris. We have conducted an expression analysis of the functional genes candidate to sex determination in the newly defined sex locus described by Picq et al (2014) using four flower types. The candidate gene Ethylene overproducer-1 (ETO1) localized in the sex locus region and which inhibits the enzyme activity of the enzyme ACS (1-aminocyclopropane-1-carboxylic acid synthase) was showed highly significantly different expression pattern according to the sex flower. Other genes studied in the sex locus do not reveal significant different expression patterns. For genes located outside of the sex locus, only the SAUR (Small auxin up RNAs) protein and the ACS gene showed different expression among sex flowers. Therefore, as ETO1 is only expressed in female and hermaphrodite flowers, it could be a good candidate for the recessive female fertility mutation and ACS copy could be implied in the reaction cascade leading to the inhibition of stamens in female flowers. However, the ETO1 only negatively interacts with type 2 ACS and our ACS phylogeny analysis confirmed that the VviACS copy is not type 2. Therefore, it is unlikely that there is such molecular interaction in grapevine. Another hypothesis could be that the molecular mechanisms that regulated the activity of VviACS2 are induced by the VvETO1 protein regulating the activity of both families of ACS type I and type 2. The last gene showing differential expression according to sex is the SAUR protein. This gene consists in early auxin response genes family playing key role in hormonal and environmental signals. Our results pointed out that one gene (ETO1) inside of the flower sex locus region and two genes (ACS, SAUR) located outside of the sex locus region, could be considered as putative candidate genes for the control of sexual traits in grapevine.

Genome-wide identification and analysis of Medicago truncatula Small auxin upregulated RNA (SAUR) gene family uncover their roles in nodule formation

Small auxin-up RNAs (SAURs) gene family, one of the three major early auxin-responsive gene families, plays a critical role in environmental responses and developmental regulation. A comprehensive identification of SAUR family genes were performed basing on the latest updated Medicago truncatula reference genome sequence. Our data showed that 133 SAUR genes were located on all eight M. truncatula chromosomes unevenly. Phylogenetic analysis indicated that the SAUR proteins from M. truncatula and Glycine max were divided into five major groups. For detail study, 12 MtSAUR genes were randomly selected from different subgroups. Three classical motifs (Motif I-III) were identified in our selected SAUR proteins and most of them were intronless genes. The qRT-PCR data showed that 12 selected MtSAUR genes could be expressed at least in one of the M. truncatula organs tested. Interestingly, MtSAUR13 was showed a specific expression in the root and root meristem. MtSAUR18, MtSAUR20, MtSAUR57 and MtSAUR91 showed highest expression levels in the flower. We also found that there was a close relationship between AuxRE number and auxin responsive expression. Expression profiles based on microarray data have provided insights into the possible function in nodule formation under different symbiotic bacterial infections. This study provides a fundamental basis for understanding the involvement of MtSAUR genes at the initiation phase of nodule formation.

SAUR15 Promotes Lateral and Adventitious Root Development via Activating H+-ATPases and Auxin Biosynthesis.

SMALL AUXIN-UP RNAs (SAURs) comprise the largest family of early auxin response genes. Some SAURs have been reported to play important roles in plant growth and development, but their functional relationships with auxin signaling remain unestablished. Here, we report Arabidopsis (Arabidopsis thaliana) SAUR15 acts downstream of the auxin response factors ARF6,8 and ARF7,19 to regulate auxin signaling-mediated lateral root (LR) and adventitious root (AR) formation. The loss-of-function mutant saur15-1 exhibits fewer LRs and ARs. By contrast, plants overexpressing SAUR15 exhibit more LRs and ARs. We find that the SAUR15 promoter contains four tandem auxin-responsive elements, which are directly bound by ARF6 and ARF7 and are essential for SAUR15 expression. LR and AR impairment in arf6 and arf7 mutants is partially reduced by ectopic expression of SAUR15 Additionally, we demonstrate that the ARF6,7-upregulated SAUR15 promotes LR and AR development using two mechanisms. On the one hand, SAUR15 interacts with PP2C-D subfamily type 2C protein phosphatases to inhibit their activities, thereby stimulating plasma membrane H+-ATPases, which drives cell expansion and facilitates LR and AR formation. On the other hand, SAUR15 promotes auxin accumulation, potentially by inducing the expression of auxin biosynthesis genes. A resulting increase in free auxin concentration likely triggers LR and AR formation, forming a feedback loop. Our study provides insights and a better understanding of how SAURs function at the molecular level in regulating auxin-mediated LR and AR development.

Small Auxin Up RNAs influence the distribution of indole-3-acetic acid and play a potential role in increasing seed size in Euryale ferox Salisb

BackgroundAquatic Euryale ferox Salisb. is an economically important crop in China and India. Unfortunately, low yield limitations seriously hinder market growth. Unveiling the control of seed size is of remarkable importance in improvement of crops. Here, we generated a new hybrid line (HL) with larger seeds by crossing South Gordon Euryale and North Gordon Euryale (WT) which hasn’t been reported before. However, the functional genes and molecular mechanisms controlling the seed size in Euryale ferox Salisb. remain unclear. In this study, we focused on the differentially expressed genes in the auxin signal transduction pathway during fruit development between HL and WT to explore candidate regulatory genes participated in regulating seed size.ResultsBoth concentration and localization of indole-3-acetic acid (IAA) at two growth stages of fruits of WT and HL were detected by LC-MS and immunofluorescence. Although IAA content between the two lines did not differ, IAA distribution was significantly different. To elucidate the mechanism and to seek the key genes underlying this difference, RNA-seq was performed on young fruits at the two selected growth stages, and differentially expressed genes related to the auxin transduction pathway were selected for further analysis.ConclusionHybrid Euryale ferox Salisb. expressed significant heterosis, resulting in non-prickly, thin-coated, large seeds, which accounted for the significantly larger yield of HL than that of WT. Our study indicated that Small Auxin Up RNAs (SAURs) -mediated localization of IAA regulates seed size in Euryale ferox Salisb. We found that some SAURs may act as a positive mediator of the auxin transduction pathway, thereby contributing to the observed heterosis.

Identification and expression analysis of the small auxin-up RNA (SAUR) gene family in apple by inducing of auxin.

The small auxin-up RNA (SAUR) family plays a vital role in the regulation of plant growth and development. We identified 80 MdSAUR genes in this study. Phylogenetic analysis indicated that the SAUR proteins from Arabidopsis, rice, and apple were divided into six groups. Of the 80 MdSAURs, 71 were randomly distributed along the 17 chromosomes, while the remaining genes were located along unassigned scafoolds. Among them, a comprehensive overview of SAUR gene family is presented, including gene structures, chromosome locations, duplication and selection pressure analyses, synteny and promoter analyses, and protein interaction. The expression profiles based on microarray data found that 80 genes showed increased expression levels in at least one tissue including seed, seedling, root, stem, leaf, flower, fruit 100daa, and harvested fruit. MdSAUR7 possibly regulate the development of flower organs, and MdSAUR15, MdSAUR24, and MdSAUR80 promote the growth of fruits by regulating cell division. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated the expression levels of 79 MdSAUR genes in leaves under exogenous IAA treatment. MdSAUR4, MdSAUR22, MdSAUR37, MdSAUR38, MdSAUR49, and MdSAUR54 were up-regulated after IAA treatment compared with the control, indicating that they may play specific roles in the IAA signaling transduction pathway. This work provided a foundation for further investigations for the functional analyses of SAURs in apple.