A peroxisomal cinnamate:CoA ligase-dependent phytohormone metabolic cascade in submerged rice germination

The mechanism underlying the ability of rice to germinate underwater is a largely enigmatic but key research question highly relevant to rice cultivation. Moreover, although rice is known to accumulate salicylic acid (SA), SA biosynthesis is poorly defined, and its role in underwater germination is unknown. It is also unclear whether peroxisomes, organelles essential to oilseed germination and rice SA accumulation, play a role in rice germination. Here, we show that submerged imbibition of rice seeds induces SA accumulation to promote germination in submergence. Two submergence-induced peroxisomal Oryza sativa cinnamate:CoA ligases (OsCNLs) are required for this SA accumulation. SA exerts this germination-promoting function by inducing indole-acetic acid (IAA) catabolism through the IAA-amino acid conjugating enzyme GH3. The metabolic cascade we identified may potentially be adopted in agriculture to improve the underwater germination of submergence-intolerant rice varieties. SA pretreatment is also a promising strategy to improve submerged rice germination in the field.

Auxin homeostasis is maintained by sly-miR167-SlARF8A/B-SlGH3.4 feedback module in the development of locular and placental tissues of tomato fruits

The locular gel, produced by the placenta, is important for fruit flavor and seed development in tomato. However, the mechanism underlying locule and placenta development is not fully understood yet. Here, we show that two SlARF transcription factors, SlARF8B and SlARF8A (SlARF8A/B), promote the development of locular and placenta tissues. The expression of both SlARF8A and SlARF8B is repressed by sly-microRNA167 (sly-miR167), allowing for the activation of auxin downstream genes. In slarf8a, slarf8b, and slarf8a/b mutants, the auxin (IAA) levels are decreased, whereas the levels of inactive IAA conjugates including IAA-Ala, IAA-Asp, and IAA-Glu are increased. We further find that SlARF8B directly inhibits the expression of SlGH3.4, an acyl acid amino synthetase that conjugates the amino acids to IAA. Disruption of such auxin balance by the increased expression of SlGH3.4 or SlGH3.2 results in defective locular and placental tissues. Taken together, our findings reveal an important regulatory module constituted by sly-miR167-SlARF8A/B-SlGH3.4 during the development of locular and placenta tissues of tomato fruits.

The Roles of GRETCHEN HAGEN3 (GH3)-Dependent Auxin Conjugation in the Regulation of Plant Development and Stress Adaptation

The precise control of free auxin (indole-3-acetic acid, IAA) gradient, which is orchestrated by biosynthesis, conjugation, degradation, hydrolyzation, and transport, is critical for all aspects of plant growth and development. Of these, the GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetase family, pivotal in conjugating IAA with amino acids, has garnered significant interest. Recent advances in understanding GH3-dependent IAA conjugation have positioned GH3 functional elucidation as a hot topic of research. This review aims to consolidate and discuss recent findings on (i) the enzymatic mechanisms driving GH3 activity, (ii) the influence of chemical inhibitor on GH3 function, and (iii) the transcriptional regulation of GH3 and its impact on plant development and stress response. Additionally, we explore the distinct biological functions attributed to IAA-amino acid conjugates.

Genome-wide identification, characterization, and expression analysis of the sweet potato (Ipomoea batatas [L.] Lam.) ARF, Aux/IAA, GH3, and SAUR gene families

BACKGROUND

Auxins are known to have roles in the tuberization process in sweet potato (Ipomoea batatas [L.] Lam.) and these effects are mediated by various auxin signalling gene families. In this study, an analysis of the sweet potato genome was performed to identify the ARF, Aux/IAA, GH3, and SAUR auxin signalling gene family members in this crop.

RESULTS

A total of 29 ARF, 39 Aux/IAA, 13 GH3, and 200 SAUR sequences were obtained, and their biochemical properties and gene expression profiles were analysed. The sequences were relatively conserved based on exon-intron structure, motif analysis, and phylogenetic tree construction. In silico expression analyses of the genes in fibrous and storage roots indicated that many sequences were not differentially expressed in tuberizing and non-tuberizing roots. However, some ARF, Aux/IAA, and SAUR genes were up-regulated in tuberizing storage roots compared to non-tuberizing fibrous roots while many GH3 genes were down-regulated. Additionally, these genes were expressed in a variety of plant parts, with some genes being highly expressed in shoots, leaves, and stems while others had higher expression in the roots. Some of these genes are up-regulated during the plant's response to various hormone treatments and abiotic stresses. Quantitative RT-PCR confirmation of gene expression was also conducted, and the results were concordant with the in silico analyses. A protein-protein interaction network was predicted for the differentially expressed genes, suggesting that these genes likely form part of a complex regulatory network that controls tuberization. These results confirm those of existing studies that show that auxin signalling genes have numerous roles in sweet potato growth and development.

CONCLUSION

This study provides useful information on the auxin signalling gene families in Ipomoea batatas and suggests putative candidates for further studies on the role of auxin signalling in tuberization and plant development.

GH3-mediated auxin inactivation attenuates multiple stages of lateral root development

Lateral root (LR) positioning and development rely on the dynamic interplay between auxin production, transport but also inactivation. Nonetheless, how the latter affects LR organogenesis remains largely uninvestigated. Here, we systematically analyze the impact of the major auxin inactivation pathway defined by GRETCHEN HAGEN3-type (GH3) auxin conjugating enzymes and DIOXYGENASE FOR AUXIN OXIDATION1 (DAO1) in all stages of LR development using reporters, genetics and inhibitors in Arabidopsis thaliana. Our data demonstrate that the gh3.1/2/3/4/5/6 hextuple (gh3hex) mutants display a higher LR density due to increased LR initiation and faster LR developmental progression, acting epistatically over dao1-1. Grafting and local inhibitor applications reveal that root and shoot GH3 activities control LR formation. The faster LR development in gh3hex is associated with GH3 expression domains in and around developing LRs. The increase in LR initiation is associated with accelerated auxin response oscillations coinciding with increases in apical meristem size and LR cap cell death rates. Our research reveals how GH3-mediated auxin inactivation attenuates LR development. Local GH3 expression in LR primordia attenuates development and emergence, whereas GH3 effects on pre-initiation stages are indirect, by modulating meristem activities that in turn coordinate root growth with LR spacing.

The many faces of lysine acylation in proteins: Phytohormones as unexplored substrates

Protein post-translational modification (PTM) is a ubiquitous process that occurs in most proteins. Lysine residues containing an ε-amino group are recognized as hotspots for the addition of different chemical groups. Lysine acetylation, extensively studied in histones, serves as an epigenetic hallmark capable of promoting changes in chromatin structure and availability. Acyl groups derived from molecules involved in carbohydrate and lipid metabolisms, such as lactate, succinate and hydroxybutyrate, were identified as lysine modifications of histones and other proteins. Lysine-acyltransferases do not exhibit significant substrate specificity concerning acyl donors. Furthermore, plant hormones harboring acyl groups often form conjugates with free amino acids to regulate their activity and function during plant physiological processes and responses, a process mediated by GH3 enzymes. Besides forming low-molecular weight conjugates, auxins have been shown to covalently modify proteins in bean seeds. Aside from auxins, other phytohormones with acyl groups are unexplored potential substrates for post-translational acylation of proteins. Using MS data searches, we revealed various proteins with lysine residues linked to auxin, abscisic acid, gibberellic acid, jasmonic acid, and salicylic acid. These findings raise compelling questions about the ability of plant hormones harboring carboxyl groups to serve as new candidates for protein acylation and acting in protein PTM and modulation.

The novel polyfluoroalkyl benzenesulfonate OBS exposure induces cell cycle arrest and senescence of rat pituitary cell GH3 via the p53/p21/RB pathway

Sodium p-perfluorous nonenoxybenzene sulfonate (OBS), an economical alternative to perfluorooctane sulfonate (PFOS) in multiple industrial fields, is widely detected in the environment. The toxicity of OBS has received increasing attention. Pituitary cells are components of the endocrine system and act as vital regulators of homeostatic endocrine balance. However, the effects of OBS on pituitary cells remain unknown. The present study explores the effects of OBS (0.5, 5, and 50μM) on GH3 rat pituitary cells after treatment for 24, 48, and 72h. We found that OBS significantly inhibited cell proliferation in GH3 cells with remarkable senescent phenotypes, including enhanced SA-β-gal activity and expression of senescence-associated secretory phenotype (SASP)-related genes, cell cycle arrest, and upregulation of the senescence-related proteins γ-H2A.X and Bcl-2. OBS caused significant cell cycle arrest of GH3 cells at the G1-phase and concomitantly downregulated the expression of some key proteins for the G1/S transition, including cyclin D1 and cyclin E1. Consistently, the phosphorylation of retinoblastoma (RB), which plays a central role in regulating the cell cycle, was prominently reduced after OBS exposure. Furthermore, OBS notably activated the p53-p21 signalling pathway in GH3 cells, as evidenced by increased p53 and p21 expressions, enhanced p53 phosphorylation, and augmented p53 nuclear import. To our knowledge, this study is the first to reveal that OBS triggers senescence in pituitary cells via the p53-p21-RB signalling pathway. Our study demonstrates a novel toxic effect of OBS in vitro, and provides new perspectives for understanding the potential toxicity of OBS.

Phylogenetic analysis, computer modeling and catalytic prediction of an Amazonian soil β-glucosidase against a soybean saponin

Saponins are amphipathic glycosides with detergent properties present in vegetables. These compounds, when ingested, can cause difficulties in absorbing nutrients from food and even induce inflammatory processes in the intestine. There is already some evidence that saponins can be degraded by β-glucosidases of the GH3 family. In the present study, we evaluated, through computational tools, the possibility of a β-glucosidase (AMBGL17) obtained from a metagenomic analysis of the Amazonian soil, to catalytically interact with a saponin present in soybean. For this, the amino acid sequence of AMBGL17 was used in a phylogenetic analysis to estimate its origin and to determine its three-dimensional structure. The 3D structure of the enzyme was used in a molecular docking analysis to evaluate its interaction with soy saponin as a ligand. The results of the phylogenetic analysis showed that AMBGL17 comes from a microorganism of the phylum Chloroflexi, probably related to species of the order Aggregatinales. Molecular docking showed that soybean saponin can interact with the catalytic site of AMBGL17, with the amino acid GLY345 being important in this catalytic interaction, especially with a β-1,2 glycosidic bond present in the carbohydrate portion of saponin. In conclusion, AMBGL17 is an enzyme with interesting biotechnological potential in terms of mitigating the anti-nutritional and pro-inflammatory effects of saponins present in vegetables used for human and animal food.

Inactivation of the entire Arabidopsis group II GH3s confers tolerance to salinity and water deficit

Indole-3-acetic acid (IAA) controls a plethora of developmental processes. Thus, regulation of its concentration is of great relevance for plant performance. Cellular IAA concentration depends on its transport, biosynthesis and the various pathways for IAA inactivation, including oxidation and conjugation. Group II members of the GRETCHEN HAGEN 3 (GH3) gene family code for acyl acid amido synthetases catalysing the conjugation of IAA to amino acids. However, the high degree of functional redundancy among them has hampered thorough analysis of their roles in plant development. In this work, we generated an Arabidopsis gh3.1,2,3,4,5,6,9,17 (gh3oct) mutant to knock out the group II GH3 pathway. The gh3oct plants had an elaborated root architecture, showed an increased tolerance to different osmotic stresses, including an IAA-dependent tolerance to salinity, and were more tolerant to water deficit. Indole-3-acetic acid metabolite quantification in gh3oct plants suggested the existence of additional GH3-like enzymes in IAA metabolism. Moreover, our data suggested that 2-oxindole-3-acetic acid production depends, at least in part, on the GH3 pathway. Targeted stress-hormone analysis further suggested involvement of abscisic acid in the differential response to salinity of gh3oct plants. Taken together, our data provide new insights into the roles of group II GH3s in IAA metabolism and hormone-regulated plant development.

The GH3 amidosynthetases family and their role in metabolic crosstalk modulation of plant signaling compounds

The Gretchen Hagen 3 (GH3) genes encoding proteins belonging to the ANL superfamily are widespread in the plant kingdom. The ANL superfamily consists of three groups of adenylating enzymes: aryl- and acyl-CoA synthetases, firefly luciferase, and amino acid-activating adenylation domains of the nonribosomal peptide synthetases (NRPS). GH3s are cytosolic, acidic amidosynthetases of the firefly luciferase group that conjugate auxins, jasmonates, and benzoate derivatives to a wide group of amino acids. In contrast to auxins, which amide conjugates mainly serve as a storage pool of inactive phytohormone or are involved in the hormone degradation process, conjugation of jasmonic acid (JA) results in biologically active phytohormone jasmonyl-isoleucine (JA-Ile). Moreover, GH3s modulate salicylic acid (SA) concentration by conjugation of its precursor, isochorismate. GH3s, as regulators of the phytohormone level, are crucial for normal plant development as well as plant defense response to different abiotic and biotic stress factors. Surprisingly, recent studies indicate that FIN219/JAR1/GH3.11, one of the GH3 proteins, may act not only as an enzyme but is also able to interact with tau-class glutathione S-transferase (GSTU) and constitutive photomorphogenic 1 (COP1) proteins and regulate light and stress signaling pathways. The aim of this work is to summarize our current knowledge of the GH3 family.

Genome-Wide Analysis, Modeling, and Identification of Amino Acid Binding Motifs Suggest the Involvement of GH3 Genes during Somatic Embryogenesis of Coffea canephora

Auxin plays a central role in growth and plant development. To maintain auxin homeostasis, biological processes such as biosynthesis, transport, degradation, and reversible conjugation are essential. The Gretchen Hagen 3 (GH3) family genes codify for the enzymes that esterify indole-3-acetic acid (IAA) to various amino acids, which is a key process in the induction of somatic embryogenesis (SE). The GH3 family is one of the principal families of early response to auxin genes, exhibiting IAA-amido synthetase activity to maintain optimal levels of free auxin in the cell. In this study, we carried out a systematic identification of the GH3 gene family in the genome of Coffea canephora, determining a total of 18 CcGH3 genes. Analysis of the genetic structures and phylogenetic relationships of CcGH3 genes with GH3 genes from other plant species revealed that they could be clustered in two major categories with groups 1 and 2 of the GH3 family of Arabidopsis. We analyzed the transcriptome expression profiles of the 18 CcGH3 genes using RNA-Seq analysis-based data and qRT-PCR during the different points of somatic embryogenesis induction. Furthermore, the endogenous quantification of free and conjugated indole-3-acetic acid (IAA) suggests that the various members of the CcGH3 genes play a crucial role during the embryogenic process of C. canephora. Three-dimensional modeling of the selected CcGH3 proteins showed that they consist of two domains: an extensive N-terminal domain and a smaller C-terminal domain. All proteins analyzed in the present study shared a unique conserved structural topology. Additionally, we identified conserved regions that could function to bind nucleotides and specific amino acids for the conjugation of IAA during SE in C. canephora. These results provide a better understanding of the C. canephora GH3 gene family for further exploration and possible genetic manipulation.

Improvements of the productivity and saccharification efficiency of the cellulolytic β-glucosidase D2-BGL in Pichia pastoris via directed evolution

BACKGROUND

β-Glucosidases are essential for cellulose hydrolysis by catalyzing the final cellulolytic degradation of cello-oligomers and cellobiose to glucose. D2-BGL is a fungal glycoside hydrolase family 3 (GH3) β-glucosidase isolated from Chaetomella raphigera with high substrate affinity, and is an efficient β-glucosidase supplement to Trichoderma reesei cellulase mixtures for the saccharification of lignocellulosic biomass.

RESULTS

We have carried out error-prone PCR to further increase catalytic efficiency of wild-type (WT) D2-BGL. Three mutants, each with substitution of two amino acids on D2-BGL, exhibited increased activity in a preliminary mutant screening in Saccharomyces cerevisiae. Effects of single amino acid replacements on catalysis efficiency and enzyme production have been investigated by subsequent expression in Pichia pastoris. Substitution F256M resulted in enhancing the tolerance to substrate inhibition and specific activity, and substitution D224G resulted in increasing the production of recombinant enzyme. The best D2-BGL mutant generated, Mut M, was constructed by combining beneficial mutations D224G, F256M and Y260D. Expression of Mut M in Pichia pastoris resulted in 2.7-fold higher production of recombinant protein, higher V_max and greater substrate inhibition tolerance towards cellobiose relative to wild-type enzyme. Surprisingly, Mut M overexpression induced the ER unfolded protein response to a level lower than that with WT D2 overexpression in P. pastoris. When combined with the T. reesei cellulase preparation Celluclast 1.5L, Mut M hydrolyzed acid-pretreated sugarcane bagasse more efficiently than WT D2.

CONCLUSIONS

D2-BGL mutant Mut M was generated successfully by following directed evolution approach. Mut M carries three mutations that are not reported in other directed evolution studies of GH3 β-glucosidases, and this mutant exhibited greater tolerance to substrate inhibition and higher V_max than wild-type enzyme. Besides the enhanced specific activity, Mut M also exhibited a higher protein titer than WT D2 when it was overexpressed in P. pastoris. Our study demonstrates that both catalytic efficiency and productivity of a cellulolytic enzyme can be enhanced via protein engineering.

Genome-wide identification of GH3 genes in Brassica oleracea and identification of a promoter region for anther-specific expression of a GH3 gene

Background

The Gretchen Hagen 3 (GH3) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors. GH3 genes, especially Group III subgroup 6 GH3 genes, and their expression patterns in economically important B. oleracea var. oleracea have not been systematically identified.

Results

As a first step to understand regulation and molecular functions of Group III subgroup 6 GH3 genes, 34 GH3 genes including four subgroup 6 genes were identified in B. oleracea var. oleracea. Synteny found around subgroup 6 GH3 genes in B. oleracea var. oleracea and Arabidopsis thaliana indicated that these genes are evolutionarily related. Although expression of four subgroup 6 GH3 genes in B. oleracea var. oleracea is not induced by auxin, gibberellic acid, or jasmonic acid, the genes show different organ-dependent expression patterns. Among subgroup 6 GH3 genes in B. oleracea var. oleracea, only BoGH3.13–1 is expressed in anthers when microspores, polarized microspores, and bicellular pollens are present, similar to two out of four syntenic A. thaliana subgroup 6 GH3 genes. Detailed analyses of promoter activities further showed that BoGH3.13–1 is expressed in tapetal cells and pollens in anther, and also expressed in leaf primordia and floral abscission zones.

Conclusions

Sixty-two base pairs (bp) region (− 340 ~ − 279 bp upstream from start codon) and about 450 bp region (− 1489 to − 1017 bp) in BoGH3.13–1 promoter are important for expressions in anther and expressions in leaf primordia and floral abscission zones, respectively. The identified anther-specific promoter region can be used to develop male sterile transgenic Brassica plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07345-9.

Thyroid disrupting effects of perfluoroundecanoic acid and perfluorotridecanoic acid in zebrafish (Danio rerio) and rat pituitary (GH3) cell line

Due to global restriction on perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA), the use of long-chain perfluoroalkyl substances (PFASs, C > 8) and their environmental occurrences have increased. PFOS and PFOA have been known for thyroid disruption, however, knowledge is still limited on thyroid disrupting effects of long-chain PFASs (C > 10). In this study, two long-chain perfluorinated carboxylic acids (PFCAs), i.e., perfluoroundecanoic acid (PFUnDA) and perfluorotridecanoic acid (PFTrDA), were chosen and investigated for thyroid disrupting effects, using zebrafish embryo/larvae and rat pituitary cell line (GH3). For comparison, PFOA was also added as a test chemical and also investigated for its thyroid disruption potential. Following a 5 d exposure to PFTrDA, zebrafish larvae showed upregulation of the genes responsible for thyroid hormone synthesis (tshβ, nkx2.1, nis, tpo, mct8) and (de)activation (dio1, dio2). In contrast, both PFUnDA and PFOA induced no regulatory changes except for upregulation of a thyroid metabolism related gene (ugt1ab). Morphological changes such as decreased eyeball size, increased yolk sac size, or deflated swim bladder, occurred following exposure to PFUnDA, PFTrDA, and PFOA. In GH3 cells, exposure to PFUnDA and PFTrDA upregulated Tshβ gene, suggesting that these PFCAs increase thyroid hormone synthesis through stimulation by Tsh. In summary, both long-chain PFCAs could cause transcriptional changes of thyroid regulating genes that may lead to increased malformation of the zebrafish larvae, but the pathway of thyroid disruption appears to be different by the chain length. Confirmation and validation in adult fish following long term exposure are warranted.

- A new perspective on formation of high-molecular weight conjugates of auxin

Gretchen Hagen 3 (GH3) acyl acid amidosynthetases are encoded by early auxin-responsive genes and catalyze an ATP-dependent biosynthesis of IAA-amino acid conjugates. An amide conjugate of IAA, indole-3-acetyl-aspartate (IAA-aspartate, IAA-Asp), is a predominant form of bound auxin in immature seeds of pea. However, there is some evidence that IAA is also able to form high molecular weight amide conjugates with proteins in pea and other plant species. In this short study we report that recombinant PsGH3 IAA-amino acid synthetase, which exhibits a preference for the formation of IAA-Asp, can also conjugate IAA with the protein fraction from immature seeds of pea (S-10 fraction). We studied [14C]IAA incorporation to the S-10 protein fraction by two assays: TLC method and protein precipitation by trichloroacetic acid (TCA). In both cases, radioactivity of [14C]IAA in the protein fraction increases in comparison to the control (without PsGH3), about 9.3- and 3.17-fold, respectively. l-Asp, as a preferred substrate in the IAA conjugation catalyzed by PsGH3, down-regulates [14C]IAA conjugation to the proteins as shown by the TLC assay (∼2.8-fold decrease) and the TCA precipitation variant (∼2-fold decrease). Moreover, l-Trp that competes with Asp for the catalytic site of PsGH3 and inhibits activity of the enzyme, diminished radioactivity of [14C]IAA-proteins about 1.2- and 2.8-fold, respectively. Taking into account that amino group of an amino acid or a protein acts as an acceptor of the indole-3-acetyl moiety from IAA-AMP intermediate during GH3-dependent conjugation, we masked amine groups (α- and ε-NH2) of the S-10 protein fraction from pea seeds by reductive alkylation. The alkylated proteins revealed about 3- and 2.8-fold lower radioactivity of [14C]IAA than non-alkylated fraction for TLC and TCA precipitation variant, respectively. This is a first study demonstrating that formation of high molecular weight IAA conjugates with proteins is catalyzed by a GH3 acyl acid amidosynthetase.

Expression Analysis of Key Auxin Biosynthesis, Transport, and Metabolism Genes of Betula pendula with Special Emphasis on Figured Wood Formation in Karelian Birch

Auxin status in woody plants is believed to be a critical factor for the quantity and quality of the wood formed. It has been previously demonstrated that figured wood formation in Karelian birch (Betula pendula Roth var. carelica (Merckl.) Hämet-Ahti) is associated with a reduced auxin level and elevated sugar content in the differentiating xylem, but the molecular mechanisms of the abnormal xylogenesis remained largely unclear. We have identified genes involved in auxin biosynthesis (Yucca), polar auxin transport (PIN) and the conjugation of auxin with amino acids (GH3) and UDP-glucose (UGT84B1) in the B. pendula genome, and analysed their expression in trunk tissues of trees differing in wood structure. Almost all the investigated genes were overexpressed in Karelian birch trunks. Although Yucca genes were overexpressed, trunk tissues in areas developing figured grain had traits of an auxin-deficient phenotype. Overexpression of GH3s and UGT84B1 appears to have a greater effect on figured wood formation. Analysis of promoters of the differentially expressed genes revealed a large number of binding sites with various transcription factors associated with auxin and sugar signalling. These data agree with the hypothesis that anomalous figured wood formation in Karelian birch may be associated with the sugar induction of auxin conjugation.

Identification and expression analysis of auxin-responsive GH3 family genes in Chinese hickory (Carya cathayensis) during grafting

The GH3 genes play vital roles in auxin homeostasis by conjugating excess auxin to amino acids. However, how GH3 genes function during grafting in Chinese hickory (Carya cathayensis) is largely unknown. Here, based on the transcriptome database, a comprehensive identification and expression profiling analysis of 12 GH3 genes in Chinese hickory were performed. Phylogenetic analysis indicated that CcGH3-x exists in a specific subfamily. To understand the roles of CcGH3 genes, tissue-specific expression and the response to different phytohormones were determined. Expression profiles of GH3 genes of Chinese hickory during grafting were analysed. The data suggested that 10 CcGH3 genes were down-regulated at an early stage of grafting, indicating that auxin homeostasis regulated by the CcGH3 family might be inhibited at initial stages. At the completion of grafting, expression levels of members of the CcGH3 family were restored to normal levels. Endogenous auxin levels were also measured, and the data showed that free auxin decreased to the lowest level at an early stage of grafting, and then increased during grafting. Auxin amino acid conjugation increased at an early stage of grafting in rootstock, and then decreased with progression of the graft union. Our results demonstrate that the reduced expression of CcGH3 family genes during grafting might contribute to the release of free auxin, making an important contribution to the recovery of auxin levels after grafting.

Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis

Auxin is well known to regulate growth and development processes. Auxin early response genes serve as a critical component of auxin signaling and mediate auxin regulation of diverse physiological processes. In the present study, a genome-wide identification and comprehensive analysis of auxin early response genes were conducted in upland cotton. A total of 71 auxin response factor (ARF), 86 Auxin/Indole-3-Acetic Acid (Aux/IAA), 63 Gretchen Hagen3 (GH3), and 194 small auxin upregulated RNA (SAUR) genes were identified in upland cotton, respectively. Phylogenetic analysis revealed that the ARF, GH3, and SAUR families were likely subject to extensive evolutionary divergence between Arabidopsis and upland cotton, while the Aux/IAA family was evolutionary conserved. Expression profiles showed that the ARF, Aux/IAA, GH3, and SAUR family genes were extensively involved in embryogenic competence acquisition of upland cotton callus. The Aux/IAA family genes generally showed a higher expression level in the non-embryogenic callus (NEC) of highly embryogenic cultivar CCRI24 than that of recalcitrant cultivar CCRI12, which may be conducive to initializing the embryogenic transformation. Auxin early response genes were tightly co-expressed with most of the known somatic embryogenesis (SE) related genes, indicating that these genes may regulate upland cotton SE by interacting with auxin early response genes.

Molecular Dynamics Gives New Insights into the Glucose Tolerance and Inhibition Mechanisms on β-Glucosidases

β-Glucosidases are enzymes with high importance for many industrial processes, catalyzing the last and limiting step of the conversion of lignocellulosic material into fermentable sugars for biofuel production. However, β-glucosidases are inhibited by high concentrations of the product (glucose), which limits the biofuel production on an industrial scale. For this reason, the structural mechanisms of tolerance to product inhibition have been the target of several studies. In this study, we performed in silico experiments, such as molecular dynamics (MD) simulations, free energy landscape (FEL) estimate, Poisson-Boltzmann surface area (PBSA), and grid inhomogeneous solvation theory (GIST) seeking a better understanding of the glucose tolerance and inhibition mechanisms of a representative GH1 β-glucosidase and a GH3 one. Our results suggest that the hydrophobic residues Y180, W350, and F349, as well the polar one D238 act in a mechanism for glucose releasing, herein called "slingshot mechanism", dependent also on an allosteric channel (AC). In addition, water activity modulation and the protein loop motions suggest that GH1 β-Glucosidases present an active site more adapted to glucose withdrawal than GH3, in consonance with the GH1s lower product inhibition. The results presented here provide directions on the understanding of the molecular mechanisms governing inhibition and tolerance to the product in β-glucosidases and can be useful for the rational design of optimized enzymes for industrial interests.

Rice group I GH3 gene family, positive regulators of bacterial pathogens

Plant GH3 genes play pivotal roles in biotic stress through involving in hormonal homeostasis by conjugation to amino acids of the free-form of salicylic acid, jasmonic acid (JA) or indole-3-acetic acid. We recently showed that rice group I GH3 gene family, with four members, are the functional JA-Ile synthetases and positively mediated rice resistance to Xanthomonas oryzae pv. oryzae (Xoo). Here, we further found that these four genes are also positive regulators conferring resistance to Xanthomonas oryzae pv. oryzicola (Xoc), the devastating bacterial pathogen of rice. The transcript of these four genes were all activated upon Xoc invasion. The overexpressing plants showed less lesion length in comparison with wild type plant accompanying with higher pathogenesis-related genes accumulation, while the triple and quadruple suppressing plants showed susceptible to Xoc with less pathogenesis-related genes accumulation. Previous and present work demonstrate that rice group I GH3 family genes act as positive regulators in the resistance to Xoo and Xoc.

Chaetomella raphigera β-glucosidase D2-BGL has intriguing structural features and a high substrate affinity that renders it an efficient cellulase supplement for lignocellulosic biomass hydrolysis

BACKGROUND

To produce second-generation biofuels, enzymatic catalysis is required to convert cellulose from lignocellulosic biomass into fermentable sugars. β-Glucosidases finalize the process by hydrolyzing cellobiose into glucose, so the efficiency of cellulose hydrolysis largely depends on the quantity and quality of these enzymes used during saccharification. Accordingly, to reduce biofuel production costs, new microbial strains are needed that can produce highly efficient enzymes on a large scale.

RESULTS

We heterologously expressed the fungal β-glucosidase D2-BGL from a Taiwanese indigenous fungus Chaetomella raphigera in Pichia pastoris for constitutive production by fermentation. Recombinant D2-BGL presented significantly higher substrate affinity than the commercial β-glucosidase Novozyme 188 (N188; K _m = 0.2 vs 2.14 mM for p-nitrophenyl β-d-glucopyranoside and 0.96 vs 2.38 mM for cellobiose). When combined with RUT-C30 cellulases, it hydrolyzed acid-pretreated lignocellulosic biomasses more efficiently than the commercial cellulase mixture CTec3. The extent of conversion from cellulose to glucose was 83% for sugarcane bagasse and 63% for rice straws. Compared to N188, use of D2-BGL halved the time necessary to produce maximal levels of ethanol by a semi-simultaneous saccharification and fermentation process. We upscaled production of recombinant D2-BGL to 33.6 U/mL within 15 days using a 1-ton bioreactor. Crystal structure analysis revealed that D2-BGL belongs to glycoside hydrolase (GH) family 3. Removing the N-glycosylation N68 or O-glycosylation T431 residues by site-directed mutagenesis negatively affected enzyme production in P. pastoris. The F256 substrate-binding residue in D2-BGL is located in a shorter loop surrounding the active site pocket relative to that of Aspergillus β-glucosidases, and this short loop is responsible for its high substrate affinity toward cellobiose.

CONCLUSIONS

D2-BGL is an efficient supplement for lignocellulosic biomass saccharification, and we upscaled production of this enzyme using a 1-ton bioreactor. Enzyme production could be further improved using optimized fermentation, which could reduce biofuel production costs. Our structure analysis of D2-BGL offers new insights into GH3 β-glucosidases, which will be useful for strain improvements via a structure-based mutagenesis approach.

Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

BACKGROUND

Auxin-induced genes regulate many aspects of plant growth and development. The Gretchen Hagen 3 (GH3) gene family, one of three major early auxin-responsive families, is ubiquitous in the plant kingdom and its members function as regulators in modulating hormonal homeostasis, and stress adaptations. Specific Auxin-amido synthetase activity of GH3 subfamily II genes is reported to reversibly inactivate or fully degrade excess auxin through the formation of amino acid conjugates. Despite these crucial roles, to date, genome-wide analysis of the GH3 gene family has not been reported in cotton.

RESULTS

We identified a total of 10 GH3 subfamily II genes in G. arboreum, 10 in G. raimondii, and 20 in G. hirsutum, respectively. Bioinformatic analysis showed that cotton GH3 genes are conserved with the established GH3s in plants. Expression pattern analysis based on RNA-seq data and qRT-PCR revealed that 20 GhGH3 genes were differentially expressed in a temporally and spatially specific manner, indicating their diverse functions in growth and development. We further summarized the organization of promoter regulatory elements and monitored their responsiveness to treatment with IAA (indole-3-acetic acid), SA (salicylic acid), GA (gibberellic acid) and BL (brassinolide) by qRT-PCR in roots and stems. These hormones seemed to regulate the expression of GH3 genes in both a positive and a negative manner while certain members likely have higher sensitivity to all four hormones. Further, we tested the expression of GhGH3 genes in the BR-deficient mutant pag1 and the corresponding wild-type (WT) of CCRI24. The altered expression reflected the true responsiveness to BL and further suggested possible reasons, at least in part, responsible for the dramatic dwarf and shriveled phenotypes of pag1.

CONCLUSION

We comprehensively identified GH3 subfamily II genes in cotton. GhGH3s are differentially expressed in various tissues/organs/stages. Their response to IAA, SA, BL and GA and altered expression in pag1 suggest that some GhGH3 genes might be simultaneously involved in multiple hormone signaling pathways. Taken together, our results suggest that members of the GhGH3 gene family could be possible candidate genes for mechanistic study and applications in cotton fiber development in addition to the reconstruction of plant architecture.

A novel isoprimeverose-producing enzyme from Phaeoacremonium minimum is active with low concentrations of xyloglucan oligosaccharides

Xyloglucan is one of the major polysaccharides found in the plant cell wall and seeds. Owing to its complex branched structure, several different hydrolases are required to degrade it. Isoprimeverose‐producing enzymes (IPase) are unique among the glycoside hydrolase 3 family in that they recognize and release a disaccharide from the nonreducing end of xyloglucan oligosaccharides. Only two IPases have been previously isolated and characterized. A novel IPase from Phaeoacremonium minimum (PmIPase) was expressed and characterized. The xylopyranosyl residue at the nonreducing end of xyloglucan oligosaccharides was essential for hydrolytic activity, and PmIPase was unable to hydrolyze cellobiose into d‐glucose. PmIPase had a K_m for xyloglucan oligosaccharide substrate that was much lower than that of the reported IPase isolated from Aspergillus oryzae. This indicates that PmIPase was able to produce isoprimeverose efficiently from low concentrations of xyloglucan oligosaccharides. PmIPase also exhibited transglycosylation activity and was able to transfer isoprimeverose units to its substrates.

Glucose tolerant and glucose stimulated β-glucosidases - A review

The β-glucosidases (β-D-glucoside glucohydrolase, EC 3.2.1.21) hydrolyze glycosidic bonds of alkyl-, amino-, or aryl-β-D-glucosides, cyanogenic glucosides, disaccharides and short oligosaccharides and can also catalyze the synthesis of glycosyl-bonds between different molecules via transglycosylation. Due to their ubiquitous phylogenetic distribution, substrate diversity and ability to both hydrolyze and synthesize glycosidic bonds, the catalysis and regulation of β-glucosidases have been extensively studied. Many β-glucosidases are inhibited by the reaction product glucose, and reduced catalytic activity may limit the biotechnological and industrial applications of these enzymes and this has stimulated the search for β-glucosidases that maintain their activity at high glucose concentrations. Studies of many glucose tolerant enzymes have been reported and due to the ongoing interest in these enzymes, here it has been reviewed this accumulated body of knowledge which provides valuable insights as to the kinetics, structure, regulation and evolution of glucose tolerant and glucose stimulated β-glucosidases.

A ripening-induced SlGH3-2 gene regulates fruit ripening via adjusting auxin-ethylene levels in tomato (Solanum lycopersicum L.)

Silencing of SlGH3-2 in tomato alters auxin and ethylene levels during fruit ripening and cause reduced lycopene accumulation in the transgenic fruits. While auxin's role during fleshy fruit ripening is widely acknowledged to be important, the physiological functions of several ripening-induced genes, especially those involved in the maintenance of cellular auxin homeostasis, largely remain under-explored. In the present study, the updated inventory shows that 24 members constitute the Gretchen-Hagen 3 (GH3) gene family in tomato. Their characterization using an expression profiling approach revealed that SlGH3-2, a member of the group II IAA-amido synthetase, is strongly induced at the commencement of fruit ripening. Phylogenetic analysis and homology modeling revealed that SlGH3-2 is the closest homolog of pepper CcGH3 and grapevine VvGH3-1. Expression profiling revealed that the mRNA level of SlGH3-2 is inhibited in ripening mutants such as ripening-inhibitor (rin) and Never-ripe (Nr). Whereas both auxin and ethylene were found to act as positive regulators of its transcript accumulation. The fruits of 35S::SlGH3-2 RNAi lines exhibited prolonged shelf-life. Both ethylene production and lycopene accumulation were affected in the fruits of SlGH3-2 silenced lines. These observations were corroborated by the altered expression of key ethylene and carotenoid biosynthesis genes such as ACS2 and PSY1, respectively, in the RNAi lines. Additionally, the SlGH3-2 silenced line fruits had higher IAA and IBA levels at the ripening stages, and showed increased transcript accumulation of several known auxin-induced SlIAA and SlGH3 genes. Altogether, the present study suggests that SlGH3-2 influences fruit ripening in tomato via modulating ethylene and auxin crosstalk, especially during the early phase.

Combined effects of resveratrol and radiation in GH3 and TtT/GF pituitary adenoma cells

OBJECTIVE

Resveratrol and radiation decrease viability in various tumor cells. This study aims to investigate combined effects of resveratrol and radiation on viability, induction of apoptosis and necrosis, and expression of apoptosis modulators in rodent GH3 and TtT/GF pituitary adenoma cells in vitro.

METHODS

Cells were incubated with 10-100 µM resveratrol. Medium and medium with ethanol served as controls. After 2 h, cells were irradiated with 0-5 Gray (Gy) and further incubated for 48-72 h. Cell viability was quantified using a hemocytometer. Cell death was assessed with an enzyme-linked immunosorbent assay (ELISA) that detects free nucleosomes in cell lysates and free nucleosomes released to the culture medium. Expression of B-cell lymphoma-2 protein (BCL-2) and BCL-2 associated Xprotein (BAX) was measured using quantitative real time-polymerase chain reaction (qRT-PCR) to analyze changes in BAX/BCL-2 ratio.

RESULTS

Resveratrol and irradiation with 4 Gy alone and in combination significantly decreased cell viability (p = 0.017 and less). In the ELISA, 10 μM resveratrol significantly induced apoptosis in TtT/GF cells at 0 Gy (p < 0.001), but not at 3 or 5 Gy. In the ELISA, 10 μM resveratrol significantly induced necrosis in GH3 cells at 0, 3 and 5 Gy (p < 0.001). While qRT-PCR did not demonstrate a significant effect of 10 µM resveratrol or radiation on expression of BAX or BCL-2, a significant increase in the BAX/BCL-2 ratio was found after irradiation with 5 Gy in GH3 cells (p = 0.0027).

CONCLUSION

While moderate irradiation solely led to inhibited proliferation, resveratrol induced cell death in rodent pituitary adenoma cells.

Preference of Arabidopsis thaliana GH3.5 acyl amido synthetase for growth versus defense hormone acyl substrates is dictated by concentration of amino acid substrate aspartate

The GH3 family of adenylating enzymes conjugate acyl substrates such as the growth hormone indole-3-acetic acid (IAA) to amino acids via a two-step reaction of acyl substrate adenylation followed by amino acid conjugation. Arabidopsis thaliana GH3.5 was previously shown to be unusual in that it could adenylate both IAA and the defense hormone salicylic acid (SA, 2-hydroxybenzoate). Our detailed studies of the kinetics of GH3.5 on a variety of auxin and benzoate substrates provides insight into the acyl preference and reaction mechanism of GH3.5. For example, we found GH3.5 activity on substituted benzoates is not defined by the substitution position as it is for GH3.12/PBS3. Most importantly, we show that GH3.5 strongly prefers Asp as the amino acid conjugate and that the concentration of Asp dictates the functional activity of GH3.5 on IAA vs. SA. Not only is Asp used in amino acid biosynthesis, but it also plays an important role in nitrogen mobilization and in the production of downstream metabolites, including pipecolic acid which propagates defense systemically. During active growth, [IAA] and [Asp] are high and the catalytic efficiency (k_cat/K_m) of GH3.5 for IAA is 360-fold higher than with SA. GH3.5 is expressed under these conditions and conversion of IAA to inactive IAA-Asp would provide fine spatial and temporal control over local auxin developmental responses. By contrast, [SA] is dramatically elevated in response to (hemi)-biotrophic pathogens which also induce GH3.5 expression. Under these conditions, [Asp] is low and GH3.5 has equal affinity (K_m) for SA and IAA with similar catalytic efficiencies. However, the concentration of IAA tends to be very low, well below the K_m for IAA. Therefore, GH3.5 catalyzed formation of SA-Asp would occur, fine-tuning localized defensive responses through conversion of active free SA to SA-Asp. Taken together, we show how GH3.5, with dual activity on IAA and SA, can integrate cellular metabolic status via Asp to provide fine control of growth vs. defense outcomes and hormone homeostasis.

Auxin transport and conjugation caught together

This article comments on: Kong Q, Ma W, Yang H, Ma G, Mantyla JJ, Benning C. 2017. The Arabidopsis WRINKLED1 transcription factor affects auxin homeostasis in roots. Journal of Experimental Botany 68, 4627–4634.

Auxin homeostasis: the DAO of catabolism

Nearly all programmed and plastic plant growth responses are at least partially regulated by auxins, such as indole-3-acetic acid (IAA). Although vectorial, long distance auxin transport is essential to its regulatory function, all auxin responses are ultimately localized in individual target cells. As a consequence, cellular auxin concentrations are tightly regulated via coordinated biosynthesis, transport, conjugation, and oxidation. The primary auxin oxidative product across species is 2-oxindole-3-acetic acid (oxIAA), followed by glucose and amino acid conjugation to oxIAA. Recently, the enzymes catalyzing the oxidative reaction were characterized in Arabidopsis thaliana. DIOXYGENASE OF AUXIN OXIDATION (DAO) comprises a small subfamily of the 2-oxoglutarate and Fe(II) [2-OG Fe(II)] dependent dioxygenase superfamily. Biochemical and genetic studies have revealed critical physiological functions of DAO during plant growth and development. Thus far, DAO has been identified in three species by homology. Here, we review historical and recent studies and discuss future perspectives regarding DAO and IAA oxidation.

Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress β-lactam antibiotic resistance

NagZ is an N-acetyl-β-d-glucosaminidase that participates in the peptidoglycan (PG) recycling pathway of Gram-negative bacteria by removing N-acetyl-glucosamine (GlcNAc) from PG fragments that have been excised from the cell wall during growth. The 1,6-anhydromuramoyl-peptide products generated by NagZ activate β-lactam resistance in many Gram-negative bacteria by inducing the expression of AmpC β-lactamase. Blocking NagZ activity can thereby suppress β-lactam antibiotic resistance in these bacteria. The NagZ active site is dynamic and it accommodates distortion of the glycan substrate during catalysis using a mobile catalytic loop that carries a histidine residue which serves as the active site general acid/base catalyst. Here, we show that flexibility of this catalytic loop also accommodates structural differences in small molecule inhibitors of NagZ, which could be exploited to improve inhibitor specificity. X-ray structures of NagZ bound to the potent yet non-selective N-acetyl-β-glucosaminidase inhibitor PUGNAc (O-(2-acetamido-2-deoxy-d-glucopyranosylidene) amino-N-phenylcarbamate), and two NagZ-selective inhibitors - EtBuPUG, a PUGNAc derivative bearing a 2-N-ethylbutyryl group, and MM-156, a 3-N-butyryl trihydroxyazepane, revealed that the phenylcarbamate moiety of PUGNAc and EtBuPUG completely displaces the catalytic loop from the NagZ active site to yield a catalytically incompetent form of the enzyme. In contrast, the catalytic loop was found positioned in the catalytically active conformation within the NagZ active site when bound to MM-156, which lacks the phenylcarbamate extension. Displacement of the catalytic loop by PUGNAc and its N-acyl derivative EtBuPUG alters the active site conformation of NagZ, which presents an additional strategy to improve the potency and specificity of NagZ inhibitors.

GH3-Mediated Auxin Conjugation Can Result in Either Transient or Oscillatory Transcriptional Auxin Responses

The conjugation of the phytohormone auxin to amino acids via members of the gene family GH3 is an important component in the auxin-degradation pathway in the model plant species Arabidopsis thaliana, as well as many other plant species. Since the GH3 genes are themselves up-regulated in response to auxin, providing a negative feedback on intracellular auxin levels, it is hypothesised that the GH3s have a role in auxin homoeostasis. To investigate this, we develop a mathematical model of auxin signalling and response that includes the auxin-inducible negative feedback from GH3 on the rate of auxin degradation. In addition, we include a positive feedback on the rate of auxin input via the auxin influx transporter LAX3, shown previously to be expressed in response to auxin and to have an important role during lateral root emergence. In the absence of the LAX3 positive feedback, we show that the GH3 negative feedback suffices to generate a transient transcriptional response to auxin in the shape of damped oscillations of the model system. When LAX3 positive feedback is present, sustained oscillations of the system are possible. Using steady-state analyses, we identify and discuss key parameters affecting the oscillatory behaviour of the model. The transient peak of auxin and subsequent transcriptional response caused by the up-regulation of GH3 represents a possible protective homoeostasis mechanism that may be used by plant cells in response to excess auxin.

Role of thyrotropin-releasing hormone in prolactin-producing cell models

Thyrotropin-releasing hormone (TRH) is a hypothalamic hypophysiotropic neuropeptide that was named for its ability to stimulate the release of thyroid-stimulating hormone in mammals. It later became apparent that it exerts a number of species-dependent hypophysiotropic activities that regulate other pituitary hormones. TRH also regulates the synthesis and release of prolactin, although whether it is a physiological regulator of prolactin that remains unclear. Occupation of the Gq protein-coupled TRH receptor in the prolactin-producing lactotroph increases the turnover of inositol, which in turn activates the protein kinase C pathway and the release of Ca(2+) from storage sites. TRH-induced signaling events also include the activation of extracellular signal-regulated kinase (ERK) and induction of MAP kinase phosphatase, an inactivator of activated ERK. TRH stimulates prolactin synthesis through the activation of ERK, whereas prolactin release occurs via elevation of intracellular Ca(2+). We have been investigating the role of TRH in a pituitary prolactin-producing cell model. Rat pituitary somatolactotroph GH3 cells, which produce and release both prolactin and growth hormone (GH), are widely used as a model for the study of prolactin- and GH-secreting cells. In this review, we describe the general action of TRH as a hypophysiotropic factor in vertebrates and focus on the role of TRH in prolactin synthesis using GH3 cells.

Jasmonic acid-isoleucine formation in grapevine (Vitis vinifera L.) by two enzymes with distinct transcription profiles

The plant hormone jasmonic acid (JA) is essential for stress responses and the formation of reproductive organs, but its role in fruit development and ripening is unclear. Conjugation of JA to isoleucine is a crucial step in the JA signaling pathway since only JA-Ile is recognized by the jasmonate receptor. The conjugation reaction is catalyzed by JA-amido synthetases, belonging to the family of Gretchen Hagen3 (GH3) proteins. Here, in vitro studies of two grapevine (Vitis vinifera L. cv Shiraz) GH3 enzymes, VvGH3-7 and VvGH3-9, demonstrated JA-conjugating activities with an overlapping range of amino acid substrates, including isoleucine. Expression studies of the corresponding genes in grape berries combined with JA and JA-Ile measurements suggested a primary role for JA signaling in fruit set and cell division and did not support an involvement of JA in the ripening process. In response to methyl JA (MeJA) treatment, and in wounded and unwounded (distal) leaves, VvGH3-9 transcripts accumulated, indicating a participation in the JA response. In contrast, VvGH3-7 was unresponsive to MeJA and local wounding, demonstrating a differential transcriptional regulation of VvGH3-7 and VvGH3-9. The transient induction of VvGH3-7 in unwounded, distal leaves was suggestive of the involvement of an unknown mobile wound signal.

The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A

Completion of the whole genome sequencing of citrus enabled us to perform genome-wide identification and functional analysis of the gene families involved in agronomic traits and morphological diversity of citrus. In this study, 22 CitARF, 11 CitGH3 and 26 CitAUX/IAA genes were identified in citrus, respectively. Phylogenetic analysis revealed that all the genes of each gene family could be subdivided into three groups and showed strong evolutionary conservation. The GH3 and AUX/IAA gene families shrank and ARF gene family was highly conserved in the citrus genome after speciation from Arabidopsis thaliana. Tissue-specific expression profiles revealed that 54 genes were expressed in at least one tissue while just 5 genes including CitARF07, CitARF20, CitGH3.04, CitAUX/IAA25 and CitAUX/IAA26 with very low expression level in all tissues tested, suggesting that the CitARF, CitGH3 and CitAUX/IAA gene families played important roles in the development of citrus organs. In addition, our data found that the expression of 2 CitARF, 4 CitGH3 and 4 AUX/IAA genes was affected by IAA treatment, and 7 genes including, CitGH3.04, CitGH3.07, CitAUX/IAA03, CitAUX/IAA04, CitAUX/IAA18, CitAUX/IAA19 and CitAUX/IAA23 were related to fruitlet abscission. This study provides a foundation for future studies on elucidating the precise role of citrus ARF, GH3 and AUX/IAA genes in early steps of auxin signal transduction and open up a new opportunity to uncover the molecular mechanism underlying citrus fruitlet abscission.

Light induces jasmonate-isoleucine conjugation via OsJAR1-dependent and -independent pathways in rice

The bioactive form of jasmonate is the conjugate of the amino acid isoleucine (Ile) with jasmonic acid (JA), which is biosynthesized in a reaction catalysed by the GH3 enzyme JASMONATE RESISTANT 1 (JAR1). We examined the biochemical properties of OsJAR1 and its involvement in photomorphogenesis of rice (Oryza sativa). OsJAR1 has a similar substrate specificities as its orthologue in Arabidopsis. However, osjar1 loss-of-function mutants did not show as severe coleoptile phenotypes as the JA-deficient mutants coleoptile photomorphogenesis 2 (cpm2) and hebiba, which develop long coleoptiles in all light qualities we examined. Analysis of hormonal contents in the young seedling stage revealed that osjar1 mutants are still able to synthesize JA-Ile conjugate in response to blue light, suggesting that a redundantly active enzyme can conjugate JA and Ile in rice seedlings. A good candidate for this enzyme is OsJAR2, which was found to be able to catalyse the conjugation of JA with Ile as well as with some additional amino acids. In contrast, if plants in the vegetative stage were mechanically wounded, the content of JA-Ile was severely reduced in osjar1, demonstrating that OsJAR1 is the most important JA-Ile conjugating enzyme in the wounding response during the vegetative stage.

Discovery of two novel β-glucosidases from an Amazon soil metagenomic library

An Amazon soil microbial community metagenomic fosmid library was functionally screened for β-glucosidase activity. Contig analysis of positive clones revealed the presence of two ORFs encoding novel β-glucosidases, AmBGL17 and AmBGL18, from the GH3 and GH1 families, respectively. Both AmBGL17 and AmBGL18 were functionally identified as β-glucosidases. The enzymatic activity of AmBGL17 was further characterized. AmBGL17 was tested with different substrates and showed highest activity on pNPβG substrate with an optimum temperature of 45 °C and an optimum pH of 6. AmBGL17 showed a Vmax of 116 mM s(-1) and Km of 0.30 ± 0.017 mM. This is the first report of β-glucosidases from an Amazon soil microbial community using a metagenomic approach.

Dynamics of the concentration of IAA and some of its conjugates during the induction of somatic embryogenesis in Coffea canephora

Most of the somatic embryogenesis (SE) process requires the presence, either before or during the embryogenic process, of at least one exogenous auxin. This exogenous auxin induces the presence of endogenous auxins, which appears to be essential for SE induction. We found that during the preincubation period of SE in Coffea canephora, there is an important increase in both free and conjugated indole-3-acetic acid (IAA), as well as indole-3-butyric acid. This increase is accompanied by an increase in the expression of YUCCA (CcYUC), TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (CcTAA1), and GRETCHEN HAGEN 3 (GH3) genes. On the other hand, most of the IAA compounds decreased during the induction of SE. The results presented in this research suggest that a balance between free IAA and its amide conjugates is necessary to allow the expression of SE-related genes.

Auxin homeostasis in plant stress adaptation response

Auxin plays a wide range of regulatory roles in diverse aspects of plant growth and developmental processes through a complex network of signaling interactions. In the May issue of Journal of Biological Chemistry, we have demonstrated that auxin homeostasis directly links growth regulation with stress adaptation responses through interactions with salicylic acid (SA) and abscisic acid (ABA) signals. In this signaling network, the endogenous auxin content is coordinately regulated through negative feedback by a group of auxin-inducible GH3 genes that encode auxin-conjugating enzymes. The Arabidopsis mutant wes1-D overexpressing a GH3 gene WES1 exhibits typical auxin-deficient traits, such as reduced growth and leaf curling, but is resistant to both biotic and abiotic stresses. In addition, various stress-regulated genes, including pathogenesis- related protein genes (PRs) and C-repeat/dehydration responsive element binding factor genes (CBFs), are up-regulated in the mutant. Consistent with these observations, WES1 is activated by pathogenic infections and abiotic stresses as well as by exogenous SA and ABA. We therefore propose that the WES1-mediated growth suppression would underlie the commonly observed symptoms of infected or stressed plants and provide a mechanism for auxin action in the fitness costs of induced resistance in plants.