GH3 Gene Research Articles

Overexpression of the RAV Transcription Factor OsAAT1 Confers Enhanced Arsenic Tolerance by Modulating Auxin Hemostasis in Rice.

Characterization of arsenic (As)-responsive genes is fundamental to solving the issue of As contamination in rice. Herein, we establish the involvement of an RAV transcription factor OsAAT1 (Arsenic Accumulation and Tolerance 1) in regulating As response in rice. The expression of OsAAT1 is significantly higher in roots and stems of rice seedlings and is clearly upregulated by higher concentrations of arsenite [As(III)]. Compared with wild-type (WT) plants, OsAAT1-overexpressed transgenic lines (OE-OsAAT1) exhibit tolerance, while OsAAT1-knockout mutants (Osaat1) are sensitive to As(III) stress. Notably, the application of exogenous 1-naphthylacetic acid (NAA) greatly enhances the As tolerance of WT and transgenic lines, with stronger effects on OE-OsAAT1. The change in OsAAT1 expression leads to the alteration of As and auxin accumulation in transgenic plants by regulating the expression of OsLsi1, OsLsi2, OsCRL4, and OsAUX1 genes. Moreover, overexpression of OsAAT1 accelerates ROS scavenging and phytochelatins (PCs) synthesis, especially with the addition of exogenous NAA. OsAAT1 localizes in the nucleus and works as a transcriptional suppressor. OsGH3-12, belonging to the auxin-responsive GH3 gene family, is the downstream target gene of OsAAT1, whose expression is extensively downregulated by As(III). These findings provide new insights into As response via auxin signaling pathway in rice.

The Genome-Wide Identification, Characterization, and Expression Patterns of the Auxin-Responsive PbGH3 Gene Family Reveal Its Crucial Role in Organ Development

The regulation of vital plant activities by hormones is governed by a family of macromolecular peptides referred to as GH3 genes. This work analyzed the expression patterns of GH3 family genes in pear tissues using transcriptome data and bioinformatics analysis. In the Bai Li pear genome, a total of 18 PbGH3 genes were identified. Comparative evolutionary studies have shown a strong association between PbGH3 and AtGH3 class I and class II proteins. The role of PbGH3 genes in growth activities and hormone regulation was revealed using gene ontology (GO) and promoter region analysis. In addition, although certain PbGH3 genes exhibited tissue-specific expression in sepals, the majority had a ubiquitous expression across all tissues. Bioinformatics and expression studies suggest that the GH3 gene family in pears may have a role in controlling the abscission of the fruit’s sepals. This work sheds light on the pear fruit sepal shedding process and may inspire further research.

The GH3 Protein from the Clubroot Pathogen Plasmodiophora brassicae Causes Hormone-Related Phenotypes in Arabidopsis thaliana

In the genome of the obligate biotrophic protist Plasmodiophora brassicae, which causes clubroot disease in the Brassicaceae family, a single gene was identified with homology to the group of GH3 proteins synthesizing amino acid conjugates with carboxylic acids. In comparison to plant members the P. brassicae GH3 protein seems to be very promiscuous with respect to the substrates converted. In vitro assays showed conversion of three different auxins (indole-3-acetic, IAA; indole-propionic, IPA; and indole-3-butyric acids, IBA), jasmonic acid (JA) and also 12-oxo-phytodienoic acid (OPDA). Auxin and Methyl-JA responsive elements were found in the promoter sequence of PbGH3. For further analysis Arabidopsis thaliana was transformed with PbGH3. Seedlings with confirmed constitutive PbGH3 protein production were grown to adult plants that were shown to produce fewer inflorescences per plant. Growth on 10 µM IAA or JA levels also altered the phenotype of the seedlings, but not so much between wild types and transgenic lines. The hormone profiles in seedlings and adult plants were examined for IAA, JA, OPDA, and respective conjugates. Transgenic seedlings displayed changes that could be partially attributed to the overexpression of a GH3 gene like lower levels of free IAA and the JA precursor cis-OPDA under control conditions, and higher levels of some auxin conjugates accumulated after IAA treatment compared to the corresponding wild types. However, the hormone patterns in adult plants were more complex and varied based on different tissue types analyzed. After inoculation with P. brassicae the transgenic plants did not show any changes in infection rate and disease index, but had higher shoot and lower root weight in infected plants compared to controls. Based on the above findings we discuss a role for PbGH3 during pathogenesis.

Genome-wide identification and expression characterization of the GH3 gene family of tea plant (Camellia sinensis)

To comprehensively understand the characteristics of the GH3 gene family in tea plants (Camellia sinensis), we identified 17 CsGH3 genes and analyzed their physicochemical properties, phylogenetic relationships, gene structures, promoters, and expression patterns in different tissues. The study showed that the 17 CsGH3 genes are distributed on 9 chromosomes, and based on evolutionary analysis, the CsGH3 members were divided into three subgroups. Gene duplication analysis revealed that segmental duplications have a significant impact on the amplification of CsGH3 genes. In addition, we identified and classified cis-elements in the CsGH3 gene promoters and detected elements related to plant hormone responses and non-biotic stress responses. Through expression pattern analysis, we observed tissue-specific expression of CsGH3.3 and CsGH3.10 in flower buds and roots. Moreover, based on predictive analysis of upstream regulatory transcription factors of CsGH3, we identified the potential transcriptional regulatory role of gibberellin response factor CsDELLA in CsGH3.14 and CsGH3.15. In this study, we found that CsGH3 genes are involved in a wide range of activities, such as growth and development, stress response, and transcription. This is the first report on CsGH3 genes and their potential roles in tea plants. In conclusion, these results provide a theoretical basis for elucidating the role of GH3 genes in the development of perennial woody plants and offer new insights into the synergistic effects of multiple hormones on plant growth and development in tea plants.

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

BackgroundAuxins 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.ResultsA 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.ConclusionThis 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.

Heterologous expression of PtAAS1 reveals the metabolic potential of the common plant metabolite phenylacetaldehyde for auxin synthesis in planta.

Aromatic aldehydes and amines are common plant metabolites involved in several specialized metabolite biosynthesis pathways. Recently, we showed that the aromatic aldehyde synthase PtAAS1 and the aromatic amino acid decarboxylase PtAADC1 contribute to the herbivory-induced formation of volatile 2-phenylethanol and its glucoside 2-phenylethyl-β-D-glucopyranoside in Populus trichocarpa. To unravel alternative metabolic fates of phenylacetaldehyde and 2-phenylethylamine beyond alcohol and alcohol glucoside formation, we heterologously expressed PtAAS1 and PtAADC1 in Nicotiana benthamiana and analyzed plant extracts using untargeted LC-qTOF-MS and targeted LC-MS/MS analysis. While the metabolomes of PtAADC1-expressing plants did not significantly differ from those of control plants, expression of PtAAS1 resulted in the accumulation of phenylacetic acid (PAA) and PAA-amino acid conjugates, identified as PAA-aspartate and PAA-glutamate. Herbivory-damaged poplar leaves revealed significantly induced accumulation of PAA-Asp, while levels of PAA remained unaltered upon herbivory. Transcriptome analysis showed that members of auxin-amido synthetase GH3 genes involved in the conjugation of auxins with amino acids were significantly upregulated upon herbivory in P. trichocarpa leaves. Overall, our data indicates that phenylacetaldehyde generated by poplar PtAAS1 serves as a hub metabolite linking the biosynthesis of volatile, non-volatile herbivory-induced specialized metabolites, and phytohormones, suggesting that plant growth and defense can be balanced on a metabolic level.

Comparative Transcriptome Analysis between Embryogenic and Non-Embryogenic Callus of Davidia involucrata

Davidia involucrata Baill. (D. involucrata), a rare and endangered wild plant, is native to China and is globally recognized as an ornamental tree species. However, D. involucrata exhibits inherent biological characteristics that contribute to its low reproductive efficiency. To address this challenge, somatic embryogenesis, a biotechnological method, offers numerous advantages, including enhanced reproductive efficiency, a large reproductive coefficient, and a complete structural composition. Consequently, somatic embryogenesis holds significant value in the propagation and genetic improvement of this particular tree species. In a previous study, we utilized immature zygotic embryos of D. involucrata as explants and induced somatic embryogenesis from embryogenic callus, thereby establishing a rapid propagation and plant regeneration scheme. In this study, we utilized Illumina RNA sequencing to compare the transcriptomes of the embryogenic callus (EC) and non-embryogenic callus (NEC) of D. involucrata. The analysis revealed 131,109 unigenes assembled from EC and NEC, and 12,806 differentially expressed genes (DEGs) were identified. To verify the authenticity of the transcriptome sequencing results, qRT-PCR was performed and 16 DEGs were screened, with the stable reference gene UBQ being selected. Our analysis focused on genes related to plant growth regulators and somatic embryogenesis, such as the Aux, IAA, ARF, GH3, AHP, ARR, CYCD, BBM, WUS, GRF, SERK, and WOX gene families. We found that certain genes in these families were significantly upregulated in EC induction compared to NEC, indicating that they play crucial roles in D. involucrata cell proliferation, differentiation, and cell totipotency. These results offer new insights into the role of these gene families in EC, and may guide efforts to improve the somatic embryo induction, culture conditions, and genetic transformation efficiency of D. involucrata.

Melatonin regulates gene expressions through activating auxin synthesis and signaling pathways.

Both melatonin and indole-3-acetic acid (IAA) are derived from tryptophan. And the most interesting and unsolved puzzle in melatonin research is that what is the relationship between melatonin and auxin? In this study, we performed transcriptome analysis with a time series method to disclose the connection of the two metabolites in soybean. Our results reveal that melatonin and IAA treatments cause substantial overlaps in gene expression changes. Common genes of melatonin and IAA treatments could be sorted into clusters with very similar expression tendency. A KEGG assay showed that exogenous applied melatonin enriched differentially expressed genes in auxin biosynthesis and signaling pathways. For details, melatonin up-regulates several YUCCA genes which participate in auxin biosynthesis; melatonin also enhances expression levels of auxin receptor coding genes, such as TIR1, AFB3 and AFB5; dozens of genes involved in auxin transport, such as AUXI and PIN, are regulated by melatonin similarly as by auxin; auxin-responsive genes, such as IAA, ARF, GH3 and SAUR-like genes, intensively respond to melatonin as well as to auxin. A DR5 promoter mediated GUS staining assay showed that low concentration of melatonin could induce auxin biosynthesis in a dosage manner, whereas high concentration of melatonin would eliminate such effect. At last, gene ontology (GO) analysis suggests that melatonin treatment has similar characteristics as auxin treatment in many processes. However, the two molecules still keep their own features respectively. For example, melatonin takes part in stress responses, while IAA treatment enriches the GO terms that related to cell growth. Taken together, exogenous applied melatonin, if not exceeds the appropriate concentration, could promote auxin responses range from biosynthesis to signaling transduction. Thus, our research is a key part to explain the auxin-like roles of melatonin in regulating plant growth.

GmIAA27 Encodes an AUX/IAA Protein Involved in Dwarfing and Multi-Branching in Soybean.

Soybean plant height and branching affect plant architecture and yield potential in soybean. In this study, the mutant dmbn was obtained by treating the cultivar Zhongpin 661 with ethylmethane sulfonate. The dmbn mutant plants were shorter and more branched than the wild type. The genetic analysis showed that the mutant trait was controlled by a semi-dominant gene. The candidate gene was fine-mapped to a 91 kb interval on Chromosome 9 by combining BSA-seq and linkage analysis. Sequence analysis revealed that Glyma.09g193000 encoding an Aux/IAA protein (GmIAA27) was mutated from C to T in the second exon of the coding region, resulting to amino acid substitution of proline to leucine. Overexpression of the mutant type of this gene in Arabidopsis thaliana inhibited apical dominance and promoted lateral branch development. Expression analysis of GmIAA27 and auxin response genes revealed that some GH3 genes were induced. GmIAA27 relies on auxin to interact with TIR1, whereas Gmiaa27 cannot interact with TIR1 owing to the mutation in the degron motif. Identification of this unique gene that controls soybean plant height and branch development provides a basis for investigating the mechanisms regulating soybean plant architecture development.

Integrated transcriptome and hormonal analysis of naphthalene acetic acid-induced adventitious root formation of tea cuttings (Camellia sinensis)

BackgroundTea plant breeding or cultivation mainly involves propagation via cuttings, which not only ensures the inheritance of the excellent characteristics of the mother plant but also facilitates mechanized management. The formation of adventitious root (AR) determines the success of cutting-based propagation, and auxin is an essential factor involved in this process. To understand the molecular mechanism underlying AR formation in nodal tea cuttings, transcriptome and endogenous hormone analysis was performed on the stem bases of red (mature)- and green (immature)-stem cuttings of ‘Echa 1 hao’ tea plant as affected by a pulse treatment with naphthalene acetic acid (NAA).ResultsIn this study, NAA significantly promoted AR formation in both red- and green-stem cuttings but slightly reduced callus formation. External application of NAA reduced the levels of endogenous indole-3-acetic acid (IAA) and cytokinin (TZR, trans-zeatin riboside). The number of DEGs (NAA vs. CK) identified in the green-stem cuttings was significantly higher than that in the red-stem cuttings, which corresponded to a higher rooting rate of green-stem cuttings under the NAA treatment. A total of 82 common DEGs were identified as being hormone-related and involved in the auxin, cytokinin, abscisic acid, ethylene, salicylic acid, brassinosteroid, and jasmonic acid pathways. The negative regulation of NAA-induced IAA and GH3 genes may explain the decrease of endogenous IAA. NAA reduced endogenous cytokinin levels and further downregulated the expression of cytokinin signalling-related genes. By the use of weighted gene co-expression network analysis (WGCNA), several hub genes, including three [cellulose synthase (CSLD2), SHAVEN3-like 1 (SVL1), SMALL AUXIN UP RNA (SAUR21)] that are highly related to root development in other crops, were identified that might play important roles in AR formation in tea cuttings.ConclusionsNAA promotes the formation of AR of tea cuttings in coordination with endogenous hormones. The most important endogenous AR inductor, IAA, was reduced in response to NAA. DEGs potentially involved in NAA-mediated AR formation of tea plant stem cuttings were identified via comparative transcriptome analysis. Several hub genes, such as CSLD2, SVL1 and SAUR21, were identified that might play important roles in AR formation in tea cuttings.

Highly Efficient Biotransformation of Phenolic Glycosides Using a Recombinant β-Glucosidase From White Rot Fungus Trametes trogii.

Phenolic glycosides are the important bioactive molecules, and their bioavailability can be influenced by enzyme hydrolysis, such as β-glucosidases (EC3.2.1.21) and other glycosyl hydrolases (GHs). Wood rotting fungi possess a superfamily of GHs, but little attention has been paid to the GHs and their potential applications in biotransformation of phenolic glycosides. In this study, two GH3 gene family members of Trametes trogii S0301, mainly expressed in the carbon sources conversion stage were cloned, and TtBgl3 coded by T_trogii_12914 showed β-glucosidase activity toward 4-nitrophenyl β-D-glucopyranoside (pNPG). The recombinant TtBgl3 preferred an intermediately neutral optimum pH with >80% of the maximum activity at pH 5.0–7.0 and was stable at a wide range of pH (5.0–10.0). Phenolic glycosides transformation experiments showed that TtBgl3 was a dual-activity enzyme with both activities of aryl-β-D-glucosidase and β-glucuronidase, and could hydrolyze the β-glucoside/glucuronide bond of phenolic glycosides. Under optimized conditions, the recombinant TtBgl3 had much higher transformation efficiency toward the β-glucoside bond of gastrodin, esculin and daidzin than β-glucuronide bond of baicalin, with the transformation rate of 100 and 50%, respectively. Our homology modeling, molecular docking, and mutational analysis demonstrated that His85 and Lys467 in the acceptor-binding pocket of TtBgl3 were the potential active sites. The point mutation of His85 and Lys467 leads to the significantly impaired catalytic activity toward pNPG and also the weak transformation efficiency toward gastrodin. These findings provide insights for the identification of novel GH3 β-glucosidases from T. trogii and other wood-rotting fungi. Furthermore, TtBgl3 might be applied as green and efficient biological catalysts in the deglycosylation of diverse phenolics to produce bioactive glycosides for drug discovery in the future.

Integrated physiological, transcriptomic and metabolomic analysis of the response of Trifolium pratense L. to Pb toxicity

Lead (Pb) interferes with plant gene expression, alters metabolite contents and affects plant growth. However, the molecular mechanism underlying the plant response to Pb is not completely understood. In the present study, Trifolium pratense L. was exposed to Pb concentrations of 0 (Pb0), 500 (Pb500), 1000 (Pb1000), 2000 (Pb2000) and 3000 (Pb3000) mg/kg in soils. Pb stress affected the ability of T. pratense to accumulate and transport Pb, increased the activity of peroxidase (POD) and the contents of malondialdehyde (MDA) and proline, decreased the amount of photosynthetic pigments and soluble proteins, and led to changes in growth and biomass. Transcriptomic and metabolomic analyses showed that Pb mainly affected eight pathways, and LHC, flavonoids, organic acids, amino acids and carbohydrates were upregulated or downregulated. Moreover, Pb500 induced the upregulation of serA, promoted the synthesis of citric acid, maintained photosynthetic pigment levels, and ultimately promoted an increase in stem length. Pb3000 induced the upregulation of ARF, GH3 and SAUR genes, but the saccharide contents and stem length decreased in response to Pb stress. We used a variety of methods to provide a molecular perspective on the mechanism underlying the response of T. pratense to Pb stress.

Novel Role of AaMYBC1 in Regulating Actinidia arguta Vine Architecture by Elongating Internode Based on Multi-Omics Analysis of Transgenic Tobacco.

The internode length affects the status of fruiting branches and shapes the vine architecture. MYB TFs (transcription factors) have been widely studied and reported to control many biological processes including secondary metabolism, abiotic stresses, growth and development, etc. However, the roles of MYB TFs in regulating internode length remain poorly understood. Here, we demonstrated that a secondary metabolism-related R2R3-MYB TF AaMYBC1 from Actinidia arguta was involved in the regulation of internode length by combined analysis of transcriptome and metabolome of transgenic tobacco plants. The metabolome analysis of OE (over-expressed tobacco) and WT (wild-typed tobacco) showed that there were a total of 1000 metabolites, 176 of which had significant differences. A key metabolite pme1651 annotated as indole 3-acetic acid belonged to phytohormone that was involved in internode length regulation. The RNA-seq analysis presented 446 differentially expressed genes (DEGs) between OE and WT, 14 of which were common DEGs in KEGG and GO enrichment. Through the combined analysis of metabolome and transcriptome in transgenic and wild-type tobacco, three key genes including two SAUR and a GH3 gene were possibly involved in internode elongation. Finally, a regulatory module was deduced to show the role of AaMYBC1 in internode elongation. Our results proposed a molecular mechanism of AaMYBC1 regulating internode length by mediated auxin signaling, implying the potential role in regulating the vine architecture.

Functional Antagonism of WRI1 and TCP20 Modulates GH3.3 Expression to Maintain Auxin Homeostasis in Roots.

Auxin is a well-studied phytohormone, vital for diverse plant developmental processes. The GH3 genes are one of the major auxin responsive genes, whose expression changes lead to modulation of plant development and auxin homeostasis. However, the transcriptional regulation of these GH3 genes remains largely unknown. WRI1 is an essential transcriptional regulator governing plant fatty acid biosynthesis. Recently, we identified that the expression of GH3.3 is increased in the roots of wri1-1 mutant. Nevertheless, in this study we found that AtWRI1 did not activate or repress the promoter of GH3.3 (proGH3.3) despite of its binding to proGH3.3. Cross-family transcription factor interactions play pivotal roles in plant gene regulatory networks. To explore the molecular mechanism by which WRI1 controls GH3.3 expression, we screened an Arabidopsis transcription factor library and identified TCP20 as a novel AtWRI1-interacting regulator. The interaction between AtWRI1 and TCP20 was further verified by several approaches. Importantly, we found that TCP20 directly regulates GH3.3 expression via binding to TCP binding element. Furthermore, AtWRI1 repressed the TCP20-mediated transactivation of proGH3.3. EMSAs demonstrated that AtWRI1 antagonized TCP20 from binding to proGH3.3. Collectively, we provide new insights that WRI1 attenuates GH3.3 expression through interaction with TCP20, highlighting a new mechanism that contributes to fine-tuning auxin homeostasis.

Engineering drought-tolerant apple by knocking down six GH3 genes and potential application of transgenic apple as a rootstock.

Drought poses a major threat to apple fruit production and quality. Because of the apple’s long juvenile phase, developing varieties with improved drought tolerance using biotechnology approaches is needed. Here, we used the RNAi approach to knock down six GH3 genes in the apple. Under prolonged drought stress, the MdGH3 RNAi plants performed better than wild-type plants and had stronger root systems, higher root-to-shoot ratio, greater hydraulic conductivity, increased photosynthetic capacity, and increased water use efficiency. Moreover, MdGH3 RNAi plants promoted the drought tolerance of the scion when they were used as rootstock, compared with wild-type and M9-T337 rootstocks. Scions grafted onto MdGH3 RNAi plants showed increased plant height, stem diameter, photosynthetic capacity, specific leaf weight, and water use efficiency. The use of MdGH3 RNAi plants as rootstocks can also increase the C/N ratio of the scion and achieve the same effect as the M9-T337 rootstock in promoting the flowering and fruiting of the scion. Notably, using MdGH3 RNAi plants as rootstocks did not reduce fruit weight and scion quality compared with using M9-T337 rootstock. Our research provides candidate genes and demonstrates a general approach that could be used to improve the drought tolerance of fruit trees without sacrificing the yield and quality of scion fruits.

Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs.

Making full use of high fiber and low-cost crop coproducts is helpful to alleviate the situation of people and livestock competing for crops. Digestion of dietary fibers in pigs is mainly through microbial fermentation in the large intestine. To reveal microbiota related to fiber digestion in pigs, fecal samples have been collected from 274 healthy female Suhuai pigs at 160 days of age under the same feeding conditions and have measured apparent neutral detergent fiber (NDF) and acid detergent fiber (ADF) digestibility. Samples from Suhuai pigs with extreme high and low apparent NDF digestibility and extreme high and low apparent ADF digestibility were subjected to shotgun metagenomic sequencing. At the species level, 62 microbial species in H_NDF group and 54 microbial species in H_ADF group were related to high fiber digestibility. Among them, Lachnospiraceae bacterium 3-1 and Alistipes sp. CAG:514 may be new types of microorganisms associated with fiber digestion. In addition, we found that more abundant GH5 and GH48 family (contribute to cellulose degradation) genes, GH39 and GH53 family (contribute to hemicellulose degradation) genes in microorganisms may contribute to the higher apparent NDF digestibility of pigs, and more abundant GH3 and GH9 family (contribute to cellulose degradation) genes in microorganisms may contribute to the higher apparent ADF digestibility of pigs. The abundance of AA4 family (helps in lignin degradation) genes in H_NDF and H_ADF groups was significantly higher than that in L_NDF and L_ADF groups, respectively (P < 0.05). Three pathways in H_NDF group and four pathways in H_ADF group are important pathways associated with degradation of non-starch polysaccharides, and their relative abundance is significantly higher than that in L_NDF and L_ADF groups, respectively. Gut microbiota of Suhuai pigs with high apparent fiber digestibility had higher abundance of genes and microbiota related to fiber digestion and may have stronger fiber digestion potential compared with low apparent fiber digestibility group. This study revealed that the characteristics of gut microbiota and microbial gene functions of pigs with high fiber apparent digestibility, which provided a theoretical basis and reference for further understanding the impact of gut microbiota on fiber digestibility of pigs.

Auxin-mediated regulation of arbuscular mycorrhizal symbiosis: A role of SlGH3.4 in tomato.

Most land plants can establish symbiosis with arbuscular mycorrhizal (AM) fungi to increase fitness to environmental challenges. The development of AM symbiosis is controlled by intricate procedures involving all phytohormones. However, the mechanisms underlying the auxin-mediated regulation of AM symbiosis remains largely unknown. Here, we report that AM colonisation promotes auxin response and indole-3-acetic acid (IAA) accumulation, but downregulates IAA biosynthesis genes in tomato(Solanum lycopersicum). External IAA application modulates the AM symbiosis by promoting arbuscule formation at low concentrations but repressing it at high concentrations. An AM-induced GH3 gene, SlGH3.4, encoding a putative IAA-amido synthetase, negatively regulates mycorrhization via maintaining cellular auxin homoeostasis. Loss of SlGH3.4 function increased free IAA content and arbuscule incidence, while constitutively overexpressing SlGH3.4 in either tomato or rice resulted in decreased IAA content, total colonisation level and arbuscule abundance in mycorrhizal roots. Several auxin-inducible expansin genes involved in AM formation or resistance to pathogen infection were upregulated in slgh3.4 mycorrhizal roots but downregulated in the SlGH3.4-overexpressing plants. Taken together, our results highlight a positive correlation between the endogenous IAA content and mycorrhization level, particularly arbuscule incidence, and suggest that the SlGH3.4-mediated auxin homoeostasis and regulation of expansin genes is involved in finely tuning the AM development.

Intensive citrus plantations suppress the microbial profiles of the β-glucosidase gene

Increases in the input of chemical fertilizer and rapid decline of soil organic matter have increased serious demand for sustainable agriculture. Cellulose is an important component of soil organic matter, which strongly affects global carbon cycle and crop yields in the agroecosystem. β-glucosidases (BG) convert cellobiose to glucose, providing carbon for soil microorganisms and plants. However, little is known about the structure of β-glucosidase gene (GH3)-harboring microbial community and its functions in response to long-term intensive cropping with frequent fertilization. In this study, quantitative PCR (qPCR) and high-throughput sequencing were used to determine the abundance of bacterial and fungal GH3 gene as well as the diversity of GH3-harboring community in intensified citrus orchards of different ages (5-year, 15-year and 30-year), or under different management practices (straw application on the surface, peanut planting between rows and control) for 15 years. The adjacent natural forest and grass soils were used as reference to investigate the effect of intensive citrus plantation on soil BG enzyme activity and the GH3 gene. The results revealed that citrus plantation significantly reduced soil GH3 gene abundance, especially for the bacterial GH3 gene. The higher abundance of bacterial GH3 gene than that of fungal GH3 gene in the soil highlighted the key role of bacterial GH3 gene in regulating soil BG enzyme activity. Among the reservoirs of the GH3 gene, Proteobacteria, Acidobacteria, Firmicutes and Actinobacteria were the main bacterial phyla, while Ascomycota was the only dominant fungal phylum. Citrus plantation caused soil bacterial community varied from Proteobacteria-dominant to Acidobacteria-dominant and reduced BG enzyme activity. The higher diversity of the bacterial community indicated that bacteria play a dominant role in the conversion of cellobiose to glucose. Citrus plantation and plantation age strongly influenced the diversity and structure of β-glucosidase gene-harboring community. A significant decline occurred in bacterial diversity along with increasing citrus plantation age. The community diversity exhibited a clear land-use specific pattern, as indicated by the obviously different community structure between the forest soil and citrus soil. Among the detected environmental factors, SOC, bacterial β-glucosidase gene abundance and the community diversity were the most important factors controlling soil BG enzyme activity. These results indicate that citrus plantation with long-term fertilization suppresses the abundance of the β-glucosidases gene, and the bacterial β-glucosidase gene contributes more to the BG enzyme activity than the fungal gene.

Two Auxinic Herbicides Affect Brassica napus Plant Hormone Levels and Induce Molecular Changes in Transcription.

With the introduction of the new auxinic herbicide halauxifen-methyl into the oilseed rape (Brassica napus) market, there is a need to understand how this new molecule interacts with indigenous plant hormones (e.g., IAA) in terms of crop response. The aim of this study was to investigate the molecular background by using different growth conditions under which three different auxinic herbicides were administered. These were halauxifen-methyl (Hal), alone and together with aminopyralid (AP) as well as picloram (Pic). Three different hormone classes were determined, free and conjugated indole-3-acetic acid (IAA), aminocyclopropane carboxylic acid (ACC) as a precursor for ethylene, and abscisic acid (ABA) at two different temperatures and growth stages as well as over time (2–168 h after treatment). At 15 °C growth temperature, the effect was more pronounced than at 9 °C, and generally, the younger leaves independent of the developmental stage showed a larger effect on the alterations of hormones. IAA and ACC showed reproducible alterations after auxinic herbicide treatments over time, while ABA did not. Finally, a transcriptome analysis after treatment with two auxinic herbicides, Hal and Pic, showed different expression patterns. Hal treatment leads to the upregulation of auxin and hormone responses at 48 h and 96 h. Pic treatment induced the hormone/auxin response already after 2 h, and this continued for the other time points. The more detailed analysis of the auxin response in the datasets indicate a role for GH3 genes and genes encoding auxin efflux proteins. The upregulation of the GH3 genes correlates with the increase in conjugated IAA at the same time points and treatments. Also, genes for were found that confirm the upregulation of the ethylene pathway.

Physcomitrium patens Mutants in Auxin Conjugating GH3 Proteins Show Salt Stress Tolerance but Auxin Homeostasis Is Not Involved in Regulation of Oxidative Stress Factors.

Salt stress is among the most challenging abiotic stress situations that a plant can experience. High salt levels do not only occur in areas with obvious salty water, but also during drought periods where salt accumulates in the soil. The moss Physcomitrium patens became a model for studying abiotic stress in non-vascular plants. Here, we show that high salt concentrations can be tolerated in vitro, and that auxin homeostasis is connected to the performance of P. patens under these stress conditions. The auxin levels can be regulated by conjugating IAA to amino acids by two members of the family of GH3 protein auxin amino acid-synthetases that are present in P. patens. Double GH3 gene knock-out mutants were more tolerant to high salt concentrations. Furthermore, free IAA levels were differentially altered during the time points investigated. Since, among the mutant lines, an increase in IAA on at least one NaCl concentration tested was observed, we treated wild type (WT) plants concomitantly with NaCl and IAA. This experiment showed that the salt tolerance to 100 mM NaCl together with 1 and 10 µM IAA was enhanced during the earlier time points. This is an additional indication that the high IAA levels in the double GH3-KO lines could be responsible for survival in high salt conditions. While the high salt concentrations induced several selected stress metabolites including phenols, flavonoids, and enzymes such as peroxidase and superoxide dismutase, the GH3-KO genotype did not generally participate in this upregulation. While we showed that the GH3 double KO mutants were more tolerant of high (250 mM) NaCl concentrations, the altered auxin homeostasis was not directly involved in the upregulation of stress metabolites.