The growing world of expansins

Alpha-expansins: more than three decades of wall creep and loosening in fruits

Expansins are proteins without catalytic activity, but able to break hydrogen bonds between cell wall polysaccharides hemicellulose and cellulose. This proteins were reported for the first time in 1992, describing cell wall extension in cucumber hypocotyls caused particularly by alpha-expansins. Although these proteins have GH45 and CBM63 domains, characteristic of enzymes related with the cleavage of cell wall polysaccharides, demonstrating in vitro that they extend plant cell wall. Its participation has been associated to molecular processes such as development and growing, fruit ripening and softening, tolerance and resistance to biotic and abiotic stress and seed germination. Structural insights, facilitated by bioinformatics approaches, are highlighted, shedding light on the intricate interactions between alpha-expansins and cell wall polysaccharides. After more than thirty years of its discovery, we want to celebrate the knowledge of alpha-expansins and emphasize their importance to understand the phenomena of disassembly and loosening of the cell wall, specifically in the fruit ripening phenomena, with this state-of-the-art dedicated to them.

Transcription factor CsMYB36 regulates fruit neck length via mediating cell expansion in cucumber

The fruit neck is an important agronomic trait of cucumber (Cucumis sativus). However, the underlying genes and regulatory mechanisms involved in fruit neck development are poorly understood. We previously identified a cucumber yellow-green peel (ygp) mutant, whose causal gene is MYB DOMAIN PROTEIN 36 (CsMYB36). This study showed that the ygp mutant exhibited a shortened fruit neck and repressed cell expansion in the fruit neck. Further functional analysis showed that CsMYB36 was also a target gene, and its expression was enriched in the fruit neck. Overexpression of CsMYB36 in the ygp mutant rescued shortened fruit necks. Furthermore, transcriptome analysis and reverse transcription quantitative PCR (RT-qPCR) assays revealed that CsMYB36 positively regulates the expression of an expansin-like A3 (CsEXLA3) in the fruit neck, which is essential for cell expansion. Yeast 1-hybrid and dual-luciferase assays revealed that CsMYB36 regulates fruit neck elongation by directly binding to the promoter of CsEXLA3. Collectively, these findings demonstrate that CsMYB36 is an important gene in the regulation of fruit neck length in cucumber plants.

Genome-wide identification of the expansin gene family in netted melon and their transcriptional responses to fruit peel cracking

Introduction

Fruit cracking not only affects the appearance of netted melons (Cucumis melo L. var. reticulatus Naud.) but also decreases their marketability.

Methods

Herein, to comprehensively understand the role of expansin (EXP) proteins in netted melon, bioinformatics methods were employed to discover the EXP gene family in the melon genome and analyze its characteristic features. Furthermore, transcriptomics analysis was performed to determine the expression patterns of melon EXP (CmEXP) genes in crack-tolerant and crack-susceptible netted melon varieties.

Discussion

Thirty-three CmEXP genes were identified. Chromosomal location analysis revealed that CmEXP gene distribution was uneven on 12 chromosomes. In addition, phylogenetic tree analysis revealed that CmEXP genes could be categorized into four subgroups, among which the EXPA subgroup had the most members. The same subgroup members shared similar protein motifs and gene structures. Thirteen duplicate events were identified in the 33 CmEXP genes. Collinearity analysis revealed that the CmEXP genes had 50, 50, and 44 orthologous genes with EXP genes in cucumber, watermelon, and Arabidopsis, respectively. However, only nine orthologous EXP genes were observed in rice. Promoter cis-acting element analysis demonstrated that numerous cis-acting elements in the upstream promoter region of CmEXP genes participate in plant growth, development, and environmental stress responses. Transcriptomics analysis revealed 14 differentially expressed genes (DEGs) in the non-cracked fruit peels between the crack-tolerant variety 'Xizhoumi 17' (N17) and the crack-susceptible variety 'Xizhoumi 25' (N25). Among the 14 genes, 11 were upregulated, whereas the remaining three were downregulated in N17. In the non-cracked (N25) and cracked (C25) fruit peels of 'Xizhoumi 25', 24 DEGs were identified, and 4 of them were upregulated, whereas the remaining 20 were downregulated in N25. In the two datasets, only CmEXPB1 exhibited consistently upregulated expression, indicating its importance in the fruit peel crack resistance of netted melon. Transcription factor prediction revealed 56 potential transcription factors that regulate CmEXPB1 expression.

Results

Our study findings enrich the understanding of the CmEXP gene family and present candidate genes for the molecular breeding of fruit peel crack resistance of netted melon.

Functional characterization of MaEXPA11 and its roles in response to biotic and abiotic stresses in mulberry

Mulberry is a traditional economic tree with various values in sericulture, ecology, food industry and medicine. Expansins (EXPs) are known as cell wall expansion related proteins and have been characterized to involve in plant development and responses to diverse stresses. In present study, twenty EXP and expansin-like (EXL) genes were identified in mulberry. RNA-seq results indicated that three EXP and EXL genes showed up-regulated expression level under sclerotiniose pathogen infection in three independent RNA-seq datasets. The most significant upregulated EXPA11 was selected as key EXP involving in response to sclerotiniose pathogen infection in mulberry. Furthermore, a comprehensive functional analysis was performed to reveal subcellular location, tissue expression profile of MaEXPA11 in mulberry. Down-regulation of MaEXPA11 using virus induced gene silence (VIGS) was performed to explore the function of MaEXPA11 in Morus alba. Results showed that MaEXPA11 can positively regulate mulberry resistance to Ciboria shiraiana infection and negatively regulate mulberry resistance to cold or drought stress.

PdeERF114 recruits PdeWRKY75 to regulate callus formation in poplar by modulating the accumulation of H2 O2 and the relaxation of cell walls

Callus formation is important for numerous biological processes in plants. Previously, we revealed that the PdeWRKY75-PdeRBOHB module positively regulates hydrogen peroxide (H2 O2 ) accumulation, thereby affecting callus formation in poplar. In this study, we identified and confirmed a transcription factor, PdeERF114, that interacts with PdeWRKY75 both in vitro and in vivo. Gene expression analysis identified both PdeRBOHB and PdeEXPB2 as downstream genes of PdeERF114 and PdeWRKY75. Overexpression (OE) and reduced-expression (RE) transgenic poplar lines for these four genes were generated, and the observation of callus formation was also performed in all plant materials. We demonstrated that PdeERF114 and PdeWRKY75 formed a protein complex and that this complex could bind W-Box motifs in the promoters of PdeRBOHB and PdeEXPB2, thereby positively regulating the expression of PdeRBOHB and PdeEXPB2. The OE/RE transgenic lines for these four genes also showed enhanced/reduced callus formation. Overall, we revealed a novel gene regulatory network for the regulation of callus formation in plants that involves four genes and regulates callus formation through two pathways: the accumulation of H2 O2 in explants and the relaxation of cell walls. In the future, the four genes could be used to enhance transformation effectiveness in genetic engineering.

Hormone-regulated expansins: Expression, localization, and cell wall biomechanics in Arabidopsis root growth

Expansins facilitate cell expansion by mediating pH-dependent cell wall (CW) loosening. However, the role of expansins in controlling CW biomechanical properties in specific tissues and organs remains elusive. We monitored hormonal responsiveness and spatial specificity of expression and localization of expansins predicted to be the direct targets of cytokinin signaling in Arabidopsis (Arabidopsis thaliana). We found EXPANSIN1 (EXPA1) homogenously distributed throughout the CW of columella/lateral root cap, while EXPA10 and EXPA14 localized predominantly at 3-cell boundaries in the epidermis/cortex in various root zones. EXPA15 revealed cell-type-specific combination of homogenous vs. 3-cell boundaries localization. By comparing Brillouin frequency shift and AFM-measured Young's modulus, we demonstrated Brillouin light scattering (BLS) as a tool suitable for non-invasive in vivo quantitative assessment of CW viscoelasticity. Using both BLS and AFM, we showed that EXPA1 overexpression upregulated CW stiffness in the root transition zone (TZ). The dexamethasone-controlled EXPA1 overexpression induced fast changes in the transcription of numerous CW-associated genes, including several EXPAs and XYLOGLUCAN:XYLOGLUCOSYL TRANSFERASEs (XTHs), and associated with rapid pectin methylesterification determined by in situ Fourier-transform infrared spectroscopy in the root TZ. The EXPA1-induced CW remodeling is associated with the shortening of the root apical meristem, leading to root growth arrest. Based on our results, we propose that expansins control root growth by a delicate orchestration of CW biomechanical properties, possibly regulating both CW loosening and CW remodeling.

Gibberellic Acid Inhibits Dendrobium nobile-Piriformospora Symbiosis by Regulating the Expression of Cell Wall Metabolism Genes

Orchid seeds lack endosperms and depend on mycorrhizal fungi for germination and nutrition acquisition under natural conditions. Piriformospora indica is a mycorrhizal fungus that promotes seed germination and seedling development in epiphytic orchids, such as Dendrobium nobile. To understand the impact of P. indica on D. nobile seed germination, we examined endogenous hormone levels by using liquid chromatography-mass spectrometry. We performed transcriptomic analysis of D. nobile protocorm at two developmental stages under asymbiotic germination (AG) and symbiotic germination (SG) conditions. The result showed that the level of endogenous IAA in the SG protocorm treatments was significantly higher than that in the AG protocorm treatments. Meanwhile, GA3 was only detected in the SG protocorm stages. IAA and GA synthesis and signaling genes were upregulated in the SG protocorm stages. Exogenous GA3 application inhibited fungal colonization inside the protocorm, and a GA biosynthesis inhibitor (PAC) promoted fungal colonization. Furthermore, we found that PAC prevented fungal hyphae collapse and degeneration in the protocorm, and differentially expressed genes related to cell wall metabolism were identified between the SG and AG protocorm stages. Exogenous GA3 upregulated SRC2 and LRX4 expression, leading to decreased fungal colonization. Meanwhile, GA inhibitors upregulated EXP6, EXB16, and EXP10-2 expression, leading to increased fungal colonization. Our findings suggest that GA regulates the expression of cell wall metabolism genes in D. nobile, thereby inhibiting the establishment of mycorrhizal symbiosis.

Transcriptome profiling reveals the genes involved in tuberous root expansion in Pueraria (Pueraria montana var. thomsonii)

BACKGROUND

Pueraria is a dry root commonly used in Traditional Chinese Medicine or as food and fodder, and tuberous root expansion is an important agronomic characteristic that influences its yield. However, no specific genes regulating tuberous root expansion in Pueraria have been identified. Therefore, we aimed to explore the expansion mechanism of Pueraria at six developmental stages (P1-P6), by profiling the tuberous roots of an annual local variety "Gange No.1" harvested at 105, 135, 165, 195, 225, and 255 days after transplanting.

RESULTS

Observations of the tuberous root phenotype and cell microstructural morphology revealed that the P3 stage was a critical boundary point in the expansion process, which was preceded by a thickening diameter and yield gain rapidly of the tuberous roots, and followed by longitudinal elongation at both ends. A total of 17,441 differentially expressed genes (DEGs) were identified by comparing the P1 stage (unexpanded) against the P2-P6 stages (expanded) using transcriptome sequencing; 386 differential genes were shared across the six developmental stages. KEGG pathway enrichment analysis showed that the DEGs shared by P1 and P2-P6 stages were mainly involved in pathways related to the "cell wall and cell cycle", "plant hormone signal transduction", "sucrose and starch metabolism", and "transcription factor (TF)". The finding is consistent with the physiological data collected on changes in sugar, starch, and hormone contents. In addition, TFs including bHLHs, AP2s, ERFs, MYBs, WRKYs, and bZIPs were involved in cell differentiation, division, and expansion, which may relate to tuberous root expansion. The combination of KEGG and trend analyses revealed six essential candidate genes involved in tuberous root expansion; of them, CDC48, ARF, and EXP genes were significantly upregulated during tuberous root expansion while INV, EXT, and XTH genes were significantly downregulated.

CONCLUSION

Our findings provide new insights into the complex mechanisms of tuberous root expansion in Pueraria and candidate target genes, which can aid in increasing Pueraria yield.

Genome-Wide Identification of Expansin Gene Family and Their Response under Hormone Exposure in Ginkgo biloba L

Expansins are pH-dependent enzymatic proteins that irreversibly and continuously facilitate cell-wall loosening and extension. The identification and comprehensive analysis of Ginkgo biloba expansins (GbEXPs) are still lacking. Here, we identified and investigated 46 GbEXPs in Ginkgo biloba. All GbEXPs were grouped into four subgroups based on phylogeny. GbEXPA31 was cloned and subjected to a subcellular localization assay to verify our identification. The conserved motifs, gene organization, cis-elements, and Gene Ontology (GO) annotation were predicted to better understand the functional characteristics of GbEXPs. The collinearity test indicated segmental duplication dominated the expansion of the GbEXPA subgroup, and seven paralogous pairs underwent strong positive selection during expansion. A majority of GbEXPAs were mainly expressed in developing Ginkgo kernels or fruits in transcriptome and real-time quantitative PCR (qRT-PCR). Furthermore, GbEXLA4, GbEXLA5, GbEXPA5, GbEXPA6, GbEXPA8, and GbEXPA24 were inhibited under the exposure of abiotic stresses (UV-B and drought) and plant hormones (ABA, SA, and BR). In general, this study expanded our understanding for expansins in Ginkgo tissues' growth and development and provided a new basis for studying GbEXPs in response to exogenous phytohormones.

Cell Wall Integrity Signaling in Fruit Ripening

Plant cell walls are essential structures for plant growth and development as well as plant adaptation to environmental stresses. Thus, plants have evolved signaling mechanisms to monitor the changes in the cell wall structure, triggering compensatory changes to sustain cell wall integrity (CWI). CWI signaling can be initiated in response to environmental and developmental signals. However, while environmental stress-associated CWI signaling has been extensively studied and reviewed, less attention has been paid to CWI signaling in relation to plant growth and development under normal conditions. Fleshy fruit development and ripening is a unique process in which dramatic alternations occur in cell wall architecture. Emerging evidence suggests that CWI signaling plays a pivotal role in fruit ripening. In this review, we summarize and discuss the CWI signaling in relation to fruit ripening, which will include cell wall fragment signaling, calcium signaling, and NO signaling, as well as Receptor-Like Protein Kinase (RLKs) signaling with an emphasis on the signaling of FERONIA and THESEUS, two members of RLKs that may act as potential CWI sensors in the modulation of hormonal signal origination and transduction in fruit development and ripening.

Postharvest High-CO2 Treatments on the Quality of Soft Fruit Berries: An Integrated Transcriptomic, Proteomic, and Metabolomic Approach

Soft fruits are appreciated for their taste qualities and for being a source of health-promoting compounds. However, their postharvest is affected by their high respiratory rates and susceptibility to fungal decay. Our aim here is to provide a perspective on the application of short-term high-CO₂ treatments at a low temperature to maintain the postharvest quality of soft fruits. This work also suggests using a multi-omics approach to better understand the role of the cell wall and phenolic compounds in maintaining quality. Finally, the contribution of high-throughput transcriptomic technologies to understand the mechanisms modulated by the short-term gaseous treatments is also highlighted.

A YABBY gene CRABS CLAW a (CRCa) negatively regulates flower and fruit sizes in tomato

CRABS CLAW (CRC) is a YABBY transcription factor that plays a pivotal role in carpel development and flower meristem determinacy. Here, we characterized a CRC homolog SlCRCa and elucidated its specific roles in tomato (Solanum lycopersicum). SlCRCa is highly expressed in the petals and stamens, and is responsive to gibberellin (GA) treatment. Overexpression of SlCRCa in tomato reduces the sizes of petals, stamens, and fruits, while the inverse phenotypes are induced by knockdown of SlCRCa. Furthermore, histological investigation suggests that the smaller or larger fruits in SlCRCa-overexpressing or SlCRCa-RNAi plants are mainly determined by the decreases or increases in cell layers and cell sizes in pericarp, respectively. Through transcriptome and qRT-PCR analyses, we speculate that SlCRCa inhibits cell division by regulating the transcription of cell division-related genes, and also suppresses cell expansion by modulating the expansin genes and GA pathway in tomato fruits. Besides, SlCRCa is involved in the feedback regulation of GA biosynthesis. Our findings reveal that SlCRCa negatively regulates fruit size by affecting cell division and cell expansion, and it is also an inhibitor of floral organ sizes in tomato.

Fruit quality parameters and volatile compounds from 'Palmer' mangoes with internal breakdown

The internal breakdown (IB) is a premature and uneven mango pulp ripening physiological disorder that is noticed only when the fruit is sliced for consumption. Thus, there is a demand for analytical methods to detect IB in mangoes to avoid consumer dissatisfaction and reduce postharvest waste. In this work, physicochemical and volatile compounds were determined to evaluate the ability to predict pulp IB. Principal components analysis (PCA) and partial least squares discriminant analysis (PLS-DA) of the data show that color, firmness, and volatiles compounds are important to give some information about the physiological changes caused by IB. The volatile compounds methacrylic acid, ethyl ester, isopentyl ethanoate, limonene oxide, (E)-2-pentenal, tetradecane, and γ-elemene were identified as chemical markers of IB. Therefore, mango physical and chemical characteristics combined with PCA and PLS-DA were successfully employed for the identification of IB in mangoes, showing significant differences between healthy and IB fruits.

A T9SS Substrate Involved in Crystalline Cellulose Degradation by Affecting Crucial Cellulose Binding Proteins in Cytophaga hutchinsonii

Cytophaga hutchinsonii is an abundant soil cellulolytic bacterium that uses a unique cellulose degradation mechanism different from those that involve free cellulases or cellulosomes. Though several proteins were identified to be important for cellulose degradation, the mechanism used by C. hutchinsonii to digest crystalline cellulose remains a mystery. In this study, chu_0922 was identified by insertional mutation and gene deletion as an important gene locus indispensable for crystalline cellulose utilization. Deletion of chu_0922 resulted in defect in crystalline cellulose utilization. The Δ0922 mutant completely lost the ability to grow on crystalline cellulose even with extended incubation, and selectively utilized the amorphous region of cellulose leading to the increased crystallinity. As a protein secreted by the type Ⅸ secretion system (T9SS), CHU_0922 was found to be located on the outer membrane, and the outer membrane localization of CHU_0922 relied on the T9SS. Comparative analysis of the outer membrane proteins revealed that the abundance of several cellulose binding proteins, including CHU_1276, CHU_1277, and CHU_1279, was reduced in the Δ0922 mutant. Further study showed that CHU_0922 is crucial for the full expression of the gene cluster containing chu_1276, chu_1277, chu_1278, chu_1279, and chu_1280 (cel9C), which is essential for cellulose utilization. Moreover, CHU_0922 is required for the cell surface localization of CHU_3220, a cellulose binding protein that is essential for crystalline cellulose utilization. Our study provides insights into the complex system that C. hutchinsonii uses to degrade crystalline cellulose. IMPORTANCE The widespread aerobic cellulolytic bacterium Cytophaga hutchinsonii, belonging to the phylum Bacteroidetes, utilizes a novel mechanism to degrade crystalline cellulose. No genes encoding proteins specialized in loosening or disruption the crystalline structure of cellulose were identified in the genome of C. hutchinsonii, except for chu_3220 and chu_1557. The crystalline cellulose degradation mechanism remains enigmatic. This study identified a new gene locus, chu_0922, encoding a typical T9SS substrate that is essential for crystalline cellulose degradation. Notably, CHU_0922 is crucial for the normal transcription of chu_1276, chu_1277, chu_1278, chu_1279, and chu_1280 (cel9C), which play important roles in the degradation of cellulose. Moreover, CHU_0922 participates in the cell surface localization of CHU_3220. These results demonstrated that CHU_0922 plays a key role in the crystalline cellulose degradation network. Our study will promote the uncovering of the novel cellulose utilization mechanism of C. hutchinsonii.

Salt Stress Promotes Abscisic Acid Accumulation to Affect Cell Proliferation and Expansion of Primary Roots in Rice

The primary root is the basic component of the root system and plays a key role in early seedling growth in rice. Its growth is easily affected by environmental cues, such as salt stress. Abscisic acid (ABA) plays an essential role in root development, but the molecular mechanism underlying ABA-regulated root growth in response to salt stress remains poorly understood. In this study, we report that salt stress inhibits primary root elongation and promotes primary root swelling. Moreover, salt stress induces the expression of ABA-responsive genes and ABA accumulation in the primary root, revealing that ABA plays an essential role in salt-modulated root growth. Transgenic lines of OsSAPK10-OE and OsABIL2-OE, which constitutively express OsSAPK10 or OsABIL2, with enhanced or attenuated ABA signaling, show increased and decreased sensitivity to salt, correspondingly. Microscopic analysis indicates that salt and ABA inhibits cell proliferation and promotes cell expansion in the root apical meristem. Transcriptome analysis showed that ABA induces the expression of EXPANSIN genes. Further investigations indicate that ABA exerts these effects largely through ABA signaling. Thus, our findings deepen our understanding of the role of ABA in controlling primary root growth in response to salt stress, and this knowledge can be used by breeders to cultivate rice varieties suitable for saline–alkali land.

The soybean β-expansin gene GmINS1 contributes to nodule development in response to phosphate starvation

Legume biological nitrogen fixation (BNF) is the most important N source in agricultural ecosystems. Nodule organogenesis from the primordia to the development of mature nodules with the ability to fix N2 largely determines BNF capacity. However, nodule growth is often limited by low phosphorus (P) availability, while the mechanisms underlying nodule development responses to P deficiency remain largely unknown. In this study, we found that nodule enlargement is severely inhibited by P deficiency, as reflected by the smaller individual nodule size from a soybean core collection in the field. Wide-ranging natural diversity in nodule size was further identified in soybeans reared in low P soils, with the FC-1 genotype outperforming FC-2 in assessments of nodulation under low P conditions. Among β-expansin members, GmINS1 expression is most abundantly enhanced by P deficiency in FC-1 nodules, and its transcript level is further displayed to be tightly associated with nodule enlargement. Four single nucleotide polymorphisms discovered in the GmINS1 promoter distinguished the FC-1 and FC-2 genotypes and accounted for the differential expression levels of GmINS1 responses to P deficiency. GmINS1 overexpression led to increases in nodule size, infected cell abundance, and N2 fixation capacity and subsequently promoted increases in N and P content, soybean biomass, and yield. Our findings provide a candidate gene for optimizing BNF capacity responses to low P stress in soybean molecular breeding programs.

HOMEODOMAIN PROTEIN8 mediates jasmonate-triggered trichome elongation in tomato

Plant hormones can adjust the physiology and development of plants to enhance their adaptation to biotic and abiotic challenges. Jasmonic acid (JA), one of the immunity hormones in plants, triggers genome-wide transcriptional changes in response to insect attack and wounding. Although JA is known to affect the development of trichomes, epidermal appendages that form a protective barrier against various stresses, it remains unclear how JA interacts with developmental programs that regulate trichome development. In this study, we show that JA affects trichome length in tomato by releasing the transcriptional repression mediated by Jasmonate ZIM (JAZ) proteins. We identified SlJAZ4, a negative regulator preferentially expressed in trichomes, as the critical component in JA signaling in tomato trichomes. We also identified a homeodomain-leucine zipper gene, SlHD8, as the downstream regulator of JA signaling that promotes trichome elongation. SlHD8 is also highly expressed in trichomes and physically interacts with SlJAZ4. Loss-of-function mutations in SlHD8 caused shorter trichomes, a phenotype that was only partially rescued by methyl jasmonate treatment. Our dual-luciferase and chromatin immunoprecipitation-quantitative PCR assays revealed that SlHD8 regulates trichome elongation by directly binding to the promoters of a set of cell-wall-loosening protein genes and activating their transcription. Together, our findings define SlHD8-SlJAZ4 as a key module mediating JA-induced trichome elongation in tomato.

Structure and Development of the Legume-Rhizobial Symbiotic Interface in Infection Threads

The intracellular infection thread initiated in a root hair cell is a unique structure associated with Rhizobium-legume symbiosis. It is characterized by inverted tip growth of the plant cell wall, resulting in a tunnel that allows invasion of host cells by bacteria during the formation of the nitrogen-fixing root nodule. Regulation of the plant-microbial interface is essential for infection thread growth. This involves targeted deposition of the cell wall and extracellular matrix and tight control of cell wall remodeling. This review describes the potential role of different actors such as transcription factors, receptors, and enzymes in the rearrangement of the plant-microbial interface and control of polar infection thread growth. It also focuses on the composition of the main polymers of the infection thread wall and matrix and the participation of reactive oxygen species (ROS) in the development of the infection thread. Mutant analysis has helped to gain insight into the development of host defense reactions. The available data raise many new questions about the structure, function, and development of infection threads.

Tomato SlBL4 plays an important role in fruit pedicel organogenesis and abscission

Abscission, a cell separation process, is an important trait that influences grain and fruit yield. We previously reported that BEL1-LIKE HOMEODOMAIN 4 (SlBL4) is involved in chloroplast development and cell wall metabolism in tomato fruit. In the present study, we showed that silencing SlBL4 resulted in the enlargement and pre-abscission of the tomato (Solanum lycopersicum cv. Micro-TOM) fruit pedicel. The anatomic analysis showed the presence of more epidermal cell layers and no obvious abscission zone (AZ) in the SlBL4 RNAi lines compared with the wild-type plants. RNA-seq analysis indicated that the regulation of abscission by SlBL4 was associated with the altered abundance of genes related to key meristems, auxin transporters, signaling components, and cell wall metabolism. Furthermore, SlBL4 positively affected the auxin concentration in the abscission zone. A dual-luciferase reporter assay revealed that SlBL4 activated the transcription of the JOINTLESS, OVATE, PIN1, and LAX3 genes. We reported a novel function of SlBL4, which plays key roles in fruit pedicel organogenesis and abscission in tomatoes.

A horizontally acquired expansin gene increases virulence of the emerging plant pathogen Erwinia tracheiphila

Erwinia tracheiphila is a bacterial plant pathogen that causes a fatal wilt infection in some cucurbit crop plants. Wilt symptoms are thought to be caused by systemic bacterial colonization through xylem that impedes sap flow. However, the genetic determinants of within-plant movement are unknown for this pathogen species. Here, we find that E. tracheiphila has horizontally acquired an operon with a microbial expansin (exlx) gene adjacent to a glycoside hydrolase family 5 (gh5) gene. Plant inoculation experiments with deletion mutants in the individual genes (Δexlx and Δgh5) and the full operon (Δexlx-gh5) resulted in decreased severity of wilt symptoms, decreased mortality rate, and impaired systemic colonization compared to the Wt strain. Co-inoculation experiments with Wt and Δexlx-gh5 rescued the movement defect of the mutant strain, suggesting that expansin and GH5 function extracellularly. Together, these results show that expansin-GH5 contributes to systemic movement through xylem, leading to rapid wilt symptom development and higher rates of plant death. The presence of expansin genes in diverse species of bacterial and fungal wilt-inducing pathogens suggests that microbial expansin proteins may be an under-appreciated virulence factor for many pathogen species.

Comparative Transcriptomic Analysis of the Development of Sepal Morphology in Tomato (Solanum Lycopersicum L.)

Sepal is an important component of the tomato flower and fruit that typically protects the flower in bud and functions as a support for petals and fruits. Moreover, sepal appearance influences the commercial property of tomato nowadays. However, the phenotype information and development mechanism of the natural variation of sepal morphology in the tomato is still largely unexplored. To study the developmental mechanism and to determine key genes related to downward sepal in the tomato, we compared the transcriptomes of sepals between downward sepal (dsp) mutation and the wild-type by RNA sequencing and found that the differentially expressed genes were dominantly related to cell expansion, auxin, gibberellins and cytokinin. dsp mutation affected cell size and auxin, and gibberellins and cytokinin contents in sepals. The results showed that cell enlargement or abnormal cell expansion in the adaxial part of sepals in dsp. As reported, auxin, gibberellins and cytokinin were important factors for cell expansion. Hence, dsp mutation regulated cell expansion to control sepal morphology, and auxin, gibberellins and cytokinin may mediate this process. One ARF gene and nine SAUR genes were dramatically upregulated in the sepal of the dsp mutant, whereas seven AUX/IAA genes were significantly downregulated in the sepal of dsp mutant. Further bioinformatic analyses implied that seven AUX/IAA genes might function as negative regulators, while one ARF gene and nine SAUR genes might serve as positive regulators of auxin signal transduction, thereby contributing to cell expansion in dsp sepal. Thus, our data suggest that 17 auxin-responsive genes are involved in downward sepal formation in the tomato. This study provides valuable information for dissecting the molecular mechanism of sepal morphology control in the tomato.

Fruit From Two Kiwifruit Genotypes With Contrasting Softening Rates Show Differences in the Xyloglucan and Pectin Domains of the Cell Wall

Fruit softening is controlled by hormonal and developmental cues, causing an upregulation of cell wall-associated enzymes that break down the complex sugar matrices in the cell wall. The regulation of this process is complex, with different genotypes demonstrating quite different softening patterns, even when they are closely related. Currently, little is known about the relationship between cell wall structure and the rate of fruit softening. To address this question, the softening of two Actinidia chinensis var. chinensis (kiwifruit) genotypes (a fast 'AC-F' and a slow 'AC-S' softening genotype) was examined using a range of compositional, biochemical, structural, and molecular techniques. Throughout softening, the cell wall structure of the two genotypes was fundamentally different at identical firmness stages. In the hemicellulose domain, xyloglucanase enzyme activity was higher in 'AC-F' at the firm unripe stage, a finding supported by differential expression of xyloglucan transglycosylase/hydrolase genes during softening. In the pectin domain, differences in pectin solubilization and location of methyl-esterified homogalacturonan in the cell wall between 'AC-S' and 'AC-F' were shown. Side chain analyses and molecular weight elution profiles of polyuronides and xyloglucans of cell wall extracts revealed fundamental differences between the genotypes, pointing towards a weakening of the structural integrity of cell walls in the fast softening 'AC-F' genotype even at the firm, unripe stage. As a consequence, the polysaccharides in the cell walls of 'AC-F' may be easier to access and hence more susceptible to enzymatic degradation than in 'AC-S', resulting in faster softening. Together these results suggest that the different rates of softening between 'AC-F' and 'AC-S' are not due to changes in enzyme activities alone, but that fundamental differences in the cell wall structure are likely to influence the rates of softening through differential modification and accessibility of specific cell wall polysaccharides during ripening.

Genome-wide identification, characterization, and expression analysis of the expansin gene family in watermelon (Citrullus lanatus)

Expansins are plant cell-wall loosening proteins involved in cell enlargement, adaptive responses to environmental stimuli, and various developmental processes. Although expansins have been characterized in many plant species, little is reported on this family in watermelon. In this study, 30 expansin genes in the watermelon genome (ClEXPs) were identified. These genes which were divided into four subfamilies (7 ClEXLAs, 2 ClEXLBs, 18 ClEXPAs, and 3 ClEXPBs) are unevenly distribute on 10 of 11 watermelon chromosomes. Chromosome mapping suggested that tandem duplication events may have played important roles in the expanding of watermelon expansins. Gene structure and motif identification revealed that same subfamily and subgroup have conserved gene structure and motif. Detection of cis-acting elements revealed that ClEXPs gene promoter regions were enriched with light-responsive elements, hormone-responsive, environmental stress-related, and development-related elements. Expression patterns of ClEXPs were investigated by qRT-PCR. The results showed that expression patterns of 15 ClEXP genes differed in three tissues. Through our own and public RNA-seq analysis, we found that ClEXPs had different expression patterns in fruit flesh, fruit rind, and seed at various developmental stages, and most of ClEXPs were highly responsive to abiotic and biotic stresses. Remarkably, 7 ClEXPs (ClEXLA1, ClEXLA6, ClEXLB1, ClEXLB2, ClEXPA5, ClEXPA10, and ClEXPA16) exhibited positive response to at least three kinds of stresses, suggesting that they might play important roles in the crosstalk of stress signal pathways. The results of this study provide useful insights for the functional identification of expansin gene family in watermelon.

Cellulose synthase interactive1- and microtubule-dependent cell wall architecture is required for acid growth in Arabidopsis hypocotyls

Auxin-induced cell elongation relies in part on the acidification of the cell wall, a process known as acid growth that presumably triggers expansin-mediated wall loosening via altered interactions between cellulose microfibrils. Cellulose microfibrils are a major determinant for anisotropic growth and they provide the scaffold for cell wall assembly. Little is known about how acid growth depends on cell wall architecture. To explore the relationship between acid growth-mediated cell elongation and plant cell wall architecture, two mutants (jia1-1 and csi1-3) that are defective in cellulose biosynthesis and cellulose microfibril organization were analyzed. The study revealed that cell elongation is dependent on CSI1-mediated cell wall architecture but not on the overall crystalline cellulose content. We observed a correlation between loss of crossed-polylamellate walls and loss of auxin- and fusicoccin-induced cell growth in csi1-3. Furthermore, induced loss of crossed-polylamellate walls via disruption of cortical microtubules mimics the effect of csi1 in acid growth. We hypothesize that CSI1- and microtubule-dependent crossed-polylamellate walls are required for acid growth in Arabidopsis hypocotyls.

Temporal expression patterns of fruit-specific α- EXPANSINS during cell expansion in bell pepper (Capsicum annuum L.)

BACKGROUND

Expansins (EXPs) facilitate non-enzymatic cell wall loosening during several phases of plant growth and development including fruit growth, internode expansion, pollen tube growth, leaf and root development, and during abiotic stress responses. In this study, the spatial and temporal expression patterns of C. annuum α- EXPANSIN (CaEXPA) genes were characterized. Additionally, fruit-specific CaEXPA expression was correlated with the rate of cell expansion during bell pepper fruit development.

RESULTS

Spatial expression patterns revealed that CaEXPA13 was up-regulated in vegetative tissues and flowers, with the most abundant expression in mature leaves. Expression of CaEXPA4 was associated with stems and roots. CaEXPA3 was expressed abundantly in flower at anthesis suggesting a role for CaEXPA3 in flower development. Temporal expression analysis revealed that 9 out of the 21 genes were highly expressed during fruit development. Of these, expression of six genes, CaEXPA5, CaEXPA7, CaEXPA12, CaEXPA14 CaEXPA17 and CaEXPA19 were abundant 7 to 21 days after anthesis (DAA), whereas CaEXPA6 was strongly expressed between 14 and 28 DAA. Further, this study revealed that fruit growth and cell expansion occur throughout bell pepper development until ripening, with highest rates of fruit growth and cell expansion occurring between 7 and 14 DAA. The expression of CaEXPA14 and CaEXPA19 positively correlated with the rate of cell expansion, suggesting their role in post-mitotic cell expansion-mediated growth of the bell pepper fruit. In this study, a ripening specific EXP transcript, CaEXPA9 was identified, suggesting its role in cell wall disassembly during ripening.

CONCLUSIONS

This is the first genome-wide study of CaEXPA expression during fruit growth and development. Identification of fruit-specific EXPAs suggest their importance in facilitating cell expansion during growth and cell wall loosening during ripening in bell pepper. These EXPA genes could be important targets for future manipulation of fruit size and ripening characteristics.

Complex Molecular Evolution and Expression of Expansin Gene Families in Three Basic Diploid Species of Brassica

Expansins are a kind of structural proteins of the plant cell wall, and they enlarge cells by loosening the cell walls. Therefore, expansins are involved in many growth and development processes. The complete genomic sequences of Brassica rapa, Brassica oleracea and Brassica nigra provide effective platforms for researchers to study expansin genes, and can be compared with analogues in Arabidopsis thaliana. This study identified and characterized expansin families in B. rapa, B. oleracea, and B. nigra. Through the comparative analysis of phylogeny, gene structure, and physicochemical properties, the expansin families were divided into four subfamilies, and then their expansion patterns and evolution details were explored accordingly. Results showed that after the three species underwent independent evolution following their separation from A. thaliana, the expansin families in the three species had increased similarities but fewer divergences. By searching divergences of promoters and coding sequences, significant positive correlations were revealed among orthologs in A. thaliana and the three basic species. Subsequently, differential expressions indicated extensive functional divergences in the expansin families of the three species, especially in reproductive development. Hence, these results support the molecular evolution of basic Brassica species, potential functions of these genes, and genetic improvement of related crops.

Transcriptome profiling reveals genes involved in spine development during CsTTG1-regulated pathway in cucumber (Cucumis sativus L.)

The cucumber (Cucumis sativus L.), a type of fleshy fruit, is covered with spines (multicellular trichomes), which have a crucial impact on the economic value of the crop. Previous studies have found that CsTTG1 plays important roles in the initiation and further differentiation of cucumber spines, but how spine formation is regulated at the molecular level by CsTTG1 remains poorly understood. In this study, we characterized a cucumber 35S:CsTTG1 transgenic T2 line, OE-2, which bears relatively large and long spines compared with the small and short spines of the wild type (WT). Phenotypic measurements and histological analyses revealed that this phenotypic change was attributed to significant increases in cell number and size. Comparison of ovary epidermis transcriptomes between OE-2 and WT by DGE (Digital Gene Expression) analysis identified 1241 differentially expressed genes, among which 712 genes were dramatically upregulated and 529 downregulated in the ovary epidermis of OE-2. XTH23 and Cyclin family genes were significantly activated in OE-2, and transcription factors (TFs) were found to participate in spine size regulation in OE-2. Further analyses confirmed that GA was implicated in the regulation of fruit spine development in cucumber. Thus, our study provides a foundation for dissecting the molecular regulatory networks of fruit spine control in cucumber.

Identification and inoculation of fungal strains from Cedrus deodara rhizosphere involve in growth and alleviation of high nitrogen stress

Cedrus deodara is economically and ethnobotanically an important forest tree and is shown to be at decline in Northern areas of Pakistan in recent years mainly due to high concentration of Nitrogen in forests. Ectomycorrhizal (ECM) association forming fungi enables the forest trees to develop optimally by absorbing water from the rhizosphere through their absorptive hyphae and by making available the nutrients by mobilization of N and P from the organic substrates. This study was conducted to identify the ECM strains from C. deodara rhizosphere and to analyse the impact of high N load on the C. deodara seedlings to establish N critical load value for coniferous forests of Pakistan. Six new fungal strains were identified from the rhizosphere of C. deodara and were registered at GenBank (NCBI) as Emmia latemarginata strain ACE1, Aspergillus terreus strain ACE2, Purpureocillium lilacinum strain ACE3, Talaromyces pinophilus strain ACE4, A. fumigatus strain ACE5 and T. pinophilus strain ACE6 with accession numbers MH145426, MH145427, MH145428, MH145429, MH145430 and MH547115. Four out of six isolated strains were inoculated with seedlings of C. deodara singly and in consortium (CN) in combination with nitrogen load of 0 (C), 25 (T1), 50 (T2), 100 kg N ha⁻¹ yr⁻¹ (T3). Agronomic, physiological and gene expression studies for ExpansinA4 (EXPA4) and Cystatins (Cys) were made to analyse the impact of fungal strains in relation to high N stress. This study suggests a positive impact of T1 (25 kg N ha⁻¹ yr⁻¹) Nitrogen load and a negative impact of T3 (100 kg N ha⁻¹ yr⁻¹) on growth parameters and expression patterns of EXPA4 and Cys genes. Peroxidase (POX) activity decreased in the order ACE5 > ACE2 > C > ACE3 > ACE1 > CN. However, the results of Superoxide dismutase (SOD) showed decreasing trend in the order ACE5 > C > CN > ACE1 > ACE2 > ACE3. Strain ACE3 was shown to have a positive impact on the seedlings in terms of growth, physiology and expression of genes. Present study suggests that newly identified fungal strains showing positive impact on the growth and physiology of C. deodara could be used for the propagation of this economically important plant in Pakistan after pathogenicity test.

An expansin-like protein expands forage cell walls and synergistically increases hydrolysis, digestibility and fermentation of livestock feeds by fibrolytic enzymes

Bacterial expansin-like proteins have synergistically increased cellulose hydrolysis by cellulolytic enzymes during the initial stages of biofuel production, but they have not been tested on livestock feeds. The objectives of this study were to: isolate and express an expansin-like protein (BsEXLX1), to verify its disruptive activity (expansion) on cotton fibers by immunodetection (Experiment 1), and to determine the effect of dose, pH and temperature for BsEXLX1 and cellulase to synergistically hydrolyze filter paper (FP) and carboxymethyl cellulose (CMC) under laboratory (Experiment 2) and simulated ruminal (Experiment 3) conditions. In addition, we determined the ability of BsEXLX1 to synergistically increase hydrolysis of corn and bermudagrass silages by an exogenous fibrolytic enzyme (EFE) (Experiment 4) and how different doses of BsEXLX1 and EFE affect the gas production (GP), in vitro digestibility and fermentation of a diet for dairy cows (Experiment 5). In Experiment 1, immunofluorescence-based examination of cotton microfiber treated without or with recombinant expansin-like protein expressed from Bacillus subtilis (BsEXLX1) increased the surface area by > 100% compared to the untreated control. In Experiment 2, adding BsEXLX1 (100 μg/g FP) to cellulase (0.0148 FPU) increased release of reducing sugars compared to cellulase alone by more than 40% (P < 0.01) at optimal pH (4.0) and temperature (50°C) after 24 h. In Experiment 3 and 4, adding BsEXLX1 to cellulase or EFE, synergistically increased release of reducing sugars from FP, corn and bermudagrass silages under simulated ruminal conditions (pH 6.0, 39°C). In Experiment 5, increasing the concentration of BsEXLX1 linearly increased (P < 0.01) GP from fermentation of a diet for dairy cows by up to 17.8%. Synergistic effects between BsEXLX1 and EFE increased in vitro NDF digestibility of the diet by 23.3% compared to the control. In vitro digestibility of hemicellulose and butyrate concentration were linearly increased by BsEXLX1 compared to the control. This study demonstrated that BsEXLX1 can improve the efficacy of cellulase and EFE at hydrolyzing pure substrates and dairy cow feeds, respectively.

Expression of Two α-Type Expansins from Ammopiptanthus nanus in Arabidopsis thaliana Enhance Tolerance to Cold and Drought Stresses

Expansins, cell-wall loosening proteins, play an important role in plant growth and development and abiotic stress tolerance. Ammopiptanthus nanus (A. nanus) is an important plant to study to understand stress resistance in forestry. In our previous study, two α-type expansins from A. nanus were cloned and named AnEXPA1 and AnEXPA2. In this study, we found that they responded to different abiotic stress and hormone signals. It suggests that they may play different roles in response to abiotic stress. Their promoters show some of the same element responses to abiotic stress and hormones, but some special elements were identified between the expansins that could be essential for their expression. In order to further testify the reliability of the above results, we conducted an analysis of β-glucuronidase (GUS) dyeing. The analysis showed that AnEXPA1 was only induced by cold stress, whereas AnEXPA2 responded to hormone induction. AnEXPA1 and AnEXPA2 transgenic Arabidopsis plants showed better tolerance to cold and drought stresses. Moreover, the ability to scavenge reactive oxygen species (ROS) was significantly improved in the transgenic plants, and expansin activity was enhanced. These results suggested that AnEXPA1 and AnEXPA2 play an important role in the response to abiotic stress. Our research contributes to a better understanding of the regulatory network of expansins and may benefit agricultural production.

Proteomic profiling of root system development proteins in chrysanthemum overexpressing the CmTCP20 gene

Plant root systems ensure the efficient absorption of water and nutrients and provide anchoring into the soil. Although root systems are a highly plastic set of traits that vary both between and among species, the basic root system morphology is controlled by inherent genetic factors. TCP20 has been identified as a key regulator of root development in plants, and yet its underlying mechanism has not been fully elucidated, especially in chrysanthemum. We found that overexpression of the CmTCP20 gene promoted both adventitious and lateral root development in chrysanthemum. To get further insight into the molecular mechanisms controlling root system development, we conducted a study employing tandem mass tag proteomic to characterize the differential root system development proteomes from CmTCP20-overexpressing and wild-type chrysanthemum root samples. Of the proteins identified, 234 proteins were found to be differentially abundant (>1.5-fold cut off, p < 0.05) in CmTCP20-overexpressing versus wild-type chrysanthemum root samples. Functional enrichment analysis indicated that the CmTCP20 gene may participate in "phytohormone signal transduction". Our findings provide a valuable perspective on the mechanisms of both adventitious and lateral root development via CmTCP20 modulation at the proteome level in chrysanthemum.

Effect of Salt Stress on Cytosine Methylation within GL2, An Arabidopsis thaliana Gene Involved in Root Epidermal Cell Differentiation. Absence of Inheritance in the Unstressed Progeny

Methylation/demethylation of cytosines is an epigenetic strategy for transcriptional regulation, allowing organisms to rapidly respond and adapt to different stimuli. In this context, and using Arabidopsis thaliana as a plant model, we explored whether an environmental stress is sufficient to trigger a change in the methylation status of Glabra-2, a master gene associated with root epidermal cell differentiation. As this gene acts mainly in the epidermis in the root, we examined the stress-driven methylation levels specifically in that tissue. We focused on the stress caused by different salt concentrations in the growth medium. When testing the effect of 20 and 75 mM NaCl, we found that there is a significant decrease in the CG methylation level of the analyzed genomic region within the epidermis. Whereas this reduction was 23% in mildly stressed plants, it turned out to be more robust (33%) in severely stressed ones. Notably, this latter epigenetic change was accompanied by an increase in the number of trichoblasts, the epidermal cell type responsible for root hair development. Analysis of an eventual inheritance of epigenetic marks showed that the non-stressed progeny (F1) of stressed plants did not inherit—in a Lamarckian fashion—the methylation changes that had been acquired by the parental individuals.

TaEXPB7-B, a β-expansin gene involved in low-temperature stress and abscisic acid responses, promotes growth and cold resistance in Arabidopsis thaliana

Low temperature is one of the primary causes of economic loss in agricultural production, and in this regard, expansin proteins are known to play important roles in plant growth and responses to various abiotic stresses and plant hormones. In order to elucidate the roles of expansin genes in the response of Dongnongdongmai 2 (D2), a highly cold-resistant winter wheat variety, to low-temperature stress, we exposed plants to a temperature of 4℃ and analysed the transcriptome of tillering nodes. Expression levels of TaEXPB7-B were significantly increased in response to both low-temperature stress and abscisic acid (ABA) treatment. To further confirm these observations, we transformed Arabidopsis plants with the β-glucuronidase (GUS) gene driven by the TaEXPB7-B promoter. GUS staining results revealed that TaEXPB7-B showed similar responses to low-temperature and ABA treatments. Our transcriptome data indicated that the AREB/ABF transcription factor gene TaWABI5 was also induced by low temperature in D2. Yeast one-hybrid experiments demonstrated that TaWABI5 binds to an ABRE cis-element in the TaEXPB7-B promoter, and overexpression of TaWABI5 in wheat protoplasts enhanced the expression of endogenous TaEXPB7-B by 7.7-fold, implying that TaWABI5 plays important roles in regulating the expression of TaEXPB7-B. Cytological data obtained from the transient expression of 35S::TaEXPB7-B-eYFP in onion epidermal cells indicated that TaEXPB7-B is cell wall localised. Overexpression of TaEXPB7-B in Arabidopsis promoted a significant increase in plant growth and increased lignin and cellulose contents. Moreover, TaEXPB7-B conferred enhanced antioxidant and osmotic regulation in transgenic Arabidopsis, thereby increasing the tolerance and survival of plants under conditions of low-temperature stress.

Identification of a cell-surface protein involved in glucose assimilation and disruption of the crystalline region of cellulose by Cytophaga hutchinsonii

The crystalline region of cellulose is the main barrier to the utilization of crystalline cellulose. Cytophaga hutchinsonii actively digests the crystalline region of cellulose by an unknown mechanism. Transposon mutagenesis was done to identify a novel gene locus chu_1557, which is required for efficient disruption of the crystalline region of cellulose, and the absence of CHU_1557 resulted in decreased glucose assimilation efficiency. The defect of the mutant in the disruption of the crystalline region of cellulose was partially retained by additional glucose or pre-culturing the mutant in a low glucose concentration medium which could improve its glucose absorption efficiency. These results suggested that extracellular glucose has important roles in the disruption of crystalline cellulose by C. hutchinsonii. Further study showed that the expression of an outer membrane protein CHU_3732 was downregulated by the absence of CHU_1557 in a low glucose concentration medium. CHU_3732 was involved in uptake of glucose and its expression was induced by a low concentration of glucose. CHU_3732 was predicted to be a porin, so we inferred that it may work as a glucose transport channel in the outer membrane. Based on these results, we deduced that CHU_1557 played a role in the process of glucose assimilation and its disruption affected the expression of other proteins related to glucose transportation such as CHU_3732, and then affected the cell growth in a low glucose concentration medium and disruption of the crystalline region of cellulose.

High-throughput 3D modelling to dissect the genetic control of leaf elongation in barley (Hordeum vulgare)

To optimize shoot growth and structure of cereals, we need to understand the genetic components controlling initiation and elongation. While measuring total shoot growth at high throughput using 2D imaging has progressed, recovering the 3D shoot structure of small grain cereals at a large scale is still challenging. Here, we present a method for measuring defined individual leaves of cereals, such as wheat and barley, using few images. Plant shoot modelling over time was used to measure the initiation and elongation of leaves in a bi-parental barley mapping population under low and high soil salinity. We detected quantitative trait loci (QTL) related to shoot growth per se, using both simple 2D total shoot measurements and our approach of measuring individual leaves. In addition, we detected QTL specific to leaf elongation and not to total shoot size. Of particular importance was the detection of a QTL on chromosome 3H specific to the early responses of leaf elongation to salt stress, a locus that could not be detected without the computer vision tools developed in this study.

iTRAQ-Based Quantitative Proteomics and Transcriptomics Provide Insights Into the Importance of Expansins During Root Development in Carrot

Carrot is an important root vegetable crop with a variety of nutrients. As the main product of carrots, the growth and development of fleshy roots directly determine the yield and quality of carrots. However, molecular mechanism underlying the carrot root formation and expansion is still limited. In our study, isobaric tags for relative and absolute quantification (iTRAQ) was utilized to explore the differentially expressed proteins (DEPs) during different developmental stages of carrot roots. Overall, 2,845 proteins were detected, of which 118 were significantly expressed in all three stages. DEPs that participated in several growth metabolisms were identified, including energy metabolism, defense metabolism, cell growth and shape regulation. Among them, two expansin proteins were obtained. A total of 30 expansin genes were identified based on the carrot genome database. Structure analysis showed that carrot expansin gene family was relatively conserved. Based on the expression analysis, we found that the expression profile of expansins genes was up-regulated during the vigorous growing period of carrot root. Furthermore, there was a consistent relationship between the expression patterns of mRNA and protein. The results indicated that expansin proteins might play important roles during root development in carrot. Our work provided useful information for understanding molecular mechanism of carrot root development.

Comparative in silico study of the differences in the structure and ligand interaction properties of three alpha-expansin proteins from Fragaria chiloensis fruit

Expansins are cell wall proteins associated with several processes, including changes in the cell wall during ripening of fruit, which matches softening of the fruit. We have previously reported an increase in expression of specific expansins transcripts during softening of Fragaria chiloensis fruit. Here, we characterized three α-expansins. Their full-length sequences were obtained, and through qRT-PCR (real-time PCR) analyses, their transcript accumulation during softening of F. chiloensis fruit was confirmed. Interestingly, differential but overlapping expression patterns were observed. With the aim of elucidating their roles, 3D protein models were built using comparative modeling methodology. The models obtained were similar and displayed cellulose binding module(CBM ) with a β-sandwich structure, and a catalytic domain comparable to the catalytic core of protein of the family 45 glycosyl hydrolase. An open groove located at the central part of each expansin was described; however, the shape and size are different. Their protein-ligand interactions were evaluated, showing favorable binding affinity energies with xyloglucan, homogalacturonan, and cellulose, cellulose being the best ligand. However, small differences were observed between the protein-ligand conformations. Molecular mechanics-generalized Born-surface area (MM-GBSA) analyses indicate the major contribution of van der Waals forces and non-polar interactions. The data provide a dynamic view of interaction between expansins and cellulose as putative cell wall ligands at the molecular scale. Communicated by Ramaswamy H. Sarma.

Quantitative Proteomics Analysis of Lettuce (Lactuca sativa L.) Reveals Molecular Basis-Associated Auxin and Photosynthesis with Bolting Induced by High Temperature

Bolting is a key process in the growth and development of lettuce (Lactuca sativa L.). A high temperature can induce early bolting, which decreases both the quality and production of lettuce. However, knowledge of underlying lettuce bolting is still lacking. To better understand the molecular basis of bolting, a comparative proteomics analysis was conducted on lettuce stems, during the bolting period induced by a high temperature (33 °C) and a control temperature (20 °C) using iTRAQ-based proteomics, phenotypic measures, and biological verifications using qRT-PCR and Western blot. The high temperature induced lettuce bolting, while the control temperature did not. Of the 5454 identified proteins, 619 proteins presented differential abundance induced by high-temperature relative to the control group, of which 345 had an increased abundance and 274 had a decreased abundance. Proteins with an abundance level change were mainly enriched in pathways associated with photosynthesis and tryptophan metabolism involved in auxin (IAA) biosynthesis. Moreover, among the proteins with differential abundance, proteins associated with photosynthesis and tryptophan metabolism were increased. These findings indicate that a high temperature enhances the function of photosynthesis and IAA biosynthesis to promote the process of bolting, which is in line with the physiology and transcription level of IAA metabolism. Our data provide a first comprehensive dataset for gaining novel understanding of the molecular basis underlying lettuce bolting induced by high temperature. It is potentially important for further functional analysis and genetic manipulation for molecular breeding to breed new cultivars of lettuce to restrain early bolting, which is vital for improving vegetable quality.

OsEXPA10 mediates the balance between growth and resistance to biotic stress in rice

OsEXPA10 gene coordinates the balance between rice development and biotic resistance. Expansins are proteins that can loosen the cell wall. Previous studies have indicated that expansin-encoding genes were involved in defense against abiotic stress, but little is known about the involvement of expansins in biotic stress. Brown planthopper (BPH) is one of the worst insect pests of rice in the Asia-Pacific planting area, and many efforts have been made to identify and clone BPH-resistance genes for use in breeding resistant cultivars. At the same time, rice blast caused by Magnaporthe grisea is one of the three major diseases that severely affect rice production worldwide. Here, we demonstrated that one rice expansin-encoding gene, OsEXPA10, functions in both rice growth and biotic resistance. Over expression of OsEXPA10 improved rice growth but also increased susceptibility to BPH infestation and blast attack, while knock-down OsEXPA10 gene expression resulted in reduced plant height and grain size, but also increased resistance to BPH and the blast pathogen. These results imply that OsEXPA10 mediates the balance between rice development and biotic resistance.

GW2 Functions as an E3 Ubiquitin Ligase for Rice Expansin-Like 1

Seed size is one of the most important traits determining the yield of cereal crops. Many studies have been performed to uncover the mechanism of seed development. However, much remains to be understood, especially at the molecular level, although several genes involved in seed size have been identified. Here, we show that rice Grain Width 2 (GW2), a RING-type E3 ubiquitin ligase, can control seed development by catalyzing the ubiquitination of expansin-like 1 (EXPLA1), a cell wall-loosening protein that increases cell growth. Microscopic examination revealed that a GW2 mutant had a chalky endosperm due to the presence of loosely packed, spherical starch granules, although the grain shape was normal. Yeast two-hybrid and in vitro pull-down assays showed a strong interaction between GW2 and EXPLA1. In vitro ubiquitination analysis demonstrated that EXPLA1 was ubiquitinated by GW2 at lysine 279 (K279). GW2 and EXPLA1 colocalized to the nucleus when expressed simultaneously. These results suggest that GW2 negatively regulates seed size by targeting EXPLA1 for degradation through its E3 ubiquitin ligase activity.

The phosphatidylinositol synthase gene (GhPIS) contributes to longer, stronger, and finer fibers in cotton

Cotton fibers are the most important natural raw material used in textile industries world-wide. Fiber length, strength, and fineness are the three major traits which determine the quality and economic value of cotton. It is known that exogenous application of phosphatidylinositols (PtdIns), important structural phospholipids, can promote cotton fiber elongation. Here, we sought to increase the in planta production of PtdIns to improve fiber traits. Transgenic cotton plants were generated in which the expression of a cotton phosphatidylinositol synthase gene (i.e., GhPIS) was controlled by the fiber-specific SCFP promoter element, resulting in the specific up-regulation of GhPIS during cotton fiber development. We demonstrate that PtdIns content was significantly enhanced in transgenic cotton fibers and the elevated level of PtdIns stimulated the expression of genes involved in PtdIns phosphorylation as well as promoting lignin/lignin-like phenolic biosynthesis. Fiber length, strength and fineness were also improved in the transgenic plants as compared to the wild-type cotton, with no loss in overall fiber yield. Our data indicate that fiber-specific up-regulation of PtdIns synthesis is a promising strategy for cotton fiber quality improvement.

On the distinct binding modes of expansin and carbohydrate-binding module proteins on crystalline and nanofibrous cellulose: implications for cellulose degradation by designer cellulosomes

Transformation of cellulose into monosaccharides can be achieved by hydrolysis of the cellulose chains, carried out by a special group of enzymes known as cellulases.

Transcriptome analysis of genes involved in secondary cell wall biosynthesis in developing internodes of Miscanthus lutarioriparius

Miscanthus is a promising lignocellulosic bioenergy crop for bioethanol production. To identify candidate genes and regulation networks involved in secondary cell wall (SCW) development in Miscanthus, we performed de novo transcriptome analysis of a developing internode. According to the histological and in-situ histochemical analysis, an elongating internode of M. lutarioriparius can be divided into three distinct segments, the upper internode (UI), middle internode (MI) and basal internode (BI), each representing a different stage of SCW development. The transcriptome analysis generated approximately 300 million clean reads, which were de novo assembled into 79,705 unigenes. Nearly 65% of unigenes was annotated in seven public databases. Comparative profiling among the UI, MI and BI revealed four distinct clusters. Moreover, detailed expression profiling was analyzed for gene families and transcription factors (TFs) involved in SCW biosynthesis, assembly and modification. Based on the co-expression patterns, putative regulatory networks between TFs and SCW-associated genes were constructed. The work provided the first transcriptome analysis of SCW development in M. lutarioriparius. The results obtained provide novel insights into the biosynthesis and regulation of SCW in Miscanthus. In addition, the genes identified represent good candidates for further functional studies to unravel their roles in SCW biosynthesis and modification.