Plant expansins: diversity and interactions with plant cell walls

The Multifunctional Anaphase Promoting Complex 7 (APC7) Gene Is Associated With Increased Plant Growth and Improved Resistance to DNA and RNA Viruses

The anaphase promoting complex 7 (AtAPC7) is an APC/C subunit expressed in different organs of Arabidopsis thaliana and conserved among eukaryotes. A variant of the complete APC7 protein, containing its C-terminal region (named APC-CT), shows a high homology with a tobacco viral replication inhibitor (IVR-like) protein that reduces plant susceptibility to RNA viruses. Here, the role of the AtAPC7 gene was investigated by characterizing Arabidopsis plants overexpressing the full-length AtAPC7 (APC7OE) and the C-terminal portion (APC7-CTOE), by phenotypical, physiological and molecular approaches. APC7OE plants showed improved growth of vegetative organs, earlier flowering and increased photosynthetic efficiency, CO2 assimilation and productivity, compared with Col-0 control plants. Conversely, APC7-CTOE plants showed reduced susceptibility to both RNA and DNA viruses, along with an improvement in plant growth, although not surpassing APC7OE plants. Altogether, the data provide evidence for the role of the AtAPC7 in regulating cell division, expansion and differentiation, accompanied by an increase in photosynthetic capacity, resulting in enhanced plant biomass and seed yield. AtAPC7-CT might reduce growth-defence trade-offs, enabling plants to simultaneously defend themselves while promoting better growth. Our findings highlight the multifunctional role of AtAPC7, unveiling the potential of its orthologous genes as valuable biotechnological tools in important crops.

Cell wall dynamic changes and signaling during plant lateral root development

Lateral roots (LRs), are an important component of plant roots, playing a crucial role in anchoring the plant in the soil and facilitating the uptake of water and nutrients. As post-embryonic organs, LRs originate from the pericycle cells of the primary root, and their formation is characterized by precise regulation of cell division and complex intercellular interactions, both of which are closely tied to cell wall regulation. Considering the rapid advances in molecular techniques over the past three decades, we reframe the understanding of the dynamic change in cell wall during LR development by summarizing the factors that precipitate these changes and their effects, as well as the regulated signals involved. Additionally, we discuss current challenges in this field and propose potential solutions.

A Fresh Look at Celery Collenchyma and Parenchyma Cell Walls Through a Combination of Biochemical, Histochemical, and Transcriptomic Analyses

Celery (Apium graveolens) can be considered as a model plant for studying pectin-enriched primary cell walls. In addition to parenchyma cells with xyloglucan-deficient walls, celery petioles contain collenchyma, a mechanical tissue with thickened cell walls of similar composition. This study presents a comprehensive analysis of these tissues at both early and late developmental stages, integrating data on polysaccharide yield, composition, localization, and transcriptome analysis. Our results reveal that young collenchyma walls possess distinct polysaccharide compositions, including higher levels of rhamnogalacturonan I (RG-I), branched galactans, esterified homogalacturonan, and xyloglucan, compared to parenchyma cells. A significant number of genes encoding proteins involved in pectin methylesterification and acetylation were upregulated in young collenchyma. Different gene isoforms encoding glycosyltransferases involved in RG-I biosynthesis were activated in both collenchyma and parenchyma, suggesting potential variations in RG-I structure and function across different primary cell walls. We identified a set of potential glycosyltransferases involved in RG-I biosynthesis in collenchyma and proposed synthase complexes for heteromannan and heteroxylan. The transcriptome data not only confirmed known biochemical traits of celery cell walls but also provided deeper insights into the peculiarities of cell wall polysaccharide metabolism, thereby helping to narrow down candidate genes for further molecular genetic studies.

Excessive accumulation of auxin inhibits protocorm development during germination of Paphiopedilum spicerianum

KEY MESSAGE

Excessive auxin accumulation inhibits protocorm development during germination of Paphiopedilum spicerianum, delaying shoot meristem formation by downregulating boundary genes (CUC1, CUC2, CLV3) and promoting fungal colonization, essential for seedling establishment. Paphiopedilum, possess high horticultural and conservational value. Asymbiotic germination is a common propagation method, but high rates of protocorm developmental arrest hinder seedling establishment. Our study found that the key difference between normally developing protocorm (NDP) and arrested developmental protocorm (ADP) is their capability for continuous cell differentiation. In ADP, cells divide without differentiating, with indole-3-acetic acid (IAA) levels being 20 times higher than that in NDP. This suggests that auxin level plays a role in protocorm cell fate determination. Exogenous application of NAA demonstrated that elevated auxin level can delay the formation of the shoot apical meristem (SAM) inside the protocorm. Gene expression analysis revealed that elevated auxin can inhibit or even halt the SAM formation through down-regulation of SAM-related genes such as CLV3, CUC1 and CUC2. High auxin levels also led to reduced cell wall rigidity by up-regulation of cell wall expanding protein (EXPB15), thereby creating ideal conditions for fungi entry. Inoculation with a compatible orchid mycorrhizal fungus (OMF) resulted in successful cell differentiation of ADP and eventually triggered the conversion of ADP to NDP. Since the protocorm is a distinct structure that facilitates the establishment of symbiotic associations with compatible OMF, we propose that the excessive auxin accumulation inside Paphiopedilum protocorm can pause the further development of protocorm and soften the cell wall. This strategy likely serves to enhance the attraction and colonization by OMFs in the native habitat of Paphiopedilum, facilitating essential symbiotic relationships necessary for their survival and growth.

Dynamic changes of heterogeneous cell wall macromolecules in differentiating conifer xylem using cytochemical localization

Tracing dynamic changes of heterogeneous cell wall components during xylem differentiation is essential for understanding the intricate architecture of wood cell walls at the individual secondary cell wall layer level. Here we employ histochemical- and immunological approaches to visualize the deposition of cellular polymers during xylem differentiation in Pinus bungeana. In axial tracheids, deposition of crystalline cellulose and glucomannan preceded xylan and lignin. Lignification was initiated in primary cell wall corners during development of the S1 layer and intensified with cell wall thickening. Immunofluorescence labeling showed an earlier deposition of glucomannan than xylan with strong presence in S1 layer corner regions at early stages of differentiation. Quantification of immunogold-labeled xylan and glucomannan showed distinct increasing trends during thickening of tracheid wall layers with xylan labeling of the S1 and S2 layers at the S3 stage greater than the S2 stage. Differential cell wall polymer deposition was evident in mature tracheid areas with glucomannan absent in warty layers. Pectins were highly concentrated in unlignified primary cell walls but decreased with axial tracheid wall differentiation. The sequence of polymer deposition in ray cells was similar but lagged behind axial tracheids with ray parenchyma remaining unlignified with thinner cell walls than ray tracheids.

Cell elongation and altered phytohormone levels play a role in establishing distyly in Averrhoa carambola

The flowers of distylous plants exhibit two distinct morphologies that facilitate precise pollen transfer. Averrhoa carambola, a woody plant characterized by distyly, has an unclear molecular regulatory mechanism underlying this trait. Its prolonged flowering period and substantial flower production render it an excellent model for investigating the distylous syndrome. This study aims to elucidate the mechanism of distyly in A. carambola and to identify the regulatory genes. The long-style cultivar 'Daguo Tianyangtao 1' and the short-style cultivar 'Daguo Tianyangtao 3' were selected as models for this investigation. We examined phenotypic characteristics, anatomical structures, and endogenous hormone content associated with distyly. Transcriptomic data were utilized to pinpoint candidate genes involved in the regulation of distyly, followed by a bioinformatics analysis these genes. The results indicate that variations in cell elongation contribute to the differential heights of stigmas and anthers in A. carambola, thereby resulting in the distylous syndrome. Auxins, Gibberellin A3 (GA3), Gibberellin A4 (GA4), and brassinolide (BL) were found to influence elongation of styles, whereas Gibberellin A1 (GA1) and GA4 affected filament elongation. Transcriptome sequencing analysis identified 34 hormone-related differentially expressed genes (DEGs) and 16 cell development-related DEGs in different morphs of pistils, and 29 hormone-related DEGs and 22 cell development-related DEGs were identified in different morphs of stamens. Four candidate genes-AcaBRU1, AcaPRE1, AcaXTH2, and AcaEXPA11-were found to possess conserved motifs characteristic of their respective families. Consequently, various plant hormones modulate the expression of response genes, leading to differences in elongation of style and filament cells between different flower types of A. carambola, thereby promoting the distylous syndrome. This study provides a theoretical basis for understanding the mechanisms of distyly formation in woody plants.

Cortical microtubules act as a template to organize nano-scale patterning of exocytosis

Targeting of exocytosis enables cellular morphogenesis, motility and polarized transport, yet relatively little is known about the targeting mechanisms in cellular systems. Here we show that the SEC/MUNC protein KEULE is a dynamic marker for individual secretory events and employ it as a live cell probe, that together with high-precision image analysis of thousands of events, reveal that cortical microtubule arrays act as two-dimensional templates that pattern exocytosis at the nano-scale in higher plant cells. This mechanism is distinct from previously described mechanisms involving motor-driven transport and defines ordered and adjacent linear domains where secretory events are higher and lower than expected, effectively redistributing exocytosis over most of the cell membrane. In addition, analysis of KEULE kinetics revealed distinct phases of assembly/disassembly that are differentially sensitive to experimental treatments that reduce exocytosis, revealing SEC/MUNC dynamics as a versatile and information rich read-out of exocytosis in vivo .

1H, 13C and 15N backbone resonance assignment of Cel45A from Phanerochaete chrysosporium

A glycoside hydrolase family 45 (GH45) enzyme from the white-rot basidiomycete fungus Phanerochaete chrysosporium (PcCel45A) was expressed in Pichia pastoris with 13C and 15N labelling. A nearly complete assignment of 1H, 13C and 15N backbone resonances was obtained, as well as the secondary structure prediction based on the assigned chemical shifts using the TALOS-N software. The predicted secondary structure was almost identical to previously published crystal structures of the same enzyme, except for differences in the termini of the sequence. This is the first NMR study using an isotopically labelled GH45 enzyme.

The C2H2-type zinc finger transcription factor ZmDi19-7 regulates plant height and organ size by promoting cell size in maize

The drought-induced protein 19 (Di19) gene family encodes a Cys2/His2 zinc-finger protein implicated in responses to diverse plant stressors. To date, potential roles of these proteins as transcription factors remain largely elusive in maize. Here, we show that ZmDi19-7 gene exerts pivotal functions in regulation of plant height and organ growth by modulating the cell size in maize. ZmDi19-7 physically interacts with ubiquitin receptor protein ZmDAR1b, which is indispensable in ubiquitination of ZmDi19-7 and affects its protein stability. Further genetic analysis demonstrated that ZmDAR1b act in a common pathway with ZmDi19-7 to regulate cell size in maize. ZmDi19-7, severing as a transcriptional factor, is significantly enriched in conserved DiBS element in the promoter region of ZmHSP22, ZmHSP18c, ZmSAUR25, ZmSAUR55, ZmSAUR7 and ZmXTH23 and orchestrates the expression of these genes involving in auxin-mediated cell expansion and protein processing in the endoplasmic reticulum. Thus, our findings demonstrate that ZmDi19-7 is an important newfound component of the ubiquitin-proteasome pathway in regulation of plant height and organ size in maize. These discoveries highlight potential targets for the genetic improvement of maize in the future.

Identification and characterization of a rice expansin-like protein with metal-binding properties

Heavy metal (HM) contamination poses significant threat to agricultural productivity. This study identified and characterized Os09g29690 (OsELP), a rice expansin-like protein. We demonstrated OsELP localizes to the cell wall and is upregulated under various abiotic stresses. Sequence analysis revealed a potential metal-binding CXXXC motif in its conserved domain. Heterologous expression of OsELP in yeast mutants (Δacr3 and Δycf1) enhanced metal tolerance under arsenate [As(V)], arsenite [As(III)], and cadmium [Cd] stress. Yeast cells expressing OsELP accumulated higher amounts of As and Cd, suggesting a potential metal-binding mechanism. This was confirmed through site-directed mutagenesis on the conserved cysteine and serine residues within OsELP. Mutants lacking cysteine residues (mutCS) reduced tolerance to As(III) and Cd but enhanced tolerance to As(V), indicating a role of cysteine in As(III) and Cd binding. Conversely, mutants lacking serine residues (mutSA) reduced tolerance to As(V), suggesting serine's involvement in As(V) binding. These findings reveal the roles of cysteine and serine residues in mediating HM tolerance and binding, confirming OsELP as a key player in HM detoxification through cell wall localization and chelation. This study provides novel insights into the molecular mechanisms of HM tolerance in plants, with potential applications in developing crops with enhanced resistance to HM toxicity.

Arabidopsis root apical meristem adaptation to an osmotic gradient condition: an integrated approach from cell expansion to gene expression

Climate change triggers abiotic stress, such as drought and high salinity, that can cause osmotic stress. Water availability can limit plant growth, and the root tip tissues initially sense it. Most experiments destined to understand root growth adaptation to osmotic stress apply homogeneous high osmotic potentials (osmotic shock) to shoots and roots. However, this treatment does not represent natural field conditions where a root may encounter increasing osmotic potentials while exploring the soil. Osmotic shock severely reduces root growth rate, decreasing cell division in the proximal meristem and reducing mature cell length. In this work, we developed an in vitro osmotic gradient experimental system with increasing osmotic potentials. The system generates a controlled osmotic gradient in the root growth zone while exposing the aerial tissues to control conditions. The osmotic gradient system allowed Arabidopsis seedlings of Col-0 and ttl1 mutant (affected in the gene TETRATRICOPEPTIDE THIOREDOXIN-LIKE 1 (TTL1)) to sustain proper root growth for 25 days, reaching osmotic potentials of -1.2 MPa. We demonstrated that roots of seedlings grown in the osmotic gradient sustain a higher root growth rate than those that were grown under a homogeneous high osmotic potential. Furthermore, we found out that the expression of some genes is modified in the roots grown in the osmotic gradient compared to those grown in osmotic shock. Our data indicate that using an osmotic gradient can improve our understanding of how plants respond to osmotic stress and help find new genes to improve plant field performance.

Origin, Evolution, and Diversification of the Expansin Family in Plants

The cell wall is a crucial feature that allows ancestral streptophyte green algae to colonize land. Expansin, an extracellular protein that mediates cell wall loosening in a pH-dependent manner, could be a powerful tool for studying cell wall evolution. However, the evolutionary trajectory of the expansin family remains largely unknown. Here, we conducted a comprehensive identification of 2461 expansins across 64 sequenced species, ranging from aquatic algae to terrestrial plants. Expansins originated in chlorophyte algae and may have conferred the ability to loosen cell walls. The four expansin subfamilies originated independently: α-expansin appeared first, followed by β-expansin, and then expansin-like A and expansin-like B, reflecting the evolutionary complexity of plant expansins. Whole genome duplication/segmental duplication and tandem duplication events greatly contributed to expanding the expansin family. Despite notable changes in sequence characteristics, the intron distribution pattern remained relatively conserved among different subfamilies. Phylogenetic analysis divided all the expansins into five clades, with genes from the same subfamily tending to cluster together. Transcriptome data from 16 species across ten lineages and qRT-PCR analysis revealed varying expression patterns of expansin genes, suggesting functional conservation and diversification during evolution. This study enhances our understanding of the evolutionary conservation and dynamics of the expansin family in plants, providing insight into their roles as cell wall-loosening factors.

Multi-omics analysis unveils early molecular responses to aluminum toxicity in barley root tip

Barley (Hordeum vulgare L.) is widely cultivated across diverse soil types, including acidic soils where aluminum (Al) toxicity is the major limiting factor. The relative Al sensitivity of barley highlights the need for a deeper understanding of early molecular responses in root tip (the primary target of Al toxicity) to develop Al-tolerant cultivars. Integrative N6-methyladenosine (m6A) modification, transcriptomic, and metabolomic analyses revealed that elevated auxin and jasmonic acid (JA) levels modulated Al-induced root growth inhibition by repressing genes involved in cell elongation and proliferation. Additionally, these pathways promoted pectin demethylation via up-regulation of genes encoding pectin methylesterases (PMEs). The up-regulation of citrate efflux transporter genes including Al-activated citrate transporter 1 (HvAACT1), and ATP-binding cassette (ABC) transporters like HvABCB25, facilitated Al exclusion and vacuolar sequestration. Enhanced activity within the phenylpropanoid pathway supported antioxidant defenses and internal chelation through the production of specific flavonoids and altered cell wall composition via lignin unit modulation. Notably, several Al-responsive genes, including HvABCB25 and transcription factors (TFs), exhibited m6A modification changes, with two microtubule associated protein 65 (MAP65) members displaying opposing regulatory patterns at both transcriptional and m6A levels, underscoring the crucial role of m6A modification in gene expression regulation. This comprehensive study provides valuable insights into the epitranscriptomic regulation of gene expression and metabolite accumulation in barley root tip under Al stress.

Differences in transcriptomic responses upon Phytophthora palmivora infection among cultivars reveal potential underlying resistant mechanisms in durian

BACKGROUND

Phytophthora palmivora is a devastating oomycete pathogen in durian, one of the most economically important crops in Southeast Asia. The use of fungicides in Phytophthora management may not be a long-term solution because of emerging chemical resistance issues. It is crucial to develop Phytophthora-resistant durian cultivars, and information regarding the underlying resistance mechanisms is valuable for smart breeding programs.

RESULTS

In this study, we conducted RNA sequencing (RNA-seq) to investigate early gene expression responses (at 8, 24, and 48 h) after the P. palmivora infection in three durian cultivars, which included one resistant cultivar (Puangmanee; PM) and two susceptible cultivars (Monthong; MT and Kradumthong; KD). We performed co-expression and differential gene expression analyses to capture gene expression patterns and identify the differentially expressed genes. The results showed that genes encoding heat shock proteins (HSPs) were upregulated in all infected durians. The expression levels of genes encoding HSPs, such as ERdj3B, were high only in infected PM. A higher level of P. palmivora resistance in PM appeared to be associated with higher expression levels of various genes encoding defense and chitin response proteins, such as lysM domain receptor-like kinases. MT had a lower resistance level than PM, although it possessed more upregulated genes during P. palmivora infection. Many photosynthetic and defense genes were upregulated in the infected MT, although their expression levels were lower than those in the infected PM. KD, the least resistant cultivar, showed downregulation of genes involved in cell wall organization or biogenesis during P. palmivora infection.

CONCLUSIONS

Our results showed that the three durian cultivars exhibited significantly different gene expression patterns in response to P. palmivora infection. The upregulation of genes encoding HSPs was common in all studied durians. The high expression of genes encoding chitin response proteins likely contributed to P. palmivora resistance in durians. Durian susceptibility was associated with low basal expression of defense genes and downregulation of several cell wall-related genes. These findings enhance our understanding of durian resistance to Phytophthora infection and could be useful for the development of elite durian cultivars.

Plant Cell Wall Loosening by Expansins

Expansins comprise an ancient group of cell wall proteins ubiquitous in land plants and their algal ancestors. During cell growth, they facilitate passive yielding of the wall's cellulose networks to turgor-generated tensile stresses, without evidence of enzymatic activity. Expansins are also implicated in fruit softening and other developmental processes and in adaptive responses to environmental stresses and pathogens. The major expansin families in plants include α-expansins (EXPAs), which act on cellulose-cellulose junctions, and β-expansins, which can act on xylans. EXPAs mediate acid growth, which contributes to wall enlargement by auxin and other growth agents. The genomes of diverse microbes, including many plant pathogens, also encode expansins designated expansin-like X. Expansins are proposed to disrupt noncovalent bonding between laterally aligned polysaccharides (notably cellulose), facilitating wall loosening for a variety of biological roles.

Identification of BpEXP family genes and functional characterization of the BpEXPA1 gene in the stems development of Betula platyphylla

Expansins (EXPs) are unique plant cell wall proteins with the ability to induce cell wall expansion and play potential roles in xylem development. In the present study, a total of 25 BpEXP genes were identified in Betula platyphylla. Results of bioinformatics analysis described that BpEXP gene family was highly conserved in the process of evolution. All these genes were clustered into four groups, EXPA (Expansin A), EXPB (Expansin B), EXLA (Expansin-like A) and EXLB (Expansin-like B), according to phylogenetic analysis and BpEXPA1 was highly homologous to PttEXP1 and PttEXP2. The results of RT-qPCR showed that BpEXPA1 was expressed higher in stems and preferentially expressed in the first internodes, followed by apical buds and the third internodes, promoter expression analysis with GUS assay demonstrated that it was expressed in developing xylem, suggesting that BpEXPA1 might be involved in the development of the primary stems of birch. Overexpression of BpEXPA1 can promote cortex cell expansion and then enlarge the cortex cell area and layer, however inhibit the secondary cell wall deposition and result in the thinner cell wall and larger lumens of xylem fiber in transgenic plants. This study will provide information for investigating the regulation mechanism of BpEXP family genes and gene resources for birch genetics improvement.

Sucrose promotes cone enlargement via the TgNGA1-TgWRKY47-TgEXPA2 module in Torreya grandis

Cone enlargement is a crucial process for seed production and reproduction in gymnosperms. Most of our knowledge of cone development is derived from observing anatomical structure during gametophyte development. Therefore, the exact molecular mechanism underlying cone enlargement after fertilization is poorly understood. Here, we demonstrate that sucrose promotes cone enlargement in Torreya grandis, a gymnosperm species with relatively low rates of cone enlargement, via the TgNGA1-TgWRKY47-TgEXPA2 pathway. Cell expansion plays a significant role in cone enlargement in T. grandis. 13C labeling and sucrose feeding experiments indicated that sucrose-induced changes in cell size and number contribute to cone enlargement in this species. RNA-sequencing analysis, transient overexpression in T. grandis cones, and stable overexpression in tomato (Solanum lycopersicum) suggested that the expansin gene TgEXPA2 positively regulates cell expansion in T. grandis cones. The WRKY transcription factor TgWRKY47 directly enhances TgEXPA2 expression by binding to its promoter. Additionally, the NGATHA transcription factor TgNGA1 directly interacts with TgWRKY47. This interaction suppresses the DNA-binding ability of TgWRKY47, thereby reducing its transcriptional activation on TgEXPA2 without affecting the transactivation ability of TgWRKY47. Our findings establish a link between sucrose and cone enlargement in T. grandis and elucidate the potential underlying molecular mechanism.

SANS investigation of fungal loosenins reveal substrate dependent impacts of protein 1 action on inter-fibril distance and packing order of cellulosic substrates

BACKGROUND

Microbial expansin-related proteins include fungal loosenins, which have been previously shown to disrupt cellulose networks and enhance the enzymatic conversion of cellulosic substrates. Despite showing beneficial impacts to cellulose processing, detailed characterization of cellulosic materials after loosenin treatment is lacking. In this study, small-angle neutron scattering (SANS) was used to investigate the effects of three recombinantly produced loosenins that originate from Phanerochaete carnosa, PcaLOOL7, PcaLOOL9, and PcaLOOL12, on the organization of holocellulose preparations from Eucalyptus and Spruce wood samples.

RESULTS

Whereas the SANS analysis of Spruce holocellulose revealed an increase in interfibril spacing of neighboring cellulose microfibrils following treatment with PcaLOOL12 and to a lesser extent PcaLOOL7, the analysis of Eucalyptus holocellulose revealed a reduction in packing number following treatment with PcaLOOL12 and to a lesser extent PcaLOOL9. Parallel SEC-SAXS characterization of PcaLOOL7, PcaLOOL9, and PcaLOOL12 indicated the proteins likely function as monomers; moreover, all appear to retain a flexible disordered N-terminus and folded C-terminal region. The comparatively high impact of PcaLOOL12 motivated its NMR structural characterization, revealing a double-psi b-barrel (DPBB) domain surrounded by three alpha-helices - the largest nestled against the DPBB core and the other two part of loops extending from the core.

CONCLUSIONS

The SANS analysis of PcaLOOL action on holocellulose samples confirms their ability to disrupt cellulose fiber networks and suggests a progression from reducing microfibril packing to increasing interfibril distance. The most impactful PcaLOOL, PcaLOOL12, was previously observed to be the most highly expressed loosenin in P. carnosa. Its structural characterization herein reveals its stabilization through two disulfide linkages, and an extended N-terminal region distal to a negatively charged and surface accessible polysaccharide binding groove.

Function Analysis of a Maize Endo-1,4-β-xylanase Gene ZmHSL in Response to High-Temperature Stress

Rising temperature is a major threat to the normal growth and development of maize, resulting in low yield production and quality. The mechanism of maize in response to heat stress remains uncertain. In this study, a maize mutant Zmhsl-1 (heat sensitive leaves) with wilting and curling leaves under high temperatures was identified from maize Zheng 58 (Z58) mutant lines generated by ethyl methanesulfonate (EMS) mutagenesis. The Zmhsl-1 plants were more sensitive to increased temperature than Z58 in the field during growth season. The Zmhsl-1 plants had lower plant height, lower yield, and lower content of photosynthetic pigments. A bulked segregant analysis coupled with whole-genome sequencing (BSA-seq) enabled the identification of the corresponding gene, named ZmHSL, which encodes an endo-β-1,4-xylanase from the GH10 family. The loss-of-function of ZmHSL resulted in reduced lignin content in Zmhsl-1 plants, leading to defects in water transport and more severe leaf wilting with the increase in temperature. RNA-seq analysis revealed that the differentially expressed genes identified between Z58 and Zmhsl-1 plants are mainly related to heat stress-responsive genes and unfolded protein response genes. All these data indicated that ZmHSL plays a key role in lignin synthesis, and its defective mutation causes changes in the cell wall structure and gene expression patterns, which impedes water transport and confers higher sensitivity to high-temperature stress.

A conserved GRAS-domain transcriptional regulator links meristem indeterminacy to sex determination in Ceratopteris gametophytes

Most land plants alternate between generations of sexual gametophytes and asexual sporophytes. Unlike seed plants, fern gametophytes are free living and grow independently of their sporophytes. In homosporous ferns such as Ceratopteris, gametophytes derived from genetically identical spores exhibit sexual dimorphism, developing as either males or hermaphrodites. Males lack meristems and promote cell differentiation into sperm-producing antheridia. In contrast, hermaphrodites initiate multicellular meristems that stay undifferentiated, sustain cell division and prothallus expansion, and drive the formation of egg-producing archegonia. Once initiating the meristem, hermaphrodites secrete the pheromone antheridiogen, which triggers neighboring slower-growing gametophytes to develop as males, while the hermaphrodites themselves remain insensitive to antheridiogen. This strategy promotes outcrossing and prevents all individuals in the colony from becoming males. This study reveals that an evolutionarily conserved GRAS-domain transcriptional regulator (CrHAM), directly repressed by Ceratopteris microRNA171 (CrmiR171), promotes meristem development in Ceratopteris gametophytes and determines the male-to-hermaphrodite ratio in the colony. CrHAM preferentially accumulates within the meristems of hermaphrodites but is excluded from differentiated antheridia. CrHAM sustains meristem proliferation and cell division through conserved hormone pathways. In the meantime, CrHAM inhibits the antheridiogen-induced conversion of hermaphrodites to males by suppressing the male program expression and preventing meristem cells from differentiating into sperm-producing antheridia. This finding establishes a connection between meristem indeterminacy and sex determination in ferns, suggesting both conserved and diversified roles of meristem regulators in land plants.

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.

Regulation of Proline Accumulation and Protein Secretion in Sorghum under Combined Osmotic and Heat Stress

Plants reprogramme their proteome to alter cellular metabolism for effective stress adaptation. Intracellular proteomic responses have been extensively studied, and the extracellular matrix stands as a key hub where peptide signals are generated/processed to trigger critical adaptive signal transduction cascades inaugurated at the cell surface. Therefore, it is important to study the plant extracellular proteome to understand its role in plant development and stress response. This study examined changes in the soluble extracellular sub-proteome of sorghum cell cultures exposed to a combination of sorbitol-induced osmotic stress and heat at 40 °C. The combined stress significantly reduced metabolic activity and altered protein secretion. While cells treated with osmotic stress alone had elevated proline content, the osmoprotectant in the combined treatment remained unchanged, confirming that sorghum cells exposed to combined stress utilise adaptive processes distinct from those invoked by the single stresses applied separately. Reactive oxygen species (ROS)-metabolising proteins and proteases dominated differentially expressed proteins identified in cells subjected to combined stress. ROS-generating peroxidases were suppressed, while ROS-degrading proteins were upregulated for protection from oxidative damage. Overall, our study provides protein candidates that could be used to develop crops better suited for an increasingly hot and dry climate.

Transcriptome- and genome-wide systematic identification of expansin gene family and their expression in tuberous root development and stress responses in sweetpotato (Ipomoea batatas)

Introduction

Expansins (EXPs) are essential components of the plant cell wall that function as relaxation factors to directly promote turgor-driven expansion of the cell wall, thereby controlling plant growth and development and diverse environmental stress responses. EXPs genes have been identified and characterized in numerous plant species, but not in sweetpotato.

Results and methods

In the present study, a total of 59 EXP genes unevenly distributed across 14 of 15 chromosomes were identified in the sweetpotato genome, and segmental and tandem duplications were found to make a dominant contribution to the diversity of functions of the IbEXP family. Phylogenetic analysis showed that IbEXP members could be clustered into four subfamilies based on the EXPs from Arabidopsis and rice, and the regularity of protein motif, domain, and gene structures was consistent with this subfamily classification. Collinearity analysis between IbEXP genes and related homologous sequences in nine plants provided further phylogenetic insights into the EXP gene family. Cis-element analysis further revealed the potential roles of IbEXP genes in sweetpotato development and stress responses. RNA-seq and qRT-PCR analysis of eight selected IbEXPs genes provided evidence of their specificity in different tissues and showed that their transcripts were variously induced or suppressed under different hormone treatments (abscisic acid, salicylic acid, jasmonic acid, and 1-aminocyclopropane-1-carboxylic acid) and abiotic stresses (low and high temperature).

Discussion

These results provide a foundation for further comprehensive investigation of the functions of IbEXP genes and indicate that several members of this family have potential applications as regulators to control plant development and enhance stress resistance in plants.

Ectopic expression of OsWOX9A alters leaf anatomy and plant architecture in rice

MAIN CONCLUSION

Ectopic expression of OsWOX9A induces narrow adaxially rolled rice leaves with larger bulliform cells and fewer large veins, probably through regulating the expression of auxin-related and expansin genes. The WUSCHEL-related homeobox (WOX) family plays a pivotal role in plant development by regulating genes involved in various aspects of growth and differentiation. OsWOX9A (DWT1) has been linked to tiller growth, uniform plant growth, and flower meristem activity. However, its impact on leaf growth and development in rice has not been studied. In this study, we investigated the biological role of OsWOX9A in rice growth and development using transgenic plants. Overexpression of OsWOX9A conferred narrow adaxially rolled rice leaves and altered plant architecture. These plants exhibited larger bulliform cells and fewer larger veins compared to wild-type plants. OsWOX9A overexpression also reduced plant height, tiller number, and seed-setting rate. Comparative transcriptome analysis revealed several differentially expressed auxin-related and expansin genes in OsWOX9A overexpressing plants, consistent with their roles in leaf and plant development. These results indicate that the ectopic expression of OsWOX9A may have multiple effects on the development and growth of rice, providing a more comprehensive picture of how the WOX9 subfamily contributes to leaf development and plant architecture.

Overexpression of Wild Soybean Expansin Gene GsEXLB14 Enhanced the Tolerance of Transgenic Soybean Hairy Roots to Salt and Drought Stresses

As a type of cell-wall-relaxing protein that is widely present in plants, expansins have been shown to actively participate in the regulation of plant growth and responses to environmental stress. Wild soybeans have long existed in the wild environment and possess abundant resistance gene resources, which hold significant value for the improvement of cultivated soybean germplasm. In our previous study, we found that the wild soybean expansin gene GsEXLB14 is specifically transcribed in roots, and its transcription level significantly increases under salt and drought stress. To further identify the function of GsEXLB14, in this study, we cloned the CDS sequence of this gene. The transcription pattern of GsEXLB14 in the roots of wild soybean under salt and drought stress was analyzed by qRT-PCR. Using an Agrobacterium rhizogenes-mediated genetic transformation, we obtained soybean hairy roots overexpressing GsEXLB14. Under 150 mM NaCl- and 100 mM mannitol-simulated drought stress, the relative growth values of the number, length, and weight of transgenic soybean hairy roots were significantly higher than those of the control group. We obtained the transcriptomes of transgenic and wild-type soybean hairy roots under normal growth conditions and under salt and drought stress through RNA sequencing. A transcriptomic analysis showed that the transcription of genes encoding expansins (EXPB family), peroxidase, H+-transporting ATPase, and other genes was significantly upregulated in transgenic hairy roots under salt stress. Under drought stress, the transcription of expansin (EXPB/LB family) genes increased in transgenic hairy roots. In addition, the transcription of genes encoding peroxidases, calcium/calmodulin-dependent protein kinases, and dehydration-responsive proteins increased significantly. The results of qRT-PCR also confirmed that the transcription pattern of the above genes was consistent with the transcriptome. The differences in the transcript levels of the above genes may be the potential reason for the strong tolerance of soybean hairy roots overexpressing the GsEXLB14 gene under salt and drought stress. In conclusion, the expansin GsEXLB14 can be used as a valuable candidate gene for the molecular breeding of soybeans.

Defying gravity: WEEP promotes negative gravitropism in peach trees by establishing asymmetric auxin gradients

Trees with weeping shoot architectures are valued for their beauty and are a resource for understanding how plants regulate posture control. The peach (Prunus persica) weeping phenotype, which has elliptical downward arching branches, is caused by a homozygous mutation in the WEEP gene. Little is known about the function of WEEP despite its high conservation throughout Plantae. Here, we present the results of anatomical, biochemical, biomechanical, physiological, and molecular experiments that provide insight into WEEP function. Our data suggest that weeping peach trees do not have defects in branch structure. Rather, transcriptomes from the adaxial (upper) and abaxial (lower) sides of standard and weeping branch shoot tips revealed flipped expression patterns for genes associated with early auxin response, tissue patterning, cell elongation, and tension wood development. This suggests that WEEP promotes polar auxin transport toward the lower side during shoot gravitropic response, leading to cell elongation and tension wood development. In addition, weeping peach trees exhibited steeper root systems and faster lateral root gravitropic response. This suggests that WEEP moderates root gravitropism and is essential to establishing the set-point angle of lateral roots from the gravity vector. Additionally, size exclusion chromatography indicated that WEEP proteins self-oligomerize, like other proteins with sterile alpha motif domains. Collectively, our results from weeping peach provide insight into polar auxin transport mechanisms associated with gravitropism and lateral shoot and root orientation.

The plant cell wall-dynamic, strong, and adaptable-is a natural shapeshifter

Mythology is replete with good and evil shapeshifters, who, by definition, display great adaptability and assume many different forms-with several even turning themselves into trees. Cell walls certainly fit this definition as they can undergo subtle or dramatic changes in structure, assume many shapes, and perform many functions. In this review, we cover the evolution of knowledge of the structures, biosynthesis, and functions of the 5 major cell wall polymer types that range from deceptively simple to fiendishly complex. Along the way, we recognize some of the colorful historical figures who shaped cell wall research over the past 100 years. The shapeshifter analogy emerges more clearly as we examine the evolving proposals for how cell walls are constructed to allow growth while remaining strong, the complex signaling involved in maintaining cell wall integrity and defense against disease, and the ways cell walls adapt as they progress from birth, through growth to maturation, and in the end, often function long after cell death. We predict the next century of progress will include deciphering cell type-specific wall polymers; regulation at all levels of polymer production, crosslinks, and architecture; and how walls respond to developmental and environmental signals to drive plant success in diverse environments.

Structure and growth of plant cell walls

Plant cells build nanofibrillar walls that are central to plant growth, morphogenesis and mechanics. Starting from simple sugars, three groups of polysaccharides, namely, cellulose, hemicelluloses and pectins, with very different physical properties are assembled by the cell to make a strong yet extensible wall. This Review describes the physics of wall growth and its regulation by cellular processes such as cellulose production by cellulose synthase, modulation of wall pH by plasma membrane H+-ATPase, wall loosening by expansin and signalling by plant hormones such as auxin and brassinosteroid. In addition, this Review discusses the nuanced roles, properties and interactions of cellulose, matrix polysaccharides and cell wall proteins and describes how wall stress and wall loosening cooperatively result in cell wall growth.

Genome-Wide Identification, Phylogenetic and Expression Analysis of Expansin Gene Family in Medicago sativa L

Expansins, a class of cell-wall-loosening proteins that regulate plant growth and stress resistance, have been studied in a variety of plant species. However, little is known about the Expansins present in alfalfa (Medicago sativa L.) due to the complexity of its tetraploidy. Based on the alfalfa (cultivar "XinjiangDaye") reference genome, we identified 168 Expansin members (MsEXPs). Phylogenetic analysis showed that MsEXPs consist of four subfamilies: MsEXPAs (123), MsEXPBs (25), MsEXLAs (2), and MsEXLBs (18). MsEXPAs, which account for 73.2% of MsEXPs, and are divided into twelve groups (EXPA-I-EXPA-XII). Of these, EXPA-XI members are specific to Medicago trunctula and alfalfa. Gene composition analysis revealed that the members of each individual subfamily shared a similar structure. Interestingly, about 56.3% of the cis-acting elements were predicted to be associated with abiotic stress, and the majority were MYB- and MYC-binding motifs, accounting for 33.9% and 36.0%, respectively. Our short-term treatment (≤24 h) with NaCl (200 mM) or PEG (polyethylene glycol, 15%) showed that the transcriptional levels of 12 MsEXPs in seedlings were significantly altered at the tested time point(s), indicating that MsEXPs are osmotic-responsive. These findings imply the potential functions of MsEXPs in alfalfa adaptation to high salinity and/or drought. Future studies on MsEXP expression profiles under long-term (>24 h) stress treatment would provide valuable information on their involvement in the response of alfalfa to abiotic stress.

Pectic-AGP is a major form of Arabidopsis AGPs

As a key component in cell walls of numerous organisms ranging from green algae to higher plants, AGPs play principal roles in many biological processes such as cell-cell adhesion and regulating Ca2+ signaling pathway as a Ca2+-capacitor. Consistently, AGP structures vary from species to species and from tissue to tissue. To understand the functions of AGPs, it is vital to know their structural differences relative to their location in the plant. Thus, AGPs were purified from different Arabidopsis tissues. Analyses of these AGPs demonstrated that the AGPs comprised covalently linked pectin and AGP, referred to as pectic-AGPs. Importantly, these pectic-AGPs were glycosylated with a remarkable variety of polysaccharides including homogalacturonan, rhamnogalacturonan-I, and type II arabinogalactan at different ratios and lengths. This result not only suggests that pectic-AGP is a major form of Arabidopsis AGPs, but also supports AGPs serve as crosslinkers covalently connecting pectins with structures tailored for tissue-specific functions.

Multifaceted roles of plant glycosyl hydrolases during pathogen infections: more to discover

MAIN CONCLUSION

Carbohydrates are hydrolyzed by a family of carbohydrate-active enzymes (CAZymes) called glycosidases or glycosyl hydrolases. Here, we have summarized the roles of various plant defense glycosidases that possess different substrate specificities. We have also highlighted the open questions in this research field. Glycosidases or glycosyl hydrolases (GHs) are a family of carbohydrate-active enzymes (CAZymes) that hydrolyze glycosidic bonds in carbohydrates and glycoconjugates. Compared to those of all other sequenced organisms, plant genomes contain a remarkable diversity of glycosidases. Plant glycosidases exhibit activities on various substrates and have been shown to play important roles during pathogen infections. Plant glycosidases from different GH families have been shown to act upon pathogen components, host cell walls, host apoplastic sugars, host secondary metabolites, and host N-glycans to mediate immunity against invading pathogens. We could classify the activities of these plant defense GHs under eleven different mechanisms through which they operate during pathogen infections. Here, we have provided comprehensive information on the catalytic activities, GH family classification, subcellular localization, domain structure, functional roles, and microbial strategies to regulate the activities of defense-related plant GHs. We have also emphasized the research gaps and potential investigations needed to advance this topic of research.

Defects in the cell wall and its deposition caused by loss-of-function of three RLKs alter root hydrotropism in Arabidopsis thaliana

Root tips can sense moisture gradients and grow into environments with higher water potential. This process is called root hydrotropism. Here, we report three closely related receptor-like kinases (RLKs) that play critical roles in root hydrotropism: ALTERED ROOT HYDROTROPIC RESPONSE 1 (ARH1), FEI1, and FEI2. Overexpression of these RLKs strongly reduce root hydrotropism, but corresponding loss-of-function mutants exhibit an increased hydrotropic response in their roots. All these RLKs show polar localization at the plasma membrane regions in root tips. The biosynthesis of the cell wall, cutin, and wax (CCW) is significantly impaired in root tips of arh1-2 fei1-C fei2-C. A series of known CCW mutants also exhibit increased root hydrotropism and reduced osmotic tolerance, similar to the characteristics of the triple mutant. Our results demonstrat that the integrity of the cell wall, cutin, and root cap wax mediate a trade-off between root hydrotropism and osmotic tolerance.

Impact of the TOR pathway on plant growth via cell wall remodeling

Plant growth is intimately linked to the availability of carbon and energy status. The Target of rapamycin (TOR) pathway is a highly relevant metabolic sensor and integrator of plant-assimilated C into development and growth. The cell wall accounts for around a third of the cell biomass, and the investment of C into this structure should be finely tuned for optimal growth. The plant C status plays a significant role in controlling the rate of cell wall synthesis. TOR signaling regulates cell growth and expansion, which are fundamental processes for plant development. The availability of nutrients and energy, sensed and integrated by TOR, influences cell division and elongation, ultimately impacting the synthesis and deposition of cell wall components. The plant cell wall is crucial in environmental adaptation and stress responses. TOR senses and internalizes various environmental cues, such as nutrient availability and stresses. These environmental factors influence TOR activity, which modulates cell wall remodeling to cope with changing conditions. Plant hormones, including auxins, gibberellins, and brassinosteroids, also regulate TOR signaling and cell wall-related processes. The connection between nutrients and cell wall pathways modulated by TOR are discussed.

The first crystal structure of a family 45 glycoside hydrolase from a brown-rot fungus, Gloeophyllum trabeum GtCel45A

Here we describe the first crystal structure of a beta-1,4-endoglucanase from a brown-rot fungus, Gloeophyllum trabeum GtCel45A, which belongs to subfamily C of glycoside hydrolase family 45 (GH45). GtCel45A is ~ 18 kDa in size and the crystal structure contains 179 amino acids. The structure is refined at 1.30 Å resolution and Rfree 0.18. The enzyme consists of a single catalytic module folded into a six-stranded double-psi beta-barrel domain surrounded by long loops. GtCel45A is very similar in sequence (82% identity) and structure to PcCel45A from the white-rot fungus Phanerochaete chrysosporium. Surprisingly though, initial hydrolysis of barley beta-glucan was almost twice as fast in GtCel45A as compared to PcCel45A.

Genomic survey and expression analysis of cellulose synthase superfamily and COBRA-like gene family in Zanthoxylum bungeanum stipule thorns

The Cellulose Synthase gene (CS) superfamily and COBRA-like (COBL) gene family are essential for synthesizing cellulose and hemicellulose, which play a crucial role in cell wall biosynthesis and the hardening of plant tissues. Our study identified 126 ZbCS and 31 ZbCOBL genes from the Zanthoxylum bungeanum (Zb) genome. Phylogenetic analysis and conservative domain analysis unfolded that ZbCS and ZbCOBL genes were divided into seven and two subfamilies, respectively. Gene duplication data suggested that more than 75% of these genes had tandem and fragment duplications. Codon usage patterns analysis indicated that the ZbCS and ZbCOBL genes prefer ending with A/T base, with weak codon preference. Furthermore, seven key ZbCS and five key ZbCOBL genes were identified based on the content of cellulose and hemicellulose and the expression characteristics of ZbCS and ZbCOBL genes in various stages of stipule thorns. Altogether, these results improve the understanding of CS and COBL genes and provide valuable reference data for cultivating Zb with soft thorns.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01432-x.

Mechanism underlying the rapid growth of Phalaenopsis equestris induced by 60Co-γ-ray irradiation

Gamma (γ)-ray irradiation is one of the important modern breeding methods. Gamma-ray irradiation can affect the growth rate and other characteristics of plants. Plant growth rate is crucial for plants. In horticultural crops, the growth rate of plants is closely related to the growth of leaves and flowering time, both of which have important ornamental value. In this study, 60Co-γ-ray was used to treat P. equestris plants. After irradiation, the plant's leaf growth rate increased, and sugar content and antioxidant enzyme activity increased. Therefore, we used RNA-seq technology to analyze the differential gene expression and pathways of control leaves and irradiated leaves. Through transcriptome analysis, we investigated the reasons for the rapid growth of P. equestris leaves after irradiation. In the analysis, genes related to cell wall relaxation and glucose metabolism showed differential expression. In addition, the expression level of genes encoding ROS scavenging enzyme synthesis regulatory genes increased after irradiation. We identified two genes related to P. equestris leaf growth using VIGS technology: PeNGA and PeEXPA10. The expression of PeEXPA10, a gene related to cell wall expansion, was down-regulated, cell wall expansion ability decreased, cell size decreased, and leaf growth rate slowed down. The TCP-NGATHA (NGA) molecular regulatory module plays a crucial role in cell proliferation. When the expression of the PeNGA gene decreases, the leaf growth rate increases, and the number of cells increases. After irradiation, PeNGA and PeEXPA10 affect the growth of P. equestris leaves by influencing cell proliferation and cell expansion, respectively. In addition, many genes in the plant hormone signaling pathway show differential expression after irradiation, indicating the crucial role of plant hormones in plant leaf growth. This provides a theoretical basis for future research on leaf development and biological breeding.

Contrasting plant transcriptome responses between a pierce-sucking and a chewing herbivore go beyond the infestation site

BACKGROUND

Plants have acquired a repertoire of mechanisms to combat biotic stressors, which may vary depending on the feeding strategies of herbivores and the plant species. Hormonal regulation crucially modulates this malleable defense response. Jasmonic acid (JA) and salicylic acid (SA) stand out as pivotal regulators of defense, while other hormones like abscisic acid (ABA), ethylene (ET), gibberellic acid (GA) or auxin also play a role in modulating plant-pest interactions. The plant defense response has been described to elicit effects in distal tissues, whereby aboveground herbivory can influence belowground response, and vice versa. This impact on distal tissues may be contingent upon the feeding guild, even affecting both the recovery of infested tissues and those that have not suffered active infestation.

RESULTS

To study how phytophagous with distinct feeding strategies may differently trigger the plant defense response during and after infestation in both infested and distal tissues, Arabidopsis thaliana L. rosettes were infested separately with the chewing herbivore Pieris brassicae L. and the piercing-sucker Tetranychus urticae Koch. Moderate infestation conditions were selected for both pests, though no quantitative control of damage levels was carried out. Feeding mode did distinctly influence the transcriptomic response of the plant under these conditions. Though overall affected processes were similar under either infestation, their magnitude differed significantly. Plants infested with P. brassicae exhibited a short-term response, involving stress-related genes, JA and ABA regulation and suppressing growth-related genes. In contrast, T. urticae elicited a longer transcriptomic response in plants, albeit with a lower degree of differential expression, in particular influencing SA regulation. These distinct defense responses transcended beyond infestation and through the roots, where hormonal response, flavonoid regulation or cell wall reorganization were differentially affected.

CONCLUSION

These outcomes confirm that the existent divergent transcriptomic responses elicited by herbivores employing distinct feeding strategies possess the capacity to extend beyond infestation and even affect tissues that have not been directly infested. This remarks the importance of considering the entire plant's response to localized biotic stresses.

Fungal loosenin-like proteins boost the cellulolytic enzyme conversion of pretreated wood fiber and cellulosic pulps

Microbial expansin-related proteins, including loosenins, can disrupt cellulose networks and increase enzyme accessibility to cellulosic substrates. Herein, four loosenins from Phanerochaete carnosa (PcaLOOLs), and a PcaLOOL fused to a family 63 carbohydrate-binding module, were compared for ability to boost the cellulolytic deconstruction of steam pretreated softwood (SSW) and kraft pulps from softwood (ND-BSKP) and hardwood (ND-BHKP). Amending the Cellic® CTec-2 cellulase cocktail with PcaLOOLs increased reducing products from SSW by up to 40 %, corresponding to 28 % higher glucose yield. Amending Cellic® CTec-2 with PcaLOOLs also increased the release of glucose from ND-BSKP and ND-BHKP by 82 % and 28 %, respectively. Xylose release from ND-BSKP and ND-BHKP increased by 47 % and 57 %, respectively, highlighting the potential of PcaLOOLs to enhance hemicellulose recovery. Scanning electron microscopy and fiber image analysis revealed fibrillation and curlation of ND-BSKP after PcaLOOL treatment, consistent with increasing enzyme accessibility to targeted substrates.

Leaf growth - complex regulation of a seemingly simple process

Understanding the underlying mechanisms of plant development is crucial to successfully steer or manipulate plant growth in a targeted manner. Leaves, the primary sites of photosynthesis, are vital organs for many plant species, and leaf growth is controlled by a tight temporal and spatial regulatory network. In this review, we focus on the genetic networks governing leaf cell proliferation, one major contributor to final leaf size. First, we provide an overview of six regulator families of leaf growth in Arabidopsis: DA1, PEAPODs, KLU, GRFs, the SWI/SNF complexes, and DELLAs, together with their surrounding genetic networks. Next, we discuss their evolutionary conservation to highlight similarities and differences among species, because knowledge transfer between species remains a big challenge. Finally, we focus on the increase in knowledge of the interconnectedness between these genetic pathways, the function of the cell cycle machinery as their central convergence point, and other internal and environmental cues.

Genome-Wide Identification of Expansins in Rubus chingii and Profiling Analysis during Fruit Ripening and Softening

Improving fruit size or weight, firmness, and shelf life is a major target for horticultural crop breeding. It is associated with the depolymerization and rearrangement of cell components, including pectin, hemicellulose, cellulose, and other structural (glyco)proteins. Expansins are structural proteins to loosen plant cell wall polysaccharides in a pH-dependent manner and play pivotal roles in the process of fruit development, ripening, and softening. Rubus chingii Hu, a unique Chinese red raspberry, is a prestigious pharmaceutical and nutraceutical dual-function food with great economic value. Thirty-three RchEXPs were predicted by genome-wide identification in this study, containing twenty-seven α-expansins (EXPAs), three β-expansins (EXPBs), one expansin-like A (EXPLA), and two expansin-like B (EXPLBs). Subsequently, molecular characteristics, gene structure and motif compositions, phylogenetic relationships, chromosomal location, collinearity, and regulatory elements were further profiled. Furthermore, transcriptome sequencing (RNA-seq) and real-time quantitative PCR assays of fruits from different developmental stages and lineages showed that the group of RchEXPA5, RchEXPA7, and RchEXPA15 were synergistically involved in fruit expanding and ripening, while another group of RchEXPA6 and RchEXPA26 might be essential for fruit ripening and softening. They were regulated by both abscisic acid and ethylene and were collinear with phylogenetic relationships in the same group. Our new findings laid the molecular foundation for improving the fruit texture and shelf life of R. chingii medicinal and edible fruit.

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.

Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice

RNA-binding proteins (RBPs) are components of the post-transcriptional regulatory system, but their regulatory effects on complex traits remain unknown. Using an integrated strategy involving map-based cloning, functional characterizations, and transcriptomic and population genomic analyses, we revealed that RBP-K (LOC_Os08g23120), RBP-A (LOC_Os11g41890), and RBP-J (LOC_Os10g33230) encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related traits. Examinations of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function normally. Additionally, RBP-J most likely affects GA pathways, resulting in considerable increases in grain and panicle lengths, but decreases in grain width and thickness. In contrast, RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport, with substantial effects on the rice grain filling process as well as grain length and weight. Evolutionarily, RBP-K is relatively ancient and highly conserved, whereas RBP-J and RBP-A are more diverse. Thus, the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency, efficiency, and versatility, as well as increased evolutionary potential. Our results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex traits. Furthermore, rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted selection.

Exogenous abscisic acid treatment regulates protein secretion in sorghum cell suspension cultures

Drought stress adversely affects plant growth, often leading to total crop failure. Upon sensing soil water deficits, plants switch on biosynthesis of abscisic acid (ABA), a stress hormone for drought adaptation. Here, we used exogenous ABA application to dark-grown sorghum cell suspension cultures as an experimental system to understand how a drought-tolerant crop responds to ABA. We evaluated intracellular and secreted proteins using isobaric tags for relative and absolute quantification. While the abundance of only ~ 7% (46 proteins) intracellular proteins changed in response to ABA, ~32% (82 proteins) of secreted proteins identified in this study were ABA responsive. This shows that the extracellular matrix is disproportionately targeted and suggests it plays a vital role in sorghum adaptation to drought. Extracellular proteins responsive to ABA were predominantly defense/detoxification and cell wall-modifying enzymes. We confirmed that sorghum plants exposed to drought stress activate genes encoding the same proteins identified in the in vitro cell culture system with ABA. Our results suggest that ABA activates defense and cell wall remodeling systems during stress response. This could underpin the success of sorghum adaptation to drought stress.

Balanced callose and cellulose biosynthesis in Arabidopsis quorum-sensing signaling and pattern-triggered immunity

The plant cell wall (CW) is one of the most important physical barriers that phytopathogens must conquer to invade their hosts. This barrier is a dynamic structure that responds to pathogen infection through a complex network of immune receptors, together with CW-synthesizing and CW-degrading enzymes. Callose deposition in the primary CW is a well-known physical response to pathogen infection. Notably, callose and cellulose biosynthesis share an initial substrate, UDP-glucose, which is the main load-bearing component of the CW. However, how these 2 critical biosynthetic processes are balanced during plant-pathogen interactions remains unclear. Here, using 2 different pathogen-derived molecules, bacterial flagellin (flg22) and the diffusible signal factor (DSF) produced by Xanthomonas campestris pv. campestris, we show a negative correlation between cellulose and callose biosynthesis in Arabidopsis (Arabidopsis thaliana). By quantifying the abundance of callose and cellulose under DSF or flg22 elicitation and characterizing the dynamics of the enzymes involved in the biosynthesis and degradation of these 2 polymers, we show that the balance of these 2 CW components is mediated by the activity of a β-1,3-glucanase (BG2). Our data demonstrate balanced cellulose and callose biosynthesis during plant immune responses.

An ex vitro hairy root system from petioles of detached soybean leaves for in planta screening of target genes and CRISPR strategies associated with nematode bioassays

MAIN CONCLUSION

The ex vitro hairy root system from petioles of detached soybean leaves allows the functional validation of genes using classical transgenesis and CRISPR strategies (e.g., sgRNA validation, gene activation) associated with nematode bioassays. Agrobacterium rhizogenes-mediated root transformation has been widely used in soybean for the functional validation of target genes in classical transgenesis and single-guide RNA (sgRNA) in CRISPR-based technologies. Initial data showed that in vitro hairy root induction from soybean cotyledons and hypocotyls were not the most suitable strategies for simultaneous performing genetic studies and nematode bioassays. Therefore, an ex vitro hairy root system was developed for in planta screening of target molecules during soybean parasitism by root-knot nematodes (RKNs). Applying this method, hairy roots were successfully induced by A. rhizogenes from petioles of detached soybean leaves. The soybean GmPR10 and GmGST genes were then constitutively overexpressed in both soybean hairy roots and tobacco plants, showing a reduction in the number of Meloidogyne incognita-induced galls of up to 41% and 39%, respectively. In addition, this system was evaluated for upregulation of the endogenous GmExpA and GmExpLB genes by CRISPR/dCas9, showing high levels of gene activation and reductions in gall number of up to 58.7% and 67.4%, respectively. Furthermore, morphological and histological analyses of the galls were successfully performed. These collective data validate the ex vitro hairy root system for screening target genes, using classical overexpression and CRISPR approaches, directly in soybean in a simple manner and associated with nematode bioassays. This system can also be used in other root pathosystems for analyses of gene function and studies of parasite interactions with plants, as well as for other purposes such as studies of root biology and promoter characterization.

The genus Arachis: an excellent resource for studies on differential gene expression for stress tolerance

Peanut Arachis hypogaea is a segmental allotetraploid in the section Arachis of the genus Arachis along with the Section Rhizomataceae. Section Arachis has several diploid species along with Arachis hypogaea and A. monticola. The section Rhizomataceae comprises polyploid species. Several species in the genus are highly tolerant to biotic and abiotic stresses and provide excellent sets of genotypes for studies on differential gene expression. Though there were several studies in this direction, more studies are needed to identify more and more gene combinations. Next generation RNA-seq based differential gene expression study is a powerful tool to identify the genes and regulatory pathways involved in stress tolerance. Transcriptomic and proteomic study of peanut plants under biotic stresses reveals a number of differentially expressed genes such as R genes (NBS-LRR, LRR-RLK, protein kinases, MAP kinases), pathogenesis related proteins (PR1, PR2, PR5, PR10) and defense related genes (defensin, F-box, glutathione S-transferase) that are the most consistently expressed genes throughout the studies reported so far. In most of the studies on biotic stress induction, the differentially expressed genes involved in the process with enriched pathways showed plant-pathogen interactions, phenylpropanoid biosynthesis, defense and signal transduction. Differential gene expression studies in response to abiotic stresses, reported the most commonly expressed genes are transcription factors (MYB, WRKY, NAC, bZIP, bHLH, AP2/ERF), LEA proteins, chitinase, aquaporins, F-box, cytochrome p450 and ROS scavenging enzymes. These differentially expressed genes are in enriched pathways of transcription regulation, starch and sucrose metabolism, signal transduction and biosynthesis of unsaturated fatty acids. These identified differentially expressed genes provide a better understanding of the resistance/tolerance mechanism, and the genes for manipulating biotic and abiotic stress tolerance in peanut and other crop plants. There are a number of differentially expressed genes during biotic and abiotic stresses were successfully characterized in peanut or model plants (tobacco or Arabidopsis) by genetic manipulation to develop stress tolerance plants, which have been detailed out in this review and more concerted studies are needed to identify more and more gene/gene combinations.

Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits

Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities.

Interaction of VvDELLA2 and VvCEB1 Mediates Expression of Expansion-Related Gene during GA-Induced Enlargement of Grape Fruit

Exogenous gibberellin treatment can promote early growth of grape fruit, but the underlying regulatory mechanisms are not well understood. Here, we show that VvDELLA2 directly regulates the activity of the VvCEB1 transcription factor, a key regulator in the control of cell expansion in grape fruit. Our results show that VvCEB1 binds directly to the promoters of cell expansion-related genes in grape fruit and acts as a transcriptional activator, while VvDELLA2 blocks VvCEB1 function by binding to its activating structural domain. The exogenous gibberellin treatment relieved this inhibition by promoting the degradation of VvDELLA2 protein, thus, allowing VvCEB1 to transcriptionally activate the expression of cell expansion-related genes. In conclusion, we conclude that exogenous GA3 treatment regulates early fruit expansion by affecting the VvDELLA-VvCEB1 interaction in grape fruit development.

Integrating ATAC-seq and RNA-seq to identify differentially expressed genes with chromatin-accessible changes during photosynthetic establishment in Populus leaves

Leaves are the primary photosynthetic organs, providing essential substances for tree growth. It is important to obtain an anatomical understanding and regulatory network analysis of leaf development. Here, we studied leaf development in Populus Nanlin895 along a development gradient from the newly emerged leaf from the shoot apex to the sixth leaf (L1 to L6) using anatomical observations and RNA-seq analysis. It indicated that mesophyll cells possess obvious vascular, palisade, and spongy tissue with distinct intercellular spaces after L3. Additionally, vacuoles fuse while epidermal cells expand to form pavement cells. RNA-seq analysis indicated that genes highly expressed in L1 and L2 were related to cell division and differentiation, while those highly expressed in L3 were enriched in photosynthesis. Therefore, we selected L1 and L3 to integrate ATAC-seq and RNA-seq and identified 735 differentially expressed genes (DEGs) with changes in chromatin accessibility regions within their promoters, of which 87 were transcription factors (TFs), such as ABI3VP1, AP-EREBP, MYB, NAC, and GRF. Motif enrichment analysis revealed potential regulatory functions for the DEGs through upstream TFs including TCP, bZIP, HD-ZIP, Dof, BBR-BPC, and MYB. Overall, our research provides a potential molecular foundation for regulatory network exploration in leaf development during photosynthesis establishment.