Genome-wide identification, phylogeny and expression analysis of the PME and PMEI gene families in maize

Phosphorus deficiency-induced cell wall pectin demethylesterification enhances cadmium accumulation in roots of Salix caprea

Regions affected by heavy metal contamination frequently encounter phosphorus (P) deficiency. Numerous studies highlight crucial role of P in facilitating cadmium (Cd) accumulation in woody plants. However, the regulatory mechanism by which P affects Cd accumulation in roots remains ambiguous. This study aims to investigate the effects of phosphorus (P) deficiency on Cd accumulation, Cd subcellular distribution, and cell wall components in the roots of Salix caprea under Cd stress. The results revealed that under P deficiency conditions, there was a 35.4% elevation in Cd content in roots, coupled with a 60.1% reduction in Cd content in shoots, compared to the P sufficiency conditions. Under deficient P conditions, the predominant response of roots to Cd exposure was the increased sequestration of Cd in root cell walls. The sequestration of Cd in root cell walls increased from 37.1% under sufficient P conditions to 66.7% under P deficiency, with pectin identified as the primary Cd binding site under both P conditions. Among cell wall components, P deficiency led to a significant 31.7% increase in Cd content within pectin compared to P sufficiency conditions, but did not change the pectin content. Notably, P deficiency significantly increased pectin methylesterase (PME) activity by regulating the expression of PME and PMEI genes, leading to a 10.4% reduction in the degree of pectin methylesterification. This may elucidate the absence of significant changes in pectin content under P deficiency conditions and the concurrent increase in Cd accumulation in pectin. Fourier transform infrared spectroscopy (FTIR) results indicated an increase in carboxyl groups in the root cell walls under P deficiency compared to sufficient P treatment. The results provide deep insights into the mechanisms of higher Cd accumulation in root mediated by P deficiency.

The adaptation of root cell wall pectin to copper toxicity in two citrus species differing in copper tolerance: remodeling and responding

Citrus species are prone to suffer from copper (Cu) toxicity because of improper application of Cu-based agrochemicals. Copper immobilization mediated by pectin methylesterase (PME) in the root cell wall (CW) is effective for Cu detoxification. However, the underlying mechanisms of the structural modification and stress responses of citrus root CW pectin to Cu toxicity have been less discussed. In the present study, seedlings of 'Shatian pummelo' (Citrus grandis L. Osbeck) and 'Xuegan' (Citrus sinensis L. Osbeck), which differ in Cu tolerance, were irrigated with nutrient solution containing 0.5 (as control), 100, 300 or 500 μM Cu for 18 weeks in sandy culture or 24 h in hydroponics. At the end of treatments in the 18-week sandy culture, Cu toxicity on CW pectin content, Cu distribution, degree of pectin methylesterification (DPM) and the PME enzyme activity were discussed. At the genome-wide level, PME gene family was identified from the two citrus species, and qRT-PCR array of citrus PMEs under control and 300 μM Cu stress for 18 weeks were performed to screen the Cu-responsive PME genes. Moreover, the candidate genes that responded to Cu toxicity were further examined within 24 h. The results showed that Cu toxicity increased the root CW pectin content. The root CW pectin under Cu toxicity was remodeled by upregulation of the expression of the Cu-responsive PME genes followed by increasing PME activity, which mainly promoted low methylesterased pectin level and the Cu content on root CW pectin. Compared with C. sinensis, C. grandis root CW had a lower DPM and higher Cu content on the Cu-stressed root CW pectin, contributing to its higher Cu tolerance. Our present study provided theoretical evidence for root CW pectin remodeling in response to Cu toxicity of citrus species.

Integration of high-throughput phenotyping, GWAS, and predictive models reveals the genetic architecture of plant height in maize

Plant height (PH) is an essential trait in maize (Zea mays) that is tightly associated with planting density, biomass, lodging resistance, and grain yield in the field. Dissecting the dynamics of maize plant architecture will be beneficial for ideotype-based maize breeding and prediction, as the genetic basis controlling PH in maize remains largely unknown. In this study, we developed an automated high-throughput phenotyping platform (HTP) to systematically and noninvasively quantify 77 image-based traits (i-traits) and 20 field traits (f-traits) for 228 maize inbred lines across all developmental stages. Time-resolved i-traits with novel digital phenotypes and complex correlations with agronomic traits were characterized to reveal the dynamics of maize growth. An i-trait-based genome-wide association study identified 4945 trait-associated SNPs, 2603 genetic loci, and 1974 corresponding candidate genes. We found that rapid growth of maize plants occurs mainly at two developmental stages, stage 2 (S2) to S3 and S5 to S6, accounting for the final PH indicators. By integrating the PH-association network with the transcriptome profiles of specific internodes, we revealed 13 hub genes that may play vital roles during rapid growth. The candidate genes and novel i-traits identified at multiple growth stages may be used as potential indicators for final PH in maize. One candidate gene, ZmVATE, was functionally validated and shown to regulate PH-related traits in maize using genetic mutation. Furthermore, machine learning was used to build predictive models for final PH based on i-traits, and their performance was assessed across developmental stages. Moderate, strong, and very strong correlations between predictions and experimental datasets were achieved from the early S4 (tenth-leaf) stage. Colletively, our study provides a valuable tool for dissecting the spatiotemporal formation of specific internodes and the genetic architecture of PH, as well as resources and predictive models that are useful for molecular design breeding and predicting maize varieties with ideal plant architectures.

Silencing of a Pectin Acetylesterase (PAE) Gene Highly Expressed in Tobacco Pistils Negatively Affects Pollen Tube Growth

Successful plant reproduction and fruit formation depend on adequate pollen and pistil development, and pollen-pistil interactions. In Nicotiana tabacum, pollen tubes grow through the intercellular spaces of pistil-specialized tissues, stigmatic secretory zone, and stylar transmitting tissue (STT). These intercellular spaces are supposed to be formed by the modulation of cell wall pectin esterification. Previously we have identified a gene preferentially expressed in pistils encoding a putative pectin acetylesterase (PAE), named NtPAE1. Here, we characterized the NtPAE1 gene and performed genome-wide and phylogenetic analyses of PAEs. We identified 30 PAE sequences in the N. tabacum genome, distributed in four clades. The expression of NtPAE1 was assessed by RT-qPCR and in situ hybridization. We confirmed NtPAE1 preferential expression in stigmas/styles and ovaries and demonstrated its high expression in the STT. Structural predictions and comparisons between NtPAE1 and functional enzymes validated its identity as a PAE. Transgenic plants were produced, overexpressing and silencing the NtPAE1 gene. Overexpressed plants displayed smaller flowers while silencing plants exhibited collapsed pollen grains, which hardly germinate. NtPAE1 silencing plants do not produce fruits, due to impaired pollen tube growth in their STTs. Thus, NtPAE1 is an essential enzyme regulating pectin modifications in flowers and, ultimately, in plant reproduction.

CRISPR/Cas9 Mutant Rice Ospmei12 Involved in Growth, Cell Wall Development, and Response to Phytohormone and Heavy Metal Stress

Pectin is one of the constituents of the cell wall, distributed in the primary cell wall and middle lamella, affecting the rheological properties and the cell wall stickiness. Pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) are the most important factors for modifying methyl esterification. In this study, 45 PMEI genes from rice (Oryza sativa L.) were screened by bioinformatics tools, and their structure, motifs, cis-acting elements in the promoter region, chromosomal distribution, gene duplication, and phylogenetic relationship were analyzed. Furthermore, CRISPR/Cas9 was used to edit the OsPMEI12 (LOC_Os03G01020) and two mutant pmei12 lines were obtained to explore the functions of OsPMEI in plant growth and development, and under cadmium (Cd) stress. Compared to wild type (WT) Nipponbare, the second inverted internodes of the mutant plants shortened significantly, resulting in the reduction in plant height at mature stage. The seed setting rate, and fresh and dry weights of the mutants were also decreased in mutant plants. In addition, the pectin methylation of pmei12 lines is decreased as expected, and the pectin content of the cell wall increased at both seedling and maturity stages; however, the cellulose and hemicellulose increased only at seedling stage. Interestingly, the growth of the pmei12 lines was better than the WT in both normal conditions and under two phytohormone (GA₃ and NAA) treatments at seedling stage. Under Cd stress, the fresh and dry weights were increased in pmei12 lines. These results indicated that OsPMEI12 was involved in the regulation of methyl esterification during growth, affected cell wall composition and agronomic traits, and might play an important role in responses to phytohormones and stress.

Identification of Genetic Variations and Candidate Genes Responsible for Stalk Sugar Content and Agronomic Traits in Fresh Corn via GWAS across Multiple Environments

The stem and leaves of fresh corn plants can be used as green silage or can be converted to biofuels, and the stalk sugar content and yield directly determine the application value of fresh corn. To identify the genetic variations and candidate genes responsible for the related traits in fresh corn, the genome-wide scan and genome-wide association analysis (GWAS) were performed. A total of 32 selective regions containing 172 genes were detected between sweet and waxy corns. Using the stalk sugar content and seven other agronomic traits measured in four seasons over two years, the GWAS identified ninety-two significant single nucleotide polymorphisms (SNPs). Most importantly, seven SNPs associated with the stalk sugar content were detected across multiple environments, which could explain 13.68–17.82% of the phenotypic variation. Accessions differing in genotype for certain significant SNPs showed significant variation in the stalk sugar content and other agronomic traits, and the expression levels of six important candidate genes were significantly different between two materials with different stalk sugar content. The genetic variations and candidate genes provide valuable resources for future studies of the molecular mechanism of the stalk sugar content and establish the foundation for molecular marker-assisted breeding of fresh corn.

Systematic analysis of the pectin methylesterase gene family in Nicotiana tabacum and reveal their multiple roles in plant development and abiotic stresses

The pectin methylesterases (PMEs) play multiple roles in regulating plant development and responses to various stresses. In our study, a total of 121 PME genes were identified in the tobacco genome, which were clustered into two groups based on phylogenetic analysis together with Arabidopsis members. The investigations of gene structure and conserved motif indicated that exon/intron and motif organizations were relatively conserved in each group. Additionally, several stress-related elements were identified in the promoter region of these genes. The survey of duplication events revealed that segmental duplications were critical to the expansion of the PME gene family in tobacco. The expression profiles analysis revealed that these genes were expressed in various tissues and could be induced by diverse abiotic stresses. Notably, NtPME029 and NtPME043, were identified as homologues with AtPME3 and AtPME31, respectively. Furthermore, NtPME029 was highly expressed in roots and the over-expression of the NtPME029 gene could promote the development of roots. While NtPME043 could be induced by salt and ABA treatments, and the over-expression of the NtPME043 gene could significantly enhance the salt-stress tolerance in tobacco. Overall, these findings may shed light on the biological and functional characterization of NtPME genes in tobacco.

Genome-wide identification of the pectin methylesterase inhibitor genes in Brassica napus and expression analysis of selected members

Pectin methylesterase inhibitors (PMEIs) modulate the status of pectin methylesterification by inhibiting the activity of pectin methylesterase (PME). Recent advances indicate PMEIs play an important role in regulating plant cell wall properties and defense responses. In this study, a genome-wide analysis of PMEI gene family in Brassica napus (B. napus) was conducted and the expression patterns of PMEI genes in response to Sclerotinia sclerotiorum (S. sclerotiorum) was investigated. A total of 190 PMEI proteins were identified from the genome of B. napus. Chromosomal location, gene structure and properties of the PMEI family were analyzed, and these features were compared with Arabidopsis thaliana (A. thaliana). A total of 123 syntenic ortholog pairs were detected from BnPMEI family by synteny analysis. Results showed the expansion of BnPMEI genes was likely predominately from whole-genome duplication (WGD) or segmental duplications. Multiple cis-elements related to plant growth and development, environmental stress responses, hormone responses were detected in the promoters of BnPMEI genes, implying they were regulated by both internal and external factors. Furthermore, expression analysis of transcriptome data combined with quantitative RT-PCR (qRT-PCR) validation identified several candidates that were strongly responsive to S. sclerotiorum infection. These BnPMEI genes are candidates for manipulation to breed novel and improved genotypes that are more resistant to sclerotinia stem rot (SSR). Extensive interactions were detected among 30 BnPMEI proteins, forming complex protein-protein interaction networks. Besides, 48 BnPMEIs showed interactions with other proteins including a range of cell wall structure-related enzymes. This study provides new insights into the evolution and function of PMEIs in B. napus and lays a foundation for breeding novel genotypes for crop improvement.

De novo transcriptome sequencing of Capsicum frutescens. L and comprehensive analysis of salt stress alleviating mechanism by Bacillus atrophaeus WU-9

Salt stress, as one of the most severe environmental stresses, can cause a series of changes in plants. However, the explanation of plant salt stress alleviating mechanism of plant growth-promoting rhizobacteria (PGPR) was hindered by the limited availability of transcriptomic information for salt stress-treated plants grown in a microorganism-controlled environment. Our previous reports have selected Bacillus atrophaeus WU-9 as PGPR significantly alleviating pepper (Capsicum frutescens. L) salt stress. In this work, the RNA-seq analysis of salt stress-treated and untreated plants, grown with and without WU-9 in a microorganism-controlled environment, was used to reveal the plant salt stress alleviating mechanisms of WU-9. Twelve sequencing libraries, prepared by treating with WU-9 and salt (150 mM NaCl for 36 h), were constructed by RNA-Seq technique. Non-inoculated seedlings mainly respond to salt stress through regulation of signal transduction, such as ethylene-activated signaling pathway, signaling and cell communication, etc. And ethylene signal participated in salt stress response in pepper through regulating defense responses, fruit ripening and senescence. WU-9 inoculation under salt stress mainly improves salt tolerance and plant growth by regulating salt stress-responding ethylene and auxin signal transduction, utilization of proline, photosynthesis, antioxidant enzyme activities and cell enlargement. Furthermore, 86 differentially expressed genes and 20 transcription factors were identified as associated with salt stress response and tolerance. Thus, this innovative transcriptomic study identified the salt stress response and alleviation in C. frutescens. L with PGPR inoculation. This result provided novel insights into the salinity alleviation in pepper regulated by PGPR.

Guard Cell-Specific Pectin METHYLESTERASE53 Is Required for Abscisic Acid-Mediated Stomatal Function and Heat Response in Arabidopsis

Pectin is a major component of the plant cell wall, forming a network that contributes to cell wall integrity and flexibility. Pectin methylesterase (PME) catalyzes the removal of methylester groups from the homogalacturonan backbone, the most abundant pectic polymer, and contributes to intercellular adhesion during plant development and different environmental stimuli stress. In this study, we identified and characterized an Arabidopsis type-II PME, PME53, which encodes a cell wall deposited protein and may be involved in the stomatal lineage pathway and stomatal functions. We demonstrated that PME53 is expressed explicitly in guard cells as an abscisic acid (ABA)-regulated gene required for stomatal movement and thermotolerance. The expression of PME53 is significantly affected by the stomatal differentiation factors SCRM and MUTE. The null mutation in PME53 results in a significant increase in stomatal number and susceptibility to ABA-induced stomatal closure. During heat stress, the pme53 mutant highly altered the activity of PME and significantly lowered the expression level of the calmodulin AtCaM3, indicating that PME53 may be involved in Ca²⁺-pectate reconstitution to render plant thermotolerance. Here, we present evidence that the PME53-mediated de-methylesterification status of pectin is directed toward stomatal development, movement, and regulation of the flexibility of the guard cell wall required for the heat response.

Genome-wide identification of PME genes, evolution and expression analyses in soybean (Glycine max L.)

BACKGROUND

Pectin methylesterase (PME) is one of pectin-modifying enzyme that affects the pectin homeostasis in cell wall and regulates plant growth and diverse biological processes. The PME genes have been well explored and characterized in different plants. Nevertheless, systematic research on the soybean (Glycine max L.) PME genes remain lacking.

RESULTS

We identified 127 Glycine max PME genes (GmPME) from the soybean Wm82.a2.v1 genome, which unevenly distributed on 20 soybean chromosomes. Phylogenetic analysis classified the GmPME genes into four clades (Group I, Group II, Group III and Group IV). GmPME gene members in the same clades displayed similar gene structures and motif patterns. The gene family expansion analysis demonstrated that segmental duplication was the major driving force to acquire novel GmPME genes compared to the tandem duplication events. Further synteny and evolution analyses showed that the GmPME gene family experienced strong purifying selective pressures during evolution. The cis-element analyses together with the expression patterns of the GmPME genes in various tissues suggested that the GmPME genes broadly participate in distinct biological processes and regulate soybean developments. Importantly, based on the transcriptome data and quantitative RT-PCR validations, we examined the potential roles of the GmPME genes in regulating soybean flower bud development and seed germination.

CONCLUSION

In conclusion, we provided a comprehensive characterization of the PME genes in soybean, and our work laid a foundation for the functional study of GmPME genes in the future.

Phloem anatomy and function as shaped by the cell wall

The partitioning of assimilated carbon is a complex process that involves the loading, long-distance transport, and subsequent unloading of carbohydrates from source to sink tissues. The network of plumbing that facilitates this coordinated process is the phloem tissue. Our understanding of the physiology of phloem transport has grown tremendously since the modern theory of mass flow was first put forward, aided by the concomitant progress of technology and experimental methodologies. Recent findings have put a renewed emphasis on the underlying anatomy of the phloem, and in particular the important role that cell walls play in enabling the high-pressure flow of photoassimilates through the sieve element. This review will briefly summarize the foundational work in phloem anatomy and highlight recent work exploring the physiology of phloem cell wall structure and mechanics.

Comparative analyses of angiosperm secretomes identify apoplastic pollen tube functions and novel secreted peptides

KEY MESSAGE

Analyses of secretomes of in vitro grown pollen tubes from Amborella, maize and tobacco identified many components of processes associated with the cell wall, signaling and metabolism as well as novel small secreted peptides. Flowering plants (angiosperms) generate pollen grains that germinate on the stigma and produce tubes to transport their sperm cells cargo deep into the maternal reproductive tissues toward the ovules for a double fertilization process. During their journey, pollen tubes secrete many proteins (secreted proteome or secretome) required, for example, for communication with the maternal reproductive tissues, to build a solid own cell wall that withstands their high turgor pressure while softening simultaneously maternal cell wall tissue. The composition and species specificity or family specificity of the pollen tube secretome is poorly understood. Here, we provide a suitable method to obtain the pollen tube secretome from in vitro grown pollen tubes of the basal angiosperm Amborella trichopoda (Amborella) and the Poaceae model maize. The previously published secretome of tobacco pollen tubes was used as an example of eudicotyledonous plants in this comparative study. The secretome of the three species is each strongly different compared to the respective protein composition of pollen grains and tubes. In Amborella and maize, about 40% proteins are secreted by the conventional "classic" pathway and 30% by unconventional pathways. The latter pathway is expanded in tobacco. Proteins enriched in the secretome are especially involved in functions associated with the cell wall, cell surface, energy and lipid metabolism, proteolysis and redox processes. Expansins, pectin methylesterase inhibitors and RALFs are enriched in maize, while tobacco secretes many proteins involved, for example, in proteolysis and signaling. While the majority of proteins detected in the secretome occur also in pollen grains and pollen tubes, and correlate in the number of mapped peptides with relative gene expression levels, some novel secreted small proteins were identified. Moreover, the identification of secreted proteins containing pro-peptides indicates that these are processed in the apoplast. In conclusion, we provide a proteome resource from three distinct angiosperm clades that can be utilized among others to study the localization, abundance and processing of known secreted proteins and help to identify novel pollen tube secreted proteins for functional studies.

Physiological, Biochemical, and Transcriptomic Responses of Neolamarckia cadamba to Aluminum Stress

Aluminum is the most abundant metal of the Earth's crust accounting for 7% of its mass, and release of toxic Al3+ in acid soils restricts plant growth. Neolamarckia cadamba, a fast-growing tree, only grows in tropical regions with acidic soils. In this study, N. cadamba was treated with high concentrations of aluminum under acidic condition (pH 4.5) to study its physiological, biochemical, and molecular response mechanisms against high aluminum stress. High aluminum concentration resulted in significant inhibition of root growth with time in N. cadamba. The concentration of Al3+ ions in the root tip increased significantly and the distribution of absorbed Al3+ was observed in the root tip after Al stress. Meanwhile, the concentration of Ca, Mg, Mn, and Fe was significantly decreased, but P concentration increased. Aluminum stress increased activities of antioxidant enzymes such as superoxide dismutase (SOD), catalase from micrococcus lysodeiktic (CAT), and peroxidase (POD) in the root tip, while the content of MDA was decreased. Transcriptome analysis showed 37,478 differential expression genes (DEGs) and 4096 GOs terms significantly associated with treatments. The expression of genes regulating aluminum transport and abscisic acid synthesis was significantly upregulated; however, the genes involved in auxin synthesis were downregulated. Of note, the transcripts of several key enzymes affecting lignin monomer synthesis in phenylalanine pathway were upregulated. Our results shed light on the physiological and molecular mechanisms of aluminum stress tolerance in N. cadamba.

Insights into the molecular control of cross-incompatibility in Zea mays

Gametophytic cross-incompatibility systems in corn have been the subject of genetic studies for more than a century. They have tremendous economic potential as a genetic mechanism for controlling fertilization without controlling pollination. Three major genetically distinct and functionally equivalent cross-incompatibility systems exist in Zea mays: Ga1, Tcb1, and Ga2. All three confer reproductive isolation between maize or teosinte varieties with different haplotypes at any one locus. These loci confer genetically separable functions to the silk and pollen: a female function that allows the silk to block fertilization by non-self-type pollen and a male function that overcomes the block of the female function from the same locus. Identification of some of these genes has shed light on the reproductive isolation they confer. The identification of both male and female factors as pectin methylesterases reveals the importance of pectin methylesterase activity in controlling the decision between pollen acceptance versus rejection, possibly by regulating the degree of methylesterification of the pollen tube cell wall. The appropriate level and spatial distribution of pectin methylesterification is critical for pollen tube growth and is affected by both pectin methylesterases and pectin methylesterase inhibitors. We present a molecular model that explains how cross-incompatibility systems may function that can be tested in Zea and uncharacterized cross-incompatibility systems. Molecular characterization of these loci in conjunction with further refinement of the underlying molecular and cellular mechanisms will allow researchers to bring new and powerful tools to bear on understanding reproductive isolation in Zea mays and related species.

A Complex Journey: Cell Wall Remodeling, Interactions, and Integrity During Pollen Tube Growth

In flowering plants, pollen tubes undergo a journey that starts in the stigma and ends in the ovule with the delivery of the sperm cells to achieve double fertilization. The pollen cell wall plays an essential role to accomplish all the steps required for the successful delivery of the male gametes. This extended path involves female tissue recognition, rapid hydration and germination, polar growth, and a tight regulation of cell wall synthesis and modification, as its properties change not only along the pollen tube but also in response to guidance cues inside the pistil. In this review, we focus on the most recent advances in elucidating the molecular mechanisms involved in the regulation of cell wall synthesis and modification during pollen germination, pollen tube growth, and rupture.

Identification of fertility-related genes for maize CMS-S via Bulked Segregant RNA-Seq

Cytoplasmic male sterility (CMS) is extensively used in maize hybrid production, and identification of genes related to fertility restoration for CMS is important for hybrid breeding. The fertility restoration of S type CMS is governed by several loci with major and minor effects, while the mechanism of fertility restoration for CMS-S is still unknown. In this study, BSR-Seq was conducted with two backcrossing populations with the fertility restoration genes, Rf3 and Rf10, respectively. Genetic mapping via BSR-Seq verified the positions of the two loci. A total of 353 and 176 differentially expressed genes (DEGs) between the male fertility and male sterile pools were identified in the populations with Rf3 and Rf10, respectively. In total, 265 DEGs were co-expressed in the two populations, which were up-regulated in the fertile plants, and they might be related to male fertility involving in anther or pollen development. Moreover, 35 and seven DEGs were specifically up-regulated in the fertile plants of the population with Rf3 and Rf10, respectively. Function analysis of these DEGs revealed that jasmonic acid (JA) signal pathway might be involved in the Rf3 mediated fertility restoration for CMS-S, while the small ubiquitin-related modifier system could play a role in the fertility restoration of Rf10.