Overexpression of the PtrNF-YA6 gene inhibits secondary cell wall thickening in poplar

The NF-Y gene family in plants plays a crucial role in numerous biological processes, encompassing hormone response, stress response, as well as growth and development. In this study, we first used bioinformatics techniques to identify members of the NF-YA family that may function in wood formation. We then used molecular biology techniques to investigate the role and molecular mechanism of PtrNF-YA6 in secondary cell wall (SCW) formation in Populus trichocarpa. We found that PtrNF-YA6 protein was localized in the nucleus and had no transcriptional activating activity. Overexpression of PtrNF-YA6 had an inhibitory effect on plant growth and development and significantly suppressed hemicellulose synthesis and SCW thickening in transgenic plants. Yeast one-hybrid and ChIP-PCR assays revealed that PtrNF-YA6 directly regulated the expression of hemicellulose synthesis genes (PtrGT47A-1, PtrGT8C, PtrGT8F, PtrGT43B, PtrGT47C, PtrGT8A and PtrGT8B). In conclusion, PtrNF-YA6 can inhibit plant hemicellulose synthesis and SCW thickening by regulating the expression of downstream SCW formation-related target genes.

WALL-ASSOCIATED KINASE Like 14 regulates vascular tissue development in Arabidopsis and tomato

Initiation of plant vascular tissue is regulated by transcriptional networks during development and in response to environmental stimuli. The WALL-ASSOCIATED KINASES (WAKs) and WAK-likes (WAKLs) are cell surface receptors involved in cell expansion and defence in cells with primary walls, yet their roles in regulation of vascular tissue development that contain secondary walls remains unclear. In this study, we showed tomato (Solanum lycopersicum) SlWAKL2 and the orthologous gene in Arabidopsis thaliana, AtWAKL14, were specifically expressed in vascular tissues. SlWAKL2-RNAi tomato plants displayed smaller fruit size with fewer seeds and vascular bundles compared to wild-type (WT) and over-expression (OE) lines. RNA-seq data showed that SlWAKL2-RNAi fruits down-regulated transcript levels of genes related to vascular tissue development compared to WT. Histological analysis showed T-DNA insertion mutant wakl14-1 had reduced plant stem length with fewer number of xylem vessels and interfascicular fibres compared to WT, with no significant differences in cellulose and lignin content. Mutant wakl14-1 also showed reduced number of vascular bundles in fruit. A proWAKL14::mCherry-WAKL14 fusion protein was able to complement wakl14-1 phenotypes and showed mCherry-WAKL14 associated with the plasma membrane. In vitro binding assays showed both SlWAKL2 and AtWAKL14 can interact with pectin and oligogalacturonides. Our results reveal novel roles of WAKLs in regulating vascular tissue development.

GhHB14_D10 and GhREV_D5, two HD-ZIP III transcription factors, play a regulatory role in cotton fiber secondary cell wall biosynthesis

KEY MESSAGE

GhHB14_D10 and GhREV_D5 regulated secondary cell wall formation and played an important role in fiber development. Cotton serves as an important source of natural fiber, and the biosynthesis of the secondary cell wall plays a pivotal role in determining cotton fiber quality. Nevertheless, the intricacies of this mechanism in cotton fiber remain insufficiently elucidated. This study investigates the functional roles of GhHB14_D10 and GhREV_D5, two HD-ZIP III transcription factors, in secondary cell wall biosynthesis in cotton fibers. Both GhHB14_D10 and GhREV_D5 were found to be localized in the nucleus with transcriptional activation activity. Ectopic overexpression of GhHB14_D10 and GhREV_D5 in Arabidopsis resulted in changed xylem differentiation, secondary cell wall deposition, and expression of genes related to the secondary cell wall. Silencing of GhHB14_D10 and GhREV_D5 in cotton led to enhanced fiber length, reduced cell wall thickness, cellulose contents and expression of secondary cell wall-related genes. Moreover, GhHB14_D10's direct interaction with GhREV_D5, and transcriptional regulation of cellulose biosynthesis genes GhCesA4-4 and GhCesA7-2 revealed their collaborative roles in secondary cell wall during cotton fiber development. Overall, these results shed light on the roles of GhHB14_D10 and GhREV_D5 in secondary cell wall biosynthesis, offering a strategy for the genetic improvement of cotton fiber quality.

The combination of uridine and nitrogen-deprivation promotes the efficient formation of astaxanthin-rich motile cells in Haematococcus pluvialis

Astaxanthin accumulation in Haematococcus pluvialis typically occurs alongside the formation of secondary cell wall (SCW), hindering astaxanthin extraction and bio-accessibility. A potential solution lies in cultivating astaxanthin-rich motile cells lacking SCW. This study explored the influence and underlying mechanism of nitrogen-deprivation (ND) on SCW formation and established a connection between pyrimidine metabolism and SCW development. Then, various pyrimidine and ND combinations were examined to cultivate astaxanthin-rich motile cells. The results indicated that, compared to the nitrogen-replete group, the combination of uridine and ND increased the proportion of motile cells by 25-33 times, achieving 95 %, and enhanced astaxanthin yield by 26.52 %. Moreover, the efficiency of astaxanthin extraction from intact, wet motile cells was 91 % - 95 %, which was 5.6-9.0 times that from non-motile cells. This study not only presents a promising method for producing astaxanthin-rich motile cells in H. pluvialis but also provides insights into the relationship between pyrimidine metabolism and SCW development.

UBC6, a ubiquitin-conjugating enzyme, participates in secondary cell wall thickening in the inflorescence stem of Arabidopsis

Secondary cell wall (SCW) thickening in plant inflorescence stems is a complicated cellular process that is essential for stem strength and biomass. Although Arabidopsis NAC transcription factor (TF) 1 (NST1) regulates the SCW thickening in anther walls, the single T-DNA-insertion mutant (nst1) does not show disrupted SCW thickening in anther endothecium, interfascicular fibers or xylem. To better understand the regulatory mechanism of this process, we generated an ethyl methanesulfonate (EMS)-mutagenized Arabidopsis population with the nst1 background. scd5 (SCW-defective mutant 5) was isolated in a forward genetic screen from the EMS mutant library, which displayed not only less lignin deposition in the interfascicular fiber and xylem than the wild type but also a pendent inflorescence stem. The EMS-induced mutation associated with the scd5 phenotype was found in the 5th exon of At2G46030 that encodes a ubiquitin-conjugating enzyme (UBC6), we thereby renamed the allele nst1 ubc6. Overexpressing UBC6 in nst1 ubc6 rescued the defective SCW, whereas disrupting UBC6 in nst1 by the CRISPR/Cas9 system caused a phenotype similar to that observed in nst1 ubc6. UBC6 was localized to the nucleus and plasma membrane, and possessed E2 ubiquitin-conjugating activity in vitro. MYB7 and MYB32 are considered as transcription repressors in the phenylpropanoid pathway and are involved in NAC TF-related transcriptional regulation in SCW thickening. UBC6 can interact with MYB7 and MYB32 and positively mediate the degradation of MYB7 and MYB32 by the 26S proteasome. Overall, these results indicated the contribution of UBC6 to SCW thickening in Arabidopsis inflorescence stems.

Functional Diversification and the Plant Secondary Cell Wall

Much evidence exists suggesting the presence of genetic functional diversification in plants, though literature associated with the role of functional diversification in the evolution of the plant secondary cell wall (SCW) has sparsely been compiled and reviewed in a recent context. This review aims to elucidate, through the examination of gene phylogenies associated with its biosynthesis and maintenance, the role of functional diversification in shaping the critical, dynamic, and characteristic organelle, the secondary cell wall. It will be asserted that gene families resulting from gene duplication and subsequent functional divergence are present and are heavily involved in SCW biosynthesis and maintenance. Furthermore, diversification will be presented as a significant driver behind the evolution of the many functional characteristics of the SCW. The structure and function of the plant cell wall and its constituents will first be explored, followed by a discussion on the phenomenon of gene duplication and the resulting genetic functional divergence that can emerge. Finally, the major constituents of the SCW and their individual relationships with duplication and divergence will be reviewed to the extent of current knowledge on the subject.

Enhancement of astaxanthin production, recovery, and bio-accessibility in Haematococcus pluvialis through taurine-mediated inhibition of secondary cell wall formation under high light conditions

This study explored the use of taurine in enhancing the production and bio-accessibility of astaxanthin in Haematococcus pluvialis, which typically forms a secondary cell wall hindering astaxanthin extraction. The biomass of taurine-treated group significantly increased by 18%, and astaxanthin yield surged by 34% in comparison to the control group. Without cell disruption, astaxanthin recovery from thin-walled cells in the taurine-treated group, using dimethyl sulfoxide and ethanol as extraction reagents, was 97% and 75%, respectively, which were 30-fold higher than those of thick-walled cells in the control group. Additionally, the cell fragmentation rate increased by 86% in taurine-treated group relative to the control group. Comparative transcriptome analysis identified taurine-induced upregulation of genes involved in the astaxanthin biosynthesis pathway and downregulation of those associated with secondary cell wall synthesis. This study thus offers an innovative taurine-based strategy to enhance astaxanthin production and bio-accessibility while shedding light on the mechanisms driving this process.

Functional investigation of five R2R3-MYB transcription factors associated with wood development in Eucalyptus using DAP-seq-ML

A multi-tiered transcriptional network regulates xylem differentiation and secondary cell wall (SCW) formation in plants, with evidence of both conserved and lineage-specific SCW network architecture. We aimed to elucidate the roles of selected R2R3-MYB transcription factors (TFs) linked to Eucalyptus wood formation by identifying genome-wide TF binding sites and direct target genes through an improved DAP-seq protocol combined with machine learning for target gene assignment (DAP-seq-ML). We applied this to five TFs including a well-studied SCW master regulator (EgrMYB2; homolog of AtMYB83), a repressor of lignification (EgrMYB1; homolog of AtMYB4), a TF affecting SCW thickness and vessel density (EgrMYB137; homolog of PtrMYB074) and two TFs with unclear roles in SCW regulation (EgrMYB135 and EgrMYB122). Each DAP-seq TF peak set (average 12,613 peaks) was enriched for canonical R2R3-MYB binding motifs. To improve the reliability of target gene assignment to peaks, a random forest classifier was developed from Arabidopsis DAP-seq, RNA-seq, chromatin, and conserved noncoding sequence data which demonstrated significantly higher precision and recall to the baseline method of assigning genes to proximal peaks. EgrMYB1, EgrMYB2 and EgrMYB137 predicted targets showed clear enrichment for SCW-related biological processes. As validation, EgrMYB137 overexpression in transgenic Eucalyptus hairy roots increased xylem lignification, while its dominant repression in transgenic Arabidopsis and Populus reduced xylem lignification, stunted growth, and caused downregulation of SCW genes. EgrMYB137 targets overlapped significantly with those of EgrMYB2, suggesting partial functional redundancy. Our results show that DAP-seq-ML identified biologically relevant R2R3-MYB targets supported by the finding that EgrMYB137 promotes SCW lignification in planta.

Two R2R3-MYB transcription factors from Chinese cedar (Cryptomeria fortunei Hooibrenk) are involved in the regulation of secondary cell wall formation

As the most abundant renewable energy source, wood comprises the secondary cell wall (SCW). SCW biosynthesis involves lignin and cellulose deposition. Increasing studies have illustrated that R2R3-MYB transcription factors (TFs) play pivotal roles in affecting lignin accumulation and SCW formation. Nevertheless, the regulatory roles of R2R3-MYBs are still unresolved in Cryptomeria fortunei Hooibrenk cambium and wood formation. To dissect the potentials of CfMYBs, we successfully cloned and intensively studied the functions of CfMYB4 and CfMYB5 in SCW formation and abiotic stress response. They both contained the conserved MYB domain capable of forming a special structure that could bind to the core motifs of downstream genes. The phylogenetic tree implied that two CfMYBs clustered into different evolutionary branches. They were predominantly expressed in the stem and were localized to the nucleus. Furthermore, CfMYB4 functioned as an activator to enhance lignin and cellulose accumulation, and increase the SCW thickness by elevating the expression levels of SCW-related genes. By contrast, CfMYB5 negatively regulated lignin and cellulose biosynthesis, and decreased SCW formation by reducing the expression of SCW biosynthetic genes. Our data not only highlight the regulatory functions of CfMYBs in lignin deposition but also provide critical insights into the development of strategies for the genetic improvement of Cryptomeria fortunei wood biomass.

Xylem development and phloem conductivity in relation to the stem mechanical strength of Paeonia lactiflora

The quality of cut Paeonia lactiflora flowers is limited by their low stem mechanical strength, but the underlying mechanism of this low strength is poorly understood. In this study, two P. lactiflora cultivars with distinct stem mechanical strengths (Chui Touhong with low stem mechanical strength and Da Fugui with high stem mechanical strength) were used as test materials. The xylem development was examined at the cellular level, and the phloem conductivity was analyzed by evaluating phloem geometry. The results showed that the secondary cell wall formation of the xylem of Chui Touhong was affected primarily in fiber cells but was affected little in vessel cells. The formation of the secondary cell walls in the xylem fiber cells of Chui Touhong was delayed, resulting in longer and thinner fiber cells with a lack of cellulose and S-lignin in the secondary cell walls. Moreover, the phloem conductivity of Chui Touhong was lower than that of Da Fugui, and more callose was accumulated in the lateral walls of the phloem sieve elements of Chui Touhong. Consequently, the delayed deposition of the secondary cell walls of the xylem fiber cells was the main factor leading to the low stem mechanical strength of Chui Touhong, and the low stem mechanical strength was closely related to the low conductivity of sieve tubes and extensive callose accumulation in the phloem. These findings provide a new perspective on enhancing P. lactiflora stem mechanical strength by targeting single cell level, and lay the foundation for future works on the correlation between phloem long-distance transport and stem mechanical strength.

Increasing production and bio-accessibility of natural astaxanthin in Haematococcus pluvialis by screening and culturing red motile cells under high light condition

The thick cell wall and low astaxanthin productivity were two important bottlenecks limiting industrial production of astaxanthin via Haematococcus pluvialis. This study reports a strategy for increasing production and bio-accessibility of astaxanthin in H. pluvialis by screening and culturing red motile cells under high light condition. Compared with the original strain NBU489, the biomass of the novel isolated strain RMS10 increased by 31.9% under low light condition, and the astaxanthin content (44.6 mg/g) increased by 53.3% after 9-day high light induction, which were readily extracted and digested without cell disruption. Subsequent transcriptomic analysis confirmed the accumulation of astaxanthin and lipids in RMS10 cells as expression of genes associated with biosynthesis of fatty acid and astaxanthin were up-regulated, while those involved in thick cell wall biosynthesis and reactive oxygen species scavenging were down-regulated in RMS10. Collectively, this study provides a simple and effective method for economical production of natural astaxanthin.

Deposition patterns of feruloylarabinoxylan during cell wall formation in moso bamboo

The feruloylarabinoxylan deposition was initiated at the formation of the secondary cell wall, especially S₂ layer in moso bamboo, which may affect crosslinking between cell wall components and plant growth. Hemicelluloses, major components of plant cell walls that are hydrogen bonded to cellulose and covalently bound to lignin, are crucial determinants of cell wall properties. Especially in commelinid monocotyledons, arabinoxylan is often esterified with ferulic acid, which is essential to crosslinking with cell wall components. However, the deposition patterns and localization of ferulic acid during cell wall formation remain unclear. In this study, developing moso bamboo (Phyllostachys pubescens) culms were used to elucidate deposition patterns of hemicelluloses including feruloylarabinoxylan. Ferulic acid content peaked with cessation of elongation growth, and thereafter decreased and remained stable as culm development proceeded. During primary cell wall (PCW) formation, xyloglucan and (1,3;1,4)-β-glucan signals were detected in all tissues. Along with culm development, arabinoxylan and feruloylarabinoxylan signals were sequentially observed in the protoxylem, vascular fibers and metaxylem, and parenchyma. Feruloylarabinoxylan signals were observed slightly later than arabinoxylan signals. Arabinoxylan signals were observed throughout the compound middle lamella and secondary cell wall (SCW), whereas the feruloylarabinoxylan signal was localized to the S₂ layer of the SCW. These results indicate that the biosynthesis of hemicelluloses is regulated in accordance with cell wall layers. Feruloylarabinoxylan deposition may be initiated at the formation of SCW, especially S₂ layer formation. Ferulic acid-mediated linkages of arabinoxylan-arabinoxylan and arabinoxylan-lignin would arise during SCW formation with the cessation of elongation growth.

Overexpression of PnMYB2 from Panax notoginseng induces cellulose and lignin biosynthesis during cell wall formation

Panax notoginseng PnMYB2 is a transcriptional activator of primary and secondary cell wall formation by promoting the PCW-specific gene CesA3 and key lignin biosynthetic gene CCoAOMT1, respectively. R2R3-MYB transcription factors play important roles in regulation secondary cell wall (SCW) formation. However, there are few reports on the functions of MYB transcription factors which involved in both primary cell wall (PCW) and SCW formation. Here, we isolated an R2R3-MYB transcription factor, PnMYB2, from Panax notoginseng roots which are widely used in Chinese traditional medicines and contain abundant cellulose and lignin. The expression pattern of PnMYB2 was similar to the accumulation pattern of cellulose and lignin contents in different organs. PnMYB2 localized in the nucleus and may function as a transcriptional activator. Overexpression of PnMYB2 in Arabidopsis thaliana enhanced cellulose and lignin biosynthesis, and remarkably increased thickness of PCW and SCW in the stem of transgenic plants compared with wild-type plants. The expression levels of genes associated with PCW-specific cellulose synthase (CesA) genes and key SCW-specific lignin biosynthetic genes were significantly increased in PnMYB2-overexpressing plants compared to the wild type plants. Furthermore, yeast one-hybrid, dual-luciferase reporter assays and electrophoretic mobility shift assays (EMSA) results verified that PnMYB2 could bind and activate the promoters of AtCesA3 and PnCesA3, which are the PCW-specific cellulose biosynthetic genes, and AtCCoAOMT1 and PnCCoAOMT1, which are the key lignin biosynthetic genes. These results demonstrated the central role of PnMYB2 in PCW-specific cellulose formation and SCW-specific lignin biosynthesis.

PtrHAT22, as a higher hierarchy regulator, coordinately regulates secondary cell wall component biosynthesis in Populus trichocarpa

Homeodomain-leucine zipper (HD-Zip) II transcription factors (TFs) have been reported to play vital roles in diverse biological processes of plants. However, it remains unclear whether HD-Zip II TFs regulate secondary cell wall (SCW) in woody plants. In this study, we performed the functional characterization of a Populus trichocarpa HD-Zip II TF, PtrHAT22, which encodes a nuclear localized transcription repressor predominantly expressing in secondary developing tissues. Overexpression of PtrHAT22 showed arrested growths, including reduced heights and diameters above the ground, small leaves, and decreased biomass. Meanwhile, the contents of lignin, cellulose, and thickness of SCW significantly decreased, whilst the content of hemicellulose obviously increased in PtrHAT22 transgenic poplar. The expressions of some wood-associated TFs and structural genes significantly changed accordingly with the alternations of SCW characteristics in PtrHAT22 transgenic poplar. Furthermore, PtrHAT22 directly repressed the promoter activities of PtrMYB20, PtrMYB28, and PtrCOMT2, and bind two cis-acting elements that were specifically enriched in their promoter regions. Taken together, our results suggested that PtrHAT22, as a higher hierarchy TF like PtrWNDs, exerted coordination regulation of poplar SCW component biosynthesis through directly and indirectly regulating structural genes and different hierarchy TFs of SCW formation network.

Comparative transcriptome analysis reveals the regulation network for fiber strength in cotton

OBJECTIVE

Determine the effect of secondary cell wall (SCW) thickness and microcrystalline cellulose content (MCC) on mature fiber strength (FS) and reveal through comparative transcriptome analysis the molecular regulation network governing FS in cotton.

RESULTS

Transmission electron microscope (TEM) analysis of two parent varieties, Prema with elite FS and 86-1 with weak fiber, revealed significant difference in the SCW but not in MCC. Transcriptome analysis revealed that genes differentially expressed during SCW thickening (20 DPA) are highly related to FS; in particular, up-regulated genes such as UDPG, CESA2, and NAC83 were important in SCW thickening, likely contributing to higher FS. GO and KEGG enrichment analysis revealed the common up-regulated genes to be enriched in carbon metabolism and terms relating to the cell wall.

CONCLUSIONS

We developed two recombinant inbred lines with elite FS, selected from the filial generation of Prema and 86-1. By comparing transcriptomic data, we revealed the gene expression network governing SCW thickness in mature fiber. Our results provide solid insights into the relationship of the SCW and FS.

Immunohistochemical analyses on two distinct internodes of stinging nettle show different distribution of polysaccharides and proteins in the cell walls of bast fibers

Stinging nettle is a perennial herbaceous species holding value as a multi-purpose plant. Indeed, its leaves and roots are phytofactories providing functional ingredients of medicinal interest and its stems produce silky and resistant extraxylary fibers (a.k.a. bast fibers) valued in the biocomposite sector. Similarly to what is reported in other fiber crops, the stem of nettle contains both lignified and hypolignified fibers in the core and cortex, respectively, and it is therefore a useful model for cell wall research. Indeed, data on nettle stem tissues can be compared to those obtained in other models, such as hemp and flax, to support hypotheses on the differentiation and development of bast fibers. The suitability of the nettle stem as model for cell wall-related research was already validated using a transcriptomics and biochemical approach focused on internodes at different developmental stages sampled at the top, middle, and bottom of the stem. We here sought to complement and enrich these data by providing immunohistochemical and ultrastructural details on young and older stem internodes. Antibodies recognizing non-cellulosic polysaccharides (galactans, arabinans, rhamnogalacturonans) and arabinogalactan proteins were here investigated with the goal of understanding whether their distribution changes in the stem tissues in relation to the bast fiber and vascular tissue development. The results obtained indicate that the occurrence and distribution of cell wall polysaccharides and proteins differ between young and older internodes and that these changes are particularly evident in the bast fibers.

Functional Analysis of Poplar Sombrero-Type NAC Transcription Factors Yields a Strategy to Modify Woody Cell Wall Properties

Woody cells generate lignocellulosic biomass, which is a promising sustainable bioresource for wide industrial applications. Woody cell differentiation in vascular plants, including the model plant poplar (Populus trichocarpa), is regulated by a set of NAC family transcription factors, the VASCULAR-RELATED NAC-DOMAIN (VND), NAC SECONDARY CELL WALL THICKENING PROMOTING FACTOR (NST)/SND, and SOMBRERO (SMB) (VNS)-related proteins, but the precise contributions of each VNS protein to wood quality are unknown. Here, we performed a detailed functional analysis of the poplar SMB-type VNS proteins PtVNS13-PtVNS16. PtVNS13-PtVNS16 were preferentially expressed in the roots of young poplar plantlets, similar to the Arabidopsis thalianaSMB gene. PtVNS13 and PtVNS14, as well as the NST-type PtVNS11, suppressed the abnormal root cap phenotype of the Arabidopsis sombrero-3 mutant, whereas the VND-type PtVNS07 gene did not, suggesting a functional gap between SMB- or NST-type VNS proteins and VND-type VNS proteins. Overexpressing PtVNS13-PtVNS16 in Arabidopsis seedlings and poplar leaves induced ectopic xylem-vessel-like cells with secondary wall deposition, and a transient expression assay showed that PtVNS13-16 transactivated woody-cell-related genes. Interestingly, although any VNS protein rescued the pendant stem phenotype of the Arabidopsis nst1-1 nst3-1 mutant, the resulting inflorescence stems exhibited distinct cell wall properties: poplar VNS genes generated woody cell walls with higher enzymatic saccharification efficiencies compared with Arabidopsis VNS genes. Together, our data reveal clear functional diversity among VNS proteins in woody cell differentiation and demonstrate a novel VNS-based strategy for modifying woody cell wall properties toward enhanced utilization of woody biomass.

Xylem vessel cell differentiation: A best model for new integrative cell biology?

Xylem vessels transport water and essential low-molecular-weight compounds throughout vascular plants. To achieve maximum performance as conductive tissues, xylem vessel cells undergo secondary cell wall deposition and programmed cell death to produce a hollow tube-like structure with a rigid outer shell. This unique process has been explored in detail from a cell biology and molecular biology perspective, culminating in the identification of the master transcriptional switches of xylem vessel cell differentiation, the VASCULAR-RELATED NAC-DOMAIN (VND) proteins. High-resolution analyses of xylem vessel cell differentiation have since accelerated and are now moving toward single cell-level dissection from a variety of directions. In this review, we introduce the current model of xylem vessel cell differentiation and discuss possible future directions in this field.

Rice Brittle Culm19 Encoding Cellulose Synthase Subunit CESA4 Causes Dominant Brittle Phenotype But has No Distinct Influence on Growth and Grain Yield

BACKGROUND

Mechanical strength is a crucial agronomic trait in rice (Oryza sativa), and brittle mutants are thought suitable materials to investigate the mechanism of cell wall formation. So far, almost all brittle mutants are recessive, and most of them are defected in multiple morphologies and/or grain yield, limiting their application in hybrid breeding and in rice straw recycling.

RESULTS

We identified a semi-dominant brittle mutant Brittle culm19 (Bc19) isolated from the japonica variety Nipponbare through chemical mutagenesis. The mutant showed the same apparent morphologies and grain yield to the wild type plant except for its weak mechanical strength. Its development of secondary cell wall in sclerenchyma cells was affected, along with reduced contents of cellulose, hemicellulose, lignin and sugars in culms and leaves. Positional cloning suggested that the Bc19 gene was allelic to OsCESA4, encoding one of the cellulose synthase A (CESA) catalytic subunits. In this mutant, a C-to-T substitution occurred in the coding sequence of BC19, causing the P507S missense mutation in its encoded product, which was located in the second cytoplasmic region of the OsCESA4 protein. Furthermore, introducing mutant gene Bc19 into the wild-type plant resulted in brittle plants, confirming that the P507S point mutation in OsCESA4 protein was responsible for the semi-dominant brittle phenotype of Bc19 mutant. Reverse correlation was revealed between cellulose contents and expression levels of mutant gene Bc19 among the homozygous mutant, the hybrid F₁ plant, and the Bc19 overexpression transgenic plants, implying that gene Bc19 might affect cellulose synthesis in a dosage-dependent manner.

CONCLUSIONS

Bc19, a semi-dominant brittle mutant allele of gene OsCESA4, was identified using map-based cloning approach. The mutated protein of Bc19 possessing the P507S missense mutation behaved in a dosage-dependent semi-dominant manner. Unique brittle effect on phenotype and semi-dominant genetic quality of gene Bc19 indicated its potential application in grain-straw dual-purpose hybrid rice breeding.

Integrative lncRNA landscape reveals lncRNA-coding gene networks in the secondary cell wall biosynthesis pathway of moso bamboo (Phyllostachys edulis)

Background

LncRNAs are extensively involved in plant biological processes. However, the lack of a comprehensive lncRNA landscape in moso bamboo has hindered the molecular study of lncRNAs. Moreover, the role of lncRNAs in secondary cell wall (SCW) biosynthesis of moso bamboo is elusive.

Results

For comprehensively identifying lncRNA throughout moso bamboo genome, we collected 231 RNA-Seq datasets, 1 Iso-Seq dataset, and 1 full-length cDNA dataset. We used a machine learning approach to improve the pipeline of lncRNA identification and functional annotation based on previous studies and identified 37,009 lncRNAs in moso bamboo. Then, we established a network of potential lncRNA-coding gene for SCW biosynthesis and identified SCW-related lncRNAs. We also proposed that a mechanism exists in bamboo to direct phenylpropanoid intermediates to lignin or flavonoids biosynthesis through the PAL/4CL/C4H genes. In addition, we identified 4 flavonoids and 1 lignin-preferred genes in the PAL/4CL/C4H gene families, which gained implications in molecular breeding.

Conclusions

We provided a comprehensive landscape of lncRNAs in moso bamboo. Through analyses, we identified SCW-related lncRNAs and improved our understanding of lignin and flavonoids biosynthesis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07953-z.

NST- and SND-subgroup NAC proteins coordinately act to regulate secondary cell wall formation in cotton

Secondary cell wall (SCW) has a strong impact on plant growth and adaptation to the environments. Previous studies have shown that NAC (NAM, ATAF1/2, and CUC2) transcription factors act as key regulators of SCW biosynthesis. However, the regulatory network triggered by NAC proteins is largely unknown, especially in cotton, a model plant for SCW development studies. Here, we show that several cotton NAC transcription factors are clustered in the same group with Arabidopsis secondary wall NACs (SWNs), including secondary wall-associated NAC domain protein1 (SND1) and NAC secondary wall thickening promoting factor1/2 (NST1/2), so we name these cotton orthologs as SND1s and NST1s. We found that simultaneous silencing of SND1s and NST1s led to severe xylem and phloem developmental defect in cotton stems, however silencing either SND1s or NST1s alone had no visible phenotype. Silencing both SND1s and NST1s but not one subgroup caused decreased expression of a set of SCW-associated genes, while over-expression of cotton SWNs in tobacco leaves resulted in SCW deposition. SWNs could bind the promoter of MYB46 and MYB83, which are highly expressed in SCW-rich tissues of cotton. In total, our data provide evidence that cotton SWNs positively and coordinately regulate SCW formation.

Genome-wide identification of fasciclin-like arabinogalactan proteins in jute and their expression pattern during fiber formation

Fasciclin-like arabinogalactan proteins (FLAs), a class of arabinogalactan proteins (AGPs) are involved in plant growth and development via cell communication and adhesion. FLAs were also associated with fiber and wood formation in plants but no information is available about the roles of FLA proteins during fibre development of jute. Here, we performed molecular characterization, evolutionary relationship and expression profiling of FLAs proteins in jute (Corchorus olitorius). In total, nineteen CoFLA genes have been identified in jute genome, which were divided into four classes like FLAs of other species based on protein structure and similarity. All CoFLAs have N-terminal signal peptide and one or two FAS domain while two FLAs lack well defined AGP region and eight FLAs were devoid of C-terminal glycosylphosphatidylinositol (GPI) anchor. Expression analysis of different regions of jute stem suggested their involvement in different fiber development stages. Four genes CoFLA 11, 12, 20, and 23 were highly or predominately expressed in fiber containing bark tissues while the expression levels of six CoFLA genes 02, 03, 04, 06, 14 and 19 were comparatively higher in stick. Higher transcripts levels of CoFLA 12 and 20 in the middle bark tissues suggest their involvement in fiber elongation. In contrast, the CoFLA 11 and 23 were more expressed in bottom bark tissues suggesting their potential involvement in secondary cell wall synthesis. Our study can serve as solid foundation for further functional exploration of FLAs and in future breeding program of jute aiming fiber improvement.

Rice OVATE family protein 6 regulates leaf angle by modulating secondary cell wall biosynthesis

Secondary cell wall not only provides rigidity and mechanical resistance to plants, but also has a large impact on plant growth and adaptation to environments. Biosynthesis of secondary cell wall is regulated by a complicated signaling transduction network; however, it is still unclear how the transcriptional regulation of secondary cell wall biosynthesis works at the molecular level. Here, we report in rice that OVATE family proteins 6 (OsOFP6) is a positive regulator in modulating expression of the genes related to biosynthesis of the secondary cell wall. Transgenic plants with knock-down of OsOFP6 by RNA interference showed increased leaf angle, which resulted from the thinner secondary cell wall with reduced amounts of cellulose and lignin, whilst overexpression of OsOFP6 in rice led to the thinker secondary cell wall with increased lignin content. Protein-protein interaction analysis revealed that OsOFP6 interacts with Oryza sativa homeobox 15 (OSH15), a class I KNOX protein. The interaction of OsOFP6 and OSH15 enhanced the transcriptional activity of OSH15 which binds to the promoter of OsIRX9 (Oryza sativa IRREGULAR XYLEM 9). Taken together, our study provides insights into the function of OsOFP6 in regulating leaf angle and the control of biosynthesis of secondary cell wall.

EgPHI-1, a PHOSPHATE-INDUCED-1 gene from Eucalyptus globulus, is involved in shoot growth, xylem fiber length and secondary cell wall properties

MAIN CONCLUSION

EgPHI-1 is a member of PHI-1/EXO/EXL protein family. Its overexpression in tobacco resulted in changes in biomass partitioning, xylem fiber length, secondary cell wall thickening and composition, and lignification. Here, we report the functional characterization of a PHOSPHATE-INDUCED PROTEIN 1 homologue showing differential expression in xylem cells from Eucalyptus species of contrasting phenotypes for wood quality and growth traits. Our results indicated that this gene is a member of the PHI-1/EXO/EXL family. Analysis of the promoter cis-acting regulatory elements and expression responses to different treatments revealed that the Eucalyptus globulus PHI-1 (EgPHI-1) is transcriptionally regulated by auxin, cytokinin, wounding and drought. EgPHI-1 overexpression in transgenic tobacco changed the partitioning of biomass, favoring its allocation to shoots in detriment of roots. The stem of the transgenic plants showed longer xylem fibers and reduced cellulose content, while the leaf xylem had enhanced secondary cell wall thickness. UV microspectrophotometry of individual cell wall layers of fibers and vessels has shown that the transgenic plants exhibit differences in the lignification of S2 layer in both cell types. Taken together, the results suggest that EgPHI-1 mediates the elongation of secondary xylem fibers, secondary cell wall thickening and composition, and lignification, making it an attractive target for biotechnological applications in forestry and biofuel crops.

Atomic force microscopy imaging of delignified secondary cell walls in liquid conditions facilitates interpretation of wood ultrastructure

Deep understanding of the physicochemical and structural characteristics of wood at the nanoscale is essential for improving wood usage in biorefining and advancing new high performance materials design. Herein, we use in situ atomic force microscopy and a simple delignification treatment to elucidate the nanoscale architecture of individual secondary cell wall layers. Advantages of this approach are: (i) minimal sample preparation that reduces the introduction of potential artifacts; (ii) prevention of structural rearrangements due to dehydration; (iii) increased accessibility to structural details masked by the lignin matrix; and (iv) possibility to complement results with other analytical techniques without sample manipulation. The methodology permits the visualization of parallel and helicoidally arranged microfibril aggregates in the S1 layer and the determination of lignin contribution to microfibril aggregates forming S2 layers. Cellulose and hemicelluloses constitute the core of the aggregates with a mean diameter of approximately 19 nm, and lignin encloses the core forming single structural entities of about 30 nm diameter. Furthermore, we highlight the implications of sample preparation and imaging parameters on the characterization of microfibril aggregates by AFM.

Root-knot nematodes modulate cell walls during root-knot formation in Arabidopsis roots

Phytoparasitic nematodes parasitize many species of rooting plants to take up nutrients, thus causing severe growth defects in the host plants. During infection, root-knot nematodes induce the formation of a characteristic hyperplastic structure called a root-knot or gall on the roots of host plants. Although many previous studies addressed this abnormal morphogenesis, the underlying mechanisms remain uncharacterized. To analyze the plant-microorganism interaction at the molecular level, we established an in vitro infection assay system using the nematode Meloidogyne incognita and the model plant Arabidopsis thaliana. Time-course mRNA-seq analyses indicated the increased levels of procambium-associated genes in the galls, suggesting that vascular stem cells play important roles in the gall formation. Conversely, genes involved in the formation of secondary cell walls were decreased in galls. A neutral sugar analysis indicated that the level of xylan, which is one of the major secondary cell wall components, was dramatically reduced in the galls. These observations were consistent with the hypothesis of a decrease in the number of highly differentiated cells and an increase in the density of undifferentiated cells lead to gall formation. Our findings suggest that phytoparasitic nematodes modulate the developmental mechanisms of the host to modify various aspects of plant physiological processes and establish a feeding site.

Isolation, cloning and expression analysis of cinnamyl alcohol dehydrogenase (CAD) involved in phenylpropanoid pathway of Erianthus arundinaceus, a wild relative of sugarcane

In this study we have cloned and characterized cinnamyl alcohol dehydrogenase (CAD) involved in phenylpropanoid pathway which can be utilized for biomass modification for improved saccharification efficiency. The full length gene CAD is of 4 kb containing four exons and three introns, among which the exon 1 and 2 of 88 and 116 bp were conserved with sorghum and Miscanthus CADs. The coding region of CAD was identified with 1098 bp open reading frame (ORF), for 365 amino acids. In the PROSITE analysis, a zinc-containing alcohol dehydrogenase signature (GHEVVGEVVEVGPEV) and an NADP-binding domain motif (GLGGLG) was identified, while the motif analysis showed unique signature sequence of "LEPYLA" at 258-264 aa which was absent in the CAD sequences of other crops. This sequence information on CAD from Erianthus a bioenergy crop might be useful for subsequent research on lignin engineering for improved biomass conversion and for unravelling the impact of lignin on cell wall mechanics.

A cotton NAC domain transcription factor, GhFSN5, negatively regulates secondary cell wall biosynthesis and anther development in transgenic Arabidopsis

NAC domain transcription factors (TFs) are plant-specific transcriptional regulators, some of which play crucial roles in secondary cell wall (SCW) biosynthesis in plants. Cotton is one of the most important natural fiber producing crops, whose mature fiber SCW contains more than 90% cellulose with very small amounts of xylan and lignin, but little is known about the molecular mechanism underlying fiber SCW formation. We previously identified seven fiber preferentially expressed NAC members, GhFSN1-7. One, GhFSN1, was demonstrated to positively regulate fiber SCW thickening, but the functions of other GhFSN members remain unknown. In this study, roles of GhFSN5 were dissected. qRT-PCR analysis showed that GhFSN5 was predominantly transcribed during the fiber SCW thickening stage. In addition, a large number of fiber SCW biosynthetic genes and SCW-related TFs were co-expressed with GhFSN5. Heterologous expression of GhFSN5 in Arabidopsis resulted in plants with smaller siliques and severe sterility. Anther dehiscence in transgenic lines was not substantially affected, but most pollen was collapsed and nonviable. Furthermore, cellulose and lignin contents in inflorescence stems as well as roots were reduced in transgenic lines, compared with the wild type. Moreover, a set of SCW biosynthetic genes for cellulose, xylan and lignin and several transcription factors involved in regulation of SCW formation were down-regulated in transgenic plants. Our findings indicate that GhFSN5 acts as a negative regulator of SCW formation and anther development and expands our understanding of transcriptional regulation of SCW biosynthesis.

Overexpression of hexose transporter CsHT3 increases cellulose content in cucumber fruit peduncle

Hexose transporters play many important roles in plant development. However, the role of hexose transporter in secondary cell wall growth has not been reported before. Here, we report that the hexose transporter gene CsHT3 is mainly expressed in cells with secondary cell walls in cucumber. Spatiotemporal expression analysis revealed that the transcript of CsHT3 mainly accumulates in the stem, petiole, tendril, and peduncle, all of which contain high cellulose levels. Immunolocalization results show that CsHT3 is localized at the sclereids in young peduncles, shifts to the phloem fiber cells during peduncle development, and then shifts again to the companion cells when the development of secondary cell walls is almost completed. Carboxyfluoresce unloading experiment indicated that carbohydrate unloading in the phloem follows an apoplastic pathway. Overexpression of CsHT3 in cucumber plant can improve the cellulose content and cell wall thickness of phloem fiber cells in the peduncle. The expression of cellulose synthase genes were increased in the CsHT3 overexpression plants. These results indicated that CsHT3 may play an important role in cellulose synthesis through promoting the expression of cellulose synthase genes.

Genome-wide identification and characterization of TALE superfamily genes in cotton reveals their functions in regulating secondary cell wall biosynthesis

BACKGROUND

Cotton fiber length and strength are both key traits of fiber quality, and fiber strength (FS) is tightly correlated with secondary cell wall (SCW) biosynthesis. The three-amino-acid-loop-extension (TALE) superclass homeoproteins are involved in regulating diverse biological processes in plants, and some TALE members has been identified to play a key role in regulating SCW formation. However, little is known about the functions of TALE members in cotton (Gossypium spp.).

RESULTS

In the present study, based on gene homology, 46, 47, 88 and 94 TALE superfamily genes were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum, respectively. Phylogenetic and evolutionary analysis showed the evolutionary conservation of two cotton TALE families (including BEL1-like and KNOX families). Gene structure analysis also indicated the conservation of GhTALE members under selection. The analysis of promoter cis-elements and expression patterns suggested potential transcriptional regulation functions in fiber SCW biosynthesis and responses to some phytohormones for GhTALE proteins. Genome-wide analysis of colocalization of TALE transcription factors with SCW-related QTLs revealed that some BEL1-like genes and KNAT7 homologs may participate in the regulation of cotton fiber strength formation. Overexpression of GhKNAT7-A03 and GhBLH6-A13 significantly inhibited the synthesis of lignocellulose in interfascicular fibers of Arabidopsis. Yeast two-hybrid (Y2H) experiments showed extensive heteromeric interactions between GhKNAT7 homologs and some GhBEL1-like proteins. Yeast one-hybrid (Y1H) experiments identified the upstream GhMYB46 binding sites in the promoter region of GhTALE members and defined the downstream genes that can be directly bound and regulated by GhTALE heterodimers.

CONCLUSION

We comprehensively identified TALE superfamily genes in cotton. Some GhTALE members are predominantly expressed during the cotton fiber SCW thicking stage, and may genetically correlated with the formation of FS. Class II KNOX member GhKNAT7 can interact with some GhBEL1-like members to form the heterodimers to regulate the downstream targets, and this regulatory relationship is partially conserved with Arabidopsis. In summary, this study provides important clues for further elucidating the functions of TALE genes in regulating cotton growth and development, especially in the fiber SCW biosynthesis network, and it also contributes genetic resources to the improvement of cotton fiber quality.

γVPE plays an important role in programmed cell death for xylem fiber cells by activating protease CEP1 maturation in Arabidopsis thaliana

The vacuolar processing enzyme (VPE) plays an important role in PCD and was originally identified as the proteinase responsible for the maturation and activation of vacuolar proteins in plants. We found that γVPE is involved in PCD of xylem fiber cells through the activation of CEP1 proproteases into mature protease in Arabidopsis. The γVPE protein was expressed specifically in cambium cells cambium, the primary phloem and the primary xylem during stem development. The recombinant γVPE appearing as a proenzyme at pH 7.0, and then transforming into a 40-kD mature enzyme at pH 5.5 in vitro by self-cleaving. The mature γVPE protein activated CEP1 maturation in vitro, whereas this activity was inhibited in the γvpe mutant. Transmission electron microscopy showed delayed PCD in fiber cells and thickening of secondary fiber cell walls in the γvpe mutant. Transcriptome analysis showed that the expression of 2001 genes was significantly altered expression in the γvpe mutants, and most of them are important for secondary cell wall formation and PCD. Our results demonstrate that γVPE is a crucial processing enzyme for xylem fiber cells PCD during stem development.

Genome-wide characterization of aspartic protease (AP) gene family in Populus trichocarpa and identification of the potential PtAPs involved in wood formation

BACKGROUND

Aspartic protease (AP) is one of four large proteolytic enzyme families that are involved in plant growth and development. Little is known about the AP gene family in tree species, although it has been characterized in Arabidopsis, rice and grape. The AP genes that are involved in tree wood formation remain to be determined.

RESULTS

A total of 67 AP genes were identified in Populus trichocarpa (PtAP) and classified into three categories (A, B and C). Chromosome mapping analysis revealed that two-thirds of the PtAP genes were located in genome duplication blocks, indicating the expansion of the AP family by segmental duplications in Populus. The microarray data from the Populus eFP browser demonstrated that PtAP genes had diversified tissue expression patterns. Semi-qRT-PCR analysis further determined that more than 10 PtAPs were highly or preferentially expressed in the developing xylem. When the involvement of the PtAPs in wood formation became the focus, many SCW-related cis-elements were found in the promoters of these PtAPs. Based on PtAP_promoter::GUS techniques, the activities of PtAP66 promoters were observed only in fiber cells, not in the vessels of stems as the xylem and leaf veins developed in the transgenic Populus tree, and strong GUS signals were detected in interfascicular fiber cells, roots, anthers and sepals of PtAP17_promoter::GUS transgenic plants. Intensive GUS activities in various secondary tissues implied that PtAP66 and PtAP17 could function in wood formation. In addition, most of the PtAP proteins were predicted to contain N- and (or) O-glycosylation sites, and the integration of PNGase F digestion and western blotting revealed that the PtAP17 and PtAP66 proteins were N-glycosylated in Populus.

CONCLUSIONS

Comprehensive characterization of the PtAP genes suggests their functional diversity during Populus growth and development. Our findings provide an overall understanding of the AP gene family in trees and establish a better foundation to further describe the roles of PtAPs in wood formation.

The transcription factor γMYB2 acts as a negative regulator of secondary cell wall thickening in anther and stem

Secondary cell wall (SCW) thickening provides the mechanical force for anther dehiscence and plays an important role in the formation of xylem structure. We have previously reported that γMYB2, a MYB coiled-coil protein, directly binds to the P1BS cis-element of the PLA₂-γ promoter and acts as a co-activator of γMYB1 in controlling the expression of PLA₂-γ. In this study, we analyzed morphological phenotypes of the constitutive overexpression (γMYB2-OE) and knock-down (γMYB2-KD) lines of γMYB2. We found that γMYB2 overexpression caused the collapse of the endothecium layer, thereby suppressing anther dehiscence and forming short infertile siliques. The γMYB2-OE also showed less cellulose deposition in the xylem and had a longer primary stem than the wild-type, while γMYB2-KD had greater cellulose accumulation and a shorter primary stem than the wild-type. We demonstrated that the male sterility and the longer primary stem in γMYB2-OE were caused by reduced expression of SCW thickening-related genes. Our results suggest that γMYB2 acts as a negative regulator in controlling the SCW thickening in Arabidopsis.

Overexpression of PsnSuSy1, 2 genes enhances secondary cell wall thickening, vegetative growth, and mechanical strength in transgenic tobacco

KEY MESSAGE

Two homologs PsnSuSy1 and PsnSuSy2 from poplar played largely similar but little distinct roles in modulating sink strength, accelerating vegetative growth and modifying secondary growth of plant. Co-overexpression of them together resulted in small but perceptible additive effects. Sucrose synthase (SuSy) acts as a crucial determinant of sink strength by controlling the conversion of sucrose into UDP-glucose, which is not only the sole precursor for cellulose biosynthesis but also an extracellular signaling molecule for plants growth. Therefore, modification of SuSy activity in plants is of utmost importance. We have isolated two SuSy genes from poplar, PsnSuSy1 and PsnSuSy2, which were preferentially expressed in secondary xylem/phloem. To investigate their functions, T2 tobacco transgenic lines of PsnSuSy1 and PsnSuSy2 were generated and then crossed to generate PsnSuSy1/PsnSuSy2 dual overexpression transgenic lines. SuSy activities in all lines were significantly increased though PsnSuSy1/PsnSuSy2 lines only exhibited slightly higher SuSy activities than either PsnSuSy1 or PsnSuSy2 lines. The significantly increased fructose and glucose, engendered by augmented SuSy activities, caused the alternations of many physiological, biochemical measures and phenotypic traits that include accelerated vegetative growth, thickened secondary cell wall, and increased stem breaking force, accompanied with altered expression levels of related pathway genes. The correlation relationships between SuSy activities and many of these traits were statistically significant. However, differences of almost all traits among three types of transgenic lines were insignificant. These findings clearly demonstrated that PsnSuSy1 and PsnSuSy2 had similar but little distinct functions and insubstantial additive effects on modulating sink strength and affecting allocation of carbon elements among secondary cell wall components.

Modification of phytosterol composition influences cotton fiber cell elongation and secondary cell wall deposition

BACKGROUND

Cotton fiber is a single cell that arises from the epidermis of ovule. It is not only a main economic product of cotton, but an ideal material for studying on the growth and development of plant cell. Our previous study indicated that phytosterol content and the ratio of campesterol to sitosterol fluctuated regularly in cotton fiber development. However, what effects of modified phytosterol content and composition on the growth and development of cotton fiber cell is unknown. In this study, we overexpressed the GhSMT2-1, a cotton homologue of sterol C-24 methyltransferase 2 gene in transgenic upland cotton plants to modify phytosterol content and composition in fiber cells and investigated the changes on fiber elongation and secondary cell wall deposition.

RESULTS

GhSMT2-1 overexpression led to changes of phytosterol content and the ratio of campesterol to sitosterol in fiber cell. At the rapid elongation stage of fiber cell, total phytosterol and sitosterol contents were increased while campesterol content was decreased in transgenic fibers when compared to control fibers. Accordingly, the ratio of campesterol to sitosterol declined strikingly. Simultaneously, the transgenic fibers were shorter and thicker than control fibers. Exogenous application of sitosterol or campesterol separately inhibited control fiber cell elongation in cotton ovule culture system in vitro. In addition, campesterol treatment partially rescued transgenic fiber elongation.

CONCLUSION

These results elucidated that modification of phytosterol content and composition influenced fiber cell elongation and secondary cell wall formation. High sitosterol or low ratio of campesterol to sitosterol suppresses fiber elongation and/or promote secondary cell wall deposition. The roles of sitosterol and campesterol were discussed in fiber cell development. There might be a specific ratio of campesterol to sitosterol in different developmental stage of cotton fibers, in which GhSMT2-1 play an important role. Our study, at a certain degree, provides novel insights into the regulatory mechanisms of fiber cell development.

Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis)

The MYB family, one of the largest transcription factor (TF) families in the plant kingdom, plays vital roles in cell formation, morphogenesis and signal transduction, as well as responses to biotic and abiotic stresses. However, the underlying function of bamboo MYB TFs remains unclear. To gain insight into the status of these proteins, a total of 85 PeMYBs, which were further divided into 11 subgroups, were identified in moso bamboo (Phyllostachys edulis) by using a genome-wide search strategy. Gene structure analysis showed that PeMYBs were significantly different, with exon numbers varying from 4 to 13. Phylogenetic analysis indicated that PeMYBs clustered into 27 clades, of which the function of 18 clades has been predicted. In addition, almost all of the PeMYBs were differently expressed in leaves, panicles, rhizomes and shoots based on RNA-seq data. Furthermore, qRT-PCR analysis showed that 12 PeMYBs related to the biosynthesis and deposition of the secondary cell wall (SCW) were constitutively expressed, and their transcript abundance levels have changed significantly with increasing height of the bamboo shoots, for which the degree of lignification continuously increased. This result indicated that these PeMYBs might play fundamental roles in SCW thickening and bamboo shoot lignification. The present comprehensive and systematic study on the members of the MYB family provided a reference and solid foundation for further functional analysis of MYB TFs in moso bamboo.

Regulation of xylem fiber differentiation by gibberellins through DELLA-KNAT1 interaction

The thickening of plant organs is supported by secondary growth, a process by which new vascular tissues (xylem and phloem) are produced. Xylem is composed of several cell types, including xylary fibers, parenchyma and vessel elements. In Arabidopsis, it has been shown that fibers are promoted by the class-I KNOX gene KNAT1 and the plant hormones gibberellins, and are repressed by a small set of receptor-like kinases; however, we lack a mechanistic framework to integrate their relative contributions. Here, we show that DELLAs, negative elements of the gibberellin signaling pathway, physically interact with KNAT1 and impair its binding to KNAT1-binding sites. Our analysis also indicates that at least 37% of the transcriptome mobilized by KNAT1 is potentially dependent on this interaction, and includes genes involved in secondary cell wall modifications and phenylpropanoid biosynthesis. Moreover, the promotion by constitutive overexpression of KNAT1 of fiber formation and the expression of genes required for fiber differentiation were still reverted by DELLA accumulation, in agreement with post-translational regulation of KNAT1 by DELLA proteins. These results suggest that gibberellins enhance fiber development by promoting KNAT1 activity.

An essential role for abscisic acid in the regulation of xylem fibre differentiation

Division of the cambial cells and their subsequent differentiation into xylem and phloem drives radial expansion of the hypocotyl. Following the transition to reproductive growth, a phase change occurs in the Arabidopsis hypocotyl. During this second phase, the relative rate of xylem production is dramatically increased compared with that of phloem, and xylem fibres that contain thick secondary cell walls also form. Using two different genetic backgrounds and different environmental conditions, we identified a set of core transcriptional changes that is associated with the switch to the second phase of growth in the hypocotyl. Abscisic acid (ABA) signalling pathways are significantly over-represented in this set of core genes. Reverse genetic analysis demonstrated that mutants that are defective in ABA-biosynthesis enzymes exhibited significantly delayed fibre production without affecting the xylem:phloem ratio, and that these effects can be reversed by the application of ABA. The altered morphology is also reflected at the transcript level, with a reduced expression of marker genes that are associated with fibre formation in aba1 mutants. Taken together, the data reveal an essential role for ABA in the regulation of fibre formation.

A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation

Identification of DIR encoding genes in flax genome. Analysis of phylogeny, gene/protein structures and evolution. Identification of new conserved motifs linked to biochemical functions. Investigation of spatio-temporal gene expression and response to stress. Dirigent proteins (DIRs) were discovered during 8-8' lignan biosynthesis studies, through identification of stereoselective coupling to afford either (+)- or (-)-pinoresinols from E-coniferyl alcohol. DIRs are also involved or potentially involved in terpenoid, allyl/propenyl phenol lignan, pterocarpan and lignin biosynthesis. DIRs have very large multigene families in different vascular plants including flax, with most still of unknown function. DIR studies typically focus on a small subset of genes and identification of biochemical/physiological functions. Herein, a genome-wide analysis and characterization of the predicted flax DIR 44-membered multigene family was performed, this species being a rich natural grain source of 8-8' linked secoisolariciresinol-derived lignan oligomers. All predicted DIR sequences, including their promoters, were analyzed together with their public gene expression datasets. Expression patterns of selected DIRs were examined using qPCR, as well as through clustering analysis of DIR gene expression. These analyses further implicated roles for specific DIRs in (-)-pinoresinol formation in seed-coats, as well as (+)-pinoresinol in vegetative organs and/or specific responses to stress. Phylogeny and gene expression analysis segregated flax DIRs into six distinct clusters with new cluster-specific motifs identified. We propose that these findings can serve as a foundation to further systematically determine functions of DIRs, i.e. other than those already known in lignan biosynthesis in flax and other species. Given the differential expression profiles and inducibility of the flax DIR family, we provisionally propose that some DIR genes of unknown function could be involved in different aspects of secondary cell wall biosynthesis and plant defense.

Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls

BACKGROUND

Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a 'typical' lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of mature cotton seed fibres is highly cellulosic and lacks lignification whereas xylem SCWs are lignocellulosic. We used cotton as a model to study different SCWs and the expression of the genes involved in their formation via RNA deep sequencing and chemical analysis of stem and seed fibre.

RESULTS

Transcriptome comparisons from cotton xylem and pith as well as from a developmental series of seed fibres revealed tissue-specific and developmentally regulated expression of several NAC transcription factors some of which are likely to be important as top tier regulators of SCW formation in xylem and/or seed fibre. A so far undescribed hierarchy was identified between the top tier NAC transcription factors SND1-like and NST1/2 in cotton. Key SCW MYB transcription factors, homologs of Arabidopsis MYB46/83, were practically absent in cotton stem xylem. Lack of expression of other lignin-specific MYBs in seed fibre relative to xylem could account for the lack of lignin deposition in seed fibre. Expression of a MYB103 homolog correlated with temporal expression of SCW CesAs and cellulose synthesis in seed fibres. FLAs were highly expressed and may be important structural components of seed fibre SCWs. Finally, we made the unexpected observation that cell walls in the pith of cotton stems contained lignin and had a higher S:G ratio than in xylem, despite that tissue's lacking many of the gene transcripts normally associated with lignin biosynthesis.

CONCLUSIONS

Our study in cotton confirmed some features of the currently accepted gene regulatory cascade for 'typical' plant SCWs, but also revealed substantial differences, especially with key downstream NACs and MYBs. The lignocellulosic SCW of cotton xylem appears to be achieved differently from that in Arabidopsis. Pith cell walls in cotton stems are compositionally very different from that reported for other plant species, including Arabidopsis. The current definition of a 'typical' primary or secondary cell wall might not be applicable to all cell types in all plant species.

Formation of wood secondary cell wall may involve two type cellulose synthase complexes in Populus

Cellulose biosynthesis is mediated by cellulose synthases (CesAs), which constitute into rosette-like cellulose synthase complexe (CSC) on the plasma membrane. Two types of CSCs in Arabidopsis are believed to be involved in cellulose synthesis in the primary cell wall and secondary cell walls, respectively. In this work, we found that the two type CSCs participated cellulose biosynthesis in differentiating xylem cells undergoing secondary cell wall thickening in Populus. During the cell wall thickening process, expression of one type CSC genes increased while expression of the other type CSC genes decreased. Suppression of different type CSC genes both affected the wall-thickening and disrupted the multilaminar structure of the secondary cell walls. When CesA7A was suppressed, crystalline cellulose content was reduced, which, however, showed an increase when CesA3D was suppressed. The CesA suppression also affected cellulose digestibility of the wood cell walls. The results suggest that two type CSCs are involved in coordinating the cellulose biosynthesis in formation of the multilaminar structure in Populus wood secondary cell walls.

VND6-induced Xylem Cell Differentiation in Arabidopsis Cell Cultures

In vitro xylem differentiation is a powerful technique that can be used to elucidate the process of xylem development that occurs deep inside plant tissues in nature. The experimental procedure described here is designed to induce metaxylem vessel differentiation at exceptionally high frequency and synchronicity using genetically engineered Arabidopsis cell suspensions. By triggering a transcriptional switch, over 80 % of the cells synchronously differentiate into xylem cells within 32 h of treatment with estradiol. Exogenous marker genes can be transiently introduced into the cells by coculturing them with transformed Agrobacterium before inducing xylem differentiation. This system is fast, easy to handle, and highly compatible with molecular and cell biology techniques used to explore xylem cell differentiation.

Comparison of four glycosyl residue composition methods for effectiveness in detecting sugars from cell walls of dicot and grass tissues

BACKGROUND

The effective use of plant biomass for biofuel and bioproduct production requires a comprehensive glycosyl residue composition analysis to understand the different cell wall polysaccharides present in the different biomass sources. Here we compared four methods side-by-side for their ability to measure the neutral and acidic sugar composition of cell walls from herbaceous, grass, and woody model plants and bioenergy feedstocks.

RESULTS

Arabidopsis, Populus, rice, and switchgrass leaf cell walls, as well as cell walls from Populus wood, rice stems, and switchgrass tillers, were analyzed by (1) gas chromatography-mass spectrometry (GC-MS) of alditol acetates combined with a total uronic acid assay; (2) carbodiimide reduction of uronic acids followed by GC-MS of alditol acetates; (3) GC-MS of trimethylsilyl (TMS) derivatives; and (4) high-pressure, anion-exchange chromatography (HPAEC). All four methods gave comparable abundance ranking of the seven neutral sugars, and three of the methods were able to quantify unique acidic sugars. The TMS, HPAEC, and carbodiimide methods provided comparable quantitative results for the specific neutral and acidic sugar content of the biomass, with the TMS method providing slightly greater yield of specific acidic sugars and high total sugar yields. The alditol acetate method, while providing comparable information on the major neutral sugars, did not provide the requisite quantitative information on the specific acidic sugars in plant biomass. Thus, the alditol acetate method is the least informative of the four methods.

CONCLUSIONS

This work provides a side-by-side comparison of the efficacy of four different established glycosyl residue composition analysis methods in the analysis of the glycosyl residue composition of cell walls from both dicot (Arabidopsis and Populus) and grass (rice and switchgrass) species. Both primary wall-enriched leaf tissues and secondary wall-enriched wood/stem tissues were analyzed for mol% and mass yield of the non-cellulosic sugars. The TMS, HPAEC, and carbodiimide methods were shown to provide comparable quantitative data on the nine neutral and acidic sugars present in all plant cell walls.

Functional conservation and divergence of Miscanthus lutarioriparius GT43 gene family in xylan biosynthesis

BACKGROUND

Xylan is the most abundant un-cellulosic polysaccharides of plant cell walls. Much progress in xylan biosynthesis has been gained in the model plant species Arabidopsis. Two homologous pairs Irregular Xylem 9 (IRX9)/9L and IRX14/14L from glycosyltransferase (GT) family 43 have been proved to play crucial roles in xylan backbone biosynthesis. However, xylan biosynthesis in grass such as Miscanthus remains poorly understood.

RESULTS

We characterized seven GT43 members in M. lutarioriparius, a promising bioenergy crop. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed that the expression of MlGT43 genes was ubiquitously detected in the tissues examined. In-situ hybridization demonstrated that MlGT43A-B and MlGT43F-G were specifically expressed in sclerenchyma, while MlGT43C-E were expressed in both sclerenchyma and parenchyma. All seven MlGT43 proteins were localized to Golgi apparatus. Overexpression of MlGT43A-E but not MlGT43F and MlGT43G in Arabidopsis irx9 fully or partially rescued the mutant defects, including morphological changes, collapsed xylem and increased xylan contents, whereas overexpression of MlGT43F and MlGT43G but not MlGT43A-E complemented the defects of irx14, indicating that MlGT43A-E are functional orthologues of IRX9, while MlGT43F and MlGT43G are functional orthologues of IRX14. However, overexpression of all seven MlGT43 genes could not rescue the mucilage defects of irx14 seeds. Furthermore, transient transactivation analyses of MlGT43A-E reporters demonstrated that MlGT43A and MlGT43B but not MlGT43C-E were differentially activated by MlSND1, MlMYB46 or MlVND7.

CONCLUSION

The results demonstrated that all seven MlGT43s are functionally conserved in xylan biosynthesis during secondary cell wall formation but diversify in seed coat mucilage xylan biosynthesis. The results obtained provide deeper insight into xylan biosynthesis in grass, which lay the foundation for genetic modification of grass cell wall components and structure to better suit for next-generation biofuel production.

BRITTLE SHEATH1 encoding OsCYP96B4 is involved in secondary cell wall formation in rice

KEY MESSAGE

Mutation of BSH1 leads to brittle sheath phenotype and reduction of very-long-chain fatty acids and their derivatives in wax. The cell wall plays an important role in plant mechanical strength. Several brittle culm mutants have been identified and characterized in rice. Here, we characterized an anther culture-derived rice brittle sheath mutant, named bsh1 and isolated BSH1 via map-based strategy. BSH1 encodes OsCYP96B4 protein, which was localized on ER membrane in the protoplast transient assay. BSH1 is mainly expressed in developing vascular tissues and the cells in which cell wall secondary thickening is occurring. Mutation in bsh1 causes changes in cell wall composition by affecting the expression of cell wall-related genes. Moreover, bsh1 shows reduced amounts of very-long-chain fatty acids and their derivatives in wax rather than the medium-chain fatty acids. In summary, BSH1 functions mainly in secondary cell wall formation, and probably in wax biosynthesis in an unidentified mechanism.

Improving total saccharification yield of Arabidopsis plants by vessel-specific complementation of caffeoyl shikimate esterase (cse) mutants

BACKGROUND

Caffeoyl shikimate esterase (CSE) was recently characterized as an enzyme central to the lignin biosynthetic pathway in Arabidopsis thaliana. The cse-2 loss-of-function mutant shows a typical phenotype of lignin-deficient mutants, including collapsed vessels, reduced lignin content, and lignin compositional shift, in addition to a fourfold increase in cellulose-to-glucose conversion when compared to the wild type. However, this mutant exhibits a substantial developmental arrest, which might outweigh the gains in fermentable sugar yield. To restore its normal growth and further improve its saccharification yield, we investigated a possible cause for the yield penalty of the cse-2 mutant. Furthermore, we evaluated whether CSE expression is under the same multi-leveled transcriptional regulatory network as other lignin biosynthetic genes and analyzed the transcriptional responses of the phenylpropanoid pathway upon disruption of CSE.

RESULTS

Transactivation analysis demonstrated that only second-level MYB master switches (MYB46 and MYB83) and lignin-specific activators (MYB63 and MYB85), but not top-level NAC master switches or other downstream transcription factors, effectively activate the CSE promoter in our protoplast-based system. The cse-2 mutant exhibited transcriptional repression of genes upstream of CSE, while downstream genes were mainly unaffected, indicating transcriptional feedback of CSE loss-of-function on monolignol biosynthetic genes. In addition, we found that the expression of CSE under the control of the vessel-specific VND7 promoter in the cse-2 background restored the vasculature integrity resulting in improved growth parameters, while the overall lignin content remained relatively low. Thus, by restoring the vascular integrity and biomass parameters of cse-2, we further improved glucose release per plant without pretreatment, with an increase of up to 36 % compared to the cse-2 mutant and up to 154 % compared to the wild type.

CONCLUSIONS

Our results contribute to a better understanding of how the expression of CSE is regulated by secondary wall-associated transcription factors and how the expression of lignin genes is affected upon CSE loss-of-function in Arabidopsis. Moreover, we found evidence that vasculature collapse is underlying the yield penalty found in the cse-2 mutant. Through a vessel-specific complementation approach, vasculature morphology and final stem weight were restored, leading to an even higher total glucose release per plant.

Expression of a fungal glucuronoyl esterase in Populus: effects on wood properties and saccharification efficiency

The secondary walls of angiosperms contain large amounts of glucuronoxylan that is thought to be covalently linked to lignin via ester bonds between 4-O-methyl-α-D-glucuronic acid (4-O-Me-GlcA) moieties in glucuronoxylan and alcohol groups in lignin. This linkage is proposed to be hydrolysed by glucuronoyl esterases (GCEs) secreted by wood-degrading fungi. We report effects of overexpression of a GCE from the white-rot basidiomycete Phanerochaete carnosa, PcGCE, in hybrid aspen (Populus tremula L. x tremuloides Michx.) on the wood composition and the saccharification efficiency. The recombinant enzyme, which was targeted to the plant cell wall using the signal peptide from hybrid aspen cellulase PttCel9B3, was constitutively expressed resulting in the appearance of GCE activity in protein extracts from developing wood. Diffuse reflectance FT-IR spectroscopy and pyrolysis-GC/MS analyses showed significant alternation in wood chemistry of transgenic plants including an increase in lignin content and S/G ratio, and a decrease in carbohydrate content. Sequential wood extractions confirmed a massive (+43%) increase of Klason lignin, which was accompanied by a ca. 5% decrease in cellulose, and ca. 20% decrease in wood extractives. Analysis of the monosaccharide composition using methanolysis showed a reduction of 4-O-Me-GlcA content without a change in Xyl contents in transgenic lines, suggesting that the covalent links between 4-O-Me-GlcA moieties and lignin protect these moieties from degradation. Enzymatic saccharification without pretreatment resulted in significant decreases of the yields of Gal, Glc, Xyl and Man in transgenic lines, consistent with their increased recalcitrance caused by the increased lignin content. In contrast, the enzymatic saccharification after acid pretreatment resulted in Glc yields similar to wild-type despite of their lower cellulose content. These data indicate that whereas PcGCE expression in hybrid aspen increases lignin deposition, the inhibitory effects of lignin are efficiently removed during acid pretreatment, and the extent of wood cellulose conversion during hydrolysis after acid pretreatment is improved in the transgenic lines possible due to reduced cell wall cross-links between cell wall biopolymers by PcGCE.

Reconstitution of a secondary cell wall in a secondary cell wall-deficient Arabidopsis mutant

The secondary cell wall constitutes a rigid frame of cells in plant tissues where rigidity is required. Deposition of the secondary cell wall in fiber cells contributes to the production of wood in woody plants. The secondary cell wall is assembled through co-operative activities of many enzymes, and their gene expression is precisely regulated by a pyramidal cascade of transcription factors. Deposition of a transmuted secondary cell wall in empty fiber cells by expressing selected gene(s) in this cascade has not been attempted previously. In this proof-of-concept study, we expressed chimeric activators of 24 transcription factors that are preferentially expressed in the stem, in empty fiber cells of the Arabidopsis nst1-1 nst3-1 double mutant, which lacks a secondary cell wall in fiber cells, under the control of the NST3 promoter. The chimeric activators of MYB46, SND2 and ANAC075, as well as NST3, reconstituted a secondary cell wall with different characteristics from those of the wild type in terms of its composition. The transgenic lines expressing the SND2 or ANAC075 chimeric activator showed increased glucose and xylose, and lower lignin content, whereas the transgenic line expressing the MYB46 chimeric activator showed increased mannose content. The expression profile of downstream genes in each transgenic line was also different from that of the wild type. This study proposed a new screening strategy to identify factors of secondary wall formation and also suggested the potential of the artificially reconstituted secondary cell walls as a novel raw material for production of bioethanol and other chemicals.

Downregulation of GAUT12 in Populus deltoides by RNA silencing results in reduced recalcitrance, increased growth and reduced xylan and pectin in a woody biofuel feedstock

BACKGROUND

The inherent recalcitrance of woody bioenergy feedstocks is a major challenge for their use as a source of second-generation biofuel. Secondary cell walls that constitute the majority of hardwood biomass are rich in cellulose, xylan, and lignin. The interactions among these polymers prevent facile accessibility and deconstruction by enzymes and chemicals. Plant biomass that can with minimal pretreatment be degraded into sugars is required to produce renewable biofuels in a cost-effective manner.

RESULTS

GAUT12/IRX8 is a putative glycosyltransferase proposed to be involved in secondary cell wall glucuronoxylan and/or pectin biosynthesis based on concomitant reductions of both xylan and the pectin homogalacturonan (HG) in Arabidopsis irx8 mutants. Two GAUT12 homologs exist in Populus trichocarpa, PtGAUT12.1 and PtGAUT12.2. Knockdown expression of both genes simultaneously has been shown to reduce xylan content in Populus wood. We tested the proposition that RNA interference (RNAi) downregulation of GAUT12.1 alone would lead to increased sugar release in Populus wood, that is, reduced recalcitrance, based on the hypothesis that GAUT12 synthesizes a wall structure required for deposition of xylan and that cell walls with less xylan and/or modified cell wall architecture would have reduced recalcitrance. Using an RNAi approach, we generated 11 Populus deltoides transgenic lines with 50 to 67% reduced PdGAUT12.1 transcript expression compared to wild type (WT) and vector controls. Ten of the eleven RNAi lines yielded 4 to 8% greater glucose release upon enzymatic saccharification than the controls. The PdGAUT12.1 knockdown (PdGAUT12.1-KD) lines also displayed 12 to 52% and 12 to 44% increased plant height and radial stem diameter, respectively, compared to the controls. Knockdown of PdGAUT12.1 resulted in a 25 to 47% reduction in galacturonic acid and 17 to 30% reduction in xylose without affecting total lignin content, revealing that in Populus wood as in Arabidopsis, GAUT12 affects both pectin and xylan formation. Analyses of the sugars present in sequential cell wall extracts revealed a reduction of glucuronoxylan and pectic HG and rhamnogalacturonan in extracts from PdGAUT12.1-KD lines.

CONCLUSIONS

The results show that downregulation of GAUT12.1 leads to a reduction in a population of xylan and pectin during wood formation and to reduced recalcitrance, more easily extractable cell walls, and increased growth in Populus.

MlWRKY12, a novel Miscanthus transcription factor, participates in pith secondary cell wall formation and promotes flowering

WRKY proteins play crucial roles in various plant processes. An AtWRKY12 homologous gene, named MlWRKY12, was isolated from Miscanthus lutarioriparius. The MlWRKY12 gene encodes a WRKY transcription factor belonging to the group IIc subfamily. MlWRKY12 is a nuclear protein. Gene expression pattern analysis revealed a relatively high MlWRKY12 expression level in rhizomes, stems and leaf sheaths. In situ hybridization analysis further demonstrated that MlWRKY12 was expressed in vascular bundle sheath, sclerenchyma and parenchyma tissues. The heterologous expression of MlWRKY12 in an atwrky12 background mutant successfully rescued the phenotype of pith cell walls caused by the defect of AtWRKY12. Most strikingly, the transgenic Arabidopsis plants overexpressing MlWRKY12 exhibited early flowering. The transcript abundance of flowering related genes was measured by quantitative RT-PCR analysis, suggesting that overexpression of MlWRKY12 in Arabidopsis had a significant impact on the expression level of CONSTANS (CO). Moreover, the expression levels of FLOWERING LOCUS T (FT), LFY (LEAFY), APETALA1 (AP1), CAULIFLOWER (CAL) and FRUITFULL (FUL) were upregulated in transgenic plants. These results demonstrated the conserved function of MlWRKY12 existing in secondary cell wall formation of monocotyledonous species and implied a possible impact of MlWRKY12 on flowering control.