Transcriptional activation of secondary wall biosynthesis by rice and maize NAC and MYB transcription factors

GhMYB7 promotes secondary wall cellulose deposition in cotton fibres by regulating GhCesA gene expression through three distinct cis-elements

Cotton fibre is the most important source for natural textiles. The secondary cell walls (SCWs) of mature cotton fibres contain the highest proportion of cellulose content (> 90%) in any plant. The onset and progression of SCW cellulose synthesis need to be tightly controlled to balance fibre elongation and cell wall deposition. However, regulatory mechanisms that control cellulose synthesis during cotton fibre growth remain elusive. Here, we conducted genetic and functional analyses demonstrating that the R2R3-MYB GhMYB7 controls cotton fibre cellulose synthesis. Overexpression of GhMYB7 in cotton sped up SCW cellulose biosynthesis in fibre cells, and led to shorter fibres with thicker walls. By contrast, RNA interference (RNAi) silencing of GhMYB7 delayed fibre SCW cellulose synthesis and resulted in elongated fibres with thinner walls. Furthermore, we demonstrated that GhMYB7 regulated cotton fibre SCW cellulose synthases by directly binding to three distinct cis-elements in the respective GhCesA4, GhCesA7 and GhCesA8 promoters. We found that this regulatory mechanism of cellulose synthesis was 'hi-jacked' also by other GhMYBs. Together, our findings uncover a hitherto-unknown mechanism that cotton fibre employs to regulate SCW cellulose synthesis. Our results also provide a strategy for genetic improvement of SCW thickness of cotton fibre.

Characterization of NAC family genes in Salvia miltiorrhiza and NAC2 potentially involved in the biosynthesis of tanshinones

The NAC (NAM, ATAF, and CUC) family members are specific transcription factors in plants. The large family is involved in many plant growth and developmental processes, as well as in abiotic/biotic stress responses. It has been well studied in the genomes of various plants, including Arabidopsis thaliana, tomato, and quinoa. However, identification and functional studies of NAC family members in medicinal Salvia miltiorrhiza are limited. Here, we systematically identified 84 NAC genes and named them according to their gene IDs in the recently sequenced genome. The phylogeny of NAC family protein sequences was analyzed using bioinformatics methods, which divided them into nine subfamilies. Then, their chromosomal locations, gene structures and conserved domains were analyzed comprehensively. To further investigate the regulatory functions of NACs in S. miltiorrhiza, we analyzed the response of 10 selected NAC genes to methyl jasmonate and used NAC2 for transgenic experiments. The overexpression of Sm-NAC2 decreased the tanshinone I and IIA contents by 56% and 62%, respectively. However, Sm-NAC2-RNAi promoted the accumulation of four tanshinones, tanshinone I, tanshinone IIA, cryptotanshinone, and dihydrotanshinone I, which increased 3.68-, 4.1-, 3.13- and 5.9- fold, respectively, compared with wild type. In the tanshinone biosynthetic pathways, the overexpression of Sm-NAC2 down-regulated CYP76AH1, and the silencing of Sm-NAC2 up-regulated the expression levels of HMGR1, DXS2, KSL2, and CYP76AH1. This study provides information on the evolution of Sm-NAC genes and their possible functions, and it lays a foundation for further research into the NAC family-associated regulation of tanshinone biosynthesis.

A regulatory network driving shoot lignification in rapidly growing bamboo

Woody bamboo is environmentally friendly, abundant, and an alternative to conventional timber. Degree of lignification and lignin content and deposition affect timber properties. However, the lignification regulatory network in monocots is poorly understood. To elucidate the regulatory mechanism of lignification in moso bamboo (Phyllostachys edulis), we conducted integrated analyses using transcriptome, small RNA, and degradome sequencing followed by experimental verification. The lignification degree and lignin content increased with increased bamboo shoot height, whereas phenylalanine ammonia-lyase and Laccase activities first increased and then decreased with shoot growth. Moreover, we identified 11,504 differentially expressed genes (DEGs) in different portions of the 13th internodes of different height shoots; most DEGs associated with cell wall and lignin biosynthesis were upregulated, whereas some DEGs related to cell growth were downregulated. We identified a total of 1,502 miRNAs, of which 687 were differentially expressed. Additionally, in silico and degradome analyses indicated that 5,756 genes were targeted by 691 miRNAs. We constructed a regulatory network of lignification, including 11 miRNAs, 22 transcription factors, and 36 enzyme genes, in moso bamboo. Furthermore, PeLAC20 overexpression increased lignin content in transgenic Arabidopsis (Arabidopsis thaliana) plants. Finally, we proposed a reliable miRNA-mediated "MYB-PeLAC20" module for lignin monomer polymerization. Our findings provide definite insights into the genetic regulation of bamboo lignification. In addition to providing a platform for understanding related mechanisms in other monocots, these insights could be used to develop strategies to improve bamboo timber properties.

Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice

Transcription factors (TFs) form the major class of regulatory genes and play key roles in multiple plant stress responses. In most eukaryotic plants, transcription factor (TF) families (WRKY, MADS-box and MYB) activate unique cellular-level abiotic and biotic stress-responsive strategies, which are considered as key determinants for defense and developmental processes. Arabidopsis and rice are two important representative model systems for dicot and monocot plants, respectively. A comprehensive comparative study on 101 OsWRKY, 34 OsMADS box and 122 OsMYB genes (rice genome) and, 71 AtWRKY, 66 AtMADS box and 144 AtMYB genes (Arabidopsis genome) showed various relationships among TFs across species. The phylogenetic analysis clustered WRKY, MADS-box and MYB TF family members into 10, 7 and 14 clades, respectively. All clades in WRKY and MYB TF families and almost half of the total number of clades in the MADS-box TF family are shared between both species. Chromosomal and gene structure analysis showed that the Arabidopsis-rice orthologous TF gene pairs were unevenly localized within their chromosomes whilst the distribution of exon–intron gene structure and motif conservation indicated plausible functional similarity in both species. The abiotic and biotic stress-responsive cis-regulatory element type and distribution patterns in the promoter regions of Arabidopsis and rice WRKY, MADS-box and MYB orthologous gene pairs provide better knowledge on their role as conserved regulators in both species. Co-expression network analysis showed the correlation between WRKY, MADs-box and MYB genes in each independent rice and Arabidopsis network indicating their role in stress responsiveness and developmental processes.

Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms

Background

Miscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production. However, knowledge of the genetic resources of this species is relatively limited, which considerably hampers further work on its biology and genetic improvement.

Results

In this study, through analyzing the transcriptome of mixed samples of leaves and stems using the latest PacBio Iso-Seq sequencing technology combined with Illumina HiSeq, we report the first full-length transcriptome dataset of M. sinensis with a total of 58.21 Gb clean data. An average of 15.75 Gb clean reads of each sample were obtained from the PacBio Iso-Seq system, which doubled the data size (6.68 Gb) obtained from the Illumina HiSeq platform. The integrated analyses of PacBio- and Illumina-based transcriptomic data uncovered 408,801 non-redundant transcripts with an average length of 1,685 bp. Of those, 189,406 transcripts were commonly identified by both methods, 169,149 transcripts with an average length of 619 bp were uniquely identified by Illumina HiSeq, and 51,246 transcripts with an average length of 2,535 bp were uniquely identified by PacBio Iso-Seq. Approximately 96 % of the final combined transcripts were mapped back to the Miscanthus genome, reflecting the high quality and coverage of our sequencing results. When comparing our data with genomes of four species of Andropogoneae, M. sinensis showed the closest relationship with sugarcane with up to 93 % mapping ratios, followed by sorghum with up to 80 % mapping ratios, indicating a high conservation of orthologs in these three genomes. Furthermore, 306,228 transcripts were successfully annotated against public databases including cell wall related genes and transcript factor families, thus providing many new insights into gene functions. The PacBio Iso-Seq data also helped identify 3,898 alternative splicing events and 2,963 annotated AS isoforms within 10 function categories.

Conclusions

Taken together, the present study provides a rich data set of full-length transcripts that greatly enriches our understanding of M. sinensis transcriptomic resources, thus facilitating further genetic improvement and molecular studies of the Miscanthus species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07971-x.

Genome-wide analysis of R2R3-MYB transcription factors family in the autopolyploid Saccharum spontaneum: an exploration of dominance expression and stress response

BACKGROUND

Sugarcane (Saccharum) is the most critical sugar crop worldwide. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes.

RESULTS

A total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genomic sequence and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which RT-qPCR validated MYB43, MYB53, MYB65, MYB78, and MYB99. Allelic expression dominance analysis implied the differential expression of alleles might be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C4 photosynthetic regulators by C4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively.

CONCLUSIONS

This is the first report on genome-wide analysis of the MYB gene family in sugarcane. SsMYBs probably played an essential role in stem development and the adaptation of various stress conditions. The results will provide detailed insights and rich resources to understand the functional diversity of MYB transcription factors and facilitate the breeding of essential traits in sugarcane.

Phylogenetic Occurrence of the Phenylpropanoid Pathway and Lignin Biosynthesis in Plants

The phenylpropanoid pathway serves as a rich source of metabolites in plants and provides precursors for lignin biosynthesis. Lignin first appeared in tracheophytes and has been hypothesized to have played pivotal roles in land plant colonization. In this review, we summarize recent progress in defining the lignin biosynthetic pathway in lycophytes, monilophytes, gymnosperms, and angiosperms. In particular, we review the key structural genes involved in p-hydroxyphenyl-, guaiacyl-, and syringyl-lignin biosynthesis across plant taxa and consider and integrate new insights on major transcription factors, such as NACs and MYBs. We also review insight regarding a new transcriptional regulator, 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, canonically identified as a key enzyme in the shikimate pathway. We use several case studies, including EPSP synthase, to illustrate the evolution processes of gene duplication and neo-functionalization in lignin biosynthesis. This review provides new insights into the genetic engineering of the lignin biosynthetic pathway to overcome biomass recalcitrance in bioenergy crops.

Molecular Genetic Characteristics of Different Scenarios of Xylogenesis on the Example of Two Forms of Silver Birch Differing in the Ratio of Structural Elements in the Xylem

Silver birch (Betula pendula Roth) is an economically important species in Northern Europe. The current research focused on the molecular background of different xylogenesis scenarios in the birch trunks. The study objects were two forms of silver birch, silver birch trees, and Karelian birch trees; the latter form is characterized by the formation of two types of wood, non-figured (straight-grained) and figured, respectively, while it is currently not clear which factors cause this difference. We identified VND/NST/SND genes that regulate secondary cell wall biosynthesis in the birch genome and revealed differences in their expression in association with the formation of xylem with different ratios of structural elements. High expression levels of BpVND7 accompanied differentiation of the type of xylem which is characteristic of the species. At the same time, the appearance of figured wood was accompanied by the low expression levels of the VND genes and increased levels of expression of NST and SND genes. We identified BpARF5 as a crucial regulator of auxin-dependent vascular patterning and its direct target—BpHB8. A decrease in the BpARF5 level expression in differentiating xylem was a specific characteristic of both Karelian birch with figured and non-figured wood. Decreased BpARF5 level expression in non-figured trees accompanied by decreased BpHB8 and VND/NST/SND expression levels compared to figured Karelian birch trees. According to the results obtained, we suggested silver birch forms differing in wood anatomy as valuable objects in studying the regulation of xylogenesis.

Xylem vessel-specific SND5 and its homologs regulate secondary wall biosynthesis through activating secondary wall NAC binding elements

Secondary cell wall biosynthesis has been shown to be regulated by a suite of transcription factors. Here, we identified a new xylem vessel-specific NAC domain transcription factor, secondary wall-associated NAC domain protein5 (SND5), in Arabidopsis thaliana and studied its role in regulating secondary wall biosynthesis. We showed that the expression of SND5 and its close homolog, SND4/ANAC075, was specifically associated with secondary wall-containing cells and dominant repression of their functions severely reduced secondary wall thickening in these cells. Overexpression of SND4/5 as well as their homologs SND2/3 fused with the activation domain of the viral protein VP16 led to ectopic secondary wall deposition in cells that are normally parenchymatous. SND2/3/4/5 regulated the expression of the same downstream target genes as do the secondary wall NAC master switches (SWNs) by binding to and activating the secondary wall NAC binding elements (SNBEs). Furthermore, we demonstrated that the poplar (Populus trichocarpa) orthologs of SND2/3/4/5 also activated SNBEs and regulated secondary wall biosynthesis during wood formation. Together, these findings indicate that SND2/3/4/5 and their poplar orthologs regulate the expression of secondary wall-associated genes through activating SNBEs and they are positioned at an upper level in the SWN-mediated transcriptional network.

The OsmiRNA166b-OsHox32 pair regulates mechanical strength of rice plants by modulating cell wall biosynthesis

The plant cell wall provides mechanical strength to support plant growth and development and to determine plant architecture. Cellulose and mixed-linkage glucan (MLG) present in primary cell wall, whereas cellulose, lignin and hemicellulose exist in secondary cell wall. Biosynthesis of the cell wall biopolymers needs the coordinated transcriptional regulation of all the biosynthetic genes. The module of OsmiR166b-OsHox32 regulates expression levels of the genes related to biosynthesis of MLG, cellulose and lignin. Transgenic plants knocking down miR166b (STTM166b) by short tandem target mimic (STTM) technology or overexpressing OsHox32 (OEHox32) showed drooping leaves and brittle culms. Due to accumulation of less lignin and cellulose, the cell wall thickness of STTM166b and OEHox32 plants was reduced when compared to that of wild-type plants. Overexpression of miR166b (OE166b) in rice plants or knocking down of OsHox32 by RNA interference (RNAiHox32) led to increased thickness of cell walls and enhanced mechanical strength of culms. Molecular analyses showed that OsmiR166b-OsHox32 pair regulates cell wall-related gene expression. OsHox32 binds to the promoters of OsCAD2 and OsCESA7 to suppress the expression levels of these two genes. The suppression of OsCAD2 is synergistic when OsHox32 is co-expressed with OSH15 (Oryza sativa homeobox 15). OsHox32 interacts with OSH15, and the START domain of OsHox32, harbouring the miR166b cleavage site, is required for the interaction of these two proteins. Our results demonstrate that OsmiR166b-OsHox32 pair plays important roles not only in plant growth and development but also in plant architecture by regulating the cell wall-related gene expression.

Abscisic acid regulates secondary cell-wall formation and lignin deposition in Arabidopsis thaliana through phosphorylation of NST1

Lignin deposition in plants is affected by environmental stress, and stress-signaling involves increases in the levels of the plant hormone abscisic acid (ABA). Here we show, using a combination of biochemical and genetic approaches, how ABA can regulate lignin biosynthesis. This involves phosphorylation of the master lignin transcription factor NST1 by a family of protein kinases (SnRK2s) that are themselves activated by phosphorylation as a result of ABA recognition by its receptor. This work provides a basis for designing trees and other biomass plants that are better adapted to stress and climate change.

Plant secondary cell-wall (SCW) deposition and lignification are affected by both seasonal factors and abiotic stress, and these responses may involve the hormone abscisic acid (ABA). However, the mechanisms involved are not clear. Here we show that mutations that limit ABA synthesis or signaling reduce the extent of SCW thickness and lignification in Arabidopsis thaliana through the core ABA-signaling pathway involving SnRK2 kinases. SnRK2.2. 3 and 6 physically interact with the SCW regulator NAC SECONDARY WALL THICKENING PROMOTING FACTOR 1 (NST1), a NAC family transcription factor that orchestrates the transcriptional activation of a suite of downstream SCW biosynthesis genes, some of which are involved in the biosynthesis of cellulose and lignin. This interaction leads to phosphorylation of NST1 at Ser316, a residue that is highly conserved among NST1 proteins from dicots, but not monocots, and is required for transcriptional activation of downstream SCW-related gene promoters. Loss of function of NST1 in the snd1 mutant background results in lack of SCWs in the interfascicular fiber region of the stem, and the Ser316Ala mutant of NST1 fails to complement this phenotype and ABA-induced lignin pathway gene expression. The discovery of NST1 as a key substrate for phosphorylation by SnRK2 suggests that the ABA-mediated core-signaling cascade provided land plants with a hormone-modulated, competitive desiccation-tolerance strategy allowing them to differentiate water-conducting and supporting tissues built of cells with thicker cell walls.

LcERF2 modulates cell wall metabolism by directly targeting a UDP-glucose-4-epimerase gene to regulate pedicel development and fruit abscission of litchi

Elucidating the biochemical and molecular basis of premature abscission in fruit crops should help develop strategies to enhance fruit set and yield. Here, we report that LcERF2 contributes to differential abscission rates and responses to ethylene in Litchi chinensis (litchi). Reduced LcERF2 expression in litchi was observed to reduce fruit abscission, concurrent with enhanced pedicel growth and increased levels of hexoses, particularly galactose, as well as pectin abundance in the cell wall. Ecoptic expression of LcERF2 in Arabidopsis thaliana caused enhanced petal abscission, together with retarded plant growth and reduced pedicel galactose and pectin contents. Transcriptome analysis indicated that LcERF2 modulates the expression of genes involved in cell wall modification. Yeast one-hybrid, dual-luciferase reporter and electrophoretic mobility shift assays all demonstrated that a UDP-glucose-4-epimerase gene (LcUGE) was the direct downstream target of LcERF2. This result was further supported by a significant reduction in the expression of the A. thaliana homolog AtUGE2-4 in response to LcERF2 overexpression. Significantly reduced pedicel diameter and enhanced litchi fruit abscission were observed in response to LcUGE silencing. We conclude that LcERF2 mediates fruit abscission by orchestrating cell wall metabolism, and thus pedicel growth, in part by repressing the expression of LcUGE.

A conservative pathway for coordination of cell wall biosynthesis and cell cycle progression in plants

The mechanism that coordinates cell growth and cell cycle progression remains poorly understood; in particular, whether the cell cycle and cell wall biosynthesis are coordinated remains unclear. Recently, cell wall biosynthesis and cell cycle progression were reported to respond to wounding. Nonetheless, no genes are reported to synchronize the biosynthesis of the cell wall and the cell cycle. Here, we report that wounding induces the expression of genes associated with cell wall biosynthesis and the cell cycle, and that two genes, AtMYB46 in Arabidopsis thaliana and RrMYB18 in Rosa rugosa, are induced by wounding. We found that AtMYB46 and RrMYB18 promote the biosynthesis of the cell wall by upregulating the expression of cell wall-associated genes, and that both of them also upregulate the expression of a battery of genes associated with cell cycle progression. Ultimately, this response leads to the development of curled leaves of reduced size. We also found that the coordination of cell wall biosynthesis and cell cycle progression by AtMYB46 and RrMYB18 is evolutionarily conservative in multiple species. In accordance with wounding promoting cell regeneration by regulating the cell cycle, these findings also provide novel insight into the coordination between cell growth and cell cycle progression and a method for producing miniature plants.

Transcriptomic Analysis of Seasonal Gene Expression and Regulation during Xylem Development in “Shanxin” Hybrid Poplar (Populus davidiana × Populus bolleana)

Xylem development is a key process for wood formation in woody plants. To study the molecular regulatory mechanisms related to xylem development in hybrid poplar P. davidiana × P. bolleana, transcriptome analyses were conducted on developing xylem at six different growth stages within a single growing season. Xylem development and differentially expressed genes in the six time points were selected for a regulatory analysis. Xylem development was observed in stem sections at different growth stages, which showed that xylem development extended from the middle of April to early August and included cell expansion and secondary cell wall biosynthesis. An RNA-seq analysis of six samples with three replicates was performed. After transcriptome assembly and annotation, the differentially expressed genes (DEGs) were identified, and a Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and expression analysis of the DEGs were performed on each sample. On average, we obtained >20 million clean reads per sample, which were assembled into 84,733 nonredundant transcripts, of which there were 17,603 unigenes with lengths >1 kb. There were 14,890 genes that were differentially expressed among the six stages. The upregulated DEGs were enriched in GO terms related to cell wall biosynthesis between S1 vs. S2 or S3 vs. S4 and, in GO terms, related to phytohormones in the S1 vs. S2 or S4 vs. S5 comparisons. The downregulated DEGs were enriched in GO terms related to cell wall biosynthesis between S4 vs. S5 or S5 vs. S6 and, in GO terms, related to hormones between S1 vs. S2 or S2 vs. S3. The KEGG pathways in the DEGs related to “phenylpropanoid biosynthesis”, “plant hormone signal transduction” and “starch and sucrose metabolism” were significantly enriched among the different stages. The DEGs related to cell expansion, polysaccharide metabolism and synthesis, lignin synthesis, transcription factors and hormones were identified. The identification of genes involved in the regulation of xylem development will increase our understanding of the molecular regulation of wood formation in trees and, also, offers potential targets for genetic manipulation to improve the properties of wood.

A natural antisense transcript acts as a negative regulator for the maize drought stress response gene ZmNAC48

Although plant-specific NAC transcription factors play crucial roles in response to abiotic stress, few reports describe the regulation of NAC genes in maize (Zea mays) by the cis-natural antisense transcripts (cis-NATs). In this study, 521 NAC genes from Gramineae were classified, of which 51 NAC genes contained cis-NATs. ZmNAC48 and cis-NATZmNAC48 co-localized to the same cell nucleus, and both transcripts responded to drought stress. Arabidopsis plants overexpressing ZmNAC48 had improved drought tolerance, lower rate of water loss, enhanced stomatal closure, and higher rates of survival. Transient expression in both maize protoplasts and tobacco leaves indicated that cis-NATZmNAC48 reduced ZmNAC48 expression. Western blotting and ribosome profiling analyses confirmed that cis-NATZmNAC48 lacked protein coding potential. Furthermore, the cis-NAT-derived small-interfering RNAs (nat-siRNAs) generated from the overlapping regions of ZmNAC48 and cis-NATZmNAC48 were detected in maize and transgenic Arabidopsis. Cis-NATZmNAC48 overexpressing maize showed higher water loss rate, increased stomatal opening, and had more dead leaves. Expression of ZmNAC48 and nat-siRNA was decreased in these plants. Taken together, our study indicates that both ZmNAC48 and cis-NATZmNAC48 are involved in plant drought stress responses, and that the double-stranded RNA-dependent mechanism is involved in the interaction between cis-NATZmNAC48 and ZmNAC48. Additionally, cis-NATZmNAC48 may negatively regulate ZmNAC48 to affect stomatal closure of maize.

XND1 Regulates Secondary Wall Deposition in Xylem Vessels through the Inhibition of VND Functions

Secondary wall deposition in xylem vessels is activated by Vascular-Related NAC Domain proteins (VNDs) that belong to a group of secondary wall NAC (SWN) transcription factors. By contrast, Xylem NAC Domain1 (XND1) negatively regulates secondary wall deposition in xylem vessels when overexpressed. The mechanism by which XND1 exerts its functions remains elusive. We employed the promoter of the fiber-specific Secondary Wall-Associated NAC Domain1 (SND1) gene to ectopically express XND1 in fiber cells to investigate its mechanism of action on secondary wall deposition. Ectopic expression of XND1 in fiber cells severely diminished their secondary wall deposition and drastically reduced the expression of SWN-regulated downstream transcription factors and secondary wall biosynthetic genes but not that of the SWN genes themselves. Transactivation analyses revealed that XND1 specifically inhibited SWN-activated expression of these downstream genes but not their MYB46-activated expression. Both the NAC domain and the C-terminus of XND1 were required for its inhibitory function and its NAC domain interacted with the DNA-binding domains of SWNs. XND1 was shown to be localized in the cytoplasm and the nucleus and its co-expression with VND6 resulted in the cytoplasmic sequestration of VND6. Furthermore, the C-terminus of XND1 was indispensable for the XND1-mediated cytoplasmic retention of VND6 and its fusion to VND6 was able to direct VND6 to the cytoplasm and render it unable to activate the gene expression. Since the XND1 gene is specifically expressed in xylem cells, these results indicate that XND1 acts through inhibiting VND functions to negatively regulate secondary wall deposition in xylem vessels.

Differentiation of Tracheary Elements in Sugarcane Suspension Cells Involves Changes in Secondary Wall Deposition and Extensive Transcriptional Reprogramming

Plant lignocellulosic biomass, mostly composed of polysaccharide-rich secondary cell walls (SCWs), provides fermentable sugars that may be used to produce biofuels and biomaterials. However, the complex chemical composition and physical structure of SCWs hinder efficient processing of plant biomass. Understanding the molecular mechanisms underlying SCW deposition is, thus, essential to optimize bioenergy feedstocks. Here, we establish a xylogenic culture as a model system to study SCW deposition in sugarcane; the first of its kind in a C4 grass species. We used auxin and brassinolide to differentiate sugarcane suspension cells into tracheary elements, which showed metaxylem-like reticulate or pitted SCW patterning. The differentiation led to increased lignin levels, mainly caused by S-lignin units, and a rise in p-coumarate, leading to increased p-coumarate:ferulate ratios. RNAseq analysis revealed massive transcriptional reprogramming during differentiation, with upregulation of genes associated with cell wall biogenesis and phenylpropanoid metabolism and downregulation of genes related to cell division and primary metabolism. To better understand the differentiation process, we constructed regulatory networks of transcription factors and SCW-related genes based on co-expression analyses. Accordingly, we found multiple regulatory modules that may underpin SCW deposition in sugarcane. Our results provide important insights and resources to identify biotechnological strategies for sugarcane biomass optimization.

Diverse Roles of MAX1 Homologues in Rice

Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious.

Major latex protein-like encoding genes contribute to Rhizoctonia solani defense responses in sugar beet

Sugar beets are attacked by several pathogens that cause root damages. Rhizoctonia (Greek for “root killer”) is one of them. Rhizoctonia root rot has become an increasing problem for sugar beet production and to decrease yield losses agronomical measures are adopted. Here, two partially resistant and two susceptible sugar beet genotypes were used for transcriptome analysis to discover new defense genes to this fungal disease, information to be implemented in molecular resistance breeding. Among 217 transcripts with increased expression at 2 days post-infection (dpi), three resistance-like genes were found. These genes were not significantly elevated at 5 dpi, a time point when increased expression of three Bet v I/Major latex protein (MLP) homologous genes BvMLP1, BvMLP2 and BvML3 was observed in the partially resistant genotypes. Quantitative RT-PCR analysis on diseased sugar beet seedlings validated the activity of BvMLP1 and BvMLP3 observed in the transcriptome during challenge by R. solani. The three BvMLP genes were cloned and overexpressed in Arabidopsis thaliana to further dissect their individual contribution. Transgenic plants were also compared to T-DNA mutants of orthologous MLP genes. Plants overexpressing BvMLP1 and BvMLP3 showed significantly less infection whereas additive effects were seen on Atmlp1/Atmlp3 double mutants. The data suggest that BvMLP1 and BvMLP3 may contribute to the reduction of the Rhizoctonia root rot disease in sugar beet. Impact on the defense reaction from other differential expressed genes observed in the study is discussed.

Overexpression of PtrMYB121 Positively Regulates the Formation of Secondary Cell Wall in Arabidopsis thaliana

MYB transcription factors have a wide range of functions in plant growth, hormone signaling, salt, and drought tolerances. In this study, two homologous transcription factors, PtrMYB55 and PtrMYB121, were isolated and their functions were elucidated. Tissue expression analysis revealed that PtrMYB55 and PtrMYB121 had a similar expression pattern, which had the highest expression in stems. Their expression continuously increased with the growth of poplar, and the expression of PtrMYB121 was significantly upregulated in the process. The full length of PtrMYB121 was 1395 bp, and encoded protein contained 464 amino acids including conserved R2 and R3 MYB domains. We overexpressed PtrMYB121 in Arabidopsis thaliana, and the transgenic lines had the wider xylem as compared with wild-type Arabidopsis. The contents of cellulose and lignin were obviously higher than those in wild-type materials, but there was no significant change in hemicellulose. Quantitative real-time PCR demonstrated that the key enzyme genes regulating the synthesis of lignin and cellulose were significantly upregulated in the transgenic lines. Furthermore, the effector-reporter experiment confirmed that PtrMYB121 bound directly to the promoters of genes relating to the synthesis of lignin and cellulose. These results suggest that PtrMYB121 may positively regulate the formation of secondary cell wall by promoting the synthesis of lignin and cellulose.

Grass secondary cell walls, Brachypodium distachyon as a model for discovery

A key aspect of plant growth is the synthesis and deposition of cell walls. In specific tissues and cell types including xylem and fibre, a thick secondary wall comprised of cellulose, hemicellulose and lignin is deposited. Secondary cell walls provide a physical barrier that protects plants from pathogens, promotes tolerance to abiotic stresses and fortifies cells to withstand the forces associated with water transport and the physical weight of plant structures. Grasses have numerous cell wall features that are distinct from eudicots and other plants. Study of the model species Brachypodium distachyon as well as other grasses has revealed numerous features of the grass cell wall. These include the characterisation of xylosyl and arabinosyltransferases, a mixed-linkage glucan synthase and hydroxycinnamate acyltransferases. Perhaps the most fertile area for discovery has been the formation of lignins, including the identification of novel substrates and enzyme activities towards the synthesis of monolignols. Other enzymes function as polymerising agents or transferases that modify lignins and facilitate interactions with polysaccharides. The regulatory aspects of cell wall biosynthesis are largely overlapping with those of eudicots, but salient differences among species have been resolved that begin to identify the determinants that define grass cell walls.

Transcriptional differentiation of UV-B protectant genes in maize landraces spanning an elevational gradient in Chiapas, Mexico

Globally, farmers cultivate and maintain crop landraces (i.e., traditional varieties). Landraces contain unique diversity shaped in part by natural and human-mediated selection and are an indispensable resource for farmers. Since environmental conditions change with elevation, crop landraces grown along elevational gradients have provided ideal locations to explore patterns of local adaptation. To further probe traits underlying this differentiation, transcriptome signatures can help provide a foundation for understanding the ways in which functional genetic diversity may be shaped by environment. In this study, we returned to an elevational gradient in Chiapas, Mexico, to assess transcriptional differentiation of genes underlying UV-B protection in locally adapted maize landraces from multiple elevations. We collected and planted landraces from three elevational zones (lowland, approximately 600 m; midland, approximately 1,550 m; highland approximately 2,100 m) in a common garden at 1,531 m. Using RNA-seq data derived from leaf tissue, we performed differential expression analysis between maize from these distinct elevations. Highland and lowland landraces displayed differential expression in phenylpropanoid and flavonoid biosynthesis genes involved in the production of UV-B protectants and did so at a rate greater than expected based on observed background transcriptional differentiation across the genome. These findings provide evidence for the differentiation of suites of genes involved in complex ecologically relevant pathways. Thus, while neutral evolutionary processes may have played a role in the observed patterns of differentiation, UV-B may have also acted as a selective pressure to differentiate maize landraces in the region. Studies of the distribution of functional crop genetic diversity across variable landscapes can aid us in understanding the response of diversity to abiotic/biotic change and, ultimately, may facilitate its conservation and utilization.

Systematic Analysis of Differential H3K27me3 and H3K4me3 Deposition in Callus and Seedling Reveals the Epigenetic Regulatory Mechanisms Involved in Callus Formation in Rice

Plant growth and development occurs through meristematic cell activity, and cell fate transition is accompanied by epigenetic modifications. Callus with cell pluripotency exhibits the ability to undergo continued cell division, and is ideal for studying plant meristematic differentiation. By comparing the differential epigenetic modifications between callus and seedling, the changes in chromatin state and effects of various epigenetic modifications on the growth and development of plants can be revealed, and the key genes related to plant growth and development can be identified, providing novel insights into the regulation of plant growth and development. In this study, we performed ChIP assays using various antibodies in rice seed-induced callus and seedlings grown for about 15 days to examine the differential deposition of H3K27me3 and H3K4me3. Furthermore, data for DNase I-hypersensitive sites in the corresponding tissues were downloaded from National Center for Biotechnology Information. We analyzed 4,562 callus H3K27me3-decreased genes especially those encoding transcription factors in callus, and found that most of the transcription factors, including AP2-ERREBP, NAC, and HB gene families, were related to growth and development. Genes related to meristemization, such as OsWOX9, OsWOX11, OsPLT4, OsPLT5, and OsSHR, were also included. In contrast, H3K4me3 positively regulated callus characteristics through its higher deposition in the callus than in the seedling. We further performed transcriptomic analysis on 45 sets of Affymetrix GeneChip arrays and identified 1,565 genes preferentially expressed in the callus. Callus development and root development in rice were found to share a common regulatory mechanism. We found that these genes, which are associated with meristems, require the removal of H3K27me3 and the deposition of H3K4me3, and DNase I-hypersensitive sites to maintain a relatively active state in the callus than in the seedling. The present study provides novel data about the epigenetic mechanisms involved in callus formation and additional resources for the study of cell division and differentiation in plants.

The transcription factor GATA10 regulates fertility conversion of a two-line hybrid tms5 mutant rice via the modulation of UbL40 expression

The thermosensitive genic male sterile 5 (tms5) mutation causes thermosensitive genic male sterility in rice (Oryza sativa) through loss of RNase Z^S1 function, which influences ubiquitin fusion ribosomal protein L40 (Ub_L40 ) messenger RNA levels during male development. Here, we used ATAC-seq, combined with analysis of H3K9ac and H3K4me2, to identify changes in accessible chromatin during fertility conversion of the two-line hybrid rice Wuxiang S (WXS) derived from a mutant tms5 allele. Furthermore, RNA-seq and bioinformatic analyses identified specific transcription factors (TFs) in differentially accessible chromatin regions. Among these TFs, only GATA10 targeted Ub_L40 . Osgata10 knockout mutations, which resulted in low expression of Ub_L40 and a tendency toward male fertility, confirmed that GATA10 regulated fertility conversion via the modulation of Ub_L40 . Meanwhile, GATA10 acted as a mediator for interactions with ERF65, which revealed that transcriptional regulation is a complex process involving multiple complexes of TFs, namely TF modules. It appears that the ERF141/MADS7/MADS50/MYB modules affect metabolic processes that control anther and pollen development, especially cell wall formation. Our analysis revealed that these modules directly or indirectly affect metabolic pathway-related genes to coordinate plant growth with proper anther development, and furthermore, that GATA10 regulates fertility conversion via the modulation of Ub_L40 expression.

Double knockout of OsWRKY36 and OsWRKY102 boosts lignification with altering culm morphology of rice

Breeding to enrich lignin, a major component of lignocelluloses, in plants contributes to enhanced applications of lignocellulosic biomass into solid biofuels and valuable aromatic chemicals. To collect information on enhancing lignin deposition in grass species, important lignocellulose feedstocks, we generated rice (Oryza sativa) transgenic lines deficient in OsWRKY36 and OsWRKY102, which encode putative transcriptional repressors for secondary cell wall formation. We used CRISPR/Cas9-mediated targeted mutagenesis and closely characterized their altered cell walls using chemical and nuclear magnetic resonance (NMR) methods. Both OsWRKY36 and OsWRKY102 mutations significantly increased lignin content by up to 28 % and 32 %, respectively. Additionally, OsWRKY36/OsWRKY102-double-mutant lines displayed lignin enrichment of cell walls (by up to 41 %) with substantially altered culm morphology over the single-mutant lines as well as the wild-type controls. Our chemical and NMR analyses showed that relative abundances of guaiacyl and p-coumarate units were slightly higher and lower, respectively, in the WRKY mutant lignins compared with those in the wild-type lignins. Our results provide evidence that both OsWRKY36 and OsWRKY102 are associated with repression of rice lignification.

Transcriptional analysis of arogenate dehydratase genes identifies a link between phenylalanine biosynthesis and lignin biosynthesis

Biogenesis of the secondary cell wall in trees involves the massive biosynthesis of the phenylalanine-derived polymer lignin. Arogenate dehydratase (ADT) catalyzes the last, and rate-limiting, step of the main pathway for phenylalanine biosynthesis. In this study, we found that transcript levels for several members of the large ADT gene family, including ADT-A and ADT-D, were enhanced in compression wood of maritime pine, a xylem tissue enriched in lignin. Transcriptomic analysis of maritime pine silenced for PpMYB8 revealed that this gene plays a critical role in coordinating the deposition of lignin with the biosynthesis of phenylalanine. Specifically, it was found that ADT-A and ADT-D were strongly down-regulated in PpMYB8-silenced plants and that they were transcriptionally regulated through direct interaction of this transcription factor with regulatory elements present in their promoters. Another transcription factor, PpHY5, exhibited an expression profile opposite to that of PpMYB8 and also interacted with specific regulatory elements of ADT-A and ADT-D genes, suggesting that it is involved in transcriptional regulation of phenylalanine biosynthesis. Taken together, our results reveal that PpMYB8 and PpHY5 are involved in the control of phenylalanine formation and its metabolic channeling for lignin biosynthesis and deposition during wood formation in maritime pine.

A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]

BACKGROUND

Tea plant (Camellia sinensis) is one of the most popular non-alcoholic beverages worldwide. In tea, lateral roots (LRs) are the main organ responsible for the absorption of moisture and mineral nutrients from the soil. Lateral roots formation and development are regulated by the nitrogen and auxin signaling pathways. In order to understand the role of auxin and nitrogen signaling in LRs formation and development, transcriptome analysis was employed to investigate the differentially expressed genes involved in lateral roots of tea plants treated with indole-3-butyric acid (IBA), N-1-naphthylphthalamic acid (NPA), low and high concentrations of nitrogen.

RESULTS

A total of 296 common differentially expressed genes were identified and annotated to four signaling pathways, including nitrogen metabolism, plant hormone signal transduction, glutathione metabolism and transcription factors. RNA-sequencing results revealed that majority of differentially expressed genes play important roles in nitrogen metabolism and hormonal signal transduction. Low nitrogen condition induced the biosynthesis of auxin and accumulation of transcripts, thereby, regulating lateral roots formation. Furthermore, metabolism of cytokinin and ethylene biosynthesis were also involved in lateral roots development. Transcription factors like MYB genes also contributed to lateral roots formation of tea plants through secondary cell wall biosynthesis. Reversed phase ultra performance liquid chromatography (RP-UPLC) results showed that the auxin concentration increased with the decreased nitrogen level in lateral roots. Thus, tea plant lateral roots formation could be induced by low nitrogen concentration via auxin biosynthesis and accumulation.

CONCLUSION

This study provided insights into the mechanisms associated with nitrogen and auxin signaling pathways in LRs formation and provides information on the efficient utilization of nitrogen in tea plant at the genetic level.

Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses

Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels.

The TuMYB46L-TuACO3 module regulates ethylene biosynthesis in einkorn wheat defense to powdery mildew

Powdery mildew disease, elicited by the obligate fungal pathogen Blumeria graminis f.sp. tritici (Bgt), causes widespread yield losses in global wheat crop. However, the molecular mechanisms governing wheat defense to Bgt are still not well understood. Here we found that TuACO3, encoding the 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase functioning in ethylene (ET) biosynthesis, was induced by Bgt infection of the einkorn wheat Triticum urartu, which was accompanied by increased ET content. Silencing TuACO3 decreased ET production and compromised wheat defense to Bgt, whereas both processes were enhanced in the transgenic wheat overexpressing TuACO3. TuMYB46L, phylogenetically related to Arabidopsis MYB transcription factor AtMYB46, was found to bind to the TuACO3 promoter region in yeast-one-hybrid and EMSA experiments. TuMYB46L expression decreased rapidly following Bgt infection. Silencing TuMYB46L promoted ET content and Bgt defense, but the reverse was observed when TuMYB46L was overexpressed. Hence, decreased expression of TuMYB46L permits elevated function of TuACO3 in ET biosynthesis in Bgt-infected wheat. The TuMYB46L-TuACO3 module regulates ET biosynthesis to promote einkorn wheat defense against Bgt. Furthermore, we found four chitinase genes acting downstream of the TuMYB46L-TuACO3 module. Collectively, our data shed a new light on the molecular mechanisms underlying wheat defense to Bgt.

A NAC-type transcription factor confers aluminium resistance by regulating cell wall-associated receptor kinase 1 and cell wall pectin

Transcriptional regulation is important for plants to respond to toxic effects of aluminium (Al). However, our current knowledge to these events is confined to a few transcription factors. Here, we functionally characterized a rice bean (Vigna umbellata) NAC-type transcription factor, VuNAR1, in terms of Al stress response. We demonstrated that rice bean VuNAR1 is a nuclear-localized transcriptional activator, whose expression was specifically upregulated by Al in roots but not in shoot. VuNAR1 overexpressing Arabidopsis plants exhibit improved Al resistance via Al exclusion. However, VuNAR1-mediated Al exclusion is independent of the function of known Al-resistant genes. Comparative transcriptomic analysis revealed that VuNAR1 specifically regulates the expression of genes associated with protein phosphorylation and cell wall modification in Arabidopsis. Transient expression assay demonstrated the direct transcriptional activation of cell wall-associated receptor kinase 1 (WAK1) by VuNAR1. Moreover, yeast one-hybrid assays and MEME motif searches identified a new VuNAR1-specific binding motif in the promoter of WAK1. Compared with wild-type Arabidopsis plants, VuNAR1 overexpressing plants have higher WAK1 expression and less pectin content. Taken together, our results suggest that VuNAR1 regulates Al resistance by regulating cell wall pectin metabolism via directly binding to the promoter of WAK1 and induce its expression.

Characterization of the Poplar R2R3-MYB Gene Family and Over-Expression of PsnMYB108 Confers Salt Tolerance in Transgenic Tobacco

The MYB, one of the largest transcription factor families in plants, is related to various biological processes. For an example, the R2R3-MYB family plays an important role in regulation of primary and secondary metabolism, plant growth and development, and responses to hormones and stresses. However, functional studies on the poplar R2R3-MYB genes are limited. In this study, we identified 207 poplar R2R3-MYB genes that are unevenly distributed on the 19 chromosomes of poplar, followed by characterization of their conserved domains. On the basis of phylogenetic analysis, these genes can be divided into 23 groups. Evidence from synteny analyses indicated that the poplar R2R3-MYB gene family is featured by tandem and segmental duplication events. On the basis of RNA-Seq data, we investigated salt responsive genes and explored their expression patterns. Furthermore, we cloned the PsnMYB108 gene from poplar, which is significantly up-regulated in roots and leaves in response to salt stress. To validate its function, we developed transgenic tobacco plants that over-express the PsnMYB108 gene. It appears that the transgenic lines are more tolerant to salt stress than the wild type does. Evidence from physiological analyses demonstrated that over-expression of PsnMYB108 may improve tobacco salt stress tolerance by increasing the reactive oxygen species scavenging ability and the accumulation of proline. These results laid the foundation for future analysis and functional studies of poplar R2R3-MYB family members, and revealed that PsnMYB108 plays an important role in improving plant salt stress tolerance.

Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effect

In plants, the phenylpropanoid pathway is responsible for the synthesis of a diverse array of secondary metabolites that include lignin monomers, flavonoids, and coumarins, many of which are essential for plant structure, biomass recalcitrance, stress defense, and nutritional quality. Our previous studies have demonstrated that Populus trichocarpa PtrEPSP-TF, an isoform of 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, has transcriptional activity and regulates phenylpropanoid biosynthesis in Populus. In this study, we report the identification of single nucleotide polymorphism (SNP) of PtrEPSP-TF that defines its functionality. Populus natural variants carrying this SNP were shown to have reduced lignin content. Here, we demonstrated that the SNP-induced substitution of 142nd amino acid (PtrEPSP-TFD142E) dramatically impairs the DNA-binding and transcriptional activity of PtrEPSP-TF. When introduced to a monocot species rice (Oryza sativa) in which an EPSP synthase isoform with the DNA-binding helix-turn-helix (HTH) motif is absent, the PtrEPSP-TF, but not PtrEPSP-TFD142E, activated genes in the phenylpropanoid pathway. More importantly, heterologous expression of PtrEPSP-TF uncovered five new transcriptional regulators of phenylpropanoid biosynthesis in rice. Collectively, this study identifies the key amino acid required for PtrEPSP-TF functionality and provides a strategy to uncover new transcriptional regulators in phenylpropanoid biosynthesis.

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.

Principles and Applications of Vibrational Spectroscopic Imaging in Plant Science: A Review

Detailed knowledge about plant chemical constituents and their distributions from organ level to sub-cellular level is of critical interest to basic and applied sciences. Spectral imaging techniques offer unparalleled advantages in that regard. The core advantage of these technologies is that they acquire spatially distributed semi-quantitative information of high specificity towards chemical constituents of plants. This forms invaluable asset in the studies on plant biochemical and structural features. In certain applications, non-invasive analysis is possible. The information harvested through spectral imaging can be used for exploration of plant biochemistry, physiology, metabolism, classification, and phenotyping among others, with significant gains for basic and applied research. This article aims to present a general perspective about vibrational spectral imaging/micro-spectroscopy in the context of plant research. Within the scope of this review are infrared (IR), near-infrared (NIR) and Raman imaging techniques. To better expose the potential and limitations of these techniques, fluorescence imaging is briefly overviewed as a method relatively less flexible but particularly powerful for the investigation of photosynthesis. Included is a brief introduction to the physical, instrumental, and data-analytical background essential for the applications of imaging techniques. The applications are discussed on the basis of recent literature.

The in vivo impact of MsLAC1, a Miscanthus laccase isoform, on lignification and lignin composition contrasts with its in vitro substrate preference

BACKGROUND

Understanding lignin biosynthesis and composition is of central importance for sustainable bioenergy and biomaterials production. Species of the genus Miscanthus have emerged as promising bioenergy crop due to their rapid growth and modest nutrient requirements. However, lignin polymerization in Miscanthus is poorly understood. It was previously shown that plant laccases are phenol oxidases that have multiple functions in plant, one of which is the polymerization of monolignols. Herein, we link a newly discovered Miscanthus laccase, MsLAC1, to cell wall lignification. Characterization of recombinant MsLAC1 and Arabidopsis transgenic plants expressing MsLAC1 were carried out to understand the function of MsLAC1 both in vitro and in vivo.

RESULTS

Using a comprehensive suite of molecular, biochemical and histochemical analyses, we show that MsLAC1 localizes to cell walls and identify Miscanthus transcription factors capable of regulating MsLAC1 expression. In addition, MsLAC1 complements the Arabidopsis lac4-2 lac17 mutant and recombinant MsLAC1 is able to oxidize monolignol in vitro. Transgenic Arabidopsis plants over-expressing MsLAC1 show higher G-lignin content, although recombinant MsLAC1 seemed to prefer sinapyl alcohol as substrate.

CONCLUSIONS

In summary, our results suggest that MsLAC1 is regulated by secondary cell wall MYB transcription factors and is involved in lignification of xylem fibers. This report identifies MsLAC1 as a promising breeding target in Miscanthus for biofuel and biomaterial applications.

Genomic resources for energy cane breeding in the post genomics era

Sugarcane is one of the most sustainable energy crops among cultivated crops presenting the highest tonnage of cultivated plants. Its high productivity of sugar, bioethanol and bioelectricity make it a promising green alternative to petroleum. Furthermore, the myriad of products that can be derived from sugarcane biomass has been driving breeding programs towards varieties with a higher yield of fiber and a more vigorous and sustainable performance: the energy cane. Here we provide an overview of the energy cane including plant description, breeding efforts, types, and end-uses. In addition, we describe recently published genomic resources for the development of this crop, discuss current knowledge of cell wall metabolism, bioinformatic tools and databases available for the community.

Comparative transcriptome and metabolome analyses provide new insights into the molecular mechanisms underlying taproot thickening in Panax notoginseng

BACKGROUND

Taproot thickening is a complex biological process that is dependent on the coordinated expression of genes controlled by both environmental and developmental factors. Panax notoginseng is an important Chinese medicinal herb that is characterized by an enlarged taproot as the main organ of saponin accumulation. However, the molecular mechanisms of taproot enlargement are poorly understood.

RESULTS

A total of 29,957 differentially expressed genes (DEGs) were identified during the thickening process in the taproots of P. notoginseng. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that DEGs associated with "plant hormone signal transduction," "starch and sucrose metabolism," and "phenylpropanoid biosynthesis" were predominantly enriched. Further analysis identified some critical genes (e.g., RNase-like major storage protein, DA1-related protein, and Starch branching enzyme I) and metabolites (e.g., sucrose, glucose, fructose, malate, and arginine) that potentially control taproot thickening. Several aspects including hormone crosstalk, transcriptional regulation, homeostatic regulation between sugar and starch, and cell wall metabolism, were identified as important for the thickening process in the taproot of P. notoginseng.

CONCLUSION

The results provide a molecular regulatory network of taproot thickening in P. notoginseng and facilitate the further characterization of the genes responsible for taproot formation in root medicinal plants or crops.

Analysis of Orthologous SECONDARY WALL-ASSOCIATED NAC DOMAIN1 (SND1) Promotor Activity in Herbaceous and Woody Angiosperms

SECONDARY WALL-ASSOCIATED NAC DOMAIN1 (SND1) is a master regulator of fibre secondary wall deposition in Arabidopsis thaliana (Arabidopsis), with homologs in other angiosperms and gymnosperms. However, it is poorly understood to what extent the fibre-specific regulation of the SND1 promoter, and that of its orthologs, is conserved between diverged herbaceous and woody lineages. We performed a reciprocal reporter gene analysis of orthologous SND1 promoters from Arabidopsis (AthSND1), Eucalyptus grandis (EgrNAC61) and Populus alba × P. grandidentata (PagWND1A) relative to secondary cell wall-specific Cellulose Synthase4 (CesA4) and CesA7 promoters, in both a non-woody (Arabidopsis) and a woody (poplar) system. β-glucuronidase (GUS) reporter analysis in Arabidopsis showed that the SND1 promoter was active in vascular tissues as previously reported and showed interfascicular and xylary fibre-specific expression in inflorescence stems, while reporter constructs of the woody plant-derived promoters were partial to the (pro)cambium-phloem and protoxylem. In transgenic P. tremula × P. alba plants, all three orthologous SND1 promoters expressed the GUS reporter similarly and preferentially in developing secondary xylem, ray parenchyma and cork cambium. Ours is the first study to reciprocally test orthologous SND1 promoter specificity in herbaceous and woody species, revealing diverged regulatory functions in the herbaceous system.

The R2R3 MYB transcription factor MYB189 negatively regulates secondary cell wall biosynthesis in Populus

Secondary cell wall (SCW) biosynthesis during wood formation in trees is controlled by a multilevel regulatory network that coordinates the expression of substantial genes. However, few transcription factors involved in the negative regulation of secondary wall biosynthesis have been characterized in tree species. In this study, we isolated an R2R3 MYB transcription factor MYB189 from Populus trichocarpa, which is expressed predominantly in secondary vascular tissues, especially in the xylem. A novel repression motif was identified in the C-terminal region of MYB189, which indicates this factor was a transcriptional repressor. Overexpression (OE) of MYB189 in Arabidopsis and poplar resulted in a significant reduction in the contents of lignin, cellulose and hemicelluloses. Vascular development in stems of MYB189 OE lines was markedly inhibited, leading to a dramatic decrease in SCW thickness of xylem fibers. Gene expression analyses showed that most of the structural genes involved in the biosynthesis of lignin, cellulose and xylans were significantly downregulated in MYB189-overexpressing poplars compared with the wild-type control. Chromatin immunoprecipitation-quantitative real-time polymerase chain reaction and transient expression assays revealed that MYB189 could directly bind to the promoters of secondary wall biosynthetic genes to repress their expression. Together, these data suggest that MYB189 acts as a repressor to regulate SCW biosynthesis in poplar.

Modified expression of ZmMYB167 in Brachypodium distachyon and Zea mays leads to increased cell wall lignin and phenolic content

One of the challenges to enable targeted modification of lignocellulosic biomass from grasses for improved biofuel and biochemical production lies within our limited understanding of the transcriptional control of secondary cell wall biosynthesis. Here, we investigated the role of the maize MYB transcription factor ZmMYB167 in secondary cell wall biosynthesis and how modified ZmMYB167 expression in two distinct grass model species affects plant biomass and growth phenotypes. Heterologous expression of ZmMYB167 in the C3 model system Brachypodium led to mild dwarf phenotypes, increased lignin (~7% to 13%) and S-lignin monomer (~11% to 16%) content, elevated concentrations of cell wall-bound p-coumaric acid (~15% to 24%) and reduced biomass sugar release (~20%) compared to controls. Overexpression of ZmMYB167 in the C4 model system Zea mays increased lignin (~4% to 13%), p-coumaric acid (~8% to 52%) and ferulic acid (~13% to 38%) content but did not affect plant growth and development nor biomass recalcitrance. Taken together, modifying ZmMYB167 expression represents a target to alter lignin and phenolic content in grasses. The ZmMYB167 expression-induced discrepancies in plant phenotypic and biomass properties between the two grass model systems highlight the challenges and opportunities for MYB transcription factor-based genetic engineering approaches of grass biomass.

Rice OsPEX1, an extensin-like protein, affects lignin biosynthesis and plant growth

Rice leucine-rich repeat extensin-like protein OsPEX1 mediates the intersection of lignin deposition and plant growth. Lignin, a major structural component of secondary cell wall, is essential for normal plant growth and development. However, the molecular and genetic regulation of lignin biosynthesis is not fully understood in rice. Here we report the identification and characterization of a rice semi-dominant dwarf mutant (pex1) with stiff culm. Molecular and genetic analyses revealed that the pex1 phenotype was caused by ectopic expression of a leucine-rich repeat extension-like gene, OsPEX1. Interestingly, the pex1 mutant showed significantly higher lignin content and increased expression levels of lignin-related genes compared with wild type plants. Conversely, OsPEX1-suppresssed transgenics displayed low lignin content and reduced transcriptional abundance of genes associated with lignin biosynthesis, indicating that the OsPEX1 mediates lignin biosynthesis and/or deposition in rice. When OsPEX1 was ectopically expressed in rice cultivars with tall stature that lacks the allele of semi-dwarf 1, well-known green revolution gene, the resulting transgenic plants displayed reduced height and enhanced lodging resistance. Our study uncovers a causative effect between the expression of OsPEX1 and lignin deposition. Lastly, we demonstrated that modulating OsPEX1 expression could provide a tool for improving rice lodging resistance.

Deposition of lignin in four species of Saccharum

We used primers designed on conserved gene regions of several species to isolate the most expressed genes of the lignin pathway in four Saccharum species. S. officinarum and S. barberi have more sucrose in the culms than S. spontaneum and S. robustum, but less polysaccharides and lignin in the cell wall. S. spontaneum, and S. robustum had the lowest S/G ratio and a lower rate of saccharification in mature internodes. Surprisingly, except for CAD, 4CL, and CCoAOMT for which we found three, two, and two genes, respectively, only one gene was found for the other enzymes and their sequences were highly similar among the species. S. spontaneum had the highest expression for most genes. CCR and CCoAOMT B presented the highest expression; 4CL and F5H showed increased expression in mature tissues; C3H and CCR had higher expression in S. spontaneum, and one of the CADs isolated (CAD B) had higher expression in S. officinarum. The similarity among the most expressed genes isolated from these species was unexpected and indicated that lignin biosynthesis is conserved in Saccharum including commercial varieties Thus the lignin biosynthesis control in sugarcane may be only fully understood with the knowledge of the promotor region of each gene.

Endoplasmic reticulum-localized UBC34 interaction with lignin repressors MYB221 and MYB156 regulates the transactivity of the transcription factors in Populus tomentosa

BACKGROUND

Regulation of lignin biosynthesis is known to occur at the level of transcription factors (TFs), of which R2R3-MYB family members have been proposed to play a central role via the AC cis-elements. Despite the important roles of TFs in lignin biosynthesis, the post-translational regulation of these TFs, particularly their ubiquitination regulation, has not been thoroughly explored.

RESULTS

We describe the discovery of a Populus tomentosa E2 ubiquitin-conjugating enzyme 34 (PtoUBC34), which is involved in the post-translational regulation of transactivation activity of lignin-associated transcriptional repressors PtoMYB221 and PtoMYB156. PtoUBC34 is localized at the endoplasmic reticulum (ER) membrane where it interacts with transcriptional repressors PtoMYB221 and PtoMYB156. This specific interaction allows for the translocation of TFs PtoMYB221 and PtoMYB156 to the ER and reduces their repression activity in a PtoUBC34 abundance-dependent manner. By taking a molecular biology approach with quantitative real-time polymerase chain reaction (qRT-PCR) analysis, we found that PtoUBC34 is expressed in all aboveground tissues of trees in P. tomentosa, and in particular, it is ubiquitous in all distinct differentiation stages across wood formation, including phloem differentiation, cambium maintaining, early and developing xylem differentiation, secondary cell wall thickening, and programmed cell death. Additionally, we discovered that PtoUBC34 is induced by treatment with sodium chloride and heat shock.

CONCLUSIONS

Our data suggest a possible mechanism by which lignin biosynthesis is regulated by ER-localized PtoUBC34 in poplar, probably through the ER-associated degradation (ERAD) of lignin-associated repressors PtoMYB221 and PtoMYB156.

Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum)

Cell wall recalcitrance is the major challenge to improving saccharification efficiency in converting lignocellulose into biofuels. However, information regarding the transcriptional regulation of secondary cell wall biogenesis remains poor in switchgrass (Panicum virgatum), which has been selected as a biofuel crop in the United States. In this study, we present a combination of computational and experimental approaches to develop gene regulatory networks for lignin formation in switchgrass. To screen transcription factors (TFs) involved in lignin biosynthesis, we developed a modified method to perform co-expression network analysis using 14 lignin biosynthesis genes as bait (target) genes. The switchgrass lignin co-expression network was further extended by adding 14 TFs identified in this study, and seven TFs identified in previous studies, as bait genes. Six TFs (PvMYB58/63, PvMYB42/85, PvMYB4, PvWRKY12, PvSND2 and PvSWN2) were targeted to generate overexpressing and/or down-regulated transgenic switchgrass lines. The alteration of lignin content, cell wall composition and/or plant growth in the transgenic plants supported the role of the TFs in controlling secondary wall formation. RNA-seq analysis of four of the transgenic switchgrass lines revealed downstream target genes of the secondary wall-related TFs and crosstalk with other biological pathways. In vitro transactivation assays further confirmed the regulation of specific lignin pathway genes by four of the TFs. Our meta-analysis provides a hierarchical network of TFs and their potential target genes for future manipulation of secondary cell wall formation for lignin modification in switchgrass.

Genome-Wide Identification of R2R3-MYB Transcription Factors Regulating Secondary Cell Wall Thickening in Cotton Fiber Development

MYB proteins represent one of the largest transcription factor (TF) families in plants, some of which act as key transcriptional regulators of secondary cell wall (SCW) biosynthesis. Cotton (Gossypium hirsutum) fiber is thought to be an ideal single-cell model to study cell elongation and SCW biosynthesis. However, little knowledge regarding the TFs controlling fiber SCW biosynthesis, particularly for R2R3-MYBs is known. By far, no comprehensive genome-wide analysis of the secondary wall-associated R2R3-MYBs has been reported in cultivated tetraploid upland cotton. In this study, we identified 419 R2R3-MYB genes by systematically examining the cotton genome. A combination of phylogenetic, RNA-seq and co-expression analyses indicated that 36 R2R3-MYBs were either preferentially or highly expressed in 20 day post anthesis (dpa) fibers and are putative SCW regulators. Among these MYB genes, 22 MYBs are homologs of known SCW MYB proteins and the other 14 MYBs are novel proteins without prior reported SCW biosynthesis-related functions. Finally, we highlighted on the roles of two MYBs named GhMYB46_D13 and GhMYB46_D9, both of which displayed the highest expression in 20 dpa fibers. Expression of GhMYB46_D13 or GhMYB46_D9 individually in Arabidopsis resulted in ectopic SCW deposition in transgenic plants. Furthermore, both GhMYB46_D13 and GhMYB46_D9 were able to activate the cotton fiber SCW cellulose synthase gene promoters. Thus, we have identified 36 R2R3-MYBs as potential SCW regulators in cotton fibers that represent strong candidates for further functional studies during fiber development and SCW thickening.

Citrus sinensis MYB Transcription Factor CsMYB85 Induce Fruit Juice Sac Lignification Through Interaction With Other CsMYB Transcription Factors

Varieties of Citrus are commercially important fruits that are cultivated worldwide and are valued for being highly nutritious and having an appealing flavor. Lignification of citrus fruit juice sacs is a serious physiological disorder that occurs during postharvest storage, for which the underlying transcriptional regulatory mechanisms remain unclear. In this study, we identified and isolated a candidate MYB transcription factor, CsMYB85, that is involved in the regulation of lignin biosynthesis in Citrus sinensis, which has homologs in Arabidopsis and other plants. We found that during juice sac lignification, CsMYB85 expression levels increase significantly, and therefore, suspected that this gene may control lignin biosynthesis during the lignification process. Our results indicated that CsMYB85 binds the CsMYB330 promoter, regulates its expression, and interacts with CsMYB308 in transgenic yeast and tobacco. A transient expression assay indicated that Cs4CL1 expression levels and lignin content significantly increased in fruit juice sacs overexpressing CsMYB85. At4CL1 expression levels and lignin content were also significantly increased in Arabidopsis overexpressing CsMYB85. We accordingly present convincing evidence for the participation of the CsMYB85 transcription factor in fruit juice sac lignification, and thereby provide new insights into the transcriptional regulation of this process in citrus fruits.

Transcriptome and metabolome reveal distinct carbon allocation patterns during internode sugar accumulation in different sorghum genotypes

Sweet sorghum accumulates large amounts of soluble sugar in its stem. However, a system-based understanding of this carbohydrate allocation process is lacking. Here, we compared the dynamic transcriptome and metabolome between the conversion line R9188 and its two parents, sweet sorghum RIO and grain sorghum BTx406 that have contrasting sugar-accumulating phenotypes. We identified two features of sucrose metabolism, stable concentrations of sugar phosphates in RIO and opposite trend of trehalose-6-phosphate (T6P) between RIO vs R9188/BTx406. Integration of transcriptome and metabolome revealed R9188 is partially active in starch metabolism together with medium sucrose level, whereas sweet sorghum had the highest sucrose concentration and remained highly active in sucrose, starch, and cell wall metabolism post-anthesis. Similar expression pattern of genes involved in sucrose degradation decreased the pool of sugar phosphates for precursors of starch and cell wall synthesis in R9188 and BTx406. Differential T6P signal between RIO vs R9188/BTx406 is associated with introgression of T6P regulators from BTx406 into R9188, including C-group bZIP and trehalose 6-phosphate phosphatase (TPP). The inverted T6P signalling in R9188 appears to down-regulate sucrose and starch metabolism partly through transcriptome reprogramming, whereas introgressed metabolic genes could be related to reduced cell wall metabolism. Our results show that coordinated primary metabolic pathways lead to high sucrose demand and accumulation in sweet sorghum, providing us with targets for genetic improvements of carbohydrate allocation in bioenergy crops.

Overexpression of ginseng patatin-related phospholipase pPLAIIIβ alters the polarity of cell growth and decreases lignin content in Arabidopsis

Background

The patatin-related phospholipase AIII family (pPLAIIIs) genes alter cell elongation and cell wall composition in Arabidopsis and rice plant, suggesting diverse commercial purposes of the economically important medicinal ginseng plant. Herein, we show the functional characterization of a ginseng pPLAIII gene for the first time and discuss its potential applications.

Methods

pPLAIIIs were identified from ginseng expressed sequence tag clones and further confirmed by search against ginseng database and polymerase chain reaction. A clone showing the highest homology with pPLAIIIβ was shown to be overexpressed in Arabidopsis using Agrobacterium. Quantitative polymerase chain reaction was performed to analyze ginseng pPLAIIIβ expression. Phenotypes were observed using a low-vacuum scanning electron microscope. Lignin was stained using phloroglucinol and quantified using acetyl bromide.

Results

The PgpPLAIIIβ transcripts were observed in all organs of 2-year-old ginseng. Overexpression of ginseng pPLAIIIβ (PgpPLAIIIβ-OE) in Arabidopsis resulted in small and stunted plants. It shortened the trichomes and decreased trichome number, indicating defects in cell polarity. Furthermore, OE lines exhibited enlarged seeds with less number per silique. The YUCCA9 gene was downregulated in the OE lines, which is reported to be associated with lignification. Accordingly, lignin was stained less in the OE lines, and the expression of two transcription factors related to lignin biosynthesis was also decreased significantly.

Conclusion

Overexpression of pPLAIIIβ retarded cell elongation in all the tested organs except seeds, which were longer and thicker than those of the controls. Shorter root length is related to auxin-responsive genes, and its stunted phenotype showed decreased lignin content.

Rice Genome-Scale Network Integration Reveals Transcriptional Regulators of Grass Cell Wall Synthesis

Grasses have evolved distinct cell wall composition and patterning relative to dicotyledonous plants. However, despite the importance of this plant family, transcriptional regulation of its cell wall biosynthesis is poorly understood. To identify grass cell wall-associated transcription factors, we constructed the Rice Combined mutual Ranked Network (RCRN). The RCRN covers >90% of annotated rice (Oryza sativa) genes, is high quality, and includes most grass-specific cell wall genes, such as mixed-linkage glucan synthases and hydroxycinnamoyl acyltransferases. Comparing the RCRN and an equivalent Arabidopsis network suggests that grass orthologs of most genetically verified eudicot cell wall regulators also control this process in grasses, but some transcription factors vary significantly in network connectivity between these divergent species. Reverse genetics, yeast-one-hybrid, and protoplast-based assays reveal that OsMYB61a activates a grass-specific acyltransferase promoter, which confirms network predictions and supports grass-specific cell wall synthesis genes being incorporated into conserved regulatory circuits. In addition, 10 of 15 tested transcription factors, including six novel Wall-Associated regulators (WAP1, WACH1, WAHL1, WADH1, OsMYB13a, and OsMYB13b), alter abundance of cell wall-related transcripts when transiently expressed. The results highlight the quality of the RCRN for examining rice biology, provide insight into the evolution of cell wall regulation, and identify network nodes and edges that are possible leads for improving cell wall composition.