Arabidopsis VASCULAR-RELATED NAC-DOMAIN6 directly regulates the genes that govern programmed cell death and secondary wall formation during xylem differentiation

HOMEODOMAIN GLABROUS2 regulates cellulose biosynthesis in seed coat mucilage by activating CELLULOSE SYNTHASE5

Numerous proteins involved in cellulose biosynthesis and assembly have been functionally characterized. Nevertheless, we have a limited understanding of the mechanisms underlying the transcriptional regulation of the genes that encode these proteins. Here, we report that HOMEODOMAIN GLABROUS2 (HDG2), a Homeobox-Leucine Zipper IV transcription factor, regulates cellulose biosynthesis in Arabidopsis (Arabidopsis thaliana) seed coat mucilage. HDG2 is a transcriptional activator with the transactivation domain located within its Leucine-Zipper domain. Transcripts of HDG2 were detected specifically in seed coat epidermal cells with peak expression at 10 d postanthesis. Disruptions of HDG2 led to seed coat mucilage with aberrant morphology due to a reduction in its crystalline cellulose content. Electrophoretic mobility shift and yeast one-hybrid assays, together with chromatin immunoprecipitation and quantitative PCR, provided evidence that HDG2 directly activates CELLULOSE SYNTHASE5 (CESA5) expression by binding to the L1-box cis-acting element in its promoter. Overexpression of CESA5 partially rescued the mucilage defects of hdg2-3. Together, our data suggest that HDG2 directly activates CESA5 expression and thus is a positive regulator of cellulose biosynthesis in seed coat mucilage.

NAC and MYB Families and Lignin Biosynthesis-Related Members Identification and Expression Analysis in Melilotus albus

Melilotus albus is an annual or biennial legume species that adapts to extreme environments via its high stress tolerance. NAC and MYB transcription factors (TFs) are involved in the regulation of lignin biosynthesis, which has not been studied in M. albus. A total of 101 MaNAC and 299 MaMYB members were identified based on M. albus genome. Chromosome distribution and synteny analysis indicated that some genes underwent tandem duplication. Ka/Ks analysis suggested that MaNACs and MaMYBs underwent strong purifying selection. Stress-, hormone- and development-related cis-elements and MYB-binding sites were identified in the promoter regions of MaNACs and MaMYBs. Five MaNACs, two MaMYBs and ten lignin biosynthesis genes were identified as presenting coexpression relationships according to weighted gene coexpression network analysis (WGCNA). Eleven and thirteen candidate MaNAC and MaMYB genes related to lignin biosynthesis were identified, respectively, and a network comprising these genes was constructed which further confirmed the MaNAC and MaMYB relationship. These candidate genes had conserved gene structures and motifs and were highly expressed in the stems and roots, and qRT-PCR further verified the expression patterns. Overall, our results provide a reference for determining the precise role of NAC and MYB genes in M. albus and may facilitate efforts to breed low-lignin-content forage cultivars in the future.

Histone methyltransferase ATX1 dynamically regulates fiber secondary cell wall biosynthesis in Arabidopsis inflorescence stem

Secondary wall thickening in the sclerenchyma cells is strictly controlled by a complex network of transcription factors in vascular plants. However, little is known about the epigenetic mechanism regulating secondary wall biosynthesis. In this study, we identified that ARABIDOPSIS HOMOLOG of TRITHORAX1 (ATX1), a H3K4-histone methyltransferase, mediates the regulation of fiber cell wall development in inflorescence stems of Arabidopsis thaliana. Genome-wide analysis revealed that the up-regulation of genes involved in secondary wall formation during stem development is largely coordinated by increasing level of H3K4 tri-methylation. Among all histone methyltransferases for H3K4me3 in Arabidopsis, ATX1 is markedly increased during the inflorescence stem development and loss-of-function mutant atx1 was impaired in secondary wall thickening in interfascicular fibers. Genetic analysis showed that ATX1 positively regulates secondary wall deposition through activating the expression of secondary wall NAC master switch genes, SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN1 (SND1) and NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1). We further identified that ATX1 directly binds the loci of SND1 and NST1, and activates their expression by increasing H3K4me3 levels at these loci. Taken together, our results reveal that ATX1 plays a key role in the regulation of secondary wall biosynthesis in interfascicular fibers during inflorescence stem development of Arabidopsis.

Proximal and Distal Parts of Sweetpotato Adventitious Roots Display Differences in Root Architecture, Lignin, and Starch Metabolism and Their Developmental Fates

Sweetpotato is an important food crop globally, serving as a rich source of carbohydrates, vitamins, fiber, and micronutrients. Sweetpotato yield depends on the modification of adventitious roots into storage roots. The underlying mechanism of this developmental switch is not fully understood. Interestingly, storage-root formation is manifested by formation of starch-accumulating parenchyma cells and bulking of the distal part of the root, while the proximal part does not show bulking. This system, where two parts of the same adventitious root display different developmental fates, was used by us in order to better characterize the anatomical, physiological, and molecular mechanisms involved in sweetpotato storage-root formation. We show that, as early as 1 and 2 weeks after planting, the proximal part of the root exhibited enhanced xylem development together with increased/massive lignin deposition, while, at the same time, the distal root part exhibited significantly elevated starch accumulation. In accordance with these developmental differences, the proximal root part exhibited up-regulated transcript levels of sweetpotato orthologs of Arabidopsis vascular-development regulators and key genes of lignin biosynthesis, while the distal part showed up-regulation of genes encoding enzymes of starch biosynthesis. All these recorded differences between proximal and distal root parts were further enhanced at 5 weeks after planting, when storage roots were formed at the distal part. Our results point to down-regulation of fiber formation and lignification, together with up-regulation of starch biosynthesis, as the main events underlying storage-root formation, marking/highlighting several genes as potential regulators, providing a valuable database of genes for further research.

Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots

BACKGROUND

Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant development and environmental adaptation. However, there are few reports about APs in fast-growing moso bamboo.

RESULT

In this study, we identified a total of 129 AP proteins (PhAPs) encoded by the moso bamboo genome. Phylogenetic and gene structure analyses showed that these 129 PhAPs could be divided into three categories (categories A, B and C). The PhAP gene family in moso bamboo may have undergone gene expansion, especially the members of categories A and B, although homologs of some members in category C have been lost. The chromosomal location of PhAPs suggested that segmental and tandem duplication events were critical for PhAP gene expansion. Promoter analysis revealed that PhAPs in moso bamboo may be involved in plant development and responses to environmental stress. Furthermore, PhAPs showed tissue-specific expression patterns and may play important roles in rapid growth, including programmed cell death, cell division and elongation, by integrating environmental signals such as light and gibberellin signals.

CONCLUSION

Comprehensive analysis of the AP gene family in moso bamboo suggests that PhAPs have experienced gene expansion that is distinct from that in rice and may play an important role in moso bamboo organ development and rapid growth. Our results provide a direction and lay a foundation for further analysis of plant AP genes to clarify their function during rapid growth.

Characterization of a High Hierarchical Regulator, PtrGATA12, Functioning in Differentially Regulating Secondary Wall Component Biosynthesis in Populus trichocarpa

In plants, GATA transcription factors (TFs) have been reported to play vital roles in to a wide range of biological processes. To date, there is still no report about the involvement and functions of woody plant GATA TFs in wood formation. In this study, we described the functional characterization of a Populus trichocarpa GATA TF, PtrGATA12, which encodes a nuclear-localized transcriptional activator predominantly expressing in developing xylem tissues. Overexpression of PtrGATA12 not only inhibited growths of most phenotypic traits and biomass accumulation, but also altered the expressions of some master TFs and pathway genes involved in secondary cell wall (SCW) and programmed cell death, leading to alternated SCW components and breaking forces of stems of transgenic lines. The significant changes occurred in the contents of hemicellulose and lignin and SCW thicknesses of fiber and vessel that increased by 13.5 and 10.8%, and 20.83 and 11.83%, respectively. Furthermore, PtrGATA12 bound directly to the promoters of a battery of TFs and pathway genes and activated them; the binding sites include two cis-acting elements that were specifically enriched in their promoter regions. Taken together, our results suggest PtrGATA12, as a higher hierarchical TF on the top of PtrWND6A, PtrWND6B, PtrMYB152, and PtrMYB21, exert a coordinated regulation of SCW components biosynthesis pathways through directly and indirectly controlling master TFs, middle-level TFs, and further downstream pathway genes of the currently known hierarchical transcription network that governs SCW formation.

Comparative analysis of transcriptomic profiling to identify genes involved in the bulged surface of pear fruit (Pyrus bretschneideri Rehd. cv. Yuluxiangli)

Pear (Pyrus spp.) belongs to the genus Pyrus, in the family Rosaceae. Some varieties of pear fruit exhibit bulged surface, which seriously affects the quality and commodity value of the pear fruit. In this study, we performed anatomical, physiological, and transcriptomic analysis to explore the mechanism of paclobutrazol (PBZ) on the bulged surface of pear fruit. The vascular bundles of flesh were more evenly distributed, and the fruit cells were more compactly arranged and smaller in size treated with PBZ. However, the auxin (IAA) content of flesh was decreased in the treated group. Furthermore, the GO and KEGG analysis of differentially expressed genes (DEGs) showed that auxin, phenylpropanoid metabolic pathways, and transcriptional factor genes were significantly enriched on the relieved bulged surface of pear fruit. And it was analyzed that some genes contained auxin responded cis-elements from the selected DEGs in the promoter region. We conclude that PBZ plays a negative role in cell division, cell elongation, and vascular bundle development on the bulged surface of pear fruit through the involvement of auxin-related genes. This study will provide a theoretical basis for the regulation of the bulged surface of pear fruit by a growth retardant agent.

SUPPLEMENTARY INFORMATION

The online version of this article (10.1007/s12298-021-00929-z) contains supplementary material, which is available to authorized users.

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.

Modes of Brassinosteroid Activity in Cold Stress Tolerance

Cold stress is a significant environmental factor that negatively affects plant growth and development in particular when it occurs during the growth phase. Plants have evolved means to protect themselves from damage caused by chilling or freezing temperatures and some plant species, in particular those from temperate geographical zones, can increase their basal level of freezing tolerance in a process termed cold acclimation. Cold acclimation improves plant survival, but also represses growth, since it inhibits activity of the growth-promoting hormones gibberellins (GAs). In addition to GAs, the steroid hormones brassinosteroids (BRs) also take part in growth promotion and cold stress signaling; however, in contrast to Gas, BRs can improve cold stress tolerance with fewer trade-offs in terms of growth and yields. Here we summarize our current understanding of the roles of BRs in cold stress responses with a focus on freezing tolerance and cold acclimation pathways.

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.

Information on the move: vascular tissue development in space and time during postembryonic root growth

Cascades of temporal and spatial regulation of gene expression play crucial roles in the vascular development in plant roots. Once vascular cell fates are determined, the timing of their differentiation is tightly controlled in a cell-autonomous manner. In contrast, extensive cell-to-cell communication contributes to the positioning and specifying of vascular cell types in the root meristem. Diverse factors moving short distances in a radial direction were found to be key contributors to these processes. Furthermore, signals from differentiated phloem were found to influence the phloem precursor and determine how the corresponding asymmetric cell division proceeded. These findings highlight the potential importance of underexplored types of intercellular communication in relation to vascular tissue development during postembryonic root growth.

Plant vascular development: mechanisms and environmental regulation

Plant vascular development is a complex process culminating in the generation of xylem and phloem, the plant transporting conduits. Xylem and phloem arise from specialized stem cells collectively termed (pro)cambium. Once developed, xylem transports mainly water and mineral nutrients and phloem transports photoassimilates and signaling molecules. In the past few years, major advances have been made to characterize the molecular, genetic and physiological aspects that govern vascular development. However, less is known about how the environment re-shapes the process, which molecular mechanisms link environmental inputs with developmental outputs, which gene regulatory networks facilitate the genetic adaptation of vascular development to environmental niches, or how the first vascular cells appeared as an evolutionary innovation. In this review, we (1) summarize the current knowledge of the mechanisms involved in vascular development, focusing on the model species Arabidopsis thaliana, (2) describe the anatomical effect of specific environmental factors on the process, (3) speculate about the main entry points through which the molecular mechanisms controlling of the process might be altered by specific environmental factors, and (4) discuss future research which could identify the genetic factors underlying phenotypic plasticity of vascular development.

Transcriptional networks regulating root vascular development

Vascular development involves multiple processes, including the establishment of vascular stem cells (e.g. procambium/cambium cells), stem cell divisions, and cell specification. A number of key transcription factors regulating vascular development have been identified, and the molecular mechanisms underlying these regulators have been keenly investigated. These studies uncovered that transcriptional regulation and phytohormone signaling have central roles in proceeding vascular developmental processes. Recent research approaches contributed to identify key transcription factors and their downstream genes, which enhanced our understanding of vascular development. This review discusses some research approaches and emerging molecular mechanisms that mediate the activation of transcriptional networks regulating root vascular development.

The Arabidopsis transcription factor LBD15 mediates ABA signaling and tolerance of water-deficit stress by regulating ABI4 expression

To survive, sessile plants must adapt to grow and develop when facing water-deficit stress. However, the molecular mechanisms underlying fine-tuning of the antagonistic action between stress response and growth remain to be determined. Here, plants overexpressing Lateral Organ Boundaries Domain 15 (LBD15) showed abscisic acid (ABA) hypersensitivity and tolerance of water-deficit stress, whereas the loss-of-function mutant lbd15 presented decreased sensitivity to ABA and increased sensitivity to water-deficit stress. Further analysis revealed that LBD15 directly binds to the promoter of the ABA signaling pathway gene ABSCISIC ACID INSENSITIVE4 (ABI4) to activate its expression, thereby forming an LBD15-ABI4 cascade to optimally regulate ABA signaling-mediated plant growth and tolerance of water-deficit stress. In addition, drought stress-induced ABA signaling promoted LBD15 expression, which directly activates expression of ABI4 to close stomata. As a result, water loss is reduced, and then water-deficit stress tolerance is increased. The results of this study reveal a molecular mechanism by which LBD15 coordinates and balances plant growth and resistance to water-deficit stress.

Isolation of dominant Arabidopsis seiv mutants defective in VND7-induced xylem vessel cell differentiation

The plant-specific NAC transcription factor VASCULAR-RELATED NAC-DOMAIN 7 (VND7) functions in xylem vessel cell differentiation in Arabidopsis thaliana. To identify novel factors regulating xylem vessel cell differentiation, we previously performed ethyl methanesulfonate mutagenesis of a transgenic 35S::VND7-VP16-GR line in which VND7 activity can be induced post-translationally by glucocorticoid treatment. We successfully isolated mutants that fail to form ectopic xylem vessel cells named seiv (suppressor of ectopic vessel cell differentiation induced by VND7) mutants. Here, we isolated eight novel dominant seiv mutants: seiv2 to seiv9. In these seiv mutants, ectopic xylem vessel cell differentiation was inhibited in aboveground but not underground tissues. Specifically, the shoot apices of the mutants, containing shoot apical meristems and leaf primordia, completely lacked ectopic xylem vessel cells. In these mutants, the VND7-induced upregulation of downstream genes was reduced, especially in shoots compared to roots. However, endogenous xylem vessel cell formation was not affected in the seiv mutants. Therefore, the seiv mutations identified in this study have repressive effects on cell differentiation in shoot meristematic regions, resulting in inhibited ectopic xylem vessel cell differentiation.

The class II KNOX transcription factors KNAT3 and KNAT7 synergistically regulate monolignol biosynthesis in Arabidopsis

The function of the transcription factor KNOTTED ARABIDOPSIS THALIANA7 (KNAT7) is still unclear since it appears to be either a negative or a positive regulator for secondary cell wall deposition with its loss-of-function mutant displaying thicker interfascicular and xylary fiber cell walls but thinner vessel cell walls in inflorescence stems. To explore the exact function of KNAT7, class II KNOTTED1-LIKE HOMEOBOX (KNOX II) genes in Arabidopsis including KNAT3, KNAT4, and KNAT5 were studied together. By chimeric repressor technology, we found that both KNAT3 and KNAT7 repressors exhibited a similar dwarf phenotype. Both KNAT3 and KNAT7 genes were expressed in the inflorescence stems and the knat3 knat7 double mutant exhibited a dwarf phenotype similar to the repressor lines. A stem cross-section of knat3 knat7 displayed an enhanced irregular xylem phenotype as compared with the single mutants, and its cell wall thickness in xylem vessels and interfascicular fibers was significantly reduced. Analysis of cell wall chemical composition revealed that syringyl lignin was significantly decreased while guaiacyl lignin was increased in the knat3 knat7 double mutant. Coincidently, the knat3 knat7 transcriptome showed that most lignin pathway genes were activated, whereas the syringyl lignin-related gene Ferulate 5-Hydroxylase (F5H) was down-regulated. Protein interaction analysis revealed that KNAT3 and KNAT7 can form a heterodimer, and KNAT3, but not KNAT7, can interact with the key secondary cell wall formation transcription factors NST1/2, which suggests that the KNAT3-NST1/2 heterodimer complex regulates F5H to promote syringyl lignin synthesis. These results indicate that KNAT3 and KNAT7 synergistically work together to promote secondary cell wall biosynthesis.

Necrotic upper tips1 mimics heat and drought stress and encodes a protoxylem-specific transcription factor in maize

Maintaining sufficient water transport during flowering is essential for proper organ growth, fertilization, and yield. Water deficits that coincide with flowering result in leaf wilting, necrosis, tassel browning, and sterility, a stress condition known as "tassel blasting." We identified a mutant, necrotic upper tips1 (nut1), that mimics tassel blasting and drought stress and reveals the genetic mechanisms underlying these processes. The nut1 phenotype is evident only after the floral transition, and the mutants have difficulty moving water as shown by dye uptake and movement assays. These defects are correlated with reduced protoxylem vessel thickness that indirectly affects metaxylem cell wall integrity and function in the mutant. nut1 is caused by an Ac transposon insertion into the coding region of a unique NAC transcription factor within the VND clade of Arabidopsis NUT1 localizes to the developing protoxylem of root, stem, and leaf sheath, but not metaxylem, and its expression is induced by flowering. NUT1 downstream target genes function in cell wall biosynthesis, apoptosis, and maintenance of xylem cell wall thickness and strength. These results show that maintaining protoxylem vessel integrity during periods of high water movement requires the expression of specialized, dynamically regulated transcription factors within the vasculature.

Processes controlling programmed cell death of root velamen radicum in an epiphytic orchid

BACKGROUND AND AIMS

Development of the velamen radicum on the outer surface of the root epidermis is an important characteristic for water uptake and retention in some plant families, particularly epiphytic orchids, for survival under water-limited environments. Velamen radicum cells derive from the primary root meristem; however, following this development, velamen radicum cells die by incompletely understood processes of programmed cell death (PCD).

METHODS

We combined the use of transmission electron microscopy, X-ray micro-tomography and transcriptome methods to characterize the major anatomical and molecular changes that occur during the development and death of velamen radicum cells of Cymbidium tracyanum, a typical epiphytic orchid, to determine how PCD occurs.

KEY RESULTS

Typical changes of PCD in anatomy and gene expression were observed in the development of velamen radicum cells. During the initiation of PCD, we found that both cell and vacuole size increased, and several genes involved in brassinosteroid and ethylene pathways were upregulated. In the stage of secondary cell wall formation, significant anatomical changes included DNA degradation, cytoplasm thinning, organelle decrease, vacuole rupture and cell wall thickening. Changes were found in the expression of genes related to the biosynthesis of cellulose and lignin, which are instrumental in the formation of secondary cell walls, and are regulated by cytoskeleton-related factors and phenylalanine ammonia-lyase. In the final stage of PCD, cell autolysis was terminated from the outside to the inside of the velamen radicum. The regulation of genes related to autophagy, vacuolar processing enzyme, cysteine proteases and metacaspase was involved in the final execution of cell death and autolysis.

CONCLUSIONS

Our results showed that the development of the root velamen radicum in an epiphytic orchid was controlled by the process of PCD, which included initiation of PCD, followed by formation of the secondary cell wall, and execution of autolysis following cell death.

Characterization of the UDP-glycosyltransferase UGT72 Family in Poplar and Identification of Genes Involved in the Glycosylation of Monolignols

Monolignols are the building blocks for lignin polymerization in the apoplastic domain. Monolignol biosynthesis, transport, storage, glycosylation, and deglycosylation are the main biological processes partaking in their homeostasis. In Arabidopsis thaliana, members of the uridine diphosphate-dependent glucosyltransferases UGT72E and UGT72B subfamilies have been demonstrated to glycosylate monolignols. Here, the poplar UGT72 family, which is clustered into four groups, was characterized: Group 1 UGT72AZ1 and UGT72AZ2, homologs of Arabidopsis UGT72E1-3, as well as group 4 UGT72B37 and UGT72B39, homologs of Arabidopsis UGT72B1-3, glycosylate monolignols. In addition, promoter-GUS analyses indicated that poplar UGT72 members are expressed within vascular tissues. At the subcellular level, poplar UGT72s belonging to group 1 and group 4 were found to be associated with the nucleus and the endoplasmic reticulum. However, UGT72A2, belonging to group 2, was localized in bodies associated with chloroplasts, as well as possibly in chloroplasts. These results show a partial conservation of substrate recognition between Arabidopsis and poplar homologs, as well as divergent functions between different groups of the UGT72 family, for which the substrates remain unknown.

WRKY15 Suppresses Tracheary Element Differentiation Upstream of VND7 During Xylem Formation

Formation of the vascular cylinder, a structure critical to water and nutrient transport in higher plants, is highly regulated. Here we identify WRKY15 as an important regulator that suppresses tracheary element (TE) differentiation in Arabidopsis (Arabidopsis thaliana). Overexpression of WRKY15 resulted in discontinuous protoxylem vessel files and TEs with reduced spiral wall thickening/lignification. Expression of a dominant-negative WRKY15 variant, WRKY15-EAR, led to extra protoxylem vessels and ectopic TEs with increased spiral wall thickening/lignification. Ectopic TE formation in the root cortex and hypocotyl/leaf epidermis reveals that the suppression of WRKY15 is sufficient to trigger the transdifferentiation of other types of cells to TEs. Expression profiling, RT-qPCR, and reporter analyses revealed that WRKY15 suppresses the expression of VASCULAR-RELATED NAC DOMAIN7 (VND7), a master transcriptional regulator that promotes TE differentiation. We propose that WRKY15 negatively regulates VND7 expression indirectly based on (1) the absence of a W-box in the promoter of VND7 and (2) the observation that WRKY15 and VND7 are expressed in different cells in the vascular cylinder, with WRKY15 expressed in the procambial cells and VND7 in the protoxylem poles of procambium and differentiating TEs. Future research is needed to reveal the details underlying the interaction of WRKY15 and VND7 in plant vascular development.

MYB44 competitively inhibits the formation of the MYB340-bHLH2-NAC56 complex to regulate anthocyanin biosynthesis in purple-fleshed sweet potato

BACKGROUND

Anthocyanins, which have important biological functions and have a beneficial effect on human health, notably account for pigmentation in purple-fleshed sweet potato tuberous roots. Individual regulatory factors of anthocyanin biosynthesis have been identified; however, the regulatory network of anthocyanin biosynthesis in purple-fleshed sweet potato is unclear.

RESULTS

We functionally determined that IbMYB340 cotransformed with IbbHLH2 in tobacco and strawberry receptacles induced anthocyanin accumulation, and the addition of IbNAC56a or IbNAC56b caused increased pigmentation. Furthermore, we confirmed the interaction of IbMYB340 with IbbHLH2 and IbNAC56a or IbNAC56b via yeast two-hybrid and firefly luciferase complementation assays; these proteins could form a MYB340-bHLH2-NAC56a or MYB340-bHLH2-NAC56b transcriptional complex to regulate anthocyanin biosynthesis by binding to the IbANS promoter rather than the IbUFGT promoter. Furthermore, it was found by a transient expression system in tobacco leaves that IbMYB44 could decrease anthocyanin accumulation. Moreover, the interaction of IbMYB44 with IbMYB340 and IbNAC56a or IbNAC56b was verified. This result suggested that IbMYB44 acts as a repressor of anthocyanin in sweet potato.

CONCLUSIONS

The repressor IbMYB44 affected anthocyanin biosynthesis by competitively inhibiting the IbMYB340-IbbHLH2-IbNAC56a or IbMYB340-IbbHLH2-IbNAC56b regulatory complex formation. Overall, the present study proposed a novel regulatory network whereby several vital TFs play key roles in regulating anthocyanin biosynthesis, and it provides strong insight into the potential mechanism underlying anthocyanin biosynthesis in sweet potato tuberous roots with purple color.

The Osmotin-Like Protein Gene PdOLP1 Is Involved in Secondary Cell Wall Biosynthesis during Wood Formation in Poplar

Osmotin-like proteins (OLPs) mediate defenses against abiotic and biotic stresses and fungal pathogens in plants. However, no OLPs have been functionally elucidated in poplar. Here, we report an osmotin-like protein designated PdOLP1 from Populus deltoides (Marsh.). Expression analysis showed that PdOLP1 transcripts were mainly present in immature xylem and immature phloem during vascular tissue development in P. deltoides. We conducted phenotypic, anatomical, and molecular analyses of PdOLP1-overexpressing lines and the PdOLP1-downregulated hybrid poplar 84K (Populus alba × Populus glandulosa) (Hybrid poplar 84K PagOLP1, PagOLP2, PagOLP3 and PagOLP4 are highly homologous to PdOLP1, and are downregulated in PdOLP1-downregulated hybrid poplar 84K). The overexpression of PdOLP1 led to a reduction in the radial width and cell layer number in the xylem and phloem zones, in expression of genes involved in lignin biosynthesis, and in the fibers and vessels of xylem cell walls in the overexpressing lines. Additionally, the xylem vessels and fibers of PdOLP1-downregulated poplar exhibited increased secondary cell wall thickness. Elevated expression of secondary wall biosynthetic genes was accompanied by increases in lignin content, dry weight biomass, and carbon storage in PdOLP1-downregulated lines. A PdOLP1 coexpression network was constructed and showed that PdOLP1 was coexpressed with a large number of genes involved in secondary cell wall biosynthesis and wood development in poplar. Moreover, based on transcriptional activation assays, PtobZIP5 and PtobHLH7 activated the PdOLP1 promoter, whereas PtoBLH8 and PtoWRKY40 repressed it. A yeast one-hybrid (Y1H) assay confirmed interaction of PtoBLH8, PtoMYB3, and PtoWRKY40 with the PdOLP1 promoter in vivo. Together, our results suggest that PdOLP1 is a negative regulator of secondary wall biosynthesis and may be valuable for manipulating secondary cell wall deposition to improve carbon fixation efficiency in tree species.

Active DNA demethylation regulates tracheary element differentiation in Arabidopsis

DNA demethylation is important for the erasure of DNA methylation. The role of DNA demethylation in plant development remains poorly understood. Here, we found extensive DNA demethylation in the CHH context around pericentromeric regions and DNA demethylation in the CG, CHG, and CHH contexts at discrete genomic regions during ectopic xylem tracheary element (TE) differentiation. While loss of pericentromeric methylation occurs passively, DNA demethylation at a subset of regions relies on active DNA demethylation initiated by DNA glycosylases ROS1, DML2, and DML3. The ros1 and rdd mutations impair ectopic TE differentiation and xylem development in the young roots of Arabidopsis seedlings. Active DNA demethylation targets and regulates many genes for TE differentiation. The defect of xylem development in rdd is proposed to be caused by dysregulation of multiple genes. Our study identifies a role of active DNA demethylation in vascular development and reveals an epigenetic mechanism for TE differentiation.

Involvement of VNS NAC-domain transcription factors in tracheid formation in Pinus taeda

Vascular plants have two types of water-conducting cells, xylem vessel cells (in angiosperms) and tracheid cells (in ferns and gymnosperms). These cells are commonly characterized by secondary cell wall (SCW) formation and programmed cell death (PCD), which increase the efficiency of water conduction. The differentiation of xylem vessel cells is regulated by a set of NAC (NAM, ATAF1/2 and CUC2) transcription factors, called the VASCULAR-RELATED NAC-DOMAIN (VND) family, in Arabidopsis thaliana Linne. The VNDs regulate the transcriptional induction of genes required for SCW formation and PCD. However, information on the transcriptional regulation of tracheid cell differentiation is still limited. Here, we performed functional analysis of loblolly pine (Pinus taeda Linne) VND homologs (PtaVNS, for VND, NST/SND, SMB-related protein). We identified five PtaVNS genes in the loblolly pine genome, and four of these PtaVNS genes were highly expressed in tissues with tracheid cells, such as shoot apices and developing xylem. Transient overexpression of PtaVNS genes induced xylem vessel cell-like patterning of SCW deposition in tobacco (Nicotiana benthamiana Domin) leaves, and up-regulated the promoter activities of loblolly pine genes homologous to SCW-related MYB transcription factor genes and cellulose synthase genes, as well as to cysteine protease genes for PCD. Collectively, our data indicated that PtaVNS proteins possess transcriptional activity to induce the molecular programs required for tracheid formation, i.e., SCW formation and PCD. Moreover, these findings suggest that the VNS-MYB-based transcriptional network regulating water-conducting cell differentiation in angiosperm and moss plants is conserved in gymnosperms.

PbMC1a/1b regulates lignification during stone cell development in pear (Pyrus bretschneideri) fruit

Programmed cell death (PCD) and secondary cell wall (SCW) thickening in pear fruit are accompanied by the deposition of cellulose and lignin to form stone cells. Metacaspase is an important protease for development, tissue renewal and PCD. The understanding of the molecular mechanism whereby pear (Pyrus) metacaspase promotes PCD and cell wall lignification is still limited. In this study, the Metacaspases gene family (PbMCs) from P. bretschneideri was identified. PbMC1a/1b was associated with lignin deposition and stone cell formation by physiological data, semiquantitative real-time polymerase chain reaction (RT-PCR) and quantitative RT-PCR (qRT-PCR). Relative to wild-type (WT) Arabidopsis, the overexpression of PbMC1a/1b increased lignin deposition and delayed growth, thickened the cell walls of vessels, xylary fibers and interfascicular fibers, and increased the expression of lignin biosynthetic genes. Yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC) and GST pull-down assays indicated that the PbMC1a/1b protein physically interacted with PbRD21. Simultaneously, the transient expression of PbMC1a/1b and PbRD21 led to significant changes in the expression of genes and lignin contents in pear fruits and flesh calli. These results indicate that PbMC1a/1b plays an important role in cell wall lignification, possibly by interacting with PbRD21 to increase the mRNA levels of some lignin synthesis-associated genes and promote the formation of stone cells in pear fruit.

A membrane-associated NAC domain transcription factor XVP interacts with TDIF co-receptor and regulates vascular meristem activity

Vascular stem cell maintenance is regulated by a peptide signaling involving Tracheary Element Differentiation Inhibitory Factor (TDIF) and Receptor TDR/PXY (Phloem intercalated with Xylem) and co-receptor BAK1 (BRI1-associated receptor kinase1). The regulatory mechanism of this signaling pathway is largely unknown despite its importance in stem cell maintenance in the vascular meristem. We report that activation of a NAC domain transcription factor XVP leads to precocious Xylem differentiation, disruption of Vascular Patterning, and reduced cell numbers in vascular bundles. We combined molecular and genetic studies to elucidate the biological functions of XVP. XVP is expressed in the cambium, localized on the plasma membrane and forms a complex with TDIF co-receptors PXY-BAK1. Simultaneous mutation of XVP and its close homologous NAC048 enhances TDIF signaling. In addition, genetics analysis indicated that XVP promotes xylem differentiation through a known master regulator VASCULAR-RELATED NAC-DOMAIN6 (VND6). Expression analyses indicate that XVP activates CLAVATA3/ESR (CLE)-related protein 44 (CLE44), the coding gene of TDIF, whereas TDIF represses XVP expression, suggesting a feedback mechanism. Therefore, XVP functions as a negative regulator of the TDIF-PXY module and fine-tunes TDIF signaling in vascular development. These results shed new light on the mechanism of vascular stem cell maintenance.

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 uncharacterized gene EVE contributes to vessel element dimensions in Populus

The radiation of angiosperms led to the emergence of the vast majority of today's plant species and all our major food crops. Their extraordinary diversification occurred in conjunction with the evolution of a more efficient vascular system for the transport of water, composed of vessel elements. The physical dimensions of these water-conducting specialized cells have played a critical role in angiosperm evolution; they determine resistance to water flow, influence photosynthesis rate, and contribute to plant stature. However, the genetic factors that determine their dimensions are unclear. Here we show that a previously uncharacterized gene, ENLARGED VESSEL ELEMENT (EVE), contributes to the dimensions of vessel elements in Populus, impacting hydraulic conductivity. Our data suggest that EVE is localized in the plasma membrane and is involved in potassium uptake of differentiating xylem cells during vessel development. In plants, EVE first emerged in streptophyte algae, but expanded dramatically among vessel-containing angiosperms. The phylogeny, structure and composition of EVE indicates that it may have been involved in an ancient horizontal gene-transfer event.

Modulation of NAC transcription factor NST1 activity by XYLEM NAC DOMAIN1 regulates secondary cell wall formation in Arabidopsis

In Arabidopsis, secondary cell walls (SCW) are formed in fiber cells and vessel cells in vascular tissue for providing plants with mechanical strength and channels for the long distance transportation of water and nutrients. NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) acts as a key gene for the initiation of SCW formation through a hierarchical transcription network. In this study, we report that NST activity is modulated by the NAC domain transcription factor XYLEM NAC DOMAIN1 (XND1) during plant growth. Using yeast two-hybrid screening and in vivo protein interaction analysis, XND1 was identified as an NST-interacting protein that modulates NST1 activity. XND1 and NST1 were co-localized in the nucleus and the interaction of XND1 with NST1 resulted in inhibition of NST1 transactivation activity. In the process of inflorescence growth, XND1 was expressed with a similar pattern to NST1. Up-regulation of XND1 in fiber cells repressed SCW formation. The study demonstrates that NST1 activity is modulated by XND1 in the regulation of secondary cell walls formation.

Differential Gene Profiling of the Heartwood Formation Process in Taiwania cryptomerioides Hayata Xylem Tissues

Taiwania (Taiwania cryptomerioides) is an important tree species in Taiwan because of the excellent properties of its wood and fascinating color qualities of its heartwood (HW), as well as the bioactive compounds therein. However, limited information is available as to the HW formation of this species. The objective of this research is to analyze the differentially expressed genes (DEGs) during the HW formation process from specific Taiwania xylem tissues, and to obtain genes that might be closely associated with this process. The results indicated that our analyses have captured DEGs representative to the HW formation process of Taiwania. DEGs related to the terpenoid biosynthesis pathway were all up-regulated in the transition zone (TZ) to support the biosynthesis and accumulation of terpenoids. Many DEGs related to lignin biosynthesis, and two DEGs related to pinoresinol reductase (PrR)/pinoresinol lariciresinol reductase (PLR), were up-regulated in TZ. These DEGs together are likely involved in providing the precursors for the subsequent lignan biosynthesis. Several transcription factor-, nuclease-, and protease-encoding DEGs were also highly expressed in TZ, and these DEGs might be involved in the regulation of secondary metabolite biosynthesis and the autolysis of the cellular components of ray parenchyma cells in TZ. These results provide further insights into the process of HW formation in Taiwania.

Hsp70 plays a role in programmed cell death during the remodelling of leaves of the lace plant (Aponogeton madagascariensis)

Lace plant leaves utilize programmed cell death (PCD) to form perforations during development. The role of heat shock proteins (Hsps) in PCD during lace plant leaf development is currently unknown. Hsp70 amounts were measured throughout lace plant leaf development, and the results indicate that it is highest before and during PCD. Increased Hsp70 amounts correlate with raised anthocyanin content and caspase-like protease (CLP) activity. To investigate the effects of Hsp70 on leaf development, whole plants were treated with either of the known regulators of PCD [reactive oxygen species (ROS) or antioxidants] or an Hsp70 inhibitor, chlorophenylethynylsulfonamide (PES-Cl). ROS treatment significantly increased Hsp70 2-fold and CLP activity in early developing leaves, but no change in anthocyanin and the number of perforations formed was observed. Antioxidant treatment significantly decreased Hsp70, anthocyanin, and CLP activity in early leaves, resulting in the fewest perforations. PES-Cl (25 μM) treatment significantly increased Hsp70 4-fold in early leaves, while anthocyanin, superoxide, and CLP activity significantly declined, leading to fewer perforations. Results show that significantly increased (4-fold) or decreased Hsp70 amounts lead to lower anthocyanin and CLP activity, inhibiting PCD induction. Our data support the hypothesis that Hsp70 plays a role in regulating PCD at a threshold in lace plant leaf development. Hsp70 affects anthocyanin content and caspase-like protease activity, and helps regulate PCD during the remodelling of leaves of lace plant, Aponogeton madagascariensis.

The Class II KNOX genes KNAT3 and KNAT7 work cooperatively to influence deposition of secondary cell walls that provide mechanical support to Arabidopsis stems

The transcription factor KNOTTED ARABIDOPSIS THALIANA7 (KNAT7) is a Class II KNOTTED1-like homeobox (KNOX2) gene that, in interfascicular fibres, acts as a negative regulator of secondary cell wall biosynthesis. In addition, knat7 loss-of-function mutants display an irregular xylem (irx) phenotype, suggesting a potential positive regulatory role in xylem vessel secondary cell wall deposition. Although our understanding of the role of KNAT7 is evolving, the function(s) of the closely related KNOX2 genes, KNAT3, KNAT4, and KNAT5, in secondary wall formation still remain unclear. We found that all four Arabidopsis KNOX2 genes were expressed in the inflorescence stems. However, only the knat3 knat7 double mutants showed a phenotype, displaying an enhanced irx phenotypes relative to the single mutants, as well as decreased interfascicular fibre cell wall thickness. Moreover, knat3 knat7 double mutants had reduced stem tensile and flexural strength compared with wild-type and single mutants. In contrast, KNAT3 overexpression resulted in thicker interfascicular fibre secondary cell walls in inflorescence stems, suggesting a potential positive regulation in interfascicular fibre secondary wall development. This work identifies KNAT3 as a potential transcriptional activator working together with KNAT7 to promote secondary cell wall biosynthesis in xylem vessels, while concurrently acting antagonistically with KNAT7 to influence secondary wall formation in interfascicular fibres.

The Progression of Xylem Vessel Cell Differentiation is Dependent on the Activity Level of VND7 in Arabidopsis thaliana

Xylem vessels are important for water conduction in vascular plants. The VASCULAR-RELATED NAC-DOMAIN (VND) family proteins, master regulators of xylem vessel cell differentiation in Arabidopsis thaliana, can upregulate a set of genes required for xylem vessel cell differentiation, including those involved in secondary cell wall (SCW) formation and programmed cell death (PCD); however, it is not fully understood how VND activity levels influence these processes. Here, we examined the Arabidopsis VND7-VP16-GR line, in which VND7 activity is post-translationally activated by treatments with different concentrations of dexamethasone (DEX), a synthetic glucocorticoid. Our observations showed that 1 nM DEX induced weak SCW deposition, but not PCD, whereas 10 or 100 nM DEX induced both SCW deposition and PCD. The decreased chlorophyll contents and SCW deposition were apparent after 24 h of 100 nM DEX treatment, but became evident only after 48 h of 10 nM DEX treatment. Moreover, the lower DEX concentrations delayed the upregulation of VND7 downstream genes, and decreased their induction levels. They collectively suggest that the regulation of VND activity is important not only to initiate xylem vessel cell differentiation, but also regulate the quality of the xylem vessels through VND-activity-dependent upregulation of the PCD- and SCW-related genes.

The Medicago truncatula nodule identity gene MtNOOT1 is required for coordinated apical-basal development of the root

BACKGROUND

Legumes can utilize atmospheric nitrogen by hosting nitrogen-fixing bacteria in special lateral root organs, called nodules. Legume nodules have a unique ontology, despite similarities in the gene networks controlling nodule and lateral root development. It has been shown that Medicago truncatula NODULE ROOT1 (MtNOOT1) is required for the maintenance of nodule identity, preventing the conversion to lateral root development. MtNOOT1 and its orthologs in other plant species -collectively called the NOOT-BOP-COCH-LIKE (NBCL) family- specify boundary formation in various aerial organs. However, MtNOOT1 is not only expressed in nodules and aerial organs, but also in developing roots, where its function remains elusive.

RESULTS

We show that Mtnoot1 mutant seedlings display accelerated root elongation due to an enlarged root apical meristem. Also, Mtnoot1 mutant roots are thinner than wild-type and are delayed in xylem cell differentiation. We provide molecular evidence that the affected spatial development of Mtnoot1 mutant roots correlates with delayed induction of genes involved in xylem cell differentiation. This coincides with a basipetal shift of the root zone that is susceptible to rhizobium-secreted symbiotic signal molecules.

CONCLUSIONS

Our data show that MtNOOT1 regulates the size of the root apical meristem and vascular differentiation. Our data demonstrate that MtNOOT1 not only functions as a homeotic gene in nodule development but also coordinates the spatial development of the root.

A Positive Feedback Loop Comprising LHW-TMO5 and Local Auxin Biosynthesis Regulates Initial Vascular Development in Arabidopsis Roots

The phytohormone auxin governs various developmental processes in plants including vascular formation. Auxin transport and biosynthesis are important factors in determining auxin distribution in tissues. Although the role of auxin transport in vein pattern formation is widely recognized, that of auxin biosynthesis in vascular development is poorly understood. Heterodimer complexes comprising two basic helix-loop-helix protein families, LONESOME HIGHWAY (LHW) and TARGET OF MONOPTEROS5 (TMO5)/TMO5-LIKE1 (T5L1), are master transcriptional regulators of the initial process of vascular development. The LHW-TMO5/T5L1 dimers regulate vascular initial cell production, vascular cell proliferation and xylem fate determination in the embryo and root apical meristem (RAM). In this study, we investigated the function of local auxin biosynthesis in initial vascular development in RAM. Results showed that LHW-T5L1 upregulated the expression of YUCCA4 (YUC4), a key auxin biosynthesis gene. The expression of YUC4 was essential for promoting xylem differentiation and vascular cell proliferation in RAM. Conversely, auxin biosynthesis was required for maintaining the expression levels of LHW, TMO5/T5L1 and their targets. Our results suggest that local auxin biosynthesis forms a positive feedback loop for fine-tuning the level of LHW-TMO5/T5L1, which is necessary for initiating vascular development.

PdWND3A, a wood-associated NAC domain-containing protein, affects lignin biosynthesis and composition in Populus

BACKGROUND

Plant secondary cell wall is a renewable feedstock for biofuels and biomaterials production. Arabidopsis VASCULAR-RELATED NAC DOMAIN (VND) has been demonstrated to be a key transcription factor regulating secondary cell wall biosynthesis. However, less is known about its role in the woody species.

RESULTS

Here we report the functional characterization of Populus deltoides WOOD-ASSOCIATED NAC DOMAIN protein 3 (PdWND3A), a sequence homolog of Arabidopsis VND4 and VND5 that are members of transcription factor networks regulating secondary cell wall biosynthesis. PdWND3A was expressed at higher level in the xylem than in other tissues. The stem tissues of transgenic P. deltoides overexpressing PdWND3A (OXPdWND3A) contained more vessel cells than that of wild-type plants. Furthermore, lignin content and lignin monomer syringyl and guaiacyl (S/G) ratio were higher in OXPdWND3A transgenic plants than in wild-type plants. Consistent with these observations, the expression of FERULATE 5-HYDROXYLASE1 (F5H1), encoding an enzyme involved in the biosynthesis of sinapyl alcohol (S unit monolignol), was elevated in OXPdWND3A transgenic plants. Saccharification analysis indicated that the rate of sugar release was reduced in the transgenic plants. In addition, OXPdWND3A transgenic plants produced lower amounts of biomass than wild-type plants.

CONCLUSIONS

PdWND3A affects lignin biosynthesis and composition and negatively impacts sugar release and biomass production.

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.

Genome-Wide Investigation of the NAC Gene Family and Its Potential Association with the Secondary Cell Wall in Moso Bamboo

NAC (NAM, ATAF, and CUC) transcription factors (TFs) are implicated in the transcriptional regulation of diverse processes and have been characterized in a number of plant species. However, NAC TFs are still not well understood in bamboo, especially their potential association with the secondary cell wall (SCW). Here, 94 PeNACs were identified and characterized in moso bamboo (Phyllostachys edulis). Based on their gene structures and conserved motifs, the PeNACs were divided into 11 groups according to their homologs in Arabidopsis. PeNACs were expressed variously in different tissues of moso bamboo, suggesting their functional diversity. Fifteen PeNACs associated with the SCW were selected for co-expression analysis and validation. It was predicted that 396 genes were co-expressed with the 15 PeNACs, in which 16 and 55 genes were involved in the lignin catabolic process and cellulose biosynthetic process respectively. As the degree of lignification in the growing bamboo shoots increased, all 15 PeNACs were upregulated with a trend of rising first and then decreasing except PeNAC37, which increased continuously. These results indicated that these PeNACs might play important roles in SCW biosynthesis and lignification in bamboo shoots. Seven of 15 PeNACs had been found positively co-expressed with seven PeMYBs, and they had similar expression patterns with those of the PeMYBs in bamboo shoots. The targeted sites of miR164 were found in 16 PeNACs, of which three PeNACs associated with SCW were validated to have an opposite expression trend to that of miR164 in growing bamboo shoots. In addition, three PeNACs were selected and verified to have self-activation activities. These results provide comprehensive information of the NAC gene family in moso bamboo, which will be helpful for further functional studies of PeNACs to reveal the molecular regulatory mechanisms of bamboo wood property.

Affinity-based high-resolution analysis of DNA binding by VASCULAR-RELATED NAC-DOMAIN7 via fluorescence correlation spectroscopy

VASCULAR-RELATED NAC-DOMAIN7 (VND7) is the master transcription factor for vessel element differentiation in Arabidopsis thaliana. To identify the cis-acting sequence(s) bound by VND7, we employed fluorescence correlation spectroscopy (FCS) to find VND7-DNA interactions quantitatively. This identified an 18-bp sequence from the promoter of XYLEM CYSTEINE PEPTIDASE1 (XCP1), a direct target of VND7. A quantitative assay for binding affinity between VND7 and the 18-bp sequence revealed the core nucleotides contributing to specific binding between VND7 and the 18-bp sequence. Moreover, by combining the systematic evolution of ligands by exponential enrichment (SELEX) technique with known consensus sequences, we defined a motif termed the Ideal Core Structure for binding by VND7 (ICSV). We also used FCS to search for VND7 binding sequences in the promoter regions of other direct targets. Taking these data together, we proposed that VND7 preferentially binds to the ICSV sequence. Additionally, we found that substitutions among the core nucleotides affected transcriptional regulation by VND7 in vivo, indicating that the core nucleotides contribute to vessel-element-specific gene expression. Furthermore, our results demonstrate that FCS is a powerful tool for unveiling the DNA-binding properties of transcription factors.

Expression Analysis of the NAC Transcription Factor Family of Populus in Response to Salt Stress

Research Highlights: Sequence phylogeny, genome organisation, gene structure, conserved motifs, promoter cis-element and expression profiling of poplar NACs related to salt stress were detected. In addition, expression of two salt-induced NACs was analysed. Background and Objectives: NAC transcription factor (TF) proteins are involved in a wide range of functions during plant development and stress-related endurance processes. To understand the function of Populus NAC TFs in salt stress tolerance, we characterised the structure and expression profile of a total of 289 NAC members. Materials and Methods: Sequence phylogeny, genome organisation, gene structure, motif composition and promoter cis-element were detected using bioinformatics. The expression pattern of Populus NAC TFs under salt stress was also detected using RNA-Seq and RT-qPCR. Results: Synteny analysis showed that 46 and 37 Populus NAC genes were involved in whole-genome duplication and tandem duplication events, respectively. The expression pattern of Populus NAC TFs under salt stress showed the expression of the 289 PtNACs of 84K poplar was induced. Similar expression trends of NACs were found in Populus simonii × P. nigra T. S. Hwang et Liang and Arabidopsis thaliana (L.) Heynh. Conclusions: The correlation analysis showed that the expression of two differentially expressed NAC genes PtNAC024 and PtNAC182 was significantly associated with most of the 63 differentially expressed genes tested. The expression of PtNAC024 and PtNAC182 in different tissues was also analysed in silico and different expression patterns were found. Together, this study provides a solid basis to explore stress-related NAC TF functions in Populus salt tolerance and 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.

Plant proteases during developmental programmed cell death

Proteases are among the key regulators of most forms of programmed cell death (PCD) in animals. Many PCD processes have also been associated with protease expression or activation in plants, However, functional evidence for the roles and actual modes of action of plant proteases in PCD remains surprisingly limited. In this review, we provide an update on protease involvement in the context of developmentally regulated plant PCD. To illustrate the diversity of protease functions, we focus on several prominent developmental PCD processes, including xylem and tapetum maturation, suspensor elimination, endosperm degradation, and seed coat formation, as well as plant senescence processes. Despite the substantial advances in the field, protease functions are often only correlatively linked to developmental PCD, and the specific molecular roles of proteases in many developmental PCD processes remain to be elucidated.

Single cell RNA sequencing and its promise in reconstructing plant vascular cell lineages

In the last decade, recent advances in single-cell RNA sequencing coupled with computational algorithms have opened new avenues to study the cell type composition of tissues and organs as well as to infer cell developmental trajectories. These technologies have been used to resolve and map atlases of tissues and organs in many animal species as well as to further order cell developmental trajectories. Despite these advances in animals, many of the current plant cell type expression profiles confound multiple developmental stages preventing an accurate monitoring of cell lineage. In this review, we propose how the application of single-cell sequencing will improve our molecular understanding of cell type differentiation. Using root vascular cells as a model, we highlight the potential of single cell transcriptomics as well as its limitations to monitor the progression of vascular maturation. By comparing cell morphology, functionality and gene expression, we aim to provide a new perspective of plant cell type differentiation.

Global Gene Expression of Seed Coat Tissues Reveals a Potential Mechanism of Regulating Seed Size Formation in Castor Bean

The physiological and molecular basis of seed size formation is complex, and the development of seed coat (derived from integument cells) might be a critical factor that determines seed size formation for many endospermic seeds. Castor bean (Ricinus communis L.), a model system of studying seed biology, has large and persistent endosperm with a hard seed coat at maturity. Here, we investigated the potential molecular mechanisms underlying seed size formation in castor bean by comparing the difference between global gene expression within developing seed coat tissues between the large-seed ZB107 and small-seed ZB306. First, we observed the cell size of seed coat and concluded that the large seed coat area of ZB107 resulted from more cell numbers (rather than cell size). Furthermore, we found that the lignin proportion of seed coat was higher in ZB306. An investigation into global gene expression of developing seed coat tissues revealed that 815 genes were up-regulated and 813 were down-regulated in ZB306 relative to ZB107. Interestingly, we found that many genes involved in regulating cell division were up-regulated in ZB107, whereas many genes involved in regulating lignin biosynthesis (including several NAC members, as well as MYB46/83 and MYB58/63) and in mediating programmed cell death (such as CysEP1 and βVPE) were up-regulated in ZB306. Furthermore, the expression patterns of the genes mentioned above indicated that the lignification of seed coat tissues was enhanced and occurred earlier in the developing seeds of ZB306. Taken together, we tentatively proposed a potential scenario for explaining the molecular mechanisms of seed coat governing seed size formation in castor bean by increasing the cell number and delaying the onset of lignification in seed coat tissues in large-seed ZB107. This study not only presents new information for possible modulation of seed coat related genes to improve castor seed yield, but also provides new insights into understanding the molecular basis of seed size formation in endospermic seeds with hard seed coat.

PvNAC1 increases biomass and enhances salt tolerance by decreasing Na+ accumulation and promoting ROS scavenging in switchgrass (Panicum virgatum L.)

Switchgrass (Panicum virgatum L.) is a bioenergy crop; thus, it is important to improve biomass to effectively produce bioethanol, particularly under adverse stress conditions. NAC transcription factors are involved in the abiotic stress response. PvNAC1 was isolated in the nucleus of switchgrass, with its C-terminal region containing a transcriptional activation domain. PvNAC1 expression was induced by dehydration, salt, H₂O₂, and abscisic acid treatments. Overexpressing (OE) PvNAC1 improved growth performance, leading to significantly taller and heavier (dry weight) plants. Moreover, cellulose content was significantly higher in OE plants, indicating that PvNAC1 plays an important role regulating growth and bioethanol production. PvNAC1 RNA interference (RNAi) switchgrass plants exhibited reduced dry weight and cellulose content. OE PvNAC1 enhanced tolerance to salt stress, through higher reactive oxygen species scavenging ability and less Na⁺ and more K⁺ accumulation in roots and shoots. RNAi plants were more sensitive to salt stress. The quantitative polymerase chain reaction results revealed that some stress responsive genes, three antioxidant enzymatic genes, and an ion homeostasis-related gene were upregulated in OE plants and downregulated in RNAi plants. These results show that PvNAC1 functions as a transcriptional activator in response to salt stress and growth.

In vitro differentiation of tracheary elements is induced by suppression of Arabidopsis phytoglobins

Differentiation of tracheary elements (TEs) in vitro was affected by the expression level of the Arabidopsis thaliana Col-0 phytoglobins (Pgbs). Over-expression of Pgb1 or Pgb2 (35S:Pgb1 or 35S:Pgb2 lines) reduced the differentiation process while suppression of either Pgb (Pgb1-RNAi or pgb2 lines) enhanced the production of TEs. The inductive effect of Pgb suppression on TE differentiation was linked to the reduced expression of the transcription factor MYC2. Suppression of this gene, observed under conditions of high NO levels or low Pgb expression, was sufficient to promote TE differentiation, while its over-expression abolished the promotive effect of Pgb suppression on the differentiation process. Cells in which MYC2 was mutated accumulated ethylene which induced the expression of the homeodomain-leucine zipper (HD-Zip) III ATHB8. Production of ethylene was reduced in cells over-expressing MYC2 in a WT or a pgb mutant background. While stabilizing procambial cell specification, ATHB8 in known to activate downstream components triggering programmed cell death (PCD) and modifications of cell wall components, required steps of the TE differentiation process. Collectively, we provide evidence that in addition to their recognised participation in stress responses, Pgbs may play a key role in the specification of cell fate during development.

A Rho-actin signaling pathway shapes cell wall boundaries in Arabidopsis xylem vessels

Patterned cell wall deposition is crucial for cell shapes and functions. In Arabidopsis xylem vessels, ROP11 GTPase locally inhibits cell wall deposition through microtubule disassembly, inducing pits in cell walls. Here, we show that an additional ROP signaling pathway promotes cell wall growth at pit boundaries. Two proteins, Boundary of ROP domain1 (BDR1) and Wallin (WAL), localize to pit boundaries and regulate cell wall growth. WAL interacts with F-actin and promotes actin assembly at pit boundaries while BDR1 is a ROP effector. BDR1 interacts with WAL, suggesting that WAL could be recruited to the plasma membrane by a ROP-dependent mechanism. These results demonstrate that BDR1 and WAL mediate a ROP-actin pathway that shapes pit boundaries. The study reveals a distinct machinery in which two closely associated ROP pathways oppositely regulate cell wall deposition patterns for the establishment of tiny but highly specialized cell wall domains.

The α-Aurora Kinases Function in Vascular Development in Arabidopsis

The Aurora kinases are serine/threonine kinases with conserved functions in mitotic cell division in eukaryotes. In Arabidopsis, Aurora kinases play important roles in primary meristem maintenance, but their functions in vascular development are still elusive. We report a dominant xdi-d mutant showing the xylem development inhibition (XDI) phenotype. Gene identification and transgenic overexpression experiments indicated that the activation of the Arabidopsis Aurora 2 (AtAUR2) gene is responsible for the XDI phenotype. In contrast, the aur1-2 aur2-2 double mutant plants showed enhanced differentiation of phloem and xylem cells, indicating that the Aurora kinases negatively affect xylem differentiation. The transcript levels of key regulatory genes in vascular cell differentiation, i.e. ALTERED PHLOEM DEVELOPMENT (APL), VASCULAR-RELATED NAC-DOMAIN 6 (VND6) and VND7, were higher in the aur1-2 aur2-2 double mutant and lower in xdi-d mutants compared with the wild-type plants, further supporting the functions of α-Aurora kinases in vascular development. Gene mutagenesis and transgenic studies showed that protein phosphorylation and substrate binding, but not protein dimerization and ubiquitination, are critical for the biological function of AtAUR2. These results indicate that α-Aurora kinases play key roles in vascular cell differentiation in Arabidopsis.

Creating vessel elements in vitro: Towards a comprehensive understanding of the molecular basis of xylem vessel element differentiation

Xylem is an essential conductive tissue in vascular plants, and secondary cell wall polymers found in xylem vessel elements, such as cellulose, hemicellulose, and lignin, are promising sustainable bioresources. Thus, understanding the molecular mechanisms underlying xylem vessel element differentiation is an important step towards increasing woody biomass and crop yields. Establishing in vitro induction systems, in which vessel element differentiation is induced by phytohormonal stimuli or by overexpression of specific transcription factors, has been vital to this research. In this review, we present an overview of these in vitro induction systems, and describe two recently developed in vitro induction systems, VISUAL (Vascular cell Induction culture System Using Arabidopsis Leaves) and the KDB system. Furthermore, we discuss the potentials and limitations of each of these new in vitro induction systems for advancing our understanding of the molecular mechanisms driving xylem vessel element differentiation.

Xylem Cell Wall Formation in Pioneer Roots and Stems of Populus trichocarpa (Torr. & Gray)

Regulation of gene expression, as determined by the genetics of the tree species, is a major factor in determining wood quality. Therefore, the identification of genes that play a role in xylogenesis is extremely important for understanding the mechanisms shaping the plant phenotype. Efforts to develop new varieties characterized by higher yield and better wood quality will greatly benefit from recognizing and understanding the complex transcriptional network underlying wood development. The present study provides a detailed comparative description of the changes that occur in genes transcription and the biosynthesis of cell-wall-related compounds during xylogenesis in Populus trichocarpa pioneer roots and stems. Even though results of microarray analysis indicated that only approximately 10% of the differentially expressed genes were common to both organs, many fundamental mechanisms were similar; e.g. the pattern of expression of genes involved in the biosynthesis of cell wall proteins, polysaccharides, and lignins. Gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) shows that the composition of monosaccharides was also very similar, with an increasing amount of xylose building secondary cell wall hemicellulose and pectins, especially in the stems. While hemicellulose degradation was typical for stems, possibly due to the intensive level of cell wall lignification. Notably, the main component of lignins in roots were guiacyl units, while syringyl units were dominant in stems, where fibers are especially needed for support. Our study is the first comprehensive analysis, at the structural and molecular level, of xylogenesis in under- and aboveground tree parts, and clearly reveals the great complexity of molecular mechanisms underlying cell wall formation and modification during xylogenesis in different plant organs.