Integrative analysis of wood biomass and developing xylem transcriptome provide insights into mechanisms of lignin biosynthesis in wood formation of Pinus massoniana

Wood formation originates in the biosynthesis of lignin and further leads to secondary cell wall (SCW) biosynthesis in woody plants. Masson pine (Pinus massoniana Lamb) is an economically important industrial timber tree, and its wood yield affects the stable development of the paper industry. However, the regulatory mechanisms of SCW formation in Masson pine are still unclear. In this study, we characterized PmMYB4, which is a Pinus massoniana MYB gene involved in SCW biosynthesis. The open reading frame (ORF) of PmMYB4 was 1473 bp, which encoded a 490 aa protein and contained two distinctive R2 and R3 MYB domains. It was shown to be a transcription factor, with the highest expression in semi-lignified stems. We overexpressed PmMYB4 in tobacco. The results indicated that PmMYB4 overexpression increased lignin deposition, SCW thickness, and the expression of genes involved in SCW formation. Further analysis indicated that PmMYB4 bound to AC-box motifs and might directly activate the promoters of genes (PmPAL and PmCCoAOMT) involved in SCW biosynthesis. In addition, PmMYB4-OE(over expression) transgenic lines had higher lignin and cellulose contents and gene expression than control plants, indicating that PmMYB4 regulates SCW mainly by targeting lignin biosynthetic genes. In summary, this study illustrated the MYB-induced SCW mechanism in Masson pine and will facilitate enhanced lignin and cellulose synthesis in genetically engineered trees.

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TheEucalyptuslinker histone variant EgH1.3 cooperates with the transcription factor EgMYB1 to control lignin biosynthesis during wood formation

New Phytologist ◽

10.1111/nph.14129 ◽

2016 ◽

Vol 213 (1) ◽

pp. 287-299 ◽

Cited By ~ 24

Author(s):

Marçal Soler ◽

Anna Plasencia ◽

Romain Larbat ◽

Cécile Pouzet ◽

Alain Jauneau ◽

...

Keyword(s):

Transcription Factor ◽

Lignin Biosynthesis ◽

Wood Formation ◽

Histone Variant

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Cloning and Functional Analysis of Lignin Biosynthesis Genes Cf4CL and CfCCoAOMT in Cryptomeria fortunei

Genes ◽

10.3390/genes10080619 ◽

2019 ◽

Vol 10 (8) ◽

pp. 619 ◽

Cited By ~ 2

Author(s):

Zhenhao Guo ◽

Hui Hua ◽

Jin Xu ◽

Jiaxing Mo ◽

Hui Zhao ◽

...

Keyword(s):

Gene Editing ◽

Bioinformatics Analysis ◽

Southern China ◽

Lignin Biosynthesis ◽

Wood Formation ◽

Primary Component ◽

Vascular Cambium ◽

Timber Species ◽

Wood Production ◽

Lignin Synthesis

Cryptomeria fortunei, also known as the Chinese cedar, is an important timber species in southern China. The primary component of its woody tissues is lignin, mainly present in secondary cell walls. Therefore, continuous lignin synthesis is crucial for wood formation. In this study, we aimed to discover key genes involved in lignin synthesis expressed in the vascular cambium of C. fortunei. Through transcriptome sequencing, we detected expression of two genes, 4CL and CCoAOMT, known to be homologous to enzymes involved in the lignin synthesis pathway. We studied the function of these genes through bioinformatics analysis, cloning, vascular cambium expression analysis, and transgenic cross-species functional validation studies. Our results show that Cf4CL and CfCCoAOMT do indeed function in the pathway of lignin synthesis and likely perform this function in C. fortunei. They are prime candidates for future (gene-editing) studies aimed at optimizing C. fortunei wood production.

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Global Transcriptomic Profile Analysis of Genes Involved in Lignin Biosynthesis and Accumulation Induced by Boron Deficiency in Poplar Roots

Biomolecules ◽

10.3390/biom9040156 ◽

2019 ◽

Vol 9 (4) ◽

pp. 156 ◽

Cited By ~ 4

Author(s):

Wan-Long Su ◽

Na Liu ◽

Li Mei ◽

Jie Luo ◽

Yi-Jie Zhu ◽

...

Keyword(s):

Histidine Kinase ◽

Theoretical Basis ◽

Reference Data ◽

Profile Analysis ◽

Expression Patterns ◽

Lignin Biosynthesis ◽

Wood Formation ◽

Boron Deficiency ◽

Rna Seq ◽

Lignin Accumulation

To uncover the transcriptomic mechanism of lignin accumulation caused by boron deficiency (BD), Nanlin895 (Populus × euramericana “Nanlin895”) was subjected to control (CK, 0.25 mg·L−1) and BD (0 mg·L−1) treatments for 3 days. RNA-Seq was carried out to survey the expression patterns of the lignin-regulated biosynthetic genes in response to BD. The results showed that 5946 genes were identified as differentially expressed genes (DEGs), 2968 (44.2%) of which were upregulated and 3318 (55.8%) of which were downregulated in response to BD. Among them, the expression of lignin monomer biosynthetic (PAL, CCR, CAD, COMT, F5H, PER/LAC) and modulated genes, for example, transcription factors (MYBs) and hormone signal regulating genes (GIDs, histidine kinase 1, coronatine-insensitive protein 1), were upregulated, and some hormone signal regulating genes, such as AUXs and BR-related (sterol methyltransferases), were downregulated under BD treatment. There are also some genes that were screened as candidates for an association with wood formation, which will be used for the further analysis of the function of lignin formation. These results provide an important theoretical basis and reference data in plant for further research on the mechanism of lignin accumulation under BD.

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Uncovering miRNA-mRNA Regulatory Modules in Developing Xylem of Pinus massoniana via Small RNA and Degradome Sequencing

International Journal of Molecular Sciences ◽

10.3390/ijms221810154 ◽

2021 ◽

Vol 22 (18) ◽

pp. 10154

Author(s):

Tengfei Shen ◽

Mengxuan Xu ◽

Haoran Qi ◽

Yuanheng Feng ◽

Zhangqi Yang ◽

...

Keyword(s):

Small Rna ◽

Target Genes ◽

Higher Plants ◽

Raw Materials ◽

Pinus Massoniana ◽

Wood Formation ◽

Mineral Elements ◽

Small Rna Sequencing ◽

Degradome Sequencing ◽

Differentially Expressed Mirnas

Xylem is required for the growth and development of higher plants to provide water and mineral elements. The thickening of the xylem secondary cell wall (SCW) not only improves plant survival, but also provides raw materials for industrial production. Numerous studies have found that transcription factors and non-coding RNAs regulate the process of SCW thickening. Pinus massoniana is an important woody tree species in China and is widely used to produce materials for construction, furniture, and packaging. However, the target genes of microRNAs (miRNAs) in the developing xylem of P. massoniana are not known. In this study, a total of 25 conserved miRNAs and 173 novel miRNAs were identified via small RNA sequencing, and 58 differentially expressed miRNAs were identified between the developing xylem (PM_X) and protoplasts isolated from the developing xylem (PM_XP); 26 of these miRNAs were significantly up-regulated in PM_XP compared with PM_X, and 32 were significantly down-regulated. A total of 153 target genes of 20 conserved miRNAs and 712 target genes of 113 novel miRNAs were verified by degradome sequencing. There may be conserved miRNA-mRNA modules (miRNA-MYB, miRNA-ARF, and miRNA-LAC) involved in softwood and hardwood formation. The results of qRT-PCR-based parallel validation were in relatively high agreement. This study explored the potential regulatory network of miRNAs in the developing xylem of P. massoniana and provides new insights into wood formation in coniferous species.

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Expression of three phenylpropanoid pathway genes in Scots pine (Pinus sylvestris L.) in open-pollinated families with differing relative wood densities during early and late wood formation

Silvae Genetica ◽

10.1515/sg-2015-0014 ◽

2015 ◽

Vol 64 (1-6) ◽

pp. 148-159 ◽

Cited By ~ 1

Author(s):

K. Kanberga-Silina ◽

A. Jansons ◽

Dainis Rungis

Keyword(s):

Gene Expression ◽

Wood Density ◽

Scots Pine ◽

Lignin Content ◽

Lignin Biosynthesis ◽

Wood Formation ◽

Phenylpropanoid Pathway ◽

Structural Development ◽

Late Wood ◽

Forestry Production

Abstract Wood volume and quality are the most important aspects of commercial forestry production, and studies of wood formation are important in order to increase the value and efficiency of forestry production. The phenylpropanoid pathway produces various compounds with diverse functions both for plant defence against biotic and abiotic stress as well as structural development. One of the main roles is monolignol production for lignin biosynthesis, which is a crucial aspect of wood formation. For this study three candidate genes involved in lignin biosynthesis were selected: phenylalanine ammonialyase (PAL1), cinnamyl alcohol dehydrogenase (CAD) and cinnamoyl-CoA reductase (CCR). Candidate gene expression was analysed in selected individuals with high and low wood density from open-pollinated Scots pine families during early wood (EW) and late wood (LW) formation and correlation between expression of these genes, total lignin content, and wood density was determined. Wood density values for analysed trees were similar within tree families but differed significantly between families with high and low wood density (p=1,06E-20). Wood density was slightly negatively correlated with lignin content (r=-0.36, p=0.038), but only in individuals in the high density wood group. In trees with low wood density, expression of the CAD gene was significantly lower in late wood formation compared to early wood (p=0.00179). In trees with high wood density, expression of the PAL1 gene was five times higher during early wood formation compared to late wood formation. A positive correlation was detected between PAL1 and CCR gene expression during early wood formation (r=0.804) and late wood formation (r=0.466).

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Integrative Analysis of the Core Fruit Lignification Toolbox in Pear Reveals Targets for Fruit Quality Bioengineering

Biomolecules ◽

10.3390/biom9090504 ◽

2019 ◽

Vol 9 (9) ◽

pp. 504 ◽

Cited By ~ 4

Author(s):

Yunpeng Cao ◽

Xiaoxu Li ◽

Lan Jiang

Keyword(s):

Fruit Quality ◽

Expression Patterns ◽

Lignin Biosynthesis ◽

Integrative Analysis ◽

Bimolecular Fluorescence Complementation ◽

Pear Fruit ◽

Cell Content ◽

Tandem Gene Duplication ◽

Stone Cell ◽

Chinese White

Stone cell content is an important factor affecting pear fruit flavor. Lignin, a major component of pear stone cells, hinders the quality and value of commercial fruit. The completion of the Chinese white pear (Pyrus bretschneideri) genome sequence provides an opportunity to perform integrative analysis of the genes encoding the eleven protein families (i.e., PAL, C4H, 4CL, HCT, C3H, CSE, CCoAOMT, CCR, F5H, COMT, and CAD) in the phenylpropanoid pathway. Here, a systematic study based on expression patterns and phylogenetic analyses was performed to identify the members of each gene family potentially involved in the lignification in the Chinese white pear. The phylogenetic analysis suggested that 35 P. bretschneideri genes belong to bona fide lignification clade members. Compared to other plants, some multigene families are expanded by tandem gene duplication, such as HCT, C3H, COMT, and CCR. RNA sequencing was used to study the expression patterns of the genes in different tissues, including leaf, petal, bud, sepal, ovary, stem, and fruit. Eighteen genes presented a high expression in fruit, indicating that these genes may be involved in the biosynthesis of lignin in pear fruit. Similarly to what has been observed for Populus trichocarpa, a bimolecular fluorescence complementation (BiFC) experiment indicated that P. bretschneideri C3H and C4H might also interact with each other to regulate monolignol biosynthesis in P. bretschneideri, ultimately affecting the stone cell content in pear fruits. The identification of the major genes involved in lignin biosynthesis in pear fruits provides the basis for the development of strategies to improve fruit quality.

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Exogenous Brassinosteroid Facilitates Xylem Development in Pinus massoniana Seedlings

International Journal of Molecular Sciences ◽

10.3390/ijms22147615 ◽

2021 ◽

Vol 22 (14) ◽

pp. 7615

Author(s):

Fuhua Fan ◽

Zijing Zhou ◽

Huijuan Qin ◽

Jianhui Tan ◽

Guijie Ding

Keyword(s):

Molecular Mechanisms ◽

Lignin Content ◽

Secondary Growth ◽

Pinus Massoniana ◽

Wood Formation ◽

Dependent Manner ◽

Xylem Development ◽

Lignin Synthesis ◽

Phenylpropanoid Biosynthesis ◽

Endogenous Phytohormone

Brassinosteroids (BRs) are known to be essential regulators for wood formation in herbaceous plants and poplar, but their roles in secondary growth and xylem development are still not well-defined, especially in pines. Here, we treated Pinus massoniana seedlings with different concentrations of exogenous BRs, and assayed the effects on plant growth, xylem development, endogenous phytohormone contents and gene expression within stems. Application of exogenous BR resulted in improving development of xylem more than phloem, and promoting xylem development in a dosage-dependent manner in a certain concentration rage. Endogenous hormone determination showed that BR may interact with other phytohormones in regulating xylem development. RNA-seq analysis revealed that some conventional phenylpropanoid biosynthesis- or lignin synthesis-related genes were downregulated, but the lignin content was elevated, suggesting that new lignin synthesis pathways or other cell wall components should be activated by BR treatment in P. massoniana. The results presented here reveal the foundational role of BRs in regulating plant secondary growth, and provide the basis for understanding molecular mechanisms of xylem development in P. massoniana.

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RNA-Seq analysis of differential gene expression in Betula luminifera xylem during the early stages of tension wood formation

PeerJ ◽

10.7717/peerj.5427 ◽

2018 ◽

Vol 6 ◽

pp. e5427 ◽

Cited By ~ 3

Author(s):

Miaomiao Cai ◽

Huahong Huang ◽

Fei Ni ◽

Zaikang Tong ◽

Erpei Lin ◽

...

Keyword(s):

Gene Expression ◽

Tension Wood ◽

Molecular Mechanisms ◽

Southern China ◽

Lignin Biosynthesis ◽

Wood Formation ◽

Cellulose Synthesis ◽

Early Stages ◽

Transcriptional Changes ◽

Betula Luminifera

Background Betula luminifera H. Winkler, which is widely distributed in southern China, is an economically important broadleaf tree species. However, little genomic information of B. luminifera is available, and little is known about the molecular mechanisms of wood formation in this species. Meanwhile, few efforts have focused on investigating the early transcriptional changes during tension wood formation in woody plants. Results A reference transcriptome dataset was first generated containing 45,700 Unigenes, and 35,135 (76.9%) Unigenes were annotated by a BLAST similarity search against four public databases. Then, based on an anatomical investigation, the global gene expression changes during the early stages of tension wood formation were analyzed. Gene expression profiling showed that a total of 13,273 Unigenes were differentially regulated during the early stages of tension wood formation. Most genes involved in cellulose and lignin biosynthesis were highlighted to reveal their biological importance in tension wood formation. In addition, the transcription levels of many genes involved in the auxin response pathway were significantly changed during the early stages of tension wood formation. Furthermore, 18 TFs co-expressed with key enzymes of cellulose synthesis were identified. Conclusions Our results revealed the transcriptional changes associated with TW formation and identified potential key genes in the regulation of this process. These results will help to dissect the molecular mechanism of wood formation and provide key candidate genes for marker-assisted selection in B. luminifera.

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Monolignol glucosides as intermediate compounds in lignin biosynthesis. Revisiting the cell wall lignification and new 13C-tracer experiments with Ginkgo biloba and Magnolia liliiflora

Holzforschung ◽

10.1515/hf-2015-0224 ◽

2016 ◽

Vol 70 (9) ◽

pp. 801-810 ◽

Cited By ~ 9

Author(s):

Noritsugu Terashima ◽

Chisato Ko ◽

Yasuyuki Matsushita ◽

Ulla Westermark

Keyword(s):

Cell Wall ◽

Early Stage ◽

Lignin Biosynthesis ◽

Wood Formation ◽

Plant Evolution ◽

Pool Size ◽

Stable Form ◽

Reaction Wood ◽

Intracellular Space ◽

Tracer Experiments

Abstract A large amount of monolignol glucosides (MLGs: p-glucocoumaryl alcohol, coniferin, syringin) are found in lignifying soft xylem near cambium and they disappear with the progress of lignification. Recently, it became a matter of debate whether those MLGs are real intermediates in lignin biosynthesis or only a storage form of monolignols outside of the main biosynthetic pathway. The latter is partly based on a misinterpretation of 14C-tracer experiments and partly on the simple generalization of the results of gene manipulation experiments concerning the flexible and complex lignification. In the present paper, it could be confirmed by the most reliable 13C-tracer method that MLGs are real intermediates in the pathway from l-phenylalanine to macromolecular lignin-polysaccharides complexes in the cell walls. This pathway via MLGs is essential for transport and programmed delivery of specific monolignols in a stable form from intracellular space to specific lignifying sites within the cell wall. The pool size of MLGs is large in most gymnosperm trees and some angiosperm species that emerged in an early stage of phylogeny, while the pool size is small in most angiosperms. This difference in pool size is reasonably understandable from the viewpoint of plant evolution, in the course of which the role of MLGs changed to meet variation in type of major cells, reaction wood formation, and postmortem lignification.

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