scholarly journals RNA Sequencing Reveals Phenylpropanoid Biosynthesis Genes and Transcription Factors for Hevea brasiliensis Reaction Wood Formation

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiangxu Meng ◽  
Yue Wang ◽  
Jia Li ◽  
Nanbo Jiao ◽  
Xiujie Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Rna Sequencing ◽  
Hevea Brasiliensis ◽  
Rubber Tree ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Industrial Applications ◽  
Normal Wood ◽  
Reaction Wood ◽  
Phenylpropanoid Biosynthesis

Given the importance of wood in many industrial applications, much research has focused on wood formation, especially lignin biosynthesis. However, the mechanisms governing the regulation of lignin biosynthesis in the rubber tree (Hevea brasiliensis) remain to be elucidated. Here, we gained insight into the mechanisms of rubber tree lignin biosynthesis using reaction wood (wood with abnormal tissue structure induced by gravity or artificial mechanical treatment) as an experimental model. We performed transcriptome analysis of rubber tree mature xylem from tension wood (TW), opposite wood (OW), and normal wood (NW) using RNA sequencing (RNA-seq). A total of 214, 1,280, and 32 differentially expressed genes (DEGs) were identified in TW vs. NW, OW vs. NW, and TW vs. OW, respectively. GO and KEGG enrichment analysis of DEGs from different comparison groups showed that zeatin biosynthesis, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant–pathogen interaction pathways may play important roles in reaction wood formation. Sixteen transcripts involved in phenylpropanoid biosynthesis and 129 transcripts encoding transcription factors (TFs) were used to construct a TF–gene regulatory network for rubber tree lignin biosynthesis. Among them, MYB, C2H2, and NAC TFs could regulate all the DEGs involved in phenylpropanoid biosynthesis. Overall, this study identified candidate genes and TFs likely involved in phenylpropanoid biosynthesis and provides novel insights into the mechanisms regulating rubber tree lignin biosynthesis.

scholarly journals Evaluation of rubber tree transcriptome and discovery of SNP and SSR from candidate genes involved in cellulose and lignin biosynthesis

2021 ◽  
Author(s):  
Ahmad Sofiman Othman ◽  
Mohd Fahmi Abu Bakar
Keyword(s):  
Rna Sequencing ◽  
Differential Expression Analysis ◽  
Economic Value ◽  
Rubber Tree ◽  
Lignin Biosynthesis ◽  
Primary Source ◽  
Wood Formation ◽  
Breeding Cycle ◽  
Nucleotide Polymorphisms ◽  
Protein Database

Hevea brasiliensis (the rubber tree) is a well-known species with high economic value, and it is the primary source of natural rubber globally. Increasing demand for furniture and related industries has made rubberwood production as important as latex production. Molecular markers such as Single Nucleotide Polymorphisms (SNPs) and Simple Sequence Repeats (SSRs) are widely used for Marker Assisted Selection (MAS) which can be detected in large quantity by transcriptome sequencing. MAS is thought to be a useful method for the development of new rubberwood clones for its shorter breeding cycle compared to a conventional breeding procedure. In this study we performed RNA sequencing (RNA-seq) on four H. brasiliensis clones (RRIM 712, RRIM 2025, RRIM 3001 and PB 314) from three tissues including bark, latex and leaf samples to identify SSRs and SNPs associated with wood-formation related genes. The RNA sequencing using the Illumina NextSeq 500 v2 platform, generated 1,697,491,922 raw reads. A total of 101,269 transcripts over 400 bp in size were obtained and similarity search of the non-redundant (nr) protein database returned 83,748 (83%) positive BLASTx hits. The transcriptome analysis was annotated using the NCBI NR (National Center for Biotechnology Information Non-Redundant), UniProtKB/Swiss-Prot, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Differential expression analysis between later-timber rubber clone and non-later-timber rubber clone on wood-formation related genes, showed genes encoding phenylalanine ammonia-lyase (PAL), caffeic acid O-methyltransferase (COMT) and cinnamoyl-CoA reductase (CCR) were highly up-regulated in a latex-timber rubber clone. In total, about 3,210,629 SNPs and 14,956 SSRs were detected with 1,786 SNPs and 31 SSRs were found for wood-formation biosynthesis of H. brasilensis from 11 lignin and cellulose gene toolboxes. After filtering and primer selection, 103 SNPs and 18 SSR markers were successfully amplified and could be useful as molecular tool for marker assisted breeding to produce new timber rubber clones.

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 ◽  
2016 ◽  
Vol 70 (9) ◽  
pp. 801-810 ◽  
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.

Comparative transcriptome profiling provides insights into endocarp lignification of walnut (Juglans Regia L.)

2020 ◽  
Author(s):  
Xiaoting Wu ◽  
Zechao Zhang ◽  
Mintao Sun ◽  
Xiuhong An ◽  
Shugang Zhao ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Juglans Regia ◽  
Expression Patterns ◽  
Lignin Biosynthesis ◽  
Transcriptome Profiling ◽  
Phenotypic Differences ◽  
Phenylpropanoid Biosynthesis ◽  
Key Genes ◽  
Main Component

Abstract Background Lignin is the main component of walnut endocarp, although we know little about the molecular mechanism of lignin formation in walnut endocarp. To understand the molecular mechanisms behind the two kinds of walnut phenotype and explore the genes involved into lignin formation, transcriptome sequencing was conducted in the walnut endocarp of the ‘Zanmei’ (ZM) and ‘Liaoning 7’ (L7) cultivars, which have different endocarp thicknesses. Compared with L7 walnut endocarp, the endocarp of ZM walnut is thicker, which decreases dehiscent nuts and compromised kernels.Results There are more differentially expressed genes (DEGs) in the ZM walnut cultivar. The DEGs involved in the phenylpropanoid biosynthesis were significantly upregulated in both cultivars 45 days after full bloom (DAFB), but more genes were upregulated in ZM than in L7. Moreover, the same DEGs showed different expression levels in the two cultivars. Most of the key genes in ZM had more different multiples than those in L7. Interestingly, when qRT-PCR was used to determine the expression of the key genes in different development stages of the two varieties, the expression patterns were different from those known in other species. Furthermore, transcription factors regulating secondary cell wall and lignin biosynthesis were identified. Quantitative real-time PCR results were consistent with transcriptome data.Conclusion In this study, transcriptome analysis was used to understand the molecular mechanisms of lignin formation in two walnut cultivars with different shell thickness. Several important key genes in the phenylpropanoid biosynthesis pathway were significantly different in the two cultivars, which may be the reason for the phenotypic differences. The analysis of transcription factors revealed that the regulation network in endocarp of walnut may be different from that of drupe such as apricot or peach. This study provides important candidate genes for exploring the complicated metabolic processes involved in the formation of walnut lignin.

scholarly journals A High-Throughput Screening System for Populus Wood-Associated Transcription Factors and Its Application to Lignin Regulation

2022 ◽  
Vol 12 ◽  
Author(s):  
Yamei Zhuang ◽  
Sihui Chen ◽  
Wenjun Lian ◽  
Li Xu ◽  
Dian Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
High Throughput ◽  
Regulatory Network ◽  
High Throughput Screening ◽  
Developmental Process ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Screening System ◽  
Regulatory Modules ◽  
Wood Development

Wood formation of trees is a complex and costly developmental process, whose regulatory network is involved in the protein-protein and protein-DNA interactions. To detect such interactions in wood development, we developed a high-throughput screening system with 517 Gal4-AD-wood-associated transcription factors (TFs) library from Populus alba × P. glandulosa cv “84K.” This system can be used for screening the upstream regulators and interacting proteins of targets by mating-based yeast-one hybrid (Y1H) and yeast-two-hybrid (Y2H) method, respectively. Multiple regulatory modules of lignin biosynthesis were identified based on this Populus system. Five TFs interacted with the 500-bp promoter fragment of PHENYLALANINE AMMONIA-LYASE 2 (PAL2), the first rate-limiting enzyme gene in the lignin biosynthesis pathway, and 10 TFs interacted with PaMYB4/LTF1, a key regulator of lignin biosynthesis. Some of these interactions were further validated by EMSA and BiFC assays. The TF-PaPAL2 promoter interaction and TF-PaMYB4 interaction revealed a complex mechanism governing the regulation of lignin synthesis in wood cells. Our high-throughput Y1H/Y2H screening system may be an efficient tool for studying regulatory network of wood formation in tree species.

scholarly journals A Novel NAC Transcription Factor From Eucalyptus, EgNAC141, Positively Regulates Lignin Biosynthesis and Increases Lignin Deposition

2021 ◽  
Vol 12 ◽  
Author(s):  
YiMing Sun ◽  
Chunxue Jiang ◽  
Ruiqi Jiang ◽  
Fengying Wang ◽  
Zhenguo Zhang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Lignin Content ◽  
Eucalyptus Grandis ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Nac Transcription Factor ◽  
Luciferase Assay ◽  
Large Set ◽  
Biosynthetic Genes

Wood formation is a complicated process under the control of a large set of transcription factors. NAC transcription factors are considered “master switches” in this process. However, few NAC members have been cloned and characterized in Eucalyptus, which is one of the most economically important woody plants. Here, we reported an NAC transcription factor from Eucalyptus grandis, EgNAC141, which has no Arabidopsis orthologs associated with xylogenesis-related processes. EgNAC141 was predominantly expressed in lignin-rich tissues, such as the stem and xylem. Overexpression of EgNAC141 in Arabidopsis resulted in stronger lignification, larger xylem, and higher lignin content. The expression of lignin biosynthetic genes in transgenic plants was significantly higher compared with wild-type plants. The transient expression of EgNAC141 activated the expression of Arabidopsis lignin biosynthetic genes in a dual-luciferase assay. Overall, these results showed that EgNAC141 is a positive regulator of lignin biosynthesis and may help us understand the regulatory mechanism of wood formation.

scholarly journals MYB Transcription Factors and Its Regulation in Secondary Cell Wall Formation and Lignin Biosynthesis during Xylem Development

2021 ◽  
Vol 22 (7) ◽  
pp. 3560
Author(s):  
Ruixue Xiao ◽  
Chong Zhang ◽  
Xiaorui Guo ◽  
Hui Li ◽  
Hai Lu
Keyword(s):  
Cell Wall ◽  
Transcription Factors ◽  
Secondary Wall ◽  
Secondary Cell Wall ◽  
Lignin Biosynthesis ◽  
Cell Wall Formation ◽  
Long Distance ◽  
Secondary Cell Wall Formation ◽  
Myb Transcription Factors ◽  
Wall Formation

The secondary wall is the main part of wood and is composed of cellulose, xylan, lignin, and small amounts of structural proteins and enzymes. Lignin molecules can interact directly or indirectly with cellulose, xylan and other polysaccharide molecules in the cell wall, increasing the mechanical strength and hydrophobicity of plant cells and tissues and facilitating the long-distance transportation of water in plants. MYBs (v-myb avian myeloblastosis viral oncogene homolog) belong to one of the largest superfamilies of transcription factors, the members of which regulate secondary cell-wall formation by promoting/inhibiting the biosynthesis of lignin, cellulose, and xylan. Among them, MYB46 and MYB83, which comprise the second layer of the main switch of secondary cell-wall biosynthesis, coordinate upstream and downstream secondary wall synthesis-related transcription factors. In addition, MYB transcription factors other than MYB46/83, as well as noncoding RNAs, hormones, and other factors, interact with one another to regulate the biosynthesis of the secondary wall. Here, we discuss the biosynthesis of secondary wall, classification and functions of MYB transcription factors and their regulation of lignin polymerization and secondary cell-wall formation during wood formation.

scholarly journals Co- and post-translational processing of the hevein preproprotein of latex of the rubber tree (Hevea brasiliensis)

1991 ◽  
Vol 266 (24) ◽  
pp. 15944-15948
Author(s):  
H.I. Lee ◽  
W.F. Broekaert ◽  
N.V. Raikhel ◽  
H. Lee
Keyword(s):  
Hevea Brasiliensis ◽  
Rubber Tree

scholarly journals Identification of New Transcription Factors that Can Promote Pluripotent Reprogramming

2021 ◽  
Author(s):  
Ping Huang ◽  
Jieying Zhu ◽  
Yu Liu ◽  
Guihuan Liu ◽  
Ran Zhang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Embryonic Stem Cells ◽  
Rna Sequencing ◽  
Human Urine ◽  
Embryonic Stem ◽  
Rna Seq ◽  
Reprogramming Efficiency ◽  
Yamanaka Factors ◽  
Urine Cells

Abstract Background Four transcription factors, Oct4, Sox2, Klf4, and c-Myc (the Yamanka factors), can reprogram somatic cells to induced pluripotent stem cells (iPSCs). Many studies have provided a number of alternative combinations to the non-Yamanaka factors. However, it is clear that many additional transcription factors that can generate iPSCs remain to be discovered. Methods The chromatin accessibility and transcriptional level of human embryonic stem cells and human urine cells were compared by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing (RNA-seq) to identify potential reprogramming factors. Selected transcription factors were employed to reprogram urine cells, and the reprogramming efficiency was measured. Urine-derived iPSCs were detected for pluripotency by Immunofluorescence, quantitative polymerase chain reaction, RNA sequencing and teratoma formation test. Finally, we assessed the differentiation potential of the new iPSCs to cardiomyocytes in vitro. Results ATAC-seq and RNA-seq datasets predicted TEAD2, TEAD4 and ZIC3 as potential factors involved in urine cell reprogramming. Transfection of TEAD2, TEAD4 and ZIC3 (in the presence of Yamanaka factors) significantly improved the reprogramming efficiency of urine cells. We confirmed that the newly generated iPSCs possessed pluripotency characteristics similar to normal H1 embryonic stem cells. We also confirmed that the new iPSCs could differentiate to functional cardiomyocytes. Conclusions In conclusion, TEAD2, TEAD4 and ZIC3 can increase the efficiency of reprogramming human urine cells into iPSCs, and provides a new stem cell sources for the clinical application and modeling of cardiovascular disease. Graphical abstract

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