scholarly journals SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa

2013 ◽  
Vol 25 (11) ◽  
pp. 4324-4341 ◽  
Author(s):  
Y.-C. Lin ◽  
W. Li ◽  
Y.-H. Sun ◽  
S. Kumari ◽  
H. Wei ◽  
...  
2019 ◽  
Vol 31 (3) ◽  
pp. 602-626 ◽  
Author(s):  
Hao Chen ◽  
Jack P. Wang ◽  
Huizi Liu ◽  
Huiyu Li ◽  
Ying-Chung Jimmy Lin ◽  
...  

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Xiaohui Yang ◽  
Zunzheng Wei ◽  
Qingzhang Du ◽  
Jinhui Chen ◽  
Qingshi Wang ◽  
...  

2019 ◽  
Vol 39 (7) ◽  
pp. 1187-1200 ◽  
Author(s):  
Bo Jiao ◽  
Xin Zhao ◽  
Wanxiang Lu ◽  
Li Guo ◽  
Keming Luo

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


Author(s):  
Zhenping Yang ◽  
Wei Wang ◽  
Yang Yang ◽  
Hongfei Chen ◽  
Jinke Wang

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Albert T. Young ◽  
Xavier Carette ◽  
Michaela Helmel ◽  
Hanno Steen ◽  
Robert N. Husson ◽  
...  

AbstractThe ability of Mycobacterium tuberculosis (Mtb) to adapt to diverse stresses in its host environment is crucial for pathogenesis. Two essential Mtb serine/threonine protein kinases, PknA and PknB, regulate cell growth in response to environmental stimuli, but little is known about their downstream effects. By combining RNA-Seq data, following treatment with either an inhibitor of both PknA and PknB or an inactive control, with publicly available ChIP-Seq and protein–protein interaction data for transcription factors, we show that the Mtb transcription factor (TF) regulatory network propagates the effects of kinase inhibition and leads to widespread changes in regulatory programs involved in cell wall integrity, stress response, and energy production, among others. We also observe that changes in TF regulatory activity correlate with kinase-specific phosphorylation of those TFs. In addition to characterizing the downstream regulatory effects of PknA/PknB inhibition, this demonstrates the need for regulatory network approaches that can incorporate signal-driven transcription factor modifications.


2021 ◽  
Vol 22 (15) ◽  
pp. 8193
Author(s):  
Daniel Pérez-Cremades ◽  
Ana B. Paes ◽  
Xavier Vidal-Gómez ◽  
Ana Mompeón ◽  
Carlos Hermenegildo ◽  
...  

Background/Aims: Estrogen has been reported to have beneficial effects on vascular biology through direct actions on endothelium. Together with transcription factors, miRNAs are the major drivers of gene expression and signaling networks. The objective of this study was to identify a comprehensive regulatory network (miRNA-transcription factor-downstream genes) that controls the transcriptomic changes observed in endothelial cells exposed to estradiol. Methods: miRNA/mRNA interactions were assembled using our previous microarray data of human umbilical vein endothelial cells (HUVEC) treated with 17β-estradiol (E2) (1 nmol/L, 24 h). miRNA–mRNA pairings and their associated canonical pathways were determined using Ingenuity Pathway Analysis software. Transcription factors were identified among the miRNA-regulated genes. Transcription factor downstream target genes were predicted by consensus transcription factor binding sites in the promoter region of E2-regulated genes by using JASPAR and TRANSFAC tools in Enrichr software. Results: miRNA–target pairings were filtered by using differentially expressed miRNAs and mRNAs characterized by a regulatory relationship according to miRNA target prediction databases. The analysis identified 588 miRNA–target interactions between 102 miRNAs and 588 targets. Specifically, 63 upregulated miRNAs interacted with 295 downregulated targets, while 39 downregulated miRNAs were paired with 293 upregulated mRNA targets. Functional characterization of miRNA/mRNA association analysis highlighted hypoxia signaling, integrin, ephrin receptor signaling and regulation of actin-based motility by Rho among the canonical pathways regulated by E2 in HUVEC. Transcription factors and downstream genes analysis revealed eight networks, including those mediated by JUN and REPIN1, which are associated with cadherin binding and cell adhesion molecule binding pathways. Conclusion: This study identifies regulatory networks obtained by integrative microarray analysis and provides additional insights into the way estradiol could regulate endothelial function in human endothelial cells.


Forests ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1002
Author(s):  
Shenquan Cao ◽  
Cong Wang ◽  
Huanhuan Ji ◽  
Mengjie Guo ◽  
Jiyao Cheng ◽  
...  

Secondary cell wall (SCW) deposition is an important process during wood formation. Although aspartic proteases (APs) have been reported to have regulatory roles in herbaceous plants, the involvement of atypical APs in SCW deposition in trees has not been reported. In this study, we characterised the Populus trichocarpa atypical AP gene PtAP66, which is involved in wood SCW deposition. Transcriptome data from the AspWood resource showed that in the secondary xylem of P. trichocarpa, PtAP66 transcripts increased from the vascular cambium to the xylem cell expansion region and maintained high levels in the SCW formation region. Fluorescent signals from transgenic Arabidopsis plant roots and transiently transformed P. trichocarpa leaf protoplasts strongly suggested that the PtAP66-fused fluorescent protein (PtAP66-GFP or PtAP66-YFP) localised in the plasma membrane. Compared with the wild-type plants, the Cas9/gRNA-induced PtAP66 mutants exhibited reduced SCW thickness of secondary xylem fibres, as suggested by the scanning electron microscopy (SEM) data. In addition, wood composition assays revealed that the cellulose content in the mutants decreased by 4.90–5.57%. Transcription analysis further showed that a loss of PtAP66 downregulated the expression of several SCW synthesis-related genes, including cellulose and hemicellulose synthesis enzyme-encoding genes. Altogether, these findings indicate that atypical PtAP66 plays an important role in SCW deposition during wood formation.


2019 ◽  
Vol 40 (1) ◽  
pp. 73-89 ◽  
Author(s):  
Manzar Abbas ◽  
Ilona Peszlen ◽  
Rui Shi ◽  
Hoon Kim ◽  
Rui Katahira ◽  
...  

Abstract Cellulose synthase A genes (CesAs) are responsible for cellulose biosynthesis in plant cell walls. In this study, functions of secondary wall cellulose synthases PtrCesA4, PtrCesA7-A/B and PtrCesA8-A/B were characterized during wood formation in Populus trichocarpa (Torr. & Gray). CesA RNAi knockdown transgenic plants exhibited stunted growth, narrow leaves, early necrosis, reduced stature, collapsed vessels, thinner fiber cell walls and extended fiber lumen diameters. In the RNAi knockdown transgenics, stems exhibited reduced mechanical strength, with reduced modulus of rupture (MOR) and modulus of elasticity (MOE). The reduced mechanical strength may be due to thinner fiber cell walls. Vessels in the xylem of the transgenics were collapsed, indicating that water transport in xylem may be affected and thus causing early necrosis in leaves. A dramatic decrease in cellulose content was observed in the RNAi knockdown transgenics. Compared with wildtype, the cellulose content was significantly decreased in the PtrCesA4, PtrCesA7 and PtrCesA8 RNAi knockdown transgenics. As a result, lignin and xylem contents were proportionally increased. The wood composition changes were confirmed by solid-state NMR, two-dimensional solution-state NMR and sum-frequency-generation vibration (SFG) analyses. Both solid-state nuclear magnetic resonance (NMR) and SFG analyses demonstrated that knockdown of PtrCesAs did not affect cellulose crystallinity index. Our results provided the evidence for the involvement of PtrCesA4, PtrCesA7-A/B and PtrCesA8-A/B in secondary cell wall formation in wood and demonstrated the pleiotropic effects of their perturbations on wood formation.


2016 ◽  
Vol 213 (1) ◽  
pp. 287-299 ◽  
Author(s):  
Marçal Soler ◽  
Anna Plasencia ◽  
Romain Larbat ◽  
Cécile Pouzet ◽  
Alain Jauneau ◽  
...  

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