skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa

Abstract

Secondary cell wall (SCW) biosynthesis is the biological process that generates wood, an important renewable feedstock for materials and energy. NAC domain transcription factors, particularly Vascular-Related NAC-Domain (VND) and Secondary Wall-Associated NAC Domain (SND) proteins, are known to regulate SCW differentiation. The regulation of VND and SND is important to maintain homeostasis for plants to avoid abnormal growth and development. We previously identified a splice variant, PtrSND1-A2 IR , derived from PtrSND1-A2 as a dominant-negative regulator, which suppresses the transactivation of all PtrSND1 family members. PtrSND1-A2 IR also suppresses the self-activation of the PtrSND1 family members except for its cognate transcription factor, PtrSND1-A2, suggesting the existence of an unknown factor needed to regulate PtrSND1-A2 . Here, a splice variant, PtrVND6-C1 IR , derived from PtrVND6-C1 was discovered that suppresses the protein functions of all PtrVND6 family members. PtrVND6-C1 IR also suppresses the expression of all PtrSND1 members, including PtrSND1-A2 , demonstrating that PtrVND6-C1 IR is the previously unidentified regulator of PtrSND1-A2 . We also found that PtrVND6-C1 IR cannot suppress the expression of its cognate transcription factor, PtrVND6-C1 . PtrVND6-C1 is suppressed by PtrSND1-A2 IR . Both PtrVND6-C1 IR and PtrSND1-A2 IR cannot suppress their cognatemore » transcription factors but can suppress all members of the other family. The results indicate that the splice variants from the PtrVND6 and PtrSND1 family may exert reciprocal cross-regulation for complete transcriptional regulation of these two families in wood formation. This reciprocal cross-regulation between families suggests a general mechanism among NAC domain proteins and likely other transcription factors, where intron-retained splice variants provide an additional level of regulation.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1402120
Grant/Contract Number:  
SC000691
Resource Type:
Published Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 114 Journal Issue: 45; Journal ID: ISSN 0027-8424
Publisher:
Proceedings of the National Academy of Sciences
Country of Publication:
United States
Language:
English

Citation Formats

Lin, Ying-Chung Jimmy, Chen, Hao, Li, Quanzi, Li, Wei, Wang, Jack P., Shi, Rui, Tunlaya-Anukit, Sermsawat, Shuai, Peng, Wang, Zhifeng, Ma, Hongyan, Li, Huiyu, Sun, Ying-Hsuan, Sederoff, Ronald R., and Chiang, Vincent L. Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa. United States: N. p., 2017. Web. doi:10.1073/pnas.1714422114.
Lin, Ying-Chung Jimmy, Chen, Hao, Li, Quanzi, Li, Wei, Wang, Jack P., Shi, Rui, Tunlaya-Anukit, Sermsawat, Shuai, Peng, Wang, Zhifeng, Ma, Hongyan, Li, Huiyu, Sun, Ying-Hsuan, Sederoff, Ronald R., & Chiang, Vincent L. Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa. United States. doi:10.1073/pnas.1714422114.
Lin, Ying-Chung Jimmy, Chen, Hao, Li, Quanzi, Li, Wei, Wang, Jack P., Shi, Rui, Tunlaya-Anukit, Sermsawat, Shuai, Peng, Wang, Zhifeng, Ma, Hongyan, Li, Huiyu, Sun, Ying-Hsuan, Sederoff, Ronald R., and Chiang, Vincent L. Mon . "Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa". United States. doi:10.1073/pnas.1714422114.
@article{osti_1402120,
title = {Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa},
author = {Lin, Ying-Chung Jimmy and Chen, Hao and Li, Quanzi and Li, Wei and Wang, Jack P. and Shi, Rui and Tunlaya-Anukit, Sermsawat and Shuai, Peng and Wang, Zhifeng and Ma, Hongyan and Li, Huiyu and Sun, Ying-Hsuan and Sederoff, Ronald R. and Chiang, Vincent L.},
abstractNote = {Secondary cell wall (SCW) biosynthesis is the biological process that generates wood, an important renewable feedstock for materials and energy. NAC domain transcription factors, particularly Vascular-Related NAC-Domain (VND) and Secondary Wall-Associated NAC Domain (SND) proteins, are known to regulate SCW differentiation. The regulation of VND and SND is important to maintain homeostasis for plants to avoid abnormal growth and development. We previously identified a splice variant, PtrSND1-A2 IR , derived from PtrSND1-A2 as a dominant-negative regulator, which suppresses the transactivation of all PtrSND1 family members. PtrSND1-A2 IR also suppresses the self-activation of the PtrSND1 family members except for its cognate transcription factor, PtrSND1-A2, suggesting the existence of an unknown factor needed to regulate PtrSND1-A2 . Here, a splice variant, PtrVND6-C1 IR , derived from PtrVND6-C1 was discovered that suppresses the protein functions of all PtrVND6 family members. PtrVND6-C1 IR also suppresses the expression of all PtrSND1 members, including PtrSND1-A2 , demonstrating that PtrVND6-C1 IR is the previously unidentified regulator of PtrSND1-A2 . We also found that PtrVND6-C1 IR cannot suppress the expression of its cognate transcription factor, PtrVND6-C1 . PtrVND6-C1 is suppressed by PtrSND1-A2 IR . Both PtrVND6-C1 IR and PtrSND1-A2 IR cannot suppress their cognate transcription factors but can suppress all members of the other family. The results indicate that the splice variants from the PtrVND6 and PtrSND1 family may exert reciprocal cross-regulation for complete transcriptional regulation of these two families in wood formation. This reciprocal cross-regulation between families suggests a general mechanism among NAC domain proteins and likely other transcription factors, where intron-retained splice variants provide an additional level of regulation.},
doi = {10.1073/pnas.1714422114},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 45,
volume = 114,
place = {United States},
year = {2017},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1073/pnas.1714422114

Citation Metrics:
Cited by: 4 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Coordinated Activation of Cellulose and Repression of Lignin Biosynthesis Pathways in Rice
journal, December 2010

  • Ambavaram, Madana M. R.; Krishnan, Arjun; Trijatmiko, Kurniawan R.
  • Plant Physiology, Vol. 155, Issue 2
  • DOI: 10.1104/pp.110.168641

Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa
journal, January 2017


A NAC transcription factor, EjNAC1 , affects lignification of loquat fruit by regulating lignin
journal, April 2015


Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O -methyltransferase activity in poplar monolignol biosynthesis
journal, June 2015

  • Wang, Jack P.; Chuang, Ling; Loziuk, Philip L.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 27
  • DOI: 10.1073/pnas.1510473112

Emerging roles of long non-coding RNA in root developmental plasticity and regulation of phosphate homeostasis
journal, June 2015


TopHat: discovering splice junctions with RNA-Seq
journal, March 2009


The Basic Helix-Loop-Helix Protein Family: Comparative Genomics and Phylogenetic Analysis
journal, May 2001


VASCULAR-RELATED NAC-DOMAIN 7 directly regulates the expression of a broad range of genes for xylem vessel formation: Direct target genes of VND7
journal, March 2011


NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants
journal, May 2015

  • Nakano, Yoshimi; Yamaguchi, Masatoshi; Endo, Hitoshi
  • Frontiers in Plant Science, Vol. 6
  • DOI: 10.3389/fpls.2015.00288

Choose your partners: dimerization in eukaryotic transcription factors
journal, May 2008

  • Amoutzias, Grigoris D.; Robertson, David L.; Van de Peer, Yves
  • Trends in Biochemical Sciences, Vol. 33, Issue 5
  • DOI: 10.1016/j.tibs.2008.02.002

Intron retention is a major phenomenon in alternative splicing in Arabidopsis
journal, September 2004


Competitive inhibition of transcription factors by small interfering peptides
journal, October 2011


Genomewide identification, classification and analysis of NAC type gene family in maize
journal, September 2015


In vitro xylem vessel elements formation from banana embryogenic cells and expression analysis of vessel development-related genes
journal, February 2015


The Role of Alternative Splicing in the Control of Immune Homeostasis and Cellular Differentiation
journal, December 2015

  • Yabas, Mehmet; Elliott, Hannah; Hoyne, Gerard
  • International Journal of Molecular Sciences, Vol. 17, Issue 1
  • DOI: 10.3390/ijms17010003

SND1, a NAC Domain Transcription Factor, Is a Key Regulator of Secondary Wall Synthesis in Fibers of Arabidopsis
journal, November 2006


A scaling normalization method for differential expression analysis of RNA-seq data
journal, March 2010


Transcription switches for protoxylem and metaxylem vessel formation
journal, August 2005


From rags to riches
journal, June 2002


The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
journal, September 2006


Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexes in planta
journal, November 2008


Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
journal, April 2012

  • Thorvaldsdottir, H.; Robinson, J. T.; Mesirov, J. P.
  • Briefings in Bioinformatics, Vol. 14, Issue 2, p. 178-192
  • DOI: 10.1093/bib/bbs017

Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis
journal, June 2007


MYB46 directly regulates the gene expression of secondary wall-associated cellulose synthases in Arabidopsis
journal, November 2012


Transcriptional repression in eukaryotes: repressors and repression mechanisms
journal, April 2003


PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors
journal, October 2013

  • Jin, Jinpu; Zhang, He; Kong, Lei
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1016

MicroProteins: small size – big impact
journal, August 2015


NAC domain function and transcriptional control of a secondary cell wall master switch: NST1 function and regulation
journal, October 2011


Function of alternative splicing
journal, February 2013


Renewable Resources for the Production of Fuels and Chemicals
journal, February 1976


Global Analysis of Direct Targets of Secondary Wall NAC Master Switches in Arabidopsis
journal, November 2010

  • Zhong, Ruiqin; Lee, Chanhui; Ye, Zheng-Hua
  • Molecular Plant, Vol. 3, Issue 6
  • DOI: 10.1093/mp/ssq062

Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa
journal, August 2012

  • Li, Q.; Lin, Y. -C.; Sun, Y. -H.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 36
  • DOI: 10.1073/pnas.1212977109

A simple improved-throughput xylem protoplast system for studying wood formation
journal, August 2014


Structure of the conserved domain of ANAC, a member of the NAC family of transcription factors
journal, February 2004


Two splice variants of the IDD14 transcription factor competitively form nonfunctional heterodimers which may regulate starch metabolism
journal, May 2011

  • Seo, Pil Joon; Kim, Mi Jung; Ryu, Jae-Yong
  • Nature Communications, Vol. 2, Issue 1
  • DOI: 10.1038/ncomms1303

Alternative splicing in plants – coming of age
journal, October 2012


Regulation of protein function by ‘microProteins’
journal, December 2010


The Sequence Alignment/Map format and SAMtools
journal, June 2009


Alternative splicing of transcription factors in plant responses to low temperature stress: mechanisms and functions
journal, April 2013


Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress
journal, April 2015

  • Filichkin, Sergei; Priest, Henry D.; Megraw, Molly
  • Current Opinion in Plant Biology, Vol. 24
  • DOI: 10.1016/j.pbi.2015.02.008

The WRKY superfamily of plant transcription factors
journal, May 2000