Literature DB >> 24300216

Genetic networks involved in poplar root response to low nitrogen.

Hairong Wei1, Yordan Yordanov2, Sapna Kumari3, Tatyana Georgieva2, Victor Busov4.   

Abstract

Perception of environmental cues and adaptation to changing environmental conditions are crucial for survival of sessile organisms like plants. This is even more important for woody perennial species like trees that can occupy a site for thousands of years. We have previously shown that under low nitrogen (LN), poplar trees display a vigorous and long-lasting root growth associated with global transcriptomic reprogramming and an activation of hierarchical genetic networks. Here we use computational analysis to better understand the network among the genes showing distinct chronological patterns of expression during the response. Our analyses confirm the previous findings, define new potential signaling pathways and the possible downstream targets of these signaling events.

Entities:  

Keywords:  Signal transduction; biological processes; low nitrogen; root specific growth; transcription factors

Mesh:

Substances:

Year:  2013        PMID: 24300216      PMCID: PMC4091351          DOI: 10.4161/psb.27211

Source DB:  PubMed          Journal:  Plant Signal Behav        ISSN: 1559-2316


  11 in total

1.  Activity of transcription factor JACKDAW is essential for SHR/SCR-dependent activation of SCARECROW and MAGPIE and is modulated by reciprocal interactions with MAGPIE, SCARECROW and SHORT ROOT.

Authors:  Hiromi Ogasawara; Ryuji Kaimi; Joseph Colasanti; Akiko Kozaki
Journal:  Plant Mol Biol       Date:  2011-09-21       Impact factor: 4.076

Review 2.  Surfing along the root ground tissue gene network.

Authors:  G Pauluzzi; F Divol; J Puig; E Guiderdoni; A Dievart; C Périn
Journal:  Dev Biol       Date:  2012-02-12       Impact factor: 3.582

3.  Nitrogen deprivation promotes Populus root growth through global transcriptome reprogramming and activation of hierarchical genetic networks.

Authors:  Hairong Wei; Yordan S Yordanov; Tatyana Georgieva; Xiang Li; Victor Busov
Journal:  New Phytol       Date:  2013-06-25       Impact factor: 10.151

4.  RSL genes are sufficient for rhizoid system development in early diverging land plants.

Authors:  Geupil Jang; Keke Yi; Nuno D Pires; Benoît Menand; Liam Dolan
Journal:  Development       Date:  2011-06       Impact factor: 6.868

5.  The rhd6 Mutation of Arabidopsis thaliana Alters Root-Hair Initiation through an Auxin- and Ethylene-Associated Process.

Authors:  J. D. Masucci; J. W. Schiefelbein
Journal:  Plant Physiol       Date:  1994-12       Impact factor: 8.340

6.  Identification of SHRUBBY, a SHORT-ROOT and SCARECROW interacting protein that controls root growth and radial patterning.

Authors:  Koji Koizumi; Kimberly L Gallagher
Journal:  Development       Date:  2013-03       Impact factor: 6.868

7.  The NAC domain transcription factors FEZ and SOMBRERO control the orientation of cell division plane in Arabidopsis root stem cells.

Authors:  Viola Willemsen; Marion Bauch; Tom Bennett; Ana Campilho; Harald Wolkenfelt; Jian Xu; Jim Haseloff; Ben Scheres
Journal:  Dev Cell       Date:  2008-12       Impact factor: 12.270

8.  Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa.

Authors:  Shanfa Lu; Quanzi Li; Hairong Wei; Mao-Ju Chang; Sermsawat Tunlaya-Anukit; Hoon Kim; Jie Liu; Jingyuan Song; Ying-Hsuan Sun; Lichai Yuan; Ting-Feng Yeh; Ilona Peszlen; John Ralph; Ronald R Sederoff; Vincent L Chiang
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-10       Impact factor: 11.205

9.  Systems approaches map regulatory networks downstream of the auxin receptor AFB3 in the nitrate response of Arabidopsis thaliana roots.

Authors:  Elena A Vidal; Tomás C Moyano; Eleodoro Riveras; Orlando Contreras-López; Rodrigo A Gutiérrez
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-11       Impact factor: 11.205

10.  An ancient mechanism controls the development of cells with a rooting function in land plants.

Authors:  Benoît Menand; Keke Yi; Stefan Jouannic; Laurent Hoffmann; Eoin Ryan; Paul Linstead; Didier G Schaefer; Liam Dolan
Journal:  Science       Date:  2007-06-08       Impact factor: 47.728

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  8 in total

1.  A network of genes associated with poplar root development in response to low nitrogen.

Authors:  Madhumita Dash; Yordan S Yordanov; Tatyana Georgieva; Sapna Kumari; Hairong Wei; Victor Busov
Journal:  Plant Signal Behav       Date:  2016-08-02

2.  Recursive random forest algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways.

Authors:  Wenping Deng; Kui Zhang; Victor Busov; Hairong Wei
Journal:  PLoS One       Date:  2017-02-03       Impact factor: 3.240

3.  Nitrogen Metabolism and Biomass Production in Forest Trees.

Authors:  Francisco M Cánovas; Rafael A Cañas; Fernando N de la Torre; María Belén Pascual; Vanessa Castro-Rodríguez; Concepción Avila
Journal:  Front Plant Sci       Date:  2018-09-28       Impact factor: 5.753

4.  Gene network analysis of poplar root transcriptome in response to drought stress identifies a PtaJAZ3PtaRAP2.6-centered hierarchical network.

Authors:  Madhumita Dash; Yordan S Yordanov; Tatyana Georgieva; Hairong Wei; Victor Busov
Journal:  PLoS One       Date:  2018-12-12       Impact factor: 3.240

5.  Genome sequence and evolution of Betula platyphylla.

Authors:  Su Chen; Yucheng Wang; Lili Yu; Tao Zheng; Sui Wang; Zhen Yue; Jing Jiang; Sapna Kumari; Chunfang Zheng; Haibao Tang; Jun Li; Yuqi Li; Jiongjiong Chen; Wenbo Zhang; Hanhui Kuang; Jon S Robertson; Patrick X Zhao; Huiyu Li; Shengqiang Shu; Yordan S Yordanov; Haijiao Huang; David M Goodstein; Ying Gai; Qi Qi; JiuMeng Min; ChunYan Xu; SongBo Wang; Guan-Zheng Qu; Andrew H Paterson; David Sankoff; Hairong Wei; Guifeng Liu; Chuanping Yang
Journal:  Hortic Res       Date:  2021-02-11       Impact factor: 6.793

6.  Bottom-up GGM algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways or processes.

Authors:  Sapna Kumari; Wenping Deng; Chathura Gunasekara; Vincent Chiang; Huann-Sheng Chen; Hao Ma; Xin Davis; Hairong Wei
Journal:  BMC Bioinformatics       Date:  2016-03-18       Impact factor: 3.169

7.  HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks.

Authors:  Xinbin Dai; Jun Li; Tingsong Liu; Patrick Xuechun Zhao
Journal:  Plant Cell Physiol       Date:  2015-12-12       Impact factor: 4.927

8.  Metabolomics and Transcriptomics Integration of Early Response of Populus tomentosa to Reduced Nitrogen Availability.

Authors:  Min Chen; Yiyi Yin; Lichun Zhang; Xiaoqian Yang; Tiantian Fu; Xiaowei Huo; Yanwei Wang
Journal:  Front Plant Sci       Date:  2021-12-08       Impact factor: 5.753

  8 in total

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