Transcriptome Analysis of Four Arabidopsis thaliana Mediator Tail Mutants Reveals Overlapping and Unique Functions in Gene Regulation

Dolan, Whitney L.; Chapple, Clint

doi:10.1534/g3.118.200573

Title: Transcriptome Analysis of Four Arabidopsis thaliana Mediator Tail Mutants Reveals Overlapping and Unique Functions in Gene Regulation

Journal Article · 26 July 2018 · G3

DOI: https://doi.org/10.1534/g3.118.200573 · OSTI ID:1510783

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Dept. of Biochemistry and Purdue Center for Plant Biology, West Lafayette, IN (United States)

The Mediator complex is a central component of transcriptional regulation in Eukaryotes. The complex is structurally divided into four modules known as the head, middle, tail and kinase modules, and in Arabidopsis thaliana, comprises 28-34 subunits. Here, we explore the functions of four Arabidopsis Medi-ator tail subunits, MED2, MED5a/b, MED16, and MED23, by comparing the impact of mutations in each on the Arabidopsis transcriptome. We find that these subunits affect both unique and overlapping sets of genes, providing insight into the functional and structural relationships between them. The mutants pri-marily exhibit changes in the expression of genes related to biotic and abiotic stress. We find evidence for a tissue specific role for MED23, as well as in the production of alternative transcripts. Together, our data help disentangle the individual contributions of these MED subunits to global gene expression and suggest new avenues for future research into their functions.

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Research Organization:: Purdue Univ., West Lafayette, IN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: FG02-07ER15905

OSTI ID:: 1510783

Journal Information:: G3, Vol. 8, Issue 9; ISSN 2160-1836

Publisher:: Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

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The TRAP100 component of the TRAP/Mediator complex is essential in broad transcriptional events and development Ito, M. The EMBO Journal, Vol. 21, Issue 13 https://doi.org/10.1093/emboj/cdf348	journal	July 2002
Requirement for RGR1 and SIN4 in RME1-dependent repression in Saccharomyces cerevisiae. Covitz, P. A.; Song, W.; Mitchell, A. P. Genetics, Vol. 138, Issue 3 https://doi.org/10.1093/genetics/138.3.577	journal	November 1994
Regulation of HIS4 expression by the Saccharomyces cerevisiae SIN4 transcriptional regulator. Jiang, Y. W.; Stillman, D. J. Genetics, Vol. 140, Issue 1 https://doi.org/10.1093/genetics/140.1.103	journal	May 1995
Enzyme activities and subcellular localization of members of the Arabidopsis glutathione transferase superfamily Dixon, David P.; Hawkins, Timothy; Hussey, Patrick J. Journal of Experimental Botany, Vol. 60, Issue 4 https://doi.org/10.1093/jxb/ern365	journal	January 2009
Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex Bourbon, Henri-Marc Nucleic Acids Research, Vol. 36, Issue 12 https://doi.org/10.1093/nar/gkn349	journal	May 2008
Conservation and Divergence of Mediator Structure and Function: Insights from Plants Dolan, Whitney L.; Chapple, Clint Plant and Cell Physiology https://doi.org/10.1093/pcp/pcw176	journal	November 2016
The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator function Knuesel, M. T.; Meyer, K. D.; Bernecky, C. Genes & Development, Vol. 23, Issue 4 https://doi.org/10.1101/gad.1767009	journal	February 2009
PHYTOCHROME AND FLOWERING TIME1/MEDIATOR25 Regulates Lateral Root Formation via Auxin Signaling in Arabidopsis Raya-González, Javier; Ortiz-Castro, Randy; Ruíz-Herrera, León Francisco Plant Physiology, Vol. 165, Issue 2 https://doi.org/10.1104/pp.114.239806	journal	April 2014
The Arabidopsis Mediator Complex Subunit16 Is a Key Component of Basal Resistance against the Necrotrophic Fungal Pathogen Sclerotinia sclerotiorum Wang, Chenggang; Yao, Jin; Du, Xuezhu Plant Physiology, Vol. 169, Issue 1 https://doi.org/10.1104/pp.15.00351	journal	July 2015
Conserved Alternative Splicing of Arabidopsis Transthyretin-Like Determines Protein Localization and S -Allantoin Synthesis in Peroxisomes Lamberto, Ilaria; Percudani, Riccardo; Gatti, Rita The Plant Cell, Vol. 22, Issue 5 https://doi.org/10.1105/tpc.109.070102	journal	May 2010
The sfr6 Mutation in Arabidopsis Suppresses Low-Temperature Induction of Genes Dependent on the CRT/DRE Sequence Motif Knight, Heather; Veale, Emma L.; Warren, Gareth J. The Plant Cell, Vol. 11, Issue 5 https://doi.org/10.1105/tpc.11.5.875	journal	May 1999
FLOWERING LOCUS C Encodes a Novel MADS Domain Protein That Acts as a Repressor of Flowering Michaels, Scott D.; Amasino, Richard M. The Plant Cell, Vol. 11, Issue 5 https://doi.org/10.1105/tpc.11.5.949	journal	May 1999
The Arabidopsis Mediator Complex Subunit16 Positively Regulates Salicylate-Mediated Systemic Acquired Resistance and Jasmonate/Ethylene-Induced Defense Pathways Zhang, Xudong; Wang, Chenggang; Zhang, Yanping The Plant Cell, Vol. 24, Issue 10 https://doi.org/10.1105/tpc.112.103317	journal	October 2012
Complexity of the Alternative Splicing Landscape in Plants Reddy, Anireddy S. N.; Marquez, Yamile; Kalyna, Maria The Plant Cell, Vol. 25, Issue 10 https://doi.org/10.1105/tpc.113.117523	journal	October 2013
The Arabidopsis Mediator Complex Subunits MED16, MED14, and MED2 Regulate Mediator and RNA Polymerase II Recruitment to CBF-Responsive Cold-Regulated Genes Hemsley, Piers A.; Hurst, Charlotte H.; Kaliyadasa, Ewon The Plant Cell, Vol. 26, Issue 1 https://doi.org/10.1105/tpc.113.117796	journal	January 2014
Mediator Complex Subunits MED2, MED5, MED16, and MED23 Genetically Interact in the Regulation of Phenylpropanoid Biosynthesis Dolan, Whitney L.; Dilkes, Brian P.; Stout, Jake M. The Plant Cell, Vol. 29, Issue 12 https://doi.org/10.1105/tpc.17.00282	journal	December 2017
The Mediator subunit SFR6/MED16 controls defence gene expression mediated by salicylic acid and jasmonate responsive pathways Wathugala, Deepthi L.; Hemsley, Piers A.; Moffat, Caroline S. New Phytologist, Vol. 195, Issue 1 https://doi.org/10.1111/j.1469-8137.2012.04138.x	journal	April 2012
Mediator subunit 16 functions in the regulation of iron uptake gene expression in Arabidopsis Zhang, Yue; Wu, Huilan; Wang, Ning New Phytologist, Vol. 203, Issue 3 https://doi.org/10.1111/nph.12860	journal	May 2014
The Arabidopsis Mediator complex subunits MED14/SWP and MED16/SFR6/IEN1 differentially regulate defense gene expression in plant immune responses Zhang, Xudong; Yao, Jin; Zhang, Yanping The Plant Journal, Vol. 75, Issue 3 https://doi.org/10.1111/tpj.12216	journal	May 2013
The Arabidopsis Mediator subunit MED16 regulates iron homeostasis by associating with EIN3/EIL1 through subunit MED25 Yang, Yan; Ou, Bin; Zhang, Jinzhe The Plant Journal, Vol. 77, Issue 6 https://doi.org/10.1111/tpj.12440	journal	February 2014
In Vivo Requirement of Activator-Specific Binding Targets of Mediator Park, J. M.; Kim, H. -S.; Han, S. J. Molecular and Cellular Biology, Vol. 20, Issue 23 https://doi.org/10.1128/mcb.20.23.8709-8719.2000	journal	December 2000
Activator-Independent Functions of the Yeast Mediator Sin4 Complex in Preinitiation Complex Formation and Transcription Reinitiation Reeves, W. M.; Hahn, S. Molecular and Cellular Biology, Vol. 23, Issue 1 https://doi.org/10.1128/mcb.23.1.349-358.2003	journal	January 2003
The Mediator complex subunits MED25/PFT1 and MED8 are required for transcriptional responses to changes in cell wall arabinose composition and glucose treatment in Arabidopsis thaliana Seguela-Arnaud, Mathilde; Smith, Caroline; Uribe, Marcos Castellanos BMC Plant Biology, Vol. 15, Issue 1 https://doi.org/10.1186/s12870-015-0592-4	journal	September 2015
The MED12-MED13 module of Mediator regulates the timing of embryo patterning in Arabidopsis Gillmor, C. S.; Park, M. Y.; Smith, M. R. Development, Vol. 137, Issue 1 https://doi.org/10.1242/dev.043174	journal	December 2009
Control of final organ size by Mediator complex subunit 25 in Arabidopsis thaliana Xu, R.; Li, Y. Development, Vol. 138, Issue 20 https://doi.org/10.1242/dev.071423	journal	September 2011
Differential Use of Signal Peptides and Membrane Domains Is a Common Occurrence in the Protein Output of Transcriptional Units Davis, Melissa J.; Hanson, Kelly A.; Clark, Francis PLoS Genetics, Vol. 2, Issue 4 https://doi.org/10.1371/journal.pgen.0020046	journal	January 2006
An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets Winter, Debbie; Vinegar, Ben; Nahal, Hardeep PLoS ONE, Vol. 2, Issue 8 https://doi.org/10.1371/journal.pone.0000718	journal	August 2007
The M ediator subunit MED 23 couples H2B mono‐ubiquitination to transcriptional control and cell fate determination Yao, Xiao; Tang, Zhanyun; Fu, Xing The EMBO Journal, Vol. 34, Issue 23 https://doi.org/10.15252/embj.201591279	journal	September 2015
Self-assembly of embryonic and two extra-embryonic stem cell types into gastrulating embryo-like structures. Sozen, Berna; Amadei, Gianluca; Cox, Andy Springer Science and Business Media LLC https://doi.org/10.17863/cam.41771	journalarticle	January 2018
Role of Arabidopsis MYC and MYB Homologs in Drought- and Abscisic Acid-Regulated Gene Expression Abe, Hiroshi; Yamaguchi-Shinozaki, Kazuko; Urao, Takeshi The Plant Cell, Vol. 9, Issue 10 https://doi.org/10.2307/3870530	journal	October 1997
Importance of Mediator complex in the regulation and integration of diverse signaling pathways in plants Samanta, Subhasis; Thakur, Jitendra K. Frontiers in Plant Science, Vol. 6 https://doi.org/10.3389/fpls.2015.00757	journal	September 2015
The Mediator Complex Subunits MED14, MED15, and MED16 Are Involved in Defense Signaling Crosstalk in Arabidopsis Wang, Chenggang; Du, Xuezhu; Mou, Zhonglin Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.01947	journal	December 2016
Plant mediator Kidd, Brendan N.; Aitken, Elizabeth A.; Schenk, Peer M. Plant Signaling & Behavior, Vol. 5, Issue 6 https://doi.org/10.4161/psb.5.6.11647	journal	June 2010
Mediator MED23 regulates basal transcription in vivo via an interaction with P-TEFb Wang, Wei; Yao, Xiao; Huang, Yan Transcription, Vol. 4, Issue 1 https://doi.org/10.4161/trns.22874	journal	January 2013
Molecular architecture of the yeast Mediator complex Robinson, Philip J.; Trnka, Michael J.; Pellarin, Riccardo eLife, Vol. 4 https://doi.org/10.7554/elife.08719	journal	September 2015
Molecular Architecture Of The Yeast Mediator Complex Robinson, Philip J.; Trnka, Michael J.; Pellarin, Riccardo Zenodo https://doi.org/10.5281/zenodo.797237	dataset	January 2015
Additional file 2: of The Mediator complex subunits MED25/PFT1 and MED8 are required for transcriptional responses to changes in cell wall arabinose composition and glucose treatment in Arabidopsis thaliana Seguela-Arnaud, Mathilde; Smith, Caroline; Uribe, Marcos Figshare https://doi.org/10.6084/m9.figshare.c.3641666_d4	dataset	January 2015

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NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies Zúñiga-León, Eduardo; Carrasco-Navarro, Ulises; Fierro, Francisco Genes, Vol. 9, Issue 12 https://doi.org/10.3390/genes9120569	journal	November 2018

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