ATL54, a RING-H2 domain protein selected by a gene co-expression network analysis, is associated with secondary cell wall formation in Arabidopsis
-
- Noda Soichiro NODA Soichiro
- Research Institute for Sustainable Humanosphere, Kyoto University
-
- Takahashi Yoshinori TAKAHASHI Yoshinori
- Research Institute for Sustainable Humanosphere, Kyoto University
-
- Tsurumaki Yuta [他] TSURUMAKI Yuta
- Research Institute for Sustainable Humanosphere, Kyoto University
-
- YAMAMURA Masaomi
- Research Institute for Sustainable Humanosphere, Kyoto University
-
- NISHIKUBO Nobuyuki
- RIKEN Plant Science Center
-
- YAMAGUCHI Masatoshi
- RIKEN Plant Science Center
-
- SAKURAI Nozomu
- Kazusa DNA Research Institute
-
- HATTORI Takefumi
- Research Institute for Sustainable Humanosphere, Kyoto University
-
- SUZUKI Hideyuki
- Kazusa DNA Research Institute
-
- DEMURA Taku
- RIKEN Plant Science Center
-
- SHIBATA Daisuke
- Kazusa DNA Research Institute
-
- SUZUKI Shiro
- Research Institute for Sustainable Humanosphere, Kyoto University
-
- UMEZAWA Toshiaki
- Research Institute for Sustainable Humanosphere, Kyoto University
Access this Article
Search this Article
Author(s)
-
- Noda Soichiro NODA Soichiro
- Research Institute for Sustainable Humanosphere, Kyoto University
-
- Takahashi Yoshinori TAKAHASHI Yoshinori
- Research Institute for Sustainable Humanosphere, Kyoto University
-
- Tsurumaki Yuta [他] TSURUMAKI Yuta
- Research Institute for Sustainable Humanosphere, Kyoto University
-
- YAMAMURA Masaomi
- Research Institute for Sustainable Humanosphere, Kyoto University
-
- NISHIKUBO Nobuyuki
- RIKEN Plant Science Center
-
- YAMAGUCHI Masatoshi
- RIKEN Plant Science Center
-
- SAKURAI Nozomu
- Kazusa DNA Research Institute
-
- HATTORI Takefumi
- Research Institute for Sustainable Humanosphere, Kyoto University
-
- SUZUKI Hideyuki
- Kazusa DNA Research Institute
-
- DEMURA Taku
- RIKEN Plant Science Center
-
- SHIBATA Daisuke
- Kazusa DNA Research Institute
-
- SUZUKI Shiro
- Research Institute for Sustainable Humanosphere, Kyoto University
-
- UMEZAWA Toshiaki
- Research Institute for Sustainable Humanosphere, Kyoto University
Abstract
Biosynthesis of plant secondary cell walls is controlled by several master transcription factors. Ubiquitin ligases, which mediate ubiquitination of proteins, including transcription factors in the protein degradation pathway, are also believed to regulate secondary wall biosynthesis; however, the exact ubiquitin ligases involved in secondary wall formation have not yet been identified. We conducted a gene co-expression network analysis and found that <i>ATL54</i>, annotated as a RING-finger protein, was highly co-expressed with several transcription factor and enzyme genes involved in secondary wall formation. A recombinant ATL54 protein showed ubiquitin ligase activity. The expression of several biosynthetic genes of cellulose, lignin, and xylan in apical portions of inflorescence stems was up-regulated by <i>ATL54</i> knock-out. The expression of <i>Xylem Cysteine Peptidase1</i> (<i>XCP1</i>), which participates in the programmed cell death process of xylem tracheary elements, was down-regulated in middle stem portions of both <i>ATL54</i>-knock-out and <i>ATL54</i>-overexpressed mutants. Alteration of <i>ATL54</i> expression levels did not, however, affect lignin and polysaccharide content and composition in whole mature stems. Our results suggest that ATL54 is an E3 ubiquitin ligase involved in secondary wall biosynthesis and programmed cell death during xylogenesis.
Journal
-
- Plant Biotechnology
-
Plant Biotechnology 30(2), 169-177, 2013-06-25
Japanese Society for Plant Cell and Molecular Biology
References: 57
-
1
- Genome-wide comparative analysis of the IQD gene families in Arabidopsis thaliana and Oryza sativa
-
ABEL S
BMC Evol Biol 5, 72, 2005
Cited by (1)
-
2
- Diversity in the architecture of ATLs, a family of plant ubiquitin-ligases, leads to recognition and targeting of substrates in different cellular environments
-
AGUILAR-HERNANDEZ V
PLoS ONE 6, e23934, 2011
Cited by (1)
-
3
- Genome-wide insertional mutagenesis of Arabidopsis thaliana
-
ALONSO JM
Science 301, 653-657, 2003
Cited by (1)
-
4
- A protocol for transient gene expression in Arabidopsis thaliana protoplasts isolated from cell suspension culture
-
AXELOS M
Plant Physiol Biochem 30, 123-128, 1992
Cited by (1)
-
5
- Comparison of five xylan synthesis mutants reveals new insight into the mechanisms of xylan synthesis
-
BROWN DM
Plant J 52, 1154-1168, 2007
Cited by (1)
-
6
-
7
- Colorimetric method for determination of sugars and related substances
-
DUBOIS M
Anal Chem 28, 350-356, 1956
Cited by (1)
-
8
- Three 4-coumarate:coenzyme A ligases in Arabidopsis thaliana represent two evolutionarily divergent classes in angiosperms
-
EHLTING J
Plant J 19, 9-20, 1999
Cited by (1)
-
9
- Characterization and dynamic analysis of Arabidopsis condensin subunits, AtCAP-H and AtCAP-H2
-
FUJIMOTO S
Planta 222, 293-300, 2005
Cited by (1)
-
10
- The Arabidopsis xylem peptidase XCP1 is a tracheary element vacuolar protein that may be a papain ortholog
-
FUNK V
Plant Physiol 128, 84-94, 2002
Cited by (1)
-
11
- Rapid acid hydrolysis of plant cell wall polysaccharides and simplified quantitative determination of their neutral monosaccharides by gas-liquid chromatography
-
HOEBLER C
J Agric Food Chem 37, 360-367, 1989
Cited by (1)
-
12
- The tyrosine kinase negative regulator c-Cbl as a RING-type, E2-dependent ubiquitin-protein ligase
-
JOAZEIRO CAP
Science 286, 309-312, 1999
Cited by (1)
-
13
- Ectopic expression of MYB46 identifies transcriptional regulatory genes involved in secondary wall biosynthesis in Arabidopsis
-
KO JH
Plant J 60, 649-665, 2009
Cited by (1)
-
14
- Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome
-
KOSAREV P
Genome Biol 3, research0016.1-research0016.12, 2002
Cited by (1)
-
15
- Transcription switches for protoxylem and metaxylem vessel formation
-
KUBO M
Genes Dev 19, 1855-1860, 2005
Cited by (1)
-
16
- Clustal W and Clustal X version 2.0
-
LARKIN MA
Bioinformatics 23, 2947-2948, 2007
Cited by (1)
-
17
- The Arabidopsis thaliana 4-coumarate : CoA ligase (4CL) gene : stress and developmentally regulated expression and nucleotide sequence of its cDNA
-
LEE D
Plant Mol Biol 28, 871-884, 1995
Cited by (1)
-
18
- The APC11 RING-H2 finger mediates E2-dependent ubiquitination
-
LEVERSON JD
Mol Biol Cell 11, 2315-2325, 2000
Cited by (1)
-
19
- RING1 E3 ligase localizes to plasma membrane lipid rafts to trigger FB1-induced programmed cell death in Arabidopsis
-
LIN SS
Plant J 56, 550-561, 2008
Cited by (1)
-
20
- The E3 ubiquitin ligase gene family in plants : regulation by degradation
-
MAZZUCOTELLI E
Curr Genomics 7, 509-522, 2006
Cited by (1)
-
21
- NAC transcription factors, NST1 and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis
-
MITSUDA N
Plant Cell 19, 270-280, 2007
Cited by (1)
-
22
- The ubiquitin-proteasome pathway and plant development
-
MOON J
Plant Cell 16, 3181-3195, 2004
Cited by (1)
-
23
- Absence of branches from xylan in Arabidopsis gux mutants reveals potential for simplification of lignocellulosic biomass
-
MORTIMER JC
Proc Natl Acad Sci USA 107, 17409-17414, 2010
Cited by (1)
-
24
- ATTED-II provides coexpressed gene networks for Arabidopsis
-
OBAYASHI T
Nucleic Acids Res 37, D987-D991, 2009
Cited by (1)
-
25
- Arabidopsis VASCULAR-RELATED NAC-DOMAIN6 directly regulates the genes that govern programmed cell death and secondary wall formation during xylem differentiation
-
OHASHI-ITO K
Plant Cell 22, 3461-3473, 2010
Cited by (1)
-
26
- MYB103 is required for FERULATE-5-HYDROXYLASE expression and syringyl lignin biosynthesis in Arabidopsis stems
-
OHMAN D
Plant J 73, 63-76, 2012
Cited by (1)
-
27
- Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module
-
OZAKI S
DNA Res 17, 105-116, 2010
Cited by (1)
-
28
- Arabidopsis irregular xylem8 and irregular xylem9 : implications for the complexity of glucuronoxylan biosynthesis
-
PENA MJ
Plant Cell 19, 549-563, 2007
Cited by (1)
-
29
- Genome-wide characterization of the lignification toolbox in Arabidopsis
-
RAES J
Plant Physiol 133, 1051-1071, 2003
Cited by (1)
-
30
- Two Arabidopsis thaliana genes encode functional pectin methylesterase inhibitors
-
RAIOLA A
FEBS Lett 557, 199-203, 2004
Cited by (1)
-
31
- Identification of 14-3-3 proteins as a target of ATL31 ubiquitin ligase, a regulator of the C/N response in Arabidopsis
-
SATO T
Plant J 68, 137-146, 2011
Cited by (1)
-
32
- CNI1/ATL31, a RING-type ubiquitin ligase that functions in the carbon/nitrogen response for growth phase transition in Arabidopsis seedlings
-
SATO T
Plant J 60, 852-864, 2009
Cited by (1)
-
33
- The plant invertase inhibitor shares structural properties and disulfide bridges arrangement with the pectin methylesterase inhibitor
-
SCOGNAMIGLIO MA
J Protein Chem 22, 363-369, 2003
Cited by (1)
-
34
- The ATL gene family from Arabidopsis thaliana and Oryza sativa comprises a large number of putative ubiquitin ligases of the RING-H2 type
-
SERRANO M
J Mol Evol 62, 434-445, 2006
Cited by (1)
-
35
- ASYMMETRIC LEAVES2-LIKE19/LATERAL ORGAN BOUNDARIES DOMAIN30 and ASL20/LBD18 regulate tracheary element differentiation in Arabidopsis
-
SOYANO T
Plant Cell 20, 3359-3373, 2008
Cited by (1)
-
36
- The cellulose synthase gene superfamily and biochemical functions of xylem-specific cellulose synthase-like genes in Populus trichocarpa
-
SUZUKI S
Plant Physiol 142, 1233-1245, 2006
Cited by (1)
-
37
- Interactions among three distinct CesA proteins essential for cellulose synthesis
-
TAYLOR NG
Proc Natl Acad Sci USA 100, 1450-1455, 2003
Cited by (1)
-
38
- Protocols for lignin analysis for Forest Biomass Analytical System of RISH, Kyoto University
-
UMEZAWA T
Res Sustainable Humanosphere (Seizonkenkenkyu) 3, 73-75, 2007
Cited by (1)
-
39
- An "electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets
-
WINTER D
PLoS ONE 2, e718, 2007
Cited by (1)
-
40
- A genome-wide analysis of Arabidopsis Rop-interactive CRIB motif-containing proteins that act as Rop GTPase targets
-
WU G
Plant Cell 13, 2841-2856, 2001
Cited by (1)
-
41
- Arabidopsis RopGAPs are a novel family of Rho GTPase-activating proteins that require the Cdc42/Rac-interactive binding motif for Rop-specific GTPase stimulation
-
WU G
Plant Physiol 124, 1625-1636, 2000
Cited by (1)
-
42
- VASCULAR-RELATED NAC-DOMAIN7 is involved in the differentiation of all types of xylem vessels in Arabidopsis roots and shoots
-
YAMAGUCHI M
Plant J 55, 652-664, 2008
Cited by (1)
-
43
- VASCULAR-RELATED NAC-DOMAIN7 directly regulates the expression of a broad range of genes for xylem vessel formation
-
YAMAGUCHI M
Plant J 66, 579-590, 2011
Cited by (1)
-
44
- The AIP2 E3 ligase acts as a novel negative regulator of ABA signaling by promoting ABI3 degradation
-
ZHANG X
Genes Dev 19, 1532-1543, 2005
Cited by (1)
-
45
- Exploiting secondary growth in Arabidopsis. Construction of xylem and bark cDNA libraries and cloning of three xylem endopeptidases
-
ZHAO C
Plant Physiol 123, 1185-1196, 2000
Cited by (1)
-
46
- SND1, a NAC domain transcription factor, is a key regulator of secondary wall synthesis in fibers of Arabidopsis
-
ZHONG R
Plant Cell 18, 3158-3170, 2006
Cited by (1)
-
47
- A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis
-
ZHONG R
Plant Cell 20, 2763-2782, 2008
Cited by (1)
-
48
- The MYB46 transcription factor is a direct target of SND1 and regulates secondary wall biosynthesis in Arabidopsis
-
ZHONG R
Plant Cell 19, 2776-2792, 2007
Cited by (1)
-
49
- MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis
-
ZHOU J
Plant Cell 21, 248-266, 2009
Cited by (1)
-
50
- Rapid analysis of transgenic rice straw using near-infrared spectroscopy
-
HATTORI Takefumi , MURAKAMI Shinya , MUKAI Mai , YAMADA Tatsuhiko , HIROCHIKA Hirohiko , IKE Masakazu , TOKUYASU Ken , SUZUKI Shiro , SAKAMOTO Masahiro , UMEZAWA Toshiaki
Plant Biotechnology 29(4), 359-366, 2012-09-25
J-STAGE References (42) Cited by (2)
-
51
- The irregular xylem9 Mutant is Deficient in Xylan Xylosyltransferase Activity
-
LEE Chanhui , O'NEILL Malcolm A. , TSUMURAYA Yoichi , DARVILL Alan G. , YE Zheng-Hua
Plant and Cell Physiology 48(11), 1624-1634, 2007-11-01
References (32) Cited by (12)
-
52
- Arabidopsis GUX Proteins Are Glucuronyltransferases Responsible for the Addition of Glucuronic Acid Side Chains onto Xylan
-
LEE Chanhui , TENG Quincy , ZHONG Ruiqin , YE Zheng-Hua
Plant Cell Physiol. 53(7), 1204-1216, 2012-07-01
References (41) Cited by (3)
-
53
- MYB83 Is a Direct Target of SND1 and Acts Redundantly with MYB46 in the Regulation of Secondary Cell Wall Biosynthesis in Arabidopsis
-
MCCARTHY Ryan L. , ZHONG Ruiqin , YE Zheng-Hua
Plant and Cell Physiology 50(11), 1950-1964, 2009-11-01
References (33) Cited by (6)
-
54
- MYB transcription factors orchestrating the developmental program of xylem vessels in Arabidopsis roots
-
NAKANO Yoshimi , NISHIKUBO Nobuyuki , GOUE Nadia , OHTANI Misato , YAMAGUCHI Masatoshi , KATAYAMA Yoshihiro , DEMURA Taku
Plant Biotechnology 27(3), 267-272, 2010-09-06
J-STAGE References (18) Cited by (3)
-
55
- Efficient and High-Throughput Vector Construction and Agrobacterium-Mediated Transformation of Arabidopsis thaliana Suspension-Cultured Cells for Functional Genomics
-
OGAWA Yoichi , DANSAKO Tomoko , YANO Kentaro , SAKURAI Nozomu , SUZUKI Hideyuki , AOKI Koh , NOJI Masaaki , SAITO Kazuki , SHIBATA Daisuke
Plant and Cell Physiology 49(2), 242-250, 2008-02-01
References (33) Cited by (10)
-
56
- Microscale alkaline nitrobenzene oxidation method for high-throughput determination of lignin aromatic components
-
YAMAMURA Masaomi , HATTORI Takefumi , SUZUKI Shiro , SHIBATA Daisuke , UMEZAWA Toshiaki
Plant Biotechnology 27(4), 305-310, 2010-09-25
J-STAGE References (12) Cited by (7)
-
57
- Occurrence of guaiacyl/p-hydroxyphenyl lignin in Arabidopsis thaliana T87 cells
-
YAMAMURA Masaomi , WADA Shohei , SAKAKIBARA Norikazu , NAKATSUBO Tomoyuki , SUZUKI Shiro , HATTORI Takefumi , TAKEDA Migiwa , SAKURAI Nozomu , SUZUKI Hideyuki , SHIBATA Daisuke , UMEZAWA Toshiaki
Plant Biotechnology 28(1), 1-8, 2011-03-25
J-STAGE References (46) Cited by (6)