Genome-Wide Identification, Evolution, and Co-expression Network Analysis of Mitogen-Activated Protein Kinase Kinase Kinases inBrachypodium distachyon.
Mitogen-activated protein kinase (MAPK) cascades are the conserved and universal signal transduction modules in all eukaryotes, which play the vital roles in plant growth, development, and in response to multiple stresses. In this study, we used bioinformatics methods to identify 86 MAPKKK protein encoded by 73 MAPKKK genes inBrachypodium. Phylogenetic analysis of MAPKKK family fromArabidopsis, rice, andBrachypodiumhas classified them into three subfamilies, of which 28 belonged to MEKK, 52 to Raf, and 6 to ZIK subfamily, respectively. Conserved protein motif, exon-intron organization, and splicing intron phase in kinase domains supported the evolutionary relationships inferred from the phylogenetic analysis. And gene duplication analysis suggested the chromosomal segment duplication happened before the divergence of the rice andBrachypodium, while all of three tandem duplicated gene pairs happened after their divergence. We further demonstrated that the MAPKKKs have evolved under strong purifying selection, implying the conservation of them. The splicing transcripts expression analysis showed that the splicesome translating longest protein tended to be adopted. Furthermore, the expression analysis of BdMAPKKKs in different organs and development stages as well as heat, virus and drought stresses revealed that the MAPKKK genes were involved in various signaling pathways. And the circadian analysis suggested there were 41 MAPKKK genes inBrachypodiumshowing cycled expression in at least one condition, of which seven MAPKKK genes expressed in all conditions and the promoter analysis indicated these genes possessed many cis-acting regulatory elements involved in circadian and light response. Finally, the co-expression network of MAPK, MAPKK, and MAPKKK inBrachypodiumwas constructed using 144 microarray and RNA-seq datasets, and ten potential MAPK cascades pathway were predicted. To conclude, our study provided the important information for evolutionary and functional characterization of MAPKKK family inBrachypodium, which will facilitate the functional analysis of BdMAPKKK genes, and also will facilitate better understanding the MAPK signal pathway inBrachypodiumand beyond.
College of Agronomy, Northwest A&F University Yangling, China.
Kewei
K
Feng
College of Agronomy, Northwest A&F University Yangling, China.
Fuyan
F
Liu
College of Agronomy, Northwest A&F University Yangling, China.
Jinwei
J
Zou
College of Agronomy, Northwest A&F University Yangling, China.
Guangwei
G
Xing
College of Agronomy, Northwest A&F University Yangling, China.
Pingchuan
P
Deng
College of Agronomy, Northwest A&F UniversityYangling, China; State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F UniversityYangling, China; Australia-China Joint Research Centre for Abiotic and Biotic Stress Management in Agriculture, Horticulture and Forestry, Northwest A&F UniversityYangling, China.
Weining
W
Song
College of Agronomy, Northwest A&F University Yangling, China.
Wei
W
Tong
College of Agronomy, Northwest A&F UniversityYangling, China; State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F UniversityYangling, China.
Xiaojun
X
Nie
Brachypodium distachyon; MAPK cascades; MAPKKK family; co-expression network; expression profiles; signal pathway
Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):373-8
11114160
Front Plant Sci. 2015 Sep 25;6:780
26442088
Nucleic Acids Res. 2009 Jan;37(Database issue):D987-91
18953027
Plant Signal Behav. 2011 Mar;6(3):316-20
21178395
Curr Opin Plant Biol. 2009 Aug;12(4):421-6
19608449
Plant Cell Physiol. 2010 Oct;51(10 ):1766-76
20802223
Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8
9843981
Trends Plant Sci. 2002 Jul;7(7):301-8
12119167
Int J Mol Sci. 2013 May 03;14(5):9643-84
23644891
Nucleic Acids Res. 2001 May 15;29(10):2145-53
11353084
Front Plant Sci. 2015 Feb 18;6:84
25741357
Nature. 2002 Feb 28;415(6875):977-83
11875555
Nature. 1998 Oct 15;395(6703):716-20
9790195
Plant Cell Physiol. 2002 Jun;43(6):675-83
12091722
Genome Res. 2003 Nov;13(11):2498-504
14597658
Int J Mol Sci. 2013 Sep 11;14(9):18740-57
24030721
Plant Physiol. 2001 Dec;127(4):1539-55
11743099
BMC Genomics. 2015 Mar 24;16:228
25886731
DNA Res. 2009 Oct;16(5):249-60
19767600
Mol Biol Evol. 2002 Mar;19(3):256-62
11861885
PLoS One. 2013;8(2):e57714
23460898
Front Plant Sci. 2015 Feb 25;6:107
25763005
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
15034147
Front Plant Sci. 2015 Jul 22;6:556
26257761
Plant Signal Behav. 2012 Nov;7(11):1488-9
22960756
DNA Res. 2010 Jun;17(3):139-53
20395279
Environ Sci Pollut Res Int. 2013 Aug;20(8):5449-60
23430734
Annu Rev Plant Biol. 2010;61:621-49
20441529
J Biol Chem. 2007 Aug 24;282(34):25020-9
17586809
Bioinformatics. 2005 May 1;21(9):2104-5
15647292
Mol Biol Evol. 2016 Jul;33(7):1870-4
27004904
Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20520-5
19910530
Plant Cell. 2012 May;24(5):2225-36
22643122
Genome Biol. 2013 Jun 25;14(6):R65
23800039
J Biol Chem. 2006 Dec 1;281(48):36969-76
17023433
BMC Plant Biol. 2014 Aug 27;14:219
25158790
Plant J. 2011 Sep;67(5):895-906
21575092
Nature. 2010 Jan 14;463(7278):178-83
20075913
Biosci Biotechnol Biochem. 2002 Nov;66(11):2429-36
12506983
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12
16845082
PLoS One. 2011;6(6):e16907
21694767
FEBS Lett. 2001 Jun 8;498(2-3):172-8
11412851
Nature. 2010 Feb 11;463(7282):763-8
20148030
Cell Res. 2008 Dec;18(12 ):1190-8
18982020
PLoS One. 2012;7(10):e46744
23082129
Front Plant Sci. 2012 Dec 06;3:271
23230446
Genome Res. 2009 Nov;19(11):1953-62
19797678
Rice (N Y). 2013 Oct 28;6(1):25
24280045
Plant J. 2014 Feb;77(4):577-88
24320620
Plant Physiol. 2011 Sep;157(1):3-13
21771916
Cell. 1993 Feb 12;72(3):427-41
8431946
Theor Appl Genet. 2006 Jul;113(2):186-95
16791686
Mol Plant. 2013 Mar;6(2):311-22
23015761
Plant Cell. 2007 Jan;19(1):63-73
17259259
Bioinformatics. 2007 Nov 1;23(21):2947-8
17846036
Curr Opin Plant Biol. 2009 Oct;12(5):615-21
19716758
Plant Cell Physiol. 1995 Jul;36(5):749-57
7551583