Identification and characteristics of SnRK genes and cold stress-induced expression profiles in Liriodendron chinense.
Cold stress
Expression pattern
Genome-wide identification
L.chinense
SnRK
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
18 Oct 2022
18 Oct 2022
Historique:
received:
26
04
2022
accepted:
09
09
2022
entrez:
17
10
2022
pubmed:
18
10
2022
medline:
20
10
2022
Statut:
epublish
Résumé
The sucrose non-fermenting 1 (SNF1)-related protein kinases (SnRKs) play a vivid role in regulating plant metabolism and stress response, providing a pathway for regulation between metabolism and stress signals. Conducting identification and stress response studies on SnRKs in plants contributes to the development of strategies for tree species that are more tolerant to stress conditions. In the present study, a total of 30 LcSnRKs were identified in Liriodendron chinense (L. chinense) genome, which was distributed across 15 chromosomes and 4 scaffolds. It could be divided into three subfamilies: SnRK1, SnRK2, and SnRK3 based on phylogenetic analysis and domain types. The LcSnRK of the three subfamilies shared the same Ser/Thr kinase structure in gene structure and motif composition, while the functional domains, except for the kinase domain, showed significant differences. A total of 13 collinear gene pairs were detected in L. chinense and Arabidopsis thaliana (A. thaliana), and 18 pairs were detected in L. chinense and rice, suggesting that the LcSnRK family genes may be evolutionarily more closely related to rice. Cis-regulation element analysis showed that LcSnRKs were LTR and TC-rich, which could respond to different environmental stresses. Furthermore, the expression patterns of LcSnRKs are different at different times under low-temperature stress. LcSnRK1s expression tended to be down-regulated under low-temperature stress. The expression of LcSnRK2s tended to be up-regulated under low-temperature stress. The expression trend of LcSnRK3s under low-temperature stress was mainly up-or down-regulated. The results of this study will provide valuable information for the functional identification of the LcSnRK gene in the future.
Sections du résumé
BACKGROUND
BACKGROUND
The sucrose non-fermenting 1 (SNF1)-related protein kinases (SnRKs) play a vivid role in regulating plant metabolism and stress response, providing a pathway for regulation between metabolism and stress signals. Conducting identification and stress response studies on SnRKs in plants contributes to the development of strategies for tree species that are more tolerant to stress conditions.
RESULTS
RESULTS
In the present study, a total of 30 LcSnRKs were identified in Liriodendron chinense (L. chinense) genome, which was distributed across 15 chromosomes and 4 scaffolds. It could be divided into three subfamilies: SnRK1, SnRK2, and SnRK3 based on phylogenetic analysis and domain types. The LcSnRK of the three subfamilies shared the same Ser/Thr kinase structure in gene structure and motif composition, while the functional domains, except for the kinase domain, showed significant differences. A total of 13 collinear gene pairs were detected in L. chinense and Arabidopsis thaliana (A. thaliana), and 18 pairs were detected in L. chinense and rice, suggesting that the LcSnRK family genes may be evolutionarily more closely related to rice. Cis-regulation element analysis showed that LcSnRKs were LTR and TC-rich, which could respond to different environmental stresses. Furthermore, the expression patterns of LcSnRKs are different at different times under low-temperature stress. LcSnRK1s expression tended to be down-regulated under low-temperature stress. The expression of LcSnRK2s tended to be up-regulated under low-temperature stress. The expression trend of LcSnRK3s under low-temperature stress was mainly up-or down-regulated.
CONCLUSION
CONCLUSIONS
The results of this study will provide valuable information for the functional identification of the LcSnRK gene in the future.
Identifiants
pubmed: 36253733
doi: 10.1186/s12864-022-08902-0
pii: 10.1186/s12864-022-08902-0
pmc: PMC9578244
doi:
Substances chimiques
Plant Proteins
0
Sucrose
57-50-1
Protein Serine-Threonine Kinases
EC 2.7.11.1
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
708Subventions
Organisme : National Natural Science Foundation of China
ID : 31971682
Informations de copyright
© 2022. The Author(s).
Références
Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21259-64
pubmed: 22160701
Biochem Biophys Res Commun. 2014 Aug 8;450(4):1679-83
pubmed: 25058458
Nat Plants. 2022 Jan;8(1):68-77
pubmed: 34949800
Plant Cell. 2013 Oct;25(10):3871-84
pubmed: 24179127
Plant J. 2018 Jan;93(1):107-118
pubmed: 29094495
Hum Genomics. 2004 Aug;1(5):335-44
pubmed: 15588494
Trends Genet. 2008 Aug;24(8):375-8
pubmed: 18586348
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11771-6
pubmed: 14504388
Dev Cell. 2015 Feb 9;32(3):278-89
pubmed: 25669882
Nature. 2007 Aug 23;448(7156):938-42
pubmed: 17671505
Cell. 2016 Oct 6;167(2):313-324
pubmed: 27716505
Genomics Proteomics Bioinformatics. 2010 Mar;8(1):77-80
pubmed: 20451164
Nucleic Acids Res. 2012 Apr;40(7):e49
pubmed: 22217600
Nature. 2009 Dec 3;462(7273):660-4
pubmed: 19924127
Nat Commun. 2020 Jan 30;11(1):613
pubmed: 32001690
Science. 2000 Nov 10;290(5494):1151-5
pubmed: 11073452
Genomics. 2011 Aug;98(2):128-36
pubmed: 21616136
Mol Plant. 2022 Feb 7;15(2):293-307
pubmed: 34562665
Nat Commun. 2020 Jan 2;11(1):12
pubmed: 31896774
Trends Biochem Sci. 1996 May;21(5):172-3
pubmed: 8871400
Plant Cell. 2022 Jan 20;34(1):616-632
pubmed: 34755865
Proc Natl Acad Sci U S A. 2015 Jun 9;112(23):7309-14
pubmed: 25997445
Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3730-4
pubmed: 10725382
Cell Res. 2011 Jul;21(7):1116-30
pubmed: 21445098
Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12625-30
pubmed: 16895985
Mol Plant. 2020 Aug 3;13(8):1194-1202
pubmed: 32585190
Proc Natl Acad Sci U S A. 2021 Jul 27;118(30):
pubmed: 34282011
Plant Sci. 2022 Jul;320:111284
pubmed: 35643609
Curr Opin Plant Biol. 2010 Jun;13(3):274-9
pubmed: 20056477
Nat Commun. 2020 Aug 25;11(1):4214
pubmed: 32843632
Nat Commun. 2020 Mar 13;11(1):1373
pubmed: 32170072
Plant Mol Biol. 1998 Jul;37(5):735-48
pubmed: 9678569
J Exp Bot. 2019 Apr 15;70(8):2239-2259
pubmed: 30870564
Plant Sci. 2011 Jul;181(1):57-64
pubmed: 21600398
BMC Plant Biol. 2022 Jan 10;22(1):25
pubmed: 35012508
Biochem J. 2009 Apr 15;419(2):247-59
pubmed: 19309312
Nature. 2020 May;581(7809):444-451
pubmed: 32461652
Plant Cell Physiol. 2013 Feb;54(2):e6
pubmed: 23299411
BMC Plant Biol. 2004 Jun 01;4:10
pubmed: 15171794
Plant Mol Biol. 2007 Mar;63(4):491-503
pubmed: 17103012
Genomics Inform. 2015 Dec;13(4):112-8
pubmed: 26865841
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
BMC Plant Biol. 2020 Jun 22;20(1):287
pubmed: 32571241
Plant Physiol. 2003 Jun;132(2):666-80
pubmed: 12805596
Plant Sci. 2020 Mar;292:110373
pubmed: 32005379
OMICS. 2011 Dec;15(12):859-72
pubmed: 22136638
Plant Mol Biol. 2003 Aug;52(6):1191-202
pubmed: 14682618
Proc Natl Acad Sci U S A. 1999 Apr 27;96(9):5322-7
pubmed: 10220464
Science. 1998 Jun 19;280(5371):1943-5
pubmed: 9632394
Plant Physiol. 2006 Aug;141(4):1316-27
pubmed: 16766677
Plant Cell. 2004 May;16(5):1163-77
pubmed: 15084714
Nat Struct Mol Biol. 2009 Dec;16(12):1230-6
pubmed: 19893533
Nat Plants. 2020 Apr;6(4):384-393
pubmed: 32231253
Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3134-9
pubmed: 25646412
J Biol Chem. 2006 Feb 24;281(8):5310-8
pubmed: 16365038
Nat Commun. 2021 Apr 28;12(1):2456
pubmed: 33911084
3 Biotech. 2020 May;10(5):209
pubmed: 32351867
Front Plant Sci. 2018 Jul 23;9:906
pubmed: 30083172
Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85
pubmed: 26673716
Dev Cell. 2002 Aug;3(2):233-44
pubmed: 12194854
EMBO J. 2001 Mar 1;20(5):1051-63
pubmed: 11230129
Int J Mol Sci. 2017 Aug 23;18(9):
pubmed: 28832544
Cell. 2006 Jun 30;125(7):1347-60
pubmed: 16814720
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W597-603
pubmed: 22661580
Mol Plant. 2016 Jun 6;9(6):926-38
pubmed: 27060495
PLoS One. 2010 Jun 28;5(6):e11335
pubmed: 20596258
Nucleic Acids Res. 2012 Jan;40(Database issue):D1202-10
pubmed: 22140109
Plant Physiol Biochem. 2018 Nov;132:287-296
pubmed: 30245342
Proc Natl Acad Sci U S A. 2021 Sep 14;118(37):
pubmed: 34504003
Mol Biol Evol. 2016 Jul;33(7):1870-4
pubmed: 27004904
Trends Plant Sci. 2008 Sep;13(9):474-82
pubmed: 18701338
Nucleic Acids Res. 2002 Jan 1;30(1):325-7
pubmed: 11752327
Plant Cell. 2002 Dec;14(12):3089-99
pubmed: 12468729
Plant Cell Environ. 2019 Mar;42(3):918-930
pubmed: 29791976
Plant Physiol. 2015 Dec;169(4):2863-73
pubmed: 26474642
Acta Crystallogr F Struct Biol Commun. 2014 Apr;70(Pt 4):509-12
pubmed: 24699751
Sci Rep. 2019 Jan 23;9(1):350
pubmed: 30674892
Plant Biotechnol J. 2019 Mar;17(3):625-637
pubmed: 30133123
J Hered. 2002 Jan-Feb;93(1):77-8
pubmed: 12011185
EMBO J. 2001 Jun 1;20(11):2742-56
pubmed: 11387208
Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3735-40
pubmed: 10725350
Plant Cell. 2021 Dec 3;33(12):3721-3742
pubmed: 34498077
Nat Plants. 2019 Jan;5(1):18-25
pubmed: 30559417
Dev Cell. 2020 Dec 7;55(5):529-543
pubmed: 33290694
J Biol Chem. 2004 Oct 1;279(40):41758-66
pubmed: 15292193