Genome-wide identification of 14-3-3 gene family and characterization of their expression in developmental stages of Solanum tuberosum under multiple biotic and abiotic stress conditions.
CSD
GF14
Orthologous
Paralogous
S. tuberosum
Journal
Functional & integrative genomics
ISSN: 1438-7948
Titre abrégé: Funct Integr Genomics
Pays: Germany
ID NLM: 100939343
Informations de publication
Date de publication:
Dec 2022
Dec 2022
Historique:
received:
13
02
2022
accepted:
25
08
2022
revised:
17
08
2022
pubmed:
2
9
2022
medline:
30
11
2022
entrez:
1
9
2022
Statut:
ppublish
Résumé
GF14 proteins are a family of conserved proteins involved in many cellular processes including transport, growth, metabolism, and stress response. However, only few reports are available regarding the 14-3-3 genes in potato. In this study, twelve 14-3-3 genes were detected in the potato genome. Based on their phylogenetic relationships, the StGF14 family members were categorized into two classes. Gene expression analysis demonstrated that StGF14h, StGF14a, and StGF14k had the highest gene expression, induced by abiotic and biotic stresses in all three tissues. The number of exons in 14-3-3 genes ranged from four to seven and most of these genes in the same subfamily had similar exon-intron patterns. The results of our study showed that the conserved motifs are similar in most of the proteins in each group. The intron-exon patterns and the composition of conserved motifs validated the 14-3-3 gene phylogenetic classification. According to the genome distribution results, 14-3-3 genes were located unevenly on the 12 Solanum tuberosum chromosomes. We find out 97 orthologous gene pairs between potato and Arabidopsis as well as 15 paralogous genes among potato genomes. Our results showed that GF-14 genes have an effective role in functional and molecular mechanisms in response to environmental stresses.
Identifiants
pubmed: 36048308
doi: 10.1007/s10142-022-00895-z
pii: 10.1007/s10142-022-00895-z
doi:
Substances chimiques
Plant Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1377-1390Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Références
Bihn EA, Paul AL, Wang SW, Erdos GW, Ferl RJ (1997) Localization of 14-3-3 proteins in the nuclei of Arabidopsis and maize. Plant J 12:1439–1445
doi: 10.1046/j.1365-313x.1997.12061439.x
pubmed: 9450348
Brandt J, Thordal-Christensen H, Vad K, Gregersen PL, Collinge DB (1992) A pathogen-induced gene of barley encodes a protein showing high similarity to a protein kinase regulator. Plant J 2:815–820
pubmed: 1302634
Bunney TD, van Walraven HS, de Boer AH (2001) 14-3-3 protein is a regulator of the mitochondrial and chloroplast ATP synthase. P N A S 98:4249–4254
doi: 10.1073/pnas.061437498
pubmed: 11274449
pmcid: 31211
Cao H, Xu Y, Yuan L, Bian Y, Wang L, Zhen S, Hu Y, Yan Y (2016) Molecular characterization of the 14-3-3 gene family in Brachypodium distachyon L. reveals high evolutionary conservation and diverse responses to abiotic stresses. Front Plant Sci 7:1099
doi: 10.3389/fpls.2016.01099
pubmed: 27507982
pmcid: 4960266
Chen Z, Fu H, Liu D, Chang PF, Narasimhan M, Ferl R, Hasegawa PM, Bressan RA (1994) A NaCl-regulated plant gene encoding a brain protein homolog that activates ADP ribosyltransferase and inhibits protein kinase C. Plant J 6:729–740
doi: 10.1046/j.1365-313X.1994.6050729.x
pubmed: 8000427
Chen F, Li Q, Sun L, He Z (2006) The rice 14-3-3 gene family and its involvement in responses to biotic and abiotic stress. DNA Res 13:53–63
doi: 10.1093/dnares/dsl001
pubmed: 16766513
Cheng C, Wang Y, Chai F, Li S, Xin H, Liang Z (2018) Genome-wide identification and characterization of the 14–3-3 family in Vitis vinifera L. during berry development and cold-and heat-stress response. BMC Genom 19:1–4
doi: 10.1186/s12864-018-4955-8
Faris JD, Li WL, Liu DJ, Chen PD, Gill BS (1999) Candidate gene analysis of quantitative disease resistance in wheat. Theor Appl Genet 98:219–225
doi: 10.1007/s001220051061
Finnie C, Andersen CH, Borch J, Gjetting S, Christensen AB, De Boer AH, Thordal-Christensen H, Collinge DB (2002) Do 14-3-3 proteins and plasma membrane H+-ATPases interact in the barley epidermis in response to the barley powdery mildew fungus? Plant Mol Biol 49:137–147
doi: 10.1023/A:1014938417267
Gao WJ, Chen Q, Zhao JY, Wang P, Li DL, Zheng K, Long YL, Jiao Y, Wang YX, Geng SW, Su XN (2020) Genome-wide identification and expression analysis of the 14-3-3 gene family in cotton (Gossypium hirsutum L.). PeerJ. 7:7950
Hajibarat Z, Saidi A, Zeinalabedini M, Gorji AM, Ghaffari MR, Shariati V, Ahmadvand R (2022) Genome-wide identification of StU-box gene family and assessment of their expression in developmental stages of Solanum tuberosum. J Genet Eng Biotechnol 20:1–21
doi: 10.1186/s43141-022-00306-7
Hill MK, Lyon KJ, Lyon BR (1999) Identification of disease response genes expressed in Gossypium hirsutum upon infection with the wilt pathogen Verticillium dahliae. Plant Mol Biol 40:289–296
doi: 10.1023/A:1006146419544
pubmed: 10412907
Li X, Wang QJ, Pan N, Lee S, Zhao Y, Chait BT, Yue Z (2011) Phosphorylation-dependent 14-3-3 binding to LRRK2 is impaired by common mutations of familial Parkinson’s disease. PLoS One 6:17153
doi: 10.1371/journal.pone.0017153
Li MY, Xu BY, Liu JH, Yang XL, Zhang JB, Jia CH, Ren LC, Jin ZQ (2012) Identification and expression analysis of four 14-3-3 genes during fruit ripening in banana (Musa acuminata L. AAA group, cv. Brazilian). Plant Cell Rep 31:369–378
doi: 10.1007/s00299-011-1172-1
pubmed: 22009053
Lozano-Durán R, Robatzek S (2015) 14-3-3 proteins in plant-pathogen interactions. Mol Plant-Microbe Interact 28:511–518
doi: 10.1094/MPMI-10-14-0322-CR
pubmed: 25584723
Malerba M, Cerana R, Crosti P (2004) Comparison between the effects of fusicoccin, Tunicamycin, and Brefeldin A on programmed cell death of cultured sycamore (Acer pseudoplatanus L.) cells. Protoplasma 224:61–70
doi: 10.1007/s00709-004-0053-7
pubmed: 15726810
Qin C, Cheng L, Shen J, Zhang Y, Cao H, Lu D, Shen C (2016) Genome-wide identification and expression analysis of the 14-3-3 family genes in Medicago truncatula. Front Plant Sci 7:320
doi: 10.3389/fpls.2016.00320
pubmed: 27047505
pmcid: 4801894
Roberts MR (2003) 14-3-3 proteins find new partners in plant cell signalling. Trends Plant Sci 8:218–223
doi: 10.1016/S1360-1385(03)00056-6
pubmed: 12758039
Roberts MR, Bowles DJ (1999) Fusicoccin, 14-3-3 proteins, and defense responses in tomato plants. Plant Physiol 119:1243–1250
doi: 10.1104/pp.119.4.1243
pubmed: 10198082
pmcid: 32008
Rosenquist M, Alsterfjord M, Larsson C, Sommarin M (2001) Data mining the Arabidopsis genome reveals fifteen 14-3-3 genes. Expression is demonstrated for two out of five novel genes. Plant Physiol 127:142–149
doi: 10.1104/pp.127.1.142
pubmed: 11553742
pmcid: 117970
Roth C, Liberles DA (2006) A systematic search for positive selection in higher plants (Embryophytes). BMC plant Biol 6:1–11
doi: 10.1186/1471-2229-6-12
Saidi A, Hajibarat Z (2020a) Application of next generation sequencing, GWAS, RNA seq, WGRS, for genetic improvement of potato (Solanum tuberosum L) under drought stress. Biocatal Agric Biotechnol 29:101801
doi: 10.1016/j.bcab.2020.101801
Saidi A, Hajibarat Z. 2020b. Computational analysis for characterization and evaluation of pentatricopeptide repeat-containing protein (PPR) in Arabidopsis thaliana. Polish J Nat Sci. 35.
Saidi A, Hajibarat Z, Hajibarat Z (2021a) Phylogeny, gene structure and GATA genes expression in different tissues of Solanaceae species. Biocatal Agric Biotechnol 35:102015
Saidi A, Hajibarat Z (2021b) Approaches for developing molecular markers associated with virus resistances in potato (Solanum tuberosum). J Plant Dis Prot 18:1–4
Seehaus K, Tenhaken R (1998) Cloning of genes by mRNA differential display induced during the hypersensitive reaction of soybean after inoculation with Pseudomonas syringae pv. glycinea. Plant Mol Biol 38:1225–1234
doi: 10.1023/A:1006036827841
pubmed: 9869427
Sehnke PC, Chung H-J, Wu K, Ferl RJ (2001) Regulation of starch accumulation by granule-associated plant 14-3-3 proteins. P Natl Acad Sci USA 98:765–770
doi: 10.1073/pnas.98.2.765
Sun G, Xie F, Zhang B (2011) Transcriptome-wide identification and stress properties of the 14-3-3 gene family in cotton (Gossypium hirsutum L.). Funct Integat Genom. 11:627–636
doi: 10.1007/s10142-011-0242-3
Tian F, Wang T, Xie Y, Zhang J, Hu J (2015) Genome-wide identification, classification, and expression analysis of 14-3-3 gene family in Populus. PLoS One 10:1–2210
Vatansever R, Ozyigit II, Filiz E, Gozukara N (2017) Genome-wide exploration of silicon (Si) transporter genes, Lsi1 and Lsi2 in plants; insights into Si-accumulation status/capacity of plants. Biometals 30:185–200
doi: 10.1007/s10534-017-9992-2
pubmed: 28091955
Wang J, Sun P, Li Y, Liu Y, Yu J, Ma X, Sun S, Yang N, Xia R, Lei T. (2017). Hierarchically aligning 10 legume Wang Y, Ling L, Jiang Z, Tan W, Liu Z, Wu L, Zhao Y, Xia S, Ma J, Wang G, Li W. Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max). Peer J. 2019 7: 7950.
Yan J, Wang J, Zhang H (2002) An ankyrin repeat-containing protein plays a role in both disease resistance and antioxidation metabolism. Plant J 29:193–202
doi: 10.1046/j.0960-7412.2001.01205.x
pubmed: 11862948