Bioinformatics of Growth-interacting Factor Genes in Foxtail Millet

ZHANG Liquan; ZHANG Haolin; LI Congcong; WEI Jianhua; ZHANG Jiewei

doi:10.19303/j.issn.1008-0384.2021.08.002

Volume 36 Issue 8

Aug. 2021

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ZHANG L Q, ZHANG H L, LI C C, et al. Bioinformatics of Growth-interacting Factor Genes in Foxtail Millet [J]. Fujian Journal of Agricultural Sciences，2021，36（8）：878−883 doi: 10.19303/j.issn.1008-0384.2021.08.002

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ZHANG L Q, ZHANG H L, LI C C, et al. Bioinformatics of Growth-interacting Factor Genes in Foxtail Millet [J]. Fujian Journal of Agricultural Sciences，2021，36（8）：878−883 doi: 10.19303/j.issn.1008-0384.2021.08.002

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Bioinformatics of Growth-interacting Factor Genes in Foxtail Millet

doi: 10.19303/j.issn.1008-0384.2021.08.002

ZHANG Liquan^1
,,
ZHANG Haolin^{1, 2
,},
LI Congcong¹,
WEI Jianhua^{1
,
,},
ZHANG Jiewei^{1
,
,}

1.
Agro-Biotechnology Research Institute, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing　100097, China
2.
College of Life Science, Shanghai Normal University, Shanghai　200234, China

Received Date: 2021-03-07
Rev Recd Date: 2021-06-06

Available Online: 2021-08-10

Publish Date: 2021-08-28

Abstract

Abstract

Objective The composition, structure, and evolution of each member of the growth-interacting factors (GIF) of the growth-regulating factors (GRF) and the transcription cofactors that closely associate with the growth, development, and stress response of plants in Setaria italica were analyzed. Method Based on the S. italica genome database and bioinformatics, the structure, characteristics, position on the chromosome, proteins similarity, secondary structure, transmembrane domain, and phosphorylation sites of the GIF genes were obtained. Result The 3 SiGIFs in S. italica genome contained 4 exons locating on the 3, 8, and 9 chromosomes. The greatest similarity between SiGIF1 and SiGIF2 was 72.04%, while the lowest was 37.08% between SiGIF1 and SiGIF3. The secondary structure consisted of 41.56%～56.60% random coils, 34.43%～35.50% alpha helix, 5.19%～11.69% beta turns and 3.23%～11.26% extended strands. The TMHMM transmembrane domain analysis showed no transmembrane domain in SiGIFs. MEME indicated that all SiGIFs contained conserved SSXT (PF05030) domain. And potential phosphorylation sites in the GIFs were predicted by analysis. Conclusion The bioinformatics revealed information on the structure, phosphorylation sites of SiGIF gene family provided crucial insights for the studies on the growth and development of plants.
- Setaria italica,
- GIF,
- gene family,
- phylogeny analysis

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References(27)

References

[1]	DEBERNARDI J M, MECCHIA M A, VERCRUYSSEN L, et al. Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity [J]. Plant Journal, 2014, 79(3): 413−426. doi: 10.1111/tpj.12567
[2]	KIM J H. Biological roles and an evolutionary sketch of the GRF-GIF transcriptional complex in plants [J]. BMB Reports, 2019, 52(4): 227−238. doi: 10.5483/BMBRep.2019.52.4.051
[3]	LEE B H, KO J H, LEE S, et al. The Arabidopsis GRF-interacting factor gene family performs an overlapping function in determining organ size as well as multiple developmental properties [J]. Plant Physiology, 2009, 151(2): 655−668. doi: 10.1104/pp.109.141838
[4]	KIM J H, KENDE H. A transcriptional coactivator, AtGIF1, is involved in regulating leaf growth and morphology in Arabidopsis [J]. PNAS, 2004, 101(36): 13374−13379. doi: 10.1073/pnas.0405450101
[5]	HORIGUCHI G, KIM G T, TSUKAYA H. The transcription factor AtGRF₅ and the transcription coactivator AN₃ regulate cell proliferation in leaf primordia of Arabidopsis thaliana [J]. The Plant Journal, 2005, 43(1): 68−78. doi: 10.1111/j.1365-313X.2005.02429.x
[6]	VERCRUYSSEN L, VERKEST A, GONZALEZ N, et al. ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development [J]. The Plant Cell, 2014, 26(1): 210−229. doi: 10.1105/tpc.113.115907
[7]	LIANG G, HE H, LI Y, et al. Molecular mechanism of microRNA396 mediating pistil development in Arabidopsis [J]. Plant Physiology, 2014, 164(1): 249−258. doi: 10.1104/pp.113.225144
[8]	ERCOLI M F, FERELA A, DEBERNARDI J M, et al. GIF transcriptional coregulators control root meristem homeostasis [J]. The Plant Cell, 2018, 30(2): 347−359. doi: 10.1105/tpc.17.00856
[9]	GAO F, WANG K, LIU Y, et al. Blocking miR396 increases rice yield by shaping inflorescence architecture [J]. Nature Plants, 2016, 2: 15196. doi: 10.1038/nplants.2015.196
[10]	NELISSEN H, EECKHOUT D, DEMUYNCK K, et al. Dynamic changes in ANGUSTIFOLIA3 complex composition reveal a growth regulatory mechanism in the maize leaf [J]. The Plant Cell, 2015, 27(6): 1605−1619. doi: 10.1105/tpc.15.00269
[11]	JIA G Q, HUANG X H, ZHI H, et al. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica) [J]. Nature Genetics, 2013, 45(8): 957−961. doi: 10.1038/ng.2673
[12]	BENNETZEN J L, SCHMUTZ J, WANG H, et al. Reference genome sequence of the model plant Setaria [J]. Nature Biotechnology, 2012, 30(6): 555−561. doi: 10.1038/nbt.2196
[13]	ZHANG G Y, LIU X, QUAN Z W, et al. Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential [J]. Nature Biotechnology, 2012, 30(6): 549−554. doi: 10.1038/nbt.2195
[14]	YANG Z R, ZHANG H S, LI X K, et al. A mini foxtail millet with an Arabidopsis-like life cycle as a C₄ model system [J]. Nature Plants, 2020, 6(9): 1167−1178. doi: 10.1038/s41477-020-0747-7
[15]	张杰伟, 丁莉萍, 陈亚娟, 等. 杨树磷酸肌醇特异性磷脂酶C基因家族鉴定与分析 [J]. 福建农业学报, 2016, 31(11):1181−1186. ZHANG J W, DING L P, CHEN Y J, et al. Genome-wide analysis and identification of phosphoinositide-specific phospholipase C gene family in poplar(Populus trichocarpa) [J]. Fujian Journal of Agricultural Sciences, 2016, 31(11): 1181−1186.(in Chinese)
[16]	BAILEY T L, JOHNSON J, GRANT C E, et al. The MEME suite [J]. Nucleic Acids Research, 2015, 43(W1): W39−W49. doi: 10.1093/nar/gkv416
[17]	GEOURJON C, DELÉAGE G. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments [J]. Bioinformatics, 1995, 11(6): 681−684. doi: 10.1093/bioinformatics/11.6.681
[18]	SIEVERS F, WILM A, DINEEN D, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega [J]. Molecular Systems Biology, 2011, 7: 539. doi: 10.1038/msb.2011.75
[19]	HUANG X Y, LIU G, ZHANG W W. Genome-wide analysis of LBD (LATERAL ORGAN BOUNDARIES domain) gene family in Brassica rapa [J]. Brazilian Archives of Biology and Technology, 2018, 61: e18180049. doi: 10.1590/1678-4324-2018180049
[20]	ZHANG J B, WANG X P, WANG Y C, et al. Genome-wide identification and functional characterization of cotton (Gossypium hirsutum) MAPKKK gene family in response to drought stress [J]. BMC Plant Biology, 2020, 20(1): 1−14. doi: 10.1186/s12870-019-2170-7
[21]	MAO J X, ZHANG X S, ZHANG W J, et al. Genome-wide identification, characterization and expression analysis of the MITF gene in Yesso scallops (Patinopecten yessoensis) with different shell colors [J]. Gene, 2019, 688: 155−162. doi: 10.1016/j.gene.2018.11.096
[22]	LU Y Z, MENG Y L, ZENG J, et al. Coordination between GROWTH-REGULATING FACTOR1 and GRF-INTERACTING FACTOR1 plays a key role in regulating leaf growth in rice [J]. BMC Plant Biology, 2020, 20(1): 200. doi: 10.1186/s12870-020-02417-0
[23]	ZAN T, ZHANG L, XIE T T, et al. Genome-wide identification and analysis of the growth-regulating factor (GRF) gene family and GRF-interacting factor family in Triticum aestivum L [J]. Biochemical Genetics, 2020, 58(5): 705−724. doi: 10.1007/s10528-020-09969-8
[24]	ZHANG J W, ZHANG Z B, ZHU D, et al. Expression and initial characterization of a Phosphoinositide-specific phospholipase C from Populus tomentosa [J]. Journal of Plant Biochemistry and Biotechnology, 2015, 24(3): 338−346. doi: 10.1007/s13562-014-0279-1
[25]	LI S C, GAO F Y, XIE K L, et al. The OsmiR396c-OsGRF4-OsGIF₁ regulatory module determines grain size and yield in rice [J]. Plant Biotechnology Journal, 2016, 14(11): 2134−2146. doi: 10.1111/pbi.12569
[26]	LIU W Y, ZHANG B, HE W Y, et al. Characterization of in vivo phosphorylation modification of differentially accumulated proteins in cotton fiber-initiation process [J]. Acta Biochimica et Biophysica Sinica, 2016, 48(8): 756−761. doi: 10.1093/abbs/gmw055
[27]	WANG Q, QIN G C, CAO M, et al. A phosphorylation-based switch controls TAA1-mediated auxin biosynthesis in plants [J]. Nature Communications, 2020, 11(1): 679. doi: 10.1038/s41467-020-14395-w