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中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志  2022, Vol. 42 Issue (12): 12-26    DOI: 10.13523/j.cb.2204077
研究报告     
Pmr1基因缺失对粟酒裂殖酵母细胞有性生殖和有丝分裂的影响及其分子机制研究*
叶姿妤1,丁祥2,鲁艳1,周丽倩1,刘欣岚2,蒲帝宏1,侯怡铃1,**()
1 西华师范大学生命科学学院 西南野生动植物资源保护教育部重点实验室 南充 637009
2 西华师范大学环境科学与工程学院 南充 637009
Effects of pmr1 Gene Deletion on Sexual Reproduction and Mitosis of Fission Yeast Cells and Its Molecular Mechanism
YE Zi-yu1,DING Xiang2,LU Yan1,ZHOU Li-qian1,LIU Xin-lan2,PU Di-hong1,HOU Yi-ling1,**()
1 Key Laboratory of Southwest China Wildlife Resource Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong 637009, China
2 College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
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摘要:

目的:pmr1基因编码P型钙转运ATP酶Pmr1,参与维持细胞壁完整性和调控胞质分裂。以粟酒裂殖酵母为模式细胞,探究pmr1缺失后对细胞有性生殖及细胞分裂中肌动蛋白环精细动力学的影响,揭示pmr1缺失后细胞异常生长过程中的关键基因和代谢通路。方法:通过细胞生长速率测定、产孢统计、绿色荧光蛋白标记肌动蛋白和活细胞成像的方法,检测pmr1缺失对细胞有丝分裂和有性生殖的影响;采用RNA-Seq对野生型菌株和pmr1Δ菌株测序和生物信息学分析,并进行qRT-PCR验证。结果:pmr1缺失后细胞生长减慢,分裂期细胞长度减小,子囊孢子长度增加,且肌动蛋白环的形成时间增加。RNA测序结果显示,mfm1mfm2mat1-Mc下调,错配修复通路cdc1exo1上调以及糖酵解/糖异生途径pgi1pfk1dld1下调是引起pmr1Δ孢子长度增加的主要因素;糖酵解/糖异生途径tdh1pgk1下调,以及脂肪酸合成代谢途径fas1fas2cut6lcf1下调导致了pmr1Δ分裂期细胞长度减小;hsp9上调是影响pmr1Δ收缩环形成时间增加的关键基因。qRT-PCR实验证实,pmr1缺失后关键基因的表达趋势与RNA-Seq结果一致。结论:pmr1缺失后,粟酒裂殖酵母细胞中错配修复通路、糖酵解/糖异生途径及脂肪酸合成代谢途径发生障碍,导致细胞及孢子形态均异常,且肌动蛋白环形成受阻,细胞增殖减缓。

关键词: pmr1基因裂殖酵母细胞分裂RNA-Seq测序代谢通路    
Abstract:

Objective: The pmr1 gene encodes P-type calcium-transporting ATPase Pmr1, which is involved in maintaining cell wall integrity and regulating cytokinesis. In this study, fission yeast was used as a model cell to explore the effects of pmr1 deletion on the sexual reproduction and dynamics of actin rings during cell mitosis, and to reveal the key genes and metabolic pathways of abnormal cell mitosis after pmr1 deletion. Methods: The effects of pmr1 deletion on cell mitosis and sexual reproduction were detected by cell growth rate measurement, spore production observation and statistics, green fluorescent protein-labeled monitoring and living cell imaging; The wild-type and pmr1Δ strain were sequenced by RNA-Seq and analyzed by bioinformatics, and verified by qRT-PCR. Results: The pmr1 deletion could slow down cell growth, decrease cell length in mitosis, increase length of sexually reproductive ascospore, and increase formation time of actin ring. RNA-sequencing results revealed that down-regulation of mfm1, mfm2 and mat1-Mc, up-regulation of cdc1 and exo1 in the mismatch repair pathway, and down-regulation of pgi1, pfk1 and dld1 in the glycolysis/gluconeogenesis pathway are the main factor of the increased spore length in the pmr1Δ; Meanwhile, the down-regulation of tdh1 and pgk1 in the glycolysis/gluconeogenesis pathway and the down-regulation of fas1, fas2, cut6 and lcf1 in the fatty acid anabolic pathway also led to the decreased cell length in mitosis of pmr1Δ; The up-regulation of hsp9 is the key gene that affected the formation time of actin ring in pmr1Δ. qRT-PCR experiments confirmed that the expression trends of key genes after pmr1 deletion were consistent with the RNA-Seq results. Conclusion: After pmr1 deletion, the mismatch repair pathway, glycolysis/gluconeogenesis pathway and fatty acid anabolic pathway are hindered in fission yeast cells, resulting in abnormal cell and spore morphology, obstruction of actin ring formation, and slowing down of cell proliferation.

Key words: pmr1 gene    Fission yeast    Cell division    RNA-Seq    Metabolic pathway
收稿日期: 2022-04-29 出版日期: 2023-01-05
ZTFLH:  Q932  
基金资助: *四川省科技厅应用基础研究(2022NSFSC0107);四川省科技厅科技成果转化项目资助项目(2022NZZJ0003)
通讯作者: 侯怡铃     E-mail: starthlh@126.com
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叶姿妤
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引用本文:

叶姿妤,丁祥,鲁艳,周丽倩,刘欣岚,蒲帝宏,侯怡铃. Pmr1基因缺失对粟酒裂殖酵母细胞有性生殖和有丝分裂的影响及其分子机制研究*[J]. 中国生物工程杂志, 2022, 42(12): 12-26.

YE Zi-yu,DING Xiang,LU Yan,ZHOU Li-qian,LIU Xin-lan,PU Di-hong,HOU Yi-ling. Effects of pmr1 Gene Deletion on Sexual Reproduction and Mitosis of Fission Yeast Cells and Its Molecular Mechanism. China Biotechnology, 2022, 42(12): 12-26.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2204077        https://manu60.magtech.com.cn/biotech/CN/Y2022/V42/I12/12

图1  pmr1基因的基因位置、PMR1蛋白结构和蛋白保守域
Strains Genotype
PT.286 h- wt
PT.287 h+ wt
PT.3850 h+ wt: Pact1-LifeAct-mGFP: LEU1
22 h- pmr1Δ: kanR
22B h? pmr1Δ: Pact1-LifeAct-mGFP: LEU1
表1  实验所用菌株及编号
图2  25℃下pmr1基因缺失对细胞生长和产孢的影响
图3  pmr1基因缺失对细胞长度和肌动蛋白环定位的影响
图4  pmr1基因缺失对肌动蛋白环形成时间、收缩时间及收缩速率的影响
Sample Clean reads Clean bases Error rate Q30 / % GC content
wt_1 46 447 832 6.97 G 0.02 94.57 41.43
wt_2 45 173 776 6.78 G 0.02 95.09 41.41
wt_3 44 388 600 6.66 G 0.03 94.11 41.23
pmr1_1 41 279 024 6.19 G 0.02 95.31 41.27
pmr1_2 41 845 000 6.28 G 0.02 95.46 41.35
pmr1_3 44 284 874 6.64 G 0.02 94.81 40.94
表2  转录组测序数据质量统计
Gene name FPKM(wt) FPKM(pmr1Δ) Gene description
gpd3 15 353.453 88 15 959.829 08 Glyceraldehyde 3-phosphate dehydrogenase Gpd3
zym1 13 760.905 16 14 307.039 34 Metallothionein Zym1
hsp9 7 879.472 53 8 560.037 92 Heat shock protein Hsp9
hsp16 6 429.324 40 6 194.116 955 Heat shock protein Hsp16
eno101 5 927.174 232 6 461.217 911 Enolase
fba1 6 012.452 647 5 818.516 153 Fructose-bisphosphate aldolase Fba1
tdh1 5 679.168 434 4 102.244 391 Glyceraldehyde-3-phosphate dehydrogenase Tdh1
pgk1 4 919.322 538 3 933.365 814 Phosphoglycerate kinase Pgk1
tef103 4 107.470 752 3 890.983 788 Translation elongation factor EF-1 alpha Ef1a-c
gpm1 3 555.484 13 3 820.980 92 Monomeric 2, 3-bisphosphoglycerate (BPG)-dependent phosphoglycerate mutase (PGAM), Gpm1
pex7 3 358.379 28 3 569.658 727 Peroxin-7
pyk1 3 488.753 815 3 564.304 155 Pyruvate kinase
lsd90 3 488.525 293 2 542.280 536 Lsd90 protein
hry1 3 423.976 852 2 454.672 867 HHE domain cation binding protein
ole1 3 069.993 526 2 462.650 536 Acyl-CoA desaturase
表3  野生型和pmr1Δ菌株高表达基因统计 ( FPKM>3 000为极高表达)
Gene name Log2FoldChange Padj Gene description
mat2-Pc 12.589 4 4.48×10-24 Silenced P-specific polypeptide Pc
mat2-Pi 9.057 1 5.97×10-12 Silenced P-specific polypeptide Pi
Tf2-13 8.503 3 2.58×10-10 Retro transposable element/transposon Tf2-type
ftm4 5.942 7 2.68×10-168 S.pombe specific 5Tm protein family
gdt1 4.297 2 0.00 Human TMEM165 homolog, implicated in calcium transport
pdc102 4.157 6 8.62×10-5 Pyruvate decarboxylase
mat1-Mi 3.759 4 4.91×10-11 Mating-type M-specific polypeptide Mm/Mi
fub2 1.577 6 3.94×10-51 PI31 proteasome regulator Fub2
map3 1.503 9 4.23×10-20 Pheromone M-factor receptor Map3
mal1 1.45 7.07×10-96 Maltase alpha-glucosidase Mal1
prl24 1.326 4 3.44×10-6 Non-coding RNA, poly(A)-bearing
nam3 1.297 2 3.68×10-3 LncRNA nam3
cox1 1.277 9 5.69×10-4 Cytochrome C oxidase subunit 1
isp3 1.046 7 1.03×10-8 Spore wall structural constituent Isp3
表4  野生型和pmr1Δ菌株上调的差异表达基因(log2FoldChange≥ 1 )
Gene name Log2FoldChange Padj Gene description
mat3-Mc -6.721 4 3.54×10-5 Mating-type m-specific HMG-box transcription factor Mc at silenced MAT3 locus
mat1-Mc -5.202 4 1.50×10-2 Mating-type m-specific polypeptide Mc
mfm2 -4.271 2 0.00 M-factor precursor Mfm2
mfm1 -2.902 0 1.57×10-78 M-factor precursor Mfm1
mam1 -1.664 9 9.75×10-115 M-factor transmembrane transporter Mam1
ght3 -1.555 4 1.20×10-54 Hexose transmembrane transporter Ght3
cig2 -1.239 3 2.30×10-6 G1/S-specific B-type cyclin Cig2
hsp3103 -1.031 0 1.99×10-35 ThiJ domain protein
cta3 -1.005 0 1.06×10-5 P-type ATPase, potassium exporting Cta3
表5  野生型和pmr1Δ菌株下调的差异表达基因(log2FoldChange≤ -1)
图5  差异表达基因火山图
图6  差异表达基因的GO富集
图7  差异表达基因的KEGG富集
图8  差异表达基因的代谢通路富集
图9  关键差异表达基因qRT-PCR验证
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