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Strategy of tuning gene expression ratio in prokaryotic cell from perspective of noise and correlation
Li, R; Xu, LF; Shi, HL; Shi, HL (reprint author), Chinese Acad Sci, Inst Theoret Phys, State Key Lab Theoret Phys, Beijing 100190, Peoples R China.
2015
发表期刊JOURNAL OF THEORETICAL BIOLOGY
卷号365期号:0页码:377-389
文章类型Article
摘要Genes are organized into operons in procaryote, and these genes in one operon generally have related functions. However, genes in the same operon are usually not equally expressed, and the ratio needs to be fine-tuned for specific functions. We examine the difference of gene expression noise and correlation when tuning the expression level at the transcriptional or translational level in a bicistronic operon driven by a constitutive or a two-state promoter. We get analytic results for the noise and correlation of gene expression levels, which is confirmed by our stochastic simulations. Both the noise and the correlation of gene expressions in an operon with a two-state promoter are higher than in an operon with a constitutive promoter. Premature termination of mRNA induced by transcription terminator in the intergenic region or changing translation rates can tune the protein ratio at the transcriptional level or at the translational level. We find that gene expression correlation between promoter-proximal and promoter-distal genes at the protein level decreases as termination increases. In contrast, changing translation rates in the normal range almost does not alter the correlation. This explains why the translation rate is a key factor of modulating gene expressions in an operon. Our results can be useful to understand the relationship between the operon structure and the biological function of a gene network, and also may help in synthetic biology design. (C) 2014 Elsevier Ltd. All rights reserved.
关键词Polar Effect The Two-state Promoter Transcription Terminator Gene Expression Correlation Operon Structure
学科领域Life Sciences & Biomedicine - Other Topics ; Mathematical & Computational Biology
资助者National Basic Research Program of China [2013CB834100] ; National Basic Research Program of China [2013CB834100] ; National Basic Research Program of China [2013CB834100] ; National Basic Research Program of China [2013CB834100] ; National Natural Science Foundation of China [11121403, 11274320] ; National Natural Science Foundation of China [11121403, 11274320] ; National Natural Science Foundation of China [11121403, 11274320] ; National Natural Science Foundation of China [11121403, 11274320] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; National Natural Science Funds for Young Scholar [11304115] ; National Natural Science Funds for Young Scholar [11304115] ; National Natural Science Funds for Young Scholar [11304115] ; National Natural Science Funds for Young Scholar [11304115] ; China Postdoctoral Science Foundation [2013M541282] ; China Postdoctoral Science Foundation [2013M541282] ; China Postdoctoral Science Foundation [2013M541282] ; China Postdoctoral Science Foundation [2013M541282] ; National Basic Research Program of China [2013CB834100] ; National Basic Research Program of China [2013CB834100] ; National Basic Research Program of China [2013CB834100] ; National Basic Research Program of China [2013CB834100] ; National Natural Science Foundation of China [11121403, 11274320] ; National Natural Science Foundation of China [11121403, 11274320] ; National Natural Science Foundation of China [11121403, 11274320] ; National Natural Science Foundation of China [11121403, 11274320] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; National Natural Science Funds for Young Scholar [11304115] ; National Natural Science Funds for Young Scholar [11304115] ; National Natural Science Funds for Young Scholar [11304115] ; National Natural Science Funds for Young Scholar [11304115] ; China Postdoctoral Science Foundation [2013M541282] ; China Postdoctoral Science Foundation [2013M541282] ; China Postdoctoral Science Foundation [2013M541282] ; China Postdoctoral Science Foundation [2013M541282]
DOIhttp://dx.doi.org/10.1016/j.jtbi.2014.11.002
关键词[WOS]SHINE-DALGARNO SEQUENCE ; MESSENGER-RNA DECAY ; ESCHERICHIA-COLI ; BACILLUS-SUBTILIS ; SINGLE-CELL ; TRANSLATION ; CODON ; BACTERIA ; OPERON ; STOCHASTICITY
收录类别SCI
语种英语
资助者National Basic Research Program of China [2013CB834100] ; National Basic Research Program of China [2013CB834100] ; National Basic Research Program of China [2013CB834100] ; National Basic Research Program of China [2013CB834100] ; National Natural Science Foundation of China [11121403, 11274320] ; National Natural Science Foundation of China [11121403, 11274320] ; National Natural Science Foundation of China [11121403, 11274320] ; National Natural Science Foundation of China [11121403, 11274320] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; National Natural Science Funds for Young Scholar [11304115] ; National Natural Science Funds for Young Scholar [11304115] ; National Natural Science Funds for Young Scholar [11304115] ; National Natural Science Funds for Young Scholar [11304115] ; China Postdoctoral Science Foundation [2013M541282] ; China Postdoctoral Science Foundation [2013M541282] ; China Postdoctoral Science Foundation [2013M541282] ; China Postdoctoral Science Foundation [2013M541282] ; National Basic Research Program of China [2013CB834100] ; National Basic Research Program of China [2013CB834100] ; National Basic Research Program of China [2013CB834100] ; National Basic Research Program of China [2013CB834100] ; National Natural Science Foundation of China [11121403, 11274320] ; National Natural Science Foundation of China [11121403, 11274320] ; National Natural Science Foundation of China [11121403, 11274320] ; National Natural Science Foundation of China [11121403, 11274320] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China [Y4KF171CJ1] ; National Natural Science Funds for Young Scholar [11304115] ; National Natural Science Funds for Young Scholar [11304115] ; National Natural Science Funds for Young Scholar [11304115] ; National Natural Science Funds for Young Scholar [11304115] ; China Postdoctoral Science Foundation [2013M541282] ; China Postdoctoral Science Foundation [2013M541282] ; China Postdoctoral Science Foundation [2013M541282] ; China Postdoctoral Science Foundation [2013M541282]
WOS类目Biology ; Mathematical & Computational Biology
引用统计
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/21111
专题理论物理所SCI论文
通讯作者Shi, HL (reprint author), Chinese Acad Sci, Inst Theoret Phys, State Key Lab Theoret Phys, Beijing 100190, Peoples R China.
推荐引用方式
GB/T 7714
Li, R,Xu, LF,Shi, HL,et al. Strategy of tuning gene expression ratio in prokaryotic cell from perspective of noise and correlation[J]. JOURNAL OF THEORETICAL BIOLOGY,2015,365(0):377-389.
APA Li, R,Xu, LF,Shi, HL,&Shi, HL .(2015).Strategy of tuning gene expression ratio in prokaryotic cell from perspective of noise and correlation.JOURNAL OF THEORETICAL BIOLOGY,365(0),377-389.
MLA Li, R,et al."Strategy of tuning gene expression ratio in prokaryotic cell from perspective of noise and correlation".JOURNAL OF THEORETICAL BIOLOGY 365.0(2015):377-389.
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