植物合成生物学领域发展态势的文献计量分析

doi:10.13560/j.cnki.biotech.bull.1985.2021-1600s

摘要/Abstract

摘要：

合成生物学作为一种颠覆性技术可应用于农业领域的创新发展,解决当前农业学科中的瓶颈问题。利用文献计量学方法从领域发表论文的时序数量分布、主题分布等探测当前合成生物学的基本态势。基于领域的主题分布可知,其中植物合成生物学这一主题是稳定存在的且主题规模处于稳定增长趋势。聚焦植物合成生物学这一主题方向,在构建引文网络的基础上利用主路径分析方法从知识流动角度探测植物合成生物学领域重要知识节点,内容涵盖介子油苷生物合成途径,重要催化酶功能解析、转录因子的调控作用,组学方法的应用,利用微生物酵母进行生物物质合成,这些内容表征了合成生物的核心理论技术。

关键词: 合成生物学, 植物合成生物学, 文献计量, 发展态势分析

Abstract:

Synthetic biology,as a disruptive technology,can be applied to solve the bottleneck problem in current agricultural disciplines. In this study,bibliometrics is used to analyze the basic situation of synthetic biology from the time series,number distribution and topic distribution of published papers in the field. Based on the topic distribution in the field,it can be seen that the topic of plant synthetic biology is steadily increasing. Focusing on the topic of plant synthetic biology,the main path analysis was used to explore the important knowledge nodes in the development process of plant synthetic biology from the perspective of knowledge flow. Based on the main path analysis method the representative content glucosinolate as the representative secondary metabolite,including the mesotrioside biosynthetic pathway,the functional analysis of important catalytic enzymes,the regulation of transcription factors,the application of omics method,and the use of microbial yeast for biomass synthesis,which respectively characterized the core theory and technology of synthetic biology.

Key words: synthetic biology, plant synthetic biology, bibliometrics, development trend analysis

郭晓真, 张学福. 植物合成生物学领域发展态势的文献计量分析[J]. 生物技术通报, 2022, 38(2): 289-296.

GUO Xiao-zhen, ZHANG Xue-fu. Analysis of the Development Trend in the Field of Plant Synthetic Biology[J]. Biotechnology Bulletin, 2022, 38(2): 289-296.

图/表 9

参考文献 17

[1]	张先恩. 中国合成生物学发展回顾与展望[J]. 中国科学:生命科学, 2019, 49(12):1543-1572.
	Zhang XE. Synthetic biology in China:Review and prospects[J]. Scientia Sinica(Vitae): 2019, 49(12):1543-1572.
[2]	江会锋. 合成生物技术助力可持续发展[J]. 生物技术通报, 2020, 36(4):1-2.
	Jiang HF. Synthetic biotechnology boosts sustainable development[J]. Biotechnology Bulletin, 2020, 36(4):1-2.
[3]	Si T, Zhao HM. A brief overview of synthetic biology research programs and roadmap studies in the United States[J]. Synthetic and Systems Biotechnology, 2016, 1(4):258-264. doi: 10.1016/j.synbio.2016.08.003 URL
[4]	Clarke LJ, Kitney RI. Synthetic biology in the UK - An outline of plans and progress[J]. Synthetic and Systems Biotechnology, 2016, 1(4):243-257. doi: 10.1016/j.synbio.2016.09.003 pmid: 29062950
[5]	陈国强, 王颖. 中国“合成生物学”973 项目研究进展[J]. 生物工程学报, 2015, 31(6):995-1008.
	Chen GQ, Wang Y. Progress in synthetic biology of “973 Funding Program” in China[J]. Chin J Biotech June, 2015, 31(6):995-1008.
[6]	孙晓, 杨鹏, 王虹扬. 农业绿色发展研究文献计量分析[J]. 中国农业资源与区划, 2021, 42(2):1-9.
	Sun X, Yang P, Wang HY. Bibliometric analysis of agricultural green development[J]. Chinese Journal of Agricultural Resources and Regional Planning, 2021, 42(2):1-9.
[7]	马瑞敏, 杨雨华. 基于节点重要性的领域主路径发现新探索[J]. 情报杂志, 2018(3):71-78, 93.
	Ma RM, Yang YH. Discovering main path of a domain based on node importance[J]. Journal of Intelligence, 2018, 37(3):71-78, 93.
[8]	Yang G, Zheng Q, Hu P, et al. Cytogenetic identification and molecular marker development for the novel stripe rust-resistant wheat-Thinopyrum intermedium translocation line WTT11[J]. aBIOTECH, 2021, 2:343-356. doi: 10.1007/s42994-021-00060-3 URL
[9]	Sun L, Wen J, Peng H, et al. The genetic and molecular basis for improving heat stress tolerance in wheat[J]. aBIOTECH, 2021, https://doi.org/10.1007/s42994-021-00064-z .
[10]	种康, 许智宏, 李家洋. 中国植物科学基础研究概[J]. 中国基础科学, 2016, 18(1):7-12.
	Chong K, Xu ZH, Li JY. Basic research panorama of plant science in China[J]. China Basic Science, 2016, 18(1):7-12.
[11]	Mikkelsen MD. Modulation of CYP79 genes and glucosinolate profiles in Arabidopsis by defense signaling pathways[J]. Plant Physiology, 2003, 131(1):298. pmid: 12529537
[12]	Mikkelsen MD, Microbial production of indolylglucosinolate through engineering of a multi-gene pathway in a versatile yeast expression platform[J]. Metabolic Engineering, 2012, 14(2):104-111. doi: 10.1016/j.ymben.2012.01.006 pmid: 22326477
[13]	Fossati E. Reconstitution of a 10-gene pathway for synjournal of the plant alkaloid dihydrosanguinarine in Saccharomyces cerevisi-ae[J]. Nature Communications, 2014, 5.
[14]	Sun T, Zhu Q, Wei Z, et al. Multi-strategy engineering greatly enhances provitamin A carotenoid accumulation and stability in Ara-bidopsis seeds[J]. aBIOTECH, 2021, 2(3):191-214. doi: 10.1007/s42994-021-00046-1 URL
[15]	张凤, 陈伟. 代谢组学在植物逆境生物学中的研究进展[J]. 生物技术通报, 2021, 37(8):1-11. doi: 10.13560/j.cnki.biotech.bull.1985.2021-0861
	Zhang F, Chen W. Research progress of metabolomics in plant stress biology[J]. Biotechnology Bulletin, 2021, 37(8):1-11.
[16]	薛勇彪, 韩斌, 种康, 等. 水稻分子模块设计研究成果与展望[J]. 中国科学院院刊, 2018, 33(9):900-908.
	Xue YB, Han B, Chong K, et al. Achievements and prospect of designer breeding by molecular modules in rice[J]. Bulletin of Chinese Academy of Sciences, 2018, 33(9):900-908.
[17]	Li J, Li Y, Ma L. Recent advances in CRISPR/Cas9 and applicati-ons for wheat functional genomics and breeding[J]. aBIOTECH, 2012, 2(3):375-385. doi: 10.1007/s42994-021-00042-5 URL

启动时间 Start-up time	项目名称 Project
2011年	人工合成细胞工厂
2011年	光合作用与人工叶片
2012年	新功能人造生物器件的构建与集成
	微生物药物创新与优产的人工合成体系
	用合成生物学方法构建生物基材料的合成新途径
2013年	合成微生物体系的适配性研究
2013年	抗逆元器件的构建和机理研究
2014年	合成生物器件干预膀胱癌的研究
2014年	微生物多细胞体系的设计与合成
2015年	生物固氮及相关抗逆模块的人工设计与系统优化

启动时间 Start-up time	项目名称 Project
2011年	人工合成细胞工厂
2011年	光合作用与人工叶片
2012年	新功能人造生物器件的构建与集成
	微生物药物创新与优产的人工合成体系
	用合成生物学方法构建生物基材料的合成新途径
2013年	合成微生物体系的适配性研究
2013年	抗逆元器件的构建和机理研究
2014年	合成生物器件干预膀胱癌的研究
2014年	微生物多细胞体系的设计与合成
2015年	生物固氮及相关抗逆模块的人工设计与系统优化

节点	内容解读
Wittstock U（2000）	Cytochrome P450CYP79A2 from Arabidopsis thaliana L. catalyzes the conversion of L-phenylalanine to phenylacetaldoxime in the biosynthesis of benzylglucosinolate
Mikkelsen MD（2000）	Cytochrome P450CYP79B2 from Arabidopsis catalyzes the conversion of tryptophan to indole-3-acetaldoxime,a precursor of indole glucosinolates and indole-3-acetic acid
Hansen CH（2001）	Cytochrome P450CYP79F1 from Arabidopsis catalyzes the conversion of dihomomethionine and trihomomethionine to the corresponding aldoximes in the biosynthesis of aliphatic glucosinolates
Mikkelsen MD（2003）	Modulation of CYP79 genes and glucosinolate profiles in Arabidopsis by defense signaling pathways
Mikkelsen MD（2004）	Arabidopsis mutants in the C-S lyase of glucosinolate biosynthesis establish a critical role for indole-3-acetaldoxime in auxin homeostasis
Grubb CD（2004）	Arabidopsis glucosyltransferase UGT74B1 functions in glucosinolate biosynthesis and auxin homeostasis
Levy M（2005）	Arabidopsis IQD1,a novel calmodulin-binding nuclear protein,stimulates glucosinolate accumulation and plant defense
Skirycz A（2006）	DOF transcription factor AtDof1.1（OBP2）is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis
Gigolashvili T（2007）	The R2R3-MYB transcription factor HAG1/MYB28 is a regulator of methionine-derived glucosinolate biosynthesis in Arabidopsis thaliana
Sonderby IE（2007）	A systems biology approach identifies a R2R3 MYB gene subfamily with distinct and overlapping functions in regulation of aliphatic glucosinolates
Malitsky S（2008）	The transcript and metabolite networks affected by the two clades of Arabidopsis glucosinolate biosynthesis regulators
Sawada Y（2009）	Omics-Based approaches to methionine side chain elongation in Arabidopsis：Characterization of the genes encoding methylthioalkylmalate isomerase and methylthioalkylmalate dehydrogenase
Sawada Y（2009）	Arabidopsis bile acid：sodium symporter family protein 5 is involved in methionine-derived glucosinolate biosynthesis
Albinsky D（2010）	Widely targeted metabolomics and coexpression analysis as tools to identify genes involved in the side-chain elongation steps of aliphatic glucosinolate biosynthesis
Sonderby IE（2010）	A complex interplay of three R2R3 MYB transcription factors determines the profile of aliphatic glucosinolates in Arabidopsis1^[C][W][OA]
Pfalz M（2011）	Metabolic engineering in nicotiana benthamiana reveals key enzyme functions in Arabidopsis indole glucosinolate modification
Mikkelsen MD（2012）	Microbial production of indolylglucosinolate through engineering of a multi-gene pathway in a versatile yeast expression platform
Fossati E（2014）	Reconstitution of a 10-gene pathway for synthesis of the plant alkaloid dihydrosanguinarine in Saccharomyces cerevisiae
Trenchard IJ（2015）	De novo production of the key branch point benzylisoquinoline alkaloid reticuline in yeast
DeLoache WC（2015）	An enzyme-coupled biosensor enables（S）-reticuline production in yeast from glucose
Galanie S（2015）	Optimization of yeast-based production of medicinal protoberberine alkaloids
Li YR（2018）	Complete biosynthesis of noscapine and halogenated alkaloids in yeast
Wang Y（2019）	Design and use of de novo cascades for the biosynthesis of new benzylisoquinoline alkaloids
Cabry MP（2019）	Structure of Papaver somniferum O-methyltransferase 1 reveals initiation of noscapine biosynthesis with implications for plant natural product methylation
Lang DE（2019）	Structure-function studies of tetrahydroprotoberberine N-methyltransferase reveal the molecular basis of stereoselective substrate recognition

节点	内容解读
Wittstock U（2000）	Cytochrome P450CYP79A2 from Arabidopsis thaliana L. catalyzes the conversion of L-phenylalanine to phenylacetaldoxime in the biosynthesis of benzylglucosinolate
Mikkelsen MD（2000）	Cytochrome P450CYP79B2 from Arabidopsis catalyzes the conversion of tryptophan to indole-3-acetaldoxime,a precursor of indole glucosinolates and indole-3-acetic acid
Hansen CH（2001）	Cytochrome P450CYP79F1 from Arabidopsis catalyzes the conversion of dihomomethionine and trihomomethionine to the corresponding aldoximes in the biosynthesis of aliphatic glucosinolates
Mikkelsen MD（2003）	Modulation of CYP79 genes and glucosinolate profiles in Arabidopsis by defense signaling pathways
Mikkelsen MD（2004）	Arabidopsis mutants in the C-S lyase of glucosinolate biosynthesis establish a critical role for indole-3-acetaldoxime in auxin homeostasis
Grubb CD（2004）	Arabidopsis glucosyltransferase UGT74B1 functions in glucosinolate biosynthesis and auxin homeostasis
Levy M（2005）	Arabidopsis IQD1,a novel calmodulin-binding nuclear protein,stimulates glucosinolate accumulation and plant defense
Skirycz A（2006）	DOF transcription factor AtDof1.1（OBP2）is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis
Gigolashvili T（2007）	The R2R3-MYB transcription factor HAG1/MYB28 is a regulator of methionine-derived glucosinolate biosynthesis in Arabidopsis thaliana
Sonderby IE（2007）	A systems biology approach identifies a R2R3 MYB gene subfamily with distinct and overlapping functions in regulation of aliphatic glucosinolates
Malitsky S（2008）	The transcript and metabolite networks affected by the two clades of Arabidopsis glucosinolate biosynthesis regulators
Sawada Y（2009）	Omics-Based approaches to methionine side chain elongation in Arabidopsis：Characterization of the genes encoding methylthioalkylmalate isomerase and methylthioalkylmalate dehydrogenase
Sawada Y（2009）	Arabidopsis bile acid：sodium symporter family protein 5 is involved in methionine-derived glucosinolate biosynthesis
Albinsky D（2010）	Widely targeted metabolomics and coexpression analysis as tools to identify genes involved in the side-chain elongation steps of aliphatic glucosinolate biosynthesis
Sonderby IE（2010）	A complex interplay of three R2R3 MYB transcription factors determines the profile of aliphatic glucosinolates in Arabidopsis1^[C][W][OA]
Pfalz M（2011）	Metabolic engineering in nicotiana benthamiana reveals key enzyme functions in Arabidopsis indole glucosinolate modification
Mikkelsen MD（2012）	Microbial production of indolylglucosinolate through engineering of a multi-gene pathway in a versatile yeast expression platform
Fossati E（2014）	Reconstitution of a 10-gene pathway for synthesis of the plant alkaloid dihydrosanguinarine in Saccharomyces cerevisiae
Trenchard IJ（2015）	De novo production of the key branch point benzylisoquinoline alkaloid reticuline in yeast
DeLoache WC（2015）	An enzyme-coupled biosensor enables（S）-reticuline production in yeast from glucose
Galanie S（2015）	Optimization of yeast-based production of medicinal protoberberine alkaloids
Li YR（2018）	Complete biosynthesis of noscapine and halogenated alkaloids in yeast
Wang Y（2019）	Design and use of de novo cascades for the biosynthesis of new benzylisoquinoline alkaloids
Cabry MP（2019）	Structure of Papaver somniferum O-methyltransferase 1 reveals initiation of noscapine biosynthesis with implications for plant natural product methylation
Lang DE（2019）	Structure-function studies of tetrahydroprotoberberine N-methyltransferase reveal the molecular basis of stereoselective substrate recognition