Analysis of Gene Clusters for Sanxiapeptin Biosynthesis by Transcriptomic Sequencing

LIU Chao; LI Kun; BAI Xiaoxuan; YANG Yuchun; XUE Yanhong; LIU Shiping

doi:10.13386/j.issn1002-0306.2020110192

Volume 42 Issue 13

Jun. 2021

Turn off MathJax

Article Contents

Abstract

References

Science and Technology of Food Industry > 2021 > 42(13): 156-162. > DOI: 10.13386/j.issn1002-0306.2020110192

LIU Chao, LI Kun, BAI Xiaoxuan, et al. Analysis of Gene Clusters for Sanxiapeptin Biosynthesis by Transcriptomic Sequencing [J]. Science and Technology of Food Industry, 2021, 42(13): 156−162. (in Chinese with English abstract). doi: 10.13386/j.issn1002-0306.2020110192.

Citation:

PDF (2599 KB)

Analysis of Gene Clusters for Sanxiapeptin Biosynthesis by Transcriptomic Sequencing

College of Life Science and Pharmacy, Key Laboratory of Functional Yeast (China National Light Industry), Three Gorges University, Yichang 443002, China

More Information

Received Date: November 22, 2020
Available Online: April 22, 2021

Graphical Abstract

Abstract

Abstract

In order to explore the biosynthesis mechanism of the sanxiapeptin, the BGISEQ-500 platform was used to determine cDNA library when the SG-4 was cultured at 200 mL for 4, 7 d and 300 mL for 7 d, and RNA-seq analysis 6.42 Gb data generated by high-throughput sequencing without reference genome. The results showed that the transcriptome sequence alignment rate was as high as 93.88%, it was found that the differential genes were mainly concentrated in the pathways of antibiotic synthesis, substance transport and redox metabolism. In the non-ribosomal peptide synthetase (NRPS, Non-ribosomal peptide synthetase) gene cluster PDE_01071, the expression trends of 21 genes were completely consistent with the content of substances, it suggested that the gene cluster PDE_01071 might be responsible for the synthesis of sanxiapeptin.
- penicillium oxalicum,
- sanxiapeptin,
- citrus,
- biosynthesis,
- comparative transcriptome,
- gene cluster

FullText(HTML)

References (32)

References

[1]	Vogt E, Künzler M. Discovery of novel fungal RiPP biosynthetic pathways and their application for the development of peptide therapeutics[J]. Applied Microbiology Biotechnology,2019,103(14):5567−5581.
[2]	Süssmuth R, Müller J, Von Döhren H, et al. Fungal cyclooligomer depsipeptides: From classical biochemistry to combinatorial biosynthesis[J]. Natural Product Reports,2011,28(1):99−124. doi: 10.1039/C001463J
[3]	Abulfathi A A, Chirehwa M, Rosenkranz B, et al. Evaluation of the effectiveness of dose individualization to achieve therapeutic vancomycin concentrations[J]. Journal Clinical Pharmacology,2018,58(9):1134−1139. doi: 10.1002/jcph.1254
[4]	Yang X, Feng P, Yin Y, et al. Cyclosporine biosynthesis in Tolypocladium inflatum benefits fungal adaptation to the environment[J]. Molecular Biology and Physiology,2018,9(5):e01211−e01218.
[5]	Zhao P, Xue Y, Li X, et al. Fungi-derived lipopeptide antibiotics developed since 2000[J]. Peptides,2019(113):52−65.
[6]	Ramm S, Krawczyk B, Süssmuth R D, et al. A Self-sacrificing N-methyltransferase is the precursor of the fungal natural product omphalotin[J]. Angewandte Chemie (International ed. in English),2017,56(33):9994−9997.
[7]	Nuti R, Goud N S, Saraswati A P, et al. Antimicrobial peptides: A promising therapeutic strategy in tackling antimicrobial resistance[J]. Current Medicinal Chemistry,2017,24:4303−4314.
[8]	Reimer J M, Aloise M N, Harrison P M, et al. Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase[J]. Nature,2016,529:239−242. doi: 10.1038/nature16503
[9]	张晨曦. 两种核糖体肽类天然产物的生物合成机制研究[D]. 上海: 上海师范大学, 2017.
[10]	Luo S, Dong S H. Recent advances in the discovery and biosynthetic study of eukaryotic RiPP natural products[J]. Molecules,2019,24(8):1541. doi: 10.3390/molecules24081541
[11]	Ortega M A, van der Donk W A. New insights into the biosynthetic logic of ribosomally synthesized and post-translationally modified peptide natural products[J]. Cell Chemical Biology,2016,23(1):31−44. doi: 10.1016/j.chembiol.2015.11.012
[12]	Ding W, Liu W Q, Jia Y, et al. Biosynthetic investigation of phomopsins reveals a widespread pathway for ribosomal natural products in ascomycetes[J]. Proceedings of the National Academy of Sciences of the United States of America,2016,113(13):3521−3526. doi: 10.1073/pnas.1522907113
[13]	Hudson G A, Mitchell D A. RiPP antibiotics: Biosynthesis and engineering potential[J]. Current Opinion in Microbiology,2018,45:61−69. doi: 10.1016/j.mib.2018.02.010
[14]	Singh M, Chaudhary S, Sareen D. Non-ribosomal peptide synthetases: Identifying the cryptic gene clusters and decoding the natural product[J]. Journal of Biosciences,2017,42(1):175−187.
[15]	韩梦瑶, 陈晶晶, 朱平, 等. 非核糖体肽合成酶研究进展[J]. 药学学报,2018,53(7):1080−1089.
[16]	潘园园, 刘钢. 中国丝状真菌次级代谢分子调控研究进展[J]. 遗传,2018,40(10):874−887.
[17]	Niu X, Thaochan N, Hu Q. Diversity of linear non-ribosomal peptide in biocontrol fungi[J]. Journal of Fungi,2020,6(2):61. doi: 10.3390/jof6020061
[18]	Boddy C N. Bioinformatics tools for genome mining of polyketide and non-ribosomal peptides[J]. J Ind Microbiol Biotechnol,2014,41:443−450. doi: 10.1007/s10295-013-1368-1
[19]	Steiniger C, Hoffmann S, Süssmuth R D, et al. Harnessing fungal nonribosomal cyclodepsipeptide synthetases for mechanistic insights and tailored engineering[J]. Chemical Science,2017,8(11):7834−7843. doi: 10.1039/C7SC03093B
[20]	Prieto C, García-Estrada C, Martín J F, et al. NRPSsp: Non-ribosomal peptide synthase substrate predictor[J]. Bioinformatics,2012,28(3):426−427.
[21]	Röttig M, Blin K, Kohlbacher O, et al. NRPSpredictor2-a web server for predicting NRPS adenylation domain specificity[J]. Nucleic Acids Research,2011,39:362−367.
[22]	Rodríguez-García A, Sola-Landa A, Barreiro C. RNA-Seq-Based comparative transcriptomics: RNA preparation and bioinformatics[J]. Methods in Molecular Biology,2017,1645:59−72.
[23]	Hrdlickova R, Toloue M, Tian B. RNA-Seq methods for transcriptome analysis[J]. Wiley Interdisciplinary Reviews-RNA,2017,8(1):10.
[24]	雷秀云. 基于RNA-Seq技术的竹红菌甲素和20-羟基蜕皮甾酮的生物合成研究[D]. 苏州: 苏州大学, 2017.
[25]	刘凤娟. 基于转录组学和代谢组学分析的山黧豆β-ODAP生物合成机制分析[D]. 咸阳: 西北农林科技大学, 2019.
[26]	刘伟, 王俊燚, 李萌, 等. 基于转录组测序的银杏类黄酮生物合成关键基因表达分析[J]. 中草药,2018,49(23):5633−5639. doi: 10.7501/j.issn.0253-2670.2018.23.024
[27]	杨宇纯, 肖梅, 薛艳红, 等. 草酸青霉中新型线性五肽的发现及对柑橘采后致腐菌拮抗活性研究[J]. 微生物学通报,2020,47 (2):481−489.
[28]	杨宇纯. 草酸青霉(Penicillium oxalicum)的线性五肽抑制柑橘采后致腐菌活性研究[D]. 宜昌: 三峡大学, 2020.
[29]	贾泽, 江云, 王智玮, 等. 炭样小单孢菌 JXNU-1 抗生素合成的转录组学分析[J]. 基因组学与应用生物学,2018,37(9):3817−3828.
[30]	魏春梅, 栾威, 代娅, 等. 比较转录组研究钛离子对紫花苜蓿基因表达的影响[J]. 应用与环境生物学,2019,25 (1):117−127.
[31]	贺润丽, 王晓英, 韩毅丽, 等. 利用转录组分析款冬萜类化合物生物合成关键酶基因及表达特征[J]. 中草药,2020,51(20):5302−5310. doi: 10.7501/j.issn.0253-2670.2020.20.024
[32]	刘超, 宋瑾怡, 熊泽, 等. 草酸青霉线性五肽生物合成的比较转录组分析[J]. 食品与生物技术学报, 2021, 40(5): 37−44. doi:10.3969/j.issn. 1673-1689.2021.05.005.

Supplements (0)

Get Citation

PDF

XML

Article Metrics

Article views (238) PDF downloads (22)

Science and Technology of Food Industry

Analysis of Gene Clusters for Sanxiapeptin Biosynthesis by Transcriptomic Sequencing

Abstract

References

Catalog

Article Metrics

Export File

Citation

Format

Content