Identification of genes related to lipopeptide synthesis in mining lipopeptide synthesis related genes of Bacillus amyloliquefaciens TF28 under different carbon sources based on transcriptome

doi:10.14088/j.cnki.issn0439-8114.2023.05.030

Abstract

Abstract: With Bacillus amyloliquefaciens TF28 as the test strain, three experimental groups were set up： glucose group （control）, fructose group and xylose group. Differential genes were identified by transcriptome sequencing, and functional analysis was carried out on the differential genes to explore the regulatory genes for lipopeptide synthesis. A total of 688 differentially expressed genes, 522 upregulated genes, and 166 downregulated genes were identified in the fructose group; a total of 855 differential genes, 691 upregulated genes, and 164 downregulated genes were identified in the xylose group. Different carbon sources changed the expression levels of global regulatory factors in the quorum sensing system and dual component system of lipopeptide synthesis in starch Bacillus subtilis TF8, and influenced the synthesis and metabolism of essential amino acids and fatty acids in lipopeptide synthesis, which provided reference for further research on the biological regulatory mechanisms of lipopeptide synthesis.

Key words: lipopeptide, Bacillus amyloliquefaciens, TF28, transcriptome, differential gene

CLC Number:

Q819

YAN Geng-xuan, WANG Xiang-xiang, TIAN Yuan, LIU Zhi-ting, ZHANG Shu-mei, XIA Hai-hua. Identification of genes related to lipopeptide synthesis in mining lipopeptide synthesis related genes of Bacillus amyloliquefaciens TF28 under different carbon sources based on transcriptome[J]. HUBEI AGRICULTURAL SCIENCES, 2023, 62(5): 172-178.

References

[1] NGALIMAT M S, YAHAYA R S R, BAHARUDIN M M A, et al. A review on the biotechnological applications of the operational group Bacillus amyloliquefaciens[J]. Microorganisms,2021, 9(3): 614.
[2] KUMAR P S, NGUEAGNI P T.A review on new aspects of lipopeptide biosurfactant: Types, production, properties and its application in the bioremediation process[J]. Journal of hazardous materials, 2021, 407: 124827.
[3] 汪水呈,曾维伟,陆兆新.Surfactin抑菌稳定性及其在米饭和面包中的应用[J].食品工业科技,2016,37(13):257-261.
[4] WEI Y H, WANG L C, CHEN W C, et al.Production and characterization of fengycin by indigenous Bacillus subtilis F29-3 originating from a potato farm[J]. International journal of molecular sciences, 2010, 11(11): 4526-4538.
[5] FARZANEH M, SHI Z Q, AHMADZADEH M, et al.Inhibition of the Aspergillus flavus growth and aflatoxin B1 contamination on pistachio nut by fengycin and surfactin-producing Bacillus subtilis UTBSP1[J]. The plant pathology journal, 2016, 32(3): 209.
[6] ZHOU L,ZHAO X,LI M,et al.Antifungal activity of silver nanoparticles synthesized by iturin against Candida albicans in vitro and in vivo[J]. Applied microbiology and biotechnology, 2021, 105(9): 3759-3770.
[7] 刘宇帅,张杰,钟瑾,等.解淀粉芽孢杆菌TF28抗菌脂肽芬芥素的分离鉴定及抑菌作用[J].中国生物工程杂志,2018,38(10):20-29.
[8] BOLGER A M,LOHSE M,USADEL B.Trimmomatic: A flexible trimmer for Illumina sequence data[J]. Bioinformatics,2014, 30(15): 2114-2120.
[9] QUINLAN A R. BEDTools: The Swiss-army tool for genome feature analysis[J]. Current protocols in bioinformatics,2014, 47(1): 11.12.1-11.12.34.
[10] LOVE M I, HUBER W, ANDERS S.Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J]. Genome biology, 2014, 15(12): 1-21.
[11] YU G, WANG L G, HAN Y, et al.clusterProfiler: An R package for comparing biological themes among gene clusters[J]. Omics: A journal of integrative biology, 2012, 16(5): 284-287.
[12] 董丽红,郭庆港,王培培,等. PhoR/PhoP双组份对枯草芽胞杆菌NCD-2菌株中surfactin合成的影响[J].植物病理学报,2018,48(1):119-127.
[13] ZHANG B, XU L, DING J, et al.Natural antimicrobial lipopeptides secreted by Bacillus spp. and their application in food preservation, a critical review[J]. Trends in food science and technology, 2022,127:26-37.
[14] YANG R, LEI S, XU X, et al.Key elements and regulation strategies of NRPSs for biosynthesis of lipopeptides by Bacillus[J]. Applied microbiology and biotechnology,2020,104(19):8077-8087.
[15] LU H,QIAN S,MUHAMMAD U,et al.Effect of fructose on promoting fengycin biosynthesis in Bacillus amyloliquefaciens fmb-60[J]. Journal of applied microbiology, 2016, 121(6): 1653-1664.
[16] JIN J, WEN J.Research progress of cyclic lipopeptides synthesized by bacillus under the guidance of synthetic biology[J]. China biotechnology, 2022,42(6):86-101.
[17] JUNG J, YU K O, RAMZI A B, et al.Improvement of surfactin production in Bacillus subtilis using synthetic wastewater by overexpression of specific extracellular signaling peptides, comX and phrC[J]. Biotechnology and bioengineering,2012,109(9): 2349-2356.
[18] SUN J, LIU Y, LIN F, et al.CodY, ComA, DegU and Spo0A controlling lipopeptides biosynthesis in Bacillus amyloliquefaciens fmb[J][J]. Journal of applied microbiology,2021,131(3):1289-1304.
[19] BANERJEE S, SEN S,BHAKAT A, et al.The lipopeptides fengycin and iturin are involved in the anticandidal activity of endophytic Bacillus sp. as determined by experimental and in silico analysis[J]. Letters in applied microbiology, 2022, 75(2): 450-459.