2025年5月4日 周日
首页 > 过刊浏览>2025年第65卷第4期 >1601-1615. DOI:10.13343/j.cnki.wsxb.20240477
PDF HTML阅读 XML下载 导出引用 引用提醒
转录-蛋白组学关联分析坎帕尼亚盐单胞菌野生型与紫外突变型菌株的差异表达基因与蛋白质
作者:
作者单位:

1.青海大学 医学院，基础医学研究中心，青海 西宁;2.青海大学 农林科学院，蔬菜遗传与生理重点实验室，青海 西宁

基金项目:

国家自然科学基金(32260019)；青海中央引导地方科技发展资金(2024ZY015)


Transcriptomics-proteomics conjoint analysis of differentially expressed genes/proteins between wild type and ultraviolet radiation-mutated Halomonas campaniensis strains
Author:
Affiliation:

1.Research Center of Basic Medical Science, Medical College, Qinghai University, Xining, Qinghai, China;2.Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai, China

Fund Project:

This work was supported by the National Natural Science Foundation of China (32260019) and the Qinghai Central Government Guide Local Science and Technology Development Fund (2024ZY015).

  • 摘要
    • | |
  • 访问统计
    • |
  • 参考文献 [36]
    • | | | |
  • 文章评论
    摘要:

    野生型坎帕尼亚盐单胞菌(Halomonas campaniensis)经9轮紫外循环诱变，获得1株高产四氢嘧啶(ectoine)的突变菌株G9-72，关于菌株差异表达基因、蛋白质以及四氢嘧啶产量暴发的分子机制有待深入探讨。目的 探讨野生菌株XH26和突变菌株G9-72的差异表达基因或蛋白质(differential expression genes/proteins, DEGs/DEPs)，并关联分析四氢嘧啶高效积聚的分子响应机制。方法 在无盐和1.5 mol/L NaCl条件下培养菌株XH26和G9-72，利用Illumina HiSeq高通量测序和定量质谱蛋白组学技术分析菌株转录组-蛋白质组学的差异变化，并采用逆转录定量PCR对显著DEGs的表达进行验证。结果 转录组学筛选出11条氨基酸代谢通路(涉及44个DEGs)与四氢嘧啶合成代谢相关；蛋白组学筛选出10条氨基酸代谢通路(涉及50个DEPs)与四氢嘧啶合成代谢相关。转录-蛋白关联分析筛选出15个显著DEGs，其中7个基因(ectB、betB、betA、asd、doeD、doeC、gabD)在2个组学中表达上调；4个基因(ItaE、gdhA、gabT、acnB)在2个组学中表达下调；3个基因(gltD、atoB、narG)在转录组学中下调，而在蛋白组学中表达上调；基因narK在转录组学中表达上调，但在蛋白组学中未检测到表达。RT-qPCR验证结果与RNA-seq测序分析一致。结论 突变菌株四氢嘧啶的积聚量暴发与代谢通路的关键基因有关(合成基因asd和ectB，分解基因doeD和doeC)，与代谢通路上游的参与基因间接相关(betB、betA、ItaE、gltD、gadA和acnB)，以及四氢嘧啶的生物合成与Ala/Asp/Glu/His代谢途径(gabD、gdhA、gabT、atoB)和氮源代谢(narK和narG)高度关联。

    Abstract:

    A mutant strain G9-72 with a high yield of ectoine was obtained from wild type Halomonas campaniensis after nine rounds of ultraviolet mutagenesis. The differentially expressed genes/proteins (DEGs/DEPs) and the molecular mechanism underlying the excessive increase in the ectoine yield remain to be explored for the mutant strain.Objective To explore the DEGs/DEPs between the wild type strain XH26 and G9-72 and decipher the molecular mechanism of efficient ectoine production by conjoint analysis.Methods A non-salt (NS, 0 mol/L NaCl) group and a high-salt (HS, 1.5 mol/L NaCl) group were designed for the culture of XH26 and G9-72. Illumina HiSeq and quantitative mass spectrometry were employed to identify the DEGs/DEPs between the two strains by transcriptomics-proteomics conjoint analysis. Furthermore, RT-qPCR was carried out to verify the expression of significant DEGs.Results The transcriptomics analysis revealed 11 amino acid metabolic pathways (44 DEGs) associated with ectoine anabolism, and the proteomics analysis revealed ten amino acid metabolic pathways (50 DEPs) associated with ectoine anabolism. The transcriptomics-proteomics conjoint analysis identified 15 significant DEGs, including seven genes (ectB, betB, betA, asd, doeD, doeC, and gabD) with up-regulated mRNA and protein level, four genes (ItaE, gdhA, gabT, and acnB) with down-regulated mRNA and protein levels, three genes (gltD, atoB, and narG) with down-regulated mRNA levels and up-regulated protein levels, and one gene narK with up-regulated mRNA level and no protein level. Additionally, the RT-qPCR results were consistent with the transcriptomics analysis.Conclusion The excessive increase in the ectoine yield of the mutant strain was associated with key genes in the ectoine metabolic pathway (including the synthesis genes asd and ectB and the catabolism genes doeD and doeC) and indirectly associated with several genes (betB, betA, ItaE, gltD, gadA, and acnB) in the upstream metabolic pathway. Notably, ectoine biosynthesis was highly associated with the Ala/Asp/Glu/His metabolic pathway (gabD, gdhA, gabT, and atoB) and nitrogen source metabolism (narK and narG).

    参考文献
    [1] CHEN YH, LU CW, SHYU YT, LIN SS. Revealing the saline adaptation strategies of the halophilic bacterium Halomonas beimenensis through high-throughput omics and transposon mutagenesis approaches[J]. Scientific Reports, 2017, 7(1): 13037.
    [2] KINDZIERSKI V, RASCHKE S, KNABE N, SIEDLER F, SCHEFFER B, PFLüGER-GRAU K, PFEIFFER F, OESTERHELT D, MARIN-SANGUINO A, KUNTE HJ. Osmoregulation in the halophilic bacterium Halomonas elongata: a case study for integrative systems biology[J]. PLoS One, 2017, 12(1): e0168818.
    [3] LI L, YANG XY, HONG R, LIU F. Combined proteomics and transcriptomics analysis of Lactococcus lactis under different culture conditions[J]. Journal of Dairy Science, 2021, 104(3): 2564-2580.
    [4] HE YZ, GONG J, YU HY, TAO Y, ZHANG S, DONG ZY. High production of ectoine from aspartate and glycerol by use of whole-cell biocatalysis in recombinant Escherichia coli[J]. Microbial Cell Factories, 2015, 14: 55.
    [5] BENíTEZ-MATEOS AI, PARADISI F. Halomonas elongata: a microbial source of highly stable enzymes for applied biotechnology[J]. Applied Microbiology and Biotechnology, 2023, 107(10): 3183-3190.
    [6] YOO W, KIM B, JEON S, KIM KK, KIM TD. Identification, characterization, and immobilization of a novel YbfF esterase from Halomonas elongata[J]. International Journal of Biological Macromolecules, 2020, 165: 1139-1148.
    [7] 田磊, 张芳, 沈国平, 高翔, 龙启福, 朱德锐. Ectoine高产菌株Halomonas sp. XH26的鉴定及紫外诱变选育[J]. 生物学杂志, 2020, 37(4): 31-35.TIAN L, ZHANG F, SHEN GP, GAO X, LONG QF, ZHU DR. Identification of high-yielding strain Halomonas sp. XH26 for producing ectoine and UV mutagenesis breeding[J]. Journal of Microbiology, 2020, 37(4): 31-35 (in Chinese).
    [8] DUTTA B, BANDOPADHYAY R. Biotechnological potentials of halophilic microorganisms and their impact on mankind[J]. Beni-Suef University Journal of Basic and Applied Sciences, 2022, 11(1): 75.
    [9] DasSARMA S, DasSARMA P. Halophiles and their enzymes: negativity put to good use[J]. Current Opinion in Microbiology, 2015, 25: 120-126.
    [10] PARWATA IP, WAHYUNINGRUM D, SUHANDONO S, HERTADI R. Heterologous ectoine production in Escherichia coli: optimization using response surface methodology[J]. International Journal of Microbiology, 2019, 2019: 5475361.
    [11] NG HS, WAN PK, NG TC, LAN JCW. Primary purification of intracellular Halomonas salina ectoine using ionic liquids-based aqueous biphasic system[J]. Journal of Bioscience and Bioengineering, 2020, 130(2): 200-204.
    [12] MORTAZAVI A, WILLIAMS BA, McCUE K, SCHAEFFER L, WOLD B. Mapping and quantifying mammalian transcriptomes by RNA-seq[J]. Nature Methods, 2008, 5(7): 621-628.
    [13] CHUNG M, BRUNO VM, RASKO DA, CUOMO CA, MU?OZ JF, LIVNY J, SHETTY AC, MAHURKAR A, DUNNING HOTOPP JC. Best practices on the differential expression analysis of multi-species RNA-seq[J]. Genome Biology, 2021, 22(1): 121.
    [14] 唐正露, 朱艳艳, 李琳, 李亮, 刘雪兰, 孙裴, 李郁. 基于转录组学与蛋白质组学对猪丹毒丝菌耐药性的研究[J]. 微生物学通报, 2021, 48(10): 3736-3752.TANG ZL, ZHU YY, LI L, LIU XL, SUN P, LI Y. Study on the resistance of Erysipelothrix rhusiopathiae based on transcriptomics and proteomics[J]. Microbiology China, 2021, 48(10): 3736-3752 (in Chinese).
    [15] REITER L, RINNER O, PICOTTI P, HüTTENHAIN R, BECK M, BRUSNIAK MY, HENGARTNER MO, AEBERSOLD R. mProphet: automated data processing and statistical validation for large-scale SRM experiments[J]. Nature Methods, 2011, 8(5): 430-435.
    [16] ROSENBERGER G, KOH CC, GUO TN, R?ST HL, KOUVONEN P, COLLINS BC, HEUSEL M, LIU YS, CARON E, VICHALKOVSKI A, FAINI M, SCHUBERT OT, FARIDI P, EBHARDT HA, MATONDO M, LAM H, BADER SL, CAMPBELL DS, DEUTSCH EW, MORITZ RL, et al. A repository of assays to quantify 10 000 human proteins by SWATH-MS[J]. Scientific Data, 2014, 1: 140031.
    [17] 海云翔, 宋敏, 杨秀娟, 蒋宜伟, 董万涛, 巩彦龙. 基于DIA蛋白质组学技术联合PRM验证探讨去卵巢骨质疏松大鼠差异蛋白表达[J]. 中药药理与临床, 2023, 39(11): 87-93.HAI YX, SONG M, YANG XJ, JIANG YW, DONG WT, GONG YL. Differential protein expression in ovariectomized osteoporosis rats based on DIA protein omics and PRM verification[J]. Pharmacology and Clinics of Chinese Materia Medica, 2023, 39(11): 87-93 (in Chinese).
    [18] ZHANG YB, LIU HH, GU D, LU XX, ZHOU XH, XIA XD. Transcriptomic analysis of PhoR reveals its role in regulation of swarming motility and T3SS expression in Vibrio parahaemolyticus[J]. Microbiological Research, 2020, 235: 126448.
    [19] McCLURE R, BALASUBRAMANIAN D, SUN Y, BOBROVSKYY M, SUMBY P, GENCO CA, VANDERPOOL CK, TJADEN B. Computational analysis of bacterial RNA-seq data[J]. Nucleic Acids Research, 2013, 41(14): e140.
    [20] G?TZ S, GARCíA-GóMEZ JM, TEROL J, WILLIAMS TD, NAGARAJ SH, NUEDA MJ, ROBLES M, TALóN M, DOPAZO J, CONESA A. High-throughput functional annotation and data mining with the Blast2GO suite[J]. Nucleic Acids Research, 2008, 36(10): 3420-3435.
    [21] FAN MH, SUN X, XU NJ, LIAO Z, LI YH, WANG JX, FAN YP, CUI DL, LI P, MIAO ZL. Integration of deep transcriptome and proteome analyses of salicylic acid regulation high temperature stress in Ulva prolifera[J]. Scientific Reports, 2017, 7(1): 11052.
    [22] 钟紫旋. 基于转录、蛋白和代谢水平联合解析白腐菌种间漆酶诱导表达机制[D]. 重庆: 西南大学博士学位论文, 2020.ZHONG ZX. Mechanism of laccase-induced expression among white rot fungi based on transcription, protein and metabolism[D]. Chongqing: Doctoral Dissertation of Southwest University, 2020 (in Chinese).
    [23] 张鑫, 王智博, 缪增强, 邢江娃, 王嵘, 李永臻, 朱德锐, 沈国平. 转录组学分析盐单胞菌四氢嘧啶合成代谢相关的表达差异基因与RT-qPCR验证[J]. 微生物学报, 2022, 62(3): 1083-1098.ZHANG X, WANG ZB, MIAO ZQ, XING JW, WANG R, LI YZ, ZHU DR, SHEN GP. Transcriptome analysis of differential genes associated with the ectoine synthesis pathway of Halomonas campaniensis under salt stress and expression verification by RT-qPCR[J]. Acta Microbiologica Sinica, 2022, 62(3): 1083-1098 (in Chinese).
    [24] WANG ZB, LI YZ, GAO X, XING JW, WANG R, ZHU DR, SHEN GP. Comparative genomic analysis of Halomonas campaniensis wild-type and ultraviolet radiation-mutated strains reveal genomic differences associated with increased ectoine production[J]. International Microbiology, 2023, 26(4): 1009-1020.
    [25] CHEN J, LIU PF, CHU XH, CHEN JW, ZHANG HW, ROWLEY DC, WANG H. Metabolic pathway construction and optimization of Escherichia coli for high-level ectoine production[J]. Current Microbiology, 2020, 77(8): 1412-1418.
    [26] JADHAV K, KUSHWAHA B, JADHAV I, SHANKAR P, GEETHADEVI A, KUMAR G, MITTAL S, SHARMA GP, PARASHAR M, PARASHAR D. Genomic analysis of a novel species Halomonas shambharensis isolated from hypersaline lake in Northwest India[J]. Molecular Biology Reports, 2021, 48(2): 1045-1053.
    [27] THOMAS J, HARDEN A. Methods for the thematic synthesis of qualitative research in systematic reviews[J]. BMC Medical Research Methodology, 2008, 8: 45.
    [28] HOBMEIER K, CANTONE M, NGUYEN QA, PFLüGER-GRAU K, KREMLING A, KUNTE HJ, PFEIFFER F, MARIN-SANGUINO A. Adaptation to varying salinity in Halomonas elongata: much more than ectoine accumulation[J]. Frontiers in Microbiology, 2022, 13: 846677.
    [29] 翟立公, 李港回, 黄菊, 蔡秋慧, 魏照辉, 何晓东, 曹睿, 王俊颖. 基于比较转录组学分析NaCl胁迫影响德尔卑沙门氏菌的耐渗机制[J]. 微生物学报, 2023, 63(8): 3219-3234.ZHAI LG, LI GH, HUANG J, CAI QH, WEI ZH, HE XD, CAO R, WANG JY. Analysis of the mechanism of NaCl stress affecting the osmotic tolerance of Salmonella delbey based on comparative transcriptomics[J]. Acta Microbiologica Sinica, 2023, 63(8): 3219-3234 (in Chinese).
    [30] LIU C. Comparative proteomics for an in-depth understanding of bioadhesion mechanisms and evolution across metazoans[J]. Journal of Proteomics, 2022, 256: 104506.
    [31] XING QH, MESBAH NM, WANG HS, ZHANG YJ, LI J, ZHAO BS. Tandem mass tag-based quantitative proteomics reveals osmotic adaptation mechanisms in Alkalicoccus halolimnae BZ-SZ-XJ29T, a halophilic bacterium with a broad salinity range for optimal growth[J]. Environmental Microbiology, 2023, 25(10): 1967-1987.
    [32] CHEN DD, FANG BZ, MANZOOR A, LIU YH, LI L, MOHAMAD OAA, SHU WS, LI WJ. Revealing the salinity adaptation mechanism in halotolerant bacterium Egicoccus halophilus EGI 80432T by physiological analysis and comparative transcriptomics[J]. Applied Microbiology and Biotechnology, 2021, 105(6): 2497-2511.
    [33] SCHNEIDER BL, KIUPAKIS AK, REITZER LJ. Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli[J]. Journal of Bacteriology, 1998, 180(16): 4278-4286.
    [34] PARK YL, CHOI TR, HAN YH, SONG HS, PARK JY, BHATIA SK, GURAV R, CHOI KY, KIM YG, YANG YH. Effects of osmolytes on salt resistance of Halomonas socia CKY01 and identification of osmolytes-related genes by genome sequencing[J]. Journal of Biotechnology, 2020, 322: 21-28.
    [35] SONG WS, KIM JH, NAMGUNG B, CHO HY, SHIN H, OH HB, HA NC, YOON SI. Complementary hydrophobic interaction of the redox enzyme maturation protein NarJ with the signal peptide of the respiratory nitrate reductase NarG[J]. International Journal of Biological Macromolecules, 2024, 262: 129620.
    [36] XIAN L, YU G, MACHO AP. The GABA transaminase GabT is required for full virulence of Ralstonia solanacearum in tomato[J]. MicroPublication Biology, 2021. DOI: 10.17912/micropub.biology.000478.
    相似文献
    引证文献
    网友评论
    网友评论
    分享到微博
    发 布
引用本文

崔金子,韩睿,乔丽娟,李永臻,邢江娃,王嵘,沈国平,朱德锐. 转录-蛋白组学关联分析坎帕尼亚盐单胞菌野生型与紫外突变型菌株的差异表达基因与蛋白质[J]. 微生物学报, 2025, 65(4): 1601-1615

复制
分享
文章指标
  • 点击次数:20
  • 下载次数: 36
  • HTML阅读次数: 22
  • 引用次数: 0
历史
  • 收稿日期:2024-08-01
  • 在线发布日期: 2025-04-12
文章二维码

科微学术

微生物学报

您是本站第 5858635 访问者

通信地址：北京市朝阳区北辰西路1号院3号 中国科学院微生物研究所   邮编：100101

电话：010-64807516    E-mail：actamicro@im.ac.cn

版权所有：微生物学报 ® 2025 版权所有