[1]刘高强,李新鹏,刘文钊,等.一株高效降解血液蛋白的枯草芽孢杆菌NWMCC0137全基因组测序及分析[J].江苏农业学报,2023,(07):1460-1471.[doi:doi:10.3969/j.issn.1000-4440.2023.07.003]
　LIU Gao-qiang,LI Xin-peng,LIU Wen-zhao,et al.Whole genome sequencing and analysis of Bacillus subtilis NWMCC0137, an efficient blood protein degrading strain[J].,2023,(07):1460-1471.[doi:doi:10.3969/j.issn.1000-4440.2023.07.003]
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一株高效降解血液蛋白的枯草芽孢杆菌NWMCC0137全基因组测序及分析()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2023年07期
页码:
1460-1471
栏目:
遗传育种·生理生化
出版日期:
2023-10-31

文章信息/Info

Title:
Whole genome sequencing and analysis of Bacillus subtilis NWMCC0137, an efficient blood protein degrading strain
作者:
刘高强1; 2; 李新鹏1; 3; 刘文钊1; 2; 周 魏1; 2; 彭乔烽1; 2; 周雪雁1; 2; 默罕默德·索布瑞·塔克瑞夫4; 丁功涛1
(1.西北民族大学生物医学研究中心中国-马来西亚国家联合实验室,甘肃兰州730030；2.西北民族大学生命科学与工程学院,甘肃兰州730030；3.西北民族大学化工学院,甘肃兰州730030；4.马来西亚国立大学工程与建筑环境学院化工系,雪兰莪州万宜43600)
Author(s):
LIU Gao-qiang1; 2; LI Xin-peng1; 3; LIU Wen-zhao1; 2; ZHOU Wei1; 2; PENG Qiao-feng1; 2; ZHOU Xue-yan1; 2; MOHAMMED Sobri-takriff4; DING Gong-tao1
(1.China-Malaysia National Joint Laboratory, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China；2.College of Life Sciences and Engineering, Northwest Minzu University, Lanzhou 730030, China；3.College of Chemical Engineering, Northwest Minzu University, Lanzhou 730030, China；4.Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment University Kebangsaan Malaysia, Bangi 43600, Malaysia)
关键词:
枯草芽孢杆菌; 全基因组; 基因功能注释; 蛋白酶
Keywords:
Bacillus subtilis; whole genome; gene function annotation; protease
分类号:
Q934.124
DOI:
doi:10.3969/j.issn.1000-4440.2023.07.003
文献标志码:
A
摘要:
NWMCC0137是从屠宰场下水道污泥中分离获得的1株高效分解血液蛋白并具有良好生物防控特性的枯草芽孢杆菌(Bacillus subtilis)。为探究枯草芽孢杆菌NWMCC0137(B.subtilis NWMCC0137)高效水解血液蛋白机制及挖掘次级代谢产物编码基因资源,利用DNBSEQ与PacBio测序平台对其进行全基因组测序并进行序列组装和基因预测、功能注释、比较基因组分析。结果表明B.subtilis NWMCC0137的基因组长度为4 215 585 bp,G+C含量为44.23%；编码基因总长度为3 711 885 bp,编码4 384个基因,编码序列占整个基因组长度的88.05%,非编码RNA中包含85个tRNA基因。在KEGG数据库中B.subtilis NWMCC0137基因组被注释到7种胞外蛋白酶编码基因,其中与丝氨酸蛋白酶相关的编码基因有8个。通过antiSMASH预测发现,菌株NWMCC0137基因组中包含7种与已知次生代谢产物合成基因簇相似度为100%的基因簇,包括产孢致死因子、聚酮类化合物、丰原素、枯草芽孢杆菌素168、儿茶酚型嗜铁素、芽孢杆菌素、杆菌溶素合成基因簇。进化分析结果表明,NWMCC0137为枯草芽孢杆菌,并且与枯草芽孢杆菌168具有很高的共线性。B.subtilis NWMCC0137基因组序列已提交至GenBank数据库,登录号为CP103066。本研究从基因层面揭示了菌株NWMCC0137的遗传信息,为该菌株应用于屠宰场血液蛋白降解及生物防控提供了参考。
Abstract:
NWMCC0137 is a Bacillus subtilis strain isolated from sewage sludge in slaughterhouses, which efficiently decomposes blood proteins and has good biological control characteristics. In order to explore the mechanism of efficient hydrolysis of blood protein by Bacillus subtilis NWMCC0137 and explore the gene resources encoded by secondary metabolites, DNBSEQ and PacBio sequencing platforms were used to sequence the whole genome, and sequence assembly, gene prediction, functional annotation and comparative genome analysis were carried out. The results showed that the genome length of Bacillus subtilis NWMCC0137 was 4 215 585 bp, and the G+C content was 44.23%. The total length of the coding gene was 3 711 885 bp, encoding 4 384 genes, accounting for 88.05% of the entire genome length. The non-coding RNA contained 85 tRNA genes. In KEGG database, Bacillus subtilis NWMCC0137 genome was annotated to seven extracellular protease coding genes, including eight coding genes related to serine protease. According to the prediction of antiSMASH, the genome of strain NWMCC0137 contained seven gene clusters with 100% similarity to the known secondary metabolite synthesis gene clusters, including sporulation killing factor, bacillaene, fengycin, sublancin 168, bacillibactin, subtilosin A and bacilysin gene clusters. The evolutionary analysis results indicated that NWMCC0137 was a Bacillus subtilis and had high collinearity with Bacillus subtilis 168. The genome sequence of Bacillus subtilis NWMCC0137 had been submitted to the GenBank database with accession number CP103066. This study revealed the genetic information of strain NWMCC0137 at the genetic level, providing a reference for its application in degrading blood proteins and biological prevention and control.

参考文献/References:

[1]BAH C S, CARNE A, MCCONNELL M A, et al. Production of bioactive peptide hydrolysates from deer,sheep,pig and cattle red blood cell fractions using plant and fungal protease preparations[J]. Food Chemistry,2016,202：458-466.
[2]LYNCH S A, MULLEN A M, O′NEILL E E, et al. Harnessing the potential of blood proteins as functional ingredients：A review of the state of the art in blood processing[J]. Comprehensive Reviews in Food Science and Food Safety,2017,16(2)：330-344.
[3]马咸莹,马石霞,周雪雁,等. 一株降解牛血液蛋白细菌的筛选及酶学性质研究[J]. 微生物学杂志,2021,41(1)：43-51.
[4]BHAT Z F, KUMAR S, BHAT H F. Bioactive peptides of animal origin：a review[J]. Journal of Food Science and Technology,2015,52(9)：5377-5392.
[5]WANG L, ZHANG B R, HAN J, et al. Optimization of hydrolysis condition of blood meal by Bacillus subtilis with response surface methodology[J]. International Biodeterioration & Biodegradation,2015,104：112-117.
[6]ZHENG Y B, ZHANG H, WANG D B, et al. Strain development and optimized fermentation conditions for blood meal using Aspergillus niger and Aspergillus oryzae[J]. Journal Microbiological Methods,2014,101：70-80.
[7]郭秀云,张开臣,孟庆丰,等. 饲用血粉加工工艺及其产品质量研究进展[J]. 中国家禽,2019,41(19)：50-54.
[8]庞伟. 猪血多肽的发酵法制备及其ACE抑制活性研究[D]. 合肥：合肥工业大学,2009.
[9]陶艳华,姚大伟,王政,等. 血红蛋白降解菌的分离筛选与鉴定[J]. 食品与生物技术学报,2009,28(6)：854-857.
[10]YAO D W, QU J, CHANG P W, et al. Production and characterization of alkaline protease from hemoglobin-degrading Bacillus pumilus NJM4 to produce fermented blood meal[J]. Journal of Food Science and Technology,2012,49(5)：626-631.
[11]崔玮琪,王红丽,王莘. 发酵猪血菌株X-17发酵条件优化[J]. 吉林农业大学学报,2015,37(4)：488-492.
[12]马咸莹. 分解牛血液蛋白菌株的筛选及其产酶特性研究[D]. 兰州：西北民族大学,2021.
[13]ZHANG H, ZHANG B R, ZHENG Y B, et al. Neutral protease expression and optimized conditions for the degradation of blood cells using recombinant Pichia pastoris[J]. International Biodeterioration and Biodegradation,2014, 93：235-240.
[14]马子豪,向军,纪晓岚,等. 1株降解牦牛血液菌株的分离鉴定[J]. 现代畜牧兽医,2022,8(8)：1-5.
[15]EARL A M, LOSICK R, KOLTER R. Ecology and genomics of Bacillus subtilis[J]. Trends in Microbiology,2008,16(6)：269-275.
[16]CHATTERJEE J, GIRI S, MAITY S, et al. Production and characterization of thermostable alkaline protease of Bacillus subtilis (ATCC 6633) from optimized solid-state fermentation[J]. Biotechnology and Applied Biochemistry,2015,62(5)：709-718.
[17]MORIKAWA M. Beneficial biofilm formation by industrial bacteria Bacillus subtilis and related species[J]. Journal of Bioscience and Bioengineering,2006,101(1)：1-8.
[18]袁萍,江明锋,官久强,等. 基于枯草芽孢杆菌多组学数据全基因组规模代谢模型与蛋白质降解模拟[J]. 东北农业大学学报,2020,51(11)：61-69.
[19]GUO X H, LI D F, LU W Q, et al. Screening of Bacillus strains as potential probiotics and subsequent confirmation of the in vivo effectiveness of Bacillus subtilis MA139 in pigs[J]. Antonie Van Leeuwenhoek,2006,90(2)：139-146.
[20]DELCHER A L, BRATKE K A, POWERS E C,et al. Identifying bacterial genes and endosymbiont DNA with Glimmer[J]. Bioinformatics,2007,23(6)：673-679.
[21]LAGESEN K, HALLIN P, RDLAND E A, et al. RNAmmer：consistent and rapid annotation of ribosomal RNA genes[J]. Nucleic Acids Research,2007,35(9)：3100-3108.
[22]LOWE T M, EDDY S R. TRNAscan-SE：a program for improved detection of transfer RNA genes in genomic sequence[J]. Nucleic Acids Research,1997,25(5)：955-964.
[23]GARDNER P P, DAUB J, TATE J G, et al. Rfam：updates to the RNA families database[J]. Nucleic Acids Research,2009,37(suppl 1)：136-140.
[24]BENSON G. Tandem repeats finder：a program to analyze DNA sequences[J]. Nucleic Acids Research,1999,27(2)：573-580.
[25]孙悦龙,刘浩,朱宝成,等. 枯草芽孢杆菌N2-10的基因组测序和比较基因组分析[J]. 微生物学通报,2023,50(1)：131-147.
[26]熊科,邓蕾,柳佳芸,等. 蛋白酶水解底物特异性机制研究进展[J]. 食品与发酵工业,2019,45(19)：292-298.
[27]CONTESINI F J, MELO R R D, SATO H H. An overview of Bacillus proteases：from production to application[J]. Critical Reviews in Biotechnology,2017,38(3)：321-334.
[28]TOYMENTSEVA A A, MASCHER T, SHARIPOVA M R. Regulatory characteristics of Bacillus pumilus protease promoters[J]. Current Microbiology,2017,74：550-559.
[29]贾仲昕,赵佳男,季芳,等. 芽孢杆菌蛋白酶基因的比较基因组学分析[J]. 广东农业科学,2022,49(5)：110-117.
[30]王宏浩,张高瑜,逯梦凡,等. 枯草芽孢杆菌ZX-11培养条件及抑菌性能研究[J]. 中国酿造,2022,41(7)：138-143.
[31]赵春晖,徐玮,冯斌,等. 七鳃鳗g型溶菌酶的分子特征和抗菌活性[J]. 中国生物化学与分子生物学报,2015,31(5)：495-504.
[32]GIMENEZ D, PHELAN A, MURPHY C D, et al. Fengycin a analogues with enhanced chemical stability and antifungal properties[J]. Organic Letters,2021,23(12)：4672-4676.
[33]刘扬科,赵天效,卢晓颖,等. 枯草芽孢杆菌YT168-6产抗菌肽sublancin的发酵工艺优化及培养基筛选的研究[J]. 中国畜牧兽医,2021,48(9)：3232-3241.
[34]戚家明,孙杉杉,张东旭,等. 芽孢杆菌BS-6基于全基因组数据的分类鉴定及拮抗能力分析[J]. 生物技术通报,2019,35(10)：111-118.
[35]DIMOPOULOU A, THEOLOGIDIS I, BENAKI D, et al. Direct antibiotic activity of bacillibactin broadens the biocontrol range of Bacillus amyloliquefaciens MBI600[J]. mSphere,2021,6(4)：e0037621.
[36]NANNAN C, VU H Q, GILLIS A, et al. Bacilysin within the Bacillus subtilis group：Gene prevalence versus antagonistic activity against gram-negative foodborne pathogens[J]. Journal of Biotechnology,2021,327：28-35.
[37]SANTOS V S V, SILVEIRA E, PEREIRA B B. Toxicity and applications of surfactin for health and environmental biotechnology[J]. Journal of Toxicology and Environmental Health,Part B：Critical Reviews,2018,21(6/7/8)：382-399.
[38]GEETHA I, MANONMANI A M. Surfactin：a novel mosquitocidal biosurfactant produced by Bacillus subtilis ssp. subtilis (VCRC B471) and influence of abiotic factors on its pupicidal efficacy[J]. Letters in Applied Microbiology,2010,51(4)：406-412.

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备注/Memo

备注/Memo:
收稿日期：2022-12-01基金项目：“科技助力经济2020”重点专项(SQ2020YFF0405583)；西北民族大学中央高校基本科研业务经费项目(31920220023)；西北民族大学中央高校基本科研业务费资助项目(31920180122)作者简介：刘高强(1996-)，男，河南周口人，硕士研究生，研究方向为环境生物技术。(E-mail)760511638@qq.com通讯作者：丁功涛，(E-mail)dinggongtao@outlook.com
更新日期/Last Update: 2023-11-17