摘要
目的
链霉菌(Streptomyces sp.) YH02是从山西运城盐湖土壤沉积物中分离的一株革兰氏阳性放线菌。解析菌株YH02的全基因组序列信息,探究其在种属进化关系中的位置,深入挖掘其次级代谢产物基因资源。
方法
利用Illumina和PacBio平台相结合的测序技术对菌株YH02进行全基因组测序,并进行基因预测、功能注释、次级代谢产物合成基因簇预测、比较基因组学分析以及形态和生理生化测定。
结果
菌株YH02基因组为一条线性染色体,全长8 285 116 bp,G+C含量为71.77%,编码7 237个开放阅读框;在GO、COG、KEGG、CAZy数据库中分别注释到2 829、5 478、4 805、279个基因;蛋白亚细胞定位分析预测到多种分泌系统相关蛋白和1 030个转运蛋白;同时预测到菌株YH02中存在32个次级代谢产物合成基因簇,涉及萜烯类、非核糖体肽类、聚酮类、核糖体合成和翻译后修饰肽类等多种天然产物的合成。比较基因组学分析揭示了15 739个泛基因组直系同源基因簇和4 267个核心基因组直系同源基因簇。基于16S rRNA基因序列的系统发育树分析显示,菌株YH02与委内瑞拉链霉菌(Streptomyces venezuelae) ATCC 10712、沙阿霉素链霉菌(Streptomyces zaomyceticus) NBC 00278亲缘关系较近,但平均核苷酸一致性(average nucleotide identity, ANI)分析小于95.00%,数字DNA-DNA杂交(digital DNA-DNA hybridization, dDDH)值小于70.00%。形态学和生理生化特性分析表明,菌株YH02在ISP 2培养基上的气生菌丝体呈现浅粉色,其对pH值、氯化钠耐受量和生长温度的耐受性与近缘菌株存在差异,且在淀粉水解能力上表现出较弱的活性,同时具有明胶液化、硝酸盐还原阳性、牛奶凝固缓慢的特性。
结论
基于基因组学和生理生化特性的分析结果,菌株YH02被确认为链霉菌属潜在新种。本研究不仅丰富了微生物物种资源库,而且为探索具有独特作用机制的天然产物提供了理论基础和潜在的遗传资源。
关键词
链霉菌属(Streptomyces)为革兰氏阳性放线菌,广泛分布于土壤、海洋生态系统以及植物组织等多种生态位
在后基因组时代,链霉菌的研究已从基因组测序及功能注释的初步阶段,发展到利用全基因组数据进行深入功能研究与应用开发的更为复杂阶
本研究从山西运城盐湖土壤沉积物中分离出一株链霉菌YH02,采用第三代测序技术对其进行了全基因组测序、功能基因注释及次级代谢基因簇分析。同时,基于16S rRNA基因序列比对结果,筛选出5株近缘链霉菌模式菌株,分别进行比较基因组分析以及形态、生理生化测定,以此确定菌株YH02的系统发育位置。旨在为探索具有新颖结构、显著生物活性和独特作用机制的天然产物提供理论基础。
1 材料与方法
1.1 菌株分离
链霉菌YH02分离自山西省运城盐湖土壤沉积物。该土壤样本于2024年2月采自运城盐湖(35°01′48.84″N,111°03′00.14″E),并在采集后的4 h内予以处理。运用标准的系列稀释法开展菌株YH02的分离操
1.2 菌株培养和全基因组测序
将菌株YH02接种于ISP 2培养基,28 ℃恒温下培养6 d。随后,转移至胰蛋白胨大豆肉汤[(tryptone soy broth, TSB),杭州微生物试剂有限公司]液体培养基,28 ℃、180 r/min继续培养5 d。发酵结束后,12 000 r/min离心20 min收集菌体,并送往上海美吉生物医药科技有限公司进行从头测序。测序过程采用PacBio的第三代单分子实时(single molecule real-time, SMRT)测序技术与第二代Illumina高通量测序平台相结合的测序技
1.3 基因组预测和功能注释
使用Glimmer、Prodigal v2.6.3和GeneMarkS v4.3软件对组装得到的基因组序列进行编码基因预测。采用Barrnap v0.9软件预测核糖体RNA (rRNA)基因,利用tRNAscan-SE v2.0.12软件预测转移RNA (tRNA)基因。其他非编码RNA (sRNA)通过Infernal v1.1.4软件进行预测,CRISPR元件借助Minced v0.2.0软件预测。基因组岛通过IslandPath-DIMOB v1.0.0软件推测得出,噬菌体由Phigaro v2.3.0软件预测。另外,运用GO (https://geneontology.org/)、eggNOG (http://eggnogdb.embl.de/)、KEGG (https://www.kegg.jp/)以及CAZy (http://www.cazy.org/)数据库,对预测的蛋白质组序列进行功能注释。
1.4 蛋白质亚细胞定位分析
通过比对PHI-base数据库(http://www.phi-base.org/)、VFDB数据库(http://www.mgc.ac.cn/VFs/)、CARD数据库(https://card.mcmaster.ca/)以及TCDB数据库(http://www.tcdb.org/),对功能性蛋白质进行注
1.5 次级代谢产物生物合成基因簇预测
运用antiSMASH v7.0软件对菌株YH02中的次级代谢产物合成基因簇进行深入分析,并预测该菌株潜在的生物合成代谢
1.6 16S rRNA基因分析和系统发育树构建
利用EzBioCloud数据库(www.ezbiocloud.net)工具从菌株YH02的基因组中提取16S rRNA基因,并上传至GenBank数据库(https://www.ncbi.nlm.nih.gov/genbank/),登录号为PQ764780。通过EzBioCloud数据库的BLAST搜索来确定最相近的亲缘关
1.7 比较基因组分析
通过菌株YH02的16S rRNA基因序列比较分析,筛选出与其系统发育关系接近的5个模式菌株,即委内瑞拉链霉菌(Streptomyces venezuelae) ATCC 10712 (CP029197.1)、沙阿霉素链霉菌(Streptomyces zaomyceticus) NBC 00278 (CP108062.1)、脱叶链霉菌(Streptomyces exfoliatus) NBC_00077 (CP108238.1)、Streptomyces vilmorinianum YP1 (CP040244.1)和加德那氏链霉菌(Streptomyces gardneri) ATCC 15439 (CP059991.1)。从NCBI genome数据库(https://www.ncbi.nlm.nih.gov/genome/)获取上述菌株的完整基因组序列与菌株YH02的全基因组序列进行比较分析。
采用OrthoMCL软件包v2.0对同源基因进行聚类分析,以确定核心基因组和泛基因组的大
平均核苷酸一致性(average nucleotide identity, ANI)被视作一种基于基因组的稳健标准,用于确定遗传相关微生物的物种身
1.8 形态和生理生化测定
菌株YH02及其近缘菌株在5种不同培养基上生长:酵母提取物麦芽提取物琼脂(ISP 2)、燕麦琼脂(ISP 3)、无机盐淀粉琼脂(ISP 4)、甘油天冬酰胺琼脂(ISP 5)和酪氨酸琼脂(ISP 7) (ISP:国际链霉菌项
2 结果与分析
2.1 菌株YH02全基因组特征分析
菌株YH02全基因组序列显示,其基因组由一条线性染色体构成,总长度为8 285 116 bp (

图1 菌株YH02的全基因组注释圈图
Figure 1 Circular maps of the complete genome of strain YH02. The circular map contains seven circles. Marked information is displayed from the outer circle to innermost, as follows: genome size, CDSs on the forward stand, CDSs on the reverse stand, rRNA and tRNA, G+C content and GC skew.
2.2 功能基因分析
2.2.1 GO功能分类
在菌株YH02基因组中,共有2 829个基因在GO数据库中获得注释。这些基因被划分至3个主要的生物学领域,即生物过程(biological process)、细胞组分(cellular component)和分子功能(molecular function) (

图2 菌株YH02基因组的GO功能分类
Figure 2 GO functional classification diagram of the genome of strain YH02. A: Biological process; B: Cellular component; C: Molecular function.
2.2.2 COG功能分类
与eggNOG数据库比较分析显示,菌株YH02基因组中共有5 478个基因被注释,并归入24个功能类别中(

图3 菌株YH02基因组的COG功能分类
Figure 3 COG functional classification diagram of the genome of strain YH02.
2.2.3 KEGG代谢途径分析
在KEGG数据库中,对菌株YH02的基因组进行注释,共鉴定出4 805个基因(

图4 菌株YH02基因组的KEGG功能分类
Figure 4 KEGG functional classification diagram of the genome of strain YH02.
2.2.4 CAZy数据库注释
通过CAZy数据库对菌株YH02进行注释分析,共鉴定出279个碳水化合物活性蛋白序列,并将其归类为六大功能类别,分别是糖苷水解酶(glycoside hydrolases, GHs)、糖基转移酶(glycosyltransferases, GTs)、多糖裂解酶(polysaccharide lyases, PLs)、碳水化合物酯酶(carbohydrate esterases, CEs)、辅助活性(auxiliary activities, AAs)以及碳水化合物结合模块(carbohydrate-binding modules, CBMs)。在这些类别中,糖苷水解酶的数量最为丰富,共有106个序列,在其中占据最大比例;其次是糖基转移酶,占比为22.9%。相比之下,碳水化合物结合模块的数量最少,仅占注释总数的1.4% (

图5 菌株YH02中碳水化合物酶分布图
Figure 5 The distribution proportion diagram of carbohydrate enzyme. AA: Auxiliary activities; CBM: Carbohydrate-binding modules; CE: Carbohydrate esterases; GH: Glycoside hydrolases; GT: Glycosyl transferases; PL: Polysaccharide lyases.
2.3 蛋白质亚定位分析
利用生物信息学工具SignalP和TMHMM进行亚细胞定位预测,共鉴定出1 620个具有跨膜螺旋的蛋白质和233个分泌蛋白。将菌株YH02的蛋白质组与CARD、PHI-base和VFDB数据库进行比较分析,共鉴定出467个与抗生素抗性相关的蛋白质。此外,还发现了1 169个与病原体-宿主互作相关的蛋白质和619个毒力因子。这些蛋白质和毒力因子在盐湖生境中可能具有非致病性的独特作用。它们可能参与分解盐湖周边的特殊有机物质以获取营养,而非侵染宿主。在应对盐湖的高盐、高碱等极端环境压力时,这些因子可能参与细胞内的渗透压调节和抗氧化防御机制,保障菌株的存活。同时,它们可能在与盐湖生态系统中的其他微生物竞争中发挥抑制作用,有助于维持微生物群落的平
2.3.1 分泌系统蛋白分析
细菌的分泌系统是一组复杂的跨膜蛋白质机器,负责将蛋白质和其他分子从细胞内部转运到细胞外环境。根据最新的研究进展,这些系统被分类为6种主要类型,即I型至VI
2.3.2 转运蛋白分析
将菌株YH02的全部蛋白质序列与TCDB数据库比对后,共鉴定出1 030个转运蛋白(

图6 菌株YH02中转运蛋白功能分类图
Figure 6 Functional classification diagram of transport proteins.
2.4 次级代谢产物生物合成基因簇的预测分析
运用Antismash v7.0软件对菌株YH02的基因组进行预测分析,共鉴定出32个与次级代谢产物生物合成相关的基因簇(
Region number | Gene cluster type | Start | End | Predicted product | Similarity (%) |
---|---|---|---|---|---|
1 | NRPS | 2 | 112 887 | Enduracidin | 14 |
2 | Lanthipeptide-class-iv | 300 441 | 323 174 | Venezuelin | 100 |
3 | NRPS | 402 054 | 453 041 | Herboxidiene | 2 |
4 | Ectoine | 583 795 | 594 212 | Ectoine | 100 |
5 | Terpene | 621 444 | 642 362 | Geosmin | 100 |
6 | Lanthipeptide-class-ii | 889 209 | 950 699 | Primycin | 5 |
7 | NRPS-like | 953 289 | 1 022 495 | Leinamycin | 22 |
8 | Indole | 1 160 109 | 1 183 373 | Rebeccamycin | 25 |
9 | CDPS | 2 348 037 | 2 368 751 | Malacidin | 5 |
10 | Siderophore | 2 988 237 | 2 998 118 | Desferrioxamin B | 100 |
11 | NRPS-like | 4 562 363 | 4 605 498 | Lankamycin | 16 |
12 | Linaridin | 5 137 647 | 5 160 275 | Cypemycin | 100 |
13 | Melanin | 5 175 473 | 5 183 729 | Istamycin | 8 |
14 | Butyrolactone | 5 545 020 | 5 554 900 | Colabomycin E | 4 |
15 | Other | 5 657 024 | 5 698 134 | A-factor | 100 |
16 | LAP | 5 703 255 | 5 762 595 | Chlorotonil A | 15 |
17 | T3PKS | 5 985 845 | 6 026 979 | Flaviolin | 50 |
18 | Siderophore | 6 074 562 | 6 086 959 | Murayaquinone | 6 |
19 | Siderophore | 6 119 730 | 6 134 556 | Ficellomycin | 3 |
20 | T1PKS | 6 279 271 | 6 381 294 | Rubradirin | 31 |
21 | RiPP-like | 6 470 007 | 6 480 677 | - | - |
22 | Butyrolactone | 6 596 825 | 6 607 776 | Coelimycin P1 | 8 |
23 | T1PKS | 6 745 282 | 6 808 200 | Formicamycins A-M | 18 |
24 | T2PKS | 6 942 292 | 7 014 832 | Alnumycin/Prealnumycin/Thalnumycin | 75 |
25 | Terpene | 7 157 915 | 7 183 759 | Hopene | 76 |
26 | RiPP-like | 7 235 466 | 7 246 348 | - | - |
27 | Melanin | 7 497 255 | 7 507 633 | Melanin | 28 |
28 | NRPS | 7 680 916 | 7 731 629 | Salinichelins | 61 |
29 | Terpene | 7 743 561 | 7 764 938 | 2-methylisoborneol | 100 |
30 | NRPS | 7 770 573 | 7 827 609 | - | - |
31 | Lanthipeptide-class-iii | 7 889 159 | 7 911 817 | - | - |
32 | Lassopeptide | 8 221 130 | 8 285 116 | Friulimicin | 15 |
-: No similar gene cluster predicted.
2.5 16S rRNA基因系统发育分析
通过对菌株YH02的16S rRNA基因序列(1 523 nt)进行BLAST分析发现,其与5个链霉菌属模式菌株的16S rRNA基因序列具有高度相似性,即S. venezuelae ATCC 10712 (99.93%)、S. zaomyceticus NBRC 13348 (99.93%)、S. exfoliatus NRRL B-2924 (99.86%)、S. vilmorinianum YP1 (99.8%)和S. gardneri NBRC 12865 (99.65%)。基于16S rRNA基因序列构建的系统发育树显示,菌株YH02与S. venezuelae ATCC 10712聚类于同一节点,且与S. zaomyceticus NBRC 13348的亲缘关系较近。这一亲缘关系在采用邻接(NJ)法和最大似然(ML)法构建的系统发育树中均得到一致体现(

图7 基于16S rRNA基因序列构建的邻接法系统发育树
Figure 7 The neighbor-joining phylogenetic tree based on 16S rRNA gene sequences of strain YH02 was constructed with closely related type species. Allostreptomyces psammosienae YIM DR400

图8 基于16S rRNA基因序列构建的最大似然法系统发育树
Figure 8 The maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences of strain YH02 was constructed with closely related type species. Allostreptomyces psammosienae YIM DR400
2.6 比较基因组分析
2.6.1 菌株YH02的核心和泛基因组
利用16S rRNA基因序列比对结果,选择与菌株YH02序列相似度较高的链霉菌属模式菌株进行全基因组比较。选定的菌株包括S. venezuelae ATCC 10712、S. zaomyceticus NBC 00278、S. exfoliatus NBC_00077、S. vilmorinianum YP1和S. gardneri ATCC 15439。通过泛基因组分析,共鉴定出15 739个直系同源基因簇(

图9 泛基因组韦恩图
Figure 9 Venn diagram of Pan-genome homology. The Venn diagram shows the number of orthologous gene clusters of the core genome (the center part) and the numbers of unique genes of each genome.
2.6.2 ANI和dDDH值计算
为了对菌株YH02进行更精确地分类,基于全基因组比对计算了6株菌株基因组之间的平均核苷酸一致性(ANI)值和DNA-DNA杂交(dDDH)值(
Similarity index | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
ANI (%) | 90.91 | 91.02 | 90.23 | 87.28 | 89.18 |
dDDH (%) | 39.80 | 47.90 | 37.20 | 35.00 | 37.20 |
1: S. venezuelae ATCC 10712; 2: S. zaomyceticus NBC 00278; 3: S. exfoliatus NBC_00077; 4: S. vilmorinianum YP1; 5: S. gardneri ATCC 15439.
2.6.3 形态和生理生化分析
基于16S rRNA基因序列比对以及ANI和dDDH计算结果,选取S. venezuelae ATCC 10712、S. zaomyceticus NBC 00278、S. exfoliatus NBC_00077与菌株YH02进行形态和生理生化特性比较,结果见
Characteristics | ||||
---|---|---|---|---|
Spore chain | Rectiflexibile | Rectiflexibile | Rectiflexibile | Flexibile/Spiral |
Aerial mass color on ISP 2 | Light pink | Yellowish gray | White | White |
Diffusion pigment on ISP 2 | - | - | nd | - |
pH range for growth | 6.0-12.0 | 6.5-7.5 | 6.5-7.5 | nd |
Maximum NaCl tolerance (%) | 5 | 2.5 | nd | 6 |
Temperature range for growth (℃) | 16-37 | 25-30 | 30 | 10-37 |
Hydrolyze of starch | w | + | + | + |
Gelatin hydrolysis | + | + | + | w |
Nitrate reduction | + | + | + | - |
Milk coagulation | w | nd | + | w |
1: Streptomyces sp. YH02; 2: S. venezuelae ATCC 10712; 3: S. zaomyceticus NBC 00278; 4: S. exfoliatus NBC_00077. +: Positive or present; -: Negative or absent; w: Weak; nd: No report.
3 讨论与结论
链霉菌属(Streptomyces)物种在多样的生态环境中展现出卓越的适应能力,使其能在极端条件下如高温、高盐和低氧环境中生长繁
运用Antismash v7.0软件进行预测分析,共鉴定出32个次级代谢产物生物合成基因簇,表明菌株 YH02具有合成多种具有不同结构和功能的次级代谢产物的能
比较基因组学分析揭示了菌株YH02的独特基因组特征,表明其在链霉菌属中的特有系统发育位置;在泛基因组分析预测的15 739个直系同源基因簇中,核心基因组的比例为27.12%,这不仅突显了链霉菌属基本生物学功能的保守性,也反映了种间遗传异质性的存
作者贡献声明
李珍华:研究构思和设计,论文撰写和修改;王佳欣:数据收集和处理;张琳婕:协助实验操作;孙宇佳:数据收集和处理;田蓉:协助实验操作;杨瑾:提供技术支持;刘缙:研究构思和设计,参与论文讨论。
利益冲突
作者声明不存在任何可能会影响本文所报告工作的已知经济利益或个人关系。
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