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贝莱斯芽孢杆菌LG37全基因组测序分析及无机氮代谢相关候选基因的筛选

刘广鑫 董晏君 赵丽娟 邓益琴 程长洪 马红玲 江建军 冯娟 郭志勋 林蠡

刘广鑫, 董晏君, 赵丽娟, 邓益琴, 程长洪, 马红玲, 江建军, 冯娟, 郭志勋, 林蠡. 贝莱斯芽孢杆菌LG37全基因组测序分析及无机氮代谢相关候选基因的筛选[J]. 南方水产科学. doi: 10.12131/20210149
引用本文: 刘广鑫, 董晏君, 赵丽娟, 邓益琴, 程长洪, 马红玲, 江建军, 冯娟, 郭志勋, 林蠡. 贝莱斯芽孢杆菌LG37全基因组测序分析及无机氮代谢相关候选基因的筛选[J]. 南方水产科学. doi: 10.12131/20210149
LIU Guangxin, DONG Yanjun, ZHAO lijuan, DENG yiqin, CHENG Changhong, MA Hongling, JIANG Jianjun, FENG juan, GUO Zhixun, LIN Li. Sequencing of whole genome of Bacillus velezensis LG37 and screening of inorganic nitrogen metabolism candidate genes[J]. South China Fisheries Science. doi: 10.12131/20210149
Citation: LIU Guangxin, DONG Yanjun, ZHAO lijuan, DENG yiqin, CHENG Changhong, MA Hongling, JIANG Jianjun, FENG juan, GUO Zhixun, LIN Li. Sequencing of whole genome of Bacillus velezensis LG37 and screening of inorganic nitrogen metabolism candidate genes[J]. South China Fisheries Science. doi: 10.12131/20210149

贝莱斯芽孢杆菌LG37全基因组测序分析及无机氮代谢相关候选基因的筛选

doi: 10.12131/20210149
基金项目: 中国水产科学研究院南海水产研究所中央级公益性科研院所基本科研业务费专项资金资助 (2020TS04);广东省重点领域研发计划项目 (2019B020215001);中国-东盟海上合作基金 (CAMC-2018F);广东省海洋与渔业厅项目 (D21822202);财政部和农业农村部国家现代农业产业技术体系资助 (CARS-48)
详细信息
    作者简介:

    刘广鑫 (1988—),男,助理研究员,博士,从事渔业生物病害防治研究。E-mail: Guangxin_liu1988@163.com

    通讯作者:

    郭志勋 (1970—),男,研究员,博士,从事渔业生物病害防治研究。E-mail: guozhixun1@163.com

    林 蠡 (1970—),男,教授,博士,从事渔业生物病害防治研究。E-mail: linli@zhku.edu.cn

  • 中图分类号: S 949

Sequencing of whole genome of Bacillus velezensis LG37 and screening of inorganic nitrogen metabolism candidate genes

  • 摘要: 前期研究发现贝莱斯芽孢杆菌 (Bacillus velezensis) LG37可高效同化无机氮,但对其机理尚不清楚。为解读其高效同化无机氮的机理,文章结合三代PacBio RS II 和二代Illumina HiSeq 2000 测序技术对贝莱斯芽孢杆菌LG37进行全基因组测序,在此基础上利用NR、KEGG、eggNOG、GO和CARD数据库进行序列注释、分析,并通过本地Blast+ 对无机氮代谢相关基因进行挖掘。测序结果表明:1) 贝莱斯芽孢杆菌LG37 的基因组大小为3 929 697 bp的环状染色体,GC 含量为46.5%,包含3 854个蛋白质编码基因、86 个tRNA 基因和27 个rRNA 基因。2) 共筛选无机氮代谢相关候选基因94 个,这些基因主要涉及编码感应蛋白、转录调控因子、转运蛋白、氧化还原酶和同化酶等,并/对基因的GO 功能进行注释分析。综上,LG37 全基因组测序及无机氮代谢相关基因的分析为芽孢杆菌降低养殖水体中无机氮的研究提供了基因水平数据,为芽孢杆菌微生态制剂降低水体中无机氮的应用研究提供了理论依据。
  • 图  1  LG37 环状基因组图谱

    从环状的外层至内层分别是:1) 基因组正向和反向基因 (COG,见右侧);2) tRNA 在正向上的标注 (红色),rRNA 基因在反向上的标注 (蓝色);3) GC 含量;4) GC skew,当 (G–C)/(G+C)>0,黄色标注,(G–C)/(G+C)<0,粉色标注。

    Figure  1.  Circular genome map of B. velezensis LG37 strain

    Rings from the outermost to the center are: 1) Genes on the forward and reverse stand (COG, see right column); 2) tRNA genes on the forward stand (red), rRNA gene on the reverse stand (blue); 3) GC content; 4) GC skew, when (G–C)/(G+C)> 0, yellow stand, (G–C)/(G+C)<0, pink stand.

    图  2  贝莱斯芽孢杆菌基于16S rDNA 序列构建的系统进化树

    Figure  2.  Neighbor-joining tree of B. velezensis LG37 based on 16S rDNA sequences

    图  3  COG功能分类

    Figure  3.  COG classification

    图  4  LG37基因功能注释KEGG代谢通路

    Figure  4.  Gene KEGG pathway classification map of LG37

    图  5  氮代谢通路 (ko00910)

    KEGG 中的基因 (绿色标注)。

    Figure  5.  Nitrogen metabolism (ko00910)

    Genes of KEGG (green stand).

    表  1  贝莱斯芽孢杆菌LG37 基因组特性

    Table  1.   Genome features of B. velezensis LG37 strain

    特性
    Feature
    数值
    Value
    基因组大小 Genome size/bp 3 929 697
    GC-含量 GC-content 46.5%
    质粒数量 Plasmid number 0
    总基因 Total genes 3 967
    蛋白编码基因 Protein-coding genes 3 854
    转运 RNA tRNA 86
    核糖体 RNA rRNA 27
    编码区域大小 Coding region size/bp 3 495 864
    编码区域GC-含量 GC-content of coding region 47.3%
    编码区域/全基因组 Coding region/Genome length 89.0%
    间隔区域大小 Intergenic region size/bp 433 833
    间隔区域占比 Ratio of intergenic region 11.0%
    下载: 导出CSV

    表  2  LG37 基因组氮代谢通路及其相关基因

    Table  2.   Related genes of nitrogen metabolism pathways of LG37

    通路
    Pathway ID
    KEGG 描述
    Pathway_description
    基因
    Gene
    ko00910 氮代谢 Nitrogen metabolism orf00490, orf00539, orf00544, orf00545, orf00546, orf00547,
    orf00817, orf01213, orf01254, orf01968, orf02226, orf02227, orf02368,
    orf03807, orf03808, orf03809, orf03810, orf03811
    M00531 同化硝酸盐还原 Assimilatory nitrate reduction orf00539, orf03807, orf03809
    M00530 异化硝酸盐还原 Dissimilatory nitrate reduction orf00544, orf00545, orf00547, orf03808, orf03809, orf03810, orf03811
    M00529 反硝化 Denitrification orf00544, orf00545, orf00547, orf03809
    M00804 反硝化完全硝化 Complete nitrification orf03809
    下载: 导出CSV

    表  3  无机氮代谢候选基因

    Table  3.   Candidate genes of inorganic nitrogen metabolism

    基因
    Gene
    大小
    Size/bp
    蛋白    
    Protein     
    GO-分子功能   
    GO-Molecular function   
    orf00084 741 Type III pantothenate kinase YacB 泛酸激酶活性
    orf00106 246 Putative septation protein SpoVG 分子功能的负调控
    orf00148 885 Pyridoxal 5'-phosphate synthase subunit PdxS 谷氨酰胺水解活性
    orf00173 2 004 Nitrate reductase YyaE 硝酸还原酶活性
    orf00246 1 416 Arginine utilization regulatory protein RocR 转录因子结合
    orf00250 1 206 Ornithine aminotransferase RocD 鸟氨酸氧酸转氨酶活性
    orf00316 963 Iron(3+)-hydroxamate-binding protein YxeB 无机离子转运与代谢
    orf00379 1 017 Respiratory nitrate reductase NarI 硝酸还原酶活性
    orf00490 1 287 Glutamate dehydrogenase RocG 谷氨酸脱氢酶 (NAD+) 活性
    orf00535 1 377 Cytochrome cd1-nitrite reductase-like YwhL 亚硝酸盐还原酶活性
    orf00539 1 131 Nitrate transporter NarT 跨膜转运
    orf00544 3 687 Nitrate reductase alpha chain NarG 硝酸还原酶活性
    orf00545 1 464 Nitrate reductase beta chain NarH 硝酸还原酶活性
    orf00546 558 Nitrate reductase NarJ 未折叠蛋白结合
    orf00547 672 Nitrate reductase gamma chain NarI 硝酸还原酶活性
    orf00608 318 Urease subunit gamma 氨基酸转运与代谢
    orf00609 375 Urease subunit beta 氨基酸转运与代谢
    orf00610 1 710 Urease subunit alpha 氨基酸转运与代谢
    orf00623 351 Nitrogen regulatory protein P-II GlnB 酶调节活性
    orf00624 1 212 Ammonium transporter NrgA 铵跨膜转运蛋白活性
    orf00630 282 Stage III sporulation protein D SpoIIID DNA结合转录因子活性
    orf00783 726 Glucosamine-6-phosphate deaminase NagB 葡萄糖胺-6-磷酸脱氨酶活性
    orf00817 582 YvdA 无机离子转运与代谢
    orf00959 2 112 YvgW 阳离子转运ATP酶活性
    orf00966 1 716 Sulfite reductase [NADPH] CysI 亚硫酸盐还原酶 (NADPH) 活性
    orf00998 1 047 ABC transporter permease protein YvrB 转运体活性
    orf01042 357 Uncharacterized protein YusI 氧化还原酶活性
    orf01058 1 398 ABC transporter ATP-binding protein ATP结合
    orf01105 237 Nitrogen-fixing NifU domain-containing protein 铁硫簇结
    orf01175 2 403 Cation:proton antiporter 单价无机阳离子跨膜转运蛋白活性
    orf01213 1 032 Nitronate monooxygenase Ncd2 硝酸单加氧酶活性
    orf01254 549 YtiB 无机离子转运与代谢
    orf01262 813 Nitrate transport system permease protein YtlD 跨膜转运蛋白活性
    orf01263 783 Nitrate ABC transporter permease YtlC 跨膜转运
    orf01264 1 005 Nitrate ABC transporter periplasmic protein YtlA ATP酶活性
    orf01290 753 Quaternary-amine-transporting ATPase 传输ATP酶活性的季铵盐化合物
    orf01357 1 191 Nitric oxide dioxygenase 一氧化氮双加氧酶活性
    orf01435 1 962 Threonine--tRNA ligase 1 ThrS ATP结合
    orf01491 225 Spore germination protein GerE DNA结合
    orf01591 657 GlnP 氨基酸转运与代谢
    orf01592 651 GlnM 氨基酸转运与代谢
    orf01593 828 GlnH 氨基酸转运与代谢
    orf01617 801 Formate/nitrite transporter 跨膜转运蛋白活性
    orf01659 726 RNA polymerase sigma factor DNA结合转录因子活性
    orf01864 855 Nitrogen assimilation regulatory protein nac DNA结合转录因子活性
    orf01911 450 Ferric uptake regulation protein DNA结合转录因子活性
    orf01968 1 275 Glutamate dehydrogenase RocG 谷氨酸脱氢酶硝酸还原酶活性
    orf02215 1 983 Nitrate reductase 硝酸还原酶活性
    orf02225 903 HTH-type transcriptional regulator GltC DNA结合转录因子活性
    orf02226 903 Glutamate synthase (NADPH/NADH) GltB 谷氨酸合酶 (NADPH) 活性
    orf02227 4 560 Glutamate synthase (NADPH/ NADH) GltD 谷氨酸合酶 (NADPH) 活性
    orf02368 1 335 Glutamine synthetase GlnA 谷氨酸氨连接酶活性
    orf02369 405 HTH-type transcriptional regulator GlnR DNA结合
    orf02384 315 Ammonium compound efflux SMR transporter 膜的组成部分
    orf02385 354 Ammonium compound efflux SMR transporter 膜的组成部分
    orf02417 261 Stage V sporulation protein S 核酸结合
    orf02418 795 2',3'-cyclic-nucleotide 2'-phosphodiesterase YmdB 2',3'-环核苷酸2'-磷酸二酯酶活性
    orf02465 723 Uridylate kinase PyrH ATP结合
    orf02483 363 Chemotaxis protein CheY 磷脂酶信号转导系统
    orf02588 783 RNA polymerase sigma factor DNA结合转录因子活性
    orf02638 930 Glutaminase 氨基酸转运与代谢
    orf02680 666 Potassium uptake protein KtrA 阳离子跨膜转运蛋白活性
    orf02747 1 914 YkvW 阳离子转运ATP酶活性
    orf02756 342 Putative transcriptional regulator 转录调控,DNA模板
    orf02787 1 353 YkrM 阳离子跨膜转运蛋白活性
    orf02794 783 Uncharacterized membrane protein YkoY 膜的组成部分
    orf02804 742 HTH-type transcriptional regulator TnrA 核心启动子结合
    orf02828 315 Ammonium compound efflux SMR transporter 膜的组成部分
    orf02830 339 Ammonium compound efflux SMR transporter 膜的组成部分
    orf02854 999 Anion permease 无机磷酸盐跨膜转运蛋白活性
    orf03008 396 ArsC family transcriptional regulator SpxA 电子转移活性
    orf03161 1 215 Cation/H (+) antiporter YhaU 溶质:质子逆向转运活性
    orf03186 396 Putative fluoride ion transporter CrcB 无机阴离子跨膜转运蛋白活性
    orf03187 360 Putative fluoride ion transporter CrcB 无机阴离子跨膜转运蛋白活性
    orf03209 435 HTH-type transcriptional regulator NsrR DNA结合
    orf03262 834 ABC-type nitrate transport system 离子跨膜转运
    orf03263 990 Putative binding protein SsuA ATP酶活性
    orf03264 768 Aliphatic sulfonates import protein SsuB 阴离子跨膜转运蛋白活性
    orf03448 720 Probable transcriptional regulatory protein 转录调控,DNA模板
    orf03546 330 Ammonium compound efflux SMR transporter 膜的组成部分
    orf03547 315 Ammonium compound efflux SMR transporter 膜的组成部分
    orf03597 963 Arsenic resistance protein 无机阴离子跨膜转运蛋白活性
    orf03677 822 Probable manganese catalase YdbD 无机离子转运与代谢
    orf03682 366 Ammonium compound efflux SMR transporter 膜的组成部分
    orf03807 1 206 Assimilatory nitrate reductase NasA 硝酸铁氧还蛋白还原酶活性
    orf03808 2 328 Nitrite reductase large subunit NasB 亚硝酸盐还原酶[NAD(P)H] 活性
    orf03809 2 133 Assimilatory nitrate reductase NasC 硝酸还原酶活性
    orf03810 2 418 Nitrite reductase [NAD(P)H] NasD 亚硝酸盐还原酶[NAD(P)H]活性
    orf03811 321 Assimilatory nitrite reductase [NAD(P)H] NasE 亚硝酸盐还原酶[NAD(P)H]活性
    orf03812 1 440 NasF 辅酶代谢
    orf03840 1 257 Transport system atp-binding protein opuaa 传输ATP酶活性的季铵盐化合物
    orf03889 984 Glutaminase 1 GlsA1 谷氨酰胺酶活性
    orf03890 1 437 GlnT 假定的钠/谷氨酰胺转运体
    orf03963 1 434 Sodium-independent anion transporter 次级活性硫酸盐跨膜转运蛋白活性
    下载: 导出CSV
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出版历程
  • 收稿日期:  2021-05-20
  • 修回日期:  2021-07-07
  • 网络出版日期:  2021-10-19

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