Please wait a minute...

中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志
中国生物工程杂志  2022, Vol. 42 Issue (11): 163-178    DOI: 10.13523/j.cb.2209022
生物信息资源     
河蟹螺原体非编码RNA及其毒力靶标的多组学系统挖掘*
欧江涛1,**(),栾筱琪1,2,卞云霞1,蒋启程1,孟玉锁1,董惠姿1,王资生1,**()
1 盐城工学院海洋与生物工程学院 盐城 224051
2 南京师范大学海洋科学与工程学院 南京 210023
Multi-omics Analysis of Spiroplasma eriocheiris Non-coding RNAs (ncRNAs) and Their Virulence Targets
OU Jiang-tao1,**(),LUAN Xiao-qi1,2,BIAN Yun-xia1,JIANG Qi-cheng1,MENG Yu-suo1,DONG Hui-zi1,WANG Zi-sheng1,**()
1 College of Ocean and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, China
2 School of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China
 全文: PDF(2272 KB)   HTML
摘要：

我国是世界最大水产养殖国,每年甲壳动物因病害造成的经济损失约为70亿元。其中,螺原体(Spiroplasma)是甲壳动物重要的致病菌之一,可造成虾蟹大面积死亡,已列入农业农村部三类疫病。非编码RNA(ncRNA)广泛存在于细菌中,其主要通过碱基配对识别靶标mRNA在转录后水平调节基因的表达,部分ncRNAs通过与蛋白质相互作用而影响蛋白质功能。近年研究表明,细菌ncRNAs在毒力调控中扮演极为重要的角色。为了研究河蟹螺原体ncRNAs在甲壳动物致病中的分子调控作用,需系统筛选鉴定螺原体感染相关的ncRNAs和毒力靶标。通过比较基因组、差异转录组、定量蛋白质组、系统生物学和分子相互作用联合研究得到:整合基因组和转录组挖掘得到河蟹螺原体ncRNAs 共54个;在体内感染和体外培养的不同时期,利用数字基因表达谱分析分别得到11个和28个差异显著ncRNAs;利用4款生物软件预测ncRNAs靶标,取交集得到423个;利用定量蛋白质组检测,鉴定出68个差异毒力蛋白,这些差异毒力蛋白与ncRNAs的30个毒力靶标中的21个相同;利用网络生物学分析得到主要的节点Hub-ncRNA共有6个;利用RNA pull-down、原核链特异性测序和LC-MS/MS综合分析,得到重要节点ncRNA SR05的互作RNA 53个、互作蛋白质120个。相关研究成果,可为诠释河蟹螺原体致病机制及其与宿主相互作用机制奠定基础,为虾蟹该疾病的综合防治提供科学依据。
关键词： 河蟹螺原体;  非编码RNA;  毒力靶标;  多组学    
Abstract:

China is the one of the largest aquaculture countries in the world, and the annual economic loss caused by diseases of crustaceans is about 7 billion RMB per year. Among them, Spiroplasma is one of the important pathogenic bacteria of crustaceans, which can cause large-scale death of crustaceans, and has been listed as a Class III epidemic disease of the Ministry of Agriculture. Non coding RNAs (ncRNAs) are widespread in bacteria. They recognize target mRNAs mainly through base pairing and regulate gene expression at the post transcriptional level. Some ncRNAs affect protein function by interacting with proteins. Recent studies have shown that bacterial ncRNAs play an important role in virulence regulation. In order to study the molecular regulatory role of Spiroplasma ncRNAs in crustaceans, it is necessary to systematically screen and identify the ncRNAs and virulence targets related to Spiroplasma infection. Through comparative genome, differential transcriptome, quantitative proteome, system biology analysis, and combined analysis of molecular interaction and bioinformatics methods, this study showed that 54 ncRNAs of Spiroplasma were obtained by integrating genome and transcriptome. Under the conditions of infection in vivo and culture in vitro, 11 and 28 significantly different ncRNAs were obtained by digital gene expression profiling. Four biological software tools were used to predict ncRNA targets, and 423 targets were obtained by intersection. Using quantitative proteomic analysis, 68 differential virulence proteins were identified, which were the same as 21 out of the 30 virulence targets of ncRNAs. Six main hub-ncRNAs were found by network biology analysis. Using RNA pull-down, prokaryotic chain specific sequencing and LC-MS/MS comprehensive analysis, 53 interacting RNAs and 120 interacting proteins of ncRNA SR05 were found. The relevant research results can lay a foundation for interpreting the pathogenic mechanism of Spiroplasma and its interaction mechanism with the host, and provide a scientific basis for the comprehensive prevention and treatment of this disease in crustaceans.
Key words: Spiroplasma eriocheiris    Non coding RNA    Virulence targets    Multi-omics
收稿日期: 2022-09-12 出版日期: 2022-12-07
ZTFLH:  Q819  
基金资助: *国家自然科学基金面上项目(31872601);盐城工学院教育教改研究项目(JYKT2022B063)
通讯作者: **电子信箱:ojt110@126.com; wzs399@126.com   
服务　　
把本文推荐给朋友
加入引用管理器
E-mail Alert
RSS
作者相关文章　　
欧江涛
栾筱琪
卞云霞
蒋启程
孟玉锁
董惠姿
王资生

引用本文:

欧江涛, 栾筱琪, 卞云霞, 蒋启程, 孟玉锁, 董惠姿, 王资生. 河蟹螺原体非编码RNA及其毒力靶标的多组学系统挖掘*[J]. 中国生物工程杂志, 2022, 42(11): 163-178.

OU Jiang-tao, LUAN Xiao-qi, BIAN Yun-xia, JIANG Qi-cheng, MENG Yu-suo, DONG Hui-zi, WANG Zi-sheng. Multi-omics Analysis of Spiroplasma eriocheiris Non-coding RNAs (ncRNAs) and Their Virulence Targets. China Biotechnology, 2022, 42(11): 163-178.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2209022    或    https://manu60.magtech.com.cn/biotech/CN/Y2022/V42/I11/163

ncRNA 开始位点 终止位点 基因长度/bp 左侧基因 右侧基因
S01 104 673 104 873 200 scrab_t01 scrab0095
S02 136 973 137 193 220 scrab0133 scrab0134
S03 172 738 172 944 206 scrab0165 scrab0166
S04 202 606 202 791 185 trxA scrab0192
S05 221 472 221 581 109 scrab0208 scrab0209
S06 272 546 272 644 98 scrab0255 scrab0256
S07 272 449 272 564 115 scrab0255 scrab0256
S08 335 627 335 690 63 ptsH scrab0324
S09 344 288 344 391 103 scrab0334 scrab0335
S10 372 027 372 195 168 scrab0357 scrab0358
S11 458 456 458 589 133 scrab0433 Scrab0434
S12 477 280 477 472 192 scrab0449 Scrab0450
S13 486 917 487 054 137 scrab0461 Scrab0462
S14 527 878 528 057 179 scrab0490 Scrab0491
S15 534 383 534 498 115 scrab0494 Scrab0495
S16 607 582 607 777 195 scrab0563 Scrab0564
S17 608 460 608 564 104 scrab0564 Scrab0565
S18 608 533 608 627 94 scrab0564 Scrab0565
S19 624 844 625 028 184 scrab0577 Scrab0578
S20 664 252 664 561 309 scrab0606 Scrab0607
S21 664 252 664 510 258 scrab0606 Scrab0607
S22 689 130 689 278 148 scrab0624 Scrab0625
S23 786 423 786 644 221 scrab0717 Scrab0718
S24 799 983 800 151 168 scrab0731 Scrab0732
S25 809 770 809 906 136 scrab0739 Scrab0740
S26 832 811 833 084 273 scrab0764 Scrab0765
S27 928 160 928 300 140 scrab0852 Scrab0853
S28 959 192 959 377 185 lgt1 Scrab0879
S29 1 048 363 1 048 516 153 scrab0953 Scrab0954
S30 1 085 695 1 085 917 222 scrab0994 scrab_t018
S31 1 089 323 1 089 455 132 scrab0998 Scrab0999
S32 1 113 737 1 114 051 314 Scrab1023 Scrab1024
S33 1 131 251 1 131 519 268 Scrab1036 Scrab1037
S34 1 206 914 1 207 087 173 Scrab1110 Scrab1111
S35 1 210 896 1 211 174 278 Scrab1113 Scrab1111
S36 1 229 830 1 230 332 502 Scrab1127 Scrab1128
S37 1 230 829 1 231 073 244 Scrab1127 Scrab1128
S38 1 291 208 1 291 515 307 Scrab1182 Scrab1183
S39 1 308 019 1 308 210 191 Scrab1197 Scrab1198
S40 1 309 173 1 309 425 252 Scrab1199 Scrab1200
S41 1 310 811 1 311 143 332 Scrab1200 Scrab1201
S42 1 310 634 1 311 143 509 Scrab1200 Scrab1201
表1  河蟹螺原体ncRNAs基因组预测结果
图1  河蟹螺原体ncRNAs长度分布示意图
序列片段类别 总测序读数(原始测序序列) 单一测序读数(同家族相同序列)
未加工的序列片段 77 998 246 18 874 896
高质量的序列片段 66 058 594 3 839 081
映射到基因组的总序列片段 65 899 039 3 708 778
映射到基因组编码区(CDS)的序列片段 1 608 363 623 506
映射到基因组的rRNA序列片段 36 807 683 2 315 767
映射到基因组的tRNA序列片段 25 983 673 608 753
映射到基因间区的序列片段 1 499 320 160 752
映射到Rfam数据库的总序列片段 53 763 838 1 851 879
映射到Rfam数据库的rRNA序列片段 26 250 950 1 051 119
映射到Rfam数据库的tRNA序列片段 25 765 791 601 942
映射到Rfam数据库的其他序列片段 1 747 097 198 818
表2  河蟹螺原体ncRNAs转录组测序序列统计分析结果
图2  河蟹螺原体ncRNAs在其基因组上的分布示意图
ncRNA 初期感染阶段 发病阶段 标准化后的log2 FC P值 FDR
SR16 — — NA NA NA
S24 1 1 0.172 493 619 0.860 778 612 0.860 778 612
SR18 2 1 -0.505 578 286 0.517 900 458 0.54 836 519
SR03 1 1 -0.827 506 381 0.479 323 794 0.539 239 268
SR09 2 3 0.631 925 238 0.324 787 272 0.389 744 727
S08 3 4 0.541 727 429 0.308 491 825 0.396 632 347
S25 2 1 -1.505 578 286 0.105 506 091 0.146 085 357
S07 1 0 -2.827 506 381 0.08 748 681 0.131 230 215
SR04 3 1 -1.827 506 381 0.022 825 508 0.037 350 831
S16 11 18 0.724 289 256 0.00 681 534 0.012 267 612
SR21 18 28 0.631 925 238 0.002 838 326 0.005 676 652
S01 0 5 3.342 418 621 3.14×10-5 7.06×10-5
SR10 26 10 -1.419 421 642 1.82×10-8 4.69×10-8
SR08 36 8 -2.139 450 387 1.18×10-18 3.54×10-18
SR05 85 23 -1.914 969 222 1.97×10-37 7.09×10-37
.0SR19 51 1 -6.499 931 723 4.19×10-50 1.88×10-49
S04 75 8 -3.223 435 057 2.79×10-57 1.68×10-56
SR01 127 31 -2.041 404 008 6.37×10-61 5.73×10-60
SR11 527 831 0.656.355 277 1.35×10-189 2.43×10-188
表3  河蟹螺原体在螃蟹体内感染条件下ncRNAs表达差异极显著结果
ncRNA 对数期 非对数期 标准化后的log2 FC P值 FDR
S06 4 3 -0.320 105 871 0.743 126 296 0.743126 296
S01 9 6 -0.542 498 292 0.414 196 207 0.424 816 623
S28 4 2 -0.905 068 372 0.402 464 138 0.423 646 461
S25 48 58 0.271 088 584 0.269 017 916 0.29 083 018
SR03 24 32 0.431 966 616 0.204 078 957 0.226 754 397
SR04 55 42 -0.387 220 067 0.132 228 024 0.151 117 742
S27 3 0 -2.642 033 966 0.098 739 931 0.117 898 425
SR17 3 0 -2.642 033 966 0.098 739 931 0.117 898 425
SR15 8 3 -1.435 583 088 0.074 534 531 0.093 168 164
SR16 27 40 0.575 557 469 0.064 877 131 0.083 712 428
SR12 9 17 0.960 002 048 0.060 750 588 0.081 000 784
SR10 485 537 0.146 901 619 0.054 159 109 0.07 470 222
SR06 4 0 -3.127 460 793 0.033 513 641 0.04 787 663
S02 11 4 -1.490 030 872 0.030 941 236 0.045 838 868
S03 10 3 -1.73 514 337 0.023 185 192 0.035 669 525
S41 0 5 4.001 822 224 0.012 394 182 0.0 202 354
SR14 0 5 4.001 822 224 0.012 394 182 0.0 202 354
S22 6 0 -3.642 033 966 0.006 797 595 0.011 821 904
S15 7 0 -3.905 068 372 0.00 238 588 0.004 337 964
S07 14 3 -2.194 574 989 0.001 872 885 0.0 035 674
S32 9 0 -4.127 460 793 0.000 848 078 0.001 696 156
S12 11 0 -4.407 568 712 0.000 183 791 0.000 386 929
S08 24 6 -2.020 545 589 8.48×10-5 0.000 188 536
SR09 16 2 -3.020 545 589 5.53×10-5 0.000 130 008
S29 14 0 -4.843 667 827 9.29×10-6 2.32×10-5
SR19 35 9 -1.957 535 792 3.94×10-6 1.05×10-5
S24 26 69 1.430 866 581 1.98×10-7 5.67×10-7
S10 21 0 -5.407 568 712 4.83×10-8 1.49×10-7
SR18 17 60 1.831 897 223 7.12×10-9 2.37×10-8
SR13 0 27 6.434 781 631 8.77×10-10 3.19×10-9
SR20 0 28 6.487 249 051 4.46×10-10 1.79×10-9
S39 29 0 -5.874 694 723 1.28×10-10 5.70×10-10
SR21 190 82 -1.21 048 138 2.44×10-14 1.22×10-13
S16 62 235 1.912 554 886 1.73×10-32 9.88×10-32
SR08 386 895 1.211 842 402 6.03×10-66 4.02×10-65
S26 16 246 3.921 968 916 1.28×10-68 1.02×10-67
SR05 792 1 754 1.146 850 808 2.71×10-128 2.71×10-127
S04 144 800 2.478 260 268 1.46×10-150 1.94×10-149
SR01 1 788 690 -1.373 469 096 9.79×10-171 1.96×10-169
SR11 2 808 1 458 -0.945 398 812 1.04×10-173 4.15×10-172
S20 — — NA NA NA
表4  河蟹螺原体在不同的生长时相下ncRNAs表达差异极显著结果
图3  河蟹螺原体ncRNAs在体外培养和体内感染不同时期的转录组调控差异
图4  河蟹螺原体ncRNAs分子靶标的4款生物学软件的综合预测结果
图5  河蟹螺原体强、弱菌株不用生长时期差异蛋白质的表达量分布火山图
基因ID 基因名称 ncRNA_ID NCBI数据库中的
蛋白质编号		 Uniprot/Swissprot蛋白数据库
(注释信息)
scrab0151 ABC型亚精胺/腐胺转运系统ATP结合蛋白 SR04 NJNU:scrab0151 亚精胺/腐胺导入ATP结合蛋白PotA
scrab0165 假定短链脱氢酶/还原酶 SR04 NJNU:scrab0165 无特征氧化还原酶C521.03
scrab0175 ATP依赖性蛋白酶ATP结合亚基ClpB SR03 NJNU:scrab0175 伴侣蛋白ClpB
scrab0193 鸟氨酸氨甲酰转移酶 SR10 NJNU:scrab0193 鸟氨酸氨基甲酰转移酶,分解代谢
scrab0264 假定磷酸泛乙烯腺苷酸转移酶 SR05 NJNU:scrab0264 磷戊烷腺苷酸转移酶
scrab0453 假定1-酰基-sn-甘油-3-磷酸酰基转移酶 SR16 NJNU:scrab0453 1-酰基-sn-甘油-3-磷酸酰基转移酶β
scrab0614 链球菌素A乙酰转移酶 SR04 NJNU:scrab0614 维吉尼亚霉素A乙酰转移酶
scrab0614 链球菌素A乙酰转移酶 SR16
scrab0698 假定胆碱激酶 S20 NJNU:scrab0698 蛋白质LicA
scrab0698 假定胆碱激酶 S26
scrab0869 假定十一烯基焦磷酸合成酶 S02 NJNU:scrab0869 异戊二烯转移酶
scrab0946 假定短链脱氢酶/还原酶 SR16 NJNU:scrab0946 3-氧酰基-[酰基载体蛋白]还原酶FabG
scrab1010 假定丝氨酸/苏氨酸蛋白激酶(C端截断) SR18 NJNU:scrab1010 丝氨酸/苏氨酸蛋白激酶PrkC
scrab1011 铜转运P型ATP酶 SR16 NJNU:scrab1011 铜输出P型ATP酶A
scrab1013 丝氨酸苏氨酸蛋白磷酸酶 SR18 NJNU:scrab1013 丝氨酸/苏氨酸磷酸酶stp
scrab1018 ABC型转运系统ATP结合蛋白 S03 NJNU:scrab1018 未鉴定的ABC转运蛋白ATP
结合蛋白YvfR
scrab1019 翻译起始因子IF-2 SR16 NJNU:scrab1019 翻译起始因子IF-2
scrab1061 蛋白转定位酶前体亚基SecA S12 NJNU:scrab1061 蛋白质转锁酶亚基SecA
scrab1088 阳离子转运ATP酶 SR12 NJNU:scrab1088 镁转运ATP酶,P型1
scrab1117 假定谷氨酰tRNA(gln)酰胺转移酶亚单位A S03 NJNU:scrab1117 谷氨酰tRNA(Gln)酰胺转移酶亚单位A
scrab1145 腐胺氨甲酰转移酶 S26 NJNU:scrab1145 腐胺氨基甲酰转移酶
scrab1164 ABC型铁硫簇组装转运系统ATP结合蛋白 SR16 NJNU:scrab1164 可能的ABC转运体ATP结合蛋白
spyM18_0273
scrab1210 假定阳离子转运ATP酶 SR16 NJNU:scrab1210 钙转运ATP酶lmo0841
表5  综合筛选的毒力靶蛋白
图6  河蟹螺原体ncRNAs、mRNAs和蛋白质的关联数据网络图
基因ID SR05正义链组 SR05反义链组 logFC P值 FDR
rrf 185 619.108 4 39 920.340 28 2.217 108 5.34×10-25 6.74×10-22
ssrA 12 922.274 37 3 515.967 002 1.877 755 2.69×10-18 1.70×10-15
SPE_RS03485 42 512.623 95 12 012.394 03 1.823 359 5.69×10-18 2.39×10-15
SPE_RS02325 58 156.043 86 17 939.776 99 1.696 654 4.06×10-15 1.28×10-12
SPE_RS03480 5 457.382 1 744.808 036 1.645 11 6.36×10-15 1.61×10-12
SPE_RS00935 55 720.301 47 18 992.953 18 1.552 635 4.44×10-13 9.35×10-11
SPE_RS05020 29 955.628 23 1 0381.288 81 1.528 656 3.73×10-12 5.88×10-10
SPE_RS05615 21 122.558 36 7 375.550 964 1.517 742 8.91×10-12 1.12×10-9
SPE_RS05035 194 321.536 2 67 954.014 03 1.515 787 5.73×10-13 1.03×10-10
ffs 32 358.822 53 11 540.250 33 1.487 349 7.30×10-12 1.02×10-9
SPE_RS05575 8 535.875 971 3 111.366 297 1.455 381 4.49×10-9 3.78×10-7
SPE_RS03530 15 095.854 73 5 793.217 381 1.381 398 1.95×10-9 1.89×10-7
SPE_RS00915 24 935.822 86 9 648.378 314 1.369 672 6.36×10-10 7.30×10-8
SPE_RS03535 18 540.765 66 7 250.496 149 1.354 295 1.95×10-9 1.89×10-7
SPE_RS03525 13 670.483 36 5 472.556 037 1.320 492 7.89×10-9 5.85×10-7
SPE_RS04995 12 961.885 73 5 206.562 456 1.315 529 1.55×10-8 1.03×10-6
SPE_RS03520 19 156.590 52 7 854.154 252 1.286 083 1.12×10-8 7.82×10-7
SPE_RS00920 36 870.242 04 15 253.028 04 1.273 246 3.93×10-9 3.54×10-7
SPE_RS00940 28 796.958 48 11 951.984 87 1.268 536 5.65×10-9 4.46×10-7
SPE_RS03550 12 724.778 07 5 657.029 63 1.169 231 4.63×10-7 2.65×10-5
SPE_RS05005 59 989.265 9 26 790.756 29 1.162 908 4.06×10-8 2.56×10-6
SPE_RS05000 45 169.010 34 20 794.821 88 1.119 031 1.57×10-7 9.42×10-6
SPE_RS00930 6 318.765 329 3 029.599 226 1.060 009 3.24×10-5 0.001 574
SPE_RS03545 12 598.525 93 6 121.238 026 1.041 112 6.08×10-6 0.000 32
SPE_RS05025 22 011.494 98 10 968.351 89 1.004 774 5.01×10-6 0.000 275
SPE_RS01375 9 721.414 3 4 860.855 09 0.999 649 2.65×10-5 0.001 337
SPE_RS00455 40 30.830 319 2 168.528 025 0.893 725 0.001 317 0.057 333
SPE_RS05010 13 046.870 56 7 028.594 6 0.892 235 7.23×10-5 0.003 382
SPE_RS03945 220.342 477 4 135.870 296 4 0.696 498 0.047 265 0.841 118
SPE_RS02385 1 186.310 353 733.958 215 1 0.692 64 0.001 422 0.059 836
SPE_RS02865 557.535 008 3 846.879 423 2 -0.602 91 0.013 798 0.446 503
SPE_RS05430 771.024 838 1 1 171.789 142 -0.603 73 0.010 194 0.367 561
rpsS 685.550 425 2 1 047.142 602 -0.610 71 0.032 696 0.723 892
SPE_RS05645 101.563 026 156.048 012 1 -0.619 08 0.041 431 0.816 972
SPE_RS04920 755.294 328 2 1 175.844 962 -0.638 46 0.005 923 0.233 607
SPE_RS06295 717.221 198 2 1 132.865 267 -0.658 91 0.033 568 0.730 395
SPE_RS03495 750.840 941 9 1 199.176 469 -0.675 12 0.011 842 0.415 115
SPE_RS06380 533.931 336 4 855.150 432 5 -0.678 93 0.027 987 0.679 225
SPE_RS03555 232.403 148 7 373.443 772 6 -0.683 82 0.016 516 0.508 377
SPE_RS04040 145.491 670 4 235.087 292 3 -0.691 57 0.032 053 0.722 341
SPE_RS03030 249.662 337 9 405.623 078 7 -0.699 87 0.006 946 0.265 617
SPE_RS02535 346.066 606 9 566.823 849 9 -0.711 33 0.015 737 0.496 51
SPE_RS00900 150.654 169 6 247.355 197 1 -0.714 39 0.043 636 0.823 293
SPE_RS04790 284.342 131 8 480.531 379 5 -0.756 36 0.013 186 0.437 929
SPE_RS02265 339.666 140 4 575.804 801 7 -0.760 65 0.018 564 0.520 781
SPE_RS05070 541.422 72 918.037 990 7 -0.761 21 0.009 527 0.353 609
SPE_RS05905 159.599 040 8 276.930 275 -0.793 62 0.045 867 0.838 908
SPE_RS06385 621.385 607 1 1 079.868 917 -0.796 41 0.017 988 0.520 781
SPE_RS03390 247.850 408 499.863 627 4 -1.011 32 0.000 547 0.024 661
SPE_RS05730 139.396 630 6 302.344 762 2 -1.113 31 0.026 266 0.649 96
SPE_RS04715 61.867 043 9 143.132 501 7 -1.206 22 0.018 998 0.521 207
SPE_RS00980 84.601 796 27 231.750 335 8 -1.445 86 0.025 943 0.649 96
SPE_RS03815 6.856 994 903 72.710 003 7 -3.339 95 0.002 813 0.114 524
表6  RNA pull-down联合链特异性测序筛选鉴定SR05互作靶基因
蛋白质编号 蛋白质名称 长度 覆盖率/%
WP_047791007.1 II型CRISPR RNA引导的核酸内切酶Cas9 1 097 130 388.3
WP_053040794.1 亚硫酸盐介导的Tau E/Saf E家族蛋白质 353 39 296.1
WP_025317127.1 多物种:HPr家族磷酸载体蛋白 87 9 087.5
WP_047791170.1 Lac I家族DNA结合转录调控因子 303 35 083.1
WP_047790930.1 tRNA二氢尿苷合酶Dus B 330 36 976.6
WP_047791774.1 磷酸糖变位酶 557 63 853.2
WP_047791107.1 腺苷琥珀酸裂解酶 433 50 121.3
WP_047791117.1 I型DNA拓扑异构酶 666 76 191.6
WP_047790935.1 单链DNA结合蛋白 153 17 035.7
WP_047791306.1 甲硫氨酸-tRNA甲酰转移酶 319 36 325.2
WP_047791018.1 硝化还原酶家族蛋白 210 23 087
WP_047791909.1 丝氨酸羟甲基转移酶 413 45 660
WP_047791406.1 FMN依赖性NADH-偶氮还原酶 200 22 667.8
表7  RNA pull-down联合LC-MS/MS筛选鉴定SR05互作蛋白
[1] 2021年全国渔业经济统计公报. 中国水产. 2022 (8): 8-9.
2021 national fishery economic statistics bulletin. Chinese aquatic products. 2022(8): 8-9.
[2] 王文. 虾蟹新型病原螺原体的发现和研究. 南京师大学报(自然科学版), 2016, 39(1): 1-13.
Wang W. Discovery and studies of a novel pathogen, Spiroplasma eriocheiris, in economically important species of crustaceans. Journal of Nanjing Normal University (Natural Science Edition), 2016, 39(1): 1-13.
[3] Wang W, Gu W, Gasparich G E, et al. Spiroplasma eriocheiris sp. nov., associated with mortality in the Chinese mitten crab, Eriocheir sinensis. International Journal of Systematic and Evolutionary Microbiology, 2011, 61(Pt 4): 703-708.
doi: 10.1099/ijs.0.020529-0 pmid: 20418415
[4] 一、二、三类动物疫病病种名录. 中国动物检疫. 2009, 26(2):1.
List of Types I, II and III animal epidemic diseases. China Animal Quarantine. 2009, 26(2):1.
[5] Peng D H, Luo X X, Zhang N, et al. Small RNA-mediated Cry toxin silencing allows Bacillus thuringiensis to evade Caenorhabditis elegans avoidance behavioral defenses. Nucleic Acids Research, 2017, 46(1): 159-173.
doi: 10.1093/nar/gkx959
[6] Das S, Lindemann C, Young B C, et al. Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation. Proceedings of the National Academy of Sciences of the United States of America, 2016, 113(22): E3101-E3110.
[7] Hör J, Gorski S A, Vogel J. Bacterial RNA biology on a genome scale. Molecular Cell, 2018, 70(5): 785-799.
doi: S1097-2765(17)30980-2 pmid: 29358079
[8] Melamed S, Peer A, Faigenbaum-Romm R, et al. Global mapping of small RNA-target interactions in bacteria. Molecular Cell, 2016, 63(5): 884-897.
doi: 10.1016/j.molcel.2016.07.026 pmid: 27588604
[9] Barquist L, Vogel J. Accelerating discovery and functional analysis of small RNAs with new technologies. Annual Review of Genetics, 2015, 49: 367-394.
doi: 10.1146/annurev-genet-112414-054804 pmid: 26473381
[10] Reinhart A A, Powell D A, Nguyen A T, et al. The prrF-encoded small regulatory RNAs are required for iron homeostasis and virulence of Pseudomonas aeruginosa. Infection and Immunity, 2015, 83(3): 863-875.
doi: 10.1128/IAI.02707-14
[11] Kinoshita-Daitoku R, Kiga K, Miyakoshi M, et al. A bacterial small RNA regulates the adaptation of Helicobacter pylori to the host environment. Nature Communications, 2021, 12: 2085.
doi: 10.1038/s41467-021-22317-7 pmid: 33837194
[12] Chen W H, van Noort V, Lluch-Senar M, et al. Integration of multi-omics data of a genome-reduced bacterium: prevalence of post-transcriptional regulation and its correlation with protein abundances. Nucleic Acids Research, 2016, 44(3): 1192-1202.
doi: 10.1093/nar/gkw004
[13] Lluch-Senar M, Delgado J, Chen W H, et al. Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium. Molecular Systems Biology, 2015, 11(1): 780.
doi: 10.15252/msb.20145558 pmid: 25609650
[14] Sauder A B, Kendall M M. A pathogen-specific sRNA influences enterohemorrhagic Escherichia coli fitness and virulence in part by direct interaction with the transcript encoding the ethanolamine utilization regulatory factor EutR. Nucleic Acids Research, 2021, 49(19): 10988-11004.
doi: 10.1093/nar/gkab863
[15] Chakravarty S, Massé E. RNA-dependent regulation of virulence in pathogenic bacteria. Frontiers in Cellular and Infection Microbiology, 2019, 9: 337.
doi: 10.3389/fcimb.2019.00337 pmid: 31649894
[16] Livny J, Brencic A, Lory S, et al. Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids Research, 2006, 34(12): 3484-3493.
doi: 10.1093/nar/gkl453
[17] Arrial R T, Togawa R C, de M Brigido M. Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis. BMC Bioinformatics, 2009, 10: 239.
doi: 10.1186/1471-2105-10-239
[18] Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nature Reviews Genetics, 2019, 20(11): 631-656.
doi: 10.1038/s41576-019-0150-2 pmid: 31341269
[19] Han K, Lory S. Toward a comprehensive analysis of posttranscriptional regulatory networks: a new tool for the identification of small RNA regulators of specific mRNAs. mBio, 2021, 12(1): e03608-e03620.
[20] Mukherjee S, Stamatis D, Bertsch J, et al. Genomes OnLine database (GOLD) v.7: updates and new features. Nucleic Acids Research, 2018, 47(D1): D649-D659.
[21] Khan M M, Ernst O, Manes N P, et al. Multi-omics strategies uncover host-pathogen interactions. ACS Infectious Diseases, 2019, 5(4): 493-505.
doi: 10.1021/acsinfecdis.9b00080 pmid: 30857388
[22] Lo A W, Moriel D G, Phan M D, et al. ‘omic’ approaches to study uropathogenic Escherichia coli virulence. Trends in Microbiology, 2017, 25(9): 729-740.
doi: 10.1016/j.tim.2017.04.006
[23] Hör J, Garriss G, di Giorgio S, et al. Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control. The EMBO Journal, 2020, 39(9): e103852.
[24] Westermann A J, Förstner K U, Amman F, et al. Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions. Nature, 2016, 529(7587): 496-501.
doi: 10.1038/nature16547
[25] Carrier M C, Lalaouna D, Massé E. Broadening the definition of bacterial small RNAs: characteristics and mechanisms of action. Annual Review of Microbiology, 2018, 72: 141-161.
doi: 10.1146/annurev-micro-090817-062607
[26] Hasin Y, Seldin M, Lusis A. Multi-omics approaches to disease. Genome Biology, 2017, 18(1): 83.
doi: 10.1186/s13059-017-1215-1 pmid: 28476144
[27] Hou L B, Du J, Ren Q L, et al. Ubiquitin-modified proteome analysis of Eriocheir sinensis hemocytes during Spiroplasma eriocheiris infection. Fish & Shellfish Immunology, 2022, 125: 109-119.
[28] Huang C, Du J, Ji B R, et al. The Eriocheir sinensis calcium/calmodulin-dependent protein kinase II activates apoptosis to resist Spiroplasma eriocheiris infection. Fish & Shellfish Immunology, 2022, 121: 223-231.
[1] 廖天赐, 郑婷, 沈林園, 赵叶, 牛丽莉, 张顺华, 朱砺. tsRNAs的作用机制及其在相关疾病中的潜在应用*[J]. 中国生物工程杂志, 2022, 42(3): 82-90.
[2] 刘美琴,高博,焦月盈,李玮,虞结梅,彭向雷,郑妍鹏,付远辉,何金生. 人呼吸道合胞病毒感染的A549细胞中长链非编码RNA表达谱研究[J]. 中国生物工程杂志, 2021, 41(2/3): 7-13.
[3] 刘天义,冯卉,SALSABEELYousuf,解领丽,苗向阳. lncRNA在动物脂肪沉积中的研究进展*[J]. 中国生物工程杂志, 2021, 41(11): 82-88.
[4] 万群,刘梦瑶,夏菁,苟理尧,唐敏,孙恃雷,张彦. 长链非编码RNA SNHG3对人乳腺癌细胞MCF-7增殖、迁移与侵袭的影响 *[J]. 中国生物工程杂志, 2019, 39(1): 13-20.
[5] 谭杨,刘胜,罗凤玲,章晓联. 结核分枝杆菌H37Rv刺激巨噬细胞后差异表达lncRNA分析及鉴定 *[J]. 中国生物工程杂志, 2018, 38(5): 1-9.
[6] 范源,罗嘉,甘麦邻,谭娅,张顺华,朱砺. 长链非编码RNA TERRA的研究进展 *[J]. 中国生物工程杂志, 2018, 38(10): 64-73.
[7] 堵晶晶, 谭镇东, 刘辰东, 巫小倩, 张培文, 张顺华, 朱砺. 长链非编码RNA的研究现状[J]. 中国生物工程杂志, 2016, 36(9): 59-74.
[8] 罗嘉, 沈林園, 李强, 李学伟, 张顺华, 朱砺. 哺乳动物中作用于非编码RNA的RNA编辑研究进展[J]. 中国生物工程杂志, 2016, 36(11): 76-82.
[9] 邱家俊, 颜景斌. 基因印记与lncRNA[J]. 中国生物工程杂志, 2014, 34(7): 63-68.
[10] 娄亮亮, 朱运峰. 长链非编码RNA及其与肿瘤关系[J]. 中国生物工程杂志, 2013, 33(7): 82-89.
[11] 黄成江, 卢向阳, 田云, 易克. miRNA研究进展[J]. 中国生物工程杂志, 2003, 23(9): 26-29.
主管：中国科学院 　主办：中国科学院文献情报中心 　中国生物技术发展中心 　中国生物工程学会