Advances on antibiotic resistance genes (ARGs) in aquaculture environment
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摘要: 抗生素对水产养殖业中水生生物疾病防治、生产线增产等发挥着重要作用，但长期滥用抗生素很可能会诱导水生生物体内产生携带抗生素抗性基因 (Antibiotic resistant genes, ARGs) 的耐药菌 (Antibiotic resistant bacteria, ARB)。ARGs在水产养殖环境中的持久性残留、迁移和传播，会埋下基因污染隐患，导致生态失衡并危害人类安全，如何遏制抗生素抗性的传播已引起全球重点关注。就水产养殖环境中ARGs的研究进展，系统总结了ARGs的污染现状及其在水产养殖环境中的来源、迁移传播和影响因素，并简述了ARGs与抗生素、微生物群落和环境因素之间的关联特性，以及抗生素、ARGs和ARB对生态环境与人类健康的影响。基于此，概述了ARGs的控制策略与去除技术，并提出了今后的研究方向，以期为水产养殖环境中ARGs污染机理的解析和抗生素抗性传播风险的控制提供科学参考。Abstract: Antibiotics play a significant role in the disease control of aquatic organisms and output increase of aquatic products. However, long-term abuse of antibiotics can result in the occurrence of antibiotic resistant bacteria (ARB) which harbor antibiotics resistance genes (ARGs) in aquatic organisms. The persistent existence, migration and spread of ARGs in aquaculture environment will potentially cause genetic pollution, destroy the ecological balance, and pose risks to human health. Therefore, how to constrain the spread of antibiotic resistance has attracted global attention. In terms of the research advancement of ARGs in aquaculture environment, this review systematically summarizes the status of ARGs pollution coupled with the source, migration and spread behavior of ARGs and their influencing factors, illustrates the correlations between ARGs and antibiotics, microbial communities and environmental factors, as well as discusses the effect of antibiotics, ARGs and ARB on ecological environment and human health. Thus, the paper reviews the management strategies and removal technologies of ARGs, and proposes the future research directions regarding ARGs, so as to provide references for revealing the pollution mechanism of ARGs and reducing the transmission risk of antibiotic resistance.
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华贵栉孔扇贝(Chalmys nobilis)具有生长快、产量高、养殖周期短等特点，是中国华南沿海地区主要的海水养殖贝种之一，具有重要的经济价值。闭壳肌是华贵栉孔扇贝主要的食用部分。目前对扇贝闭壳肌的研究较少，主要有闭壳肌与其他性状的相关性研究，如墨西哥湾扇贝(Argopecten irradians concentricus)体质量和壳长与闭壳肌质量紧密相关[1]；华贵栉孔扇贝软体部质量对闭壳肌质量的直接影响最大，其次是壳宽[2]；影响虾夷扇贝(C. farreri)闭壳肌质量的主要因素是壳宽[3]；另外闭壳肌颜色和蛋白分布也有涉及[4-5]。但很少见到闭壳肌生长和发育的相关研究。
肌肉生长抑制素myostatin (MSTN)是转化生长因子-β (transforming growth factor-beta)超家族的成员，在动物肌肉生长和发育过程中起负调控作用[6]。Myostatin蛋白包括1个分泌信号序列、蛋白水解处理位点、含有9个半胱氨酸残基的保守型羧基末端区[7-8]。Myostatin的前体蛋白由信号序列、N-末端前肽区域和1个活性配基的C-末端区域组成[7-8]。前体蛋白经过2次蛋白质水解切割后，Myostatin即可活化[8-9]。成熟的Myostatin蛋白是一个C-末端由二硫键连接的二聚体，与MSTN基因受体结合，从而发挥其生物活性[8-9]。
目前在海湾扇贝(A. irradians)、栉孔扇贝 (C. farreri)、华贵栉孔扇贝、贻贝(Mytilus chilensis)、小狮爪海扇蛤(Nodipecten subnodosus)和竹蛏(Sinonovacula constricta)等贝类中有myostatin基因的研究报道[10-16]。Morelos等[14]研究1龄小狮爪海扇蛤一年中myostatin在闭壳肌中的表达情况、闭壳肌质量和肌纤维数量和大小，证实myostatin表达和闭壳肌性状有关联。在一些贝类中发现MSTN有与生长性状相关联的SNP位点[15,17-18]。Hu等[11]预测了栉孔扇贝MSTN启动子中有MEF2、COMP、MTBF、E-box等调控元件。
笔者已获得了华贵栉孔扇贝MSTN启动子序列[16]。本研究拟对启动子序列进行生物信息学分析。通过构建不同缺失长度的报告基因系统，检测启动子的转录活性，为今后进一步研究MSTN基因的调控机制奠定基础。
1. 材料与方法
1.1 实验材料
华贵栉孔扇贝采购于广东深圳南澳，剪取其闭壳肌组织，液氮冷冻后放置于– 80 ℃冰箱保存。
1.2 实验方法
1.2.1 DNA提取
用海洋动物DNA提取试剂盒(天根)提取DNA，终质量浓度为50 ng·mL–1，– 20 ℃保存备用。
1.2.2 myostatin启动子的生物信息学分析
笔者已获得myostatin基因启动子序列[16]。用在线软件BDGP (http://www.fruitfly.org/seq_tools/promoter.html)预测核心启动子区域和转录起始位点(transcription start site，TSS)。用MatInspector软件预测潜在的转录因子结合位点。用MethPrimer软件(http://www.urogene.org/methprimer2/)预测CpG岛。
1.2.3 不同长度片段表达载体构建
根据潜在的转录因子结合位点分析结果，设计6个正向引物和1个反向引物。上、下游引物分别添加KpnⅠ和HindⅢ酶切位点和保护碱基(表1)。以PGL-22为正向引物，P1322A为反向引物，扩增出最长的启动子片段，胶回收后，连接到pMD18-T载体，转化到DH5α大肠杆菌中，挑单克隆菌送上海生工生物工程有限公司测序。测序正确后，用质粒提取试剂盒(生工)提取质粒，以质粒DNA为模板，分别以PGL-102、PGL-274、PGL-534、PGL-995和PGL-1143为正向引物，P1322A为反向引物，通过PCR扩增不同片段长度的MSTN基因启动子片段，随后连接转化，测序验证序列正确后提取质粒。
表 1 实验所用引物Table 1. Primers used in this experiment引物
primer序列 (5'−3')
sequencePGL-22 CGGggtaccACACGGCGAAAAAATGGAGC PGL-102 CGGggtaccGGATGCCATAAATCAAAACCACAAC PGL-274 CGGggtaccAAAACGCCGCCAAACG PGL-534 CGGggtaccACTTCAGGCTGTATCGCAAAT PGL-995 CGGggtaccACCCGTTGGCAGCGTTCA PGL-1143 CGGggtaccTCTAAATGCTAACCCTTGTGCTG P1322A CTAaagcttTATAGCGGTTACGTTACAGATGGTT 注：小写字体为酶切位点 Note: Lowercase letters represent restriction enzyme loci. 用KpnⅠ和HindⅢ2种内切酶同时在37 ℃水浴酶切含有不同长度片段的pMD18-T重组质粒和pGL3-basic质粒，分别纯化后，用Solution I连接酶(TaKaRa) 16 ℃连接过夜，转化到DH5α大肠杆菌中，用去内毒素质粒提取试剂盒(OMEGA)提取重组质粒，测序以验证序列是否正确。
1.2.4 细胞培养
在24孔培养板中接种HEK293T细胞，使转染时细胞密度在70%~80%。所用培养基为DMEM高糖培养基(Hyclone)，加入10% FBS (Gibco)。细胞放置于37 ℃、5% CO2培养箱中培养约20 h。
1.2.5 瞬时转染
内参质粒为pRL-TK (Promega)，分别将各pGL3-basic重组质粒和内参质粒以20∶1的比例共转染到细胞。转染对照组为pGL3-basic载体和pRL-TK载体。每组做5个平行。瞬时转染采用转染试剂盒Lipofectamine 2000 Transfection Reagent (Invitrogen)，根据试剂盒的说明进行实验。
1.2.6 双荧光素酶活性检测
用萤光素酶检测试剂盒Dual-Luciferase®Reporter Assay System(Promega)分析报告基因Luciferase活性。转染24 h后，吸去旧的培养基，加入1×PBS清洗1~2次，吸出PBS后，每孔中加入细胞裂解液PLB (passive lysis buffer，Promega) 200 μL，室温孵育10 min；将裂解液10 000 r·min–1离心5 min，取上清作为待测液；取100 μL裂解液上清加入96孔发光板中，加入100 μL萤火虫荧光素酶检测工作液(碧云天)，吹吸混匀；上机测发光值，积分时间5 s；加入海肾荧光素酶检测工作液(碧云天) 100 μL，吹吸混匀，用化学发光分析仪BK-L96C (中生北控)监测发光值。用SPSS 19.0软件中的单因素方差分析检测各样品间差异的显著性。
2. 结果
2.1 华贵栉孔扇贝MSTN基因启动子的生物信息学分析
华贵栉孔扇贝MSTN基因5'调控区序列长1 358 bp (GenBank登录号：KY888888)。BDGP预测有4个TSS，分别为位于ATG上游第70个碱基“A”，第233个碱基“G”，第1 059个碱基“A”和第1 299个碱基“T”(图1)。核心启动子区在–100~–51 bp。MatInspector在线软件分析潜在的转录因子结合位点包括MEF2、MEF3、FoxO、MTBF和MyoD等，存在1个TATA-box (位于–92~–86bp)和2个E-box顺式作用元件 (图1)。MethPrimer软件预测无CpG岛。
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图 1 MSTN启动子序列分析下划直线表示转录因子结合位点，下划波浪线为顺式作用元件，斜体表示核心启动子区域，阴影部分表示转录起始位点Figure 1. Analysis of MSTN gene promoter sequenceThe potential transcription factor binding sites are straightly underlined. The cis-regulatory elements are wavily underlined. Core promoter region is in italic. Nucletide of each transcription start sites are in shadow.2.2 MSTN基因启动子不同长度片段的扩增和表达载体构建
6个正向引物(PGL-22、PGL-102、PGL-274、PGL-534、PGL-995和PGL-1143)和1个下游引物(P1322A)分别扩增出6个长度不同的启动子片段，长度依次为1 301 bp、1 221 bp、1 049 bp、789 bp、328 bp和180 bp (图2)。构建的pGL3-basic重组质粒名字与正向引物名字一一对应，即PGL-22、PGL-102、PGL-274、PGL-534、PGL-995和PGL-1143，经测序确定序列正确。
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图 2 MSTN基因启动子不同长度片段的扩增电泳图电泳顺序：PGL-22、PGL-102、PGL-274、PGL-534、PGL-995、PGL-1143、DL2 000Figure 2. Electrophoretograms of MSTN gene promoter with different lengthsElectrophoresis order: PGL-22, PGL-102, PGL-274, PGL-534, PGL-995, PGL-1143, DL2 0002.3 MSTN启动子活性分析
将构建的6个不同长度缺失片段pGL3-basic重组质粒分别与pRL-TK质粒共转染到HEK293T细胞。pGL3-basic空载体作为阴性对照。荧光素酶活性检测结果见图3，6个启动子片段的pGL3-basic重组载体与阴性对照pGL-basic空载体相比，荧光强度均有显著性差异(P<0.05)。除PGL-22和PGL-274外，其他启动子片段的荧光强度彼此间均有显著性差异(P<0.05)。PGL-534的转录活性最高，其次为PGL-274、PGL-22和PGL-102，最低为PGL-995。
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图 3 MSTN启动子不同长度片段的相对活性相同字母表示差异不显著，不同字母表示差异显著(P<0.05)Figure 3. Relative luciferase activity of MSTN gene with different lengthsThe same letters indicate no significant difference, while different letters indicate significant difference (P<0.05).3. 讨论
启动子是基因的“开关”，决定着基因的活动。通过生物信息学预测启动子上的顺式作用元件和反式作用因子，是研究启动子结构和功能的基础。
本研究对华贵栉孔扇贝MSTN启动子序列进行生物信息学分析，结果显示核心启动子区为–100~–51 bp。华贵栉孔扇贝MSTN启动子包含4个TSS，分别位于起始密码ATG上游的第70、第233、第1 059和第1 299个碱基。栉孔扇贝和人的MSTN启动子有3个TSS[11,19]，但在牛中只有1个[20]。TATA-box是真核生物启动子中重要组成部分，在猪[21]、大黄鱼 (Larimichthys crocea)[22]、栉孔扇贝[11]和华贵栉孔扇贝MSTN启动子中均发现有1个TATA-box，金头鲷 (Sparus aurata) MSTN启动子有2个TATA-box[23]。在大黄鱼和金头鲷MSTN启动子中，还检测到CAAT-box，但在扇贝中均未发现。E-box (核心序列为5'-CANNTG-3')在以上物种MSTN启动子中均检测到，说明E-box在不同物种MSTN启动子区域具有保守性。E-box突变会降低启动子活性[24]。E-box能被生肌调控家族因子(myogenic regular factor，MRFs)中的碱基螺旋-环-螺旋(bHLH)结构特异性识别，从而调控MSTN的转录[25]。
华贵栉孔扇贝MSTN启动子中存在的转录因子结合位点有MEF2、MEF3、FoxO、MTBF和MyoD。在其他物种中也发现有一样的转录因子结合位点，如在栉孔扇贝中发现MEF2和MTBF[11]，在金头鲷中发现MEF2[23]，在猪中发现MEF2和MyoD[21]，在牛中发现MEF2、MyoD和FoxO1[26]。均为肌肉特异性相关的转录因子结合位点，参与MSTN基因的转录和表达[27-28]。MEF2广泛存在于肌肉细胞中，可与许多肌肉特异性基因的启动子结合[29]。MEF2有MEF2A、MEF2B、MEF2C、MEF2D等4种亚型。
CpG岛主要存在于启动子或第一外显子中，在基因表达调控中起负调控作用。本研究未发现华贵栉孔扇贝MSTN启动子存在CpG岛，这与栉孔扇贝MSTN启动子的分析结果相同。
报告基因是检测启动子活性的常用方法。本研究构建了6个不同缺失片段的启动子报告基因，发现它们都有转录活性。这些报告基因均包含核心启动子区域，说明预测的核心启动子区域结果可靠。6个不同缺失片段启动子的转录活性与启动子长度无关。如PGL-534的活性最高，但该序列并不是最长。这说明MSTN启动子序列中有的序列是促进该基因表达的调控元件，有的则是抑制该基因表达的调控元件。这些表达元件在一起产生作用，产生不同的转录活性。如PGL-1143转录活性比PGL-995的强，说明–216~–364 bp区域可能存在负调控基因表达的转录因子结合位点；PGL-995的转录活性远低于PGL-534，说明–364~–825 bp区域可能存在正调控基因表达的转录因子结合位点。这些推论还需要进一步研究证实。
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图 1 水产环境中ARGs的来源、迁移与传播
Figure 1. Source, migration and spread behavior of ARGs in aquaculture environment
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图 2 水产养殖环境中ARGs与抗生素、微生物群落和环境因素之间的关联特性
Figure 2. Correlations between ARGs and antibiotics, microbial communities and environmental factors in aquaculture environment
表 1 现有技术对ARGs的去除效果
Table 1 Reduction efficiency of ARGs by existing technologies
去除技术
Removal technology去除原理
Removal principle去除效果
Reduction efficiency参考文献
Reference添加大孔吸附树脂
Adding macroporous adsorption resin (MAR)MAR是一种多孔交联聚合物，能够降低ARGs和微生物群落的丰度，并且通过吸附重金属以降低其对ARGs的协同效应和选择压力。 ARGs (14.14%~99.44%)和MGEs (47.83%~99.48%)的丰度显著降低。 [101] UV/氯消毒
UV/chlorineUV/氯协同作用可以有效灭活ARB、打破ARGs结构并抑制其水平转移。 UV (320 mJ·cm−2)/氯(2 mg·L−1)协同作用下，ARGs的去除率增强了1~1.5 log。 [102] 臭氧后处理
Ozone post-treatment臭氧具有高氧化电位 (2.07 V)，可以有效去除ARGs和ARB。 胞内ARGs (iARGs)的去除率达到89%。 [103] 高铁酸盐
Ferrate高铁酸盐作为一种高价铁基氧化剂，其强氧化电位能够直接去除ARGs，且具备较强的杀菌效能，能够灭活携带ARGs的细菌，从而抑制其垂直转移。 高铁酸盐的剂量为10 mg-Fe·L−1时，ARGs的去除率达到1.10~4.37 log。 [104] 生物过滤
Biofiltration水体中的微生物会附着在过滤介质 (石英砂、颗粒活性炭和无烟煤等) 表面并形成生物膜。 ARGs平均丰度降低了0.97 log。 [105] 污泥处理湿地
Sludge treatment wetlands (STWs)STWs法是传统沙干化床和垂直流人工湿地的联合技术，剩余污泥进入湿地后会形成不同污泥层，而植物在其中生长，有利于稳定污泥、减少污泥体积并去除ARGs等污染物。 磺胺类ARGs的丰度降低了21%。 [106] 
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