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非洲豬瘟病毒的基因特征

2020-02-04 07:31謝春芳于瑞嵩董世娟陳冰清
國外畜牧學(xué)·豬與禽 2020年12期
關(guān)鍵詞:復(fù)雜性多樣性

謝春芳 于瑞嵩 董世娟 陳冰清

摘? 要:由非洲豬瘟病毒(African Swine Fever Virus,ASFV)引起的非洲豬瘟(African Swine Fever,ASF)會給豬群的健康造成極其嚴重的危害。ASFV是大分子病毒,基因組成分復(fù)雜而且多變,這是研究ASFV的主要難點之一。ASFV以大分子DNA病毒的獨特方式進行基因的轉(zhuǎn)錄、復(fù)制、翻譯和表達。目前ASFV有超過150個開放閱讀框編碼的結(jié)構(gòu)蛋白和各種酶等,能在宿主細胞中增殖并適應(yīng)宿主細胞中的抗病毒應(yīng)答環(huán)境。了解ASFV的基因特征可以為找到有效控制和治療非洲豬瘟的方法提供基因組學(xué)方面的理論依據(jù)。

關(guān)鍵詞:非洲豬瘟病毒;基因特征;復(fù)雜性;多樣性

中圖分類號:S852.6 文獻標(biāo)志碼:C 文章編號:1001-0769(2020)12-0040-08

非洲豬瘟病毒(African Swine Fever Virus,ASFV)是非洲豬瘟病毒科(Asfarviridae)非洲豬瘟病毒屬(Asfivirus)唯一的成員,是雙鏈DNA大分子病毒,基因組長度介于170 kb~193 kb,編碼150~167個蛋白,其基因組從DNA的兩條鏈上讀取,基因緊密間隔,病毒基因組末端由堿基不完全配對的發(fā)夾環(huán)共價閉合。發(fā)夾環(huán)以兩種形式存在,互補并相互反轉(zhuǎn),與終端相鄰的是多種串聯(lián)的反向重復(fù)序列。大多數(shù)ASFV毒株的基因組GC含量*為38%,GC含量相對較低的區(qū)域位于基因組兩端的左可變區(qū)(Left Variable Region,LVR)和右可變區(qū)(Right Variable Region,RVR),容易發(fā)生基因變異的多基因家族(Multigene Family,MGF)分布于LVR和RVR[1-2]。

1? 與復(fù)制和轉(zhuǎn)錄相關(guān)的基因

細胞被ASFV感染后,病毒DNA開始在細胞核周圍復(fù)制,F(xiàn)1055L蛋白在復(fù)制的起始時結(jié)合DNA,并與DNA起始酶融合。病毒基因組編碼病毒基因轉(zhuǎn)錄和復(fù)制所需的酶、參與DNA堿基切除修復(fù)(Base Excision Repair,BER)途徑的酶、逃逸免疫的酶、多基因家族蛋白(MGF360、MGF110、MGF100、MGF505)、功能性蛋白、結(jié)構(gòu)蛋白和許多目前未知的蛋白。ASFV編碼基因有150多個,ASFV基因編碼早期表達的蛋白主要包括與基因組復(fù)制相關(guān)的蛋白、后期轉(zhuǎn)錄因子及與免疫逃逸相關(guān)的MGFs蛋白;ASFV結(jié)構(gòu)蛋白主要在感染后期表達[3-6]。

ASFV的轉(zhuǎn)錄機制類似于真核RNA聚合酶Ⅱ(RNA polymerase Ⅱ,RNAPⅡ)系統(tǒng),包括一個(8-亞基)ASFV RNAP和TATA結(jié)合蛋白(TATA Binding Protein,TBP)、轉(zhuǎn)錄起始因子Ⅱ B(Transcription Initiation Factor Ⅱ B,TFⅡB)、延伸因子(Transcription Elongation Factor Ⅱ,TFⅡ)以及DNA結(jié)合蛋白pA104R和拓撲異構(gòu)酶Ⅱ pPⅡ92R[3,7-9]。

在感染ASFV的細胞中,病毒顆粒包含早期基因轉(zhuǎn)錄所需的所有酶和因子,病毒基因組轉(zhuǎn)錄不依賴宿主RNA聚合酶。在ASFV基因組中,與轉(zhuǎn)錄起始位點(Transcription Start Site,TSS)重疊的起始子(Initiator,Inr)元件是區(qū)分早期和晚期基因啟動子的一個特征。早期基因Inr是一個TANA四核苷酸基序,其中N沒有核苷酸偏好,ASFV基因的Inr與TSS重疊,早期表達基因啟動子的特征序列是TA(TSS);而晚期基因Inr表現(xiàn)出對序列TATA的強烈偏好,晚期表達基因啟動子的特征是序列TATA(TSS)。早期基因和晚期基因與5-非翻譯區(qū)(5Untranslated Regions,5-UTRs)的長度有關(guān),即mRNA N端與翻譯起始密碼子之間的距離,晚期基因的5-UTR比早期基因的5-UTR短,晚期基因的AT含量高于早期基因的;在TSS的上游有一個保守區(qū),分別對應(yīng)早期啟動子基序(Early Promoter Motif,EPM)和晚期啟動子基序(Late Promoter Motif,LPM),早期保守區(qū)的序列比晚期保守區(qū)的有更高的保守性。ASFV啟動子沒有一致的序列,但是編碼鏈中7個或更多個連續(xù)的胸腺嘧啶殘基(7 thymidylate residues,7T motif)是mRNA C端的形成信號[3,11-13]。

為了維持ASFV基因組的完整性,ASFV進化出了自己的堿基切除修復(fù)(Base Excision Repair,BER)系統(tǒng)。該系統(tǒng)包括abasic(AP)核酸內(nèi)切酶(AP endonuclease)、修復(fù)聚合酶(repair Polymerase,PolX)和連接酶(Ligase,LIG)。這些酶的主要功能是維持病毒基因組的完整性,還在ASFV的基因突變和基因型形成中發(fā)揮重要作用,修復(fù)細胞內(nèi)環(huán)境對ASFV產(chǎn)生的病毒DNA損傷。ASFV PolX包含5-磷酸基團(5-P)結(jié)合囊的結(jié)構(gòu)域,ASFV LIG N端包含DNA結(jié)合域,其中ASFV AP是BER系統(tǒng)中的關(guān)鍵酶,ASFV pE296R基因編碼病毒的AP。AP屬于Ⅱ類AP內(nèi)切酶家族,主要催化無堿基位點AP 5端的DNA裂解反應(yīng),生成3-羥基和5-脫氧核糖磷酸(deoxyRibose Phosphate,dRP)。ASFV AP具有3→5核酸外切酶、3-磷酸二酯酶和核苷酸切割修復(fù)(Nucleotide Incision Repair,NIR)活性,對ASFV在宿主細胞中的存活起著至關(guān)重要的作用,pE296R基因的缺失極大地降低了ASFV在細胞中的生長[14-19]。

2? 與結(jié)構(gòu)蛋白相關(guān)的基因

ASFV的形態(tài)為二十面體,病毒粒子分核心、內(nèi)衣殼、內(nèi)膜、外衣殼和外膜共五層,目前已知有19個基因編碼結(jié)構(gòu)蛋白。

ASFV A104R基因編碼pA104R核蛋白,細胞被ASFV感染后2 h,轉(zhuǎn)錄病毒A104R基因,在感染后期細胞表達pA104R。pA104R是病毒的組蛋白樣蛋白,與DNA高度親和,與DNA結(jié)合位點長約11 nt~20 nt,pA104R上的精氨酸69殘基和脯氨酸74殘基對pA104R結(jié)合DNA的活性起關(guān)鍵作用[20-22]。

ASFV CP2475L基因編碼病毒的多蛋白220(polyprotein 220,pp220),其水解產(chǎn)物是病毒核殼的主要結(jié)構(gòu)蛋白p150、p37、p34和p14;CP530R基因編碼病毒的另一個多蛋白pp62,其主要水解產(chǎn)物是蛋白p35和p15。p150、p37、p34和p14、p35和p15是形成核殼的主要蛋白[23]。

ASFV D117L基因編碼p17蛋白,其既是內(nèi)膜蛋白又是衣殼蛋白;二十面體衣殼蛋白(Capsid protein)包括p72、M1249L、p17、p49和H240R,其中p72是主要的衣殼結(jié)構(gòu)蛋白,編碼基因B646L是晚期表達的蛋白;B438L基因編碼另一個衣殼蛋白p49,其位于二十面體衣殼的頂點,是一個頂點蛋白;M1249L基因編碼的蛋白連接了二十面體中兩個相鄰的五邊體,形成了三邊體的邊[24-26]。

p54蛋白是一個免疫原性衣殼結(jié)構(gòu)蛋白,編碼P54蛋白的基因在編碼區(qū)有兩組串聯(lián)重復(fù)序列(tandem repeat sequence),第一組由15個核苷酸的六次重復(fù)組成,第二組由12個核苷酸的二次不完全重復(fù)組成[27]。

3? 與酶相關(guān)的基因

ASFV基因編碼轉(zhuǎn)錄并加工mRNAs需要的蛋白和酶,其中EP1242L、C147L、NP1450L、H359L、D205R、CP80R編碼6個與RNAⅡ型多聚酶類似的亞基。NP868R基因編碼mRNA帽酶的3個結(jié)構(gòu)域:三磷酸酶、胍基轉(zhuǎn)移酶和甲基轉(zhuǎn)移酶。I226R基因和I243L基因在獨立啟動子的控制下,在ASFV感染的多個階段能轉(zhuǎn)錄多種mRNA[28-29]。

ASFV P1192R基因編碼病毒的Ⅱ型拓撲異構(gòu)酶(topoisomerase Ⅱ),pP1192R酶能夠通過去乙?;饔盟沙贒NA的超螺旋結(jié)構(gòu),P1192R基因在病毒感染后2 h開始轉(zhuǎn)錄,在感染后16 h轉(zhuǎn)錄達到高峰。ASFV B318L基因編碼反式丙烯酰胺轉(zhuǎn)移酶,反式丙烯酰胺轉(zhuǎn)移酶在體外催化法尼基二磷酸和異戊烯基二磷酸縮合合成二磷酸或二磷酸長鏈,B318L基因包含一個氨基末端疏水序列和所有異戊二烯轉(zhuǎn)移酶的特征區(qū)域[30-31]。

ASFV G1211R(G1207R)基因位于96 365 nt~ 99 997 nt,該基因閱讀框內(nèi)的起始密碼子是第2個ATP,而不是第1個ATP,基因序列具有串聯(lián)重復(fù),對磷乙酸敏感。該基因在病毒感染的早期和晚期都表達蛋白,表達α樣DNA螺旋酶,蛋白大小為139.8 KDa,等電點pI為8.2。ASFV RNA螺旋酶pQP509L和pQ706L在病毒感染的中晚期出現(xiàn)。ASFV C962R基因編碼NTP酶,ASFV G1211R基因編碼DNA多聚酶,E301R基因編碼增殖細胞核抗原樣蛋白(Proliferating Cell Nuclear Antigen,PCNA-like protein),該蛋白與DNA多聚酶直接作用于ASFV DNA,鉗住DNA酶到DNA鏈[32-35]。

ASFV O174L基因編碼DNA聚合酶β樣蛋白,一個屬于X族DNA聚合酶的修復(fù)性DNA聚合酶。聚合酶X在病毒感染時能有效通過堿基切除修復(fù)(Base Excision Repair,BER)修復(fù)單核苷酸DNA斷裂,隨著豬巨噬細胞突變頻率的增加,ASFV聚合酶X基因的缺失導(dǎo)致DNA損傷的累積,這種特殊的基因?qū)S持病毒的遺傳信息至關(guān)重要。ASFV I1215L基因編碼病毒的泛素結(jié)合酶,調(diào)節(jié)宿主細胞的泛素-蛋白酶體系統(tǒng)(ubiquitin-proteasome system, UPS)。pI1215L泛素結(jié)合酶能在pH 4~9、4 ℃~42 ℃環(huán)境中始終保持活性。I1215L基因在細胞感染ASFV的早期開始轉(zhuǎn)錄,在感染后2 h和16 h分別達到轉(zhuǎn)錄高峰,pI1215L泛素結(jié)合酶可能參與病毒生命周期的不同階段。在病毒感染的中后期,即病毒DNA復(fù)制、轉(zhuǎn)錄和翻譯的活躍時期,pI1215L泛素結(jié)合酶在細胞質(zhì)內(nèi)的“病毒工廠”內(nèi)可以被檢測到[36-39]。

4? 與免疫相關(guān)的基因

ASFV的免疫抑制及免疫逃避主要與其多基因家族基因編碼的蛋白相關(guān)。ASFV基因組內(nèi)的多樣性主要分布于基因組左右兩端區(qū)域,左端35 kb和右端15 kb的兩個區(qū)域包含了多個多基因家族,包括MGF360、MGF505、MGF110、MGF100、MGF530等。MGF505和MGF360是ASFV的毒力因子,可用于疫苗的設(shè)計;MGF360和MGF505/530能抑制誘導(dǎo)和影響Ⅰ型干擾素的作用;MGF360和MGF505拷貝數(shù)的減少不影響病毒的復(fù)制,但能減弱病毒的毒力;MGF505-7R(A 528R)基因編碼的蛋白抑制Ⅰ型和Ⅱ型干擾素信號途徑,抑制細胞內(nèi)JAK激酶(一類信號分子)和信號轉(zhuǎn)導(dǎo)與轉(zhuǎn)錄激活因子(Signal Transducer and Activator of Transcription,STAT)(一類信號分子)的通路途徑(JAK-STAT passway)以及干擾素刺激基因(Interferon Stimulated Gene,ISG)的表達;MGF110基因包含一個信號肽,是一個多樣性基因,位于基因組LVR,容易發(fā)生基因缺失;MGF基因受其自身啟動子的控制[40-45]。

多基因家族具有相似的序列特征,在不同的基因組中,多家族基因的數(shù)量和序列是可變的。多基因家族成員MGF100、MGF110、MGF300、MGF360、MGF505/530和p22家族成員的得失是ASFV基因組變異最常見的原因,它們位于左端40 kb和右端20 kb內(nèi)。MGF505和MGF360開放閱讀框(Open Reading Frame, ORF)的突變與ASFV的毒力密切相關(guān);ASFV MGF110基因在LVR中的缺失與衰減表型相關(guān)。MGF 110-7 L、MGF 505-5 R、K145R、I267L、DP60R第一個基因發(fā)生G→A突變,但突變是沉默的,對蛋白質(zhì)氨基酸序列沒有任何影響;在MGF505-5R基因中檢測到其他G→A突變,導(dǎo)致纈氨酸突變?yōu)楫惲涟彼?,MGF-505-4R ORF的天冬氨酸突變?yōu)樘於0?MGF 360-16 R ORF插入A后引起與下游編碼DP63R的閱讀框融合;單個堿基非同義突變導(dǎo)致MGF505-9R(賴氨酸突變?yōu)楣劝彼幔﹩我话被崽鎿Q和NP419L(天冬酰胺突變?yōu)榻z氨酸);MGF505-5R的纈氨酸突變?yōu)楫惲涟彼醄46-48]。

5? 基因突變和變異

ASFV p72基因最早用于基因分型。p72基因中A、C、G和T所占的比例分別為: 0.273 3、0.240 8、0.187 4和0.298 6,根據(jù)C端p72基因分類法,ASFV的基因變異多達22種以上。感染基因Ⅱ型ASFV的豬會出現(xiàn)臨床癥狀,感染基因Ⅸ型ASFV的豬則無臨床癥狀。EP402R基因編碼的CD2v是ASFV血紅素吸附及抑制相關(guān)的蛋白,是ASFV血清學(xué)分型的依據(jù)[49-51]。

2014年至2018年,在歐洲和中國的ASFV分離株中發(fā)現(xiàn)了許多不同基因的累積突變。在不同基因和基因間區(qū)域的ASFV分離株中已經(jīng)發(fā)現(xiàn)了多個單核苷酸的變化,包括一些預(yù)測翻譯蛋白的移碼和截短的變化。K145R基因內(nèi)C→A突變導(dǎo)致另一種替代,即絲氨酸突變?yōu)槔野彼?。在I267L基因中發(fā)現(xiàn)了T→A突變,導(dǎo)致異亮氨酸突變?yōu)楸奖彼?。在DP60R基因中檢測到了其序列特有的最后一個變異,單個A的插入引起了閱讀框移位,導(dǎo)致開放閱讀框延長14 nt,編碼O174L的ORF基因序列中有14個堿基插入;在QP383R、KP177R、CP204L和MGF 360-16 R ORFs之間的基因間區(qū)域(位置21 588 nt~24 589 nt)也容易有堿基的插入;QP383R ORF一個堿基的缺失或者一個A的插入使12個連續(xù)密碼子移碼;KP177R ORF中插入A導(dǎo)致了閱讀框移位,從而導(dǎo)致假定的蛋白質(zhì)截短(基因缺失);CP204L ORF中雙重TT插入引起了閱讀框移位,導(dǎo)致終止密碼子的過早出現(xiàn),并導(dǎo)致蛋白質(zhì)C端最后幾個殘基的截短;E184L基因中還檢測到其他獨特的G→A突變;B602Ll基因中的小規(guī)模串聯(lián)重復(fù)序列數(shù)量增加[52-58]。

6? 小結(jié)

綜上所述,ASFV基因組有150多個開放閱讀框,編碼150多個蛋白,其中50多個是結(jié)構(gòu)蛋白;基因組兩端主要編碼與免疫相關(guān)的多基因家族,兩端可變區(qū)LVR和RVR以及中央可變區(qū)的基因容易發(fā)生基因堿基突變和變異。ASFV基因組的數(shù)量龐大而且復(fù)雜、易變,導(dǎo)致對ASFV的研究充滿了挑戰(zhàn)。目前科技界對ASFV的認識還非常有限,還有許多未知基因等待去探索了解。

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