Karasev A V, Boyko V P, Gowda S, Nikolaeva O V, Hilf M E, Koonin E V, Niblett C L, Cline K, Gumpf D J, Lee R F
Citrus Research and Education Center, University of Florida, Lake Alfred 33850-2299, USA.
Virology. 1995 Apr 20;208(2):511-20. doi: 10.1006/viro.1995.1182.
The sequence of the entire genome of citrus tristeza virus (CTV), Florida isolate T36, was completed. The 19,296-nt CTV genome encodes 12 open reading frames (ORFs) potentially coding for at least 17 protein products. The 5'-proximal ORF 1a starts at nucleotide 108 and encodes a large polyprotein with calculated MW of 349 kDa containing domains characteristic of (from 5' to 3') two papain-like proteases (P-PRO), a methyltransferase (MT), and a helicase (HEL). Alignment of the putative P-PRO sequences of CTV with the related proteases of beet yellows closterovirus (BYV) and potyviruses allowed the prediction of catalytic cysteine and histidine residues as well as two cleavage sites, namely Val-Gly/Gly for the 5' proximal P-PRO domain and Met-Gly/Gly for the 5' distal P-PRO domain. The autoproteolytic cleavage of the polyprotein at these sites would release two N-terminal leader proteins of 54 and 55 kDa, respectively, and a 240-kDa C-terminal fragment containing MT and HEL domains. The apparent duplication of the leader domain distinguishes CTV from BYV and accounts for most of the size increase in the ORF 1a product of CTV. The downstream ORF 1b encodes a 57-kDa putative RNA-dependent RNA polymerase (RdRp), which is probably expressed via a +1 ribosomal frameshift. Sequence analysis of the frameshift region suggests that this +1 frameshift probably occurs at a rare arginine codon CGG and that elements of the RNA secondary structure are unlikely to be involved in this process. The complete polyprotein resulting from this frameshift event has a calculated MW of 401 kDa and after cleavage of the two N-terminal leaders would yield a 292-kDa protein containing the MT, HEL, and RdRp domains. Phylogenetic analysis of the three replication-associated domains, MT, HEL, and RdRp, indicates that CTV and BYV form a separate closterovirus lineage within the alpha-like supergroup of positive-strand RNA viruses. Two gene blocks or modules can be easily identified in the CTV genome. The first includes the replicative MT, HEL, and RdRp genes and is conserved throughout the entire alpha-like superfamily. The second block consists of five ORFs, 3 to 7, conserved among closteroviruses, including genes for the CTV homolog of HSP70 proteins and a duplicate of the coat protein gene. The 3'-terminal ORFs 8 to 11 encode a putative RNA-binding protein (ORF 11), and three proteins with unknown functions; this gene array is poorly conserved among closteroviruses.(ABSTRACT TRUNCATED AT 400 WORDS)
柑橘衰退病毒（CTV）佛罗里达分离株T36的全基因组序列已完成测定。该病毒基因组全长19296个核苷酸，编码12个开放阅读框（ORF），可能至少编码17种蛋白质产物。5'端近端的ORF 1a起始于核苷酸108，编码一个计算分子量为349 kDa的大的多聚蛋白，该多聚蛋白包含（从5'到3'）两个类木瓜蛋白酶（P-PRO）、一个甲基转移酶（MT）和一个解旋酶（HEL）的结构域。将CTV假定的P-PRO序列与甜菜黄化病毒（BYV）和马铃薯Y病毒属相关蛋白酶进行比对，可预测出催化性半胱氨酸和组氨酸残基以及两个切割位点，即5'近端P-PRO结构域的Val-Gly/Gly和5'远端P-PRO结构域的Met-Gly/Gly。多聚蛋白在这些位点的自催化切割将分别释放两个N端前导蛋白，分子量分别为54 kDa和55 kDa，以及一个包含MT和HEL结构域的240 kDa C端片段。前导结构域的明显重复使CTV区别于BYV，并导致CTV的ORF 1a产物大部分分子量增加。下游的ORF 1b编码一个57 kDa的假定RNA依赖性RNA聚合酶（RdRp），它可能通过+1核糖体移码表达。移码区域的序列分析表明，这种+1移码可能发生在罕见的精氨酸密码子CGG处，且RNA二级结构元件不太可能参与这一过程。由该移码事件产生的完整多聚蛋白计算分子量为401 kDa，在切割两个N端前导蛋白后将产生一个包含MT、HEL和RdRp结构域的292 kDa蛋白质。对三个与复制相关的结构域MT、HEL和RdRp进行系统发育分析表明，CTV和BYV在正链RNA病毒的α样超群中形成一个独立的长线形病毒谱系。在CTV基因组中可以很容易地识别出两个基因模块。第一个模块包括复制性MT、HEL和RdRp基因，在整个α样超家族中是保守的。第二个模块由5个ORF（3至7）组成，在长线形病毒中保守，包括HSP70蛋白的CTV同源基因和外壳蛋白基因的一个重复拷贝。3'端的ORF 8至11编码一个假定的RNA结合蛋白（ORF 11）和三个功能未知的蛋白；这个基因阵列在长线形病毒中保守性较差。（摘要截短至400字）
