Sequence analysis of the porcine transmissible gastroenteritis coronavirus nucleocapsid protein gene

The 3' end of the 20-kb genome of the Purdue strain of porcine transmissible gastroenteritis coronavirus (TGEV) was copied into cDNA after priming with oligo(dT) and the double-stranded product was cloned into the PstI site of the pUC9 vector. One clone of 2.0-kb contained part of the poly(A) tail and was sequenced in its entirety using the chemical method of Maxam and Gilbert. Another clone of 0.7 kb also contained part of the poly(A) tail and was sequenced in part to confirm the primary structure of the most 3' end of the genome. Two potential, nonoverlapping genes were identified within the 3'-terminal 1663-base sequence from an examination of open reading frames. The first gene encodes a 382-amino acid protein of 43,426 mol wt, that is the apparent nucleocapsid protein on the basis of size, chemical properties, and amino acid sequence homology with other coronavirus nucleocapsid proteins. It is flanked on its 5' side by at least part of the matrix protein gene. The second encodes a hypothetical 78-amino acid protein of 9101 mol wt that is hydrophobic at both ends. A 3'-proximal noncoding sequence of 276 bases was also determined and a conserved stretch of 9 nucleotides near the poly(A) tail was found to be common among TGEV, the mouse hepatitis coronavirus, and the avian infectious bronchitis coronavirus.     

Sequence comparison of the N genes of five strains of the coronavirus mouse hepatitis virus suggests a three domain structure for the nucleocapsid protein

To obtain information about the structure and evolution of the nucleocapsid (N) protein of the coronavirus mouse hepatitis virus (MHV), we determined the entire nucleotide sequences of the N genes of MHV-A59, MHV-3, MHV-S, and MHV-1 from cDNA clones. At the nucleotide level, the N gene sequences of these viral strains, and that of MHV-JHM, were more than 92% conserved overall. Even higher nucleotide sequence identity was found in the 3' untranslated regions (3' UTRs) of the five strains, which may reflect the role of the 3' UTR in negative-strand RNA synthesis. All five N genes were found to encode markedly basic proteins of 454 or 455 residues having at least 94% sequence identity in pairwise comparisons. However, amino acid sequence divergences were found to be clustered in two short segments of N, putative spacer regions that, together, constituted only 11% of the molecule. Thus, the data suggest that the MHV N protein is composed of three highly conserved structural domains connected to each other by regions that have much less constraint on their amino acid sequences. The first two conserved domains contain most of the excess of basic amino acid residues; by contrast, the carboxy-terminal domain is acidic. Finally, we noted that four of the five N genes contain an internal open reading frame that potentially encodes a protein of 207 amino acids having a large proportion of basic and hydrophobic residues.     

Synthesis and subcellular localization of the murine coronavirus nucleocapsid protein

The synthesis and processing of the nucleocapsid protein (pp60) of the JHM strain of murine coronaviruses were examined. Pulse-chase experiments showed that pp60 was synthesized initially as a protein of approximately 57,000 in molecular weight (p57). Immunoprecipitation using mouse anti-JHMV antiserum indicated that p57 was virus specific. Immunoprecipitation with monoclonal antibodies specific for pp60 showed that p57 was antigenically related to pp60 and was not phosphorylated, while the intracellular protein that comigrated with the virion nucleocapsid protein, pp60, was phosphorylated. The p57 was found exclusively in the cytosol while the majority of pp60 was associated with the membrane fraction but pp60 was not an integral membrane protein.     

SARS冠状病毒N蛋白的克隆与表达

目的　克隆和表达SARS冠状病毒N蛋白 ,并分析其免疫学活性。方法　采用RT PCR从SARS冠状病毒RNA中扩增出编码N蛋白的基因 ;经克隆和测序分析后 ,亚克隆至表达载体pGEX 4T 2 ,转化大肠杆菌JM10 9,PCR和双酶切鉴定 ;阳性菌株经IPTG诱导 ,SDS PAGE分析 ;大量诱导表达N蛋白 ,亲和层析予以纯化 ;免疫印迹分析纯化蛋白对SARS的诊断效果 ;用纯化的融合蛋白免疫小鼠观察其诱导的抗体应答。结果　RT PCR扩增出N蛋白基因的特异片段 ,获得的阳性克隆序列与Gen Bank中登录的SARS冠状病毒的N蛋白基因序列同源性为 99.8% ;N蛋白基因被亚克隆到表达载体pGEX 4T 2 ,在JM10 9中表达了N蛋白 ,表达的蛋白经亲和层析获得纯化 ;纯化蛋白能被SARS病人血清识别 ;免疫小鼠诱导产生了高滴度的抗体。结论　成功构建了SARS冠状病毒N蛋白的重组表达质粒 ,在大肠杆菌中表达的N蛋白融合蛋白具有良好的免疫学活性。     

Sequence analysis of the nucleocapsid and phosphoprotein genes of avian pneumoviruses circulating in the US

Avian pneumovirus (APV) has recently been described as the cause of a new respiratory syndrome in turkey flocks in the United States. We here describe the complete sequence of the nucleocapsid (N) and phosphoprotein (P) genes of this emerging APV (APV/US). Our results show 59 and 61% nucleotide sequence identity of the APV/US N gene with N genes of previously described European APV subgroups A and B, respectively. The P gene of APV/US showed only 53% nucleotide sequence identity with the ortholog from APV subgroup A. Phylogenetic analyses of both N and P genes clearly demonstrate that the APV/US lineage is evolutionarily related but distinct from European APVs. Moreover, sequence analysis of the N and P genes from two laboratory adapted isolates of APV/US (APV/MN-1a and APV/MN-1b) and from ten clinical samples from APV-infected turkeys suggests only modest level of amino acid divergence in the N (0-0.3%) and P (0-1.4%) proteins. Taken together, the results of this study indicate support that APV/US represents a new subgroup (subgroup C) of APV and show that there is limited heterogeneity in the N and P genes of APV/US isolates.     

Sequence analysis of the nucleoprotein genes of three enterotropic strains of murine coronavirus

Summary The nucleotide sequences of the nucleoprotein genes of three enterotropic strains of the murine coronavirus mouse hepatitis virus (MHV-Y, MHV-RI and DVIM) were determined and compared with previously reported sequences of three polytropic (respiratory) strains (MHV-A59, MHV-JHM and MHV-S). Greater than 92% homology was found among the six strains by pair-wise comparison at the nucleotide level. The genes encoded proteins of 451 to 455 residues and the deduced amino acid sequences were more than 91% homologous. A unique deletion of twelve nucleotides was found at the carboxy terminus of MHV-Y and a three nucleotide deletion was found in MHV-RI, which corresponded to the one previously reported in MHV-A59 and MHV-S. Two internal open reading frames were found within the coding region of the nucleoprotein, the smaller one was specific for the enterotropic strains. It could potentially encode a truncated version of the hypothetical protein described for MHV-A59 and MHV-S. Sequence relationship of the N gene showed no correlation with tissue tropism and no sequence or even single amino acid change unique to either tropism group was found. This indicates that the nucleoprotein of MHV probably has no part in the determination of the primary tissue tropism of an MHV strain. The role of the potential internal protein warrants further investigation.     

Sequence analysis of the turkey coronavirus nucleocapsid protein gene and 3' untranslated region identifies the virus as a close relative of infectious bronchitis virus

The 3' end of the turkey coronavirus (TCV) genome (1740 bases) including the nucleocapsid (N) gene and 3' untranslated region (UTR) were sequenced and compared with published sequences of other avian and mammalian coronaviruses. The deduced sequence of the TCV N protein was determined to be 409 amino acids with a molecular mass of approximately 45 kDa. The TCV N protein was identical in size and had greater than 90% amino acid identity with published N protein sequences of infectious bronchitis virus (IBV); less than 21% identity was observed with N proteins of bovine coronavirus and transmissible gastroenteritis virus. The 3' UTR showed some variation among the three TCV strains examined, with two TCV strains, Minnesota and Indiana, containing 153 base segments which are not present in the NC95 strain. Nucleotide sequence identity between the 3' UTRs of TCV and IBV was greater than 78%. Similarities in both size and sequence of TCV and IBV N proteins and 3' UTRs provide additional evidence that these avian coronaviruses are closely related.     

Characterization of protein-protein interactions between the nucleocapsid protein and membrane protein of the SARS coronavirus

The human coronavirus, associated with severe acute respiratory syndrome (SARS-CoV), was identified and molecularly characterized in 2003. Sequence analysis of the virus indicates that there is only 20% amino acid (aa) identity with known coronaviruses. Previous studies indicate that protein-protein interactions amongst various coronavirus proteins are critical for viral assembly. Yet, little sequence homology between the newly identified SARS-CoV and those previously studied coronaviruses suggests that determination of protein-protein interaction and identification of amino acid sequences, responsible for such interaction in SARS-CoV, are necessary for the elucidation of the molecular mechanism of SARS-CoV replication and rationalization of anti-SARS therapeutic intervention. In this study, we employed mammalian two-hybrid system to investigate possible interactions between SARS-CoV nucleocapsid (N) and the membrane (M) proteins. We found that interaction of the N and M proteins takes place in vivo and identified that a stretch of amino acids (168-208) in the N protein may be critical for such protein-protein interactions. Importantly, the same region has been found to be required for multimerization of the N protein (He et al., 2004) suggesting this region may be crucial in maintaining correct conformation of the N protein for self-interaction and interaction with the M protein.     

SARS冠状病毒N蛋白单克隆抗体的制备及鉴定

目的 制备SARS冠状病毒(SARS-CoV)N蛋白特异性单克隆抗体(McAb)，为SARS的快速诊断及致病机制的研究提供实验材料。方法 用纯化的重组SARS-CoVN蛋白免疫BALB/c小鼠，经细胞融合和亚克隆后获得分泌针对N蛋白的杂交瘤细胞株，用Western blot和间接免疫荧光法检测这些细胞株分泌的单克隆抗体特异性，并将N蛋白分3段表达初步定位单克隆抗体识别表位所在区域。结果 通过细胞融合和3轮克隆化，筛选出分泌抗N蛋白的6个杂交瘤细胞株。Western blot及免疫荧光显示，获得的McAb可与SARS-CoVN蛋白及SARS-CoV发生特异性反应，有4个细胞株分泌的抗体的识别位点位于N蛋白N端，2个位于C端。结论 获得了SARS-CoV特异性单克隆抗体并进行了初步定位，可用于SARS的早期诊断及致病机制研究。     

Antigenic and cellular localisation analysis of the severe acute respiratory syndrome coronavirus nucleocapsid protein using monoclonal antibodies

A member of the family of coronaviruses has previously been identified as the cause of the severe acute respiratory syndrome (SARS). In this study, several monoclonal antibodies against the nucleocapsid protein have been generated to examine distribution of the nucleocapsid in virus-infected cells and to study antigenic regions of the protein. Confocal microscopic analysis identified nucleocapsids packaged in vesicles in the perinuclear area indicating viral synthesis at the endoplasmic reticulum and Golgi apparatus. The monoclonal antibodies bound to the central and carboxyterminal half of the nucleocapsid protein indicating prominent exposure and immunogenicity of this part of the protein. Antibodies recognised both linear and conformational epitopes. Predictions of antigenicity using mathematical modelling based on hydrophobicity analysis of SARS nucleoprotein could not be confirmed fully. Antibody binding to discontinuous peptides provides evidence that amino acids 274-283 and 373-382 assemble to a structural unit particularly rich in basic amino acids. In addition, amino acids 286-295, 316-325 and 361-367 that represent the epitope recognised by monoclonal antibody 6D11C1 converge indicating a well-structured C-terminal region of the SARS virus nucleocapsid protein and functional relationship of the peptide regions involved. Alternatively, dimerisation of the nucleocapsid protein may result in juxtaposition of the amino acid sequences 316-325 and 361-367 on one nucleoprotein molecule to amino acid 286-295 on the second peptide. The monoclonal antibodies will be available to assess antigenicity and immunological variabilities between different SARS CoV strains.     

In vitro assembly of bovine rotavirus nucleocapsid protein

The nucleocapsid protein (VP6) of bovine rotavirus was purified from in vitro-derived single shelled particles by CaCl2 or LiCl treatment. The protein exhibits polymorphism. Specifically, hexamers and small hexagonal lattices were present in many of the samples. Tubular particles formed between pH 5.0 and 9.0 were moderately stable to changes in temperature and ionic strength and were shown to be composed of nucleocapsid protein. Their formation is fully reversible. Spherical particles resembling single-shelled virus formed at pH 4.0. A novel structure in the form of sheets composed of a small-hole lattice formed in samples shifted from pH 6.0 to 4.0. The results demonstrate the importance of the nucleocapsid protein and of protein-protein interactions for rotavirus assembly.     

APOBEC3G cytidine deaminase association with coronavirus nucleocapsid protein

We previously reported that replacing HIV-1 nucleocapsid (NC) domain with SARS-CoV nucleocapsid (N) residues 2-213, 215-421, or 234-421 results in efficient virus-like particle (VLP) production at a level comparable to that of wild-type HIV-1. In this study we demonstrate that these chimeras are capable of packaging large amounts of human APOBEC3G (hA3G), and that an HIV-1 Gag chimera containing the carboxyl-terminal half of human coronavirus 229E (HCoV-229E) N as a substitute for NC is capable of directing VLP assembly and efficiently packaging hA3G. When co-expressed with SARS-CoV N and M (membrane) proteins, hA3G was efficiently incorporated into SARS-CoV VLPs. Data from GST pull-down assays suggest that the N sequence involved in N-hA3G interactions is located between residues 86 and 302. Like HIV-1 NC, the SARS-CoV or HCoV-229E N-associated with hA3G depends on the presence of RNA, with the first linker region essential for hA3G packaging into both HIV-1 and SARS-CoV VLPs. The results raise the possibility that hA3G is capable of associating with different species of viral structural proteins through a potentially common, RNA-mediated mechanism.     

SARS病毒N蛋白的表达与DNA疫苗的构建

目的：在大肠杆菌中表达SARS冠状病毒核衣壳N蛋白，并构建其DNA疫苗。方法：构建含N基因的原核表达载体pQEN，并在大肠杆菌M15中表达N蛋白。采用NP亲和层析法纯化目的蛋白。将N基因克隆入真核表达载体pSecTagB中，构建真核重组质粒pSecN。以其免疫小鼠制备抗血清，并用ELISA法检测其与大肠杆菌中表达的重组N蛋白及天然全病毒N蛋白的反应性。结果：重组N蛋白能与DNA疫苗免疫的小鼠血清以及SARS患者血清发生特异性反应；SARS—CoV病毒颗粒也可与DNA疫苗免疫的小鼠血清发生特异性反应。结论：重组N蛋白保留了病毒的一些特异性抗原表位，可作为用ELISA法检测SARS—CoV的抗原。构建的DNA疫苗可在小鼠体内产生高效价的抗SARS病毒N蛋白的特异性抗体，从而为该疫苗的开发奠定了基础。     

SARS冠状病毒核衣壳蛋白的重组表达及其单克隆抗体的制备

目的: 表达SARS冠状病毒核衣壳蛋白(N蛋白),并以表达产物为免疫原制备特异性单克隆抗体 (mAb)。方法: 采用RT- PCR方法, 从灭活的病毒抗原标本中扩增编码N蛋白的基因。测序确认后, 再亚克隆至原核表达载体中。从SDS -PAGE凝胶中回收原核表达产物后免疫BALB/c小鼠, 经融合、筛选制备特异性mAb。结果: 从标本中扩增出 1 269bp的DNA, 测序结果证实为N蛋白基因。将该基因克隆至原核表达载体中后, 在大肠杆菌中获得了较好的表达。表达产物经SDS- PAGE后, 在Mr约为 43 000处可见 1条明显的诱导表达带。Westernblot的结果表明, 该电泳带与SARS患者的恢复期血清呈特异的免疫反应。从SDS- PAGE凝胶中回收表达产物并免疫BALB/c小鼠, 制备出 3株抗N蛋白的mAb。这些mAb与SDS- PAGE凝胶上Mr约为 43 000的蛋白带也呈现很强的免疫反应。结论: 所获的重组N蛋白及特异性mAb, 将为进一步建立SARS病毒感染早期诊断的方法奠定了基础。