Genomic sequence and virulence evaluation of MN184A-like porcine reproductive and respiratory syndrome virus in Japan.

In this study, a porcine reproductive and respiratory syndrome virus (PRRSV) that was isolated from a 9-week-old diseased pig on a farm in Japan with a high mortality rate during 2007-2008 was characterized. This unique isolate, designated as Jpn5-37, did not have a high nucleotide identity in open reading frame 5 against any Japanese isolates. Among all available type 2 PRRSV complete genome sequences, Jpn5-37 shared the highest nucleotide identity (93.6%) with virulent strain MN184A. The genomic characteristics of Jpn5-37 were highly conserved with respect to the virulent MN184A, including a continuous eight amino acid deletion in the nonstructural protein 2 region. Moreover, virus distribution, viremia and the gross and microscopic characteristics of lesions were investigated in pigs 10 days post-inoculation to elucidate the pathogenicity of the isolate. Intranasal inoculation was found to rapidly result in viremia and dissemination of the Jpn5-37 isolate to several tissues in a similar manner to EDRD1; however, the amounts of Jpn5-37 RNA in serum were significantly greater. Similarly, the quantities of Jpn5-37 viral RNA in all organs tested tended to be higher than with EDRD1 infection. Mean rectal temperatures were significantly higher in the Jpn5-37-inoculated than in the control group at 4 and 6 days post infection (dpi) and in the EDRD1-inoculated group at 6 and 8 dpi. These results suggest that the Jpn5-37 strain replicates and is more efficiently distributed to the organs than is EDRD1 under the same conditions.

A single nucleotide polymorphism of porcine MX2 gene provides antiviral activity against vesicular stomatitis virus.

The objective was to determine if single nucleotide polymorphisms (SNPs) in porcine MX2 gene affect its antiviral potential. MX proteins are known to suppress the multiplication of several viruses, including influenza virus and vesicular stomatitis virus (VSV). In domestic animals possessing highly polymorphic genome, our previous research indicated that a specific SNP in chicken Mx gene was responsible for its antiviral function. However, there still has been no information about SNPs in porcine MX2 gene. In this study, we first conducted polymorphism analysis in 17 pigs of MX2 gene derived from seven breeds. Consequently, a total of 30 SNPs, of which 11 were deduced to cause amino acid variations, were detected, suggesting that the porcine MX2 is very polymorphic. Next, we classified MX2 into eight alleles (A1-A8) and subsequently carried out infectious experiments with recombinant VSVΔG*-G to each allele. In A1-A5 and A8, position 514 amino acid (514 aa) of MX2 was glycine (Gly), which did not inhibit VSV multiplication, whereas in A6 and A7, 514 aa was arginine (Arg), which exhibited the antiviral ability against VSV. These results demonstrate that a SNP at 514 aa (Gly-Arg) of porcine MX2 plays a pivotal role in the antiviral activity as well as that at 631 aa of chicken Mx.

Structural and functional annotation of the porcine immunome.

BACKGROUND: The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the structure and function of genes comprising the pig immunome are not well-characterized. The completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems. RESULTS: The Immune Response Annotation Group (IRAG) used computational curation and manual annotation of the swine genome assembly 10.2 (Sscrofa10.2) to refine the currently available automated annotation of 1,369 immunity-related genes through sequence-based comparison to genes in other species. Within these genes, we annotated 3,472 transcripts. Annotation provided evidence for gene expansions in several immune response families, and identified artiodactyl-specific expansions in the cathelicidin and type 1 Interferon families. We found gene duplications for 18 genes, including 13 immune response genes and five non-immune response genes discovered in the annotation process. Manual annotation provided evidence for many new alternative splice variants and 8 gene duplications. Over 1,100 transcripts without porcine sequence evidence were detected using cross-species annotation. We used a functional approach to discover and accurately annotate porcine immune response genes. A co-expression clustering analysis of transcriptomic data from selected experimental infections or immune stimulations of blood, macrophages or lymph nodes identified a large cluster of genes that exhibited a correlated positive response upon infection across multiple pathogens or immune stimuli. Interestingly, this gene cluster (cluster 4) is enriched for known general human immune response genes, yet contains many un-annotated porcine genes. A phylogenetic analysis of the encoded proteins of cluster 4 genes showed that 15% exhibited an accelerated evolution as compared to 4.1% across the entire genome. CONCLUSIONS: This extensive annotation dramatically extends the genome-based knowledge of the molecular genetics and structure of a major portion of the porcine immunome. Our complementary functional approach using co-expression during immune response has provided new putative immune response annotation for over 500 porcine genes. Our phylogenetic analysis of this core immunome cluster confirms rapid evolutionary change in this set of genes, and that, as in other species, such genes are important components of the pig's adaptation to pathogen challenge over evolutionary time. These comprehensive and integrated analyses increase the value of the porcine genome sequence and provide important tools for global analyses and data-mining of the porcine immune response.

Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence.

BACKGROUND: Along with the draft sequencing of the pig genome, which has been completed by an international consortium, collection of the nucleotide sequences of genes expressed in various tissues and determination of entire cDNA sequences are necessary for investigations of gene function. The sequences of expressed genes are also useful for genome annotation, which is important for isolating the genes responsible for particular traits. RESULTS: We performed a large-scale expressed sequence tag (EST) analysis in pigs by using 32 full-length-enriched cDNA libraries derived from 28 kinds of tissues and cells, including seven tissues (brain, cerebellum, colon, hypothalamus, inguinal lymph node, ovary, and spleen) derived from pigs that were cloned from a sow subjected to genome sequencing. We obtained more than 330,000 EST reads from the 5'-ends of the cDNA clones. Comparison with human and bovine gene catalogs revealed that the ESTs corresponded to at least 15,000 genes. cDNA clones representing contigs and singlets generated by assembly of the EST reads were subjected to full-length determination of inserts. We have finished sequencing 31,079 cDNA clones corresponding to more than 12,000 genes. Mapping of the sequences of these cDNA clones on the draft sequence of the pig genome has indicated that the clones are derived from about 15,000 independent loci on the pig genome. CONCLUSIONS: ESTs and cDNA sequences derived from full-length-enriched libraries are valuable for annotation of the draft sequence of the pig genome. This information will also contribute to the exploration of promoter sequences on the genome and to molecular biology-based analyses in pigs.

Two immune-based methods using immortalized porcine kidney macrophages for quantifying neutralizing activity against porcine reproductive and respiratory syndrome virus-2.

Porcine reproductive and respiratory syndrome virus (PRRSV) causes a serious infectious disease in pigs in farms worldwide. Neutralizing antibody titer is an effective index for evaluating immunity to PRRSV; however, PRRSV has different neutralizing cross-reactivity between strains. Therefore, quantitative measurement of neutralizing antibody titers against field PRRSV strains would be required to evaluate whether neutralizing antibodies in pigs could possess neutralizing activity against individual or multiple strains. Immune-based methods, such as image cytometry (ICM) and cell-based enzyme-linked immune sorbent assay (ELISA), are quantitative and can be used to evaluate many samples. Using immortalized porcine kidney macrophages (IPKMs), which are highly susceptible to infection from field PRRSV-2 strains compared with other cell lines, immune-based methods could enable the evaluation of the neutralizing activity of porcine serum against field strains of PRRSV-2 that are difficult to isolate in conventional cells. In summary, we adapted two methods, namely ICM and cell-based ELISA, to IPKMs for quantitative neutralizing antibody titer measurements. Two immune-based methods using IPKMs are adequate for quantifying neutralizing activity of porcine serum against PRRSV-2, including field strains.

Identification of a second gene associated with variation in vertebral number in domestic pigs.

BACKGROUND: The number of vertebrae in pigs varies and is associated with body size. Wild boars have 19 vertebrae, but European commercial breeds for pork production have 20 to 23 vertebrae. We previously identified two quantitative trait loci (QTLs) for number of vertebrae on Sus scrofa chromosomes (SSC) 1 and 7, and reported that an orphan nuclear receptor, NR6A1, was located at the QTL on SSC1. At the NR6A1 locus, wild boars and Asian local breed pigs had the wild-type allele and European commercial-breed pigs had an allele associated with increased numbers of vertebrae (number-increase allele). RESULTS: Here, we performed a map-based study to define the other QTL, on SSC7, for which we detected genetic diversity in European commercial breeds. Haplotype analysis with microsatellite markers revealed a 41-kb conserved region within all the number-increase alleles in the present study. We also developed single nucleotide polymorphisms (SNPs) in the 450-kb region around the QTL and used them for a linkage disequilibrium analysis and an association study in 199 independent animals. Three haplotype blocks were detected, and SNPs in the 41-kb region presented the highest associations with the number of vertebrae. This region encodes an uncharacterized hypothetical protein that is not a member of any other known gene family. Orthologs appear to exist not only in mammals but also birds and fish. This gene, which we have named vertnin (VRTN) is a candidate for the gene associated with variation in vertebral number. In pigs, the number-increase allele was expressed more abundantly than the wild-type allele in embryos. Among candidate polymorphisms, there is an insertion of a SINE element (PRE1) into the intron of the Q allele as well as the SNPs in the promoter region. CONCLUSIONS: Genetic diversity of VRTN is the suspected cause of the heterogeneity of the number of vertebrae in commercial-breed pigs, so the polymorphism information should be directly useful for assessing the genetic ability of individual animals. The number-increase allele of swine VRTN was suggested to add an additional thoracic segment to the animal. Functional analysis of VRTN may provide novel findings in the areas of developmental biology.

Susceptibility of immortalized porcine kidney macrophages to porcine reproductive and respiratory syndrome virus-2 infection.

Porcine reproductive and respiratory syndrome virus (PRRSV) displays restricted tropism to porcine alveolar macrophages in nature. Meanwhile, non-porcine cell lines derived from African green monkey kidney cell lines are permissive to PRRSV, resulting in their widespread use in PRRSV research. Furthermore, genetically modified cell lines expressing receptors targeted by PRRSV have been established. We previously established porcine immortalized kidney-derived macrophages (IPKMs) that maintained typical macrophage function. In the present study, we demonstrated the advantages of IPKMs for PRRSV research. IPKMs expressed receptors for PRRSV such as CD163 and CD169. The efficiency of virus isolation from field biological samples was higher for IPKMs than for MARC-145 cells. Five different clusters of North American type PRRSV were propagated in IPKMs. Four field strains continuously produced progeny viruses during 10 continuous passages. The efficiency of virus isolation from field biological samples and continuous progeny virus production in the sequential passages using IPKMs indicated that these cells are good vessels for PRRSV research.

Dexamethasone enhances CD163 expression in porcine IPKM immortalized macrophages.

In our previous study, we established a unique porcine macrophage cell line, immortalized porcine kidney-derived macrophages (IPKM). The purpose of the present study was to further elucidate the characteristics of IPKM. CD163 is a scavenger receptor for the hemoglobin-haptoglobin complex and is used as a phenotypic marker of anti-inflammatory M2 macrophages. The expression of CD163 is enhanced by dexamethasone (DEX), a potent steroidal anti-inflammatory drug, in human and rodent macrophages in vitro. Therefore, we investigated the effects of DEX on CD163 expression in porcine IPKM. Treatment with DEX markedly enhanced CD163 expression in the IPKM. In addition, we found that SB203580, a selective inhibitor of p38 mitogen-activated protein kinase (MAPK), blocked the effects of DEX, suggesting that the p38 MAPK signaling pathway is involved in the regulation of the DEX-induced enhancement of CD163 expression. Since CD163 is considered to be a putative receptor for the porcine reproductive and respiratory syndrome virus (PRRSV), the effects of DEX on the infection of IPKM by PRRSV were evaluated. Although the IPKM were susceptible to infection by the Fostera PRRSV vaccine strain, DEX treatment did not affect the propagation of the virus in the IPKM. This suggests that the DEX-induced enhancement of CD163 expression alone is not sufficient to facilitate the infection of IPKM by PRRSV.

Polymorphism distribution and structural conservation in RNA-sensing Toll-like receptors 3, 7, and 8 in pigs.

BACKGROUND: Viral genomic RNA-both single-stranded (ss) and double-stranded (ds)-is recognized by RNA-sensing Toll-like receptors (TLRs), notably TLR3 (dsRNA), TLR7 (ssRNA), and TLR8 (ssRNA). However, our knowledge of the roles of porcine TLR3, 7, and 8 in antiviral immunity is inadequate. METHODS: From information on exon-intron boundaries obtained through comparisons of the genomic and cDNA sequences, polymorphisms in the coding sequences of each gene were detected in 84 male pigs of 11 breeds. RESULTS: Genomic structures are conserved between pigs and humans. The RNA-sensing TLR genes had fewer polymorphisms causing amino acid alterations than did the cell-surface TLR genes, but the alterations were distributed with a similar bias toward ectodomains. CONCLUSIONS: The low level of diversity of substitutive polymorphisms in RNA-sensing TLRs than cell-surface ones implies that polymorphisms severely affecting function have been eliminated by selection pressure during longstanding pig breeding. GENERAL SIGNIFICANCE: Recognition of virus-derived RNA is critical in host defense against infection. These results should provide a useful clue to analysis of the association between polymorphisms in RNA-sensing TLRs and disease resistance.

Cloning, expression, and polymorphisms of natural killer cell receptor NCR1 in pigs.

NCR1 (NKp46) is expressed on the surfaces of natural killer cells and recognizes hemagglutinin on the influenza virus. We cloned the NCR1 gene in pigs and found that porcine NCR1 was minimally expressed in the thymus, suggesting that NCR1 could be a useful marker of natural killer cells in pigs. We observed three nonsynonymous single nucleotide polymorphisms and one deletion of three nucleotides in the coding sequence of porcine NCR1; these may affect the function of NCR1. The polymorphisms detected here may be useful markers for breeding for influenza resistance in pigs.

Molecular cloning and characterization of porcine Mx2 gene.

Mx, an interferon-inducible protein, is found in various vertebrates and confers resistance to several RNA viruses. At least two Mx proteins occur in vertebrates, and these proteins are key components of innate defense against viral infection. In mice and humans, the two Mx genes have different antiviral activities. Both Mx1 and Mx2 have also been detected in pigs, although only a partial sequence of porcine Mx2 has been reported, and there is no information on its antiviral activity. Here, we report the structure of the intact porcine Mx2 gene having an open reading frame of 2136 bp. We also determined the sequence of the genomic region containing the entire porcine Mx2 gene in addition to Mx1 gene. A weak constitutive expression of porcine Mx2 mRNA and endogenous Mx2 protein was observed in interferon-untreated cells. Porcine endogenous Mx2 protein showed nuclear localization. Furthermore, assays using NIH3T3 cells transfected with Mx genes showed that porcine Mx2 possessed antiviral activity against influenza, although this activity was lower than that of human MxA. This report is the first to describe the intact porcine Mx2 gene, which is a functional gene that may play a key role in the clearance of viruses in pigs.

Differences in distribution of single nucleotide polymorphisms among intracellular pattern recognition receptors in pigs.

Pathogens localized extracellularly or incorporated into endosomes are recognized mainly by Toll-like receptors, whereas pathogens and pathogen-derived molecules that invade into the cytoplasm of host cells typically are recognized by intracellular pattern recognition receptors (PRRs), such as retinoic acid-inducible gene (RIG)-like helicases (RLHs) and nucleotide-binding oligmerization domain (NOD)-like receptors (NLRs). RIG-I and melanoma differentiation-associated gene 5 (MDA5), which belong to the RLH family, recognize viral genomic RNA, whereas NOD2, a member of the NLR family, responds to microbial peptidoglycans. These receptors may play an important role in pig opportunistic infectious diseases, such as pneumonia and diarrhea, which markedly impair livestock productivity, such that polymorphisms of these receptor genes are potential targets of pig breeding to increase disease resistance. Here, we report single nucleotide polymorphisms (SNPs) in porcine DDX58, IFIH1, and NOD2, which encode RIG-I, MDA5, and NOD2, respectively. Interestingly, compared with DDX58 and IFIH1, NOD2 abounded in nonsynonymous SNPs both throughout the coding sequence and in sequences encoding domains important for ligand recognition, such as helicase domains for RIG-I and MDA5 and leucine-rich repeats in NOD2. These differences in the distribution of SNPs in intracellular PRRs may parallel the diversity of their ligands, which include nucleic acids and peptidoglycans.

Genomic structure of eight porcine chemokine receptors and intergene sharing of an exon between CCR1 and XCR1.

We completely sequenced a 516,013-bp portion of the porcine genome that encompassed a cluster of genes for chemokine (C-C motif) receptors (CC chemokine receptors). We identified genes for six CC chemokine receptors (CCR1, CCR2, CCR3, CCR5, CCR9, and CCRL2) and two other chemokine receptors (CXCR6 and XCR1) in this region. Clarification of the entire structure of the region and the respective genes revealed their high conservation among human, mouse, and pig. Interestingly, much of the 5'UTR of porcine XCR1 shared an identical sequence with CCR1; this sharing does not occur in humans or mice. This finding suggests a mechanism for posttranscriptional switching of tandem-located genes in mammals that depends on alternative splicing. Furthermore, our findings contribute to analyses of lymphocyte trafficking and the functions of immune cells in pigs and other artiodactyls.

Essential role of the yolk syncytial layer for the development of isolated blastoderms from medaka embryos.

To investigate a possible role of the yolk syncytial layer (YSL) in the development of the medaka embryo, blastoderms were isolated at different stages of embryogenesis either with or without the layer and were incubated in a culture medium. The blastoderms from cleavage stage embryos (stage 8-9), in which the YSL had not yet formed, developed into an irregular mass of cells. But some of the blastoderms isolated with the YSL from the blastula embryos (stage 10) developed into embryo-like structures with apparent body axes and contained differentiated organs, such as the eye, ear, contractile heart, yolk sac-like sphere and posterior body trunk with notochord. The proportion of such explants increased as the developmental stage proceeded. However, the proportion was much smaller when blastoderms were isolated at the blastula stage without the YSL. These results suggest that the YSL is essential for the development of embryonic structures. At stage 12 (early gastrula), the frequency of formation of such structures was the same among blastoderms with or without the YSL, so that these embryos are apparently committed for pattern formation.

Polymorphisms and the antiviral property of porcine Mx1 protein.

We determined the cDNA sequences of the type I interferon-inducible proteins, pig Mx1 from PK(15) and LLC-PK1 cells, and compared the antiviral activities of both Mx proteins, including Mx1 polymorphisms against vesicular stomatitis virus (VSV). Mx1 cDNA derived from PK(15) cells had an 11 bp-deletion in the 3' end of the coding region, and was estimated to encode 8 amino acid substitutions and a 23 amino acid extension compared to that from LLC-PK1 cells. VSV replication was inhibited in the 3T3 cells expressing Mx1 mRNA after the cDNA was transfected. However, the efficiency of this inhibition was not different between the cells expressing Mx1 mRNA from both PK and LLC. These results indicate that pig Mx1 protein confers resistance to VSV.

Concise and broadly applicable method for determining the genomic sequences of North-American-type porcine reproductive and respiratory syndrome viruses in various clusters.

We developed a concise and broadly applicable method for accurate genomic sequencing of North American genotype (NA-type) porcine reproductive and respiratory syndrome viruses (PRRSVs) that overcomes high genetic variability of the viruses. The method, designated "combination of consensus oligonucleotide reverse transcription and multiple displacement amplification" (CORT-MDA), involves reverse-transcription of viral RNA followed by shotgun sequencing after amplification using only 11 degenerate oligonucleotide primers; these primers were designed against consensus regions within the open reading frames of the 124 NA-type PRRSV strains with reported full-length genomic sequences. Sequencing of the 192 shotgun clones generated per virus showed 80% to 94% coverage on the reported PRRSV genomic sequence, such that only 2 or 3 unread regions had to be resequenced after PCR amplification using custom primers. Direct sequencing of RT-PCR products confirmed absolute consistency between sequences determined by the CORT-MDA method and those from RT-PCR. These results suggest that our method is applicable to diverse NA-type viruses.

Genomic survey of polymorphisms in pattern recognition receptors and their possible relationship to infections in pigs.

Recent progress in the accumulation of pig genomic information has enabled us to comprehensively explore polymorphisms in pig genes. One of our targets for exploration has been the genes encoding molecules related to pathogen recognition, such as pattern recognition receptors (PRRs). PRRs play a role in the innate immune system, and possess various members such as Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-like helicases (RLHs), and C-type lectin-like receptors (CLRs). PRRs are required for the monitoring of pathogens; therefore, polymorphisms in PRRs may influence molecular functions such as ligand recognition. There have been many studies on the relationship between polymorphisms within PRR genes and disease susceptibility in humans and mice. Our studies have revealed that porcine PRR genes possess many nonsynonymous polymorphisms, particularly in regions encoding the ectodomains of TLRs localized on the cell surface. The genes encoding TLRs located on the membrane of intracellular compartments, and cytoplasmic PRRs such as NLRs and RLHs, also possessed nonsynonymous polymorphisms. Several observations indicate that there are relationships between polymorphisms in PRR or related genes and disease susceptibility in livestock animals including pig. Such information may contribute to breeding aimed at disease resistance, and effective vaccine design.

A rapid and cost-effective method for sequencing pooled cDNA clones by using a combination of transposon insertion and Gateway technology.

Large-scale cDNA-sequencing projects require an efficient strategy for mass sequencing. Here we describe a method for sequencing pooled cDNA clones using a combination of transposon insertion and Gateway technology. Our method reduces the number of shotgun clones that are unsuitable for reconstruction of cDNA sequences, and has the advantage of reducing the total costs of the sequencing project.

Polymorphisms in pattern recognition receptors and their relationship to infectious disease susceptibility in pigs.

BACKGROUND: Pattern recognition receptors (PRRs), including Toll-like receptors (TLRs), are censoring receptors for molecules derived from bacteria, viruses, and fungi. The PRR system is a prerequisite for proper responses to pathogens, for example by cytokine production, resulting in pathogen eradication. Many cases of polymorphisms in PRR genes affecting the immune response and disease susceptibility are known in humans and mice. METHODS: We surveyed polymorphisms in pig genes encoding PRRs and investigated the relationship between some of the detected polymorphisms and molecular function or disease onset. RESULTS: Nonsynonymous polymorphisms abounded in pig TLR genes, particularly in the region corresponding to the ectodomains of TLRs expressed on the cell surface. Intracellular TLRs such as TLR3, TLR7, and TLR8, and other intracellular PRRs, such as the peptidoglycan receptor NOD2 and viral RNA receptors RIG-I and MDA5, also possessed nonsynonymous polymorphisms. Several of the polymorphisms influenced molecular functions such as ligand recognition. Polymorphisms in the PRR genes may be related to disease susceptibility in pigs: pigs with a particular allele of TLR2 showed an increased tendency to contract pneumonia. CONCLUSIONS: We propose the possibility of pig breeding aimed at disease resistance by the selection of PRR gene alleles that affect pathogen recognition.

Genomic sequence encoding diversity segments of the pig TCR delta chain gene demonstrates productivity of highly diversified repertoire.

To better understand the function and diversity of gammadelta T cells, we determined the genomic sequence encoding diversity (D) segments of the porcine TCR delta chain and its upstream regions, because pigs and other artiodactyls have relatively high proportions of gammadelta T cells. The revealed sequence contained 28 variable (V) alpha/delta segments, including 4 TRDV1 and at least 6 Ddelta segments, a much higher number than in humans and mice. All 6 of the Ddelta segments that had canonical recombination signal sequences were functionally utilized in expressed TCR delta chain genes. The multiplicity of Ddelta segments enabled the use of more than 3 Ddelta segments in a single functional TCR delta chain. The increased number of TCR delta segments was acquired by the duplication of the germline sequence, which occurred after the divergence of artiodactyls from primates and rodents. These data demonstrate that the pig is able to generate a highly diversified repertoire of TCR delta chain molecules.