Abstract
Porcine reproductive and respiratory syndrome (PRRS) has devastated pig industries worldwide for many years. It is caused by a small RNA virus (PRRSV), which targets almost exclusively pig monocytes or macrophages. In the present study, five SAGE (serial analysis of gene expression) libraries derived from 0 hour mock-infected and 6, 12, 16 and 24 hours PRRSV-infected porcine alveolar macrophages (PAMs) produced a total 643,255 sequenced tags with 91,807 unique tags. Differentially expressed (DE) tags were then detected using the Bayesian framework followed by gene/mRNA assignment, arbitrary selection and manual annotation, which determined 699 DE genes for reactome analysis. The DAVID, KEGG and REACTOME databases assigned 573 of the DE genes into six biological systems, 60 functional categories and 504 pathways. The six systems are: cellular processes, genetic information processing, environmental information processing, metabolism, organismal systems and human diseases as defined by KEGG with modification. Self-organizing map (SOM) analysis further grouped these 699 DE genes into ten clusters, reflecting their expression trends along these five time points. Based on the number one functional category in each system, cell growth and death, transcription processes, signal transductions, energy metabolism, immune system and infectious diseases formed the major reactomes of PAMs responding to PRRSV infection. Our investigation also focused on dominant pathways that had at least 20 DE genes identified, multi-pathway genes that were involved in 10 or more pathways and exclusively-expressed genes that were included in one system. Overall, our present study reported a large set of DE genes, compiled a comprehensive coverage of pathways, and revealed system-based reactomes of PAMs infected with PRRSV. We believe that our reactome data provides new insight into molecular mechanisms involved in host genetic complexity of antiviral activities against PRRSV and lays a strong foundation for vaccine development to control PRRS incidence in pigs.
Highlights
Porcine reproductive and respiratory syndrome (PRRS), known as Mystery Swine Disease, Blue Ear Disease, Porcine Endemic Abortion and Respiratory Syndrome (PEARS) and Swine Infertility Respiratory Syndrome (SIRS), was first reported in USA in 1987 and in Europe in 1990 [1,2]
Five serial analysis of gene expression (SAGE) libraries constructed from the 0 hour mock-infected and 6, 12, 16 and 24 hour PRRSV-infected cells produced a total of 643,255 sequenced tags, which allowed identification of 91,807 unique tags among these five time points (Figure 1)
As porcine alveolar macrophages (PAMs) were infected with PRRSV, we anticipated the existence of viral mRNA tags in the cells
Summary
Porcine reproductive and respiratory syndrome (PRRS), known as Mystery Swine Disease, Blue Ear Disease, Porcine Endemic Abortion and Respiratory Syndrome (PEARS) and Swine Infertility Respiratory Syndrome (SIRS), was first reported in USA in 1987 and in Europe in 1990 [1,2]. PRRSV causes severe reproductive failure of the sow, including third-trimester abortions, early farrowing with stillborns, mummies, neonatal death and weak piglets, agalactia and mastitis, and prolonged anoestrus and delayed return to estrus post-weaning. Respiratory disease is the major clinical sign in neonatal pigs and is characterized by fever, interstitial pneumonia, eyelid edema, periocular edema, blue discoloration of the ears and shaking [3,4]. The mortality in neonatal pigs infected with PRRSV can reach 100%. Some PRRSV-infected boars demonstrate a loss of libido, lethargy, lowered sperm volume and decreased fertility
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