Deletion Clones Research Articles

CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells.

The pluripotency of embryonic stem cells (ESCs) is maintained by a small group of master transcription factors including Oct4, Sox2 and Nanog. These core factors form a regulatory circuit controlling the transcription of a number of pluripotency factors including themselves. Although previous studies have identified transcriptional regulators of this core network, the cis-regulatory DNA sequences required for the transcription of these key pluripotency factors remain to be defined. We analyzed epigenomic data within the 1.5 Mb gene-desert regions around the Sox2 gene and identified a 13kb-long super-enhancer (SE) located 100kb downstream of Sox2 in mouse ESCs. This SE is occupied by Oct4, Sox2, Nanog, and the mediator complex, and physically interacts with the Sox2 locus via DNA looping. Using a simple and highly efficient double-CRISPR genome editing strategy we deleted the entire 13-kb SE and characterized transcriptional defects in the resulting monoallelic and biallelic deletion clones with RNA-seq. We showed that the SE is responsible for over 90% of Sox2 expression, and Sox2 is the only target gene along the chromosome. Our results support the functional significance of a SE in maintaining the pluripotency transcription program in mouse ESCs.

Disruption of microRNA-21 by TALEN leads to diminished cell transformation and increased expression of cell–environment interaction genes

MicroRNA-21 is dysregulated in many cancers and fibrotic diseases. Since miR-21 suppresses several tumor suppressor and anti-apoptotic genes, it is considered a cancer therapeutic target. Antisense oligonucleotides are commonly used to inhibit a miRNA; however, blocking miRNA function via an antagomir is temporary, often only achieves a partial knock-down, and may be complicated by off-target effects. Here, we used transcription activator-like effector nucleases (TALENs) to disrupt miR-21 in cancerous cells. Individual deletion clones were screened and isolated without drug selection. Sequencing and quantitative RT-PCR identified clones with no miR-21 expression. The loss of miR-21 led to subtle but global increases of mRNAs containing miR-21 target sequences. Cells without miR-21 became more sensitive to cisplatin and less transformed in culture and in mouse xenografts. In addition to the increase of PDCD4 and PTEN protein, mRNAs for COL4A1, JAG1, SERPINB5/Maspin, SMAD7, and TGFBI – all are miR-21 targets and involved in TGFβ and fibrosis regulation – were significantly upregulated in miR-21 knockout cells. Gene ontology and pathway analysis suggested that cell–environment interactions involving extracellular matrix can be an important miR-21 pathogenic mechanism. The study also demonstrates the value of using TALEN-mediated microRNA gene disruption in human pathobiological studies.

Generation of Human Immunodeficiency Virus–1 Long Terminal Repeat Reporter Genes by Rapid Polymerase Chain Reaction–Mediated Mutagenesis

Objective: The development of a human immunodeficiency virus (HIV)–1 promoter reporter system is critical for investigating transcription activity of the virus. We designed a modified overlap extension PCR method for single round site-directed mutagenesis of the long terminal repeat (LTR) segment of HIV-1. Methods: The procedure consists of overlap extension PCR, DpnI digestion, and product transformation. Wild-type and serial sequence deletion clones of HIV-1 LTR were constructed. Basal transcription activity was also measured. Results: The overall efficiency for obtaining the desired products was 53.2%. The reporter assay indicated the importance of the second NF-ĸB cis-element and surrounding regions in mediating the regulation of HIV-1 transcription. Conclusion: The technique we investigated is suitable for highthroughput functional studies of virus-host interaction.

Molecular characterization and intermolecular interaction of coat protein of Prunus necrotic ringspot virus: implications for virus assembly

Coat protein (CP) and RNA3 from Prunus necrotic ringspot virus (PNRSV-rose), the most prevalent virus infecting rose in India, were characterized and regions in the coat protein important for self-interaction, during dimer formation were identified. The sequence analysis of CP and partial RNA 3 revealed that the rose isolate of PNRSV in India belongs to PV-32 group of PNRSV isolates. Apart from the already established group specific features of PV-32 group member's additional group-specific and host specific features were also identified. Presence of methionine at position 90 in the amino acid sequence alignment of PNRSV CP gene (belonging to PV-32 group) was identified as the specific conserved feature for the rose isolates of PNRSV. As protein-protein interaction plays a vital role in the infection process, an attempt was made to identify the portions of PNRSV CP responsible for self-interaction using yeast two-hybrid system. It was found (after analysis of the deletion clones) that the C-terminal region of PNRSV CP (amino acids 153-226) plays a vital role in this interaction during dimer formation. N-terminal of PNRSV CP is previously known to be involved in CP-RNA interactions, but our results also suggested that N-terminal of PNRSV CP represented by amino acids 1-77 also interacts with C-terminal (amino acids 153-226) in yeast two-hybrid system, suggesting its probable involvement in the CP-CP interaction.

Promoter variants in the MSMB gene associated with prostate cancer regulate MSMB/NCOA4 fusion transcripts.

Beta-microseminoprotein (MSP)/MSMB is an immunoglobulin superfamily protein synthesized by prostate epithelial cells and secreted into seminal plasma. Variants in the promoter of the MSMB gene have been associated with the risk of prostate cancer (PCa) in several independent genome-wide association studies. Both MSMB and an adjacent gene, NCOA4, are subjected to transcriptional control via androgen response elements. The gene product of NCOA4 interacts directly with the androgen receptor as a co-activator to enhance AR transcriptional activity. Here, we provide evidence for the expression of full-length MSMB-NCOA4 fusion transcripts regulated by the MSMB promoter. The predominant MSMB-NCOA4 transcript arises by fusion of the 5'UTR and exons 1-2 of the MSMB pre-mRNA, with exons 2-10 of the NCOA4 pre-mRNA, producing a stable fusion protein, comprising the essential domains of NCOA4. Analysis of the splice sites of this transcript shows an unusually strong splice acceptor at NCOA4 exon 2 and the presence of Alu repeats flanking the exons potentially involved in the splicing event. Transfection experiments using deletion clones of the promoter coupled with luciferase reporter assays define a core MSMB promoter element located between -27 and -236 of the gene, and a negative regulatory element immediately upstream of the start codon. Computational network analysis reveals that the MSMB gene is functionally connected to NCOA4 and the androgen receptor signaling pathway. The data provide an example of how GWAS-associated variants may have multiple genetic and epigenetic effects.

Molecular Fingerprinting of Hsp27 Anti‐Apoptotic Activity

Apoptosis is an evolutionarily conserved mechanism crucial to the homeostasis of cell numbers, tissue development, and immune response. Several checkpoints regulate the activation of apoptosis, including heat shock protein 27 (Hsp27), an anti‐apoptotic regulator that blocks several steps in the apoptotic cascade. However, the structural basis for this protective effect remains unknown.Increased cardiomyocyte (CM) apoptosis contributes to cardiovascular disease (CVD) in doxorubicin (dox)‐treated cancer patients. CM apoptosis requires the activation of caspase‐3, a key evolutionarily conserved protease. We showed that Hsp27 associates with and inhibits caspase‐3, but the exact mechanisms remain unknown. The goal of this study was to determine the structural‐functional relationships responsible for the anti‐apoptotic activity of Hsp27. Serial deletion clones of Hsp27 were used to fingerprint the Hsp27 domains responsible for the association with caspase‐3 and inhibition of apoptosis. We identified different molecular signatures responsible for caspase‐3 association and the regulation of cytochrome c. These findings contribute to the understanding of Hsp27 anti‐apoptotic function and will aid in the development of anti‐apoptotic peptide therapies for the prevention of CVD in cancer patients.This research was funded by AHA SURF and ASC URS to JCT and RO1 HL075040 and NSF‐MCB 0542244 to AID

The p19 protein of Grapevine Algerian latent virus is a determinant of systemic infection of Chenopodium quinoa

A previous study showed that both Grapevine Algerian latent virus (GALV) and Tomato bushy stunt virus (TBSV) systemically infect Nicotiana benthamiana, but GALV causes systemic infection whereas TBSV causes only local lesions in Chenopodium quinoa (C. quinoa). We recently isolated GALV strain Naju (GALV-N) from Limonium sinense and TBSV strain Sacheon (TBSV-S) from tomato. Both viruses belong to the genus Tombusvirus and have a similar genome organization. To identify determinants of systemic infection of GALV-N in C. quinoa in the current study, we generated infectious clones and capsid protein (CP)-deletion clones for the two viruses and confirmed that CP of GALV-N is required for systemic infection of C. quinoa due to its primary structural role in virus assembly. Through the use of chimeras, we identified a viral factor in addition to CP that contributes to systemic infection by GALV-N. Inactivation of the p19 demonstrated that host-specific activities of p19 are necessary for efficient systemic infection of C. quinoa by GALV-N. Our study is the first report to determine the viral factors required for systemic infection of GALV in C. quinoa.

Viral Interferon Regulatory Factors Are Critical for Delay of the Host Immune Response against Rhesus Macaque Rhadinovirus Infection

Kaposi's sarcoma-associated herpesvirus (KSHV) and the closely related gamma-2 herpesvirus rhesus macaque (RM) rhadinovirus (RRV) are the only known viruses to encode viral homologues of the cellular interferon (IFN) regulatory factors (IRFs). Recent characterization of a viral IRF (vIRF) deletion clone of RRV (vIRF-knockout RRV [vIRF-ko RRV]) demonstrated that vIRFs inhibit induction of type I and type II IFNs during RRV infection of peripheral blood mononuclear cells. Because the IFN response is a key component to a host's antiviral defenses, this study has investigated the role of vIRFs in viral replication and the development of the immune response during in vivo infection in RMs, the natural host of RRV. Experimental infection of RMs with vIRF-ko RRV resulted in decreased viral loads and diminished B cell hyperplasia, a characteristic pathology during acute RRV infection that often develops into more severe lymphoproliferative disorders in immune-compromised animals, similar to pathologies in KSHV-infected individuals. Moreover, in vivo infection with vIRF-ko RRV resulted in earlier and sustained production of proinflammatory cytokines and earlier induction of an anti-RRV T cell response compared to wild-type RRV infection. These findings reveal the broad impact that vIRFs have on pathogenesis and the immune response in vivo and are the first to validate the importance of vIRFs during de novo infection in the host.

Maximal transcriptional activation of piscine soluble Toll-like receptor 5 by the NF-κB subunit p65 and flagellin

Toll-like receptor 5 (TLR5), which is highly conserved from lower to higher vertebrates, is an important pattern recognition receptor (PRR) for bacterial flagellin. However, a soluble form of TLR5 (TLR5S) was identified in fish that is not present in mammals. To better understand the transcriptional regulation of TLR5S gene in fish, we determined the TLR5S 5′-flanking sequence region from flounder ( Paralichthys olivaceus) and assayed its promoter activity in Hirame natural embryo (HINAE) cells. The 5′-flanking region of TLR5S (715 bp) contains sequence elements for two AP-1 binding sites, two C/EBP sites, and one NF-κB site. To elucidate the functional significance of these sites, deletion clones and a site-directed mutant of NF-κB were generated. We estimated the luciferase activity in flagellin- or lipopolysaccharide-stimulated HINAE cells. The co-transfection of p65 with the wild-type TLR5S promoter greatly increased luciferase activity by more than nine-fold compared with the NF-κB mutant. Wild-type TLR5S promoter activity was increased synergistically by more than 159.5-fold in the presence of flagellin and p65. Furthermore, it was determined that the level of TRL5S mRNA was up-regulated by p65 and flagellin using a quantitative PCR. Additionally, translocation of TLR5S in the HINAE-TLR5S stable cell line after flagellin stimulation was observed by confocal microscopy. These results suggest that NF-κB and flagellin are essential components that act as a transcription factor and ligand, respectively, for maximal induction of the TLR5S promoter.

Liposome-based DNA carriers may induce cellular stress response and change gene expression pattern in transfected cells

BackgroundDuring functional studies on the rat stress-inducible Hspa1b (hsp70.1) gene we noticed that some liposome-based DNA carriers, which are used for transfection, induce its promoter activity. This observation concerned commercial liposome formulations (LA), Lipofectin and Lipofectamine 2000. This work was aimed to understand better the mechanism of this phenomenon and its potential biological and practical consequences.ResultsWe found that a reporter gene driven by Hspa1b promoter is activated both in the case of transient transfections and in the stably transfected cells treated with LA. Using several deletion clones containing different fragments of Hspa1b promoter, we found that the regulatory elements responsible for most efficient LA-driven inducibility were located between nucleotides -269 and +85, relative to the transcription start site. Further studies showed that the induction mechanism was independent of the classical HSE-HSF interaction that is responsible for gene activation during heat stress. Using DNA microarrays we also detected significant activation of the endogenous Hspa1b gene in cells treated with Lipofectamine 2000. Several other stress genes were also induced, along with numerous genes involved in cellular metabolism, cell cycle control and pro-apoptotic pathways.ConclusionsOur observations suggest that i) some cationic liposomes may not be suitable for functional studies on hsp promoters, ii) lipofection may cause unintended changes in global gene expression in the transfected cells.

In this issue: Proteomics 9/2009

AbstractIn this issue of Proteomics you will find the following highlighted articles:Rafting on the pondIt seems that any river with a drop of more than 20‐30 cm/km is a candidate for a commercially viable rafting business. Biochemical rafters are pickier. They need a detergent‐resistant lipid raft where they can set up their signaling system. Kim et al. examined the changes in the raft molecules involved in insulin stimulated pre‐adipocyte to adipocyte differentiation (adipogenesis). A substantial number of adipocyte raft‐specific proteins were identified by immunoblots and confirmed by 2‐DE MS. A protein of particular interest was gC1qR, specific for mature adipocyte rafts, which also binds complement C1q and a number of other extracellular proteins (vitronectin, fibrinogen, hyaluronic acids . . .). Down‐regulation of gC1qR by siRNA was paralleled by reduction of insulin signaling through gC1qR, through the insulin receptor, and prevented adipogenesis. The rafts also were home to a variety of mitochondrial proteins during adipogenesis.Kim, K.‐B. et al., Proteomics 2009, 9, 2373‐2382.E. coli chaperone SurA is recognizedSurA was a sad protein. It was sad because it couldn't get promoted without proof that it had done a good job on its current assignment. But what was that assignment? Being a good little protein, it did its best to never make a mistake and its good was very good, making thousands of perfect cycles. Still, no‐one noticed. Then one day, Vertommen et al. decided to give SurA a rest (actually its clone rested). After creating the deletion clone, they fired up the proteome machines to see what had changed. The lab was quiet as the proteomers collected their results. They sat down with the data and looked and talked, studied and talked. They finally came to a conclusion: SurA was indeed a chaperone and was responsible for transport of eight important bbarrel proteins across the periplasmic space to the outer membrane! And now a publication!Vertommen, D.. et al., Proteomics 2009, 9, 2432‐2443.Aphid saliva: solvent, glue, caulk, . . .Children learn quickly that if they don't wash their faces properly, a mother's wet thumb will finish the job. If hair won't stay where it belongs, you can always use saliva. Spots on your glasses or your computer monitor? Aphids and mosquitoes extend the uses even further. Carolan et al. report on the active components of saliva of the pea aphid (Acrythosiphon pisum), an agricultural pest that attacks legumes. The researchers used mass spectrometry, RNAi, and various types of electrophoresis to identify the nine proteins secreted in pea aphid saliva. From the complete genome sequence, four proteins could be identified by homology: a metalloprotease [M2], a zinc [M1] protease, both probably cleaving plant defensive peptides, a glucose oxidoreductase that probably detoxifies phytochemicals, and a relative of regucalsin, which might suppress Ca+2 mediated defense. Three of the proteins could not be matched to any known proteins.Carolan, J. C. et al., Proteomics 2009, 9, 2457‐2467.

Cover Picture: Proteomics 9/2009

AbstractIn this issue of Proteomics you will find the following highlighted articles:Rafting on the pondIt seems that any river with a drop of more than 20‐30 cm/km is a candidate for a commercially viable rafting business. Biochemical rafters are pickier. They need a detergent‐resistant lipid raft where they can set up their signaling system. Kim et al. examined the changes in the raft molecules involved in insulin stimulated pre‐adipocyte to adipocyte differentiation (adipogenesis). A substantial number of adipocyte raft‐specific proteins were identified by immunoblots and confirmed by 2‐DE MS. A protein of particular interest was gC1qR, specific for mature adipocyte rafts, which also binds complement C1q and a number of other extracellular proteins (vitronectin, fibrinogen, hyaluronic acids . . .). Down‐regulation of gC1qR by siRNA was paralleled by reduction of insulin signaling through gC1qR, through the insulin receptor, and prevented adipogenesis. The rafts also were home to a variety of mitochondrial proteins during adipogenesis.Kim, K.‐B. et al., Proteomics 2009, 9, 2373‐2382.E. coli chaperone SurA is recognizedSurA was a sad protein. It was sad because it couldn't get promoted without proof that it had done a good job on its current assignment. But what was that assignment? Being a good little protein, it did its best to never make a mistake and its good was very good, making thousands of perfect cycles. Still, no‐one noticed. Then one day, Vertommen et al. decided to give SurA a rest (actually its clone rested). After creating the deletion clone, they fired up the proteome machines to see what had changed. The lab was quiet as the proteomers collected their results. They sat down with the data and looked and talked, studied and talked. They finally came to a conclusion: SurA was indeed a chaperone and was responsible for transport of eight important bbarrel proteins across the periplasmic space to the outer membrane! And now a publication!Vertommen, D.. et al., Proteomics 2009, 9, 2432‐2443.Aphid saliva: solvent, glue, caulk, . . .Children learn quickly that if they don't wash their faces properly, a mother's wet thumb will finish the job. If hair won't stay where it belongs, you can always use saliva. Spots on your glasses or your computer monitor? Aphids and mosquitoes extend the uses even further. Carolan et al. report on the active components of saliva of the pea aphid (Acrythosiphon pisum), an agricultural pest that attacks legumes. The researchers used mass spectrometry, RNAi, and various types of electrophoresis to identify the nine proteins secreted in pea aphid saliva. From the complete genome sequence, four proteins could be identified by homology: a metalloprotease [M2], a zinc [M1] protease, both probably cleaving plant defensive peptides, a glucose oxidoreductase that probably detoxifies phytochemicals, and a relative of regucalsin, which might suppress Ca+2 mediated defense. Three of the proteins could not be matched to any known proteins.Carolan, J. C. et al., Proteomics 2009, 9, 2457‐2467.

Tolfenamic Acid Increases EGR‐1 Expression through a PKC/ERK Dependent Pathway in Human Colorectal Cancer Cells

Considerable evidence indicates that the use of non‐steroidal anti‐inflammatory drugs (NSAIDs) reduces the mortality of colorectal cancer in a cyclooxygenase (COX)‐independent manner. Tolfenamic acid (TA) has been selected as a potent chemopreventive agent for cancer therapy because of its inhibitory effect on tumorigenesis in pancreatic cancer models. In the present study, we sought to the anti‐cancer effect of TA in human colorectal cancer. The mechanisms by which TA affects anti‐tumorigenesis involve the induction of the proapoptotic protein EGR‐1 in human colorectal cancer cells. TA treatment inhibited cell proliferation and induced apoptosis in HCT‐116 cells. Electrical impedance study showed that TA resulted in a decrease of the normalized impedance components which reflect increasing numbers of apoptotic cells. Ectopic expression of EGR‐1 increased apoptosis, and siRNA of EGR‐1 reduced TA‐induced apoptosis. TA treatment induced approximately 5.5‐fold induction of luciferase activity of EGR‐1 promoter. Subsequently, the results of the luciferase assay using internal deletion clones showed that the EBS and CREB/ATF binding sites in the EGR‐1 promoter are required for TA‐induced EGR‐1 transactivation. Experiments using kinase inhibitors and siRNA transfection implied the involvement of the PKC/ERK pathway in TA‐induced EGR‐1 expression. These results demonstrate a role of EGR‐1 in TA‐induced anti‐tumorigenesis in human colorectal cancer cells.

The Dystonia-associated Protein TorsinA Modulates Synaptic Vesicle Recycling

The loss of a glutamic acid residue in the AAA-ATPase (ATPases associated with diverse cellular activities) torsinA is responsible for most cases of early onset autosomal dominant primary dystonia. In this study, we found that snapin, which binds SNAP-25 (synaptosome-associated protein of 25,000 Da) and enhances the association of the SNARE complex with synaptotagmin, is an interacting partner for both wild type and mutant torsinA. Snapin co-localized with endogenous torsinA on dense core granules in PC12 cells and was recruited to perinuclear inclusions containing mutant DeltaE-torsinA in neuroblastoma SH-SY5Y cells. In view of these observations, synaptic vesicle recycling was analyzed using the lipophilic dye FM1-43 and an antibody directed against an intravesicular epitope of synaptotagmin I. We found that overexpression of wild type torsinA negatively affects synaptic vesicle endocytosis. Conversely, overexpression of DeltaE-torsinA in neuroblastoma cells increases FM1-43 uptake. Knockdown of snapin and/or torsinA using small interfering RNAs had a similar inhibitory effect on the exo-endocytic process. In addition, down-regulation of torsinA causes the persistence of synaptotagmin I on the plasma membrane, which closely resembles the effect observed by the overexpression of the DeltaE-torsinA mutant. Altogether, these findings suggest that torsinA plays a role together with snapin in regulated exocytosis and that DeltaE-torsinA exerts its pathological effects through a loss of function mechanism. This may affect neuronal uptake of neurotransmitters, such as dopamine, playing a role in the development of dystonic movements.

LPT1 Encodes a Membrane-bound O-Acyltransferase Involved in the Acylation of Lysophospholipids in the Yeast Saccharomyces cerevisiae

Phospholipids are major components of cellular membranes that participate in a range of cellular processes. Phosphatidic acid (PA) is a key molecule in the phospholipid biosynthetic pathway. In Saccharomyces cerevisiae, SLC1 has been identified as the gene encoding lysophosphatidic acid acyltransferase, which catalyzes PA synthesis. However, despite the importance of PA, disruption of SLC1 does not affect cell viability (Nagiec, M. M., Wells, G. B., Lester, R. L., and Dickson, R. C. (1993) J. Biol. Chem. 268, 22156-22163). We originally aimed to identify the acetyl-CoA:lyso platelet-activating factor acetyltransferase (lysoPAF AT) gene in yeast. Screening of a complete set of yeast deletion clones (4741 homozygous diploid clones) revealed a single mutant strain, YOR175c, with a defect in lysoPAF AT activity. YOR175c has been predicted to be a member of the membrane-bound O-acyltransferase superfamily, and we designated the gene LPT1. An Lpt1-green fluorescent protein fusion protein localized at the endoplasmic reticulum. Other than lysoPAF AT activity, Lpt1 catalyzed acyltransferase activity with a wide variety of lysophospholipids as acceptors, including lysophosphatidic acid, lysophosphatidylcholine, lysophosphatidylethanolamine, lysophosphatidylglycerol, lysophosphatidylinositol, and lysophosphatidylserine. A liquid chromatography-mass spectrometry analysis indicated that lysophosphatidylcholine and lysophosphatidylethanolamine accumulated in the Deltalpt1 mutant strain. Although the Deltalpt1 mutant strain did not show other detectable defects, the Deltalpt1 Deltaslc1 double mutant strain had a synthetic lethal phenotype. These results indicate that, in concert with Slc1, Lpt1 plays a central role in PA biosynthesis, which is essential for cell viability.

Identification and functional analysis of the origins of DNA replication in the Cydia pomonella granulovirus genome

The entire genome of Cydia pomonella granulovirus (CpGV) was systematically screened for origins of DNA replication, using an infection-dependent DNA replication assay in the granulovirus-permissive Cydia pomonella cell line, Cp14R. All seven cosmids in an overlapping library that covered the CpGV genome were found to replicate in the assay. A genomic library of 32 overlapping plasmids was subsequently screened. Plasmids that replicated were in turn subcloned into 1-2 kbp overlapping fragments. Eleven subclones replicated, each containing at least one of the 13 single-copy 74-76 bp imperfect palindromes, previously identified in the CpGV genome as possible origins of replication. Genome fragments of 156 bp, each containing one of the 13 palindromes, were cloned to verify replication and provided confirmation that these 13 palindromes are the only origins of replication in the genome. A real-time PCR method was developed for the quantification of DNA replication, which eliminated the need for Southern blotting and hybridization. A set of deletion clones allowed further quantitative characterization of one of the palindromes. The previously proposed non-homologous region origin of replication did not replicate in the assay.

Blocking of Interferon-Induced Jak-Stat Signaling by Japanese Encephalitis Virus NS5 through a Protein Tyrosine Phosphatase-Mediated Mechanism

Japanese encephalitis virus (JEV), a mosquito-borne flavivirus that causes severe human disease, has been shown to block the interferon (IFN)-induced Janus kinase signal transducer and activation of transcription (Jak-Stat) signaling cascade by preventing Tyk2 tyrosine phosphorylation and Stat activation. In this study, we demonstrate that expression of the JEV nonstructural protein NS5 readily blocked IFN-stimulated Jak-Stat signaling events such as Stat1 nuclear translocation and tyrosine phosphorylation of Tyk2 and Stat1. The region of JEV NS5 responsible for Stat1 suppression was identified using various deletion clones. Deletion of 83 N-terminal residues of JEV NS5, but not the 143 C-terminal residues, abolished its ability to block IFN-stimulated Stat1 activation. The role of JEV NS5 as an IFN antagonist was further demonstrated by its ability to block the induction of interferon-stimulated genes and the antiviral effect of IFN-alpha against the IFN-sensitive encephalomyocarditis virus, which appears to replicate and kill cells that express NS5 even with alpha IFN treatment. Furthermore, the molecular mechanism responsible for IFN antagonism by NS5 probably involves protein tyrosine phosphatases (PTPs), as the IFN-blocking events in both JEV-infected and NS5-expressing cells were reversed by sodium orthovanadate, a broad-spectrum inhibitor of PTPs. We suggest that JEV NS5 is an IFN antagonist and that it may play a role in blocking IFN-stimulated Jak-Stat signaling via activation of PTPs during JEV infection.

Characterization of monoclonal antibodies directed against the canine distemper virus nucleocapsid protein

We have established four monoclonal antibodies (MAbs) against the nucleocapsid protein (NP) of canine distemper virus (CDV). A competitive binding assay has revealed that the MAbs are directed against two antigenic domains. An immunofluorescence assay using a series of deletion clones of the NP and an immunoprecipitation assay using the NP have revealed that two of the MAbs recognize the C-terminal region of the NP while the other two recognize the tertiary structure of the N-terminal domain. These MAbs reacted with all eight strains of CDV used in this study, but showed different reactivities against measles virus and rinderpest virus.

Involvement of the LlaKR2I Methylase in Expression of the AbiR Bacteriophage Defense System in Lactococcus lactis subsp. lactis biovar diacetylactis KR2

The native lactococcal plasmid, pKR223, from Lactococcus lactis subsp. lactis biovar diacetylactis KR2 encodes two distinct bacteriophage-resistant mechanisms, the LlaKR2I restriction and modification (R/M) system and the abortive infection (Abi) mechanism, AbiR, that impedes bacteriophage DNA replication. This study completed the characterization of AbiR, revealing that it is the first Abi system to be encoded by three genes, abiRa, abiRb, and abiRc, arranged in an operon and that it requires the methylase gene from the LlaKR2I R/M system. An analysis of deletion and insertion clones demonstrated that the AbiR operon was toxic in L. lactis without the presence of the LlaKR2I methylase, which is required to protect L. lactis from AbiR toxicity. The novelty of the AbiR system resides in its original gene organization and the unusual protective role of the LlaKR2I methylase. Interestingly, the AbiR genetic determinants are flanked by two IS982 elements generating a likely transposable AbiR composite. This observation not only substantiated the novel function of the LlaKR2I methylase in the AbiR system but also illustrated the evolution of the LlaKR2I methylase toward a new and separate cellular function. This unique structure of both the LlaKR2I R/M system and the AbiR system may have contributed to the evolution of the LlaKR2I methylase toward a novel role comparable to that of the cell cycle-regulated methylases that include Dam and CcrM methylases. This new role for the LlaKR2I methylase offers a unique snapshot into the evolution of the cell cycle-regulated methylases from an existing R/M system.

Dimerization of the cardiac ankyrin protein CARP: Implications for MARP titin-based signaling

Cardiac ankyrin repeat protein (CARP) and its two close homologs ankrd2 (Arpp) and DARP correspond to a conserved gene family of muscle ankyrin repeat proteins (MARPs). All three genes respond to a variety of stress/strain injury signals with their cytokine-like induction and can associate with the elastic region of titin/connectin. Recently, both CARP and ankrd2 were observed to be elevated in cardiac diseases as well as muscular dystrophies, implicating their joined signaling in muscle diseases. Here we show that CARP in the yeast two-hybrid system (YTH) interacts with itself and desmin. To further verify the YTH data and to investigate possible CARP subunit structure(s), we expressed CARP in E. coli. Expressed CARP has an apparent mobility of about 70 kDa on gel filtration, corresponding to a dimeric species. Yeast two-hybrid experiments using amino- and carboxyterminal deletion clones suggest that CARP, ankrd2, and DARP contain potential coiled-coil dimerization motifs within their unique aminoterminal domains that mediate the formation of homo-dimers. In contrast, we could not detect the formation of hetero-dimers between CARP, ankrd2, and DARP. Therefore, when CARP, ankrd2 and DARP are upregulated in disease/stress states, they are likely to be sorted into distinct structural protein complexes since CARP within the MARP family contains a unique aminoterminal dimerization motif.