Biomedical subjects

Saumendra N Sarkar

Publications and source records attributed to Saumendra N Sarkar.

12 recordsLinked to original sources

PubMed2006

Two tyrosine residues of Toll-like receptor 3 trigger different steps of NF-kappa B activation.

Innate immune response to viral infection is often triggered by Toll-like receptor 3 (TLR3)-mediated signaling by double-stranded (ds) RNA, which culminates in the activation of the transcription factor NF-kappaB and induction of NF-kappaB-driven genes. We demonstrated that dsRNA-induced phosphorylation of two specific tyrosine residues, 759 and 858, of TLR3 was necessary and sufficient for complete activation of the NF-kappaB pathway. When Tyr-759 of TLR3 was mutated, gene induction was inhibited, although NF-kappaB was partially activated. It was released from IkappaB and translocated to the nucleus but failed to bind to the kappaB site of the target A20 gene promoter. This defect could be attributed to incomplete phosphorylation of the RelA (p65) subunit of NF-kappaB, as revealed by two-dimensional gel analyses of p65, isolated from dsRNA-treated cells expressing either wild type TLR3 or the Tyr-759 --> Phe mutant TLR3. Thus, two phosphotyrosine residues of TLR3 activate two distinct pathways, one leading to NF-kappaB release and the other leading to its phosphorylation.

Cell Line↗

PubMed2005

Natural mutations in a 2'-5' oligoadenylate synthetase transgene revealed residues essential for enzyme activity.

Unlike other RNA polymerases, 2'-5' oligoadenylate synthetases, a family of interferon-induced enzymes, catalyze the formation of 2'-5', not 3'-5', phosphodiester bonds. Moreover, to be active, these proteins require double-stranded RNA as a cofactor. We have been identifying the specific residues of these proteins that impart their novel properties. Here, we report the identity of three such residues that underwent natural mutations in a transgenic mouse line. When deliberately introduced into recombinant proteins, each of these mutations rendered the protein enzymatically inactive. In an effort to understand the roles of these residues in enzyme activity, new mutants carrying other residues in one of these three sites were generated. Detailed characterization of the properties of the mutant proteins revealed that Lys 404 is needed for proper binding of the acceptor substrate, Pro 500 provides structural flexibility to the protein, and Ser 471 is probably required for its proper folding. This study illustrates the power of using natural mutations in transgenes as guides for studying structure-function relationships of proteins.

2',5'-Oligoadenylate Synthetase↗

PubMed2005

Transcriptional signaling by double-stranded RNA: role of TLR3.

Mammalian Toll-like receptors recognize components of invading microbes and trigger the first line of innate immune response that is mediated by transcriptional induction of a large number of cellular genes. Toll-like receptor 3 (TLR3) is thought to be a major mediator of cellular response to viral infection, because it responds to double-stranded (ds) RNA, a common by-product of viral replication. This article is focused on the nature of the signaling pathways activated by TLR3 and dsRNA. The genes induced by TLR3 activation include those that encode secreted antiviral cytokines, such as interferon (IFN), and those that encode intracellular viral stress-inducible proteins. Recent studies have revealed several unique features of TLR3 signaling that are highlighted here. Specifically, we discuss the roles of receptor tyrosine phosphorylation, PI3 kinase and two-step activation of the transcription factors, IRF-3 and NF-kappaB, in mediating TLR3-signaling.

Animals↗

PubMed2005

Hitching RIG to action.

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Adaptor Proteins, Signal Transducing↗

PubMed2005

Assays for the interferon-induced enzyme 2',5' oligoadenylate synthetases.

Inhibition of protein synthesis by interferon treatment is mediated by two major pathways: the 2'-5'-linked oligoadenylates [2-5 (A)] synthetase-RNase L pathway and the double-stranded ribonucleic acid-dependent protein kinase-mediated pathway. 2-5 (A) synthetases are unique interferon-inducible enzymes that, upon activation by double-stranded RNA, polymerize adenosine triphosphate (ATP) to 2-5 (A) synthases. These 2-5 (A) synthetases bind and activate the latent RNase L, causing RNA degradation. In addition to the three major size classes of enzymatically active oligoadenylate synthetase proteins, at least one inactive oligoadenylate synthetase is known in human and mouse. Structure-function studies and recent crystal structure determination have identified several distinct sites in these proteins responsible for different biochemical functions. RNase L is the only known protein that binds to 2-5 (A) synthetases with very high affinity. Gene knockout studies of RNase L have identified its role in antiviral actions of interferon and in apoptosis. Recently, it has also been implicated in prostate cancer metastasis. In this chapter we describe several methodologies for studying biochemical and physiological properties of the 2-5 (A) synthetase-RNase L pathway.

2',5'-Oligoadenylate Synthetase↗

PubMed2004

Novel roles of TLR3 tyrosine phosphorylation and PI3 kinase in double-stranded RNA signaling.

Double-stranded RNA (dsRNA), a frequent byproduct of virus infection, is recognized by Toll-like receptor 3 (TLR3) to mediate innate immune response to virus infection. TLR3 signaling activates the transcription factor IRF-3 by its Ser/Thr phosphorylation, accompanied by its dimerization and nuclear translocation. It has been reported that the Ser/Thr kinase TBK-1 is essential for TLR3-mediated activation and phosphorylation of IRF-3. Here we report that dsRNA-activated phosphorylation of two specific tyrosine residues of TLR3 is essential for initiating two distinct signaling pathways. One involves activation of TBK-1 and the other recruits and activates PI3 kinase and the downstream kinase, Akt, leading to full phosphorylation and activation of IRF-3. When PI3 kinase is not recruited to TLR3 or its activity is blocked, IRF-3 is only partially phosphorylated and fails to bind the promoter of the target gene in dsRNA-treated cells. Thus, the PI3K-Akt pathway plays an essential role in TLR3-mediated gene induction.

Active Transport, Cell Nucleus↗

PubMed2004

Novel functions of proteins encoded by viral stress-inducible genes.

The interferon (IFN) system is the first line of defense against viral infection in vertebrates. It is well known that IFN synthesis is induced by viral infection and secreted IFN act upon as yet uninfected neighboring cells to prepare them for combating oncoming virus infection. The products of IFN-stimulated genes (ISG), which number in hundreds, mediate this antiviral action of IFN. Recent evidence suggests that many of these genes are also induced directly by double-stranded RNA (dsRNA), a common byproduct of virus infection, or by other viral products. We refer to this family of genes, on which this article is focused, as viral stress-inducible genes (VSIG). First, we will discuss the different signaling pathways that lead to induce transcription of these genes in response to different agents. Second, we will review the available information about the inducibility of different VSIG by IFN, dsRNA, and viruses. In this article, we will review the functions of proteins encoded by selected members of the VSIG family. Because most of these proteins affect many aspects of cellular physiology, the information presented here is important for understanding not only the nature of host response to virus infection but also cellular responses to cytokines, such as IFN and exogenous dsRNA, which is known to signal through Toll-like receptor 3 (TLR3). Finally, we will present a future perspective and point out the main gaps of our knowledge in the field.

2',5'-Oligoadenylate Synthetase↗

PubMed2003

Crystal structure of the 2'-specific and double-stranded RNA-activated interferon-induced antiviral protein 2'-5'-oligoadenylate synthetase.

2'-5'-oligoadenylate synthetases are interferon-induced, double-stranded RNA-activated antiviral enzymes which are the only proteins known to catalyze 2'-specific nucleotidyl transfer. This crystal structure of a 2'-5'-oligoadenylate synthetase reveals a structural conservation with the 3'-specific poly(A) polymerase that, coupled with structure-guided mutagenesis, supports a conserved catalytic mechanism for the 2'- and 3'-specific nucleotidyl transferases. Comparison with structures of other superfamily members indicates that the donor substrates are bound by conserved active site features while the acceptor substrates are oriented by nonconserved regions. The 2'-5'-oligoadenylate synthetases are activated by viral double-stranded RNA in infected cells and initiate a cellular response by synthesizing 2'-5'-oligoadenylates, which in turn activate RNase L. This crystal structure suggests that activation involves a domain-domain shift and identifies a putative dsRNA activation site that is probed by mutagenesis, thus providing structural insight into cellular recognition of viral double-stranded RNA.

2',5'-Oligoadenylate Synthetase↗

PubMed2002

Double-stranded RNA signaling by Toll-like receptor 3 requires specific tyrosine residues in its cytoplasmic domain.

Double-stranded (ds) RNA, a common product of viral infection, can induce transcription of many cellular genes, including the 561 gene that encodes P56, a regulator of protein synthesis. Here, we report that induction of the 561 mRNA by exogenous dsRNA is mediated by Toll-like receptor 3 (TLR3), and it requires no new protein synthesis. Because gene induction by dsRNA is blocked by inhibitors of tyrosine kinases, we investigated the potential roles of the five tyrosine residues present in the cytoplasmic domain of TLR3 by their individual and combinatorial mutations. Transfection assays, using a reporter gene driven by the 561 promoter, identified specific tyrosine residues to be essential for TLR3 signaling. This conclusion was further validated in permanent cell lines expressing tyrosine-mutant TLR3 proteins; in some of these cell lines dsRNA failed to induce the 561 mRNA. Our results provide the first demonstration of the importance of TLR3 cytoplasmic tyrosine residues in dsRNA signaling.

Cell Line↗

PubMed2002

Crisscross enzymatic reaction between the two molecules in the active dimeric P69 form of the 2'-5' oligodenylate synthetase.

2'-5' oligoadenylate (2-5 (A)) synthetases are major components of the antiviral pathways induced by interferons. In the presence of double-stranded RNA, they polymerize ATP to form 2-5 (A) oligomers that, in turn, activate the latent ribonuclease RNase L, causing mRNA degradation. These enzymes, unlike other nucleotidyl transferases, catalyze 2'-5', not 3'-5', phosphodiester bond formation between substrates bound to the acceptor and donor sites. Moreover, unlike other members of this extended family, the P69 isozyme of 2-5 (A) synthetase functions as a homodimer. Here, we report that the need for P69 dimerization is because of a crisscross enzyme reaction joining two substrate molecules bound to two opposite subunits. Consequently, although homodimers of mutants in the previously identified acceptor site, the donor site, or the catalytic site were inactive, selective heterodimers of the mutants were active because of subunit complementation. The catalytic site had to be present in the same subunit that contained the acceptor site, whereas the donor site had to be provided by the other subunit. These results allowed us to design a mutant protein that acted as a dominant-negative inhibitor of wt P69 but not of another isozyme of 2-5 (A) synthetase.

2',5'-Oligoadenylate Synthetase↗

PubMed2002

Identification of the substrate-binding sites of 2'-5'-oligoadenylate synthetase.

2'-5'-Oligoadenylate synthetases are interferon-induced enzymes that upon activation by double-stranded RNA polymerize ATP to 2'-5'-linked oligoadenylates. In our continuing effort to understand the mechanism of catalysis by these enzymes, we used photo affinity cross-linking and peptide mapping to identify the substrate-binding sites of the P69 isozyme of human 2'-5'-oligoadenylate synthetases. Radiolabeled azido 2'-5'-oligoadenylate dimers were enzymatically synthesized and used as ligands for cross-linking to the P69 protein by exposure to ultraviolet light. The radiolabeled protein was digested with trypsin, and two ligand-cross-linked peptides were purified by immobilized aluminum affinity chromatography followed by reverse phase high pressure liquid chromatography. The peptides were identified by mass spectrometry and peptide sequencing and were found to correspond to residues 420-425 and 539-547 of P69. To examine the functional importance of the cross-linking sites, specific residues in the two peptides were mutated. When residues in the two sites were mutated individually, ligand cross-linking was selectively eliminated at the mutated site, and the enzyme activity was lost almost completely. Using substrates that can serve either as a donor or as an acceptor but not both, we could identify one of the sites as the acceptor and the other as the donor site.

2',5'-Oligoadenylate Synthetase↗

PubMed2002

The proapoptotic 9-2 isozyme of 2-5 (A) synthetase cannot substitute for the sperm functions of the proapoptotic protein, Bax.

The 9-2 isozyme of 2-5 (A) synthetase has cellular proapoptotic functions that are mediated not by enzyme activity but by the Bcl-2 homology domain 3 present in its unique carboxyl-terminal region. Another proapoptotic cellular protein is Bax, whose absence in the Bax(-/-) mice causes male sterility due to abnormal sperm differentiation. In this study, we examined whether transgenic 9-2 expression can substitute for the in vivo reproductive function of Bax. To achieve this goal, a sperm-specific promoter was used to drive the expression of 9-2 in the sperm of transgenic mice. By selective cross-breeding, the transgene was transferred to Bax(-/-) mice to generate the experimental mouse line (Bax(-/-), 9-2(+/+)). The male experimental mice were sterile, and their testes maintained the structural abnormality found in Bax(-/-) mice. Thus, the male reproduction functions of Bax could not be replaced by the 9-2 isozyme of 2-5 (A) synthetase.

2',5'-Oligoadenylate Synthetase↗