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Chapter 26 : Effects of Picornavirus Proteinases on Host Cell Transcription

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Effects of Picornavirus Proteinases on Host Cell Transcription, Page 1 of 2

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Abstract:

Poliovirus (PV) is known to shut off both host cell transcription and translation. It is believed that the shutoff of host cell transcription in PV-infected cells increases the pool of free ribonucleotides that the PV-encoded RNA-dependent RNA polymerase (Pol) uses to transcribe and replicate the viral genomic RNA. In support of this theory, PV first shuts off Pol I-mediated transcription in the cell that accounts for greater than 50% of all host cell transcription. The authors have used in vitro transcription systems for understanding the mechanism by which PV shuts off host cell transcription catalyzed by RNA Pol I, II, and III. Infection of susceptible cells with PV results in rapid and dramatic changes in macromolecular metabolism, including the shutoff of host cell transcription. Early attempts to identify the cellular components of the transcriptional machinery inactivated by picornavirus infection focused on the polymerases. To examine whether 3C is sufficient to cause inhibition of host cell transcription seen in virus-infected cells, 3C was cloned into the eukaryotic expression vector pCDNA. The role of the 3C protease in host cell transcription shutoff is clear from both genetic and biochemical analyses. PV is an RNA virus, which replicates in the cytoplasm of infected cells. To shut off host cell transcription, one or more viral gene products must enter the nucleus of the infected host cell. The viral precursor 3CD has protease activity and is able to autocatalyze the formation of 3C and 3D polypeptides.

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26

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Small Nuclear RNA
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RNA Polymerase II
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Figures

Image of FIGURE 1
FIGURE 1

Schematic diagram of preinitiation complex assembly for RNA Pol II, Pol I, and Pol III transcription. (A) Basal and activated transcription complex formation at the TATA box is shown. TBP plus five TAFs constitute TFIID. TFIIA through TFIIF are general transcription factors. Pol II is RNA polymerase II. Activator proteins (AP) bind to upstream activator sites and interact with the basal complex (indicated by two-headed arrow) to promote activated transcription. Single-headed arrow shows transcription start site. (B) RNA Pol I transcription requires cooperative binding of UBF and SL1 (TBP plus three TAFs) to rRNA promoter. (C) RNA Pol III transcription requires binding of TFIIIC to B-box internal promoter and recruitment of TFIIIB (TBP plus TAFs) and Pol III.

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26
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Image of FIGURE 2
FIGURE 2

Effect of purified 3C on basal and activated transcription. Nuclear extracts prepared from uninfected HeLa cells were treated with -expressed and purified 3C before being used in an in vitro transcription reaction. (A) TATA-, (B) TATA-plus-INR-, (C) SPl-plus-TATA-, and (D) SPl-plus-INR-mediated transcription was determined in the absence (lanes 1) or presence of bacterially expressed purified wild-type 3Cpro (lanes 2) or an inactive protease mutant, 3C-147S (lanes 3).

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26
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Image of FIGURE 3
FIGURE 3

Sequence and potential poliovirus protease cleavage sites in TBR (A) Predicted amino acid sequence of human TBP is shown. Three glutamine-glycine (QG) sites are boxed, and a tyrosine-glycine (YG) site is circled. The lower panel shows predicted size of TBP if it is cleaved by 3C at the QG sites and by 2A at the YG site. The predicted molecular mass of TBP is 37.4 kDa, but the apparent molecular mass in our sodium dodecyl sulfate gels is 41 kDa. (B) Western blot analysis of recombinant purified TBP treated with recombinant purified 2A and 3C. Bacterially expressed and purified TBP (lane 1) was incubated with increasing amounts of 2A (lanes 2 to 4) or Δ2Α (lane 5), 3C (lane 7), or both 2A and 3C (lane 6). 2Apro alone was also run alongside as a control (lane 8). Mock- and PV-infected HeLa cell extracts (lanes 9 and 10, respectively) were also analyzed. The position of full-length TBP is indicated by an arrow. The positions of 3C- and 2A-cleaved TBP are indicated by a square and an asterisk, respectively.

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26
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Image of FIGURE 4
FIGURE 4

Inhibition of basal transcription by PV. Transcription from the (A) TATA and (B) TATA plus INR in cell extracts prepared from mock-infected (M), wild-type PV-infected (P), and PV Sei 3C-02 mutant-infected (S) cells is shown.

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26
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Image of FIGURE 5
FIGURE 5

Restoration of transcription by TBR Recombinant TBP was added to mock-infected and PV-infected cell extracts. These TBP-supplemented extracts were then used for in vitro transcriptional analysis. The DNA templates used for transcription contained (A) SP1 plus TATA, (B) SP1 plus INR, and (C) INR plus TATA sequence elements. Transcription reactions were performed with mock-infected nuclear extract (lanes 1) and mock-infected nuclear extracts supplemented with increasing amounts of TBP (lanes 2 and 3). Transcription reactions were also performed with PV-infected extracts prepared 4 h postinfection (lanes 4) and PV-infected extracts supplemented with increasing amounts of TBP (lanes 5 and 6). The amount of TBP added is indicated at the top. Panel Β has the pBR/Hpall marker in the far-left lane.

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26
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Image of FIGURE 6
FIGURE 6

Restoration of transcription by TBP in heat-inactivated PV-infected extracts. Transcription from (A) TATA + SP1 and (B) TATA promoter was carried out in either unheated or heated (47°C for 15 min) mock-infected (M) or PV-infected (PV) cell extract in the presence or absence of purified TBP as indicated.

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26
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Image of FIGURE 7
FIGURE 7

Gel retardation analysis of TBP binding to the TATA box following 3C treatment. Gel retardation assays were performed with purified TBP without 3C (lane 1) or treated with 1, 4, or 8 µg of 3C (lanes 2 through 4) or 8 µg of bovine serum albumin (BSA) (lane 5). Lane 6 contained 8 µg of 3C but not TBP.

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26
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Image of FIGURE 8
FIGURE 8

(A) Predicted amino acid sequence and potential 3C cleavage sites in CREB. Two glutamine-glycine (QG) sites are boxed. (B) Identification of the 3C cleavage site in CREB. Site-diiected mutagenesis was used to replace the QG pairs at positions 172 and 187 with valine-aspartate pairs. The wild type (WT; lanes 1 and 2) and mutants CI (position 172; lanes 3 and 4) and C2 (position 187; lanes 5 and 6) were translated in the presence of [S]methionine. The in vitro translated proteins were incubated with buffer (–; lanes 1, 3, and 5) or purified 3C ( + ; lanes 2, 4, and 6). Labeled products were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The positions of molecular mass (in kilodaltons) markers are indicated on the left, and the positions of full-length CREB and cleaved products are indicated by arrows on the right.

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26
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Image of FIGURE 9
FIGURE 9

(A) Modular structure of the transcriptional activator, Oct-1. Three domains, the N-terminal transcription-activation domain (Dl), the DNA-binding domain (homeodomain) (DII), and the C-terminal domain (Dili), are shown. The numbers at the bottom indicate positions of amino acids constituting each domain. Numbers at the top indicate potential QG cleavage sites. The position of Oct-1 (amino acids 723 to 743) shown near the C terminus was used for the preparation of antibodies to Oct-1. (B) Western blot analysis of Oct-1 treated with 3C Mock-infected nuclear extracts (M) were incubated with 0.1, 1, and 4 µ.g of 3C (lanes 3, 4, and 5, respectively) or 4 µg of heat-treated 3C (lane 6) at 30°C for 4 h. Mock-infected and PV-infected extracts prepared 3 h postinfection were also run on the same gel (lanes 1 and 2, respectively). Position of the full-length Oct-1 is indicated by an arrow and that of cleaved Oct- 1 is indicated by an asterisk. The sizes of the molecular weight markers are on the left in kilodaltons. (C) Western blot analysis of purified Oct-1 treated with recombinant, purified 3CPurified Oct-1 was treated with buffer (lane 3) or 4 µg of 3C (lane 4). Lanes 1 and 2 show Western blot analysis of mock-infected or PV-infected extracts prepared 3 h postinfection.

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26
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Image of FIGURE 10
FIGURE 10

Poliovirus 3C protease mediates shutoff of RNA Pol III transcription. (A) In vitro transcription analysis of cell extracts prepared at different times after infection of cells with wild-type or Sel 3C-02 mutant PV. The numbers at the top indicate time of infection or mock infection. The correctly initiated VA I transcript position is indicated. (B) Gel retardation analysis of B-box binding activity of extracts (4, 8, and 12 µg) from HeLa cells infected for 5.5 h with wild-type or the 3C mutant virus Sel 3C-02. (C) In vitro transcriptional analysis of TFIIIC treated directly with 3C. Untreated, 3C-treated, or mutant (C147S) 3C-treated TFIIIC was added to reactions containing TFIIIB and Pol III. The VA I transcript is shown. (D) Transcription analysis of TFIIIC recovered from nuclear extracts of cells transfected with no DNA (lane 1), 3Cpro DNA (lanes 2, 3, and 4), 3C DNA in reverse orientation (lane 5), and pUC18 vector (lane 6). Lane 7 is the same as lane 4 except purified TFIIIC was added to the reaction before the start of transcription.

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26
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Image of FIGURE 11
FIGURE 11

(A) Fragments of TFIIIC used to generate antisera. The TFIIICα amino acid sequence is diagrammed; the fragments shown below were expressed as His-tagged polypeptides in and used to generate antisera. The positions of QG bonds, preferred cleavage sites for PV 3C, are indicated above the diagram. (B) Mapping of the N-terminal 3C cleavage site in TFIIICα. Immunoblots were performed with Ab2 on uncleaved PC-C (lane 1), 3C-cleaved PC-C (lane 2), and in vitro transcribed and translated pTMIIICα1-732 (lane 3) and pTMIIICαl-740 (lane 4).

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26
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Image of FIGURE 12
FIGURE 12

Kinetics of inhibition of rRNA transcription correlates with alteration in UCE complex mobility. (A) Pol 1 transcription (indicated by large arrowhead) was examined in extracts prepared from mock-infected (4 h, M4) and PV-infected HeLa cells at 2, 3, and 4 h postinfection (P, P, P). (B) Gel retardation analysis was performed using cell-free extracts and [P]UMP-labeled promoter sequence (lanes 1 to 4). Specificity of protein binding to the promoter was examined by competition gel retardation analysis with mock (lanes 5 to 7) and PV-infected extract (lanes 8 to 10) and addition of no RNA (lanes 5 and 8), unlabeled UCE RNA (lanes 6 and 9), and nonspecific RNA (lanes 7 and 10).

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26
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Image of FIGURE 13
FIGURE 13

Schematic diagram of preinitiation complex assembly for RNA Pol III- and Pol II-catalyzed SnRNA transcription. (A) Basal transcription from Pol Ill-catalyzed U6 SnRNA transcription requires cooperative binding of TBP to TATA box and SNAPc to the PSE. Activated transcription requires interaction (shown by double-headed arrow) of the basal complex formed at the PSE with the activator Oct-1 bound at the DSE. Single-headed arrow shows transcription start site. (B) RNA Pol II-catalyzed basal transcription from the U2 SnRNA promoter requires binding of SNAPc to PSE and possibly binding of other general Pol II factors. Activated transcription requires interaction (double-headed arrow) between Oct-1 bound to DSE with the basal complex at PSE.

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26
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Tables

Generic image for table
TABLE 1

Summary of transcription factors cleaved by poliovirus proteases 3C and 2A

ND, not determined.

Citation: Dasgupta A, Yalamanchili P, Clark M, Kliewer S, Fradkin L, Rubinstein S, Das S, Shen Y, Weidman M, Banerjee R, Datta U, Igo M, Kundu P, Barat B, Berk A. 2002. Effects of Picornavirus Proteinases on Host Cell Transcription, p 321-335. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch26

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