Preferential interaction of the mRNA proofreading factor TFIIS zinc ribbon with rU·dA base pairs correlates with its function

The transcriptional factor TFIIS helps overcome elongation barriers and enhances proofreading by RNA polymerase II. These TFIIS functions may be modulated by the TFIIS zinc ribbon domain through interactions with nucleic acids in the elongation complex. Within this zinc ribbon domain, the dipeptide...

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Main Authors: Sitikov, Albert S., Yoon, Ho Sup, Jeon, Choon Ju, Agarwal, Kan
Other Authors: School of Biological Sciences
Format: Article
Language:English
Published: 2012
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Online Access:https://hdl.handle.net/10356/94267
http://hdl.handle.net/10220/7472
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spelling sg-ntu-dr.10356-942672020-03-07T12:18:17Z Preferential interaction of the mRNA proofreading factor TFIIS zinc ribbon with rU·dA base pairs correlates with its function Sitikov, Albert S. Yoon, Ho Sup Jeon, Choon Ju Agarwal, Kan School of Biological Sciences DRNTU::Science::Biological sciences::Biochemistry The transcriptional factor TFIIS helps overcome elongation barriers and enhances proofreading by RNA polymerase II. These TFIIS functions may be modulated by the TFIIS zinc ribbon domain through interactions with nucleic acids in the elongation complex. Within this zinc ribbon domain, the dipeptide sequences Asp261-Glu262 and Arg276-Trp277 have been shown to be critical for its function by mutant analysis. The sequence Asp261-Glu262 has been suggested to participate in metal binding within the RNA polymerase II active site. We now show that the sequence Arg276-Trp277 interacts with nucleic acids through a combination of electrostatic and stacking interactions. The interaction of the indole side chain of the tryptophan residue with nucleic acid bases is demonstrated by a characteristic and reversible decrease in the zinc ribbon fluorescence intensity as a function of oligonucleotide concentration. These interactions are salt sensitive (maximum interaction at 200 mM and no interaction at 500 mM NaCl), suggesting that the tryptophan stacking with nucleic acid base accompanies electrostatic contacts. The oligonucleotide−zinc ribbon interactions exhibit small but significant base preferences, as shown by the dependence of Keq on base composition, with decreasing Keq in the order U > T > A > C >> G. Within the variety of homopolymeric single- and double-stranded deoxy- and ribooligonucleotides, the oligonucleotide rU12-18·dA20 exhibited a 2−6-fold binding preference relative to other oligonucleotides. This preferential binding of the zinc ribbon to sequences composed of rU·dA base pairs, which are generally associated with elongation blocks, may help in overcoming elongation barriers. Since the mRNA proofreading and enhancement of elongation involve cleavage of ribonucleotide of the mismatched pair and the weakly paired rU·dA nucleotides, but not the stably paired rC·dG nucleotides, we propose that the Arg276-Trp277 sequence in the TFIIS zinc ribbon may serve as a scanner connected to the transcript cleavage apparatus for weakly paired or mismatched nucleotides by employing indole ring stacking with the bases as a criterion of determining their subsequent removal. The striking similarity in preference for mismatched and weakly paired nucleotides for binding and for excision suggests a functional relationship between binding and cleavage reactions. 2012-01-25T05:58:55Z 2019-12-06T18:53:32Z 2012-01-25T05:58:55Z 2019-12-06T18:53:32Z 1998 1998 Journal Article Yoon, H., Sitikov, A. S., Jeon, C., & Agarwal, K. (1998). Preferential Interaction of the mRNA Proofreading Factor TFIIS Zinc Ribbon with rU·dA Base Pairs Correlates with Its Function. Biochemistry, 37(35), 12104-12112. https://hdl.handle.net/10356/94267 http://hdl.handle.net/10220/7472 10.1021/bi980924n en Biochemistry © 1998 American Chemical Society.
institution Nanyang Technological University
building NTU Library
country Singapore
collection DR-NTU
language English
topic DRNTU::Science::Biological sciences::Biochemistry
spellingShingle DRNTU::Science::Biological sciences::Biochemistry
Sitikov, Albert S.
Yoon, Ho Sup
Jeon, Choon Ju
Agarwal, Kan
Preferential interaction of the mRNA proofreading factor TFIIS zinc ribbon with rU·dA base pairs correlates with its function
description The transcriptional factor TFIIS helps overcome elongation barriers and enhances proofreading by RNA polymerase II. These TFIIS functions may be modulated by the TFIIS zinc ribbon domain through interactions with nucleic acids in the elongation complex. Within this zinc ribbon domain, the dipeptide sequences Asp261-Glu262 and Arg276-Trp277 have been shown to be critical for its function by mutant analysis. The sequence Asp261-Glu262 has been suggested to participate in metal binding within the RNA polymerase II active site. We now show that the sequence Arg276-Trp277 interacts with nucleic acids through a combination of electrostatic and stacking interactions. The interaction of the indole side chain of the tryptophan residue with nucleic acid bases is demonstrated by a characteristic and reversible decrease in the zinc ribbon fluorescence intensity as a function of oligonucleotide concentration. These interactions are salt sensitive (maximum interaction at 200 mM and no interaction at 500 mM NaCl), suggesting that the tryptophan stacking with nucleic acid base accompanies electrostatic contacts. The oligonucleotide−zinc ribbon interactions exhibit small but significant base preferences, as shown by the dependence of Keq on base composition, with decreasing Keq in the order U > T > A > C >> G. Within the variety of homopolymeric single- and double-stranded deoxy- and ribooligonucleotides, the oligonucleotide rU12-18·dA20 exhibited a 2−6-fold binding preference relative to other oligonucleotides. This preferential binding of the zinc ribbon to sequences composed of rU·dA base pairs, which are generally associated with elongation blocks, may help in overcoming elongation barriers. Since the mRNA proofreading and enhancement of elongation involve cleavage of ribonucleotide of the mismatched pair and the weakly paired rU·dA nucleotides, but not the stably paired rC·dG nucleotides, we propose that the Arg276-Trp277 sequence in the TFIIS zinc ribbon may serve as a scanner connected to the transcript cleavage apparatus for weakly paired or mismatched nucleotides by employing indole ring stacking with the bases as a criterion of determining their subsequent removal. The striking similarity in preference for mismatched and weakly paired nucleotides for binding and for excision suggests a functional relationship between binding and cleavage reactions.
author2 School of Biological Sciences
author_facet School of Biological Sciences
Sitikov, Albert S.
Yoon, Ho Sup
Jeon, Choon Ju
Agarwal, Kan
format Article
author Sitikov, Albert S.
Yoon, Ho Sup
Jeon, Choon Ju
Agarwal, Kan
author_sort Sitikov, Albert S.
title Preferential interaction of the mRNA proofreading factor TFIIS zinc ribbon with rU·dA base pairs correlates with its function
title_short Preferential interaction of the mRNA proofreading factor TFIIS zinc ribbon with rU·dA base pairs correlates with its function
title_full Preferential interaction of the mRNA proofreading factor TFIIS zinc ribbon with rU·dA base pairs correlates with its function
title_fullStr Preferential interaction of the mRNA proofreading factor TFIIS zinc ribbon with rU·dA base pairs correlates with its function
title_full_unstemmed Preferential interaction of the mRNA proofreading factor TFIIS zinc ribbon with rU·dA base pairs correlates with its function
title_sort preferential interaction of the mrna proofreading factor tfiis zinc ribbon with ru·da base pairs correlates with its function
publishDate 2012
url https://hdl.handle.net/10356/94267
http://hdl.handle.net/10220/7472
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