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W2003735948 abstract "Yeast S-II was found to stimulate yeast RNA polymerase II only and not mouse RNA polymerase II. To identify the molecular region of S-II that defines species specificity, we constructed six hybrid S-II molecules consisting of three regions from yeast and/or Ehrlich cell S-II and examined their activity in terms of RNA polymerase II specificity and suppression of 6-azauracil sensitivity in the yeast S-II null mutant. We found that the region 132–270 (amino acid positions) of yeast S-II is indispensable for specific interaction with yeast RNA polymerase II in vitroand for suppression of 6-azauracil sensitivity in vivo. The corresponding region of Ehrlich cell S-II, the region 132–262, was also shown to be essential for its interaction with mouse RNA polymerase II. This region is known to be less conserved than the N- and C-terminal regions in the S-II family suggesting that it is important in the interaction with transcription machinery proteins in a tissue and/or species-specific manner. Yeast S-II was found to stimulate yeast RNA polymerase II only and not mouse RNA polymerase II. To identify the molecular region of S-II that defines species specificity, we constructed six hybrid S-II molecules consisting of three regions from yeast and/or Ehrlich cell S-II and examined their activity in terms of RNA polymerase II specificity and suppression of 6-azauracil sensitivity in the yeast S-II null mutant. We found that the region 132–270 (amino acid positions) of yeast S-II is indispensable for specific interaction with yeast RNA polymerase II in vitroand for suppression of 6-azauracil sensitivity in vivo. The corresponding region of Ehrlich cell S-II, the region 132–262, was also shown to be essential for its interaction with mouse RNA polymerase II. This region is known to be less conserved than the N- and C-terminal regions in the S-II family suggesting that it is important in the interaction with transcription machinery proteins in a tissue and/or species-specific manner. Transcription initiation is a complex process that involves protein-protein and protein-nucleic acid interactions, and factors participating in this process have been extensively characterized (1Buratowski S. Cell. 1994; 77: 1-3Abstract Full Text PDF PubMed Scopus (264) Google Scholar, 2Tjian R. Maniatis T. Cell. 1994; 77: 5-8Abstract Full Text PDF PubMed Scopus (953) Google Scholar, 3Orphanides G. Lagrange T. Reinberg D. Genes Dev. 1996; 10: 2657-2683Crossref PubMed Scopus (843) Google Scholar, 4Roeder R.G. Trends Biochem. Sci. 1996; 21: 327-335Abstract Full Text PDF PubMed Scopus (718) Google Scholar). On the other hand, regulation of gene expression at the transcription elongation level has been less thoroughly studied. Recently, it has become evident that various cellular and viral genes are regulated at the level of transcription elongation (5Spencer C. Groudine M. Oncogene. 1990; 5: 777-785PubMed Google Scholar, 6Kerppola T.K. Kane C.M. FASEB J. 1991; 5: 2833-2842Crossref PubMed Scopus (91) Google Scholar, 7Kane C.M. Conaway R.C. Conaway J.W. Transcription: Mechanisms and Regulation. Raven Press, Ltd., New York1993: 279-296Google Scholar, 8Aso T. Conaway J.W. Conaway R.C. FASEB J. 1995; 9: 1419-1428Crossref PubMed Scopus (55) Google Scholar). Thus, transcription elongation is likely to also be a crucial step for eukaryotic gene expression that involves various transcription elongation factors such as S-II (TFIIS) (9Sekimizu K. Nakanishi Y. Mizuno D. Natori S. Biochemistry. 1979; 18: 1582-1588Crossref PubMed Scopus (56) Google Scholar, 10Natori S. Mol. Cell. Biochem. 1982; 46: 173-187Crossref PubMed Scopus (33) Google Scholar), Elongin (SIII) (11Bradsher J.N. Jackson K.W. Conaway R.C. Conaway J.W. J. Biol. Chem. 1993; 268: 25587-25593Abstract Full Text PDF PubMed Google Scholar,12Aso T. Lane W.S. Conaway J.W. Conaway R.C. Science. 1995; 269: 1439-1443Crossref PubMed Scopus (289) Google Scholar), TFIIF (13Price D.H. Sluder A.E. Greenleaf A.L. Mol. Cell. Biol. 1989; 9: 1465-1475Crossref PubMed Scopus (133) Google Scholar, 14Kephart D.D. Wang B.Q. Burton Z.F. Price D.H. J. Biol. Chem. 1994; 269: 13536-13543Abstract Full Text PDF PubMed Google Scholar, 15Gu W. Reines D. J. Biol. Chem. 1995; 270: 11238-11244Abstract Full Text Full Text PDF PubMed Scopus (70) Google Scholar), and ELL (16Shilatifard A. Lane W.S. Jackson K.W. Conaway R.C. Conaway J.W. Science. 1996; 271: 1873-1876Crossref PubMed Scopus (279) Google Scholar).Transcription elongation factor S-II was originally purified from mouse Ehrlich ascites tumor cells as a specific stimulatory protein of RNA polymerase II, and it was thought to participate in eukaryotic transcription (9Sekimizu K. Nakanishi Y. Mizuno D. Natori S. Biochemistry. 1979; 18: 1582-1588Crossref PubMed Scopus (56) Google Scholar, 10Natori S. Mol. Cell. Biochem. 1982; 46: 173-187Crossref PubMed Scopus (33) Google Scholar, 17Sekimizu K. Kobayashi N. Mizuno D. Natori S. Biochemistry. 1976; 15: 5064-5070Crossref PubMed Scopus (65) Google Scholar, 18Sekimizu K. Yokoi H. Natori S. J. Biol. Chem. 1982; 257: 2719-2721Abstract Full Text PDF PubMed Google Scholar, 19Ueno K. Sekimizu K. Mizuno D. Natori S. Nature. 1979; 277: 145-146Crossref PubMed Scopus (33) Google Scholar). Subsequently, S-II was purified from various organisms and was shown to enable RNA polymerase II to read through blocks of transcription elongation within the transcription units of many eukaryotic genes by promoting cleavage of the 3′-end of the nascent RNA by RNA polymerase II (20Reines D. Chamberlin M.J. Kane C.M. J. Biol. Chem. 1989; 264: 10799-10809Abstract Full Text PDF PubMed Google Scholar, 21Reines D. Ghanoumi P. Li Q. Mote Jr., J. J. Biol. Chem. 1992; 267: 15516-15522Abstract Full Text PDF PubMed Google Scholar, 22Reines D. Conaway J.W. Conaway R.C. Trends Biochem. Sci. 1996; 21: 351-355Abstract Full Text PDF PubMed Scopus (120) Google Scholar, 23SivaRaman L. Reines D. Kane C.M. J. Biol. Chem. 1990; 265: 14554-14560Abstract Full Text PDF PubMed Google Scholar, 24Izban M.G. Luse D.S. Genes Dev. 1992; 6: 1342-1356Crossref PubMed Scopus (226) Google Scholar, 25Izban M.G. Luse D.S. J. Biol. Chem. 1993; 268: 12864-12873Abstract Full Text PDF PubMed Google Scholar, 26Reines D. J. Biol. Chem. 1992; 267: 3795-3800Abstract Full Text PDF PubMed Google Scholar, 27Reines D. Mote Jr., J. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 1917-1921Crossref PubMed Scopus (92) Google Scholar, 28Gu W. Powell W. Mote Jr., J. Reines D. J. Biol. Chem. 1993; 268: 25604-25616Abstract Full Text PDF PubMed Google Scholar, 29Guo H. Price D.H. J. Biol. Chem. 1993; 268: 18762-18770Abstract Full Text PDF PubMed Google Scholar, 30Kassavetis G.A. Geiduschek E.P. Science. 1993; 259: 944-945Crossref PubMed Scopus (66) Google Scholar).Previously, we purified and characterized S-II from Saccharomyces cerevisiae (31Nakanishi T. Nakano A. Nomura K. Sekimizu K. Natori S. J. Biol. Chem. 1992; 267: 13200-13204Abstract Full Text PDF PubMed Google Scholar, 32Nakanishi T. Shimoaraiso M. Kubo T. Natori S. J. Biol. Chem. 1995; 270: 8991-8995Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar). Yeast S-II was found to contain an N-terminal region of 73 residues and a C-terminal region, including a zinc ribbon motif, that are relatively well conserved in the S-II proteins of many other species (33Qian X. Gonzani S.N. Yoon H.S. Jeon C.J. Agarwal K. Weiss M.A. Biochemistry. 1993; 32: 9944-9959Crossref PubMed Scopus (115) Google Scholar, 34Qian X. Jeon C. Yoon H.S. Agarwal K. Weiss M.A. Nature. 1993; 365: 277-279Crossref PubMed Scopus (111) Google Scholar). A gene disruption experiment revealed that the S-II null mutant is viable but becomes sensitive to 6-azauracil.During the study of yeast S-II, we found that there is a strict species specificity in the combination of S-II and RNA polymerase II. Yeast S-II did not stimulate mouse RNA polymerase II and vice versa. To identify the region of the S-II molecule that prescribes species specificity, we constructed various hybrid clones between yeast and Ehrlich cell S-II. We found that the region between Pro-131 and Phe-270 is needed for yeast S-II to interact with yeast RNA polymerase II and thus to suppress 6-azauracil sensitivity of S-II null mutant in vivo. The N- and C-terminal regions were shown to be interchangeable between yeast and Ehrlich cell S-II without loss of function.DISCUSSIONIt is known that the N- and C-terminal regions of S-II are relatively well conserved among various species. In particular, the sequence identity of the first 30–40 C-terminal residues is over 70% among S-II family proteins. Previously, we demonstrated that yeast S-II consists of 309 amino acid residues and that at least the first 147 N-terminal residues are dispensable for the stimulation of RNA polymerase II in vitro and the suppression of 6-azauracil sensitivity in S-II null mutants in vivo. Of the remaining 162 residues, 49 C-terminal residues were shown to be essential for S-II activity, but nothing was known about the remaining 113 residues.In this paper we have demonstrated for the first time that most of these residues are related to species specificity in the interaction with RNA polymerase II. It is known that Ehrlich cell S-II has polymerase specificity and cannot stimulate mouse RNA polymerase I (17Sekimizu K. Kobayashi N. Mizuno D. Natori S. Biochemistry. 1976; 15: 5064-5070Crossref PubMed Scopus (65) Google Scholar). The sequences of S-II are relatively well conserved among various organisms, so the species specificity of S-II in terms of the stimulation of RNA polymerase II had not been examined. We clearly demonstrated that yeast S-II cannot stimulate mouse RNA polymerase II and vice versa, and this species specificity was roughly ascribed to the above mentioned 113 residues.By constructing various hybrid molecules of yeast and Ehrlich cell S-II, we have demonstrated that the region 132–270 (or 262 in the case of Ehrlich cell S-II), consisting of 138 residues, determines the species specificity and that the above mentioned 113 residues are included in this region. Recent structural analysis of yeast S-II revealed that it is composed of three distinctive structural domains, termed domains I (1–105/124), II (106/125–246), and III (247–309) (47Morin P.E. Awrey D.E. Edwards A.M. Arrowsmith C.H. Proc. Natl. Sci. Acad. U. S. A. 1996; 93: 10604-10608Crossref PubMed Scopus (37) Google Scholar). We divided yeast S-II into three regions on the basis of previous deletion experiments (32Nakanishi T. Shimoaraiso M. Kubo T. Natori S. J. Biol. Chem. 1995; 270: 8991-8995Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar) and sequence comparison with Ehrlich cell S-II. The region 132–270 is located between domain II and domain III and does not contain the zinc ribbon.Agarwal et al. (48Agarwal K. Baek K.H. Jeon C.J. Miyamoto K. Ueno A. Yoon H.S. Biochemistry. 1991; 30: 7842-7851Crossref PubMed Scopus (71) Google Scholar) showed that the region 100–230 of human S-II is required for binding to human RNA polymerase II in vitro. As human S-II and Ehrlich cell S-II are very similar, the region 100–230 of human S-II may correspond to the region 132–262 of Ehrlich cell S-II; however, it is not known whether Ehrlich cell S-II stimulates human RNA polymerase II. Cipres-Palacin and Kane (49Cipres-Palacin G. Kane C.M. Proc. Natl. Acad. Sci. U. S. A. 1994; 91: 8087-8091Crossref PubMed Scopus (38) Google Scholar) prepared two mutants of human S-II, named TFIIS5 (E174A, E175A) and TFIIS7 (K187A, E175A), and showed that those residues are critical for arrest relief activity of S-II. As all these residues are located in the region corresponding to the region 132–262 of Ehrlich cell S-II, these mutants are likely to have lost the ability to interact with RNA polymerase II of the same species.This report presents two unique findings as follows: 1) yeast and Ehrlich cell S-II were not interchangeable in either in vitro or in vivo transcription systems, and 2) less conserved sequences in the region 132–270 (or 262) of S-II were found to define species specificity. These findings suggest that this region and possible S-II binding site of RNA polymerase II co-evolved in yeast and mice. The other two regions were shown to be interchangeable between yeast and Ehrlich cell S-II. The third region, region 271–309 (262–301 in the case of Ehrlich cell S-II), is crucial for the stimulation of RNA polymerase II (32Nakanishi T. Shimoaraiso M. Kubo T. Natori S. J. Biol. Chem. 1995; 270: 8991-8995Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar), so the molecular mechanism of the stimulation of RNA synthesis by S-II is the same regardless of the species. Therefore, identifying the region of RNA polymerase II that interacts with the region 132–270 of S-II will provide a clue about the regulation of transcription at the level of elongation.It is noteworthy that both the YEY and YYE hybrid molecules were expressed in yeast and migrated into nuclei. It is difficult to assign the nuclear transport signal to a region of S-II, but these nuclear localization experiments rule out the possibility that the failure of YEY to suppress 6-aqzauracil sensitivity of an S-II deletion strain is simply due to mislocalization of this hybrid protein. Transcription initiation is a complex process that involves protein-protein and protein-nucleic acid interactions, and factors participating in this process have been extensively characterized (1Buratowski S. Cell. 1994; 77: 1-3Abstract Full Text PDF PubMed Scopus (264) Google Scholar, 2Tjian R. Maniatis T. Cell. 1994; 77: 5-8Abstract Full Text PDF PubMed Scopus (953) Google Scholar, 3Orphanides G. Lagrange T. Reinberg D. Genes Dev. 1996; 10: 2657-2683Crossref PubMed Scopus (843) Google Scholar, 4Roeder R.G. Trends Biochem. Sci. 1996; 21: 327-335Abstract Full Text PDF PubMed Scopus (718) Google Scholar). On the other hand, regulation of gene expression at the transcription elongation level has been less thoroughly studied. Recently, it has become evident that various cellular and viral genes are regulated at the level of transcription elongation (5Spencer C. Groudine M. Oncogene. 1990; 5: 777-785PubMed Google Scholar, 6Kerppola T.K. Kane C.M. FASEB J. 1991; 5: 2833-2842Crossref PubMed Scopus (91) Google Scholar, 7Kane C.M. Conaway R.C. Conaway J.W. Transcription: Mechanisms and Regulation. Raven Press, Ltd., New York1993: 279-296Google Scholar, 8Aso T. Conaway J.W. Conaway R.C. FASEB J. 1995; 9: 1419-1428Crossref PubMed Scopus (55) Google Scholar). Thus, transcription elongation is likely to also be a crucial step for eukaryotic gene expression that involves various transcription elongation factors such as S-II (TFIIS) (9Sekimizu K. Nakanishi Y. Mizuno D. Natori S. Biochemistry. 1979; 18: 1582-1588Crossref PubMed Scopus (56) Google Scholar, 10Natori S. Mol. Cell. Biochem. 1982; 46: 173-187Crossref PubMed Scopus (33) Google Scholar), Elongin (SIII) (11Bradsher J.N. Jackson K.W. Conaway R.C. Conaway J.W. J. Biol. Chem. 1993; 268: 25587-25593Abstract Full Text PDF PubMed Google Scholar,12Aso T. Lane W.S. Conaway J.W. Conaway R.C. Science. 1995; 269: 1439-1443Crossref PubMed Scopus (289) Google Scholar), TFIIF (13Price D.H. Sluder A.E. Greenleaf A.L. Mol. Cell. Biol. 1989; 9: 1465-1475Crossref PubMed Scopus (133) Google Scholar, 14Kephart D.D. Wang B.Q. Burton Z.F. Price D.H. J. Biol. Chem. 1994; 269: 13536-13543Abstract Full Text PDF PubMed Google Scholar, 15Gu W. Reines D. J. Biol. Chem. 1995; 270: 11238-11244Abstract Full Text Full Text PDF PubMed Scopus (70) Google Scholar), and ELL (16Shilatifard A. Lane W.S. Jackson K.W. Conaway R.C. Conaway J.W. Science. 1996; 271: 1873-1876Crossref PubMed Scopus (279) Google Scholar). Transcription elongation factor S-II was originally purified from mouse Ehrlich ascites tumor cells as a specific stimulatory protein of RNA polymerase II, and it was thought to participate in eukaryotic transcription (9Sekimizu K. Nakanishi Y. Mizuno D. Natori S. Biochemistry. 1979; 18: 1582-1588Crossref PubMed Scopus (56) Google Scholar, 10Natori S. Mol. Cell. Biochem. 1982; 46: 173-187Crossref PubMed Scopus (33) Google Scholar, 17Sekimizu K. Kobayashi N. Mizuno D. Natori S. Biochemistry. 1976; 15: 5064-5070Crossref PubMed Scopus (65) Google Scholar, 18Sekimizu K. Yokoi H. Natori S. J. Biol. Chem. 1982; 257: 2719-2721Abstract Full Text PDF PubMed Google Scholar, 19Ueno K. Sekimizu K. Mizuno D. Natori S. Nature. 1979; 277: 145-146Crossref PubMed Scopus (33) Google Scholar). Subsequently, S-II was purified from various organisms and was shown to enable RNA polymerase II to read through blocks of transcription elongation within the transcription units of many eukaryotic genes by promoting cleavage of the 3′-end of the nascent RNA by RNA polymerase II (20Reines D. Chamberlin M.J. Kane C.M. J. Biol. Chem. 1989; 264: 10799-10809Abstract Full Text PDF PubMed Google Scholar, 21Reines D. Ghanoumi P. Li Q. Mote Jr., J. J. Biol. Chem. 1992; 267: 15516-15522Abstract Full Text PDF PubMed Google Scholar, 22Reines D. Conaway J.W. Conaway R.C. Trends Biochem. Sci. 1996; 21: 351-355Abstract Full Text PDF PubMed Scopus (120) Google Scholar, 23SivaRaman L. Reines D. Kane C.M. J. Biol. Chem. 1990; 265: 14554-14560Abstract Full Text PDF PubMed Google Scholar, 24Izban M.G. Luse D.S. Genes Dev. 1992; 6: 1342-1356Crossref PubMed Scopus (226) Google Scholar, 25Izban M.G. Luse D.S. J. Biol. Chem. 1993; 268: 12864-12873Abstract Full Text PDF PubMed Google Scholar, 26Reines D. J. Biol. Chem. 1992; 267: 3795-3800Abstract Full Text PDF PubMed Google Scholar, 27Reines D. Mote Jr., J. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 1917-1921Crossref PubMed Scopus (92) Google Scholar, 28Gu W. Powell W. Mote Jr., J. Reines D. J. Biol. Chem. 1993; 268: 25604-25616Abstract Full Text PDF PubMed Google Scholar, 29Guo H. Price D.H. J. Biol. Chem. 1993; 268: 18762-18770Abstract Full Text PDF PubMed Google Scholar, 30Kassavetis G.A. Geiduschek E.P. Science. 1993; 259: 944-945Crossref PubMed Scopus (66) Google Scholar). Previously, we purified and characterized S-II from Saccharomyces cerevisiae (31Nakanishi T. Nakano A. Nomura K. Sekimizu K. Natori S. J. Biol. Chem. 1992; 267: 13200-13204Abstract Full Text PDF PubMed Google Scholar, 32Nakanishi T. Shimoaraiso M. Kubo T. Natori S. J. Biol. Chem. 1995; 270: 8991-8995Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar). Yeast S-II was found to contain an N-terminal region of 73 residues and a C-terminal region, including a zinc ribbon motif, that are relatively well conserved in the S-II proteins of many other species (33Qian X. Gonzani S.N. Yoon H.S. Jeon C.J. Agarwal K. Weiss M.A. Biochemistry. 1993; 32: 9944-9959Crossref PubMed Scopus (115) Google Scholar, 34Qian X. Jeon C. Yoon H.S. Agarwal K. Weiss M.A. Nature. 1993; 365: 277-279Crossref PubMed Scopus (111) Google Scholar). A gene disruption experiment revealed that the S-II null mutant is viable but becomes sensitive to 6-azauracil. During the study of yeast S-II, we found that there is a strict species specificity in the combination of S-II and RNA polymerase II. Yeast S-II did not stimulate mouse RNA polymerase II and vice versa. To identify the region of the S-II molecule that prescribes species specificity, we constructed various hybrid clones between yeast and Ehrlich cell S-II. We found that the region between Pro-131 and Phe-270 is needed for yeast S-II to interact with yeast RNA polymerase II and thus to suppress 6-azauracil sensitivity of S-II null mutant in vivo. The N- and C-terminal regions were shown to be interchangeable between yeast and Ehrlich cell S-II without loss of function. DISCUSSIONIt is known that the N- and C-terminal regions of S-II are relatively well conserved among various species. In particular, the sequence identity of the first 30–40 C-terminal residues is over 70% among S-II family proteins. Previously, we demonstrated that yeast S-II consists of 309 amino acid residues and that at least the first 147 N-terminal residues are dispensable for the stimulation of RNA polymerase II in vitro and the suppression of 6-azauracil sensitivity in S-II null mutants in vivo. Of the remaining 162 residues, 49 C-terminal residues were shown to be essential for S-II activity, but nothing was known about the remaining 113 residues.In this paper we have demonstrated for the first time that most of these residues are related to species specificity in the interaction with RNA polymerase II. It is known that Ehrlich cell S-II has polymerase specificity and cannot stimulate mouse RNA polymerase I (17Sekimizu K. Kobayashi N. Mizuno D. Natori S. Biochemistry. 1976; 15: 5064-5070Crossref PubMed Scopus (65) Google Scholar). The sequences of S-II are relatively well conserved among various organisms, so the species specificity of S-II in terms of the stimulation of RNA polymerase II had not been examined. We clearly demonstrated that yeast S-II cannot stimulate mouse RNA polymerase II and vice versa, and this species specificity was roughly ascribed to the above mentioned 113 residues.By constructing various hybrid molecules of yeast and Ehrlich cell S-II, we have demonstrated that the region 132–270 (or 262 in the case of Ehrlich cell S-II), consisting of 138 residues, determines the species specificity and that the above mentioned 113 residues are included in this region. Recent structural analysis of yeast S-II revealed that it is composed of three distinctive structural domains, termed domains I (1–105/124), II (106/125–246), and III (247–309) (47Morin P.E. Awrey D.E. Edwards A.M. Arrowsmith C.H. Proc. Natl. Sci. Acad. U. S. A. 1996; 93: 10604-10608Crossref PubMed Scopus (37) Google Scholar). We divided yeast S-II into three regions on the basis of previous deletion experiments (32Nakanishi T. Shimoaraiso M. Kubo T. Natori S. J. Biol. Chem. 1995; 270: 8991-8995Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar) and sequence comparison with Ehrlich cell S-II. The region 132–270 is located between domain II and domain III and does not contain the zinc ribbon.Agarwal et al. (48Agarwal K. Baek K.H. Jeon C.J. Miyamoto K. Ueno A. Yoon H.S. Biochemistry. 1991; 30: 7842-7851Crossref PubMed Scopus (71) Google Scholar) showed that the region 100–230 of human S-II is required for binding to human RNA polymerase II in vitro. As human S-II and Ehrlich cell S-II are very similar, the region 100–230 of human S-II may correspond to the region 132–262 of Ehrlich cell S-II; however, it is not known whether Ehrlich cell S-II stimulates human RNA polymerase II. Cipres-Palacin and Kane (49Cipres-Palacin G. Kane C.M. Proc. Natl. Acad. Sci. U. S. A. 1994; 91: 8087-8091Crossref PubMed Scopus (38) Google Scholar) prepared two mutants of human S-II, named TFIIS5 (E174A, E175A) and TFIIS7 (K187A, E175A), and showed that those residues are critical for arrest relief activity of S-II. As all these residues are located in the region corresponding to the region 132–262 of Ehrlich cell S-II, these mutants are likely to have lost the ability to interact with RNA polymerase II of the same species.This report presents two unique findings as follows: 1) yeast and Ehrlich cell S-II were not interchangeable in either in vitro or in vivo transcription systems, and 2) less conserved sequences in the region 132–270 (or 262) of S-II were found to define species specificity. These findings suggest that this region and possible S-II binding site of RNA polymerase II co-evolved in yeast and mice. The other two regions were shown to be interchangeable between yeast and Ehrlich cell S-II. The third region, region 271–309 (262–301 in the case of Ehrlich cell S-II), is crucial for the stimulation of RNA polymerase II (32Nakanishi T. Shimoaraiso M. Kubo T. Natori S. J. Biol. Chem. 1995; 270: 8991-8995Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar), so the molecular mechanism of the stimulation of RNA synthesis by S-II is the same regardless of the species. Therefore, identifying the region of RNA polymerase II that interacts with the region 132–270 of S-II will provide a clue about the regulation of transcription at the level of elongation.It is noteworthy that both the YEY and YYE hybrid molecules were expressed in yeast and migrated into nuclei. It is difficult to assign the nuclear transport signal to a region of S-II, but these nuclear localization experiments rule out the possibility that the failure of YEY to suppress 6-aqzauracil sensitivity of an S-II deletion strain is simply due to mislocalization of this hybrid protein. It is known that the N- and C-terminal regions of S-II are relatively well conserved among various species. In particular, the sequence identity of the first 30–40 C-terminal residues is over 70% among S-II family proteins. Previously, we demonstrated that yeast S-II consists of 309 amino acid residues and that at least the first 147 N-terminal residues are dispensable for the stimulation of RNA polymerase II in vitro and the suppression of 6-azauracil sensitivity in S-II null mutants in vivo. Of the remaining 162 residues, 49 C-terminal residues were shown to be essential for S-II activity, but nothing was known about the remaining 113 residues. In this paper we have demonstrated for the first time that most of these residues are related to species specificity in the interaction with RNA polymerase II. It is known that Ehrlich cell S-II has polymerase specificity and cannot stimulate mouse RNA polymerase I (17Sekimizu K. Kobayashi N. Mizuno D. Natori S. Biochemistry. 1976; 15: 5064-5070Crossref PubMed Scopus (65) Google Scholar). The sequences of S-II are relatively well conserved among various organisms, so the species specificity of S-II in terms of the stimulation of RNA polymerase II had not been examined. We clearly demonstrated that yeast S-II cannot stimulate mouse RNA polymerase II and vice versa, and this species specificity was roughly ascribed to the above mentioned 113 residues. By constructing various hybrid molecules of yeast and Ehrlich cell S-II, we have demonstrated that the region 132–270 (or 262 in the case of Ehrlich cell S-II), consisting of 138 residues, determines the species specificity and that the above mentioned 113 residues are included in this region. Recent structural analysis of yeast S-II revealed that it is composed of three distinctive structural domains, termed domains I (1–105/124), II (106/125–246), and III (247–309) (47Morin P.E. Awrey D.E. Edwards A.M. Arrowsmith C.H. Proc. Natl. Sci. Acad. U. S. A. 1996; 93: 10604-10608Crossref PubMed Scopus (37) Google Scholar). We divided yeast S-II into three regions on the basis of previous deletion experiments (32Nakanishi T. Shimoaraiso M. Kubo T. Natori S. J. Biol. Chem. 1995; 270: 8991-8995Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar) and sequence comparison with Ehrlich cell S-II. The region 132–270 is located between domain II and domain III and does not contain the zinc ribbon. Agarwal et al. (48Agarwal K. Baek K.H. Jeon C.J. Miyamoto K. Ueno A. Yoon H.S. Biochemistry. 1991; 30: 7842-7851Crossref PubMed Scopus (71) Google Scholar) showed that the region 100–230 of human S-II is required for binding to human RNA polymerase II in vitro. As human S-II and Ehrlich cell S-II are very similar, the region 100–230 of human S-II may correspond to the region 132–262 of Ehrlich cell S-II; however, it is not known whether Ehrlich cell S-II stimulates human RNA polymerase II. Cipres-Palacin and Kane (49Cipres-Palacin G. Kane C.M. Proc. Natl. Acad. Sci. U. S. A. 1994; 91: 8087-8091Crossref PubMed Scopus (38) Google Scholar) prepared two mutants of human S-II, named TFIIS5 (E174A, E175A) and TFIIS7 (K187A, E175A), and showed that those residues are critical for arrest relief activity of S-II. As all these residues are located in the region corresponding to the region 132–262 of Ehrlich cell S-II, these mutants are likely to have lost the ability to interact with RNA polymerase II of the same species. This report presents two unique findings as follows: 1) yeast and Ehrlich cell S-II were not interchangeable in either in vitro or in vivo transcription systems, and 2) less conserved sequences in the region 132–270 (or 262) of S-II were found to define species specificity. These findings suggest that this region and possible S-II binding site of RNA polymerase II co-evolved in yeast and mice. The other two regions were shown to be interchangeable between yeast and Ehrlich cell S-II. The third region, region 271–309 (262–301 in the case of Ehrlich cell S-II), is crucial for the stimulation of RNA polymerase II (32Nakanishi T. Shimoaraiso M. Kubo T. Natori S. J. Biol. Chem. 1995; 270: 8991-8995Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar), so the molecular mechanism of the stimulation of RNA synthesis by S-II is the same regardless of the species. Therefore, identifying the region of RNA polymerase II that interacts with the region 132–270 of S-II will provide a clue about the regulation of transcription at the level of elongation. It is noteworthy that both the YEY and YYE hybrid molecules were expressed in yeast and migrated into nuclei. It is difficult to assign the nuclear transport signal to a region of S-II, but these nuclear localization experiments rule out the possibility that the failure of YEY to suppress 6-aqzauracil sensitivity of an S-II deletion strain is simply due to mislocalization of this hybrid protein." @default.
W2003735948 created "2016-06-24" @default.
W2003735948 creator A5042593421 @default.
W2003735948 creator A5066791630 @default.
W2003735948 creator A5081184238 @default.
W2003735948 creator A5090667783 @default.
W2003735948 date "1997-10-01" @default.
W2003735948 modified "2023-10-03" @default.
W2003735948 title "Identification of the Region in Yeast S-II That Defines Species Specificity in Its Interaction with RNA Polymerase II" @default.
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