SemOpenAlex |

SemOpenAlex

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2014275427> ?p ?o ?g. }

Showing items 1 to 100 of ±104 with 100 items per page.

W2014275427 endingPage "9221" @default.
W2014275427 startingPage "9215" @default.
W2014275427 abstract "Three different cDNAs coding for putative plant plastid sigma70-type transcription initiation factors have recently been cloned and sequenced from Arabidopsis thaliana. We have analyzed the evolutionary conservation of function(s) of the N-terminal and C-terminal halves of these three sigma factors by in vitro transcription studies using heterologous transcription systems and by complementation assays usingEscherichia coli thermosensitive rpoD mutants. Our results indicate differences and similarities of the three plant factors and their prokaryotic ancestors. The functions of the N-terminal parts of the plant sigma factors are considerably different from the function of the N-terminal part of the principal sigma70 factor of E. coli. On the other hand, the C-terminal parts have kept at least two characteristics when compared with their prokaryotic ancestors: 1) they can distinguish between different promoter structures, and 2) one of them is capable of fully complementing E. coli rpoD mutants, i.e.recognizing all essential E. coli promoters that are used by the E. coli principal sigma70 factor. This shows for the first time in vivo a strong evolutionary conservation of cis- and trans-acting elements between the prokaryotic and the plant plastid transcriptional machinery. Three different cDNAs coding for putative plant plastid sigma70-type transcription initiation factors have recently been cloned and sequenced from Arabidopsis thaliana. We have analyzed the evolutionary conservation of function(s) of the N-terminal and C-terminal halves of these three sigma factors by in vitro transcription studies using heterologous transcription systems and by complementation assays usingEscherichia coli thermosensitive rpoD mutants. Our results indicate differences and similarities of the three plant factors and their prokaryotic ancestors. The functions of the N-terminal parts of the plant sigma factors are considerably different from the function of the N-terminal part of the principal sigma70 factor of E. coli. On the other hand, the C-terminal parts have kept at least two characteristics when compared with their prokaryotic ancestors: 1) they can distinguish between different promoter structures, and 2) one of them is capable of fully complementing E. coli rpoD mutants, i.e.recognizing all essential E. coli promoters that are used by the E. coli principal sigma70 factor. This shows for the first time in vivo a strong evolutionary conservation of cis- and trans-acting elements between the prokaryotic and the plant plastid transcriptional machinery. polymerase chain reaction The higher plant plastid genome is transcribed by two different transcriptional systems (reviewed in Ref. 1.Hess W.R. Börner T. Int. Rev. Cytol. 1999; 190: 1-59Crossref PubMed Google Scholar). One of the two systems is phage-like and its evolutionary origin is still unclear (2.Lerbs-Mache S. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 5509-5513Crossref PubMed Scopus (141) Google Scholar, 3.Hedtke B. Börner T. Weihe A. Science. 1997; 277: 809-811Crossref PubMed Scopus (299) Google Scholar). The other system is of the prokaryotic type revealing the cyanobacterial origin of present-day chloroplasts (4.Iratni R. Baeza L. Andreeva A. Mache R. Lerbs-Mache S. Genes Dev. 1994; 8: 2928-2938Crossref PubMed Scopus (53) Google Scholar, 5.Hu J. Bogorad L. Proc. Natl. Acad. Sci. U. S. A. 1990; 87: 1531-1535Crossref PubMed Scopus (123) Google Scholar, 6.Hu J. Troxler R.F. Bogorad L. Nucleic Acids Res. 1991; 19: 3431-3434Crossref PubMed Scopus (55) Google Scholar). All polypeptides that are necessary to build up the core enzyme of the prokaryotic-type plastid RNA polymerase are still encoded in the plastid genome (7.Shinozaki K. Ohme M. Tanaka M. Wakasugi T. Hayashida N. Matsubayashi T. Zaita N. Chunwongse J. Obokata J. Yamaguchi-Shinozaki K. Ohto C. Torazawa K. Meng B.Y. Sugita M. Deno H. Kamogashira T. Yamada K. Kusuda J. Takaiwa F. Kato A. Tohdoh N. Shimada H. Sugiura M. EMBO J. 1986; 5: 2043-2049Crossref PubMed Scopus (1856) Google Scholar, 1.Hess W.R. Börner T. Int. Rev. Cytol. 1999; 190: 1-59Crossref PubMed Google Scholar). However, genes corresponding to sigma-like transcription initiation factors that are indispensable for the activity of this type of enzyme (reviewed in Ref. 8.Helmann J.D. Chamberlin M.J. Ann. Rev. Biochem. 1988; 57: 839-872Crossref PubMed Scopus (713) Google Scholar) are not found on the plastid genomes (7.Shinozaki K. Ohme M. Tanaka M. Wakasugi T. Hayashida N. Matsubayashi T. Zaita N. Chunwongse J. Obokata J. Yamaguchi-Shinozaki K. Ohto C. Torazawa K. Meng B.Y. Sugita M. Deno H. Kamogashira T. Yamada K. Kusuda J. Takaiwa F. Kato A. Tohdoh N. Shimada H. Sugiura M. EMBO J. 1986; 5: 2043-2049Crossref PubMed Scopus (1856) Google Scholar, 1.Hess W.R. Börner T. Int. Rev. Cytol. 1999; 190: 1-59Crossref PubMed Google Scholar). These genes have been transferred to the nucleus during evolution (9.Isono K. Shimizu M. Yoshimoto K. Niwa Y. Satoh K. Yokota A. Kobayashi H. Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 14948-14953Crossref PubMed Scopus (115) Google Scholar).The existence of more than one sigma-like transcription factor in higher plant plastids had been suggested several years ago on the basis of biochemical approaches for spinach and mustard (10.Tiller K. Eisermann A. Link G. Eur. J. Biochem. 1991; 198: 93-99Crossref PubMed Scopus (66) Google Scholar, 11.Tiller K. Link G. Plant Mol. Biol. 1993; 21: 503-513Crossref PubMed Scopus (51) Google Scholar, 12.Lerbs S. Bräutigam E. Mache R. Mol. Gen. Genet. 1988; 211: 459-464Crossref Scopus (50) Google Scholar). However, the corresponding genes have not been cloned. Only recently, six different cDNAs showing strong sequence similarity with genes coding for prokaryotic-like sigma70-type initiation factors have been cloned and sequenced from Arabidopsis thaliana(accession numbers: SIG1, dbj: AB004820 and emb: Y15362; SIG2, dbj:AB004821 and emb: Y14567; SIG3, dbj: AB004822; SIG4, gb: AF101075; SIG5, emb: Y18550; and SIG6, emb: AJ250812). For three of them, it has been shown that the corresponding proteins are transported into the chloroplasts (9.Isono K. Shimizu M. Yoshimoto K. Niwa Y. Satoh K. Yokota A. Kobayashi H. Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 14948-14953Crossref PubMed Scopus (115) Google Scholar, 14.Kanamaru K. Fujiwara M. Seki M. Katagiri T. Nakamur M. Mochizuki N. Nagatani A. Shinozaki K. Tanaka K. Takahashi H. Plant Cell Physiol. 1999; 40: 832-842Crossref PubMed Scopus (65) Google Scholar), but the function of these putative transcription factors in the regulation of plastid gene expression is not clear. In particular, it is not clear why several sigma70-type factors have been conserved during evolution, despite an important reduction of (plastid) genome size.Prokaryotic sigma factors can be classified into two families. Members of the first family are similar to the Escherichia colisigma70 factor, whereas members of the other family are similar to the E. coli sigma54 factor. The sigma70 family of transcription factors can be further subdivided into two or three groups. One primary sigma factor is required to ensure that “housekeeping functions” are performed, and alternative sigma factors direct transcriptional responses to changing environmental conditions (8.Helmann J.D. Chamberlin M.J. Ann. Rev. Biochem. 1988; 57: 839-872Crossref PubMed Scopus (713) Google Scholar). Although both groups of sigma70 factors are similar with respect to their amino acid sequence, they recognize different sequences at the two promoter elements localized –10 and –35 base pairs upstream of the transcription start sites (reviewed in 8 and 15).In the present study, we attempted to obtain information about the evolutionary conservation of components of the transcriptional machinery between prokaryotes and higher plant plastids. With this aim, we analyzed differences of the three plant sigma factors with respect to promoter recognition by in vitro transcription, and we determined the plant analogue to the primary sigma factor ofE. coli by complementation of E. coli rpoD(ts) mutants. For the first time, we show in vivo complementation of a protein of the E. colitranscriptional machinery by a protein of the plastid transcriptional machinery.DISCUSSIONThree different cDNAs coding for potential plastid-localized sigma70-type transcription initiation factors have recently been cloned and sequenced from A. thaliana (9.Isono K. Shimizu M. Yoshimoto K. Niwa Y. Satoh K. Yokota A. Kobayashi H. Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 14948-14953Crossref PubMed Scopus (115) Google Scholar, 23.Tanaka K. Tozawa Y. Mochizuki N. Shinozaki K. Nagatani A. Wakasa K. Takahashi H. FEBS Lett. 1997; 413: 309-313Crossref PubMed Scopus (106) Google Scholar), and the existence of a multigene family of sigma factors has been suggested forZea mays (24.Tan S. Troxler R. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 5316-5321Crossref PubMed Scopus (42) Google Scholar). Meanwhile, the list of Arabidopsissigma-like factors has been extended to six (SIG1– SIG6; see accession numbers listed above). Considering the small size of the plastid genome compared with that of bacteria or cyanobacteria, the existence of several sigma-like factors in plastids is quite surprising. It suggests that these factors might play different roles in plastid gene expression.The sigma70 transcription factor family is well characterized in prokaryotes such as E. coli and B. subtilis. It is subdivided into two (8.Helmann J.D. Chamberlin M.J. Ann. Rev. Biochem. 1988; 57: 839-872Crossref PubMed Scopus (713) Google Scholar) or three (25.Gruber T.M. Bryant D.A. J. Bacteriol. 1997; 179: 1734-1747Crossref PubMed Google Scholar) groups including primary and alternative sigma factors. In the present study, we analyzed whether the two-group system has been conserved in higher plant plastids, i.e. whether a functional specialization might explain the existence of several sigma-like factors in photosynthetically active plastids. We have used in vitroand in vivo approaches to study the evolutionary conservation of components of the transcriptional machinery between prokaryotes and higher plant plastids and to characterize the function(s) of three of the six different plant plastid sigma-like factors. Expression and complementation studies (Figs. 1 and 4) of full-length and truncated plant plastid sigma polypeptides in E. coli indicate that the functions of the N-terminal parts of the plant sigma factors differ considerably from those of the corresponding portion of the principal sigma70 factor of E. coli. High level production of the full-length protein in E. coli was only achieved for SIG2. However, SIG2 does not activate transcription in a heterologous system with E. coli core enzyme (Fig. 2). This might explain why it was possible to produce this protein in high amounts in E. coli.To reveal and analyze specificity in promoter recognition of the three plant sigma-like factors, we used truncated polypeptides that harbor only the conserved regions 2–4. In this way, we avoid differences in promoter-RNA polymerase interactions that may arise from different functions of the different N-terminal sequences of these factors. In addition, it has been shown previously that the intact sigma70 factor of E. coli does not bind to DNA but that the cleavage of the N-terminal part of the factor transforms it into a DNA-binding protein (16.Dombroski A., J. Walter W.A. Record M.T. Siegele D.A. Gross C.A. Cell. 1992; 70: 501-512Abstract Full Text PDF PubMed Scopus (276) Google Scholar). Therefore, we supposed that it should be possible to reveal promoter specificity by using truncated sigma factors. We analyzed transcription factor-RNA polymerase-promoter interactions either by reconstitution of the truncated polypeptides with the E. coli core enzyme or by competition of the truncated polypeptides with the E. coli holoenzyme followed by in vitro transcription. These experiments clearly demonstrate differences in the recognition of three selected plastid promoters, rrn-P1, rrn-P2, and rbcL. SIG3 recognizes all three promoters, i.e. it is the least specific of the three regulatory proteins. SIG2 recognizes specifically the rrn-P1 promoter, and SIG1 recognizes only therbcL promoter (Figs. 2, 3, and 6). The analysis of several truncated SIG3 proteins shows that SIG3 might contain an inhibition domain that is similar to the pro sequence of B. subtilissigma K. However, we could not detect proteolytic cleavage of SIG3 inArabidopsis. Nevertheless, our experiments suggest a function of this domain in the regulation of SIG3 activity. Instead of proteolytic cleavage, the activity of SIG3 might be regulated by posttranslational conformational changes that modify the accessibility of this putative inhibition domain.If we compare the three plastid promoter structures with the consensus sequence recognized by the principal sigma70 factor ofE. coli, we find that the rbcL promoter has the highest similarity with the E. coli consensus (Fig.1 C). SIG1 recognizes specifically only the rbcL promoter, as analyzed by in vitro transcription, suggesting that SIG1 is the plant analogue to the primary sigma factor of E. coli. This hypothesis is further supported by the in vivo analysis of the hybrid sigma factors (Fig. 4). For this analysis, the N-terminal part of the E. coli primary ς70 factor (region 1) was fused to the different C-terminal parts of the three plant sigma factors (regions 2–4). Region 1 had been shown to be important for open and ternary complex formation (26.Wilson C. Dombroski A.J. J. Mol. Biol. 1997; 267: 60-74Crossref PubMed Scopus (99) Google Scholar) and to induce conformational changes into the holoenzyme that are important for correct promoter recognition (27.Wilson Bowers C. Dombroski A.J. EMBO J. 1999; 18: 709-716Crossref PubMed Scopus (29) Google Scholar). Parts of regions 2 and 4 are important for the recognition of consensus –10 and –35 DNA sequences (for review, see Ref. 8.Helmann J.D. Chamberlin M.J. Ann. Rev. Biochem. 1988; 57: 839-872Crossref PubMed Scopus (713) Google Scholar). Thus, differences in promoter recognition and initiation of these hybrid sigma factors ought to be due to differences in the 3′ plant-specific part of the constructs. Results show that of the three tested hybrid sigma factors, only SIG1 fully complements the E. coli thermosensitiverpoD mutants.Our results indicate that the three higher plant plastid sigma70-like proteins have at least three characteristics in common with their prokaryotic ancestors: 1) they are composed of specific functional domains; 2) they distinguish between different promoter structures; and 3) only one of them (SIG1) is capable of recognizing all essential E. coli promoters that are recognized by the E. coli principal sigma70factor in vivo in E. coli. Therefore, we consider SIG1 to be the plant analogue to the primary sigma factor of E. coli. Interestingly, sequence alignment of all sixArabidopsis sigma factors to all five sigma factors localized on the Synechocystis genome (13.Kaneko T. Sato S. Kotani H. Tanaka A. Asamizu E. Nakamura Y. Miyajima N. Hirosawa M. Sugiura M. Sasamoto S. Kimura T. Hosouchi T. Matsuno A. Muraki A. Nakazaki N. Naruo K. Okumura S. Shimpo S. Takeuchi C. Wada T. Watanabe A. Yamada M. Yasuda M. Tabata S. DNA Res. 1996; 3: 185-209Crossref PubMed Scopus (239) Google Scholar) shows that SIG1 has the strongest sequence similarity and/or identity to all of the cyanobacterial sigma factors (Table I). Thus, SIG1 is the most prokaryotic-like plant sigma factor. The other plant sigma factors might have evolved in coordination with the transformation of a unicellular organism, the cyanobacterial ancestor, into an integrated part of a multicellular organism, the present-day plastid. The in vivo function of the SIG2-specificrrn-P1 promoter is still unclear (4.Iratni R. Baeza L. Andreeva A. Mache R. Lerbs-Mache S. Genes Dev. 1994; 8: 2928-2938Crossref PubMed Scopus (53) Google Scholar), 2S. Lerbs-Mache, unpublished results. and the activity of SIG3 might be regulated by posttranslational modification(s). Therefore, our results suggest specific functions for SIG2 and SIG3 that are related either to plant development and/or changes of environmental conditions. Experiments are in progress in our laboratory to analyze the function of the three plant sigma factors duringA. thaliana development using an antisense approach.Table IAmino acid sequence similarities and identities between cyanobacterial and plant ς factorsSyn1, orf sll2012; Syn2, ofr sll1689; Syn3, orf sll0306; Syn4, orf sll0184; Syn5, slr0653. Open table in a new tab The higher plant plastid genome is transcribed by two different transcriptional systems (reviewed in Ref. 1.Hess W.R. Börner T. Int. Rev. Cytol. 1999; 190: 1-59Crossref PubMed Google Scholar). One of the two systems is phage-like and its evolutionary origin is still unclear (2.Lerbs-Mache S. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 5509-5513Crossref PubMed Scopus (141) Google Scholar, 3.Hedtke B. Börner T. Weihe A. Science. 1997; 277: 809-811Crossref PubMed Scopus (299) Google Scholar). The other system is of the prokaryotic type revealing the cyanobacterial origin of present-day chloroplasts (4.Iratni R. Baeza L. Andreeva A. Mache R. Lerbs-Mache S. Genes Dev. 1994; 8: 2928-2938Crossref PubMed Scopus (53) Google Scholar, 5.Hu J. Bogorad L. Proc. Natl. Acad. Sci. U. S. A. 1990; 87: 1531-1535Crossref PubMed Scopus (123) Google Scholar, 6.Hu J. Troxler R.F. Bogorad L. Nucleic Acids Res. 1991; 19: 3431-3434Crossref PubMed Scopus (55) Google Scholar). All polypeptides that are necessary to build up the core enzyme of the prokaryotic-type plastid RNA polymerase are still encoded in the plastid genome (7.Shinozaki K. Ohme M. Tanaka M. Wakasugi T. Hayashida N. Matsubayashi T. Zaita N. Chunwongse J. Obokata J. Yamaguchi-Shinozaki K. Ohto C. Torazawa K. Meng B.Y. Sugita M. Deno H. Kamogashira T. Yamada K. Kusuda J. Takaiwa F. Kato A. Tohdoh N. Shimada H. Sugiura M. EMBO J. 1986; 5: 2043-2049Crossref PubMed Scopus (1856) Google Scholar, 1.Hess W.R. Börner T. Int. Rev. Cytol. 1999; 190: 1-59Crossref PubMed Google Scholar). However, genes corresponding to sigma-like transcription initiation factors that are indispensable for the activity of this type of enzyme (reviewed in Ref. 8.Helmann J.D. Chamberlin M.J. Ann. Rev. Biochem. 1988; 57: 839-872Crossref PubMed Scopus (713) Google Scholar) are not found on the plastid genomes (7.Shinozaki K. Ohme M. Tanaka M. Wakasugi T. Hayashida N. Matsubayashi T. Zaita N. Chunwongse J. Obokata J. Yamaguchi-Shinozaki K. Ohto C. Torazawa K. Meng B.Y. Sugita M. Deno H. Kamogashira T. Yamada K. Kusuda J. Takaiwa F. Kato A. Tohdoh N. Shimada H. Sugiura M. EMBO J. 1986; 5: 2043-2049Crossref PubMed Scopus (1856) Google Scholar, 1.Hess W.R. Börner T. Int. Rev. Cytol. 1999; 190: 1-59Crossref PubMed Google Scholar). These genes have been transferred to the nucleus during evolution (9.Isono K. Shimizu M. Yoshimoto K. Niwa Y. Satoh K. Yokota A. Kobayashi H. Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 14948-14953Crossref PubMed Scopus (115) Google Scholar). The existence of more than one sigma-like transcription factor in higher plant plastids had been suggested several years ago on the basis of biochemical approaches for spinach and mustard (10.Tiller K. Eisermann A. Link G. Eur. J. Biochem. 1991; 198: 93-99Crossref PubMed Scopus (66) Google Scholar, 11.Tiller K. Link G. Plant Mol. Biol. 1993; 21: 503-513Crossref PubMed Scopus (51) Google Scholar, 12.Lerbs S. Bräutigam E. Mache R. Mol. Gen. Genet. 1988; 211: 459-464Crossref Scopus (50) Google Scholar). However, the corresponding genes have not been cloned. Only recently, six different cDNAs showing strong sequence similarity with genes coding for prokaryotic-like sigma70-type initiation factors have been cloned and sequenced from Arabidopsis thaliana(accession numbers: SIG1, dbj: AB004820 and emb: Y15362; SIG2, dbj:AB004821 and emb: Y14567; SIG3, dbj: AB004822; SIG4, gb: AF101075; SIG5, emb: Y18550; and SIG6, emb: AJ250812). For three of them, it has been shown that the corresponding proteins are transported into the chloroplasts (9.Isono K. Shimizu M. Yoshimoto K. Niwa Y. Satoh K. Yokota A. Kobayashi H. Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 14948-14953Crossref PubMed Scopus (115) Google Scholar, 14.Kanamaru K. Fujiwara M. Seki M. Katagiri T. Nakamur M. Mochizuki N. Nagatani A. Shinozaki K. Tanaka K. Takahashi H. Plant Cell Physiol. 1999; 40: 832-842Crossref PubMed Scopus (65) Google Scholar), but the function of these putative transcription factors in the regulation of plastid gene expression is not clear. In particular, it is not clear why several sigma70-type factors have been conserved during evolution, despite an important reduction of (plastid) genome size. Prokaryotic sigma factors can be classified into two families. Members of the first family are similar to the Escherichia colisigma70 factor, whereas members of the other family are similar to the E. coli sigma54 factor. The sigma70 family of transcription factors can be further subdivided into two or three groups. One primary sigma factor is required to ensure that “housekeeping functions” are performed, and alternative sigma factors direct transcriptional responses to changing environmental conditions (8.Helmann J.D. Chamberlin M.J. Ann. Rev. Biochem. 1988; 57: 839-872Crossref PubMed Scopus (713) Google Scholar). Although both groups of sigma70 factors are similar with respect to their amino acid sequence, they recognize different sequences at the two promoter elements localized –10 and –35 base pairs upstream of the transcription start sites (reviewed in 8 and 15). In the present study, we attempted to obtain information about the evolutionary conservation of components of the transcriptional machinery between prokaryotes and higher plant plastids. With this aim, we analyzed differences of the three plant sigma factors with respect to promoter recognition by in vitro transcription, and we determined the plant analogue to the primary sigma factor ofE. coli by complementation of E. coli rpoD(ts) mutants. For the first time, we show in vivo complementation of a protein of the E. colitranscriptional machinery by a protein of the plastid transcriptional machinery. DISCUSSIONThree different cDNAs coding for potential plastid-localized sigma70-type transcription initiation factors have recently been cloned and sequenced from A. thaliana (9.Isono K. Shimizu M. Yoshimoto K. Niwa Y. Satoh K. Yokota A. Kobayashi H. Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 14948-14953Crossref PubMed Scopus (115) Google Scholar, 23.Tanaka K. Tozawa Y. Mochizuki N. Shinozaki K. Nagatani A. Wakasa K. Takahashi H. FEBS Lett. 1997; 413: 309-313Crossref PubMed Scopus (106) Google Scholar), and the existence of a multigene family of sigma factors has been suggested forZea mays (24.Tan S. Troxler R. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 5316-5321Crossref PubMed Scopus (42) Google Scholar). Meanwhile, the list of Arabidopsissigma-like factors has been extended to six (SIG1– SIG6; see accession numbers listed above). Considering the small size of the plastid genome compared with that of bacteria or cyanobacteria, the existence of several sigma-like factors in plastids is quite surprising. It suggests that these factors might play different roles in plastid gene expression.The sigma70 transcription factor family is well characterized in prokaryotes such as E. coli and B. subtilis. It is subdivided into two (8.Helmann J.D. Chamberlin M.J. Ann. Rev. Biochem. 1988; 57: 839-872Crossref PubMed Scopus (713) Google Scholar) or three (25.Gruber T.M. Bryant D.A. J. Bacteriol. 1997; 179: 1734-1747Crossref PubMed Google Scholar) groups including primary and alternative sigma factors. In the present study, we analyzed whether the two-group system has been conserved in higher plant plastids, i.e. whether a functional specialization might explain the existence of several sigma-like factors in photosynthetically active plastids. We have used in vitroand in vivo approaches to study the evolutionary conservation of components of the transcriptional machinery between prokaryotes and higher plant plastids and to characterize the function(s) of three of the six different plant plastid sigma-like factors. Expression and complementation studies (Figs. 1 and 4) of full-length and truncated plant plastid sigma polypeptides in E. coli indicate that the functions of the N-terminal parts of the plant sigma factors differ considerably from those of the corresponding portion of the principal sigma70 factor of E. coli. High level production of the full-length protein in E. coli was only achieved for SIG2. However, SIG2 does not activate transcription in a heterologous system with E. coli core enzyme (Fig. 2). This might explain why it was possible to produce this protein in high amounts in E. coli.To reveal and analyze specificity in promoter recognition of the three plant sigma-like factors, we used truncated polypeptides that harbor only the conserved regions 2–4. In this way, we avoid differences in promoter-RNA polymerase interactions that may arise from different functions of the different N-terminal sequences of these factors. In addition, it has been shown previously that the intact sigma70 factor of E. coli does not bind to DNA but that the cleavage of the N-terminal part of the factor transforms it into a DNA-binding protein (16.Dombroski A., J. Walter W.A. Record M.T. Siegele D.A. Gross C.A. Cell. 1992; 70: 501-512Abstract Full Text PDF PubMed Scopus (276) Google Scholar). Therefore, we supposed that it should be possible to reveal promoter specificity by using truncated sigma factors. We analyzed transcription factor-RNA polymerase-promoter interactions either by reconstitution of the truncated polypeptides with the E. coli core enzyme or by competition of the truncated polypeptides with the E. coli holoenzyme followed by in vitro transcription. These experiments clearly demonstrate differences in the recognition of three selected plastid promoters, rrn-P1, rrn-P2, and rbcL. SIG3 recognizes all three promoters, i.e. it is the least specific of the three regulatory proteins. SIG2 recognizes specifically the rrn-P1 promoter, and SIG1 recognizes only therbcL promoter (Figs. 2, 3, and 6). The analysis of several truncated SIG3 proteins shows that SIG3 might contain an inhibition domain that is similar to the pro sequence of B. subtilissigma K. However, we could not detect proteolytic cleavage of SIG3 inArabidopsis. Nevertheless, our experiments suggest a function of this domain in the regulation of SIG3 activity. Instead of proteolytic cleavage, the activity of SIG3 might be regulated by posttranslational conformational changes that modify the accessibility of this putative inhibition domain.If we compare the three plastid promoter structures with the consensus sequence recognized by the principal sigma70 factor ofE. coli, we find that the rbcL promoter has the highest similarity with the E. coli consensus (Fig.1 C). SIG1 recognizes specifically only the rbcL promoter, as analyzed by in vitro transcription, suggesting that SIG1 is the plant analogue to the primary sigma factor of E. coli. This hypothesis is further supported by the in vivo analysis of the hybrid sigma factors (Fig. 4). For this analysis, the N-terminal part of the E. coli primary ς70 factor (region 1) was fused to the different C-terminal parts of the three plant sigma factors (regions 2–4). Region 1 had been shown to be important for open and ternary complex formation (26.Wilson C. Dombroski A.J. J. Mol. Biol. 1997; 267: 60-74Crossref PubMed Scopus (99) Google Scholar) and to induce conformational changes into the holoenzyme that are important for correct promoter recognition (27.Wilson Bowers C. Dombroski A.J. EMBO J. 1999; 18: 709-716Crossref PubMed Scopus (29) Google Scholar). Parts of regions 2 and 4 are important for the recognition of consensus –10 and –35 DNA sequences (for review, see Ref. 8.Helmann J.D. Chamberlin M.J. Ann. Rev. Biochem. 1988; 57: 839-872Crossref PubMed Scopus (713) Google Scholar). Thus, differences in promoter recognition and initiation of these hybrid sigma factors ought to be due to differences in the 3′ plant-specific part of the constructs. Results show that of the three tested hybrid sigma factors, only SIG1 fully complements the E. coli thermosensitiverpoD mutants.Our results indicate that the three higher plant plastid sigma70-like proteins have at least three characteristics in common with their prokaryotic ancestors: 1) they are composed of specific functional domains; 2) they distinguish between different promoter structures; and 3) only one of them (SIG1) is capable of recognizing all essential E. coli promoters that are recognized by the E. coli principal sigma70factor in vivo in E. coli. Therefore, we consider SIG1 to be the plant analogue to the primary sigma factor of E. coli. Interestingly, sequence alignment of all sixArabidopsis sigma factors to all five sigma factors localized on the Synechocystis genome (13.Kaneko T. Sato S. Kotani H. Tanaka A. Asamizu E. Nakamura Y. Miyajima N. Hirosawa M. Sugiura M. Sasamoto S. Kimura T. Hosouchi T. Matsuno A. Muraki A. Nakazaki N. Naruo K. Okumura S. Shimpo S. Takeuchi C. Wada T. Watanabe A. Yamada M. Yasuda M. Tabata S. DNA Res. 1996; 3: 185-209Crossref PubMed Scopus (239) Google Scholar) shows that SIG1 has the strongest sequence similarity and/or identity to all of the cyanobacterial sigma factors (Table I). Thus, SIG1 is the most prokaryotic-like plant sigma factor. The other plant sigma factors might have evolved in coordination with the transformation of a unicellular organism, the cyanobacterial ancestor, into an integrated part of a multicellular organism, the present-day plastid. The in vivo function of the SIG2-specificrrn-P1 promoter is still unclear (4.Iratni R. Baeza L. Andreeva A. Mache R. Lerbs-Mache S. Genes Dev. 1994; 8: 2928-2938Crossref PubMed Scopus (53) Google Scholar), 2S. Lerbs-Mache, unpublished results. and the activity of SIG3 might be regulated by posttranslational modification(s). Therefore, our results suggest specific functions for SIG2 and SIG3 that are related either to plant development and/or changes of environmental conditions. Experiments are in progress in our laboratory to analyze the function of the three plant sigma factors duringA. thaliana development using an antisense approach.Table IAmino acid sequence similarities and identities between cyanobacterial and plant ς factorsSyn1, orf sll2012; Syn2, ofr sll1689; Syn3, orf sll0306; Syn4, orf sll0184; Syn5, slr0653. Open table in a new tab Three different cDNAs coding for potential plastid-localized sigma70-type transcription initiation factors have recently been cloned and sequenced from A. thaliana (9.Isono K. Shimizu M. Yoshimoto K. Niwa Y. Satoh K. Yokota A. Kobayashi H. Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 14948-14953Crossref PubMed Scopus (115) Google Scholar, 23.Tanaka K. Tozawa Y. Mochizuki N. Shinozaki K. Nagatani A. Wakasa K. Takahashi H. FEBS Lett. 1997; 413: 309-313Crossref PubMed Scopus (106) Google Scholar), and the existence of a multigene family of sigma factors has been suggested forZea mays (24.Tan S. Troxler R. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 5316-5321Crossref PubMed Scopus (42) Google Scholar). Meanwhile, the list of Arabidopsissigma-like factors has been extended to six (SIG1– SIG6; see accession numbers listed above). Considering the small size of the plastid genome compared with that of bacteria or cyanobacteria, the existence of several sigma-like factors in plastids is quite surprising. It suggests that these factors might play different roles in plastid gene expression. The sigma70 transcription factor family is well characterized in prokaryotes such as E. coli and B. subtilis. It is subdivided into two (8.Helmann J.D. Chamberlin M.J. Ann. Rev. Biochem. 1988; 57: 839-872Crossref PubMed Scopus (713) Google Scholar) or three (25.Gruber T.M. Bryant D.A. J. Bacteriol. 1997; 179: 1734-1747Crossref PubMed Google Scholar) groups including primary and alternative sigma factors. In the present study, we analyzed whether the two-group system has been conserved in higher plant plastids, i.e. whether a functional specialization might explain the existence of several sigma-like factors in photosynthetically active plastids. We have used in vitroand in vivo approaches to study the evolutionary conservation of components of the transcriptional machinery between prokaryotes and higher plant plastids and to characterize the function(s) of three of the six different plant plastid sigma-like factors. Expression and complementation studies (Figs. 1 and 4) of full-length and truncated plant plastid sigma polypeptides in E. coli indicate that the functions of the N-terminal parts of the plant sigma factors differ considerably from those of the corresponding portion of the principal sigma70 factor of E. coli. High level production of the full-length protein in E. coli was only achieved for SIG2. However, SIG2 does not activate transcription in a heterologous system with E. coli core enzyme (Fig. 2). This might explain why it was possible to produce this protein in high amounts in E. coli. To reveal and analyze specificity in promoter recognition of the three plant sigma-like factors, we used truncated polypeptides that harbor only the conserved regions 2–4. In this way, we avoid differences in promoter-RNA polymerase interactions that may arise from different functions of the different N-terminal sequences of these factors. In addition, it has been shown previously that the intact sigma70 factor of E. coli does not bind to DNA but that the cleavage of the N-terminal part of the factor transforms it into a DNA-binding protein (16.Dombroski A., J. Walter W.A. Record M.T. Siegele D.A. Gross C.A. Cell. 1992; 70: 501-512Abstract Full Text PDF PubMed Scopus (276) Google Scholar). Therefore, we supposed that it should be possible to reveal promoter specificity by using truncated sigma factors. We analyzed transcription factor-RNA polymerase-promoter interactions either by reconstitution of the truncated polypeptides with the E. coli core enzyme or by competition of the truncated polypeptides with the E. coli holoenzyme followed by in vitro transcription. These experiments clearly demonstrate differences in the recognition of three selected plastid promoters, rrn-P1, rrn-P2, and rbcL. SIG3 recognizes all three promoters, i.e. it is the least specific of the three regulatory proteins. SIG2 recognizes specifically the rrn-P1 promoter, and SIG1 recognizes only therbcL promoter (Figs. 2, 3, and 6). The analysis of several truncated SIG3 proteins shows that SIG3 might contain an inhibition domain that is similar to the pro sequence of B. subtilissigma K. However, we could not detect proteolytic cleavage of SIG3 inArabidopsis. Nevertheless, our experiments suggest a function of this domain in the regulation of SIG3 activity. Instead of proteolytic cleavage, the activity of SIG3 might be regulated by posttranslational conformational changes that modify the accessibility of this putative inhibition domain. If we compare the three plastid promoter structures with the consensus sequence recognized by the principal sigma70 factor ofE. coli, we find that the rbcL promoter has the highest similarity with the E. coli consensus (Fig.1 C). SIG1 recognizes specifically only the rbcL promoter, as analyzed by in vitro transcription, suggesting that SIG1 is the plant analogue to the primary sigma factor of E. coli. This hypothesis is further supported by the in vivo analysis of the hybrid sigma factors (Fig. 4). For this analysis, the N-terminal part of the E. coli primary ς70 factor (region 1) was fused to the different C-terminal parts of the three plant sigma factors (regions 2–4). Region 1 had been shown to be important for open and ternary complex formation (26.Wilson C. Dombroski A.J. J. Mol. Biol. 1997; 267: 60-74Crossref PubMed Scopus (99) Google Scholar) and to induce conformational changes into the holoenzyme that are important for correct promoter recognition (27.Wilson Bowers C. Dombroski A.J. EMBO J. 1999; 18: 709-716Crossref PubMed Scopus (29) Google Scholar). Parts of regions 2 and 4 are important for the recognition of consensus –10 and –35 DNA sequences (for review, see Ref. 8.Helmann J.D. Chamberlin M.J. Ann. Rev. Biochem. 1988; 57: 839-872Crossref PubMed Scopus (713) Google Scholar). Thus, differences in promoter recognition and initiation of these hybrid sigma factors ought to be due to differences in the 3′ plant-specific part of the constructs. Results show that of the three tested hybrid sigma factors, only SIG1 fully complements the E. coli thermosensitiverpoD mutants. Our results indicate that the three higher plant plastid sigma70-like proteins have at least three characteristics in common with their prokaryotic ancestors: 1) they are composed of specific functional domains; 2) they distinguish between different promoter structures; and 3) only one of them (SIG1) is capable of recognizing all essential E. coli promoters that are recognized by the E. coli principal sigma70factor in vivo in E. coli. Therefore, we consider SIG1 to be the plant analogue to the primary sigma factor of E. coli. Interestingly, sequence alignment of all sixArabidopsis sigma factors to all five sigma factors localized on the Synechocystis genome (13.Kaneko T. Sato S. Kotani H. Tanaka A. Asamizu E. Nakamura Y. Miyajima N. Hirosawa M. Sugiura M. Sasamoto S. Kimura T. Hosouchi T. Matsuno A. Muraki A. Nakazaki N. Naruo K. Okumura S. Shimpo S. Takeuchi C. Wada T. Watanabe A. Yamada M. Yasuda M. Tabata S. DNA Res. 1996; 3: 185-209Crossref PubMed Scopus (239) Google Scholar) shows that SIG1 has the strongest sequence similarity and/or identity to all of the cyanobacterial sigma factors (Table I). Thus, SIG1 is the most prokaryotic-like plant sigma factor. The other plant sigma factors might have evolved in coordination with the transformation of a unicellular organism, the cyanobacterial ancestor, into an integrated part of a multicellular organism, the present-day plastid. The in vivo function of the SIG2-specificrrn-P1 promoter is still unclear (4.Iratni R. Baeza L. Andreeva A. Mache R. Lerbs-Mache S. Genes Dev. 1994; 8: 2928-2938Crossref PubMed Scopus (53) Google Scholar), 2S. Lerbs-Mache, unpublished results. and the activity of SIG3 might be regulated by posttranslational modification(s). Therefore, our results suggest specific functions for SIG2 and SIG3 that are related either to plant development and/or changes of environmental conditions. Experiments are in progress in our laboratory to analyze the function of the three plant sigma factors duringA. thaliana development using an antisense approach. Syn1, orf sll2012; Syn2, ofr sll1689; Syn3, orf sll0306; Syn4, orf sll0184; Syn5, slr0653. We are grateful to H. Geiselmann for helpful discussions during the preparation of the manuscript, and we thank H. Pesey for photographic work." @default.
W2014275427 created "2016-06-24" @default.
W2014275427 creator A5007203419 @default.
W2014275427 creator A5039009013 @default.
W2014275427 creator A5044297306 @default.
W2014275427 creator A5080857100 @default.
W2014275427 date "2000-03-01" @default.
W2014275427 modified "2023-09-27" @default.
W2014275427 title "Evolutionary Conservation of C-terminal Domains of Primary Sigma70-type Transcription Factors between Plants and Bacteria" @default.
W2014275427 cites W1530712791 @default.
W2014275427 cites W1560298788 @default.
W2014275427 cites W1743360482 @default.
W2014275427 cites W1970538130 @default.
W2014275427 cites W1972478044 @default.
W2014275427 cites W1996958791 @default.
W2014275427 cites W2001605466 @default.
W2014275427 cites W2007498342 @default.
W2014275427 cites W2012275337 @default.
W2014275427 cites W2018926318 @default.
W2014275427 cites W2020932446 @default.
W2014275427 cites W2025625996 @default.
W2014275427 cites W2036935628 @default.
W2014275427 cites W2056943636 @default.
W2014275427 cites W2065176599 @default.
W2014275427 cites W2078340918 @default.
W2014275427 cites W2081753166 @default.
W2014275427 cites W2090609263 @default.
W2014275427 cites W2092530456 @default.
W2014275427 cites W2112172921 @default.
W2014275427 cites W2115024759 @default.
W2014275427 cites W2116844374 @default.
W2014275427 cites W2122360878 @default.
W2014275427 cites W2125739542 @default.
W2014275427 cites W2142443870 @default.
W2014275427 cites W2164249947 @default.
W2014275427 cites W2179908318 @default.
W2014275427 cites W4253647815 @default.
W2014275427 doi "https://doi.org/10.1074/jbc.275.13.9215" @default.
W2014275427 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/10734058" @default.
W2014275427 hasPublicationYear "2000" @default.
W2014275427 type Work @default.
W2014275427 sameAs 2014275427 @default.
W2014275427 citedByCount "67" @default.
W2014275427 countsByYear W20142754272012 @default.
W2014275427 countsByYear W20142754272013 @default.
W2014275427 countsByYear W20142754272015 @default.
W2014275427 countsByYear W20142754272017 @default.
W2014275427 countsByYear W20142754272018 @default.
W2014275427 countsByYear W20142754272020 @default.
W2014275427 countsByYear W20142754272021 @default.
W2014275427 countsByYear W20142754272022 @default.
W2014275427 crossrefType "journal-article" @default.
W2014275427 hasAuthorship W2014275427A5007203419 @default.
W2014275427 hasAuthorship W2014275427A5039009013 @default.
W2014275427 hasAuthorship W2014275427A5044297306 @default.
W2014275427 hasAuthorship W2014275427A5080857100 @default.
W2014275427 hasBestOaLocation W20142754271 @default.
W2014275427 hasConcept C104317684 @default.
W2014275427 hasConcept C127413603 @default.
W2014275427 hasConcept C138885662 @default.
W2014275427 hasConcept C179926584 @default.
W2014275427 hasConcept C185592680 @default.
W2014275427 hasConcept C2779664074 @default.
W2014275427 hasConcept C41895202 @default.
W2014275427 hasConcept C523546767 @default.
W2014275427 hasConcept C54355233 @default.
W2014275427 hasConcept C76155785 @default.
W2014275427 hasConcept C86339819 @default.
W2014275427 hasConcept C86803240 @default.
W2014275427 hasConcept C95444343 @default.
W2014275427 hasConceptScore W2014275427C104317684 @default.
W2014275427 hasConceptScore W2014275427C127413603 @default.
W2014275427 hasConceptScore W2014275427C138885662 @default.
W2014275427 hasConceptScore W2014275427C179926584 @default.
W2014275427 hasConceptScore W2014275427C185592680 @default.
W2014275427 hasConceptScore W2014275427C2779664074 @default.
W2014275427 hasConceptScore W2014275427C41895202 @default.
W2014275427 hasConceptScore W2014275427C523546767 @default.
W2014275427 hasConceptScore W2014275427C54355233 @default.
W2014275427 hasConceptScore W2014275427C76155785 @default.
W2014275427 hasConceptScore W2014275427C86339819 @default.
W2014275427 hasConceptScore W2014275427C86803240 @default.
W2014275427 hasConceptScore W2014275427C95444343 @default.
W2014275427 hasIssue "13" @default.
W2014275427 hasLocation W20142754271 @default.
W2014275427 hasOpenAccess W2014275427 @default.
W2014275427 hasPrimaryLocation W20142754271 @default.
W2014275427 hasRelatedWork W1920751942 @default.
W2014275427 hasRelatedWork W1991523530 @default.
W2014275427 hasRelatedWork W2002128513 @default.
W2014275427 hasRelatedWork W2020824267 @default.
W2014275427 hasRelatedWork W2031436818 @default.
W2014275427 hasRelatedWork W2057739827 @default.
W2014275427 hasRelatedWork W2075354549 @default.
W2014275427 hasRelatedWork W2782497155 @default.
W2014275427 hasRelatedWork W4251051526 @default.
W2014275427 hasRelatedWork W2092874662 @default.
W2014275427 hasVolume "275" @default.