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A novel phage-encoded transcription antiterminator acts by suppressing bacterial RNA polymerase pausing.

Berdygulova Z, Esyunina D, Miropolskaya N, Mukhamedyarov D, Kuznedelov K, Nickels BE, Severinov K, Kulbachinskiy A, Minakhin L - Nucleic Acids Res. (2012)

Bottom Line: Gp39 also accelerates transcription elongation by decreasing RNAP pausing and backtracking but does not significantly affect the rates of catalysis of individual reactions in the RNAP active center.However, in contrast to Q and N, gp39 does not depend on NusA or other auxiliary factors for its activity.To our knowledge, gp39 is the first characterized phage-encoded transcription factor that affects every step of the transcription cycle and suppresses transcription termination through its antipausing activity.

View Article: PubMed Central - PubMed

Affiliation: Waksman Institute of Microbiology, Piscataway, NJ 08854, USA.

ABSTRACT
Gp39, a small protein encoded by Thermus thermophilus phage P23-45, specifically binds the host RNA polymerase (RNAP) and inhibits transcription initiation. Here, we demonstrate that gp39 also acts as an antiterminator during transcription through intrinsic terminators. The antitermination activity of gp39 relies on its ability to suppress transcription pausing at poly(U) tracks. Gp39 also accelerates transcription elongation by decreasing RNAP pausing and backtracking but does not significantly affect the rates of catalysis of individual reactions in the RNAP active center. We mapped the RNAP-gp39 interaction site to the β flap, a domain that forms a part of the RNA exit channel and is also a likely target for λ phage antiterminator proteins Q and N, and for bacterial elongation factor NusA. However, in contrast to Q and N, gp39 does not depend on NusA or other auxiliary factors for its activity. To our knowledge, gp39 is the first characterized phage-encoded transcription factor that affects every step of the transcription cycle and suppresses transcription termination through its antipausing activity.

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The binding sites of gp39 and other antiterminator proteins on the Tth RNAP TEC structure (21). The template and non-template DNA strands are shown in blue and brown, respectively, RNA is red. The β flap domain is dark green; the putative gp39-binding site is shown with red circle. β′ Zn finger [1], zipper [2] and lid [3] are shown as black lines. The proposed binding sites of the Xp10 p7 (β′ residue Glu4) and λ Q proteins (β flap tip helix) are shown in dark blue. The β′ coiled-coil (β′CC) and β gate-loop (GL) targeted by proteins of RfaH/NusG family are shown in green. The β′ bridge helix (BH) is gray.
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gkr1285-F7: The binding sites of gp39 and other antiterminator proteins on the Tth RNAP TEC structure (21). The template and non-template DNA strands are shown in blue and brown, respectively, RNA is red. The β flap domain is dark green; the putative gp39-binding site is shown with red circle. β′ Zn finger [1], zipper [2] and lid [3] are shown as black lines. The proposed binding sites of the Xp10 p7 (β′ residue Glu4) and λ Q proteins (β flap tip helix) are shown in dark blue. The β′ coiled-coil (β′CC) and β gate-loop (GL) targeted by proteins of RfaH/NusG family are shown in green. The β′ bridge helix (BH) is gray.

Mentions: Gp39 binds to the Thermus RNAP β flap domain that has emerged as a common target for factors affecting the elongation and termination properties of the TEC. Indeed, a number of elongation, termination and antitermination factors in E. coli were shown to bind to β flap (Figure 7, see ‘Introduction’ section). The β flap is located along the nascent RNA exit pathway and either interacts with or is physically close to RNA hairpins that cause pausing or termination (36,37). The flap is flexibly connected to the RNAP mainframe and its interactions with the nascent transcript may cause it to change its position, inducing long-range allosteric changes in the RNAP active center, which have been proposed to occur during termination (3,36,37). Thus, a factor that binds the β flap may influence every step of the termination process, including RNAP pausing at the terminator, formation of secondary structures in the nascent RNA and induction of long-range rearrangements in the RNAP active center, ultimately leading to RNA : DNA hybrid melting and TEC dissociation.Figure 7.


A novel phage-encoded transcription antiterminator acts by suppressing bacterial RNA polymerase pausing.

Berdygulova Z, Esyunina D, Miropolskaya N, Mukhamedyarov D, Kuznedelov K, Nickels BE, Severinov K, Kulbachinskiy A, Minakhin L - Nucleic Acids Res. (2012)

The binding sites of gp39 and other antiterminator proteins on the Tth RNAP TEC structure (21). The template and non-template DNA strands are shown in blue and brown, respectively, RNA is red. The β flap domain is dark green; the putative gp39-binding site is shown with red circle. β′ Zn finger [1], zipper [2] and lid [3] are shown as black lines. The proposed binding sites of the Xp10 p7 (β′ residue Glu4) and λ Q proteins (β flap tip helix) are shown in dark blue. The β′ coiled-coil (β′CC) and β gate-loop (GL) targeted by proteins of RfaH/NusG family are shown in green. The β′ bridge helix (BH) is gray.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC3351154&req=5

gkr1285-F7: The binding sites of gp39 and other antiterminator proteins on the Tth RNAP TEC structure (21). The template and non-template DNA strands are shown in blue and brown, respectively, RNA is red. The β flap domain is dark green; the putative gp39-binding site is shown with red circle. β′ Zn finger [1], zipper [2] and lid [3] are shown as black lines. The proposed binding sites of the Xp10 p7 (β′ residue Glu4) and λ Q proteins (β flap tip helix) are shown in dark blue. The β′ coiled-coil (β′CC) and β gate-loop (GL) targeted by proteins of RfaH/NusG family are shown in green. The β′ bridge helix (BH) is gray.
Mentions: Gp39 binds to the Thermus RNAP β flap domain that has emerged as a common target for factors affecting the elongation and termination properties of the TEC. Indeed, a number of elongation, termination and antitermination factors in E. coli were shown to bind to β flap (Figure 7, see ‘Introduction’ section). The β flap is located along the nascent RNA exit pathway and either interacts with or is physically close to RNA hairpins that cause pausing or termination (36,37). The flap is flexibly connected to the RNAP mainframe and its interactions with the nascent transcript may cause it to change its position, inducing long-range allosteric changes in the RNAP active center, which have been proposed to occur during termination (3,36,37). Thus, a factor that binds the β flap may influence every step of the termination process, including RNAP pausing at the terminator, formation of secondary structures in the nascent RNA and induction of long-range rearrangements in the RNAP active center, ultimately leading to RNA : DNA hybrid melting and TEC dissociation.Figure 7.

Bottom Line: Gp39 also accelerates transcription elongation by decreasing RNAP pausing and backtracking but does not significantly affect the rates of catalysis of individual reactions in the RNAP active center.However, in contrast to Q and N, gp39 does not depend on NusA or other auxiliary factors for its activity.To our knowledge, gp39 is the first characterized phage-encoded transcription factor that affects every step of the transcription cycle and suppresses transcription termination through its antipausing activity.

View Article: PubMed Central - PubMed

Affiliation: Waksman Institute of Microbiology, Piscataway, NJ 08854, USA.

ABSTRACT
Gp39, a small protein encoded by Thermus thermophilus phage P23-45, specifically binds the host RNA polymerase (RNAP) and inhibits transcription initiation. Here, we demonstrate that gp39 also acts as an antiterminator during transcription through intrinsic terminators. The antitermination activity of gp39 relies on its ability to suppress transcription pausing at poly(U) tracks. Gp39 also accelerates transcription elongation by decreasing RNAP pausing and backtracking but does not significantly affect the rates of catalysis of individual reactions in the RNAP active center. We mapped the RNAP-gp39 interaction site to the β flap, a domain that forms a part of the RNA exit channel and is also a likely target for λ phage antiterminator proteins Q and N, and for bacterial elongation factor NusA. However, in contrast to Q and N, gp39 does not depend on NusA or other auxiliary factors for its activity. To our knowledge, gp39 is the first characterized phage-encoded transcription factor that affects every step of the transcription cycle and suppresses transcription termination through its antipausing activity.

Show MeSH