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Insights into how Spt5 functions in transcription elongation and repressing transcription coupled DNA repair.

Li W, Giles C, Li S - Nucleic Acids Res. (2014)

Bottom Line: Through its KOW4-5 domains, Spt5 extensively interacts with Rpb4/7.Deletion of Spt5 KOW4-5 domains decreases transcription elongation and derepresses TCR.Our findings suggest that Spt5 is a key coordinator for holding the RNAP II complex in a closed conformation that is highly competent for transcription elongation but repressive to TCR.

View Article: PubMed Central - PubMed

Affiliation: Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA.

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Related in: MedlinePlus

Architecture of interactions between Spt4/5 and RNAP II. (A) Locations of Spt4 and different domains of Spt5 on RNAP II. The sources of the RNAP II structure are the same as those of Figure 1E. Spt4, the NGN domain of Spt5, Rpb1, Rbp2, Rbp4 and Rpb7 are shown in colors as indicated. Other subunits of RNAP II are shown in gray. The template DNA, non-template DNA and RNA transcript are shown as blue, greencyan and red ribbon structures, respectively. Residues of RNAP II that cross-linked to Spt5 are shown in purple. The Spt4/Spt5-NGN structure [PDB 2EXU (10)] is docked onto the RNAP II clamp based on the archaeal Spt4/5-RNAP clamp structure (9) and our Bpa cross-linking data. The likely locations of the Spt5 KOW domains are marked with red dashed-line ellipses. (B) Schematic cut-away view of the interaction architecture. The dashed line indicates the open clamp position observed in the absence of Rpb4/7 [PDB 1I50 (44)].
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Figure 3: Architecture of interactions between Spt4/5 and RNAP II. (A) Locations of Spt4 and different domains of Spt5 on RNAP II. The sources of the RNAP II structure are the same as those of Figure 1E. Spt4, the NGN domain of Spt5, Rpb1, Rbp2, Rbp4 and Rpb7 are shown in colors as indicated. Other subunits of RNAP II are shown in gray. The template DNA, non-template DNA and RNA transcript are shown as blue, greencyan and red ribbon structures, respectively. Residues of RNAP II that cross-linked to Spt5 are shown in purple. The Spt4/Spt5-NGN structure [PDB 2EXU (10)] is docked onto the RNAP II clamp based on the archaeal Spt4/5-RNAP clamp structure (9) and our Bpa cross-linking data. The likely locations of the Spt5 KOW domains are marked with red dashed-line ellipses. (B) Schematic cut-away view of the interaction architecture. The dashed line indicates the open clamp position observed in the absence of Rpb4/7 [PDB 1I50 (44)].

Mentions: In view of the observations that the archaeal Spt5 NGN interacts with the RNAP clamp and has close proximity to the protrusion (9), it is highly likely that the yeast Spt5 NGN interacts with Rpb1 through the clamp domain and with Rpb2 through the protrusion domain. Spt4 may bind to the other side of the Spt5 NGN and point away from RNAP II (Figure 3A and B). Based on our findings that the Spt5 KOW4 interacts with Rpb1, Rpb4 and Rpb7 (Supplementary Table S8), this domain is likely to reside in the indentation between the Rpb1 clamp and the Rpb4/7 stalk. The Spt5 KOW5 may also reside in or be close to the indentation, as this domain cross-links to Rpb1 and the KOW4-5 linker cross-links to Rpb4. The Spt5 KOW3 may interact with the clamp region that is between the coiled coil and the base of the clamp. The KOW1, which is adjacent to the NGN, and KOW2, which is adjacent to KOW3, may also reside in or be close to the region between the coiled coil and the base of the clamp, although we did not detect direct interactions of the KOW1-2 with any RNAP II subunits. It is possible that the KOW1–2 domains of Spt5 bulge away from the RNAP II surface. The acidic and CTR domains of Spt5 might not directly interact with RNAP II. This is supported by previous studies showing that the acidic and CTR domains of Spt5 are not required for binding of Spt5 to RNAP II (23,41-43). We must note that the proposed model of Spt4/5-RNAP II interaction architecture is based on non-exhaustive Bpa substitutions.


Insights into how Spt5 functions in transcription elongation and repressing transcription coupled DNA repair.

Li W, Giles C, Li S - Nucleic Acids Res. (2014)

Architecture of interactions between Spt4/5 and RNAP II. (A) Locations of Spt4 and different domains of Spt5 on RNAP II. The sources of the RNAP II structure are the same as those of Figure 1E. Spt4, the NGN domain of Spt5, Rpb1, Rbp2, Rbp4 and Rpb7 are shown in colors as indicated. Other subunits of RNAP II are shown in gray. The template DNA, non-template DNA and RNA transcript are shown as blue, greencyan and red ribbon structures, respectively. Residues of RNAP II that cross-linked to Spt5 are shown in purple. The Spt4/Spt5-NGN structure [PDB 2EXU (10)] is docked onto the RNAP II clamp based on the archaeal Spt4/5-RNAP clamp structure (9) and our Bpa cross-linking data. The likely locations of the Spt5 KOW domains are marked with red dashed-line ellipses. (B) Schematic cut-away view of the interaction architecture. The dashed line indicates the open clamp position observed in the absence of Rpb4/7 [PDB 1I50 (44)].
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Related In: Results  -  Collection

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Figure 3: Architecture of interactions between Spt4/5 and RNAP II. (A) Locations of Spt4 and different domains of Spt5 on RNAP II. The sources of the RNAP II structure are the same as those of Figure 1E. Spt4, the NGN domain of Spt5, Rpb1, Rbp2, Rbp4 and Rpb7 are shown in colors as indicated. Other subunits of RNAP II are shown in gray. The template DNA, non-template DNA and RNA transcript are shown as blue, greencyan and red ribbon structures, respectively. Residues of RNAP II that cross-linked to Spt5 are shown in purple. The Spt4/Spt5-NGN structure [PDB 2EXU (10)] is docked onto the RNAP II clamp based on the archaeal Spt4/5-RNAP clamp structure (9) and our Bpa cross-linking data. The likely locations of the Spt5 KOW domains are marked with red dashed-line ellipses. (B) Schematic cut-away view of the interaction architecture. The dashed line indicates the open clamp position observed in the absence of Rpb4/7 [PDB 1I50 (44)].
Mentions: In view of the observations that the archaeal Spt5 NGN interacts with the RNAP clamp and has close proximity to the protrusion (9), it is highly likely that the yeast Spt5 NGN interacts with Rpb1 through the clamp domain and with Rpb2 through the protrusion domain. Spt4 may bind to the other side of the Spt5 NGN and point away from RNAP II (Figure 3A and B). Based on our findings that the Spt5 KOW4 interacts with Rpb1, Rpb4 and Rpb7 (Supplementary Table S8), this domain is likely to reside in the indentation between the Rpb1 clamp and the Rpb4/7 stalk. The Spt5 KOW5 may also reside in or be close to the indentation, as this domain cross-links to Rpb1 and the KOW4-5 linker cross-links to Rpb4. The Spt5 KOW3 may interact with the clamp region that is between the coiled coil and the base of the clamp. The KOW1, which is adjacent to the NGN, and KOW2, which is adjacent to KOW3, may also reside in or be close to the region between the coiled coil and the base of the clamp, although we did not detect direct interactions of the KOW1-2 with any RNAP II subunits. It is possible that the KOW1–2 domains of Spt5 bulge away from the RNAP II surface. The acidic and CTR domains of Spt5 might not directly interact with RNAP II. This is supported by previous studies showing that the acidic and CTR domains of Spt5 are not required for binding of Spt5 to RNAP II (23,41-43). We must note that the proposed model of Spt4/5-RNAP II interaction architecture is based on non-exhaustive Bpa substitutions.

Bottom Line: Through its KOW4-5 domains, Spt5 extensively interacts with Rpb4/7.Deletion of Spt5 KOW4-5 domains decreases transcription elongation and derepresses TCR.Our findings suggest that Spt5 is a key coordinator for holding the RNAP II complex in a closed conformation that is highly competent for transcription elongation but repressive to TCR.

View Article: PubMed Central - PubMed

Affiliation: Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA.

Show MeSH
Related in: MedlinePlus