Conformation of the RNA polymerase II C-terminal domain: circular dichroism of long and short fragments

Bienkiewicz, Ewa A.; Woody, A. Young M.; Woody, Robert W.

doi:10.1006/jmbi.2000.3545

Cited by 81 publications

(96 citation statements)

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“…Thus our NMR and SAXS data are strongly consistent with Dm CTD free in solution adopting a spatially heterogeneous ensemble that is highly dynamic on the approximately nanosecond timescale. This observation is consistent with prior reports which concluded that short CTD-derived peptides are predominantly random in solution, lacking long-range order or temporally persistent tertiary structure 14,15,27,28 . In summary, the unphosphorylated state CTD2 0 is highly disordered, temporally dynamic and contains nearly all trans-proline.…”

Section: Transgenic Flies Reveal a Ctd Region Needed For Developmentsupporting

confidence: 93%

Phosphorylation Induces Sequence-Specific Conformational Switches in the RNA Polymerase II C-Terminal Domain

Showalter

Gibbs

2017

Biophysical Journal

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The carboxy-terminal domain (CTD) of the RNA polymerase II (Pol II) large subunit cycles through phosphorylation states that correlate with progression through the transcription cycle and regulate nascent mRNA processing. Structural analyses of yeast and mammalian CTD are hampered by their repetitive sequences. Here we identify a region of the Drosophila melanogaster CTD that is essential for Pol II function in vivo and capitalize on natural sequence variations within it to facilitate structural analysis. Mass spectrometry and NMR spectroscopy reveal that hyper-Ser5 phosphorylation transforms the local structure of this region via proline isomerization. The sequence context of this switch tunes the activity of the phosphatase Ssu72, leading to the preferential de-phosphorylation of specific heptads. Together, context-dependent conformational switches and biased dephosphorylation suggest a mechanism for the selective recruitment of cis-proline-specific regulatory factors and region-specific modulation of the CTD code that may augment gene regulation in developmentally complex organisms.

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Section: Transgenic Flies Reveal a Ctd Region Needed For Developmentsupporting

confidence: 93%

Phosphorylation Induces Sequence-Specific Conformational Switches in the RNA Polymerase II C-Terminal Domain

Showalter

Gibbs

2017

Biophysical Journal

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“…It has been derived for use with short proline-rich sequences. The models of Park et al (14) and Bienkiewicz et al (35) are more suitable for use with proline-poor sequences.…”

Section: Resultsmentioning

confidence: 99%

“…We are assuming that 100% PPII helix content corresponds to a rigid PPII helix, which one could debate. Our lower bound is estimated from data for a peptide containing no proline (36) and, furthermore, makes use of other, approximate models for estimating PPII content (14,35). As noted above, these prior models are not suitable for use with our poly(proline)-based peptides.…”

Section: Resultsmentioning

confidence: 99%

Host−Guest Study of Left-Handed Polyproline II Helix Formation

et al. 2001

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The importance of the left-handed polyproline II (PPII) helical conformation has recently become apparent. This conformation generally is involved in two important functions: protein-protein interactions and structural integrity. PPII helices play vital roles in a variety of processes including signal transduction, transcription, and cell motility. Proline-rich regions of sequence are often assumed to adopt this structure. Remarkably, little is known about the physical determinants of this secondary structure type. In this study, we have explored the formation of PPII helices by a short poly(proline) peptide. In addition, the results from experiments used to determine the propensities for apolar residues, plus glycine, asparagine, and glutamine, to adopt this structure in a poly(proline)-based host peptide are reported here. Proline possesses the highest intrinsic propensity, with glutamine, alanine, and glycine having surprisingly high propensities.-Branched residues possess the lowest propensities of the residues examined. It is postulated that propensities possessed by apolar residues are due in part to peptide-solvent interactions, and that the remarkably high propensity possessed by glutamine may be due to a side chain to backbone hydrogen bond. These data are the first step toward a molecular understanding of the formation of this important, and yet little studied, secondary structure.In recent years, the left-handed polyproline II (PPII) 1 helical conformation has been elevated from the status of a relatively rare and seemingly uninteresting secondary structure to one that is surprisingly common and of the utmost importance. This structure plays a central role in numerous vital processes including signal transduction, transcription, cell motility, and the immune response. Proline-rich ligands of the cytoskeletal protein profilin (1), as well as those of the SH3, WW, and EVH1 protein interaction domains, are bound in this conformation (2). The peptide ligands of class II MHC molecules are also bound in the PPII conformation (3). PPII helices are major features of collagens (4) and plant cell wall proteins (5). The PPII helix is believed to be the dominant conformation for many proline-rich regions of sequence (PRRs) (6). Sequences not rich in proline also adopt this structure. For example, poly(lysine), poly(glutamate), and poly(aspartate) peptides form PPII helices (7). Around 2% of all residues in known protein structures are found in PPII helices at least four residues long (8, 9). As many as 10% of all residues are found in the PPII conformation, although not necessarily as part of PPII helices (10). PPII helices have also been hypothesized to be a major component of protein denatured states (11-14), giving them a role in a most fundamental process. Recently, Blanch et al. (15) have suggested that the PPII helix might be the precursor conformation in amyloid formation. Given the preceding, it is truly remarkable how little is known about the physical determinants of the PPII helical conformat...

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“…The circular dichroism of tandem heptad fragments indicates that at least eight repeats are necessary to achieve a secondary structure resembling that of the full-length mouse CTD (46). It is interesting that this also is the minimum number of heptads needed to convey viability in yeast (43).…”

Section: Discussionmentioning

confidence: 99%

Evolution of the RNA polymerase II C-terminal domain

Stiller

Hall

2002

Proc. Natl. Acad. Sci. U.S.A.

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In recent years a great deal of biochemical and genetic research has focused on the C-terminal domain (CTD) of the largest subunit (RPB1) of DNA-dependent RNA polymerase II. This strongly conserved domain of tandemly repeated heptapeptides has been linked functionally to important steps in the initiation and processing of mRNA transcripts in both animals and fungi. Although they are absolutely required for viability in these organisms, C-terminal tandem repeats do not occur in RPB1 sequences from diverse eukaryotic taxa. Here we present phylogenetic analyses of RPB1 sequences showing that canonical CTD heptads are strongly conserved in only a subset of eukaryotic groups, all apparently descended from a single common ancestor. Moreover, eukaryotic groups in which the most complex patterns of ontogenetic development occur are descended from this CTD-containing ancestor. Consistent with the results of genetic and biochemical investigations of CTD function, these analyses suggest that the enhanced control over RNA polymerase II transcription conveyed by acquired CTD͞protein interactions was an important step in the evolution of intricate patterns of gene expression that are a hallmark of large, developmentally complex eukaryotic organisms. development ͉ RPB1 ͉ transcription E ach of the core subunits present in all cellular DNAdependent RNA polymerase (pol) enzymes shares a common evolutionary origin (1, 2). The largest of these subunits contains eight highly conserved domains, designated regions A through H (2), which are common to all prokaryotic and eukaryotic homologues (3). Unlike all other members of this protein family, however, the largest subunit of eukaryotic RNA pol II has an additional C-terminal domain (CTD), comprising a varied number of tandemly repeated heptapeptides with the consensus sequence Tyr-1-Ser-2-Pro-3-Thr-4 -Ser-5-Pro-6 -Ser-7 (4). In animals and yeast, where the mechanics of transcription are understood most clearly, the CTD has become a focal point of investigations into the interactions between RNA pol II and a variety of transcription-related proteins.Reversible phosphorylation of the CTD regulates the cycling of RNA pol II between a hypophosphorylated (IIO) form, which is competent to enter the preinitiation complex, and a hyperphosphorylated (IIA) form capable of processive transcript elongation (5). Throughout this cycle the CTD binds essential transcription-related proteins that help to regulate gene expression (6-9), promote efficient elongation (10), and effectively couple transcription to pre-mRNA processing (11-15). So central is its role in these interactions that the CTD has been called, by one reviewer, ''the tail that wags the dog'' of RNA pol II (16).Tandemly repeated CTD heptads occur in all RNA pol II largest subunits isolated to date from animals, fungi, and green plants. Given the importance of the CTD for pol II function, it is not surprising that it has been conserved so strongly during the evolution of these groups. A typical CTD also is present in certain protists;...

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Conformation of the RNA polymerase II C-terminal domain: circular dichroism of long and short fragments

Cited by 81 publications

References 81 publications

Phosphorylation Induces Sequence-Specific Conformational Switches in the RNA Polymerase II C-Terminal Domain

Phosphorylation Induces Sequence-Specific Conformational Switches in the RNA Polymerase II C-Terminal Domain

Host−Guest Study of Left-Handed Polyproline II Helix Formation

Evolution of the RNA polymerase II C-terminal domain

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