Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5

Zhou, Karen; Kuo, Wei Hung William; Fillingham, Jeffrey; Greenblatt, Jack

doi:10.1073/pnas.0806302106

Cited by 141 publications

(201 citation statements)

References 55 publications

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“…7C, the slower migrating band reflecting the phosphorylated Spt5 cannot be detected in bur2⌬ cells. This indicates that the Bur kinase is responsible for phosphorylation of Spt5 at the CTR, in agreement with two recent reports (60,61).…”

Section: Phosphorylation Of the Spt5 Ctr Domain By Bur Kinase Plays Asupporting

confidence: 81%

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The C-terminal Repeat Domain of Spt5 Plays an Important Role in Suppression of Rad26-independent Transcription Coupled Repair

Ding

LeJeune

2010

Journal of Biological Chemistry

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In eukaryotic cells, transcription coupled nucleotide excision repair (TCR) is believed to be initiated by RNA polymerase II (Pol II) stalled at a lesion in the transcribed strand of a gene. Rad26, the yeast homolog of the human Cockayne syndrome group B (CSB) protein, plays an important role in TCR. Spt4, a transcription elongation factor that forms a complex with Spt5, has been shown to suppress TCR in rad26⌬ cells. Here we present evidence that Spt4 indirectly suppresses Rad26-independent TCR by protecting Spt5 from degradation and stabilizing the interaction of Spt5 with Pol II. We further found that the C-terminal repeat (CTR) domain of Spt5, which is dispensable for cell viability and is not involved in interactions with Spt4 and Pol II, plays an important role in the suppression. The Spt5 CTR is phosphorylated by the Bur kinase. Inactivation of the Bur kinase partially alleviates TCR in rad26⌬ cells. We propose that the Spt5 CTR suppresses Rad26-independent TCR by serving as a platform for assembly of a multiple protein suppressor complex that is associated with Pol II. Phosphorylation of the Spt5 CTR by the Bur kinase may facilitate the assembly of the suppressor complex. Nucleotide excision repair (NER)2 is a conserved DNA repair mechanism capable of removing a variety of helix-distorting lesions, such as UV-induced cyclobutane pyrimidine dimers (CPDs) (1). NER can be grouped into two pathways: global genomic repair (GGR), which refers to repair throughout the genome, and transcription coupled repair (TCR), which refers to a repair mechanism that is dedicated to the transcribed strand of actively transcribed genes (2). In the yeast Saccharomyces cerevisiae, Rad7, Rad16 (3), and Elc1 (4) are specifically required for GGR, but dispensable for TCR. Rad7 and Rad16 form a complex that binds specifically to UV-damaged DNA in an ATP-dependent manner and has DNA-dependent ATPase activity (5). Elc1 has been shown to be a component of a ubiquitin ligase that contains Rad7 and Rad16, and is responsible for regulating the levels of Rad4 protein in response to UV damage (6, 7). It has also been suggested that Elc1 is a component of another ubiquitin ligase complex, which contains Ela1, Cul3, and Roc1 but not Rad7 and Rad16 (8,9). The role of Elc1 in GGR may not be subsidiary to that of Rad7 and Rad16 (4).The mechanistic details of TCR are relatively well understood in Escherichia coli. The transcription repair coupling factor Mfd targets the transcribed strand for repair by recognizing a stalled RNA polymerase and actively recruiting the NER machinery to the transcription blocking lesion as it dissociates the stalled RNA polymerase (10). Conversely, the TCR mechanisms in eukaryotes appear to be extremely complicated (for reviews, see Refs. 11 and 12). In mammalian cells, Cockayne syndrome group A (CSA) and B (CSB) proteins are specifically required for TCR, but dispensable for GGR (13-16). Like its human homolog CSB, the yeast Rad26 plays an important role in TCR but is dispensable for GGR (17). Both human CSB (18) ...

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Section: Phosphorylation Of the Spt5 Ctr Domain By Bur Kinase Plays Asupporting

confidence: 81%

“…It was found recently that the Spt5 CTR is a platform for the association of proteins that promote both transcription elongation and histone modification in transcribed regions (61). One protein complex recruited by the Spt5 CTR is PAF (61).…”

Section: Discussionmentioning

confidence: 99%

The C-terminal Repeat Domain of Spt5 Plays an Important Role in Suppression of Rad26-independent Transcription Coupled Repair

Ding

LeJeune

2010

Journal of Biological Chemistry

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“…Bur1 regulates transcription elongation by phosphorylating the Spt5 elongation factor (23). As predicted by our data, mutation of neither GCN5 nor ESA1 were able to fully eliminate the acetylation signal observed on this protein (Fig.…”

Section: Fig 4 Analysis Of Sites Targeted By Sirtuin Gcn5 and Esa1supporting

confidence: 60%

“…These proteins function in diverse biological processes and include proteins known to function in the same complex or pathway. For example, acetylated peptides from both the Bur1 kinase and its target Spt5 (23,24), a regulator of transcription elongation, were classified as high-confidence hits in our analyses (supplemental Table S1 and Fig. 2A).…”

Section: Resultsmentioning

confidence: 99%

Acetylome Profiling Reveals Overlap in the Regulation of Diverse Processes by Sirtuins, Gcn5, and Esa1

Downey

Johnson

Davey

et al. 2015

Molecular & Cellular Proteomics

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Although histone acetylation and deacetylation machineries (HATs and HDACs) regulate important aspects of cell function by targeting histone tails, recent work highlights that non-histone protein acetylation is also pervasive in eukaryotes. Here, we use quantitative mass-spectrometry to define acetylations targeted by the sirtuin family, previously implicated in the regulation of non-histone protein acetylation. To identify HATs that promote acetylation of these sites, we also performed this analysis in gcn5 (SAGA) and esa1 (NuA4) mutants. We observed strong sequence specificity for the sirtuins and for each of these HATs. Although the Gcn5 and Esa1 consensus sequences are entirely distinct, the sirtuin consensus overlaps almost entirely with that of Gcn5, suggesting a strong coordination between these two regulatory enzymes. Furthermore, by examining global acetylation in an ada2 mutant, which dissociates Gcn5 from the SAGA complex, we found that a subset of Gcn5 targets did not depend on an intact SAGA complex for targeting. Our work provides a framework for understanding how HAT and HDAC enzymes collaborate to regulate critical cellular processes related to growth and division. Molecular & Cellular

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“…In yeast, the BUR kinase is important for the phosphorylation of Spt5 in vivo and can also phosphorylate the Spt5 CTR in vitro (109). It has been suggested that the CTR may serve as a platform to recruit other elongation factors such as the PAF complex (106,109).…”

Section: Discussionmentioning

confidence: 99%

Histone Variant H2A.Z and RNA Polymerase II Transcription Elongation

Santisteban

Hang

Smith

2011

Molecular and Cellular Biology

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Nucleosomes containing histone variant H2A.Z (Htz1) serve to poise quiescent genes for activation and transcriptional initiation. However, little is known about their role in transcription elongation. Here we show that dominant mutations in the elongation genes SPT5 and SPT16 suppress the hypersensitivity of htz1⌬ strains to drugs that inhibit elongation, indicating that Htz1 functions at the level of transcription elongation. Direct kinetic measurements of RNA polymerase II (Pol II) movement across the 9.5-kb GAL10p-VPS13 gene revealed that the elongation rate of polymerase is 24% slower in the absence of Htz1. We provide evidence for two nonexclusive mechanisms. First, we observed that both the phospho-Ser2 levels in the elongating isoform of Pol II and the loading of Spt5 and Elongator over the GAL1 open reading frame (ORF) depend on Htz1. Second, in the absence of Htz1, the density of nucleosome occupancy is increased over the GAL10p-VPS13 ORF and the chromatin is refractory to remodeling during active transcription. These results establish a mechanistic role for Htz1 in transcription elongation and suggest that Htz1-containing nucleosomes facilitate Pol II passage by affecting the correct assembly and modification status of Pol II elongation complexes and by favoring efficient nucleosome remodeling over the gene.Transcription by RNA polymerase II (Pol II) takes place on a compositionally and topologically complex chromatin template at multiple steps, including promoter activation, transcription initiation, elongation, and termination. A number of mechanisms facilitate the initiation of gene transcription on chromatin templates. Two of the most prominent of these are the remodeling of nucleosomes by DNA-dependent ATPase complexes and the covalent posttranslational modification of histone proteins (20,90). At a minimum, these pathways are thought to act by establishing a permissive chromatin structure at gene promoters, allowing access of site-specific transcription factors and the subsequent recruitment of polymerase and the general factors (25,69).

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Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5

Cited by 141 publications

References 55 publications

The C-terminal Repeat Domain of Spt5 Plays an Important Role in Suppression of Rad26-independent Transcription Coupled Repair

The C-terminal Repeat Domain of Spt5 Plays an Important Role in Suppression of Rad26-independent Transcription Coupled Repair

Acetylome Profiling Reveals Overlap in the Regulation of Diverse Processes by Sirtuins, Gcn5, and Esa1

Histone Variant H2A.Z and RNA Polymerase II Transcription Elongation

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