scholarly journals Insights into Transcriptional Regulation by Individual H3K4 Methylation Marks in S. Cerevisiae

Author(s):  
Neha Deshpande ◽  
Rachel A Jordan ◽  
Shelley Henderson Pozzi ◽  
Mary Bryk

Abstract Set1 is a lysine methyltransferase in S. cerevisiae that catalyzes the mono, di and tri methylation of the fourth lysine on the amino terminal tail of histone H3 (H3K4). Set1-like methyltransferases are evolutionarily conserved, and research has linked their function to developmental gene regulation and several cancers in higher eukaryotes. Set1 is a member of the multiprotein COMPASS complex in S. cerevisiae. The H3K4 methylation activity of COMPASS regulates gene expression and chromosome segregation in vivo. The three distinct methyl marks on histone H3K4 act in discrete ways to regulate transcription. Trimethylation of H3K4 is usually associated with active transcription whereas dimethylation of H3K4 is associated with gene repression. In this study, amino acid substitution mutants of SET1 that encode partial function Set1 proteins capable of H3K4me1, H3K4me1 and H3K4me2, or H3K4me1and H3K4me3 were analyzed to learn more about the roles of individual H3K4 methyl marks in transcription. The findings reveal a previously unappreciated role for H3K4me1 in activation of transcription of the HIS3 gene in S. cerevisiae cultures grown under histidine-starvation conditions. Surprisingly, induction of the HIS3 gene in cultures grown under histidine starvation is not accompanied by significant changes in the profiles of H3K4-methylated nucleosomes at the HIS3 gene in SET1 wild-type strains and set1 partial-function mutants. The data show that H3K4me1 supports induction of HIS3 mRNA to wild-type levels under histidine-starvation conditions and that higher-order H3K4 methylation (H3K4me2 and H3K4me3) is not required.

1987 ◽  
Vol 7 (1) ◽  
pp. 294-304 ◽  
Author(s):  
D Pilgrim ◽  
E T Young

Alcohol dehydrogenase isoenzyme III (ADH III) in Saccharomyces cerevisiae, the product of the ADH3 gene, is located in the mitochondrial matrix. The ADH III protein was synthesized as a larger precursor in vitro when the gene was transcribed with the SP6 promoter and translated with a reticulocyte lysate. A precursor of the same size was detected when radioactively pulse-labeled proteins were immunoprecipitated with anti-ADH antibody. This precursor was rapidly processed to the mature form in vivo with a half-time of less than 3 min. The processing was blocked if the mitochondria were uncoupled with carbonyl cyanide m-chlorophenylhydrazone. Mutant enzymes in which only the amino-terminal 14 or 16 amino acids of the presequence were retained were correctly targeted and imported into the matrix. A mutant enzyme that was missing the amino-terminal 17 amino acids of the presequence produced an active enzyme, but the majority of the enzyme activity remained in the cytoplasmic compartment on cellular fractionation. Random amino acid changes were produced in the wild-type presequence by bisulfite mutagenesis of the ADH3 gene. The resulting ADH III protein was targeted to the mitochondria and imported into the matrix in all of the mutants tested, as judged by enzyme activity. Mutants containing amino acid changes in the carboxyl-proximal half of the ADH3 presequence were imported and processed to the mature form at a slower rate than the wild type, as judged by pulse-chase studies in vivo. The unprocessed precursor appeared to be unstable in vivo. It was concluded that only a small portion of the presequence contains the necessary information for correct targeting and import. Furthermore, the information for correct proteolytic processing of the presequence appears to be distinct from the targeting information and may involve secondary structure information in the presequence.


1992 ◽  
Vol 12 (9) ◽  
pp. 4084-4092
Author(s):  
P C McCabe ◽  
H Haubruck ◽  
P Polakis ◽  
F McCormick ◽  
M A Innis

The rap1A gene encodes a 21-kDa, ras-related GTP-binding protein (p21rap1A) of unknown function. A close structural homolog of p21rap1A (65% identity in the amino-terminal two-thirds) is the RSR1 gene product (Rsr1p) of Saccharomyces cerevisiae. Although Rsr1p is not essential for growth, its presence is required for nonrandom selection of bud sites. To assess the similarity of these proteins at the functional level, wild-type and mutant forms of p21rap1A were tested for complementation of activities known to be fulfilled by Rsr1p. Expression of p21rap1A, like multicopy expression of RSR1, suppressed the conditional lethality of a temperature-sensitive cdc24 mutation. Point mutations predicted to affect the localization of p21rap1A or its ability to cycle between GDP and GTP-bound states disrupted suppression of cdc24ts, while other mutations in the 61-65 loop region improved suppression. Expression of p21rap1A could not, however, suppress the random budding phenotype of rsr1 cells. p21rap1A also apparently interfered with the normal activity of Rsrlp, causing random budding in diploid wild-type cells, suggesting an inability of p21rap1A to interact appropriately with Rsr1p regulatory proteins. Consistent with this hypothesis, we found an Rsr1p-specific GTPase-activating protein (GAP) activity in yeast membranes which was not active toward p21rap1A, indicating that p21rap1A may be predominantly GTP bound in yeast cells. Coexpression of human Rap1-specific GAP suppressed the random budding due to expression of p21rap1A or its derivatives, including Rap1AVal-12. Although Rap1-specific GAP stimulated the GTPase of Rsr1p in vitro, it did not dominantly interfere with Rsr1p function in vivo. A chimera consisting of Rap1A1-165::Rsr1p166-272 did not exhibit normal Rsr1p function in the budding pathway. These results indicated that p21rap1A and Rsr1p share at least partial functional homology, which may have implications for p21rap1A function in mammalian cells.


1990 ◽  
Vol 10 (6) ◽  
pp. 2801-2808 ◽  
Author(s):  
D T Mooney ◽  
D B Pilgrim ◽  
E T Young

Point mutations in the presequence of the mitochondrial alcohol dehydrogerase isoenzyme (ADH III) have been shown to affect either the import of the precursor protein into yeast mitochondria in vivo or its processing within the organelle. In the present work, the behavior of these mutants during in vitro import into isolated mitochondria was investigated. All point mutants tested were imported with a slower initial rate than that of the wild-type precursor. This defect was corrected when the precursors were treated with urea prior to import. Once imported, the extent of processing to the mature form of mutant precursors varied greatly and correlated well with the defects observed in vivo. This result was not affected by prior urea treatment. When matrix extracts enriched for the processing protease were used, this defect was shown to be due to failure of the protease to efficiently recognize or cleave the presequence, rather than to a lack of access to the precursor. The rate of import of two ADH III precursors bearing internal deletions in the leader sequence was similar to those of the point mutants, whereas a deletion leading to the removal of the 15 amino-terminal amino acids was poorly imported. The mature amino terminus of wild-type ADH III was determined to be Gln-25. Mutant m01 (Ser-26 to Phe), which reduced the efficiency of cleavage in vitro by 80%, was cleaved at the correct site.


1990 ◽  
Vol 10 (6) ◽  
pp. 3194-3203 ◽  
Author(s):  
A Andrianopoulos ◽  
M J Hynes

The positively acting regulatory gene amdR of Aspergillus nidulans coordinately regulates the expression of five structural genes involved in the catabolism of certain amides (amdS), omega amino acids (gatA and gabA), and lactams (lamA and lamB) in the presence of omega amino acid inducers. Analysis of the amdR gene showed that it contains three small introns, heterogeneous 5' and 3' transcription sites, and multiple AUG codons prior to the major AUG initiator. The predicted amdR protein sequence has a cysteine-rich "zinc finger" DNA-binding motif at the amino-terminal end, four putative acidic transcription activation motifs in the carboxyl-terminal half, and two sequences homologous to the simian virus 40 large T antigen nuclear localization motif. These nuclear localization sequences overlap the cysteine-rich DNA-binding motif. A series of 5', 3', and internal deletions were examined in vivo for transcription activator function and showed that the amdR product contains at least two activation regions in the carboxyl-terminal half. Each of these activator amdR product contains at least two activation regions in the carboxyl-terminal half. Each of these activator regions may function independently, but both are required for wild-type levels of transcription activation. A number of the amdR deletion products were found to compete with the wild-type amdR product in vivo. Development of a rapid method for the localization of amdR mutations is presented, and using this technique, we localized and sequenced the mutation in the semiconstitutive amdR6c allele. The amdR6c missense mutation occurs in the middle of the gene, and it is suggested that it results in an altered protein which activates gene expression efficiently in the absence of an inducer.


1997 ◽  
Vol 17 (10) ◽  
pp. 5679-5687 ◽  
Author(s):  
C P Chang ◽  
Y Jacobs ◽  
T Nakamura ◽  
N A Jenkins ◽  
N G Copeland ◽  
...  

The Pbx1 and Meis1 proto-oncogenes code for divergent homeodomain proteins that are targets for oncogenic mutations in human and murine leukemias, respectively, and implicated by genetic analyses to functionally collaborate with Hox proteins during embryonic development and/or oncogenesis. Although Pbx proteins have been shown to dimerize with Hox proteins and modulate their DNA binding properties in vitro, the biochemical compositions of endogenous Pbx-containing complexes have not been determined. In the present study, we demonstrate that Pbx and Meis proteins form abundant complexes that comprise a major Pbx-containing DNA binding activity in nuclear extracts of cultured cells and mouse embryos. Pbx1 and Meis1 dimerize in solution and cooperatively bind bipartite DNA sequences consisting of directly adjacent Pbx and Meis half sites. Pbx1-Meis1 heterodimers display distinctive DNA binding specificities and cross-bind to a subset of Pbx-Hox sites, including those previously implicated as response elements for the execution of Pbx-dependent Hox programs in vivo. Chimeric oncoprotein E2a-Pbx1 is unable to bind DNA with Meis1, due to the deletion of amino-terminal Pbx1 sequences following fusion with E2a. We conclude that Meis proteins are preferred in vivo DNA binding partners for wild-type Pbx1, a relationship that is circumvented by its oncogenic counterpart E2a-Pbx1.


2007 ◽  
Vol 189 (7) ◽  
pp. 2825-2833 ◽  
Author(s):  
Ray A. Larsen ◽  
Gail E. Deckert ◽  
Kyle A. Kastead ◽  
Surendranathan Devanathan ◽  
Kimberly L. Keller ◽  
...  

ABSTRACT The cytoplasmic membrane protein TonB couples the protonmotive force of the cytoplasmic membrane to active transport across the outer membrane of Escherichia coli. The uncleaved amino-terminal signal anchor transmembrane domain (TMD; residues 12 to 32) of TonB and the integral cytoplasmic membrane proteins ExbB and ExbD are essential to this process, with important interactions occurring among the several TMDs of all three proteins. Here, we show that, of all the residues in the TonB TMD, only His20 is essential for TonB activity. When alanyl residues replaced all TMD residues except Ser16 and His20, the resultant “all-Ala Ser16 His20” TMD TonB retained 90% of wild-type iron transport activity. Ser16Ala in the context of a wild-type TonB TMD was fully active. In contrast, His20Ala in the wild-type TMD was entirely inactive. In more mechanistically informative assays, the all-Ala Ser16 His20 TMD TonB unexpectedly failed to support formation of disulfide-linked dimers by TonB derivatives bearing Cys substitutions for the aromatic residues in the carboxy terminus. We hypothesize that, because ExbB/D apparently cannot efficiently down-regulate conformational changes at the TonB carboxy terminus through the all-Ala Ser16 His20 TMD, the TonB carboxy terminus might fold so rapidly that disulfide-linked dimers cannot be efficiently trapped. In formaldehyde cross-linking experiments, the all-Ala Ser16 His20 TMD also supported large numbers of apparently nonspecific contacts with unknown proteins. The all-Ala Ser16 His20 TMD TonB retained its dependence on ExbB/D. Together, these results suggest that a role for ExbB/D might be to control rapid and nonspecific folding that the unregulated TonB carboxy terminus otherwise undergoes. Such a model helps to reconcile the crystal/nuclear magnetic resonance structures of the TonB carboxy terminus with conformational changes and mutant phenotypes observed at the TonB carboxy terminus in vivo.


1994 ◽  
Vol 14 (12) ◽  
pp. 7839-7854 ◽  
Author(s):  
S M Althoff ◽  
S W Stevens ◽  
J A Wise

Signal recognition particle (SRP) is a cytoplasmic ribonucleoprotein required for targeting a subset of presecretory proteins to the endoplasmic reticulum (ER) membrane. Here we report the results of a series of experiments to define the function of the Schizosaccharomyces pombe homolog of the 54-kDa subunit of mammalian SRP. One-step gene disruption reveals that the Srp54 protein, like SRP RNA, is essential for viability in S. pombe. Precursor to the secretory protein acid phosphatase accumulates in cells in which Srp54 synthesis has been repressed under the control of a regulated promoter, indicating that S. pombe SRP functions in protein targeting. In common with other Srp54 homologs, the S. pombe protein has a modular structure consisting of an amino-terminal G (GTPase) domain and a carboxyl-terminal M (methionine-rich) domain. We have analyzed the effects of 17 site-specific mutations designed to alter the function of each of the four GTPase consensus motifs individually. Several alleles, including some with relatively conservative amino acid substitutions, confer lethal or conditional phenotypes, indicating that GTP binding and hydrolysis are critical to the in vivo role of the protein. Two mutations (R to L at position 194 [R194L] and R194H) which were designed, by analogy to oncogenic mutations in rats, to dramatically decrease the catalytic rate and one (T248N) predicted to alter nucleotide binding specificity produce proteins that are unable to support growth at 18 degrees C. Consistent with its design, the R194L mutant hydrolyzes GTP at a reduced rate relative to wild-type Srp54 in enzymatic assays on immunoprecipitated proteins. In strains that also contain wild-type srp54, this mutant protein, as well as others designed to be locked in a GTP-bound conformation, exhibits temperature-dependent dominant inhibitory effects on growth, while a mutant predicted to be GDP locked does not interfere with the function of the wild-type protein. These results form the basis of a simple model for the role of GTP hydrolysis by Srp54 during the SRP cycle.


2005 ◽  
Vol 52 (2) ◽  
pp. 541-544 ◽  
Author(s):  
Liu Rongrong ◽  
Wang Lixia ◽  
Lin Zhongping

Cre recombinase from bacteriophage P1 is widely used in both in vitro and in vivo DNA manipulations. Based on a structural and functional analysis, three deleted cre mutants were constructed and expressed in Escherichia coli. Mutated recombinases were purified and their recombination activities were determined in vitro. Our results revealed that the mutant with amino-terminal deletion retains the recombination activity as high as wild type Cre; however, the carboxy-terminal deletion and the middle region deletion both lead to a complete loss of the recombinase function.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 326-326
Author(s):  
Alessandro Zarpellon ◽  
Reha Celikel ◽  
Richard McClintock ◽  
James R. Roberts ◽  
G. Loredana Mendolicchio ◽  
...  

Abstract Abstract 326 In spite of two known crystal structures, the mechanisms supporting the interaction between the amino terminal domain of glycoprotein (GP) Ibα (GPIb-N) and α-thrombin (FIIa) are still debated, and a controversial issue concerns the involvement of FIIa exosites I and II in binding. Competition for exosite I could influence processes important for hemostasis and thrombosis. Both known crystal structures show two independent contact interfaces between GPIb-N and bound FIIa in a conformation that involves each exosite interacting with a different GPIb-N molecule. This notwithstanding, a majority of investigators in the field has concluded that exosite II is solely required for FIIa binding to GPIb-N, suggesting that the interface with exosite I is the consequence of crystal packing. The goal of this work was to probe experimentally the role of FIIa exosites in GPIb-N binding. Human GPIb-N contains three Tyr residues (at positions 276, 278 and 279) that can undergo post-translational sulfation (sulfated Tyr = Tys), although this was not the case for Tyr278 in the known crystal structures. To address this discrepancy, we expressed GPIb-N in Drosophila cells - which endogenously contain a single tyrosylprotein sulfotransferase (TPST) gene - co-transfected with human TPST-2, and showed that we could obtain different GPIb-N species with 0 to 3 sulfate moles/protein moles. Using these different GPIb-N forms immobilized onto a surface plasmon resonance (SPR) chip, we determined that the kD of human FIIa binding decreased from 1290 to 89 nM going from 0 to 3 sulfate moles/protein moles. We crystallized the fully sulfated GPIb-N complexed with FIIa and found that Tys278 established contacts not previously seen with exosite II (residues Arg35 and Lys236), thus explaining the contribution of full sulfation to maximal binding efficiency. To establish the effect of TPST-2 on the process of sulfation, we compared the affinity of FIIa binding to distinct wild type GPIb-N species of known sulfate content with that to GPIb-N mutants containing distinct single, double or triple Tyr “Phe substitutions (Phe differs from Tyr for the lack of an OH group and cannot be sulfated) in which the identity of Tys residues could be established. We found that TPST-2 favors Tyr sulfation in the order 276–278-279, which is more efficient for a complete process than the order 276–279 predominant in the absence of TPST-2. We then used different Tyr "Phe (Y to F) mutants to evaluate the effects of the substitution preventing sulfation on FIIa binding to GPIb-N in solution or immobilized onto a SPR chip. We fount that the Y276F mutant had no capacity to form a soluble complex with FIIa, while Y279F could complex about as much FIIa as fully sulfated wild type GPIb-N (82 vs 99% FIIa incorporation). Of note, both Y276F and Y279F mutants had a complete to nearly complete loss of FIIa binding activity in the SPR system. In the crystal structure, the sulfate group on Tys279 establishes three close contacts (3.1, 3.3, 2.8 □) with Trp148 in a FIIa loop neighboring exosite I. On the other hand, Tys276 has closer contacts than Tys279 with residues in exosite II, suggesting that the latter may be sufficient for FIIa binding when GPIb-N is in solution but not immobilized onto a surface. To confirm this hypothesis, we used specific aptamer inhibitors of FIIa exosite II (HD22) or I (HD1) and found that the latter, similar to the Y279F substitution, indeed had no effect on FIIa-GPIb-N soluble complex formation (thus ruling out possible allosteric effects on exosite II influencing GPIb-N binding) but completely prevented FIIa binding to immobilized GPIb-N. Of note, as shown by crystallographic evidence, bound HD1 alters the orientation of Trp148 in manner that would oppose the interaction with Tys279 in GPIb-N, providing a structural explanation for the similar functional effects of the mutation and the inhibitor. Finally, we expressed transgenically wild type or Y279F mutant human GPIbα to replace the homologous chain in the GPIb-IX-V complex of murine platelets and showed that the mutation almost completely impairs FIIa binding to platelets, which is also prevented by inhibition of exosite I with HD1. These results provide functional evidence and a structural explanation for a key role of exosite I, concurrently with exosite II, for FIIa binding to GPIbα. Additional studies are now demonstrating that interfering with this interaction modifies responses to vascular injury in vivo. Disclosures: No relevant conflicts of interest to declare.


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