DNA-Binding Specificity of Mcm1: Operator Mutations That Alter DNA-Bending and Transcriptional Activities by a MADS Box Protein

Acton, Thomas; Zhong, Hualin; Vershon, Andandrew K.

doi:10.1128/mcb.17.4.1881

Cited by 62 publications

(82 citation statements)

References 54 publications

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“…6A. Mcm1 binds as a dimer to its cognate sequence to produce a 66°bend in the DNA at multiple sites in ARS120 (1,66). We have shown that Mcm1 binds cooperatively to four MCEs in the C domain of ARS120 to protect four clustered sequences spanning a 250-bp region.…”

Section: Discussionmentioning

confidence: 99%

Mcm1 Promotes Replication Initiation by Binding Specific Elements at Replication Origins

Chang

Donato

Chan

et al. 2004

Molecular and Cellular Biology

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Replication of DNA must be inherently accurate and precisely regulated. It is therefore not surprising that the mechanism for the initiation of DNA replication is both complex and conserved. Initiation of DNA synthesis involves the assembly of a multicomponent complex at designated sites known as replication origins. While the protein components of the prereplication complex (pre-RC) used in this initiation process are conserved in all eukaryotes (5), there is little in common between the nucleotide sequences of replication origins within each eukaryote and between different eukaryotes (29).In Saccharomyces cerevisiae, replication origins (ORI) consist of defined sequences of about 200 bp that can replicate autonomously independently of their native chromosomal environment. These autonomously replicating sequences (ARSs) are modular in structure. They contain a ubiquitous 11-bp (5Ј-WTTTAYRTTTW) ARS consensus sequence (ACS) (11,22,63) where the origin recognition complex (ORC) binds (4). In certain ARSs, a 10-of-11 match of the ACS is sufficient for ORC recognition (64). The ACS is essential but not sufficient for autonomous replication. cis elements on the 5Ј (C domain) or the 3Ј (B domain) flanking sequences of the ACS are also required (12). Elements in the B domain of one particular ARS, ARS1, have been characterized in great detail. Three elements, known as B1, B2, and B3, have been identified (44). B1 is protected by the ORC (55), whereas B3 is protected by Abf1 (41) or Mcm1 (17) in in vitro footprinting analyses. Initiation of DNA synthesis at ARS1 has been mapped to a region between the B1 and B2 elements (6). Two of the three B elements in combination with the ACS are sufficient to promote autonomous replication. Although B elements of different ARSs are not conserved in nucleotide sequence, they are interchangeable between certain ARSs (31, 54, 61). The differences in size and modular composition of replication origins suggest that there are many ways to assemble a functional replication origin from a finite set of modules (60)(61)(62)65). The plasticity in the organization of replication origins is further illustrated by the dispensability of the B elements altogether in the presence of the C domain in several telomeric ARSs (13). However, because the C domain is generally larger, elements in the C domain have not been characterized.The redundant functions of the B and C domains in promoting replication initiation suggest that although the process of pre-RC assembly may be conserved, there are many ways to create an environment conducive to this assembly process. The concept of alternative pathways for creating an environment for pre-RC assembly is especially appealing in higher eukaryotes, where there appears not to be a unifying mechanism for site selection for pre-RC assembly. In Xenopus oocytes, replication initiation occurs at random sequences (38). In mammalian cells, initiation occurs at multiple sites within replication zones that are defined by their chromosomal contexts rather than nucleotide...

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Section: Discussionmentioning

confidence: 99%

Mcm1 Promotes Replication Initiation by Binding Specific Elements at Replication Origins

Chang

Donato

Chan

et al. 2004

Molecular and Cellular Biology

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“…It was previously known that four of the genes found in this cluster, CLB1, CLB2, SWI5, and BUD4, are regulated by a combination of two transcription factors, Mcm1p and SFF (Althoefer et al, 1995;Sanders and Herskowitz, 1996). Mcm1p binds to the consensus TTACCNAAT-TNGGTAA (Acton et al, 1997), whereas, on the basis of three of these genes, SFF was thought to bind to the consensus sequence GTMAACAA. Furthermore, transcription of CLB1, CLB2, and SWI5 was known to be induced by Clb2p activity, possibly because of posttranslational activation of SFF (Amon et al, 1993).…”

Section: The S and M Clustersmentioning

confidence: 99%

Comprehensive Identification of Cell Cycle–regulated Genes of the YeastSaccharomyces cerevisiaeby Microarray Hybridization

Spellman

Sherlock

Zhang

et al. 1998

MBoC

4,313

117

4,374

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We sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA microarrays and samples from yeast cultures synchronized by three independent methods: ␣ factor arrest, elutriation, and arrest of a cdc15 temperature-sensitive mutant. Using periodicity and correlation algorithms, we identified 800 genes that meet an objective minimum criterion for cell cycle regulation. In separate experiments, designed to examine the effects of inducing either the G1 cyclin Cln3p or the B-type cyclin Clb2p, we found that the mRNA levels of more than half of these 800 genes respond to one or both of these cyclins. Furthermore, we analyzed our set of cell cycle-regulated genes for known and new promoter elements and show that several known elements (or variations thereof) contain information predictive of cell cycle regulation. A full description and complete data sets are available at

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“…Oligonucleotides containing mutant URS1 H sites were also cloned into the SalI site of pUC18, and the 58-bp HindIII/BamHI fragments containing these sites were used in the EMSAs described below. Plasmids pAV73, p⌬SS, and pTBA30 are derivatives of pLG⌬312S and contain a CYC1-lacZ fusion under the control of the CYC1 promoter (1,17,46). These plasmids differ only by the presence (pAV73) or absence (p⌬SS and pTBA30) of the endogenous CYC1 UAS sites.…”

Section: Methodsmentioning

confidence: 99%

Analysis of a Meiosis-Specific URS1 Site: Sequence Requirements and Involvement of Replication Protein A

Gailus‐Durner

Chintamaneni

Wilson

et al. 1997

Molecular and Cellular Biology

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URS1 is a transcriptional repressor site found in the promoters of a wide variety of yeast genes that are induced under stress conditions. In the context of meiotic promoters, URS1 sites act as repressor sequences during mitosis and function as activator sites during meiosis. We have investigated the sequence requirements of the URS1 site of the meiosis-specific HOP1 gene (URS1 H ) and have found differences compared with a URS1 site from a nonmeiotic gene. We have also observed that the sequence specificity for meiotic activation at this site differs from that for mitotic repression. Base pairs flanking the conserved core sequence enhance meiotic induction but are not required for mitotic repression of HOP1. Electrophoretic mobility shift assays of mitotic and meiotic cell extracts show a complex pattern of DNA-protein complexes, suggesting that several different protein factors bind specifically to the site. We have determined that one of the complexes of URS1 H is formed by replication protein A (RPA). Although RPA binds to the double-stranded URS1 H site in vitro, it has much higher affinity for single-stranded than for double-stranded URS1 H , and one-hybrid assays suggest that RPA does not bind to this site at detectable levels in vivo. In addition, conditional-lethal mutations in RPA were found to have no effect on URS1 H -mediated repression. These results suggest that although RPA binds to URS1 H in vitro, it does not appear to have a functional role in transcriptional repression through this site in vivo.

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DNA-Binding Specificity of Mcm1: Operator Mutations That Alter DNA-Bending and Transcriptional Activities by a MADS Box Protein

Cited by 62 publications

References 54 publications

Mcm1 Promotes Replication Initiation by Binding Specific Elements at Replication Origins

Mcm1 Promotes Replication Initiation by Binding Specific Elements at Replication Origins

Comprehensive Identification of Cell Cycle–regulated Genes of the YeastSaccharomyces cerevisiaeby Microarray Hybridization

Analysis of a Meiosis-Specific URS1 Site: Sequence Requirements and Involvement of Replication Protein A

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