Francisco Malagón

Transient Reversal of RNA Polymerase II Active Site Closing Controls Fidelity of Transcription Elongation

To study fidelity of RNA polymerase II (Pol II), we analyzed properties of the 6-azauracil-sensitive and TFIIS-dependent E1103G mutant of rbp1 (rpo21), the gene encoding the catalytic subunit of Pol II in Saccharomyces cerevisiae. Using an in vivo retrotransposition-based transcription fidelity assay, we observed that rpb1-E1103G causes a 3-fold increase in transcription errors. This mutant showed a 10-fold decrease in fidelity of transcription elongation in vitro. The mutation does not appear to significantly affect translocation state equilibrium of Pol II in a stalled elongation complex. Primarily, it promotes NTP sequestration in the polymerase active center. Furthermore, pre-steady-state analyses revealed that the E1103G mutation shifted the equilibrium between the closed and the open active center conformations toward the closed form. Thus, open conformation of the active center emerges as an intermediate essential for preincorporation fidelity control. Similar mechanisms may control fidelity of DNA-dependent DNA polymerases and RNA-dependent RNA polymerases.

Mitotic recombination in yeast: elements controlling its incidence.

Mitotic recombination is an important mechanism of DNA repair in eukaryotic cells. Given the redundancy of the eukaryotic genomes and the presence of repeated DNA sequences, recombination may also be an important source of genomic instability. Here we review the data, mainly from the budding yeast S. cerevisiae, that may help to understand the spontaneous origin of mitotic recombination and the different elements that may control its occurrence. We cover those observations suggesting a putative role of replication defects and DNA damage, including double‐strand breaks, as sources of mitotic homologous recombination. An important part of the review is devoted to the experimental evidence suggesting that transcription and chromatin structure are important factors modulating the incidence of mitotic recombination. This is of great relevance in order to identify the causes and risk factors of genomic instability in eukaryotes. Copyright

Rpb9 Subunit Controls Transcription Fidelity by Delaying NTP Sequestration in RNA Polymerase II

Rpb9 is a small non-essential subunit of yeast RNA polymerase II located on the surface on the enzyme. Deletion of the RPB9 gene shows synthetic lethality with the low fidelity rpb1-E1103G mutation localized in the trigger loop, a mobile element of the catalytic Rpb1 subunit, which has been shown to control transcription fidelity. Similar to the rpb1-E1103G mutation, the RPB9 deletion substantially enhances NTP misincorporation and increases the rate of mismatch extension with the next cognate NTP in vitro. Using pre-steady state kinetic analysis, we show that RPB9 deletion promotes sequestration of NTPs in the polymerase active center just prior to the phosphodiester bond formation. We propose a model in which the Rpb9 subunit controls transcription fidelity by delaying the closure of the trigger loop on the incoming NTP via interaction between the C-terminal domain of Rpb9 and the trigger loop. Our findings reveal a mechanism for regulation of transcription fidelity by protein factors located at a large distance from the active center of RNA polymerase II.

Genetic Interactions of DST1 in Saccharomyces cerevisiae Suggest a Role of TFIIS in the Initiation-Elongation Transition

TFIIS promotes the intrinsic ability of RNA polymerase II to cleave the 3′-end of the newly synthesized RNA. This stimulatory activity of TFIIS, which is dependent upon Rpb9, facilitates the resumption of transcription elongation when the polymerase stalls or arrests. While TFIIS has a pronounced effect on transcription elongation in vitro, the deletion of DST1 has no major effect on cell viability. In this work we used a genetic approach to increase our knowledge of the role of TFIIS in vivo. We showed that: (1) dst1 and rpb9 mutants have a synthetic growth defective phenotype when combined with fyv4, gim5, htz1, yal011w, ybr231c, soh1, vps71, and vps72 mutants that is exacerbated during germination or at high salt concentrations; (2) TFIIS and Rpb9 are essential when the cells are challenged with microtubule-destabilizing drugs; (3) among the SDO (synthetic with Dst one), SOH1 shows the strongest genetic interaction with DST1; (4) the presence of multiple copies of TAF14, SUA7, GAL11, RTS1, and TYS1 alleviate the growth phenotype of dst1 soh1 mutants; and (5) SRB5 and SIN4 genetically interact with DST1. We propose that TFIIS is required under stress conditions and that TFIIS is important for the transition between initiation and elongation in vivo.

DIFFERENTIAL INTRACHROMOSOMAL HYPER-RECOMBINATION PHENOTYPE OF SPT4 AND SPT6 MUTANTS OF S. CEREVISIAE

Abstract  In order to test whether mutations affecting transcription also affect DNA recombination, we have determined the influence of a number of snf/swi and spt/sin transcriptional regulatory mutations on the recombination of a DNA inverted repeat. Among the nine different mutations analyzed, we found that spt4 and spt6 confer a significant hyper-recombination phenotpye. Both mutations produced increases in the frequencies of reciprocal exchange/gene conversion and deletion events ranging from 1- to 15-fold above the wild-type levels, as determined in six direct repeat systems and one inverted repeat. The frequency of mitotic recombination between homologs, determined at one chromosomal locus, was not affected. We discuss the intrachromosomal hyper-recombination phenotype of spt4 an spt6 on the basis of the possible functions of SPT4 and SPT6 on transcriptional regulation and on chromatin structure.

The Fidelity of Transcription RPB1 (RPO21) MUTATIONS THAT INCREASE TRANSCRIPTIONAL SLIPPAGE IN S. CEREVISIAE

Background: Yeast RNA polymerase II domains involved in maintenance of transcription register are unknown. Results: We isolated and biochemically characterized RPB1 mutations leading to register loss (transcription slippage). Conclusion: All RPB1 mutations affect slippage localize close to the active center and near the secondary pore of RNA polymerase II. Significance: Our results shed light on the mechanism of slippage by eukaryotic RNA polymerases. The fidelity of RNA synthesis depends on both accurate template-mediated nucleotide selection and proper maintenance of register between template and RNA. Loss of register, or transcriptional slippage, is particularly likely on homopolymeric runs in the template. Transcriptional slippage can alter the coding capacity of mRNAs and is used as a regulatory mechanism. Here we describe mutations in the largest subunit of Saccharomyces cerevisiae RNA polymerase II that substantially increase the level of transcriptional slippage. Alleles of RPB1 (RPO21) with elevated slippage rates were identified among 6-azauracil-sensitive mutants and were also isolated using a slippage-dependent reporter gene. Biochemical characterization of polymerase II isolated from these mutants confirms elevated levels of transcriptional slippage.

Genetic stability and DNA rearrangements associated with a 2 x 1.1-Kb perfect palindrome in Escherichia coli.

Abstract We show that circular plasmids containing perfect palindromic regions of 2 × 1.1 kb can be propagated in sbcC strains of Escherichia coli, a result that is at variance with the well known observation that λ DNA cannot tolerate palindromic regions larger than 2 × 265 bp. However, a significant fraction of these palindrome-containing plasmids can be recovered from E. coli strains either as linear molecules with hairpins at their ends or as head-to-head dimers, both in a RuvC-and RusA-independent manner. Our results suggests that large palindromes may form cruciforms in E. coli. However, palindrome-associated DNA rearrangements occur by a process that does not require any known cruciform resolvase activity. Our data support a replication-dependent model for the induction of DNA rearrangements by perfect palindromes.

Construction and genetic analysis of S. cerevisiae deletants of six novel ORFs from chromosome II.

We have constructed S. cerevisiae strains carrying genomic deletions of six ORFs from the left arm of chromosome II (YBL018c, YBL019w, YBL024w, YBL042c, YBL043w and YBL046w) in both FY1679 and W303 backgrounds. We have found that YBL018c is an essential gene in yeast, whereas the other five genes are non‐essential. We have developed plasmids carrying deletion cassettes that can be used to delete any of the six genes in S. cerevisiae by transforming to G418‐resistance, as well as centromeric plasmids containing the cognate genes. Copyright