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Full-Text Articles in Molecular Biology
Transcriptional Cross Talk Within The Mar-Sox-Rob Regulon In Escherichia Coli Is Limited To The Rob And Marrab Operons, Lon Chubiz, George Glekas, Christopher Rao
Transcriptional Cross Talk Within The Mar-Sox-Rob Regulon In Escherichia Coli Is Limited To The Rob And Marrab Operons, Lon Chubiz, George Glekas, Christopher Rao
Biology Department Faculty Works
Bacteria possess multiple mechanisms to survive exposure to various chemical stresses and antimicrobial compounds. In the enteric bacterium Escherichia coli, three homologous transcription factors—MarA, SoxS, and Rob—play a central role in coordinating this response. Three separate systems are known to regulate the expression and activities of MarA, SoxS, and Rob. However, a number of studies have shown that the three do not function in isolation but rather are coregulated through transcriptional cross talk. In this work, we systematically investigated the extent of transcriptional cross talk in the mar-sox-rob regulon. While the three transcription factors were found to have the potential …
Rna Processing Of Nitrogenase Transcripts In The Cyanobacterium Anabaena Variabilis, Justin Ungerer, Brenda Pratte, Teresa Thiel
Rna Processing Of Nitrogenase Transcripts In The Cyanobacterium Anabaena Variabilis, Justin Ungerer, Brenda Pratte, Teresa Thiel
Biology Department Faculty Works
Little is known about the regulation of nitrogenase genes in cyanobacteria. Transcription of the nifH1 and vnfH genes, encoding dinitrogenase reductases for the heterocyst-specific Mo-nitrogenase and the alternative V-nitrogenase, respectively, was studied by using a lacZ reporter. Despite evidence for a transcription start site just upstream of nifH1 and vnfH, promoter fragments that included these start sites did not drive the transcription of lacZ and, for nifH1, did not drive the expression of nifHDK1. Further analysis using larger regions upstream of nifH1 indicated that a promoter within nifU1 and a promoter upstream of nifB1 both contributed to expression of nifHDK1, …
Computational Design Of Orthogonal Ribosomes, Lon Chubiz, Christopher Rao
Computational Design Of Orthogonal Ribosomes, Lon Chubiz, Christopher Rao
Biology Department Faculty Works
Orthogonal ribosomes (o-ribosomes), also known as specialized ribosomes, are able to selectively translate mRNA not recognized by host ribosomes. As a result, they are powerful tools for investigating translational regulation and probing ribosome structure. To date, efforts directed towards engineering o-ribosomes have involved random mutagenesisbased approaches. As an alternative, we present here a computational method for rationally designing o-ribosomes in bacteria. Working under the assumption that base-pair interactions between the 16S rRNA and mRNA serve as the primary mode for ribosome binding and translational initiation, the algorithm enumerates all possible extended recognition sequences for 16S rRNA and then chooses those …
Mer1p Is A Modular Splicing Factor Whose Function Depends On The Conserved U2 Snrnp Protein Snu17p, Marc Spingola, Javier Armisen, Manuel Ares
Mer1p Is A Modular Splicing Factor Whose Function Depends On The Conserved U2 Snrnp Protein Snu17p, Marc Spingola, Javier Armisen, Manuel Ares
Biology Department Faculty Works
Mer1p activates the splicing of at least three pre‐mRNAs (AMA1, MER2, MER3) during meiosis in the yeast Saccharomyces cerevisiae. We demonstrate that enhancer recognition by Mer1p is separable from Mer1p splicing activation. The C‐terminal KH‐type RNA‐binding domain of Mer1p recognizes introns that contain the Mer1p splicing enhancer, while the N‐terminal domain interacts with the spliceosome and activates splicing. Prior studies have implicated the U1 snRNP and recognition of the 5′ splice site as key elements in Mer1p‐activated splicing. We provide new evidence that Mer1p may also function at later steps of spliceosome assembly. First, Mer1p can activate splicing of introns …
Test Of Intron Predictions Reveals Novel Splice Sites, Alternatively Spliced Mrnas And New Introns In Meiotically Regulated Genes Of Yeast, Carrie Davis, Leslie Grate, Marc Spingola, Manuel Ares
Test Of Intron Predictions Reveals Novel Splice Sites, Alternatively Spliced Mrnas And New Introns In Meiotically Regulated Genes Of Yeast, Carrie Davis, Leslie Grate, Marc Spingola, Manuel Ares
Biology Department Faculty Works
Correct identification of all introns is necessary to discern the protein-coding potential of a eukaryotic genome. The existence of most of the spliceosomal introns predicted in the genome of Saccharomyces cerevisiae remains unsupported by molecular evidence. We tested the intron predictions for 87 introns predicted to be present in non-ribosomal protein genes, more than a third of all known or suspected introns in the yeast genome. Evidence supporting 61 of these predictions was obtained, 20 predicted intron sequences were not spliced and six predictions identified an intron-containing region but failed to specify the correct splice sites, yielding a successful prediction …
Genome-Wide Bioinformatic And Molecular Analysis Of Introns In Saccharomyces Cerevisiae, Marc Spingola, Leslie Grate, David Haussler, Manuel Ares
Genome-Wide Bioinformatic And Molecular Analysis Of Introns In Saccharomyces Cerevisiae, Marc Spingola, Leslie Grate, David Haussler, Manuel Ares
Biology Department Faculty Works
Introns have typically been discovered in an ad hoc fashion: introns are found as a gene is characterized for other reasons. As complete eukaryotic genome sequences become available, better methods for predicting RNA processing signals in raw sequence will be necessary in order to discover genes and predict their expression. Here we present a catalog of 228 yeast introns, arrived at through a combination of bioinformatic and molecular analysis. Introns annotated in the Saccharomyces Genome Database (SGD) were evaluated, questionable introns were removed after failing a test for splicing in vivo, and known introns absent from the SGD annotation were …
Ms2 Coat Protein Mutants Which Bind Qβ Rna, Marc Spingola, David Peabody
Ms2 Coat Protein Mutants Which Bind Qβ Rna, Marc Spingola, David Peabody
Biology Department Faculty Works
The coat proteins of the RNA phages MS2 and Qβ are structurally homologous, yet they specifically bind different RNA structures. In an effort to identify the basis of RNA binding specificity we sought to isolate mutants that convert MS2 coat protein to the RNA binding specificity of Qβ. A library of mutations was created which selectively substitutes amino acids within the RNA binding site. Genetic selection for the ability to repress translation from the Qβ translational operator led to the isolation of several MS2 mutants that acquired binding activity for Qβ RNA. Some of these also had reduced abilities to …