Yeast Upf proteins required for RNA surveillance affect global expression of the yeast transcriptome.

mRNAs are monitored for errors in gene expression by RNA surveillance, in which mRNAs that cannot be fully translated are degraded by the nonsense-mediated mRNA decay pathway (NMD). RNA surveillance ensures that potentially deleterious truncated proteins are seldom made. NMD pathways that promote surveillance have been found in a wide range of eukaryotes. In Saccharomyces cerevisiae, the proteins encoded by the UPF1, UPF2, and UPF3 genes catalyze steps in NMD and are required for RNA surveillance. In this report, we show that the Upf proteins are also required to control the total accumulation of a large number of mRNAs in addition to their role in RNA surveillance. High-density oligonucleotide arrays were used to monitor global changes in the yeast transcriptome caused by loss of UPF gene function. Null mutations in the UPF genes caused altered accumulation of hundreds of mRNAs. The majority were increased in abundance, but some were decreased. The same mRNAs were affected regardless of which of the three UPF gene was inactivated. The proteins encoded by UPF-dependent mRNAs were broadly distributed by function but were underrepresented in two MIPS (Munich Information Center for Protein Sequences) categories: protein synthesis and protein destination. In a UPF(+) strain, the average level of expression of UPF-dependent mRNAs was threefold lower than the average level of expression of all mRNAs in the transcriptome, suggesting that highly abundant mRNAs were underrepresented. We suggest a model for how the abundance of hundreds of mRNAs might be controlled by the Upf proteins.

A factor required for nonsense-mediated mRNA decay in yeast is exported from the nucleus to the cytoplasm by a nuclear export signal sequence.

In Saccharomyces cerevisiae, Upf3p is required for nonsense-mediated mRNA decay (NMD). Although localized primarily in the cytoplasm, Upf3p contains three sequence elements that resemble nuclear localization signals (NLSs) and two sequence elements that resemble nuclear export signals (NESs). We found that a cytoplasmic reporter protein localized to the nucleus when fused to any one of the three NLS-like sequences of Upf3p. A nuclear reporter protein localized to the cytoplasm when fused to one of the NES-like sequences (NES-A). We present evidence that NES-A functions to signal the export of Upf3p from the nucleus. Combined alanine substitutions in the NES-A element caused a re-distribution of Upf3p to a subnuclear location identified as the nucleolus and conferred an Nmd- phenotype. Single mutations in NES-A failed to affect the distribution of Upf3p and were Nmd+. When an NES element from HIV-1 Rev was inserted near the C terminus of a mutant Upf3p containing multiple mutations in NES-A, the cytoplasmic distribution typical of wild-type Upf3p was restored but the cells remained phenotypically Nmd-. These results suggest that NES-A is a functional nuclear export signal. Combined mutations in NES-A may cause multiple defects in protein function leading to an Nmd- phenotype even when export is restored.

Promoter-specific repression of fimB expression by the Escherichia coli nucleoid-associated protein H-NS.

The H-NS protein is a major component of the Escherichia coli nucleoid. Mutations in hns, the gene encoding H-NS, have pleiotropic effects on the cell altering both the expression of a variety of unlinked genes and the inversion rate of the DNA element containing the fimA promoter. We investigated the interaction between H-NS and fimB, the gene encoding the bidirectional recombinase that catalyzes fimA promoter flipping. In beta-galactosidase assays, we found that fimB expression increased approximately fivefold in an hns2-tetR insertion mutant. In gel mobility shift assays with purified H-NS, we have also shown that H-NS bound directly and cooperatively to the fimB promoter region with greater affinity than for any other known H-NS-regulated gene. Furthermore, this high-affinity interaction resulted in a promoter-specific inhibition of fimB transcription. The addition of purified H-NS to an in vitro transcription system yielded a fivefold or greater reduction in fimB-specific mRNA production. However, the marked increase in cellular FimB levels in the absence of H-NS was not the primary cause of the mutant rapid inversion phenotype. These results are discussed in regard to both H-NS as a transcriptional repressor of fimB expression and its role in regulating type 1 pilus promoter inversion.

Relationship between yeast polyribosomes and Upf proteins required for nonsense mRNA decay.

In yeast, the accelerated rate of decay of nonsense mutant mRNAs, called nonsense-mediated mRNA decay, requires three proteins, Upf1p, Upf2p, and Upf3p. Single, double, and triple disruptions of the UPF genes had nearly identical effects on nonsense mRNA accumulation, suggesting that the encoded proteins function in a common pathway. We examined the distribution of epitope-tagged versions of Upf proteins by sucrose density gradient fractionation of soluble lysates and found that all three proteins co-distributed with 80 S ribosomal particles and polyribosomes. Treatment of lysates with RNase A caused a coincident collapse of polyribosomes and each Upf protein into fractions containing 80 S ribosomal particles, as expected for proteins that are associated with polyribosomes. Mutations in the cysteine-rich (zinc finger) and RNA helicase domains of Upf1p caused loss of function, but the mutant proteins remained polyribosome-associated. Density gradient profiles for Upf1p were unchanged in the absence of Upf3p, and although similar, were modestly shifted to fractions lighter than those containing polyribosomes in the absence of Upf2p. Upf2p shifted toward heavier polyribosome fractions in the absence of Upf1p and into fractions containing 80 S particles and lighter fractions in the absence of Upf3p. Our results suggest that the association of Upf2p with polyribosomes typically found in a wild-type strain depends on the presence and opposing effects of Upf1p and Upf3p.

Using a new inbred fish model and cultured fish tissue cells to study Aeromonas hydrophila and Yersinia ruckeri pathogenesis.

An inbred strain of the southern platyfish, Xiphophorus maculatus, was used as a host for Aeromonas hydrophila and Yersinia ruckeri infections. The infections were initiated by holding the platyfish in inoculation baths containing dilutions of virulent A. hydrophila or Y. ruckeri strains. Inoculating the platyfish in this manner resulted in a dose-dependent mortality over a range of bacterial input from 10(5) to 10(8) A. hydrophila and 10(6) to 10(8) Y. ruckeri/ml. Clinical manifestations of A. hydrophila infections were noted in infected platyfish that eventually died, but not in platyfish that survived. In this model, the Y. ruckeri infected fish died before obvious signs of infection were detected. The A. hydrophila strain used to establish the infections was recovered from the kidney and intestine of infected fish that died, but not from survivors receiving the same inoculation dose. Both infective bacteria were tested for the ability to invade a number of different fish and human cultured cells. A hydrophila strain TF7 did not invade of the cells tested, whereas the Y. ruckeri strain invaded fish derived cultured cells, but not human derived Hep-2 cells.

Hsc66, an Hsp70 homolog in Escherichia coli, is induced by cold shock but not by heat shock.

Hsc66 is the second identified Hsp70 protein in Escherichia coli. Mutations in hscA, the gene encoding Hsc66, compensate for some phenotypic effects of a mutation in hns, a gene encoding the cold-inducible, nucleoid-associated protein H-NS. Expression of hscA was not induced upon heat shock but was induced approximately 11-fold 3 h after a shift from 37 to 10 degrees C. Furthermore, hscA was induced upon chloramphenicol addition, which induces the synthesis of other cold-inducible genes. Mapping of the transcription initiation site showed that hscA was cotranscribed with an upstream dnaJ-like gene, hscB; thus, hscB was also cold inducible. The hscBA promoter did not contain a Y-box element found in some cold-inducible promoters. Using two-dimensional electrophoresis, we identified Hsc66 under static 37 degrees C growth conditions and showed that Hsc66 was induced, as well as hscA, 3 h after a cold shock. Growth of an hscA mutant following cold shock was monitored relative to that of an isogenic wild-type strain. While cold shock adaptation as a function of growth rate was not significantly impaired in an hscA mutant, the expression of at least five other proteins was altered in this mutant following cold shock. On the basis of the homology to Hsp70 proteins and the induction following cold shock, we speculate that Hsc66 functions as a cold shock molecular chaperone.

Mutations in a gene encoding a new Hsp70 suppress rapid DNA inversion and bgl activation, but not proU derepression, in hns-1 mutant Escherichia coli.

Mutations in hns, the gene encoding the nucleoid-associated protein H-NS, affect both the expression of many specific unlinked genes and the inversion rate of the DNA segment containing the pilA promoter in Escherichia coli. A second-site mutation, termed hscA1, compensated for the effect of an hns-1 mutant allele on the pilA promoter inversion rate and on activation of the bgl operon. The proU operon, induced in an hns-1 background, remained derepressed in an hns-1 hscA1 strain and was induced at an intermediate level in an hns hscA1 strain. An insertion mutant allele, hscA2-cat, conferred the same partial hns-1 compensatory phenotype as the hscA1 allele. The hscA gene encoded a 66-kDa protein product that is a member of the Hsp70 protein class. The gene encoding this product is part of a bicistronic operon that is preceded by a possible sigma 32 promoter and also encodes a 21-kDa protein with significant homology to the DnaJ protein family. The mutation defining the hscA1 allele resulted in a phenylalanine substituting a conserved serine residue located in the ATP-binding region of other Hsp70 proteins.