Transformation of psi- Saccharomyces cerevisiae to psi+ with DNA co-purified with 3 micron circles

Ribosomal RNA Modulates Aggregation of the Podospora Prion Protein HET-s

The role of the nucleic acids in prion aggregation/disaggregation is becoming more and more evident. Here, using HET-s prion from fungi Podospora anserina (P. anserina) as a model system, we studied the role of RNA, particularly of different domains of the ribosomal RNA (rRNA), in its aggregation process. Our results using Rayleigh light scattering, Thioflavin T (ThT) binding, transmission electron microscopy (TEM) and cross-seeding assay show that rRNA, in particular the domain V of the major rRNA from the large subunit of the ribosome, substantially prevents insoluble amyloid and amorphous aggregation of the HET-s prion in a concentration-dependent manner. Instead, it facilitates the formation of the soluble oligomeric “seeds”, which are capable of promoting de novo HET-s aggregation. The sites of interactions of the HET-s prion protein on domain V rRNA were identified by primer extension analysis followed by UV-crosslinking, which overlap with the sites previously identified for the protein-folding activity of the ribosome (PFAR). This study clarifies a missing link between the rRNA-based PFAR and the mode of propagation of the fungal prions.

[PSI(+)] turns 50

The year 2015 sees the fiftieth anniversary of the publication of a research paper that underpins much of our understanding of fungal prion biology, namely "ψ, a cytoplasmic suppressor of super-suppressor in yeast" by Brian Cox. Here we show how our understanding of the molecular nature of the [PSI(+)] determinant evolved from an 'occult' determinant to a transmissible amyloid form of a translation termination factor. We also consider the impact studies on [PSI] have had--and continue to have--on prion research. To demonstrate this, leading investigators in the yeast prion field who have made extensive use of the [PSI(+)] trait in their research, provide their own commentaries on the discovery and significance of [PSI].

Tools for the study of ribosome-borne protein folding activity

In addition to its role in protein synthesis, which involves a peptidyl transferase activity, the ribosome has also been described to be able to assist protein folding, at least in vitro, as presented in a Research Highlight (Das, et al., Biotechnol. J. 2008). This in vitro-described ribosome-borne protein folding activity (RPFA) is yet poorly characterized in vivo, in part because of the lack of tools to study its biological significance. There is substantial evidence documenting RPFA in vitro, and an assay intended to detect this activity in vivo has been set up in bacteria, but this assay is indirect. In this review, we describe the different tools and tests currently available to study RPFA. We put a special emphasis on the various available inhibitors of this activity and in particular, we discuss the use of 6-aminophenanthridine (6AP) and guanabenz (GA), two antiprion drugs that were very recently shown to specifically inhibit RPFA in vitro without any significant effect on the activity of the ribosome in protein synthesis. Therefore, these drugs should allow determining the potential biological role of RPFA. Importantly, the biological activity of 6AP and GA suggest a possible involvement of RPFA in human proteinopathies.

Protein folding activity of ribosomal RNA is a selective target of two unrelated antiprion drugs

BACKGROUND

6-Aminophenanthridine (6AP) and Guanabenz (GA, a drug currently in use for the treatment of hypertension) were isolated as antiprion drugs using a yeast-based assay. These structurally unrelated molecules are also active against mammalian prion in several cell-based assays and in vivo in a mouse model for prion-based diseases.

METHODOLOGY/PRINCIPAL FINDINGS

Here we report the identification of cellular targets of these drugs. Using affinity chromatography matrices for both drugs, we demonstrate an RNA-dependent interaction of 6AP and GA with the ribosome. These specific interactions have no effect on the peptidyl transferase activity of the ribosome or on global translation. In contrast, 6AP and GA specifically inhibit the ribosomal RNA-mediated protein folding activity of the ribosome.

CONCLUSION/SIGNIFICANCE

6AP and GA are therefore the first compounds to selectively inhibit the protein folding activity of the ribosome. They thus constitute precious tools to study the yet largely unexplored biological role of this protein folding activity.

The genetic control of the formation and propagation of the [PSI+] prion of yeast

It is over 40 years since it was first reported that the yeast Saccahromyces cerevisiae contains two unusual cytoplasmic 'genetic' elements: [PSI(+)] and [URE3]. Remarkably the underlying determinants are protein-based rather than nucleic acid-based, i.e., that they are prions, and we have already learnt much about their inheritance and phenotypic effects from the application of 'classical' genetic studies alongside the more modern molecular, cellular and biochemical approaches. Of particular value has been the exploitation of chemical mutagens and 'antagonistic' mutants which directly affect the replication and/or transmission of yeast prions. In this Chapter we describe what has emerged from the application of classical and molecular genetic studies, to the most intensively studied of the three native yeast prions, the [PSI(+)] prion.

[PSI+]: an epigenetic modulator of translation termination efficiency

The [PSI+] factor of the yeast Saccharomyces cerevisiae is an epigenetic regulator of translation termination. More than three decades ago, genetic analysis of the transmission of [PSI+] revealed a complex and often contradictory series of observations. However, many of these discrepancies may now be reconciled by a revolutionary hypothesis: protein conformation-based inheritance (the prion hypothesis). This model predicts that a single protein can stably exist in at least two distinct physical states, each associated with a different phenotype. Propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other. Mounting genetic and biochemical evidence suggests that the determinant of [PSI+] is the nuclear encoded Sup35p, a component of the translation termination complex. Here we review the series of experiments supporting the yeast prion hypothesis and provide another look at the 30 years of work preceding this theory in light of our current state of knowledge.

[PSI] and [URE3] as yeast prions

[URE3] is a non-Mendelian genetic element that mimics recessive mutations in the chromosomal URE2 gene making cells derepressed for nitrogen catabolic enzymes. [PSI] is a non-Mendelian enhancer of readthrough of translational termination similar in its effects to some mutations in the chromosomal SUP35 gene. Three lines of evidence led to the proposal that both [URE3] and [PSI] are prions, infectious proteins analogous to the scrapie agent mediating transmissible spongiform encephalopathies of mammals. 1) Both [PSI] and [URE3] are reversibly curable. 2) [PSI] propagation requires SUP35 and [URE3] propagation requires URE2 with recessive chromosomal mutants having the same phenotypes as the presence of the respective dominant non-Mendelian element. 3) Overproduction of Sup35p and Ure2p increases the frequency of cells acquiring [PSI] or [URE3], respectively.

Cytoplasmic inheritance. Prion-like factors in yeast

Some non-Mendelian genetic factors in yeast have properties reminiscent of prions; inheritance of these prion-like factors may involve the autocatalytic conversion of a protein from one metastable state to another.

Expression and inheritance of the yeast extrachromosomal element psi do not depend on RNA polymerase I

The extrachromosomal element psi affects translation fidelity in the yeast Saccharomyces cerevisiae by increasing the efficiency of tRNA-mediated ochre suppression. The nature of the psi factor is unknown, although there is evidence that 3-microns circles from psi+ strains can be used to transform psi- cells to psi+. The 3-microns circles are extrachromosomal copies of the repeating ribosomal DNA unit, which is organized into two transcription units: the 35s rRNA precursor transcribed by RNA polymerase I, and the 5s rRNA transcribed by RNA polymerase III. We used a strain containing a mutation in RNA polymerase I to test whether psi expression and inheritance depended on RNA polI. Neither expression nor inheritance of psi requires intact RNA polI.

Multicopy SUP35 gene induces de-novo appearance of psi-like factors in the yeast Saccharomyces cerevisiae

Previously, we have shown that plasmid-mediated multiplication of Saccharomyces cerevisiae wild-type SUP35 gene leads to omnipotent suppression and is incompatible with psi-factor, which is an endogenous extrachromosomal suppressor. Here, we describe a frequent de-novo appearance of psi-like factors in mitotic progeny of yeast transformants containing multicopy SUP35 gene.

Interactions between chromosomal omnipotent suppressors and extrachromosomal effectors in Saccharomyces cerevisiae

Chromosomal omnipotent suppressor mutations recovered in psi+ strains of Saccharomyces cerevisiae were brought into psi- cytoplasm. SUP46, SUP138 and SUP139 acted as dominant omnipotent suppressors in the psi- cytoplasm though their suppressor activity was substantially reduced. SUP46 and SUP138 conferred recessive thermosensitivity and antibiotic sensitivity in psi- cytoplasm as in psi+ cytoplasm. On the other hand, sup111 through sup115, which acted as recessive omnipotent suppressors in the psi+ cytoplasm, manifested no, or very low, suppressor activity in the psi- cytoplasm. They, however, still enhanced the efficiency of the SUP29 tRNA suppressor in psi- cytoplasm. A multicopy plasmid carrying the wild-type SUP35 gene enhanced the efficiency of sup111 in psi- cytoplasm.

Nonconventional yeasts: their genetics and biotechnological applications

To date, more than 500 species of yeasts have been described. Most of the genetic and biochemical studies have, however, been carried out with Saccharomyces cerevisiae. Although a considerable amount of knowledge has been accumulated on fundamental processes and biotechnological applications of this industrially important yeast, the large variety of other yeast genera and species may offer various advantages for experimental study as well as for product formation in biotechnology. The genetic investigation of these so-called unconventional yeasts is poorly developed and information about corresponding data is dispersed. It is the aim of this review to summarize and discuss the main results of genetic studies and biotechnological applications of unconventional yeasts and to serve as a guide for scientists who wish to enter this field or are interested in only some aspects of these yeasts.