Nonsense codon suppression in fission yeast due to mutations of tRNA(Ser.11) and translation release factor Sup35 (eRF3)

Chromatin-mediated regulators of meiotic recombination revealed by proteomics of a recombination hotspot

Background

Meiotic recombination hotspots control the frequency and distribution of Spo11 (Rec12)-initiated recombination in the genome. Recombination occurs within and is regulated in part by chromatin structure, but relatively few of the many chromatin remodeling factors and histone posttranslational modifications (PTMs) have been interrogated for a role in the process.

Results

We developed a chromatin affinity purification and mass spectrometry-based approach to identify proteins and histone PTMs that regulate recombination hotspots. Small (4.2 kbp) minichromosomes (MiniCs) bearing the fission yeast ade6-M26 hotspot or a basal recombination control were purified approximately 100,000-fold under native conditions from meiosis; then, associated proteins and histone PTMs were identified by mass spectrometry. Proteins and PTMs enriched at the hotspot included known regulators (Atf1, Pcr1, Mst2, Snf22, H3K14ac), validating the approach. The abundance of individual histones varied dynamically during meiotic progression in hotspot versus basal control MiniCs, as did a subset of 34 different histone PTMs, implicating these as potential regulators. Measurements of basal and hotspot recombination in null mutants confirmed that additional, hotspot-enriched proteins are bona fide regulators of hotspot activation within the genome. These chromatin-mediated regulators include histone H2A-H2B and H3-H4 chaperones (Nap1, Hip1/Hir1), subunits of the Ino80 complex (Arp5, Arp8), a DNA helicase/E3 ubiquitin ligase (Rrp2), components of a Swi2/Snf2 family remodeling complex (Swr1, Swc2), and a nucleosome evictor (Fft3/Fun30).

Conclusions

Overall, our findings indicate that a remarkably diverse collection of chromatin remodeling factors and histone PTMs participate in designating where meiotic recombination occurs in the genome, and they provide new insight into molecular mechanisms of the process.

Electronic supplementary material

The online version of this article (10.1186/s13072-018-0233-x) contains supplementary material, which is available to authorized users.

Generation of an arginine-tRNA-adapted Saccharomyces cerevisiae strain for effective heterologous protein expression

The tRNA population reflects the codon bias of the organism and affects the translation of heterologous target mRNA molecules. In this study, Saccharomyces cerevisiae strains with modified levels of rare tRNA were engineered, that allowed efficient generation of recombinant proteins with unfavorable codon usage. We established a novel synthetic tRNA expression cassette and verified functional nonsense suppressor tRNA^GlnS_CUA generation in a stop codon read-through assay with a modified β-galactosidase reporter gene. Correlation between altered tRNA and protein level was shown by survival of copper sensitive S. cerevisiae cells in the presence of copper ions by an increased transcription of tRNA^Arg_CCG molecules, recognizing rare codons in a modified CUP1 gene. Genome integration of tRNA expression cassette led to the generation of arginine-tRNA-adapted S. cerevisiae strains, which showed elevated tRNA levels (tRNA^Arg_CCG, tRNA^Arg_GCG and tRNA^Arg_UCG) pairing to rare codons. The modified strain MNY3 revealed a considerably improved monitoring of protein-protein interaction from Aspergillus fumigatus bait and prey sequences in yeast two-hybrid experiments. In future, this principle to overcome limited recombinant protein expression by tRNA adaption of expression strains instead of codon adaption might provide new designer yeast cells for an efficient protein production and for improved genome-wide protein-protein interaction analyses.

Unique properties of multiple tandem copies of the M26 recombination hotspot in mitosis and meiosis in Schizosaccharomyces pombe

The M26 hotspot of the fission yeast Schizosaccharomyces pombe is one of the best-characterized eukaryotic hotspots of recombination. The hotspot requires a seven bp sequence, ATGACGT, that serves as a binding site for the Atf1-Pcr1 transcription factor, which is also required for activity. The M26 hotspot is active in meiosis but not mitosis and is active in some but not all chromosomal contexts and not on a plasmid. A longer palindromic version of M26, ATGACGTCAT, shows significantly greater activity than the seven bp sequence. Here, we tested whether the properties of the seven bp sequence were also true of the longer sequence by placing one, two, or three copies of the sequence into the ade6 gene, where M26 was originally discovered. These constructs were tested for activity when located on a plasmid or on a chromosome in mitosis and meiosis. We found that two copies of the 10bp M26 motif on a chromosome were significantly more active for meiotic recombination than one, but no further increase was observed with three copies. However, three copies of M26 on a chromosome created an Atf1-dependent mitotic recombination hotspot. When located on a plasmid, M26 also appears to behave as a mitotic recombination hotspot; however, this behavior most likely results from Atf1-dependent inter-allelic complementation between the plasmid and chromosomal ade6 alleles.

Dual role of ribosome-associated chaperones in prion formation and propagation

Chaperones of the diverse ubiquitous Hsp70 family are involved in the regulation of ordered self-perpetuating protein aggregates (amyloids and prions), implicated in both devastating diseases and protein-based inheritance. Yeast ribosome-associated chaperone complex (RAC), composed of the Hsp40 protein Zuo1 and non-canonical Hsp70 protein Ssz1, mediates association of the Hsp70 chaperone Ssb with translating ribosomes. Ssb participates in co-translational protein folding, regulation of premature translation termination, and ribosome biogenesis. The loss of Ssb or disruption of RAC results in the increased formation of [PSI ⁺], a prion form of the translation termination factor Sup35 (eRF3). This implicates co-translational protein misfolding in de novo prion formation. However, RAC disruption also destabilizes pre-existing [PSI ⁺] prions, as Ssb, released from ribosomes to the cytosol in the absence of RAC, antagonizes the function of the major cytosolic chaperone, Ssa, in prion propagation. The mechanism of the Ssa/Ssb antagonism is currently under investigation and may include a competition for substrates and/or co-chaperones. Notably, yeast cells with wild-type RAC also release Ssb to the cytosol in certain unfavorable growth conditions, and Ssb contributes to increased prion loss in these conditions. This indicates that the circulation of Ssb between the ribosome and cytosol may serve as a physiological regulator of the formation and propagation of self-perpetuating protein aggregates. Indeed, RAC and Ssb modulate toxicity of some aggregating proteins in yeast. Mammalian cells lack the Ssb ortholog but contain a RAC counterpart, apparently recruiting other Hsp70 protein(s). Thus, amyloid modulation by ribosome-associated chaperones could be applicable beyond yeast.