Adaptive expression responses in the Pol-γ null strain of S. pombe depleted of mitochondrial genome

Chu, Zhaoqing; Li, Juntao; Eshaghi, Majid; Karuturi, R. Krishna Murthy; Lin, Kui; Liu, Jianhua

doi:10.1186/1471-2164-8-323

Cited by 22 publications

(21 citation statements)

References 33 publications

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“…A ptp1-1 mutant strain (Cy0989) depleted of mtDNA (49,64) was included as a negative control. This mutant strain contains a nuclear mutation, ptp1-1 , which allows S. pombe cells to grow in the absence of mtDNA (49,64).…”

Section: Resultsmentioning

confidence: 99%

The Schizosaccharomyces pombe PPR protein Ppr10 associates with a novel protein Mpa1 and acts as a mitochondrial translational activator

Wang

Yan

Zhang

et al. 2017

Nucleic Acids Research

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The pentatricopeptide repeat (PPR) proteins characterized by tandem repeats of a degenerate 35-amino-acid motif function in all aspects of organellar RNA metabolism, many of which are essential for organellar gene expression. In this study, we report the characterization of a fission yeast Schizosaccharomyces pombe PPR protein, Ppr10 and a novel Ppr10-associated protein, designated Mpa1. The ppr10 deletion mutant exhibits growth defects in respiratory media, and is dramatically impaired for viability during the late-stationary phase. Deletion of ppr10 affects the accumulation of specific mitochondrial mRNAs. Furthermore, deletion of ppr10 severely impairs mitochondrial protein synthesis, suggesting that Ppr10 plays a general role in mitochondrial protein synthesis. Ppr10 interacts with Mpa1 in vivo and in vitro and the two proteins colocalize in the mitochondrial matrix. The ppr10 and mpa1 deletion mutants exhibit very similar phenotypes. One of Mpa1's functions is to maintain the normal protein level of Ppr10 protein by protecting it from degradation by the mitochondrial matrix protease Lon1. Our findings suggest that Ppr10 functions as a general mitochondrial translational activator, likely through interaction with mitochondrial mRNAs and mitochondrial translation initiation factor Mti2, and that Ppr10 requires Mpa1 association for stability and function.

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Section: Resultsmentioning

confidence: 99%

The Schizosaccharomyces pombe PPR protein Ppr10 associates with a novel protein Mpa1 and acts as a mitochondrial translational activator

Wang

Yan

Zhang

et al. 2017

Nucleic Acids Research

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“…This creates a deletion of serine 817, a residue conserved in Cryptococcus species, but within a large, 200-residue insertion found only in basidiomycete genomes. Polymerase γ has been shown to be essential in the maintenance of the mitochondrial genome in both S. cerevisiae (Foury 1989) and Schizosaccharomyces pombe (Chu et al 2007). As we estimated the number of mitochondrial genomes per cell to be similar between F0 and F2 (11 and 9, respectively, based on read coverage), there is likely no phenotypic effect from this mutation.…”

Section: Resultsmentioning

confidence: 99%

Comparative Genomics of Serial Isolates of Cryptococcus neoformans Reveals Gene Associated With Carbon Utilization and Virulence

Ormerod

Morrow

Chow

et al. 2013

G3 Genes|Genomes|Genetics

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The opportunistic fungal pathogen Cryptococcus neoformans is a leading cause of mortality among the human immunodeficiency virus/acquired immunodeficiency syndrome population and is known for frequently causing life-threatening relapses. To investigate the potential contribution of in-host microevolution to persistence and relapse, we have analyzed two serial isolates obtained from a patient with acquired immunodeficiency syndrome who suffered an initial and relapse episode of cryptococcal meningoencephalitis. Despite being identical by multilocus sequence typing, the isolates differ phenotypically, exhibiting changes in key virulence factors, nutrient acquisition, metabolic profiles, and the ability to disseminate in an animal model. Whole-genome sequencing uncovered a clonal relationship, with only a few unique differences. Of these, two key changes are expected to explain the phenotypic differences observed in the relapse isolate: loss of a predicted AT-rich interaction domain protein and changes in copy number of the left and right arms of chromosome 12. Gene deletion of the predicted transcriptional regulator produced changes in melanin, capsule, carbon source use, and dissemination in the host, consistent with the phenotype of the relapse isolate. In addition, the deletion mutant displayed altered virulence in the murine model. The observed differences suggest the relapse isolate evolved subsequent to penetration of the central nervous system and may have gained dominance following the administration of antifungal therapy. These data reveal the first molecular insights into how the Cryptococcus neoformans genome changes during infection of humans and the manner in which microevolution progresses in this deadly fungal pathogen.

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“…Without a highdepth global TSS profiling, detailed analysis of the core promoter elements and the promoter classes could not be carried out. Given the importance of these model systems in a broad range of studies, [22][23][24][25][26][27] the lack of information on their promoter analysis could limit our ability to utilize these simpler organisms in deciphering the relationship between the promoter structure and gene regulations.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of core promoter structures inSchizosaccharomyces pombewith DeepCAGE

Hou

Bai

et al. 2015

RNA Biology

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The core promoter, which immediately flanks the transcription start site (TSS), plays a critical role in transcriptional regulation of eukaryotes. Recent studies on higher eukaryotes have revealed an unprecedented complexity of core promoter structures that underscores diverse regulatory mechanisms of gene expression. For unicellular eukaryotes, however, the structures of core promoters have not been investigated in detail. As an important model organism, Schizosaccharomyces pombe still lacks the precise annotation for TSSs, thus hampering the analysis of core promoter structures and their relationship to higher eukaryotes. Here we used a deep sequencing-based approach (DeepCAGE) to generate 16 million uniquely mapped tags, corresponding to 93,736 positions in the S. pombe genome. The high-resolution TSS landscape enabled identification of over 8,000 core promoters, characterization of 4 promoter classes and observation of widespread alternative promoters. The landscape also allowed precise determination of the representative TSSs within core promoters, thus redefining the 5' UTR for 82.8% of S. pombe genes. We further identified the consensus initiator (Inr) sequence--PyPyPuN(A/C)(C/A), the TATA-enriched region (between position -25 and -37) and an Inr immediate downstream motif--CC(T/A)(T/C)(T/C/A)(A/G)CCA(A/T/C), all of which were associated with highly expressed promoters. In conclusion, the detailed analysis of core promoters not only significantly improves the genome annotation of S. pombe, but also reveals that this unicellular eukaryote shares a highly similar organization in the core promoters with higher eukaryotes. These findings lend additional evidence for the power of this model system in delineating complex regulatory processes in multicellular organisms, despite its perceived simplicity.

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Adaptive expression responses in the Pol-γ null strain of S. pombe depleted of mitochondrial genome

Cited by 22 publications

References 33 publications

The Schizosaccharomyces pombe PPR protein Ppr10 associates with a novel protein Mpa1 and acts as a mitochondrial translational activator

The Schizosaccharomyces pombe PPR protein Ppr10 associates with a novel protein Mpa1 and acts as a mitochondrial translational activator

Comparative Genomics of Serial Isolates of Cryptococcus neoformans Reveals Gene Associated With Carbon Utilization and Virulence

Genome-wide analysis of core promoter structures inSchizosaccharomyces pombewith DeepCAGE

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