The transcriptome of Candida albicans mitochondria and the evolution of organellar transcription units in yeasts

Abstract

BackgroundYeasts show remarkable variation in the organization of their mitochondrial genomes, yet there is little experimental data on organellar gene expression outside few model species. Candida albicans is interesting as a human pathogen, and as a representative of a clade that is distant from the model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Unlike them, it encodes seven Complex I subunits in its mtDNA. No experimental data regarding organellar expression were available prior to this study.MethodsWe used high-throughput RNA sequencing and traditional RNA biology techniques to study the mitochondrial transcriptome of C. albicans strains BWP17 and SN148.ResultsThe 14 protein-coding genes, two ribosomal RNA genes, and 24 tRNA genes are expressed as eight primary polycistronic transcription units. We also found transcriptional activity in the noncoding regions, and antisense transcripts that could be a part of a regulatory mechanism. The promoter sequence is a variant of the nonanucleotide identified in other yeast mtDNAs, but some of the active promoters show significant departures from the consensus. The primary transcripts are processed by a tRNA punctuation mechanism into the monocistronic and bicistronic mature RNAs. The steady state levels of various mature transcripts exhibit large differences that are a result of posttranscriptional regulation. Transcriptome analysis allowed to precisely annotate the positions of introns in the RNL (2), COB (2) and COX1 (4) genes, as well as to refine the annotation of tRNAs and rRNAs. Comparative study of the mitochondrial genome organization in various Candida species indicates that they undergo shuffling in blocks usually containing 2–3 genes, and that their arrangement in primary transcripts is not conserved. tRNA genes with their associated promoters, as well as GC-rich sequence elements play an important role in these evolutionary events.ConclusionsThe main evolutionary force shaping the mitochondrial genomes of yeasts is the frequent recombination, constantly breaking apart and joining genes into novel primary transcription units. The mitochondrial transcription units are constantly rearranged in evolution shaping the features of gene expression, such as the presence of secondary promoter sites that are inactive, or act as “booster” promoters, simplified transcriptional regulation and reliance on posttranscriptional mechanisms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2078-z) contains supplementary material, which is available to authorized users.

Traditional and novel tools to probe the mitochondrial metabolism in health and disease

“…Two methods have been used to decipher mitochondrial transcriptomes: (1) directional RNA sequencing, which measures the abundance of RNA from each strand of mtDNA, and (2) parallel analysis of RNA ends, which makes it possible to study the processing, termini, and annotation of mitochondrial transcripts . RNAseq has been used to determine mitochondrial proteomes in humans and the yeasts Saccharomyces cerevisiae and Candida albicans . In addition, RNAseq has been used to study the levels of mitochondrial and nuclear transcripts of OXPHOS subunits and assembly factors.…”

Experimental evolution ofCandida albicansunder hypoxia and heat shock reveals nuclear genome variants and mitochondrial methylome alterations

“…The methylated mtDNA cytosines are mainly distributed inside introns, exons and intergenic regions (Figure 8). C. albicans mtDNA transcription is polycistronic, and there are only 8 promoters involved in the regulation of 8 transcription units (TU) (Kolondra et al, 2015).…”

The S. pombe mitochondrial transcriptome

“…Processing of the 5 ′ -end of COB, ATP6/8, and VAR1 additionally requires a putative 5 ′ -to 3 ′ -exonuclease Pet127 (Lipinski et al 2010). In Candida albicans, the 5 ′ -and 3 ′ -ends of mitochondrial RNAs (mt-RNAs) are generated by mt-tRNA processing enzymes except for the 3 ′ -ends of NAD1, COX3, NAD3, and RNS that are likely to be generated by transcription termination (Kolondra et al 2015).…”