Biology subjects

Knorre, D. A.

Publications and source records attributed to Knorre, D. A..

2 recordsLinked to original sources

bioRxiv2023

ORFanes in mitochondrial genomes of marine polychaete Polydora

Most characterised metazoan mitochondrial genomes are compact and encode a small set of proteins that are essential for oxidative phosphorylation. However, in rare cases, invertebrate taxa have additional open reading frames (ORFs) in their mtDNA sequences. Here, we sequenced and analysed the mitochondrial genome of a polychaete worm, Polydora cf. ciliata, part of whose life cycle takes place in low-oxygen conditions. In the mitogenome, we found three "ORFane" regions (1063, 427, and 519 bp) that have no resemblance to any standard metazoan mtDNA gene but lack stop codons in one of the reading frames. Similar regions are found in the mitochondrial genomes of three other Polydora species and Bocardiella hamata. All five species share the same gene order in their mitogenomes, which differ from that of other known spionidae mitogenomes. By analysing the ORFane sequences, we found that they are under negative selection pressure, contain conservative regions, and harbour predicted transmembrane domains.The codon adaptation indices (CAIs) of the ORFan genes were in the same range of values as the CAI of conventional protein-coding genes in corresponding mitochondrial genomes. Together, this suggests that ORFanes encode functional proteins. We speculate that the ORFanes originated from the conventional mitochondrial protein-coding genes which were duplicated when the Polydora/Bocardiella species complex separated from the rest of the Spionidae. Significance statementMetazoan mitochondrial genomes usually contain a conservative set of genes and features. However, mitogenomes of some species contain ORFanes - putative protein-coding genes without clear homology with other known sequences. In this study, we analysed three ORFanes in mitochondria of species of the genera Polydora and Bocardiella, which were absent in all other representatives of Spionidae. To the best of our knowledge, ORFanes havent been described in Annelida before. Sequence analysis of the ORFanes suggests they contain conservative regions and are likely translated into functional proteins. Our study features an uncommon case where new protein-coding genes emerged in the mitochondrial genomes of metazoa.

evolutionary biology↗

bioRxiv2021

The adaptive role of cell death in yeast communities stressed with macrolide antifungals

Microorganisms cooperate with each other to protect themselves from environmental stressors. An extreme case of such cooperation is regulated cell death for the benefit of other cells. Dying cells can provide surviving cells with nutrients or induce their stress-response by transmitting an alarm signal; however, the role of dead cells in microbial communities is unclear. Here we searched for types of stressors the protection from which can be achieved by death of a subpopulation of cells. Thus, we compared the survival of Saccharomyces cerevisiae cells upon exposure to various stressors in the presence of additionally supplemented living versus dead cells. We found that dead cells contribute to yeast community resistance against macrolide antifungals (e.g. amphotericin B [AmB] and filipin) to a greater extent than living cells. Dead yeast cells absorbed more macrolide filipin than control cells because they exposed intracellular sterol-rich membranes. We also showed that, upon the addition of lethal concentrations of AmB, supplementation with AmB-sensitive cells but not with AmB-resistant cells enabled the survival of wild-type cells. Together, our data suggests that cell-to-cell heterogeneity in sensitivity to AmB can be an adaptive mechanism helping yeast communities to resist macrolides, which are naturally occurring antifungal agents. ImportanceEukaryotic microorganisms harbour elements of programmed cell death (PCD) mechanisms that are homologous to the PCD of multicellular metazoa. However, it is still debated whether microbial PCD has an adaptive role or the processes of cell death are an aimless operation in self-regulating molecular mechanisms. Here, we demonstrated that dying yeast cells provide an instant benefit for their community by absorbing macrolides, which are bacteria-derived antifungals. Our results illustrate the principle that the death of a microorganism can contribute to the survival of its kin and suggest that early plasma membrane permeabilization improves community-level protection. The latter makes a striking contrast to the manifestations of apoptosis in higher eukaryotes, the process by which plasma membranes maintain integrity.

microbiology↗