Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss
Lewis, William H. ; Lind, Anders E. ; Sendra, Kacper M. ; Onsbring, Henning ; Williams, Tom A. ; Esteban, Genoveva F. ; Hirt, Robert P. ; Ettema, Thijs J.G. ; Embley, T.M. - \ 2020
Molecular Biology and Evolution 37 (2020)2. - ISSN 0737-4038 - p. 524 - 539.
anaerobic metabolism - evolution - genomics - hydrogenosomes - microbial eukaryotes - mitochondria
Hydrogenosomes are H2-producing mitochondrial homologs found in some anaerobic microbial eukaryotes that provide a rare intracellular niche for H2-utilizing endosymbiotic archaea. Among ciliates, anaerobic and aerobic lineages are interspersed, demonstrating that the switch to an anaerobic lifestyle with hydrogenosomes has occurred repeatedly and independently. To investigate the molecular details of this transition, we generated genomic and transcriptomic data sets from anaerobic ciliates representing three distinct lineages. Our data demonstrate that hydrogenosomes have evolved from ancestral mitochondria in each case and reveal different degrees of independent mitochondrial genome and proteome reductive evolution, including the first example of complete mitochondrial genome loss in ciliates. Intriguingly, the FeFe-hydrogenase used for generating H2 has a unique domain structure among eukaryotes and appears to have been present, potentially through a single lateral gene transfer from an unknown donor, in the common aerobic ancestor of all three lineages. The early acquisition and retention of FeFe-hydrogenase helps to explain the facility whereby mitochondrial function can be so radically modified within this diverse and ecologically important group of microbial eukaryotes.
RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration
Onsbring, Henning ; Jamy, Mahwash ; Ettema, Thijs J.G. - \ 2018
Current Biology 28 (2018)8. - ISSN 0960-9822 - p. 1281 - 1288.e3.
cell damage repair - cell regeneration - ciliate - microbial eukaryotes - protist - RNA-seq - single-cell transcriptomics - Stentor
While ciliates of the genus Stentor are known for their ability to regenerate when their cells are damaged or even fragmented, the physical and molecular mechanisms underlying this process are poorly understood. To identify genes involved in the regenerative capability of Stentor cells, RNA sequencing of individual Stentor polymorphus cell fragments was performed. After splitting a cell over the anterior-posterior axis, the posterior fragment has to regenerate the oral apparatus, while the anterior part needs to regenerate the hold fast. Altogether, differential expression analysis of both posterior and anterior S. polymorphus cell fragments for four different post-split time points revealed over 10,000 upregulated genes throughout the regeneration process. Among these, genes involved in cell signaling, microtubule-based movement, and cell cycle regulation seemed to be particularly important during cellular regeneration. We identified roughly nine times as many upregulated genes in regenerating S. polymorphus posterior fragments as compared to anterior fragments, indicating that regeneration of the anterior oral apparatus is a complex process that involves many genes. Our analyses identified several expanded groups of genes, such as dual-specific tyrosine-(Y)-phosphorylation-regulated kinases and MORN domain-containing proteins that seemingly act as key regulators of cellular regeneration. In agreement with earlier morphological and cell biological studies [1, 2], our differential expression analyses indicate that cellular regeneration and vegetative division share many similarities. Onsbring et al. sequence transcriptomes of individual bisections of regenerating cells of the giant heterotrichous ciliate Stentor polymorphus. Their differential expression analysis reveals that protein phosporylation, microtubule-based processes, and genes involved in the cell cycle are important for cellular regeneration.
Molecular Investigation of the Ciliate Spirostomum semivirescens, with First Transcriptome and New Geographical Records
Hines, Hunter N. ; Onsbring, Henning ; Ettema, Thijs J.G. ; Esteban, Genoveva F. - \ 2018
Protist 169 (2018)6. - ISSN 1434-4610 - p. 875 - 886.
anaerobic respiration - Heterotrich. - Protist - RNA-seq - stop codon - symbiotic algae
The ciliate Spirostomum semivirescens is a large freshwater protist densely packed with endosymbiotic algae and capable of building a protective coating from surrounding particles. The species has been rarely recorded and it lacks any molecular investigations. We obtained such data from S. semivirescens isolated in the UK and Sweden. Using single-cell RNA sequencing of isolates from both countries, the transcriptome of S. semivirescens was generated. A phylogenetic analysis identified S. semivirescens as a close relative to S. minus. Additionally, rRNA sequence analysis of the green algal endosymbiont revealed that it is closely related to Chlorella vulgaris. Along with the molecular species identification, an analysis of the ciliates’ stop codons was carried out, which revealed a relationship where TGA stop codon frequency decreased with increasing gene expression levels. The observed codon bias suggests that S. semivirescens could be in an early stage of reassigning the TGA stop codon. Analysis of the transcriptome indicates that S. semivirescens potentially uses rhodoquinol-dependent fumarate reduction to respire in the oxygen-depleted habitats where it lives. The data also shows that despite large geographical distances (over 1,600 km) between the sampling sites investigated, a morphologically-identical species can share an exact molecular signature, suggesting that some ciliate species, even those over 1 mm in size, could have a global biogeographical distribution.