Complex microbes

Complex microbes

Decoding gene expression regulation in ciliates

Department of Biochemistry and Molecular Biophysics, University of Columbia, New York, USA 

Ciliates are unicellular eukaryotes with two nuclei: a germline micronucleus (abbreviated MIC) with a 1Gb genome and a somatic nucleus (macronucleus or MAC) that specializes in gene expression. In Oxytricha trifallax, our main laboratory model organism, the MAC genome develops from a copy of the germline genome by excision of 90-95% of its chromosome sequences, rearrangement of the 225,000 remaining pieces, and elaborate DNA splicing. This complex process involves both RNA factors transmitted epigenetically and partially-domesticated transposases, very abundant in the germline genome.

The MAC genome has a unique architecture: it is composed of ~ 20,000 tiny chromosomes that average just 3 kb and often carry a single gene. Only ~100bp non-coding sequences remain on each side of most genes, which poses the challenging question of the location of signals for gene expression regulation. Very little is known about cis- signals and trans-factors regulating gene expression.

Identification of new type of RNA editing in the mitochondrial genome of a very divergent marine micro-eukaryote.

Centre Robert-Cedergren, Université de Montréal, Québec, Canada 

Gene expression in eukaryotes with peculiar genome architecture may differ substantially from mainstream eukaryotes. Diplonemids present arguably one of the most deviant/peculiar mitochondrial genome architecture known with their genes in pieces.

  • Analysis of the mitochondrial transcriptome (RNA seq) and identification of a unique type of RNA editing
  • In silico identification of candidate components of the trans-splicing machinery.
  • Modelisation of the 3D structure of an intriguing RNA ligase 2 and analysis by molecular dynamics simulation. 
  • Nuclear and mitochondrial genome assembly (DNA seq) and annotation

From Valach M., Moreira S., Burger G. Trends In Genetics (2016) , Figure 2
(A) Appearance of the diplonemid Rhynchopus euleeides (drawing based on scanning microscopy, kindly provided by S. Teijeiro). Left, trophic state with large subapical flagellar pocket (‘mouth’; the two flagella do not emerge). Right, a free-swimming ‘swarmer’ [Roy, J. et al. (2007)]. (B) Diplonemids’ placement in the eukaryotic tree. The topology is taken from [Derelle, R. et al. (2015)]. (C) mtDNA structure and gene expression. The constant region (dark blue) is common to the two classes of mitochondrial chromosomes. The class-specific regions (bright and pale blue) are adjacent to the cassette (light gray). Each cassette contains a gene fragment (module m1 to m3, yellow shades). Transcription starts and ends within the constant region, thus transcripts require extensive end processing. Substitution editing at clustered sites is illustrated for module 1, symbolized by the dinucleotide CA that is converted to UI. U-appendage RNA editing is shown for module 2, to which two Us are added at its 30 end prior to trans-splicing. Module 3 undergoes polyadenylation.