Georg Hausner

Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases.

Catalytic RNAs are often regarded as molecular fossils from the RNA World, yet it is usually difficult to get more specific information about their evolution. Here we have investigated the coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases (RTs). Unlike group I introns, there has been no obvious reshuffling between intron RNA structures and ORFs. Of the six classes of intron structures that encode ORFs, three are conventional forms of group II A1, B1, and B2 secondary structures, whereas the remaining classes are bacterial, are possibly associated with the most primitive ORFs, and have unusual features and hybrid features of group IIA and group IIB intron structures. Based on these data, we propose a new model for the evolution of group II introns, designated the retroelement ancestor hypothesis, which predicts that the major RNA structural forms of group II introns developed through coevolution with the intron-encoded protein rather than as independent catalytic RNAs, and that most ORF-less introns are derivatives of ORF-containing introns. The model is supported by the distribution of ORF-containing and ORF-less introns, and by numerous examples of ORF-less introns that contain ORF remnants.

DO GALEATE-ASCOSPORE MEMBERS OF THE CEPHALOASCACEAE, ENDOMYCETACEAE AND OPHIOSTOMATACEAE SHARE A COMMON PHYLOGENY?

Using partial small subunit ribosomal gene sequences we show that yeast-like genera that produce galeate (hat-shaped) ascospores and similar-spored members of the Ophiostomatales do not form a monophyletic group. Based on distance and parsimony methods Cephaloascusfragrans and Endomyces decipiens failed to form a monophyletic grouping with species of Ceratocystis sensu stricto and Ophiostoma. Instead these yeast species clustered with Saccharomyces cerevisiae, Kluyveromyces lactis, and Torulaspora delbrueckii in >99% of both the distance and parsimony majority-rule consensus trees generated using the statistical method of bootstrapping. Therefore galeate ascospores appear to be an example of convergent evolution in fungi and by itself this trait should not be considered as an indicator of evolutionary relatedness.

Molecular evolutionary analysis based on the amino acid sequence of catalase

Heme-containing catalase sequences from 20 different organisms representing prokaryotes, fungi, animals, and plants have been compiled for phylogenetic reconstruction. Phylogenies based on distance and parsimony analysis show that fungal and animal catalases can be derived from one ancestor, whereas bacterial catalases fail to form a monophyletic group. Plant catalases appear to form a second class of catalases that arose independently from a possible prokaryotic ancestor.

Ceratocystiopsis: a reappraisal based on molecular criteria

Analysis of partial rDNA sequences from both the small and large subunit genes of species of Ceratocystiopsis suggests they represent a polyphyletic group. Therefore the production of falcate-like ascospores, the key feature of this genus, is an example of convergent evolution. The partial rDNA sequences also show that the majority of Ceratocystiopsis spp. can be placed in Ophiostoma along with Certocystis ips , a conclusion supported at the 100% confidence level by bootstrap analysis. Therefore we formally reduce Ceratocystiopsis to synonymy with Ophiostoma and provide the necessary new combinations in Ophiostoma . However, C. proteae, C. falcata , and C. alba are shown to have a very distant relationship with Ophisotoma , and their taxonomic position remains unresolved.

Complete genome sequence of sporisorium scitamineum and biotrophic interaction transcriptome with sugarcane

Sporisorium scitamineum is a biotrophic fungus responsible for the sugarcane smut, a worldwide spread disease. This study provides the complete sequence of individual chromosomes of S. scitamineum from telomere to telomere achieved by a combination of PacBio long reads and Illumina short reads sequence data, as well as a draft sequence of a second fungal strain. Comparative analysis to previous available sequences of another strain detected few polymorphisms among the three genomes. The novel complete sequence described herein allowed us to identify and annotate extended subtelomeric regions, repetitive elements and the mitochondrial DNA sequence. The genome comprises 19,979,571 bases, 6,677 genes encoding proteins, 111 tRNAs and 3 assembled copies of rDNA, out of our estimated number of copies as 130. Chromosomal reorganizations were detected when comparing to sequences of S. reilianum, the closest smut relative, potentially influenced by repeats of transposable elements. Repetitive elements may have also directed the linkage of the two mating-type loci. The fungal transcriptome profiling from in vitro and from interaction with sugarcane at two time points (early infection and whip emergence) revealed that 13.5% of the genes were differentially expressed in planta and particular to each developmental stage. Among them are plant cell wall degrading enzymes, proteases, lipases, chitin modification and lignin degradation enzymes, sugar transporters and transcriptional factors. The fungus also modulates transcription of genes related to surviving against reactive oxygen species and other toxic metabolites produced by the plant. Previously described effectors in smut/plant interactions were detected but some new candidates are proposed. Ten genomic islands harboring some of the candidate genes unique to S. scitamineum were expressed only in planta. RNAseq data was also used to reassure gene predictions.

Evolution of rDNA ITS1 and ITS2 sequences and RNA secondary structures within members of the fungal genera Grosmannia and Leptographium.

The two internal transcribed spacers (ITS) of the nuclear ribosomal (r) DNA tandem repeat were examined in ophiostomatoid fungi belonging to the genera Grosmannia and Leptographium and closely-related taxa. Although the DNA sequence of the ITS region evolves rapidly, core features of the RNA secondary structure of the ITS1 and ITS2 segments are conserved. The results demonstrate that structural conservation of GC-rich helical regions is facilitated primarily through compensatory base changes (CBCs), hemi-CBCs, and compensating insertions/deletions (indels), although slippage of the RNA strand is potentially an additional mechanism for maintaining basepairing interactions. The major conclusion of the structural analysis of both ITS segments is that two factors appear to be involved in limiting the type of changes observed: a high GC bias for both ITS1 and ITS2 and structural constraints at the RNA level.

6 - Fungal Mitochondrial Genomes, Plasmids and Introns

Within the fungi mitochondrial genomes can exist as either linear or circular molecules, whose size variation is mostly due to the presence or absence of optional introns, and size variation in the intergenic regions. Optional introns can be either group I or group II introns, which are potential ribozymes that, in part, catalyze their own removal from the precursor RNA transcript. Mitochondria can also contain autonomously replicating DNA molecules, that are either derived from the mitochondrial DNA or represent true plasmids that show no homology with the mitochondrial chromosome. True plasmids are mostly cryptic in nature, and may have a different evolutionary origin from that of the mitochondrial host-genome. Amongst true plasmids at least three different categories can be recognized: (1) Circular plasmids encoding a DNA polymerase; (2) linear plasmids with terminal inverted repeats encoding a DNA and an RNA polymerase and; (3) retroplasmids, which are linear or circular plasmids that encode a reverse transcriptase. These different groups of true plasmids probably arose independently of one another, and were either vertically transmitted from the original endosymbiont that gave rise to the mitochondrion, or invaded the mitochondrion at various times during fungal evolution.

Molecular Evolution of the mtDNA Encoded rps3 Gene Among Filamentous Ascomycetes Fungi with an Emphasis on the Ophiostomatoid Fungi

The mitochondrial ribosomal protein S3 (rps3) gene within the fungi is extremely diverse in location and organization, some versions of this gene have been incorporated into a group I intron, others appear to have gained large insertions, microsatellite expansions, or have been invaded by homing endonucleases. Among the ascomycetes fungi the group I intron encoded version of rps3 appears to have a rather complex evolutionary history including first the acquisition of rps3 by a group I intron (mL2449), the loss of the mL2499 intron and the establishment of rps3 as a free-standing gene, and the eventual loss of the intron derived version of rps3.

Bacterial group I introns: mobile RNA catalysts

Group I introns are intervening sequences that have invaded tRNA, rRNA and protein coding genes in bacteria and their phages. The ability of group I introns to self-splice from their host transcripts, by acting as ribozymes, potentially renders their insertion into genes phenotypically neutral. Some group I introns are mobile genetic elements due to encoded homing endonuclease genes that function in DNA-based mobility pathways to promote spread to intronless alleles. Group I introns have a limited distribution among bacteria and the current assumption is that they are benign selfish elements, although some introns and homing endonucleases are a source of genetic novelty as they have been co-opted by host genomes to provide regulatory functions. Questions regarding the origin and maintenance of group I introns among the bacteria and phages are also addressed.

Introns, Mobile Elements, and Plasmids

The organellar mobilome mainly consists of mobile group I and II introns, homing endonuclease genes, and plasmids. Group I and II introns can be distinguished from each other by their sequences, secondary and tertiary RNA structures, and splicing mechanisms. These introns are potential ribozymes catalyzing their own removal from the precursor RNA transcripts. Organellar plasmids are presumed to be cryptic, although some plasmids have been associated with genetic defects. Plasmids are also of interest as, within some yeast species, plasmids appear to have been co-opted into the maintenance of telomeres in linear mitochondrial chromosomes.