Biology subjects

Prohaska, S. J.

Publications and source records attributed to Prohaska, S. J..

7 recordsLinked to original sources

bioRxiv2026

Functional class 2 CCA-adding enzymes in Asgard archaea and their implications for eukaryogenesis

CCA-adding enzymes are essential for transfer RNA (tRNA) maturation and translation among all domains of life. A long-standing dogma holds that archaea encode exclusively class one CCA-adding enzymes (CCA1), whereas bacteria and eukaryotes encode class two enzymes (CCA2), creating a perceived strict evolutionary separation between archaeal and eukaryotic CCA-adding enzymes. Here, we show that this view is incorrect. We identify widespread CCA2 enzymes across multiple archaeal superphyla, including Asgard archaea, and demonstrate that these enzymes are functional enzymes and can replace their archaeal CCA1 counterparts. Within Heimdallarchaeia, the proposed closest archaeal relatives of eukaryotes, we identify distinct clades with different CCA-adding enzyme repertoires that trace back to independent bacterial sources. One Heimdallarchaeia lineage exhibits strongest similarity to Bacteroidota/Chlorobiota/Rhodothermota, a bacterial group previously implicated in early gene contributions to eukaryogenesis. CCA-adding enzymes from early-branching eukaryotes share this deep signature, indicating that predecessors of the eukaryotic enzymes had already been long-established and functionally adapted within the ancestral Asgardian gene pool. Together, these findings challenge a central paradigm of CCA-adding enzyme evolution and provide molecular-level support for the ancestral integration and subsequent transmission of bacterial functions prior to or during eukaryogenesis, aligning with current evolutionary frameworks such as the Heimdall nucleation-decentralized innovation-hierarchical import (HDH) model.

evolutionary biology↗

bioRxiv2025

Telomerase RNA gene duplications drive telomeric repeatdiversity and evolution in Andrena bees

Most organisms in the animal kingdom require a non-coding telomerease RNA (TR) in conjunction with the telomerase reverse transcriptase (TERT) to add telomere tandem repeats to chromosome ends to genomic instability. Recent studies reported an extensive diversity in the sequence of telomeric repeats in some insect species. Our investigation of TR genes in the Andrena genus provides convincing evidence for the presence of multiple TR gene copies with different template sequences for synthesis of distinct telomeric repeat sequences in several species. In this study we describe the structure, genomic coordinates and abundance of these TR genes, and correlate our findings with the levels of tandem repeats found in DNAseq data. Based on an analysis of the synthenic context of these newly predicted TR genes, we show evidence for the existence of multiple TR paralogs that diverged during the evolution of the genus Andrena. To our knowledge this is the first time such a phenomenon is observed in animals, although recently reported for plants. Interestingly, the comprehensive annotation of all TERT genes found in yet unannotated Andrena species shows no corresponding evolutionary changes in related TERT proteins encoded by a single copy gene. Our study suggests an evolutionary mechanism for diversification of telomeric repeat sequences in certain insect species through telomerase RNA gene duplication.

bioinformatics↗

bioRxiv2025

Multiomics reveal associations between CpG methylation, histone modifications and transcription in a species that has lost DNMT3, the Colorado potato beetle

Insects display exceptional phenotypic plasticity, which can be mediated by epigenetic modifications, including CpG methylation and histone modifications. In vertebrates, both are interlinked and CpG methylation is associated with gene repression. However, little is known about these regulatory systems in invertebrates, where CpG methylation is mainly restricted to gene bodies of transcriptionally active genes. A widely conserved mechanism involves the co-transcriptional deposition of H3K36 trimethylation and the targeted methylation of unmethylated CpGs by the de novo DNA methyltransferase DNMT3. However, DNMT3 has been lost multiple times in invertebrate lineages raising the question of how the links between CpG methylation, histone modifications and gene expression are affected by its loss. Here, we report the epigenetic landscape of Leptinotarsa decemlineata, a beetle species that has lost DNMT3 but retained CpG methylation. We combine RNA-seq, enzymatic methyl-seq and CUT&Tag to study CpG methylation and patterns of H3K36me3 and H3K27ac histone modifications on a genome-wide scale. Despite the loss of DNMT3, H3K36me3 mirrors CpG methylation patterns. Together, they give rise to signature profiles for expressed and non-expressed genes. H3K27ac patterns, which show no association with CpG methylation, have a prominent peak at the transcription start site that is predictive of expressed genes. Our study provides new insights into the evolutionary flexibility of epigenetic modification systems that urge caution when generalizing across species. Research highlightsDespite lacking DNMT3, EM-seq revealed CpG methylation in the Colorado potato beetle. CUT&Tag showed an association of H3K36me3 and H3K27ac with transcription, while only H3K36me3 aligns with CpG methylation, demonstrating epigenetic flexibility.

evolutionary biology↗

bioRxiv2021

Evolution of DNA methylation across Ecdysozoa

DNA methylation is a crucial, abundant mechanism of gene regulation in vertebrates. It is less prevalent in many other metazoan organisms and completely absent in some key model species, such as D. melanogaster and C. elegans. We report here a comprehensive study of the presence and absence of DNA methyltransferases (DNMTs) in 138 Ecdysozoa, covering Arthropoda, Nematoda, Priapulida, Onychophora, and Tardigrada. Three of these phyla have not been investigated for the presence of DNA methylation before. We observe that the loss of individual DNMTs independently occurred multiple times across ecdysozoan phyla. We computationally predict the presence of DNA methylation based on CpG rates in coding sequences using an implementation of Gaussian Mixture Modelling, MethMod. Integrating both analysis we predict two previously unknown losses of DNA methylation in Ecdysozoa, one within Chelicerata (Mesostigmata) and one in Tardigrada. In the early-branching Ecdysozoa Priapulus caudatus we predict the presence of a full set of DNMTs and the presence of DNA methylation. We are therefore showing a very diverse and independent evolution of DNA methylation in different ecdysozoan phyla spanning a phylogenetic range of more than 700 million years.

evolutionary biology↗

bioRxiv2018

Genome-wide features of introns are evolutionary decoupled among themselves and from genome size throughout Eukarya

The impact of spliceosomal introns on genome and organismal evolution remains puzzling. Here, we investigated the correlative associations among genome-wide features of introns from protein-coding genes (e.g., size, density, genome-content, repeats), genome size and multicellular complexity on 461 eukaryotes. Thus, we formally distinguished simple from complex multicellular organisms (CMOs), and developed the program GenomeContent to systematically estimate genomic traits. We performed robust phylogenetic controlled analyses, by taking into account significant uncertainties in the tree of eukaryotes and variation in genome size estimates. We found that changes in the variation of some intron features (such as size and repeat composition) are only weakly, while other features measuring intron abundance (within and across genes) are not, scaling with changes in genome size at the broadest phylogenetic scale. Accordingly, the strength of these associations fluctuates at the lineage-specific level, and changes in the length and abundance of introns within a genome are found to be largely evolving independently throughout Eukarya. Thereby, our findings are in disagreement with previous estimations claiming a concerted evolution between genome size and introns across eukaryotes. We also observe that intron features vary homogeneously (with low repetitive composition) within fungi, plants and stramenophiles; but they vary dramatically (with higher repetitive composition) within holozoans, chlorophytes, alveolates and amoebozoans. We also found that CMOs and their closest ancestral relatives are characterized by high intron-richness, regardless their genome size. These patterns contrast the narrow distribution of exon features found across eukaryotes. Collectively, our findings unveil spliceosomal introns as a dynamically evolving non-coding DNA class and strongly argue against both, a particular intron feature as key determinant of eukaryotic gene architecture, as well as a major mechanism (adaptive or non-adaptive) behind the evolutionary dynamics of introns over a large phylogenetic scale. We hypothesize that intron-richness is a pre-condition to evolve complex multicellularity.

evolutionary biology↗

bioRxiv2017

Large-Scale Evolutionary Patterns of Protein Domain Distributions in Eukaryotes

The genomic inventory of protein domains is an important indicator of an organisms regulatory and metabolic capabilities. Existing gene annotations, however, can be plagued by substantial ascertainment biases that make it difficult to obtain and compare quantitative domain data. We find that quantitative trends across the Eukarya can be investigated based on a combination of gene prediction and standard domain annotation pipelines. Species-specific training is required, however, to account for the genomic peculiarities in many lineages. In contrast to earlier studies we find wide-spread statistically significant avoidance of protein domains associated with distinct functional high-level gene-ontology terms.\n\n1998 ACM Subject Classification J.3 Life and Medical Sciences

bioinformatics↗

bioRxiv2016

Design Specifications for Cellular Regulation

A critical feature of all cellular processes is the ability to control the rate of gene or protein expression and metabolic flux in changing environments through regulatory feedback. We review the many ways that regulation is represented through causal, logical and dynamical components. Formalizing the nature of these components promotes effective comparison among distinct regulatory networks and provides a common framework for the potential design and control of regulatory systems in synthetic biology.

systems biology↗