Biology subjects

Köstlbacher, S.

Publications and source records attributed to Köstlbacher, S..

5 recordsLinked to original sources

bioRxiv2026

Asgard archaeal origin of microtubules

Eukaryotic cells change their shapes, actively segregate their DNA and contain membrane networks, facilitated by a complex cytoskeleton containing actin filaments, microtubules made from tubulin, and other components. These filaments have ancient evolutionary origins since actin- and tubulin-like proteins form prokaryotic cytoskeletons in archaea and bacteria. Bona fide eukaryotic F-actin can be traced back to crenarchaea and Asgard archaea, which are the closest known relatives of eukaryotes. A possible Asgard archaeal origin of microtubules was suggested recently with the discovery of a lokiarchaeon containing AtubAB mini microtubules that share architectural features with their eukaryotic counterparts. Using phylogenetic analyses of metagenomic data, here we report the broad occurrence of tubulins in Asgard archaea. Biochemical and structural analyses showed that one of our newly discovered heimdallarchaeial AtubAB tubulin pairs forms four-protofilament mini-microtubules that show dynamic instability and are inhibited by the tubulin drug maytansine. Our work raises the possibility that microtubule architecture and dynamics evolved in Asgard archaea prior to eukaryogenesis.

cell biology↗

bioRxiv2024

The Escherichia coli replication initiator DnaA is titrated on the chromosome

DNA replication initiation is orchestrated in many prokaryotes by the replication initiator DnaA. Two models for regulation of DnaA activity in Escherichia coli have been proposed: the switch between an active and inactive form of DnaA, and the titration of DnaA on the E. coli chromosome. Although proposed decades ago, experimental evidence of a titration-based control mechanism is still lacking. Here, we first identified a conserved high-density region of binding motifs near the origin of replication, an advantageous trait for titration of DnaA. We then investigated the mobility of DnaA by single-particle tracking microscopy in wild-type and deletion mutants E. coli strains, while monitoring cellular size and DNA content. Our results indicate that the chromosome of E. coli controls the free amount of DnaA in a growth rate-dependent fashion. Finally, we provide insights on the relevance of DnaA titration in stabilising DNA replication by preventing re-initiation events during slow growth.

molecular biology↗

bioRxiv2023

Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switching

Our knowledge of archaeal diversity and evolution has expanded rapidly in the past decade. However, hardly any genomes of the phylum Korarchaeota have been obtained due to the difficulty in accessing their natural habitats and - possibly - their limited abundance. As a result, many aspects of Korarchaeota biology, physiology and evolution remain enigmatic. Here, we expand this phylum with five high-quality metagenome-assembled genomes. This improved taxon sampling combined with sophisticated phylogenomic analyses robustly places Korarchaeota at the base of TACK and Asgard clades, revisiting the phylums long-assumed position. Furthermore, we observe a clear split between terrestrial and marine thermal clades. Gene tree-aware ancestral reconstructions suggest that the last Korarchaeota common ancestor was a thermophilic autotroph. In contrast, Korarchaeaceae, the lineage where environmental transitions occurred, shifted towards a heterotrophic lifestyle. Terrestrial Korarchaeota gained many cas and CARF genes indicating they may need to manage viral infections. Together, our study provides new insights into these early diverging Archaea and suggests that gradual gene gain and loss shaped their adaptation to different thermal environments. ImportanceKorarchaeota are an ancient group of archaea, but their biology, physiology and evolution have remained obscure. Analysis of five novel Korarchaeota MAGs, and publicly available reference data provides robust phylogenomic evidence that Korarchaeota are placed at the base of Asgard archaea and TACK, revisiting the phylums long-assumed position. Gene content reconstruction suggests a versatile thermophilic and autotrophic last Korarchaeota common ancestor. Environmental distribution surveying of public databases places all Korarchaeota in thermophilic environments and indicates that their habitat is limited to hydrothermal vents and hot springs. Our modeling indicates at least two transitions linked to habitat switching between these environments in the evolutionary history of Korarchaeota. Both are linked to a significant alteration of the inferred ancestral gene content, including a shift towards a heterotrophic and potential scavenging lifestyle. Furthermore, hot spring Korarchaeota acquired various genes participating in resistance to viruses, suggesting they may need to manage frequent viral threats.

microbiology↗

bioRxiv2022

One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus

Bacterial endosymbionts of the groups Wolbachia, Cardinium and Rickettsiaceae are well-known for their diverse effects on their arthropod hosts, ranging from mutualistic relationships to reproductive phenotypes. Here, we analyzed a unique system in which the dwarf spider Oedothorax gibbosus is co-infected with up to five different endosymbionts affiliated with Wolbachia, Candidatus Tisiphia (formerly Torix group Rickettsia), Cardinium, and Rhabdochlamydia. Using short-read genome sequencing data, we show that the endosymbionts are heterogeneously distributed among O. gibbosus populations and are frequently found co-infecting spider individuals. To study this intricate host-endosymbiont system on a genome resolved level, we used long-read sequencing to reconstruct closed genomes of the Wolbachia, Ca. Tisiphia and Cardinium endosymbionts. We provide insights in the ecology and evolution of the endosymbionts and shed light on the interactions with their spider host. We detected high quantities of transposable elements in all endosymbiont genomes and provide evidence that ancestors of the Cardinium, Ca. Tisiphia and Wolbachia endosymbionts have co-infected the same hosts in the past. Our findings contribute to broadening our knowledge about endosymbionts infecting one of the largest animal phyla on earth and show the usefulness of transposable elements as an evolutionary "contact-tracing" tool. Data summaryAll supporting data, code and protocols have been provided within the article or through supplementary data files. Seven supplementary figures and seven supplementary tables are available with the online version of this article. Sequencing data used in this study was generated and previously published by Hendrickx et al., 2021. Genome assemblies generated in this study have been deposited under the project PRJEB52003 at DDBJ/ENA/GenBank. The MAG of R. oedothoracis OV001 was deposited at DDBJ/ENA/GenBank under the sample SAMN28026840. The genome of Candidatus Rhabdochlamydia oedothoracis W744x776 was previously published by Halter et al., 2022 and is available at DDBJ/ENA/GenBank (accession: CP075587-CP075588). The collection of genomes and proteomes, all files for phylogenetic analyses including gene alignments, concatenated alignments, and tree files, and original output files of the HGT and SNP predictions used in this study are available at zenodo (https://doi.org/10.5281/zenodo.6362846).

genomics↗

bioRxiv2020

Acquisition of a type 3 secretion signal in an housekeeping enzyme shaped glycogen metabolism in Chlamydia

The obligate intracellular bacteria Chlamydia trachomatis store glycogen in the lumen of the vacuoles in which they grow. Glycogen catabolism generates glucose-1-phosphate (Glc1P), while the bacteria are capable of taking up only glucose-6-phosphate (Glc6P). We tested whether the conversion of Glc1P into Glc6P could be catalyzed by a phosphoglucomutase (PGM) of host or bacterial origin. We found no evidence for the presence of the host enzyme in the vacuole. In C. trachomatis, two proteins are potential PGMs. By reconstituting the reaction, and by complementing PGM deficient fibroblasts, we demonstrated that only CT295 displayed robust PGM activity. Furthermore, we showed that glycogen accumulation by a subset of Chlamydia species correlated with the presence of a type three secretion (T3S) signal in their PGM. In conclusion, we established that the conversion of Glc1P into Glc6P was accomplished by a bacterial PGM, through the acquisition of a T3S signal in a "housekeeping" gene.

microbiology↗