Biology subjects

Stach, T.

Publications and source records attributed to Stach, T..

5 recordsLinked to original sources

bioRxiv2026

Intracellular genomic variability driven by cellular compartmentalization in the giant bacterium Achromatium spp

Bacteria of the genus Achromatium harbor hundreds of chromosomes that were previously suggested to be genetically diverse. By sequencing multiple regions from individual cells, we demonstrate that chromosomes within a single cell differ in nucleotide and amino acid sequence, reaching levels of divergence well below accepted bacterial species boundaries and below the range associated with homologous recombination. Sequencing of dividing cells further revealed that daughter cells inherit distinct chromosome populations, a mode of inheritance previously associated with sexual reproduction in eukaryotes. Combining subcellular sequencing with high-resolution microscopy, we reconstruct the three-dimensional cellular architecture of Achromatium and show that extensive intracellular heterogeneity arises from the spatial segregation of chromosome populations by the cells internal structure, which limits genome-wide recombination. Our findings establish cellular architecture as a determinant of genome evolution in giant polyploid bacteria and identify spatial genome segregation as a mechanism enabling the maintenance and inheritance of divergent chromosome populations in bacteria.

microbiology↗

bioRxiv2025

Submersion and oxidative stress triggers pyrenoid formation, carbon concentration-related protein remodeling and sub-plastidial rearrangements in hornworts

Plastids are important for controlling acclimation of plants to environmental changes. In hornworts, chloroplasts may contain a RuBisCO-enriched protein matrix, a pyrenoid-like structure, which enables them to perform a biophysical carbon concentration mechanism (CCM) at the single-cell level- a unique feature among land plants. However, much remains unknown about the function, formation, and regulation of hornwort pyrenoids, especially as they are unaffected by changes in atmospheric CO2. Here, we tested whether submersion and hyperoxia induce pyrenoid formation and CCM. By subjecting Anthoceros agrestis, a pyrenoid-forming hornwort species, and A. fusiformis, which develops no pyrenoids, to a series of submersion experiments and analyzing their molecular, physiological, and cell-morphological response patterns using label-free proteomics and transmission electron microscopy, with additional in silico analysis, we identified a core set of CCM candidate genes. Under submersion, both species expressed CCM-associated protein homologs, whereas hyperoxia induced or diminished the expression of CCM-like homologs in a species-specific manner. We discovered that a carbonic anhydrase, a CAH3 homolog, as well as thylakoid bicarbonate transporter (LCI11-like) are upregulated under both conditions in A. agrestis, but not in A. fusiformis, suggesting that an algae-like mechanism of bicarbonate pumping into the thylakoid lumen and CO2 conversion exists in A. agrestis. Corroborating these molecular findings, an ultrastructural analysis of plastids revealed increases in pyrenoid-like structures and rearrangements during submersion in A. agrestis, whereas A. fusiformis accumulated lipid droplets between thylakoid stacks. Together, our data highlight hornworts distinct acclimation strategies to adverse environmental conditions, highlighting the relevance of their pyrenoids and CCM. Significance statementCarbon concentration via pyrenoids, densely packed matrices of a CO2-fixing enzyme, holds significant biotechnological promise for enhancing crop resilience. Studying mechanisms underlying pyrenoid formation in hornworts--the only land plants to naturally develop pyrenoids--is of exceptional interest due to their evolutionary closeness to crops. This study closes a knowledge gap by showing that hornworts use pyrenoids and a carbon-concentrating mechanism to adapt to submersion and hyperoxia, allowing them to thrive under regular transitions between atmospheric and submerged environments, resembling conditions during plants water-to-land transition. Species lacking pyrenoids accumulate lipid droplets instead, in addition to altering developmental and physiological pathways. Together, this work highlights hornworts remarkable versatility and untapped potential in advancing our understanding of plant adaptation to terrestrial life.

plant biology↗

bioRxiv2023

Time- and lineage-resolved transcriptional profiling uncovers gene expression programs and clonal relationships that underlie human T lineage specification

T cells develop from multi-potent hematopoietic progenitors in the thymus and provide adaptive protection against pathogens and cancer. However, the emergence of human T cell-competent blood progenitors, and their subsequent specification to the T lineage, has been challenging to capture in real time. Here, we leveraged a pluripotent stem cell differentiation system to understand the transcriptional dynamics and cell fate restriction events that underlie this critical developmental process. Time-resolved single cell RNA sequencing revealed that cell-cycle exit, downregulation of the multipotent hematopoietic program, and upregulation of >90 lineage-associated transcription factors all occur within a highly co-ordinated and narrow developmental window. Computational gene-regulatory network inference elucidated the transcriptional logic of T lineage specification, uncovering an important role for YBX1. We mapped the differentiation cell fate hierarchy using transcribed lineage barcoding and mathematical trajectory inference and discovered that mast and myeloid potential bifurcate from each other early in haematopoiesis, upstream of T lineage restriction. Collectively, our analyses provide a quantitative, time-resolved model of human T cell specification with relevance for regenerative medicine and developmental immunology.

immunology↗

bioRxiv2022

The common oral parasitic protozoan Entamoeba gingivalis forms cysts in response to antibiotic treatment

The eukaryotic protozoan Entamoeba gingivalis (E.g.) is strongly associated with inflamed periodontal pockets. Unlike other obligate anaerobic Entamoeba species, it is considered to not have a life cycle of actively dividing trophozoites and dormant cysts. Accordingly, it has been regarded as non-infectious. To investigate if E.g is capable of encystation in response to adverse environmental conditions, we cultivated clinical isolates of E.g. collected from inflamed periodontal pockets in antibiotics for 8 days. The cytomorphological and ultrastructure forms of the amoeba were investigated by transmission and scanning electron microscopy to reveal cyst formation. We observed exocysts and the encapsulated trophozoids separated by an intra-cystic space, a dense poorly vesiculated cytoplasma and polygonal surface areas of cysts. The cysts walls were composed of chitin. Cysts were conspicuously smaller compared to trophozoids and lacked pseudo- and filipodia. We did not observe multi-nucleated trophozoids after antibiotic induces encystation. Cyst formation in E.g may explain why established treatment approaches often do not stop periodontal tissue destruction during periodontitis and periimplantitis.

microbiology↗

bioRxiv2020

A lipocalin mediates unidirectional haem biomineralization in malaria parasites

During blood stage development, malaria parasites are challenged with the detoxification of enormous amounts of haem released during the proteolytic catabolism of erythrocytic haemoglobin. They tackle this problem by sequestering haem into bioinert crystals known as haemozoin. The mechanisms underlying this biomineralization process remain enigmatic. Here, we demonstrate that both rodent and human malaria parasite species secrete and internalize a lipocalin-like protein, PV5, to control haem crystallization. Transcriptional deregulation of PV5 in the rodent parasite Plasmodium berghei results in inordinate elongation of haemozoin crystals, while conditional PV5 inactivation in the human malaria agent Plasmodium falciparum causes excessive multi-directional crystal branching. Although haemoglobin processing remains unaffected, PV5-deficient parasites generate less haemozoin. Electron diffraction analysis indicates that despite the distinct changes in crystal morphology neither the crystalline order nor unit cell of haemozoin are affected by impaired PV5 function. Deregulation of PV5 expression renders P. berghei hypersensitive to the antimalarial drugs artesunate, chloroquine, and atovaquone, resulting in accelerated parasite clearance following drug treatment in vivo. Together, our findings demonstrate the Plasmodium-tailored role of a lipocalin family member in haemozoin formation and underscore the haem biomineralization pathway as an attractive target for therapeutic exploitation. SIGNIFICANCEDuring blood stage development, the malaria parasite replicates inside erythrocytes of the vertebrate host, where it engulfs and digests most of the available haemoglobin. This results in release of the oxygen-binding prosthetic group haem, which is highly toxic in its unbound form. The parasite crystallizes the haem into an insoluble pigment called haemozoin, a process that is vital for parasite survival and which is exploited in antimalarial therapy. We demonstrate that the parasite uses a protein called PV5 in haemozoin formation and that interfering with PV5 expression can increase the parasites sensitivity to antimalarial drugs during blood infection. An improved understanding of the mechanisms underlying haem sequestration will provide valuable insights for future drug development efforts.

microbiology↗