Biology subjects

Walter, I.

Publications and source records attributed to Walter, I..

5 recordsLinked to original sources

bioRxiv2026

The gene-like promoter and transcription of LTR retrotransposons.

Transcriptional regulation is one of the fundamental approaches for young plants to cope with environmental fluctuations and maintain active development. The transposable element (TE) subclass long terminal-repeat retrotransposons (LTR-RTs) can act as additional regulators for genes through enhancer and promoter activity, but their promoters, transcription initiation, and contributions during maize development remain uncharacterized. Here, we developed IsoClassifier to resolve the transcription start site (TSS) and RNA isoforms of LTR-RTs based on long-read transcriptomics, delineating LTR U3 regions as the native promoter and enhancer of LTR-RTs. We reveal conserved motifs associated with core promoter activity in transcribed LTR-RTs that are highly comparable to gene promoters. Further, we found that LTR-RT transcription in maize was dominated by spliced, long non-coding RNA. Finally, a genome-wide coexpression analysis revealed that LTR-RTs are transcribed as hub-like elements in coexpression networks, suggesting important roles in gene regulation. We conclude that LTR-RTs have similar promoter compositions to gene promoters and likely share similar transcription regulation programs.

plant biology↗

bioRxiv2025

Detection of vasculogenic mimicry in equine ocular, oronasal, and genital squamous cell carcinoma

Squamous cell carcinoma (SCC) is the most common malignant tumor disease in horses. It predominantly affects the ocular, oronasal, and anogenital region. Equine SCC is difficult to treat, also because important aspects of SCC development and metastasis are still unclear. We previously provided evidence that equine SCC cells can adopt a stem cell-like phenotype as a hallmark of malignant progression. Here, we investigated whether equine SCCs harbor endothelial-like tumor cells that form an alternative network of pseudo-vessels better known as vasculogenic mimicry (VM). Following histopathological diagnosis, 43 equine SCCs or precursor lesions (15 ocular, 14 genital, 14 oronasal tumors) were PCR-screened for equine papillomavirus (EcPV) infection. Subsequently, formalin-fixed paraffin-embedded-sections of all tumors were analyzed by Periodic Acid-Schiff (PAS) reaction and immunohistochemical (IHC) staining for endothelial cell marker CD31. Obtained micrographs were evaluated by a scientific board to unanimously identify sections of intact tumor tissue displaying PAS-positive, CD31-negative lumens harboring erythrocytes. Thirteen lesions exhibiting these features were subjected to triple immunofluorescence (IF) staining for CD31, pan-cytokeratin (KRT) and type 4 collagen (Col4) or alpha smooth muscle actin (SMA) to confirm the presence of VM, and to determine whether pericytes have a role in this phenomenon. All genital and 50% of oronasal lesions scored positive for EcPV type 2, whilst ocular lesions tested negative. One mandibular SCC harbored EcPV type 5. Six genital, three oronasal, and four ocular tumors unambiguously exhibited VM as revealed by CD31-/PAS+ vessel-like structures containing erythrocytes, the detection of CD31-negative cells lining their lumens, and the presence of Col4 and SMA in this lining. Detection of these two proteins in the context of VM suggests that VM-forming cancer cells recruit pericytes to enhance channel formation and stability. To our knowledge, this is the first report providing evidence of VM in equine cancer, and more generally, SCC in animals.

cancer biology↗

bioRxiv2025

Overcoming Fluorescence Loss in mEOS-based AAA+ Unfoldase Reporters Through Covalent Linkage

Recent work has demonstrated that the soluble photoconvertable fluorescent protein mEOS can be a reporter for AAA+ (ATPases Associated with diverse cellular Activities) unfoldase activity. Given that many AAA+ proteins process membrane proteins, we sought to adapt mEOS for use with membrane protein substrates. However, direct genetic fusion of mEOS to a membrane protein completely abolished fluorescence, severely limiting the utility of mEOS for studying AAA+ proteins. To circumvent this challenge, we separately purified mEOS and a AAA+ degron, covalently linked them via Sortase, and photoconverted the linked construct. This innovative approach preserves fluorescence and enables functional analysis, offering a broadly applicable platform for the study of membrane associated AAA+ proteins.

biochemistry↗

bioRxiv2024

Energetic requirements and mechanistic plasticity in Msp1-mediated substrate extraction from lipid bilayers

AAA+ proteins are essential molecular motors involved in numerous cellular processes, yet their mechanism of action in extracting membrane proteins from lipid bilayers remains poorly understood. One roadblock for mechanistic studies is the inability to generate subunit specific mutations within these hexameric proteins. Using the mitochondrial AAA+ protein Msp1 as a model, we created covalently linked dimers with varying combinations of wild type and catalytically inactive E193Q mutations. The wide range of ATPase rates in these constructs allows us to probe how Msp1 uses the energy from ATP hydrolysis to perform the thermodynamically unfavorable task of removing a transmembrane helix (TMH) from a lipid bilayer. Our in vitro and in vivo assays reveal a non-linear relationship between ATP hydrolysis and membrane protein extraction, suggesting a minimum ATP hydrolysis rate is required for effective TMH extraction. While structural data often supports a sequential clockwise/2-residue step (SC/2R) mechanism for ATP hydrolysis, our biochemical evidence suggests mechanistic plasticity in how Msp1 coordinates ATP hydrolysis between subunits, potentially allowing for robustness in processing challenging substrates. This study enhances our understanding of how Msp1 coordinates ATP hydrolysis to drive mechanical work and provides foundational insights about the minimum energetic requirements for TMH extraction and the coordination of ATP hydrolysis in AAA+ proteins.

biochemistry↗

bioRxiv2019

Satellite DNA landscapes after allotetraploidisation of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes

If two related plant species hybridise, their genomes are combined within a single nucleus, thereby forming an allotetraploid. How the emerging plant balances two co-evolved genomes is still a matter of ongoing research. Here, we focus on satellite DNA (satDNA), the fastest turn-over sequence class in eukaryotes, aiming to trace its emergence, amplification and loss during plant speciation and allopolyploidisation. As a model, we used Chenopodium quinoa Willd. (quinoa), an allopolyploid crop with 2n=4x=36 chromosomes. Quinoa originated by hybridisation of an unknown female American Chenopodium diploid (AA genome) with an unknown male Old World diploid species (BB genome), dating back 3.3 to 6.3 million years. Applying short read clustering to quinoa (AABB), C. pallidicaule (AA), and C. suecicum (BB) whole genome shotgun sequences, we classified their repetitive fractions, and identified and characterised seven satDNA families, together with the 5S rDNA model repeat. We show unequal satDNA amplification (two families) and exclusive occurrence (four families) in the AA and BB diploids by read mapping as well as Southern, genomic and fluorescent in situ hybridisation. As C. pallidicaule harbours a unique satDNA profile, we are able to exclude it as quinoas parental species. Using quinoa long reads and scaffolds, we detected only limited evidence of interlocus homogenisation of satDNA after allopolyploidisation, but were able to exclude dispersal of 5S rRNA genes between subgenomes. Our results exemplify the complex route of tandem repeat evolution through Chenopodium speciation and allopolyploidisation, and may provide sequence targets for the identification of quinoas progenitors.

plant biology↗