Biology subjects

Seidel, M.

Publications and source records attributed to Seidel, M..

13 recordsLinked to original sources

bioRxiv2026

Macroalgal fucoidan can activate the biological carbon pump

Macroalgae secrete complex carbohydrate polymers, their extracellular matrix, as protection against microbial degradation. By resisting breakdown, these carbohydrates can contribute to marine carbon sequestration, though mechanisms, extent, and timescales remain unknown. Using ship-based sampling and experiments, we found that brown macroalgae release 1.7-4.2% of carbon fixation as fucoidan, equivalent to 0.32-0.88 mg fucoidan per gram of dry seaweed tissue per day. A Bayesian model trained on our empirical data, coupled with Monte Carlo simulations suggests an annual global release of 13-37 megatons fucoidan carbon. Moreover, degradation resistance combined with surface-activity enabled fucoidan to act as glue that cross-linked allochthonous organic carbon including microbes and proteins into marine snow. Notably, substantial fucoidan exudation was universally conserved across all tested species and regions. Thus, any brown macroalgal species can be used e.g. via aquafarming to enhance the formation of marine snow.

ecology↗

bioRxiv2026

Ubiquitin selective ribosome profiling reveals systematic principles of co-translational quality control

Protein biogenesis is a stress- and error-sensitive process that can lead to nascent protein misfolding and aggregation, challenging cellular proteostasis.1 Co-translational ubiquitination (CTU) is a critical surveillance mechanism,2,3 yet its regulatory principles remain unclear due to limited known substrates and the lack of translatome-wide methods to query CTU. Here, we introduce UbSeRP, an approach that enables ubiquitin linkage-specific, and translatome-wide mapping of CTU. Focusing on ribosome-associated quality control (RQC), we expand the known endogenous RQC substrates in S. cerevisiae from few4-7 to thousands, reveal that only a subset of all identified disomes undergoes RQC, and uncover biophysical features of nascent chains that predict RQC engagement. We also identify widespread RQC-independent ubiquitination of nascent proteins, implicating broader roles of CTU in protein complex assembly. In a chronological aging model, we show that aging remodels translation and diminishes RQC engagement, favoring RQC-independent proteasomal pathways. Our findings provide systematic insight into the determinants and adaptability of CTU in maintaining proteostasis under changing physiological conditions.

biochemistry↗

bioRxiv2025

DNA methylation around transcription start sites not globally associated with transcription in natural and synthetic hexaploid wheat

Epigenetic mechanisms including DNA methylation are assumed to play crucial roles in the maintenance of genome integrity, regulation of gene expression and development, and their increasing exploitation in breeding applications is anticipated. However, the relationship between DNA methylation and gene expression remains ambiguous and difficult to generalize. Here we explored the hypothesized causality between the level of transcription and cytosine methylation at the 5 end of genes (around transcription start sites and start codons) in relation to whole-genome duplication in natural and synthetic allohexaploid wheat (Triticum/Aegilops complex). Using transcriptomes and a sequence capture protocol coupled with bisulfite sequencing, we observed sometimes significant, but overall very weak associations between gene expression and 5 end methylation on a genome-wide scale. In synthetic wheat allohexaploids, global methylation differences between subgenomes are not triggered by the polyploidization, as the subgenome patterns are rather faithfully inherited from parents. A small number of genes differentially methylated between the parents and synthetics was consistently recovered in reciprocal synthetics and subsequent generations. Differences in transcription between homeologs are not clearly associated with 5 end methylation in either natural or synthetic wheat. Overall, allopolyploidization triggers only minor methylation changes around transcription start sites and start codons of nascent wheat allopolyploids, and these are not statistically associated with differential expression. Although there is a measurable methylation difference between expressed and non-expressed genes, our results do not support the hypothesis that 5 end DNA methylation is engaged in the regulation of gene expression in natural and synthetic wheat. SIGNIFICANCE STATEMENTWhile agenome shock hypothesis predicts extensive transcriptomic and epigenetic reorganization after polyploidization, DNA methylation patterns around transcription start sites are generally undisturbed in nascent wheat allohexaploids. Although this stability might indicate importance for gene regulation, a clear relationship between DNA methylation and transcription was not observed either on a genome-wide scale, or among triads of homeologous genes.

genomics↗

bioRxiv2025

Decoding the functional role of the calcium ATPase YloB in microbially induced calcite precipitation and sporulation in Solibacillus silvestris

Calcium homeostasis is essential for bacterial physiology, yet its regulation and role in specialized processes such as microbially induced calcite precipitation (MICP) and sporulation remain poorly understood. Here, we characterized the sole annotated P-type calcium ATPase in Solibacillus silvestris, which was previously shown to be upregulated under MICP conditions. We named the protein YloB based on homology to the Bacillus subtilis protein. Structural modeling confirmed that YloB possesses the conserved domains and motifs typical of calcium binding P-type ATPases. Deletion of yloB did not affect growth under elevated calcium levels nor did it reduce MICP yields, indicating that YloB is dispensable for calcium detoxification and biomineralization. In contrast, {Delta}yloB cells produced only partially dehydrated spores with severely reduced heat resistance, a defect rescued by complementation. A YloB-mNeonGreen fluorescent fusion localized specifically to the cell membrane surrounding the forespore during early engulfment, and was retained at this site throughout the remainder of sporulation. A transcriptional PyloB-msfGFP reporter demonstrated that yloB transcription was induced in the early stages of sporulation, but did not respond to a calcium stimulus. These results show that YloB does not act to detoxify calcium from the cytoplasm of S. silvestris, but rather functions to pump calcium into the forespore, enabling Ca-dipicolinic acid accumulation and proper spore maturation. Our study reveals a specialized role for a bacterial calcium ATPase in sporulation, distinguishing calcium transport for endospore development from biomineralization and global calcium homeostasis.

microbiology↗

bioRxiv2023

During heat stress in Myxococcus xanthus, the CdbS PilZ domain protein, along with two PilZ-DnaK chaperones, perturbs chromosome organization and accelerates cell death

C-di-GMP is a bacterial second messenger that regulates diverse processes in response to environmental or cellular cues. The nucleoid-associated protein (NAP) CdbA in Myxococcus xanthus binds c-di-GMP and DNA in a mutually exclusive manner in vitro. CdbA is essential for viability, and CdbA depletion causes defects in chromosome organization, leading to a block in cell division and, ultimately, cell death. Most NAPs are not essential; therefore, to explore the paradoxical cdbA essentiality, we isolated suppressor mutations that restored cell viability without CdbA. Most mutations mapped to cdbS, which encodes a stand-alone c-di-GMP binding PilZ domain protein, and caused loss-of-function of cdbS. Cells lacking CdbA and CdbS or only CdbS were fully viable and had no defects in chromosome organization. CdbA depletion caused post-transcriptional upregulation of CdbS accumulation, and this CdbS over-accumulation was sufficient to disrupt chromosome organization and cause cell death. CdbA depletion also caused increased accumulation of CsdK1 and CsdK2, two unusual PilZ-DnaK chaperones. During CdbA depletion, CsdK1 and CsdK2, in turn, stabilized CdbS, thereby enabling its increased accumulation and toxicity. Moreover, we demonstrate that heat stress, possibly involving an increased cellular c-di-GMP concentration, induces the CdbA/CsdK1/CsdK2/CdbA system, causing a CsdK1- and CsdK2-dependent increase in CdbS accumulation. Thereby this system accelerates heat stress-induced chromosome mis-organization and cell death. Collectively, this work describes a unique system that contributes to regulated cell death in M. xanthus and suggests a link between c-di-GMP signaling and regulated cell death in bacteria. Author summaryThe nucleotide-based second messenger c-di-GMP in bacteria controls numerous processes in response to environmental or cellular cues. Typically, these processes are related to lifestyle transitions between motile and sessile behaviors. However, c-di-GMP also regulates other processes. In Myxococcus xanthus, CdbA is a DNA-binding and nucleoid-associated protein that helps to organize the large chromosome. CdbA binds c-di-GMP and DNA in a mutually exclusive manner. While other nucleoid-associated proteins are not essential, CdbA is essential. Here, we show that the crucial function of CdbA is to maintain the level of the c-di-GMP-binding PilZ-domain protein CdbS appropriately low. The CdbS level is not only increased upon depletion of CdbA but also in response to heat stress. Under both conditions, the increased CdbS level perturbs chromosome organization and ultimately causes cell death. The CdbA/CdbS system represents a unique system that contributes to regulated cell death in M. xanthus and suggests a link between c-di-GMP signaling and regulated cell death.

microbiology↗

bioRxiv2023

A transcriptome-based phylogeny of Scarabaeoidea confirms the sister group relationship of dung beetles and phytophagous pleurostict scarabs (Coleoptera)

Scarab beetles (Scarabaeidae) are a diverse and ecologically important group of angiosperm-associated insects. As conventionally understood, scarab beetles comprise two major lineages: dung beetles and the phytophagous Pleurosticti. However, previous phylogenetic analyses have not been able to convincingly answer the question whether or not the two lineages form a monophyletic group. Here we report our results from phylogenetic analyses of more than 4,000 genes mined from transcriptomes of more than 50 species of Scarabaeidae and other Scarabaeoidea. Our results provide convincing support for the monophyly of Scarabaeidae, confirming the debated sister group relationship of dung beetles and phytophagous pleurostict scarabs. Supermatrix-based maximum likelihood and multispecies coalescent phylogenetic analyses strongly imply the subfamily Melolonthinae as currently understood being paraphyletic. We consequently suggest various changes in the systematics of Melolonthinae: Sericinae Kirby, 1837 stat. rest. and sensu n. to include the tribes Sericini, Ablaberini and Diphucephalini, and Sericoidinae Erichson, 1847 stat. rest. and sensu n. to include the tribes Automoliini, Heteronychini, Liparetrini, Maechidiini, Scitalini, Sericoidini, and Phyllotocini. Both subfamilies appear to consistently form a monophyletic sister group to all remaining subfamilies so far included within pleurostict scarabs except Orphninae. Our results represent a major step towards understanding the diversification history of one of the largest angiosperm-associated radiations of beetles.

zoology↗

bioRxiv2022

Co-translational binding of importins to nascent proteins

Various cellular quality control mechanisms support proteostasis. While, ribosome-associated chaperones prevent misfolding of nascent chains during translation, importins were shown to prevent the aggregation of specific cargoes in a post-translational mechanism prior the import into the nucleoplasm. Here, we hypothesized that importins may already bind ribosome-associated cargo in a co-translational manner. We systematically measured the nascent chain association of all importins in Saccharomyces cerevisiae by selective ribosome profiling. We identified a subset of importins that bind to a wide range of nascent, often uncharacterized cargoes. This included ribosomal proteins, chromatin remodelers and RNA binding proteins that are aggregation prone in the cytosol. We show that importins act consecutively with other ribosome-associated chaperones. Thus, the nuclear import system is directly intertwined with nascent chain folding and chaperoning. One-Sentence SummaryWe describe an unanticipated connection between co-translational protein chaperoning and the nuclear import system.

molecular biology↗

bioRxiv2022

New estimates of genome size in Orthoptera and their evolutionary implications

Animal genomes vary widely in size, and much of their architecture and content remains poorly understood. Even among related groups, such as orders of insects, genomes may vary in size by orders of magnitude - for reasons unknown. The largest known insect genomes were repeatedly found in Orthoptera, e.g., Podisma pedestris (1C = 16.93 pg), Stethophyma grossum (1C = 18.48 pg) and Bryodemella holdereri (1C = 18.64 pg). While all these species belong to the suborder of Caelifera, the ensiferan Deracantha onos (1C = 19.60 pg) was recently found to have the largest genome. Here, we present new genome size estimates of 50 further species of Ensifera (superfamilies Gryllidea, Tettigoniidea) and Caelifera (Acrididae, Tetrigidae) based on flow cytometric measurements. We found that Bryodemella tuberculata (Caelifera: Acrididae) has the so far largest measured genome of all insects with 1C = 21.96 pg (21.48 gBp). Species with 2n = 16 and 2n = 22 chromosomes have significantly larger genomes than species with other chromosome counts. Gryllidea genomes vary between 1C = 0.95 and 2.88 pg, and Tetrigidae between 1C = 2.18 and 2.41, while the genomes of all other studied Orthoptera range in size from 1C = 1.37 to 21.96 pg. Reconstructing ancestral genome sizes based on a phylogenetic tree of mitochondrial genomic data, we found genome size values of >15.84 pg only for the nodes of Bryodemella holdereri / B. tuberculata and Chrysochraon dispar / Euthystira brachyptera. The predicted values of ancestral genome sizes are 6.19 pg for Orthoptera, 5.37 pg for Ensifera, and 7.28 pg for Caelifera. The reasons for the large genomes in Orthoptera remain largely unknown, but a duplication seems unlikely as chromosome numbers do not differ. Sequence-based genomic studies may shed light on the underlying evolutionary mechanisms.

genomics↗

bioRxiv2022

Gene amplifications cause high-level resistance against albicidin in Gram-negative bacteria

Antibiotic resistance is a continuously increasing concern for public health care. Understanding resistance mechanisms and their emergence is crucial for the development of new antibiotics and their effective use. Here, we report the discovery of a gene amplification-based mechanism that imparts an up to 1000-fold increase in resistance levels against the antibiotic albicidin. We show that this mechanism protects Salmonella Typhimurium and Escherichia coli by increasing the copy number of the GyrI-like transcription regulator STM3175 (YgiV) which binds albicidin. X-ray crystallography and molecular docking studies reveal a conserved binding motif that can interact with aromatic building blocks of albicidin. Phylogenetic studies suggest that this resistance mechanism is ubiquitous in Gram-negative bacteria and our experiments confirm that STM3175 homologs can convey resistance in pathogens such as Vibrio vulnificus and Pseudomonas aeruginosa.

microbiology↗

bioRxiv2021

Co-translational assembly counteracts promiscuous interactions

During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examined structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally tested candidate structural motifs and identified several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assembled co-translationally in only one but not all of the relevant assembly pathways. Our results highlight the regulatory complexity of assembly pathways.

molecular biology↗

bioRxiv2021

Lateral Undulation Aids Biological and Robotic Earthworm Anchoring and Locomotion

Earthworms (Lumbricus terrestris) are characterized by soft, highly flexible and extensible bodies, and are capable of locomoting in most terrestrial environments. Previous studies of earthworm movement have focused on the use of retrograde peristaltic gaits in which controlled contraction of longitudinal and circular muscles results in waves of shortening/thickening and thinning/lengthening of the hydrostatic skeleton. These waves can propel the animal across ground as well as into soil. However, worms can also benefit from axial body bends during locomotion. Such lateral undulation dynamics can aid locomotor function via hooking/anchoring (to provide propulsion), modify travel orientation (to avoid obstacles and generate turns) and even generate snake-like undulatory locomotion in environments where peristaltic locomotion results in poor performance. To the best of our knowledge, the important aspects of locomotion associated with the lateral undulation of an earthworm body are yet to be systematically investigated. In this study, we observed that within confined environments, the worm uses lateral undulation to anchor its body to the walls of their burrows and tip (nose) bending to search the environment. This relatively simple locomotion strategy drastically improved the performance of our soft bodied robophysical model of the earthworm both in a confined (in an acrylic tube) and above-ground heterogeneous environment (rigid pegs), where the peristaltic gait often fails. In summary, lateral undulation facilitates the mobility of earthworm locomotion in diverse environments and can play an important role in the creation of low cost soft robotic devices capable of traversing a variety of environments.

animal behavior and cognition↗

bioRxiv2019

Seagrass excretes sugars to their rhizosphere making them the sweet spots in the sea

Seagrasses are one of the most efficient sinks of carbon dioxide on Earth1: They bury carbon 35 times faster than tropical rainforests on a per unit area basis2. While we know that carbon sequestration in terrestrial plants is intimately linked to the microorganisms living in their soils3-6, the interactions of seagrasses with their rhizospheres are poorly understood. We show that three seagrass species from two oceans excrete simple sugars, mainly sucrose, into their rhizosphere that accumulate to over 200 {micro}M. Such high concentrations are at least 80 times higher than previously observed in the ocean, and surprising, as sugars are quickly consumed by microorganisms. In situ analyses and incubation experiments indicated that phenolic compounds from the seagrass inhibited microbial consumption of sucrose. Metagenomic and metatranscriptomic analyses of the microbial communities in the seagrass rhizosphere revealed that many members had the genes for degrading sucrose, but these were only expressed by a few specialists that also expressed genes for degrading phenolics. Our results explain why sucrose accumulates under seagrass meadows, where it comprises as much as 40% of the dissolved organic carbon. Destruction of extant seagrass canopies would allow sediment microorganisms to consume the tremendous deposits of sucrose buried underneath their meadows, thereby releasing large amounts of CO2 into the oceans and atmosphere.

microbiology↗

bioRxiv2019

The de novo reference genome and transcriptome assemblies of the wild tomato species Solanum chilense

BackgroundWild tomato species, like Solanum chilense, are important germplasm resources for enhanced biotic and abiotic stress resistance in tomato breeding. In addition, S. chilense serves as a model system to study adaptation of plants to drought and to investigate the evolution of seed banks. However to date, the absence of a well annotated reference genome in this compulsory outcrossing, very diverse species limits in-depth studies on the genes involved.\n\nFindingsWe generated [~]134 Gb of DNA and 157 Gb of RNA sequence data of S chilense, which yielded a draft genome with an estimated length of 914 Mb in total encoding 25,885 high-confidence (hc) predicted gene models, which show homology to known protein-coding genes of other tomato species. Approximately 71% (18,290) of the hc gene models are additionally supported by RNA-seq data derived from leaf tissue samples. A benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models retrieved 93.3% BUSCO genes, which is in the current range of high-quality genomes for non-inbred plants. To further verify the genome annotation completeness and accuracy, we manually inspected the NLR resistance gene family and assessed its assembly quality. We revealed the existence of unique gene families of NLRs to S. chilense. Comparative genomics analyses of S. chilense, cultivated tomato S. lycopersicum and its wild relative S. pennellii revealed similar levels of highly syntenic gene clusters between the three species.\n\nConclusionsWe generated the first genome and transcriptome sequence assembly for the wild tomato species Solanum chilense and demonstrated its value in comparative genomics analyses. We make these genomes available for the scientific community as an important resource for studies on adaptation to biotic and abiotic stress in Solanaceae, on evolution of self-incompatibility, and for tomato breeding.

plant biology↗