Biology subjects

Kiefer, C.

Publications and source records attributed to Kiefer, C..

9 recordsLinked to original sources

bioRxiv2026

Why woodiness repeatedly evolves--and disappears

Derived woodiness--the evolution of woody growth from herbaceous ancestors--has arisen hundreds of times across flowering plants, yet the environmental conditions associated with its repeated evolution remain poorly understood. Here, we analyse woodiness evolution in the mustard family (Brassicaceae; ~4,150 species) using a time-calibrated phylogeny of 2,927 species, including 374 of the 385 known woody species, together with global growth-form and climatic niche data. We infer 231 independent origins of woodiness alongside 176 reversals to herbaceousness, indicating that woodiness evolves repeatedly but remains evolutionarily unstable. Although woody species are enriched on islands, most occur on the mainland, where woodiness is consistently associated with drought and reduced frost. Correlated-evolution analyses reveal that drought is associated primarily with the persistence of woodiness, whereas reduced frost is associated with gains of woodiness and increased frost with its loss. These findings identify distinct climatic associations with the gain, persistence, and loss of woody growth forms.

evolutionary biology↗

bioRxiv2026

Combination of enhanced gene activation and cell death causes lethal inflammatory pulmonary fibrosis

The current paradigm of inflammatory disease etiology is that it is caused by an aberrant increase in either gene activation or cell death. Studying the linear ubiquitin (linUb) chain assembly complex (LUBAC) was instrumental in proving that immune-receptor-dependent cell death can cause inflammatory disease. As LUBAC regulates both, gene activation and cell death, it can, however, also serve to evaluate the inflammatory-disease-initiating role of gene activation. Investigating mice with two different gene-activation-enhancing point mutations in LUBAC components showed that aberrantly increased gene activation in Hoil 1C458A/C458A mice did not cause pathology. In contrast, in HoipN101A/N101A mice it led to untoward cell death which, unexpectedly, was required for pathological inflammation, culminating in lethal lung fibrosis resembling human idiopathic pulmonary fibrosis (IPF). Hence, we here uncover a new etiology of inflammation, whereby aberrantly enhanced gene activation can be root cause of pathological, fibrogenic inflammation, yet intriguingly via inducing untoward cell death.

cell biology↗

bioRxiv2026

Mechanisms regulating combination effect of antibody-drug conjugates and cancer immunotherapy

Antibody-drug conjugates (ADCs) have emerged as a transformative class of cancer therapeutics with important challenges still to be addressed. Combination of ADC with immunotherapy is a promising strategy but mechanisms and effective application remain to be determined. We evaluated ADC combinations with T cell engagers (TCEs) and checkpoint inhibitors (CPI). ADC-TCE combinations produced robust antitumor activity independent of antigen and payload and persisted despite ADC-related T cell loss. Efficacy was dominated by a direct effect of ADC on tumor cells. ADCs induced autophagy that upregulated TNF receptors (TNFRs) and mannose-6-phosphate receptors (M6PR). When ADCs were combined with TCEs TNF released by T cells was primarily responsible for potent antitumor effect of combination. In contrast, M6PR was dispensable for ADC-TCE activity but critical for combinations with CPI expanded antigen-specific T cells via enhanced granzyme B uptake. These data reveal a unifying, target- and payload-agnostic mechanism enabling rational ADC-immunotherapy combinations. SignificanceThis is first evidence that ADC-induced tumor cell autophagy via up-regulation of TNFR and M6PR could be responsible for potent antitumor effect of combination of ADC with TCE. TCEs exploit a TNF-TNFR axis, whereas antigen-specific T cells leverage granzyme B-M6PR uptake. This mechanistic framework explains broad ADC-TCE synergy and guides rational selection of ADC-immunotherapy combinations beyond checkpoint blockade.

immunology↗

bioRxiv2025

Split or spread - A spatio-temporal framework for the evolution of annual Arabis (Brassicaceae) in Eurasia

Life history in plants appears to be an important determining factor for the capacity to cope with major environmental change. Consequently, the evolutionary history of life form may have constrained significantly present-day biogeographic distribution patterns of phylogenetically related species, which had either to adapt or migrate during Pleistocene climatic fluctuations. In particular in Brassicaceae the molecular basis of monocarpic and polycarpic flowering behavior is well understood, and it is thought that both traits are reciprocally conversed. The Brassicaceae consist in total of c. 25% of monocarpic species. However, species-rich tribes such as Arabideae consist of only 8% monocarpic species indicating evolutionary and environmental constrain towards life history transition. Here we utilized whole plastid genome sequencing through next-generation sequencing (NGS) to investigate the spatio-temporal timing of the evolution of annual species in the tribe Arabideae (Brassicaceae). Based on these data, we conducted phylogenetic reconstructions, divergence time estimations, and plastid haplotype distribution analyses. Past and present ecological niche modeling was performed for monocarpic taxa from three different Arabideae clades, Arabis auriculata, Arabis nova subsp. iberica, and Arabis montbretiana. With the integration of these approaches, we test the hypothesis that the evolution of monocarpic species in tribe Arabideae at low frequency is associated with large-scale biogeographic patterns reflecting migration rather than adaptation or reversals.

evolutionary biology↗

bioRxiv2024

Unravelling complex hybrid and polyploid evolutionary relationships using phylogenetic placement of paralogs from target enrichment data

Phylogenomic datasets comprising hundreds of genes have become the standard for plant systematics and phylogenetics. However, large scale phylogenomic studies often exclude polyploids and hybrids due to the challenges in assessing paralog status of targeted loci and incorporating them into tree reconstruction methods. Using a target enrichment dataset of 1081 genes from 452 samples from the Brassicaceae tribe Arabideae, including many hybrid and high ploidy taxa, we developed a novel approach to disentangle the evolutionary history of this phylogenetically and taxonomically challenging clade. Our approach extends beyond commonly used gene tree-species tree reconciliation techniques by using phylogenetic placement, a method adopted from metagenomics, of paralogous sequences into a diploid tree. We call this approach Paralog PhyloGenomics (PPG), and show how it allows for the simultaneous assessment of the origins of ancient and recent hybrids and autopolyploids, and the detection of nested polyploidization events. Additionally, we demonstrate how synonymous substitution rates provide further evidence for the mode of polyploidization, specifically to distinguish between allo- and autopolyploidization, and to identify hybridization events involving a ghost lineage. Our approach will be a valuable addition to phylogenomic methods available for the study of polyploids.

evolutionary biology↗

bioRxiv2022

Differential expression analysis of sexual and apomictic Boechera uncovers FAS4 as crucial for gametogenesis

During sexual reproduction of higher plants, seed formation is initiated by double fertilization of egg and central cell. In contrast, pseudogamous apomicts form embryos asexually by parthenogenesis of the egg, but initiation of endosperm development still depends on central cell fertilization. It can be envisioned that these differences are determined during gametogenesis and specification of gametophytic cells. To deepen the understanding of the transcriptional basis underlying sexual and apomictic reproduction, we applied tissue type-specific RNA-Seq. We compared expression in reproductive tissues of different Boechera accessions at distinct developmental stages. This confirmed previous evidence for an enrichment of RNA helicases at onset of reproductive development. We further identified a small number of members of this gene family as differentially expressed in female reproductive ovule tissues harbouring mature gametophytes from apomictic and sexual accessions. This included homologues of A. thaliana FASCIATED STEM 4 (FAS4) and of ENHANCED SILENCING PHENOTYPE 3 (ESP3), which have previously been identified as potential candidates for gametogenesis and apomixis, respectively. Unlike in A. thaliana, for either of them additional homologues or copies of related genes are present in Boechera, indicating complex evolutionary histories. As the expression patterns implied potential roles of FAS4 during gametogenesis, we first studied A. thaliana lines carrying mutant alleles. Indeed, we observed defects during male and female gametogenesis and severely reduced transmission efficiencies through both parents. In conclusion, our study identifies FAS4 as crucial for plant reproduction and suggests the potential for sub-functionalization of additional homologous genes in Boechera to shape reproductive development.

plant biology↗

bioRxiv2022

Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene icehouse origin of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodate Arabidopsis. With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology.

evolutionary biology↗

bioRxiv2020

The Arabidopsis V-ATPase is localized to the TGN/EE via a seed plant specific motif and acts in a partially redundant manner with the tonoplast enzyme

Vacuolar-type H+-ATPases (V-ATPases) are versatile proton pumps that control the pH of many intracellular compartments in all eukaryotic cells. The localization of the Arabidopsis V-ATPase was previously shown to be determined by the isoforms of subunit a (VHA-a). The incorporation of VHA-a1 targets the V-ATPase to the trans-Golgi network/early endosome (TGN/EE) whilst the incorporation of VHA-a2 or VHA-a3 targets the V-ATPase to the tonoplast. By employing chimeric proteins and site directed mutagenesis we identified a targeting domain (a1-TD) containing an acidic cluster in the N-terminus of VHA-a1 that serves as both an ER export signal and as a TGN retention motif. The a1-TD is conserved among seed plants and we confirmed experimentally that its presence is predictive of TGN/EE- localization. In contrast to many other non-seed plants, the liverwort Marchantia polymorpha encodes only a single VHA-a subunit (MpVHA-a) and we show here that it is predominantly localized at the tonoplast. In our attempts to determine if MpVHA-a can functionally replace the Arabidopsis VHA-a isoforms, we used CRISPR/Cas9 to generate null-alleles lacking VHA-a1 and discovered that its function is essential for male gametophyte development but can be replaced by VHA-a2 and VHA-a3 during vegetative growth.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2020

Cytokinin-promoted secondary growth and nutrient storage in the perennial stem zone of Arabis alpina

Perennial plants maintain their life span through several growth seasons. Arabis alpina serves as model Brassicaceae species to study perennial traits. A. alpina lateral stems have a proximal vegetative zone with a dormant bud zone, and a distal senescing seed-producing inflorescence zone. We addressed the questions of how this zonation is distinguished at the anatomical level, whether it is related to nutrient storage, and which signals affect the zonation. We found that the vegetative zone exhibits secondary growth, which we termed the perennial growth zone (PZ). High-molecular weight carbon compounds accumulate there in cambium and cambium derivatives. Neither vernalization nor flowering were requirements for secondary growth and sequestration of storage compounds. The inflorescence zone with only primary growth, termed annual growth zone (AZ), or roots exhibited different storage characteristics. Following cytokinin application, cambium activity was enhanced and secondary phloem parenchyma was formed in the PZ and also in the AZ. In transcriptome analysis cytokinin-related genes represented enriched gene ontology terms and were expressed at higher level in PZ than AZ. Thus, A. alpina uses primarily the vegetative PZ for nutrient storage, coupled to cytokinin-promoted secondary growth. This finding lays a foundation for future studies addressing signals for perennial growth. HighlightArabis alpina stems have a perennial zone with secondary growth, where cambium and derivatives store high-molecular weight compounds independent of vernalization. Cytokinins are signals for the perennial secondary growth zone.

plant biology↗