Ute Krämer

Centromeres are critical for accurate segregation of chromosomes and are often composed of megabases of tandemly arranged satellite repeats. Yet, despite their conserved function, the DNA sequence of centromeres is, paradoxically, rapidly evolving. To understand the nature of centromeric sequence turnover, we assembled 417 centromeres from nine species representing the entire Arabidopsis genus. In the genus, centromeres are formed by four main satellite repeats with homologous sequences forming central arrays and minor repeat types. We identify the ancestral centromeric repeat type for the Arabidopsis genus and three independent turnovers to different repeats: (1) a complete turnover in A. thaliana, (2) a turnover of seven out of the eight centromeres in the ancestor of A. cebennensis and A. pedemontana, (3) turnovers of three to five centromeres in the genomes of A. halleri and A. lyrata. Most centromeric repeats are also present throughout the genome with shared syntenic locations between Arabidopsis species, and some being similar to parts of transposable elements and genes, suggesting that centromeric repeats originate outside of the centromeres. In allotetraploid A. suecica we find that the repeats from centromeric arrays on one subgenome can transpose and invade the other, likely via transposable element activity. All four main centromeric repeats can recruit the CENH3 (CENP-A) histone variant, however, when a new repeat successfully proliferates in an old array, CENH3 is primarily recruited to the new array marking functional take over. Complete centromeric turnovers occurred in species that experienced severe bottlenecks in their evolutionary history, where new centromeric alleles may have been fixed by genetic drift. Yet, we also observe segregation distortion between two different centromeric repeat types in A. lyrata, suggestive of centromere drive and we propose that both drift and drive contribute to centromeric repeat turnover. Together, our findings reveal the origin of centromeric repeats, mechanisms of repeat proliferation and spread, and the evolutionary dynamics of centromeric repeat turnovers in the Arabidopsis genus.

Soil pH is an influential abiotic environmental factor. Here, we identify responses to central stimuli associated with calcareous alkaline soils in Arabidopsis and comparatively explore the potential of the closely related Arabidopsis halleri for addressing how plants cope with local soil pH. We profiled the root transcriptome upon applying a set of hydroponic treatments—low bioavailable iron (Fe), alkaline pH and both in combination. Among the known Fe deficiency responses (ferrome), pervasively Fe‐deficiency responsive transcripts (pIDR) encoding the transcription factor PYE and its targets responded co‐directionally to Fe deficiency also at pH 7.5. A distinct subgroup of additionally alkaline‐pH‐responsive transcripts (aAPRs), comprising FIT and FIT‐dependent genes, showed a co‐directional response to pH 7.5 even with available Fe. Root hair densities in both species increased at an alkaline pH. Compared with A. thaliana , A. halleri accessions from soils of contrasting pH showed elevated tolerance to low‐Fe and alkaline pH based on chlorophyll content and root growth. A. halleri from high‐pH soils convergently exhibited longer and less branched root systems, more stable ionomes across conditions, and attenuated root growth at alkaline pH with Fe. Our findings provide insights into Fe‐deficiency regulatory networks and identify soil pH‐related phenotypic divergence within A. halleri and across species.

Summary: The causal factors shaping plant-associated microbiota are incompletely known. Elevated concentrations of the micronutrients zinc (Zn), manganese (Mn) and copper (Cu), and exposure to non-essential trace elements including cadmium (Cd) and arsenic (As), can be toxic. Here we explored whether differences in metal(loid) sensitivity between plants and bacteria influence phyllosphere bacterial community composition. 224 representative Arabidopsis thaliana phyllosphere bacterial strains were screened on metal(loid) concentration series in synthetic media. We obtained leaf apoplastic fluid ionomes for comparisons with bacteriotoxicity profiles, and tested for relationships between strain-wise metal(loid) tolerances, phylogeny and gene content. Leaf apoplastic Zn ²⁺ and Cd ²⁺ concentrations were the most likely to arrest growth of metal-sensitive bacteria in planta . Soil bacterial strains were several-fold more sensitive to both these metals than leaf strains, consistent with selection for increased bacterial Zn and Cd tolerance in the phyllosphere. Strains known to govern bacterial community structure were metal-sensitive, with only minor influences of between-metal and between-strain interactions. Bacterial genus explained considerable proportions of the variances in metal(loid)-related gene content and tolerance phenotypes. Bacterial Cd tolerance correlated with the presence and copy number of known Cd-related genes. Our results suggest that plant metal homeostasis contributes to structuring bacterial communities in the leaf endosphere.

Annually, chloroplasts fix 258 billion tons of CO2 through photosynthesis. Photosynthesis and other biochemical pathways require specific amounts of metal ions in the organelle. Transport proteins in the plastid inner envelope maintain the organellar ion homeostasis. Despite substantial progress over the last decades, many genes encoding plastid ion channels and ion carriers or their regulators remain unknown. To fill this knowledge gap, detailed information on the elemental composition of chloroplasts ie, a plastid ionome, is needed. This will allow us to compare mutants of transporter candidates with wild-type plants. Here, we provide quantitative descriptions of chloroplast ionomes from Arabidopsis thaliana, the metal hyperaccumulator Arabidopsis halleri, Pisum sativum, and Nicotiana benthamiana and analyze similarities and distinctions. Using A. thaliana, we show that plastid ionomes can be genetically manipulated. Chloroplasts of OLIGOPEPTIDE TRANSPORTER3 (OPT3)-deficient mutants contain 14-fold more iron, likely associated with stromal FERRITIN. The removal of FERRITIN in opt3 mutants leads to a substantial decrease in plastid and leaf iron, pointing to an important role of ferritins in shaping the chloroplast ionome. Our study reveals that chloroplast ferritins can be turned into iron sinks. Since crop biofortification to fight hidden hunger has become a global mission, this research provides groundwork to reach this goal.

Following gene duplication, the evolutionary trajectories of gene copies can be shaped by various processes including mutation, selection, recombination and interlocus, i.e., non-allelic, gene conversion (IGC). To explore dynamics and consequences of these processes, we developed a mathematical model that simulates the early evolution of recently duplicated, tandemly arrayed paralogous gene copies with positive selection on the new gene copy. We compared the results of our model to sequence variation in the three tandemly arrayed Arabidopsis halleri HEAVY METAL ATPase 4 ( HMA4 ) gene copies, which are known to undergo IGC. We find that the effective rates of IGC vary within genes, resulting in a mosaic pattern of divergence. Informed by empirical data, our model captures the impact of IGC on the diversity within each gene copy and the divergence among them. By tailoring the model to the AhHMA4 gene copies, we demonstrate the model’s flexibility and its potential to provide insights into the evolutionary dynamics driving the evolution of tandemly arrayed paralogues. This study enhances our understanding of the balance between concerted evolution and divergence in the early evolution of gene families following gene duplication.

Annually, chloroplasts fix 258 billion tons of CO ₂ through photosynthesis. Photosynthesis and other biochemical pathways require specific amounts of metal ions in the organelle. Transport proteins in the plastid inner envelope maintain the organellar ion homeostasis. Despite substantial progress over the last decades, many genes encoding for plastid ion channels and ion carriers or their regulators remain unknown. To fill this knowledge gap, detailed information on the elemental composition of chloroplasts i.e., a plastid ionome, is needed. This will allow to compare mutants of transporter candidates with wild-types. Here, we provide quantitative descriptions of chloroplast ionomes from Arabidopsis thaliana, the metal hyperaccumulator Arabidopsis halleri , Pisum sativum , and Nicotiana benthamiana and analyze similarities and distinctions. Using A. thaliana, we show that plastid ionomes can be genetically manipulated. Chloroplasts of oligopeptide transporter3 ( opt3 )-deficient mutants contain 14-fold more iron, which they deposit into stromal FERRITIN. The removal of FERRITIN in opt3 mutants leads to a substantial decrease in plastid and leaf iron pointing to important signaling linked to the chloroplast ionome. Our study reveals that chloroplasts can be turned into large iron storages. Since crop biofortification to fight hidden hunger has become a global mission, this research provides groundwork to reach this goal.

MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important regulatory roles in plant genomes. While some miRNA genes are deeply conserved, the majority appear to be species-specific, raising the question of how they emerge and integrate into cellular regulatory networks. To address this question, we first performed a detailed annotation of miRNA genes in the closely related Arabidopsis halleri and A. lyrata, then evaluated their phylogenetic conservation across 87 plant species. We then characterized the process by which newly emerged miRNA genes progressively acquire the properties of “canonical” miRNA genes, in terms of size and stability of the hairpin precursor, loading of their cleavage products into Argonaute proteins, and potential to regulate downstream target genes. Analysis of nucleotide polymorphism distribution along the hairpin sequence (stem, mature miRNA, terminal loop) revealed that the selective constraints on recently emerged miRNA genes were initially weak, gradually increasing toward evolutionarily conserved miRNA genes. Our results illustrate the rapid birth-and-death of miRNA genes in plant genomes, and provide a detailed picture of the evolutionary progression toward canonical miRNAs by which a small fraction of de novo formed miRNA genes eventually integrate into “core” biological processes.

The micronutrient zinc (Zn) is often poorly available but toxic when present in excess, so a tightly controlled Zn homoeostasis network operates in all organisms. This review summarizes our present understanding of plant Zn homoeostasis. In Arabidopsis, about 1,900 Zn-binding metalloproteins require Zn as a cofactor. Abundant Zn metalloproteins reside in plastids, mitochondria and peroxisomes, emphasizing the need to address how Zn reaches these proteins. Apo–Zn metalloproteins do not acquire Zn²⁺ from a cytosolic pool of free cations, but instead through associative ligand exchange from Zn-buffering molecules. The importance of cytosolic thiols in Zn buffering suggests that, besides elevated Zn influx, a more oxidized redox state is also predicted to cause elevated labile-bound Zn levels, consistent with the suppression of a Zn deficiency marker under oxidative stress. Therefore, we consider a broadened physiological scope in plants for a possible signalling role of Zn²⁺, experimentally supported only in animals to date.

Diphthamide is a posttranslationally modified histidine residue of eukaryotic TRANSLATION ELONGATION FACTOR 2 (eEF2) and the target of diphtheria toxin in human cells. In yeast and mammals, the 4Fe–4S cluster-containing proteins Dph1 and Dph2 catalyze the first biosynthetic step of diphthamide formation. Here, we identify Arabidopsis (Arabidopsis thaliana) DPH2 and show that it is required for diphthamide biosynthesis, localizes to the cytosol, and interacts physically with AtDPH1. Arabidopsis dph2 mutants form shorter primary roots and smaller rosettes than the wild type, similar to dph1 mutants which we characterized previously. Additionally, increased ribosomal -1 frameshifting error rates and attenuated TARGET OF RAPAMYCIN (TOR) kinase activity in dph2 mutants also phenocopy the dph1 mutant. Beyond the known heavy metal hypersensitivity and heat shock tolerance of dph1, we show here that both dph1 and dph2 mutants are hypersensitive to elevated light intensities and oxidative stress and that wild-type Arabidopsis seedlings accumulate diphthamide-unmodified eEF2 under oxidative stress. Both mutants share the deregulation of 1,186 transcripts associated with several environmental and hormone responses. AtDPH1 and AtDPH2 do not complement the corresponding mutants of Saccharomyces cerevisiae. In summary, DPH2 and DPH1 interact to function inter-dependently in diphthamide formation, the maintenance of translational fidelity, wild-type growth rates, and TOR kinase activation, and they contribute to mitigating damage from elevated light intensities and oxidative stress. Under oxidative stress, a dose-dependent loss of diphthamide could potentiate downstream effects in a feed-forward loop. This work advances our understanding of translation and its interactions with growth regulation and stress responses in plants.