Biology subjects

Zenker, S.

Publications and source records attributed to Zenker, S..

5 recordsLinked to original sources

bioRxiv2024

Many transcription factor families have evolutionarily conserved binding motifs in plants

Transcription factors control gene expression during development and in response to a broad range of internal and external stimuli. They regulate promoter activity by directly binding cis- regulatory elements in DNA. The angiosperm Arabidopsis thaliana contains more than 1,500 annotated transcription factors, each containing a DNA-binding domain that is used to define transcription factor families. Analyzing binding motifs of 686 and the binding sites of 335 A. thaliana transcription factors as well as motifs of 92 transcription factors from other plants, we identified a constrained vocabulary of 74 conserved motifs spanning 50 families in plants. Among 21 transcription factor families, we found one core motif for all analyzed members and between 2 and 72% overlapping binding sites. Five families show conservation of the motif along phylogenetic clades. Five families including the C2H2 zinc finger family show high diversity among motifs in plants, suggesting potential for neofunctionalization of duplicated transcription factors based on the motif recognized. For conserved motifs we tested if they remained conserved since at least 450 million years ago by determining the binding motifs of 17 orthologous transcription factors from 11 families in M. polymorpha using amplified DNA affinity purification sequencing. We detected nearly identical binding motifs as predicted from the angiosperm data. Taken together, the results show a large repertoire of overlapping binding sites within a TF family and species and a high degree of binding motif conservation for at least 450 million years. The results indicate more potential for evolution in cis- rather than trans-regulatory elements.

plant biology↗

bioRxiv2024

Regulation of Crassulacean Acid Metabolism at the protein level in the CAM plant Kalanchoë laxiflora

Crassulacean acid metabolism (CAM) is an adaptation to environments where water availability is seasonal or extremely low. It serves to ensure survival and/ or maintain productivity in these adverse environments. CAM has repeatedly evolved although it requires a large and complex set of enzymes and transporters and regulatory processes to control metabolite flux and pools. To test potential regulatory levels, we analyze the CAM plant Kalanchoe laxiflora embedded in the context of available CAM genome and transcriptome sequences. We show that CAM associated transcripts and proteins do not show a binary on/off pattern between day and night in K. laxiflora. Instead, we observe that many CAM plants display shared amino acid changes compared to C3 plants especially in starch metabolism. Phosphoproteomics identifies phosphoproteome changes in K. laxiflora between day and night. Taken together, the analyses demonstrate the CAM photosynthesis is regulated at the levels of transcripts and proteins. One sentence summaryRegulation of CAM cannot be explained by transcript and protein abundance alone but is also dependent on adaptive changes in proteins and posttranslational modifications.

plant biology↗

bioRxiv2024

Study of excess manganese stress response highlights the central role of manganese exporter Mnx for holding manganese homeostasis in the cyanobacterium Synechocystis sp. PCC 6803

Cellular levels of the essential micronutrient manganese (Mn) need to be carefully balanced within narrow boarders. In cyanobacteria, sufficient Mn supply is critical for assuring the function of the oxygen-evolving complex as central part of the photosynthetic machinery. However, Mn accumulation is fatal for the cells. The reason for the observed cytotoxicity is unclear. To understand the causality behind Mn toxicity in cyanobacteria, we investigated the impact of excess Mn on physiology and global gene expression in the model organism Synechocystis sp. PCC 6803. We compared the response of the wild type and the knock-out mutant in the manganese exporter (Mnx), {Delta}mnx, which is disabled in the export of surplus Mn and thus functions as model for toxic Mn overaccumulation. While growth and pigment accumulation in {Delta}mnx was severely impaired 24 h after addition of 10-fold Mn, the wild type was not affected and thus mounted an adequate transcriptional response. RNA-seq data analysis revealed that the Mn stress transcriptomes were partly resembling an iron limitation transcriptome. However, the expression of iron limitation signature genes isiABDC was not affected by the Mn treatment, indicating that Mn excess is not accompanied by iron limitation in Synechocystis. We suggest that the Ferric uptake regulator, Fur, gets partially mismetallated under Mn excess conditions and thus interferes with an iron-dependent transcriptional response. To encounter mismetallation and other Mn-dependent problems on protein level, the cells invest into transcripts of ribosomes, proteases, and chaperones. In case of the {Delta}mnx mutant the consequences of the disability to export excess Mn from the cytosol manifest in additionally impaired energy metabolism and oxidative stress transcriptomes with fatal outcome. This study emphasizes the central importance of Mn homeostasis and the transporter Mnxs role in restoring and holding it.

microbiology↗

bioRxiv2023

Transcription factors operate on a limited vocabulary of binding motifs in Arabidopsis thaliana

Predicting gene expression from promoter sequence requires understanding of the different signal integration points within a promoter. Sequence-specific transcription factors (TFs) binding to their cognate TF binding motifs control gene expression in eukaryotes by activating and repressing transcription. Their interplay generates complex expression patterns in reaction to environmental conditions and developmental cues. We hypothesized that signals are not only integrated by different TFs binding various positions in a promoter, but also by single TF binding motifs onto which multiple TFs can bind. Analyzing 2,190 binding motifs, we identified only 76 core TF binding motifs in plants. Twenty-one TF protein families act highly specific and bind a single conserved motif. Four TF families are classified as semi-conserved as they bind up to four motifs within a family, with divisions along phylogenetic groups. Five TF families bind diverse motifs. Expression analyses revealed high competition within TF families for the same binding motif. The results show that singular binding motifs act as signal integrators in plants where a combination of binding affinity and TF abundance likely determine the output.

systems biology↗

bioRxiv2023

Transcription factors mediating regulation of photosynthesis

Photosynthesis by which plants convert carbon dioxide to sugars using the energy of light is fundamental to life as it forms the basis of nearly all food chains. Surprisingly, our knowledge about its transcriptional regulation remains incomplete. Effort for its agricultural optimization have mostly focused on post-translational regulatory processes1-3 but photosynthesis is regulated at the post-transcriptional4 and the transcriptional level5. Stacked transcription factor mutations remain photosynthetically active5,6 and additional transcription factors have been difficult to identify possibly due to redundancy6 or lethality. Using a random forest decision tree-based machine learning approach for gene regulatory network calculation7 we determined ranked candidate transcription factors and validated five out of five tested transcription factors as controlling photosynthesis in vivo. The detailed analyses of previously published and newly identified transcription factors suggest that photosynthesis is transcriptionally regulated in a partitioned, non-hierarchical, interlooped network.

plant biology↗