Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants

Wulf D, Bräutigam A. Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants. bioRxiv. 2023.Gene regulatory networks based on transcription factors control development and environmental responses in plants. Networks calculated by the machine learning algorithm random forest decision tree-based regression for the grasses barley, maize, wheat, Brachypodium, sorghum, and rice compared with Arabidopsis and an alga show substantial conservation. The degree of conservation depends on phylogenetic closeness. The processes, which are conserved between all species include basic cellular functions while the processes conserved in the grasses also more specific gene ontology terms. In the three species with a carbon concentration mechanism, photorespiration is partially disassociated from photosynthetic regulation. In contrast, in the C4 species, the regulation of C4 genes associates with photosynthetic regulation. The comparative analyses reveal conserved transcription factors, which control photosynthesis in seed plants but not in the alga. An analysis pipeline for the general transfer of information between the small weed Arabidopsis and the commercially relevant grasses is presented

Using Publicly Available RNA-seq Data for Expression Analysis of Genes of Interest

Wulf D, Bräutigam A, Eisenhut M. Using Publicly Available RNA-seq Data for Expression Analysis of Genes of Interest. Methods in Molecular Biology. 2024;2792:241-250.RNA-seq data in publicly available repositories enable the efficient reanalysis of transcript abundances in existing experiments. Graphical user interfaces usually only allow the visual inspection of a single gene and of predefined experiments. Here, we describe how experiments are selected from the Sequence Read Archive or the European Nucleotide Archive, how data is efficiently mapped onto a reference transcriptome, and how global transcript abundances and patterns are inspected. We exemplarily apply this analysis pipeline to study the expression of photorespiration-related genes in photosynthetic organisms, such as cyanobacteria, and to identify conditions under which photorespiratory transcript abundances are enhanced. © 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

Local DNA shape is a general principle of transcription factor binding specificity in Arabidopsis thaliana

Sielemann J, Wulf D, Schmidt R, Bräutigam A. Local DNA shape is a general principle of transcription factor binding specificity in Arabidopsis thaliana. Nature Communications. 2021;12(1): 6549.**Abstract** Understanding gene expression will require understanding where regulatory factors bind genomic DNA. The frequently used sequence-based motifs of protein-DNA binding are not predictive, since a genome contains many more binding sites than are actually bound and transcription factors of the same family share similar DNA-binding motifs. Traditionally, these motifs only depict sequence but neglect DNA shape. Since shape may contribute non-linearly and combinational to binding, machine learning approaches ought to be able to better predict transcription factor binding. Here we show that a random forest machine learning approach, which incorporates the 3D-shape of DNA, enhances binding prediction for all 216 testedArabidopsis thalianatranscription factors and improves the resolution of differential binding by transcription factor family members which share the same binding motif. We observed that DNA shape features were individually weighted for each transcription factor, even if they shared the same binding sequence

Complete Genome Sequence of Pseudomonas sp. Strain MM213, an Isolate from a Brookside in Bielefeld, Germany

Verwaaijen B, Cevahir Ö, Hitz F, Römmich J, Wulf D. Complete Genome Sequence of Pseudomonas sp. Strain MM213, an Isolate from a Brookside in Bielefeld, Germany. Microbiology Resource Announcements. 2022: e0086621.Here, we report the genome sequence of Pseudomonas sp. strain MM213, isolated from brookside soil in Bielefeld, Germany. The genome is complete and consists of 6,746,355bp, with a GC content of 59.4% and 6,145 predicted protein-coding sequences. Pseudomonas sp. strain MM213 is part of the Pseudomonas mandelii group

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

Zenker S, Wulf D, Meierhenrich A, et al. Dataset for "Transcription factors operate on a limited vocabulary of binding motifs in Arabidopsis thaliana". Bielefeld University; 2023.Supplemental dataset for the publication "Transcription factors operate on a limited vocabulary of binding motifs in *Arabidopsis thaliana*". Contains binding data from the publication "Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape" (O'Malley et al. 2016, 10.1016/j.cell.2016.04.038) mapped onto promoters of all nuclear encoded genes in *A. thaliana*. Visualizations available as interactive htmls

Whole-Genome Sequence of Pseudomonas sp. Strain MM211, Isolated from Soil in Langenfeld, Germany

Wulf D, Arndt J, Bleile IE, Bramers C, Gülpen PL, Verwaaijen B. Whole-Genome Sequence of Pseudomonas sp. Strain MM211, Isolated from Soil in Langenfeld, Germany. Microbiology Resource Announcements. 2022;11(2): e0104821.Here, we present the genome sequence of Pseudomonas sp. strain MM211, which was isolated from garden soil. The complete circular genome consists of a 5,281,862-bp chromosome, with a GC content of 61.5%

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

Zenker S, Wulf D, Meierhenrich A, et al. Transcription factors operate on a limited vocabulary of binding motifs in Arabidopsis thaliana. bioRxiv. 2023.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

Ubiquitin ligase component LRS1 and transcription factor CrHy5 act as a light switch for photoprotection in Chlamydomonas

Lämmermann N, Wulf D, Chang KS, et al. Ubiquitin ligase component LRS1 and transcription factor CrHy5 act as a light switch for photoprotection in Chlamydomonas. bioRxiv. 2020.Survival under excess light conditions requires the light-induced accumulation of protein LHCSR3 and other photoprotection factors, to enable efficient energy-dependent quenching in the green microalgaChlamydomonas reinhardtii. Here, we demonstrate that the high light-tolerant phenotype of mutanthit1is caused by a de-repression of promoters belonging to photoprotection genes, which in turn results from an inactivation of the E3 ubiquitin ligase substrate adaptor LRS1. Transcriptome analyses ofhit1revealed massive alterations of gene expression modulation as a consequence of perturbed LRS1 function, indicating its role as a crown regulator. In conjunction with random forest-based network modeling, these transcriptome analyses predicted that LRS1 controls photoprotection gene expression via an algal HY5 homolog as its prime transcription factor target. CrHY5 binds to T-box elements present in the promoters of these genes and its inactivation in thehit1mutant via CRISPR-Cas9 genome editing, confirmed the regulatory connection between LRS1 and CrHY5, predicted by the network analysis

Multiple transcription factors mediate acclimation of Chlamydomonas to light stress

Wulf D, Kruger FJ, Klages LJ, et al. Multiple transcription factors mediate acclimation of Chlamydomonas to light stress. bioRxiv. 2023.Light as a substrate for photosynthesis may be a boon or a bane. To thrive, photosynthetic organisms must constantly respond to changing light and CO2 conditions by balancing energy harvest and consumption in a highly dynamic way. Two major safeguard measures of photoacclimation, that is photoprotection and carbon concentrating mechanism, underlie tight transcriptional control, leading to expression changes under high light and limited CO2 with different dynamics for both systems. Here, by using a consensus gene regulatory network inferred by employing a compendium of 1,869 RNA-seq datasets, we identified and validated in vivo eight candidate transcription factors (TFs) that contribute to photoacclimation in Chlamydomonas reinhardtii. Target gene analyses indicate that the TFs act individually in associated pathways but also influence each other in expression, and function as network parts with partial redundancy with respect to photoprotection. The analyses unveil that stress responses in Chlamydomonas are mediated by a complex, interconnected network of TFs rather than a hierarchical system where multiple regulators can influence each other and target gene expression and thereby mitigate the effects of loss