Article
Biochemistry & Molecular Biology
Haihong Guo, Malte Prell, Hiltrud Koenigs, Nengwei Xu, Tanja Waldmann, Benita Hermans-Sachweh, Elisa Ferrando-May, Bernhard Luescher, Ferdinand Kappes
Summary: The DEK oncoprotein regulates cellular chromatin function through protein-protein interactions, with its unique pseudo-SAP/SAP-box domain speculated to play a role in transmitting DNA modulating activities. Random mutagenesis combined with the Bacterial Growth Inhibition Screen (BGIS) was used to generate DNA-binding null mutants, overcoming previous technical limitations. Re-expression of a DEK-DBN mutant failed to reduce the increase in nuclear size compared to wild type in newly established human DEK knockout cells, indicating the importance of DEK-DNA interactions in cellular chromatin organization.
Article
Immunology
Zhe Chen, Dawei Huo, Lei Li, Zhilong Liu, Zhigang Li, Shuangnian Xu, Yongxiu Huang, Weiru Wu, Chengfang Zhou, Yuanyuan Liu, Mei Kuang, Feng Wu, Hui Li, Pengxu Qian, Guanbin Song, Xudong Wu, Jieping Chen, Yu Hou
Summary: DEK plays a crucial role in preserving hematopoietic stem cell potential by regulating chromatin accessibility and quiescence-associated gene expression, which is partly dependent on mTOR signaling.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Plant Sciences
Wei Zong, Bo Zhao, Yanpeng Xi, Yogendra Bordiya, Hyungwon Mun, Nicholas A. Cerda, Dong-Hwan Kim, Sibum Sung
Summary: The DEK proteins, DEK3 and DEK4, play a role in controlling the floral transition in Arabidopsis by interacting with chromatin to promote the expression of flowering repressors. They also affect histone modifications at specific gene loci and interact with RNA polymerase II to facilitate gene expression.
Article
Biochemistry & Molecular Biology
Jinglong Zhou, Lihong Zhao, Yajie Wu, Xiaojian Zhang, Sheng Cheng, Feng Wei, Yalin Zhang, Heqin Zhu, Yi Zhou, Zili Feng, Hongjie Feng
Summary: The study revealed the crucial role of GhDEK2D in cotton against Verticillium dahliae (Vd), and silencing of this gene reduces resistance. Homozygous overexpression of GhDEK2D in transgenic Arabidopsis enhances resistance to Verticillium wilt (Vw), suggesting GhDEK2D as a potential molecular target for improving cotton resistance to Vw.
PLANT SIGNALING & BEHAVIOR
(2022)
Article
Plant Sciences
Syed Muhammad Muntazir Mehdi, Michal Wojciech Szczesniak, Agnieszka Ludwikow
Summary: Abscisic acid (ABA) affects plant physiology by regulating gene expression. The AtBro1 gene plays a crucial role in the plant's response to abiotic stress, such as drought and salt stress. ABA stimulates stress-resistance responses through the activation of AtBro1.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Yao-Shun Yang, Xi-Zheng Jia, Qian-Yun Lu, Sun-Li Cai, Xue-Ting Huang, Shu-Hua Yang, Chris Wood, Yue-Hong Wang, Jiao-Jiao Zhou, Yi-Ding Chen, Jin-Shu Yang, Wei-Jun Yang
Summary: This study identified and isolated chemoradiotherapy-resistant CSCs in quiescent state with high capacity of tumor-initiation and tumorsphere formation from three types of breast tumors in mice. Experiments revealed DEK as essential for CSC activation, and exogenous DEK was used to trigger quiescence exit of CSCs. The study provides insights into the mechanism of quiescent CSC activation and may offer new clinical opportunities for removal of quiescence-linked therapy resistance.
Article
Plant Sciences
Xiaoqing Meng, Siyuan Liu, Chengbin Zhang, Junna He, Daifu Ma, Xin Wang, Tingting Dong, Fen Guo, Jing Cai, Tiandan Long, Zongyun Li, Mingku Zhu
Summary: In this study, a stress-induced transcription factor named IbNAC3 from sweet potato was identified. IbNAC3 was found to enhance the tolerance of Arabidopsis to single and combined salt and drought stresses. It interacts with a group of NAC transcription factors and regulates the expression of downstream target genes, thus affecting stress tolerance. Additionally, IbNAC3 regulates the ubiquitin pathway and abscisic acid signaling to modulate the combined stress tolerance.
Article
Plant Sciences
Chao-Yuan Yu, Oshin Sharma, Phong H. T. Nguyen, Chynthia D. Hartono, Kazue Kanehara
Summary: SVBL, the closest homolog of SVB, modulates plant growth and trichome development with SVB in Arabidopsis thaliana, resulting in dwarfed plant growth in double mutants and enhanced defects in trichome development. This study highlights the pivotal role of SVB and SVBL in affecting a specific subset of known trichome developmental regulators in higher plants.
Article
Multidisciplinary Sciences
Agnieszka Pierzynska-Mach, Isotta Cainero, Michele Oneto, Elisa Ferrando-May, Luca Lanzano, Alberto Diaspro
Summary: Epigenetic dysregulation in cancer is being investigated through DEK protein, which modulates chromatin topology. Overexpression of DEK is associated with spatial correlation with histone marks corresponding to gene promoters, but not with enhancers. Additionally, the colocalization of DEK and histone marks is lower in non-invasive breast cancer cells compared to highly invasive cells.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Yulia Kargapolova, Rizwan Rehimi, Huelya Kayserili, Joanna Bruehl, Konstantinos Sofiadis, Anne Zirkel, Spiros Palikyras, Athanasia Mizi, Yun Li, Goekhan Yigit, Alexander Hoischen, Stefan Frank, Nicole Russ, Jonathan Trautwein, Bregje van Bon, Christian Gilissen, Magdalena Laugsch, Eduardo Gade Gusmao, Natasa Josipovic, Janine Altmueller, Peter Nuernberg, Gernot Laengst, Frank J. Kaiser, Erwan Watrin, Han Brunner, Alvaro Rada-Iglesias, Leo Kurian, Bernd Wollnik, Karim Bouazoune, Argyris Papantonis
Summary: Members of the CHD chromatin remodeler family are implicated in human pathologies, however CHD6 remained poorly studied. Here, the authors show that CHD6 binds to and regulates autophagy and stress response genes across cell types. They identify a clinical mutation that affects its ability to recruit cofactors, leading to impaired autophagy induction and DNA repair.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Arsheed H. Sheikh, Kashif Nawaz, Naheed Tabassum, Marilia Almeida-Trapp, Kiruthiga G. Mariappan, Hanna Alhoraibi, Naganand Rayapuram, Manuel Aranda, Martin Groth, Heribert Hirt
Summary: The mutants of Arabidopsis H1 histones, H1.1 and H1.2 double mutants and H1.1, H1.2, and H1.3 triple mutants, were found to be resistant to Pseudomonas syringae and Botrytis cinerea infections. Transcriptome analysis revealed that H1s play a crucial role in regulating the expression of defense genes during pathogen challenge. Overall, the study demonstrates the role of H1 as a molecular gatekeeper in modulating the chromatin landscape of defense genes during plant-pathogen interaction.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Agronomy
Eryong chen, Bo Shen
Summary: Plant growth and crop productivity are greatly influenced by abiotic stress. WD40 repeat-containing proteins are crucial for the development and environmental adaptation of eukaryotes. The study cloned a stress response gene, OsABT, from rice and found that it plays a positive role in response to salt stress and a negative role in response to drought stress in Arabidopsis. OsABT enhances tolerance to ABA and salt stress during plant seedling development.
Article
Multidisciplinary Sciences
Jekaterina Truskina, Jingyi Han, Elina Chrysanthou, Carlos S. Galvan-Ampudia, Stephanie Laine, Geraldine Brunoud, Julien Mace, Simon Bellows, Jonathan Legrand, Anne-Maarit Bagman, Margot E. Smit, Ondrej Smetana, Arnaud Stigliani, Silvana Porco, Malcolm J. Bennett, Ari Pekka Mahonen, Francois Parcy, Etienne Farcot, Francois Roudier, Siobhan M. Brady, Anthony Bishopp, Teva Vernoux
Summary: Genes encoding the class A auxin-response factor group of plant transcriptional activators reside in constitutively open chromatin, enabling their continual regulation by transcriptional repressors to modulate auxin signalling throughout development.
Article
Plant Sciences
Jovanka Vladejic, Fen Yang, Eva Dvorak Tomastikova, Jaroslav Dolezel, Jan J. Palecek, Ales Pecinka
Summary: Plants have a sophisticated molecular network to maintain the integrity of genetic information and repair damaged DNA. This study identified and analyzed four uncharacterized Arabidopsis BCP proteins, with BCP1 being the most interesting candidate due to its sensitivity to DNA damage. It was found that BCP1 is regulated by SOG1 and is involved in homology-based repair.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Yaoguang Yu, Wei Fu, Jianqu Xu, Yawen Lei, Xin Song, Zhenwei Liang, Tao Zhu, Yuhui Liang, Yuanhao Hao, Liangbing Yuan, Chenlong Li
Summary: The Arabidopsis thaliana bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and play critical roles in genomic targeting. These BRDs interact directly with multiple SWI/SNF subunits, including the BRAHMA (BRM) catalytic subunit, to control gene expression and developmental processes. The bromodomains of BRDs are essential for genomic targeting of SWI/SNF complexes.
Article
Chemistry, Analytical
Claudia Ctortecka, Karel Stejskal, Gabriela Krssakova, Sasha Mendjan, Karl Mechtler
Summary: Advancements in single-cell proteomics workflows have enhanced sensitivity and reproducibility for characterizing unknown biological phenomena. The introduction of multiplexed single-cell proteomics has led to a trend of combining single-cell measurements with abundant carriers to improve precursor selection and identification accuracy, although extreme carrier spikes may affect quantitative accuracy. Narrowly titrated carrier spikes have been found to provide comparable sensitivity with superior accuracy, while alternative multiplexing strategies can help evaluate data quality. Ultimately, optimized experimental designs for multiplexed proteomics of trace samples can lead to improved quantitative accuracy and elevated replicate overlap.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Claudia Ctortecka, Gabriela Krssakova, Karel Stejskal, Josef M. Penninger, Sasha Mendjan, Karl Mechtler, Johannes Stadlmann
Summary: The combination of single-cell transcriptomics and proteomics has significantly advanced our understanding of basic biology and disease. A novel data analysis pipeline, using DIA and TMT methods, allows for reproducible comparison of protein expression profiles across hundreds of samples.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Christin Naumann, Marcus Heisters, Wolfgang Brandt, Philipp Janitza, Carolin Alfs, Nancy Tang, Alicia Toto Nienguesso, Jorg Ziegler, Richard Imre, Karl Mechtler, Yasin Dagdas, Wolfgang Hoehenwarter, Gary Sawers, Marcel Quint, Steffen Abel
Summary: Access to inorganic phosphate profoundly affects cellular activities and plant performance. This study reveals that Arabidopsis LPR1 acts as a phosphate-dependent cue to adjust root meristem maintenance by sensing subtle concentration differentials of external Fe availability via Fe redox signaling and cell wall modification.
Article
Multidisciplinary Sciences
Christoph Neumayr, Vanja Haberle, Leonid Serebreni, Katharina Karner, Oliver Hendy, Ann Boija, Jonathan E. Henninger, Charles H. Li, Karel Stejskal, Gen Lin, Katharina Bergauer, Michaela Pagani, Martina Rath, Karl Mechtler, Cosmas D. Arnold, Alexander Stark
Summary: This paper investigates different types of enhancers and their reliance on cofactors. The authors find that some enhancers can function without commonly used cofactors, regulating distinct gene regulatory programs.
Article
Oncology
Lukas Leiendecker, Tobias Neumann, Pauline S. Jung, Shona M. Cronin, Thomas L. Steinacker, Alexander Schleiffer, Michael Schutzbier, Karl Mechtler, Thibault Kervarrec, Estelle Laurent, Kamel Bachiri, Etienne Coyaud, Rajmohan Murali, Klaus J. Busam, Babak Itzinger-Monshi, Reinhard Kirnbauer, Lorenzo Cerroni, Eduardo Calonje, Arno Rutten, Frank Stubenrauch, Klaus G. Griewank, Thomas Wiesner, Anna C. Obenauf
Summary: This study reveals the presence of human papillomavirus 42 (HPV42) in 96% of digital papillary adenocarcinoma (DPA), a cancer occurring on fingers and toes. It shows that HPV42, previously considered nononcogenic, behaves similarly to oncogenic, high-risk HPVs. Machine learning analysis indicates that HPV-driven transformation induces a germ cell-like transcriptional program conserved across all HPV-driven cancers, with implications for early detection, diagnosis, and therapy.
Article
Biochemical Research Methods
Sebastian Dorl, Stephan Winkler, Karl Mechtler, Viktoria Dorfer
Summary: Spectral library search enables more sensitive peptide identification in tandem mass spectrometry experiments, but suffers from limited availability of high-quality libraries and the difficulty of creating decoy spectra for result validation. MS Ana is a new spectral library search engine that addresses these issues by allowing the use of curated or predicted libraries and providing robust false discovery control through its own decoy library generation algorithm. In benchmark tests, MS Ana outperformed database search, achieving 36% more spectrum matches and 4% more proteins identified in single-shot human cell-line data. The quality of result validation was demonstrated through tests on synthetic peptide pools, and the importance of library selection was highlighted by comparing the performance of different publicly available human spectral libraries.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Friederike Leesch, Laura Lorenzo-Orts, Carina Pribitzer, Irina Grishkovskaya, Josef Roehsner, Anastasia Chugunova, Manuel Matzinger, Elisabeth Roitinger, Katarina Belacic, Susanne Kandolf, Tzi-Yang Lin, Karl Mechtler, Anton Meinhart, David Haselbach, Andrea Pauli
Summary: Using mass spectrometry and cryo-electron microscopy, the study provides molecular evidence that ribosomes transition from a dormant state to an active state during early embryogenesis. Dormant ribosomes are associated with four conserved factors that stabilize ribosomes and repress translation. Addition of recombinant zebrafish Dap1b protein can block translation and reconstitute the dormant ribosome state in vitro.
Article
Chemistry, Analytical
Manuel Matzinger, Elisabeth Mueller, Gerhard Duernberger, Peter Pichler, Karl Mechtler
Summary: We report a comprehensive workflow that includes improved strategies for all steps, from cell lysis to data analysis. The workflow is easy to implement even for novice users, thanks to the use of convenient-to-handle 1 μL sample volume and standardized 384-well plates. Using advanced micro-pillar columns, ultrashort gradient lengths down to 5 minutes were tested for high throughput. By benchmarking different acquisition methods and data analysis algorithms, the workflow achieved identification of 1790 proteins in a single cell using data-dependent acquisition (DDA), and more than 2200 proteins from single-cell level input using data-independent acquisition (DIA) in a 20-minute active gradient. The workflow also demonstrated its suitability for differentiating two cell lines, indicating its potential for cellular heterogeneity determination.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Leonid Serebreni, Lisa-Marie Pleyer, Vanja Haberle, Oliver Hendy, Anna Vlasova, Vincent Loubiere, Filip Nemcko, Katharina Bergauer, Elisabeth Roitinger, Karl Mechtler, Alexander Stark
Summary: Different classes of promoters have distinct mechanisms of transcription initiation, resulting in either focused or dispersed initiation patterns.
Review
Biochemical Research Methods
Manuel Matzinger, Rupert L. Mayer, Karl Mechtler
Summary: Mapping proteomic fingerprints to transcriptomic data is crucial for understanding gene expression and phenotype. Despite challenges in protein amplification and lack of established gold standard workflows, advances in microfluidics, sample separation, data acquisition, and analysis have improved the analysis of tiny sample amounts. Sensitivity, robustness, and throughput are still urgent needs, and label-free single-cell mass spectrometry is a promising strategy for unbiased quantification. This review focuses on recent advances in label-free single-cell mass spectrometry workflows and provides guidance for method selection and future prospects.
Article
Multidisciplinary Sciences
Andreas Lackner, Michael Mueller, Magdalena Gamperl, Delyana Stoeva, Olivia Langmann, Henrieta Papuchova, Elisabeth Roitinger, Gerhard Duernberger, Richard Imre, Karl Mechtler, Paulina A. A. Latos
Summary: The Erf-NCoR1/2 complex controls trophoblast differentiation by linking signalling with transcriptional repression.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Jaydeep Sidhaye, Philipp Trepte, Natalie Sepke, Maria Novatchkova, Michael Schutzbier, Gerhard Duernberger, Karl Mechtler, Juergen A. Knoblich
Summary: By analyzing the transcriptome and epigenome during human corticogenesis, important gene regulatory networks have been identified. Through the use of human brain organoids, specific transcriptome and proteome analyses were conducted, revealing gene expression modules during cortical development. One module involving mTOR-mediated regulation of translation was investigated, showing that partial inhibition of ribosomal genes translation prevents premature translation of differentiation markers, crucial for maintaining the accuracy of cortical development.
Article
Biochemical Research Methods
Micha J. J. Birklbauer, Manuel Matzinger, Fraenze Mueller, Karl Mechtler, Viktoria Dorfer
Summary: In the paper "Cross-linking Mass Spectrometry 2.0", the authors present an updated version of the MS Annika search engine, which accurately identifies cross-linked peptides and introduces a novel scoring function. The evaluation shows that MS Annika 2.0 outperforms other search engines in terms of true unique cross-link detection and false discovery rate estimation.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Plant Sciences
Chao Feng, Elisabeth Roitinger, Otto Hudecz, Maria Cuacos, Jana Lorenz, Veit Schubert, Baicui Wang, Rui Wang, Karl Mechtler, Stefan Heckmann
Summary: During meiotic prophase I, the meiotic chromosome axis is essential for synapsis and meiotic recombination progression. TurboID-based proximity labelling enables the identification of proximate proteins in meiotic cells of A. thaliana. This proteomic profiling helps uncover known and new meiotic proteins in rare cell types like meiotic cells.
Article
Multidisciplinary Sciences
Friederike Leesch, Laura Lorenzo-Orts, Carina Pribitzer, Irina Grishkovskaya, Josef Roehsner, Anastasia Chugunova, Manuel Matzinger, Elisabeth Roitinger, Katarina Belacic, Susanne Kandolf, Tzi-Yang Lin, Karl Mechtler, Anton Meinhart, David Haselbach, Andrea Pauli
Summary: Using mass spectrometry and cryo-electron microscopy analyses, we show that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis in zebrafish and Xenopus laevis. Dormant ribosomes are associated with conserved factors that form two modules, responsible for stabilizing ribosomes and repressing translation. A newly discovered translational inhibitor, Dap1b, is found to play a key role in maintaining the dormant state of ribosomes.
