A5080279154- Mitochondrial Function and Pathology
- RNA and protein synthesis mechanisms
- Transgenic Plants and Applications
- Heat shock proteins research
- CRISPR and Genetic Engineering
- Plant Molecular Biology Research
- Plant Virus Research Studies
- Plant Reproductive Biology
- Genomics and Chromatin Dynamics
- ATP Synthase and ATPases Research
- Photosynthetic Processes and Mechanisms
- Genomics and Phylogenetic Studies
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Plant tissue culture and regeneration
- RNA modifications and cancer
- Plant Micronutrient Interactions and Effects
- RNA Research and Splicing
- Microbial Community Ecology and Physiology
- Linguistic Education and Pedagogy
- Toxin Mechanisms and Immunotoxins
- Rice Cultivation and Yield Improvement
- Gene expression and cancer classification
- Research in Cotton Cultivation
- Chromosomal and Genetic Variations
University of Washington
2020-2024
Heinrich Heine University Düsseldorf
2024
Cluster of Excellence on Plant Sciences
2024
University of Tübingen
2015-2020
The exchange of metabolites between the mitochondrial matrix and cytosol depends on β-barrel channels in outer membrane α-helical carrier proteins inner membrane. essential translocase (TIM) chaperones escort these through intermembrane space, but structural mechanistic details remain elusive. We have used an integrated biology approach to reveal functional principle TIM chaperones. Multiple clamp-like binding sites hold a translocation-competent elongated form, thus mimicking...
Mitochondrial β-barrel proteins are synthesized on cytosolic ribosomes and must be specifically targeted to the organelle before their integration into mitochondrial outer membrane. The signal that assures such precise targeting its recognition by remained obscure. In present study we show a specialized β-hairpin motif is this long searched for signal. We demonstrate synthetic peptide competes with import of harbouring fused passenger domains mitochondria. Furthermore, from targets...
Mitochondrial β-barrel proteins are encoded in the nucleus, translated by cytosolic ribosomes, and then imported into organelle. Recently, a detailed understanding of intramitochondrial import pathway was obtained. In contrast, it is still completely unclear how newly synthesized reach mitochondrial surface an import-competent conformation. this study, we show that Hsp70 chaperones their Hsp40 cochaperones Ydj1 Sis1 interact with proteins. These interactions highly relevant for proper...
Genetic engineering of
Most mitochondrial proteins are synthesized in the cytosol prior to their import into organelle. It is commonly accepted that cytosolic factors required for delivering precursor surface and keeping newly an import-competent conformation. However, identity of such defined contribution process mostly unknown. Using a presequence-containing model protein site-directed photo-crosslinking approach yeast cells we identified chaperones Hsp70 (Ssa1) Hsp90 (Hsp82) as well cochaperones, Sti1 Ydj1,...
Abstract Enhancers are cis-regulatory elements that shape gene expression in response to numerous developmental and environmental cues. In animals, several models have been proposed explain how enhancers integrate the activity of multiple transcription factors. However, it remains largely unclear plant factor activity. Here, we use Plant STARR-seq characterize 3 light-responsive enhancers—AB80, Cab-1, rbcS-E9—derived from genes associated with photosynthesis. Saturation mutagenesis revealed...
Mitochondria originated from proteobacterial endosymbionts, and their transition to organelles was tightly linked establishment of the protein import pathways. The initial most proteins is mediated by translocase outer membrane (TOM). Although TOM common all forms mitochondria, an unexpected diversity subunits between eukaryotic lineages has been predicted. However, experimental knowledge limited a few organisms, so far, it remains unsettled whether triplet-pore or twin-pore structure...
Chaperones are essential for assisting protein folding and transferring poorly soluble proteins to their functional locations within cells. Hydrophobic interactions drive promiscuous chaperone-client binding, but our understanding of how additional enable client specificity is sparse. Here, we decipher what determines binding two chaperones (TIM8·13 TIM9·10) different integral membrane proteins, the all-transmembrane mitochondrial carrier Ggc1 Tim23, which has an disordered hydrophilic...
Abstract The 3’ end of a gene, often called terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, massively parallel reporter assay, to measure the activity over 50,000 terminators from plants Arabidopsis thaliana Zea mays . We characterize thousands plant terminators, including many that outperform bacterial commonly used in plants. Terminator is species-specific, differing tobacco leaf maize protoplast assays. While...
A special group of mitochondrial outer membrane (MOM) proteins spans the several times via multiple helical segments. Such multispan are synthesized on cytosolic ribosomes before their targeting to mitochondria and insertion into MOM. Previous work recognized import receptor Tom70 (MIM) complex, both residents MOM, as required for optimal biogenesis these proteins. However, involvement is not sufficient explain either entire pathway or its regulation. To identify additional factors that...
Abstract The 3’ end of a gene, often called terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, massively parallel reporter assay, to measure the activity over 50,000 terminators from plants Arabidopsis thaliana Zea mays . We characterize thousands plant terminators, including many that outperform bacterial commonly used in plants. Terminator is species-specific, differing tobacco leaf maize protoplast assays. While...
Abstract Deep learning has become a popular tool to study cis-regulatory function. Yet efforts design software for deep-learning analyses in regulatory genomics that are findable, accessible, interoperable and reusable (FAIR) have fallen short of fully meeting these criteria. Here we present elucidating the utility genomic elements with neural nets (EUGENe), FAIR toolkit analysis sequences deep learning. EUGENe consists set modules subpackages executing key functionality workflow: (1)...
Abstract Targeted engineering of plant gene expression holds great promise for ensuring food security and producing biopharmaceuticals in plants. However, this requires thorough knowledge cis -regulatory elements order to precisely control either endogenous or introduced genes. To generate knowledge, we used a massively parallel reporter assay measure the activity nearly complete sets promoters from Arabidopsis, maize sorghum. We demonstrate that core promoter – notably TATA-box as well GC...
Abstract Faced with accelerating climate change and rapid population growth, we need crops higher yields greater resilience to ensure food security. Crop genome engineering will likely play a major role in meeting future needs. However, do not understand plant gene regulation well enough target achieve predictable outcomes. Therefore, study regulatory DNA its interactions–the grammar – plants using high-throughput assays computational approaches.
Abstract Insulators are cis -regulatory elements that separate transcriptional units, whereas silencers repress transcription regardless of their position. In plants, these remain largely uncharacterized. Here, we use the massively parallel reporter assay Plant STARR-seq with short fragments eight large insulators to identify more than 100 block enhancer activity. The can be combined generate powerful abolish capacity strong viral 35S activate minimal promoter. Unexpectedly, when tested...
Abstract Deep learning (DL) has become a popular tool to study cis-regulatory element function. Yet efforts design software for DL analyses in genomics that are Findable, Accessible, Interoperable and Reusable (FAIR) have fallen short of fully meeting these criteria. Here we present EUGENe ( E lucidating the U tility G enomic lements with Ne ural Nets), FAIR toolkit analysis labeled sets nucleotide sequences DL. consists set modules empower users execute key functionality workflow: 1)...
ABSTRACT Genetic engineering of cis -regulatory elements in crop plants is a promising strategy to ensure food security. However, such currently hindered by our limited knowledge plant elements. Here, we adapted STARR-seq — technology for the high-throughput identification enhancers its use transiently transformed tobacco leaves. We demonstrate that optimal placement reporter construct enhancer sequences from virus, pea and wheat was just upstream minimal promoter, none these four known...
ABSTRACT Enhancers are cis -regulatory elements that shape gene expression in response to numerous developmental and environmental cues. In animals, several models have been proposed explain how enhancers integrate the activity of multiple transcription factors. However, it remains largely unknown plant factor activity. Here, we use Plant STARR-seq characterize three light-responsive enhancers— AB80 , Cab-1 rbcS-E9 —derived from genes active photosynthesis. Saturation mutagenesis reveals...
Chaperones are essential for assisting protein folding, and transferring poorly soluble proteins to their functional locations within cells. Hydrophobic interactions drive promiscuous chaperone–client binding, but our understanding how additional enable client specificity is sparse. Here we decipher what determines binding of two chaperones (TIM8·13, TIM9·10) different integral membrane proteins, the alltransmembrane mitochondrial carrier Ggc1, Tim23 which has an disordered hydrophilic...