Biology subjects

Krieger, C.

Publications and source records attributed to Krieger, C..

4 recordsLinked to original sources

bioRxiv2026

PTMOverlay: A Proteomic Tool to Visualize Post-Translational Modifications Across Evolution

Evolutionary conservation has been considered a hallmark of essential basic functions in cells. Therefore, the study of evolutionarily conserved post-translational modifications (PTMs) can provide insight into their role in protein function. In this context, mass spectrometry can identify and quantify thousands of PTM sites. However, a major bottleneck lies in analyzing the large amounts of data collected by the mass spectrometer. Here we address the need for a protein sequence alignment tool for multiple PTMs across several species. We developed a tool named PTMOverlay that takes peptide identification output files and overlays PTM sites onto multiple protein sequence alignments. Examining 31 bacteria isolates, we combined their protein sequences with select PTM types, including acetylation, phosphorylation, monomethylation, dimethylation, and trimethylation. The tool revealed a variety of conserved modification sites on the bacterial central carbon metabolism. Further structural analysis revealed possible interactions between methylated arginine and lysine residues with phosphothreonine/serine sites on the homodimer interface of enolase. Overall, this tool can parse large amounts of mass spectrometry data and allows for more informed and efficient selection of sites for future studies of protein function.

systems biology↗

bioRxiv2021

20-hydroxyecdysone (20E) signaling regulates amnioserosa morphogenesis during Drosophila dorsal closure: Ecdysone receptor modulates gene expression in a complex with the AP-1 component, Jun

Steroid hormones influence diverse biological processes throughout the animal life cycle, including metabolism, stress resistance, reproduction, and lifespan. In insects, the steroid hormone, 20-hydroxyecdysone (20E), is the central regulator of molting and metamorphosis, and has been shown to play roles in tissue morphogenesis. For example, amnioserosa contraction, which is a major driving force in Drosophila dorsal closure (DC), is defective in embryos mutant for 20E biosynthesis. Here, we show that 20E signaling modulates the transcription of several DC participants in the amnioserosa and other dorsal tissues during late embryonic development, including the zipper locus, which encodes for non-muscle myosin II heavy chain. Canonical 20E signaling typically involves the binding of Ecdysone receptor (EcR) and Ultraspiracle heterodimers to ecdysone-response elements (EcREs) within the promoters of ecdysone-responsive genes to drive their expression. During DC, we provide evidence that 20E signaling instead acts in parallel to the JNK cascade via a direct interaction between EcR and the AP-1 component, Jun, which together binds to genomic regions containing AP-1 binding sites but no EcREs to control gene expression. Our work demonstrates a novel mode of action for 20E signaling in Drosophila that likely functions beyond DC, and may provide further insights into mammalian steroid hormone receptor interactions with AP-1.

developmental biology↗

bioRxiv2019

The engulfment receptor Draper organizes the postsynaptic spectrin cytoskeleton into corrals containing synaptic proteins and promotes synaptic renewal

The spectrin cytoskeleton is required for development of the Drosophila neuromuscular junction (NMJ) but its role is unclear. Here we show that the muscle spectrin lattice functions to corral membrane-associated synaptic proteins and limit their lateral mobility. Drosophila adducin, Hts, is required for integrity of the spectrin cytoskeleton and disruption of Hts function results in failure of the corrals. The spectrin cytoskeleton is itself patterned at the muscle membrane by the engulfment receptor Draper (Drpr) through regulation of Hts. We find patches of membrane where the spectrin cytoskeleton is organized into bilaterally symmetric patterns, which coincide with a field of Drpr-dependent structures similar to phagocytic pseudopods. The bilaterally symmetric patterns are likely created by folds of the muscle membrane in the pseudopods. We present evidence that the folds trap nascent boutons of motor neurons, leading to boutons with a bilaterally symmetric organization of the postsynaptic membrane. Drpr thus acts as a sensor of synaptic damage that promotes synaptogenesis.

developmental biology↗

bioRxiv2019

Homeodomain-interacting protein kinase (Hipk) is required for nervous system and muscle structure and function

Homeodomain-interacting protein kinases (Hipk) have been previously associated with cell proliferation and cancer, however, their effects in the nervous system are less well understood. We have used Drosophila melanogaster to evaluate the effects of altered Hipk expression on the nervous system and muscle. Using genetic manipulation of Hipk expression we demonstrate that knockdown and over-expression of Hipk produces early adult lethality, partially due to the effects on the nervous system and muscle involvement. We find that optimal levels of Hipk are critical for the function of dopaminergic neurons and glial cells in the nervous system, as well as muscle. Furthermore, manipulation of Hipk affects the structure of the larval neuromuscular junction (NMJ) and increases motor neuron axonal branching. Hipk regulates the phosphorylation of the synapse-associated cytoskeletal protein Hts (adducin) and modulates the expression of two important protein kinases, Calcium-calmodulin protein kinase II (CaMKII) and Partitioning-defective 1 (PAR-1), all of which may alter neuromuscular function and influence lethality. Hipk also modifies the distribution of an important nuclear protein, TBPH, the fly orthologue of TAR DNA-binding protein 43 (TDP-43), which may have relevance for understanding motor neuron diseases.

neuroscience↗