Biology subjects

Baumeister, R.

Publications and source records attributed to Baumeister, R..

5 recordsLinked to original sources

bioRxiv2024

Targeting the paralog protein for degradation accounts for the opposite roles of NRBP1 and NRBP2 in regulating LINE1 retrotransposition

Gene duplication generates paralogs undergoing diverse fates during evolution and serves as a potent catalyst of biological complexity. Paralogs frequently share redundant functions and may also exhibit antagonistic activities by competing for common interaction partners. Here we show that the gene paralogs NRBP1 and NRBP2 oppositely regulate LINE1 retrotransposition, via influencing integrity of the LINE1 ribonucleoprotein complex. We demonstrate that the opposite roles of NRBP1 and NRBP2 are not results of a competitive mechanism, but rather due to targeting NRBP1 for proteasome-mediated decay by NRBP2, probably through heterodimer formation. Moreover, our phylogenetic analysis shows that the regulatory function of NRBP2 may be acquired later during evolution, suggesting that evolutionary pressure has favored this functional fine-tuning of NRBP1. In summary, our discovery not only identifies NRBP1/2 as novel LINE1 regulators and implicates their involvement in human pathogenesis, but also provides a novel insight into the regulatory details arising from gene duplication.

cell biology↗

bioRxiv2022

Pseudokinase HPO-11 inhibits nonsense-mediated decay to ensure genome stability in C. elegans

DNA double-strand breaks (DSBs) are highly toxic DNA lesions that can induce mutations and chromosome rearrangement therefore causing genome instability (GIN). In response to DSBs, cells activate the DNA damage response by hierarchical assembly of signaling and repair mechanisms. This involves recruitment of the repair factors at DSB sites, local chromatin remodeling, cell cycle arrest and, eventually, DNA repair or apoptosis. Studies investigating mechanisms ensuring genome stability have so far mostly focused on DNA-protein interactions and signal transduction in response to DNA damage. Emerging evidence in the last decade suggests that post-transcriptional control of gene expression by RNA-binding proteins also participates in maintaining genome integrity. However, how specific control of RNA fate mechanistically affects genome stability is still poorly understood. Here, we report that the pseudokinase HPO-11 ensures genome integrity in C. elegans. Loss of hpo-11 leads to accumulation of R-loops, increased DSBs and germline apoptosis, as well as an elevated mutation rate in the somatic cells. In addition, inhibition of nonsense mediated decay (NMD) reduces DSBs and germline apoptosis in the absence of hpo-11. We find that HPO-11 physically interacts with SMG-2, the core factor of NMD, and prevents degradation of specific transcripts by NMD, thus contributing to maintenance of genome stability. Furthermore, knock-down of hpo-11 human homologs NRBP1/2 also results in increased DNA DSBs, and NRBP1/2 physically interact with the human SMG-2 orthologue UPF1. In summary, our work identifies an evolutionarily conserved role of HPO-11 to protect genome stability via suppressing abnormal mRNA decay by NMD.

molecular biology↗

bioRxiv2020

G3BP1 tethers the TSC complex to lysosomes and suppresses mTORC1 in the absence of stress granules

G3BP1 (Ras GTPase-activating protein-binding protein 1) is widely recognized as a core component of stress granules (SG), non-membranous RNA-protein-assemblies required for cellular survival under stress. We report that in the absence of SG, G3BP1 acts as lysosomal anchor of the Tuberous Sclerosis Complex (TSC) protein complex. By tethering the TSC complex to lysosomes, G3BP1 suppresses signaling through the metabolic master regulator mTORC1 (mechanistic target of rapamycin complex 1). Like the known TSC complex subunits, G3BP1 suppresses phenotypes related to mTORC1 hyperactivity in the context of tumors and neuronal dysfunction. Thus, G3BP1 is not only a core component of SG but also a key element of lysosomal TSC-mTORC1 signaling. HighlightsThe bona fide stress granule component G3BP1 O_LIis a key element of the TSC-mTORC1 signaling axis. C_LIO_LItethers the TSC complex to lysosomes. C_LIO_LIprevents mTORC1 hyperactivation by metabolic stimuli. C_LIO_LIsuppresses mTORC1-driven cancer cell motility and epileptiform activity. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/044081v3_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@77cb4forg.highwire.dtl.DTLVardef@c4d1a0org.highwire.dtl.DTLVardef@19e83acorg.highwire.dtl.DTLVardef@1d6a378_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2019

LF4/MOK and a CDK-related kinase regulate the number and length of cilia in Tetrahymena

The length of cilia is controlled by a poorly understood mechanism that involves members of the conserved RCK kinase group, and among them, the LF4/MOK kinases. In Tetrahymena, a loss of an LF4/MOK ortholog, LF4A, lengthened the locomotory cilia, but also reduced their total number per cell. Without LF4A, cilia assembled faster and showed signs of increased intraflagellar transport (IFT). Consistently, overproduced LF4A shortened cilia and downregulated the IFT. GFP-tagged LF4A, expressed in the native locus and imaged by total internal reflection microscopy, was enriched at the basal bodies and distributed along the shafts of cilia. Within cilia, most LF4A-GFP particles were immobile and a few either diffused or moved by IFT. A forward genetic screen identified a CDK-related kinase, CDKR1, whose loss-of-function suppressed the shortening of cilia caused by overexpression of LF4A, by reducing its kinase activity. A loss of CDKR1 alone lengthened both the locomotory and oral cilia. CDKR1 resembles other known ciliary CDK-related kinases: LF2 of Chlamydomonas, mammalian CCRK and DYF-18 of C. elegans, in lacking the cyclin-binding motif and acting upstream of RCKs. We propose that the total LF4/MOK activity per cilium is dependent on both its activation by an upstream CDK-related kinase and cilium length. Previous studies showed that the rate of assembly is high in growing cilia and decreases as cilia elongate to achieve the steady-state length. We propose that in a longer cilium, the IFT components, which travel from the base to the tip, are subjected to a higher dose of inhibition by the uniformly distributed LF4/MOK. Thus, in a feedback loop, LF4/MOK may translate cilium length into proportional inhibition of IFT, to balance the rates of assembly and disassembly at steady-state.\n\nAuthor summaryCilia are conserved organelles that generate motility and mediate vital sensory functions, including olfaction and vision. Cilia that are either too short or too long fail to generate proper forces or responses to extracellular signals. Several cilia-based diseases (ciliopathies) are associated with defects in cilia length. Here we use the multiciliated model protist Tetrahymena, to study a conserved protein kinase whose activity shortens cilia, LF4/MOK. We find that cells lacking an LF4/MOK kinase of Tetrahymena, LF4A, have excessively long, but also fewer cilia. We show that LF4A decreases the intraflagellar transport, a motility that shuttles ciliary precursors from the cilium base to the tip. Live imaging revealed that LF4A is distributed along cilium length and remains mostly immobile, likely due to its anchoring to ciliary microtubules. We proposed that in longer cilia, the intraflagellar transport machinery is exposed to a higher dose of inhibition by LF4A, which could decrease the rate of cilium assembly, to balance the rate of cilium disassembly in mature cilia that maintain stable length.

cell biology↗

bioRxiv2017

Combined flow cytometry and high throughput image analysis for the study of essential genes in Caenorhabditis elegans

BackgroundThe advancement in automated image based microscopy platforms coupled with high throughput liquid workflows has facilitated the design of large scale screens utilizing multicellular model organisms such as Caenorhabditis elegans to identify genetic interactions, therapeutic drugs or disease modifiers. However, the analysis of essential genes has lagged behind because lethal or sterile mutations pose a bottleneck for high throughput approaches.\n\nResultsIn C. elegans, non-conditional lethal mutations can be maintained in heterozygosis using chromosome balancers, commonly labelled with GFP in the pharynx. Moreover gene-expression is typically monitored by the use of fluorescent reporters marked with the same fluorophore. Therefore, the separation of the different populations of animals at early larval stages represents a challenge. Here, we develop a sorting strategy capable of selecting homozygous mutants carrying a GFP stress reporter from GFP-balanced animals at early larval stages. Because sorting is not completely error-free, we develop an automated high-throughput image-analysis protocol that identifies and discards animals carrying the chromosome balancer. We demonstrate the experimental usefulness of combining sorting of homozygous lethal mutants and automated image-analysis in a functional genomic RNAi screen for genes that genetically interact with mitochondrial prohibitin (PHB). Lack of PHB results in embryonic lethality, while, homozygous PHB deletion mutants develop into sterile adults due to maternal contribution and strongly induce the mitochondrial unfolded protein response (UPRmt). In a chromosome-wide RNAi screen for C. elegans genes having human orthologues, we uncover both, known and new PHB genetic interactors affecting the UPRmt and growth.\n\nConclusionsA systematic way to analyse genetic interactions of essential genes in multicellular organisms is lacking. The method presented here allows the study of balanced lethal mutations in a high-throughput manner and can be easily adapted depending on the users requirements. Therefore, it will serve as a useful resource for the C. elegans community for probing new biological aspects of essential nematode genes as well as the generation of more comprehensive genetic networks.

genetics↗