Biology subjects

Shen, Y.

Publications and source records attributed to Shen, Y..

At least 271 records · Page 15Linked to original sources

bioRxiv2022

An evolutionally conserved archaeal KEOPS complex functions in DNA repair

KEOPS is a multi-subunit protein complex conserved in eukaryotes and archaea. It is composed of Pcc1, Kae1, Bud32, Cgi121, and Gon7 in eukaryotes and is primarily involved in N6-threonylcarbamoyl adenosine (t6A) modification of tRNAs. Recently, KEOPS is reported to participate in homologous recombination repair in yeast. To characterize the KEOPS in archaea (aKEOPS), we conducted genetic and biochemical analyses of its encoding genes in the hyperthermophilic archaeon Saccharolobus islandicus. We show that aKEOPS also possesses five subunits, Pcc1, Kae1, Bud32, Cgi121, and Pcc1-like (or Gon7-like), just as eukaryotic KEOPS. Pcc1-like has physical interactions with Kae1 and Pcc1 and can mediate the monomerization of the dimeric subcomplex (Kae1-Pcc1-Pcc1-Kae1), suggesting that Pcc1-like is a functional homolog of the eukaryotic Gon7 subunit. Strikingly, none of the genes encoding aKEOPS subunits, including Pcc1 and Pcc1-like, can be deleted in the wild type and in a t6A modification complementary strain named TsaKI, implying that aKEOPS complex is essential for an additional cellular process in this archaeon. Knock-down of the Cgi121 subunit leads to severe growth retardance in the wild type which is partially rescued in TsaKI. These results suggest that aKEOPS plays an essential role independent of cellular t6A modification level. In addition, archaeal Cgi121 possesses dsDNA-binding activity which relies on its tRNA 3 CCA tail binding module. Our study clarifies the subunit organization of archaeal KEOPS and suggests of an origin of eukaryotic Gon7. The study also reveals a possible link between the function in t6A modification and the additional function presumably homologous recombination.

microbiology↗

bioRxiv2022

Solid/liquid coexistence during aging of FUS condensates

A wide range of macromolecules undergo phase separation, forming biomolecular condensates in living cells. These membraneless organelles are typically highly dynamic, formed in a reversible manner, and carry out important functions in biological systems. Crucially, however, a further liquid-to-solid transition of the condensates can lead to irreversible pathological aggregation and cellular dysfunction associated with the onset and development of neurodegenerative diseases. Despite the importance of this liquid-to-solid transition of proteins, the mechanism by which it is initiated in normally functional condensates is unknown. Here we show, by measuring the changes in structure, dynamics and mechanics in time and space, that FUS condensates do not uniformly convert to a solid gel, but rather that liquid and gel phases co-exist simultaneously within the same condensate, resulting in highly inhomogeneous structures. We introduce two new optical techniques, dynamic spatial mapping and reflective confocal dynamic speckle microscopy, and use these to further show that the liquid-to-solid transition is initiated at the interface between the dense phase within condensates and the dilute phase. These results reveal the importance of the spatiotemporal dimension of the liquid-to-solid transition and highlight the interface of biomolecular condensates as a key element in driving pathological protein aggregation.

biophysics↗

bioRxiv2022

Proteome capacity constraints favor respiratory ATP generation

Cells face competing metabolic demands. These include efficient use of both limited substrates and limited proteome capacity, as well as flexibility to deal with different environments. Flexibility requires spare enzyme capacity, which is proteome inefficient. ATP generation can occur via fermentation or respiration. Fermentation is much less substrate-efficient, but often assumed to be more proteome efficient 1-3, thereby favoring fast-growing cells engaging in aerobic glycolysis 4-8. Here, however, we show that mitochondrial respiration is actually more proteome-efficient than aerobic glycolysis. Instead, aerobic glycolysis arises from cells maintaining the flexibility to grow also anaerobically. These conclusions emerged from an unbiased assessment of metabolic regulatory mechanisms, integrating quantitative metabolomics, proteomics, and fluxomics, of two budding yeasts, Saccharomyces cerevisiae and Issatchenkia orientalis, the former more fermentative and the latter respiratory. Their energy pathway usage is largely explained by differences in proteome allocation. Each organisms proteome allocation is remarkably stable across environmental conditions, with metabolic fluxes predominantly regulated at the level of metabolite concentrations. This leaves extensive spare biosynthetic capacity during slow growth and spare capacity of their preferred bioenergetic machinery when it is not essential. The greater proteome-efficiency of respiration is also observed in mammals, with aerobic glycolysis occurring in yeast or mammalian cells that maintain a fermentation-capable proteome conducive to both aerobic and anaerobic growth.

systems biology↗

bioRxiv2022

Next-generation large-scale binary protein interaction network for Drosophila

Generating reference maps of the interactome networks underlying most cellular functions can greatly illuminate genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. Here, we applied state-of-the-art experimental and bioinformatics methods to identify high-confidence binary protein-protein interactions (PPIs) for Drosophila melanogaster. We performed four all-by-all yeast two-hybrid (Y2H) screens of >10,000 Drosophila proteins, resulting in the FlyBi dataset of 8,723 PPIs among 2,939 proteins. As part of this effort, we tested subsets of our data and data from previous PPI datasets using an orthogonal assay, which allowed us to normalize data quality across datasets. Next, we integrated our FlyBi data with previous PPI data, resulting in an expanded, high-confidence binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6,511 proteins. These data are accessible through the Molecular Interaction Search Tool (MIST) and other databases. To assess the utility of the PPI resource, we used novel interactions from the FlyBi dataset to generate an autophagy interaction network that we validated in vivo using two different autophagy-related assays. We found that deformed wings (dwg) encodes a protein that is both a regulator and a target of autophagy. Altogether, the resources generated in this project provide a strong foundation for building high-confidence new hypotheses regarding protein networks and function.

cell biology↗

bioRxiv2022

The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles

Functional genomics experiments are invaluable for understanding mechanisms of gene regulation. However, comprehensively performing all such experiments, even across a fixed set of sample and assay types, is often infeasible in practice. A promising alternative to performing experiments exhaustively is to, instead, perform a core set of experiments and subsequently use machine learning methods to impute the remaining experiments. However, questions remain as to the quality of the imputations, the best approaches for performing imputations, and even what performance measures meaningfully evaluate performance of such models. In this work, we address these questions by comprehensively analyzing imputations from 23 imputation models submitted to the ENCODE Imputation Challenge. We find that measuring the quality of imputations is significantly more challenging than reported in the literature, and is confounded by three factors: major distributional shifts that arise because of differences in data collection and processing over time, the amount of available data per cell type, and redundancy among performance measures. Our systematic analyses suggest several steps that are necessary, but also simple, for fairly evaluating the performance of such models, as well as promising directions for more robust research in this area.

bioinformatics↗

bioRxiv2022

Why is Babesia not killed by artemisinin like Plasmodium?

Babesia spp. are intraerythrocytic apicomplexan organisms digesting hemoglobin similar to intraerythrocytic Plasmodium spp. However, unlike Plasmodium spp., Babesia spp. are not sensitive to artemisinin, The difference between Babesia genomes and Plasmodium genomes revealed that smaller Babesia genomes lack numerous genes, especially haem synthesis-related genes. Single-cell sequencing analysis showed that different groups of B. microti with expressed pentose phosphate pathway (PPP)-related, DNA replication-related, antioxidation-related, glycolysis-related, and glutathione-related genes were not as sensitive to artemether as P. yoelii 17XNL. Especially, PPP-related, DNA replication-related, and glutathione-related genes were inactively expressed compared with P. yoelii 17XNL. Adding iron supply in vivo can promote the reproduction of B. microti. These results suggest that Babesia spp. lack a similar mechanism to that in malaria parasites, by which haem or iron in hemoglobin is utilized, but it likely leads to their insensitivity to artemisinin in turn. Author summaryBabesia and Plasmodium are similar in many ways, from morphology to life history. In particular, both ingest and break down hemoglobin. However, compared with Plasmodium, Babesia cannot form hemozoin with less pathogenicity and insensitivity to artemisinin. Recent studies suggest that artemisinin can kill malaria parasites through free-radical and iron-capture effects, indicating that iron and haem play a key role in the sensitivity of malaria parasites to artemisinin. The Babesia genome is smaller and does not contain haem synthesis-related genes, indicating low requirements and utilization of haem and iron (HI). Moreover, we found that the expression of PPP-related and DNA replication-related genes is not active, distinctly different from malaria parasites. However, adding iron supply in vivo can increase the infection rate of B. microti. Therefore, we hypothesized that Babesia lacks mechanisms for the efficient utilization of HI, resulting in low requirements for HI, and therefore insensitivity to artemisinin.

evolutionary biology↗

bioRxiv2022

Cross-Modality and Self-Supervised Protein Embedding for Compound-Protein Affinity and Contact Prediction

MotivationComputational methods for compound-protein affinity and contact (CPAC) prediction aim at facilitating rational drug discovery by simultaneous prediction of the strength and the pattern of compound-protein interactions. Although the desired outputs are highly structure-dependent, the lack of protein structures often makes structure-free methods rely on protein sequence inputs alone. The scarcity of compound-protein pairs with affinity and contact labels further limits the accuracy and the generalizability of CPAC models. ResultsTo overcome the aforementioned challenges of structure naivety and labelled-data scarcity, we introduce cross-modality and self-supervised learning, respectively, for structure-aware and task-relevant protein embedding. Specifically, protein data are available in both modalities of 1D amino-acid sequences and predicted 2D contact maps, that are separately embedded with recurrent and graph neural networks, respectively, as well as jointly embedded with two cross-modality schemes. Furthermore, both protein modalities are pretrained under various self-supervised learning strategies, by leveraging massive amount of unlabelled protein data. Our results indicate that individual protein modalities differ in their strengths of predicting affinities or contacts. Proper cross-modality protein embedding combined with self-supervised learning improves model generalizability when predicting both affinities and contacts for unseen proteins. AvailabilityData and source codes are available at https://github.com/Shen-Lab/CPAC. Contactyshen@tamu.edu Supplementary informationSupplementary data are included.

bioinformatics↗

bioRxiv2022

Multipartite super-enhancers function in an orientation-dependent manner

Transcriptional enhancers regulate gene expression in a developmental-stage and cell-specific manner. They were originally defined as individual regulatory elements that activate expression regardless of distance and orientation to their cognate genes. Genome-wide studies have shown that the mammalian enhancer landscape is much more complex, with different classes of individual enhancers and clusters of enhancer-like elements combining in additive, synergistic and redundant manners, possibly acting as single, integrated regulatory elements. These so-called super-enhancers are largely defined as clusters of enhancer-like elements which recruit particularly high levels of Mediator and often drive high levels of expression of key lineage-specific genes. Here, we analysed 78 erythroid-specific super-enhancers and showed that, as units, they preferentially interact in a directional manner, to drive expression of their cognate genes. Using the well characterised -globin super-enhancer, we show that inverting this entire structure severely downregulates -globin expression and activates flanking genes 5 of the super-enhancer. Our detailed genetic dissection of the -globin locus clearly attributes the clusters functional directionality to its sequence orientation, demonstrating that, unlike regular enhancers, super-enhancers act in an orientation-dependent manner. Together, these findings identify a novel emergent property of super-enhancers and revise current models by which enhancers are thought to contact and activate their cognate genes.

molecular biology↗

bioRxiv2022

Structural basis for the enhanced infectivity and immune evasion of Omicron subvariants

The Omicron variants of SARS-CoV-2 have recently become the globally dominant variants of concern in the COVID-19 pandemic. At least five major Omicron sub-lineages have been characterized: BA.1, BA.2, BA.3, BA.4 and BA.5. They all possess over 30 mutations on the Spike (S) protein. Here we report the cryo-EM structures of the trimeric S proteins from the five subvariants, of which BA.4 and BA.5 share the same mutations of S protein, each in complex with the surface receptor ACE2. All three receptor binding domains of S protein from BA.2 and BA.4/BA.5 are "up", while the BA.1 S protein has two "up" and one "down". The BA.3 S protein displays increased heterogeneity, with the majority in the all "up" RBD state. The differentially preferred conformations of the S protein are consistent with their varied transmissibilities. Analysis of the well defined S309 and S2K146 epitopes reveals the underlie immune evasion mechanism of Omicron subvariants.

biochemistry↗

bioRxiv2022

Human iPSC-derived neuron of 16p11.2 deletion reveals haplotype-specific expression of MAPK3 and its contribution to variable NDD phenotypes

Recurrent proximal 16p11.2 deletion (16p11.2del) is risk factor of diverse neurodevelopmental disorders (NDDs) with variable penetrance. Although previous human induced pluripotent stem cell (hiPSC) models of 16p11.2del confirmed disrupted neuron development, it is not known which gene(s) at this interval are mainly responsible for the abnormal cellular phenotypes and how the NDD penetrance is regulated. After haplotype phasing of 16p11.2 region, we generated hiPSCs for two 16p11.2del families with distinct residual haplotypes and variable NDD phenotypes. We also differentiated the hiPSCs to cortical neural cells and demonstrated MAPK3 as a driver signal of 16p11.2 region contributing to the dysfunctions in multiple pathways related to neuron development, which leads to altered morphological or electrophysiological properties in neuron cells. Furthermore, residual haplotype-specific MAPK3 expression was identified in 16p11.2del neuron cells, associating MAPK3 down-expression with the minor allele of the residual haplotype. Ten SNPs of the residual haplotype are mapped as enhancer SNPs (enSNPs) of MAPK3, eight enSNPs were functionally validated by luciferase assays, implying enSNPs contribute to residual haplotype-specific MAPK3 expression via cis-regulation. Finally, the analyses of three different patient cohorts showed that the residual haplotype of 16p11.2del is associated with variable NDD phenotypes.

genetics↗

bioRxiv2022

Bifidobacterium infantis-mediated herpes simplex virus-TK/ganciclovir treatment inhibits cancer metastasis

Previous studies have found that Bifidobacterium infantis-mediated herpes simplex virus-TK/ganciclovir (BF-TK/GCV) reduces the expression of VEGF and CD146 which implies tumor metastasis inhibition. However, the mechanism of BF-TK/GCV inhibits tumor metastasis is still not fully studied. Here, we comprehensively identified and quantified protein expression profiling for the first time in gastric cancer (GC) cells MKN-45 upon BF-TK/GCV treatment using quantitative proteomics. A total of 159 and 72 differential expression proteins (DEPs) were significantly changed in BF-TK/GCV / BF-TK and BF-TK/GCV / BF/GCV groups. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed some enriched metastasis-related pathways such as gap junction and cell adhesion molecules pathways. Moreover, transwell assay proved that BF-TK/GCV inhibited the invasion and migration of tumor cells. Furthermore, immunohistochemistry (IHC) demonstrated that BF-TK/GCV reduced the expression of HIF-1A, MTOR, NF-{kappa}B1-p105, VCAM1, CEBPB and CXCL12, which were associated with tumor metastasis. In summary, besides apoptosis, BF-TK/GCV also inhibited tumor metastasis, which deepened and expanded the understanding of BF-TK/GCV anti-tumor mechanisms.

cancer biology↗

bioRxiv2022

A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea

Cell cycle regulation is of paramount importance for all forms of life. Here we report that a conserved and essential cell cycle-specific transcription factor (designated as aCcr1) and its viral homologs control cell division in Sulfolobales. We show that the transcription level of accr1 reaches peak during active cell division (D-phase) subsequent to the expression of CdvA, an archaea-specific cell division protein. Cells over-expressing the 58-aa-long RHH (ribbon-helix-helix) family cellular transcription factor as well as the homologs encoded by large spindle-shaped viruses Acidianus two-tailed virus (ATV) and Sulfolobus monocaudavirus 3 (SMV3) display significant growth retardation and cell division failure, manifested as enlarged cells with multiple chromosomes. aCcr1 over-expression results in downregulation of 17 genes (>4-folds) including cdvA. A conserved motif, aCcr1-box, located between the TATA-binding box and the translation initiation site in the promoters of 13 out of the 17 highly repressed genes, is critical for aCcr1 binding. The aCcr1-box is present in the promoters of cdvA genes across Sulfolobales, suggesting that aCcr1-mediated cdvA repression is an evolutionarily conserved mechanism by which archaeal cells dictate cytokinesis progression, whereas their viruses take advantage of this mechanism to manipulate the host cell cycle.

microbiology↗

bioRxiv2022

Chiral Derivatization-enabled Discrimination and Visualization of Proteinogenic Amino Acids by Ion Mobility Mass Spectrometry

The importance of chiral amino acids (AAs) in living organisms has been widely recognized since the discovery of endogenous D-AAs as potential biomarkers in several metabolic disorders. Chiral analysis by ion mobility spectrometry-mass spectrometry (IMS-MS) has the advantages of high speed and sensitivity but is still in its infancy. Here, a N-(2,4-dinitro-5-fluorophenyl)-L-alaninamide (FDAA) derivatization is combined with trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) for chiral AA analysis. For the first time, we demonstrate the simultaneous separation of 19 pairs of chiral proteinogenic AAs in a single fixed condition TIMS-MS run. The utility of this approach presents for mouse brain extracts by direct-infusion TIMS-MS. The robust separation ability in complex biological sample was proven in MALDI TIMS mass spectrometry imaging (MSI) as well by directly depositing 19 pairs of AAs on a tissue slide following on-tissue derivatization. In addition, endogenous chiral amino acids were also detected and distinguished. The developed methods show compelling application prospects in biomarker discovery and biological research. Entry for the Table of Contents O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/498692v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@19af718org.highwire.dtl.DTLVardef@d457d7org.highwire.dtl.DTLVardef@d2f932org.highwire.dtl.DTLVardef@e64831_HPS_FORMAT_FIGEXP M_FIG C_FIG The combination of chiral derivatization and trapped ion mobility-mass spectrometry provides the first insights into the separation of 19 pairs of chiral proteinogenic D/L-amino acids in a single run and further visualization of chiral amino acids under complex biological matrix.

biochemistry↗

bioRxiv2022

Upf3a is dispensable for nonsense-mediated mRNA decay in mouse pluripotent and somatic cells

Nonsense-mediated mRNA decay (NMD) is a highly conserved regulatory mechanism of post-transcriptional gene expression in eukaryotic cells. NMD plays essential roles in mRNA quality and quantity control, and thus safeguards multiple biological processes including embryonic stem cell differentiation and organogenesis. UPF3A and UPF3B in vertebrate species, originated from a single UPF3 gene in yeast, are key factors in the NMD machinery. While UPF3B is a well-recognized weak NMD-promoting factor, whether UPF3A functions in promoting or suppressing NMD is under debate. In this study, we generated a Upf3a conditional knockout mouse strain, and established multiple lines of embryonic stem cells and somatic cells without UPF3A. Through extensive analysis on the expressions of 33 NMD targets, we found UPF3A neither represses NMD in mouse embryonic stem cells, somatic cells, nor in major organs including the liver, spleen, and thymus. Our study reinforces that UPF3A is dispensable for NMD when UPF3B is present. Furthermore, UPF3A may weakly and selectively promote NMD in certain murine organs. Summary blurbWe generated a new Upf3a inducible knockout mouse model and showed that UPF3A does not repress expressions of NMD target genes in embryonic stem cells, somatic fibroblasts, as well as multiple tissues from adult mice.

cell biology↗

bioRxiv2022

Renal ischemia-reperfusion injury attenuated by exosomes extracted from splenic ischemic preconditioning

ObjectiveTo investigate the protective effects of the exosomes extracted from splenic ischemic preconditioning (sIPC) on renal ischemia-reperfusion (IR) injury. Materials and methodsSplenic ischemic preconditioning(sIPC)was conducted on mice in vivo 24 hours before the start of renal ischemia-reperfusion (IR) injury experiment, and serum exosomes derived from sIPC mice were infused into the mice model of renal ischemia-reperfusion injury. The kidney tissue and serum were collected 24 hours later. The morphological changes and inflammation in ischemia-reperfusion kidneys were determined by hematoxylin-eosin (HE) staining.Then the apoptosis of kidney tissue sections were detected by TUNEL staining, Ki-67 immunohistochemical staining was used to assess the proliferation.In addition, the levels of pro-inflammatory cytokines including TNF-, IL-1{beta} and SCr in serum were measured by ELISA. In vitro, we extracted exosomes from mouse spleen fibroblasts pretreated with hypoxia and reoxygenation (H/R) and administered them to mouse renal epithelial cells.Furthermore, for the hypoxia-reoxygenation model of renal epithelial cells, TUNEL and flow cytometry were used to evalutaed cell apoptosis;Then ELISA was used to measure the levels of TNF- and IL-1{beta} in the cell supernatant, Bax and Bcl-2 were measured by Western Blotting. ResultsHE staining showed that the renal injury caused by ischemia-reperfusion attenuated after sIPC. TUNEL staining showed that renal tissue apoptosis was greatly reduced after sIPC or injection of exosomes extracted from splenic fibroblast hypoxia-reoxygenation model. Ki-67 staining showed that the positive rates of IRI+sIPC group, IRI+mSF(H/R)-exo group, IRI+mSF(H/R+PBS)-exo group were close, higher than IRI group but lower than sham group. ELISA test of kidney tissue showed that the serum creatinine, TNF- and IL-1{beta} induced by IRI decreased with sIPC and addition of the above-mentioned exosomes.In vitro, the exosomes extracted from the hypoxia-reoxygenation model of splenic fibroblasts had the same protective effect on hypoxia-reoxygenated mouse renal epithelial cells model, and this protective effect disappears after the addition of exosome inhibitors.TUNEL and flow cytometry showed that the exosomes reduced the apoptosis. The ELISA test results showed that the levels of TNF- and IL-1{beta} in the H/R group increased significantly, but decreased due to the splenic fibroblast exosomes treated with starvation.While the exosome inhibitors inhibited the effects of exosomes.Western blot results showed that the Bax expression level of the H/R group increased, and the Bcl-2 decreased.While the starvation-treated splenic fibroblast exosomes decreased the Bax level and increased the Bcl-2 level. ConclusionsThe exosomes extracted from splenic ischemic preconditioning exerted a protective capacity to attenuate renal IR injury.

pathology↗

bioRxiv2022

Phase separation of Myc differentially regulates gene transcription

Dysregulation and enhanced expression of MYC transcription factors (TFs) including MYC and MYCN contribute to the majority of human cancers. For example, MYCN is amplified up to several hundred-fold in high-risk neuroblastoma. The resulting overexpression of N-myc aberrantly activates genes that are not activated at low N-myc levels and drives proliferation and cell survival. Whether increasing N-myc levels simply mediate binding to lower-affinity binding sites in the genome or fundamentally changes the activation process remains unclear. One such activation mechanism that could become important above threshold levels of N-myc is the formation of aberrant transcriptional condensates through phase separation. Phase separation has recently been linked to transcriptional regulation, but how strongly it contributes to gene activation remains unclear. Here we characterized the phase behavior of N-myc and showed that it can form dynamic condensates that bear the hallmarks of transcriptional activity. We tested the contribution of phase separation to N-myc-mediated gene expression by using a chemogenetic tool that allowed us to compare non-phase-separated and phase-separated conditions at identical N-myc levels, which both showed a strong impact on gene expression compared to no N-myc expression. However, we found that only a small fraction of <3% of N-myc-regulated genes is further affected by phase separation, but that these events include the activation of key oncogenes and the repression of tumor suppressors. Indeed, phase separation increases cell survival by [~]15% corroborating the biological effects of the transcriptional changes. However, our results also show that >97% of N-myc-regulated genes are not affected by N-myc phase separation, highlighting that transcription can be activated effectively by diffuse complexes of TFs with the transcriptional machinery.

cell biology↗

bioRxiv2022

Endogenous Rab38 regulates LRRK2's membrane recruitment and substrate Rab phosphorylation in melanocytes

Point mutations in LRRK2 cause Parkinsons Disease and augment LRRK2s kinase activity. However, cellular pathways that enhance LRRK2 kinase function have not been identified. While overexpressed Rab29 draws LRRK2 to Golgi membranes to increase LRRK2 kinase activity, there is little evidence that endogenous Rab29 performs this function under physiological conditions. Here we identify Rab38 as a novel physiological regulator of LRRK2. In mouse melanocytes, which express high levels of Rab38, Rab32, and Rab29, knockdown of Rab38 but not Rab32 or Rab29 decreases phosphorylation of multiple LRRK2 substrates, including Rab10 and Rab12, by both exogenous and endogenous LRRK2. In B16-F10 mouse melanoma cells, Rab38 drives LRRK2 membrane association, and overexpressed kinase-active but not kinase-inactive LRRK2 shows striking pericentriolar recruitment, which is dependent on the presence of endogenous Rab38 but not Rab32 or Rab29. Deletion or mutation of LRRK2 at the Rab38 binding site in the N-terminal armadillo domain decreases LRRK2 membrane association, pericentriolar recruitment, and ability to phosphorylate Rab10. Consistently, overexpression of LRRK2350-550, a fragment that encompasses the Rab38 binding site, blocks endogenous LRRK2s phosphorylation of Thr73-Rab10. Finally, disruption of BLOC-3, the guanine nucleotide exchange factor for Rab38 and 32, inhibits Rab38s regulation of LRRK2. In sum, our data identify Rab38 as a physiologic regulator of LRRK2 function and lend support to a model in which LRRK2 plays a central role in Rab GTPase coordination of vesicular trafficking.

cell biology↗

bioRxiv2022

Biosensor optimization using a FRET pair based on mScarlet red fluorescent protein and an mScarlet-derived green fluorescent protein

Genetically encoded biosensors based on Forster resonance energy transfer (FRET) are indispensable tools for monitoring biochemical changes in cells. Green and red fluorescent protein-based FRET pairs offer advantages over the classically employed cyan and yellow fluorescent protein pairs, such as better spectral separation, lower phototoxicity, and less autofluorescence. Here, we describe the development of an mScarlet-derived green fluorescent protein (designated as mWatermelon) and its use as a FRET donor to the red fluorescent protein mScarlet-I as a FRET acceptor. We tested the functionality of this FRET pair by engineering biosensors for the detection of protease activity, Ca2+, and K+. Furthermore, we described a strategy to enhance the FRET efficiency of these biosensors by modulating the intramolecular association between mWatermelon and mScarlet-I.

bioengineering↗