Sucrose Gradient Fractionation Research Articles

Bacterial Envelope Fractionation.

Numerous bioinformatics tools allow predicting the localization of membrane proteins in the outer or inner membrane of Escherichia coli with high precision. Nevertheless, it might be desirable to experimentally verify such predictions or to assay the correct localization of recombinant or mutated variants of membrane proteins. Here we describe two methods (preferential detergent solubilization and sucrose-gradient fractionation) that allow to fractionate Gram-negative bacterial membranes and subsequently to enrich inner or outer membrane proteins.

Role of Lipid Rafts on LRP8 Signaling Triggered by Anti-β2-GPI Antibodies in Endothelial Cells.

Antiphospholipid antibody syndrome is an autoimmune disease characterized by thrombosis and/or pregnancy morbidity in association with circulating antiphospholipid antibodies, mainly anti-β2 glycoprotein 1 antibodies (anti-β2-GPI antibodies). Previous studies demonstrated that the signaling pathway may involve lipid rafts, plasma membrane microdomains enriched in glycosphingolipid and cholesterol. In this study, we analyzed the signaling pathway of LRP8/ApoER2, a putative receptor of anti-β2-GPI antibodies, through lipid rafts in human endothelial cells. LRP8, Dab2 and endothelial nitric oxide synthase (e-NOS) phosphorylation were evaluated using Western blot, Nitric Oxide (NO) production with cytofluorimetric analysis, LRP8 enrichment in lipid rafts via sucrose gradient fractionation, and scanning confocal microscopy analysis of its association with ganglioside GM1 was also conducted. The analyses demonstrated that affinity-purified anti-β2-GPI antibodies induced LRP8 and Dab-2 phosphorylation, together with a significant decrease in e-NOS phosphorylation, with consequent decrease in NO intracellular production. These effects were almost completely prevented by Methyl-β-cyclodextrin (MβCD), indicating the involvement of lipid rafts. It was supported with the observation of LRP8 enrichment in lipid raft fractions and its association with ganglioside GM1, detected with scanning confocal microscopy. These findings demonstrate that LRP8 signaling triggered by anti-β2-GPI antibodies in endothelial cells occurs through lipid rafts. It represents a new task for valuable therapeutic approaches, such as raft-targeted therapy, including cyclodextrins and statins.

Human brain microvascular endothelial cells release different types of P-glycoprotein-containing extracellular vesicles upon exposure to doxorubicin

In the brain, the efflux transporter P-glycoprotein (Pgp) is predominantly located on the luminal membrane of microvascular endothelial cells (BMECs) that form the blood-brain barrier. In addition, Pgp is localized in intracellular organelles involved in Pgp traffic and cycling and, by the release of extracellular vesicles (EVs), in intercellular Pgp transfer to cells with low Pgp expression. We recently described that drug exposure of a human BMEC line (hCMEC/D3) induces the release of Pgp-EGFP-containing EVs; however, the nature of the Pgp-enriched vesicles was not characterized. The two main categories of EVs are exosomes and microvesicles, which differ in origin, size, and molecular cargo. In the present study, we performed similar experiments with hCMEC/D3 cells in the absence and presence of doxorubicin and isolated and characterized the EVs released by the cells during the experiments by differential ultracentrifugation with/without subsequent sucrose gradient fractionation of EV pellets, proteomic profiling, EV size analysis, and confocal fluorescence microscopy. Using cocultures of hCMEC/D3 wildtype cells and cells transduced with MDR1-EGFP or monocultures of hCMEC/D3-MDR1-EGFP cells, we found release of both Pgp-enriched exosomes and microvesicles but analysis of the exosomal marker protein Rab7 indicated that doxorubicin increased particularly the release of exosomes. Transfer experiments with isolated EVs demonstrated EV endocytosis by recipient cells. EV release from BMECs in response to anticancer drugs such as doxorubicin likely serves different functions, including non-genetic intercellular transfer of a resistance phenotype to neighboring BMECs and a mechanism of drug extrusion that contributes to brain protection against potentially toxic chemotherapeutic drugs.

Cyclodextrin-Mediated Cholesterol Depletion Induces Adiponectin Secretion in 3T3-L1 Adipocytes.

Adipocytes store a significant amount of cholesterol and triglycerides. However, whether cholesterol modulates adipocyte function remains largely unknown. We modulated the cholesterol level in adipocytes to examine its effect on the secretion of adiponectin, an important hormone specifically secreted by adipocytes. Treating differentiated 3T3-L1 adipocytes with 4 mM methyl-β-cyclodextrin (MβCD), a molecule with a high affinity for cholesterol, rapidly depleted cholesterol in adipocytes. Interestingly, MβCD treatment increased adiponectin in the medium without affecting its intracellular level, suggesting a modulation of secretion. By contrast, cholesterol addition did not affect adiponectin secretion, suggesting that cholesterol-depletion-induced intracellular cholesterol trafficking, but not reduced cholesterol level, accounted for MβCD-induced adiponectin secretion. MβCD-induced adiponectin secretion was reduced after 10 μg/mL U18666A treatment that suppressed cholesterol transport out of late endosomes/lysosomes. Depleting Niemann-Pick type C1 (NPC1) or NPC2 proteins, which mediate endosomal/lysosomal cholesterol export, consistently reduced MβCD-induced adiponectin secretion. Furthermore, treatment with 1 μM bafilomycin A1, which neutralized acidic endosomes/lysosomes, also attenuated MβCD-induced adiponectin secretion. Finally, MβCD treatment redistributed cellular adiponectin to lower-density fractions in sucrose gradient fractionation. Our results show that MβCD-mediated cholesterol depletion elevates the secretion of adiponectin, highlighting the involvement of endosomes and lysosomes in adiponectin secretion in adipocytes.

Uptake of oomycete RXLR effectors into host cells by clathrin-mediated endocytosis.

Filamentous (oomycete and fungal) plant pathogens deliver cytoplasmic effector proteins into host cells to facilitate disease. How RXLR effectors from the potato late blight pathogen Phytophthora infestans enter host cells is unknown. One possible route involves clathrin-mediated endocytosis (CME). Transient silencing of NbCHC, encoding clathrin heavy chain, or the endosome marker gene NbAra6 encoding a Rab GTPase in the model host Nicotiana benthamiana, attenuated P. infestans infection and reduced translocation of RXLR effector fusions from transgenic pathogen strains into host cells. By contrast, silencing PP1c isoforms, susceptibility factors not required for endocytosis, reduced infection but did not attenuate RXLR effector uptake. Endosome enrichment by ultracentrifugation and sucrose gradient fractionation revealed co-localization of RXLR effector Pi04314-RFP with clathrin-coated vesicles. Immunopurification of clathrin- and NbAra6-associated vesicles during infection showed that RXLR effectors Pi04314-RFP and AvrBlb1-RFP, but not apoplastic effector PiSCR74-RFP, were co-immunoprecipitated during infection with pathogen strains secreting these effectors. Tandem mass spectrometry analyses of proteins co-immunoprecipitated with NbAra6-GFP during infection revealed enrichment of host proteins associated with endocytic vesicles alongside multiple pathogen RXLR effectors, but not apoplastic effectors, including PiSCR74, which do not enter host cells. Our data show that the uptake of P. infestans RXLR effectors into plant cells occurs via CME.

Purification of Active Photosystem I-Light Harvesting Complex I from Plant Tissues.

This method is used to isolate Photosystem I (PSI) together with the Light Harvesting Complex I (LHCI), its native antenna, from plants. PSI-LHCI is a large membrane protein complex coordinating hundreds of light harvesting and electron transport factors and is the most efficient light harvesting system found in nature. Photons absorbed by the four LHCA antenna proteins that make up LHCI are transferred through excitonic interaction to the PSI core reaction center and are used to facilitate light-driven charge separation across the thylakoid membrane, providing reducing power and energy for carbon fixation in photoautotrophic organisms. The high quantum efficiency of PSI makes this complex an excellent model to study light-driven energy transfer. In this protocol, plant tissue is mechanically homogenized, and the chloroplasts are separated from the bulk cellular debris by filtration and centrifugation. The isolated chloroplasts are then osmotically lysed, and the thylakoid membranes are recovered via centrifugation and solubilized using the detergent n-dodecyl-beta-maltoside. The solubilized material is loaded onto an anion exchange column to collect most of the chlorophyll-containing complexes. Larger complexes are precipitated from the solution, resuspended in a small volume, and loaded on sucrose gradients to separate the major chlorophyll-containing complexes. The resulting sucrose gradient fractions are characterized to identify the band of interest containing PSI-LHCI. This protocol is highly similar to the protocol used in the crystallization of plant PSI-LHCI with some simplifications and relies on methods developed over the years in the lab of Nathan Nelson.

Ribosomal RNA-based epitranscriptomic regulation of chondrocyte translation and proteome in osteoarthritis

Osteoarthritis-related cartilage extracellular matrix remodelling is dependent on changes in chondrocyte protein expression. Yet, the role of ribosomes in chondrocyte translation regulation is unknown. In this exploratory study, we investigated ribosomal RNA (rRNA) epitranscriptomic-based ribosome heterogeneity in human articular chondrocytes and its relevance for osteoarthritis. Sequencing-based rRNA 2'-O-methylation profiling analysis (RiboMethSeq) was performed on non-OA primary human articular chondrocytes (n=5) exposed for 14 days to osteoarthritic synovial fluid (14 donors, pooled, 20% v/v). The SW1353 SNORD71 KO cell pool was generated using LentiCRISPRv2/Cas9. The mode of translation initiation and fidelity were determined by dual-luciferase reporters. The cellular proteome was analysed by LC-MS/MS and collagen type I protein expression was evaluated by immunoblotting. Loading of COL1A1 mRNA into polysomes was determined by sucrose gradient ultracentrifugation and fractionation. We discovered that osteoarthritic synovial fluid instigates site-specific changes in the rRNA 2'-O-me profile of primary human articular chondrocytes. We identified five sites with differential 2'-O-me levels. The 2'-O-me status of 5.8S-U14 (one of identified differential 2'-O-me sites; decreased by 7.7%, 95% CI [0.9% to 14.5%]) was targeted by depleting the level of its guide snoRNA SNORD71 (50% decrease, 95% CI [33% to 64%]). This resulted in an altered ribosome translation modus (e.g CrPV IRES, FC 3, 95% CI [2.2 to 4.1]) and promoted translation of COL1A1 mRNA which led to increased levels of COL1A1 protein (FC 1.7, 95% CI [1.3 to 2.0]). Our data identify a novel concept suggesting that articular chondrocytes employ rRNA epitranscriptomic mechanisms in osteoarthritis development.

The role of the γ subunit in the photosystem of the lowest-energy phototrophs

Purple phototrophic bacteria use a 'photosystem' consisting of light harvesting complex 1 (LH1) surrounding the reaction centre (RC) that absorbs far-red-near-infrared light and converts it to chemical energy. Blastochloris species, which harvest light >1000 nm, use bacteriochlorophyll b rather than the more common bacteriochlorophyll a as their major photopigment, and assemble LH1 with an additional polypeptide subunit, LH1γ, encoded by multiple genes. To assign a role to γ, we deleted the four encoding genes in the model Blastochloris viridis. Interestingly, growth under halogen bulbs routinely used for cultivation yielded cells displaying an absorption maximum of 825 nm, similar to that of the RC only, but growth under white light yielded cells with an absorption maximum at 972 nm. HPLC analysis of pigment composition and sucrose gradient fractionation demonstrate that the white light-grown mutant assembles RC-LH1, albeit with an absorption maximum blue-shifted by 46 nm. Wavelengths between 900-1000 nm transmit poorly through the atmosphere due to absorption by water, so our results provide an evolutionary rationale for incorporation of γ; this polypeptide red-shifts absorption of RC-LH1 to a spectral range in which photons are of lower energy but are more abundant. Finally, we transformed the mutant with plasmids encoding natural LH1γ variants and demonstrate that the polypeptide found in the wild type complex red-shifts absorption back to 1018 nm, but incorporation of a distantly related variant results in only a moderate shift. This result suggests that tuning the absorption of RC-LH1 is possible and may permit photosynthesis past its current low-energy limit.

PS1 Affects the Pathology of Alzheimer's Disease by Regulating BACE1 Distribution in the ER and BACE1 Maturation in the Golgi Apparatus.

Neuritic plaques are one of the major pathological hallmarks of Alzheimer's disease. They are formed by the aggregation of extracellular amyloid-β protein (Aβ), which is derived from the sequential cleavage of amyloid-β precursor protein (APP) by β- and γ-secretase. BACE1 is the main β-secretase in the pathogenic process of Alzheimer's disease, which is believed to be a rate-limiting step of Aβ production. Presenilin 1 (PS1) is the active center of the γ-secretase that participates in the APP hydrolysis process. Mutations in the PS1 gene (PSEN1) are the most common cause of early onset familial Alzheimer's disease (FAD). The PSEN1 mutations can alter the activity of γ-secretase on the cleavage of APP. Previous studies have shown that PSEN1 mutations increase the expression and activity of BACE1 and that BACE1 expression and activity are elevated in the brains of PSEN1 mutant knock-in mice, compared with wild-type mice, as well as in the cerebral cortex of FAD patients carrying PSEN1 mutations, compared with sporadic AD patients and controls. Here, we used a Psen1 knockout cell line and a PS1 inhibitor to show that PS1 affects the expression of BACE1 in vitro. Furthermore, we used sucrose gradient fractionation combined with western blotting to analyze the distribution of BACE1, combined with a time-lapse technique to show that PS1 upregulates the distribution and trafficking of BACE1 in the endoplasmic reticulum, Golgi, and endosomes. More importantly, we found that the PSEN1 mutant S170F increases the distribution of BACE1 in the endoplasmic reticulum and changes the ratio of mature BACE1 in the trans-Golgi network. The effect of PSEN1 mutations on BACE1 may contribute to determining the phenotype of early onset FAD.

Expression of miRNA-Targeted and Not-Targeted Reporter Genes Shows Mutual Influence and Intercellular Specificity

The regulation of translation by RNA-induced silencing complexes (RISCs) composed of Argonaute proteins and micro-RNAs is well established; however, the mechanisms underlying specific cellular responses to miRNAs and how specific complexes arise are not completely clear. To explore these questions, we performed experiments with Renilla and firefly luciferase reporter genes transfected in a psiCHECK-2 plasmid into human HCT116 or Me45 cells, where only the Renilla gene contained sequences targeted by microRNAs (miRNAs) in the 3'UTR. The effects of targeting were miRNA-specific; miRNA-21-5p caused strong inhibition of translation, whereas miRNA-24-3p or Let-7 family caused no change or an increase in reporter Renilla luciferase synthesis. The mRNA-protein complexes formed by transcripts regulated by different miRNAs differed from each other and were different in different cell types, as shown by sucrose gradient centrifugation. Unexpectedly, the presence of miRNA targets on Renilla transcripts also affected the expression of the co-transfected but non-targeted firefly luciferase gene in both cell types. Renilla and firefly transcripts were found in the same sucrose gradient fractions and specific anti-miRNA oligoribonucleotides, which influenced the expression of the Renilla gene, and also influenced that of firefly gene. These results suggest that, in addition to targeted transcripts, miRNAs may also modulate the expression of non-targeted transcripts, and using the latter to normalize the results may cause bias. We discuss some hypothetical mechanisms which could explain the observed miRNA-induced effects.

Multiplexed Analysis of Human uORF Regulatory Functions During the ISR Using PoLib-Seq.

Protein synthesis is a highly regulated essential process. As such, it is subjected to substantial regulation in response to stress. One hallmark of the Integrated Stress Response (ISR) is the immediate shutdown of most translation through phosphorylation of the alpha subunit of translation initiation factor eIF2 and activation of eIF4E binding proteins. While these posttranslational modifications largely inhibit cap-dependent translation, many mRNA resist this inhibition by alternative translation mechanisms involving cis-regulatory sequences and structures in 5' transcript leaders, including upstream Open Reading Frames (uORFs), Internal Ribosome Entry Sites (IRESes), and Cap-Independent Translation Elements (CITEs). Studies of uORF and IRES activity are often performed on a gene-by-gene basis; however, high-throughput methods have recently emerged. Here, we describe a protocol for Polysome Library Sequencing (PoLib-Seq; Fig. 1), a multiplexed assay of reporter gene translation that can be used during the ISR. A designer library of reporter RNAs are transfected into tissue-culture cells, and their translation is assayed via sucrose gradient fractionation followed by high-throughput sequencing. As an example, we include PoLib-seq results simultaneously assaying translation of wildtype and uORF mutant human ATF4 reporter RNAs, recapitulating the known function of uORF1 in resisting translational inhibition during the ISR.

Abstract 2901: Pdcd4 inhibits slug translation to suppress E-cadherin expression and invasion in colon tumor cells

Abstract Programmed cell death 4 (Pdcd4) has been demonstrated to function as a tumor suppressor and protein translation inhibitor. We previously reported that knockdown of Pdcd4 down-regulated E-cadherin expression. E-cadherin is a key regulator for tumor cell invasion and metastasis, whose expression is controlled by transcription repressors Snail, Slug, ZEB1/2, and Twist. Both Slug and Snail have been shown to repress E-cadherin expression and contribute to tumor progression in various cancers including colon cancer. Here, we reported that knockdown of Pdcd4 increased Slug protein level but not SLUG mRNA level in colon tumor cells. Conversely, over-expression of Pdcd4 decreased Slug expression. Using sucrose gradient fractionation assays, Pdcd4 knockdown was found to increase the population of SLUG mRNA in the polysomal fractions. These results indicate that Pdcd4 translationally regulates Slug expression. To understand the mechanism by which Pdcd4 regulates Slug translation, the SLUG 5' untranslated region (5'UTR) was cloned and fused with luciferase reporter and named as 5'UTR-Slug-Luc. Knockdown of Pdcd4 significantly enhanced the translation of 5'UTR-Slug-Luc while ectopic expression of Pdcd4 repressed the translation of 5'UTR-Slug-Luc, suggesting that SLUG 5'UTR is an essential element for Pdcd4 to inhibit Slug translation. Moreover, cells treated with silvestrol, an inhibitor for translation initiation factor 4A (eIF4A), significantly suppressed Slug translation. In addition, ectopic expression of Pdcd4 inhibited Slug translation and thereby decreased E-cadherin expression. By contrast, Pdcd4(D418A), a mutant that does not bind with eIF4A, failed to suppress the expression of Slug and E-cadherin. These findings suggest that Pdcd4-inhibited Slug translation is through suppressing eIF4A. Furthermore, knockdown of Slug in Pdcd4 knockdown cells restored the E-cadherin expression and reversed the invasive capacity induced by Pdcd4 knockdown, indicating that up-regulation of Slug contributes to Pdcd4-knockdown enhanced invasion. Taken together, this study demonstrates that Pdcd4 inhibits translation of Slug to regulate E-cadherin expression and invasion in colon tumor cells. Citation Format: Qing Wang, Jiang Zhu, Hsin-Sheng Yang. Pdcd4 inhibits slug translation to suppress E-cadherin expression and invasion in colon tumor cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2901.

Distinct features of the Leishmaniacap-binding protein LeishIF4E2 revealed by CRISPR-Cas9 mediated hemizygous deletion.

Leishmania parasites cycle between sand-fly vectors and mammalian hosts adapting to alternating environments by stage-differentiation accompanied by changes in the proteome profiles. Translation regulation plays a central role in driving the differential program of gene expression since control of gene regulation in Leishmania is mostly post-transcriptional. The Leishmania genome encodes six eIF4E paralogs, some of which bind a dedicated eIF4G candidate, and each eIF4E is assumed to have specific functions with perhaps some overlaps. However, LeishIF4E2 does not bind any known eIF4G ortholog and was previously shown to comigrate with the polysomal fractions of sucrose gradients in contrast to the other initiation factors that usually comigrate with pre-initiation and initiation complexes. Here we deleted one of the two LeishIF4E2 gene copies using the CRISPR-Cas9 methodology. The deletion caused severe alterations in the morphology of the mutant cells that became round, small, and equipped with a very short flagellum that did not protrude from its pocket. Reduced expression of LeishIF4E2 had no global effect on translation and growth, unlike other LeishIF4Es; however, there was a change in the proteome profile of the LeishIF4E2(+/-) cells. Upregulated proteins were related mainly to general metabolic processes including enzymes involved in fatty acid metabolism, DNA repair and replication, signaling, and cellular motor activity. The downregulated proteins included flagellar rod and cytoskeletal proteins, as well as surface antigens involved in virulence. Moreover, the LeishIF4E2(+/-) cells were impaired in their ability to infect cultured macrophages. Overall, LeishIF4E2 does not behave like a general translation factor and its function remains elusive. Our results also suggest that the individual LeishIF4Es perform unique functions.

Photoreceptor cilia, in contrast to primary cilia, grant entry to a partially assembled BBSome.

The BBSome is a protein complex consisting of BBS1, BBS2, BBS4, BBS5, BBS7, BBS8, BBS9 and BBS18 that associates with intraflagellar transport complexes and specializes in ciliary trafficking. In primary cilia, ciliary entry requires the fully assembled BBSome as well as the small GTPase, ARL6 (BBS3). Retinal photoreceptors possess specialized cilia. In light of key structural and functional differences between primary and specialized cilia, we examined the principles of BBSome recruitment to photoreceptor cilia. We performed sucrose gradient fractionation using retinal lysates of Bbs2-/-, Bbs7-/-, Bbs8-/- and Bbs3-/- mice to determine the status of BBSome assembly, then determined localization of BBSome components using immunohistochemistry. Surprisingly, we found that a subcomplex of the BBSome containing at least BBS1, BBS5, BBS8 and BBS9 is recruited to cilia in the absence of BBS2 or BBS7. In contrast, a BBSome subcomplex consisting of BBS1, BBS2, BBS5, BBS7 and BBS9 is found in Bbs8-/- retinas and is denied ciliary entry in photoreceptor cells. In addition, the BBSome remains fully assembled in Bbs3-/- retinas and can be recruited to photoreceptor cilia in the absence of BBS3. We compared phenotypic severity of their retinal degeneration phenotypes. These findings demonstrate that unlike primary cilia, photoreceptor cilia admit a partially assembled BBSome meeting specific requirements. In addition, the recruitment of the BBSome to photoreceptor cilia does not require BBS3. These findings indicate that the ciliary entry of the BBSome is subjected to cell-specific regulation, particularly in cells with highly adapted forms of cilia such as photoreceptors.

Accessing the Human Pluripotent Stem Cell Translatome by Polysome Profiling.

Polysome profiling is a technique that uses sucrose density gradient ultracentrifugation to separate complexes of mRNAs associated with one or more ribosomes. Here we describe polysome profiling analysis in human pluripotent stem cells (hPSCs) using a continuous ultraviolet spectrophotometer and a gradient fractionator. We provide protocols for processing sucrose gradient fractions for isolation of RNA for RT-qPCR or large-scale sequencing analysis, used to establish the translational status of specific mRNAs and identify the role of noncoding RNA in translation.

Characterization of raft microdomains in bovine mammary tissue during lactation: How they are modulated by fatty acid treatments

The objective of the current study was first to characterize lipid raft microdomains isolated as detergent-resistant membranes (DRM) from mammary gland tissue, and second to determine how dietary fatty acids (FA) such as conjugated linoleic acid (CLA), 19:1 cyclo, and long-chain n-3 polyunsaturated FA affect lipid raft markers of mammary cells, and to finally establish relationships between these markers and lactation performance in dairy cows. Eight Holstein cows were used in a replicated 4 × 4 Latin square design with periods of 28 d. For the first 14 d, cows received daily an abomasal infusion of (1) 406 g of a saturated FA supplement (112 g of 16:0 + 230 g of 18:0) used as a control; (2) 36 g of a CLA supplement (13.9 g of trans-10,cis-12 18:2) + 370 g of saturated FA; (3) 7 g of Sterculia fetida oil (3.1 g of 19:1 cyclo, STO) + 399 g of saturated FA; or (4) 406 g of fish oil (55.2 g of cis-5,cis-8,cis-11,cis-14,cis-17 20:5 + 59.3 g of cis-4,cis-7,cis-10,cis-13,cis-16,cis-19 22:6, FO). Mammary biopsies were harvested on d 14 of each infusion period and were followed by a 14-d washout interval. Cholera toxin subunit B, which specifically binds to ganglioside M-1 (GM-1), a lipid raft marker, was used to assess its distribution in DRM. Infusions of CLA, STO, and FO were individually compared with the control, and significance was declared at P ≤ 0.05. Milk fat yield was decreased with CLA and FO, but was not affected by STO. Milk lactose yield was decreased with CLA and STO, but was not affected by FO. Mammary tissue shows a strong GM-1-signal enrichment in isolated DRM from mammary gland tissue. Caveolin (CAV) and flotillin (FLOT) are 2 proteins considered as lipid raft markers and they are present in DRM from mammary gland tissue. Distributions of GM-1, CAV-1, and FLOT-1 showed an effect of treatments determined by their subcellular distributions in sucrose gradient fractions. Regardless of treatments, data showed positive relationships between the yield of milk fat, protein, and lactose, and the abundance GM-1 in DRM fraction. Milk protein yield was positively correlated with relative proportion of FLOT-1 in the soluble fraction, whereas lactose yield was positively correlated with relative proportion of CAV-1 in the DRM fractions. Infusion of CLA decreased mRNA abundance of CAV-1, FLOT-1, and FLOT-2. Regardless of treatments, a positive relationship was observed between fat yield and mRNA abundance of FLOT-2. In conclusion, although limited to a few markers, results of the current experiment raised potential links between variation in specific biologically active component of raft microdomains in bovine mammary gland and lactation performances in dairy cows.

EDF1 coordinates cellular responses to ribosome collisions.

Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation combined with quantitative proteomics to systematically identify proteins associated with collided ribosomes. This approach identified Endothelial differentiation-related factor 1 (EDF1) as a novel protein recruited to collided ribosomes during translational distress. Cryo-electron microscopic analyses of EDF1 and its yeast homolog Mbf1 revealed a conserved 40S ribosomal subunit binding site at the mRNA entry channel near the collision interface. EDF1 recruits the translational repressors GIGYF2 and EIF4E2 to collided ribosomes to initiate a negative-feedback loop that prevents new ribosomes from translating defective mRNAs. Further, EDF1 regulates an immediate-early transcriptional response to ribosomal collisions. Our results uncover mechanisms through which EDF1 coordinates multiple responses of the ribosome-mediated quality control pathway and provide novel insights into the intersection of ribosome-mediated quality control with global transcriptional regulation.

Isolation of Extracellular Vesicles from Leishmania spp.

Exosomes, a class of extracellular vesicles, are released by eukaryotes, bacteria, and archaea, as evident from both in vitro and in vivo studies. These nano-sized double-membraned vesicles play an important role in cell-to-cell communication, dysregulation of the immune system, and pathogenesis in a number of diseases, including leishmaniasis. Leishmania is a genus of obligate intracellular parasites, which infect host macrophages, are transmitted through the bite of a sandfly, and are shown to secrete exosomes with immunomodulatory activities. Given the importance of these vesicles in Leishmania spp. virulence, it is necessary to perform appropriate isolation and characterization in order to further study their relevance in the parasite's infectious life cycle. In this chapter, we describe four methods for the isolation of extracellular vesicles derived from Leishmania species including ultracentrifugation, polyethylene glycol-based precipitation, size-exclusion chromatography, and sucrose-gradient fractionation. Further, we describe the preparation of isolated samples for characterization by nanoparticle tracking analysis, transmission electron microscopy, and proteomic profiling.

CircPCMTD1: A Protein-Coding Circular RNA That Regulates DNA Synthesis in Leukemic Myeloblasts

Introduction: The prognostic and biologic significance of circular RNAs (circRNAs) in patients with acute myeloid leukemia has recently been reported. Circular PCMTD1 (circPCMTD1) was among the circRNAs that were prognostic in this disease. Herein, we study the functional role of circPCMTD1 in leukemia. Methods: We used RNase H-recruiting, locked nucleic acid-modified oligonucleotides (gapmers) for knock-down (KD) experiments. Cell cycle analyses were performed with bromodeoxyuridine and 7-actinomycin D staining. Apoptosis was assessed with annexin V and propidium iodide staining. Chloro-deoxyuridine (CldU) and iodo-deoxyuridine (IdU) were used for DNA fiber assays. Results: To study the biologic function of circPCMTD1, we performed KD experiments using anti-circPCMTD1 gapmers in K562 and LAMA84 leukemia cell lines. Anti-circPCMTD1 gapmers specifically degraded the circular transcript without affecting the levels of the linear PCMTD1 (linPCMTD1). CircPCMTD1-KD led to a potent G2/M blockade and increased the percent of apoptotic blasts in both the K562 and LAMA84 cell lines. In contrast, linPCMTD1-KD did not have a significant effect on cell cycle progression or the viability of myeloblasts. Mass cytometry (CyTOF) experiments validated the cell cycle blockade after circPCMTD1-KD. In addition, CyTOF experiments identified an increase of H2AX phosphorylation, as an early downstream event of circPCMTD1-KD. We validated this finding with western blots and could also show that circPCMTD1-KD led to an increase in the phosphorylation of the ATM, ATR, CHK1, DNA-PK and RPA32 proteins. Further, we performed sequential labeling with CldU and IdU in cells treated with circPCMTD1-KD versus control, and conducted DNA fiber assays. We detected a global decrease in the length of CldU- and IdU-labeled fibers as well as of the IdU/CldU ratio in the circPCMTD1-KD cells. Taken together these data indicate that circPCMTD1-KD causes impaired DNA replication in leukemic cells. To identify proteins with which circPCMTD1 interacts, we performed ribonucleoprotein complex purification and comparative proteomics analyses, using the RAP-MS technique (McHugh et al, Nature 2015;521:232). We identified METTL3 as a strong candidate binder of circPCMTD1. We validated the METTL3-circPCMTD1 interaction by RNA Immunoprecipitation experiments. We also found enrichment of circPCMTD1 in capture experiments from total RNA with an anti-N6-methyladenosine (m6A) antibody compared to control. METTL3-mediated, high m6A status has been associated with protein-coding potential of circRNAs (Yang et al, Cell Res 2017;27:626). To evaluate whether circPCMTD1 interacts with the translational machinery of the leukemic blasts, we performed sucrose gradient fractionation and targeted polysome profiling and we found enrichment of the circPCMTD1 in the 80S monosomes, and both light and heavy molecular weight polysomal fractions. In search of an open reading frame, we identified a stop codon in the 5' UTR of exon 2 of the PCMTD1 transcript. While this stop codon should have no functional relevance for the linPCMTD1, it was in-frame with a start codon also contained in the circPCMTD1. We generated an antibody against a region specific for the circPCMTD1-derived peptide. The antibody detected a protein of 35 kD, which was depleted after circPCMTD1-KD. We next performed immunoprecipitation experiments followed by mass spectrometry analysis, using our custom antibody. These showed a strong and specific enrichment of the BLM, TOP3A and RMI1 proteins in the circPCMTD1 samples. Each interaction was validated with reciprocal co-immunoprecipitation experiments. BLM, TOP3A and RMI1 form the BTR complex, which is implicated in DNA replication and repair. CircPCMTD1-KD had no effect on the total amount of each of the three proteins but reduced their interaction and the amount of the formed BTR complex. Biotin labeling and capture of newly synthetized DNA with the iPOND technique showed a significant decrease in the presence of the BTR complex on the sites of active DNA replication after circPCMTD1-KD. Conclusions: C ircPCMTD1 is a circRNA with protein-coding potential. The circPCMTD1-derived peptide interacts with BLM, TOP3A and RMI1 and facilitates the formation of the BTR complex. In this context, circPCMTD1 is indispensable for the proliferation of leukemic myeloblasts as circPCMTD1-KD impairs DNA replication. Disclosures Behbehani: Fluidigm corporation: Other: Travel funding.

Modeling and plasmid expression of gene fragment of Ki67 protein biomarker

In eukaryotes, ribosome assembly is a rate-limiting step in ribosomal biogenesis that takes place in a distinctive subnuclear organelle, the nucleolus. How ribosomes get assembled at the nucleolar site by forming initial preribosomal complexes remains poorly characterized. In this study, using several human and murine cell lines, we developed a method for isolation of native mammalian preribosomal complexes by lysing cell nuclei through mild sonication. A sucrose gradient fractionation of the nuclear lysate resolved several ribonucleoprotein (RNP) complexes containing rRNAs and ribosomal proteins. Characterization of the RNP complexes with MS-based protein identification and Northern blotting–based rRNA detection approaches identified two types of preribosomes we named here as intermediate preribosomes (IPRibs) and composed preribosome (CPRib). IPRib complexes comprised large preribosomes (105S to 125S in size) containing the rRNA modification factors and premature rRNAs. We further observed that a distinctive CPRib complex consists of an 85S preribosome assembled with mature rRNAs and a ribosomal biogenesis factor, Ly1 antibody–reactive (LYAR), that does not associate with premature rRNAs and rRNA modification factors. rRNA-labeling experiments uncovered that IPRib assembly precedes CPRib complex formation. We also found that formation of the preribosomal complexes is nutrient-dependent because the abundances of IPRib and CPRib decreased substantially when cells were either deprived of amino acids or exposed to an mTOR kinase inhibitor. These findings indicate that preribosomes form via dynamic and nutrient-dependent processing events and progress from an intermediate to a composed state during ribosome maturation.