Cell Fractionation and the Identification of Host Proteins Involved in Plant-Virus Interactions

Plant viruses depend on host cellular factors for their replication and movement. There are cellular proteins that change their localization and/or expression and have a proviral role or antiviral activity and interact with or target viral proteins. Identification of those proteins and their roles during infection is crucial for understanding plant-virus interactions and to design antiviral resistance in crops. Important host proteins have been identified using approaches such as tag-dependent immunoprecipitation or yeast two hybridization that require cloning individual proteins or the entire virus. However, the number of possible interactions between host and viral proteins is immense. Therefore, an alternative method is needed for proteome-wide identification of host proteins involved in host-virus interactions. Here, we present cell fractionation coupled with mass spectrometry as an option to identify protein-protein interactions between viruses and their hosts. This approach involves separating subcellular organelles using differential and/or gradient centrifugation from virus-free and virus-infected cells (1) followed by comparative analysis of the proteomic profiles obtained for each subcellular organelle via mass spectrometry (2). After biological validation, prospect host proteins with proviral or antiviral roles can be subject to fundamental studies in the context of basic biology to shed light on both virus replication and cellular processes. They can also be targeted via gene editing to develop virus-resistant crops.

G1P3/IFI6, an interferon stimulated protein, promotes the association of RAB5+ endosomes with mitochondria in breast cancer cells

G1P3/IFI6 is an interferon stimulated gene with antiapoptotic, prometastatic, and antiviral functions. Despite its pleiotropic functions, subcellular localization of G1P3 remains unclear. Using biochemical- and confocal microscopic approaches, this study identified the localization of G1P3 in organelles of the endomembrane system and in the mitochondria of breast cancer cells. In cell fractionation studies, both interferon-induced endogenous- and stably expressed G1P3 cofractionated with affinity-isolated mitochondria. Results of the protease protection assay have suggested that ~24% of mitochondrial G1P3 resides within the mitochondria. Conforming to this, confocal microscopy studies of cells stably expressing epitope-tagged G1P3 (MCF-7/G1P3-FLAG), identified its localization in mitochondria (~38%) as well as in ER, trans-Golgi network (TGN), lysosomes, and in RAB5 positive (RAB5+ ) endosomes. These results suggested the trafficking of G1P3 from TGN into endolysosomes. Both G1P3 and RAB5 were known to confer apoptosis resistance through mitochondrial stabilization. Therefore, the effects of G1P3 on the localization of RAB5 in mitochondria were tested. Compared to vector control, the co-occurrence of RAB5 with the mitochondria was increased by 1.5-fold in MCF-7/G1P3-FLAG expressing cells (p ≤ .005). Taken together, our results demonstrate a role for G1P3 to promote the association of RAB5+ endosomes with mitochondria and provide insight into yet another mechanism of G1P3-induced cancer cell survival.

In Vitro Characterization of a Threonine-Ligated Molybdenyl-Sulfide Cluster as a Putative Cyanide Poisoning Antidote; Intracellular Distribution, Effects on Organic Osmolyte Homeostasis, and Induction of Cell Death

Binuclear molybdenum sulfur complexes are effective for the catalytic conversion of cyanide into thiocyanate. The complexes themselves exhibit low toxicity and high aqueous solubility, which render them suitable as antidotes for cyanide poisoning. The binuclear molybdenum sulfur complex [(thr)Mo2O2(μ-S)2(S2)]- (thr - threonine) was subjected to biological studies to evaluate its cellular accumulation and mechanism of action. The cellular uptake and intracellular distribution in human alveolar (A549) cells, quantified by inductively coupled plasma mass spectrometry (ICP-MS) and cell fractionation methods, revealed the presence of the compound in cytosol, nucleus, and mitochondria. The complex exhibited limited binding to DNA, and using the expression of specific protein markers for cell fate indicated no effect on the expression of stress-sensitive channel components involved in cell volume regulation, weak inhibition of cell proliferation, no increase in apoptosis, and even a reduction in autophagy. The complex is anionic, and the sodium complex had higher solubility compared to the potassium. As the molybdenum complex possibly enters the mitochondria, it is considered as a promising remedy to limit mitochondrial cyanide poisoning following, e.g., smoke inhalation injuries.

The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited

Ribosome biogenesis is one cell function-defining process. It depends on efficient transcription of rDNAs in the nucleolus as well as on the cytosolic synthesis of ribosomal proteins. For newly transcribed rRNA modification and ribosomal protein assembly, so-called small nucleolar RNAs (snoRNAs) and ribosome biogenesis factors (RBFs) are required. For both, an inventory was established for model systems like yeast and humans. For plants, many assignments are based on predictions. Here, RNA deep sequencing after nuclei enrichment was combined with single molecule species detection by northern blot and in vivo fluorescence in situ hybridization (FISH)-based localization studies. In addition, the occurrence and abundance of selected snoRNAs in different tissues were determined. These approaches confirm the presence of most of the database-deposited snoRNAs in cell cultures, but some of them are localized in the cytosol rather than in the nucleus. Further, for the explored snoRNA examples, differences in their abundance in different tissues were observed, suggesting a tissue-specific function of some snoRNAs. Thus, based on prediction and experimental confirmation, many plant snoRNAs can be proposed, while it cannot be excluded that some of the proposed snoRNAs perform alternative functions than are involved in rRNA modification.

Organellar Maps Through Proteomic Profiling - A Conceptual Guide

Protein subcellular localization is an essential and highly regulated determinant of protein function. Major advances in mass spectrometry and imaging have allowed the development of powerful spatial proteomics approaches for determining protein localization at the whole cell scale. Here, a brief overview of current methods is presented, followed by a detailed discussion of organellar mapping through proteomic profiling. This relatively simple yet flexible approach is rapidly gaining popularity, because of its ability to capture the localizations of thousands of proteins in a single experiment. It can be used to generate high-resolution cell maps, and as a tool for monitoring protein localization dynamics. This review highlights the strengths and limitations of the approach and provides guidance to designing and interpreting profiling experiments.

Proteomic Analysis Reveals that Topoisomerase 2A is Associated with Defective Sperm Head Morphology

Male infertility is widespread and estimated to affect 1 in 20 men. Although in some cases the etiology of the condition is well understood, for at least 50% of men, the underlying cause is yet to be classified. Male infertility, or subfertility, is often diagnosed by looking at total sperm produced, motility of the cells and overall morphology. Although counting spermatozoa and their associated motility is routine, morphology assessment is highly subjective, mainly because of the procedure being based on microscopic examination. A failure to diagnose male-infertility or sub-fertility has led to a situation where assisted conception is often used unnecessarily. As such, biomarkers of male infertility are needed to help establish a more consistent diagnosis. In the present study, we compared nuclear extracts from both high- and low-quality spermatozoa by LC-MS/MS based proteomic analysis. Our data shows that nuclear retention of specific proteins is a common facet among low-quality sperm cells. We demonstrate that the presence of Topoisomerase 2A in the sperm head is highly correlated to poor head morphology. Topoisomerase 2A is therefore a potential new biomarker for confirming male infertility in clinical practice.

Spatiotemporal Organization of the E. coli Transcriptome: Translation Independence and Engagement in Regulation

RNA localization in eukaryotes is a mechanism to regulate transcripts fate. Conversely, bacterial transcripts were not assumed to be specifically localized. We previously demonstrated that E. coli mRNAs may localize to where their products localize in a translation-independent manner, thus challenging the transcription-translation coupling extent. However, the scope of RNA localization in bacteria remained unknown. Here, we report the distribution of the E. coli transcriptome between the membrane, cytoplasm, and poles by combining cell fractionation with deep-sequencing (Rloc-seq). Our results reveal asymmetric RNA distribution on a transcriptome-wide scale, significantly correlating with proteome localization and prevalence of translation-independent RNA localization. The poles are enriched with stress-related mRNAs and small RNAs, the latter becoming further enriched upon stress in an Hfq-dependent manner. Genome organization may play a role in localizing membrane protein-encoding transcripts. Our results show an unexpected level of intricacy in bacterial transcriptome organization and highlight the poles as hubs for regulation.

A toolbox for the immunomagnetic purification of signaling organelles

Homeostasis and the complex functions of organisms and cells rely on the sophisticated spatial and temporal regulation of signaling in different intra- and extracellular compartments and via different mediators. We here present a set of fast and easy to use protocols for the target-specific immunomagnetic enrichment of receptor containing endosomes (receptosomes), plasma membranes, lysosomes and exosomes. Isolation of subcellular organelles and exosomes is prerequisite for and will advance their detailed subsequent biochemical and functional analysis. Sequential application of the different subprotocols allows isolation of morphological and functional intact organelles from one pool of cells. The enrichment is based on a selective labelling using receptor ligands or antibodies together with superparamagnetic microbeads followed by separation in a patented matrix-free high-gradient magnetic purification device. This unique magnetic chamber is based on a focusing system outside of the empty separation column, generating an up to 3 T high-gradient magnetic field focused at the wall of the column.

Settling the m6A debate: methylation of mature mRNA is not dynamic but accelerates turnover

This Outlook discusses the study published in this issue by Ke et al., which clarifies the role of N⁶-methyladenosine (m⁶A) in mRNA biogenesis and function and shows that m⁶A methylation levels negatively correlate with transcript half-life but are not required for most pre-mRNA splicing events.

Post-transcriptional modification of RNA nucleosides has been implicated as a pivotal regulator of mRNA biology. In this issue of Genes & Development, Ke and colleagues (pp. 990–1006) provide insights into the temporal and spatial distribution of N⁶-methyladenosine (m⁶A) in RNA transcripts by analyzing different subcellular fractions. Using a recently developed biochemical approach for detecting m⁶A, the researchers show that m⁶A methylations are enriched in exons and are added to transcripts prior to splicing. Although m⁶A addition is widely thought to be readily reversible, they demonstrate in HeLa cells that once RNA is released from chromatin, the modifications are surprisingly static. This study integrates data from previous publications to clarify conflicting conclusions regarding the role of m⁶A in mRNA biogenesis and function. Ke and colleagues found that m⁶A methylation levels negatively correlate with transcript half-life but are not required for most pre-mRNA splicing events.

m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover

Understanding the biologic role of N⁶-methyladenosine (m⁶A) RNA modifications in mRNA requires an understanding of when and where in the life of a pre-mRNA transcript the modifications are made. We found that HeLa cell chromatin-associated nascent pre-mRNA (CA-RNA) contains many unspliced introns and m⁶A in exons but very rarely in introns. The m⁶A methylation is essentially completed upon the release of mRNA into the nucleoplasm. Furthermore, the content and location of each m⁶A modification in steady-state cytoplasmic mRNA are largely indistinguishable from those in the newly synthesized CA-RNA or nucleoplasmic mRNA. This result suggests that quantitatively little methylation or demethylation occurs in cytoplasmic mRNA. In addition, only ∼10% of m⁶As in CA-RNA are within 50 nucleotides of 5' or 3' splice sites, and the vast majority of exons harboring m⁶A in wild-type mouse stem cells is spliced the same in cells lacking the major m⁶A methyltransferase Mettl3. Both HeLa and mouse embryonic stem cell mRNAs harboring m⁶As have shorter half-lives, and thousands of these mRNAs have increased half-lives (twofold or more) in Mettl3 knockout cells compared with wild type. In summary, m⁶A is added to exons before or soon after exon definition in nascent pre-mRNA, and while m⁶A is not required for most splicing, its addition in the nascent transcript is a determinant of cytoplasmic mRNA stability.

Intracellular PK/PD Relationships of Free and Liposomal Doxorubicin: Quantitative Analyses and PK/PD Modeling

Nanomedicines are widely studied for intracellular delivery of cancer drugs. However, the relationship between intracellular drug concentrations and drug responses are poorly understood. In this study, cellular and nuclear concentrations of doxorubicin were quantified with LC/MS after cell exposure with free and liposomal doxorubicin (pH-sensitive and pegylated liposomes). Cellular uptake of pegylated liposomes was low (∼3-fold extracellular concentrations) compared with doxorubicin in free form and pH-sensitive liposomes (up to 280-fold extracellular concentrations) in rat glioma (BT4C) and renal clear cell carcinoma (Caki-2) cells. However, after the cell exposure with pegylated liposomes, intracellular doxorubicin was distributed into the nuclear compartment in both cell types. Despite high drug concentrations in the nuclei, Caki-2 cells showed strong resistance toward doxorubicin. A model was successfully built to describe PK/PD relationship between drug concentrations in nucleus and cytotoxic responses in BT4C cells. This model is the first step to link target site concentration of doxorubicin into its effect and can be a useful part of more comprehensive future in vivo PK/PD models.

Nuclear localization and functional characteristics of voltage-gated potassium channel Kv1.3

It is widely known that ion channels are expressed in the plasma membrane. However, a few studies have suggested that several ion channels including voltage-gated K(+) (Kv) channels also exist in intracellular organelles where they are involved in the biochemical events associated with cell signaling. In the present study, Western blot analysis using fractionated protein clearly indicates that Kv1.3 channels are expressed in the nuclei of MCF7, A549, and SNU-484 cancer cells and human brain tissues. In addition, Kv1.3 is located in the plasma membrane and the nucleus of Jurkat T cells. Nuclear membrane hyperpolarization after treatment with margatoxin (MgTX), a specific blocker of Kv1.3 channels, provides evidence for functional channels at the nuclear membrane of A549 cells. MgTX-induced hyperpolarization is abolished in the nuclei of Kv1.3 silenced cells, and the effects of MgTX are dependent on the magnitude of the K(+) gradient across the nuclear membrane. Selective Kv1.3 blockers induce the phosphorylation of cAMP response element-binding protein (CREB) and c-Fos activation. Moreover, Kv1.3 is shown to form a complex with the upstream binding factor 1 in the nucleus. Chromatin immunoprecipitation assay reveals that Sp1 transcription factor is directly bound to the promoter region of the Kv1.3 gene, and the Sp1 regulates Kv1.3 expression in the nucleus of A549 cells. These results demonstrate that Kv1.3 channels are primarily localized in the nucleus of several types of cancer cells and human brain tissues where they are capable of regulating nuclear membrane potential and activation of transcription factors, such as phosphorylated CREB and c-Fos.

Constitutive expression of a COOH-terminal leucine mutant of lysosome-associated membrane protein-1 causes its exclusive localization in low density intracellular vesicles

Lysosome-associated membrane protein-1 (LAMP-1) is a type I transmembrane protein with a short cytoplasmic tail that possesses a lysosome-targeting signal of GYQTI(382)-COOH. Wild-type (WT)-LAMP-1 was exclusively localized in high density lysosomes, and efficiency of LAMP-1's transport to lysosomes depends on its COOH-terminal amino acid residue. Among many different COOH-terminal amino acid substitution mutants of LAMP-1, a leucine-substituted mutant (I382L) displays the most efficient targeting to late endosomes and lysosomes [Akasaki et al. (2010) J. Biochem. 148: , 669-679]. In this study, we generated two human hepatoma cell lines (HepG2 cell lines) that stably express WT-LAMP-1 and I382L, and compared their intracellular distributions. The subcellular fractionation study using Percoll density gradient centrifugation revealed that WT-LAMP-1 had preferential localization in the high density secondary lysosomes where endogenous human LAMP-1 was enriched. In contrast, a major portion of I382L was located in a low density fraction. The low density fraction also contained approximately 80% of endogenous human LAMP-1 and significant amounts of endogenous β-glucuronidase and LAMP-2, which probably represents occurrence of low density lysosomes in the I382L-expressing cells. Double immunofluorescence microscopic analyses distinguished I382L-containing intracellular vesicles from endogenous LAMP-1-containing lysosomes and early endosomes. Altogether, constitutive expression of I382L causes its aberrant intracellular localization and generation of low density lysosomes, indicating that the COOH-terminal isoleucine is critical for normal localization of LAMP-1 in the dense lysosomes.

Intracellular activation of gelatinase A (72-kDa type IV collagenase) by normal fibroblasts

Normal fibroblasts cultured as monolayers secrete matrix metalloproteinases (MMP), including gelatinase A (72-kDa type IV collagenase) as inactive zymogens. Previously we found that normal fibroblasts cultured in a type I collagen lattice (dermal equivalent) secrete active gelatinase A. Here we show that the activation of progelatinase A occurs within the cell and that the activator copurifies with Golgi membranes. Cell extracts of fibroblasts cultured in collagen lattices contain active 62-kDa gelatinase A at least 4-6 h before active enzyme is detected in the culture medium. Pulse-chase experiments confirm these results. The activator is membrane-bound and localizes to the Golgi-enriched fraction. Highly purified plasma membranes from lattice cultures are unable to convert gelatinase A from the zymogen to its active form. The activator may be a metalloproteinase because EDTA prevents activation of exogenous proenzyme by membrane fractions. Membrane-type MMP1, the enzyme thought to be responsible for activation of gelatinase A on the plasma membrane of tumor cells, shows no significant change in either mRNA or protein levels during lattice culture. Intracellular levels of gelatinase A mRNA and protein increase during the culture period, and tissue inhibitor of metalloproteinases concentration does not change. Because of the greater availability of tissue inhibitor of metalloproteinases-free proenzyme as a substrate for the activator, it is possible that membrane-type MMP1 is the activating enzyme. In that case, malignant transformation may involve a change in the localization of the activator to the plasma membrane.

In vivo delayed rejection of tumors and inhibition of delayed-type hypersensitivity by HT-29 human colonic adenocarcinoma cell line

Products secreted by HT-29 human colonic adenocarcinoma cells (DMEM-HT-29) mediated strong suppressive activity of in vitro lymphoproliferative responses to several mitogens. In vivo administration of DMEM-HT-29 both inhibited the afferent limb of delayed-type hypersensitivity against the Mc FiFi2(s) syngeneic fibrosarcoma and delayed the rejection of these tumor cells by immunized animals. Transfer experiments prior or after cell fractionation did not demonstrate suppressor cells induced by DMEM-HT-29. This suggests that DMEM-HT-29 produces its effect by directly interacting with macrophage and/or T cells at the sensitization stage of the antitumor immune response.

Regulation of herpesvirus macromolecular synthesis: nuclear retention of nontranslated viral RNA sequences

We report two instances of selective accumulation of herpes simplex 1 RNA transcripts in different compartments of infected HEp-2 cells. In the first, transcripts derived from about 50% of the viral DNA accumulated in the nuclei of cells 8 hr after infection. However, only 40-42% of the DNA was represented in transcripts accumulating in both cytoplasm and polyribosomes. A more striking disparity in the distribution of transcripts between nuclei and cytoplasm occurred when viral infection was initiated and maintained for several hours in the absence of protein synthesis. RNA complementary to about 50% of the viral DNA accumulated in the nuclei, while transcripts derived from only about 10% of the DNA were detectable in the cytoplasm. The transcripts that were selectively transported in the presence of cycloheximide seem to be functional messenger RNA molecules, since they were found on polysomes immediately after cycloheximide reversal. In contrast, RNA retained in the nuclei during the period of cycloheximide treatment was not mobilized when protein synthesis subsequently resumed. The two instances of selective RNA transport observed during herpesvirus infection suggest that only viral transcripts competent to function in translation are exported from the nucleus.

Immunological functions of lymphocytes fractionated with antigen-derivatized fibers

Specific antigen-binding cells from spleens of immune and nonimmune mice were isolated by the method of fiber fractionation. After removal from the fibers, these cells were assayed for their viability, their ability to rebind to fibers of the same specificity, and their in vivo response to the antigen after transfer to syngeneic irradiated recipients. These experiments indicate that the fiber method yields highly enriched populations of specific antigen-binding cells that are viable and include antigen-sensitive bone marrow-derived cells capable of undergoing mitosis and differentiating into antibody-secreting cells.

Specific fractionation of immune cell populations

Antigen-binding cells from spleens of immune and nonimmune mice were isolated by the method of fiber fractionation. Binding of the lymphoid cells to derivatives of nylon fibers made with various antigens was prevented by the presence of the respective free antigen, as well as by antibodies to mouse immunoglobulins. Antigen-binding cells specific for dinitrophenyl groups were separated from direct and indirect plaque-forming cells of the same specificity. Spleen cells from immune and nonimmune animals were fractionated according to their relative affinities for antigen, and the percentage of antigen-binding cells in the spleens of nonimmune animals was estimated. A comparison of the numbers and relative affinities of immunoglobulin receptors of immune and nonimmune populations indicated that after immunization only those antigen-binding cells of higher affinities were increased in number. This finding suggests that the specificity of clonal selection depends not only upon the binding of antigen to a lymphoid cell but also upon the capacity of that cell to be triggered to mature and replicate.

Temperature-dependent intracellular distribution of thyroxine in amphibian liver

Rana catesbeiana tadpoles were injected with [(14)C]thyroxine, and the subcellular distribution of the labeled hormone was determined. At 25 degrees the amount of isotope found in the liver was maximal after 1-2 hr and then rapidly decreased to a relatively constant value. A large percentage of the hormone was found associated with the purified nuclei isolated 24 hr after injection of [(14)C]thyroxine. Injection of [(14)C]thyroxine into tadpoles maintained at 5 degrees resulted in a much slower but constant accumulation of isotope in the liver, with virtually no movement of thyroxine into the cell nucleus. Thyroxine was bound very tightly to the chromatin fraction of the nucleus, but extraction and chromatography revealed no chemical modification of the thyroxine itself. These results suggest the presence of two temperature-dependent processes: one concerned with the transport of thyroxine into the liver cell and a second concerned with the transport of the intracellular thyroxine into the cell nucleus. It is proposed that the latter process is involved in the low-temperature inhibition of thyroxine-induced metamorphosis.