Inside Mammalian Cells Research Articles

G-quadruplexes in the mitochondrial genome - a cause for instability.

Accumulation of mutations such as deletions in mitochondrial DNA is associated with ageing, cancer and human genetic disorders. These deletions are often flanked by GC-skewed sequence motifs that can potentially fold into secondary non-B DNA conformations. G-quadruplexes are emerging as key initiators of mitochondrial genomic instability. In this issue, Dahal etal provide an insilico analysis of sequence motifs that can fold into altered DNA structures in mitochondrial genomic regions that contain frequent deletions. They show the formation of five G-quadruplexes near such frequent breakpoints using biochemical and biophysical approaches invitro and more importantly inside mammalian cells. Comment on: https://doi.org/10.1111/febs.16113.

Analysis of In Vivo Transcriptome of Intracellular Bacterial Pathogen Salmonella enterica serovar Typhmurium Isolated from Mouse Spleen.

Salmonella enterica serovar Typhimurium (S. Typhimurium) is an important intracellular pathogen that poses a health threat to humans. This study tries to clarify the mechanism of Salmonella survival and reproduction in the host. In this study, high-throughput sequencing analysis was performed on RNA extracted from the strains isolated from infected mouse spleens and an S. Typhimurium reference strain (ATCC 14028) based on the BGISEQ-500 platform. A total of 1340 significant differentially expressed genes (DEGs) were screened. Functional annotation revealed DEGs associated with regulation, metabolism, transport and binding, pathogenesis, and motility. Through data mining and literature retrieval, 26 of the 58 upregulated DEGs (FPKM > 10) were not reported to be related to the adaptation to intracellular survival and were classified as candidate key genes (CKGs) for survival and proliferation in vivo. Our data contribute to our understanding of the mechanisms used by Salmonella to regulate virulence gene expression whilst replicating inside mammalian cells.

Naphthalimide based fluorescent organic nanoparticles in selective sensing of Fe3+ and as a diagnostic probe for Fe2+/Fe3+ transition.

Fluorescent organic nanoparticles (FONPs) have attracted considerable attention as a practical and effective platform for sensing and imaging applications. The present article delineates the fabrication of FONPs derived from the naphthalimide based histidine appended amphiphile, NID. The self-assembly of NID in 99 vol% water in DMSO led to the formation of FONPs through J-type aggregation. Aggregation-induced emission (AIE) was observed due to the pre-associated excimer of NID with bluish green emission at 470 nm along with intramolecular charge transfer (ICT). The emission of NID FONPs was utilized for selective sensing of Fe3+ and bioimaging of Fe3+ inside mammalian cells. The fluorescence intensity of the FONPs was quenched with the gradual addition of Fe3+ due to the formation of a 1 : 1 stoichiometric complex with the histidine residue of NID. The morphology of the FONPs transformed from spherical to spindle upon the complex formation of NID with Fe3+. The limit of detection (LOD) of this AIE based turn-off chemosensor for Fe3+ was found to be 12.5 ± 1.2 μM having high selectivity over other metal ions. On the basis of the very low cytotoxicity and selective sensing of Fe3+, NID FONPs were successfully employed for bioimaging of Fe3+ ions through fluorescence quenching within mammalian cells (NIH3T3, B16F10). Considering the varying oxidative stress inside different cells, NID FONPs were used for detecting Fe2+ to Fe3+ redox state transition selectively inside cancer cells (B16F10) in comparison to non-cancerous cells (NIH3T3). Selective sensing of cancer cells was substantiated by co-culture experiment and flow cytometry. Hence, NID FONPs can be a selective diagnostic probe for cancer cells owing to their higher H2O2 content.

Graphene Quantum Dots As Intracellular Imaging-Based Temperature Sensors

Non-invasive temperature sensing is necessary for the analysis of biological processes occurring in the human body including cellular enzyme activity, protein expression, and ion regulation. Considering that a variety of such biological processes occur at the microscopic scale, a novel mechanism allowing for the detection of the temperature changes in microscopic environments is desired. One-dimensional graphene quantum dots can serve as agents for such detection: they are promising non-invasive probes that because of their 2-5 nm size and optical sensitivity to temperature change enable sub-cellular resolution imaging. Both biocompatible bottom-up synthesized nitrogen-doped graphene quantum dots and quantum dots produced from reduced graphene oxide via top-down approach exhibit temperature-induced fluorescence variations. This response observed for the first time is utilized for deterministic temperature sensing in bulk suspension as well as inside mammalian cells. Distinctive quenching of quantum dot fluorescence by up to 19.8% is observed, in a temperature range from 25℃ to 49℃, in aqueous solution, while the intensity is restored to the original values as the temperature decreases back to 25℃. A similar trend is observed in vitro in HeLa cells as the cellular temperature is increased from 25℃ to 41℃. Our findings suggest that the temperature-dependent fluorescence quenching of bottom-up and top-down-synthesized graphene quantum dots can serve as a non-invasive, reversible, and deterministic mechanism for temperature sensing in microscopic sub-cellular biological environments.

Engineering a Magnetic Protein Crystal

Magnetogenetics is a new field that leverages genetically encoded proteins and protein assemblies that are sensitive to magnetic fields to study and manipulate cell behavior. Theoretical studies show that many proposed magnetogenetic proteins do not contain enough iron to generate substantial magnetic forces. Here, we have engineered a genetically encoded ferritin-containing protein crystal that grows inside mammalian cells. Each of these crystals contains more than 10 million ferritin subunits and is capable of mineralizing substantial amounts of iron. When isolated from cells and loaded with iron in vitro, these crystals generate magnetic forces that are 9 orders of magnitude larger than the forces from the single ferritin cages used in previous studies. These protein crystals are attracted to an applied magnetic field and move toward magnets even when internalized into cells. While additional studies are needed to realize the full potential of magnetogenetics, these results demonstrate the feasibility of engineering protein assemblies for magnetic sensing.

Engineering a Genetically Encoded Magnetic Protein Crystal.

Magnetogenetics is a new field that leverages genetically encoded proteins and protein assemblies that are sensitive to magnetic fields to study and manipulate cell behavior. Theoretical studies show that many proposed magnetogenetic proteins do not contain enough iron to generate substantial magnetic forces. Here, we have engineered a genetically encoded ferritin-containing protein crystal that grows inside mammalian cells. Each of these crystals contains more than 10 million ferritin subunits and is capable of mineralizing substantial amounts of iron. When isolated from cells and loaded with iron in vitro, these crystals generate magnetic forces that are 9 orders of magnitude larger than the forces fromthe single ferritin cages used in previous studies. These protein crystals are attracted to an applied magnetic field and move toward magnets even when internalized into cells. While additional studies are needed to realize the full potential of magnetogenetics, these results demonstrate the feasibility of engineering protein assemblies for magnetic sensing.

DNP-Supported Solid-State NMR Spectroscopy of Proteins Inside Mammalian Cells.

Elucidating at atomic level how proteins interact and are chemically modified in cells represents a leading frontier in structural biology. We have developed a tailored solid‐state NMR spectroscopic approach that allows studying protein structure inside human cells at atomic level under high‐sensitivity dynamic nuclear polarization (DNP) conditions. We demonstrate the method using ubiquitin (Ub), which is critically involved in cellular functioning. Our results pave the way for structural studies of larger proteins or protein complexes inside human cells, which have remained elusive to in‐cell solution‐state NMR spectroscopy due to molecular size limitations.

DNP‐Supported Solid‐State NMR Spectroscopy of Proteins Inside Mammalian Cells

AbstractElucidating at atomic level how proteins interact and are chemically modified in cells represents a leading frontier in structural biology. We have developed a tailored solid‐state NMR spectroscopic approach that allows studying protein structure inside human cells at atomic level under high‐sensitivity dynamic nuclear polarization (DNP) conditions. We demonstrate the method using ubiquitin (Ub), which is critically involved in cellular functioning. Our results pave the way for structural studies of larger proteins or protein complexes inside human cells, which have remained elusive to in‐cell solution‐state NMR spectroscopy due to molecular size limitations.

Host Cytosolic Glutathione Sensing by a Membrane Histidine Kinase Activates the Type VI Secretion System in an Intracellular Bacterium.

Type VI secretion systems (T6SSs) are major virulence mechanisms in many Gram-negative bacteria, but the physiological signals that activate them are not well understood. The T6SS1 of Burkholderia pseudomallei is essential for pathogenesis in mammalian hosts and is only expressed when the bacterium is intracellular. We found that signals for T6SS1 activation reside in the host cytosol. Through site-directed mutagenesis and biochemical studies, we identified low molecular weight thiols, particularly glutathione, as the signal sensed by a periplasmic cysteine residue (C62) on the histidine kinase sensor VirA. Upon glutathione exposure, dimeric VirA is converted to monomers via reduction at C62. When glutathione in the host was depleted, T6SS1 expression was abrogated, and bacteria could no longer induce multinucleate giant cell formation, the hallmark of T6SS1 function. Therefore, intracellular bacteria exploit the abundance of glutathione in host cytosol as a signal for expression of virulence at the appropriate time and place.

Two-Photon Fluorescence Imaging of Single Fluorescent Proteins Inside Mammalian Cells

Exciting progress has been made recently in biophysical techniques that allow optical imaging of single molecules in live cells. However, imaging of single fluorescent proteins in live cells is usually limited to bacteria that are small in size or proteins that are on the cell surface, where excitation through total internal reflection can be used to reduce fluorescence background and achieve single-molecule sensitivity. Eukaryotic cells are typically larger in size with higher autofluorescence background. To achieve single-molecule sensitivity deep inside a eukaryotic cell is thus challenging. We have used two-photon fluorescence excited by infrared lasers to reduce autofluorescence background. We show that single green fluorescent proteins can be imaged deep inside a mammalian cell using two-photon fluorescence. Discrete stepwise photobleaching of enhanced green fluorescent proteins was observed. The single-molecule fluorescence intensity analysis and on-time distribution indicate that two-photon fluorescence is detectable at the single-molecule level deep inside a eukaryotic cell. Moreover, it is not necessary to use a pulsed laser for two-photon fluorescence excitation. A continuous-wave laser that is routinely used for optical tweezers can be used to excite two-photon fluorescence and achieve single-molecule sensitivity. These advantages could significantly benefit future application of this single-molecule technique in biological studies. We present applications of our technique, and demonstrate two-photon fluorescence imaging of eukaryotic cells at single-molecule level.

Expression of antibodies using single‐open reading frame vector design and polyprotein processing from mammalian cells

We describe a novel polyprotein precursor-based approach to express antibodies from mammalian cells. Rather than expressing heavy and light chain proteins from separate expression units, the antibody heavy and light chains are contained in one single-open reading frame (sORF) separated by an intein gene fused in frame. Inside mammalian cells this ORF is transcribed into a single mRNA, and translated into one polypeptide. The antibody heavy and light chains are separated posttranslationally, assembled into the functional antibody molecule, and secreted into culture medium. It is demonstrated that Pol I intein from P. horikoshii mediates protein splicing and cleavage reactions in mammalian cells, in the context of antibody heavy and light chain amino acid sequences. To allow the separation of antibody heavy chain, light chain, and the intein, we investigated a number of intein mutations designed to inhibit intein-mediated splicing but preserve cleavage reactions. We have also designed constructs in which the signal peptide downstream from intein has altered hydrophobicity. The use of some of these mutant constructs resulted in more efficient antibody secretion, highlighting areas that can be further explored in improving such an expression system. An antibody secreted using one of the sORF constructs was characterized. This antibody has correct N-terminal sequences for both of its heavy and light chains, correct heavy and light chain MW as well as intact MW as measured by mass spectrometry. Its affinity to antigen, as measured by surface plasmon resonance (SPR), is indistinguishable from that of the same antibody produced using conventional method.

Mechanism of therapeutic effectiveness of cefixime against typhoid fever.

beta-Lactams have been considered ineffective against organisms growing inside mammalian cells because of their poor penetration into cells. However, cefixime has been shown to be clinically effective against typhoid fever. The probable mechanism of therapeutic effectiveness of cefixime against typhoid fever was investigated using Salmonella enterica serovar Typhimurium instead of S. enterica serovar Typhi both in a cellular and in a mouse infection model. Cefixime was able to inhibit the growth of serovar Typhimurium inhabiting monocyte-derived THP-1 cells. Elongation of serovar Typhimurium in THP-1 cells was observed microscopically. Apparent morphological changes of serovar Typhimurium in THP-1 cells were also observed by electron microscopy. The concentration of cefixime inside THP-1 cells was almost half (46 to 48%) of the concentration outside the cells when serovar Typhimurium coexisted in the solution. The length of time after oral dosing (8 mg/kg) that cefixime was present-calculated from levels in serum-at a concentration above the MIC at which 90% of the serovar Typhi organisms inside human cells were inhibited was presumed to be more than 12 h. Cefixime also showed excellent activity in the mouse systemic and oral infection models based on infections caused by serovar Typhimurium. It is concluded that a fair amount of cefixime can enter mammalian cells and inhibit the growth of bacteria inside cells when the bacteria are sensitive enough to cefixime, as are serovars Typhimurium and Typhi.