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Chimia 2016Artificial organelles, molecular factories and nanoreactors are membrane-bound systems envisaged to exhibit cell-like functionality. These constitute liposomes,... (Review)
Review
Artificial organelles, molecular factories and nanoreactors are membrane-bound systems envisaged to exhibit cell-like functionality. These constitute liposomes, polymersomes or hybrid lipo-polymersomes that display different membrane-spanning channels and/or enclose molecular modules. To achieve more complex functionality, an artificial organelle should ideally sustain a continuous influx of essential macromolecular modules (i.e. cargoes) and metabolites against an outflow of reaction products. This would benefit from the incorporation of selective nanopores as well as specific trafficking factors that facilitate cargo selectivity, translocation efficiency, and directionality. Towards this goal, we describe how proteinaceous cargoes are transported between the nucleus and cytoplasm by nuclear pore complexes and the biological trafficking machinery in living cells (i.e. nucleocytoplasmic transport). On this basis, we discuss how biomimetic control may be implemented to selectively import, compartmentalize and accumulate diverse macromolecular modules against concentration gradients in artificial organelles.
Topics: Biological Transport; Cell Nucleus; Cytoplasm
PubMed: 27363369
DOI: 10.2533/chimia.2016.413 -
Frontiers in Cellular and Infection... 2016Intracellular bacterial pathogens replicate within eukaryotic cells and display unique adaptations that support key infection events including invasion, replication,... (Review)
Review
Intracellular bacterial pathogens replicate within eukaryotic cells and display unique adaptations that support key infection events including invasion, replication, immune evasion, and dissemination. From invasion to dissemination, all stages of the intracellular bacterial life cycle share the same three-dimensional cytosolic space containing the host cytoskeleton. For successful infection and replication, many pathogens hijack the cytoskeleton using effector proteins introduced into the host cytosol by specialized secretion systems. A subset of effectors contains eukaryotic-like motifs that mimic host proteins to exploit signaling and modify specific cytoskeletal components such as actin and microtubules. Cytoskeletal rearrangement promotes numerous events that are beneficial to the pathogen, including internalization of bacteria, structural support for bacteria-containing vacuoles, altered vesicular trafficking, actin-dependent bacterial movement, and pathogen dissemination. This review highlights a diverse group of obligate intracellular bacterial pathogens that manipulate the host cytoskeleton to thrive within eukaryotic cells and discusses underlying molecular mechanisms that promote these dynamic host-pathogen interactions.
Topics: Actin Cytoskeleton; Bacteria; Bacterial Proteins; Cytoplasm; Eukaryotic Cells; Host-Pathogen Interactions; Microtubules; Protein Transport; Vacuoles
PubMed: 27713866
DOI: 10.3389/fcimb.2016.00107 -
Autophagy Apr 2011
Topics: Autophagy; Cell Membrane; Cytoplasm; Databases, Bibliographic; Models, Biological; Phagosomes
PubMed: 21258205
DOI: 10.4161/auto.7.4.14730 -
Journal of Molecular Biology Nov 2018Phase transitions that alter the physical state of ribonucleoprotein particles contribute to the spacial and temporal organization of the densely packed intracellular... (Review)
Review
Phase transitions that alter the physical state of ribonucleoprotein particles contribute to the spacial and temporal organization of the densely packed intracellular environment. This allows cells to organize biologically coupled processes as well as respond to environmental stimuli. RNA plays a key role in phase separation events that modulate various aspects of RNA metabolism. Here, we review the role that RNA plays in ribonucleoprotein phase separations.
Topics: Animals; Cytoplasm; Humans; Organelles; Phase Transition; RNA; Ribonucleoproteins
PubMed: 29753780
DOI: 10.1016/j.jmb.2018.05.003 -
The Journal of Cell Biology Sep 1993
Review
Topics: Animals; Cell Nucleus; Cytoplasm; Humans; Nuclear Envelope
PubMed: 8354697
DOI: 10.1083/jcb.122.5.977 -
American Journal of Physiology. Cell... Jun 2010Present-day cellular systems biology is producing data on an unprecedented scale. This field has generated a renewed interest in the holistic, "system" character of cell... (Review)
Review
Present-day cellular systems biology is producing data on an unprecedented scale. This field has generated a renewed interest in the holistic, "system" character of cell structure-and-function. Underlying the data deluge, however, there is a clear and present need for a historical foundation. The origin of the "system" view of the cell dates to the birth of the protoplasm concept. The 150-year history of the role of "protoplasm" in cell biology is traced. It is found that the "protoplasmic theory," not the "cell theory," was the key 19th-century construct that drove the study of the structure-and-function of living cells and set the course for the development of modern cell biology. The evolution of the "protoplasm" picture into the 20th century is examined by looking at controversial issues along the way and culminating in the current views on the role of cytological organization in cellular activities. The relevance of the "protoplasmic theory" to 21st-century cellular systems biology is considered.
Topics: Animals; Biomedical Research; Cell Physiological Phenomena; Cytoplasm; Cytoskeleton; History, 19th Century; History, 20th Century; History, 21st Century; Humans; Models, Biological; Systems Biology; Terminology as Topic; Water
PubMed: 20200206
DOI: 10.1152/ajpcell.00016.2010 -
PLoS Genetics Aug 2022In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject...
In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, resulting in daily fluctuations of RNA accumulation and affecting the distribution of transcripts in different subcellular compartments. Our study analysed the nuclear and cytoplasmic, poly(A) and total transcriptomes of mouse livers collected over the course of a day. These data provide a genome-wide temporal inventory of enrichment in subcellular RNA, and revealed specific signatures of splicing, nuclear export and cytoplasmic mRNA stability related to transcript and gene lengths. Combined with a mathematical model describing rhythmic RNA profiles, we could test the rhythmicity of export rates and cytoplasmic degradation rates of approximately 1400 genes. With nuclear export times usually much shorter than cytoplasmic half-lives, we found that nuclear export contributes to the modulation and generation of rhythmic profiles of 10% of the cycling nuclear mRNAs. This study contributes to a better understanding of the dynamic regulation of the transcriptome during the day-night cycle.
Topics: Animals; Cell Nucleus; Cytoplasm; Liver; Mice; RNA; Transcriptome
PubMed: 35921362
DOI: 10.1371/journal.pgen.1009903 -
Postepy Higieny I Medycyny... Nov 2012Autophagy is a catabolic process involving the degradation of long-lived proteins and organelles through the lysosomal machinery. In eukaryotic cells, among the three... (Review)
Review
Autophagy is a catabolic process involving the degradation of long-lived proteins and organelles through the lysosomal machinery. In eukaryotic cells, among the three types of autophagy the most extensively studied is macroautophagy. Macroautophagy (hereafter referred to as autophagy) is characterized by sequestration of bulk cytoplasm in double-membrane vesicles, called autophagosomes, which ultimately fuse with lysosomes, resulting in degradation of their contents. Autophagy is responsible for the maintenance of intracellular homeostasis and enables cell survival under stress conditions. However, this process is also involved in the pathogenesis of diverse diseases, including cancers. In the cancer cell, autophagy plays a dual role, as a mechanism responsible for protecting or killing the cell. In most cases chemotherapy-induced autophagy in tumor cells is a prosurvival response which potentially leads to development of drug resistance. However, autophagy can also lead to cell death, thus enhancing treatment efficacy. It is important for the anticancer therapy to find the type of cancer cells which are susceptible to autophagy and to determine whether the autophagy induced by the applied therapy leads to cells' death or their survival and subsequently to therapy resistance. In this review, the molecular mechanism of macroautophagy and the most important signaling transduction pathways involved in regulation of this process in cancer cells are presented. The dual function of autophagy in tumorigenesis and the implications of autophagy modulation for cancer therapy are also discussed.
Topics: Apoptosis; Autophagy; Cell Death; Cell Survival; Cytoplasm; Eukaryotic Cells; Humans; Lysosomes; Neoplasms; Organelles; Signal Transduction
PubMed: 23175348
DOI: 10.5604/17322693.1021109 -
Current Biology : CB May 2012The critical importance of controlling the size and number of intracellular organelles has led to a variety of mechanisms for regulating the formation and growth of... (Review)
Review
The critical importance of controlling the size and number of intracellular organelles has led to a variety of mechanisms for regulating the formation and growth of cellular structures. In this review, we explore a class of mechanisms for organelle growth control that rely primarily on the cytoplasm as a 'limiting pool' of available material. These mechanisms are based on the idea that, as organelles grow, they incorporate subunits from the cytoplasm. If this subunit pool is limited, organelle growth will lead to depletion of subunits from the cytoplasm. Free subunit concentration therefore provides a measure of the number of incorporated subunits and thus the current size of the organelle. Because organelle growth rates are typically a function of subunit concentration, cytoplasmic depletion links organelle size, free subunit concentration, and growth rates, ensuring that as the organelle grows, its rate of growth slows. Thus, a limiting cytoplasmic pool provides a powerful mechanism for size-dependent regulation of growth without recourse to active mechanisms to measure size or modulate growth rates. Variations of this general idea allow not only for size control, but also cell-size-dependent scaling of cellular structures, coordination of growth between similar structures within a cell, and the enforcement of singularity in structure formation, when only a single copy of a structure is desired. Here, we review several examples of such mechanisms in cellular processes as diverse as centriole duplication, centrosome and nuclear size control, cell polarity, and growth of flagella.
Topics: Cytoplasm; Organelles
PubMed: 22575475
DOI: 10.1016/j.cub.2012.03.046 -
Chemical Reviews Feb 2024Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with... (Review)
Review
Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.
Topics: Phase Separation; Macromolecular Substances; Cytoplasm; Bacteria; Homeostasis
PubMed: 38331392
DOI: 10.1021/acs.chemrev.3c00622