On the biophysical mechanism of the circum-hour cell rhythm and its role in metabolism

The universal biophysical mechanism of "circum-hour" oscillations of parameters and properties of various cells and their organelles was considered. The mechanism is the result of nonspecific responses of cells to any damaging agents. At the basis of the "circum-hour" mechanism is the earlier reported inverse dependence of the activity of enzymes on the concentration of low-molecular weight organic substances in medium. The universal character of "circum-hour" oscillations and their probable relationship with the acceleration of metabolism was shown using automatic scanning analyzers of microobjects on numerous objects: cells, cell organelles and compartments.     

Directed import of macromolecules into mitochondria

Mitochondria are multifunctional organelles of eukaryotic cells that provide the energy for the cells by oxidative phosphorylation, play an important role in the apoptosis and take part in Fe-S clusters formation, fatty acids oxidation and synthesis of some aminoacids. They contain their own genome and are able to transcribe and to translate it. However, the vast majority of the macromolecules which function inside the mitochondria are imported into these organelles from the cytoplasm. The imported macromolecules include proteins and several types of small RNAs. Protein import is a universal process and its mechanism is conserved among all species. This mechanism is now known in detail. RNA import was shown to occur in several groups of eukaryotes, while the pool of imported RNA molecules varies in different organisms. Although the knowledge about the mechanisms of RNA import is less extensive than for the proteins, it becomes clear that these mechanisms are not universal among all the species possessing this pathway. In this review, we summarize the data about the import of macromolecules mentioned above into mitochondria.     

Sustained simultaneous glycolytic and insulin oscillations in beta-cells

Chemical oscillation in glycolysis induced by glucose is an universal feature in all living cells. In beta-cells this is accompanied by sustained oscillations of concentration of insulin, which helps to keep the blood glucose level within optimum limits. Experiments in this regard had shown that the glycolytic and insulin oscillations are almost consistently in phase and their time periods are very close to each other at both high and low initial concentration of glucose. Experiments have also demonstrated the dynamical transition between the states of glycolytic oscillations indicating a saturation behaviour of glucose transporters at a higher glucose flow rate. We propose a phenomenological model to understand these simultaneous oscillations and how glycolysis provides a mechanism for pulsatory insulin secretion in the light of these basic experimental issues.     

Organellar peptide deformylases: universality of the N-terminal methionine cleavage mechanism

Most mature proteins do not retain their initial N-terminal amino acid (methionine in the cytosol and N-formyl methionine in the organelles). Recent studies have shown that dedicated machinery is involved in this process in plants. In addition to cytosolic and organelle-targeted methionine aminopeptidases, organellar peptide deformylases have been identified. Here, we attempt to answer questions about the mechanism, specificity and significance of N-terminal methionine cleavage in plant organelles. It seems to be universal because orthologues of plant deformylases are found in most living organisms.     

STIM1 and STIM2 are located in the acidic Ca2+ stores and associates with Orai1 upon depletion of the acidic stores in human platelets

Mammalian cells accumulate Ca2+ into agonist-sensitive acidic organelles, vesicles that possess a vacuolar proton-ATPase. Acidic Ca2+ stores include secretory granules and lysosome-related organelles. Current evidence clearly indicates that acidic Ca2+ stores participate in cell signaling and function, including the activation of store-operated Ca2+ entry in human platelets upon depletion of the acidic stores, although the mechanism underlying the activation of store-operated Ca2+ entry controlled by the acidic stores remains unclear. STIM1 has been presented as the endoplasmic reticulum Ca2+ sensor, but its role sensing intraluminal Ca2+ concentration in the acidic stores has not been investigated. Here we report that STIM1 and STIM2 are expressed in the lysosome-related organelles and dense granules in human platelets isolated by immunomagnetic sorting. Depletion of the acidic Ca2+ stores using the specific vacuolar proton-ATPase inhibitor, bafilomycin A1, enhanced the association between STIM1 and STIM2 as well as between these proteins and the plasma membrane channel Orai1. Depletion of the acidic Ca2+ stores also induces time-dependent co-immunoprecipitation of STIM1 with the TRPC proteins hTRPC1 and hTRPC6, as well as between Orai1 and both TRPC proteins. In addition, bafilomycin A1 enhanced the association between STIM2 and SERCA3. These findings demonstrate the location of STIM1 and STIM2 in the acidic Ca2+ stores and their association with Ca2+ channels and ATPases upon acidic stores discharge.     

Delayed Feedback Model of Axonal Length Sensing

A fundamental question in cell biology is how the sizes of cells and organelles are regulated at various stages of development. Size homeostasis is particularly challenging for neurons, whose axons can extend from hundreds of microns to meters (in humans). Recently, a molecular-motor-based mechanism for axonal length sensing has been proposed, in which axonal length is encoded by the frequency of an oscillating retrograde signal. In this article, we develop a mathematical model of this length-sensing mechanism in which advection-diffusion equations for bidirectional motor transport are coupled to a chemical signaling network. We show that chemical oscillations emerge due to delayed negative feedback via a Hopf bifurcation, resulting in a frequency that is a monotonically decreasing function of axonal length. Knockdown of either kinesin or dynein causes an increase in the oscillation frequency, suggesting that the length-sensing mechanism would produce longer axons, which is consistent with experimental findings. One major prediction of the model is that fluctuations in the transport of molecular motors lead to a reduction in the reliability of the frequency-encoding mechanism for long axons.     

Cytoplasmic streaming in plants

Plant cells are surrounded by a cell wall composed of polysaccharides and hence can change neither their form nor their position. However, active movement of organelles (cytoplasmic streaming or protoplasmic streaming) is observed in plant cells, and involvement of the actin/myosin system in these processes has been suggested. Successful biochemical and biophysical approaches to studying myosins have extensively promoted the understanding of the molecular mechanism underlying these phenomena.     

MLN64 is involved in actin-mediated dynamics of late endocytic organelles

MLN64 is a late endosomal cholesterol-binding membrane protein of an unknown function. Here, we show that MLN64 depletion results in the dispersion of late endocytic organelles to the cell periphery similarly as upon pharmacological actin disruption. The dispersed organelles in MLN64 knockdown cells exhibited decreased association with actin and the Arp2/3 complex subunit p34-Arc. MLN64 depletion was accompanied by impaired fusion of late endocytic organelles and delayed cargo degradation. MLN64 overexpression increased the number of actin and p34-Arc-positive patches on late endosomes, enhanced the fusion of late endocytic organelles in an actin-dependent manner, and stimulated the deposition of sterol in late endosomes harboring the protein. Overexpression of wild-type MLN64 was capable of rescuing the endosome dispersion in MLN64-depleted cells, whereas mutants of MLN64 defective in cholesterol binding were not, suggesting a functional connection between MLN64-mediated sterol transfer and actin-dependent late endosome dynamics. We propose that local sterol enrichment by MLN64 in the late endosomal membranes facilitates their association with actin, thereby governing actin-dependent fusion and degradative activity of late endocytic organelles.     

Plant coated vesicles

Abstract. Coated vesicles are organelles frequently encountered in many plant cell types often in association with the plasma membrane, Golgi apparatus, partially coated reticulum and multivesicular bodies. They are readily identified by a characteristic cage or basket composed of interlocking triskelions of the protein clathrin which are bound to the surface of the vesicle membrane. Although their transport function has been well studied and characterized in mammalian systems, the possible importance of coated vesicles as transport organelles in plant cells is only just beginning to be explored. In this review, the authors describe the structure of higher plant coated vesicles and discuss their possible involvement in the endocytosis of marcromolecules, in exocytosis and in the intracellular transport of material between cytoplasmic compartments. Their possible role in maintaining the macromolecular composition of the plasma membrane whilst allowing recycling of excess lipid bilayer and their potential application as vehicles for the introduction of foreign macromolecules into plant cells are discussed.     

Stability of the saccadic oculomotor system

A variety of different types of instability has been found in the saccadic system of humans. Some of the instabilities correspond to clinical conditions, whereas others are inherent in the normal saccadic system. How can these instabilities arise within the mechanism of normal saccadic eye movements? A physiologically-based model of the saccadic system predicts that horizontal saccadic oscillations will occur with excessive mutual inhibition between the left and right burst cells and with underaction of the pause cells. The amplitudes and frequencies of the oscillations had ranges of 0–6° and 6–20 cycles per second, respectively. Application of stability analysis techniques to the model reveals that development of the oscillations can be explained by the Hopf bifurcation mechanism. Future development of this approach will involve classifying pathological instabilities of the saccadic system according to the bifurcation involved in their generation.     

Directed import of macromolecules into mitochondria

Mitochondria are multifunctional eukaryotic organelles that provide cells with energy via oxidative phosphorylation. They participate in the formation of Fe-S clusters, oxidation of fatty acids, and synthesis of certain amino acids and play an important role in apoptosis. Mitochondria have their own genome and are able to transcribe and translate it. However, most macromolecules functioning in mitochondria, such as proteins and some small RNAs, are imported from the cytoplasm. Protein import into mitochondria is a universal process, and its mechanism is very similar in all eukaryotic cells. Today this mechanism is known in detail. At the same time, the RNA import was discovered only in several eukaryotic groups. Nevertheless, it is proposed that this process is typical for most species. A set of imported RNA molecules varies in different organisms. Although the knowledge about the mechanisms of RNA import is less extensive than that of protein import, it becomes clear that these mechanisms greatly differ between different species. The review summarizes information about the import of such macromolecules into mitochondria.     

Alternative splicing modulates the frequency-dependent response of CaMKII to Ca(2+) oscillations

Ca(2+) oscillations are required in various signal trans duction pathways, and contain information both in their amplitude and frequency. Remarkably, the Ca(2+)/calmodulin(CaM)-dependent protein kinase II (CaMKII) can decode such frequencies. A Ca(2+)/CaM-stimulated autophosphorylation leads to Ca(2+)/CaM-independent (autonomous) activity of the kinase that outlasts the initial stimulation. This autonomous activity increases exponentially with the frequency of Ca(2+) oscillations. Here we show that three beta-CaMKII splice variants (beta(M), beta and beta(e)') have very similar specific activity and maximal autonomy. However, their autonomy generated by Ca(2+) oscillations differs significantly. A mechanistic basis was found in alterations of the CaM activation constant and of the initial rate of autophosphorylation. Structurally, the splice variants differ only in a variable 'linker' region between the kinase and association domains. Therefore, we propose that differences in relative positioning of kinase domains within multimeric holoenzymes are responsible for the observed effects. Notably, the beta-CaMKII splice variants are differentially expressed, even among individual hippocampal neurons. Taken together, our results suggest that alternative splicing provides cells with a mechanism to modulate their sensitivity to Ca(2+) oscillations.     

Biophysical basis for principles of universality of speech perception

There is increasing evidence that the synergistic interaction of the objectively accepted low-frequency rhythm and the subjectively accepted high-frequency sound is a source of speech "sense". The lack of one of these components or of their synergistic interaction results in the loss of "sense" of the acoustic signal being perceived. As for the universality of perception of the sound component of speech, there is a model of sound perception, which ensures this universality. This model describes the dynamics of audition using the synchronization model of oscillations in the Ruell-Takens scenario of transition to chaos. The oscillations are described by Hopf bifurcations known to be structurally stable, which just provides the universality of sound perception. However, up till now, nothing was known about the mechanism of rhythm. It was shown in our study that the mechanism of rhythm is described by the Feigenbaum scenario of transition to chaos. Upon transition from oscillations to chaos, this scenario incorporates a critical point near which the dynamics of the system is described in an universal way.     

Direct Targeting of Proteins from the Cytosol to Organelles: The ER versus Endosymbiotic Organelles

In eukaryotic cells consisting of many different types of organelles, targeting of organellar proteins is one of the most fundamental cellular processes. Proteins belonging to the endoplasmic reticulum (ER), chloroplasts and mitochondria are targeted individually from the cytosol to their cognate organelles. As the targeting to these organelles occurs in the cytosol during or after translation, the most crucial aspect is how specific targeting to these three organelles can be achieved without interfering with other targeting pathways. For these organelles, multiple mechanisms are used for targeting proteins, but the exact mechanism used depends on the type of protein and organelle, the location of targeting signals in the protein and the location of the protein in the organelle. In this review, we discuss the various mechanisms involved in protein targeting to the ER, chloroplasts and mitochondria, and how the targeting specificity is determined for these organelles in plant cells .     

Modeling the synchronization of yeast respiratory oscillations

The budding yeast Saccharomyces cerevisiae exhibits autonomous oscillations when grown aerobically in continuous culture with ethanol as the primary carbon source. A single cell model that includes the sulfate assimilation and ethanol degradation pathways recently has been developed to study these respiratory oscillations. We utilize an extended version of this single cell model to construct large cell ensembles for investigation of a proposed synchronization mechanism involving hydrogen sulfide. Ensembles with as many as 10,000 cells are used to simulate population synchronization and to compute transient number distributions from asynchronous initial cell states. Random perturbations in intracellular kinetic parameters are introduced to study the synchronization of single cells with small variations in their unsynchronized oscillation periods. The cell population model is shown to be consistent with available experimental data and to provide insights into the regulatory mechanisms responsible for the synchronization of yeast metabolic oscillations.     

Dynein, dynactin, and kinesin II's interaction with microtubules is regulated during bidirectional organelle transport

The microtubule motors, cytoplasmic dynein and kinesin II, drive pigmented organelles in opposite directions in Xenopus melanophores, but the mechanism by which these or other motors are regulated to control the direction of organelle transport has not been previously elucidated. We find that cytoplasmic dynein, dynactin, and kinesin II remain on pigment granules during aggregation and dispersion in melanophores, indicating that control of direction is not mediated by a cyclic association of motors with these organelles. However, the ability of dynein, dynactin, and kinesin II to bind to microtubules varies as a function of the state of aggregation or dispersion of the pigment in the cells from which these molecules are isolated. Dynein and dynactin bind to microtubules when obtained from cells with aggregated pigment, whereas kinesin II binds to microtubules when obtained from cells with dispersed pigment. Moreover, the microtubule binding activity of these motors/dynactin can be reversed in vitro by the kinases and phosphatase that regulate the direction of pigment granule transport in vivo. These findings suggest that phosphorylation controls the direction of pigment granule transport by altering the ability of dynein, dynactin, and kinesin II to interact with microtubules.     

Biogenesis of the protein storage vacuole crystalloid

We identify new organelles associated with the vacuolar system in plant cells. These organelles are defined biochemically by their internal content of three integral membrane proteins: a chimeric reporter protein that moves there directly from the ER; a specific tonoplast intrinsic protein; and a novel receptor-like RING-H2 protein that traffics through the Golgi apparatus. Highly conserved homologues of the latter are expressed in animal cells. In a developmentally regulated manner, the organelles are taken up into vacuoles where, in seed protein storage vacuoles, they form a membrane-containing crystalloid. The uptake and preservation of the contents of these organelles in vacuoles represents a unique mechanism for compartmentalization of protein and lipid for storage.     

Molecular and functional aspects of parasite invasion

Apicomplexan parasites have evolved an efficient mechanism to gain entry into non-phagocytic cells, hence challenging their hosts by the establishment of infection in immuno-privileged tissues. Gliding motility is a prerequisite for the invasive stage of most apicomplexans, allowing them to migrate across tissues, and actively invade and egress host cells. In the late 1960s, detailed morphological studies revealed that motile apicomplexans share an elaborate architecture comprising a subpellicular cytoskeleton and apical organelles. Since 1993, the development of technologies for transient and stable transfection have provided powerful tools with which to identify gene products associated with these structures and organelles, as well as to understand their functions. In combination with access to several parasite genomes, it is now possible to compare and contrast the strategies and molecular machines that have been selectively designed by distinct life stages within a species, or by different apicomplexan species, to optimize infection.     

Snapping magnetosome chains by asymmetric cell division in magnetotactic bacteria

The mechanism by which prokaryotic cells organize and segregate their intracellular organelles during cell division has recently been the subject of substantial interest. Unlike other microorganisms, magnetotactic bacteria (MTB) form internal magnets (known as magnetosome chain) for magnetic orientation, and thus face an additional challenge of dividing and equipartitioning this magnetic receptor to their daughter cells. Although MTB have been investigated more than four decades, it is only recently that the basic mechanism of how MTB divide and segregate their magnetic organelles has been addressed. In this issue of Molecular Microbiology, the cell cycle of the model magnetotactic bacterium, Magnetospirillum gryphiswaldense is characterized by Katzmann and co-workers. The authors have found that M. gryphiswaldense undergoes an asymmetric cell division along two planes. A novel wedge-like type of cellular constriction is observed before separation of daughter cells and magnetosome chains, which is assumed to help cell cope with the magnetic force within the magnetosome chain. The data shows that the magnetosome chain becomes actively recruited to the cellular division site, in agreement with the previous suggestions described by Staniland et al. (2010), and the actin-like protein MamK is likely involved in this fast polar-to-midcell translocalization. With the use of cryo-electron tomography, an arc-shaped Z ring is observed near the division site, which is assumed to trigger the asymmetric septation of cell and magnetosome chain.