Mucolipidosis Type IV Protein TRPML1‐Dependent Lysosome Formation

Lysosomes are dynamic organelles that undergo cycles of fusion and fission with themselves and with other organelles. Following fusion with late endosomes to form hybrid organelles, lysosomes are reformed as discrete organelles. This lysosome reformation or formation is a poorly understood process that has not been systematically analyzed and that lacks known regulators. In this study, we quantitatively define the multiple steps of lysosome formation and identify the first regulator of this process.      

Influence of translocation track on the motion of intra-axonally transported organelles in human nerve

The mechanism by which organelles are transported bidirectionally in axoplasm is still unknown; however, evidence of a key role for microtubules in many nonmammalian models has been established. We have observed common or shared tracks within the axoplasm of human nerves along which multiple organelles of varying size and shape are bidirectionally transported. Organelles traveling anterogradely and retrogradely were visualized by video-enhanced differential interference contrast optics and analyzed with the aid of computer-image-processing techniques. Speeds of translocating organelles were determined at eight to 16 translocation points along a path or "track." Each translocation speed was plotted against its corresponding position on the track to develop a "speed/position diagram." Regardless of mean organelle speed or direction of motion, organelles sharing a common track exhibited similar patterns of "speeding up" and "slowing down" relative to position along the track. Speed position data for organelles translocating the local axonal region of a common track showed no unique patterns (not different from a uniform distribution, p less than 0.05). The unique speed/position patterns exhibited by common tracks were not necessarily related to the patterns of other tracks in the immediate vicinity (distance between tracks of less than 0.50 micron). These findings suggest that there are "common tracks" shared by organelles moving retrogradely and anterogradely; both the organelles and the "track" associated with its translocation play a role in the resultant motion of that organelle; the influence exerted by a common track on the motion of an organelle results in a pattern of speed changes related to position along the track.     

Catalase-negative peroxisomes in human embryonic liver

Hepatic peroxisomes in human embryos with a menstrual age of 6 and 7 weeks have been examined via catalase cytochemistry. In the younger sample, the organelles show no catalase activity, their matrix being pale and coarsely reticular. In the 7-week specimen, the peroxisome population consists of catalase-positive and catalase-negative organelles. The latter have a morphology identical to that of the 6-week sample and represent 66% of the population. The positive organelles show a pronounced staining hetereogeneity. Together with the simultaneous presence of negative organelles, this might reflect the onset of catalase import into the peroxisomes during this period. Catalase heterogeneity excludes a continuous exchange of matrix contents; moreover, interconnections between peroxisomes have not been observed, and no cluster formation occurs. The data therefore also suggest that catalase is imported into individual, preexisting organelles in embryonic liver. The three peroxisomal -oxidation enzymes become detectable by immunocytochemistry only later during development. Morphological indications for a rapidly dividing population, such as elongated and/or tailed organelles, have not been observed. Morphometry has revealed that, in these early stages, the organelles are significantly smaller than the peroxisomes of fetal and adult human liver.     

Co-operative dynamics in organelles

Some organelles produce elementary life phenomena which are characterized by the spontaneous formation and/or maintenance of ordered macroscopic dynamics like e.g. the shortening of sarcomeres in striated muscle and the transmission of electrical impulses in an axon. It has been widely accepted that such organelles are organized molecular systems where molecular elements work independently under constraint of a more or less rigid and regular structure of the system. On the other hand, such organelles should be regarded as self-organizing systems if the ordered macroscopic dynamics are self-organized. As the macroscopic dynamics gradually emerge, the microscopic dynamics of its elements become linked to each other through a feedback loop. It is crucial for the feedback loop to operate that the macroscopic dynamics are "free" in their behavior. In the present paper, it is pointed out that the traditional view of independent molecular elements has been obtained from experiments in which, by means of external constraint, the macroscopic dynamics is "clamped". Under such conditions, the self-organizing system may behave as an organized one. Based on synergetics we propose criterions for proving self-organizing systems, and, by applying the criterions, we conclude that skeletal muscle actomysin is a co-operative element in the sense of self-organization.     

Morphometric analysis of gold particles in low-label cell compartments.

Quantitative estimation of the binding of gold-conjugated ligands to various cell organelles has become a commonly used method to quantify the amount of ligand-binding sites associated with those organelles. However, often a small percentage of organelles is labeled or the density of gold labeling is low. We have defined the "gold-labeled region" as a zone that has a boundary defined by the localization of the outermost gold particles. Such a phenomenon was recently observed in a study of the internalization of gold-labeled native surfactant into lamellar bodies of cultured pulmonary type II cells. We estimated the size and density of gold-labeled regions in lamelar bodies using a simple stereological approach and demonstrated that the low percentage of gold-labeled organelles can be explained as a result of the probability of random selecting through the labeled areas. Our method, which permits use of transmission electron microscopy to calculate the true parameters of gold-labeled regions, can significantly facilitate analyses of ligand binding to various cell compartments.     

Organelles in fast axonal transport

The present minireview describes experiments carried out, in short-term crush-operated rat nerves, using immunofluorescence and cytofluorimetric scanning techniques to study endogenous substances in anterograde and retrograde fast axonal transport. Vesicle membrane components p38 (synaptophysin) and SV2 are accumulating on both sides of a crush, but a larger proportion of p38 (about 3/4) than of SV2 (about 1/2) is recycling toward the cell body, compared to the amount carried with anterograde transport. Matrix peptides, such as CGRP, ChRA, VIP, and DBH are recycling to a minor degree, although only 10-20% of surface-associated molecules, such as synapsins and kinesin, appear to recycle. The described methodological approach to study the composition of organelles in fast axonal transport, anterograde as compared to retrograde, is shown to be useful for investigating neurobiological processes. We make use of the "in vivo chromatography" process that the fast axonal transport system constitutes. Only substances that are in some way either stored in, or associated with, transported organelles can be clearly observed to accumulate relative to the crush region. Emphasis in this paper was given to the synapsins, because of diverging results published concerning the degree of affiliation with various neuronal organelles. Our previously published results have indicated that in the living axons the SYN I is affiliated with mainly anterogradely fast transported organelles. Therefore, some preliminary, previously unpublished results on the accumulations of the four different synapsins (SYN Ia, SYN Ib, SYN IIa, and SYN IIb), using antisera specific for each of the four members of the synapsin family, are described. It was found that SYN Ib clearly has a stronger affiliation to anterogradely transported organelles than SYN Ia, and that both SYN IIa and SYN IIb are bound to some degree to transported organelles.     

Intracellular organelle networks: Understanding their organization and communication through systems-level modeling and analysis

Background

Membrane-bound intracellular organelles are biochemically distinct compartments used by eukaryotic cells for serving specialized physiological functions and organizing their internal environment. Recent studies revealed surprisingly extensive communication between these organelles and highlighted the network nature of their organization and communication. Since organization and communication of the organelles are carried out at the systems level through their networks, systems-level studies are essential for understanding the underlying mechanisms.

Methods

We reviewed recent studies that used systems-level quantitative modeling and analysis to understand organization and communication of intracellular organelle networks.

Results

We first review modeling and analysis studies on how fusion/fission and degradation/biogenesis, two essential and closely related classes of activities of individual organelles, collectively mediate the dynamic organization of their networks. We then turn to another important aspect of the dynamic organization of the organelle networks, namely how organelles are physically connected within their networks, a property referred to as the topology of the networks in mathematics, and summarize some of their distinct properties. Lastly, we briefly review modeling and analysis studies that aim to understand communication between different organelle networks, focusing on cellular calcium homeostasis as an example. We conclude with a brief discussion of future directions for research in this area.

Conclusion

Together, the reviewed studies provide critical insights into how diverse activities of individual organelles collectively mediate the organization and communication of their networks. They demonstrate the essential role of systemslevel modeling and analysis in understanding complex behavior of such networks.

     

Cell Biology of Prokaryotic Organelles

Mounting evidence in recent years has challenged the dogma that prokaryotes are simple and undefined cells devoid of an organized subcellular architecture. In fact, proteins once thought to be the purely eukaryotic inventions, including relatives of actin and tubulin control prokaryotic cell shape, DNA segregation, and cytokinesis. Similarly, compartmentalization, commonly noted as a distinguishing feature of eukaryotic cells, is also prevalent in the prokaryotic world in the form of protein-bounded and lipid-bounded organelles. In this article we highlight some of these prokaryotic organelles and discuss the current knowledge on their ultrastructure and the molecular mechanisms of their biogenesis and maintenance.The emergence of eukaryotes in a world dominated by prokaryotes is one of the defining moments in the evolution of modern day organisms. Although it is clear that the central metabolic and information processing machineries of eukaryotes and prokaryotes share a common ancestry, the origins of the complex eukaryotic cell plan remain mysterious. Eukaryotic cells are typified by the presence of intracellular organelles that compartmentalize essential biochemical reactions whereas their prokaryotic counterparts generally lack such sophisticated subspecialization of the cytoplasmic space. In most cases, this textbook categorization of eukaryotes and prokaryotes holds true. However, decades of research have shown that a number of unique and diverse organelles can be found in the prokaryotic world raising the possibility that the ability to form organelles may have existed before the divergence of eukaryotes from prokaryotes (Shively 2006).Skeptical readers might wonder if a prokaryotic structure can really be defined as an organelle. Here we categorize any compartment bounded by a biological membrane with a dedicated biochemical function as an organelle. This simple and broad definition presents cells, be they eukaryotes or prokaryotes, with a similar set of challenges that need to be addressed to successfully build an intracellular compartment. First, an organism needs to mold a cellular membrane into a desired shape and size. Next, the compartment must be populated with the proper set of proteins that carry out the activity of the organelle. Finally, the cell must ensure the proper localization, maintenance and segregation of these compartments across the cell cycle. Eukaryotic cells perform these difficult mechanistic steps using dedicated molecular pathways. Thus, if connections exist between prokaryotic and eukaryotic organelles it seems likely that relatives of these molecules may be involved in the biogenesis and maintenance of prokaryotic organelles as well.Prokaryotic organelles can be generally divided into two major groups based on the composition of the membrane layer surrounding them. First are the cellular structures bounded by a nonunit membrane such a protein shell or a lipid monolayer (Shively 2006). Well-known examples of these compartments include lipid bodies, polyhydroxy butyrate granules, carboxysomes, and gas vacuoles. The second class consists of those organelles that are surrounded by a lipid-bilayer membrane, an arrangement that is reminiscent of the canonical organelles of the eukaryotic endomembrane system. Therefore, this article is dedicated to a detailed exploration of three prokaryotic lipid-bilayer bounded organelle systems: the magnetosomes of magnetotactic bacteria, photosynthetic membranes, and the internal membrane structures of the Planctomycetes. In each case, we present the most recent findings on the ultrastructure of these organelles and highlight the molecular mechanisms that control their formation, dynamics, and segregation. We also highlight some protein-bounded compartments to present the reader with a more complete view of prokaryotic compartmentalization.     

Calcium regulation in endosymbiotic organelles of plants

In plant cells calcium-dependent signaling pathways are involved in a large array of biological processes in response to hormones, biotic/abiotic stress signals and a variety of developmental cues. This is generally achieved through binding of calcium to diverse calcium-sensing proteins, which subsequently control downstream events by activating or inhibiting biochemical reactions. Regulation by calcium is considered as a eukaryotic trait and has not been described for prokaryotes. Nevertheless, there is increasing evidence indicating that organelles of prokaryotic origin, such as chloroplasts and mitochondria, are integrated into the calcium-signaling network of the cell. An important transducer of calcium in these organelles appears to be calmodulin. In this review we want to give an overview over present data showing that endosymbiotic organelles harbour calcium-dependent biological processes with a focus on calmodulin-regulation.Key words: mitochondria, chloroplasts, calcium, calmodulin, EF-hand proteins     

Circadian changes in microtubules,synaptic ribbons and synaptic ribbon fields in the pinealocytes of the baboon (Papio ursinus)

Summary In baboons kept under controlled lighting conditions, microtubules (MT) are readily seen in the perikaryal cytoplasm and in the perivascular processes of pinealocytes. A significant increase in the number of MT, single synaptic ribbons (SR) and the formation of synaptic ribbon fields (RF, i.e. organelles which consist of multiple dense rodlets or plates, and vesicles), occur during the dark phase of a circadian light-dark cycle. MT may act as tracks for the oriented flow of vesicles derived from the smooth endoplasmic reticulum, to cytoplasmic sites where RF are being formed. The origin of the dense rodlets of RF remains unknown. Structural differences between SR and RF indicate that the latter organelles are not directly involved in impulse propagation between adjacent baboon pinealocytes. RF may function as storage organelles for some of the pineal secretory products which are formed in large amounts during the dark phase.     

Accelerated sliding of pollen tube organelles along Characeae actin bundles regulated by Ca2+

Pollen tubes show active cytoplasmic streaming. We isolated organelles from pollen tubes and tested their ability to slide along actin bundles in characean cell models. Here, we show that sliding of organelles was ATP-dependent and that motility was lost after N-ethylmaleimide or heat treatment of organelles. On the other hand, cytoplasmic streaming in pollen tube was inhibited by either N-ethylmaleimide or heat treatment. These results strongly indicate that cytoplasmic streaming in pollen tubes is supported by the "actomyosin"-ATP system. The velocity of organelle movement along characean actin bundles was much higher than that of the native streaming in pollen tubes. We suggested that pollen tube "myosin" has a capacity to move at a velocity of the same order of magnitude as that of characean myosin. Moreover, the motility was high at Ca2+ concentrations lower than 0.18 microM (pCa 6.8) but was inhibited at concentration higher than 4.5 microM (pCa 5.4). In conclusion, cytoplasmic streaming in pollen tubes is suggested to be regulated by Ca2+ through "myosin" inactivation.     

Toxoplasma gondii Syntaxin 6 Is Required for Vesicular Transport Between Endosomal‐Like Compartments and the Golgi Complex

Apicomplexans are obligate intracellular parasites that invade the host cell in an active process that relies on unique secretory organelles (micronemes, rhoptries and dense granules) localized at the apical tip of these highly polarized eukaryotes. In order for the contents of these specialized organelles to reach their final destination, these proteins are sorted post‐Golgi and it has been speculated that they pass through endosomal‐like compartments (ELCs), where they undergo maturation. Here, we characterize a Toxoplasma gondii homologue of Syntaxin 6 (TgStx6), a well‐established marker for the early endosomes and trans Golgi network (TGN) in diverse eukaryotes. Indeed, TgStx6 appears to have a role in the retrograde transport between ELCs, the TGN and the Golgi, because overexpression of TgStx6 results in the development of abnormally shaped parasites with expanded ELCs, a fragmented Golgi and a defect in inner membrane complex maturation. Interestingly, other organelles such as the micronemes, rhoptries and the apicoplast are not affected, establishing the TGN as a major sorting compartment where several transport pathways intersect. It therefore appears that Toxoplasma has retained a plant‐like secretory pathway .     

Peroxisomes as a cellular source of reactive nitrogen species signal molecules

Peroxisomes are single membrane-bounded subcellular organelles with an essentially oxidative type of metabolism and are probably the major sites of intracellular H₂O₂ production. These organelles also generate superoxide radicals () and besides catalase they have a complex battery of antioxidative enzymes. In recent years the existence of l-arginine-dependent nitric oxide synthase (NOS) activity and the generation of the reactive nitrogen species (RNS) nitric oxide (NO) have been demonstrated in plant peroxisomes. The inter-cellular and intracellular NO carrier S-nitrosoglutathione (GSNO) can be generated inside peroxisomes and the presence of this RNS has been demonstrated in peroxisomes from several plant species. This review analyzes the available evidence concerning the properties of the NOS activity and the generation of the RNS messengers NO and GSNO in peroxisomes in the context of the cellular function of these organelles as a source of RNS signaling molecules. The important physiological functions displayed by NO and other RNS in intra- and inter-cellular communication in different organisms indicate that more attention should be payed to the RNS signaling function of peroxisomes in human, animal and fungal cells, where it is very likely that similar mechanisms to those found in plant peroxisomes are also operative.     

Negative staining of whole cells: transmission electron microscopy of peripheral organelles in rat venous endothelial cells.

The study of whole negatively stained cells has revealed details of cellular organelles in rat venous endothelial cells. In particular, details of surface membrane organelles and small tubular structures were demonstrated. The surface membrane organelles which appeared "vesicular-like" were found to be connected with small tubular attachments. These findings were correlated with those described by other techniques. It is significant that this simple technique appears to permit the demonstration of fine details of three-dimensional cytoplasmic structures.     

Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'amitochondriate' diplomonads and retortamonads

Diplomonads, retortamonads, and "Carpediemonas-like" organisms (CLOs) are a monophyletic group of protists that are microaerophilic/anaerobic and lack typical mitochondria. Most diplomonads and retortamonads are parasites, and the pathogen Giardia intestinalis is known to possess reduced mitochondrion-related organelles (mitosomes) that do not synthesize ATP. By contrast, free-living CLOs have larger organelles that superficially resemble some hydrogenosomes, organelles that in other protists are known to synthesize ATP anaerobically. This group represents an excellent system for studying the evolution of parasitism and anaerobic, mitochondrion-related organelles. Understanding these evolutionary transitions requires a well-resolved phylogeny of diplomonads, retortamonads and CLOs. Unfortunately, until now the deep relationships amongst these taxa were unresolved due to limited data for almost all of the CLO lineages. To address this, we assembled a dataset of up to six protein-coding genes that includes representatives from all six CLO lineages, and complements existing rRNA datasets. Multigene phylogenetic analyses place CLOs as well as the retortamonad Chilomastix as a paraphyletic basal assemblage to the lineage comprising diplomonads and the retortamonad Retortamonas. In particular, the CLO Dysnectes was shown to be the closest relative of the diplomonads + Retortamonas clade, with strong support. This phylogeny is consistent with a drastic degeneration of mitochondrion-related organelles during the evolution from a free-living organism resembling extant CLOs to a probable parasite/commensal common ancestor of diplomonads and Retortamonas.     

Glutathione transporters

Background

Glutathione (GSH) is synthesized in the cytoplasm but there is a requirement for glutathione not only in the cytoplasm, but in the other organelles and the extracellular milieu. GSH is also imported into the cytoplasm. The transports of glutathione across these different membranes in different systems have been biochemically demonstrated. However the molecular identity of the transporters has been established only in a few cases.

Scope of review

An attempt has been made to present the current state of knowledge of glutathione transporters from different organisms as well as different organelles. These include the most well characterized transporters, the yeast high-affinity, high-specificity glutathione transporters involved in import into the cytoplasm, and the mammalian MRP proteins involved in low affinity glutathione efflux from the cytoplasm. Other glutathione transporters that have been described either with direct or indirect evidences are also discussed.

Major conclusions

The molecular identity of a few glutathione transporters has been unambiguously established but there is a need to identify the transporters of other systems and organelles. There is a lack of direct evidence establishing transport by suggested transporters in many cases. Studies with the high affinity transporters have led to important structure-function insights.

General significance

An understanding of glutathione transporters is critical to our understanding of redox homeostasis in living cells. By presenting our current state of understanding and the gaps in our knowledge the review hopes to stimulate research in these fields. This article is part of a Special Issue entitled Cellular functions of glutathione.     

The Movement of Coiled Bodies Visualized in Living Plant Cells by the Green Fluorescent Protein

Coiled bodies are nuclear organelles that contain components of at least three RNA-processing pathways: pre-mRNA splicing, histone mRNA 3'- maturation, and pre-rRNA processing. Their function remains unknown. However, it has been speculated that coiled bodies may be sites of splicing factor assembly and/or recycling, play a role in histone mRNA 3'-processing, or act as nuclear transport or sorting structures. To study the dynamics of coiled bodies in living cells, we have stably expressed a U2B"-green fluorescent protein fusion in tobacco BY-2 cells and in Arabidopsis plants. Time-lapse confocal microscopy has shown that coiled bodies are mobile organelles in plant cells. We have observed movements of coiled bodies in the nucleolus, in the nucleoplasm, and from the periphery of the nucleus into the nucleolus, which suggests a transport function for coiled bodies. Furthermore, we have observed coalescence of coiled bodies, which suggests a mechanism for the decrease in coiled body number during the cell cycle. Deletion analysis of the U2B" gene construct has shown that the first RNP-80 motif is sufficient for localization to the coiled body.     

On vesicles and membrane compartments

Summary Two different mechanisms have been proposed to explain transport along the endocytic and biosynthetic transport routes in cells. The first involves stable compartments connected by vesicular traffic while the second argues that the key organelles (early endosomes or the cis Golgi) form de novo by fusion of vesicles and subsequently mature into later forms. In the first part of this article, I propose a classification that distinguishes between stable, preexisting membrane compartments and vesicles that are, by definition, transient organelles. In this scheme, compartments, but not vesicles, are capable of homotypic fusion while vesicles, but not compartments, are able to mature, a process defined as an irreversible set of biochemical events which lead to a physiologically distinct end-state of the vesicle prior to its vectorial fusion with a target compartment. In the second part, I summarize my current ideas about the ultrastructural organization of the ER-Golgi region. Finally, I review the cell biology of selected examples of different vesicle types in order to exemplify the fascinating diversity of functions that this class of membrane organelles has evolved.Abbreviations COP coatomer - ECV endosome carrier vesicle - ER endoplasmic reticulum - HRP horseradish peroxidase - IC intermediate compartment between ER and Golgi - MVB multivesicular body - NSF N-ethyl maleimide sensitive factor - SNAPS soluble NSF associated proteins - TGN trans Golgi network Dedicated to Professor Eldon H. Newcomb in recognition of his contributions to cell biology     

Organelles in Blastocystis that blur the distinction between mitochondria and hydrogenosomes

Blastocystis is a unicellular stramenopile of controversial pathogenicity in humans. Although it is a strict anaerobe, Blastocystis has mitochondrion-like organelles with cristae, a transmembrane potential and DNA. An apparent lack of several typical mitochondrial pathways has led some to suggest that these organelles might be hydrogenosomes, anaerobic organelles related to mitochondria. We generated 12,767 expressed sequence tags (ESTs) from Blastocystis and identified 115 clusters that encode putative mitochondrial and hydrogenosomal proteins. Among these is the canonical hydrogenosomal protein iron-only [FeFe] hydrogenase that we show localizes to the organelles. The organelles also have mitochondrial characteristics, including pathways for amino acid metabolism, iron-sulfur cluster biogenesis, and an incomplete tricarboxylic acid cycle as well as a mitochondrial genome. Although complexes I and II of the electron transport chain (ETC) are present, we found no evidence for complexes III and IV or F1Fo ATPases. The Blastocystis organelles have metabolic properties of aerobic and anaerobic mitochondria and of hydrogenosomes. They are convergently similar to organelles recently described in the unrelated ciliate Nyctotherus ovalis. These findings blur the boundaries between mitochondria, hydrogenosomes, and mitosomes, as currently defined, underscoring the disparate selective forces that shape these organelles in eukaryotes.     

Occurrence, characterization and development of two different types of microbodies in the nematophagous fungus Arthrobotrys oligospora

Abstract The occurrence of microbodies in different cells of the nematophagous fungus Arthrobotrys oligospora has been investigated. In the predacious phase this organism forms complex 3-dimensional network traps. Mature trap cells generally were crowded with "special" microbodies which possessed an electron dense matrix and were surrounded by a membrane of approx. 9 nm. These organelles developed during the early stages of trap formation and were derived from specialized regions of the endoplasmic reticulum. Cytochemical staining experiments revealed that the electron-dense microbodies contained catalase and d -amino acid oxidase and thus must be considered peroxisomal in nature. Electron-dense bodies were absent in normal vegetative cells of the fungus. These cells contained "normal" microbodies which developed from each other by the separation of small organelles from mature ones. As in yeasts, the metabolic function of these latter organelles was dependent upon environmental conditions.