Guidelines for a Morphometric Analysis of Prokaryotic and Eukaryotic Cells by Scanning Electron Microscopy

The invention of a scanning electron microscopy (SEM) pushed the imaging methods and allowed for the observation of cell details with a high resolution. Currently, SEM appears as an extremely useful tool to analyse the morphology of biological samples. The aim of this paper is to provide a set of guidelines for using SEM to analyse morphology of prokaryotic and eukaryotic cells, taking as model cases Escherichia coli bacteria and B-35 rat neuroblastoma cells. Herein, we discuss the necessity of a careful sample preparation and provide an optimised protocol that allows to observe the details of cell ultrastructure (≥ 50 nm) with a minimum processing effort. Highlighting the versatility of morphometric descriptors, we present the most informative parameters and couple them with molecular processes. In this way, we indicate the wide range of information that can be collected through SEM imaging of biological materials that makes SEM a convenient screening method to detect cell pathology.

Isolation of an archaeon at the prokaryote-eukaryote interface

The origin of eukaryotes remains unclear1-4. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea5,6. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon-'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1-is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea6, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle-engulf-endogenize (also known as E3) model.

BUSCA: an integrative web server to predict subcellular localization of proteins

Here, we present BUSCA (http://busca.biocomp.unibo.it), a novel web server that integrates different computational tools for predicting protein subcellular localization. BUSCA combines methods for identifying signal and transit peptides (DeepSig and TPpred3), GPI-anchors (PredGPI) and transmembrane domains (ENSEMBLE3.0 and BetAware) with tools for discriminating subcellular localization of both globular and membrane proteins (BaCelLo, MemLoci and SChloro). Outcomes from the different tools are processed and integrated for annotating subcellular localization of both eukaryotic and bacterial protein sequences. We benchmark BUSCA against protein targets derived from recent CAFA experiments and other specific data sets, reporting performance at the state-of-the-art. BUSCA scores better than all other evaluated methods on 2732 targets from CAFA2, with a F1 value equal to 0.49 and among the best methods when predicting targets from CAFA3. We propose BUSCA as an integrated and accurate resource for the annotation of protein subcellular localization.

How does solvation in the cell affect protein folding and binding?

The cellular environment is highly diverse and capable of rapid changes in solute composition and concentrations. Decades of protein studies have highlighted their sensitivity to solute environment, yet these studies were rarely performed in situ. Recently, new techniques capable of monitoring proteins in their natural context within a live cell have emerged. A recurring theme of these investigations is the importance of the often-neglected cellular solvation environment to protein function. An emerging consensus is that protein processes in the cell are affected by a combination of steric and non-steric interactions with this solution. Here we explain how protein surface area and volume changes control these two interaction types, and give recent examples that highlight how even mild environmental changes can alter cellular processes.

Tracking the Movement of a Single Prokaryotic Cell in Extreme Environmental Conditions

Many bacterial species move toward favorable habitats. The flagellum is one of the most important machines required for the motility in solution and is conserved across a wide range of bacteria. The motility machinery is thought to function efficiently with a similar mechanism in a variety of environmental conditions, as many cells with similar machineries have been isolated from harsh environments. To understand the common mechanism and its diversity, microscopic examination of bacterial movements is a crucial step. Here, we describe a method to characterize the swimming motility of cells in extreme environmental conditions. This microscopy system enables acquisition of high-resolution images under high-pressure conditions. The temperature and oxygen concentration can also be manipulated. In addition, we also describe a method to track the movement of swimming cells using an ImageJ plugin. This enables characterization of the swimming motility of the selected cells.

Ultrastructural Heterogeneity of Carbonaceous Material in Ancient Cherts: Investigating Biosignature Origin and Preservation

Opaline silica deposits on Mars may be good target sites where organic biosignatures could be preserved. Potential analogues on Earth are provided by ancient cherts containing carbonaceous material (CM) permineralized by silica. In this study, we investigated the ultrastructure and chemical characteristics of CM in the Rhynie chert (c. 410 Ma, UK), Bitter Springs Formation (c. 820 Ma, Australia), and Wumishan Formation (c. 1485 Ma, China). Raman spectroscopy indicates that the CM has experienced advanced diagenesis or low-grade metamorphism at peak metamorphic temperatures of 150-350°C. Raman mapping and micro-Fourier transform infrared (micro-FTIR) spectroscopy were used to document subcellular-scale variation in the CM of fossilized plants, fungi, prokaryotes, and carbonaceous stromatolites. In the Rhynie chert, ultrastructural variation in the CM was found within individual fossils, while in coccoidal and filamentous microfossils of the Bitter Springs and formless CM of the Wumishan stromatolites ultrastructural variation was found between, not within, different microfossils. This heterogeneity cannot be explained by secondary geological processes but supports diverse carbonaceous precursors that experienced differential graphitization. Micro-FTIR analysis found that CM with lower structural order contains more straight carbon chains (has a lower R3/2 branching index) and that the structural order of eukaryotic CM is more heterogeneous than prokaryotic CM. This study demonstrates how Raman spectroscopy combined with micro-FTIR can be used to investigate the origin and preservation of silica-permineralized organics. This approach has good capability for furthering our understanding of CM preserved in Precambrian cherts, and potential biosignatures in siliceous deposits on Mars.

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.

Sculpting the bacterial cell

Prokaryotes come in a wide variety of shapes, determined largely by natural selection, physical constraints, and patterns of cell growth and division. Because of their relative simplicity, bacterial cells are excellent models for how genes and proteins can directly determine morphology. Recent advances in cytological methods for bacteria have shown that distinct cytoskeletal filaments composed of actin and tubulin homologs are important for guiding growth patterns of the cell wall in bacteria, and that the glycan strands that constitute the wall are generally perpendicular to the direction of growth. This cytoskeleton-directed cell wall patterning is strikingly reminiscent of how plant cell wall growth is regulated by microtubules. In rod-shaped bacilli, helical cables of actin-like MreB protein stretch along the cell length and orchestrate elongation of the cell wall, whereas the tubulin-like FtsZ protein directs formation of the division septum and the resulting cell poles. The overlap and interplay between these two systems and the peptidoglycan-synthesizing enzymes they recruit are the major driving forces of cylindrical shapes. Round cocci, on the other hand, have lost their MreB cables and instead must grow mainly via their division septum, giving them their characteristic round or ovoid shapes. Other bacteria that lack MreB homologs or even cell walls use distinct cytoskeletal systems to maintain their distinct shapes. Here I review what is known about the mechanisms that determine the shape of prokaryotic cells.

Intracellular minerals and metal deposits in prokaryotes

Thanks to the work of Terrance J. Beveridge and other pioneers in the field of metal-microbe interactions, prokaryotes are well known to sequester metals and other ions intracellularly in various forms. These forms range from poorly ordered deposits of metals to well-ordered mineral crystals. Studies on well-ordered crystalline structures have generally focused on intracellular organelles produced by magnetotactic bacteria that are ubiquitous in terrestrial and marine environments that precipitate Fe(3)O(4) or Fe(3)S(4), Fe-bearing minerals that have magnetic properties and are enclosed in intracellular membranes. In contrast, studies on less-well ordered minerals have focused on Fe-, As-, Mn-, Au-, Se- and Cd-precipitates that occur intracellularly. The biological and environmental function of these particles remains a matter of debate.

On the origin of eukaryotic cytoskeleton

The origin of eukaryote-specific cytoskeletal proteins is an issue which is closely related to the origin of the domain Eukarya. As nearly all of these proteins are not found in prokaryotes, the prokaryotic origin of eukaryotic cytoskeletal network suggested by most models is questionable. Eukaryotic cytoskeletal proteins might descend from subpopulations of pre-cells co-existing with Bacteria and Archaea prior to the origin of eukaryotes. The pre-karyote (the host for a-proteobacterial ancestors of mitochondria) might have already possessed eukaryotic-like cytoskeleton. A possible role for viruses in the origin of eukaryotic cytoskeletal proteins is discussed. Viruses parasitizing on pre-cells and/or on the pre-karyote might have themselves used several eukaryotic-like cytoskeletal proteins for segregation and packing of their genomes.

The hidden side of the prokaryotic cell: rediscovering the microbial world

How many different forms of life exist and how they are evolutionarily related is one of the most challenging problems in biology. In 1962, Roger Y. Stanier and Cornelis B. van Niel proposed "the concept of a bacterium" and thus allowed (micro)biologists to divide living organisms into two primary groups: prokaryotes and eukaryotes. Initially, prokaryotes were believed to be devoid of any internal organization or other characteristics typical of eukaryotes, due to their minute size and deceptively simple appearance. However, the last few decades have demonstrated that the structure and function of the prokaryotic cell are much more intricate than initially thought. We will discuss here two characteristics of prokaryotic cells that were not known to Stanier and van Niel but which now allow us to understand the basis of many characteristics that are fully developed in eukaryotic cells: First, it has recently become clear that bacteria contain all of the cytoskeletal elements present in eukaryotic cells, demonstrating that the cytoskeleton was not a eukaryotic invention; on the contrary, it evolved early in evolution. Essential processes of the prokaryotic cell, such as the maintenance of cell shape, DNA segregation, and cell division, rely on the cytoskeleton. Second, the accumulation of intracellular storage polymers, such as polyhydroxyalkanoates (a property studied in detail by Stanier and colleagues), provides a clear evolutionary advantage to bacteria. These compounds act as a "time-binding" mechanism, one of several prokaryotic strategies to increases survival in the Earth's everchanging environments.

Flagellar apparatus of south-seeking many-celled magnetotactic prokaryotes

Magnetotactic bacteria orient and migrate along geomagnetic field lines. Each cell contains membrane-enclosed, nano-scale, iron-mineral particles called magnetosomes that cause alignment of the cell in the geomagnetic field as the bacteria swim propelled by flagella. In this work we studied the ultrastructure of the flagellar apparatus in many-celled magnetotactic prokaryotes (MMP) that consist of several Gram-negative cells arranged radially around an acellular compartment. Flagella covered the organism surface, and were observed exclusively at the portion of each cell that faced the environment. The flagella were helical tubes never as long as a complete turn of the helix. Flagellar filaments varied in length from 0.9 to 3.8 micro m (average 2.4 +/- 0.5 micro m, n = 150) and in width from 12.0 to 19.5 nm (average 15.9 +/- 1.4 nm, n = 52), which is different from previous reports for similar microorganisms. At the base of the flagella, a curved hook structure slightly thicker than the flagellar filaments was observed. In freeze-fractured samples, macromolecular complexes about 50 nm in diameter, which possibly corresponded to part of the flagella basal body, were observed in both the P-face of the cytoplasmic membrane and the E-face of the outer membrane. Transmission electron microscopy showed that magnetosomes occurred in planar groups in the cytoplasm close and parallel to the organism surface. A striated structure, which could be involved in maintaining magnetosomes fixed in the cell, was usually observed running along magnetosome chains. The coordinated movement of the MMP depends on the interaction between the flagella of each cell with the flagella of adjacent cells of the microorganism.

Single molecule studies of molecular diffusion in cellular membranes: Determining membrane structure

Since the advent of single particle/molecule microscopies, researchers have applied these techniques to understanding the fluid membranes of cells. By observing diffusion of membrane proteins and lipids in live cell membranes of eukaryotic cells, it has been found that membranes contain a mosaic of fluid compartments. Such structure may be instrumental in understanding key characteristics of the membrane. Recent single molecule observations on prokaryotic cell membranes will also be discussed.

Prokaryotic photosynthesis and phototrophy illuminated

Genome sequencing projects are revealing new information about the distribution and evolution of photosynthesis and phototrophy. Although coverage of the five phyla containing photosynthetic prokaryotes (Chlorobi, Chloroflexi, Cyanobacteria, Proteobacteria and Firmicutes) is limited and uneven, genome sequences are (or soon will be) available for >100 strains from these phyla. Present knowledge of photosynthesis is almost exclusively based on data derived from cultivated species but metagenomic studies can reveal new organisms with novel combinations of photosynthetic and phototrophic components that have not yet been described. Metagenomics has already shown how the relatively simple phototrophy based upon rhodopsins has spread laterally throughout Archaea, Bacteria and eukaryotes. In this review, we present examples that reflect recent advances in phototroph biology as a result of insights from genome and metagenome sequencing.

Unidentified extracellular prokaryotes within the byssal threads of the deep-sea vent musselBathymodiolus azoricus

Bacterial symbiosis and/or parasitism is widespread in hydrothermal bivalves, and is typically developed in gills, with a lower incidence in mantle and digestive glands, while it has never been described in byssus. Using ultrastructural examination, we provide evidence for the existence of a potentially new group of filamentous prokaryotic organism inBathymodiolus azoricusbyssus, with putative parasitic influence. Additionally, a cystic, undefined organism was found with an unclear physiological role within the spongy net of the byssus plaque. Our results indicate that in spite of its antibacterial protective sheath, byssus gives access to prokaryotic organisms becoming prone to failure through damaged collagen fibres.

Long-distance calls between cells connected by tunneling nanotubules

Long membrane tethers between cells, known as membrane nantotubes or tunneling nanotubules, create supracellular structures that allow multiple cell bodies to act in a synchronized manner. Calcium fluxes, vesicles, and cell-surface components can all traffic between cells connected by nanotubes. Thus, complex and specific messages can be transmitted between multiple cells, and the strength of signal will suffer relatively little with the distance traveled, as compared to the use of soluble factors to transmit messages. Connecting multiple antigen-presenting cells, for example, can help amplify and coordinate immune responses that are distal to an antigenic site. Conversely, because the ability of a pathogen to spread between cells is a key determinant of its capacity to multiply, pathogens may exploit nanotubes for their own transmission.

A “flip–flop” rotation stage for routine dual-axis electron cryotomography

Electron cryotomography can be used to solve the three-dimensional structures of individual large macromolecules, assemblies, and even small intact cells to medium (approximately 4-8 nm) resolution in a near-native state, but restrictions in the range of accessible views are a major limitation. Here we report on the design, characterization, and demonstration of a new "flip-flop" rotation stage that allows facile and routine collection of two orthogonal tilt-series of cryosamples. Single- and dual-axis tomograms of a variety of samples are compared to illustrate qualitatively the improvement produced by inclusion of the second tilt-series. Exact quantitative expressions are derived for the volume of the remaining "missing pyramid" in reciprocal space. When orthogonal tilt-series are recorded to +/-65 degrees in each direction, as this new cryostage permits, only 11% of reciprocal space is left unmeasured. The tomograms suggest that further improvement could be realized, however, through better software to align and merge dual-axis tilt-series of cryosamples.

The new bacterial cell biology: moving parts and subcellular architecture

Recent advances have demonstrated that bacterial cells have an exquisitely organized and dynamic subcellular architecture. Like their eukaryotic counterparts, bacteria employ a full complement of cytoskeletal proteins, localize proteins and DNA to specific subcellular addresses at specific times, and use intercellular signaling to coordinate multicellular events. The striking conceptual and molecular similarities between prokaryotic and eukaryotic cell biology thus make bacteria powerful model systems for studying fundamental cellular questions.

New insights into the structural organization of eukaryotic and prokaryotic cytoskeletons using cryo-electron tomography

Cryo-electron tomography (cryo-ET) is an emerging imaging technology that combines the potential of three-dimensional (3-D) imaging at molecular resolution (<5 nm) with a close-to-life preservation of the specimen. In conjunction with pattern recognition techniques, it enables us to map the molecular landscape inside cells. The application of cryo-ET to intact cells provides novel insights into the structure and the spatial organization of the cytoskeleton in prokaryotic and eukaryotic cells.

[Ultrastructural basis of interactions between prokaryotes and eukaryotes in different symbiotic models]

This paper reviews the Author's contribution to the knowledge of the ultrastructural basis of the prokaryote-eukaryote interactions in different models assessed by an ultrastructural approach. In agreement with the hypothesis of the origin of eukaryotic cells, which are chimeras of several prokaryotes with different morpho-functional specializations, symbiosis had major consequence for evolution of life. In Arthropods, one of the most successful lifestyles, the presence of endosymbiotic prokaryotes, plays an important role in their metabolism. In some cases, genome integration has occurred in the endosymbiotic relationships with the host, proving that intracellular symbiosis is not merely a nutritional supplement. Intracellular symbiotic bacteria are also described in nematodes. In particular, the presence of intracellular Wolbachia in filariae, even if its function is not yet completely known, influences positively the reproductive biology and the survival of the host, as proved by antibiotic treatment against this bacterium. The ultrastructural images reported in this review were obtained using different species of cockroaches, termites, ticks and filarial nematodes. The traditional methods of transmission (TEM), scansion (SEM) and immuno electron microscopy were used. In addition, also freeze-fracture and deep-etching techniques were employed. The cockroaches and the primitive termite Mastotermes darwiniensis host symbiotic bacteria in the ovary and in specialized cells (bacteriocytes) of the fat body. These bacteria have the typical cell boundary profile of gram-negative bacteria and are enveloped in a vacuolar membrane produced by the host cell. Molecular sequence data of 16S rDNA of endosymbionts of five species of cockroaches and M. darwiniensis indicate that they are members of the Flavobacteria-bacteroides group and that the infection occurred in an ancestor common to cockroaches and termites probably after the end of the Paleozoic (250 Ma BP). The symbiotic bacteria are transmitted transovarially and, during embryogenesis, they are integrated into the morphogenetic processes. In particular, we were able to demonstrate that the origin of the bacteriocyte should be looked for in the cells of the haemocyte line (embryonic plasmatocytes). The eggs are infected by the bacteria emerging from the bacteriocytes of the ovaric fat body and, at the end of the vitellogenesis, they are actively phagocytized by the egg membrane. In filarial nematodes, intracellular bacteria belonging to the genus Wolbachia have been described: they have evolved an obligatory mutualistic association with their host. In fact, antibiotic treatments lead to the clearance of bacteria and this loss produces a negative impact on reproduction and survival of the filarial host. We evidenced, by TEM, the degenerative events occurring during the embriogenesis of Brugia pahangi and Dirofilaria immitis after tetracycline treatment. The data suggest that the Wolbachia play a direct role in worm metabolism. Finally, a new additional model of the prokaryote-eukaryote interaction has been described: we have recently discovered a new intracellular alpha-proteobacterium, named Iric ES1, which resides in the ovarian tissues of the tick Ixodes ricinus. The intriguing characteristic of this bacterium is its ability to invade and consume the ovaric mitochondria. From an evolutionary perspective, it is interesting to note that Iric ES1 enters mitochondria in a similar way to that employed by the "predatory" bacterium Bdellovibrio bacteriovorus.

Insights into the regulation of transcription by scanning force microscopy

The scanning force microscope (SFM) is a valuable tool for the structural analysis of complexes between protein(s) and DNA. In recent years the application of scanning force microscopy to the field of transcription regulation has been reported in numerous studies. Using this technique, novel insights could be obtained into the architecture and dynamics of complexes, which are relevant to the transcription process and the mechanisms by which this process is regulated. In this article an overview is given of SFM studies addressing, in particular, topics in the field of transcription in prokaryotic organisms.

Another cytoskeleton in the closet

Many eukaryotic cells contain up to three families of cytoskeletal proteins that are responsible for the spatial organization of the cell. Although the prokaryotic origins of the actin and tubulin families have now been established, the origin of the third was unknown. In this issue of Cell, provide evidence that the third family, comprising the intermediate filaments, also has origins in bacteria and is responsible for producing curved cells.

Cytoskeletons in prokaryotes

Not only eukaryotes, but also prokaryotes possess a cytoskeleton. Tubulin-related bacterial protein FtsZ, and actin-related bacterial proteins MreB/Mbl have recently been described as constituents of bacterial cytoskeletons. Genes coding for MreB/Mbl could only be found in elongated bacteria, not in coccoid forms. It was speculated that constituents of today's eukaryotic cytoskeleton (tubulin, actin) may have evolved from prokaryotic precursor proteins closely related to today's bacterial proteins FtsZ and MreB/Mbl. Prior to the description of proteins MreB/Mbl, evidence had been obtained for the existence of a shape-preserving cytoskeleton ubiquitously present in all bacteria. In the meantime, structural studies allow to speculate on a possible role of bacterial elongation factor Tu (EF-Tu) as a structural element in such a "cytoskeletal web". EF-Tu was long known to form fibrillar structures in vitro; now experimental data accumulate, pointing towards formation of intracellular protofilaments containing EF-Tu, and networks thereof as well. In addition, results of these structural studies suggest a so far unknown mode of complex formation of EF-Tu with active ribosomes: ribosomes/polysomes were seen to be attached to intracellular protofilaments. Implications for the understanding of EF-Tu-ribosome interaction, and a role of such a kind of putative protofilaments as a general site of attachment for cellular functional macromolecules are discussed. The notion is discussed that an EF-Tu-containing cytoskeletal web might have been the "primary" or "basic" kind of prokaryotic cytoskeleton, already in existence prior to the "invention" of precursors of today's MreB.

Cell shape, division and development: the 2002 American Society for Microbiology (ASM) conference on prokaryotic development

In the last decade, the use of cytological techniques, together with the analysis of complete genomes, has dramatically advanced our understanding of bacterial development. Work on several well-developed model systems such as Bacillus subtilis, Caulobacter crescentus, Myxococcus xanthus and Streptomyces spp., has provided us with an in-depth understanding of processes such as sporulation, multicellular behaviour and the bacterial cell cycle. At the same time, these studies have revolutionized our view of the bacterial cell and shown it to be a highly complex entity with spatial and temporal organization. The recent American Society for Microbiology (ASM) conference on prokaryotic development demonstrated that several laboratories have now started to connect data obtained through functional genomic analysis with subcellular organization, thereby generating three-dimensional regulatory networks. This meeting report highlights new findings in the field, such as regulation of protein localization during sporulation and the cell cycle, control of cell-cell interaction and the initiation of cell division.

Rotary protein motors

Three protein motors have been unambiguously identified as rotary engines: the bacterial flagellar motor and the two motors that constitute ATP synthase (F(0)F(1) ATPase). Of these, the bacterial flagellar motor and F(0) motors derive their energy from a transmembrane ion-motive force, whereas the F(1) motor is driven by ATP hydrolysis. Here, we review the current understanding of how these protein motors convert their energy supply into a rotary torque.

Elemental characterization of microorganism granules by EFTEM in the tube wall of a deep-sea vent invertebrate

Microorganisms colonizing the exoskeletons of the tube worm Riftia pachyptila are described at the ultrastructural level. The prokaryotic cells from the worm tube wall differ from those colonizing the exoskeleton outer surface in the presence of an electron dense granule. The morphology and distribution of these bacteria-like cells are described. Prokaryotic organisms are assembled in nodules which increased in size in the oldest part of the exoskeleton. The aspect, location and elemental composition of the intracellular granules are determined. Most of them (100 nm in diameter) are located close to the cell membrane and exhibit a homogeneous and amorphous content. EDX and EFTEM microanalyses show that these structures contain phosphorus, oxygen and iron. All together these data suggest that these granules are iron polyphosphates. These structures may act as energy sources for making ATP during anoxic conditions as existing in hydrothermal environments.

Molecular evolution of proteasomes

Proteasomes are large, multisubunit proteases that are found, in one form or another, in all domains of life and play a critical role in intracellular protein degradation. Although they have substantial structural similarity, the proteasomes of bacteria, archaea, and eukaryotes show many differences in architecture and subunit composition. This article discusses possible paths by which proteasomes may have evolved from simple precursors to the highly complicated and diverse complexes observed today.

The intracellular localization of the proteasome

In summary, localization of proteasomes does appear to be important in the regulation of proteolysis. In yeast, a discrete localization is observed at the nuclear periphery for cells undergoing mitotic growth. This localization is clearly important as degradation by the ubiquitin/proteasome pathway is impaired in mutants that mislocalize proteasomes. In mammalian cells, proteasomes are present throughout the cell. However, the proteasome does appear to be enriched at the MTOC upon aggresome formation. The inhibition of the ubiquitin/proteasome pathway in aggresome-containing cells could provide an explanation for the pathogenicity of a number of neurodegenerative diseases.

Prokaryote infections in the New Zealand scallops Pecten novaezelandiae and Chlamys delicatula

Four intracellular prokaryotes are reported from the scallops Pecten novaezelandiae Reeve, 1853 and Chlamys delicatula Hutton, 1873. Elongated (1025 x 110 nm), irregular (390 x 200 nm), or toroidal (410 x 200 nm) mollicute-like organisms (M-LOs) occurred free in the cytoplasm in the digestive diverticular epithelial cells of both scallop species. Those in P. novaezelandiae bore osmiophilic blebs that sometimes connected the organisms together, and some had a rod-like protrusion, both of which resemble the blebs and tip structures of pathogenic mycoplasmas. The M-LOs in C. delicatula had a slightly denser core than periphery. Round M-LOs, 335 x 170 nm, occurred free in the cytoplasm of agranular haemocytes in P. novaezelandiae, without apparent harm to the host cell. In P. novaezelandiae, 2 types of highly prevalent (95 to 100%) basophilic inclusions in the branchial epithelium contained Rickettsia-like organisms (R-LOs). Type 1 inclusions occurred in moderately hypertrophied, intensely basophilic cells, 8 to 10 microm in diameter, containing elongate intracellular R-LOs, 2000 x 500 nm. Type 2 inclusions were elongated and moderately basophilic in markedly hypertrophic branchial epithelial cells, 50 x 20 microm in diameter, containing intracellular organisms 500 x 200 nm in diameter. The possible roles of these organisms in pathogenesis is discussed.

Macromolecular crowding: an important but neglected aspect of the intracellular environment

Biological macromolecules have evolved over billions of years to function inside cells, so it is not surprising that researchers studying the properties of such molecules, either in extracts or in purified form, take care to control factors that reflect the intracellular environment, such as pH, ionic strength and composition, redox potential and the concentrations of relevant metabolites and effector molecules. There is one universal aspect of the cellular interior, however, that is largely neglected--the fact that it is highly crowded with macromolecules. It is proposed that the addition of crowding agents should become as routine as controlling pH and ionic strength if we are to meet the objective of studying biological molecules under more physiologically relevant conditions.

[Role of hypothalamic nonapeptides in interaction of prokaryotic and eukaryotic cells]

The role of hypothalamic nonapeptides in the interaction of prokaryotic and eukaryotic cells was studied in the experimental setting. Nonapeptides were found to stimulate the adaptive and regenerative properties of eukaryotic cells and they are likely to have an antimicrobic effect on prokaryotic ones. The paper discusses the modulating role of nonapeptides in the establishment of symbiotic relations in the bacterial agent-host system.

Protein folding in vivo: the importance of molecular chaperones

The contribution of the two major cytosolic chaperone systems, Hsp70 and the cylindrical chaperonins, to cellular protein folding has been clarified by a number of recent papers. These studies found that, in vivo, a significant fraction of newly synthesized polypeptides transit through these chaperone systems in both prokaryotic and eukaryotic cells. The identification and characterization of the cellular substrates of chaperones will be instrumental in understanding how proteins fold in vivo.

Using discriminant function for prediction of subcellular location of prokaryotic proteins

The discriminant function algorithm was introduced to predict the subcellular location of proteins in prokaryotic organisms from their amino-acid composition. The rate of correct prediction for the three possible subcellular locations of prokaryotic proteins studied by Reinhardt and Hubbard (Nucleic Acid Research, 1998, 26:2230-2236) was 90% by the self-consistency test, and 87% by the jackknife test. These rates are considerably higher than the results recently reported by them using the neural network method. Furthermore, the test procedure adopted here is also more rigorous. The core of the current algorithm is the covariance matrix, through which the collective interactions among different amino-acid components of a protein can be reflected. It is anticipated that, owing to the intimate correlation of the function of a protein with its subcellular location, the current algorithm will become a useful tool for the systematic analysis of genome data.

Preservation of cell structures in permafrost: a model for exobiology

The present report is the first contribution toward a comprehensive fine-structural study of microbial cells from permafrost. Prokaryotes with a variety of cell wall types demonstrate high stability of cell structure after long-term cryopreservation in frozen soils and sediments of the Arctic. The surface capsular layers that were a salient feature of the cells both in situ and on nutrient media may be an adaptation to low temperature. To the extent that permafrost regions on Earth approximate Martian conditions, preservation of cell structure there can serve as the basis for predictions about preservation in Martian permafrost sediments.

The application of fractal geometric analysis to microscopic images

Fractal geometry is a relatively new tool for the quantitative microscopist that is a more valid way of measuring dimensions of complex irregular objects than the integer-dimensional geometries (such as Euclidean geometry). This review discusses the theory of fractal geometry using the classic examples of the Von Koch curve, the Cantor set and the Sierpinski gasket. The problems of describing the dimensions of these objects are discussed and the concept of fractal dimensionality is introduced. Methods for measuring fractal dimensions are discussed, including their implementation on microcomputer-based image analysis systems . The advantages and problems of fractal geometric analysis are discussed and current applications in the field of microscopy are reviewed.

On the origin of mitosing cells. 1967

A theory of the origin of eukaryotic cells ("higher" cells which divide by classical mitosis) is presented. By hypothesis, three fundamental organelles: the mitochondria, the photosynthetic plastids and the (9+2) [9(2)+2] basal bodies [kinetosomes] of flagella [undulipodia] were themselves once free-living (prokaryotic) cells. The evolution of photosynthesis under the anaerobic [anoxic] conditions of the early atmosphere to form anaerobic bacteria, photosynthetic bacteria and eventually blue-green algae (and protoplastids) is described. The subsequent evolution of aerobic metabolism in prokayotes to form aerobic bacteria (protoflagella [undulipodia] and protomitochondria) presumably occurred during the transition to the oxidizing atmosphere. Classical mitosis evolved in protozoan-type cells millions of years after the evolution of photosynthesis. A plausible scheme for the origin of classical mitosis in primitive amoeboflagellates [amoebomastigotes] is presented. During the course of the evolution of mitosis, photosynthetic plastids (themselves derived from prokaryotes) were symbolically acquired by some of these protozoans to form the ["eukaryotic" deleted] algae and the green plants. The cytological, biochemical and paleontological evidence for this theory is presented, along with suggestions for further possible experimental verification. The implications of this scheme for the systematics of the lower [smaller] organisms is discussed.

Flagella in prokaryotes and lower eukaryotes

During the past year, significant advances have been made in the understanding of both prokaryotic and eukaryotic flagella. About 50 genes are dedicated to the assembly and operation of bacterial flagella. Recent discoveries have advanced our understanding of how these genes are regulated and how their products assemble into a functional, rotating organelle. The dynein arms of eukaryotic flagella are now also better understood. Several genes that are found in the mechanochemical macroassemblies have been cloned, and other loci have been identified, suggesting that there is even greater complexity than first expected.

E.coli hemolysin interactions with prokaryotic and eukaryotic cell membranes

The hemolysin toxin (HlyA) is secreted across both the cytoplasmic and outer membranes of pathogenic Escherichia coli and forms membrane pores in cells of the host immune system, causing cell dysfunction and death. The processes underlying the interaction of HlyA with the bacterial and mammalian cell membranes are remarkable. Secretion of HlyA occurs without a periplasmic intermediate and is directed by an uncleaved C-terminal targetting signal and the HlyB and HlyD translocator proteins, the former being a member of a transporter superfamily central to import and export of a wide range of substrates by prokaryotic and eukaryotic cells. The separate process by which HlyA is targetted to mammalian cell membranes is dependent upon fatty acylation of a non-toxic precursor, proHlyA. This is achieved by a novel mechanism directed by the activator protein HlyC, which binds to an internal proHlyA recognition sequence and provides specificity for the transfer of fatty acid from cellular acyl carrier protein.

Ribosomes from trichomonad protozoa have prokaryotic characteristics

1. Ribosomes from cells of the genera Trichomonas and Tritrichomonas have been isolated and characterized. The ribosomes from each organism had a sedimentation coefficient of 70S in calibrated sucrose gradients and the subunits sedimented as 50S and 30S particles under the same conditions. 2. The major ribosomal RNAs from each species were identical in size to prokaryotic ribosomal RNAs when examined by denaturing gel electrophoresis. The ribosomes contained both 5.8S and 5S RNAs. 3. The ribosomal proteins were compared by the methods of two-dimensional gel electrophoresis and reversed phase HPLC. Electrophoresis of the ribosomal proteins in two different gel systems indicated the presence of 56 proteins in T. gallinae, 40 in T. bactrachorum and 45 in the Tritrichomonas sp. The protein molecular mass range was 8.5-40 kDa. 4. The HPLC analysis confirmed the protein number established by the gel methods. 5. Both methods of analysis revealed greater similarities between the ribosomal proteins of the 2 Tritrichomonas sp. than between those of the more distantly related T. gallinae and T. bactrachorum.

An unusual symbiont from the gut of surgeonfishes may be the largest known prokaryote

Symbionts first reported from the gut of a Red Sea surgeonfish, Acanthurus nigrofuscus (family Acanthuridae), were subsequently described as Epulopiscium fishelsoni. The taxonomic position of this very large (up to 576 microns in length) microorganism has previously been designated in the literature as either uncertain or eukaryotic. We suggest that similar symbionts from Great Barrier Reef surgeonfish may be prokaryotes, which together with E. fishelsoni from the Red Sea may represent the largest known forms of this cell type. Features identifying the symbionts as prokaryotes include the presence of bacterial-type flagella and a bacterial nucleoid and the absence of a nucleus or any other membrane-bound organelle.

Characterization of the str operon genes from Spirulina platensis and their evolutionary relationship to those of other prokaryotes

A 5.3 kb DNA segment containing the str operon (ca. 4.5 kb) of the cyanobacterium Spirulina platensis has been sequenced. The str operon includes the structural genes rpsL (ribosomal protein S12), rpsG (ribosomal protein S7), fus (translation elongation factor EF-G) and tuf (translation elongation factor EF-Tu). From the nucleotide sequence of this operon, the primary structures of the four gene products have been derived and compared with the available corresponding structures from eubacteria, archaebacteria and chloroplasts. Extensive homologies were found in almost all cases and in the order S12 greater than EF-Tu greater than EF-G greater than S7; the largest homologies were generally found between the cyanobacterial proteins and the corresponding chloroplast gene products. Overall codon usage in S. platensis was found to be rather unbiased.