Chemoautotrophic endosymbioses: contemporary models for symbiogenesis?

Oxygen appears to be one of the key factors in understanding the evolution of life on Earth. Almost absent during more than 2 billion years, its subsequent increase is correlated with the emergence of oxygenic photosynthesis by Cyanobacteria, followed by aerobic Prokaryotes and eventually Eukaryotes, all primitively aerobic, and more recently, the development of complex multicellular organisms. However, in some reduced environments, still present at the surface of the Earth and even more so in ocean depths (hydrothermal vents, cold seeps, massive organic falls,...), anaerobic or micro-aerobic Prokaryotes continue to grow, including some chemoautotrophic bacteria deriving energy from sulfide oxidation for instance. A few Metazoa have managed to collaborate with such chemoautotroph Prokaryotes, the most abundant species forming endosymbiotic associations. The most studied of these endosymbioses (the mussels Bathymodiolus, the vestimentiferan tubeworm Riftia pachyptila, or the clams Calyptogena) have revealed important differences in the degree of interdependence between host and symbionts, and in the mode of symbiont transmission. The evolutive process of these symbioses is reminiscent of the primary endosymbioses which have given rise to the organelles of heterotrophic Eukaryotes (mitochondria) and phototrophic Eukaryotes (chloroplasts). The study of these modern days biological models could shed light on symbiogenesis itself and also potentially reveal thiotrophic Eukaryotes as a new lineage.     

Ultrastructural and biochemical nuclear aspects of Eukaryote classification: Independent evolution of the dinoflagellates as a sister group of the actual Eukaryotes?

Structural and functional features of the dinoflagellate nucleus are examined and compared to those commonly found in Prokaryotes and in Eukaryotes. It appears that dinoflagellate protists, while showing several ancestral characters also found in Prokaryotes are above the prokaryote level in terms of their organization but below that of the other Eukaryotes. Some characters are typical of dinoflagellate nuclei alone, and no correspondence is found in either bacterial nucleoïd or typical eukaryote nuclei. This supports Loeblich's (1976) proposal that dinoflagellate evolution may have been independent of that of the Eukaryotes. This concept can now be refined using an argumentation plansensu Hennig (Hennig and Schlee, 1978) and appears to be in accordance with the Mesokaryote model introduced by Dodge (1965).     

A unified theory for estimation of cardiac output, volumes of distribution and renal clearance from indicator dilution curves.

The assembly of cellular structures is considered to be a linear process that begins with the synthesis of structural molecules. At various points during assembly, additional genetic information may be required for proper assembly. Based on the location of genetic information expression during assembly, structure biogenesis can be grouped into four categories: (1) those which require only information for the synthesis of structural macromolecules; (2) those which require information for the post-translational modification of precursor structural macromolecules; (3) those which require genetic information for the actual assembly step; and (4) those which require information for post-assembly modification of the structure. Examples are given to illustrate and document each of these types of assembly reactions. Further, the usefulness of this scheme for understanding intracellular and extracellular assembly processes is discussed.     

Large‐scale analysis of intrinsic disorder flavors and associated functions in the protein sequence universe

Intrinsic disorder (ID) in proteins has been extensively described for the last decade; a large‐scale classification of ID in proteins is mostly missing. Here, we provide an extensive analysis of ID in the protein universe on the UniProt database derived from sequence‐based predictions in MobiDB. Almost half the sequences contain an ID region of at least five residues. About 9% of proteins have a long ID region of over 20 residues which are more abundant in Eukaryotic organisms and most frequently cover less than 20% of the sequence. A small subset of about 67,000 (out of over 80 million) proteins is fully disordered and mostly found in Viruses. Most proteins have only one ID, with short ID evenly distributed along the sequence and long ID overrepresented in the center. The charged residue composition of Das and Pappu was used to classify ID proteins by structural propensities and corresponding functional enrichment. Swollen Coils seem to be used mainly as structural components and in biosynthesis in both Prokaryotes and Eukaryotes. In Bacteria, they are confined in the nucleoid and in Viruses provide DNA binding function. Coils & Hairpins seem to be specialized in ribosome binding and methylation activities. Globules & Tadpoles bind antigens in Eukaryotes but are involved in killing other organisms and cytolysis in Bacteria. The Undefined class is used by Bacteria to bind toxic substances and mediate transport and movement between and within organisms in Viruses. Fully disordered proteins behave similarly, but are enriched for glycine residues and extracellular structures.     

Exploring prokaryotic diversity: there are other molecular worlds

Prokaryotes are the major source of biological diversity on earth. This is not simply because of the large number of species present, or because of their diverse growth conditions and environmental niches populated by them, but because of the wealth of genes, metabolic pathways and molecular processes that are only found in prokaryotic cells. Therefore, Bacteria and Archaea (and their phages) cannot be considered any longer as miniaturized models of Eukaryotes, but as a genuine source of unique biological processes that are mediated by unique sets of genes and molecular devices. A true understanding of complex biological phenomena will require a deeper knowledge of this vast prokaryotic world. The second European Molecular Biology Organization (EMBO) conference on Molecular Microbiology entitled 'Exploring Prokaryotic Diversity' explored many aspects of this newly emerging interest in the prokaryotic world.     

胞外和胞内菌胞外囊泡的功能及应用

细胞外囊泡(Extracellular Vesicles,EVs)是从细胞膜上脱落或者分泌的双层膜结构的囊泡状小体.真核生物、细菌、古细菌和支原体等具有细胞结构的生物均能够释放EVs.细菌分泌的EVs含有DNA、RNA及蛋白质等多种成分,其在细菌毒力保持、免疫逃逸、细菌间物质运输、宿主细胞免疫调节、宿主转录基因调节、耐...     

Immunological characterization of a major transformation-sensitive fibroblast cell surface glycoprotein. Localization, redistribution, and role in cell shape

The major cell surface glycoprotein of chick embryo fibroblasts, cellular fibronectin (formerly known as CSP or LETS protein), was purified and used to produce monospecific antisera. After affinity purification, the anti-fibronectin was used to investigate fibronectin's localization, its transfer from intracellular to extracellular pools, its antibody-induced redistribution on the cell surface, and its role in cell shape. Anti-fibronectin localizes to extracellular fibrils located under and between sparse cells, and to a dense matrix that surrounds confluent cells. Cellular fibronectin is also present in granular intracytoplasmic structures containing newly synthesized fibronectin before secretion. This intracellular staining disappears 2 h after treatment with cycloheximide or puromycin, and returns after removal of these protein synthesis inhibitors. In pulse-chase experiments using cycloheximide, fibronectin was sequentially transferred from the intracellular to the fibrillar extracellular forms. Transformation of chick fibroblasts results in decreases in both extracellular and intracellular fibronectin, and in altered cell shape. Treatment of untransformed chick fibroblasts with anti-fibronectin results in rapid (30 min) alteration to a rounder cell shape resembling that of many transformed cells. These rapid shape changes are followed by a slow, antibody-induced redistribution of fibronectin to supranuclear caplike structures. This "capping" is inhibited by metabolic inhibitors. Reconstitution of cell surface fibronectin onto transformed cells restores a more normal fibroblastic phenotype. The reconstituted fibronectin on these cells organizes into fibrillar patterns similar to those of untransformed cells. As with untransformed cells, treatment of these reconstituted cells with anti-fibronectin also results in cell rounding and "capping" of fibronectin.     

The crowd you're in with: Effects of different types of crowding agents on protein aggregation

The intracellular environment contains high concentrations of macromolecules occupying up to 30% of the total cellular volume. Presence of these macromolecules decreases the effective volume available for the proteins in the cell and thus increases the effective protein concentrations and stabilizes the compact protein conformations. Macromolecular crowding created by various macromolecules such as proteins, nucleic acids, and carbohydrates has been shown to have a significant effect on a variety of cellular processes including protein aggregation. Most studies of macromolecular crowding have used neutral, flexible polysaccharides that function primarily via excluded volume effect as model crowding agents. Here we have examined the effects of more rigid polysaccharides on protein structure and aggregation. Our results indicate that rigid and flexible polysaccharides influence protein aggregation via different mechanisms and suggest that, in addition to excluded volume effect, changes in solution viscosity and non-specific protein–polymer interactions influence the structure and dynamics of proteins in crowded environments.     

细胞穿膜肽介导蛋白/多肽类药物输送的研究进展

在当前药物研发中,蛋白/多肽类药物占据着重要地位。然而,此类药物大多需进入细胞内才能发挥作用,故细胞摄取率低的问 题成为制约其发展的关键因素。细胞穿膜肽是一类富含精氨酸的短肽,自身具有较强的生物膜穿透能力,可携带多种大分子甚至是纳米 粒入胞。因此,穿膜肽被广泛应用于药物输送,且基于穿膜肽介导药物胞内输送,成为解决蛋白/多肽类药物入胞问题的优选策略。主 要综述穿膜肽介导蛋白/多肽类药物输送用于不同疾病治疗的研究进展。     

Autophagy and related mechanisms of lysosome-mediated protein degradation

Lysosomes play a central role in the degradation of extracellular and intracellular macromolecules. These organelles contain hydrolytic enzymes capable of degrading proteins, proteoglycans, nucleic acids, and lipids. The mechanisms involved in the delivery of such intracellular compounds to the lysosome have been characterized in several recent studies. The sequestration of intracellular macromolecules for intralysosomal degradation can occur by crinophagy, hsc73-mediated carrier transport, or autophagy. The major route of delivery of cellular proteins and RNA into lysosomes is by autophagy. Furthermore, autophagy is regulated by nutrients and hormones, thus allowing the cell to adjust its degradative state to environmental changes.     

The release of radioactive nucleic acids and mucoproteins by trypsin and ethylenediaminetetra-acetate treatment of baby-hamster cells in tissue culture

Monolayers of baby-hamster kidney cells were grown on glass in tissue culture and harvested with trypsin or EDTA in order to investigate the cell surface macromolecules removed by these cell-disaggregating agents. The release of nucleic acids from the cells during the harvesting procedure was monitored by labelling the cellular RNA with [5-(3)H]uridine and the cellular DNA with [2-(14)C]thymidine. Treatment of the cells with EDTA was found to cause an increase in the permeability of the plasma membrane with 7.6% of the cellular RNA, but less than 1% of the cellular DNA, being released. Moreover, 61% of the cells harvested with EDTA were permeable to Trypan Blue. With crude trypsin, lysis of the cell occurred with the release of similar amounts of RNA and DNA amounting to about 11% of the total cellular nucleic acid. In contrast, crystalline trypsin released only 1% of the cellular nucleic acids. Since virtually all the cells (99%) after harvesting in crystalline trypsin were impermeable to Trypan Blue, this method was suitable for obtaining cell surface macromolecules without contamination by intracellular damage. [1-(14)C]Glucosamine was incorporated by the cells only into bound hexosamines and sialic acids. [By monitoring the release of radioactivity in high-molecular-weight material in such experiments a measure of the release of macromolecules containing amino sugars was obtained.] Of the total macromolecules containing amino sugars in the cells 33%, 24% and 13% were released when the cells were harvested with crude trypsin, crystalline trypsin or EDTA respectively. Crystalline trypsin also released 39% of the total sialic acid of the cell, whereas less than 1% of the cellular sialic acid was present in the EDTA-treated fraction. It is concluded that the macromolecules containing amino sugars released with crude trypsin and EDTA are likely to be heavily contaminated with intracellular material. However, the macromolecules released by crystalline trypsin appear to come from the cell surface.     

The Nuclear Pore Complex and Nuclear Transport

Internal membrane bound structures sequester all genetic material in eukaryotic cells. The most prominent of these structures is the nucleus, which is bounded by a double membrane termed the nuclear envelope (NE). Though this NE separates the nucleoplasm and genetic material within the nucleus from the surrounding cytoplasm, it is studded throughout with portals called nuclear pore complexes (NPCs). The NPC is a highly selective, bidirectional transporter for a tremendous range of protein and ribonucleoprotein cargoes. All the while the NPC must prevent the passage of nonspecific macromolecules, yet allow the free diffusion of water, sugars, and ions. These many types of nuclear transport are regulated at multiple stages, and the NPC carries binding sites for many of the proteins that modulate and modify the cargoes as they pass across the NE. Assembly, maintenance, and repair of the NPC must somehow occur while maintaining the integrity of the NE. Finally, the NPC appears to be an anchor for localization of many nuclear processes, including gene activation and cell cycle regulation. All these requirements demonstrate the complex design of the NPC and the integral role it plays in key cellular processes.Taxonomically speaking, all life on earth falls into one of two fundamental groups, the prokaryotes and the eukaryotes. The prokaryotes, the first group to evolve, are single cell organisms bounded by a single membrane. About 1.5 billion years later, a series of evolutionary innovations led to the emergence of eukaryotes. Eukaryotes have multiple inner membrane structures that allow for compartmentalization within the cell, and therefore differentiation of the cell and regulation within it. Ultimately, the greater cellular complexity of eukaryotes allowed them to adopt a multicellular lifestyle, as seen in the plants, fungi and animals of today (reviewed in Field and Dacks 2009).Internal membrane bound structures sequester all genetic material in eukaryotic cells. The most prominent of these structures, which gives the eukaryotes their Greek-rooted name, is the nucleus—the central “kernel” (gr. “karyo-”) of the cell. The nucleus is bounded by a double membrane termed the nuclear envelope (NE), which separates the nucleoplasm and genetic material from the surrounding cytoplasm. However the genetic material in the nucleus is not totally isolated from the rest of the cell. Studded throughout the NE are portals called nuclear pore complexes (NPCs). The NPC is a highly selective, bidirectional transporter for a tremendous range of cargoes. Going into the nucleus, these cargoes include inner nuclear membrane proteins and all the proteins in the nucleoplasm. Going out are RNA-associated proteins that are assembled into ribosomal subunits or messenger ribonucleoproteins (mRNPs). Once transported, the NPC must ensure these cargos are retained in their respective nuclear and cytoplasmic compartments. All the while the NPC must prevent the passage of nonspecific macromolecules, yet allow the free diffusion of water, sugars, and ions. These many types of nuclear transport are regulated at multiple stages, providing a powerful extra level of cellular control that is not necessary in prokaryotes. Assembly, maintenance, and repair of the NPC must somehow occur while maintaining the integrity of the NE. Finally, the NPC appears to be an anchor for localization of many nuclear processes, including gene activation and cell cycle regulation (reviewed in Ahmed and Brickner 2007; Hetzer and Wente 2009). All these requirements demonstrate the complex design of the NPC and the integral role it plays in key cellular processes.     

The cellular-induced decay of DMPO spin adducts of .OH and .O2

In a recent report, it was concluded that DMPO, often considered the spin trap of choice for detection of superoxide and hydroxyl radical adducts in biological systems, may be unsuitable for many biological uses because of its instability in cellular systems. It was demonstrated in red blood cells and in hamster V79 cells that the DMPO spin adducts of .O2- and .OH are metabolized very rapidly so that even if formed, they may not be detected in many experiments with cells. Because of the potential importance of these findings to experiments already reported on the occurrence of oxygen radicals in cellular systems, and the implications of these findings for future experiments, we have extended the studies on DMPO to other cellular, systems. We have also investigated the role of oxygen in this system because it has been shown recently that very hypoxic cells reduce some nitroxides much more rapidly than oxic cells and therefore it seemed possible that the rapid loss of radical adducts of DMPO was due to the hypoxic conditions under which the previous experiments were carried out. The results of the present experiments indicate that the loss of the DMPO spin adducts occurs in other cell systems as well, that the decomposition rate is independent of the concentration of oxygen, and that the final products of cellular metabolism of DMPO adducts are different from those of most nitroxides. There is no evidence that intracellular DMPO-spin adducts of oxygen radicals can be observed under conditions similar to those used in this study. We conclude that DMPO is not likely to be a suitable agent for studying intracellular oxygen radicals.     

柠檬醛抗黄曲霉作用的分子机理

以多组分山苍子[Litsea cubeba(Lour)Per]香精油作为复合中药模型。以该香精油中主要抗菌成分柠檬醛为中药靶部位,以能分泌致癌毒素的黄曲霉单细胞作为药物作用对象,吸收当今医学影像领域先进的科学技术,采用多学科交叉策略,将多维显微、瑞利光散射(Rayleigh scattering)、电镜与生化分析4项技术构筑平台, 从细胞、亚细胞和生物大分子三个水平,研究柠檬醛作用于黄曲霉的动静态过程,阐明模拟的中药方剂靶部位对细胞整体的作用规律.发现该醛不仅能改变黄曲霉细胞膜的形态结构、物理学特性及其生物学功能(如对物质吸收的选择通透性,细胞体积调节机制等),而且使细胞膜产生脂质过氧化损伤;进入细胞后,既作用于细胞器(如线粒体、细胞核等),使其产生损伤及区域性分布;又通过干扰细胞内大分子拥挤状态,导致细胞内生物大分子构象的改变、高含量类大分子缔合反应不可逆增强以及因生化反应区域效应丧失而产生的新陈代谢紊乱,揭示该醛能使黄曲霉孢子失去萌发力、菌丝体生长被抑制及产生孢子的能力,在于黄曲霉细胞膜、细胞器及大分子失去了正常结构、功能及相关的调节机制.在实现对柠檬醛抗黄曲霉机理阐明的过程中,在研究思路和方法上进行全新的探索.     

Macromolecular NMR spectroscopy for the non-spectroscopist

NMR spectroscopy is a powerful tool for studying the structure, function and dynamics of biological macromolecules. However, non-spectroscopists often find NMR theory daunting and data interpretation nontrivial. As the first of two back-to-back reviews on NMR spectroscopy aimed at non-spectroscopists, the present review first provides an introduction to the basics of macromolecular NMR spectroscopy, including a discussion of typical sample requirements and what information can be obtained from simple NMR experiments. We then review the use of NMR spectroscopy for determining the 3D structures of macromolecules and examine how to judge the quality of NMR-derived structures.     

Mechanisms of intercellular adhesion.

Investigations into cellular adhesion, both of a biochemical and biophysical nature, have not yet produced an established theory or widely accepted hypothesis to explain the mechanics of this fundamental biological process although much information concerning the structure and function of the mammalian cell surface has been gained. At the present time there is increasing evidence to suggest that cellular adhesion is mediated by specific cell surface macromolecules which are capable of forming protein-carbohydrate complexes possibly resembling those found between plant lectins and their carbohydrate substrates.     

Cytotoxic effects induced by oxidative stress in cultured mammalian cells and protection provided by Hsp27 expression

There is currently great interest in the development of methods to analyze intracellular redox state and the cellular damages generated by oxidative stress. General methods for analyzing reactive oxygen species and glutathione level are presented together with more recently developed protocols to analyze the consequences of oxidative stress on the oxidation of macromolecules. Finally, techniques to study modalities of constitutive expression of Hsp27 in mammalian cells are considered as well as methods used to determine the protective activity of this small heat shock protein against the deleterious effects induced by oxidative stress.     

Botulinum Neurotoxin Light Chain Inhibits Norepinephrine Secretion in PC12 Cells at an Intracellular Membranous or Cytoskeletal Site

Botulinum neurotoxin (NT) is a potent inhibitor of neurotransmitter secretion, but its intracellular mechanism and site of action are unknown. In this study, the intracellular action of NT was investigated by rendering the secretory apparatus of PC12 cells accessible to macromolecules by a recently described "cell cracking" procedure. Soluble cytoplasmic factors were depleted from permeabilized cells by washing to generate cell "ghosts" which retained cellular structural components and intracellular organelles (including secretory granules). The PC12 cell ghosts exhibited Ca(2+)-activated [3H]norepinephrine release which was enhanced by cytosolic proteins and MgATP. PC12 cell ghosts provide the opportunity to distinguish the intracellular action of NT on soluble cytoplasmic components versus structural cellular components. The 150-kDa NT and the 50-kDa light chain of serotypes E and B, and to a lesser extent type A, inhibited Ca(2+)-activated [3H]norepinephrine release in PC12 ghosts, but not in intact PC12 cells. The 100-kDa heavy chain had no effect. This indicates that NT acts at an intracellular site in these cells permeabilized by "cell cracking." The inhibition of secretion by NT was rapid and irreversible under the incubation conditions used. NT inhibition of [3H]-norepinephrine release from PC12 ghosts occurred in the absence of cytosolic proteins and MgATP and was not reversed by the addition of cytosolic proteins and MgATP, indicating that NT acts at an intracellular membranous or cytoskeletal site.     

Intracellular signal transduction as a factor in the development of "smart" biomaterials for bone tissue engineering

Signal transduction involves studying the intracellular mechanisms that govern cellular responses to external stimuli such as hormones, cytokines, and also cell adhesion to biomaterials surfaces. Several events have been shown to be responsible for cellular adhesion and adaptation onto different surfaces. For instance, cytoskeletal rearrangements during cell adhesion require the recruitment of specific protein tyrosine kinases into focal adhesion structures that promote transient focal adhesion kinase and Src phosphorylations, initially modulating cell behavior. In addition, the phosphorylation of tyrosine (Y) residues have been generally accepted as a critical regulator of a wide range of cell-related processes, including cell proliferation, migration, differentiation, survival signalling, and energy metabolism. The understanding of the signaling involved on the mechanisms of osteoblast adhesion, proliferation, and differentiation on implant surfaces is fundamental for the successful design of novel "smart" materials, potentially decreasing the repair time, thereby allowing for faster patient rehabilitation.