Perspectives on the origin of microfilaments, microtubules, the relevant chaperonin system and cytoskeletal motors--a commentary on the spirochaete origin of flagella

Differential size-dependent response patterns and antibiotic resistance development mechanism in anammox consortia

Antibiotic resistance is a global threat to human and animal health. Anaerobic ammonia oxidation (anammox) is an efficient and innovative wastewater treatment technology, which can be served as a promising approach to teat antibiotic wastewater. This study systematically investigated effects of sulfamethazine on the performance, microbial community dynamics and the resistome in anammox systems inoculated with different-sized granular sludge. The activity and performance of small (< 0.5 mm) anammox granules were more susceptible to sulfamethazine stress than those of medium (0.5-1.0 mm) and large (1.0-2.0 mm) granules. Sulfamethazine addition greatly increased the diversity and abundance of mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs). Based on the metagenomic analysis, the horizontal transfer of ARGs in the anammox system was upregulated through bacterial oxidative stress, pili synthesis and type IV secretion system. In addition, two strains of sulfamethazine-resistant bacteria (Pseudomonas asiatica sp. nov. and Pseudomonas shirazica sp. nov.) were isolated from the anammox system. Their whole genome sequencing results showed that the most abundant plasmid was pkF7158B, which mediated the horizontal transfer of two main multidrug resistance genes (cpxR and mexB). This work provides a holistic insight into microbial heterogeneity of different-sized anammox granular sludge and their evolution and resistance development mechanism.

Proteomic profiling of rabbit embryonic stem cells derived from parthenotes and fertilized embryos

Rabbit embryonic stem (rES) cells can be derived from various sources of embryos. However, understanding of the gene expression profile, which distincts embryonic stem (ES) cells from other cell types, is still extremely limited. In this study, we compared the protein profiles of three independent lines of rabbit cells, i.e., fibroblasts, fertilized embryo-derived stem (f-rES) cells, and parthenote-derived ES (p-rES) cells. Proteomic analyses were performed using two-dimensional gel electrophoresis (2-DE) and mass spectrometry. Collectively, the expression levels of 100 out of 284 protein spots differed significantly among these three cell types (p<0.05). Of those differentially expressed spots, 91% were identified in the protein database and represented 63 distinct proteins. Proteins with known identities are mainly localized in the cytoplasmic compartments (48%), nucleus (14%), and cytoskeletal machineries (13%). These proteins were majorly involved in biological functions of energy and metabolic pathways (25%), cell growth and maintenance (25%), signal transduction (14%), and protein metabolisms (10%). When protein expression levels among cell types were compared, six proteins associated with a variety of cellular activities, including structural constituents of the cytoskeleton (tubulins), structural molecule (KRT8), catalytic molecules (α-enolase), receptor complex scaffold (14-3-3 protein sigma), microfilament motor proteins (Myosin-9), and heat shock protein (HSP60), were found highly expressed in p-rES cells. Two proteins related to HSP activity and structural constituent of cytoskeleton in f-rES cells, and one structural molecule activity protein in fibroblasts showed significantly higher expression levels (p<0.05). Marker protein expressions in f-rES and p-rES cells were further confirmed by Western blotting and immunocytochemical staining. This study demonstrated unique proteomic profiles of the three rabbit cell types and revealed some novel proteins differentially expressed between f-rES and p-rES cells. These analyses provide insights into rES cell biology and would invite more in-depth studies toward rES cell applications.

Sphingosine-1-phosphate receptors stimulate macrophage plasma-membrane actin assembly via ADP release, ATP synthesis and P2X7R activation

Eukaryotic plasma membranes assemble actin filaments within seconds of activation of many receptors, especially during chemotaxis. Here, serum or sphingosine-1-phosphate stimulation of J774 and RAW macrophages released ADP within seconds into the extracellular medium, along with an adenylate kinase activity that converted ADP to ATP. ATP then activated the P2X7 receptor (P2X7R) that was necessary for a peak of plasma-membrane actin assembly within 5 to 10 seconds in P2X7R-expressing J774, RAW and primary macrophages. Neither actin assembly nor characteristic P2X7R channel activity was seen in response to ATP in P2X7R-knockout macrophages, as detected by patch-clamp analysis. Since P2X7R has been shown previously to form a macromolecular complex with actin we propose that it is involved in the membrane assembly of actin. Our data reveal a surprisingly rapid and complex relay of signaling and externalization events that precede and control actin assembly induced by sphingosine-1-phosphate. The overall model we present is strongly supported by the data presented in the accompanying paper that focuses on latex bead phagosomes.

Lipids regulate P2X7-receptor-dependent actin assembly by phagosomes via ADP translocation and ATP synthesis in the phagosome lumen

Latex bead phagosomes isolated from J774 macrophages polymerize actin. We show here that five lipids--phosphatidylinositol-4-phosphate, phosphatidylinositol-(4,5)-bisphosphate, sphingosine-1-phosphate (S1P), ceramide-1-phosphate and phosphatidic acid--stimulate both actin assembly and transport of ADP across the phagosomal membrane into the lumen. Once there, this ADP is converted to ATP by adenylate kinase activity. High luminal ATP concentrations correlated well with phagosome actin assembly under different conditions. The ATP-binding P2X7 receptor (P2X7R) was detected in phagosomes. Although S1P stimulated actin assembly by phagosomes from P2X7R-containing bone marrow macrophages, S1P-stimulated actin assembly was inhibited in phagosomes from cells lacking P2X7R. We propose that luminal ATP accumulates in response to selected lipids and activates the P2X7R that signals across the phagosomal membrane to trigger actin assembly on the cytoplasmic membrane surface. In the accompanying paper by Kuehnel et al. (doi:10.1242/jcs.034207), more evidence is provided in support of this model from the analysis of actin assembly at the plasma membrane of intact macrophages.

Molecular modeling of the axial and circumferential elastic moduli of tubulin

Microtubules play a number of important mechanical roles in almost all cell types in nearly all major phylogenetic trees. We have used a molecular mechanics approach to perform tensile tests on individual tubulin monomers and determined values for the axial and circumferential moduli for all currently known complete sequences. The axial elastic moduli, in vacuo, were found to be 1.25 GPa and 1.34 GPa for alpha- and beta-bovine tubulin monomers. In the circumferential direction, these moduli were 378 MPa for alpha- and 460 MPa for beta-structures. Using bovine tubulin as a template, 269 homologous tubulin structures were also subjected to simulated tensile loads yielding an average axial elastic modulus of 1.10 +/- 0.14 GPa for alpha-tubulin structures and 1.39 +/- 0.68 GPa for beta-tubulin. Circumferentially the alpha- and beta-moduli were 936 +/- 216 MPa and 658 +/- 134 MPa, respectively. Our primary finding is that that the axial elastic modulus of tubulin diminishes as the length of the monomer increases. However, in the circumferential direction, no correlation exists. These predicted anisotropies and scale dependencies may assist in interpreting the macroscale behavior of microtubules during mitosis or cell growth. Additionally, an intergenomic approach to investigating the mechanical properties of proteins may provide a way to elucidate the evolutionary mechanical constraints imposed by nature upon individual subcellular components.

Intracellular proadrenomedullin-derived peptides decorate the microtubules and contribute to cytoskeleton function

Adrenomedullin (AM) and proadrenomedullin N-terminal 20 peptide (PAMP) are secretory hormones, but it is not unusual to find them in intracellular compartments. Using yeast-2 hybrid technology, we found interactions between AM and several microtubule-associated proteins (MAPs), and between PAMP and tubulin. Expression of fluorescent-tagged AM and PAMP as well as immunofluorescence for the native peptides showed a complete decoration of the microtubules and colocalization with other MAPs. PAMP, but not AM, bound to tubulin in vitro and destabilized tubulin polymerization. Down-regulation of the gene coding for both AM and PAMP through small interfering RNA technology resulted in morphological changes, microtubule stabilization, increase in posttranslational modifications of tubulin such as acetylation and detyrosination, reduction in cell motility, and partial arrest at the G2 phase of the cell cycle, when compared with cells transfected with the same vector carrying a scrambled sequence. These results show that PAMP is a novel MAP, whereas AM may be exerting more subtle effects in regulating cytoskeleton function.

Cell evolution and the problem of membrane topology

Cells somehow evolved from primordial chemistry and their emergence depended on the co-evolution of the cytoplasm, a genetic system and the cell membrane. It is widely believed that the cytoplasm evolved inside a primordial lipid vesicle, but here I argue that the earliest cytoplasm could have co-evolved to high complexity outside a vesicle on the membrane surface. An invagination of the membrane, aided by an early cytoskeletal system, may have formed the first cells--initially within primordial vesicles.

Intelligent design and biological complexity

Before any intelligence can appear, a world endowed with the potential for being experienced as a body of phenomena has to be existent. Indeed, if there is to be an intelligence, there first has to be something intelligible. Hence, when an intelligence is present, "creation" must already have taken place. Nevertheless, biological complexity has been deemed by some to be one of the privileged points of insertion of a supernatural intelligence endowed with temporal and causal primacy. In the course of a critical review, it is pointed out that the spectacle of nature's spontaneous tinkering with the structures and performances of informational macromolecules and with interactive connections among these molecules suggests that intelligence and design are absent from evolution. Nor is intelligent design required for explaining biological complexity, which can increase spontaneously as a byproduct of combinatorial intermolecular gambles and of the restoration of molecular damage wrought by mutations. One of the possible molecular pathways to spontaneous evolutionary increases in complexity is described.

Evolution of intraflagellar transport from coated vesicles and autogenous origin of the eukaryotic cilium

The cilium/flagellum is a sensory-motile organelle ancestrally present in eukaryotic cells. For assembly cilia universally rely on intraflagellar transport (IFT), a specialised bidirectional transport process mediated by the ancestral and conserved IFT complex. Based on the homology of IFT complex proteins to components of coat protein I (COPI) and clathrin-coated vesicles, we propose that the non- vesicular, membrane-bound IFT evolved as a specialised form of coated vesicle transport from a protocoatomer complex. IFT thus shares common ancestry with all protocoatomer derivatives, including all vesicle coats and the nuclear pore complex (NPC). This has major implications for the evolutionary origin of the cilium. First, it reinforces the tenet that duplication and divergence of pre-existing structures, rather than symbiosis, were the major themes during cilium evolution. Second, it suggests that the initial step in the autogenous origin of the cilium was the establishment of a membrane patch with transmembrane proteins transported by the ancestral vesicle-coating IFT complex. We propose a scenario for how the initial membrane patch gradually protruded to enhance exposure to the environment, then started to move, and finally compartmentalised to render receptor signalling and ciliary beating more efficient.

The Cytomatrix as a Cooperative System of Macromolecular and Water Networks

Water was called by Szent-Gyorgi "life's mater and matrix, mother and medium." This chapter considers both aspects of his statement. Many astrobiologists argue that some, if not all, of Earth's water arrived during cometary bombardments. Amorphous water ices of comets possibly facilitated organization of complex organic molecules, kick-starting prebiotic evolution. In Gaian theory, Earth retains its water as a consequence of biological activity. The cell cytomatrix is a proteinaceous matrix/lattice incorporating the cytoskeleton, a pervasive, holistic superstructural network that integrates metabolic pathways. Enzymes of metabolic pathways are ordered in supramolecular clusters (metabolons) associated with cytoskeleton and/or membranes. Metabolic intermediates are microchanneled through metabolons without entering a bulk aqueous phase. Rather than being free in solution, even major signaling ions are probably clustered in association with the cytomatrix. Chloroplasts and mitochondria, like bacteria and archaea, also contain a cytoskeletal lattice, metabolons, and channel metabolites. Eukaryotic metabolism is mathematically a scale-free or small-world network. Enzyme clusters of bacterial origin are incorporated at a pathway level that is architecturally archaean. The eucaryotic cell may be a product of serial endosymbiosis, a chimera. Cell cytoplasm is approximately 80% water. Water is indisputably a conserved structural element of proteins, essential to their folding, specificity, ligand binding, and to enzyme catalysis. The vast literature of organized cell water has long argued that the cytomatrix and cell water are an entire system, a continuum, or gestalt. Alternatives are offered to mainstream explanations of cell electric potentials, ion channel, enzyme, and motor protein function, in terms of high-order cooperative systems of ions, water, and macromolecules. This chapter describes some prominent concepts of organized cell water, including vicinal water network theory, the association-induction hypothesis, wave-cluster theory, phase-gel transition theories, and theories of low- and high-density water polymorphs.

New symbiotic hypothesis on the origin of eukaryotic flagella

The origin of eukaryotic flagella has long been a mystery. Here we review the possibility that flagella sprouted evolutionarily from the eukaryotic cell proper seems very unlikely because it is hard to imagine what function and benefit in natural selection the flagella would have provided to the cells when they first emerged as simple buds. Lynn Margulis' 1970 spirochete hypothesis, though popular still, has never been confirmed. Moreover, the absence of tubulin and axonemal dynein in the spirochetes and the incapability of the bacterial and eukaryotic membranes' making a continuum now suggest that the hypothesis is outdated. Tubulin genes were recently identified in a new bacteria division, verrucomicrobia, and microtubules have also been found in one of these species, epixenosomes, the defensive ectosymbionts. On the basis of these data, we propose a new symbiotic hypothesis: that the mid-ancestor of eukaryotic cells obtained epixenosomelike verrucomicrobia as defensive ectosymbionts and the ectosymbionts later became endosymbiotic. They still, however, protruded from the surface of their host to play their role. Later, many genes were lost or incorporated into the host genome. Finally, the genome, the bacterial membrane, and the endosymbiotic vesicle membrane were totally lost, and fingerlike protrusions with microtubules formed. As the cells grew larger, the defensive function of the protrusions eventually weakened and then vanished. Some of the protrusions took on a new role in cell movement, which led them to evolve into flagella. The key step in this process was that the dynein obtained from the host evolved into axonemal dyneins, attaching onto the microtubules and forming motile axonemes. Our hypothesis is unproven, but it offers a possible explanation that is consistent with current scientific thought. We hope that our ideas will stimulate additional studies on the origin of eukaryotic flagella and on investigations of verrucomicrobia. Whether such studies confirm, refine, or replace our hypothesis, they should nevertheless further our understanding of the origin of eukaryotic cells.