Phylogenetic and regional variations in brain gangliosides of tetrapods.

1. Ganglioside patterns were analyzed from four neural tissues (medulla, midbrain, forebrain and retina) in a representative from each of the four tetrapod classes. 2. Regional variations in ganglioside patterns were noted within some species, but differences were greater across phylogenetic lines. 3. These results suggest that evolutionary history plays a greater role than neural differentiation in the expression of brain ganglioside patterns.     

Phylogenetic and ontogenetic study of neuropeptide Y-containing nerves in the liver

Summary The distribution of neuropeptide Y was investigated by light and electron microscopic immunohistochemistry in the liver of various vertebrates including the eel, carp, bullfrog, turtle, chicken, mouse, rat, guinea-pig, dog, monkey and human. The ontogenetic development of neuropeptide Y was also studied in the mouse liver. In all species examined except the eel, neuropeptide Y-like immunoreactivity was detected in nerve fibres. In the carp, bullfrog, turtle, chicken, mouse and rat, positive fibres were distributed around the wall of hepatic vessels and the bile duct of the Glisson's sheath. The density of the positive fibres increased with evolution. On the other hand, in the guinea-pig, dog, monkey and human, numerous neuropeptide Y-positive fibres were observed not only in the Glisson's sheath but also in the liver parenchyma. Positive fibres formed a dense network to surround hepatocytes. The present immunoelectron microscopic study has confirmed that neuropeptide Y-positive terminals are closely apposing to hepatocytes. Ontogenetically, neuropeptide Y-positive fibres were first found in embryonic liver of 19-day-old mice. Positive fibres increased with age and the highest peak was seen one week after birth. This ontogenetic pattern has suggested that neuropeptide Y plays a certain role in developing liver.     

The role of neuropeptide S and neuropeptide S receptor 1 in regulation of respiratory function in mice

Genome-wide screening and positional cloning have linked neuropeptide S receptor 1 (NPSR1) with asthma and airway hyperresponsiveness. However, the mechanism by which NPSR1 regulates pulmonary responses remains elusive. Because neuropeptide S and its receptor NPSR1 are expressed in brain regions that regulate respiratory rhythm, and Npsr1-deficient mice have impaired stress and anxiety responses, we aimed to investigate whether neuropeptide S and NPSR1 regulate respiratory function through a central-mediated pathway. After neuropeptide S intracerebroventricular administration, respiratory responses of wildtype and Npsr1-deficient mice were monitored by whole-body or invasive plethysmography with or without serial methacholine inhalation. Airway inflammatory and hyperresponsiveness were assessed in allergen-challenged (ovalbumin or Aspergillus fumigatus) Npsr1-deficient mice. Analysis of breathing patterns by whole-body plethysmography revealed that intracerebroventricular neuropeptide S, as compared with the artificial cerebral spinal fluid control, increased respiratory frequency and decreased tidal volume in an NPSR1-dependent manner but did not affect enhanced pause. Following serial methacholine inhalation, intracerebroventricular neuropeptide S increased respiratory frequency in wildtype mice, but not in Npsr1-deficient mice, and had no effect on tidal volume. Intracerebroventricular neuropeptide S significantly reduced airway responsiveness to methacholine as measured by whole-body plethysmography. Npsr1 deletion had no impact on airway inflammation or hyperresponsiveness in ovalbumin- or A. fumigatus-induced experimental asthma. Our results demonstrate that neuropeptide S and NPSR1 regulate respiratory function through a central nervous system-mediated pathway.     

Phylogenetic analysis of AAA proteins

AAA ATPases form a large protein family with manifold cellular roles. They belong to the AAA+ superfamily of ringshaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. Phylogenetic analyses have suggested the existence of five major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, and the MSP1/katanin/spastin group), as well as a number of deeply branching minor clades. These analyses however have been characterized by a lack of consistency in defining the boundaries of the AAA family. We have used cluster analysis to delineate unambiguously the group of AAA sequences within the AAA+ superfamily. Phylogenetic and cluster analysis of this sequence set revealed the existence of a sixth major AAA clade, comprising the mitochondrial, membrane-bound protein BCS1 and its homologues. In addition, we identified several deep branches consisting mainly of hypothetical proteins resulting from genomic projects. Analysis of the AAA N-domains provided direct support for the obtained phylogeny for most branches, but revealed some deep splits that had not been apparent from phylogenetic analysis and some unexpected similarities between distant clades. It also revealed highly degenerate D1 domains in plant MSP1 sequences and in at least one deeply branching group of hypothetical proteins (YC46), showing that AAA proteins with two ATPase domains arose at least three times independently.     

Partial processing of the neuropeptide Y precursor in transfected CHO cells

The activation of regulatory peptides by post-translational modification of their biosynthetic precursors is generally thought to occur only in neuroendocrine cells. We have selected clones of Chinese hamster ovary cells, a non-neuroendocrine cell line, which were transfected with a eukaryotic expression vector coding for the precursor for neuropeptide Y. Although the majority of the immunoreactive NPY was found in the form of pro-NPY, some degree of intracellular proteolytic processing of the precursor occurred in all clones. Part of the intracellular NPY immunoreactivity was even correctly amidated. Extracellular degradation of pro-NPY in the tissue culture medium generated immunoreactivity which corresponded in size to NPY. It is concluded that precursor processing can occur in non-neuroendocrine cells both as a biological process within the cells and as apparent processing, degradation in the tissue culture medium.     

Phylogenetic mixture models for proteins

Standard protein substitution models use a single amino acid replacement rate matrix that summarizes the biological, chemical and physical properties of amino acids. However, site evolution is highly heterogeneous and depends on many factors: genetic code; solvent exposure; secondary and tertiary structure; protein function; etc. These impact the substitution pattern and, in most cases, a single replacement matrix is not enough to represent all the complexity of the evolutionary processes. This paper explores in maximum-likelihood framework phylogenetic mixture models that combine several amino acid replacement matrices to better fit protein evolution.We learn these mixture models from a large alignment database extracted from HSSP, and test the performance using independent alignments from TREEBASE.We compare unsupervised learning approaches, where the site categories are unknown, to supervised ones, where in estimations we use the known category of each site, based on its exposure or its secondary structure. All our models are combined with gamma-distributed rates across sites. Results show that highly significant likelihood gains are obtained when using mixture models compared with the best available single replacement matrices. Mixtures of matrices also improve over mixtures of profiles in the manner of the CAT model. The unsupervised approach tends to be better than the supervised one, but it appears difficult to implement and highly sensitive to the starting values of the parameters, meaning that the supervised approach is still of interest for initialization and model comparison. Using an unsupervised model involving three matrices, the average AIC gain per site with TREEBASE test alignments is 0.31, 0.49 and 0.61 compared with LG (named after Le & Gascuel 2008 Mol. Biol. Evol. 25, 1307-1320), WAG and JTT, respectively. This three-matrix model is significantly better than LG for 34 alignments (among 57), and significantly worse for 1 alignment only. Moreover, tree topologies inferred with our mixture models frequently differ from those obtained with single matrices, indicating that using these mixtures impacts not only the likelihood value but also the output tree. All our models and a PhyML implementation are available from http://atgc.lirmm.fr/mixtures.     

Processing of pro-hormone precursor proteins

Peptide-hormones and other biologically active peptides are synthesized as higher molecular weight precursor proteins (pro-proteins) which must undergo post-translational modification to yield the bioactive peptide(s). These post-translational enzymatic events include limited endoproteolysis and may include other modifications of the generated peptide such as limited exopeptidase digestion, N-terminal acetylation, C-terminal amidation, and formation of N-terminal pyroglutamyl residues (pyrrolation). The secretory vesicle hypothesis, one of the major hypotheses regarding processing, states that the initial endoproteolytic event occurs upon formation of the secretory vesicle (or granule) or within the secretory vesicle from which the bioactive peptides are released. Two different endoproteinases which are likely to be physiologically relevant processing enzymes of pro-atrial natriuretic factor and pro-gonadotropin releasing hormone precursor protein, respectively, have recently been discovered in our laboratory and are discussed as model enzymes in the context of this hypothesis. The results indicate that the precursor protein and its complement of processing enzymes are co-packaged into the secretory granule. Evidence is presented to support the idea that the specific sequence and conformation (secondary structural features) of the processing recognition site within the precursor protein likely contribute in large part to the basis for limited endoproteolysis. In the pro-hormones studied, the recognition site is an extended sequence of five to seven residues which likely exists as a beta-turn at the surface of the precursor protein. By extending our results to appropriate protein sequences in the National Biomedical Research Foundation database, we are suggesting that in addition to the doublet of basic amino acids, the primary processing recognition site in pro-hormone precursor proteins often contains a monobasic amino acid or a strongly polar residue (Glu or Asp) in close sequence proximity to the doublet of basic residues.     

Phylogenetic analysis of RhoGAP domain-containing proteins

Proteins containing an Rho GTPase-activating protein （RhoGAP） domain work as molecular switches involved in the regulation of diverse cellular functions. The ability of these GTPases to regulate a wide number of cellular processes comes from their interactions with multiple effectors and inhibitors, including the RhoGAP family, which stimulates their intrinsic GTPase activity. Here, a phylogenetic approach was applied to study the evolutionary relationship among 59 RhoGAP domain-containing proteins. The sequences were aligned by their RhoGAP domains and the phylogenetic hypotheses were generated using Maximum Parsimony and Bayesian analyses. The character tracing of two traits, GTPase activity and presence of other domains, indicated a significant phylogenetic signal for both of them.     

Onset of neurophysin self-association upon neurophysin/neuropeptide hormone precursor biosynthesis

32P-Labelled washed rabbit platelets were incubated with 0.6 nM platelet activating factor (PAF-acether), giving a full aggregation and release response within 30-60 s. The major phospholipid changes observed under these conditions were: (1) An increased labelling of phosphatidic acid (PA) within 10 s and of phosphatidylinositol (MPI) at 30 s, reflecting the activation of the MPI cycle via the cytosolic phospholipase C; (2) an enhancement of phosphatidylinositol-4-phosphate (DPI) and phosphatidylinositol-4,5-bisphosphate (TPI) labelling at later incubation times; (3) an early degradation of TPI with a counterbalancing formation of DPI. The latter changes suggest a receptor-mediated stimulation of TPI-phosphomonoesterase, the role of which in the mechanism of platelet activation is discussed.     

The appearance of photosynthetic proteins in developing maize leaves

Soybean (Glycine max (L.) Merr.) protoplasts have been surface-labelled with cationized ferritin, and the fate of the label has been followed ultrastructurally. Endocytosis of the label occurs via the coated-membrane system. The pathway followed by the label, once it has been taken into the interior of the protoplast, appears to be similar to that found during receptor-mediated endocytosis in animal cells. Cationized ferritin is first seen in coated vesicles but rapidly appears in smooth vesicles. Labelled, partially coated vesicles are occasionally observed, indicating that the smooth vesicles may have arisen by the uncoating of coated vesicles. Structures which eventually become labelled with cationized ferritin include multivesicular bodies, dictyosomes, large smooth vesicles, and a system of partially coated reticula.Abbreviation CF cationized ferritin     

Temperature and hypoxia in ectothermic tetrapods

 

(1)

Interactions between temperature and hypoxia in ectothermic tetrapods (reptiles and amphibians) are reviewed.     

Structural studies of a neuropeptide precursor protein with an RGD proteolytic site

The snail Lymnaea stagnalis produces a neuropeptide precursor protein that contains seven Arg-Gly-Asp (RGD) sites. These sites are recognized and cleaved by one or more prohormone convertases in the first processing step to yield mature neuropeptides in the secretory pathway. Conformations of two synthetic RGD-containing peptides derived from the L. stagnalis precursor protein were determined by NMR spectroscopy. The peptides were tested in a platelet aggregation assay for RGD activity and were processed in vitro by PC2 and furin. The native peptide with a proline following the RGD site has minimal structure around the RGD region, does not inhibit platelet aggregation, and is properly processed by the enzymes PC2 and furin. A variant of the native fragment with a serine following the RGD sequence has a significant amount of a reverse turn around the RGD region, is a potent inhibitor of platelet aggregation, and is processed with the same specificity as the native fragment. The large conformational differences between the two peptides provide a molecular mechanism for effects of proline residues following the RGD site and suggest that precursor processing is influenced more by flexibility than by the conformation of the processing site.     

Anxiolytic-like effect of neuropeptide S in the rat defensive burying

Neuropeptide S (NPS) has been recently identified as the endogenous ligand of a previously orphan G-protein-coupled receptor now named NPSR. Both NPS and its receptor are expressed in the brain, where they modulate different functions. In particular, it has been demonstrated that intracerebroventricular (i.c.v.) injection of NPS in rodents increases wakefulness and promotes anxiolytic-like effects. In the present study we used the defensive burying (DB) test in rats to further investigate the action of human NPS (0.1–10 nmol, i.c.v.) on anxiety-related behaviors. Diazepam (1.5 mg/kg, i.p.) and caffeine (20 mg/kg, i.p.) were used in parallel experiments as standard anxiolytic and anxiogenic drugs, respectively. None of the tested drugs produced statistical differences in the latency to contact the probe, burying behavior latency, number of shocks received or immobility/freezing duration. Caffeine increased cumulative burying behavior and the buried bedding height in a statistically significant manner thus promoting anxiogenic like effects. Opposite results were obtained with diazepam that significantly reduced these behavioral parameters. The anxiolytic-like action of diazepam was mimicked by NPS that reduced cumulative burying behavior in a dose dependent manner. Collectively, robust anxiolytic-like effects were recorded in response to NPS in the DB test. These results are of particular interest since the outcome of this assay is marginally influenced by drug effects on locomotor activity. In conclusion, we provide further evidence that NPS evokes genuine anxiolytic-like effects in the rat; therefore NPSR selective agonists are worthy of development as innovative drugs for the treatment of anxiety disorders.     

Phylogenetic analysis of fungal centromere H3 proteins

Centromere H3 proteins (CenH3's) are variants of histone H3 specialized for packaging centromere DNA. Unlike canonical H3, which is among the most conserved of eukaryotic proteins, CenH3's are rapidly evolving, raising questions about orthology and conservation of function across species. To gain insight on CenH3 evolution and function, a phylogenetic analysis was undertaken on CenH3 proteins drawn from a single, ancient lineage, the Fungi. Using maximum-likelihood methods, a credible phylogeny was derived for the conserved histone fold domain (HFD) of 25 fungal CenH3's. The collection consisted mostly of hemiascomycetous yeasts, but also included basidiomycetes, euascomycetes, and an archaeascomycete. The HFD phylogeny closely recapitulated known evolutionary relationships between the species, supporting CenH3 orthology. The fungal CenH3's lacked significant homology in their N termini except for those of the Saccharomyces/Kluyveromyces clade that all contained a region homologous to the essential N-terminal domain found in Saccharomyces cerevisiae Cse4. The ability of several heterologous CenH3's to function in S. cerevisiae was tested and found to correlate with evolutionary distance. Domain swapping between S. cerevisiae Cse4 and the noncomplementing Pichia angusta ortholog showed that species specificity could not be explained by the presence or absence of any recognized secondary structural element of the HFD.     

Processing of precursor proteins by plant mitochondria

Precursor proteins from Neurospora crassa were correctly processed by a matrix extract from Vicia faba and cauliflower mitochondria. Processing yielded mature protein of the same molecular mass as mature Neurospora protein. The processing activity has two components. One is antigenically related to and of the same molecular mass as the processing enhancing protein of Neurospora. The second component was not recognized by antibody to the matrix processing protease from Neurospora mitochondria. The second component also houses the protease activity. Similar results were obtained using precursors to both the F1 beta subunit of the mitochondrial F0F1 ATPase and subunit V of the Rieske FeS complex from Neurospora. The beta subunit of the F0F1 ATPASE was processed to the mature form. Subunit V of the Rieske FeS complex was processed to the intermediate form only. Additional processing seen during import into plant mitochondria is not catalyzed by these proteins.     

A supertree of early tetrapods

A genus-level supertree for early tetrapods is built using a matrix representation of 50 source trees. The analysis of all combined trees delivers a long-stemmed topology in which most taxonomic groups are assigned to the tetrapod stem. A second analysis, which excludes source trees superseded by more comprehensive studies, supports a deep phylogenetic split between lissamphibian and amniote total groups. Instances of spurious groups are rare in both analyses. The results of the pruned second analysis are mostly comparable with those of a recent, character-based and large-scale phylogeny of Palaeozoic tetrapods. Outstanding areas of disagreement include the branching sequence of lepospondyls and the content of the amniote crown group, in particular the placement of diadectomorphs as stem diapsids. Supertrees are unsurpassed in their ability to summarize relationship patterns from multiple independent topologies. Therefore, they might be used as a simple test of the degree of corroboration of nodes in the contributory analyses. However, we urge caution in using them as a replacement for character-based cladograms and for inferring macroevolutionary patterns.