Nuclear envelope transmembrane proteins (NETs) that are up-regulated during myogenesis

Background  

The nuclear lamina is a protein meshwork lining the inner nuclear membrane, which contains a polymer of nuclear lamins associated with transmembrane proteins of the inner nuclear membrane. The lamina is involved in nuclear structure, gene expression, and association of the cytoplasmic cytoskeleton with the nucleus. We previously identified a group of 67 novel putative nuclear envelope transmembrane proteins (NETs) in a large-scale proteomics analysis. Because mutations in lamina proteins have been linked to several human diseases affecting skeletal muscle, we examined NET expression during differentiation of C2C12 myoblasts. Our goal was to identify new nuclear envelope and lamina components whose expression is coordinated with muscle differentiation.     

Neutrophil elastase cleaves laminin-332 (laminin-5) generating peptides that are chemotactic for neutrophils

Proteolytic processing of laminin-332 by matrix metalloproteinase (MMP)-2 and MMP-14 has been shown to yield fragments that are promigratory for epithelial cells. During acute and chronic inflammation, proteases are elaborated by neutrophils and macrophages that can degrade basement membranes. We investigated the susceptibility of laminin-332 to degradation by the following neutrophil and macrophage proteases: neutrophil elastase (NE), cathepsin G, proteinase-3, and MMPs-2, -8, -9, and -12. Protease-specific differences were seen in the capacity to cleave the individual chains of laminin-332. NE and MMP-12 showed the greatest activity toward the gamma2 chain, generating a fragment similar in size to the gamma2x fragment generated by MMP-2. The digestion pattern of laminin-332 by degranulated neutrophils was nearly identical to that generated with NE alone. Digestion by supernatants of degranulated neutrophils was blocked by an inhibitor of NE, and NE-deficient neutrophils were essentially unable to digest laminin-332, suggesting that NE is the major neutrophil-derived protease that degrades laminin-332. In vivo, laminin gamma2 fragments were found in the bronchoalveolar lavage fluid of wild-type mice treated with lipopolysaccharide, whereas that obtained from NE-deficient mice showed a different cleavage pattern. In addition, NE cleaved a synthetic peptide derived from the region of human laminin gamma2 containing the MMP-2 cleavage site, suggesting that NE may generate laminin-332 fragments that are also promigratory. Both laminin-332 fragments generated by NE digestion and NE-digested laminin gamma2 peptide were found to be chemotactic for neutrophils. Collectively, these data suggest that degradation of laminin-332 by NE generates fragments with important biological activities.     

Designing TIMP (tissue inhibitor of metalloproteinases) variants that are selective metalloproteinase inhibitors

The tissue inhibitors of metalloproteinases (TIMPs) are endogenous inhibitors of the matrix metalloproteinases (MMPs), enzymes that play central roles in the degradation of extracellular matrix components. The balance between MMPs and TIMPs is important in the maintenance of tissues, and its disruption affects tissue homoeostasis. Four related TIMPs (TIMP-1 to TIMP-4) can each form a complex with MMPs in a 1:1 stoichiometry with high affinity, but their inhibitory activities towards different MMPs are not particularly selective. The three-dimensional structures of TIMP-MMP complexes reveal that TIMPs have an extended ridge structure that slots into the active site of MMPs. Mutation of three separate residues in the ridge, at positions 2, 4 and 68 in the amino acid sequence of the N-terminal inhibitory domain of TIMP-1 (N-TIMP-1), separately and in combination has produced N-TIMP-1 variants with higher binding affinity and specificity for individual MMPs. TIMP-3 is unique in that it inhibits not only MMPs, but also several ADAM (a disintegrin and metalloproteinase) and ADAMTS (ADAM with thrombospondin motifs) metalloproteinases. Inhibition of the latter groups of metalloproteinases, as exemplified with ADAMTS-4 (aggrecanase 1), requires additional structural elements in TIMP-3 that have not yet been identified. Knowledge of the structural basis of the inhibitory action of TIMPs will facilitate the design of selective TIMP variants for investigating the biological roles of specific MMPs and for developing therapeutic interventions for MMP-associated diseases.     

Two different H-type subunits from pea seed (Pisum sativum) ferritin that are responsible for fast Fe(II) oxidation

It was established that ferritin from pea seed is composed of 26.5 and 28.0kDa subunits, but the relationship between the two subunits is unclear. The present study by both MALDI-TOF-MS and MS/MS indicated that the 28.0kDa subunit is distinct from the 26.5kDa subunit although they might share high homology in amino acid sequence, a result suggesting that pea seed ferritin is encoded by at least two genes. This result is not consistent with previous proposal that the 28.0kDa subunit is converted into the 26.5kDa subunit upon cleavage of its N-terminal sequence by free radical. Also, present results indicated that pea seed ferritin contains two different kinds of ferroxidase centers located in the 28.0 and 26.5kDa subunits, respectively. This is an exception among all known ferritins. Therefore, it is of special interest to know the role of the two subunits in iron oxidative deposition. Spectrophotometric titration and stopped flow results indicated that 48 ferrous ions can be bound and oxidized by oxygen at the ferroxidase sites, demonstrating that all of the ferroxidase sites are active and involved in fast Fe(II) oxidation. However, unlike H and L subunits in horse spleen ferritin (HoSF), both the 28.0 and 26.5 subunits lack cooperation in iron turnover into the inner cavity of pea seed ferritin.     

Aggressive communication in fulmars (Fulmarus glacialis) competing for food

A simple model which considers communication of subjective resource value during aggressive encounters is developed. If different behavioural patterns differ in effectiveness (probability of winning) the model predicts that: (1) the expected cost should differ for different behaviour patterns; (2) when effectiveness increases, the associated cost should increase; and (3) the optimal choice should be influenced by the value the resource represents for the animal. These predictions were tested on field data from 1383 interactions between fulmars competing for food. In these interactions, one bird was the ‘owner’ who defended the food item and during the time of ownership ate pieces of the food item. The owner was regularly challenged and take-overs occurred in 22% of interactions. The effectiveness of a given behaviour pattern was measured as the proportion of interactions won. The cost was measured as the proportion of interactions that entailed physical fighting. Resource value was estimated indirectly by comparing time as owner with choice of behaviour. The results indicate that an animal's choice of behaviour influenced its probability of victory, and expected cost, and that effectiveness and cost correlate positively. Furthermore, the frequency with which different behaviours were observed is influenced by the value of the resource for the bird.     

Evidence that the nonparenchymal cells of the liver are the principal source of cholesteryl ester transfer protein in primates

Previous studies showed that 90% or more of the cholesteryl ester transfer protein (CETP) mRNA is contained in the liver of cynomolgus monkeys. The purpose of this study was to determine if the parenchymal cells (hepatocytes) were the hepatic cell type that contained that mRNA. The parenchymal and nonparenchymal cells were separated by standard methods, and the CETP, apoA-I, apoB, and apoE mRNA content of the preparation determined at each step in the purification process. ApoA-I and apoB are produced only in the parenchymal cells; apoE is produced by both cell types. The mRNA measurements showed that the CETP mRNA: apoA-I mRNA and the CETP mRNA: apoB mRNA ratios were more than 2500-fold greater in the nonparenchymal cell preparation than in the starting material, and that the purified parenchymal cell fraction was virtually devoid of CETP mRNA. In situ hybridization studies showed that, whereas the apoA-I mRNA signal was evenly distributed over the tissue section, the CETP mRNA signal was associated with the hepatic sinusoids, suggesting that it was the hepatic sinusoidal cells that were principally responsible for the high CETP mRNA levels in the liver. We conclude that the nonparenchymal cells are the principal source of CETP in the cynomolgus monkey.     

Some labels that are recognized on landmarks by the honeybee (Apis mellifera)

Freely flying bees were trained in a situation that resembled the natural task of a bee arriving at a foraging site that was located by a landmark. The bees' task was to locate the reward in the arm of the Y-choice apparatus, where a black pattern on a white background was displayed in one arm versus a white target in the other arm, at a range of 27 cm. The alternative patterns for the training included previously identified cues. They were: an oblique bar, three parallel oblique bars, an oblique grating, a square cross, six spokes, a large or a small spot, a spotty modulation, or a ring. The trained bees were given a variety of interleaved tests to discover the labels they had used to identify the patterns. A label is defined as the coincidence of cues that contributed to the recognition of a single landmark. The bees learned, firstly, the black area at the expected place, secondly, modulation caused by edges at the expected place. These cues were quantified and always available. In addition, the orientation cue was learned from a grating that covered the target, but was ignored in a single bar. The bees learned the positions of the centres of black and of radial symmetry. In tests, they also recognized unfamiliar cues that were not displayed in the training. The cues and preferences were similar to those used to discriminate between two targets. The new experiments validate some old conclusions that have been controversial for 40 years.     

Microtubule-dependent plus- and minus end-directed motilities are competing processes for nuclear targeting of adenovirus

Adenovirus (Ad) enters target cells by receptor-mediated endocytosis, escapes to the cytosol, and then delivers its DNA genome into the nucleus. Here we analyzed the trafficking of fluorophore-tagged viruses in HeLa and TC7 cells by time-lapse microscopy. Our results show that native or taxol-stabilized microtubules (MTs) support alternating minus- and plus end-directed movements of cytosolic virus with elementary speeds up to 2.6 micrometer/s. No directed movement was observed in nocodazole-treated cells. Switching between plus- and minus end-directed elementary speeds at frequencies up to 1 Hz was observed in the periphery and near the MT organizing center (MTOC) after recovery from nocodazole treatment. MT-dependent motilities allowed virus accumulation near the MTOC at population speeds of 1-10 micrometer/min, depending on the cell type. Overexpression of p50/dynamitin, which is known to affect dynein-dependent minus end-directed vesicular transport, significantly reduced the extent and the frequency of minus end-directed migration of cytosolic virus, and increased the frequency, but not the extent of plus end-directed motility. The data imply that a single cytosolic Ad particle engages with two types of MT-dependent motor activities, the minus end- directed cytoplasmic dynein and an unknown plus end- directed activity.     

Genes that are uniquely stress regulated in salt overly sensitive (sos) mutants

Repetitive rounds of differential subtraction screening, followed by nucleotide sequence determination and northern-blot analysis, identified 84 salt-regulated (160 mM NaCl for 4 h) genes in Arabidopsis wild-type (Col-0 gl1) seedlings. Probes corresponding to these 84 genes and ACP1, RD22BP1, MYB2, STZ, and PAL were included in an analysis of salt responsive gene expression profiles in gl1 and the salt-hypersensitive mutant sos3. Six of 89 genes were expressed differentially in wild-type and sos3 seedlings; steady-state mRNA abundance of five genes (AD06C08/unknown, AD05E05/vegetative storage protein 2 [VSP2], AD05B11/S-adenosyl-L-Met:salicylic acid carboxyl methyltransferase [SAMT], AD03D05/cold regulated 6.6/inducible2 [COR6.6/KIN2], and salt tolerance zinc finger [STZ]) was induced and the abundance of one gene (AD05C10/circadian rhythm-RNA binding1 [CCR1]) was reduced in wild-type plants after salt treatment. The expression of CCR1, SAMT, COR6.6/KIN2, and STZ was higher in sos3 than in wild type, and VSP2 and AD06C08/unknown was lower in the mutant. Salt-induced expression of VSP2 in sos1 was similar to wild type, and AD06C08/unknown, CCR1, SAMT, COR6.6/KIN2, and STZ were similar to sos3. VSP2 is regulated presumably by SOS2/3 independent of SOS1, whereas the expression of the others is SOS1 dependent. AD06C08/unknown and VSP2 are postulated to be effectors of salt tolerance whereas CCR1, SAMT, COR6.6/KIN2, and STZ are determinants that must be negatively regulated during salt adaptation. The pivotal function of the SOS signal pathway to mediate ion homeostasis and salt tolerance implicates AD06C08/unknown, VSP2, SAMT, 6.6/KIN2, STZ, and CCR1 as determinates that are involved in salt adaptation.     

Phylotranscriptomics of Swertiinae (Gentianaceae) reveals that key floral traits are not phylogenetically correlated

Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth. Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups. The subtribe Swertiinae (Gentianaceae) comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries. Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu, representing the range of floral diversity, using data from the nuclear and plastid genomes. Extensive topological conflicts were present between the nuclear and plastome trees. Three of the 15 genera represented by multiple species are polyphyletic in both trees. Key floral traits including corolla type, absence or presence of lobe scales, nectary type, nectary position, and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation. We also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits. These results highlight the complex evolutionary history of this subtribe. The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity.     

Application of principal component analysis for the optimisation of lead(II) biosorption

Current study was focused on optimising lead(II) biosorption carried out by living cells of Arthrospira platensis using Principal Component Analysis. Various experimental conditions were considered: initial metal concentration (50 and 100 mg/l), solution pH (4.0, 4.5, 5.0, 5.5) and contact time (10, 20, 30, 40, 50 and 60 min) at constant rotary speed 200 rpm. It was found that when the biomass was separated from experimental solutions by the filtration, almost 50% of initial metal dose was removed by the filter paper. Moreover, pH was the most important parameter influencing examined processes. The Principal Component Analysis indicated that the most optimum conditions for lead(II) biosorption were metal initial concentration 100 mg/l, pH 4.5 and time 60 min. According to the analysis of the first component it might be stated that the lead(II) uptake increases in time. In overall, it was found to be useful for analysing data obtained in biosorption experiments and eliminating insignificant experimental conditions. Experimental data fitted Langmuir and Dubinin–Radushkevich models indicating that physical and chemical absorption take place at the same time. Further studies are necessary to verify how sorption–desorption cycles affect A. platensis cells.     

Evidence that there are only two tRNA(Phe) genes in Escherichia coli.

pheV, one of the genes that code for tRNA(Phe), was deleted from the chromosome of a strain of Escherichia coli K-12. As a consequence of this mutation, expression of pheA, the gene for chorismate mutase P-prephenate dehydratase, the first enzyme in the terminal pathway of phenylalanine biosynthesis, was derepressed. Similar derepression of pheA has been reported in pheR mutants of E. coli K-12 (J. Gowrishankar and J. Pittard, J. Bacteriol. 150:1130-1137, 1982). Attempts to introduce a pheR mutation into the delta pheV strain failed under circumstances suggesting that this combination of mutations is lethal. Southern blot analysis of pheV+ and delta pheV strains indicated that there are only two tRNA(Phe) genes in E. coli. It is recommended that the names pheU and pheV be retained for these genes.     

Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species

Background  

The Bacteroidetes and Chlorobi species constitute two main groups of the Bacteria that are closely related in phylogenetic trees. The Bacteroidetes species are widely distributed and include many important periodontal pathogens. In contrast, all Chlorobi are anoxygenic obligate photoautotrophs. Very few (or no) biochemical or molecular characteristics are known that are distinctive characteristics of these bacteria, or are commonly shared by them.     

Structural analysis of fertilin(beta) cyclic peptide mimics that are ligands for alpha6beta1 integrin.

The NMR structural analysis of two fertilin(beta) mimics cyclo(EC2DC1)YNH2, 1, and cyclo(D2EC2D1C1)YNH2, 2 is described. Both of these mimics are moderate inhibitors of sperm-egg binding with IC50 values of 500 microm in a mouse in vitro fertilization assay. For peptide 1, the optimized conformations that best match the NMR data have a pseudo-type II' beta-turn with the linker and Glu at the i+1 and i+2 positions, respectively. The EC2D1C1 sequence is in a nonclassical (type IV) beta-turn. For peptide 2, the conformation that best matches the NMR data has two turns: a pseudo-type II' beta-turn in the D2EC2D1 sequence followed by a nonclassical beta-turn in the EC2D1C1 sequence. The Cbeta-Cbeta distance between E and D1 in peptide 1 is 9.1 A, in peptide 2, it is 7.7 A. Thus, one possibility for the high IC50 values of these cyclic peptides is that the acidic residues are not constrained to a sufficiently tight turn, and thus much entropy must still be lost upon binding to the alpha6beta1 integrin. This explains why the cyclic peptides are the same as linear peptides at inhibiting sperm-egg binding.     

Novel receptors for melatonin that mediate pigment dispersion are present in some melanophores of the pencil fish (Nannostomus)

1. Comparing the daytime and the night-time pigmentary patterns of the skin of the pencil fish, Nannostomus beckfordi, we noticed that specific regions of dark spots that were part of the night-time pattern became pale during the day.2. Microscopic observations revealed that melanosomes in the melanophores in those regions were aggregated during the day but became dispersed at night.3. These melanophores responded to melatonin by dispersal of melanosomes while the cells on other parts of the body responded to melatonin by aggregation of the pigment in the normal way.4. The melanophores that responded to melatonin by pigment dispersion responded normally to other hormones and neurotransmitters, as did those on other parts of the skin.5. The results indicate that, in addition to the known melatonin receptor that mediates the aggregation of melanosomes, there also exists an unusual receptor which mediates the dispersion of pigment in melanophores. We have tentatively designated this receptor the ‘beta-melatonin receptor’.