Rate matrices for analyzing large families of protein sequences.

We propose and study a new approach for the analysis of families of protein sequences. This method is related to the LogDet distances used in phylogenetic reconstructions; it can be viewed as an attempt to embed these distances into a multidimensional framework. The proposed method starts by associating a Markov matrix to each pairwise alignment deduced from a given multiple alignment. The central objects under consideration here are matrix-valued logarithms L of these Markov matrices, which exist under conditions that are compatible with fairly large divergence between the sequences. These logarithms allow us to compare data from a family of aligned proteins with simple models (in particular, continuous reversible Markov models) and to test the adequacy of such models. If one neglects fluctuations arising from the finite length of sequences, any continuous reversible Markov model with a single rate matrix Q over an arbitrary tree predicts that all the observed matrices L are multiples of Q. Our method exploits this fact, without relying on any tree estimation. We test this prediction on a family of proteins encoded by the mitochondrial genome of 26 multicellular animals, which include vertebrates, arthropods, echinoderms, molluscs, and nematodes. A principal component analysis of the observed matrices L shows that a single rate model can be used as a rough approximation to the data, but that systematic deviations from any such model are unmistakable and related to the evolutionary history of the species under consideration.     

A low-resolution model of crystalline methionyl-transfer RNA synthetase from Escherichia coli

When submitted to a controlled proteolysis by trypsin, native methionyl-tRNA synthetase from Escherichia coli (a dimer of molecular weight 172,000) yields a well-defined fragment of molecular weight 64,000 composed of one single polypeptide chain. This fragment retains full specificity towards methionine and tRNA^met, and has unimpaired activity in both the activation reaction and aminoacyl-tRNA formation. Crystals of this active fragment have been studied by X-ray crystallography and, using two isomorphous heavy-atom derivatives, a 4 Å electron density map has been calculated.The molecule appears as an elongated ellipsoid of overall dimensions 90 Å × 43 Å × 43 Å. It is clearly built of two parts separated by a large cleft. The volume of one of these “domains” is approximately twice that of the other; these results are consistent with our present knowledge of the chemistry of the protein.     

Response of vegetation and vertebrate fauna to 23 years of fire exclusion in a tropical Eucalyptus open forest,Northern Territory,Australia

Abstract This opportunistic study compares the vegetation, fuel loads and vertebrate fauna of part of a 120‐ha block of tropical open forest protected from fire for 23 years, and an adjacent block burnt annually over this period. Total fuel loads did not differ significantly between the unburnt and annually burnt sites, but their composition was markedly different, with far less grassy fuel, but far more litter fuel, in the unburnt block. There were major differences between treatments in the composition of trees and shrubs, manifest particularly in the number of stems. There was no overall difference in plant species richness between the two treatments, but richness of woody species was far higher in the unburnt treatment, and of annual and perennial grasses, and perennial herbs in the annually burnt treatment. Change in plant species composition from annually burnt to unburnt treatment was directional, in that there was a far higher representation of rainforest‐associated species (with the percentage of woody stems attributable to ‘rainforest’ species increasing from 24% of all species in the annually burnt treatment to 43% in the unburnt treatment, that of basal area from 9% to 30%, that of species richness from 8% to 17%, and that of cover from 12 to 47%). The vertebrate species composition varied significantly between treatments, but there was relatively little difference in species richness (other than for a slightly richer reptile fauna in the unburnt treatment). Again, there was a tendency for species that were more common in the unburnt treatment to be rainforest‐associated species. The results from this study suggest that there is a sizeable and distinct set of species that are associated with relatively long‐unburnt environments, and hence that are strongly disadvantaged under contemporary fire regimes. We suggest that such species need to be better accommodated by fire management through strategic reductions in the frequency of burning.     

Evolution of genes,evolution of species: the case of aminoacyl-tRNA synthetases

All of the aminoacyl-tRNA synthetase (aaRS) sequences currently available in the data banks have been subjected to a systematic analysis aimed at finding gene duplications, genetic recombinations, and horizontal transfers. Evidence is provided for the occurrence (or probable occurrence) of such phenomena within this class of enzymes. In particular, it is suggested that the monomeric PheRS from the yeast mitochondrion is a chimera of the alpha and beta chains of the standard tetrameric protein. In addition, it is proposed that the dimeric and tetrameric forms of GlyRS are the result of a double and independent acquisition of the same specificity within two different subclasses of aaRS. The phylogenetic reconstructions of the evolutionary histories of the genes encoding aaRS are shown to be extremely diverse. While large segments of the population are consistent with the broad grouping into the three Woesian domains, some phylogenetic reconstructions do not place the Archae and the Eucarya as sister groups but, rather, show a gram-negative bacteria/eukaryote clustering. In addition, many individual genes pose difficulties that preclude any simple evolutionary scheme. Thus, aaRS's are clearly a paradigm of F. Jacob's "odd jobs of evolution" but, on the whole, do not call into question the evolutionary scenario originally proposed by Woese and subsequently refined by others.     

Die Haploidie der MÄnnchen und die Endopolyploidie in Einigen Geweben von Haplothrips (Thysanoptera)

Zusammenfassung Die Spermatogonien sind haploid, die Oögonien diploid, die Chromosomenzahl beträgt bei Haplothrips statices n=15. Die Ganglienzellen und die Nervenmutterzellen sind bei Männchen haploid, bei Weibchen diploid.Haploid sind bei den Männchen auch die Zellen der Epidermis, der Tracheenmatrix und des Hinterdarniepithels mindestens bis zur Pronymphe.Es findet demnach während der Entwicklung der von Haplothrips keine allgemeine Aufregulierung (Diploidisierung) der Zellen statt.Fettkörper, Mitteldarmepithel, Malpighigefäße und Oenocyten werden polyploid bis zu 32n. Dabei teilen sich im Fettkörper mindestens noch die 16-ploiden Zellkerne. Während im Mitteldarmepithel, den Malpighigefäßen und vermutlich auch im Fettkörper das Verhältnis der Polyploidie von l2 entsprechend der haploiden Ausgangsbasis der männlichen Zellen erhalten bleibt, wächst die Mehrzal der Oenocyten bei den Männchen stärker als bei den Weibchen.Mit Unterstützung der Deutschen Forschungsgemeinschaft.     

Beef liver L-glutamate dehydrogenase mechanism: Presteady state study of the catalytic reduction of 2.oxoglutarate by NADPH

The mechanism of the reduction of 2.oxoglutarate by NADPH and addition of NH₄⁺ catalyzed by L-glutamate dehydrogenase was investigated with the stopped flow technique, following dihydronicotinamide absorbance and fluorescence changes. We make conspicuous, as in the reverse reaction, the existence of prestationnary events, the characteristics of which strongly depend on the ligand addition order. If the E-NADPH-2.oxoglutarate complex is preformed, saturated with regard to each ligand, there is a burst associated with the oxidation of 0.7 mole of NADPH per mole of protomer, a first order process with a velocity constant of 300 ± 50 sec^?1. If this complex is not preformed, the burst has reduced amplitude and velocity constants, differences that suggest an isomerization step following the binding processes. Whichever the incubation order, the later evolution follows an exponential decrease towards equilibrium with a velocity constant depending on the ligand concentration up to an extrapolated value of 27 sec^?1, a step corresponding to the dissociation of the reaction products.     

Crystal structure study of Opsanus tau parvalbumin by multiwavelength anomalous diffraction

The crystal structure of a small calcium-binding protein, the parvalbumin IIIf from Opsanus tau in which Tb was substituted for Ca, has been analysed by multiwavelength anomalous diffraction. Data at a resolution of 2.3 A were collected at three wavelengths near the L3 absorption edge of Tb (1.645-1.650 A), using the synchrotron radiation emitted by a storage ring and a multiwire proportional counter. The phases of the reflections were determined from this single derivative, without native data. Prior to any refinement, the resulting electron density map shows a good agreement with the model of the homologous carp parvalbumin in regions of identical amino-acid sequence.     

Non Mycobacterial Virulence Genes in the Genome of the Emerging Pathogen Mycobacterium abscessus

Mycobacterium abscessus is an emerging rapidly growing mycobacterium (RGM) causing a pseudotuberculous lung disease to which patients with cystic fibrosis (CF) are particularly susceptible. We report here its complete genome sequence. The genome of M. abscessus (CIP 104536T) consists of a 5,067,172-bp circular chromosome including 4920 predicted coding sequences (CDS), an 81-kb full-length prophage and 5 IS elements, and a 23-kb mercury resistance plasmid almost identical to pMM23 from Mycobacterium marinum. The chromosome encodes many virulence proteins and virulence protein families absent or present in only small numbers in the model RGM species Mycobacterium smegmatis. Many of these proteins are encoded by genes belonging to a “mycobacterial” gene pool (e.g. PE and PPE proteins, MCE and YrbE proteins, lipoprotein LpqH precursors). However, many others (e.g. phospholipase C, MgtC, MsrA, ABC Fe(3+) transporter) appear to have been horizontally acquired from distantly related environmental bacteria with a high G+C content, mostly actinobacteria (e.g. Rhodococcus sp., Streptomyces sp.) and pseudomonads. We also identified several metabolic regions acquired from actinobacteria and pseudomonads (relating to phenazine biosynthesis, homogentisate catabolism, phenylacetic acid degradation, DNA degradation) not present in the M. smegmatis genome. Many of the “non mycobacterial” factors detected in M. abscessus are also present in two of the pathogens most frequently isolated from CF patients, Pseudomonas aeruginosa and Burkholderia cepacia. This study elucidates the genetic basis of the unique pathogenicity of M. abscessus among RGM, and raises the question of similar mechanisms of pathogenicity shared by unrelated organisms in CF patients.     

Chronic administration of losartan reverses cardiovascular changes in hypertensive fructose-fed rats.

The cluster of risk factors including hyperinsulinemia, insulin resistance, hypertriglyceridemia and hypertension has been called syndrome X. Several evidences link the insulin resistance syndrome with endothelial dysfunction. Since the participation of the renin-angiotensin system (RAS) in this pathology is still unclear, the present study examined the effect of chronic administration of an angiotensin AT1 receptor antagonist, losartan (L), on endothelial nitric oxide synthase (eNOS) activity in aortic endothelium and cardiac tissue, and on the proliferation of primary cultured aortic smooth muscle cells (SMC), obtained from fructose-fed rats (FFR), an experimental model of syndrome X Male Wistar rats were used: Control, FFR and FFR+L (n = 8 in each group). After 8 weeks, tissue samples were obtained and 10% fetal calf serum (FCS) proliferative effect was examined in SMC by 3H-thymidine incorporation and cell counting. The eNOS activity was estimated in aortic endothelial lining and cardiac homogenates by conversion of 3H-arginine into 3H-citrulline. FFR aortic SMC showed a significantly increased 10% FCS-induced 3H-thymidine incorporation and cell number compared to controls. FFR aortic and cardiac eNOS activities were significantly decreased. Chronic treatment with L decreased systolic blood pressure,reverted cardiac hypertrophy, abolished the increased SMC proliferation and restoredeNOS activity. These data confirm that changes in SMC proliferation and endothelial dysfunction at different levels of the cardiovascular system are involved in syndrome "X", and that AT1 receptor blocking can revert those changes, suggesting an important role of the RAS, possibly mediated by AT2 receptors and kinins, in the physiopathological mechanisms of this model.