Pseudomonas aeruginosa diaminopimelate decarboxylase: evolutionary relationship with other amino acid decarboxylases

The lysA gene encodes meso-diaminopimelate (DAP) decarboxylase (E.C.4.1.1.20), the last enzyme of the lysine biosynthetic pathway in bacteria. We have determined the nucleotide sequence of the lysA gene from Pseudomonas aeruginosa. Comparison of the deduced amino acid sequence of the lysA gene product revealed extensive similarity with the sequences of the functionally equivalent enzymes from Escherichia coli and Corynebacterium glutamicum. Even though both P. aeruginosa and E. coli are Gram-negative bacteria, sequence comparisons indicate a greater similarity between enzymes of P. aeruginosa and the Gram- positive bacterium C. glutamicum than between those of P. aeruginosa and E. coli enzymes. Comparison of DAP decarboxylase with protein sequences present in data bases revealed that bacterial DAP decarboxylases are homologous to mouse (Mus musculus) ornithine decarboxylase (E.C.4.1.1.17), the key enzyme in polyamine biosynthesis in mammals. On the other hand, no similarity was detected between DAP decarboxylases and other bacterial amino acid decarboxylases.      

THE EFFECTS OF SODIUM CHLORIDE ON HIGHER PLANTS

(1) This review concentrates on the effect of sodium chloride on the growth of higher plants, being primarily concerned with relatively high concentrations i.e. 50 mmol 1^-1 and above, though something is also said about those instances when sodium acts as a micronutrient. Emphasis is placed on particular species or genera for which enough information is available to discuss possible mechanisms. (2) Trace amounts of sodium are required for the growth of plants using the C₄ pathway of carbon fixation and may also be important in plants with Crassulacean acid metabolism. (3) The increased growth of Beta vulgaris brought about by sodium chloride can in part be explained by a sparing effect on potassium. However, growth is still increased when sufficient potassium is available. Complementary studies with rubidium indicate that the hormone balance in the plant may be changed. Sodium chloride also increases the level of sucrose in storage roots and allows beet plants to withstand water stress more readily, possibly by increased turgor pressure. (4) Sodium chloride increases production of dry matter in C₄ species of Atriplex under conditions of low relative humidity because water loss is reduced and photo-synthesis hardly affected. (5) Succulence in many plants is stimulated by salinity. The essential basis of the phenomenon is an increased water potential gradient between the leaf and the external medium. In some instances, it is the accumulation of chloride which is important; in others it is the accumulation of cations, when potassium can be as effective as sodium. (6) Salinity reduces the final area achieved by growing leaves. Most of the studies have been made on Phaseolus vulgaris and an important early event is the reduction in the rate of expansion of the epidermal cells and this may be accompanied by a decrease in their number. Reduction of epidermal cell size is a result of water stress; sodium chloride may directly affect cell division, though water stress cannot be ruled out. Whether salinity brings about inhibition of cell division depends upon the calcium content of the medium – a high content is accompanied solely by a reduction in epidermal cell size. (7) Hormones, as yet unspecified, may play an important part in response of a growing leaf to salinity. However, there is no evidence that sodium chloride per se has an effect on hormone balance within the plant. So far, any measured changes in levels of specific hormones can be ascribed to the osmotic effects of the saline medium. (8) Two estimates by flux analysis of cytoplasmic concentration of sodium in plants growing in conditions of high salinity give a value of around 150 mmol 1^-1. There is no similar information for chloride. Other techniques (histochemistry and X-ray micro-probe analysis) give questionable information. (9) There is now extensive information to show that enzymes of halophytes (other than ATPases) do not differ significantly from those of other higher plants with respect to their sensitivity in vitro to sodium chloride. There is a need for further work with respect to the activity of enzymes in the presence of those metabolites which have the highest cytoplasmic concentration. (10) Sodium-stimulated ATPases have been isolated from plant cells but their distribution amongst higher plants is restricted. (11) There are a number of reports of changed metabolism brought about by saline treatments but it is not clear how far the effects of sodium chloride and water stress are confounded. (12) Sodium appears to increase the sucrose levels in sugar beet by an inhibitory effect on product starch-granule-bound ADP-glucose starch synthase. (13) Reversal of a sodium pump located at the plasmalemma might have an effect on cell turgor. (14) Sodium (like other monovalent cations) causes loss of materials from plant cells, possibly through an effect on carrier proteins; calcium prevents this from happening. Calcium also allows plants to grow better in saline conditions by a depression of sodium uptake by and transport within the plant. The properties and composition of the membranes of mesophytes and halophytes need to be compared. (15) A saline medium exerts a major effect on plant growth through water stress to which a halophyte must adapt. As well as this, the cytoplasmic concentration of sodium chloride must be kept lower than the total cellular concentration of the salt. Unless this happens, it is likely that enzymic activity will be reduced due, in some instances, to an unspecific effect of a high concentration of monovalent cations and/or chloride and in other instances to competition between sodium and other cations, specifically potassium, for activation sites on enzymes, e.g. pyruvate kinase. (16) Further work is required to separate the osmotic effects from the specific effect of sodium chloride after it has entered the plant. As well as this, it has become clear that more information is needed about the mineral nutrition of halophytes.     

Recognizing the forest for the trees: testing temporal patterns of cladogenesis using a null model of stochastic diversification

Computer simulations are developed and employed to examine the expected temporal distributions of nodes under a null model of stochastic lineage bifurcation and extinction. These Markovian models of phylogenetic process were constructed so as to permit direct comparisons against empirical phylogenetic trees generated from molecular or other information available solely from extant species. For replicate simulated phylads with n extant species, cumulative distribution functions (cdf's) of branching times were calculated, and compared (using the Kolmogorov-Smirnov test statistic D) to those from three published empirical trees. Molecular phylogenies for columbine plants and avian cranes showed statistically significant departures from the null expectations, in directions indicating recent and ancient species' radiations, respectively, whereas a molecular phylogeny for the Drosophila virilis species group showed no apparent historical clustering of branching events. Effects of outgroup choice and phylogenetic frame of reference were investigated for the columbines and found to have a predictable influence on the types of conclusions to be drawn from such analyses. To enable other investigators to statistically test for nonrandomness in temporal cladogenetic pattern in empirical trees generated from data on extant species, we present tables of mean cdf's and associated probabilities under the null model for expected branching times in phylads of varying size. The approaches developed in this report complement and extend those of other recent methods for employing null models to assess the statistical significance of pattern in evolutionary trees.      

The Effect of Salinity on Growth of Phaseolus vulgaris L.: I. Anatomical Changes in the First Trifoliate Leaf

When plants of Phaseolus vulgaris were grown in culture solutioncontaining 48 m mol l^–1 sodium chloride, the first trifoliateleaves were always smaller in area than those of control plants.The leaves of the salt-treated plants however could become thicker.This increase in thickness was brought about by the increasein the thickness of the spongy parenchyma layer. The palisadeparenchyma layer was always thinner than that in the controlleaves. While these latter leaves expanded predominantly bycell division, this only held for the early stages of expansionof the leaves of salt-treated plants. In this case cell divisionceased when the leaves were about half their maximal size andfurther increase in area was brought about by an increase involume of the spongy parenchyma cells.     

Amino acid size, charge, hydropathy indices and matrices for protein structure analysis

Background  

Prediction of protein folding and specific interactions from only the sequence (ab initio) is a major challenge in bioinformatics. It is believed that such prediction will prove possible if Anfinsen's thermodynamic principle is correct for all kinds of proteins, and all the information necessary to form a concrete 3D structure is indeed present in the sequence.     

Differential binding of lectins IL-2 and CSL to candida albicans and cancer cells

The demonstration that interleukin 2 (IL-2) is a lectin specific for oligomannosides allows to understand a new function for this cytokine: as a bifunctional molecule when bound to its receptor ss, IL-2 associates the latter which the CD3/TCR complex, interacting with oligosaccharides of CD3 through its carbohydrate-recognition domain (Zanetta et al. , 1996, Biochem. J., 318, 49-53). This induces the tyrosine phosphorylation of the IL-2R beta by ++p56(lck) , the first step of the IL-2-dependent signaling. Since this specific association is disrupted in vitro by oligomannosides with five and six mannose residues, we made the hypothesis that pathogenic cells or microorganisms could bind IL-2, consequently disturbing the IL-2- dependent response. This study shows that the pathogenic yeast Candida albicans (in contrast with nonpathogenic yeasts) binds high amounts of IL-2 as did cancer cells. In contrast with cancer cells, yeasts do not bind the Man6GlcNAc2-specific lectin CSL, an endogenous "amplifier of activation signals" (Zanetta et al. , 1995, Biochem. J., 311, 629-636).