Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion

The diaminopimelic acid pathway of lysine biosynthesis has been suggested to provide attractive targets for the development of novel antibacterial drugs. Here we report the characterization of two enzymes from this pathway in the human pathogen Pseudomonas aeruginosa, utilizing structural biology, biochemistry and genetics. We show that tetrahydrodipicolinate N-succinyltransferase (DapD) from P. aeruginosa is specific for the L-stereoisomer of the amino substrate L-2-aminopimelate, and its D-enantiomer acts as a weak inhibitor. The crystal structures of this enzyme with L-2-aminopimelate and D-2-aminopimelate, respectively, reveal that both compounds bind at the same site of the enzyme. Comparison of the binding interactions of these ligands in the enzyme active site suggests misalignment of the amino group of D-2-aminopimelate for nucleophilic attack on the succinate moiety of the co-substrate succinyl-CoA as the structural basis of specificity and inhibition. P. aeruginosa mutants where the dapA gene had been deleted were viable and able to grow in a mouse lung infection model, suggesting that DapA is not an optimal target for drug development against this organism. Structure-based sequence alignments, based on the DapA crystal structure determined to 1.6 Å resolution revealed the presence of two homologues, PA0223 and PA4188, in P. aeruginosa that could substitute for DapA in the P. aeruginosa PAO1ΔdapA mutant. In vitro experiments using recombinant PA0223 protein could however not detect any DapA activity.     

Protein trafficking to plastids: one theme, many variations

Plastids are a diverse group of essential organelles in plants that include chloroplasts. The biogenesis and maintenance of these organelles relies on the import of thousands of nucleus-encoded proteins. The complexity of plastid structure has resulted in the evolution of at least four general import pathways that target proteins into and across the double membrane of the plastid envelope. Several of these pathways can be further divided into specialty pathways that mediate and regulate the import of specific classes of proteins. The co-ordination of import by these specialized pathways with changes in gene expression is critical for plastid and plant development. Moreover, protein import is acutely regulated in response to physiological and metabolic changes within the cell. In the present review we summarize the current knowledge of the mechanism of import via these pathways and highlight the regulatory mechanisms that integrate the plastid protein-trafficking pathways with the developmental and metabolic state of the plant.     

Cysteine synthase (CysM) of Mycobacterium tuberculosis is an O-phosphoserine sulfhydrylase: evidence for an alternative cysteine biosynthesis pathway in mycobacteria

The biosynthesis of cysteine is a crucial metabolic pathway supplying a building block for de novo protein synthesis but also a reduced thiol as a component of the oxidative defense mechanisms that appear particularly vital in the dormant state of Mycobacterium tuberculosis. We here show that the cysteine synthase CysM is, in contrast to previous annotations, an O-phosphoserine-specific cysteine synthase. CysM belongs to the fold type II pyridoxal 5'-phosphate-dependent enzymes, as revealed by the crystal structure determined at 2.1-angstroms resolution. A model of O-phosphoserine bound to the enzyme suggests a hydrogen bonding interaction of the side chain of Arg220 with the phosphate group as a key feature in substrate selectivity. Replacement of this residue results in a significant loss of specificity for O-phosphoserine. Notably, reactions with sulfur donors are not affected by the amino acid replacement. The specificity of CysM toward O-phosphoserine together with the previously established novel mode of sulfur delivery via thiocarboxylated CysO (Burns, K. E., Baumgart, S., Dorrestein, P. C., Zhai, H., McLafferty, F. W., and Begley, T. P. (2005) J. Am. Chem. Soc. 127, 11602-11603) provide strong evidence for an O-phosphoserine-based cysteine biosynthesis pathway in M. tuberculosis that is independent of both O-acetylserine and the sulfate reduction pathway. The existence of an alternative biosynthetic pathway to cysteine in this pathogen has implications for the design strategy aimed at inhibition of this metabolic route.     

Maternal care in the rockpool amphipod Apherusa jurinei: developmental and environmental cues

There is evidence that active, pre-emergence maternal brood care in amphipod crustaceans may be associated with ‘harsh’ environmental conditions. We examined, in the rockpool amphipod Apherusa jurinei, behavioural activities that may function as a form of active brood care. Only ovigerous females showed ‘curl’ and ‘stretch’ activities, with consequent flushing of the brood pouch and cycling of the eggs therein. There was a significant decline in these activities as embryonic development advanced and brood care almost ceased when well-developed embryos showed a heart pulse and self-ventilation. We propose that this pattern of brood care reflects changes in the physiological requirements of embryos as they develop within the egg membrane. In addition, ovigerous females showed significantly higher levels of brood care under lowered oxygen conditions. They achieved this by increasing the average duration of the ‘stretch’ component, with other brood care components remaining constant. Thus, developmental and environmental cues alter the components of active brood care in distinct ways. Experimental removal showed that the physical presence of eggs in the brood pouch is important in controlling the expression of brood care activities. However, females with all of their eggs removed continued to brood at low levels, suggesting that a maternal state also controls brood care. The sophisticated expression of active maternal brood care in amphipods under ‘harsh’ environmental conditions such as rockpools has implications both for individual reproductive success and the distribution and abundance of brooding versus nonbrooding species. Copyright 2002 Published by Elsevier Science Ltd on behalf of The Association for the Study of Animal Behaviour     

Statistical comparison of proximity matrices: applications in animal behaviour

Animal behaviour studies often require the diagnosis and statistical evaluation of patterns among individuals of a group. However, association values derived for all pairs of individuals are mathematically interrelated and, hence, difficult to evaluate. A general method of matrix comparison, called the Mantel test, is described which accounts for such interdependencies. In this test, two square difference matrices are compared to determine whether a statistical association exists between corresponding elements. For example, distances in one of the matrices might represent differences in songs for each pair of a group of birds, while distances in the other matrix could be the geographic distances between each of the same bird pairs; the test would assess whether or not birds close to one another have songs that are more similar than those pairs that are located further apart geographically. Distances in the matrices can be of a variety of sorts (depending on the application), including for instance geographic distances, morphological differences, or behavioural differences. The test has wide applicability in studies of animal behaviour, and we present three examples. First, dialects of splendid sunbirds (Nectarinia coccinigaster) were investigated to determine whether local or regional patterns of geographic variation in song were present, and whether birds with similar dialects were concentrated within the same habitat. Second, dominance hierarchies of white-throated sparrows (Zonotrichia albicollis) and dark-eyed juncos (Junco hyemalis oreganus) were analysed by constructing appropriate hypothesis matrices that were contrasted against a matrix summarizing behavioural interrelationships of flock members. In the third application, involving progressions of yellow baboons (Papio cynocephalus), an approach was developed to assess whether members of a given sex occur adjacent (or at least closer) to one another in progression order more often than expected by chance, and also whether individuals of a given sex tend to be found at or near the end of a progression more frequently than predicted. Other possible applications of the Mantel test are discussed, and a detailed computational example is included.     

Primary structure of the Dolichos biflorus seed lectin

The Dolichos biflorus seed lectin is a tetramer composed of equal amounts of two subunit types. The subunit types are structurally very similar, yet only the larger subunit exhibits the ability to bind carbohydrate. A cDNA clone representing the entire coding region of the D. biflorus lectin mRNA has been sequenced. This cDNA represents 1075 nucleotides of seed lectin mRNA encoding a polypeptide of Mr = 29,674. Analysis of the deduced sequence indicates that the NH2 termini and COOH termini of both lectin subunits are present within the mRNA coding region. This information supports previous data indicating that both subunits of the lectin are encoded by a single mRNA and that the difference between the subunit types apparently arises by the proteolytic removal of a 10-amino acid sequence from the COOH terminus of the larger subunit. Comparison of the D. biflorus seed lectin sequence to the sequence of other leguminous seed lectins indicates regions of extensive homology. The residues of concanavalin A involved in metal binding are highly conserved in the D. biflorus lectin, but those involved in saccharide binding show a much lower degree of conservation. Prediction of the secondary conformation of the D. biflorus polypeptide suggests that structures involved in the formation of quaternary structure in concanavalin A are also conserved.