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.     

Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis

QTL detection experiments in livestock species commonly use the half-sib design. Each male is mated to a number of females, each female producing a limited number of progeny. Analysis consists of attempting to detect associations between phenotype and genotype measured on the progeny. When family sizes are limiting experimenters may wish to incorporate as much information as possible into a single analysis. However, combining information across sires is problematic because of incomplete linkage disequilibrium between the markers and the QTL in the population. This study describes formulæ for obtaining MLEs via the expectation maximization (EM) algorithm for use in a multiple-trait, multiple-family analysis. A model specifying a QTL with only two alleles, and a common within sire error variance is assumed. Compared to single-family analyses, power can be improved up to fourfold with multi-family analyses. The accuracy and precision of QTL location estimates are also substantially improved. With small family sizes, the multi-family, multi-trait analyses reduce substantially, but not totally remove, biases in QTL effect estimates. In situations where multiple QTL alleles are segregating the multi-family analysis will average out the effects of the different QTL alleles.     

The structure of 3-methylaspartase from Clostridium tetanomorphum functions via the common enolase chemical step.

Methylaspartate ammonia-lyase (3-methylaspartase, MAL; EC ) catalyzes the reversible anti elimination of ammonia from L-threo-(2S,3S)-3-methylaspartic acid to give mesaconic acid. This reaction lies on the main catabolic pathway for glutamate in Clostridium tetanomorphum. MAL requires monovalent and divalent cation cofactors for full catalytic activity. The enzyme has attracted interest because of its potential use as a biocatalyst. The structure of C. tetanomorphum MAL has been solved to 1.9-A resolution by the single-wavelength anomalous diffraction method. A divalent metal ion complex of the protein has also been determined. MAL is a homodimer with each monomer consisting of two domains. One is an alpha/beta-barrel, and the other smaller domain is mainly beta-strands. The smaller domain partially occludes the C terminus of the barrel and forms a large cleft. The structure identifies MAL as belonging to the enolase superfamily of enzymes. The metal ion site is located in a large cleft between the domains. Potential active site residues have been identified based on a combination of their proximity to a metal ion site, molecular modeling, and sequence homology. In common with all members of the enolase superfamily, the carboxylic acid of the substrate is co-ordinated by the metal ions, and a proton adjacent to a carboxylic acid group of the substrate is abstracted by a base. In MAL, it appears that Lys(331) removes the alpha-proton of methylaspartic acid. This motif is the defining mechanistic characteristic of the enolase superfamily of which all have a common fold. The degree of structural conservation is remarkable given only four residues are absolutely conserved.     

Complement components and terminal complement complex in oesophageal smooth muscle of patients with achalasia.

This study investigates whether patients with achalasia exhibit autoimmune reactions with subsequent complement activation within oesophageal smooth muscle, vessels and neurones. Oesophageal muscular biopsies from 8 patients undergoing surgery for achalasia and from 6 patients operated for oesophageal cancer were investigated by immunofluorescence for the presence of the complement components C1q, C4, C3c, C3d, C9 and the C9 neoantigen of the terminal C5b-C9 complement complex. Tissues were also investigated for the expression of immunoglobulins (G,A,M) and of the antigens of rubella and varicella zoster viruses. In addition, sera of both patient groups were tested for the presence of autoantibodies against Auerbach's plexus. The terminal complement complex C5b-C9 was found within muscle cells from all patients with achalasia but in only one specimen from a patient with cancer. Two patients with achalasia also exhibited the terminal complement complex as well as IgM within ganglion cells. Muscle cells stained positive for the complement component C9 in all five patients with achalasia in whom this test was performed but in none of the control tissues. In addition, sera from four patients with achalasia contained antibodies against Auerbach's plexus. Studies for the complement components C1q, C4, C3c and for antigens of rubella and varicella zoster viruses revealed negative results in all patients and controls. The results of this study suggest that a complement activation is involved in the autoimmune pathogenesis of achalasia. However, the triggering mechanism of this phenomenon remains to be determined.     

Theoretical considerations and probability models for the somatic development of the T-cell repertoire

A theory about the somatic development of the T-cell repertoire is described which explains the high proportion of alloreactive T lymphocytes as a side effect resulting from two biologically important selection processes. It is assumed that the T-cell receptors contain two binding sites X and Y similar to the two V regions of the B-cell receptors and immunoglobulin molecules, but with a different specificity repertoire as a result of the two selection processes. The first selection process is mediated by T-lineage inducer cells, which have already been postulated by Zinkernagel. They are believed to induce only cells with a binding site Y that can bind to major histocompatibility antigens (MHA) on the inducer cells. This selection forces the T-cell system to recognize preferentially cell-bound antigens; and it introduces under certain circumstances a high degree of self-MHA restriction and self-reactivity, and also a low degree of alloreactivity on the basis of cross-reactivity. The subsequent second selection process serves the purpose of self-tolerance induction. This process is expected under certain circumstances to result in a loss self-reactivity combined with a partial loss of self-restriction and selective enrichment of alloreactive T cells. Probability models are presented to illustrate how the two selection processes shape the T-cell repertoire and how the proportion of alloreactive cells is increased under special circumstances. It is possible that some T-cell subclasses are not affected by the second selection and maintain the primary repertoire. The theory is, in contrast to major competing theories, compatible with the assumption that the original V gene repertoires for the T-cell receptors are random.     

Organic Fertilization and Sufficient Nutrient Status in Prehistoric Agriculture? – Indications from Multi-Proxy Analyses of Archaeological Topsoil Relicts

Neolithic and Bronze Age topsoil relicts revealed enhanced extractable phosphorus (P) and plant available inorganic P fractions, thus raising the question whether there was targeted soil amelioration in prehistoric times. This study aimed (i) at assessing the overall nutrient status and the soil organic matter content of these arable topsoil relicts, and (ii) at tracing ancient soil fertilizing practices by respective stable isotope and biomarker analyses. Prehistoric arable topsoils were preserved in archaeological pit fillings, whereas adjacent subsoils served as controls. One Early Weichselian humic zone represented the soil status before the introduction of agriculture. Recent topsoils served as an additional reference. The applied multi-proxy approach comprised total P and micronutrient contents, stable N isotope ratios, amino acid, steroid, and black carbon analyses as well as soil color measurements. Total contents of P and selected micronutrients (I, Cu, Mn, Mo, Se, Zn) of the arable soil relicts were above the limits for which nutrient deficiencies could be assumed. All pit fillings exhibited elevated δ¹⁵N values close to those of recent topsoils (δ¹⁵N>6 to 7‰), giving first hints for prehistoric organic N-input. Ancient legume cultivation as a potential source for N input could not be verified by means of amino acid analysis. In contrast, bile acids as markers for faecal input exhibited larger concentrations in the pit fillings compared with the reference and control soils indicating faeces (i.e. manure) input to Neolithic arable topsoils. Also black carbon contents were elevated, amounting up to 38% of soil organic carbon, therewith explaining the dark soil color in the pit fillings and pointing to inputs of burned biomass. The combination of different geochemical analyses revealed a sufficient nutrient status of prehistoric arable soils, as well as signs of amelioration (inputs of organic material like charcoal and faeces-containing manure).     

Production of d-ribose by fermentation

The production of d-ribose by fermentation has received much attention lately, possibly because of the use of this pentose to synthesize antiviral and anticancer drugs. This review briefly outlines the methods that have been used to synthesize d-ribose since it was identified in yeast RNA, and focuses in particular on the latest developments in d-ribose fermentation, which have led to d-ribose yields that exceed 90 g/l. Furthermore, the various transketolase-deficient d-ribose-producing mutants that are used, and the biochemical and genetic rationales applied to select them or to enhance their d-ribose productivities, are dealt with. Attention is also drawn to the unusual pleiotropic characteristics of the mutant strains, as well as to the industrial and academic applications of d-ribose. Received: 29 January 1997 / Received revision: 13 March 1997 / Accepted: 15 March 1997     

Health and chemical burdens of fish species from polluted and hyper-eutrophic freshwater ecosystems in South Africa

Three aquatic ecosystems in South Africa, the Hartbeespoort, Klipvoor and Bospoort Dams, are classified as hyper-eutrophic, because of high nutrient loads and chemical pollution. Water and two fish species, Clarias gariepinus and Cyprinus carpio, were collected from these dams to assess the impact of eutrophication and chemical pollutants on their health status. Water and muscle samples were analysed for organic and inorganic chemicals. Condition factor was determined and a necropsy performed to note any macroscopic abnormalities. A histology-based fish health assessment was done on the liver, kidney, gills and gonads. A number of fish from the three dams exhibited livers with fatty change and focal discoloration, skin lesions and parasites within the visceral cavity. The prevalence and severity of histopathology in the liver resulted in higher liver index values than the index values for kidneys and gills. Aluminium, silicon and chromium were detected in the water and muscle tissue. The DDT metabolite p,p’-DDE was present in both species, as well as in fish from the reference site, Marico-Bosveld Dam. Only C. gariepinus from Hartbeespoort Dam had p,p’-DDD levels higher than 5 µg g^?1 per edible portion. Water from hyper-eutrophic dams adversely affects the health of freshwater fish.