The genome of the simian and human malaria parasite Plasmodium knowlesi.

Plasmodium knowlesi is an intracellular malaria parasite whose natural vertebrate host is Macaca fascicularis (the 'kra' monkey); however, it is now increasingly recognized as a significant cause of human malaria, particularly in southeast Asia. Plasmodium knowlesi was the first malaria parasite species in which antigenic variation was demonstrated, and it has a close phylogenetic relationship to Plasmodium vivax, the second most important species of human malaria parasite (reviewed in ref. 4). Despite their relatedness, there are important phenotypic differences between them, such as host blood cell preference, absence of a dormant liver stage or 'hypnozoite' in P. knowlesi, and length of the asexual cycle (reviewed in ref. 4). Here we present an analysis of the P. knowlesi (H strain, Pk1(A+) clone) nuclear genome sequence. This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome and other sequenced Plasmodium genomes. In contrast to other Plasmodium genomes, putative variant antigen families are dispersed throughout the genome and are associated with intrachromosomal telomere repeats. One of these families, the KIRs, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry.

Continuous infusions of midazolam and interrupted hydration - such as insulin infusions without glucose?

The Liverpool Care Pathway (LCP) for the dying patient is a UK care pathway covering palliative care options for patients in the final days or hours of life; it has recently been recommended for decommission in the UK following an independent review. The pathway was widely implemented in UK hospitals in part because of governmental financial incentives. One of the criticisms of the LCP included reports of the rapid escalation to continuous infusions of sedatives in patients who then became quickly unconscious and unable to communicate.

Complete genome sequence of the plant pathogen Erwinia amylovora strain ATCC 49946.

Erwinia amylovora causes the economically important disease fire blight that affects rosaceous plants, especially pear and apple. Here we report the complete genome sequence and annotation of strain ATCC 49946. The analysis of the sequence and its comparison with sequenced genomes of closely related enterobacteria revealed signs of pathoadaptation to rosaceous hosts.

The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.

Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod belonging to the genus Corynebacterium and the actinomycete group of organisms. The organism produces a potent bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which causes the symptoms of diphtheria. This potentially fatal infectious disease is controlled in many developed countries by an effective immunisation programme. However, the disease has made a dramatic return in recent years, in particular within the Eastern European region. The largest, and still on-going, outbreak since the advent of mass immunisation started within Russia and the newly independent states of the former Soviet Union in the 1990s. We have sequenced the genome of a UK clinical isolate (biotype gravis strain NCTC13129), representative of the clone responsible for this outbreak. The genome consists of a single circular chromosome of 2 488 635 bp, with no plasmids. It provides evidence that recent acquisition of pathogenicity factors goes beyond the toxin itself, and includes iron-uptake systems, adhesins and fimbrial proteins. This is in contrast to Corynebacterium's nearest sequenced pathogenic relative, Mycobacterium tuberculosis, where there is little evidence of recent horizontal DNA acquisition. The genome itself shows an unusually extreme large-scale compositional bias, being noticeably higher in G+C near the origin than at the terminus.

A mutation causing constitutive synthesis of the pyruvate dehydrogenase complex in Escherichia coli is located within the pdhR gene.

The aceE-aceF-lpd genes encoding the pyruvate dehydrogenase (PDH) complex of Escherichia coli are preceded by a gene encoding a putative transcriptional regulator, PdhR (formerly designated GenA). Enzymological tests and studies with pdhR-lacZ and aceE-lacZ translational fusions have shown that a constitutive mutation (acec816), which increases PDH complex synthesis to the pyruvate-induced level in the absence of inducer, is recessive to the wild-type pdhR gene in trans. Sequence comparisons further showed that the acec816 mutation affects a single site in the pdhR gene leading to an Arg118 (CGU)-->Cys (UGU) substitution in the PdhR protein. The results support the view that synthesis of the PDH complex is regulated from the pdhR promoter of a pdhR-aceEF-lpd operon.

Identification of a fatty acyl responsive regulator (FarR) in Escherichia coli.

FarR (formerly P30) has been identified as a fatty acid and fatty acyl-CoA responsive DNA-binding protein. It is encoded by the farR gene (g30) in the citric acid cycle gene cluster of E. coli (gltA-sdhCDAB-sucABCD-farR). The amplified FarR protein specifically bound to the farR promoter (PfarR) and exhibited weak binding to the citrate synthase and lipoamide dehydrogenase promoters. Binding at PfarR was abolished by long-chain fatty acids and their CoA thioesters. In DNaseI footprints, FarR binding at PfarR protected two sites, each characterised by two related 10-bp direct repeats. It is suggested that FarR autoregulates farR expression and may modulate citric acid cycle expression in response to long-chain fatty acids.

How the presence of three iron binding sites affects the iron storage function of the ferritin (EcFtnA) of Escherichia coli.

The iron storage proteins, ferritins, are found in all organisms which use iron. Here iron storage processes in the Escherichia coli ferritin (EcFtnA) are compared with those in human H-type ferritin (HuHF). Both proteins contain dinuclear iron centres that enable the rapid oxidation of 2 Fe(II) by O2. The presence of a third iron binding site in EcFtnA, although not essential for fast oxidation, causes the O2/Fe ratio to increase from 2 to 3-4. In EcFtnA the rate of iron oxidation falls markedly after the oxidation of 48 Fe(II) atoms/molecule probably because some of it remains at the oxidation site. However a compensatory physiological advantage is conferred because this iron is more readily available to meet the cell's needs.

Gene discovery in Plasmodium chabaudi by genome survey sequencing.

The first genome survey sequencing of the rodent malaria parasite Plasmodium chabaudi is presented here. In 766 sequences, 131 putative gene sequences have been identified by sequence similarity database searches. Further, 7 potential gene families, four of which have not previously been described, were discovered. These genes may be important in understanding the biology of malaria, as well as offering potential new drug targets. We have also identified a number of candidate minisatellite sequences that could be helpful in genetic studies. Genome survey sequencing in P. chabaudi is a productive strategy in further developing this in vivo model of malaria, in the context of the malaria genome projects.

M13 cloning of mung bean nuclease digested PCR fragments as a means of gap closure within A/T-rich, genome sequencing projects.

Obtaining the complete DNA sequence of a genome is often not straightforward. After standard shotgun sequencing strategies have been employed there are often gaps remaining and these can be the most intractable regions, frequently containing repeat sequences, "uncloneable" sequences and/or regions of potential secondary structure or differential base composition. In genomes with a high A/T content, such as Plasmodium falciparum and Dictyostelium discoideum, solving these gaps is a particularly difficult problem as the sequences concerned are "fragile" and easily denatured, commonly uncloneable and have a paucity of good oligonucleotide priming sites. Reported here is a simple, yet reliable method for determining the sequence of A/T-rich gap-spanning PCR products. This method relies on the slippage of the specificity of mung bean nuclease so that it digests A/T-rich double-stranded DNA into a set of deletion fragments that can then be cloned into M13, sequenced and the original sequence assembled therefrom.

Unusual features in organisation of capsular polysaccharide-related genes of C. jejuni strain X.

PCR probing of the genome of Campylobacter jejuni strain X using conserved capsular polysaccharide (CPS)-related genes allowed elucidation of a complete sequence of the respective gene cluster (cps). This is the largest known Campylobacter cps cluster (38 kb excluding flanking kps regions), which includes a number of genes not detected in other Campylobacter strains. Sequence analysis suggests genetic rearrangements both within and outside the cps gene cluster, a mechanism which may be responsible for mosaic organisation of sugar transferase-related genes leading to structural variability of the capsular polysaccharide (CPS).

Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli.

The repressor of the pdhR-aceEF-lpd operon of Escherichia coli, PdhR, was amplified to 23% of total cell protein and purified to homogeneity by heparin-agarose and cation-exchange chromatography. The purified protein is a monomer (M(r) 29,300) which binds specifically to DNA fragments containing the pdh promoter (Ppdh) in the absence of pyruvate. The pdh operator was identified by DNase I footprinting as a region of hyphenated dyad symmetry, +11AATTGGTaagACCAATT+27, situated just downstream of the transcript start site. In vitro transcription from Ppdh was repressed > 1000-fold by PdhR and this repression was antagonized in a concentration-dependent manner by its co-effector, pyruvate. Studies on RNA polymerase binding at Ppdh showed that RNA polymerase protects the -44 to +21 region in the absence of PdhR, but no RNA polymerase binding or protection upstream of +9 could be detected in the presence of PdhR. It is concluded that PdhR represses transcription by binding to an operator site centred at +19 such that effective binding of RNA polymerase is prevented.

Short-insert libraries as a method of problem solving in genome sequencing.

As the Human Genome Project moves into its sequencing phase, a serious problem has arisen. The same problem has been increasingly vexing in the closing phase of the Caenorhabditis elegans project. The difficulty lies in sequencing efficiently through certain regions in which the templates (DNA substrates for the sequencing process) form complex folded secondary structures that are inaccessible to the enzymes. The solution, however, is simply to break them up. Specifically, the offending fragments are sonicated heavily and recloned, as much smaller fragments, into pUC vector. The sequences obtained from the resulting library can subsequently be assembled, free from the effects of secondary structure, to produce high-quality, complete sequence. Because of the success and simplicity of this procedure, we have begun to use it for the sequencing of all regions in which standard primer walking has been at all difficult.

The pdhR-aceEF-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex.

Transcript mapping and studies with lacZ translational fusions have shown that the pdhR gene (formerly genA) is the proximal gene of the pdhR-aceE-aceF-lpd operon encoding the pyruvate dehydrogenase (PDH) complex of Escherichia coli. A pdhR-lpd read-through transcript (7.4 kb) initiating at the pyruvate-inducible pdh promoter, and a smaller lpd transcript (1.7 kb) initiating at the independent lpd promoter, were identified. Evidence showing that the pdhR gene product negatively regulates the synthesis of the PdhR protein and the PDH complex via the pdh promoter was obtained, with pyruvate (or a derivative) serving as the putative inducing coeffector. The partially purified PdhR protein was also found to specifically retard and protect DNA fragments containing the pdh promoter region. The pdh promoter was not strongly controlled by ArcA, FNR or CRP.

Iron(II) oxidation by H chain ferritin: evidence from site-directed mutagenesis that a transient blue species is formed at the dinuclear iron center.

The iron storage molecule, ferritin, consists of an iron core surrounded by a shell of 24 protein subunits, which, in mammals, are of two types, H and L. Prior to storage of iron as a hydrous ferric oxide within the protein shell, Fe(II) is catalytically oxidized at dinuclear centers within H chains. When 48 Fe(II) atoms/molecule were added to 1 microM recombinant human H chain apoferritin (apo-HuHF), in 0.1 M Mes (pH 6.5), oxidation was 80% complete within about 0.2 s while 99% of the Fe(II) was oxidized within 10 s. A broad visible absorption band (400-800 nm, with a maximum at 650 nm) appeared during the fast phase of Fe(II) oxidation. It reached a plateau at 0.2-0.3 s and then declined while Fe(II) oxidation proceeded to completion and absorbance in the near-UV (300-400 nm) increased. The transient visible species was not observed when Tyr-34 was replaced by phenylalanine or when other conserved amino acids at the ferroxidase centers were substituted by residues which are unable to bind iron or which alter the charge balance. When a second increment of 48 iron atoms was added, 10 min after the first, the visible absorbance was absent and the rate of oxidation slower. Restoration of full oxidative activity took over 24 h. The data indicate that the fast oxidation of Fe(II) by apo-HuHF and the transient visible absorbance associated with it are due to Fe(II) oxidation at the ferroxidase centers.

Dinuclear center of ferritin: studies of iron binding and oxidation show differences in the two iron sites.

The ferroxidase activity of human ferritin has previously been associated with a diiron site situated centrally within the four-helix bundle of H-type chains (HuHF). However, direct information about the site of Fe(II) binding has been lacking, and events between Fe(II) binding and its oxidation have not previously been studied. A sequential stopped-flow assay has now been developed to enable the dissection of binding and oxidation. It depends on the ability of 1,10-phenanthroline to complex protein-bound Fe(II) and to distinguish it from the more immediately available free Fe(II). This approach, aided by the use of site-directed variants, indicates that in HuHF and the non-heme ferritin of Escherichia coli the first 48 Fe(II) atoms/molecule added are bound and oxidized at the dinuclear centers. At a constant iron concentration, the rate of Fe(II) oxidation was maximal for additions of 2 Fe(II) atoms/subunit, consistent with a two-electron oxidation of the Fe(II) pair. Although, at low Fe(II)/protein ratios, no cooperativity in Fe(II) binding was observed; a preferred order of binding was deduced [Fe(II) binding first at site A and then at site B]. Binding of Fe(II) at both sites was essential for fast oxidation. Modification of site A ligands resulted in slow iron binding and slow oxidation. Modification of site B did not prevent Fe(II) binding at site A but greatly reduced its oxidation rate. These differences may mean that dioxygen is initially bound to Fe(II) at site B.

Stages in iron storage in the ferritin of Escherichia coli (EcFtnA): analysis of Mössbauer spectra reveals a new intermediate.

Iron uptake into the nonheme ferritin of Escherichia coli (EcFtnA) and its site-directed variants have been investigated by Mössbauer spectroscopy. EcFtnA, like recombinant human H chain ferritin (HuHF), oxidized Fe(II) at a dinuclear ferroxidase center situated at a central position within each subunit. As with HuHF, Mössbauer subspectra observed between 1 min and 24 h after Fe(II) addition were assigned to Fe(III) monomers, "c", mu-oxo-bridged dimers, "b", and clusters, "a", the latter showing magnetically split spectra, "d", at 4.1 K. Like those of HuHF, the mu-oxo-bridged dimers were formed at the ferroxidase centers. However, the analysis also revealed the presence of a new type of dimer, "e" (QS1 = 0.38 mm/s, IS1 = 0.51 mm/s and QS2 = 0.72 mm/s, IS2 = 0.50 mm/s), and this was also assigned to the ferroxidase center. Dimers "b" appeared to be converted to dimers "e" over time. Subspectra "e" became markedly asymmetric at temperatures above 90 K, suggesting that the two Fe(III) atoms of dimers "e" were more weakly coupled than in the mu-oxo-bridged dimers "b", possibly due to OH- bridging. Monomeric Fe(III), giving relaxation spectra "c", was assigned to a unique site C that is near the dinuclear center. In EcFtnA all three iron atoms seemed to be oxidized together. In contrast to HuHF, no Fe(III) clusters were observed 24 h after the aerobic addition of 48 Fe(II) atoms/molecule in wild-type EcFtnA. This implies that iron is more evenly distributed between molecules in the bacterial ferritins, which may account for its greater accessibility.

Tyrosyl radical formation during the oxidative deposition of iron in human apoferritin.

The radical chemistry of ferritin is incompletely understood. The present study was undertaken to investigate the production of radicals in H-chain recombinant human ferritin (HuHF) and mixed H/L-chain horse spleen ferritin (HoSF) and the potential role of radicals in the oxidative deposition of iron in these proteins. Radical production follows distinct pathways for the two proteins; an intact H-chain ferroxidase site is required for radical generation in both of them, however. With the H-chain HuHF, an EPR spectrum characteristic of a tyrosyl radical is seen following Fe2+ oxidation by O2 and, based on measurements with site-directed variants, is suggested to arise from residue Tyr-34 located in the vicinity of the ferroxidase site. The observation of this radical correlates with the observation of a 400-600 nm absorbance seen in stopped-flow kinetics studies which seems to require the presence of Tyr-34 (Bauminger et al. (1993) Biochem. J. 296, 709-714). The data are inconsistent, however, with the Tyr-34 radical being critically important in the protein-catalyzed mechanism of iron oxidation. Unlike HuHF, the radicals observed in L-chain-rich HoSF appear to arise from hydroxyl radical damage to the protein through Fenton chemistry. These latter radicals also appear to be centered on aromatic amino acids and may be derived from histidine.

Spectroscopic and voltammetric characterisation of the bacterioferritin-associated ferredoxin of Escherichia coli.

The bacterioferritin-associated ferredoxin (Bfd) of Escherichia coli is a 64-residue polypeptide encoded by the bfd gene located upstream of the gene (bfr) encoding the iron-storage haemoprotein, bacterioferritin. The Bfd sequence resembles those of the approximately 60-residue domains found in NifU proteins (required for metallocluster assembly), nitrite reductases, and Klebsiella pneumoniae nitrate reductase. These related-domains contain four well-conserved cysteine residues, which are thought to function as ligands to a [2Fe-2S] cluster. The Bfd protein was over-produced, purified, and characterised. Bfd was found to be a positively-charged monomer containing two iron atoms and two labile sulphides. Ultraviolet-visible, EPR, variable-temperature magnetic-circular dichroism and resonance Raman spectroscopies, together with cyclic voltogram measurements, revealed the presence of a [2Fe-2S]2+,+ centre (E1/2 = -254 mV) having remarkably similar properties to the Fe-S cluster of NifU. Bfd may thus be a 2Fe ferredoxin participating either in release/delivery of iron from/to bacterioferritin (or other iron complexes), or in iron-dependent regulation of bfr expression.

The complex repeats of Dictyostelium discoideum.

In the course of determining the sequence of the Dictyostelium discoideum genome we have characterized in detail the quantity and nature of interspersed repetitive elements present in this species. Several of the most abundant small complex repeats and transposons (DIRS-1; TRE3-A,B; TRE5-A; skipper; Tdd-4; H3R) have been described previously. In our analysis we have identified additional elements. Thus, we can now present a complete list of complex repetitive elements in D. discoideum. All elements add up to 10% of the genome. Some of the newly described elements belong to established classes (TRE3-C, D; TRE5-B,C; DGLT-A,P; Tdd-5). However, we have also defined two new classes of DNA transposable elements (DDT and thug) that have not been described thus far. Based on the nucleotide amount, we calculated the least copy number in each family. These vary between <10 up to >200 copies. Unique sequences adjacent to the element ends and truncation points in elements gave a measure for the fragmentation of the elements. Furthermore, we describe the diversity of single elements with regard to polymorphisms and conserved structures. All elements show insertion preference into loci in which other elements of the same family reside. The analysis of the complex repeats is a valuable data resource for the ongoing assembly of whole D. discoideum chromosomes.