The apicoplast: a review of the derived plastid of apicomplexan parasites

The apicoplast is a plastid organelle, homologous to chloroplasts of plants, that is found in apicomplexan parasites such as the causative agents of Malaria Plasmodium spp. It occurs throughout the Apicomplexa and is an ancient feature of this group acquired by the process of endosymbiosis. Like plant chloroplasts, apicoplasts are semi-autonomous with their own genome and expression machinery. In addition, apicoplasts import numerous proteins encoded by nuclear genes. These nuclear genes largely derive from the endosymbiont through a process of intracellular gene relocation. The exact role of a plastid in parasites is uncertain but early clues indicate synthesis of lipids, heme and isoprenoids as possibilities. The various metabolic processes of the apicoplast are potentially excellent targets for drug therapy.     

Cryptosporidium: Genomic and biochemical features

Recent progress in understanding the unique biochemistry of the two closely related human enteric pathogens Cryptosporidium parvum and Cryptosporidium hominis has been stimulated by the elucidation of the complete genome sequences for both pathogens. Much of the work that has occurred since that time has been focused on understanding the metabolic pathways encoded by the genome in hopes of providing increased understanding of the parasite biology, and in the identification of novel targets for pharmacological interventions. However, despite identifying the genes encoding enzymes that participate in many of the major metabolic pathways, only a hand full of proteins have actually been the subjects of detailed scrutiny. Thus, much of the biochemistry of these parasites remains a true mystery.     

Nucleus-encoded genes for plastid-targeted proteins in Helicosporidium: functional diversity of a cryptic plastid in a parasitic alga

Plastids are the organelles of plants and algae that house photosynthesis and many other biochemical pathways. Plastids contain a small genome, but most of their proteins are encoded in the nucleus and posttranslationally targeted to the organelle. When plants and algae lose photosynthesis, they virtually always retain a highly reduced "cryptic" plastid. Cryptic plastids are known to exist in many organisms, although their metabolic functions are seldom understood. The best-studied example of a cryptic plastid is from the intracellular malaria parasite, Plasmodium, which has retained a plastid for the biosynthesis of fatty acids, isoprenoids, and heme by the use of plastid-targeted enzymes. To study a completely independent transformation of a photosynthetic plastid to a cryptic plastid in another alga-turned-parasite, we conducted an expressed sequence tag (EST) survey of Helicosporidium. This parasite has recently been recognized as a highly derived green alga. Based on phylogenetic relationships to other plastid homologues and the presence of N-terminal transit peptides, we have identified 20 putatively plastid-targeted enzymes that are involved in a wide variety of metabolic pathways. Overall, the metabolic diversity of the Helicosporidium cryptic plastid exceeds that of the Plasmodium plastid, as it includes representatives of most of the pathways known to operate in the Plasmodium plastid as well as many others. In particular, several amino acid biosynthetic pathways have been retained, including the leucine biosynthesis pathway, which was only recently recognized in plant plastids. These two parasites represent different evolutionary trajectories in plastid metabolic adaptation.     

Computational prediction of human metabolic pathways from the complete human genome

Background  

We present a computational pathway analysis of the human genome that assigns enzymes encoded therein to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary first step toward quantitative modeling of metabolism.     

Assessing the impact of Plasmodium falciparum genome sequencing

With the publication of the complete sequences for chromosomes 2 and 3 and the increasing availability of shotgun sequence covering most of its genome, Plasmodium falciparum biology is entering its post-genomic era. Analysis of the results generated to date has identified higher-order organisation of gene families involved in parasite pathology, provided information regarding the unique biology of this parasite and allowed the identification of potential chemotherapeutic drug targets. Continuing efforts to complete the P. falciparum genome and the availability of sequences from other protozoan parasites will facilitate a broader understanding of their biology, particularly with respect to their pathogenicity.     

Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas

Phytoplasmas and mycoplasmas are two groups of important pathogens in the bacterial class Mollicutes. Because of their economical and clinical importance, these obligate pathogens have attracted much research attention. However, difficulties involved in the empirical study of these bacteria, particularly the fact that phytoplasmas have not yet been successfully cultivated outside of their hosts despite decades of attempts, have greatly hampered research progress. With the rapid advancements in genome sequencing, comparative genome analysis provides a new approach to facilitate our understanding of these bacteria. In this study, our main focus is to investigate the evolution of gene content in phytoplasmas, mycoplasmas, and their common ancestor. By using a phylogenetic framework for comparative analysis of 12 complete genome sequences, we characterized the putative gains and losses of genes in these obligate parasites. Our results demonstrated that the degradation of metabolic capacities in these bacteria has occurred predominantly in the common ancestor of Mollicutes, prior to the evolutionary split of phytoplasmas and mycoplasmas. Furthermore, we identified a list of genes that are acquired by the common ancestor of phytoplasmas and are conserved across all strains with complete genome sequences available. These genes include several putative effectors for the interactions with hosts and may be good candidates for future functional characterization.     

Genotype networks in metabolic reaction spaces

Background  

A metabolic genotype comprises all chemical reactions an organism can catalyze via enzymes encoded in its genome. A genotype is viable in a given environment if it is capable of producing all biomass components the organism needs to survive and reproduce. Previous work has focused on the properties of individual genotypes while little is known about how genome-scale metabolic networks with a given function can vary in their reaction content.     

Metabolic complexity in the RNA world and implications for the origin of protein synthesis

Summary A model is presented for the evolution of metabolism and protein synthesis in a primitive, acellular RNA world. It has been argued previously that the ability to perform metabolic functions logically must have preceded the evolution of a message-dependent protein synthetic machinery and that considerable metabolic complexity was achieved by ribo-organisms (i.e., organisms in which both genome and enzymes are comprised of RNA). The model proposed here offers a mechanism to account for the gradual development of sophisticated metabolic activities by ribo-organisms and explains how such metabolic complexity would lead subsequently to the synthesis of genetically encoded polypeptides. RNA structures ancestral to modern ribosomes, here termed metabolosomes, are proposed to have functioned as organizing centers that coordinated, using base-pairing interactions, the order and nature of adaptor-mounted substrate/catalyst interactions in primitive metabolic pathways. In this way an ancient genetic code for metabolism is envisaged to have predated the specialized modern genetic code for protein synthesis. Thus, encoded amino acids initially would have been used, in conjunction with other encoded metabolites, as building blocks for biosynthetic pathways, a role that they retain in the metabolism of contemporary organisms. At a later stage the encoded amino acids would have been condensed together on similar RNA metabolosome structures to form the first genetically determined, and therefore biologically meaningful, polypeptides. On the basis of codon distributions in the modern genetic code it is argued that the first proteins to have been synthesized and used by ribo-organisms were predominantly hydrophobic and likely to have performed membrane-related functions (such as forming simple pore structures), activities essential for the evolution of membrane-enclosed cells.     

The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolic enzymes and their organization into metabolic pathways. Currently, it contains information on over 400 enzymes. In the last year the enzyme page was enhanced to contain more internal and external links; it also displays the different metabolic pathways in which each enzyme participates. In collaboration with the Nomenclature Commission of the International Union of Biochemistry and Molecular Biology, 35 UM-BBD enzymes were assigned complete EC codes during 2000. Bacterial oxygenases are heavily represented in the UM-BBD; they are known to have broad substrate specificity. A compilation of known reactions of naphthalene and toluene dioxygenases were recently added to the UM-BBD; 73 and 108 were listed respectively. In 2000 the UM-BBD is mirrored by two prestigious groups: the European Bioinformatics Institute and KEGG (the Kyoto Encyclopedia of Genes and Genomes). Collaborations with other groups are being developed. The increased emphasis on UM-BBD enzymes is important for predicting novel metabolic pathways that might exist in nature or could be engineered. It also is important for current efforts in microbial genome annotation.     

Replication and partitioning of the apicoplast genome of Toxoplasma gondii is linked to the cell cycle and requires DNA polymerase and gyrase

Apicomplexans are the causative agents of numerous important infectious diseases including malaria and toxoplasmosis. Most of them harbour a chloroplast-like organelle called the apicoplast that is essential for the parasites’ metabolism and survival. While most apicoplast proteins are nuclear encoded, the organelle also maintains its own genome, a 35 kb circle. In this study we used Toxoplasma gondii to identify and characterise essential proteins involved in apicoplast genome replication and to understand how apicoplast genome segregation unfolds over time. We demonstrated that the DNA replication enzymes Prex, DNA gyrase and DNA single stranded binding protein localise to the apicoplast. We show in knockdown experiments that apicoplast DNA Gyrase A and B, and Prex are required for apicoplast genome replication and growth of the parasite. Analysis of apicoplast genome replication by structured illumination microscopy in T. gondii tachyzoites showed that apicoplast nucleoid division and segregation initiate at the beginning of S phase and conclude during mitosis. Thus, the replication and division of the apicoplast nucleoid is highly coordinated with nuclear genome replication and mitosis. Our observations highlight essential components of apicoplast genome maintenance and shed light on the timing of this process in the context of the overall parasite cell cycle.     

The novel heme oxygenase-like protein from Plasmodiumfalciparum converts heme to bilirubin IXα in the apicoplast

The metabolic pathways in apicoplasts of human malaria parasites are promising drug targets. The apicomplexan parasites exhibit delayed cell death when their apicoplast is impaired, but the metabolic pathways within apicoplasts are poorly understood. A nuclear-encoded heme oxygenase (HO)-like protein with an apicoplast-targeted bipartite transit peptide was identified in the Plasmodiumfalciparum genome. Purified mature recombinant PfHO protein converted heme into bilirubin IXα as confirmed by high-performance liquid chromatography. In addition, PfHO required an iron chelator such as deferoxamine for complete activity. These observations lead to the conclusion that a novel enzymatic heme degradation system is present in human malaria parasites.     

Eco Cyc: encyclopedia of Escherichia coli genes and metabolism.

The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactions into 129 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc has many references to the primary literature, and is a (qualitative) computational model of E. coli metabolism. EcoCyc is available at URL http://ecocyc. PangeaSystems.com/ecocyc/     

Metabolic potential of the organic‐solvent tolerant Pseudomonas putida DOT‐T1E deduced from its annotated genome

Pseudomonas putida DOT‐T1E is an organic solvent tolerant strain capable of degrading aromatic hydrocarbons. Here we report the DOT‐T1E genomic sequence (6 394 153 bp) and its metabolic atlas based on the classification of enzyme activities. The genome encodes for at least 1751 enzymatic reactions that account for the known pattern of C, N, P and S utilization by this strain. Based on the potential of this strain to thrive in the presence of organic solvents and the subclasses of enzymes encoded in the genome, its metabolic map can be drawn and a number of potential biotransformation reactions can be deduced. This information may prove useful for adapting desired reactions to create value‐added products. This bioengineering potential may be realized via direct transformation of substrates, or may require genetic engineering to block an existing pathway, or to re‐organize operons and genes, as well as possibly requiring the recruitment of enzymes from other sources to achieve the desired transformation.     

Apicomplexan mitochondrial metabolism: a story of gains, losses and retentions

Apicomplexans form a large group of obligate intracellular parasites that occupy diverse environmental niches. To adapt to their hosts, these parasites have evolved sophisticated strategies to access host-cell nutrients and minimize exposure to the host's defence mechanisms. Concomitantly, they have drastically reshaped their own metabolic functions by retaining, losing or gaining genes for metabolic enzymes. Although several Apicomplexans remain experimentally intractable, bioinformatic analyses of their genomes have generated preliminary metabolic maps. Here, we compare the metabolic pathways of five Apicomplexans, focusing on their different mitochondrial functions, which highlight their adaptation to their individual intracellular habitats.