The Wolbachia Genome of Brugia malayi: Endosymbiont Evolution within a Human Pathogenic Nematode

Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial parasitic nematode Brugia malayi. Although, quantitatively, the genome is even more degraded than those of closely related Rickettsia species, Wolbachia has retained more intact metabolic pathways. The ability to provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely to be Wolbachia's principal contribution to the mutualistic relationship, whereas the host nematode likely supplies amino acids required for Wolbachia growth. Genome comparison of the Wolbachia endosymbiont of B. malayi (wBm) with the Wolbachia endosymbiont of Drosophila melanogaster (wMel) shows that they share similar metabolic trends, although their genomes show a high degree of genome shuffling. In contrast to wMel, wBm contains no prophage and has a reduced level of repeated DNA. Both Wolbachia have lost a considerable number of membrane biogenesis genes that apparently make them unable to synthesize lipid A, the usual component of proteobacterial membranes. However, differences in their peptidoglycan structures may reflect the mutualistic lifestyle of wBm in contrast to the parasitic lifestyle of wMel. The smaller genome size of wBm, relative to wMel, may reflect the loss of genes required for infecting host cells and avoiding host defense systems. Analysis of this first sequenced endosymbiont genome from a filarial nematode provides insight into endosymbiont evolution and additionally provides new potential targets for elimination of cutaneous and lymphatic human filarial disease

The genome of Brucella melitensis

The genome of Brucella melitensis strain 16M was sequenced and contained 3,294,931bp distributed over two circular chromosomes. Chromosome I was composed of 2,117,144bp and chromosome II has 1,177,787bp. A total of 3198 ORFs were predicted. The origins of replication of the chromosomes are similar to each other and to those of other α-proteobacteria. Housekeeping genes such as those that encode for DNA replication, protein synthesis, core metabolism, and cell-wall biosynthesis were found on both chromosomes. Genes encoding adhesins, invasins, and hemolysins were also identified. © 2002 Elsevier Science B.V. All rights reserved

Metabolic Network Analysis-Based Identification of Antimicrobial Drug Targets in Category A Bioterrorism Agents

<div><p>The 2001 anthrax mail attacks in the United States demonstrated the potential threat of bioterrorism, hence driving the need to develop sophisticated treatment and diagnostic protocols to counter biological warfare. Here, by performing flux balance analyses on the fully-annotated metabolic networks of multiple, whole genome-sequenced bacterial strains, we have identified a large number of metabolic enzymes as potential drug targets for each of the three Category A-designated bioterrorism agents including <i>Bacillus anthracis, Francisella tularensis and Yersinia pestis</i>. Nine metabolic enzymes- belonging to the coenzyme A, folate, phosphatidyl-ethanolamine and nucleic acid pathways common to all strains across the three distinct genera were identified as targets. Antimicrobial agents against some of these enzymes are available. Thus, a combination of cross species-specific antibiotics and common antimicrobials against shared targets may represent a useful combinatorial therapeutic approach against all Category A bioterrorism agents.</p></div

Comparative Genome-Scale Metabolic Reconstruction and Flux Balance Analysis of Multiple Staphylococcus aureus Genomes Identify Novel Antimicrobial Drug Targets▿ †

Mortality due to multidrug-resistant Staphylococcus aureus infection is predicted to surpass that of human immunodeficiency virus/AIDS in the United States. Despite the various treatment options for S. aureus infections, it remains a major hospital- and community-acquired opportunistic pathogen. With the emergence of multidrug-resistant S. aureus strains, there is an urgent need for the discovery of new antimicrobial drug targets in the organism. To this end, we reconstructed the metabolic networks of multidrug-resistant S. aureus strains using genome annotation, functional-pathway analysis, and comparative genomic approaches, followed by flux balance analysis-based in silico single and double gene deletion experiments. We identified 70 single enzymes and 54 pairs of enzymes whose corresponding metabolic reactions are predicted to be unconditionally essential for growth. Of these, 44 single enzymes and 10 enzyme pairs proved to be common to all 13 S. aureus strains, including many that had not been previously identified as being essential for growth by gene deletion experiments in S. aureus. We thus conclude that metabolic reconstruction and in silico analyses of multiple strains of the same bacterial species provide a novel approach for potential antibiotic target identification

Essential enzymes and its associated reactions identified by FBA are categorized into specific metabolic systems of Category A bacteria. B: <i>B. anthracis</i>, F: <i>F. tularensis</i>, Y: <i>Y. pestis.</i>

<p>Essential enzymes and its associated reactions identified by FBA are categorized into specific metabolic systems of Category A bacteria. B: <i>B. anthracis</i>, F: <i>F. tularensis</i>, Y: <i>Y. pestis.</i></p

Genome features, with ORFs and functions, EC numbers, metabolic reactions, transport and metabolites of Category A bacterial agents.

<p>Genome features, with ORFs and functions, EC numbers, metabolic reactions, transport and metabolites of Category A bacterial agents.</p

Comparisons of predicted essential enzymes encoding genes shared by all three Category A agents to experimentally identified essential genes across various pathogenic bacteria.

<p><i>Vc: Vibrio cholera N116961, Bs: Bacillus subtilis 168, Ec: E. coli MG1655, Hi: Haemophilus influenzae Rd KW20, Sp: Streptococcus pneumoniae, Fn: Francisella tularensis sub spp novicida U112, Ab: Acinetobacter baylyi ADP1, Pa: Pseudomonas aeruginosa UCBPP-PA14, Se: Salmonella enterica serv Typhi, Sa: Staphylococcus aureus N315, Mg: Mycoplasma genitalium G37, Mt: Mycobacterium tuberculosis H37Rv, Mp: Mycoplasma pulmonis UAB CTIP and Hp: Helicobacter pylori 26695. “+” Indicates as essential, “− ” Indicates as non-essential.</i></p

Common metabolic enzyme targets in the three Category A bacteria.

<p>Nine shared essential enzymes in several major pathways were identified across all Category A bacteria and are marked by “X”.</p