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

Yong-Yeol Ahn, Deok-Sun Lee, Henry Burd, William Blank, Vinayak Kapatral 

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 Bacillus anthracis, Francisella tularensis and Yersinia pestis. 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.

Published: January 15, 2014DOI: 10.1371/journal.pone.0085195

Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis.

Anderson I, Sorokin A, Kapatral V, Reznik G, Bhattacharya A, Mikhailova N, Burd H, Joukov V, Kaznadzey D, Walunas T, Markd'Souza, Larsen N, Pusch G, Liolios K, Grechkin Y, Lapidus A, Goltsman E, Chu L, Fonstein M, Ehrlich SD, Overbeek R, Kyrpides N, Ivanova N.

Genome features of the Bacillus cereus group genomes (representative strains of Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis sub spp. israelensis) were analyzed and compared with the Bacillus subtilis genome. A core set of 1381 protein families among the four Bacillus genomes, with an additional set of 933 families common to the B. cereus group, was identified. Differences in signal transduction pathways, membrane transporters, cell surface structures, cell wall, and S-layer proteins suggesting differences in their phenotype were identified. The B. cereus group has signal transduction systems including a tyrosine kinase related to two-component system histidine kinases from B. subtilis. A model for regulation of the stress responsive sigma factor sigmaB in the B. cereus group different from the well studied regulation in B. subtilis has been proposed. Despite a high degree of chromosomal synteny among these genomes, significant differences in cell wall and spore coat proteins that contribute to the survival and adaptation in specific hosts has been identified.

FEMS Microbiol Lett. 2005 Sep 15;250(2):175-84.

Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis.

Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V,
Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A, Chu L, Mazur M, Goltsman E,
Larsen N, D'Souza M, Walunas T, Grechkin Y, Pusch G, Haselkorn R, Fonstein M,
Ehrlich SD, Overbeek R, Kyrpides N.

Bacillus cereus is an opportunistic pathogen causing food poisoning manifested by
diarrhoeal or emetic syndromes. It is closely related to the animal and human
pathogen Bacillus anthracis and the insect pathogen Bacillus thuringiensis, the
former being used as a biological weapon and the latter as a pesticide. B.
anthracis and B. thuringiensis are readily distinguished from B. cereus by the
presence of plasmid-borne specific toxins (B. anthracis and B. thuringiensis) and
capsule (B. anthracis). But phylogenetic studies based on the analysis of
chromosomal genes bring controversial results, and it is unclear whether B.
cereus, B. anthracis and B. thuringiensis are varieties of the same species or
different species. Here we report the sequencing and analysis of the type strain
B. cereus ATCC 14579. The complete genome sequence of B. cereus ATCC 14579
together with the gapped genome of B. anthracis A2012 enables us to perform
comparative analysis, and hence to identify the genes that are conserved between
B. cereus and B. anthracis, and the genes that are unique for each species. We
use the former to clarify the phylogeny of the cereus group, and the latter to
determine plasmid-independent species-specific markers.

Nature. 2003 May 1;423(6935):87-91.

The genome sequence of the facultative intracellular pathogen Brucella melitensis.

DelVecchio VG, Kapatral V, Redkar RJ, Patra G, Mujer C, Los T, Ivanova N,
Anderson I, Bhattacharyya A, Lykidis A, Reznik G, Jablonski L, Larsen N, D'Souza
M, Bernal A, Mazur M, Goltsman E, Selkov E, Elzer PH, Hagius S, O'Callaghan D,
Letesson JJ, Haselkorn R, Kyrpides N, Overbeek R.

Brucella melitensis is a facultative intracellular bacterial pathogen that causes
abortion in goats and sheep and Malta fever in humans. The genome of B.
melitensis strain 16M was sequenced and found to contain 3,294,935 bp distributed
over two circular chromosomes of 2,117,144 bp and 1,177,787 bp encoding 3,197
ORFs. By using the bioinformatics suite ERGO, 2,487 (78%) ORFs were assigned
functions. The origins of replication of the two chromosomes are similar to those
of other alpha-proteobacteria. Housekeeping genes, including those involved in
DNA replication, transcription, translation, core metabolism, and cell wall
biosynthesis, are distributed on both chromosomes. Type I, II, and III secretion
systems are absent, but genes encoding sec-dependent, sec-independent, and
flagella-specific type III, type IV, and type V secretion systems as well as
adhesins, invasins, and hemolysins were identified. Several features of the B.
melitensis genome are similar to those of the symbiotic Sinorhizobium meliloti.

Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):443-8. Epub 2001 Dec 26.