Functional genomics of Pasteuria penetrans, an obligate hyperparasite of root-knot nematodes, Meloidogyne spp.

摘要

The gram-positive, endospore-forming bacterium Pasteuria penetrans is an obligate parasite of root-knot nematodes, Meloidogyne spp., which themselves are parasites of plants. Pasteuria penetrans has a demonstrated ability to control root-knot nematodes, thus making it an ideal biological alternative to chemical nematicides.; Currently, the genome of P. penetrans is being sequenced. Comparative genomic analyses between a partial P. penetrans genome and complete genomes of five closely related Bacillus spp. using BLAST homology searches revealed genome colinearity and microsynteny. Conservation of essential genes for basic developmental, metabolic and physiological processes was observed. The presence of putative competence pathway gene members implies that similar regulatory mechanisms may govern these processes in Pasteuria. Transposable elements may have been active during the evolution of these bacterial genomes, a conclusion supported by the presence of genes encoding transposon-like proteins within the genomes and chromosomal inversions. Therefore, it is plausible that P. penetrans is regulated by biochemical processes similar to those controlling its close relatives, the Bacillus spp. This information will provide insight into understanding mechanisms of host recognition, germination and virulence.; Codon- and protein-level phylogenetic analyses have been done on 46 single or concatenated sporulation genes from six Bacillus members, including P. penetrans, using maximum likelihood and Bayesian approaches. Concatenated and single gene trees consistently positioned P. penetrans near nonparasitic Bacillus species. The nonsynonymous and synonymous rate ratios were surveyed to infer proteins and sites within proteins under diversifying selection. Phylogenies indicate that P. penetrans diverged prior to its Bacillus relatives and that it is more closely related to nonparasitic members of this group. Overall, the inferred phylogenies of sporulation proteins showed a tendency toward purifying selection, resulting in conservation of amino acid residues. However, certain membrane proteins yielded alternative phylogenies compared to the concatenated set, which may indicate a role in host-parasite interactions.; Mass production of endospores remains a challenge to the implementation of P. penetrans as a root-knot nematode biocontrol agent. In vitro culturing investigations with metal titrations have been performed which augmented growth and sporulation of P. penetrans over previous reports. These findings suggest a potential for metalloregulation of growth and sporulation in P. penetrans.; The Spo0F protein is a sporulation response regulator that is central for integrating stress signals necessary to trigger the differentiation of vegetative cells into environmentally-resistant, dormant spores. Structural and functional analyses revealed similarities and differences between P. penetrans Spo0F, the well-characterized B. subtilis Spo0F, and Spo0F proteins from other closely related Bacillus spp. All Spo0F proteins assayed have a conserved negatively-charged active site and display a similar three-dimensional conformation as observed by NMR and inferred by in silico modeling methods. P. penetrans Spo0F is surprisingly more hydrophobic and possesses a significantly higher instability index than Bacillus counterparts. The inherent difference of P. penetrans Spo0F, possibly due in part to the ecological niche the bacterium inhabits, affects its stability during in vitro manipulations, but has no apparent compromises to in vivo functionality.