The Ravel Laboratory for Microbial Genomics
PROJECTS
Whole genome sequencing of the biocontrol agent Lysobacter enzymogenes.
Collaborators: Donald Kobayashi, Rutgers University.
Funding: USDA
Project objectives:
1)Determine the genome sequence of Lysobacter enzymogenes.
2)Annotate and compare the genome to functionally and taxonomically-related organisms to better understand the general biology, parasitic lifestyle and biological control capacity of the organism.
3)Utilize draft and complete sequences of the genome as a teaching tool to enhance pre- and post-baccalaurate education in nucleotide sequence analysis and genome annotation.
4)Provide genome information to the research community, end users and general public.
Lysobacter enzymogenes is rapidly emerging as a microbial species of ecological and agricultural relevance. Known primarily as a prolific producer of enzymes and antibiotics, the species is gaining recognition for a number of novel features stemming from its ecological diversity, industrial applications, and most notably, unique biotic interactions. Recent studies indicate L. enzymogenes is capable of establishing unique pathogenic interactions with a broad range of hosts that include lower plants and microbial eukaryotic hosts (described in further detail below). This promiscuous behavior provides a unique opportunity to establish L. enzymogenes as a model organism for pathogenic interaction studies with lower organisms.
study the fundamental basis of universal host cell processes such as innate immune responses and programmed cell death. However, with the exception of the cosmopolitan pathogen, Pseudomonas aeruginosa, few model pathogens have been available for comparative interaction studies with these host systems. L. enzymogenes differs from P. aeruginosa not only in pathogenicity mechanisms, but also in its unique host range, which is specific towards lower organisms. Availability of the genome sequence of L. enzymogenes will provide access to the molecular mechanisms that underlie the extraordinary range of biotic interactions.
A.2. The genus Lysobacter. The genus currently belongs to the family Xanthomonadaceae within the gamma proteobacteria and includes the four accepted species of L. enzymogenes, L. antibioticus, L. gummosus and L. brunescens. Recent improvements in methods to taxonomically position bacterial strains have resulted in reclassification of strains and proposals for new species within the genus. Lysobacter spp. display a number of unique, distinct traits that separate them from other taxonomically and ecologically related microbes. Their genomes consist of relatively high G+C content typically ranging between the 65-72%, and they lack flagella, but are capable of movement by gliding motility . The feature of gliding motility alone has piqued the interest of many, since the role of gliding bacteria in soil ecology is poorly understood. In addition, while a number of different mechanisms have been proposed for gliding motility among a wide range of bacterial species, the genetic mechanism in Lysobacter remains unknown. Members of the Lysobacter group have gained broad spectrum interest for production of extracellular enzymes. The group is also regarded as a rich source for production of novel antibiotics, such as β-lactams containing substituted side chains, macrocyclic lactams and macrocyclic peptide antibiotics.
Lysobacter spp. generally have been described as ubiquitous inhabitants of soil and water [2]. Their presence has been largely ignored in the past, since members often lack predominance in sample screenings when using conventional isolation procedures. Because of improved molecular methods of identification and better descriptions for the Lysobacter genus, however, their agricultural relevance is becoming increasingly evident, especially as members of ecologically significant microbial communities associated with plants. Recent evidence suggests that Lysobacter spp. may occupy a range of ecological niches beyond those associated with plants, including a broad range of ‘extreme’ environments. For example, phylogenetic analyses of 16s rDNA depict Lysobacter clades that included clones obtained from hydrothermal vents, isolates from Mt. Pinatobo mud flows and upflow anaerobic blanket sludge reactors, and an iron-oxidizing, microaerophilic lithotroph.
A.3. Rationale for sequencing L. enzymogenes. L. enzymogenes is the most represented species of the genus described in the literature. As the species name implies, L. enzymogenes is a prolific producer of secreted enzymes, many of which have depolymerizing activity. As a consequence, the species not only has been used as a system of study for understanding enzymatic processes, but also as a source of metabolically novel enzymes that can be used for practical purposes, such as various proteases with highly specific activities, antibiotic resistance, and antibiotic activities.
