Biology Reference
In-Depth Information
Chapter 9
Metabolic Analysis
Kennan Kellaris Salinero, Keith Keller, William S. Feil, Helene Feil,
Stephan Trong, Genevieve Di Bartolo, and Alla Lapidus
INTRODUCTION
Initial interest in
Dechloromonas aromatica
strain RCB arose from its ability to
anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlo-
robenzoate, toluene, and xylene, creating interest in using this organism for bioreme-
diation. Little physiological data has been published for this microbe. It is considered
to be a free-living organism.
The a priori prediction that the
D. aromatica
genome would contain previously
characterized “central” enzymes to support anaerobic aromatic degradation of ben-
zene proved to be false, suggesting the presence of novel anaerobic aromatic deg-
radation pathways in this species. These missing pathways include the benzylsucci-
nate synthase (
Bss
ABC) genes (responsible for fumarate addition to toluene) and the
central benzoyl-CoA pathway for monoaromatics. In depth analyses using existing
TIGRfam, clusters of orthologs gene (COG), and InterPro models, and the creation of
de novo
hidden Markov models (HMM) models, indicate a highly complex lifestyle
with a large number of environmental sensors and signaling pathways, including a
relatively large number of GGDEF domain signal receptors and multiple quorum sen-
sors. A number of proteins indicate interactions with an as yet unknown host, as indi-
cated by the presence of predicted cell host remodeling enzymes, effector enzymes,
hemolysin-like proteins, adhesins, nitrous oxide (NO) reductase, and both type III and
type VI secretory complexes. Evidence of biofi lm formation including a proposed
exopolysaccharide complex and exosortase (epsH) are also present. Annotation de-
scribed in this chapter also reveals evidence for several metabolic pathways that have
yet to be observed experimentally, including a sulfur oxidation (
soxFCDYZAXB
) gene
cluster, Calvin cycle enzymes, and proteins involved in nitrogen fi xation in other spe-
cies (including RubisCo, ribulose-phosphate 3-epimerase, and
nif
gene families, re-
spectively).
Analysis of the
D. aromatica
genome indicates there is much to be learned regard-
ing the metabolic capabilities, and life-style, for this microbial species. Examples of
recent gene duplication events in signaling as well as dioxygenase clusters are present,
indicating selective gene family expansion as a relatively recent event in
D. aromati-
ca's
evolutionary history. Gene families that constitute metabolic cycles presumed to
create
D. aromatica's
environmental “foot-print” indicate a high level of diversifi ca-
