Biology Reference
In-Depth Information
noted for the initial two annotation runs, Joint Genome Institute's, done at Oak Ridge
National Laboratories--ORNL, and VIMSS).
The most defi nitive functional classifi cation, TIGRfams, initially defi ned approxi-
mately 10% of the proteins in this genome; as of this writing, 33% of predicted proteins
in the
D. aromatica
genome are covered by TIGRfams, leaving 2,802 genes with no
TIGRfam classifi cation. Many proteins in the current and initial non-covered sets were
investigated further using K. Sjölander's HMM building protocols (many of which
are available at [http://phylogenomics.berkeley.edu]), to supplement TIGRfams. The
COG assignments were used for classifi cation in the families of signaling proteins,
but specifi c function predictions for these proteins also required further analyses. The
metabolic and signaling pathways are discussed below, and the identity of orthologs
within these pathways are based on analysis of phylogenomic profi les of clusters ob-
tained by HMM analysis, with comparison to proteins having experimentally defi ned
function.
Anaerobic Aromatic Degradation--Absence of Known Enzymes Indicates
Novel Pathways
One of the more striking findings is the absence of known key enzymes for monoaro-
matic degradation under anaerobic conditions. One of the primary metabolic capabili-
ties of interest for this microbe is anaerobic degradation of benzene. Fumarate addi-
tion to toluene via BssABCD is recognized as the common mechanism for anaerobic
degradation by a phylogenomically diverse population of microbes [14-16] and has
been called “the paradigm of anaerobic hydrocarbon oxidation” [17]. Benzoyl-CoA
is likewise considered a central intermediate in anaerobic degradation, and is further
catabolized via benzoyl-CoA reductase (BcrAB) [17]. Populated KEGG maps in the
IMG and VIMSS databases, based on BLAST analyses, indicate the presence of some
of the enzymes previously characterized as belonging to the Bss pathway in
D. aro-
matica
, yet more careful analysis shows the candidate enzymes to be members of a
general family, rather than true orthologs of the enzymes in question. The majority of
catabolic enzymes of interest for
D. aromatica
are not covered by TIGRfams or COGs
families. For this reason Flower Power clustering, SCI-PHY subfamily clade analysis,
and HMM scoring were used to ascertain the presence or absence of proteins of inter-
est. The most reliable prediction-of-function approaches for genomically sequenced
protein orfs are obtained using the more computationally intensive HMM modeling
and scoring utilities. This allows the protein in question to be assessed by phylogenetic
alignment to protein families or sub-families with experimentally known function,
providing much more accurate predictions [18, 19].
To explore the apparent lack of anaerobic aromatic degradation pathways expected
to be present in this genome, all characterized anaerobic aromatic degradation path-
ways from
A. aromaticum
EbN1 [20] were defi ned by HMMs to establish presence or
absence of proteins in both the
D. aromatica
and
Azoarcus
BH72 genomes (these three
genomes comprise nearest-neighbor species in currently sequenced species. In
A.
aromaticum
EbN1, 10 major catabolic pathways have been found for anaerobic aromatic
degradation, and nine of the 10 converge on benzoyl-CoA [21]. A key catalytic enzyme
or subunit for each enzymatic step was used as a seed sequence to recruit proteins from a
