Biology Reference
In-Depth Information
Potential gene family expansion is indicated in several functional groups, includ-
ing the following: signaling proteins (including cAMP signaling, histidine kinases,
and others),
Mhp
-like aromatic oxidation complexes, nitrogen metabolism proteins,
and transport proteins.
Most duplications indicate that a single gene, rather than sets of genes, were repli-
cated. An exception is the Tra/Type IV transport cluster (VIMSS582581-582601 and
VIMSS582864-582884) noted previously. In the protein sets for the histidine kinase/
response regulator, duplication of histidine kinase appears to occur without duplica-
tion of the adjacent response regulator. The paralogs created by recent duplication
events are typically found well-removed from one another on the chromosome, al-
though some tandem repeats of single genes were noted. However, the highest percent
identity was not found between pairs of genes in tandem repeats.
CONCLUSION
Dechloromonas aromatica
strain RCB appears to support a highly complex lifestyle
which might involve biofilm formation and interaction with a eukaryotic host. It lacks
predicted enzyme families for anaerobic aromatic catabolism, though it supports deg-
radation of several aromatic species in the absence of oxygen. The enzymes respon-
sible for this metabolic function remain to be identified and characterized. It also en-
codes proteins suggestive of the ability to fix nitrogen and CO
2
, as well as thiosulfate
oxidation. Converse to aromatic degradation, these enzymatic functionalities have yet
to be experimentally demonstrated. In short, this genome was full of surprises.
The utility of TIGRfams and COGs families in these analyses cannot be over-
stated. New releases of TIGRfams during the course of this analysis provided new
insights and identifi ed new functionality (malonate degradation cluster, PEP-Cterm
transport and the epsH putative translocon, and urea degradation all were identifi ed
in the TIGRfam 7.0 additions). The HMM model building and assessment utilized
as the major annotation approach for this study was employed to cover those protein
families of interest that are not currently covered by TIGRfams. We utilized K. Sjö-
lander's modeling and analysis tools, which are highly similar to those used to produce
TIGRfams models. Overall, the extensive use of HMMs during this analysis allowed
high confi dence in predicted protein function, as well as certainty that several families
of previously characterized anaerobic degradation enzymes for aromatic compounds
are not present (e.g., BssABCD and BcrAB).
KEYWORDS
•
Benzylsuccinate synthase
•
Clusters of orthologs gene
•
Dechloromonas aromatic
•
Open reading frames
•
Paralogs
•
Poly-hydroxyalkanoates
