Biology Reference
In-Depth Information
Cellular Interactions with Community/Environment—Secretion
Type I Secretion
Fifteen transport clusters include a TolC-like outer membrane component, and recent
gene family expansion is noted within several families of ABC transporters for this
genome. The TolC was originally identified in
E. coli
as the channel that exports he-
molysin [43], and hemolysin-like proteins are encoded in this genome. Two groups
of ABC transporters occur as a cluster of five transport genes; these five-component
transporters have been implicated in the uptake of external macromolecules [44].
The presence of putative lytic factors, lipases, proteases, antimicrobials, invasins,
hemolysins, RTXs, and colicins near potential type I transport systems indicate that
these might be effector molecules used by
D. aromatica
for interactions with host cells
(e.g., for cell wall remodeling). Iron acquisition is likely to be supported by a putative
FeoAB protein cluster (VIMSS583997, 583998), as well as several siderophore-like
receptors and a putative FhuE protein (outer membrane receptor for ferric iron uptake;
VIMSS583312). Other effector-type proteins, likely to be involved in cell/host interac-
tions (and which in some species have a role in pathogenicity [45]), are present in this
genome. Adhesins, haemagglutinins, and oxidative stress neutralizers are relatively
abundant in
D. aromatica
. A number of transporters occur near the six putative soluble
lytic murein transglycosylases, indicating possible cell wall remodeling capabilities
for host colonization in conjunction with the potential effector molecules noted above.
Homologs of these transporters were shown to support invasin-type functions in other
microbes [45]. Interaction with a host is further implicated by: VIMSS581582, encod-
ing a potential cell wall-associated hydrolase, VIMSS581622, encoding a predicted
ATPase, and VIMSS3337824/formerly 581623, encoding a putative membrane-bound
lytic transglycosylase.
Eleven tandem copies of a 672 nucleotide insert comprise a region of the chromo-
some that challenged the correct assembly of the genome, and fi nishing this region
was the fi nal step for the sequencing phase of this project (see Materials and Meth-
ods). Unexpectedly, analysis of this region revealed a potential orf encoding a very
large protein that has been variously predicted at 4,854, 2,519, or 2,491 amino ac-
ids in size during sequential automated protein prediction analyses (VIMSS3337779/
formerly 582095). This putative protein, even in its smallest confi guration, contains
a hemolysin-type calcium-binding region, a cadherin-like domain, and several RTX
domains, which have been associated with adhesion and virulence. Internal repeats of
up to 100 residues with multiple copies have also been found in proteins from
Vibrio
,
Colwellia
, Bradyrhizobium, and
Shewanella
spp. (termed “VCBS” proteins as defi ned
by TIGRfam1965).
Other potential effector proteins include: three hemolysin-like proteins adjacent
to type I transporters, eight proteins with a predicted hemolysin-related function,
including VIMSS583067, a hemolysin activation/secretion protein, VIMSS580979,
hemolysin A, VIMSS583372, phospholipase/hemolysin, VIMSS581868, a ho-
molog of hemolysin III, predicted by TIGRfam1065 to have cytolytic capability,
VIMSS582079, a transport/hemolysin, and VIMSS581408, a general hemolysin. Five
predicted proteins have possible LysM/invasin domains, including: VIMSS580547,
