Biology Reference
In-Depth Information
domain response regulators have been implicated in root colonization in
Pseudomonas
putida
(Matilla et al., 2007); in
E. coli
the GGDEF domain-containing YddV protein
upregulates the transcription of a number of cell wall modifi cation enzymes [42], and
in point of fact,
D. aromatica's
VIMSS581804, a GGDEF domain containing homolog
of the YddV
E. coli
protein, occurs upstream of a cluster of 16 cell wall division pro-
teins (encoded by VIMSS581805-581820).
Figure 3.
Number of predicted signaling proteins versus total protein count. Microbial genomes,
displaying total number of predicted open reading frames (orfs, left axis) and total number of
predicted signaling proteins (defined as COG T, right axis). Microbes displaying a high number
of signaling orfs relative to total predicted proteins are labeled (above COG T line), as well as two
large-sized genomes having a relatively low number of annotated COG T proteins (labeled below
COG T line).
Figure 4.
Overview of predicted metabolic cycles, membrane transporters, and signaling proteins
in
D. aromatica
. Various metabolic cycles, secretory apparatus, and signaling cascades predicted in
the annotation process are depicted. TM: transmembrane. Gene names are discussed in the relevant
sections of this chapter. Areas of the cell depicting nitrogen, hydrogen, carbon, and sulfur cycles are
indicated by “N”, “H”, “C”, and “S”.
