Reactive design patterns

<p><b>Twitching zones on (a) soft vs. (b) hard agar for multiple twitching phenotypes.</b> On soft agar (0.5%) in panel (a), mutants <i>fimU</i> and <i>comA</i> twitch a comparable amount to the wildtype, while <i>comP</i> and <i>comE</i> are substantially impaired in agreement with <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182139#pone.0182139.g003" target="_blank">Fig 3</a>. Panel (b) shows the same mutants but now on hard agar (1.5%). In this case all diameters are comparable.</p

Competence and twitching phenotypes of null mutations.

<p>All data in this figure were taken using complex media and incubating at 37°C. Both competence and twitching assays were performed on agar: 1.5% for competence and 0.5% for twitching. Color scheme is the same as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182139#pone.0182139.g001" target="_blank">Fig 1</a>. Like symbols indicate that genes are part of the same operon. All data points contain multiple measurements for both competence and twitching. Error bars represent the standard deviation of multiple measurements. For the x-axis standard deviation is given by where x = log and ΔTE is defined as the standard deviation from the mean transformation efficiency, . The detection limit for competence is 10⁻⁹ and for twitching is 0.4. Data points that fall below either detection limit appear on the graph in a “below detection limit” region. Their position within this region has no physical interpretation beyond indicating that they fall below this limit.</p

Model of the ADP1 type IV pilus with associated competence and signal transduction proteins.

<p>Components of the model are predicted by homology from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182139#pone.0182139.t001" target="_blank">Table 1</a> and are supported by data in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182139#pone.0182139.g003" target="_blank">Fig 3</a>.</p

Protein motif diagrams of the type IV pilin proteins encoded by ADP1.

<p>Length in amino acids is indicated along the top, with pilins diagrammed below. Pilins absolutely required for both twitching and competence are in boldface. Pfam motifs are indicated by filled, labeled boxes. The Pfam motif names are: N = PF07963.11 Prokaryotic N-terminal methylation motif; Pilin = PF00114.18 Pilin (bacterial filament); GspH = PF12019.7 Type II transport protein GspH; PilW = PF16074.4 Type IV Pilus-assembly protein W; PilX_N = PF14341.5 PilX N-terminal; ComP_DUS = PF16732.4 Type IV minor pilin ComP, DNA uptake sequence receptor.</p

Alignment of PilT and PilU retraction motors from ADP1.

<p>A. The length of the primary sequence is indicated above with Pfam motifs found in both proteins diagrammed below. T2SSE = Type II/IV secretion system protein; AAA_30 = AAA_proteins. AAA_30 domains contain a P-loop motif with Walker A and Walker B motifs. Such motifs are identified using multiple sequence alignments. B. Pairwise alignment of PilT and PilU. Identical amino acids are indicated by a vertical line connecting them while: and. represent higher and lower degrees of chemical similarity between the two amino acids, respectively. Boldface amino acids are part of the Pfam motifs diagrammed in A while the blue text indicates more specifically the AAA_30 motifs.</p

Alignment of FimU and FimT pilins from ADP1.

<p>A. The length of the primary sequence is indicated above with Pfam motifs found in both proteins diagrammed below. N = PF07963.11; GspH = PF12019.7. Such motifs are identified using multiple sequence alignments. B. Pairwise alignment of FimU and FimT. Identical amino acids are indicated by a vertical line connecting them while: and. represent higher and lower degrees of chemical similarity between the two amino acids, respectively. Boldface amino acids are part of the Pfam motifs diagrammed in A.</p

Type IV pilus protein homologs in ADP1.

<p>Type IV pilus protein homologs in ADP1.</p

Full-length homologs of competence and twitching proteins encoded by the ADP1 genome.

<p>Full-length homologs of competence and twitching proteins encoded by the ADP1 genome.</p