Conserved domains of PilQ.

<p>Panel <b>A.</b> Conserved domains of MxPilQ (901 residues) and TtPilQ (757 residues) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070144#pone.0070144-MarchlerBauer1" target="_blank">[58]</a>. The conserved feature are drawn to scale and areindicated by shaded letters below both protein. Each has the PilQ region at their C-terminus consisting of the highly conserved Secretin domain and the region immediately N-terminal of secretin (Secretin_N). Two AMIN domains <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070144#pone.0070144-deSouza1" target="_blank">[59]</a> are found at the N-terminus of MxPilQ but not TtPilQ. The brackets and the labels above indicate the different Y2H constructs and/or subdomains in each protein. Panel <b>B.</b> Structural alignment of the N-termini of TtPilQ and the T2SS secretin GspD from Enterotoxigenic <i>E. coli</i> (ETEC) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070144#pone.0070144-Kelley1" target="_blank">[50]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070144#pone.0070144-Korotkov3" target="_blank">[55]</a>. The boundaries between N0 and N1 as well as N1 and N2 subdomains in GspD are indicated by arrows (↑). The secondary structure of GspD from crystallography and that of TtPilQ predicted from modeling are indicated below and above the aligned sequences, respectively, with β strands represented by block arrows and α helices by cylinders.</p

Plasmids used in this study.

<p>Plasmids used in this study.</p

Interactions among <i>M. xanthus</i> Pil proteins detected by Y2H mating protocol.

*<p>The first column and first row indicate proteins fused to GAD and GBD, respectively. Diploid cells containing the indicated pair of fusions were examined for growth on SD-His and SD-Ade plates. Plus (+), growth on both plates; minus (−), growth on neither plates.</p

Pairwise interactions among Pil proteins in Y2H system.

<p>Panels <b>A</b> and <b>B</b>. Interactions among <i>M. xanthus</i> Pil proteins. Panels <b>C, D</b> and <b>E</b>. Interactions among <i>T. thermophilus</i> Pil proteins. The first and second columns on the left of each panel indicate Pil proteins or fragments fused to GAD and GBD in Y2H plasmids by their last letter, respectively. V indicates an empty Y2H vector. N0, N1, N2 and their combinations are represented by their numerals only. Last row in each panel contained the positive control with T-antigen (T) and p53 (53). The left half of each panel shows growth on SD-His and the right on SD-Ade plates, respectively. The spots in each row in a panel were inoculated by serial dilutions of the same yeast cells with the indicated Y2H plasmids. See text and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070144#s2" target="_blank">Materials and Methods</a> for details.</p

Quantification of β-galactosidase in Y2H experiment.

<p>The upper and lower panels show the β-galactosidase activity for Pil protein interactions in Y2H experiments from <i>M. xanthus</i> and <i>T. thermophilus</i>, respectively. The values for β-galactosidase activity were the average of three independent experiments and samples in each experiment were analyzed in triplicate. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070144#pone-0070144-g004" target="_blank">Figure 4</a> for protein designations under each panel. The bars for the vector controls are shaded for comparison. See text and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070144#s2" target="_blank">Materials and Methods</a> for more details.</p

An integrated T4P structure.

<p>Pil proteins in this model are represented by their single letter designations. OM, outer membrane; IM, inner membrane. This integrated T4P structure, which consists of the indicated Pil protein at the minimum, may exist in the absence of the pilus filament. The interactions of PilB with PilC and PilM are inferred from genetic analysis and they may be either direct or indirect. See main text for details.</p

<i>Myxococcus xanthus</i> strains used in this study.

<p><i>Myxococcus xanthus</i> strains used in this study.</p

<i>pilB^WA</i> suppresses some but not all T4P⁻<i>pil</i> deletions in EPS production.

<p>EPS levels were analyzed on plates with the fluorescent dye Calcofluor white (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070144#s2" target="_blank">Materials and Methods</a>). The presence of fluorescence indicates EPS⁺ and its absence EPS⁻. Each strip shows two strains, the upper is a strain with the indicated mutation(s) in a <i>pilB⁺</i> background and the lower in the <i>pilB^WA</i> background. Strains used are YZ690 (Δ<i>pilA</i>), YZ1573 (Δ<i>pilA pilB^WA</i>), DK10417 (Δ<i>pilC</i>), YZ1182 (Δ<i>pilC pilB^WA</i>), YZ1860 (Δ<i>pilM</i>), YZ1185 (Δ<i>pilM pilB^WA</i>), DK11135 (Δ<i>pilG</i>), YZ1183 (Δ<i>pilG pilB^WA</i>), DK11133 (Δ<i>pilH</i>), YZ1181 (Δ<i>pilH pilB^WA</i>), DK11132 (Δ<i>pilI</i>), YZ1184 (Δ<i>pilI pilB^WA</i>), YZ1191 (Δ<i>pilA</i> Δ<i>pilQ</i>) and YZ1190 (Δ<i>pilA</i> Δ<i>pilQ pilB^WA</i>). <i>pilB^WA</i> failed to suppress Δ<i>pilN</i>, Δ<i>pilO</i>, Δ<i>pilP</i> and Δ<i>pilQ</i> as it did Δ<i>pilC</i> and Δ<i>pilM</i> (data not shown).</p

Additional file 9: Figure S7. of Occurrence, diversity and community structure of culturable atrazine degraders in industrial and agricultural soils exposed to the herbicide in Shandong Province, P.R. China

BOX-PCR typing of ERIC type B isolates. Lanes are designated by the strain names. Lane T – pattern of the species type strain A. ureafaciens CGMCC 1.1897T. Lanes M contain a 100 bp DNA Ladder (Takara Biotechnology (Dalian) Co., Ltd., China). (TIF 1179 kb

Table_1_Identification of the toxin components of Rhizoctonia solani AG1-IA and its destructive effect on plant cell membrane structure.doc

Rice sheath blight is a fungal disease caused mainly by Rhizoctonia solani AG1-IA. Toxins are a major pathogenic factor of R. solani, and some studies have reported their toxin components; however, there is no unified conclusion. In this study, we reported the toxin components and their targets that play a role in R. solani AG1-IA. First, toxins produced by R. solani AG1-IA were examined. Several important phytotoxins, including benzoic acid (BZA), 5-hydroxymethyl-2-furanic aid (HFA), and catechol (CAT), were identified by comparative analysis of secondary metabolites from AG1-IA, AG1-IB, and healthy rice. Follow-up studies have shown that the toxin components of this fungus can rapidly disintegrate the biofilm structure while maintaining the content of host plant membrane components, thereby affecting the organelles, which may also explain the lack of varieties highly resistant to sheath blight.</p