Additional file 1 of Oligoribonuclease mediates high adaptability of P. aeruginosa through metabolic conversion

Supplementary Material 1: Supplementary Figure S1-S5. Supplementary Table S1-S

DataSheet2_Influential factors on urine EV DNA methylation detection and its diagnostic potential in prostate cancer.ZIP

The value of Extracellular vesicles (EVs) diagnostic markers is widely recognized. However, current research on EV DNA remains limited. This study investigates the biological properties, preprocessing factors, and diagnostic potential of EV DNA. We found that DNA positive vesicles account for 23.3% ± 6.7% of the urine total EV, with a large amount of DNA attached to the outside. EV DNA fragments are large, there is no significant effect on uEV DNA when store urine less than 6 h at 4°C. In addition, the influence of different EV extraction methods on methylation detection is also minor. More importantly, RASSF1A methylation in urine total EV DNA can distinguish between PCa and BPH, with an AUC of 0.874. Our results suggest the potential of urine EV DNA as a novel marker for PCa diagnosis. This provides a new idea for the study of urinary tumor markers.</p

DataSheet1_Influential factors on urine EV DNA methylation detection and its diagnostic potential in prostate cancer.zip

The value of Extracellular vesicles (EVs) diagnostic markers is widely recognized. However, current research on EV DNA remains limited. This study investigates the biological properties, preprocessing factors, and diagnostic potential of EV DNA. We found that DNA positive vesicles account for 23.3% ± 6.7% of the urine total EV, with a large amount of DNA attached to the outside. EV DNA fragments are large, there is no significant effect on uEV DNA when store urine less than 6 h at 4°C. In addition, the influence of different EV extraction methods on methylation detection is also minor. More importantly, RASSF1A methylation in urine total EV DNA can distinguish between PCa and BPH, with an AUC of 0.874. Our results suggest the potential of urine EV DNA as a novel marker for PCa diagnosis. This provides a new idea for the study of urinary tumor markers.</p

Schematic modular pipeline of ThioFinder.

<p>Schematic modular pipeline of ThioFinder.</p

ThioFinder: A Web-Based Tool for the Identification of Thiopeptide Gene Clusters in DNA Sequences

<div><p>Thiopeptides are a growing class of sulfur-rich, highly modified heterocyclic peptides that are mainly active against Gram-positive bacteria including various drug-resistant pathogens. Recent studies also reveal that many thiopeptides inhibit the proliferation of human cancer cells, further expanding their application potentials for clinical use. Thiopeptide biosynthesis shares a common paradigm, featuring a ribosomally synthesized precursor peptide and conserved posttranslational modifications, to afford a characteristic core system, but differs in tailoring to furnish individual members. Identification of new thiopeptide gene clusters, by taking advantage of increasing information of DNA sequences from bacteria, may facilitate new thiopeptide discovery and enrichment of the unique biosynthetic elements to produce novel drug leads by applying the principle of combinatorial biosynthesis. In this study, we have developed a web-based tool ThioFinder to rapidly identify thiopeptide biosynthetic gene cluster from DNA sequence using a profile Hidden Markov Model approach. Fifty-four new putative thiopeptide biosynthetic gene clusters were found in the sequenced bacterial genomes of previously unknown producing microorganisms. ThioFinder is fully supported by an open-access database ThioBase, which contains the sufficient information of the 99 known thiopeptides regarding the chemical structure, biological activity, producing organism, and biosynthetic gene (cluster) along with the associated genome if available. The ThioFinder website offers researchers a unique resource and great flexibility for sequence analysis of thiopeptide biosynthetic gene clusters. ThioFinder is freely available at <a href="http://db-mml.sjtu.edu.cn/ThioFinder/">http://db-mml.sjtu.edu.cn/ThioFinder/</a>.</p> </div

List of the HMM-profiles of the protein families or domains involved in thiopeptide biosynthesis.

<p>List of the HMM-profiles of the protein families or domains involved in thiopeptide biosynthesis.</p

Relationship between biosynthetic gene cluster features and the thiopeptide side ring system.

<p>Selected examples of thiopeptides of different types exhibit distinct chemical signatures. MR denotes macrocyclic ring; SR, light grey, side ring. In classical classification<b>,</b> Thiopeptides are classified into series a-e according to the oxidative state of the central heterocyclic ring (Pink, 6-membered N heterocycle, including pyrimidine). Three types of thiopeptide gene cluster biosynthetic we proposed makes use of the conserved amino acid sequences of enzyme that produce characteristic indolyl (MIA) or quinolinic acid (QA) residues, which are often found in the side rings of some thiopeptides. Type I, characterized by a side ring containing the indolyl structure (blue, MIA). MIA is synthesized from L-Trp by conserved NosL-like enzymes encoded by one of the grey ORFs. Type II thiopeptides contain side rings with quinaldic acid (orange, QA), which is formed by two enzymes, a hypothetical amidotransferase and a putative ester cyclase for the epoxide ring intermediate. Type III, contains the macro-circular structure but no side ring, and no genes for synthesizing L-trp derivatives (MIA or QA).</p

General and specific features of thiopeptidebiosynthetic gene clusters.

<p>(A) Organization of the biosynthetic genes, as exemplified by that for nosiheptide utilized as the reference in this study. The red (dehydratases, creating C = C double bonds in seryl, cysteinyl or threonyl residues), blue (azole formation from cysteinyl residues), and yellow arrows (formation of 6-membered nitrogen heterocycle by interaction of two seryl residues) indicate ORFs that have orthologs in all known thiopeptide biosynthetic gene clusters. Small black arrow, gene for the precursor peptide (<100 aa). Some thiopeptide gene clusters contain several (up to5) almost identical precursor peptide genes. Grey, genes that are not conserved between gene clusters, presumably creating the remarkable diversity of thiopeptides. (B) Enzymatic reactions resulting in the highly modified, circular, precursor of a typical thiopeptide. A macro-circular structure, joined at the 6-membered nitrogen heterocycle (yellow) is found in all thiopeptides. Shapes: orange oval with capital letter, natural amino acid; blue pentagon, azole; red square with parallel lines indicating the double bond, dehydroamino acid; yellow hexagon, and six-membered nitrogen ring. Lower case letters indicate the original amino acid residue. (C) Classification of thiopeptide biosynthetic gene clusters. MIA indolyl; QA, quinaldic acid. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045878#pone-0045878-g004" target="_blank">Figure 4</a> for more details.</p

<i>NDRG2</i> overexpression inhibits proliferation of human bladder cancer cells.

<p>(A and B) Colony formation assay. Upregulation of <i>NDRG2</i> inhibits colony formation. (C) The cell growth curves of T24 cells by MTT method. All the assays were repeated independently for at least three times. The results are shown as the mean ± SD (*=p<0.001).</p

Overexpression of <i>NDRG2</i> suppresses human bladder cancer cell invasion, migration and expression of MMP-2 and MMP-9.

<p>(A) Invasion analysis of T24 cells treated with LEN-<i>NDRG2</i>. The invasion ability was estimated using Transwell coated with Matrigel. The invasiveness of LEN-<i>NDRG2</i> group cells was significantly lower than that in the other two groups. **p<0.001. (B) Migration analysis of T24 cells treated with LEN-<i>NDRG2</i>. The migration ability was estimated using Transwell uncoated with Matrigel. The migration ability of LEN-<i>NDRG2</i> group cells was significantly lower than that in the other two groups. **p<0.001. (C and D) Expression of MMP-2 and MMP-9 were measured after T24 cells were infected with LEN-<i>NDRG2</i>. LEN-<i>NDRG2</i> group reduced MMP-2 and MMP-9 expression compared to the other groups (** p<0.01).</p