- networks in Pseudomonas syringae. - Results: In this study, we investigated global gene expression profiles of PstDC3000 and PssB728a and their. - A total of 1886 and 1562 differentially expressed genes (DEGs) were uncovered between the (p)ppGpp 0 mutants and the wild-type in PstDC3000 and PssB728a, respectively. - Comparative transcriptomics identified 1613 common DEGs, as well as 444 and 293 unique DEGs in PstDC3000 and PssB728a, respectively. - Functional cluster analysis revealed that (p) ppGpp positively regulated a variety of virulence-associated genes, including type III secretion system (T3SS), type VI secretion system (T6SS), cell motility, cell division, and alginate biosynthesis, while negatively regulated multiple basic physiological processes, including DNA replication, RNA processes, nucleotide biosynthesis, fatty acid metabolism, ribosome protein biosynthesis, and amino acid metabolism in both PstDC3000 and PssB728a. - Conclusion: In this study, comparative transcriptomic analysis reveals common regulatory networks in both PstDC3000 and PssB728a mediated by (p) ppGpp in HMM. - In both P. - Moreover, cell sizes of the (p)ppGpp 0 mutants were increased and their survival on plant surfaces was significantly decreased at 24 h after in- oculation [26, 27], indicating that (p) ppGpp plays a major role in regulating gene expression for growth, survival and virulence. - In this study, we performed a glo- bal transcriptomic analysis to compare gene expression between PstDC3000 and its relA/spoT/fpRel triple mutant ((p)ppGpp 0 PstDC3000. - syringae systems to illus- trate their similarities or differences in the global ef- fects of the (p)ppGpp-mediated stringent response.. - In total to reads for each biological sample were generated for PstDC3000 and its triple mutant ((p)ppGpp 0 PstDC3000. - PCA plot clearly showed that the first two components (PC1 and PC2) explained about 91 and 87% of the variability in the datasets for PstDC3000 and PssB728a and their corre- sponding mutant strains, respectively (Fig. - 0.05 between PstDC3000 and PssB728a and its corresponding (p)ppGpp 0 mutant, were respect- ively identified. - a PC1 and PC2 explain data variability of 79.4 and 8.2%, respectively, for PstDC3000 and its (p)ppGpp 0 mutant. - c Expression of the desA, pspto_1775, infA, avrE1, iaaL and csrA2 genes in the relA/. - d Expression of the cstA, actP, acsA, mtiD, cspC and ksgA genes in the relA/spoT ((p)ppGpp 0 ) mutant strain as compared with PssB728a grown in hrp-inducing medium at 3 h post-inoculation. - The qRT-PCR results showed that expression of selected genes was mostly in similar trend as those of the RNA-seq data (Fig. - In total, 1202 DEGs for PstDC3000 and 1009 DEGs for PssB728a were functionally separated into 20 out of 21 known function categories (Fig. - In general, most of the DEGs categorized as T3SS, signal transduction, cell motility, and carbohydrate metabolism were positively regulated by (p)ppGpp. - In order to determine the similarities and differences be- tween effects of (p) ppGpp in PstDC3000 and PssB728a, a comparative transcriptomic analysis was performed. - In the genomes of PstDC3000 and PssB728a, there are 5483 and 5137 protein-coding genes, respectively [6]. - Additional file 3: Table S3), representing about three fourths of the genomes. - The remaining 1273 and 927 genes are unique for PstDC3000 and PssB728a, respectively (Fig. - When DEGs of the (p)ppGpp 0 PstDC3000 mutant versus PstDC3000 (Fig. - 3, Ring 4) were mapped to the corresponding genes in the genome, similar expression patterns for homologous genes in PstDC3000 and PssB728a. - These results suggested that (p) ppGpp exhibited similar effects on global gene expression in both PstDC3000 and PssB728a in HMM. - 0.05 and at least one |log 2 FC| value ≥1) in comparison of the (p)ppGpp 0 PstDC3000 mutant versus PstDC3000 and the (p)ppGpp 0 PssB728a mutant versus PstB728a (Additional file 3: Table S4). - A total of 444 and 293 unique DEGs, which were regu- lated by (p) ppGpp in PstDC3000 and PssB728a, respect- ively, were also identified (Additional file 4: Table S6 &. - Among the six different secretion systems [28–30], T3SS specif- ically secretes and translocates effector proteins from the bacteria to the cytoplasm of the host cell through the needle-like apparatus [31, 32]. - T3SS is a key pathogen- icity factor in both PstDC3000 and PssB728a and injects effector proteins into host cells to suppress host defense and cause disease . - In the regulatory networks of P. - and (p)ppGpp 0 PssB728a mutants, indicating that (p) ppGpp is required for activating T3SS in both PstDC3000 and PssB728a. - One of the three T6SSs in Pseudomonas aeruginosa and. - In this study, 28 pu- tative T6SS-associated genes of PstDC3000 and 25 T6SS- related genes of PssB728a were down-regulated in the (p)ppGpp 0 PstDC3000 and (p)ppGpp 0 PssB728a mutants, re- spectively (Fig. - Transcriptomic data showed that 27 genes involved in cell motility were down- regulated in PstDC3000 and PssB728a, including type IV pilus biogenesis (pil), flagellar (flg) and chemotaxis (che) genes (Additional file 3: Table S4). - a PstDC3000 and (p)ppGpp 0 PstDC3000 . - motility of the (p)ppGpp 0 PstDC3000 and (p)ppGpp 0 PssB728a. - Previous studies have reported that cells of the (p)ppGpp 0 PstDC3000 and (p)ppGpp 0 PssB728a mutants was much longer than those of PstDC3000 and PssB728a in HMM medium and on plant surfaces [26, 27]. - The products of the ftsA, ftsQ and ftsZ genes are respon- sible for controlling cell division and cell wall metabol- ism [44]. - These results might explain why cell sizes of the (p)ppGpp 0 PstDC3000 and (p)ppGpp 0 PssB728a mutants were increased under such stress conditions.. - Alginate is one of the EPS molecules reported to be a virulence factor in P.. - The first ring (outside ring) showed PstDC3000 and PssB728a genome. - The sky blue region represents homologues genes between PstDC3000 and PssB728a. - the height of the plot represents the percentage of sequence identity (40 to 100. - The fourth ring represents log 2 FC of the (p)ppGpp 0 PssB728a versus PssB728a, red and blue bar represents log 2 FC ≥ 1 and log 2 FC ≤ -1 with a corrected p value <. - PstDC3000 and (p)ppGpp 0 PssB728a versus PssB728a (Fig. - These results suggest that (p) ppGpp acts as an important internal signal to positively regulate virulence- associated factors in both PstDC3000 and PssB728a.. - Our results showed that 93 translation factors were up-regulated in the (p)ppGpp 0 PstDC3000 and. - Overexpression of the acetyl-CoA carboxylase (acc) and acetyl-CoA synthetase (acsA) genes could lead to in- creased fatty acid biosynthesis [83, 84]. - Our results showed that (p) ppGpp suppressed 66 coen- zyme metabolism-related genes in both PstDC3000 and PssB728a, including the ribDEF gene cluster, which is in- volved in riboflavin biosynthesis [92–94], nadACD gene cluster (regulate niacin biosynthesis) and the hemACFHL gene cluster (Additional file 5: Table S12). - On the other hand, 29 carbohydrate metabolism-related genes in PstDC3000 and PssB728a were negatively controlled by (p) ppGpp, including rpiA (encoding ribose 5-phosphate isomerase), mqo (encoding malate:quinone oxidoreductase), and tpiA (encoding triosephosphate isomerase) (Additional file 5: Table S12).. - Differential regulation by (p) ppGpp in PstDC3000 and PssB728a. - How- ever, different phytotoxins are produced in PstDC3000 and PssB728a. - These results indicated that (p) ppGpp positively activate toxin gene expression to promote bacterial viru- lence in both PstDC3000 and PssB728a.. - Fifteen T6SS genes on HSI-I cluster in PssB728a, and 18 T6SS genes on HSI-II cluster, but no genes on HSI-I in PstDC3000, were positively regulated by (p) ppGpp (Table 3), indicating that different T6SSs may be regulated differently by (p) ppGpp in PstDC3000 and PssB728a. - Furthermore, we found that some homologous genes in PstDC3000 and PssB728a were. - Table 1 Differential gene regulation by (p) ppGpp in PstDC3000 and PssB728a Homolog genes inversely regulated. - mutant, but down-regulated in the (p)ppGpp 0 PssB728a mu- tant. - 7 is based on our global transcription data as well as previously reported results in PstDC3000 and Pss728a [16, 17]. - SpoT/FpRel systems are activated in PstDC3000 and PssB728a, leading to accumulation of (p)ppGpp. - In both PstDC3000 and PssB728a, (p) ppGpp suppresses biosynthesis of DNA replication, RNA pro- cesses, ribosome proteins, nucleotide metabolism, amino acid metabolism and fatty acid metabolism and other basic physical processes, and at the same time, activates the expression of T3SS, T6SS, cell motility, cell division, EPS and phytotoxin to promote viru- lence and survival.. - The wild-type PstDC3000 and its relA/spoT/fpRel triple mutant ((p)ppGpp 0 PstDC3000. - Overnight cultures of the bacterial strains were collected by centrifugation, and washed with HMM for three time.. - The suspensions were adjusted to OD 600 = 0.2 in HMM and incubated in 5 ml HMM at 18 °C for 3 h. - The quantity and quality of RNA samples was Table 2 List of phytotoxin genes differentially regulated by (p) ppGpp in PstDC3000 and PssB728a. - DEGs were differentially expressed genes in the (p)ppGpp 0 PstDC3000 and (p)ppGpp 0 PssB728a with p-value <. - Table 3 List of T6SS genes differentially regulated by (p) ppGpp in PstDC3000 and PssB728a. - Table 4 List of homologous genes regulated by (p) ppGpp in opposite ways in PstDC3000 and PssB728a. - (p)ppGpp 0 PssB728a. - AE016853.1) and PssB728a (accession. - Identification of homologous and unique genes in PstDC3000 and PssB728a. - Coding sequences in the genomes of PstDC3000 and PssB728a were downloaded from the NCBI database.. - 10 − 2 and 40% identity were used to distinguish homologues and unique genes be- tween PstDC3000 and PssB728a.. - List of homologues and unique genes via comparative analysis of PstDC3000 and PssB728a genomes. - List of homologues genes in both PstDC3000 and PssB728a regulated by (p) ppGpp in a similar way. - List of homologues genes in both PstDC3000 and PssB728a inversely regulated by (p)ppGpp.. - The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.. - Pseudomonas syringae pv. - tomato: the right pathogen, of the right plant, at the right time. - Comparison of the complete genome sequences of Pseudomonas syringae pv. - Regulation of the type III secretion system in phytopathogenic bacteria. - Stress response regulators identified through genome- wide transcriptome analysis of the (p) ppGpp dependent response in Rhizobium etli. - Regulation of the co-evolved HrpR and HrpS AAA + proteins required for Pseudomonas syringae pathogenicity. - Hcp2, a secreted protein of the phytopathogen Pseudomonas syringae pv. - The division inhibitor EzrA contains a seven-residue patch required for maintaining the dynamic nature of the medial FtsZ ring. - Assembly dynamics of the bacterial MinCDE system and spatial regulation of the Z ring. - Cell division inhibitors SulA and MinCD prevent formation of the FtsZ ring. - Topological regulation of cell division in Escherichia coli involves rapid pole to pole oscillation of the division inhibitor MinC under the control of MinD and MinE. - Involvement of the EPS alginate in the virulence and epiphytic fitness of Pseudomonas syringae pv. - Characterization of the DNA damage-inducible helicase DinG from Escherichia coli. - Identification of the e- subunit of Escherichia coli DNA polymerase III holoenzyme as the dnaQ gene product: a fidelity subunit for DNA replication. - Importance of the positive charge cluster in Escherichia coli ribonuclease HI for the effective binding of the substrate. - Cloning and sequencing of the adenylate kinase gene (adk) of Escherichia coli. - Optimization of the heme biosynthesis pathway for the production of 5-aminolevulinic acid in Escherichia coli. - Role of the Escherichia coli glgX gene in glycogen metabolism. - CsrA regulates trans-lation of the Escherichia coli carbon starvation gene, cstA,by blocking ribosome access to the cstA transcript. - Transcription profiling of the stringent response in Escherichia coli. - Characterization of the salA, syrF, and syrG regulatory genes located at the right border of the syringomycin gene cluster of Pseudomonas syringae pv. - Homologues of the RNA binding protein RsmA in Pseudomonas syringae pv. - The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv
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