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Microbiological Research
Urban & Fischer Verlag DmbH & Co.
Microbiological Research

Urban & Fischer Verlag DmbH & Co.

0944-5013

Microbiological Research/Journal Microbiological ResearchSCIEIAHCI
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    EppR, a new LysR-family transcription regulator, positively influences phenazine biosynthesis in the plant growth-promoting rhizobacterium Pseudomonas chlororaphis G05

    Chi, XiaoyanWang, YanhuaMiao, JingWang, Wei...
    10页
    查看更多>>摘要：Pseudomonas chlororaphis G05 has the capability to repress the mycelial growth of many phytopathogenic fungi by producing and secreting certain antifungal compounds, including phenazines and pyrrolnitrin. Although some regulatory genes have been identified to be involved in antifungal metabolite production, the regulatory mechanism and pathway of phenazine-1-carboxylic acid biosynthesis remain poorly defined. To identify more new regulatory genes, we applied transposon mutagenesis with the chromosomal lacZ fusion strain G05 Delta phz:: lacZ as an acceptor. In the white conjugant colony G05W05, a novel transcriptional regulator gene, eppR, was verified to be interrupted by the transposon mini-Tn5Kan. To evaluate the specific function of eppR, we created a set of eppR-deletion mutants, including G05 Delta eppR, G05 Delta phz::lacZ Delta eppR and G05 Delta prn::lacZ Delta eppR. By quantifying the production of antifungal compounds and beta-galactosidase expression, we found that the expression of the phenazine biosynthetic gene cluster (phz) and the production of phenazine-1-carboxylic acid were markedly reduced in the absence of EppR. Moreover, the pathogen suppression test verified that the yield of phenazine-1carboxylic acid was significantly decreased when eppR was deleted in frame. At the same time, no changes in the expression of the phzI/phzR quorum-sensing (QS) system and the production of N-acyl homoserine lactones (AHLs) and pyrrolnitrin were found in the EppR-deficient mutant. In addition, chromosomal fusion analyses and quantitative real-time polymerase chain reaction (qRT-PCR) results also showed that EppR could positively mediate the expression of the phz cluster at the posttranscriptional level. In summary, EppR is specifically essential for phenazine biosynthesis but not for pyrrolnitrin biosynthesis in P. chlororaphis.
      原文链接:
    • NSTL
    • Elsevier

    iTRAQ-based proteomic analysis of Bacillus subtilis strain NCD-2 regulated by PhoPR two-component system: A comparative analysis with transcriptomics revealed the regulation for fengycin production by branched chain amino acids

    Fu, YifanGuo, QinggangDong, LihongLiu, Xiaomeng...
    10页
    查看更多>>摘要：The PhoPR two-component system (TCS) is a signal transduction pathway to regulate the phosphate starvation response in Bacillus subtilis and regulated fengycin production in strain NCD-2 under low phosphate condition. The purpose of this study was to characterize the proteome level responses in the phoP-null mutant (MP) and the phoR-null mutant (MR), and to integrate the proteomics with the transcriptomic data obtained previously. The metabolic pathway for fengycin was predicted based on omics analysis as well as molecular genetics assay. Results showed the proteins and genes associated with biosynthesis of branched chain amino acids (BCAAs) were regulated by PhoPR TCS, and liquid chromatography mass spectrometry (LC-MS) analysis also confirmed that the production of BCAAs was down-regulated in the MP and MR mutants, when compared to wild-type strain NCD-2. Protein network analysis showed that the BCAA metabolism was linked to the biosynthesis of lipopeptides. The MP and MR strains decreased the fengycin production when cultured in modified Landy medium supplied with 0.42 mM phosphate, however, the fengycin production could be restored when the glutamic acid was replaced with BCAAs that were added to modified Landy medium. The lpdV gene, which is responsible for the BCAA degradation process, was deleted in strain NCD-2. Compared with the wild-type strain, the lpdV mutant produced significantly less fengycin in the medium supplied with BCAAs. Considered together, the results of this study indicate that the PhoPR TCS regulates fengycin production by affecting BCAA biosynthesis.
      原文链接:
    • NSTL
    • Elsevier

    Genomic and transcriptomic analysis screening key genes for (+)-valencene biotransformation to (+)-nootkatone in Yarrowia lipolytica

    Li, XiaoRen, Jing-NanFan, GangHe, Jin...
    14页
    查看更多>>摘要：Yarrowia lipolytica is a kind of unconventional yeast, which is widely used in food industry because of its safety. (+)-Nootkatone, the ketone derivatives of (+)-valencene, possesses typical grapefruit aroma and is used as aromatics and medicines. It was found that Yarrowia lipolytica was an efficient biocatalyst for the transformation of (+)-valencene to (+)-nootkatone. Thus, it was meaningful to explore the genome features and the gene expression differences of strain Yarrowia lipolytica during (+)-valencene biotransformation, and to study the detailed bioconversion pathways. The results showed that the Yarrowia lipolytica genome was about 20.49 Mb, which encoded 6 137 protein coding genes. There were 1 167 differentially expressed genes (DEGs) in Y_V_36h ((+)-valencene-treated condition) compared to Y_36h ((+)-valencene-untreated blank). During biotransformation, the expression of genes related to the biosynthesis of secondary metabolites and most of ATP-binding cassette (ABC) transporters were significantly up-regulated. In addition, the expression of genes involved in energy metabolism decreased. Moreover, the enzymes participated in (+)-valencene biotransformation were inducible and they were inhibited by cytochrome P450 inhibitors. Several differentially expressed genes related to cytochrome P450 and dehydrogenase (gene2800, gene2911 and gene3152) were significantly up-regulated and might be responsible for converting (+)-valencene to (+)-nootkatone. The RT-qPCR experiment of ten DEGs were further verified and confirmed the reliability of transcriptome results. This study provided a basis for exploring the related genes and molecular regulatory mechanism of (+)-nootkatone biosynthesis from (+)-valencene by Yarrowia lipolytica.
      原文链接:
    • NSTL
    • Elsevier

    Lactobacillus and intestinal diseases: Mechanisms of action and clinical applications

    Huang, RoujieWu, FeiZhou, QianWei, Wei...
    22页
    查看更多>>摘要：The gut microbial ecosystem, which is a collection of the host-microbiota interactions and the inter-species interplay among bacteria-dominated microbiota, has become a research hotspot due to its contribution to host health in recent years. Lactobacillus, which has worldwide usage in fermented dairy products, has aroused increasing attention and becomes one of the commonly used probiotics given its promising applications in intestinal health and disease, though it occupies a relatively small proportion of the intestinal microbiota. In the review, we first update the current understanding of determinants of Lactobacillus abundance in the intestinal tract. We then review evidence from animal models to human trials that provided insights into Lactobacillus's applications in common intestinal disorders including the Helicobacter pylori infection, colorectal cancer, diarrhea, inflammatory bowel disease, and irritable bowel syndrome. Mechanisms underlying the probiotic role of Lactobacillus are finally discussed in five aspects: microbial interactions, the improvement of intestinal barrier function, the immunoregulation, the anticancer activity, and the metabolic regulation. This review aims to yield a profound understanding of how Lactobacillus will contribute to disease prevention and individualized therapies in future clinical practice, and to inspire novel microbial strategies utilizing both probiotics and their products in the fields of biology and medicine.
      原文链接:
    • NSTL
    • Elsevier

    Exploring biocontrol and growth-promoting potential of multifaceted PGPR isolated from natural suppressive soil against the causal agent of chickpea wilt

    Fatima, IqraHakim, SughraImran, AsmaAhmad, Niaz...
    13页
    查看更多>>摘要：Chickpea is an important nutritive food crop both for humans and animals. Chickpea wilt caused by Fusarium oxysporum f.sp. ciceris (Foc) results in huge yield losses every year. Chickpea being a food crop requires the development of an eco-friendly bio-pesticide to effectively control the chickpea wilt disease. In this study, more than 50 bacterial stains isolated from the rhizosphere of healthy plants growing in wilt sick soil were examined for their Foc antagonist activities. Out of these, 17 strains showing > 90% growth inhibition of Foc were then characterized for their plant growth-promoting (PGP) and biocontrol traits. The biocontrol and PGP traits identified include amylase, hydrogen cyanide, protease, cellulase, chitinase activities, p-solubilization, nitrogen fixing, and indole-3-acetic acid production. Two bacterial strains, IR-27 and IR-57, exhibiting the highest Foc proliferation inhibition and the PGP potential along with a consortium of four different strains (Serratia sp. IN-1, Serratia sp. IS-1, Enterobacter sp. IN-2, Enterobacter sp. IN-6) were used for controlling the chickpea wilt disease and growth promotion of the chickpea plants. Confocal laser scanning microscopy revealed their root colonization ability with partial or complete elimination of broken Foc mycelia and hyphae from roots. The bacterial inoculations particularly the consortium significantly suppressed the disease and improved the overall root morphology traits (root length, root surface area, root volume, forks, tips, and crossings), resulting in enhanced growth of the chickpea plants. Significant changes in growth (107% increase in root length, 23% increase in shoot length, and 54% increase in branches) in Foc-challenged plants were observed when inoculated with the consortium. Further investigations revealed that the chickpea plants inoculated with bacterial strains induced the expression of a number of key defence enzymes, including the phenylalanine ammonia lyase, peroxidase, polyphenol peroxidase, beta-1,3 glucanase, which might have helped the plants to thwart the pathogen attack. These findings indicate the potential of our identified bacterial strains to be used as a natural biopesticide for controlling the chickpea wilt disease.
      原文链接:
    • NSTL
    • Elsevier

    The role of quorum sensing, biofilm formation, and iron acquisition as key virulence mechanisms in Acinetobacter baumannii and the corresponding anti-virulence strategies

    Law, Soffi Kei KeiTan, Hock Siew
    17页
    查看更多>>摘要：Acinetobacter baumannii is a nosocomial pathogen responsible for several serious infections, including pneu-monia, sepsis, and meningitis. The propensity of this bacterium to rapidly acquire antibiotic resistance leads to the emergence and spread of multidrug-resistant A. baumannii strains. As a result, antibiotics are becoming less effective in treating infections caused by this pathogen. In recent years, increasing efforts have focused on developing therapeutic compounds that could reduce the ability of A. baumannii to establish infection by inhibiting the virulence factors and pathogenesis of this pathogen without interfering with the bacterial viability. These alternative therapeutic options may impose milder selective pressure, reducing the likelihood of anti-virulence resistance development. To develop novel anti-virulence therapies, an in-depth understanding of the bacterial virulence mechanisms is crucial to identifying potential drug targets. This review summarises the latest discoveries about the virulence of A. baumannii, focusing on quorum sensing, biofilm formation, and iron acquisition, along with the corresponding anti-virulence strategies. This article also elaborates on the practical challenges involved in developing anti-virulence drugs. Therapeutic agents that target bacterial virulence factors may play a crucial role in controlling infection in the human host. Combining anti-virulence agents with existing antibiotics could enhance the therapeutic potential of these antibiotics against A. baumannii. Although anti-virulence therapy has been envisioned as an attractive alternative to overcome antimicrobial resistance, addi-tional research on the possibility of developing resistance against anti-virulence drugs is encouraged to evaluate the sustainability of these strategies. Moreover, future studies on the efficacy of anti-virulence therapy against a diverse panel of clinical isolates and in polymicrobial A. baumannii infections are required to provide more valuable information about its clinical application.
      原文链接:
    • NSTL
    • Elsevier

    Putative probiotics decrease cell viability and enhance chemotherapy effectiveness in human cancer cells: role of butyrate and secreted proteins

    Doublier, S.Cirrincione, S.Scardaci, R.Botta, C....
    12页
    查看更多>>摘要：Recent advances have highlighted probiotic role in preventing colorectal cancer, by promoting differentiation, inhibiting proliferation, and inducing apoptosis in colonocytes. Here, three ascertained probiotics (L. rhamnosus GG ATCC 53103, L. reuterii DSM 17938 and L. johnsonii LC1) and four food-isolated putative probiotics (L. plantarum S2, L. plantarum O2, L. pentosus S3, L. rhamnosus 14E4) were investigated for their ability to adhere to HT29 cancer cells and to inhibit their and the chemoresistant counterpart (HT29-dx cells) proliferation. Three putative probiotics (S2, S3 and 14E4) were able to decrease viability of both sensitive and chemo-resistant HT-29 cells. Supposing this effect related to secreted metabolites (namely short chain fatty acids (SCFA), exopolysaccharides (EPS) and extracellular proteins) we tested the efficacy of extracellular extracts and butyrate with or without the chemotherapeutic agent doxorubicin (DOXO) (10 mu M, 4 h). Increased production of mitochondrial reactive oxygen species (ROS) in HT29 and HT29-dx cells was observed. Moreover, cell exposure to DOXO (10 mu M, 24 h) and extracellular extracts (48 h) reduced cell viability. Comparative phenotypic and secretome analyses on the effective/non effective strains, revealed quantitative/qualitative differences in EPS content and protein profiles, suggesting that P40, phage-tail-like and capsid-like proteins may be also involved. These results suggest that food-isolated bacteria releasing bioactive compounds (butyrate, EPS and peculiar proteins) may control cancer cell proliferation and improve their response to chemotherapy.
      原文链接:
    • NSTL
    • Elsevier

    Secretome analysis of Trichoderma reesei RUT-C30 and Penicillium oxalicum reveals their synergic potential to deconstruct sugarcane and energy cane biomasses

    Ribeiro Correa, Thamy LiviaBarreto Roman, Ellen KarenCassoli, Juliana da Silvados Santos, Leandro Vieira...
    10页
    查看更多>>摘要：The conversion of lignocellulosic polymers into monomeric sugars demands a plethora of enzymatic activities generally not produced by a single microorganism and induced by the carbon source. In this vein, this work investigates the synergy between the enzymes secreted by the cellulolytic model fungi Trichoderma reesei RUT C30 (TR) and Penicillium oxalicum (PO) to deconstruct sugarcane straw (SCS) and energy cane bagasse (ECB). TR and PO secrete a similar profile of cellulose-active enzymes resulting in a comparable conversion of SCS and ECB into glucose. The synergy between the enzymes produced by both fungi to break down the cellulose fraction becomes evident by the improvement of glucose titers from similar to 35-54% and from similar to 10-17% in SCS and ECB conditions, respectively, reached with the mixture of the secretomes of both fungi. The effect of a hemicellulaseenriched secretome produced by TR is particularly seen in SCS where the xylose yield reached similar to 15% compared to 5% by PO, remaining unaltered following the mixture of secretomes. However, the secretion of enzymes active in the decorations of the main chain polymers possibly aid PO to access the hemicellulose fraction of ECB reaching xylose yields similar to TR in this condition.
      原文链接:
    • NSTL
    • Elsevier

    Recovering metagenome-assembled genomes from shotgun metagenomic sequencing data: Methods, applications, challenges, and opportunities

    Zhou, YunyanLiu, MinYang, Jiawen
    13页
    查看更多>>摘要：Reference genomes are essential for analyzing the metabolic and functional potentials of microbiomes. However, microbial genome resources are limited because most of microorganisms are difficult to culture. Genome binning is a culture-independent approach that can recover a vast number of microbial genomes from short-read high throughput shotgun metagenomic sequencing data. In this review, we summarize methods commonly used for reconstructing metagenome-assembled genomes (MAGs) to provide a reference for researchers to choose propriate software programs among the numerous and complicated tools and pipelines that are available for these analyses. In addition, we discuss application prospects, challenges, and opportunities for recovering MAGs from metagenomic sequencing data.
      原文链接:
    • NSTL
    • Elsevier

    PP2A(Rts1) antagonizes Rck2-mediated hyperosmotic stress signaling in yeast

    Hollenstein, D. M.Veis, J.Romanov, N.Gerecova, G....
    9页
    查看更多>>摘要：In Saccharomyces cerevisiae, impairment of protein phosphatase PP2A(Rts1) leads to temperature and hyperosmotic stress sensitivity, yet the underlying mechanism and the scope of action of the phosphatase in the stress response remain elusive. Using a quantitative mass spectrometry-based approach we have identified a set of putative substrate proteins that show both hyperosmotic stress-and PP2A(Rts1)-dependent changes in their phosphorylation pattern. A comparative analysis with published MS-shotgun data revealed that the phosphorylation status of many of these sites is regulated by the MAPKAP kinase Rck2, suggesting that the phosphatase antagonizes Rck2 signaling. Detailed gel mobility shift assays and protein-protein interaction analysis strongly indicate that Rck2 activity is directly regulated by PP2A(Rts1) via a SLiM B56-family interaction motif, revealing how PP2A(Rts1) influences the response to hyperosmotic stress in Yeast.
      原文链接:
    • NSTL
    • Elsevier