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Molecular Plant-microbe Interactions :... Sep 2023spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the...
spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including AvOP, A1501, DSM4166, 6HT33bT, and sp. strain K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from , , and . Today, this island is conserved in spp. from different geographical locations, which, in turn, have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind -driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N) and improving plant N content. We describe -plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signaling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions and differs at sufficient and deficient N. The molecular controls behind different plant responses are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind -driven nitrogen fixation and to point to possible agricultural solutions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
PubMed: 36989040
DOI: 10.1094/MPMI-10-22-0223-CR -
Toxins Nov 2022and the produced aflatoxins cause great hazards to food security and human health across all countries. The control of and aflatoxins in grains during storage is of...
and the produced aflatoxins cause great hazards to food security and human health across all countries. The control of and aflatoxins in grains during storage is of great significance to humans. In the current study, bacteria strain YM6 isolated from sea sediment was demonstrated effective in controlling by the production of anti-fungal volatiles. According to morphological characteristics and phylogenetic analysis, strain YM6 was identified as YM6 can produce abundant volatile compounds which could inhibit mycelial growth and conidial germination of . Moreover, it greatly prevented fungal infection and aflatoxin production on maize and peanuts during storage. The inhibition rate was 100%. Scanning electron microscopy further supported that the volatiles could destroy the cell structure of and prevent conidia germination on the grain surface. Gas chromatography/mass spectrometry revealed that dimethyl trisulfide (DMTS) with a relative abundance of 13% is the most abundant fraction in the volatiles from strain YM6. The minimal inhibitory concentration of DMTS to conidia is 200 µL/L (compound volume/airspace volume). Thus, we concluded that YM6 and the produced DMTS showed great inhibition to , which could be considered as effective biocontrol agents in further application.
Topics: Humans; Aspergillus flavus; Aflatoxins; Pseudomonas stutzeri; Phylogeny
PubMed: 36422962
DOI: 10.3390/toxins14110788 -
MSphere Jun 2024The RNA chaperone Hfq acts as a global regulator of numerous biological processes, such as carbon/nitrogen metabolism and environmental adaptation in plant-associated...
UNLABELLED
The RNA chaperone Hfq acts as a global regulator of numerous biological processes, such as carbon/nitrogen metabolism and environmental adaptation in plant-associated diazotrophs; however, its target RNAs and the mechanisms underlying nitrogen fixation remain largely unknown. Here, we used enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing to identify hundreds of Hfq-binding RNAs probably involved in nitrogen fixation, carbon substrate utilization, biofilm formation, and other functions. Collectively, these processes endow strain A1501 with the requisite capabilities to thrive in the highly competitive rhizosphere. Our findings revealed a previously uncharted landscape of Hfq target genes. Notable among these is , encoding an isomerase necessary for nitrogenase reductase solubility; , encoding an ammonium transporter; , encoding a carbohydrate porin; and , encoding a chemotaxis protein. Furthermore, we identified more than 100 genes of unknown function, which expands the potential direct regulatory targets of Hfq in diazotrophs. Our data showed that Hfq directly interacts with the mRNA of regulatory proteins (RsmA, AlgU, and NifA), regulatory ncRNA RsmY, and other potential targets, thus revealing the mechanistic links in nitrogen fixation and other metabolic pathways.
IMPORTANCE
Numerous experimental approaches often face challenges in distinguishing between direct and indirect effects of Hfq-mediated regulation. New technologies based on high-throughput sequencing are increasingly providing insight into the global regulation of Hfq in gene expression. Here, enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing was employed to identify the Hfq-binding sites and potential targets in the root-associated A1501 and identify hundreds of novel Hfq-binding RNAs that are predicted to be involved in metabolism, environmental adaptation, and nitrogen fixation. In particular, we have shown Hfq interactions with various regulatory proteins' mRNA and their potential targets at the posttranscriptional level. This study not only enhances our understanding of Hfq regulation but, importantly, also provides a framework for addressing integrated regulatory network underlying root-associated nitrogen fixation.
Topics: Pseudomonas stutzeri; Host Factor 1 Protein; Nitrogen Fixation; Gene Expression Regulation, Bacterial; Plant Roots; RNA, Bacterial; Gene Expression Profiling; Gene Regulatory Networks; Bacterial Proteins; High-Throughput Nucleotide Sequencing; Transcriptome; Rhizosphere
PubMed: 38747590
DOI: 10.1128/msphere.00762-23 -
Environmental Research Jul 2023Biodegradation, harnessing the metabolic versatility of microorganisms to reduce agrochemical contaminations, is commonly studied with enriched planktonic cells but...
Biodegradation, harnessing the metabolic versatility of microorganisms to reduce agrochemical contaminations, is commonly studied with enriched planktonic cells but overlooking the dominant lifestyle of microorganisms is to form biofilms, which compromises the efficiency of biodegradation in natural environment. Here, we employed a carbofuran-degrading bacterium Pseudomonas stutzeri PS21 to investigate how the bacterial biofilms formed and responded to agrochemicals. First, the PS21 biofilms formed with a core of bacterial cells enclosing with extracellular polymeric substances (EPSs), and the biofilms were active and resilient when exposed to carbofuran (up to 50 mg L). The formation was regulated by the second messenger bis-(3'-5')-cyclic di-guanosine monophosphate signaling, which strengthened the structural resistance and metabolic basis of biofilms to remain the degrading efficiency as comparable as the planktonic cells. Second, carbofuran distributed heterogeneously in the near-biofilm microenvironment via the covalent adsorption of biofilms, which provided a spontaneous force that enhanced the combination of carbofuran with biofilms to maintain high degrading activity. Additionally, we elucidated the biodegradation was driven by the integrated metabolic system of biofilms involving the extracellular enzymes located in the EPSs. This study exhibited the structural and metabolic advantages of microbial biofilms, highlighting the attractive potentials of exploring biofilm-based strategies to facilitate the in-situ bioremediation of organic contaminations.
Topics: Biodegradation, Environmental; Pseudomonas stutzeri; Carbofuran; Biofilms; Extracellular Polymeric Substance Matrix; Bacteria
PubMed: 37068725
DOI: 10.1016/j.envres.2023.115894 -
International Journal of Molecular... Feb 2022Rhamnolipids are becoming an important class of glycolipid biosurfactants. Herein, we describe for the first time the enzymatic synthesis of rhamnose fatty acid esters...
Rhamnolipids are becoming an important class of glycolipid biosurfactants. Herein, we describe for the first time the enzymatic synthesis of rhamnose fatty acid esters by the transesterification of rhamnose with fatty acid vinyl esters, using lipase from as a biocatalyst. The use of this lipase allows excellent catalytic activity in the synthesis of 4--acylrhamnose (99% conversion and full regioselectivity) after 3 h of reaction using tetrahydrofuran (THF) as the reaction media and an excess of vinyl laurate as the acyl donor. The role of reaction conditions, such as temperature, the substrates molar ratio, organic reaction medium and acyl donor chain-length, was studied. Optimum conditions were found using 35 °C, a molar ratio of 1:3 (rhamnose:acyldonor), solvents with a low logP value, and fatty acids with chain lengths from C4 to C18 as acyl donors. In hydrophilic solvents such as THF and acetone, conversions of up to 99-92% were achieved after 3 h of reaction. In a more sustainable solvent such as 2-methyl-THF (2-MeTHF), high conversions were also obtained (86%). Short and medium chain acyl donors (C4-C10) allowed maximum conversions after 3 h, and long chain acyl donors (C12-C18) required longer reactions (5 h) to get 99% conversions. Furthermore, scaled up reactions are feasible without losing catalytic action and regioselectivity. In order to explain enzyme regioselectivity and its ability to accommodate ester chains of different lengths, homology modelling, docking studies and molecular dynamic simulations were performed to explain the behaviour observed.
Topics: Biocatalysis; Enzymes, Immobilized; Esterification; Esters; Fatty Acids; Hydrophobic and Hydrophilic Interactions; Laurates; Lipase; Pseudomonas stutzeri; Rhamnose; Solvents; Vinyl Compounds
PubMed: 35216354
DOI: 10.3390/ijms23042239 -
Environmental Microbiology Jan 2021MerF, a proposed bacterial mercury transporter, was surprisingly found to play key roles in the flagellum biogenesis and motility but not mercuric resistance of the...
MerF, a proposed bacterial mercury transporter, was surprisingly found to play key roles in the flagellum biogenesis and motility but not mercuric resistance of the deep-sea bacterium Pseudomonas stutzeri 273 in our previous study. However, the mechanism behind this interesting discovery has not been elucidated. Here, we firstly applied the combined transcriptomic and proteomic analysis to the P. stutzeri 273 wild type and merF deletion mutant. The results showed that expressions of extracellular flagellar components and FliS, a key factor controlling the biogenesis of extracellular flagellar filament, were significantly downregulated in the merF deletion mutant. In combination of genetic and biochemical methods, MerF was further demonstrated to regulate the expression of fliS via directly binding to its promoter, which is consistent with the discovery that MerF is essential for bacterial flagellum biogenesis and motility. Importantly, the expression of merF and fliS could be simultaneously upregulated by different heavy metals and MerF homologues exist in both bacterial and archaeal domains. To the best of our knowledge, this is the first report linking the heavy metal transporter and the flagellum biogenesis and motility in microorganisms, which provides a good model to investigate the unexplored adaptation strategies of deep-sea microbes against harsh conditions.
Topics: Bacterial Proteins; Cation Transport Proteins; Flagella; Gene Expression Regulation, Bacterial; Proteomics; Pseudomonas stutzeri; Seawater; Transcriptional Activation
PubMed: 33047460
DOI: 10.1111/1462-2920.15275 -
Environmental Research Feb 2023Wastewater treatment plants (WWTP) are considered sources of bioaerosols emission that negatively affects the surrounding atmosphere. This study focused on Pseudomonas...
Wastewater treatment plants (WWTP) are considered sources of bioaerosols emission that negatively affects the surrounding atmosphere. This study focused on Pseudomonas sp. Emissions in bioaerosols from a WWTP that adopts the AO treatment process, and their inactivation through ultraviolet (UV) radiation. High-throughput sequencing was used to assay the microbial population, and functional composition profiles were predicted using 16 S rRNA sequencing data with PICRUSt2. Recorded emission levels of airborne bacteria and Pseudomonas sp. In WWTP were 130 ± 83-6113 ± 3015 CFU/m and 0-6431 ± 1945 CFU/m, respectively. Bioaerosol emissions presented site-related and temporal variation. Over 80% of Pseudomonas sp. Were attached to coarse particles with sizes over 2.1 μm. Bioaerosol concentration and particle-size distribution in the air were closely related to ambient temperature, relative humidity, light intensity, and wind speed. Exposure to 45.67 μW/cm UV radiation led to a significant decline in bioaerosol concentrations in the air, and reduction rate reached 89.16% and 95.77% for airborne bacteria and Pseudomonas sp., respectively. The results suggested that UV radiation can be an effective method in reducing bioaerosols. Compared with other bacteria, Pseudomonas stutzeri and Bacillus sp. Are more resistant to UV radiation. The abundance of antibiotic resistance genes noticeably receded when exposed to UV irradiation. The relative abundance of cationic antimicrobial peptide resistance, categorized under human diseases in KEGG (level 3), significantly decreased in Pseudomonas sp. After 120 min of UV irradiation. This study provides a novel insight into the control of bioaerosol emissions carrying pathogenic bacteria.
Topics: Humans; Wastewater; Air Microbiology; Pseudomonas; Bacteria; Aerosols; Water Purification
PubMed: 36549495
DOI: 10.1016/j.envres.2022.115129 -
Biochimica Et Biophysica Acta. Proteins... Feb 2021The trehalose biosynthesis pathway has recently received attention for therapeutic intervention combating infectious diseases caused by bacteria, helminths or fungi....
The trehalose biosynthesis pathway has recently received attention for therapeutic intervention combating infectious diseases caused by bacteria, helminths or fungi. Trehalose-6-phosphate phosphatase (TPP) is a key enzyme of the most common trehalose biosynthesis pathway and a particularly attractive target owing to the toxicity of accumulated trehalose-6-phosphate in pathogens. Here, we characterised TPP-like proteins from bacterial pathogens implicated in nosocomial infections in terms of their steady-state kinetics as well as pH- and metal-dependency of their enzymatic activity. Analysis of the steady-state kinetics of recombinantly expressed enzymes from Acinetobacter baumannii, Corynebacterium diphtheriae and Pseudomonas stutzeri yielded similar kinetic parameters as those of other reported bacterial TPPs. In contrast to nematode TPPs, the divalent metal ion appears to be bound only weakly in the active site of bacterial TPPs, allowing the exchange of the resident magnesium ion with other metal ions. Enzymatic activity comparable to the wild-type enzyme was observed for the TPP from P. stutzeri with manganese, cobalt and nickel. Analysis of the enzymatic activity of S. maltophilia TPP active site mutants provides evidence for the involvement of four canonical aspartate residues as well as a strictly conserved histidine residue of TPP-like proteins from bacteria in the enzyme mechanism. That histidine residue is a member of an interconnected network of five conserved residues in the active site of bacterial TPPs which likely constitute one or more functional units, directly or indirectly cooperating to enhance different aspects of the catalytic activity.
Topics: Acinetobacter baumannii; Bacterial Infections; Catalytic Domain; Corynebacterium diphtheriae; Glucosyltransferases; Humans; Pseudomonas stutzeri; Sugar Phosphates; Trehalose
PubMed: 33171283
DOI: 10.1016/j.bbapap.2020.140564 -
Biotechnology Reports (Amsterdam,... Sep 2020Alginate is a group of water-soluble linear polysaccharides comprising of variable units of α-l-guluronic and β-d-mannuronic acid. The alginates are in high demand in...
Alginate is a group of water-soluble linear polysaccharides comprising of variable units of α-l-guluronic and β-d-mannuronic acid. The alginates are in high demand in biomedical, pharmaceutical and bioengineering applications. In the present study, we have isolated a strain of that has potential alginate synthesis. The biochemical and physiochemical characteristic including Carbazole assay, DSC, FTIR and H NMR were confirmed the alginate synthesis efficacy by . Evaluation of alginate for the removal of heavy metals such as Chromium, Cobalt and Lead showed that it effectively adsorbs heavy metals. Further analysis of gelling ability and cytotoxicity evaluation revealed that the alginate can be reconstituted as hydrogel and scaffold. Overall, our findings suggest that the strain may be used to produce alginate at commercial level that has the potential bioremediation and biomedical applications.
PubMed: 32874945
DOI: 10.1016/j.btre.2020.e00517 -
Bioresources and Bioprocessing May 2022Prokaryotic Argonaute (pAgo) proteins are well-known oligonucleotide-directed endonucleases, which contain a conserved PIWI domain required for endonuclease activity....
BACKGROUND
Prokaryotic Argonaute (pAgo) proteins are well-known oligonucleotide-directed endonucleases, which contain a conserved PIWI domain required for endonuclease activity. Distantly related to pAgos, PIWI-RE family, which is defined as PIWI with conserved R and E residues, has been suggested to exhibit divergent activities. The distinctive biochemical properties and physiological functions of PIWI-RE family members need to be elucidated to explore their applications in gene editing.
RESULTS
Here, we describe the catalytic performance and cellular functions of a PIWI-RE family protein from Pseudomonas stutzeri (PsPIWI-RE). Structural modelling suggests that the protein possesses a PIWI structure similar to that of pAgo, but with different PAZ-like and N-terminal domains. Unlike previously reported pAgos, recombinant PsPIWI-RE acts as an RNA-guided DNA nuclease, as well as a DNA-guided RNA nuclease. It cleaves single-stranded DNA at temperatures ranging from 20 to 65 °C, with an optimum temperature of 45 °C. Mutation at D525 or D610 significantly reduced its endonuclease activity, confirming that both residues are key for catalysis. Comparing with wild-type, mutant with PIWI-RE knockout is more sensitive to ciprofloxacin as DNA replication inhibitor, suggesting PIWI-RE may potentially be involved in DNA replication.
CONCLUSION
Our study provides the first insights into the programmable nuclease activity and biological function of the unknown PIWI-RE family of proteins, emphasizing their important role in vivo and potential application in genomic DNA modification.
PubMed: 38647609
DOI: 10.1186/s40643-022-00539-x