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Frontiers in Genetics 2020Many bacteria belonging to are plant growth-promoting rhizobacteria (PGPR) with the potential to promote plant growth and suppress phytopathogens and have been used as...
Comparative and Functional Analyses of Two Sequenced Genomes Provides Insights Into Their Potential Genes Related to Plant Growth-Promoting Features and Biocontrol Mechanisms.
Many bacteria belonging to are plant growth-promoting rhizobacteria (PGPR) with the potential to promote plant growth and suppress phytopathogens and have been used as biological control agents (BCAs). However, the growth promotion and biocontrol mechanisms of have not been thoroughly elucidated thus far. In this investigation, the genome sequences of two strains, ZF129 and ZF197, with broad anti-pathogen activities and potential for growth promotion were comparatively studied. Comparative and functional analyses of the two sequenced genomes showed that the ZF129 genome consists of one 5,703,931 bp circular chromosome and two 79,020 bp and 37,602 bp plasmids, designated pAP1 and pAP2, respectively. The complete genome sequence of ZF197 consists of one 5,507,169 bp circular chromosome and one 32,065 bp plasmid, designated pAP197. Phylogenetic analysis revealed that ZF129 is highly similar to two strains, HY96-2 and SQR-21, while ZF197 is highly similar to strain J. The genes responsible for secondary metabolite synthesis, plant growth-promoting traits, and systemic resistance inducer production were compared between strains ZF129 and ZF197 as well as other strains. The results indicated that the variation of the corresponding genes or gene clusters between strains ZF129 and ZF197 may lead to different antagonistic activities of their volatiles or cell-free supernatants against . This work indicates that plant growth promotion by is largely mediated by phytohormone production, increased nutrient availability and biocontrol mechanisms. This study provides an in-depth understanding of the genome architecture of , revealing great potential for the application of this bacterium in the fields of agriculture and horticulture as a PGPR.
PubMed: 33391337
DOI: 10.3389/fgene.2020.564939 -
RNA Biology Nov 2021Nine distinct classes of self-cleaving ribozymes are known to date, of which the pistol ribozyme class was discovered only 5 years ago. Self-cleaving ribozymes are able...
Nine distinct classes of self-cleaving ribozymes are known to date, of which the pistol ribozyme class was discovered only 5 years ago. Self-cleaving ribozymes are able to cleave their own phosphodiester backbone at a specific site with rates much higher than those of spontaneous RNA degradation. Our study focuses on a bioinformatically predicted pistol ribozyme from the bacterium . We provide a biochemical characterization of this ribozyme, which includes an investigation of the effect of various metal ions on ribozyme cleavage and a kinetic analysis of ribozyme activity under increasing Mg concentrations and pH. Based on the obtained results, we discuss a possible catalytic role of divalent metal ions. Moreover, we investigated the ligation activity of the pistol ribozyme - an aspect that has not been previously analysed for this ribozyme class. We determined that the pistol ribozyme is almost fully cleaved at equilibrium with the ligation rate constant being nearly 30-fold lower than the cleavage rate constant. In summary, we have characterized an additional representative of this recently discovered ribozyme class isolated from . We expect that our biochemical characterization of a pistol representative in a cultivatable, genetically tractable organism will support our future investigation of the biological roles of this ribozyme class in bacteria.
Topics: Biocatalysis; Catalytic Domain; Computational Biology; Kinetics; Models, Molecular; Nucleic Acid Conformation; Paenibacillus polymyxa; RNA, Catalytic
PubMed: 33622172
DOI: 10.1080/15476286.2021.1874706 -
Frontiers in Microbiology 2020Bacteria belonging to the genus were frequently isolated from legume nodules. The nodule-inhabiting as a resource of biocontrol and plant growth-promoting endophytes...
Bacteria belonging to the genus were frequently isolated from legume nodules. The nodule-inhabiting as a resource of biocontrol and plant growth-promoting endophytes has rarely been explored. This study explored the nodule-inhabiting ' antifungal activities and biocontrol potentials against broad-spectrum important phytopathogenic fungi. We collected strains which were isolated from nodules of , , , , , or and belong to , , , , , , or closely related to , or . These nodule-inhabiting showed diverse antagonistic activities against five phytopathogenic fungi (, , , , and ). Six strains within the complex showed broad-spectrum and potent activities against all the five pathogens, and produced multiple hydrolytic enzymes, siderophores, and lipopeptide fusaricidins. Fusaricidins are likely the key antimicrobials responsible for the broad-spectrum antifungal activities. The nodule-inhabiting strains within the complex were able to epiphytically and endophytically colonize the non-host wheat plants, produce indole acetic acids (IAA), and dissolve calcium phosphate and calcium phytate. strains RP20, RP51, and RP62 could fix N. RP51 and sp. RP31, which showed potent plant colonization and plant growth-promotion competence, effectively control fungal infection . Genome mining revealed that all strains ( = 76) within the complex contain gene encoding indole-3-pyruvate decarboxylase for biosynthesis of IAA, 96% ( = 73) contain the cluster for biosynthesis of fusaricidins, and 43% ( = 33) contain the cluster for nitrogen fixation. Together, our study highlights that endophytic strains within the complex have a high probability to be effective biocontrol agents and biofertilizers and we propose an effective approach to screen strains within the complex.
PubMed: 33537018
DOI: 10.3389/fmicb.2020.618601 -
3 Biotech Jul 2021Glycosylation is a prominent biological mechanism, affecting the structural and functional diversity of many natural products. In this study, a novel thermostable...
UNLABELLED
Glycosylation is a prominent biological mechanism, affecting the structural and functional diversity of many natural products. In this study, a novel thermostable uridine diphosphate-dependent glycosyltransferase gene PpGT1 was cloned from NJPI29 and recombinantly expressed in WB600. The purified PpGT1 had a molecular weight of 45 kDa, as estimated using SDS-PAGE. The PpGT1 could catalyze the glycosylation of vanillic acid, methyl vanillate, caffeic acid, cinnamic alcohol, and ferulic acid. Moreover, PpGT1 possessed good thermostability and retained 80% of its original activity even after 12 h of incubation at 45 °C. In addition, PpGT1 remained stable within a neutral to alkaline pH range as well as in the presence of metal ions. The synthesis of methyl vanillate 4--β-D-glucoside by purified PpGT1 reached a yield 3.58 mM in a system with pH 8.0, 45 °C, 12 mM UDP-Glc, and 4 mM methyl vanillate. 3D-structure-based amino acid sequence alignments revealed that the catalytic residues and C-terminated PSPG motif were conserved. These unusual properties indicated that PpGT1 is a candidate UGT for valuable natural product industrial applications.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s13205-021-02855-z.
PubMed: 34109099
DOI: 10.1007/s13205-021-02855-z -
Life (Basel, Switzerland) Apr 2022Pepper is vulnerable to soil-borne fungal pathogens such as and . The potential of beneficial rhizosphere microorganisms to control and f.sp. was evaluated in pepper...
Pepper is vulnerable to soil-borne fungal pathogens such as and . The potential of beneficial rhizosphere microorganisms to control and f.sp. was evaluated in pepper plants. and were isolated from rhizospheric soil samples of healthy pepper plants. In vitro, both isolates caused clear reductions in the radial growth of root rot and wilt pathogens. Scanning electron microscopy displayed lysis and abnormal shape of the pathogens in dual cultures with and . The incidence and severity of root rot and wilt diseases were significantly reduced in pepper plants treated with the growth-promoting fungi (PGPF isolates; GF19-1, GF18-3, and sp. GS8-3), , or in comparison to the control. Moreover, the induction treatments led to increased pepper growth compared with their control. The defense related gene () expression was shown to be significantly higher in the treated plants than in the control plants. In conclusion, the antagonistic isolates ( and ) and PGPF isolates have a clear impact on the prevention of root rot and wilt diseases in pepper plants incited by and f.sp. The expression of the gene added to the evidence that PGPF isolates generate systemic resistance to pathogen infections.
PubMed: 35455078
DOI: 10.3390/life12040587 -
Microbiology Resource Announcements Jan 2022Paenibacillus polymyxa SRT9.1 is an epiphytic bacterium capable of inhibiting plant-pathogenic bacteria. The strain has potential for development as a biocontrol agent...
Paenibacillus polymyxa SRT9.1 is an epiphytic bacterium capable of inhibiting plant-pathogenic bacteria. The strain has potential for development as a biocontrol agent for use in agriculture. We report the whole-genome sequence of Paenibacillus polymyxa SRT9.1, consisting of 6,754,470 bp and 7,878 coding sequences, with an average G+C content of 45%.
PubMed: 35049350
DOI: 10.1128/mra.01097-21 -
Frontiers in Bioengineering and... 2024The demand for highly robust and metabolically versatile microbes is of utmost importance for replacing fossil-based processes with biotechnological ones. Such an...
The demand for highly robust and metabolically versatile microbes is of utmost importance for replacing fossil-based processes with biotechnological ones. Such an example is the implementation of DSM 365 as a novel platform organism for the production of value-added products such as 2,3-butanediol or exopolysaccharides. For this, a complete genome sequence is the first requirement towards further developing this host towards a microbial chassis. A genome sequencing project has just been reported for DSM 365 showing a size of 5,788,318 bp with a total of 47 contigs. Herein, we report the first complete genome sequence of DSM 365, which consists of 5,889,536 bp with 45 RNAs, 106 tRNAs, 5,370 coding sequences and an average GC content of 45.6%, resulting in a closed genome of 365. The additional nucleotide data revealed a novel NRPS synthetase that may contribute to the production of tridecaptin. Building on these findings, we initiated the top-down construction of a chassis variant of . In the first stage, single knock-out mutants of non-essential genomic regions were created and evaluated for their biological fitness. As a result, two out of 18 variants showed impaired growth. The remaining deletion mutants were combined in two genome-reduced variants which either lack the production of endogenous biosynthetic gene clusters (GR1) or non-essential genomic regions including the insertion sequence IS (GR2), with a decrease of the native genome of 3.0% and 0.6%, respectively. Both variants, GR1 and GR2, showed identical growth characteristics to the wild-type. Endpoint titers of 2,3-butanediol and EPS production were also unaffected, validating these genome-reduced strains as suitable for further genetic engineering.
PubMed: 38605990
DOI: 10.3389/fbioe.2024.1378873 -
Applied Microbiology and Biotechnology Dec 2019The focus of this study was to investigate the effects of luxS, a key regulatory gene of the autoinducer-2 (AI-2) quorum sensing (QS) system, on the biofilm formation...
The focus of this study was to investigate the effects of luxS, a key regulatory gene of the autoinducer-2 (AI-2) quorum sensing (QS) system, on the biofilm formation and biocontrol efficacy against Ralstonia solanacearum by Paenibacillus polymyxa HY96-2. luxS mutants were constructed and assayed for biofilm formation of the wild-type (WT) strain and luxS mutants of P. polymyxa HY96-2 in vitro and in vivo. The results showed that luxS positively regulated the biofilm formation of HY96-2. Greenhouse experiments of tomato bacterial wilt found that from the early stage to late stage postinoculation, the biocontrol efficacy of the luxS deletion strain was the lowest with 50.70 ± 1.39% in the late stage. However, the luxS overexpression strain had the highest biocontrol efficacy with 75.66 ± 1.94% in the late stage. The complementation of luxS could restore the biocontrol efficacy of the luxS deletion strain with 69.84 ± 1.09% in the late stage, which was higher than that of the WT strain with 65.94 ± 2.73%. Therefore, we deduced that luxS could promote the biofilm formation of P. polymyxa HY96-2 and further promoted its biocontrol efficacy against R. solanacearum.
Topics: Bacterial Proteins; Biofilms; Biological Control Agents; Carbon-Sulfur Lyases; Gene Expression Regulation, Bacterial; Solanum lycopersicum; Paenibacillus polymyxa; Plant Diseases; Quorum Sensing; Ralstonia solanacearum
PubMed: 31686149
DOI: 10.1007/s00253-019-10162-0 -
International Journal of Molecular... Apr 2021NifS and NifU (encoded by and ) are generally dedicated to biogenesis of the nitrogenase Fe-S cluster in diazotrophs. However, and are not found in N-fixing strains,...
NifS and NifU (encoded by and ) are generally dedicated to biogenesis of the nitrogenase Fe-S cluster in diazotrophs. However, and are not found in N-fixing strains, and the mechanisms involved in Fe-S cluster biosynthesis of nitrogenase is not clear. Here, we found that the genome of WLY78 contains the complete operon, a partial operon, a -like gene, two -like genes (-like and ), and two genes. Deletion and complementation studies showed that the , and genes of the operon, and -like and genes were involved in the Fe-S cluster biosynthesis of nitrogenase. Heterologous complementation studies demonstrated that the -like gene of WLY78 is interchangeable with , but WLY78 SufCDB cannot be functionally replaced by NifU. In addition, and are able to complement the WLY78 mutant. Our findings thus indicate that the NifS-like and SufCDB proteins are the specific sulfur donor and the molecular scaffold, respectively, for the Fe-S cluster formation of nitrogenase in WLY78. YutI can be an Fe-S cluster carrier involved in nitrogenase maturation in WLY78.
Topics: Bacterial Proteins; Genes, Bacterial; Iron-Sulfur Proteins; Nitrogenase; Paenibacillus polymyxa
PubMed: 33916504
DOI: 10.3390/ijms22073771 -
Microbiological Research Jan 2020Biocontrol has emerged in recent years as an alternative to pesticides. Given the importance of environmental preservation using biocontrol, in this study two...
Inhibition of Rhizoctonia solani RhCh-14 and Pythium ultimum PyFr-14 by Paenibacillus polymyxa NMA1017 and Burkholderia cenocepacia CACua-24: A proposal for biocontrol of phytopathogenic fungi.
Biocontrol has emerged in recent years as an alternative to pesticides. Given the importance of environmental preservation using biocontrol, in this study two antagonistic bacteria against phytopathogenic fungi were isolated and evaluated. These bacterial strains, identified as Paenibacillus polymyxa NMA1017 and Burkholderia cenocepacia CACua-24, inhibited (70 to 80%) the development of two phytopathogens of economic importance: the fungus Rhizoctonia solani RhCh-14, isolated from chili pepper, and the oomycete Pythium ultimum PyFr-14, isolated from tomato. The spectrum was not limited to the previous pathogens, but also to other phytopathogenic fungus, some bacteria and other oomycetes. Fungi-bacteria microcultures observed with optical and scanning electron microscopy revealed hyphae disintegration and pores formation. The antifungal activity was found also in the supernatant, suggesting a diffusible compound is present. Innocuous tests on tobacco leaves, blood agar, bean seed germination and in Galleria mellonella larvae showed that strain NMA1017 has the potential to be a biocontrol agent. Greenhouse experiments with bean plants inoculated with P. polymyxa exhibited the efficacy to inhibit the growth of R. solani and P. ultimum. Furthermore, P. polymyxa NMA1017 showed plant growth promotion activities, such as siderophore synthesis and nitrogen fixation which can contribute to the crop development.
Topics: Antifungal Agents; Burkholderia cenocepacia; Paenibacillus polymyxa; Pest Control, Biological; Plant Diseases; Pythium; Rhizoctonia; Nicotiana
PubMed: 31586859
DOI: 10.1016/j.micres.2019.126347