Isolation and characterization of peptide antibiotics LI-F04 and polymyxin B6 produced by Paenibacillus polymyxa strain JSa-9

Paenibacillus polymyxa JSa-9 had been found to produce five cyclic LI-F type antibiotics which were released into culture medium in accordance with our previous report. In this study, another three kinds of antagonistic compounds were extracted from P. polymyxa JSa-9 cell pellets and (or) spores by methanol. Using high performance liquid chromatography (HPLC) method, two antagonistic fractions were separated and collected from the methanol extract. One showed inhibition against Escherichia coli and Staphylococcus aureus, while the other was active against Aspergillus niger and S. aureus. By means of electrospray ionization mass spectroscopy (ESI-MS), infrared spectroscopy (IR), and amino acid analysis, two kinds of compounds from fraction B with molecular masses of 901 and 915 Da were characterized as the linear lipopeptide analogs of antibiotics LI-F04a and LI-F04b, respectively. Another antimicrobial substance from fraction A could be attributed to polymyxin B₆.     

Identification of LI-F type antibiotics and di-n-butyl phthalate produced by Paenibacillus polymyxa

Paenibacillus polymyxa strain JSa-9, a soil isolate that displayed antibacterial and antifungal activities in vitro, had been found to produce two types of antimicrobial substances. The two compounds were extracted from the fermentation broth of JSa-9 using ethyl acetate and subsequently purified by high performance liquid chromatography. By means of liquid chromatography-mass spectrometry and tandem mass spectrometry analysis, one of two antagonistic compounds was determined as di-n-butyl phthalate. And another was characterized as a mixture of related peptides of molecular masses of 883, 897, 911, 947, and 961 Da, with the most likely structure of them determined to be a cyclic depsipeptide with an unusual 15-guanidino-3-hydroxypentadecanoic acid moiety bound to a free amino group. These peptides were therefore members of the LI-F group of cyclic depsipeptides.     

Isolation and partial characterization of antibacterial lipopeptide produced by <Emphasis Type="Italic">Paenibacillus polymyxa</Emphasis> HKA-15 against phytopathogen <Emphasis Type="Italic">Xanthomonas campestris</Emphasis> pv. phaseoli M-5

An antibacterial metabolite was isolated from Paenibacillus polymyxa HKA-15, a soybean bacterial endophyte. The purification of the crude metabolite from Paenibacillus polymyxa HKA-15 was done by column chromatography. In TLC, a spot with an R _f value of 0.86 (±0.02) from the purified fraction showed bioactivity against Xanthomonas campestris pv. phaseoli M-5. In SDS-PAGE, the purified antibiotic was separated in the molecular weight range of 3.5 kDa. The exact molecular weight of the active compound was identified as 1,347.7 Da using MS-MS analysis. Infra red spectrum and ¹H NMR analysis showed the presence of amino acids and fatty acids in the active compound. The characterization of the antibacterial compound revealed its lipopeptide nature. In an agar diffusion assay, the crude metabolite showed a broad spectrum of activity, being able to inhibit the growth of the fungal pathogen, Rhizoctonia bataticola, Macrophomina phaseolina and Fusarium udum. A stronger inhibition was observed against bacterial pathogens viz., X. campestris pv.phaseoli M-5, X. campestris pv. phaseoli CP-1-1, Xanthomonas oryzae, Ralstonia solanacearum and Micrococcus luteus.     

多粘类芽胞杆菌KM2501-1杀南方根结线虫活性产物研究

【目的】南方根结线虫(Meloidogyne incognita)是一种危害严重的土传性植物病原线虫,给农业生产造成了巨大的经济损失,前期研究发现多粘类芽胞杆菌(Panebacillus polymyxa) KM2501-1具有很好的温室防治南方根结线虫效果,且可产生多种挥发性杀线虫活性物质,但对其非挥发性产物是否有杀线虫活性没有研究。本研究拟进一步分离鉴定其产生的杀线虫活性代谢产物,发掘新的杀线虫药物。【方法】对菌株KM2501-1进行液体发酵并离心收集发酵上清液,通过硅胶柱层析、高效液相色谱分离等方法得到高纯度的杀线虫活性物质,并通过液相色谱质谱联用分析、核磁共振等技术鉴定杀线虫活性物质的结构。【结果】生物活性检测显示,多粘类芽胞杆菌KM2501-1发酵上清液具有较强的南方根结线虫触杀活性,并能有效抑制南方根结线虫卵孵化,体外杀线虫效率高达87.66%,抑制卵孵化效率达92.26%。结构鉴定结果显示多粘类芽胞杆菌产生的杀线虫活性物质为环二肽类物质cyclo (Pro-Phe),800 mg/L的cyclo(Pro-Phe)杀线虫效率达84.75%。进一步的显微观测结果表明,与对照组相比,活性物质cyclo(Pro-Phe)处理后的根结线虫肠道组织紊乱、结构发生破坏。【结论】多粘类芽胞杆菌KM2501-1产生的cyclo (Pro-Phe)是一个具有杀线虫新功能的活性物质,其可能通过破坏线虫肠道杀死线虫。     

Biocontrol of <Emphasis Type="Italic">Meloidogyne javanica</Emphasis> by <Emphasis Type="Italic">Rhizobium</Emphasis> and plant growth-promoting rhizobacteria on lentil

Biocontrol of the root-knot nematode Meloidogyne javanica was studied on lentil using plant growth-promoting rhizobacteria (PGPR) namely Pseudomonas putida, P. alcaligenes, Paenibacillus polymyxa and Bacillus pumilus and root nodule bacterium Rhizobium sp. Pseudomonas putida caused greater inhibitory effect on the hatching and penetration of M. javanica followed by P. alcaligenes, P. polymyxa and B. pumilus. Inoculation of any PGPR species alone or together with Rhizobium increased plant growth both in M. javanica-inoculated and -uninoculated plants. Inoculation of Rhizobum caused greater increase in plant growth than caused by any species of plant growth-promoting rhizobacteria in nematode-inoculated plants. Among PGPR, P. putida caused greater increase in plant growth and higher reduction in galling and nematode multiplication followed by P. alcaligenes, P. polymyxa and B. pumilus. Combined use of Rhizobium with any species of PGPR caused higher reduction in galling and nematode multiplication than their individual inoculation. Use of Rhizobium plus P. putida caused maximum reduction in galling and nematode multiplication followed by Rhizobium plus P. alcaligens. Pseudomonas putida caused greater root colonization and siderophore production followed by P. alcaligenes, P. polymyxa and B. pumilus. Analysis of the protein bands of these four species by SDS-PAGE revealed that P. putida had a different protein band profile compared to the protein profiles of P. alcaligenes, P. polymyxa and B. pumilus. However, the protein profiles of P. acaligenes, P. polymyxa and B. pumilus were similar.     

Evaluation of promoter sequences for the secretory production of a Clostridium thermocellum cellulase in Paenibacillus polymyxa

Due to their high secretion capacity, Gram-positive bacteria from the genus Bacillus are important expression hosts for the high-yield production of enzymes in industrial biotechnology; however, to date, strains from only few Bacillus species are used for enzyme production at industrial scale. Herein, we introduce Paenibacillus polymyxa DSM 292, a member of a different genus, as a novel host for secretory protein production. The model gene cel8A from Clostridium thermocellum was chosen as an easily detectable reporter gene with industrial relevance to demonstrate heterologous expression and secretion in P. polymyxa. The yield of the secreted cellulase Cel8A protein was increased by optimizing the expression medium and testing several promoter sequences in the expression plasmid pBACOV. Quantitative mass spectrometry was used to analyze the secretome in order to identify promising new promoter sequences from the P. polymyxa genome itself. The most abundantly secreted host proteins were identified, and the promoters regulating the expression of their corresponding genes were selected. Eleven promoter sequences were cloned and tested, including well-characterized promoters from Bacillus subtilis and Bacillus megaterium. The best result was achieved with the promoter for the hypothetical protein PPOLYM_03468 from P. polymyxa. In combination with the optimized expression medium, this promoter enabled the production of 5475 U/l of Cel8A, which represents a 6.2-fold increase compared to the reference promoter P_aprE. The set of promoters described in this work covers a broad range of promoter strengths useful for heterologous expression in the new host P. polymyxa.

     

Colistin A and colistin B among inhibitory substances of <Emphasis Type="Italic">Paenibacillus polymyxa</Emphasis> JB05-01-1

Recently, we isolated and reported the antagonism of Paenibacillus polymyxa JB05-01-1 (P. polymyxa JB05-01-1) against Gram-negative bacteria. Here, we provide more insights and attribute the abovementioned antagonism to the production of colistins A and B, which were purified by Amberlite column exchange, C18 column hydrophobicity, superdex 75 16/60 gel filtration chromatography connected to fast protein liquid chromatography and identified by MALDI TOF/TOF, and manual nanospray analysis. The amount of colistin A and colistin B recovered from 500 ml of culture supernatant was about 0.05 mg. The specific activity and the average recovery of the eluted substances were 5,120 AU/mg and 1.1%, respectively. The minimal inhibitory concentrations of the purified colistins against Escherichia coli O157:H7 and Pseudomonas fluorescens LRC R73 were 0.13 and 0.62 μg/ml, respectively.     

A new approach to the production of the recombinant SOD protein by methylotrophic <Emphasis Type="Italic">Pichia pastoris</Emphasis>

The gene for the copper, zinc–superoxide dismutase (SOD) from the yeast Saccharomyces cerevisiae was cloned, characterized, and overexpressed in the methylotrophic Pichia pastoris. The sod gene sequence obtained is 465 bp and encodes 154 amino acid residues. The sod gene sequence was cloned into the pPIC9K vector, yielding pAB22. The linearized pAB22 DNA, digested with restriction enzyme SacI, was transformed into the genome of the GS115 strain of yeast P. pastoris. The overexpressed SOD protein was shown to have immunologically biological activity and to be enzymatically active. The SOD protein was purified from the cultured yeast by ammonium sulfate precipitation and diethylaminoethyl–cellulose column chromatography. This relatively simple purification method produced a single band on analysis by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), which indicated that the SOD protein obtained attained to higher purity and specific activity.     

Isolation and Characterization of Transposon-Insertional Mutants from <Emphasis Type="Italic">Paenibacillus </Emphasis><Emphasis Type="Italic">polymyxa</Emphasis> E681 Altering the Biosynthesis of Indole-3-Acetic Acid

We screened a mini-Tn10 insertional mutant library of the spore-forming bacterium Paenibacillus polymyxa E681 with variable indole-3-acetic acid (IAA) productivity. Four mutants, of which two showed a decrease in IAA production and the other two showed an increase in IAA production, were finally selected. Further analyses demonstrated different levels of IAA intermediates from culture supernatant of wild-type strain and mutants. In addition, mutants showed different promotions on the early growth of 10-day-old maize in terms of the increase in shoot and root weights. DNA fragments flanking the transposon insertion in four mutants were cloned and sequenced. The target sites of insertion were gene gpr1, disrupted at two sites, 49 bp downstream of the spo0F gene, and relA/spoT homologue, which codes for GPR1/FUN34/YaaH family protein, stage 0 sporulation protein F, and RelA/SpoT domain protein, respectively. This evidence suggests that there may be a number of genes involved in the regulation of IAA biosynthesis of P. polymyxa.     

Purification and Characterization of Biliverdin-binding Protein from Larval Hemolymph of the Swallowtail Butterfly,Papilio xuthus L.

The biliverdin-binding protein from the larval hemolymph of the swallowtail butterfly, Papilio xuthus L., was purified and characterized. The crude biliverdin-binding protein, obtained by ammonium sulfate fractionation, was purified in two steps, the first one by gel filtration chromatography and the second one by ion-exchange chromatography. The molecular mass of the purified protein was analyzed by SDS-polyacrylamide gel electrophoresis and estimated to be 21 kDa. The N-amino terminal sequence of P. xuthus biliverdin-binding protein analyzed up to the 19th residue showed that 42% of the amino acid sequence are sequence similarity to the bilin-binding protein from Pieris brassicae. These results suggest that the P. xuthus biliverdin-binding protein belongs to the insecticyanin-type.     

Artificial consortium that produces riboflavin regulates distribution of acetoin and 2,3‐butanediol by Paenibacillus polymyxa CJX518

The introduction of an NADH/NAD⁺ regeneration system can regulate the distribution between acetoin and 2,3‐butanediol. NADH regeneration can also enhance butanol production in coculture fermentation. In this work, a novel artificial consortium of Paenibacillus polymyxa CJX518 and recombinant Escherichia coli LS02T that produces riboflavin (VB₂) was used to regulate the NADH/NAD⁺ ratio and, consequently, the distribution of acetoin and 2,3‐butanediol by P. polymyxa. Compared with a pure culture of P. polymyxa, the level of acetoin was increased 76.7% in the P. polymyxa and recombinant E. coli coculture. Meanwhile, the maximum production and yield of acetoin in an artificial consortium with fed‐batch fermentation were 57.2 g/L and 0.4 g/g glucose, respectively. Additionally, the VB₂ production of recombinant E. coli could maintain a relatively low NADH/NAD⁺ ratio by changing NADH dehydrogenase activity. It was also found that 2,3‐butanediol dehydrogenase activity was enhanced and improved acetoin production by the addition of exogenous VB₂ or by being in the artificial consortium that produces VB₂. These results illustrate that the coculture of P. polymyxa and recombinant E. coli has enormous potential to improve acetoin production. It was also a novel strategy to regulate the NADH/NAD⁺ ratio to improve the acetoin production of P. polymyxa.     

Cloning and characterization of a novel CoA-ligase gene from <Emphasis Type="BoldItalic">Penicillium chrysogenum</Emphasis>

A novel phenylacetic acid (PAA)-induced CoA-ligase-encoding gene, designated as phlC, has been cloned from penicillin-producing fungus Penicillium chrysogenum. The open reading frame of phlC cDNA was 1671 bp and encoded a 556 amino acid residues protein with the consensus AMP binding site and a peroxisomal targeting signal 1 on its C terminus. The deduced amino acid sequence showed 37% and 38% identity with characterized P. chrysogenum Phl and PhlB protein, respectively. Functional recombinant PhlC protein was overexpressed in Escherichia coli. The purified recombinant enzyme was capable to convert PAA into its corresponding CoA ester with a specific activity of 129.5 ± 3.026 pmol/min per mg protein. Similar to Phl and PhlB, PhlC displayed broad substrate spectrum and showed higher activities to medium- and long-chain fatty acids. The catalytic properties of PhlC have been determined and compared to those of Phl and PhlB.     

β-Chemokines Are Produced in Lungs of Mice with Mycoplasma Respiratory Disease

The abilities of Bacillus polymyxa and Bacillus thuringiensis to survive on the rice phyllospere were compared; it was found that B. polymyxa colonizes the crop better. This study also showed that B. polymyxa inoculation to rice plants increased the shoot and the root growth of the crop. Efforts were made to introduce the cry1Ac gene of B. thuringiensis subsp. kurstaki into B. polymyxa so that the application of such transgenic B. polymyxa strains would prove to be dually beneficial to rice crops both as a biopesticide and as a biofertilizer. Immunoblot analysis of the recombinant organism containing the cry1Ac gene, strain BP113, indicated efficient expression of this gene in the heterologous host. Bioassays with the first instar larvae of the yellow stem borer of rice (Scirpophaga incertulas) revealed that the protein preparations from BP113 were toxic. Received: 12 August 1998 / Accepted: 25 September 1998     

Toxin-binding proteins isolated from yellow mealworm <Emphasis Type="Italic">Tenebrio molitor</Emphasis> and wax moth <Emphasis Type="Italic">Galleria mellonella</Emphasis>

A 67-kDa protein that can specifically bind the activated Cry9A endotoxin under ligand-blotting conditions was purified from midgut epithelium apical membranes of wax moth Galleria mellonella by affinity chromatography. N-Terminal amino acid sequencing enabled identification of this protein as aminopeptidase N. In similar experiments, 66- and 58-kDa proteins specific to endotoxin Cry3A were isolated from the midgut epithelium apical membranes of Tenebrio molitor larvae. Mass spectrometry showed close similarity of the 58-kDa protein to the Tenebrio molitor α-amylase.     

Isolation and Identification of a Novel Antifungal Protein from a Rhizobacterium Bacillus subtilis Strain F3

Bacillus subtilis strain F3, isolated from peach rhizosphere soil, is an antifungal bacterium against many plant pathogens. In this study, the antifungal protein was isolated and purified by ammonium sulphate and chromatography, then identified by mass spectrum analysis. By sequential chromatography of Sephadex G‐50, DEAE‐Sephadex A‐25 anion exchange and Sephadex G‐100, a fraction designated as F3A was isolated to show a single protein band in SDS‐PAGE and be antagonistic towards Monilinia fructicola. The peptide mass fingerprinting of the protein band of F3A had high similarity with the amino acid sequences of several flagellin protein of B. subtilis. There were seven amino acid fragments matched with the protein having the highest score, and sequence coverage was 33%. F3A showed a strongly inhibitory effect to the growth and sporulation of M. fructicola. There were little aerial hyphae and conidia at the antifungal zone, and the hyphae were abnormal with some cell wall collapse and several vacuoles in cells.     

Isolation of bioactive antibiotic peptides from Bacillus brevis and Bacillus polymyxa against Botrytis grey mould in strawberry

Abstract

Grey mould caused by Botrytis cinerea is a devastating disease that results in extensive yield losses to strawberry. Bacillus brevis (Brevibacillus brevis) and Bacillus polymyxa (Paenibacillus polymyxa), which showed strong antifungal activity against B. cinerea, were isolated from the phyllosphere of strawberry plants. The advantage of using these bacteria is that the biochemistry and physiology of production of antibiotic peptides antimicrobial substances is well documented. A study was conducted to assess the activity of both Bacilli and their antibiotic peptides produced against B. cinerea in strawberry plants in vitro and in vivo. In vitro bioassay, both Bacilli have strongly inhibited pathogen germination, growth and extra-cellular enzyme production. Bacillus brevis was generally the most effective in reducing Botrytis growth. Gramicidin S and polymyxin B peptide antibiotics were extracted from culture filtrate of B. brevis and B. polymyxa, respectively, purified by silica thin chromatography and identified by high performance liquid chromatography. Germination, growth rate and production of extra-cellular enzymes were more sensitive to both antibiotics. Gramicidin S was the most active against B. cinerea with a minimal inhibitory concentration of 15 μmol/l. Polymyxin B also showed activity against B. cinerea at 25 μmol/l. Under controlled conditions (18 – 22°C, 90% relative humidity and 12 h photoperiod), strawberry plants were sprayed with pathogens (10⁵ spores/ml), antagonists (from 10⁵ to 10⁸ cells/ml) and antibiotic peptides (0 – 30 μmol/l) for reducing grey mould. Disease incidence was decreased in the presence of B. brevis. Both antibiotic peptides inhibited Botrytis growth that was observed by scanning electron microscopy. The plant leaves adsorbed significant amounts of antibiotics which reached from 46.1 to 67.5% of the original solution. Under natural field conditions, these biocontrol and antibiotic peptides at different concentrations were evaluated in 2003/2004 and 2004/2005 seasons against Botrytis grey mould. Treating plants with B. brevis exhibited a significant high activity against the development of Botrytis disease on strawberry. Gramicidin S showed a strong potential in reducing disease incidence, followed by polymyxin B, and acted as a fungicide to the pathogen growth. Inhibition of B. cinerea by both Bacilli was similar to equivalent levels of their antibiotics produced. In addition, these treatments significantly reduced the development of Botrytis and increased fruit yield. It can be suggested that B. brevis and B. polymyxa may be considered as potential biocontrol agents against Botrytis grey mould on strawberry based on the production of antifungal peptides. Therefore, gramicidin S and polymyxin B products are considered as biocontrol agents and may play a significant role in the future for practical applications in strawberry management systems.     

Purification and Identification of a Novel Leucine Aminopeptidase from <Emphasis Type="Italic">Bacillus thuringiensis israelensis</Emphasis>

A novel leucine aminopeptidase was purified from a Bacillus thuringiensis israelensis (Bti) culture. The purification stages included heating the concentrated supernatant to 65°C for 90 min, anion-exchange chromatography by DEAE cellulose, and hydrophobic chromatography by phenyl Sepharose. The specific activity of leucine aminopeptidase after the hydrophobic chromatography increased by 215.5-fold and the yield was 16%. The molecular weight of the active enzyme was 59 kDa. Mass spectrometry analysis of the 59-kDa leucine aminopeptidase revealed that this protein has at least 41% homology with the cytosol leucine aminopeptidase produced by Bacillus cereus. Maximal leucine aminopeptidase activity occurred at 65°C, pH 10 toward leucine as the amino acid terminus. The enzyme was strongly inhibited by bestatin, dithiothreitol, and 1,10-phenanthroline, indicating that the enzyme might be considered as a metallo-aminopeptidase that has disulfide bonds at the catalytic site or at a region that influences its configuration. Examination of the purified leucine aminopeptidase’s effect on the activation of the protoxin Cyt1Aa from Bti revealed that when it acts synergistically with Bti endogenous proteases, it has only a minor role in the processing of Cyt1Aa into an active toxin.     

Molecular characterization of a cDNA for a cysteine-rich antifungal protein from<Emphasis Type="Italic">Capsicum annuum</Emphasis>

We have isolated a cDNA clone for the antifungal protein,CaAFP, from hot pepper,Capsicum annuum L. Its open reading frame encodes 85 amino acids, including 8 cysteine residues. CaAFP consists of three domains: a signal peptide, a chitin-binding domain, and a C-terminal peptide domain. The deduced amino acid sequence of the chitin-binding domain shows 92% and 85% similarity to the same domain from PnAMPs and hevein, respectively. Southern blot analysis indicated that CaAFP is present as a single copy, while the northern blots revealed that the clone is highly expressed in the leaves and flower buds, but not in the roots. However, wounding treatments and chemicals generally known to induce PR proteins did not stimulate its expression.In situ hybridization also showed that CaAFP is expressed in the parenchyma cells of the floral sepals. As seen in our functional analysis, this clone was expressed inEscherichia coli, and the fusion protein was purified using nickel-affinity column chromatography. This purified AFP fusion protein inhibited spore germination and appressoria formation in several plant pathogenic fungi, includingFusarium oxisporum andColletotrichum gloeosporioides. Our results suggest CaAFP is an antifungal protein that defends developing seeds against pathogen invasion while also having a specific biological role during floral development.