Antagonistic Activities of Novel Peptides from Bacillus

Oct 23, 2015 - Young Gwon Kim†, Hee Kyoung Kang†, Kee-Deok Kwon§, Chang Ho Seo§, Hyang Burm Lee#, and Yoonkyung Park†‡. † Department of ...
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Antagonistic activities of novel peptides from Bacillus amyloliquefaciens PT14 against Fusarium solani and F. oxysporum YOUNG GWON KIM, Hee-Kyoung Kang, KEE-DEOK KWON, CHANG HO SEO, HYANG BURM LEE, and Yoonkyung Park J. Agric. Food Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jafc.5b04068 • Publication Date (Web): 23 Oct 2015 Downloaded from http://pubs.acs.org on October 27, 2015

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Journal of Agricultural and Food Chemistry

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Antagonistic

activities

of

novel

peptides

from

Bacillus

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amyloliquefaciens PT14 against Fusarium solani and F. oxysporum

3 4

YOUNG GWON KIM†,#, HEE KYOUNG KANG†,#, KEE-DEOK KWON§, CHANG HO

5

SEO§, HYANG BURM LEE¶ AND YOONKYUNG PARK†, ‡, *

6 7



Department of Biomedical Science, Chosun University, Gwangju 61452, Korea

8

§

Department of Bioinformatics, Kongju National University, Kongju 32588, Korea

9



College of Agriculture and Life Sciences, Chonnam National University, Gwangju

10

61186, Korea

11



Research Center for Proteineous Materials, Chosun University, Gwangju 61452, Korea

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TITLE RUNNING HEAD: Antagonistic activities of PT14 peptides

14 15

*Corresponding author (e-mail [email protected]; fax 82-62-225-6758).

16 17 18 19 20 21 22



Research Center for Proteineous Materials (RCPM), Chosun University. Department of Biomedical Science and BK21 Research Team for Protein Activity Control, Chosun University. §

#

These authors contributed equally to this work

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ABSTRACT: Bacillus species have recently drawn attention due to their potential use

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in the biological control of fungal diseases. Here we report on the antifungal activity of

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novel peptides isolated from Bacillus amyloliquefaciens PT14. Reverse-phase high

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performance liquid chromatography revealed that B. amyloliquefaciens PT14 produces

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five peptides (PT14-1, 2, 3, 4a and 4b) that exhibit antifungal activity but are inactive

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against bacterial strains. In particular, PT14-3 and PT14-4a showed broad spectrum

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antifungal activity against Fusarium solani and F. oxysporum. The PT14-4a N-terminal

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amino acid sequence was identified through Edman degradation, and a BLAST

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homology analysis showed it not to be identical to any other protein or peptide. PT14-4a

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displayed strong fungicidal activity with minimal inhibitory concentrations of 3.12

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mg/L (F. solani) and 6.25 mg/L (F. oxysporum), inducing severe morphological

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deformation in the conidia and hyphae. On the other hand, PT14-4a had no detectable

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hemolytic activity. This suggests PT14-4a has the potential to serve as an antifungal

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agent in clinical therapeutic and crop-protection applications.

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KEYWORDS: Bacillus amyloliquefaciens, antifungal peptide, biological control,

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Fusarium oxysporum, Fusarium solani

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■ INTRODUCTION

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Plant diseases caused by viruses, bacteria and fungi are responsible for significant crop

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losses and reductions in the quality and safety of agricultural products. They cause, for

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example, wilt and rot diseases that diminish the commercial production of numerous

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important agricultural and ornamental plant species, including tomatoes, bananas,

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cotton and tulip bulbs.1 One deadly pathogen infecting agricultural products is

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Fusarium oxysporum. Unfortunately, once F. oxysporum is established in the soil, it can

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be extremely difficult to eradicate, as its chlamydospores can remain dormant and infect

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the soil for many years. F. oxysporum f. sp. spinaciae is an important pathogen in

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spinach and is typically found in fields where the F. oxysporum population is high.2,3 It

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is also a major component of a seedling disease complex.2 Up to now, farmers have

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mainly relied on chemical pesticides to control this fungus; however, use of chemical

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pesticides inevitably leads to environmental pollution and microbial tolerance to the

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chemicals.4 For those reasons as well as for their potent bactericidal and/or fungicidal

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activities over a broad spectrum of microorganisms and their low propensity to induce

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tolerance, antimicrobial peptides have been attracting attention.

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In recent years, several groups have explored the potential use of rhizosphere-

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associated bacteria (Bacillus, Pseudomonas and Burkholderia spp.) as biological control

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agents.5-7 Among these, Bacillus spp., which occur ubiquitously in the soil, are

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considered to be natural “factories” for production of a wide array of biologically active

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compounds against soil-borne and post-harvest pathogens, including Fusarium spp.,

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Rhizoctonia spp., Pythium spp. and Aspergillus spp.8,10-12 In addition, they form

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endospores that are highly resistant to unfavorable environmental conditions.8,9

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Consequently, strains such as B. subtilis, B. megaterium, and B. cereus have already

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been developed as commercial biocontrol agents.13,14

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Bacillus amyloliquefaciens is closely related to B. subtilis and is able to produce a

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variety of structurally diverse antimicrobial compounds, more than half of which are

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cyclic or linear lipopeptides.9 The cyclic lipopeptides, which include the iturin group

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(iturins, mycosubtilins, and bacillomycins), the surfactin group and the fengycin group

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(fengycin A, fengycin B, and fengycin C),15 have well-recognized potential for use in

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biotechnology and biomedical applications related to their excellent antibacterial,

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antiviral, antitumoral, antifungal and antimycoplasmic activities.16 The objectives of the

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present study were to (a) investigate antagonistic effects of the peptides isolated from B.

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amyloliquefaciens PT14 against F. solani and F. oxysporum under in vitro conditions;

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(b) purify PT14 peptides by RP-HPLC, perform chemical profiling by MALDI-

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TOF/MS, and analyze their N-terminal sequences; (c) conduct antifungal assays with

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PT14 peptides, using disc diffusion, micro-well dilution, and scanning electron

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microscopy.

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■ MATERIALS AND METHODS

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Bacterial strains and chemicals. A total of 14 Bacillus amyloliquefaciens

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strains isolated from soil were provided by the Environment Microorganism Laboratory,

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Chonnam National University (Gwangju, Korea).

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For antifungal and antimicrobial assays, the following strains were obtained from

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the Korea Collection for Type Cultures (KCTC) at the Korea Research Institute of

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Bioscience and Biotechnology (KRIBB, Daejon, Korea): F. solani (KCTC 6326), F.

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oxysporum (KCTC 16909), Trichoderma harzianum (KCTC 6043), Staphylococcus

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aureus (KCTC 1621) and Escherichia coli (KCTC 1682).

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A SPE 900 mg Lrg Pore C18 column was purchased from Maxi-CleanTM (USA). A

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reverse-phase C18 HPLC column for purification of peptides was purchased from

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Shimadzu Corporation (Kyoto, Japan). Acetonitrile and water (HPLC grade) were

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obtained from Burdick & Jackson Inc. (Muskegon, MI, USA), and trifluoroacetic acid

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(TFA) was obtained from Merck. The Luria-Bertani (LB) medium used for B.

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amyloliquefaciens culture and other media were purchased from Difco Laboratories Inc.

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(Detroit, MI, USA). All other chemicals and reagents were of analytical grade.

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Screening B. amyloliquefaciens for antifungal activity. To isolate effective

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antagonists against F. oxysporum, F. solani, and Trichoderma harzianum, 14 B.

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amyloliquefaciens strains were screened using paper/agar disc assays for their antifungal

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activity. Of these, five strains (PT1, PT2, PT5, PT13, and PT14) exhibited strong

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antagonistic activity against F. oxysporum, F. solani, and T. harzianum in the assays

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(Supplementary Figure 1A). The strongest antagonistic activity was exhibited by PT14,

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which formed an 18-mm inhibition zone against F. solani in the agar diffusion assay

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(Supplementary Figure 1B, Supplementary Table 1). Thus, B. amyloliquefaciens 5

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PT14 was selected for subsequent physiological and biological analyses.

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Isolation and purification of antifungal proteins. B. amyloliquefaciens was

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grown at 37°C in 700 mL LB medium. After incubation for 24 h (to stationary growth

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phase) in a shaking incubator (120 rpm), the culture medium was centrifuged at 14,000

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× g for 30 min to remove the cells. The supernatants were then filtered through a 185-

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mm paper after SPE C18 column purification to remove remaining cells and LB medium.

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Peptides exhibiting antifungal activity were separated by RP-HPLC on a C18

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reverse phase column (VP-ODS, 4.6 × 250 mm) using a HPLC system (Shimadzu

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Corporation, Japan) previously equilibrated with 0.1% (v/v) trifluoroacetic acid in

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HPLC-grade water containing 5% acetonitrile. Elution was performed using a linear

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gradient of 0.1% (v/v) TFA in water (solvent A) and 0.1% (v/v) TFA in acetonitrile

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(solvent B) at a flow rate of 1 mL/min as follows: PT14 fractions were eluted in the

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presence of 40% solvent B for 15 min, 40-65% solvent B for 45 min and 65-95% for 65

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min. Fractions eluted between 30 min and 45 min were pooled, dried using a vacuum

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concentrator, and then successively subjected for further purification under the same

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conditions. The eluate was monitored by measurement of the absorbance at 215 nm, and

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each peak fraction was collected and assayed for antifungal activity.

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Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis

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(SDS-PAGE). Electrophoresis of low-molecular-mass peptides was performed

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according to the method of Schagger and Jagow17 on 16.5% polyacrylamide gel. After

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electrophoresis, the gel was stained with Coomassie Brilliant Blue G-250. The

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molecular weight markers in Tricine SDS-PAGE included triosephosphate isomerase

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from rabbit muscle (26.6 kDa), myoglobin from horse heart (17 kDa), α-lactalbumin

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from bovine milk (14.2 kDa), aprotinin from bovine lung (6.5 kDa), oxidized insulin 6

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chain B from bovine pancreas (3.5 kDa) and bradykinin (1 kDa). Protein

determination.

Matrix-assisted

laser

desorption/ionization

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(MALDI-MS) was performed in linear mode using an Axima-CFR MALDI-TOF mass

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spectrometer (Kratos Analytical, Manchester, UK). The protein concentration was

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determined according to the method of Bradford (1972)18 using bovine serum albumin

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(BSA) as the calibration standard.

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N-terminal amino acid sequence analysis. The N-terminal amino acid

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sequences of the purified peptides were analyzed using automated Edman degradation

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in a pulse liquid automatic sequencer (Applied Biosystems Inc., model 491) at the

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Korean Basic Science Institute (Seoul, Korea). The amino acid sequence was then

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compared to sequences from the NCBI database using the BLAST program.

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Antifungal assay. Assays for antifungal activity toward phytopathogenic fungi

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were carried out in petri dishes containing potato dextrose agar (PDA; Difco

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Laboratories Inc.). After development of a mycelial colony, sterile black paper disks (6

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mm in diameter) were placed 0.5 cm away from the rim of the colony. Aliquots of

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purified peptide in 10 mM PBS buffer (pH 7.4) were layered onto the disks, and the

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plates were incubated at 28°C for 18 h to allow mycelial growth.

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The minimal inhibitory concentrations (MICs) of the purified peptides against the

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fungal strains were determined as described by Moor et al.19 The MIC was defined in

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this study as the lowest concentration of peptide that inhibited fungal growth. After

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fungal strains were grown at 28°C in PDA agar plates, the fungal conidia were collected

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using 0.08% Triton X-100 and seeded at a density of 2 × 104 spore/mL (counted using a

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hemocytometer) in the wells of a 96-well plate (Nunc F96 microtiter plates, Denmark)

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containing YM medium. Serially diluted peptide solutions (final concentrations: 50, 25, 7

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12.5, 6.25 and 3.125 mg/L) were then added to the wells, and wells not receiving

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peptide were used as negative controls. The plate was then incubated overnight at 28°C,

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after which morphological changes to the conidia were examined using an ECLIPSE

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TE300 phase contrast microscope (Nikon, Japan). Identical assays examining the effects

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of the peptides on fungal hyphae were also performed.

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Antibacterial assay. Antibacterial activity was tested by measuring the

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inhibition of bacterial growth in sterile 96-well plates. Serial dilutions of sample

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solutions were added to the wells to final concentrations ranging from 0.78 to 100 µg.

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Then after adding bacteria to the wells (5 × 105 cfu/mL), the plate was incubated

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overnight at 37°C. Control assays contained all components, except the test sample.

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MICs were determined based on the increase in optical density at 600 nm measured

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using a Microtiter ELISA Reader after incubation for 18 h at 37°C.

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Circular dichroism (CD) spectroscopy. CD spectra were recorded at 25°C on

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a Jasco J-810 spectropolarimeter (JASCO Inc., Easton, MD, USA) equipped with a

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temperature control unit. A quartz cell with a 0.1-cm path length was used with a 50 µM

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peptide solution under the indicated conditions [various concentrations of peptide and

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1.5 mM liposomes (PC:CH, 10:1 w/w and PE:PG, 7:3 w/w) or 10 mM sodium

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phosphate buffer (pH 7.4). To improve the signal-to-noise ratio, five scans from 190-

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250 nm were acquired for each condition and averaged. The acquired CD signal spectra

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were then converted to the mean residue ellipticity using the following equation:

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[θ] = θobs /10ᆞlᆞc

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where θobs is the measured signal (ellipticity) in millidegrees, l is the optical path length

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of the cell in cm, and c is the concentration of peptide in mol/L [mean residue molar

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concentration: c = number of residues in the constructed of peptide × the molar

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concentration of the peptide].

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Hemolysis. Hemolytic activity was assessed using human red blood cells

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(hRBCs) collected from healthy donors. Fresh hRBCs were collected by centrifugation

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at 800 × g for 10 min and washed tree times with PBS. Peptides dissolved in PBS were

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then added to 100 µL of stock hRBCs suspended in PBS (final hRBC concentration, 8%

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v/v), after which the samples were incubated for 60 min at 37°C with agitation,

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followed by centrifugation for 10 min at 800 × g. The absorbance (A) of the

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supernatants was then assessed at 414 nm; hRBCs in PBS (Ablank) or 0.1% Triton X-100

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(Atriton) serving as negative and positive controls, respectively. Percent hemolysis was

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calculated according to the equation:

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% Hemolysis = [(Asample − Ablank)/(Atriton − Ablank)] × 100

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Each measurement was conducted in triplicate.

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■ RESULTS AND DISCUSSION

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Recently reported effects of antifungal peptides from bacteria. In recent

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years, there has been increasing interest in the safety of agricultural products.20 For

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organic crops, in particular, biological disease controls are important.21-22 Reports from

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several studies provide strong evidence that strains of B. amyloliquefaciens12,

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significantly reduce disease severity in a variety of hosts,28 and they are currently being

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used commercially in biological control products, owing to their excellent antagonist

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effects and high stability.29

23-27

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Bacteria express a wide array of antifungal peptides. For instance, peptides with

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antifungal activity towards Alternaria brassicicola have been isolated from the

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fermentation broth of B. subtilis CL2T.30 In addition, iturin A and surfactin, two

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antifungal lipopeptides, have also been isolated from B. subtilis,31 while tensin is an

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antifungal cyclic lipopeptide from P. fluorescens.32 Tensin acts against F. solani by

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causing a reduction in radial mycelial extension and an increase in branching and rosette

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formation. Lipopeptides exhibiting fungicidal, bactericidal and insecticidal activities

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have most commonly been isolated from B. thuringiensis CMB26,33 though a novel

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antifungal peptide produced by another Bacillus strain, B-TL2, has been purified from

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tobacco stems.34 However, only few short linear antifungal/antimicrobial peptides

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produced by Bacillus strain are reported in the literature. Kening et al. (1999) pointed

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out that B. subtilis produces bacilysin, a small peptide containing an N-terminal alanine

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residue, and L-anticapsin, which is involved in synthesis of nucleotides, amino acids

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and coenzymes and causes the lysis of Candida albicans.35 Some strains of B. subtilis

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also produce chlorotetaine, a chlorinated derivative of bacilysin with similar antifungal

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activity.36 10

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For that reason, we tested B. amyloliquefaciens for its potential use against three

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plant fungal pathogens, F. solani, F. oxysporum and T. harzianum. Of those, F. solani is

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a phytopathogenic fungus and an important causal agent of several crop diseases,

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including root and stem rot in peas, sudden death syndrome in soybeans, foot rot in

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beans and dry rot in potatos,37-40 while F. oxysporum is a phytopathogenic fungus that

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affects tomato crops, causing huge losses to farmers.41 From B. amyloliquefaciens, we

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were able to isolate several small antifungal peptides that suppressed those fungi.

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Purification of antifungal peptides from B. amyloliquefaciens PT14. Using

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RP-HPLC we detected four main peaks that had retention times of 30 to 42 min and

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were eluted using a 40-65% gradient (Figure 1A). The peak fractions exhibiting

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antifungal activity were collected, pooled (Figure 1C), and confirmed by Tricine-SDS-

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PAGE, which showed single bands of molecular weights ranging from 1 to 3.5 kDa

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(Figure 1B). However, exact molecular masses of the PT14 peptides could not be

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determined by SDS-PAGE. In addition, peak 4 was separated into two peaks, 4a and 4b

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in the 2nd RP-HPLC (Figure 2A). Consistent with that finding, when subjected to

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MALDI-TOF/MS analysis, compounds 1, 2, 3, 4a and 4b exhibited m/z peaks at 1454.4,

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1478.5, 1463.2, 1514.0 and 1516.9, respectively (Supplementary Figure 2, Figure 2B).

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When these substances were tested in antifungal assays against F. oxysporum, F.

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solani and T. harzianum, compounds 1, 2, 3 and 4, corresponding to the peaks shown in

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Figure 1C, exhibited potent growth inhibiting activity against all three fungal strains.

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Note that peptides 4a and 4b exhibited antifungal activities at different concentrations

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(Supplementary Figure 3). MALDI-TOF/MS analysis and antifungal activity assay

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confirmed PT-14a and PT-4b as different peptides.

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Antifungal activity assay. We next assessed the antifungal activities of PT14-1, 11

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2, 3, 4a and 4b by using spectrophotometrics and microscopy to evaluate their inhibitory

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capacity against F. solani and F. oxysporum conidial germination and hyphae growth.

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The MICs for each of the peptides are listed in Table 1. After incubation for 24 h, PT14-

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3 and PT14-4a at 3.12 mg/L (log10 = 0.49) for F. solani and 6.25 mg/L (log10 = 0.80) for

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F. oxysporum completely inhibited conidial germination (100% growth inhibition)

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(Figure 3). PT14-4b completely inhibited the germination of F. solani conidia at 25

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mg/L (log10 = 1.40), but F. oxysporum conidia were able to germinate and grow even in

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the presence of 25 µg/mL peptide, though 100% growth inhibition was achieved at 50

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mg/L (log10 = 1.70) (Figure 3). PT14-1 and PT14-2 also completely inhibited the

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growth of F. oxysporum at 50 mg/L; at 6.25 µg/mL, PT14-1 and PT14-2 inhibited

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growth of F. oxysporum by 59% and 74%, respectively (Figure 3). Notably, none of the

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peptides tested exhibited antibacterial activity against gram-positive S. aureus or gram-

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negative E. coli (MIC >100 mg/L).

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Photomicrographs of F. solani and F. oxysporum mycelia were taken after a 12 h

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growth period, and the effect of PT14-4a on hyphal morphology was monitored and

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compared with the morphology of untreated hyphae. As shown in Figure 4, in control

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cultures, without an antagonistic peptide, conidial spores had their typical canoe shape

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and hyphae grew actively, displaying equal widths, even surfaces and active branching.

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By contrast, treatment with PT14-4a resulted in conidia being greatly deformed and

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exhibiting a damaged morphology characterized by lateral expansion, budding and

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uneven surfaces. The antifungal activities of PT14-1, 2, 3, 4a, and 4b against F.

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oxysporum and F. solani were detected as hyphal swelling, indicating inhibition of the

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hyphal growth (Supplementary Figures 4 and 5). Treating the hyphae with PT14-4a

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caused their structures to become severely distorted and condensed with enlarged 12

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vacuoles and conglobated apical tips (Figure 4). The altered conidial morphology

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induced in F. oxysporum and F. solani by PT14-3 and 4a, including the hyphal swelling,

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suggests the peptides may irreversibly inactivate cellular machinery within the fungi.

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However, whether the peptides directly or indirectly inhibit the catalytic activities of

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cellular enzymes remains unknown.

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Toxicity of PT14 peptides. The toxicity of the peptides against eukaryotic cells

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was assessed based on their ability to lyse hRBCs at concentrations ranging from 3.52

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to 450 µg/mL (Figure 5). The percent hemolysis was determined by measuring the

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absorbance of the supernatant from a hRBC suspension incubated with PT14-1, 2, 3, 4a,

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4b or melittin. The PT14 peptides did not induce hemolysis, even at the highest

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concentration tested. By contrast, melittin, which is known to be highly cytotoxic and

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hemolytic, induced lysis even at the lowest concentration tested.

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PT14-4a identification. In an effort to identify the peptides, the sequences of the

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N-terminal 14 residues were determined. The N-terminal amino acid sequence of the

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purified PT14-4a peptide was YLEALEAESITTGV. A BLAST homology analysis

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revealed the sequence of 4a to be most similar to the corresponding N-terminal amino

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acid sequences of Temporin-1Ca from a green frog Rana clamitans, North America

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(GenBank ID in NCBI: P82880, similarity: 46.66 %) and Caerin 3.5 from skin dorsal

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glands of Australian dainty green tree frog, Litoria gracilenta (P0C2A9, 40.9%).

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However, the sequence of PT14-4a was not identical to that of any other protein,

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suggesting it is a novel antifungal peptide. Figure 2B shows single charged potassium

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adducts [M+K]+ of PT14-4a with m/z value of 1514.0, corresponding to 1495 Da, the

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MALDI-TOF/MS result of PT14-4a. MALDI-TOF/MS result of PT14-4a and its

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theoretical molecular weight fit well with its amino acid sequence determined by Edman 13

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degradation.

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PT14-4a secondary structure. PT14-4a has an amphipathic helical structure, as

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indicated by the helical wheel projection in Figure 6A, which also shows it carries a

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negative charge (-3) and low hydrophobicity (H, 0.469). CD spectral analysis of the

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secondary structures of PT14-3 and PT14-4a in a membrane environment showed that

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both PT14-3 and PT14-4a have little helicity in aqueous solution or in a bacterial

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membrane mimetic environment (PE:PG vesicles, 7:3 w/w), but exhibit a high degree of

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α-helical structure in a fungal membrane mimetic environment (PC:CH vesicles, 10:1

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w/w) (Figure 6B-D). PT14-4a displayed a positive band at 197 nm and a negative band

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at 210 nm in PC:CH vesicles (Figure 6C), indicating that its side chains partitioned

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preferentially into the more rigid and hydrophobic environment of the lipid bilayer.

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Using the secondary structure predictor server K2D3,42 the percentage of α-helix in both

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PT14-3 and PT14-4a was calculated to be 80% in the presence of PC:CH vesicles (10:1

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w/w), but much lower (