Supplemental Data

Isolation of a new antibacterial peptide achromosin from Streptomyces achromogenes subsp. achromogenes based on genome mining

Authors: Issara Kaweewan 1, Mayumi Ohnishi-Kameyama2, Shinya Kodani1,3,4*

Affiliations: 1Graduate School of Integrated Science and Technology, Shizuoka University, 836

Ohya, Suruga-ku, Shizuoka 422-8529 Japan; 2Food Research Institute, NARO, 2–1-12 Kan-nondai,

Tsukuba, Ibaraki 305-8642 Japan; 3College of Agriculture, Academic Institute, Shizuoka University,

836 Ohya, Suruga-ku, Shizuoka 422-8529 Japan; 4Graduate School of Science and Technology,

Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529 Japan

*To whom correspondence should be addressed: Shinya Kodani, College of Agriculture, Academic

Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529 Japan, Tel/Fax;

+81(54)238-5008, E-mail; kodani.shinya@shizuoka.ac.jp

Materials and Methods

Table S1. Putative functions of proteins encoded by genes within the putative achromosin biosynthetic gene clusterTable S2. Fragment ions detected by MALDI-TOF-MS/MS of achromosinTable S3. Fragment ions detected by MALDI-TOF-MS/MS of BNPS-skatole cleaved achromosinFig. S1. HPLC chromatogram of achromosin

Fig. S2. ESI-TOF-MS analysis of achromosin

Fig. S3. Amino acid content analysis of achromosinFig. S4. ESI-TOF-MS analysis of BNPS-skatole cleaved achromosin

Fig. S5. Antibacterial activity of achromosin against Micrococcus luteus

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Materials and Methods

Bacterial strains

The microorganisms (Bacterial strains including Streptomyces achromogenes subsp.

achromogenes NBRC12735T, Escherichia coli NBRC 102203T, Pseudomonas aeruginosa NBRC

12689T, Serratia marcescens NBRC102204T, Bacillus subtilis NBRC 13719T, Staphylococcus aureus

NBRC 100910T, Micrococcus luteus NBRC 3333T, Streptomyces antibioticus NBRC3117; Yeast

strains including Saccharomyces cerevisiae NBRC 2376, Schizosaccharomyces pombe NBRC0340,

Kloeckera apiculata NBRC 0154; fungi strains including Aspergillus niger NBRC 33023T,

Aspergillus oryzae NBRC 4290, Mucor hiemalis NBRC 9405T) were obtained from the NBRC

culture collection (NITE Biological Resource Center, Japan).

Genome mining for lasso peptide biosynthetic genes

The lasso peptide maturation of actinobacteria is catalyzed by proteins encoded by genes C, B1, and

B2.1 The amino acid sequences of chaxapeptin biosynthetic genes (cptC: ALT06553.1,

cptB1:ALT06554.1, and cptB2:ALT06555.1) were used to search homologous genes in bacteria by

protein BLAST program (blastp).2 The maturation protein coding genes for achromosin were found

by the search ( acrC/cptC: 37% identity, 51% positive matches, acrB1/cptB1: 40% identity, 54%

positive matches, acrB2/cptB2: 55% identity, 69% positive matches) from the NCBI database.3

Isolation of achromosin

Streptomyces achromogenes subsp. achromogenes NBRC12735T was cultured using 5L of ISP2 agar

medium4 for 7 days at 30 °C. The aerial hyphae and spore cells on the agar surface were harvested

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with steel spatula. Double volume of MeOH was added to the harvested cells, followed by filtration

with paper filter (Whatman No. 1, GE Healthcare Life Sciences, Little Chalfont, UK). The MeOH

extract was concentrated to an aqueous residue using rotary evaporation. The aqueous residue was

subjected to open column chromatography using hydrophobic resin CHP-20P (Mitsubishi Chemical,

Tokyo, Japan), eluted with 10% MeOH, 60% MeOH, and 100% MeOH. The 100% MeOH fraction

was subjected to HPLC purification using an ODS column (4.6 × 250 mm, Wakopak Handy-ODS,

Wako Pure Chemical Industries, Ltd., Osaka, Japan) with gradient elution from 20 to 70% MeCN

containing 0.05% trifluoroacetic acid for 20 min with UV detector set at 220 nm to yield 5.0 mg of

achromosin (Retention time: 16.7 min, Fig. S1).

BNPS-skatole reaction

Achromosin solution (100 μL, 4 mg/mL MeOH) was dried in the microtube by incubation at 50 °C

for 24 h. The peptide was subjected to cleavage reaction by adding 100 μL of BNPS-skatole solution

(2 mg/mL acetic acid) and 10 μL of distilled water.5 The solution was incubated at 90 °C for 1 hour.

Acetic acid was completely evaporated using rotary evaporator. After evaporation, 300 μL of

chloroform and 500 μL of distilled water were added to the reaction mixture. After two-layer

partition, water-soluble layer was transferred to a new micro tube. After adding 500 μL of MeOH,

the reaction mixture was analyzed by an HPLC system. The conditions for HPLC analysis were as

follows; HPLC column, Wakopak Handy-ODS (4.6 mm × 250 mm; Wako Pure Chemical Industries,

Ltd.); mobile phase A, MeCN containing 0.05% trifluoroacetic acid; mobile phase B, 0.05%

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trifluoroacetic acid; flow rate, 1 mL/min; gradient of increasing the mixing rate of mobile phase A

from 20% to 50% for 20 min (linear gradient); UV detector, 220 nm.

Amino acid analysis

The amino acid content of achromosin was determined by HPLC analysis of PTC-derivatized

amino acids.6 For hydrolysis, achromosin (0.2 mg) was incubated in 100 μL of 6N HCl at 110 °C for

16 h. Aliquot of 40 μL of hydrolyzed sample, or aliquot of 10 μL of amino acid mixture standard

solution (Wako Pure Chemical Industries, LTD.) was evaporated by a freeze dryer. Aliquots of 20

μL of ethanol/water/triethylamine (2/2/1, v/v/v) were added to each sample and evaporated by a

freeze dryer. For PTC-derivatization of amino acids, aliquots of 50μl of

ethanol/water/triethylamine/phenylisocyanate (7/1/1/1, v/v/v/v) were added to each sample, and

derivatization was accomplished by incubation at room temperature for 20 min. After evaporation

using a freeze dryer, 1.0 ml of PTC-derivatized amino acid mobile phase A (60 mM CH3COONa

aqueous solution pH 6.0/MeCN, 6:94) was added to dissolve each sample. The PTC-derivatized

samples were analyzed using an HPLC system (PU980 system, JASCO, Tokyo, Japan). The

conditions for HPLC analysis were following: HPLC column, Wakopak Handy-ODS (4.6 mm × 250

mm; Wako Pure Chemical Industries, Ltd.); mobile phase A (60mM CH3COONa aqueous solution

pH 6.0/MeCN, 6:94); mobile phase B (60mM CH3COONa aqueous solution pH 6.0/MeCN, 60:40);

flow rate, 1 ml/min; gradient of mobile phase B, 5% to 65% from 0 to 30 min (linear gradient); UV

detector, 254 nm.

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Mass spectrometry experiments

The sample solution was mixed with the matrix -cyano-4-hydroxycinnamic acid (Bruker

Daltonics, MA, USA) solution and was spotted on a target plate. Matrix-assisted laser

desorption/ionization (MALDI)-time-of-flight (TOF)/TOF mass spectra were recorded on a 4800

plus TOF/TOF analyzer (AB SCIEX, CA, USA) in positive ion mode with an acceleration voltage of

20 kV. The accurate mass was analyzed using an electrospray ionization (ESI) Fourier-transform ion

cyclotron resonance (FT-ICR) mass spectrometer (solarix XR, Bruker Daltonics) as the solution of

50% acetonitrile including 0.1% formic acid in positive ion mode. The mass spectrometers were

tuned and calibrated using calibration standards of the peptide mixture (Peptide Calibration Standard

II, Bruker Daltonics) and YOKUDELNA (JEOL, Tokyo, Japan), respectively, prior to the

measurements.

Antimicrobial assay

By using a paper disk diffusion assay (6 mm paper disk in diameter, thick type) in the same

manner of our previous report,7 the antimicrobial activity of achromosin was measured against all the

test microorganisms. Achromosin was dissolved in MeOH at the concentration of 1 mg/mL. The

test microorganisms including E. coli, P. aeruginosa, S. marcescens, B. subtilis, S. aureus, M. luteus,

A. niger, A. oryzae, and M. hiemalis were inoculated onto nutrient agar medium.8 The test

microroganisms including S. antibioticus, S. cerevisiae, S. pombe, and K. apiculata were inoculated

onto ISP2 agar medium.4 Paper disks with 10 μg of achromosin (10 μL, 1 mg/mL solution in

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MeOH) were placed onto the surface of the agar medium with the testing microorganism, and paper

disk with MeOH (10 μL) was used as a negative control. After incubation for 2 days at 30C, the

diameter of the inhibitory zone was measured for evaluation of antimicrobiol activity.

References

1. Arnison, P. G.; Bibb, M. J.; Bierbaum, G.; Bowers, A. A.; Bugni, T. S.; Bulaj, G.; Camarero,

J. A.; Campopiano, D. J.; Challis, G. L.; Clardy, J.; Cotter, P. D.; Craik, D. J.; Dawson, M.; Dittmann,

E.; Donadio, S.; Dorrestein, P. C.; Entian, K. D.; Fischbach, M. A.; Garavelli, J. S.; Goransson, U.;

Gruber, C. W.; Haft, D. H.; Hemscheidt, T. K.; Hertweck, C.; Hill, C.; Horswill, A. R.; Jaspars, M.;

Kelly, W. L.; Klinman, J. P.; Kuipers, O. P.; Link, A. J.; Liu, W.; Marahiel, M. A.; Mitchell, D. A.;

Moll, G. N.; Moore, B. S.; Muller, R.; Nair, S. K.; Nes, I. F.; Norris, G. E.; Olivera, B. M.; Onaka,

H.; Patchett, M. L.; Piel, J.; Reaney, M. J.; Rebuffat, S.; Ross, R. P.; Sahl, H. G.; Schmidt, E. W.;

Selsted, M. E.; Severinov, K.; Shen, B.; Sivonen, K.; Smith, L.; Stein, T.; Sussmuth, R. D.; Tagg, J.

R.; Tang, G. L.; Truman, A. W.; Vederas, J. C.; Walsh, C. T.; Walton, J. D.; Wenzel, S. C.; Willey, J.

M.; van der Donk, W. A., Ribosomally synthesized and post-translationally modified peptide natural

products: overview and recommendations for a universal nomenclature. Nat Prod Rep 2013, 30, 108-

60.

2. Gish, W.; States, D. J., Identification of protein coding regions by database similarity search.

Nat Genet 1993, 3, 266-72.

3. Sayers, E. W.; Barrett, T.; Benson, D. A.; Bryant, S. H.; Canese, K.; Chetvernin, V.; Church,

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D. M.; DiCuccio, M.; Edgar, R.; Federhen, S.; Feolo, M.; Geer, L. Y.; Helmberg, W.; Kapustin, Y.;

Landsman, D.; Lipman, D. J.; Madden, T. L.; Maglott, D. R.; Miller, V.; Mizrachi, I.; Ostell, J.;

Pruitt, K. D.; Schuler, G. D.; Sequeira, E.; Sherry, S. T.; Shumway, M.; Sirotkin, K.; Souvorov, A.;

Starchenko, G.; Tatusova, T. A.; Wagner, L.; Yaschenko, E.; Ye, J., Database resources of the

National Center for Biotechnology Information. Nucleic Acids Res 2009, 37, D5-15.

4. Shirling, E. B.; Gottlieb, D., Methods for characterization of Streptomyces species. Int. J.

Syst. Bacteriol. 1966, 16, 313-340.

5. Fontana, A., Modification of tryptophan with BNPS-skatole (2-(2-nitrophenylsulfenyl)-3-

methyl-3-bromoindolenine). Methods Enzymol 1972, 25, 419-23.

6. Heinrikson, R. L.; Meredith, S. C., Amino acid analysis by reverse-phase high-performance

liquid chromatography: precolumn derivatization with phenylisothiocyanate. Anal Biochem 1984,

136, 65-74.

7. Kodani, S.; Murao, A.; Hidaki, M.; Sato, K.; Ogawa, N., Isolation and structural

determination of a new macrolide, makinolide, from the newly isolated Streptomyces sp. MK-30. J

Antibiot (Tokyo) 2012, 65, 331-4.

8. Wright, H. D., The importance of adequate reduction of peptone in the preparation of media

for the pneumococcus and other organisms. J. Pathol. Bacteriol. 1933, 37, 257-282.

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Table S1 Putative functions of proteins encoded by genes within the putative achromosin biosynthetic gene cluster

*Similarity/identity

Table S2. Fragment ions detected by MALDI-TOF-MS/MS of achromosin

Table S3. Fragment ions detected by MALDI TOF-MS/MS of BNPS-skatole cleaved achromosin

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Gene Accession no. Size (aa)

Putative function (domain organization)

BLAST search

Closest homolog (accession no.); origin %*

acrA Not annotated 42 precursor peptide cptA(ALT06552.1); Streptomyces leeuwenhoekii

68/46

acrC WP_063755122.1 616 asparagine synthase

asparagine synthase (WP_051815273.1); Streptomyces lavenduligriseus

94/91

acrB1 WP_037654159.1 95 Coenzyme PQQ synthesis protein D

hypothetical protein (WP_030776557.1); Streptomyces lavenduligriseus

85/83

acrB2 WP_037654156.1 150 Transglutaminase hypothetical protein (WP_030776559.1); Streptomyces lavenduligriseus

94/92

Fragment ion

Observed mass [Da] Calculated mass [Da] Mass error [Da]

b13 1526.64 1526.74 -0.1b12 1340.58 1340.66 -0.08b11 1227.50 1227.58 -0.08b10 1041.42 1041.50 -0.08b9 928.34 928.42 -0.08b8 827.28 827.36 -0.08y2 320.07 320.12 -0.05y3 433.13 433.21 -0.08y4 619.20 619.29 -0.09y6 833.33 833.42 -0.09

Fragment ion

Observed mass [Da] Calculated mass [Da] Mass error [Da]

b3 1073.45 1073.49 -0.04b2 960.37 960.41 -0.04b1+H2O 877.33 877.36 -0.03y7 762.31 762.34 -0.03y6 705.28 705.32 -0.04y5 592.20 592.23 -0.03y4 535.18 535.21 -0.03y3 448.15 448.18 -0.03y2 320.10 320.12 -0.02

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Fig. S1. HPLC chromatogram of achromosin

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Fig. S2. ESI-TOF-MS analysis of achromosin

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Fig. S3. Amino acid content analysis of achromosin

Upper: HPLC chromatogram of PTC derivatives of achromosin hydrolysate

Bottom: HPLC chromatogram of PTC derivatives of standard amino acids

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Fig. S4. ESI-TOF-MS analysis of 'BNPS-skatole cleaved achromosin

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Fig. S5. Antibacterial activity of achromosin against Micrococcus luteus

Left: 10 μg of achromosin (10 μL on a disk, 1 mg/mL solution in MeOH)

Right: negative control (inoculation of 10 μL MeOH on a disk)

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