Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/CK_2.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/CF_4.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/CF_2.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/CK_3.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/CF_1.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/CK_1.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/EB_2_220706085659.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/EB_3_220705122037.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/EB_1_220705223842.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/EB_2_220706085659.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/EB_3_220705122037.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/CK_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/CF_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/CK_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/EB_1_220705223842.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/CK_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/CF_4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD067784/CF_2.rawprimaryOK200swhan@cau.ac.krSang-Wook HanMass SpectrometryBottom-up proteomicsBrevibacillus brevisEdeine bErwinia amylovorahttps://www.ebi.ac.uk/pride/archive/projects/PXD067784Cell Suspension CultureCell CultureE. amylovora TS3128 was grown overnight in LB medium (Luria Bertani; 10 g of tryptone, 5 g of yeast extract, and 10 g of NaCl per liter) at 28°C. A 1 mL aliquot of the overnight culture was inoculated into 100 mL of LB medium containing CF (0.1%) and EB1 (1.25 µg/mL), corresponding to the IC50 values determined from the antibacterial activity assay. A total of nine samples were harvested at OD600 of 0.6 by centrifugation at 7300 × g for 15 min at 28°C. Harvested cells (0.5 g fresh weight) were resuspended in 1 mL of 50 mM Tris-HCl (pH 7.8) and washed twice. The washed cells were lysed in 1 mL of buffer containing 6 M guanidine-HCl, 10 mM DTT, and 50 mM Tris-HCl (pH 7.8), followed by sonication on ice using an Ultrasonic Processor (Cole Parmer, Vernon Hills, IL, USA) with 10 cycles of 10 s on/60 s off. Cell lysates were centrifuged at 8000 × g for 20 min at 4°C, and the soluble protein fraction was collected. Protein concentration was determined using a bicinchoninic acid protein assay kit (Thermo Fisher Scientific, Rockford, IL, USA). For reduction and alkylation, 1000 μg of protein extract was incubated at 60°C for 1 h, treated with 100 mM iodoacetamide for 1 h in the dark, and subsequently incubated with 20 mM DTT for 1 h. Proteins were precipitated with ice-cold trichloroacetic acid for 12 h at 4°C, recovered by centrifugation (15,700 ×g, 30 min, 4°C), and washed three times with 1 mL of acetone. The resulting pellets were air-dried for 2 h in a clean bench and resuspended in 50 mM ammonium bicarbonate (pH 7.8). For tryptic digestion, 300 µg of proteins was digested with 8 µg of trypsin at 37°C for 18 h. The digested peptides were acidified with 0.4% trifluoroacetic acid and purified using Sep-Pak Vac 1cc tC18 cartridges (Waters Corporation, Milford, MA, USA). Peptides were eluted with eluted with 1 mL of 50% acetonitrile containing 0.1% trifluoroacetic acid, dried for 6 h using a Centrifugal Evaporator CVE-2100 (EYELA, Tokyo, Japan), and then resuspended in 0.4% acetic acid. Peptide concentrations were quantified using the bicinchoninic acid protein assay kit (Thermo Fisher Scientific).Pride- Mass spectrometry analysis One μg of tryptic-digested peptides from the nine samples were analyzed using a split-free nano LC system (EASY-nLC II; Thermo Fisher Scientific) coupled to an LTQ Velos Pro mass spectrometer (Thermo Fisher Scientific) operated in nanospray ion mode. Peptides were loaded onto a C18 column (7.5 cm, MAGIC C18AQ 200A, 5 µm; Michrom BioResources, Auburn, CA, USA) and separated at a flow rate of 300 nL/min using a 420 min linear gradient (solvent A: water with 0.1% formic acid; solvent B: 100% acetonitrile with 0.1% formic acid). Mass spectra were obtained in a data-dependent acquisition mode over an m/z range of 300–2000. Dynamic exclusion was permitted with 1 repeat count, 0.5 repeat duration, and 3 min exclusion duration. Charge states of 2+ and 3+ were selected, and the six most intense ions from each full MS scan were sequentially selected for fragmented in the linear ion trap, with data recorded in centroid mode. - Protein/peptide identification Spectra from LC-MS/MS analysis were identified and quantified using a Thermo Proteome Discoverer 1.3 (ver. 1.3.0.399) with the SEQUEST search algorithm. Protein and peptide identification were performed according to previously described procedures. Briefly, the E. amylovora strain TS3128 genome database (accession no. CP056034.1 for chromosome and CP056035.1 for plasmid) from the National Center for Biotechnology Information was used as the reference. A target-decoy strategy was employed to increase confidence. Search parameters included trypsin as the proteolytic enzyme with up to two missed cleavages, a precursor mass tolerance of 100 ppm, and methionine oxidation as a variable modification. Peptides were filtered at a 1% false discovery rate using reversed database searches, and only those with probability scores ≥20 were accepted. Proteins were considered present when at least two unique peptides were identified. Identified proteins were further validated and compared using Scaffold 4 (Proteome Software, Portland, OR, USA). For quantitative analyses, peptide-spectrum matches (PSMs) were extracted after removing decoy proteins. PSM values were normalized against the total PSMs per sample. Only proteins detected in all three biological replicates were included in the comparative analysis. Normalized PSMs were averaged across replicates, and proteins showing at least two-fold abundance differences were considered differentially abundant. For statistical analyses, PSM values from three independent replicates were evaluated using Student’s t-test (Microsoft Excel, version 2019), with P < 0.05 considered significant. Identified proteins were subsequently categorized into functional groups using clusters of orthologous groups (COG) analysis.ProteomicsSang-Wook HanDepartment of Plant Science and Technology, Chung-Ang University, Anseong, Republic of KoreaPARTIALErwinia Amylovoraswhan@cau.ac.kr41742721 Kim YS, Rhyu H, Kim B, Van Nguyen M, Han JW, Choi GJ, Son H, Han SW, Kim H. Proteomic Insights into the Antibacterial Mechanism of Brevibacillus brevis HK544 Producing Edeine B1 against Erwinia amylovora. Plant Pathol J. 2026 42(2):215-221 10.5423/ppj.nt.12.2025.0185Chung-Ang UniversitySouth KoreaRecently, we reported that Brevibacillus brevis HK544, which produces edeine B1 (EB1), exhibits promising antimicrobial activity against plant pathogens. To elucidate its antibacterial mechanisms against Erwinia amylovora, the causal agent of fire blight, we conducted label-free shotgun proteomic analysis of E. amylovora TS3128 treated with B. brevis culture filtrate (CF) or purified EB1. Comparative analysis showed significant (over twofold) changes in 45 of 624 and 81 of 846 quantified proteins following CF and EB1 treatments, respectively. Functional categorization revealed altered abundances of proteins associated with energy production, ribosome biogenesis, and cell wall/membrane/ envelope biogenesis in both treatments. Notably, 42 and 75 translation-related proteins were differentially expressed in CF- and EB1-treated samples, respectively, consistent with the proposed translation-inhibitory activity of EB1. These findings provide insights into the cellular targets and antibacterial mode of action of B. brevis HK544 and EB1, supporting their potential as biocontrol agents against fire blight.Proteomic Insights into the Antibacterial Mechanism of Brevibacillus brevis HK544 Producing Edeine B1 against Erwinia amylovora.Kim Yeong Seok YS, Rhyu Haerim H, Kim Bomin B, Van Nguyen Minh M, Han Jae Woo JW, Choi Gyung Ja GJ, Son Hokyoung H, Han Sang-Wook SW, Kim Hun HfalseProteomic Insights into the Antibacterial Mechanism of Brevibacillus brevis HK544 and Edeine B1 against Erwinia amylovora- Identification of proteins whose expression was affected by B. brevis culture filtrate (CF) and purified EB1 in Erwinia amylovora str. TS3128 - Shotgun proteomic analysis was used - Three conditions were used with three biological replicates (total 9 samples). CK: no treatment (control). CF: treatment of B. brevis culture filtrate. EB : treatment of 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