{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/SDRF_PRIDE_Compliant_Soybean_Proteomics.txt"],"Xml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/mqpar.xml"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/Soybean_BacillusHT1_Rep3.raw.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/Soybean_BacillusHT3_Rep3.raw.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/Soybean_Control_Rep1.raw.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/Soybean_BacillusHT3_Rep2.raw.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/Soybean_BacillusHT2_Rep3.raw.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/Soybean_BacillusHT2_Rep2.raw.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/Soybean_BacillusHT1_Rep2.raw.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/Soybean_BacillusHT2_Rep1.raw.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/Soybean_Control_Rep3.raw.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/Soybean_BacillusHT1_Rep1.raw.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/Soybean_BacillusHT3_Rep1.raw.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/Soybean_Control_Rep2.raw.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065756/txt.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["donald.smith@mcgill.ca"],"submitter":["Haleema Tariq"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Endophyte-host interaction","Proteomic reprogramming","Bacillus strains","Soybean microbiome","Label-free proteomics"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD065756"],"sample_protocol":["Shotgun proteomics analysis was performed on soybean plants grown from seeds coated with Bacillus strains HT1, HT2, and HT3 at a concentration of 10⁷ CFU per seed prior to germination. Trifoliate leaves harvested after 28 days of planting were flash frozen in liquid nitrogen. A biological replicate was constructed by pooling the three technical replicates from each experiment. The collected leaf samples were dried in a lyophilizer and the total protein was extracted using a plant total protein extraction kit (Sigma-Aldrich, St. Louis, MO, USA). Approximately 100 mg of the fine powder was placed in sterile Eppendorf tubes and 1 mL of ice-cold methanol-protease cocktail inhibitor (Cat. No. 15468-7, Sigma-Aldrich Co., St. Louis, MO, USA) was added; the resulting mix was vortexed, incubated at -20°C for 2 hours and centrifuged for 10 minutes at 4°C (Micro12, Fisher Scientific, Denver Instrument Co., USA). Following the removal of the supernatant, ice-cold methanol was added and incubated overnight, followed by centrifugation at 13,000 rpm for 10 minutes, followed by incubation in ice-cold methanol again for 1 hour and centrifugation at the same speed. A similar incubation in acetone (Cat. no. 179124, Sigma-Aldrich, Co., St. Louis, MO, USA) was performed to remove phenolics and secondary metabolites that might interfere with the LC-MS/MS analysis. Following the removal of acetone from the samples, wash buffer solution (RW4) was added, vortexed for 30 seconds, and incubated for 30 minutes at room temperature (22°C). The samples were centrifuged at 13,000 rpm for 10 minutes, and the supernatants were carefully collected in sterile tubes, which constituted the total proteins from leaves. Proteins were quantified using the Lowry method (Lowry et al 1951) and a sample of 10 μg of proteins in 20 μL of 1M urea were analyzed for untargeted proteomics at the Institute de Recherches Cliniques de Montréal (IRCM) for label-free shotgun proteomics. Total extracted proteins from trifoliate leaves were tryptic digested before analyses by LC-MS/MS on a Velos Orbitrap instrument (Thermo Fisher Scientific, Waltham, MA, USA). LC-MS analysis was performed according to Subramanian et al. (2016)."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Raw mass spectrometry (MS) data were processed using MaxQuant software (version v2.6.7.0). The spectra were searched against the Glycine max (85,130 sequences; accessed on June 2025) database from UniProtKB (http://www.uniprot.org/). An initial precursor mass tolerance of 15 ppm was applied. Trypsin was specified as the digestion enzyme, allowing up to two missed cleavages and a fragment ion mass tolerance of 20 ppm. Carbamidomethylation of cysteine was set as a fixed modification, while N-terminal acetylation and methionine oxidation were treated as variable modifications. A global false discovery rate (FDR) threshold of <1% was applied for both peptide-spectrum matches (PSMs) and protein identifications. Only proteins identified by at least two unique peptides and consistently detected in at least two replicates per sample were considered confidently identified and selected for downstream analysis. Protein quantification was carried out using LFQ based on peptide intensities. Match-between-runs functionality was enabled to align quantification data across replicates."],"omics_type":["Proteomics"],"labhead":["Donald Smith"],"instrument_platform":[""],"labhead_affiliation":["McGill University Canada"],"submission_type":["PARTIAL"],"species":["Glycine Max X Glycine Soja"],"submitter_mail":["haleema.tariq@mail.mcgill.ca"],"publication":["41455887 Tariq H, Dutilleul P, Geddes-McAlister J, Geitmann A, Smith DL. Plant growth-promoting Bacillus strains modulate early soybean development via proteome remodeling. BMC Plant Biol. 2025 26(1):178 10.1186/s12870-025-07972-y"],"submitter_affiliation":["McGill University"],"submitter_country":["Canada"],"pubmed_abstract":["Plant adaptation to environmental stress involves tightly regulated cellular, molecular, and biochemical responses. Among these, microbe-assisted strategies have gained attention, particularly the role of the plant microbiome (phytomicrobiome) in promoting growth and stress resilience. Soybean (Glycine max), a major agricultural crop, actively recruits beneficial microbes through root-secreted secondary metabolites, fostering symbiotic interactions with endophytic bacteria. However, the direct and indirect impacts of root-associated endophytes on plant development remain incompletely understood. In this study, we investigated three Bacillus strains (HT1, HT2, and HT3) isolated previously from the soybean root microbiome.16 S rRNA analysis indicates that HT1 and HT2 are closely related to the Bacillus velezensis and HT3 to the Bacillus thuringiensis lineage although more detailed analyses are warranted for genus identification. These strains were selected for their demonstrated plant growth-promoting and biocontrol activities. Bacillus-HT1 and HT2 significantly enhanced soybean seed germination, while Bacillus-HT3 promoted leaf area expansion significantly compared to the control, indicating strain-specific developmental effects. To elucidate the molecular basis of these effects, we conducted shotgun proteomic profiling of soybean leaves. Enrichment analysis revealed distinct functional signatures, with Bacillus HT1 and HT2 associated with pathways linked to cellular component organization, microtubule dynamics, and organelle function, and Bacillus-HT3 inducing broader enrichment of photosynthesis, chloroplast organization, and biosynthetic processes. These findings suggest that HT1 and HT2 promote early developmental transitions, while HT3 enhances vegetative growth through large-scale metabolic reprogramming. Notably, proteins such as anthranilate synthase and proteasome subunit alpha type were differentially abundant, pointing to the potential involvement of auxin biosynthesis and ubiquitin-proteasome-mediated regulation but, the actual roles of these pathways remain to be validated. These findings provide mechanistic insights into how specific Bacillus strains modulate soybean development at the molecular level and highlight their potential for use as bio-inoculants to enhance crop productivity and resilience under stress conditions."],"pubmed_title":["Plant growth-promoting Bacillus strains modulate early soybean development via proteome remodeling."],"pubmed_authors":["Tariq H H, Dutilleul P P, Geddes-McAlister J J, Geitmann A A, Smith D L DL"],"additional_accession":[]},"is_claimable":false,"name":"Plant Growth-Promoting Bacillus Strains Modulate Soybean Development via Proteome Remodelling","description":"we investigated three Bacillus strains (HT1, HT2, and HT3) isolated from the soybean root microbiome for their potential plant growth-promoting and biocontrol activities. Bacillus-HT1 and HT2 significantly enhanced soybean seed germination, while Bacillus-HT3 promoted leaf area expansion, indicating strain-specific developmental effects. To elucidate the molecular basis of these effects, we conducted shotgun proteomic profiling of soybean leaves. The analysis revealed significant modulation of proteins involved in key biological processes, including amino acid metabolism, biosynthesis of cellular nitrogen and aromatic compounds, and cellular component organization and biogenesis. Notably, proteins such as anthranilate synthase and proteasome subunit alpha type were differentially expressed, suggesting the activation of growth- and defense-related pathways. These findings provide mechanistic insights into how specific Bacillus strains modulate soybean development at the molecular level and highlight their potential for use as bio-inoculants to enhance crop productivity and resilience under stress 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