, 15:16 | Cite as

Metabolic and proteomic alteration in phytohormone-producing endophytic Bacillus amyloliquefaciens RWL-1 during methanol utilization

  • Raheem Shahzad
  • Abdul Latif Khan
  • Muhammad Waqas
  • Ihsan Ullah
  • Saqib Bilal
  • Yoon-Ha Kim
  • Sajjad Asaf
  • Sang-Mo Kang
  • In-Jung LeeEmail author
Original Article



Methanol utilization by bacteria is important for various industrial processes. Methylotrophic bacteria are taxonomically diverse and some species promote plant growth and induce stress tolerance. However, methylotrophic potential of bacterial endophytes is poorly understood.


The current study aimed to evaluate the metabolomic and proteomic changes in endophytic Bacillus amyloliquefaciens RWL-1 caused by its methanol utilization and the resultant influence on its phytohormone production.


B. amyloliquefaciens RWL-1 was grown in LB medium with different concentrations [0 (control), 0.5, 1, 1.5, 2, 2.5, 3, 3.5, and 4%) of methanol to examine its methylotrophic potential. SDS-PAGE analysis was carried out for bacterial protein confirmation. Moreover, the phytohormones (indole 3 acetic acid (IAA), gibberellins (GAs), abscisic acid (ABA)) produced by RWL-1 in methanol supplemented medium were quantified by GC-MS/SIM (6890N Network GC system, and 5973 Network Mass Selective Detector; Agilent Technologies, Santa Clara, CA, USA), while the antioxidants were estimated spectrophotometrically (T60 UV-VIS spectrophotometer, Leicester, UK). The amino acid quantification was carried out by amino acid analyzer (HITACHI L-8900, Japan). Furthermore, Nano-liquid chromatography (LC)–MS/MS analysis was performed with an Agilent system (Wilmington, DE, USA) for proteomic analysis while mascot algorithm (Matrix science, USA) was used to identify peptide sequences present in the protein sequence database.


RWL-1 showed significant growth in media supplemented with 2 and 3.5% methanol, when compared with other concentrations. Mass spectroscopy analysis revealed that RWL-1 utilizes methanol efficiently as a carbon source. In the presence of methanol, RWL-1 produced significantly higher levels of IAA but lower levels of ABA, when compared with the control. Further, enzymatic antioxidants and functional amino acids were significantly up-regulated, with predominant expression of glutamic acid and alanine. Nano-liquid chromatography, quadrupole time-of-flight analysis, and quantitative analysis of methanol-treated bacterial cells showed expression of eight different types of proteins, including detoxification proteins, unrecognized and unclassified enzymes with antioxidant properties, proteases, metabolism enzymes, ribosomal proteins, antioxidant proteins, chaperones, and heat shock proteins.


Results demonstrate that RWL-1 can significantly enhance its growth by utilizing methanol, and could produce phytohormones when growing in methanol-supplemented media, with increased expression of specific proteins and different biochemicals. These results will be useful in devising strategies for utilizing methylotrophic bacterial endophytes as alternative promoters of plant growth.

Graphical abstract

Understanding RWL-1 ability to utilize methanol. The survival and phytohormones production by Bacillus amyloliquefaciens RWL-1 in methanol supplemented media whistle inducing metabolic and proteomic changes.


Methanol utilization Phytohormones Antioxidants Amino acids Proteomics 



This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2017R1D1A1B04035601).

Authors contributions

RS presented the idea, carried out the experiment, collected data and wrote the manuscript. ALK, MW and IU contributed to data analysis and manuscript drafting. SB, Y-HK, SA and S-MK helped in biochemical analysis. I-JL, as the team leader, supervised the design and conducting of all the experiments, and provided the relevant facilities, financial support, and mentorship. All authors have read and approved the final manuscript.

Compliance with ethical standards

Consent for publication

Not applicable.

Conflict of interest

All authors have no competing interests.

Ethics approval and consent to participate

Not applicable.


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Raheem Shahzad
    • 1
  • Abdul Latif Khan
    • 2
  • Muhammad Waqas
    • 3
  • Ihsan Ullah
    • 4
  • Saqib Bilal
    • 1
  • Yoon-Ha Kim
    • 1
  • Sajjad Asaf
    • 2
  • Sang-Mo Kang
    • 5
  • In-Jung Lee
    • 1
    Email author
  1. 1.School of Applied BiosciencesKyungpook National UniversityDaeguRepublic of Korea
  2. 2.Natural and Medical Science Research CenterUniversity of NizwaNizwaOman
  3. 3.Department of Agriculture ExtensionBunerPakistan
  4. 4.Department of Biological Sciences, Faculty of scienceKing Abdulaziz UniversityJeddahSaudi Arabia
  5. 5.Institute of Agricultural Science and TechnologyKyungpook National UniversityDaeguRepublic of Korea

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