Malaysian Journal of Analytical Sciences, Vol 28 No 4 (2024): 939 - 955

 

IN SILICO AND MS/MS-BASED APPROACHES TO INVESTIGATE PROTEIN-PROTEIN INTERACTION NETWORKS IN Staphylococcus aureus BIOFILM

 

(Pendekatan Berasaskan In Silico dan MS/MS Untuk Mengkaji Jaringan Interaksi Protein-Protein dalam Biofilem Staphylococcus aureus)

 

Nawal Zulkiply1, Norfatimah Mohamed Yunus1, Hamidah Idris2, Wan Syaidatul Aqma Wan Mohd Noor3, Saiful Anuar Karsani4, Mohd Fakharul Zaman Raja Yahya1 *

 

1Faculty of Applied Sciences, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia

2Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900 Tanjung Malim, Perak, Malaysia

3Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia

4Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia

 

*Corresponding author: fakharulzaman@uitm.edu.my

 

 

Received: 7 September 2023; Accepted: 7 May 2024; Published:  27 August 2024

 

 

Abstract

Staphylococcus aureus is a Gram-positive pathogen inhabiting soft tissues like the epidermis and nasal cavity. Currently, there is limited knowledge of the protein-protein interaction (PPI) networks in S. aureus biofilm. The present study aimed to characterize S. aureus proteins and their interaction networks using an in silico approach and to identify the proteins expressed in S. aureus biofilm using tandem mass spectrometry. Initially, a preliminary characterization of the PPI networks in S. aureus was conducted using the STRING 12.0 database. Subsequently, S. aureus biofilm was developed in a 6-well microplate and harvested at 6 h, 12 h, 18 h, and 24 h. The expression of proteins in S. aureus biofilm was determined using a combination of one-dimensional SDS-PAGE and HPLC-ESI-MS/MS. The in silico results demonstrated that 147 biological processes, 46 molecular functions, 17 cellular components, and 15 biological pathways were significantly enriched (p <0.05) in the PPI networks of S. aureus. S. aureus biofilm proteins identified from the SDS-PAGE gel bands, such as L-lactate dehydrogenase (quinone), chaperone protein DnaK, and serine hydroxymethyltransferase, corroborated the findings obtained from the preliminary in silico work. In conclusion, the formation of biofilm by S. aureus may involve complex PPI networks.

 

Keywords: biofilm, in silico, protein-protein interaction network, Staphylococcus aureus, tandem mass spectrometry 

 

Abstrak

Staphylococcus aureus adalah patogen Gram-positif yang mendiami tisu lembut seperti epidermis dan rongga hidung. Pada masa ini terdapat pengetahuan terhad tentang rangkaian interaksi protein-protein dalam biofilm S. aureus. Kerja-kerja ini dilakukan untuk mencirikan protein S. aureus dan rangkaian interaksinya menggunakan pendekatan dalam siliko dan untuk mengenal pasti protein yang dinyatakan dalam biofilm S. aureus menggunakan spektrometri jisim tandem. Pencirian awal rangkaian interaksi protein-protein dalam S. aureus telah dilakukan menggunakan pangkalan data STRING 12.0. Kemudian, biofilm S. aureus telah dibangunkan dalam plat mikro 6-telaga dan dituai pada 6 jam, 12 jam, 18 jam dan 24 jam. Ekspresi protein dalam biofilm S. aureus ditentukan menggunakan gabungan SDS-PAGE satu dimensi dan HPLC-ESI-MS/MS. Keputusan kajian in silico menunjukkan bahawa terdapat 147 proses biologi, 46 fungsi molekul, 17 komponen selular, dan 15 laluan biologi didapati diperkaya dengan ketara (P<0.05) dalam rangkaian interaksi protein-protein S. aureus. Protein biofilm S. aureus yang dikenalpasti daripada jalur gel SDS-PAGE seperti L-lactate dehydrogenase (quinone), protein pendamping DnaK, dan serine hydroxymethyltransferase, mengesahkan penemuan yang diperoleh daripada kajian awal in silico. Kesimpulannya, pembentukan biofilm oleh S. aureus mungkin melibatkan rangkaian interaksi protein-protein yang kompleks.

 

Kata kunci: biofilem, in silico, jaringan interaksi protein-protein, Staphylococcus aureus, spektrometri jisim ganda

 

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