Trends in Biotechnology
Scientific LifeThe Biofilms Structural Database
Section snippets
Biofilms in Health
Biofilms are heterogeneous and complex structures of microorganisms, typically adhered to a surface and presenting sophisticated singular and collective behaviors. Bacteria in biofilms are embedded in a self-produced matrix of extracellular polymeric substances (EPS) composed of (glyco)proteins, (glyco)lipids, mono- or poly-saccharides, extracellular DNA, minerals, and water [1]. This protected mode of growth allows bacteria to survive in hostile environments. In the health context, some
Strategies for Inhibiting Biofilm Formation
Antibacterial strategies focusing on inhibiting cellular growth often induce antimicrobial resistance by imposing a strong selective pressure on bacteria. By contrast, alternatives that target the processes associated with biofilm formation and development, which include bacterial motility, cell adhesion, biofilm dispersion, the synthesis of EPS, and also cell-to-cell communication or quorum sensing (QS), can be more efficient [5,6], as these processes are less amenable to induce antimicrobial
The Shift from the Cellular to the Molecular Level
Over the past few years, there has been an immense increase in the number of 3D structures (particularly X-ray) of proteins and enzymes associated with biofilm formation and development. The data associated with these structures, together with the vast body of work dispersed throughout the scientific literature – including kinetic and mutagenesis data, amino acid sequences, and inhibitory activity of known molecules – offers new opportunities to understand biofilms at a structural and atomic
Data Selection
The main focus of the BSD is at the molecular level. However, biofilm research integrates several different scales. Therefore, the database was designed to create a comprehensive repository of structural data on biofilm research that could integrate with the information available in other databases, beyond the molecular level, to link different fields. An intensive literature search was performed to extract the relevant structural information about the proteins and enzymes involved in biofilm
Organization of the Database
The BSD is organized in a simple and intuitive manner. Each entry in the database corresponds to one atomic structure with a unique PDB code. A total of 425 PDB entries are currently included, corresponding to a total of 133 unique proteins (Figure 1A). Each entry is identified through the PDB code associated with the corresponding structure in the PDB and by the name of the protein. Entries are classified by protein category and mechanism. The term ‘category’ refers to the general and main
Concluding Remarks
The BSD is a free-access catalogue containing the structures of all known proteins and enzymes involved in biofilm formation. This database is a tool that helps to visualize, explore, and understand biofilm targets to design and develop new and effective antibiofilm drugs and to understand the structure and activity of proteins and enzymes involved in biofilm development. The interface is easy to use and accessible to anyone wishing to start their work in this field.
Acknowledgments
This work was supported by national funds from Fundação para a Ciência e a Tecnologia (grant numbers: SFRH/BD/137844/2018, SFRH/BD/115396/2016, IF/00052/2014, UID/Multi/04378/2019, UIDB/04378/2020, PTDC/QUI-QIN/30649/2017, UID/QUI/50006/2019, and NORTE-01-0145-FEDER-000011) and the Interreg SUDOE NanoDesk (SOE1/P1/E0215; UP). This work was also financially supported by: Base Funding – UIDB/00511/2020 of LEPABE, funded by national funds through the FCT/MCTES (PIDDAC), projects
References (15)
Bacterial biofilm and associated infections
J. Chinese Med. Assoc.
(2018)A review of current and emergent biofilm control strategies
LWT Food Sci. Technol.
(2010)- et al.
The biofilm matrix
Nat. Rev. Microbiol.
(2010) Strategies for combating bacterial biofilms: a focus on anti-biofilm agents and their mechanisms of action
Virulence
(2018)Targeting microbial biofilms: current and prospective therapeutic strategies
Nat. Rev. Microbiol.
(2017)Targeting the bacterial protective armour; challenges and novel strategies in the treatment of microbial biofilm
Materials (Basel)
(2018)Biofilm dispersal: multiple elaborate strategies for dissemination of bacteria with unique properties
Mol. Microbiol.
(2017)
Cited by (0)
- 4
These authors contributed equally to this work.