Computational investigation for modeling the protein–protein interaction of TasA(28–261)–TapA(33–253): a decisive process in biofilm formation by Bacillus subtilis

AbstractBiofilms have significant role in microbial persistence, antibiotic resistance and chronic infections; consequently, there is a pressing need for development of novel “anti-biofilm strategies”. One of the fundamental mechanisms involved in biofilm formation is protein-protein interactions of ‘amyloid like proteins’ (ALPs) in extracellular matrix. Such interactions could be potential targets for development of novel anti-biofilm strategies; therefore, assessing the structural features of these interactions could be of great scientific value. Characterization of biomolecular interaction with conventional structure biology tools including X-Ray diffraction and Nuclear Magnetic Resonance is technically challenging, expensive and time-consuming. In contrast, modelling such interactions is time-efficient, economical and might provide deeper understanding of structural basis of interactions. Therefore, during the present study, protein-protein interaction of TasA(28-261)–TapA(33-253) (which is a decisive process for biofilm formation by Bacillus subtilis) was modeled using in silico approaches viz., molecular modelling, protein-protein docking and molecular dynamics simulations. Results identified amino-acid residues present within intrinsically disordered regions of both proteins to be critical for interaction. These results were further supported with PCA and FEL analyses. Results presented here represent novel finding and we hypothesize that aa identified during the present study could be targeted for inhibition of biofilm formation by B. subtilis.

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Bacillus subtilis Glutamine Synthetase Controls Gene Expression through a Protein-Protein Interaction with Transcription Factor TnrA

Cell ◽

10.1016/s0092-8674(01)00572-4 ◽

2001 ◽

Vol 107 (4) ◽

pp. 427-435 ◽

Cited By ~ 93

Author(s):

Lewis V Wray ◽

Jill M Zalieckas ◽

Susan H Fisher

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Bacillus Subtilis ◽

Glutamine Synthetase ◽

Protein Interaction ◽

Protein Protein Interaction ◽

Transcription Factor Tnra

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A LysM Domain Intervenes in Sequential Protein-Protein and Protein-Peptidoglycan Interactions Important for Spore Coat Assembly inBacillus subtilis

Journal of Bacteriology ◽

10.1128/jb.00642-18 ◽

2018 ◽

Vol 201 (4) ◽

Cited By ~ 3

Author(s):

Fatima C. Pereira ◽

Filipa Nunes ◽

Fernando Cruz ◽

Catarina Fernandes ◽

Anabela L. Isidro ◽

...

Keyword(s):

Bacillus Subtilis ◽

Protein Interaction ◽

Interaction Domain ◽

Content Type ◽

Protein Protein Interaction ◽

Lysm Domain ◽

Binding Function ◽

Morphogenetic Protein ◽

Tight Connection

ABSTRACTAt a late stage in spore development inBacillus subtilis, the mother cell directs synthesis of a layer of peptidoglycan known as the cortex between the two forespore membranes, as well as the assembly of a protective protein coat at the surface of the forespore outer membrane. SafA, the key determinant of inner coat assembly, is first recruited to the surface of the developing spore and then encases the spore under the control of the morphogenetic protein SpoVID. SafA has a LysM peptidoglycan-binding domain, SafALysM, and localizes to the cortex-coat interface in mature spores. SafALysMis followed by a region, A, required for an interaction with SpoVID and encasement. We now show that residues D10 and N30 in SafALysM, while involved in the interaction with peptidoglycan, are also required for the interaction with SpoVID and encasement. We further show that single alanine substitutions on residues S11, L12, and I39 of SafALysMthat strongly impair binding to purified cortex peptidoglycan affect a later stage in the localization of SafA that is also dependent on the activity of SpoVE, a transglycosylase required for cortex formation. The assembly of SafA thus involves sequential protein-protein and protein-peptidoglycan interactions, mediated by the LysM domain, which are required first for encasement then for the final localization of the protein in mature spores.IMPORTANCEBacillus subtilisspores are encased in a multiprotein coat that surrounds an underlying peptidoglycan layer, the cortex. How the connection between the two layers is enforced is not well established. Here, we elucidate the role of the peptidoglycan-binding LysM domain, present in two proteins, SafA and SpoVID, that govern the localization of additional proteins to the coat. We found that SafALysMis a protein-protein interaction module during the early stages of coat assembly and a cortex-binding module at late stages in morphogenesis, with the cortex-binding function promoting a tight connection between the cortex and the coat. In contrast, SpoVIDLysMfunctions only as a protein-protein interaction domain that targets SpoVID to the spore surface at the onset of coat assembly.

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A Computational Investigation of Small-Molecule Engagement of Hot Spots at Protein–Protein Interaction Interfaces

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.7b00181 ◽

2017 ◽

Vol 57 (9) ◽

pp. 2250-2272 ◽

Cited By ~ 7

Author(s):

David Xu ◽

Yubing Si ◽

Samy O. Meroueh

Keyword(s):

Small Molecule ◽

Protein Interaction ◽

Hot Spots ◽

Computational Investigation ◽

Protein Protein Interaction

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An expanded protein-protein interaction network in Bacillus subtilis reveals a group of hubs: Exploration by an integrative approach

PROTEOMICS ◽

10.1002/pmic.201000791 ◽

2011 ◽

Vol 11 (15) ◽

pp. 2981-2991 ◽

Cited By ~ 39

Author(s):

Elodie Marchadier ◽

Rut Carballido-López ◽

Sophie Brinster ◽

Céline Fabret ◽

Peggy Mervelet ◽

...

Keyword(s):

Bacillus Subtilis ◽

Protein Interaction ◽

Protein Interaction Network ◽

Interaction Network ◽

Integrative Approach ◽

Protein Protein Interaction ◽

Protein Protein Interaction Network

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A Multimodal Strategy Used by a Large c-di-GMP Network

Journal of Bacteriology ◽

10.1128/jb.00703-17 ◽

2018 ◽

Vol 200 (8) ◽

Cited By ~ 23

Author(s):

Kurt M. Dahlstrom ◽

Alan J. Collins ◽

Georgia Doing ◽

Jaclyn N. Taroni ◽

Timothy J. Gauvin ◽

...

Keyword(s):

Protein Interaction ◽

Biofilm Formation ◽

Model Building ◽

Mutational Analysis ◽

Bacterial Biofilm ◽

Transcriptional Analysis ◽

Physical Interaction ◽

Dependent Manner ◽

Protein Protein Interaction ◽

Two Hybrid

ABSTRACTThePseudomonas fluorescensgenome encodes more than 50 proteins predicted to be involved in c-di-GMP signaling. Here, we demonstrated that, tested across 188 nutrients, these enzymes and effectors appeared capable of impacting biofilm formation. Transcriptional analysis of network members across ∼50 nutrient conditions indicates that altered gene expression can explain a subset of but not all biofilm formation responses to the nutrients. Additional organization of the network is likely achieved through physical interaction, as determined via probing ∼2,000 interactions by bacterial two-hybrid assays. Our analysis revealed a multimodal regulatory strategy using combinations of ligand-mediated signals, protein-protein interaction, and/or transcriptional regulation to fine-tune c-di-GMP-mediated responses. These results create a profile of a large c-di-GMP network that is used to make important cellular decisions, opening the door to future model building and the ability to engineer this complex circuitry in other bacteria.IMPORTANCECyclic diguanylate (c-di-GMP) is a key signaling molecule regulating bacterial biofilm formation, and many microbes have up to dozens of proteins that make, break, or bind this dinucleotide. A major open issue in the field is how signaling specificity is conferred in the unpartitioned space of a bacterial cell. Here, we took a systems approach, using mutational analysis, transcriptional studies, and bacterial two-hybrid analysis to interrogate this network. We found that a majority of enzymes are capable of impacting biofilm formation in a context-dependent manner, and we revealed examples of two or more modes of regulation (i.e., transcriptional control with protein-protein interaction) being utilized to generate an observable impact on biofilm formation.

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Interaction of Porphyromonas gingivalis with Oral Streptococci Requires a Motif That Resembles the Eukaryotic Nuclear Receptor Box Protein-Protein Interaction Domain

Infection and Immunity ◽

10.1128/iai.00366-08 ◽

2008 ◽

Vol 76 (7) ◽

pp. 3273-3280 ◽

Cited By ~ 51

Author(s):

Carlo Amorin Daep ◽

Richard J. Lamont ◽

Donald R. Demuth

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Nuclear Receptor ◽

Protein Interaction ◽

Biofilm Formation ◽

Amino Acid Substitutions ◽

Oral Streptococci ◽

Interaction Domain ◽

Protein Protein Interaction ◽

Streptococcal Antigen

ABSTRACT Porphyromonas gingivalis initially colonizes the oral cavity by interacting with organisms in supragingival plaque, such as the oralis group of oral streptococci. This interaction involves the association of the streptococcal antigen I/II with the minor fimbrial antigen (Mfa1) of P. gingivalis. Our previous studies showed that a peptide (BAR) derived from antigen I/II inhibits P. gingivalis adherence and subsequent biofilm formation on streptococcal substrates. In addition, screening a combinatorial peptide library identified select amino acid substitutions in the NITVK active region of BAR that increased the adherence of P. gingivalis to streptococci. Here we report that incorporating these residues in a synthetic peptide results in more-potent inhibition of P. gingivalis adherence and biofilm formation (I50 [50% inhibition] at 0.52 μM versus I50 at 1.25 μM for BAR). In addition, a second structural motif in BAR, comprised of the amino acids KKVQDLLKK, was shown to contribute to P. gingivalis adherence to streptococci. Consistent with this, the KKVQDLLKK and NITVK motifs are conserved only in antigen I/II proteins expressed by the oralis group of streptococci, which interact with P. gingivalis. Interestingly, the primary and secondary structures and the functional characteristics of the amphipathic VQDLL core α-helix resemble the consensus nuclear receptor (NR) box protein-protein interacting domain sequence (LXXLL) of eukaryotes. BAR peptides containing amino acid substitutions with the potential to disrupt the secondary structure of VQDLL were less-effective inhibitors of P. gingivalis adherence and biofilm formation, suggesting that the α-helical character of VQDLL is important. Furthermore, replacing the lysines that flank VQDLL with acidic amino acids also reduced inhibitory activity, suggesting that the association of VQDLL with Mfa1 may be stabilized by a charge clamp. These results indicate that the Mfa1-interacting interface of streptococcal antigen I/II encompasses both the KKVQDLLKK and NITVK motif and suggest that the adherence of P. gingivalis to streptococci is driven by a protein-protein interaction domain that resembles the eukaryotic NR box. Thus, both motifs must be taken into account in designing potential peptidomimetics that target P. gingivalis adherence and biofilm formation.

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