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Enzymology and Protein Engineering

Solution Structure of Acidocin B, a Circular Bacteriocin Produced by Lactobacillus acidophilus M46

Jeella Z. Acedo, Marco J. van Belkum, Christopher T. Lohans, Ryan T. McKay, Mark Miskolzie, John C. Vederas
C. A. Elkins, Editor
Jeella Z. Acedo
Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Marco J. van Belkum
Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Christopher T. Lohans
Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Ryan T. McKay
Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Mark Miskolzie
Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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John C. Vederas
Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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C. A. Elkins
Roles: Editor
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DOI: 10.1128/AEM.04265-14
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  • FIG 1
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    FIG 1

    (A) Sequence alignment of subgroup II circular bacteriocins using Clustal W (36). Conserved, conservative, and semiconservative substitutions are indicated by asterisks, colons, and semicolons, respectively. The previously proposed N-terminal amino acid for acidocin B is in brackets (22). (B) Schematic representation of the acidocin B gene cluster. The solid arrow indicates the structural bacteriocin gene aciA; the hatched arrow indicates aciT, encoding an ATP-binding protein; open arrows indicate aciB, aciC, aciD, aciI, and aciE, encoding proteins containing putative transmembrane domains. (C) Acidocin B precursor peptide. The cleavage site during maturation is indicated.

  • FIG 2
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    FIG 2

    MALDI-TOF mass spectrum of acidocin B showing singly and doubly charged species consistent with an average molecular mass of 5,621.5 Da.

  • FIG 3
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    FIG 3

    CD profile of acidocin B in SDS (solid line) and DPC (dashed line) micelles. The peptide exhibited similar α-helical contents in both micelles.

  • FIG 4
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    FIG 4

    NMR solution structure of acidocin B (PDB code 2MWR): helix 1 is in blue, helix 2 is in purple, helix 3 is in cyan, and helix 4 is in orange. The arrow indicates the linkage of the N and C termini.

  • FIG 5
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    FIG 5

    (A) Solution structure of acidocin B showing the amphipathicity of the helices. Hydrophobic residues are in green, while hydrophilic residues are in white. The arrow indicates the linkage of the N and C termini. (B) Hydrophobic surface map as generated from PyMOL (34). (C) Electrostatic potential surface map calculated using the APBS functionality of the PDB2PQR (version 1.8) online pipeline (35). Cationic regions are shown in red, while anionic regions are in blue.

  • FIG 6
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    FIG 6

    Predicted structures of gassericin A and butyrivibriocin AR10 derived from homology modeling (SWISS-MODEL) (37) using the structure of acidocin B as the template. Basic residues are shown in red, and acidic residues are in blue. The arrow indicates the N- to C-terminal linkage.

  • FIG 7
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    FIG 7

    Multiple-sequence alignment of known and putative (indicated by source organisms) subgroup II circular bacteriocin precursors using Clustal W (36). The known circular bacteriocins are acidocin B, gassericin A, and butyrivibriocin AR10. The UniProt accession numbers are in parentheses. The region corresponding to leader peptide sequences is underlined, and the highly conserved asparaginyl cleavage site is marked by an asterisk. Conserved residues (similarity threshold of 80%) are highlighted in black.

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  • TABLE 1

    Characteristics of predicted proteins encoded by the acidocin B gene clustera

    ProteinSize (aa)TMFunctionNo. of identical amino acids/total (% identity) relative to gassericin A gene cluster homologs
    AciB1745Unknown173/174 (99.4)
    AciC602Unknown60/60 (100)
    AciA912Acidocin B precursor88/91 (96.7)
    AciD1624Unknown, DUF95 family160/162 (98.8)
    AciI531Immunity53/53 (100)
    AciT2260ATP-binding protein225/226 (99.6)
    AciE2126Membrane transporter209/212 (98.6)
    • ↵a aa, amino acids; TM, number of putative transmembrane domains.

  • TABLE 2

    MS/MS sequences of fragments of acidocin B after trypsin-chymotrypsin digestion

    FragmentLinear sequenceObserved m/zChargeCalculated m/z
    1--WIADQF779.3881779.365
    2---IADQFGIHL507.27621,013.534
    3---IADQFGIHLATGT672.36021,343.688
    4------------------KLLDAVASGASLGTAF760.92921,520.825
    5-------------------LLDAVASGASLGTAF696.88621,392.730
    6-----------------------------------AILGV472.2901472.306
    7--------------------------------------GVTLPAW743.4471743.401
    8---------------------------------------------ALAAAGAL657.4461657.386
    9IY---------------------------------------------AAAGALGATAA1,120.61911,120.592
    Complete sequenceaIYWIADQFGIHLATGTARKLLDAVASGASLGTAFAAILGVTLPAWALAAAGALGATAA
    • ↵a Ala-17, Arg-18, and Ala-35 were inferred from the deduced amino acid sequence from DNA sequence analysis.

Additional Files

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    Files in this Data Supplement:

    • Supplemental file 1 -

      Chemical shift assignments for acidocin B (Table S1), structure calculation statistics for acidocin B (Table S2), RP-­HPLC trace (Fig. S1), superimposition of the 20 lowest energy conformers calculated for acidocin B (Fig. S2), hydrophobic surface maps (Fig. S3), and molecular phylogenetic analysis (Fig. S4).

      PDF, 1.7M

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Solution Structure of Acidocin B, a Circular Bacteriocin Produced by Lactobacillus acidophilus M46
Jeella Z. Acedo, Marco J. van Belkum, Christopher T. Lohans, Ryan T. McKay, Mark Miskolzie, John C. Vederas
Applied and Environmental Microbiology Mar 2015, 81 (8) 2910-2918; DOI: 10.1128/AEM.04265-14

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Solution Structure of Acidocin B, a Circular Bacteriocin Produced by Lactobacillus acidophilus M46
Jeella Z. Acedo, Marco J. van Belkum, Christopher T. Lohans, Ryan T. McKay, Mark Miskolzie, John C. Vederas
Applied and Environmental Microbiology Mar 2015, 81 (8) 2910-2918; DOI: 10.1128/AEM.04265-14
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