Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a novel macromolecular assembly

Xu, X.; Ruiz, R.; Adipietro, K. A.; Peralta, C.; Ben-Hail, D.; Varney, K. M.; Cook, M. E.; Roth, B. M.; Wilder, P. T.; Cleveland, T.; Grishaev, A.; Neu, H.; Michel, S.; Yu, W.; Beckett, D.; Rustandi, R. R.; Lancaster, C.; Loughney, J. W.; Krsitopeit, A.; Christanti, S.; Olson, J. W.; MacKerell, A. D.; des Georges, A.; Pozharski, E.; Weber, D. J.

doi:10.1101/833699

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bioRxiv · 10.1101/833699

Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a novel macromolecular assembly

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Abstract

Targeting Clostridium difficile infection (CDI) is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent CDI often has a binary toxin termed the C. difficile toxin (CDT), in addition to the enterotoxins TsdA and TsdB. CDT has an enzymatic component, termed CDTa, and a pore-forming or delivery subunit termed CDTb. CDTb was characterized here using a combination of single particle cryoEM, X-ray crystallography, NMR, and other biophysical methods. In the absence of CDTa, two novel di-heptamer structures for activated CDTb (aCDTb; 1.0 MDa) were solved at atomic resolution including a symmetric (SymCDTb; 3.14 [A]) and an asymmetric form (AsymCDTb; 2.84 [A]). Roles played by two receptor-binding domains of aCDTb were of particular interest since RBD1 lacks sequence homology to any other known toxin, and the RBD2 domain is completely absent in other well-studied heptameric toxins (i.e. anthrax). For AsymCDTb, a novel Ca2+ binding site was discovered in RBD1 that is important for its stability, and RBD2 was found to be critical for host cell toxicity and the novel di-heptamer fold for both forms of aCDTb. Together, these studies represent a starting point for structure-based drug-discovery strategies to targeting CDT in the most severe strains of CDI. SIGNIFICANCE STATEMENTThere is a high burden from C. difficile infection (CDI) throughout the world, and the Center for Disease Control (CDC) reports more than 500,000 cases annually in the United States, resulting in an estimated 15,000 deaths. In addition to the large clostridial toxins, TcdA/TcdB, a third C. difficile binary toxin (CDT) is associated with the most serious outbreaks of drug resistant CDI in the 21st century. Here, structural biology and biophysical approaches were used to characterize the cell binding component of CDT, termed CDTb, at atomic resolution. Surprisingly, two novel structures were solved from a single sample that help to explain the molecular underpinnings of C. difficile toxicity. These structures will also be important for targeting this human pathogen via structure-based therapeutic design methods.

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Xu, X., Ruiz, R., Adipietro, K. A., Peralta, C., Ben-Hail, D., Varney, K. M., Cook, M. E., Roth, B. M., Wilder, P. T., Cleveland, T., Grishaev, A., Neu, H., Michel, S., Yu, W., Beckett, D., Rustandi, R. R., Lancaster, C., Loughney, J. W., Krsitopeit, A., Christanti, S., Olson, J. W., MacKerell, A. D., des Georges, A., Pozharski, E., Weber, D. J.. 2019-11-08. Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a novel macromolecular assembly. https://doi.org/10.1101/833699

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