An increase in surface hydrophobicity mediates chaperone activity in N-chlorinated proteins

Varatnitskaya, M.; Fasel, J.; Müller, A.; Lupilov, N.; Shi, Y.; Fuchs, K.; Krewing, M.; Jung, C.; Jacob, T.; Sitek, B.; Bandow, J. E.; Carroll, K. S.; Leichert, L. I.

doi:10.1101/2021.10.26.465855

bioRxiv · 10.1101/2021.10.26.465855

An increase in surface hydrophobicity mediates chaperone activity in N-chlorinated proteins

Varatnitskaya, M.·Fasel, J.·Müller, A.·Lupilov, N.·Shi, Y.·Fuchs, K.·Krewing, M.·Jung, C.·Jacob, T.·Sitek, B.·Bandow, J. E.·Carroll, K. S.·Leichert, L. I.

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Abstract

Under physiological conditions, Escherichia coli RidA is an enamine/imine deaminase, which promotes the release of ammonia from reactive enamine/imine intermediates. However, when modified by hypochlorous acid (HOCl), as produced by the host defense, RidAHOCl turns into a potent chaperone-like holdase that can effectively protect the proteome of E. coli during oxidative stress. We previously reported that the activation of RidAs chaperone-like function coincides with the addition of at least seven and up to ten chlorine atoms. These atoms are reversibly added to basic amino acids in RidAHOCl and removal by reducing agents leads to inactivation. Nevertheless, it remains unclear, which residues in particular need to be chlorinated for activation. Here, we employ a combination of LC-MS/MS analysis, a chemo-proteomic approach, and a mutagenesis study to identify residues responsible for RidAs chaperone-like function. Through LC-MS/MS of digested RidAHOCl, we obtained direct evidence of the chlorination of one arginine residue (and, coincidentally, two tyrosine residues), while other N- chlorinated residues could not be detected, presumably due to the instability of the modification and its potential interference with a proteolytic digest. Therefore, we established a chemoproteomic approach using 5-(dimethylamino) naphthalene-1-sulfinic acid (DANSO2H) as a probe to label N-chlorinated lysines. Using this probe, we were able to detect the N-chlorination of six additional lysine residues. Moreover, using a mutagenesis study to genetically probe the role of single arginine and lysine residues, we found that the removal of arginines R105 and R128 leads to a substantial reduction of RidAHOCls chaperone activity. These results, together with structural analysis, confirm that the chaperone activity of RidA is concomitant with the loss of positive charges on the protein surface, leading to an increased overall protein hydrophobicity. Molecular modelling of RidAHOCl and the rational design of a RidA variant that shows chaperone activity even in the absence of HOCl further supports our hypothesis. Our data provide a molecular mechanism for HOCl-mediated chaperone activity found in RidA and a growing number of other HOCl-activated chaperones.

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Varatnitskaya, M., Fasel, J., Müller, A., Lupilov, N., Shi, Y., Fuchs, K., Krewing, M., Jung, C., Jacob, T., Sitek, B., Bandow, J. E., Carroll, K. S., Leichert, L. I.. 2021-10-27. An increase in surface hydrophobicity mediates chaperone activity in N-chlorinated proteins. https://doi.org/10.1101/2021.10.26.465855

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