Crystal Structure and Biochemical Analysis Suggest That YjoB ATPase is a Putative Substrate-specific Molecular Chaperone

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2022 Oct 3

PMID 36191235

Authors

Eunju Kwon

Pawan Dahal

Dong Young Kim

Affiliations

Soon will be listed here.

Abstract

AAA+ ATPases are ubiquitous proteins associated with most cellular processes, including DNA unwinding and protein unfolding. Their functional and structural properties are typically determined by domains and motifs added to the conserved ATPases domain. Currently, the molecular function and structure of many ATPases remain elusive. Here, we report the crystal structure and biochemical analyses of YjoB, a AAA+ protein. The crystal structure revealed that the YjoB hexamer forms a bucket hat-shaped structure with a porous chamber. Biochemical analyses showed that YjoB prevents the aggregation of vegetative catalase KatA and gluconeogenesis-specific glyceraldehyde-3 phosphate dehydrogenase GapB but not citrate synthase, a conventional substrate. Structural and biochemical analyses further showed that the internal chamber of YjoB is necessary for inhibition of substrate aggregation. Our results suggest that YjoB, conserved in the class Bacilli, is a potential molecular chaperone acting in the starvation/stationary phases of growth.

References

Holm L . DALI and the persistence of protein shape. Protein Sci. 2019; 29(1):128-140. PMC: 6933842. DOI: 10.1002/pro.3749. View

Iyer L, Leipe D, Koonin E, Aravind L . Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol. 2004; 146(1-2):11-31. DOI: 10.1016/j.jsb.2003.10.010. View

Wagener N, Ackermann M, Funes S, Neupert W . A pathway of protein translocation in mitochondria mediated by the AAA-ATPase Bcs1. Mol Cell. 2011; 44(2):191-202. DOI: 10.1016/j.molcel.2011.07.036. View

Huang X, Gaballa A, Cao M, Helmann J . Identification of target promoters for the Bacillus subtilis extracytoplasmic function sigma factor, sigma W. Mol Microbiol. 1999; 31(1):361-71. DOI: 10.1046/j.1365-2958.1999.01180.x. View

Otwinowski Z, Minor W . Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997; 276:307-26. DOI: 10.1016/S0076-6879(97)76066-X. View

Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg L . Improvements to the APBS biomolecular solvation software suite. Protein Sci. 2017; 27(1):112-128. PMC: 5734301. DOI: 10.1002/pro.3280. View

Goloubinoff P, Mogk A, Zvi A, Tomoyasu T, Bukau B . Sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network. Proc Natl Acad Sci U S A. 1999; 96(24):13732-7. PMC: 24133. DOI: 10.1073/pnas.96.24.13732. View

Erdmann R, Wiebel F, Flessau A, Rytka J, Beyer A, Frohlich K . PAS1, a yeast gene required for peroxisome biogenesis, encodes a member of a novel family of putative ATPases. Cell. 1991; 64(3):499-510. DOI: 10.1016/0092-8674(91)90234-p. View

Cruciat C, Hell K, Folsch H, Neupert W, Stuart R . Bcs1p, an AAA-family member, is a chaperone for the assembly of the cytochrome bc(1) complex. EMBO J. 1999; 18(19):5226-33. PMC: 1171593. DOI: 10.1093/emboj/18.19.5226. View

10.

Karshikoff A, Ladenstein R . Proteins from thermophilic and mesophilic organisms essentially do not differ in packing. Protein Eng. 1998; 11(10):867-72. DOI: 10.1093/protein/11.10.867. View

11.

Hohl T, Parlati F, Wimmer C, Rothman J, Sollner T, Engelhardt H . Arrangement of subunits in 20 S particles consisting of NSF, SNAPs, and SNARE complexes. Mol Cell. 1998; 2(5):539-48. PMC: 5496501. DOI: 10.1016/s1097-2765(00)80153-7. View

12.

Hanson P, Whiteheart S . AAA+ proteins: have engine, will work. Nat Rev Mol Cell Biol. 2005; 6(7):519-29. DOI: 10.1038/nrm1684. View

13.

Barton G . ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng. 1993; 6(1):37-40. DOI: 10.1093/protein/6.1.37. View

14.

Bol D, Yasbin R . Analysis of the dual regulatory mechanisms controlling expression of the vegetative catalase gene of Bacillus subtilis. J Bacteriol. 1994; 176(21):6744-8. PMC: 197032. DOI: 10.1128/jb.176.21.6744-6748.1994. View

15.

Niwa H, Tsuchiya D, Makyio H, Yoshida M, Morikawa K . Hexameric ring structure of the ATPase domain of the membrane-integrated metalloprotease FtsH from Thermus thermophilus HB8. Structure. 2002; 10(10):1415-23. DOI: 10.1016/s0969-2126(02)00855-9. View

16.

BEERS Jr R, SIZER I . A spectrophotometric method for measuring the breakdown of hydrogen peroxide by catalase. J Biol Chem. 1952; 195(1):133-40. View

17.

Burton B, Baker T . Mu transpososome architecture ensures that unfolding by ClpX or proteolysis by ClpXP remodels but does not destroy the complex. Chem Biol. 2003; 10(5):463-72. DOI: 10.1016/s1074-5521(03)00102-9. View

18.

Frickey T, Lupas A . Phylogenetic analysis of AAA proteins. J Struct Biol. 2004; 146(1-2):2-10. DOI: 10.1016/j.jsb.2003.11.020. View

19.

Vivian J, Callis P . Mechanisms of tryptophan fluorescence shifts in proteins. Biophys J. 2001; 80(5):2093-109. PMC: 1301402. DOI: 10.1016/S0006-3495(01)76183-8. View

20.

Cao M, Wang T, Ye R, Helmann J . Antibiotics that inhibit cell wall biosynthesis induce expression of the Bacillus subtilis sigma(W) and sigma(M) regulons. Mol Microbiol. 2002; 45(5):1267-76. DOI: 10.1046/j.1365-2958.2002.03050.x. View