ATP binding by an F1Fo ATP synthase ε subunit is pH dependent, suggesting a diversity of ε subunit functional regulation in bacteria
It is a conjecture that the ε subunit regulates ATP hydrolytic function of the F1Fo ATP synthase in bacteria. This has been proposed by the ε subunit taking an extended conformation, with a terminal helix probing into the central architecture of the hexameric catalytic domain, preventing ATP hydroly...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-02-01
|
| Series: | Frontiers in Molecular Biosciences |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1059673/full |
| _version_ | 1797894025644081152 |
|---|---|
| author | Alexander Krah Alexander Krah Timothy Vogelaar Sam I. de Jong Jolyon K. Claridge Peter J. Bond Peter J. Bond Duncan G. G. McMillan Duncan G. G. McMillan |
| author_facet | Alexander Krah Alexander Krah Timothy Vogelaar Sam I. de Jong Jolyon K. Claridge Peter J. Bond Peter J. Bond Duncan G. G. McMillan Duncan G. G. McMillan |
| author_sort | Alexander Krah |
| collection | DOAJ |
| description | It is a conjecture that the ε subunit regulates ATP hydrolytic function of the F1Fo ATP synthase in bacteria. This has been proposed by the ε subunit taking an extended conformation, with a terminal helix probing into the central architecture of the hexameric catalytic domain, preventing ATP hydrolysis. The ε subunit takes a contracted conformation when bound to ATP, thus would not interfere with catalysis. A recent crystallographic study has disputed this; the Caldalkalibacillus thermarum TA2.A1 F1Fo ATP synthase cannot natively hydrolyse ATP, yet studies have demonstrated that the loss of the ε subunit terminal helix results in an ATP synthase capable of ATP hydrolysis, supporting ε subunit function. Analysis of sequence and crystallographic data of the C. thermarum F1Fo ATP synthase revealed two unique histidine residues. Molecular dynamics simulations suggested that the protonation state of these residues may influence ATP binding site stability. Yet these residues lie outside the ATP/Mg2+ binding site of the ε subunit. We then probed the effect of pH on the ATP binding affinity of the ε subunit from the C. thermarum F1Fo ATP synthase at various physiologically relevant pH values. We show that binding affinity changes 5.9 fold between pH 7.0, where binding is weakest, to pH 8.5 where it is strongest. Since the C. thermarum cytoplasm is pH 8.0 when it grows optimally, this correlates to the ε subunit being down due to ATP/Mg2+ affinity, and not being involved in blocking ATP hydrolysis. Here, we have experimentally correlated that the pH of the bacterial cytoplasm is of critical importance for ε subunit ATP affinity regulated by second-shell residues thus the function of the ε subunit changes with growth conditions. |
| first_indexed | 2024-04-10T07:02:15Z |
| format | Article |
| id | doaj.art-f451c47f4bd443398ca14dbf15b94ad4 |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-04-10T07:02:15Z |
| publishDate | 2023-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-f451c47f4bd443398ca14dbf15b94ad42023-02-27T18:20:20ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2023-02-011010.3389/fmolb.2023.10596731059673ATP binding by an F1Fo ATP synthase ε subunit is pH dependent, suggesting a diversity of ε subunit functional regulation in bacteriaAlexander Krah0Alexander Krah1Timothy Vogelaar2Sam I. de Jong3Jolyon K. Claridge4Peter J. Bond5Peter J. Bond6Duncan G. G. McMillan7Duncan G. G. McMillan8Korea Institute for Advanced Study, School of Computational Sciences, Seoul, South KoreaBioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, SingaporeDepartment of Biotechnology, Delft University of Technology, Delft, NetherlandsDepartment of Biotechnology, Delft University of Technology, Delft, NetherlandsSchool of Fundamental Sciences, Massey University, Palmerston North, New ZealandBioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, SingaporeDepartment of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biotechnology, Delft University of Technology, Delft, NetherlandsSchool of Fundamental Sciences, Massey University, Palmerston North, New ZealandIt is a conjecture that the ε subunit regulates ATP hydrolytic function of the F1Fo ATP synthase in bacteria. This has been proposed by the ε subunit taking an extended conformation, with a terminal helix probing into the central architecture of the hexameric catalytic domain, preventing ATP hydrolysis. The ε subunit takes a contracted conformation when bound to ATP, thus would not interfere with catalysis. A recent crystallographic study has disputed this; the Caldalkalibacillus thermarum TA2.A1 F1Fo ATP synthase cannot natively hydrolyse ATP, yet studies have demonstrated that the loss of the ε subunit terminal helix results in an ATP synthase capable of ATP hydrolysis, supporting ε subunit function. Analysis of sequence and crystallographic data of the C. thermarum F1Fo ATP synthase revealed two unique histidine residues. Molecular dynamics simulations suggested that the protonation state of these residues may influence ATP binding site stability. Yet these residues lie outside the ATP/Mg2+ binding site of the ε subunit. We then probed the effect of pH on the ATP binding affinity of the ε subunit from the C. thermarum F1Fo ATP synthase at various physiologically relevant pH values. We show that binding affinity changes 5.9 fold between pH 7.0, where binding is weakest, to pH 8.5 where it is strongest. Since the C. thermarum cytoplasm is pH 8.0 when it grows optimally, this correlates to the ε subunit being down due to ATP/Mg2+ affinity, and not being involved in blocking ATP hydrolysis. Here, we have experimentally correlated that the pH of the bacterial cytoplasm is of critical importance for ε subunit ATP affinity regulated by second-shell residues thus the function of the ε subunit changes with growth conditions.https://www.frontiersin.org/articles/10.3389/fmolb.2023.1059673/fullF1Fo ATP synthaseregulation-physiologicalalkaliphile bacteriaaerobepolyextreme environments |
| spellingShingle | Alexander Krah Alexander Krah Timothy Vogelaar Sam I. de Jong Jolyon K. Claridge Peter J. Bond Peter J. Bond Duncan G. G. McMillan Duncan G. G. McMillan ATP binding by an F1Fo ATP synthase ε subunit is pH dependent, suggesting a diversity of ε subunit functional regulation in bacteria Frontiers in Molecular Biosciences F1Fo ATP synthase regulation-physiological alkaliphile bacteria aerobe polyextreme environments |
| title | ATP binding by an F1Fo ATP synthase ε subunit is pH dependent, suggesting a diversity of ε subunit functional regulation in bacteria |
| title_full | ATP binding by an F1Fo ATP synthase ε subunit is pH dependent, suggesting a diversity of ε subunit functional regulation in bacteria |
| title_fullStr | ATP binding by an F1Fo ATP synthase ε subunit is pH dependent, suggesting a diversity of ε subunit functional regulation in bacteria |
| title_full_unstemmed | ATP binding by an F1Fo ATP synthase ε subunit is pH dependent, suggesting a diversity of ε subunit functional regulation in bacteria |
| title_short | ATP binding by an F1Fo ATP synthase ε subunit is pH dependent, suggesting a diversity of ε subunit functional regulation in bacteria |
| title_sort | atp binding by an f1fo atp synthase ε subunit is ph dependent suggesting a diversity of ε subunit functional regulation in bacteria |
| topic | F1Fo ATP synthase regulation-physiological alkaliphile bacteria aerobe polyextreme environments |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1059673/full |
| work_keys_str_mv | AT alexanderkrah atpbindingbyanf1foatpsynthaseesubunitisphdependentsuggestingadiversityofesubunitfunctionalregulationinbacteria AT alexanderkrah atpbindingbyanf1foatpsynthaseesubunitisphdependentsuggestingadiversityofesubunitfunctionalregulationinbacteria AT timothyvogelaar atpbindingbyanf1foatpsynthaseesubunitisphdependentsuggestingadiversityofesubunitfunctionalregulationinbacteria AT samidejong atpbindingbyanf1foatpsynthaseesubunitisphdependentsuggestingadiversityofesubunitfunctionalregulationinbacteria AT jolyonkclaridge atpbindingbyanf1foatpsynthaseesubunitisphdependentsuggestingadiversityofesubunitfunctionalregulationinbacteria AT peterjbond atpbindingbyanf1foatpsynthaseesubunitisphdependentsuggestingadiversityofesubunitfunctionalregulationinbacteria AT peterjbond atpbindingbyanf1foatpsynthaseesubunitisphdependentsuggestingadiversityofesubunitfunctionalregulationinbacteria AT duncanggmcmillan atpbindingbyanf1foatpsynthaseesubunitisphdependentsuggestingadiversityofesubunitfunctionalregulationinbacteria AT duncanggmcmillan atpbindingbyanf1foatpsynthaseesubunitisphdependentsuggestingadiversityofesubunitfunctionalregulationinbacteria |