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Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes

Journal Article · · PLoS ONE

Unraveling the metabolism of Treponema pallidum is a key component to understanding the pathogenesis of the human disease that it causes, syphilis. For decades, it was assumed that glucose was the sole carbon/energy source for this parasitic spirochete. But the lack of citric-acid-cycle enzymes suggested that alternative sources could be utilized, especially in microaerophilic host environments where glycolysis should not be robust. Recent bioinformatic, biophysical, and biochemical evidence supports the existence of an acetogenic energy-conservation pathway in T . pallidum and related treponemal species. In this hypothetical pathway, exogenous D-lactate can be utilized by the bacterium as an alternative energy source. Herein, we examined the final enzyme in this pathway, acetate kinase (named TP0476), which ostensibly catalyzes the generation of ATP from ADP and acetyl-phosphate. We found that TP0476 was able to carry out this reaction, but the protein was not suitable for biophysical and structural characterization. We thus performed additional studies on the homologous enzyme (75% amino-acid sequence identity) from the oral pathogen Treponema vincentii , TV0924. This protein also exhibited acetate kinase activity, and it was amenable to structural and biophysical studies. We established that the enzyme exists as a dimer in solution, and then determined its crystal structure at a resolution of 1.36 Å, showing that the protein has a similar fold to other known acetate kinases. Mutation of residues in the putative active site drastically altered its enzymatic activity. A second crystal structure of TV0924 in the presence of AMP (at 1.3 Å resolution) provided insight into the binding of one of the enzyme’s substrates. On balance, this evidence strongly supported the roles of TP0476 and TV0924 as acetate kinases, reinforcing the hypothesis of an acetogenic pathway in pathogenic treponemes.

Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-76SF00515; AC02-06CH11357
OSTI ID:
2498416
Journal Information:
PLoS ONE, Journal Name: PLoS ONE Journal Issue: 1 Vol. 20; ISSN 1932-6203
Publisher:
Public Library of Science (PLoS)Copyright Statement
Country of Publication:
United States
Language:
English

References (42)

Molecular insights into the enzymatic diversity of flavin-trafficking protein (Ftp; formerly ApbE) in flavoprotein biogenesis in the bacterial periplasm journal December 2015
Inhibition of bacterial FMN transferase: A potential avenue for countering antimicrobial resistance journal November 2021
Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts journal January 2008
SEDNTERP: a calculation and database utility to aid interpretation of analytical ultracentrifugation and light scattering data journal February 2023
Size-Distribution Analysis of Macromolecules by Sedimentation Velocity Ultracentrifugation and Lamm Equation Modeling journal March 2000
Size-Distribution Analysis of Proteins by Analytical Ultracentrifugation: Strategies and Application to Model Systems journal February 2002
Direct Sedimentation Analysis of Interference Optical Data in Analytical Ultracentrifugation journal April 1999
Acetate kinase from Veillonella alcalescens. Regulation of enzyme activity by succinate and substrates. journal May 1976
Calculations and Publication-Quality Illustrations for Analytical Ultracentrifugation Data book January 2015
HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties journal February 2018
Crystal Structures of ADP and AMPPNP-bound Propionate Kinase (TdcD) from Salmonella typhimurium: Comparison with Members of Acetate and Sugar Kinase/Heat Shock Cognate 70/Actin Superfamily journal September 2005
Inference of Macromolecular Assemblies from Crystalline State journal September 2007
Structural, Bioinformatic, and In Vivo Analyses of Two Treponema pallidum Lipoproteins Reveal a Unique TRAP Transporter journal March 2012
Structural and Thermodynamic Characterization of the Interaction between Two Periplasmic Treponema pallidum Lipoproteins that are Components of a TPR-Protein-Associated TRAP Transporter (TPAT) journal June 2012
Investigation of the Methanosarcina thermophila Acetate Kinase Mechanism by Fluorescence Quenching journal December 2007
Syphilis journal October 2017
Treponema pallidum, the syphilis spirochete: making a living as a stealth pathogen journal October 2016
Array programming with NumPy journal September 2020
Highly accurate protein structure prediction with AlphaFold journal July 2021
Accurate structure prediction of biomolecular interactions with AlphaFold 3 journal May 2024
SciPy 1.0: fundamental algorithms for scientific computing in Python journal February 2020
ColabFold: making protein folding accessible to all journal May 2022
Site-directed Mutational Analysis of Active Site Residues in the Acetate Kinase from Methanosarcina thermophila journal September 2001
The TP0796 Lipoprotein of Treponema pallidum Is a Bimetal-dependent FAD Pyrophosphatase with a Potential Role in Flavin Homeostasis journal February 2013
Structural and Kinetic Analyses of Arginine Residues in the Active Site of the Acetate Kinase from Methanosarcina thermophila journal January 2005
The PnrA (Tp0319; TmpC) Lipoprotein Represents a New Family of Bacterial Purine Nucleoside Receptor Encoded within an ATP-binding Cassette (ABC)-like Operon in Treponema pallidum journal January 2006
Crystal Structure of the Tp34 (TP0971) Lipoprotein of Treponema pallidum: IMPLICATIONS OF ITS METAL-BOUND STATE AND AFFINITY FOR HUMAN LACTOFERRIN journal December 2006
Characterization of the phosphotransacetylase-acetate kinase pathway for ATP production inPorphyromonas gingivalis journal January 2019
The HHpred interactive server for protein homology detection and structure prediction journal July 2005
Dali server: conservation mapping in 3D journal May 2010
Deciphering key features in protein structures with the new ENDscript server journal April 2014
Phaser crystallographic software journal July 2007
Coot model-building tools for molecular graphics journal November 2004
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions journal November 2004
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Structures of substrate- and nucleotide-bound propionate kinase fromSalmonella typhimurium: substrate specificity and phosphate-transfer mechanism journal July 2015
Complete Genome Sequence of Treponema pallidum, the Syphilis Spirochete journal July 1998
Biophysical and Bioinformatic Analyses Implicate the Treponema pallidum Tp34 Lipoprotein (Tp0971) in Transition Metal Homeostasis journal October 2012
Urkinase: Structure of Acetate Kinase, a Member of the ASKHA Superfamily of Phosphotransferases journal January 2001
Long-Term In Vitro Culture of the Syphilis Spirochete Treponema pallidum subsp. pallidum journal June 2018
Biophysical and biochemical studies support TP0094 as a phosphotransacetylase in an acetogenic energy-conservation pathway in Treponema pallidum journal May 2023
Protein Identification and Analysis Tools on the ExPASy Server book January 2005