Structural and Functional Evolution of Bacterial Polyphospha
Posted on：
2024-04-29 16:36
Phosphorus plays an important role in the origin of life, and it is widely found in living organisms as a key component in biological molecules such as nucleic acids, phospholipids and phosphate esters. The polyP is a linear negatively-charged inorganic polymer consisting of tens to hundreds of orthophosphate residues linked by high-energy phosphoanhydride bonds, and might serve as a plausible source of phosphorus and energy. In bacteria, polyP metabolism is controlled by polyP kinase (PPK) for polyP synthesis by using ATP or GTP as the substrates, and exopolyphosphatase (PPX) for polyP degradation. Understanding the structure basis of PPX is crucial to reveal polyP degradation mechanism. However, little is known about the molecular basis and structural evolution of PPX.
On 29th Apr 2024, Professor Ruhong Zhou from Institute of Quantitative Biology, Zhejiang University and Professor Bing Tian, Professor Ye Zhao and Professor Yuejin Hua from College of Life Sciences, Zhejiang University have published an article ‘Structural Evolution of Bacterial Polyphosphate Degradation Enzyme for Phosphorus Cycling’ (https://onlinelibrary.wiley.com/doi/10.1002/advs.202309602), revealing PPX structure varies in the length of ɑ-helical interdomain linker (ɑ-linker) across various bacteria, which is negatively correlated with their enzymatic activity and thermostability. The study provides insights into the interdomain linker length-dependent evolution of PPXs, which shed light on enzymatic adaption for phosphorus cycling during natural evolution. The article was selected as the front cover.
Protein crystal structures of PPX homologs from different bacterial species were studied and PPX proteins adopt distinct dimer conformations with varying lengths of the α-helical interdomain linker (designated ɑ-linker) between the N- and C-terminus. Regression analysis showed a negative correlation between the dimer interface and α-linker length, indicating that the extended α-linker could modulate the interactions between the domains, resulting in changes of quaternary structure. It was found that the length of α-linker in PPXs varies among bacteria, and had an impact on the interactions between the two domains thus affecting the dimer configuration of PPX. Among the PPXs from different bacterial species, those with shorter α-linkers exhibited stronger enzyme activities. This negative correlation was also identified using artificially modified PPXs with extended or shortened α-linkers: the shorter the linker, the stronger the activity of PPX. Combined with crystal structures and computational biology techniques, the authors concluded that polyP interacted with two conserved loops and positively charged residues in the polyP binding pocket. Molecular simulation further demonstrated that shortening of the α-linker could increase the interactions between the C-terminus and N-terminus, thereby reducing the center of mass distance between the two loops involved in polyP binding and increasing the atom contact number between polyP and the binding pocket.
The authors verified the relationship of ɑ-linker length with the activity of PPXs in the extremophilic phylum Deinococcus-Thermus by combing multiple sequence alignments, phylogenetic analysis, and protein structure analysis via AlphaFold 2. The thermophilic bacteria tended to have PPXs with shorter ɑ-linkers, higher polyP hydrolysis activity, and thermostability, in contrast with those of the thermolabile bacteria from Deinococcus. The formation of a short ɑ-linker secondary structure might enhance the utilization of polyP as a phosphorus source. Artificial variants of PPX with different ɑ-linker lengths were constructed and confirmed the negative correlation between the polyP hydrolysis activity and the length of the α-linker in PPX. Therefore, ɑ-linker may play an important role in PPX evolution and environmental adaptation of bacteria. The work proposed an ɑ-linker based protein structure evolution model for rational design and directed evolution of enzymes.
The work was at the interaction of adversity biology, computational biology, and structural biology, and was financially supported by grants from the National Key R&D Program of China, and grants from the National Natural Science Foundation of China etc.
