Expression, purification, and characterization of cold-adapted inorganic pyrophosphatase from psychrophilic Shewanella sp. AS-11

A cold‐active esterase enhances mesophilic properties through Mn 2+ binding

A key aspect of adaptation to cold environments is the production of cold-active enzymes by psychrophilic organisms. These enzymes not only have high activity at low temperatures, but also exhibit remarkable structural flexibility and thermolability. In this context, the role of metal ions has been little explored, and the few available studies seem to suggest that metal binding counteracts structural flexibility. This article reports an investigation into the role of the binding of manganese ion (Mn²⁺ ) in the thermal adaptation of an esterase (M-Est) of the GDSx family, identified in the genome of the Antarctic bacterium Marinomonas sp. ef1. M-Est is specific for esters containing acetate groups and turned out to be a highly thermolabile cold-active enzyme, with a catalysis optimum temperature of 5 °C and a melting temperature of 31.7 °C. A combination of biochemical and computational analyses, including molecular dynamics simulations, revealed that M-Est binds Mn²⁺ ions via a single binding site located on the surface of the enzyme, close to the active site. Although the interaction between M-Est and Mn²⁺ induces only local conformational changes involving the active site, quite surprisingly they trigger an improvement in both thermal stability and catalytic efficiency under mild temperature conditions. These results, together with the conservation of the Mn²⁺ binding site among psychrophilic and psychrotolerant homologues, suggest that Mn²⁺ binding may be a useful, albeit atypical, strategy to mitigate the detrimental effects of temperature on true cold-active enzymes.

X-ray Crystallography and Electron Paramagnetic Resonance Spectroscopy Reveal Active Site Rearrangement of Cold-Adapted Inorganic Pyrophosphatase

Inorganic pyrophosphatase (PPase) catalyses the hydrolysis reaction of inorganic pyrophosphate to phosphates. Our previous studies showed that manganese (Mn) activated PPase from the psychrophilic bacterium Shewanella sp. AS-11 (Mn-Sh-PPase) has a characteristic temperature dependence of the activity with an optimum at 5 °C. Here we report the X-ray crystallography and electron paramagnetic resonance (EPR) spectroscopy structural analyses of Sh-PPase in the absence and presence of substrate analogues. We successfully determined the crystal structure of Mn-Sh-PPase without substrate and Mg-activated Sh-PPase (Mg-Sh-PPase) complexed with substrate analogue (imidodiphosphate; PNP). Crystallographic studies revealed a bridged water placed at a distance from the di-Mn centre in Mn-Sh-PPase without substrate. The water came closer to the metal centre when PNP bound. EPR analysis of Mn-Sh-PPase without substrate revealed considerably weak exchange coupling, whose magnitude was increased by binding of substrate analogues. The data indicate that the bridged molecule has weak bonds with the di-Mn centre, which suggests a 'loose' structure, whereas it comes closer to di-Mn centre by substrate binding, which suggests a 'well-tuned' structure for catalysis. Thus, we propose that Sh-PPase can rearrange the active site and that the 'loose' structure plays an important role in the cold adaptation mechanism.

Proteome Analysis of Poplar Seed Vigor

Seed vigor is a complex property that determines the seed’s potential for rapid uniform emergence and subsequent growth. However, the mechanism for change in seed vigor is poorly understood. The seeds of poplar (Populus × Canadensis Moench), which are short-lived, were stored at 30°C and 75±5% relative humidity for different periods of time (0–90 days) to obtain different vigor seeds (from 95 to 0% germination). With decreasing seed vigor, the temperature range of seed germination became narrower; the respiration rate of the seeds decreased markedly, while the relative electrolyte leakage increased markedly, both levelling off after 45 days. A total of 81 protein spots showed a significant change in abundance (≥ 1.5-fold, P < 0.05) when comparing the proteomes among seeds with different vigor. Of the identified 65 proteins, most belonged to the groups involved in metabolism (23%), protein synthesis and destination (22%), energy (18%), cell defense and rescue (17%), and storage protein (15%). These proteins accounted for 95% of all the identified proteins. During seed aging, 53 and 6 identified proteins consistently increased and decreased in abundance, respectively, and they were associated with metabolism (22%), protein synthesis and destination (22%), energy (19%), cell defense and rescue (19%), storage proteins (15%), and cell growth and structure (3%). These data show that the decrease in seed vigor (aging) is an energy-dependent process, which requires protein synthesis and degradation as well as cellular defense and rescue.