Novel DNA-Binding Activity Exhibited by Poly(aspartic acid) Hydrolase-1 Inhibits Poly(aspartic acid) Hydrolase...

Area of Science:

• Biochemistry
• Environmental Science
• Polymer Science

Background:

• Biodegradable polymers like poly(aspartic acid) (PAA) are crucial for reducing environmental pollution.
• Polymer hydrolases (PAH) are enzymes that degrade PAA, offering a sustainable alternative to traditional superabsorbent polymers.
• Understanding PAH-substrate interactions is key to optimizing their environmental applications.

Purpose of the Study:

• To characterize the interaction between poly(aspartic acid) hydrolases (PAH) and DNA.
• To investigate the impact of DNA binding on PAH enzymatic activity and PAA biodegradation.
• To propose a model for PAH localization and function in extracellular biofilm environments.

Main Methods:

• DNA binding assays using PahZ1 homologues from *Sphingomonas* sp. KT-1 and *Pedobacter* sp. KP-2.
• Determination of binding affinities (K_D,app) for single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA).
• Enzyme activity assays using gel permeation chromatography to assess PAA biodegradation inhibition.

Main Results:

• PahZ1 homologues exhibit nanomolar binding affinities for both ssDNA and dsDNA.
• PahZ1_KT-1 binds ssDNA and dsDNA with K_D,app values of 81 ± 14 nM and 19 ± 1 nM, respectively.
• dsDNA binding significantly inhibits PAH-catalyzed PAA biodegradation.

Conclusions:

• Polymer hydrolases (PAH) bind to DNA with high affinity.
• DNA binding acts as an inhibitory mechanism for PAH-mediated PAA biodegradation.
• PAH-DNA interaction may facilitate enzyme localization to extracellular PAA in biofilms, aiding nutrient acquisition.