Crystal structure of the adenylation domain from an ε-poly-l-lysine synthetase provides molecular mechanism for substrate specificity

Engineering functional homopolymeric amino acids: from biosynthesis to design

Homopolymeric amino acids (HPAs) are a class of microbial polymers that can be classified into two categories: anionic and cationic HPAs. Notable examples include γ-poly-glutamic acid (γ-PGA) and ε-poly-L-lysine (ε-PL) that have wide-ranging applications in medicine, food, and agriculture. The primary method of manufacture is through microbial synthesis. In recent decades significant efforts have been made to enhance the production of HPAs, specifically focusing on γ-PGA and ε-PL. We comprehensively review current advances in understanding the synthetic mechanisms as well as metabolic engineering and fermentation process techniques to improve the production of HPAs. In addition, we discuss the major challenges and solutions associated with desired structure regulation of HPAs and the development of novel structures.

Design and optimization of ε-poly-l-lysine with specific functions for diverse applications

ε-Poly-l-lysine (ε-PL) is a natural homo-poly(amino acid) which can be produced by microorganisms. With the advantages in broad-spectrum antimicrobial activity, biodegradability, and biocompatibility, ε-PL has been widely used as a preservative in the food industry. Different molecular architectures endow ε-PL and ε-PL-based materials with versatile applications. However, the microbial synthesis of ε-PL is currently limited by low efficiencies in genetic engineering and molecular architecture modification. This review presents recent advances in ε-PL production and molecular architecture modification of microbial ε-PL, with a focus on the current challenges and solutions for the improvement of the productivity and diversity of ε-PL. In addition, we highlight recent examples where ε-PL has been applied to expand the versability of edible films and nanoparticles in various applications. Commercial production and the challenges and future research directions in ε-PL biosynthesis are also discussed. Currently, although the main use of ε-PL is as a food preservative, ε-PL and ε-PL-based polymers have shown excellent application potential in biomedical fields. With the development of synthetic biology, the design and synthesis of ε-PL with a customized molecular architecture are possible in the near future. ε-PL-based polymers with specific functions will be a new trend in biopolymer manufacturing.

Structural and functional insights into δ-poly-L-ornithine polymer biosynthesis from Acinetobacter baumannii

Cationic homo-polyamino acid (CHPA) peptides containing isopeptide bonds of diamino acids have been identified from Actinomycetes strains. However, none has been reported from other bacteria. Here, we report a δ-poly-L-ornithine synthetase from Acinetobacter baumannii, which we name PosA. Surprisingly, structural analysis of the adenylation domain and biochemical assay shows L-ornithine as the substrate for PosA. The product from the enzymatic reaction was purified and identified as poly-L-ornithine composed of 7-12 amino acid units. Chemical labeling of the polymer confirmed the isopeptide linkage of δ-poly-L-ornithine. We examine the biological activity of chemically synthesized 12-mer δ-poly-L-ornithine, illustrating that the polymer may act as an anti-fungal agent. Structures of the isolated adenylation domain from PosA are presented with several diamino acids and biochemical assays identify important substrate binding residues. Structurally-guided genome-mining led to the identification of homologs with different substrate binding residues that could activate additional substrates. A homolog from Bdellovibrionales sp. shows modest activity with L-arginine but not with any diamino acids observed to be substrates for previously examined CHPA synthetases. Our study indicates the possibility that additional CHPAs may be produced by various microbes, supporting the further exploration of uncharacterized natural products.

Recent advances in the structural analysis of adenylation domains in natural product biosynthesis

Adenylation (A) domains catalyze the biosynthetic incorporation of acyl building blocks into nonribosomal peptides and related natural products by selectively transferring acyl substrates onto cognate carrier proteins (CP). The use of noncanonical acyl units, such as nonproteinogenic amino acids and keto acids, by A domains expands the structural diversity of natural products. Furthermore, interrupted A domains, which have embedded auxiliary domains, are able to modify the incorporated acyl units. Structural information on A domains is important for rational protein engineering to generate unnatural compounds. In this review, we summarize recent advances in the structural analysis of A domains. First, we discuss the mechanisms by which A domains recognize noncanonical acyl units. We then focus on the interactions of A domains with CP domains and embedded auxiliary domains.