Promiscuous Installation of d-Amino Acids in Gene-Encoded Peptides

Research on enhancing enzymatic degradation of anti-digestive peptides containing D-amino acids through N-terminal acetylation

The incorporation of D-amino acids can influence the structure and enzymatic stability of proteins or peptides, especially when they are introduced at enzyme cleavage sites, significantly inhibiting the enzymatic hydrolysis of peptides. The abnormal accumulation of these peptides has been linked to age-related conditions, including cataracts and Alzheimer's disease. N-terminal acetylation, an essential post-translational modification, significantly enhances the physicochemical properties of peptides and plays an essential role in regulating their performance within biological systems. This research examined the impact of N-terminal acetylation on the enzymatic hydrolysis of peptides incorporating D-amino acids. Enzymatic activity assessments showed that N-terminal acetylation greatly promoted the enzymatic breakdown of these peptides by Proteinase K (PROK), with the substrate decay rate constant for the acetylated peptide Ac-6-w increasing by 17.5 times. This enhancement was specific to serine-type proteases, which exhibited a comparable cleavage pattern. Molecular docking further demonstrated that N-terminal acetylation improved interactions within the catalytic triad of serine proteases, leading to faster enzymatic degradation. The results provide novel insights into the impact of N-terminal acetylation on the enzymatic behavior of peptides incorporating D-amino acids, and they propose a potential approach for targeting these peptides to preserve normal physiological functions.

Synthetic Biology in Natural Product Biosynthesis

Synthetic biology has played an important role in the renaissance of natural products research during the post-genomics era. The development and integration of new tools have transformed the workflow of natural product discovery and engineering, generating multidisciplinary interest in the field. In this review, we summarize recent developments in natural product biosynthesis from three different aspects. First, advances in bioinformatics, experimental, and analytical tools to identify natural products associated with predicted biosynthetic gene clusters (BGCs) will be covered. This will be followed by an extensive review on the heterologous expression of natural products in bacterial, fungal and plant organisms. The native host-independent paradigm to natural product identification, pathway characterization, and enzyme discovery is where synthetic biology has played the most prominent role. Lastly, strategies to engineer biosynthetic pathways for structural diversification and complexity generation will be discussed, including recent advances in assembly-line megasynthase engineering, precursor-directed structural modification, and combinatorial biosynthesis.

Enabling Access to Novel Bacterial Biosynthetic Potential From ONT Draft Genomic Data

Natural products comprise a wide diversity of compounds with a range of biological activities, including antibiotics, anti-inflammatory and anti-tumoral molecules. However, we can only access a small portion of these compounds due to various technical difficulties. We have herein developed a novel and efficient approach for accessing biosynthetic gene clusters (BGCs) that encode natural products from soil bacteria. The pipeline uses a combination of long-read sequencing, antiSMASH for BGC identification and Transformation-associated recombination (TAR) for cloning the BGCs. We hypothesized that a genome assembly using Oxford Nanopore Technology (ONT) sequencing could facilitate the detection of large BGCs at a relatively fast and low-cost DNA sequencing. Despite the relative low accuracy and sequence mistakes due to high GC content and sequence repetitions frequently found in BGC containing bacteria, we demonstrate that ONT long-read sequencing and antiSMASH are effective for identifying novel BGCs and enabling TAR cloning to isolate the BGC in a desired vector. We applied this pipeline on a previously non-sequenced myxobacteria Aetherobacter fasciculatus SBSr002. Our approach enabled us to clone a previously unknown BGC into a genome engineering-ready vector, illustrating the capabilities of this powerful and cost-effective strategy.

De novo design of ribosomally synthesized and post-translationally modified peptides

In nature, peptides are enzymatically modified to constrain their structure and introduce functional moieties. De novo peptide structures could be built by combining enzymes from different pathways, but determining the rules of their use is difficult. We present a biophysical model to combine enzymes sourced from bacterial ribosomally synthesized and post-translationally modified peptide (RiPP) gene clusters. Using a pipeline to evaluate more than 1,000 peptides, the model was parameterized under uniform conditions in Escherichia coli for enzymes from different classes (graspetide, spliceotide, pantocin, cyanobactin, glycocin, lasso peptide and lanthipeptide). Synthetic leader peptides with recognition sequences for up to three enzymes were designed to modify core sequences sharing no identity to natural RiPPs. Empirically, RiPPs with the desired modifications constituted 7-67% of the total peptides produced, and 6 of our 8 peptide designs were successfully modified. This work is an example of the design of enzyme-modified peptides and libraries, using a framework that can be expanded to include new enzymes and chemical moieties.

Illuminating Substrate Preferences of Promiscuous F420H2-Dependent Dehydroamino Acid Reductases with 4-Track mRNA Display

Stereoselective reduction of dehydroamino acids is a common biosynthetic strategy to introduce d-amino acids into peptidic natural products. The reduction, often observed during the biosynthesis of lanthipeptides, is performed by dedicated dehydroamino acid reductases (dhAARs). Enzymes from the three known dhAAR families utilize nicotinamide, flavin, or F420H2 coenzymes as hydride donors, and little is known about the catalysis performed by the latter family proteins. Here, we perform a bioinformatics-guided identification and large-scale in vitro characterization of five F420H2-dependent dhAARs. We construct an mRNA display-based pipeline for ultrahigh throughput substrate specificity profiling of the enzymes. The pipeline relies on a 4-track selection strategy to deliver large quantities of clean data, which were leveraged to build accurate substrate fitness models. Our results identify a remarkably promiscuous enzyme, referred to as MaeJC, that is capable of installing d-Ala residues into arbitrary substrates with minimal recognition requirements. We integrate MaeJC into a thiopeptide biosynthetic pathway to produce d-amino acids-containing thiopeptides, demonstrating the utility of MaeJC for the programmable installation of d-amino acids in ribosomal peptides.

Using LanM Enzymes to Modify Glucagon-Like Peptides 1 and 2 in E.coli

Selective modification of peptides is often exploited to improve pharmaceutically relevant properties of bioactive peptides like stability, circulation time, and potency. In Nature, natural products belonging to the class of ribosomally synthesized and post-translationally modified peptides (RiPPs) are known to install a number of highly attractive modifications with high selectivity. These modifications are installed by enzymes guided to the peptide by corresponding leader peptides that are removed as the last step of biosynthesis. Here, we exploit leader peptides and their matching enzymes to investigate the installation of D-Ala post-translationally in a critical position in the hormones, glucagon-like peptides (GLP) 1 and 2. We also offer insight into how precursor peptide design can modulate the modification pattern achieved.

Direct Detection of the α-Carbon Radical Intermediate Formed by OspD: Mechanistic Insights into Radical S-Adenosyl-l-methionine Peptide Epimerization

OspD is a radical S-adenosyl-l-methionine (SAM) peptide epimerase that converts an isoleucine (Ile) and valine (Val) of the OspA substrate to d-amino acids during biosynthesis of the ribosomally synthesized and post-translationally modified peptide (RiPP) natural product landornamide A. OspD is proposed to carry out this reaction via α-carbon (Cα) H-atom abstraction to form a peptidyl Cα radical that is stereospecifically quenched by hydrogen atom transfer (HAT) from a conserved cysteine (Cys). Here we use site-directed mutagenesis, freeze-quench trapping, isotopic labeling, and electron paramagnetic resonance (EPR) spectroscopy to provide new insights into the OspD catalytic mechanism including the direct observation of the substrate peptide Cα radical intermediate. The putative quenching Cys334 was changed to serine to generate an OspD C334S variant impaired in HAT quenching. The reaction of reduced OspD C334S with SAM and OspA freeze-quenched at 15 s exhibits a doublet EPR signal characteristic of a Cα radical coupled to a single β-H. Using isotopologues of OspA deuterated at either Ile or Val, or both Ile and Val, reveals that the initial Cα radical intermediate forms exclusively on the Ile of OspA. Time-dependent freeze quench coupled with EPR spectroscopy provided evidence for loss of the Ile Cα radical concomitant with gain of a Val Cα radical, directly demonstrating the N-to-C directionality of epimerization by OspD. These results provide direct evidence for the aforementioned OspD-catalyzed peptide epimerization mechanism via a central Cα radical intermediate during RiPP maturation of OspA, a mechanism that may extend to other proteusin peptide epimerases.

A Promiscuous rSAM Enzyme Enables Diverse Peptide Cross-linking

Ribosomally produced and post-translationally modified polypeptides (RiPPs) are a diverse group of natural products that are processed by a variety of enzymes to their biologically relevant forms. PapB is a member of the radical S-adenosyl-l-methionine (rSAM) superfamily that introduces thioether cross-links between Cys and Asp residues in the PapA RiPP. We report that PapB has high tolerance for variations in the peptide substrate. Our results demonstrate that branched side chains in the thiol- and carboxylate-containing residues are processed and that lengthening of these groups to homocysteine and homoglutamate does not impair the ability of PapB to form thioether cross-links. Remarkably, the enzyme can even cross-link a peptide substrate where the native Asp carboxylate moiety is replaced with a tetrazole. We show that variations to residues embedded between the thiol- and carboxylate-containing residues are tolerated by PapB, as peptides containing both bulky (e.g., Phe) and charged (e.g., Lys) side chains in both natural L- and unnatural D-forms are efficiently cross-linked. Diastereomeric peptides bearing (2S,3R)- and (2S,3S)-methylaspartate are processed by PapB to form cyclic thioethers with markedly different rates, suggesting the enzymatic hydrogen atom abstraction event for the native Asp-containing substrate is diastereospecific. Finally, we synthesized two diastereomeric peptide substrates bearing E- and Z-configured γ,δ-dehydrohomoglutamate and show that PapB promotes addition of the deoxyadenosyl radical (dAdo•) instead of hydrogen atom abstraction. In the Z-configured γ,δ-dehydrohomoglutamate substrate, a fraction of the dAdo-adduct peptide is thioether cross-linked. In both cases, there is evidence for product inhibition of PapB, as the dAdo-adducts likely mimic the native transition state where dAdo• is poised to abstract a substrate hydrogen atom. Collectively, these findings provide critical insights into the arrangement of reacting species in the active site of the PapB, reveal unusual promiscuity, and highlight the potential of PapB as a tool in the development peptide therapeutics.

Engineering ribosomally synthesized and posttranslationally modified peptides as new antibiotics

The rise of antimicrobial resistance is an urgent public health threat demanding the invention of new drugs to combat infections. Naturally sourced nonribosomal peptides (NRPs) have a long history as antimicrobial drugs. Through recent advances in genome mining and engineering technologies, their ribosomally synthesized and posttranslationally modified peptide (RiPP) counterparts are poised to further contribute to the arsenal of anti-infectives. As natural products from diverse organisms involved in interspecies competition, many RiPPs already possess antimicrobial activities that can be further optimized as drug candidates. Owing to the mutability of precursor protein genes that encode their core structures and the availability of diverse posttranslational modification (PTM) enzymes with broad substrate tolerances, RiPP systems are well suited to engineer complex peptides with desired functions.

Emulating nonribosomal peptides with ribosomal biosynthetic strategies

Peptide natural products are important lead structures for human drugs and many nonribosomal peptides possess antibiotic activity. This makes them interesting targets for engineering approaches to generate peptide analogues with, for example, increased bioactivities. Nonribosomal peptides are produced by huge mega-enzyme complexes in an assembly-line like manner, and hence, these biosynthetic pathways are challenging to engineer. In the past decade, more and more structural features thought to be unique to nonribosomal peptides were found in ribosomally synthesised and posttranslationally modified peptides as well. These streamlined ribosomal pathways with modifying enzymes that are often promiscuous and with gene-encoded precursor proteins that can be modified easily, offer several advantages to produce designer peptides. This review aims to provide an overview of recent progress in this emerging research area by comparing structural features common to both nonribosomal and ribosomally synthesised and posttranslationally modified peptides in the first part and highlighting synthetic biology strategies for emulating nonribosomal peptides by ribosomal pathway engineering in the second part.

Leveraging Substrate Promiscuity of a Radical S-Adenosyl-L-methionine RiPP Maturase toward Intramolecular Peptide Cross-Linking Applications

Radical S-adenosyl-l-methionine (RS) enzymes operate on a variety of substrates and catalyze a wide range of complex radical-mediated transformations. Radical non-α-carbon thioether peptides (ranthipeptides) are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs). The RS enzyme PapB catalyzes the formation of thioether cross-links between Cys/Asp (or Cys/Glu) residues located in six Cys-X3-Asp/Glu motifs. In this report, using a minimal substrate that contains a single cross-link motif, we explore the substrate scope of the PapB and show that the enzyme is highly promiscuous and will accept a variety of Cys-X n -Asp sequences where n = 0-6. Moreover, we show that the enzyme will introduce in-line and nested thioether cross-links independently in peptide sequences that contain two motifs derived from the wild-type sequence. Additionally, the enzyme accepts peptides that contain d-amino acids at either the Cys or the Asp position. These observations are leveraged to produce a thioether cyclized analogue of the FDA-approved therapeutic agent octreotide, with a Cys-Glu cross-link replacing the disulfide that is found in the drug. These findings highlight the remarkable substrate tolerance of PapB and show the utility of RS RiPP maturases in biotechnological applications.

Insights into post-translational modification enzymes from RiPPs: A toolkit for applications in peptide synthesis

The increasing length and complexity of peptide drug candidates foster the development of novel strategies for their manufacture, which should include sustainable and efficient technologies. In this context, including enzymatic catalysis in the production of peptide molecules has gained interest. Here, several enzymes from ribosomally synthesized and post-translationally modified peptides biosynthesis pathways are reviewed, with attention to their capacity to introduce stability-promoting structural features on peptides, providing an initial framework towards their use in therapeutic peptide production processes.

Nocathioamides, Uncovered by a Tunable Metabologenomic Approach, Define a Novel Class of Chimeric Lanthipeptides

The increasing number of available genomes, in combination with advanced genome mining techniques, unveiled a plethora of biosynthetic gene clusters (BGCs) coding for ribosomally synthesized and post-translationally modified peptides (RiPPs). The products of these BGCs often represent an enormous resource for new and bioactive compounds, but frequently, they cannot be readily isolated and remain cryptic. Here, we describe a tunable metabologenomic approach that recruits a synergism of bioinformatics in tandem with isotope- and NMR-guided platform to identify the product of an orphan RiPP gene cluster in the genomes of Nocardia terpenica IFM 0406 and 0706T . The application of this tactic resulted in the discovery of nocathioamides family as a founder of a new class of chimeric lanthipeptides I.