scholarly journals Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fredarla S. Miller ◽  
Kathryn K. Crone ◽  
Matthew R. Jensen ◽  
Sudipta Shaw ◽  
William R. Harcombe ◽  
...  
Keyword(s):  
Natural Product ◽  
Biological Membrane ◽  
Shewanella Oneidensis ◽  
Structural Constraints ◽  
Peptide Backbone ◽  
Amide Bonds ◽  
Type Iv ◽  
Precursor Peptide ◽  
Modified Peptides ◽  
Conformational Rearrangements

AbstractPeptide backbone α-N-methylations change the physicochemical properties of amide bonds to provide structural constraints and other favorable characteristics including biological membrane permeability to peptides. Borosin natural product pathways are the only known ribosomally encoded and posttranslationally modified peptides (RiPPs) pathways to incorporate backbone α-N-methylations on translated peptides. Here we report the discovery of type IV borosin natural product pathways (termed ‘split borosins’), featuring an iteratively acting α-N-methyltransferase and separate precursor peptide substrate from the metal-respiring bacterium Shewanella oneidensis. A series of enzyme-precursor complexes reveal multiple conformational states for both α-N-methyltransferase and substrate. Along with mutational and kinetic analyses, our results give rare context into potential strategies for iterative maturation of RiPPs.

scholarly journals Diverse Protein Architectures and α-N-Methylation Patterns Define Split Borosin RiPP Biosynthetic Gene Clusters

2021 ◽  
Author(s):  
Aman S. Imani ◽  
Aileen R. Lee ◽  
Nisha Vishwanathan ◽  
Floris de Waal ◽  
Michael F. Freeman
Keyword(s):  
Markov Models ◽  
Sequence Similarity ◽  
Shewanella Oneidensis ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Peptide Backbone ◽  
Reading Frame ◽  
Type Iv ◽  
Modified Peptides

Borosins are ribosomally synthesized and post-translationally modified peptides (RiPPs) with α-N-methylations installed on the peptide backbone that impart unique properties like proteolytic stability to these natural products. The borosin RiPP family was initially reported only in fungi until our recent discovery and characterization of a Type IV split borosin system in the metal-respiring bacterium Shewanella oneidensis. Here, we used hidden Markov models and sequence similarity networks to identify over 1,600 putative pathways that show split borosin biosynthetic gene clusters are widespread in bacteria. Noteworthy differences in precursor and α-N-methyltransferase open reading frame sizes, architectures, and core peptide properties allow further subdivision of the borosin family into six additional discrete structural types, of which five have been validated in this study.

scholarly journals Global Genome Mining Reveals the Distribution of Diverse Thioamidated RiPP Biosynthesis Gene Clusters

2021 ◽  
Vol 12 ◽  
Author(s):  
Jessie James Limlingan Malit ◽  
Chuanhai Wu ◽  
Ling-Li Liu ◽  
Pei-Yuan Qian
Keyword(s):  
Protein Pair ◽  
Genome Mining ◽  
Gene Clusters ◽  
Cytotoxic Activities ◽  
Related Gene ◽  
Peptide Backbone ◽  
Precursor Peptide ◽  
Wide Range ◽  
Biosynthesis Gene ◽  
Modified Peptides

Thioamidated ribosomally synthesized and post-translationally modified peptides (RiPPs) are recently characterized natural products with wide range of potent bioactivities, such as antibiotic, antiproliferative, and cytotoxic activities. These peptides are distinguished by the presence of thioamide bonds in the peptide backbone catalyzed by the YcaO-TfuA protein pair with its genes adjacent to each other. Genome mining has facilitated an in silico approach to identify biosynthesis gene clusters (BGCs) responsible for thioamidated RiPP production. In this work, publicly available genomic data was used to detect and illustrate the diversity of putative BGCs encoding for thioamidated RiPPs. AntiSMASH and RiPPER analysis identified 613 unique TfuA-related gene cluster families (GCFs) and 797 precursor peptide families, even on phyla where the presence of these clusters have not been previously described. Several additional biosynthesis genes are colocalized with the detected BGCs, suggesting an array of possible chemical modifications. This study shows that thioamidated RiPPs occupy a widely unexplored chemical landscape.

scholarly journals Structure Prediction and Synthesis of a New Class of Macrocyclic Peptide Natural Products

2020 ◽  
Author(s):  
graham a hudson ◽  
Annie R. Hooper ◽  
Adam J. DiCaprio ◽  
David Sarlah ◽  
Douglas Mitchell
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Structure Prediction ◽  
Gene Clusters ◽  
Leader Peptide ◽  
Biosynthetic Gene Clusters ◽  
New Class ◽  
Precursor Peptide ◽  
Modified Peptides ◽  
Subsequent Elimination

<p>Owing to advances in genomic sequencing and bioinformatics, the breadth of natural product biosynthetic gene clusters (BGCs) has meteorically risen. This remains true for ribosomally synthesized and post-translationally modified peptides (RiPPs), where the rate of bioinformatically identifying clusters vastly outpaces characterization efforts. Uniting bioinformatics and enzymological knowledge to predict the chemical product(s) of a RiPP BGC with total chemical synthesis to obtain the natural compound is an effective platform for investigating cryptic gene clusters. Herein, we report the bioinformatic identification of a biosynthetically divergent class of RiPP bearing a subset of enzymes involved in thiopeptide biosynthesis. These natural products were predicted based on BGC architecture to undergo a formal, enzymatic [4+2]-cycloaddition with subsequent elimination of the leader peptide and water to produce a tri-substituted pyridine-based macrocycle. Bearing a pyridine similar to thiopeptides but lacking the ubiquitous thiazole heterocycles, these new RiPPs were termed pyritides. One of the predicted natural products was chemically synthesized using an 11-step synthesis. This structure was verified to be chemically identical by an orthogonal chemoenzymatic synthesis utilizing the precursor peptide and the cognate [4+2]-cycloaddition enzyme. The chemoenzymatic platform was used to synthesize a second in-cluster pyritide product as well as analogs from other bioinformatically identified pyritide BGCs. This work exemplifies complementary bioinformatic, enzymological, and synthetic techniques to characterize a structurally distinct class of RiPP natural product.</p>

scholarly journals Structure Prediction and Synthesis of a New Class of Macrocyclic Peptide Natural Products

2020 ◽  
Author(s):  
graham a hudson ◽  
Annie R. Hooper ◽  
Adam J. DiCaprio ◽  
David Sarlah ◽  
Douglas Mitchell
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Structure Prediction ◽  
Gene Clusters ◽  
Leader Peptide ◽  
Biosynthetic Gene Clusters ◽  
New Class ◽  
Precursor Peptide ◽  
Modified Peptides ◽  
Subsequent Elimination

<p>Owing to advances in genomic sequencing and bioinformatics, the breadth of natural product biosynthetic gene clusters (BGCs) has meteorically risen. This remains true for ribosomally synthesized and post-translationally modified peptides (RiPPs), where the rate of bioinformatically identifying clusters vastly outpaces characterization efforts. Uniting bioinformatics and enzymological knowledge to predict the chemical product(s) of a RiPP BGC with total chemical synthesis to obtain the natural compound is an effective platform for investigating cryptic gene clusters. Herein, we report the bioinformatic identification of a biosynthetically divergent class of RiPP bearing a subset of enzymes involved in thiopeptide biosynthesis. These natural products were predicted based on BGC architecture to undergo a formal, enzymatic [4+2]-cycloaddition with subsequent elimination of the leader peptide and water to produce a tri-substituted pyridine-based macrocycle. Bearing a pyridine similar to thiopeptides but lacking the ubiquitous thiazole heterocycles, these new RiPPs were termed pyritides. One of the predicted natural products was chemically synthesized using an 11-step synthesis. This structure was verified to be chemically identical by an orthogonal chemoenzymatic synthesis utilizing the precursor peptide and the cognate [4+2]-cycloaddition enzyme. The chemoenzymatic platform was used to synthesize a second in-cluster pyritide product as well as analogs from other bioinformatically identified pyritide BGCs. This work exemplifies complementary bioinformatic, enzymological, and synthetic techniques to characterize a structurally distinct class of RiPP natural product.</p>

Engineering “Antimicrobial Peptides” and Other Peptides to Modulate Protein-Protein Interactions in Cancer

2020 ◽  
Vol 20 (32) ◽  
pp. 2970-2983
Author(s):  
Samuel J.S. Rubin ◽  
Nir Qvit
Keyword(s):  
Antimicrobial Peptides ◽  
Protein Interactions ◽  
Anticancer Agents ◽  
Cancer Therapeutics ◽  
Target Cells ◽  
Protein Protein Interactions ◽  
Peptide Backbone ◽  
Modified Peptides ◽  
Selective Death ◽  
Drug Leads

Antimicrobial peptides (AMPs) are a class of peptides found across a wide array of organisms that play key roles in host defense. AMPs induce selective death in target cells and orchestrate specific or nonspecific immune responses. Many AMPs exhibit native anticancer activity in addition to antibacterial activity, and others have been engineered as antineoplastic agents. We discuss the use of AMPs in the detection and treatment of cancer as well as mechanisms of AMP-induced cell death. We present key examples of cathelicidins and transferrins, which are major AMP families. Further, we discuss the critical roles of protein-protein interactions (PPIs) in cancer and how AMPs are well-suited to target PPIs based on their unique drug-like properties not exhibited by small molecules or antibodies. While peptides, including AMPs, can have limited stability and bioavailability, these issues can be overcome by peptide backbone modification or cyclization (e.g., stapling) and by the use of delivery systems such as cellpenetrating peptides (CPPs), respectively. We discuss approaches for optimizing drug properties of peptide and peptidomimetic leads (modified peptides), providing examples of promising techniques that may be applied to AMPs. These molecules represent an exciting resource as anticancer agents with unique therapeutic advantages that can target challenging mechanisms involving PPIs. Indeed, AMPs are suitable drug leads for further development of cancer therapeutics, and many studies to this end are underway.

Peptide Modifications: Versatile Tools in Peptide and Natural Product Syntheses

Synlett ◽  
2019 ◽  
Vol 30 (11) ◽  
pp. 1289-1302 ◽  
Author(s):  
Phil Servatius ◽  
Lukas Junk ◽  
Uli Kazmaier
Keyword(s):  
Amino Acids ◽  
Natural Product ◽  
Bond Activation ◽  
Bond Formation ◽  
Side Chain ◽  
Peptide Backbone ◽  
Claisen Rearrangements ◽  
The Past ◽  
Allylic Alkylations ◽  
Peptide Modifications

Peptide modifications via C–C bond formation have emerged as valuable tools for the preparation and alteration of non-proteinogenic amino acids and the corresponding peptides. Modification of glycine subunits in peptides allows for the incorporation of unusual side chains, often in a highly stereoselective manner, orchestrated by the chiral peptide backbone. Moreover, modifications of peptides are not limited to the peptidic backbone. Many side-chain modifications, not only by variation of existing functional groups, but also by C–H functionalization, have been developed over the past decade. This account highlights the synthetic contributions made by our group and others to the field of peptide modifications and their application in natural product syntheses.1 Introduction2 Peptide Backbone Modifications via Peptide Enolates2.1 Chelate Enolate Claisen Rearrangements2.2 Allylic Alkylations2.3 Miscellaneous Modifications3 Side-Chain Modifications3.1 C–H Activation3.1.1 Functionalization via Csp3–H Bond Activation3.2.2 Functionalization via Csp2–H Bond Activation3.2 On Peptide Tryptophan Syntheses4 Conclusion

Distorting Malaria Peptide Backbone Structure to Enable Fitting into MHC Class II Molecules Renders Modified Peptides Immunogenic and Protective

2003 ◽  
Vol 46 (11) ◽  
pp. 2250-2253 ◽  
Author(s):  
Gladys Cifuentes ◽  
Manuel Elkin Patarroyo ◽  
Mauricio Urquiza ◽  
Luis E. Ramirez ◽  
Claudia Reyes ◽  
...  
Keyword(s):  
Mhc Class Ii ◽  
Class Ii ◽  
Peptide Backbone ◽  
Modified Peptides ◽  
Backbone Structure ◽  
Mhc Class Ii Molecules

scholarly journals High-resolution structure of a type IV pilin from the metal-reducing bacterium Shewanella oneidensis

2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Manuela Gorgel ◽  
Jakob Jensen Ulstrup ◽  
Andreas Bøggild ◽  
Nykola C Jones ◽  
Søren V Hoffmann ◽  
...  
Keyword(s):  
High Resolution ◽  
Shewanella Oneidensis ◽  
Type Iv ◽  
High Resolution Structure ◽  
Type Iv Pilin ◽  
Resolution Structure

scholarly journals Understanding Thioamitide Biosynthesis Using Pathway Engineering and Untargeted Metabolomics

2020 ◽  
Author(s):  
Tom H. Eyles ◽  
Natalia M. Vior ◽  
Rodney Lacret ◽  
Andrew W. Truman
Keyword(s):  
Biosynthetic Pathway ◽  
Gene Clusters ◽  
Untargeted Metabolomics ◽  
Pathway Engineering ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Heterologous Host ◽  
Detailed Understanding ◽  
Precursor Peptide ◽  
Modified Peptides

ABSTRACTThiostreptamide S4 is a thioamitide, a family of promising antitumour ribosomally synthesised and post-translationally modified peptides (RiPPs). The thioamitides are one of the most structurally complex RiPP families, yet very few thioamitide biosynthetic steps have been elucidated, even though the gene clusters of multiple thioamitides have been identified. We hypothesised that engineering the thiostreptamide S4 gene cluster in a heterologous host could provide insights into its biosynthesis when coupled with untargeted metabolomics and targeted mutations of the precursor peptide. Modified gene clusters were constructed, and in-depth metabolomics enabled a detailed understanding of the biosynthetic pathway, including the identification of an effector-like protein critical for amino acid dehydration. We use this biosynthetic understanding to bioinformatically identify new widespread families of RiPP biosynthetic gene clusters, paving the way for future RiPP discovery and engineering.

scholarly journals Biosynthesis and secretion of the microbial sulfated peptide RaxX and binding to the rice XA21 immune receptor

2019 ◽  
Vol 116 (17) ◽  
pp. 8525-8534 ◽  
Author(s):  
Dee Dee Luu ◽  
Anna Joe ◽  
Yan Chen ◽  
Katarzyna Parys ◽  
Ofir Bahar ◽  
...  
Keyword(s):  
Immune Response ◽  
Biological Process ◽  
Peptide Hormone ◽  
Xanthomonas Oryzae ◽  
Targeted Proteomics ◽  
Mature Peptide ◽  
Immune Receptor ◽  
High Affinity ◽  
Precursor Peptide ◽  
Modified Peptides

The rice immune receptor XA21 is activated by the sulfated microbial peptide required for activation of XA21-mediated immunity X (RaxX) produced byXanthomonas oryzaepv.oryzae(Xoo). Mutational studies and targeted proteomics revealed that the RaxX precursor peptide (proRaxX) is processed and secreted by the protease/transporter RaxB, the function of which can be partially fulfilled by a noncognate peptidase-containing transporter component B (PctB). proRaxX is cleaved at a Gly–Gly motif, yielding a mature peptide that retains the necessary elements for RaxX function as an immunogen and host peptide hormone mimic. These results indicate that RaxX is a prokaryotic member of a previously unclassified and understudied group of eukaryotic tyrosine sulfated ribosomally synthesized, posttranslationally modified peptides (RiPPs). We further demonstrate that sulfated RaxX directly binds XA21 with high affinity. This work reveals a complete, previously uncharacterized biological process: bacterial RiPP biosynthesis, secretion, binding to a eukaryotic receptor, and triggering of a robust host immune response.

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