Articoli di riviste: "Ribosomally synthesized and post-Translationally modified peptides"

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Jeanne Dit Fouque, K., H. Lavanant, S. Zirah, J. D. Hegemann, C. D. Fage, M. A. Marahiel, S. Rebuffat e C. Afonso. "General rules of fragmentation evidencing lasso structures in CID and ETD". Analyst 143, n. 5 (2018): 1157–70. http://dx.doi.org/10.1039/c7an02052j.

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Lasso peptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by a mechanically interlocked structure in which the C-terminal tail of the peptide is threaded and trapped within an N-terminal macrolactam ring.

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Ma, Suze, e Qi Zhang. "Linaridin natural products". Natural Product Reports 37, n. 9 (2020): 1152–63. http://dx.doi.org/10.1039/c9np00074g.

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Linaridins, defined as linear, dehydrated (arid) peptides, are a small but growing family of natural products belonging to the ribosomally synthesized and post-translationally modified peptide (RiPP) superfamily.

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Jimenez, Elsie C. "Bromotryptophan and its Analogs in Peptides from Marine Animals". Protein & Peptide Letters 26, n. 4 (28 marzo 2019): 251–60. http://dx.doi.org/10.2174/0929866526666190119170020.

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Bromotryptophan is a nonstandard amino acid that is rarely incorporated in ribosomally synthesized and post-translationally modified peptides (ribosomal peptides). Bromotryptophan and its analogs sometimes occur in non-ribosomal peptides. This paper presents an overview of ribosomal and non-ribosomal peptides that are known to contain bromotryptophan and its analogs. This work further covers the biological activities and therapeutic potential of some of these peptides.

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Sikandar, Asfandyar, e Jesko Koehnke. "The role of protein–protein interactions in the biosynthesis of ribosomally synthesized and post-translationally modified peptides". Natural Product Reports 36, n. 11 (2019): 1576–88. http://dx.doi.org/10.1039/c8np00064f.

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Ruijne, Fleur, e Oscar P. Kuipers. "Combinatorial biosynthesis for the generation of new-to-nature peptide antimicrobials". Biochemical Society Transactions 49, n. 1 (13 gennaio 2021): 203–15. http://dx.doi.org/10.1042/bst20200425.

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Abstract (sommario):

Natural peptide products are a valuable source of important therapeutic agents, including antibiotics, antivirals and crop protection agents. Aided by an increased understanding of structure–activity relationships of these complex molecules and the biosynthetic machineries that produce them, it has become possible to re-engineer complete machineries and biosynthetic pathways to create novel products with improved pharmacological properties or modified structures to combat antimicrobial resistance. In this review, we will address the progress that has been made using non-ribosomally produced peptides and ribosomally synthesized and post-translationally modified peptides as scaffolds for designed biosynthetic pathways or combinatorial synthesis for the creation of novel peptide antimicrobials.

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Zhang, Dan, Yu He, Yang Ye, Yanni Ma, Peng Zhang, Hongxia Zhu, Ningzhi Xu e Shufang Liang. "Little Antimicrobial Peptides with Big Therapeutic Roles". Protein & Peptide Letters 26, n. 8 (11 settembre 2019): 564–78. http://dx.doi.org/10.2174/1573406415666190222141905.

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Antimicrobial Peptides (AMPs) are short amphipathic biological molecules generally with less than 100 amino acids. AMPs not only present high bioactivities against bacteria, fungi or protists-induced infections, but also play important roles in anticancer activity, immune response and inflammation regulation. AMPs are classified as ribosomally synthesized, non-ribosomally synthesized and post-translationally modified, non-ribosomally synthesized ones and several synthetic or semisynthetic peptides according to their synthesis with or without the involvement of ribosomes. The molecular characterization and bioactivity action mechanisms are summarized for several ribosomally synthesized AMPs and main non-ribosomally synthesized members (cyclopeptides, lipopeptides, glycopeptides, lipoglycopeptides). We also analyze challenges and new strategies to overcome drug resistance and application limitations for AMP discovery. In conclusion, the growing novel small molecular AMPs have huge therapeutic potentials of antibacterial, antiviral, anticancer and immunoregulatory bioactivities through new techniquesdriven drug discovery strategy including bioinformatics prediction, de novo rational design and biosynthesis.

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Rowe, Sam M., e David R. Spring. "The role of chemical synthesis in developing RiPP antibiotics". Chemical Society Reviews 50, n. 7 (2021): 4245–58. http://dx.doi.org/10.1039/d0cs01386b.

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This tutorial review discusses the potential of ribosomally synthesised and post-translationally modified peptides (RiPPs) as antimicrobials and looks at the chemical synthesis of three classes of RiPP: lasso peptides, cyclotides, and lanthipeptides.

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Fu, Yuxin, Ate H. Jaarsma e Oscar P. Kuipers. "Antiviral activities and applications of ribosomally synthesized and post-translationally modified peptides (RiPPs)". Cellular and Molecular Life Sciences 78, n. 8 (2 febbraio 2021): 3921–40. http://dx.doi.org/10.1007/s00018-021-03759-0.

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AbstractThe emergence and re-emergence of viral epidemics and the risks of antiviral drug resistance are a serious threat to global public health. New options to supplement or replace currently used drugs for antiviral therapy are urgently needed. The research in the field of ribosomally synthesized and post-translationally modified peptides (RiPPs) has been booming in the last few decades, in particular in view of their strong antimicrobial activities and high stability. The RiPPs with antiviral activity, especially those against enveloped viruses, are now also gaining more interest. RiPPs have a number of advantages over small molecule drugs in terms of specificity and affinity for targets, and over protein-based drugs in terms of cellular penetrability, stability and size. Moreover, the great engineering potential of RiPPs provides an efficient way to optimize them as potent antiviral drugs candidates. These intrinsic advantages underscore the good therapeutic prospects of RiPPs in viral treatment. With the aim to highlight the underrated antiviral potential of RiPPs and explore their development as antiviral drugs, we review the current literature describing the antiviral activities and mechanisms of action of RiPPs, discussing the ongoing efforts to improve their antiviral potential and demonstrate their suitability as antiviral therapeutics. We propose that antiviral RiPPs may overcome the limits of peptide-based antiviral therapy, providing an innovative option for the treatment of viral disease.

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Han, Sang-Woo, e Hyung-Sik Won. "Advancements in the Application of Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs)". Biomolecules 14, n. 4 (15 aprile 2024): 479. http://dx.doi.org/10.3390/biom14040479.

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Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a significant potential for novel therapeutic applications because of their bioactive properties, stability, and specificity. RiPPs are synthesized on ribosomes, followed by intricate post-translational modifications (PTMs), crucial for their diverse structures and functions. PTMs, such as cyclization, methylation, and proteolysis, play crucial roles in enhancing RiPP stability and bioactivity. Advances in synthetic biology and bioinformatics have significantly advanced the field, introducing new methods for RiPP production and engineering. These methods encompass strategies for heterologous expression, genetic refactoring, and exploiting the substrate tolerance of tailoring enzymes to create novel RiPP analogs with improved or entirely new functions. Furthermore, the introduction and implementation of cutting-edge screening methods, including mRNA display, surface display, and two-hybrid systems, have expedited the identification of RiPPs with significant pharmaceutical potential. This comprehensive review not only discusses the current advancements in RiPP research but also the promising opportunities that leveraging these bioactive peptides for therapeutic applications presents, illustrating the synergy between traditional biochemistry and contemporary synthetic biology and genetic engineering approaches.

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Gordon, Catriona H., Emily Hendrix, Yi He e Mark C. Walker. "AlphaFold Accurately Predicts the Structure of Ribosomally Synthesized and Post-Translationally Modified Peptide Biosynthetic Enzymes". Biomolecules 13, n. 8 (12 agosto 2023): 1243. http://dx.doi.org/10.3390/biom13081243.

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Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing class of natural products biosynthesized from a genetically encoded precursor peptide. The enzymes that install the post-translational modifications on these peptides have the potential to be useful catalysts in the production of natural-product-like compounds and can install non-proteogenic amino acids in peptides and proteins. However, engineering these enzymes has been somewhat limited, due in part to limited structural information on enzymes in the same families that nonetheless exhibit different substrate selectivities. Despite AlphaFold2’s superior performance in single-chain protein structure prediction, its multimer version lacks accuracy and requires high-end GPUs, which are not typically available to most research groups. Additionally, the default parameters of AlphaFold2 may not be optimal for predicting complex structures like RiPP biosynthetic enzymes, due to their dynamic binding and substrate-modifying mechanisms. This study assessed the efficacy of the structure prediction program ColabFold (a variant of AlphaFold2) in modeling RiPP biosynthetic enzymes in both monomeric and dimeric forms. After extensive benchmarking, it was found that there were no statistically significant differences in the accuracy of the predicted structures, regardless of the various possible prediction parameters that were examined, and that with the default parameters, ColabFold was able to produce accurate models. We then generated additional structural predictions for select RiPP biosynthetic enzymes from multiple protein families and biosynthetic pathways. Our findings can serve as a reference for future enzyme engineering complemented by AlphaFold-related tools.

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Tan, Stephanie, Gaelen Moore e Justin Nodwell. "Put a Bow on It: Knotted Antibiotics Take Center Stage". Antibiotics 8, n. 3 (11 agosto 2019): 117. http://dx.doi.org/10.3390/antibiotics8030117.

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Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large class of natural products produced across all domains of life. The lasso peptides, a subclass of RiPPs with a lasso-like structure, are structurally and functionally unique compared to other known peptide antibiotics in that the linear peptide is literally “tied in a knot” during its post-translational maturation. This underexplored class of peptides brings chemical diversity and unique modes of action to the antibiotic space. To date, eight different lasso peptides have been shown to target three known molecular machines: RNA polymerase, the lipid II precursor in peptidoglycan biosynthesis, and the ClpC1 subunit of the Clp protease involved in protein homeostasis. Here, we discuss the current knowledge on lasso peptide biosynthesis as well as their antibiotic activity, molecular targets, and mechanisms of action.

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Russell, Alicia H., e Andrew W. Truman. "Genome mining strategies for ribosomally synthesised and post-translationally modified peptides". Computational and Structural Biotechnology Journal 18 (2020): 1838–51. http://dx.doi.org/10.1016/j.csbj.2020.06.032.

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Schröder, Maria-Paula, Isabel P.-M. Pfeiffer e Silja Mordhorst. "Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry". Beilstein Journal of Organic Chemistry 20 (18 luglio 2024): 1652–70. http://dx.doi.org/10.3762/bjoc.20.147.

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This review article aims to highlight the role of methyltransferases within the context of ribosomally synthesised and post-translationally modified peptide (RiPP) natural products. Methyltransferases play a pivotal role in the biosynthesis of diverse natural products with unique chemical structures and bioactivities. They are highly chemo-, regio-, and stereoselective allowing methylation at various positions. The different possible acceptor regions in ribosomally synthesised peptides are described in this article. Furthermore, we will discuss the potential application of these methyltransferases as powerful biocatalytic tools in the synthesis of modified peptides and other bioactive compounds. By providing an overview of the various methylation options available, this review is intended to emphasise the biocatalytic potential of RiPP methyltransferases and their impact on the field of natural product chemistry.

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Sánchez-Hidalgo, Marina, Jesús Martín e Olga Genilloud. "Identification and Heterologous Expression of the Biosynthetic Gene Cluster Encoding the Lasso Peptide Humidimycin, a Caspofungin Activity Potentiator". Antibiotics 9, n. 2 (7 febbraio 2020): 67. http://dx.doi.org/10.3390/antibiotics9020067.

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Humidimycin (MDN-0010) is a ribosomally synthesized and post-translationally modified peptide (RiPP) belonging to class I lasso peptides, and is structurally related to siamycins, which have been shown to have strong antimicrobial activities against Gram-positive bacteria and to possess anti-HIV activity. Humidimycin was isolated from the strain Streptomyces humidus CA-100629, and was shown to synergize the activity of the fungal cell wall inhibitor caspofungin. In this work, the biosynthetic gene cluster of humidimycin was identified by genome mining of S. humidus CA-100629, cloned by Gibson assembly, and heterologously expressed.

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Letzel, Anne-Catrin, Sacha J. Pidot e Christian Hertweck. "Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in anaerobic bacteria". BMC Genomics 15, n. 1 (2014): 983. http://dx.doi.org/10.1186/1471-2164-15-983.

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Hug, Joachim J., Jan Dastbaz, Sebastian Adam, Ole Revermann, Jesko Koehnke, Daniel Krug e Rolf Müller. "Biosynthesis of Cittilins, Unusual Ribosomally Synthesized and Post-translationally Modified Peptides from Myxococcus xanthus". ACS Chemical Biology 15, n. 8 (8 luglio 2020): 2221–31. http://dx.doi.org/10.1021/acschembio.0c00430.

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Luo e Dong. "Recent Advances in the Discovery and Biosynthetic Study of Eukaryotic RiPP Natural Products". Molecules 24, n. 8 (18 aprile 2019): 1541. http://dx.doi.org/10.3390/molecules24081541.

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Abstract (sommario):

Natural products have played indispensable roles in drug development and biomedical research. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a group of fast-expanding natural products attribute to genome mining efforts in recent years. Most RiPP natural products were discovered from bacteria, yet many eukaryotic cyclic peptides turned out to be of RiPP origin. This review article presents recent advances in the discovery of eukaryotic RiPP natural products, the elucidation of their biosynthetic pathways, and the molecular basis for their biosynthetic enzyme catalysis.

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Hubrich, Florian, Alessandro Lotti, Thomas A. Scott e Jörn Piel. "Uncovering Novel Peptide Chemistry from Bacterial Natural Products". CHIMIA International Journal for Chemistry 75, n. 6 (30 giugno 2021): 543–47. http://dx.doi.org/10.2533/chimia.2021.543.

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Nature has evolved a remarkable array of biosynthetic enzymes that install diverse chemistries into natural products (NPs), bestowing them with a range of important biological properties that are of considerable therapeutic value. This is epitomized by the ribosomally synthesized and post-translationally modified peptides (RiPPs), a class of peptide natural products that undergo extensive post-translational modifications to produce structurally diverse bioactive peptides. In this review, we provide an overview of our research into the proteusin RiPP family, describing characterized members and the maturation enzymes responsible for their unique chemical structures and biological activities. The diverse enzymology identified in the first two proteusin pathways highlights the enormous potential of the RiPP class for new lead structures and novel pharmacophore-installing maturases as biocatalytic tools for drug discovery efforts.

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Zhong, Zheng, Beibei He, Jie Li e Yong-Xin Li. "Challenges and advances in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs)". Synthetic and Systems Biotechnology 5, n. 3 (settembre 2020): 155–72. http://dx.doi.org/10.1016/j.synbio.2020.06.002.

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Truman, Andrew W. "Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides". Beilstein Journal of Organic Chemistry 12 (20 giugno 2016): 1250–68. http://dx.doi.org/10.3762/bjoc.12.120.

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Abstract (sommario):

Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a large class of natural products that are remarkably chemically diverse given an intrinsic requirement to be assembled from proteinogenic amino acids. The vast chemical space occupied by RiPPs means that they possess a wide variety of biological activities, and the class includes antibiotics, co-factors, signalling molecules, anticancer and anti-HIV compounds, and toxins. A considerable amount of RiPP chemical diversity is generated from cyclisation reactions, and the current mechanistic understanding of these reactions will be discussed here. These cyclisations involve a diverse array of chemical reactions, including 1,4-nucleophilic additions, [4 + 2] cycloadditions, ATP-dependent heterocyclisation to form thiazolines or oxazolines, and radical-mediated reactions between unactivated carbons. Future prospects for RiPP pathway discovery and characterisation will also be highlighted.

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Teber, Rabeb, e Shuichi Asakawa. "In Silico Screening of Bacteriocin Gene Clusters within a Set of Marine Bacillota Genomes". International Journal of Molecular Sciences 25, n. 5 (22 febbraio 2024): 2566. http://dx.doi.org/10.3390/ijms25052566.

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Due to their potential application as an alternative to antibiotics, bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by bacteria, have received much attention in recent years. To identify bacteriocins within marine bacteria, most of the studies employed a culture-based method, which is more time-consuming than the in silico approach. For that, the aim of this study was to identify potential bacteriocin gene clusters and their potential producers in 51 marine Bacillota (formerly Firmicutes) genomes, using BAGEL4, a bacteriocin genome mining tool. As a result, we found out that a majority of selected Bacillota (60.78%) are potential bacteriocin producers, and we identified 77 bacteriocin gene clusters, most of which belong to class I bacteriocins known as RiPPs (ribosomally synthesized and post-translationally modified peptides). The identified putative bacteriocin gene clusters are an attractive target for further in vitro research, such as the production of bacteriocins using a heterologous expression system.

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Glassey, Emerson, Andrew M. King, Daniel A. Anderson, Zhengan Zhang e Christopher A. Voigt. "Functional expression of diverse post-translational peptide-modifying enzymes in Escherichia coli under uniform expression and purification conditions". PLOS ONE 17, n. 9 (19 settembre 2022): e0266488. http://dx.doi.org/10.1371/journal.pone.0266488.

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RiPPs (ribosomally-synthesized and post-translationally modified peptides) are a class of pharmaceutically-relevant natural products expressed as precursor peptides before being enzymatically processed into their final functional forms. Bioinformatic methods have illuminated hundreds of thousands of RiPP enzymes in sequence databases and the number of characterized chemical modifications is growing rapidly; however, it remains difficult to functionally express them in a heterologous host. One challenge is peptide stability, which we addressed by designing a RiPP stabilization tag (RST) based on a small ubiquitin-like modifier (SUMO) domain that can be fused to the N- or C-terminus of the precursor peptide and proteolytically removed after modification. This is demonstrated to stabilize expression of eight RiPPs representative of diverse phyla. Further, using Escherichia coli for heterologous expression, we identify a common set of media and growth conditions where 24 modifying enzymes, representative of diverse chemistries, are functional. The high success rate and broad applicability of this system facilitates: (i) RiPP discovery through high-throughput “mining” and (ii) artificial combination of enzymes from different pathways to create a desired peptide.

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Sukmarini, Linda. "Marine Bacterial Ribosomal Peptides: Recent Genomics- and Synthetic Biology-Based Discoveries and Biosynthetic Studies". Marine Drugs 20, n. 9 (24 agosto 2022): 544. http://dx.doi.org/10.3390/md20090544.

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Marine biodiversity is represented by an exceptional and ample array of intriguing natural product chemistries. Due to their extensive post-translational modifications, ribosomal peptides—also known as ribosomally synthesized and post-translationally modified peptides (RiPPs)—exemplify a widely diverse class of natural products, endowing a broad range of pharmaceutically and biotechnologically relevant properties for therapeutic or industrial applications. Most RiPPs are of bacterial origin, yet their marine derivatives have been quite rarely investigated. Given the rapid advancement engaged in a more powerful genomics approach, more biosynthetic gene clusters and pathways for these ribosomal peptides continue to be increasingly characterized. Moreover, the genome-mining approach in integration with synthetic biology techniques has markedly led to a revolution of RiPP natural product discovery. Therefore, this present short review article focuses on the recent discovery of RiPPs from marine bacteria based on genome mining and synthetic biology approaches during the past decade. Their biosynthetic studies are discussed herein, particularly the organization of targeted biosynthetic gene clusters linked to the encoded RiPPs with potential bioactivities.

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Hwang, Hyeon-Jeong, Youngsang Nam, Chanhee Jang, Eun La Kim, Eun Seo Jang, Yeo Jin Lee e Seoung Rak Lee. "Anticancer Ribosomally Synthesized and Post-Translationally Modified Peptides from Plants: Structures, Therapeutic Potential, and Future Directions". Current Issues in Molecular Biology 47, n. 1 (26 dicembre 2024): 6. https://doi.org/10.3390/cimb47010006.

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Cancer remains a significant medical challenge, necessitating the discovery of novel therapeutic agents. Ribosomally synthesized and post-translationally modified peptides (RiPPs) from plants have emerged as a promising source of anticancer compounds, offering unique structural diversity and potent biological activity. This review identifies and discusses cytotoxic RiPPs across various plant families, focusing on their absolute chemical structures and reported cytotoxic activities against cancer cell lines. Notably, plant-derived RiPPs such as rubipodanin A and mallotumides A–C demonstrated low nanomolar IC50 values against multiple cancer cell types, highlighting their therapeutic potential. By integrating traditional ethnobotanical knowledge with modern genomic and bioinformatic approaches, this study underscores the importance of plant RiPPs as a resource for developing innovative cancer treatments. These findings pave the way for further exploration of plant RiPPs, emphasizing their role in addressing the ongoing challenges in oncology and enhancing the repertoire of effective anticancer therapies.

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do Amaral, Samuel Cavalcante, Patrick Romano Monteiro, Joaquim da Silva Pinto Neto, Gustavo Marques Serra, Evonnildo Costa Gonçalves, Luciana Pereira Xavier e Agenor Valadares Santos. "Current Knowledge on Microviridin from Cyanobacteria". Marine Drugs 19, n. 1 (4 gennaio 2021): 17. http://dx.doi.org/10.3390/md19010017.

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Cyanobacteria are a rich source of secondary metabolites with a vast biotechnological potential. These compounds have intrigued the scientific community due their uniqueness and diversity, which is guaranteed by a rich enzymatic apparatus. The ribosomally synthesized and post-translationally modified peptides (RiPPs) are among the most promising metabolite groups derived from cyanobacteria. They are interested in numerous biological and ecological processes, many of which are entirely unknown. Microviridins are among the most recognized class of ribosomal peptides formed by cyanobacteria. These oligopeptides are potent inhibitors of protease; thus, they can be used for drug development and the control of mosquitoes. They also play a key ecological role in the defense of cyanobacteria against microcrustaceans. The purpose of this review is to systematically identify the key characteristics of microviridins, including its chemical structure and biosynthesis, as well as its biotechnological and ecological significance.

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Wang, Wei, S. Cyrus Khojasteh e Dian Su. "Biosynthetic Strategies for Macrocyclic Peptides". Molecules 26, n. 11 (1 giugno 2021): 3338. http://dx.doi.org/10.3390/molecules26113338.

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Macrocyclic peptides are predominantly peptide structures bearing one or more rings and spanning multiple amino acid residues. Macrocyclization has become a common approach for improving the pharmacological properties and bioactivity of peptides. A variety of ribosomal-derived and non-ribosomal synthesized cyclization approaches have been established. The biosynthesis of backbone macrocyclic peptides using seven new emerging methodologies will be discussed with regard to the features and strengths of each platform rather than medicinal chemistry tools. The mRNA display variant, known as the random nonstandard peptide integrated discovery (RaPID) platform, utilizes flexible in vitro translation (FIT) to access macrocyclic peptides containing nonproteinogenic amino acids (NAAs). As a new discovery approach, the ribosomally synthesized and post-translationally modified peptides (RiPPs) method involves the combination of ribosomal synthesis and the phage screening platform together with macrocyclization chemistries to generate libraries of macrocyclic peptides. Meanwhile, the split-intein circular ligation of peptides and proteins (SICLOPPS) approach relies on the in vivo production of macrocyclic peptides. In vitro and in vivo peptide library screening is discussed as an advanced strategy for cyclic peptide selection. Specifically, biosynthetic bicyclic peptides are highlighted as versatile and attractive modalities. Bicyclic peptides represent another type of promising therapeutics that allow for building blocks with a heterotrimeric conjugate to address intractable challenges and enable multimer complexes via linkers. Additionally, we discuss the cell-free chemoenzymatic synthesis of macrocyclic peptides with a non-ribosomal catalase known as the non-ribosomal synthetase (NRPS) and chemo-enzymatic approach, with recombinant thioesterase (TE) domains. Novel insights into the use of peptide library tools, activity-based two-hybrid screening, structure diversification, inclusion of NAAs, combinatorial libraries, expanding the toolbox for macrocyclic peptides, bicyclic peptides, chemoenzymatic strategies, and future perspectives are presented. This review highlights the broad spectrum of strategy classes, novel platforms, structure diversity, chemical space, and functionalities of macrocyclic peptides enabled by emerging biosynthetic platforms to achieve bioactivity and for therapeutic purposes.

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Wu, Chunyu, e Wilfred A. van der Donk. "Engineering of new-to-nature ribosomally synthesized and post-translationally modified peptide natural products". Current Opinion in Biotechnology 69 (giugno 2021): 221–31. http://dx.doi.org/10.1016/j.copbio.2020.12.022.

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Hetrick, Kenton J., e Wilfred A. van der Donk. "Ribosomally synthesized and post-translationally modified peptide natural product discovery in the genomic era". Current Opinion in Chemical Biology 38 (giugno 2017): 36–44. http://dx.doi.org/10.1016/j.cbpa.2017.02.005.

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Miranda, Kevin Jace, Saif Jaber, Dana Atoum, Subha Arjunan, Rainer Ebel, Marcel Jaspars e RuAngelie Edrada-Ebel. "Pseudomonassin, a New Bioactive Ribosomally Synthesised and Post-Translationally Modified Peptide from Pseudomonas sp. SST3". Microorganisms 11, n. 10 (15 ottobre 2023): 2563. http://dx.doi.org/10.3390/microorganisms11102563.

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Abstract (sommario):

Genome mining and metabolomics have become valuable tools in natural products research to evaluate and identify potential new chemistry from bacteria. In the search for new compounds from the deep-sea organism, Pseudomonas sp. SST3, from the South Shetland Trough, Antarctica, a co-cultivation with a second deep-sea Pseudomonas zhaodongensis SST2, was undertaken to isolate pseudomonassin, a ribosomally synthesised and post-translationally modified peptide (RiPP) that belongs to a class of RiPP called lasso peptides. Pseudomonassin was identified using a genome-mining approach and isolated by means of mass spectrometric guided isolation. Extensive metabolomics analysis of the co-cultivation of Pseudomonas sp. SST3 and P. zhaodongensis SST2, Pseudomonas sp. SST3 and Escherichia coli, and P. zhaodongensis SST2 and E. coli were performed using principal component analysis (PCA) and orthogonal projections to latent structures discriminant analysis (OPLS-DA), which revealed potential new metabolites in the outlier regions of the co-cultivation, with other metabolites identified previously from other species of Pseudomonas. The sequence of pseudomonassin was completely deduced using high collision dissociation tandem mass spectrometry (HCD-MS/MS). Preliminary studies on its activity against the pathogenic P. aeruginosa and its biofilm formation have been assessed and produced a minimum inhibitory concentration (MIC) of 63 μg/mL and 28 μg/mL, respectively.

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Kriger, Draco, Michael A. Pasquale, Brigitte G. Ampolini e Jonathan R. Chekan. "Mining raw plant transcriptomic data for new cyclopeptide alkaloids". Beilstein Journal of Organic Chemistry 20 (11 luglio 2024): 1548–59. http://dx.doi.org/10.3762/bjoc.20.138.

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In recent years, genome and transcriptome mining have dramatically expanded the rate of discovering diverse natural products from bacteria and fungi. In plants, this approach is often more limited due to the lack of available annotated genomes and transcriptomes combined with a less consistent clustering of biosynthetic genes. The recently identified burpitide class of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products offer a valuable opportunity for bioinformatics-guided discovery in plants due to their short biosynthetic pathways and gene encoded substrates. Using a high-throughput approach to assemble and analyze 700 publicly available raw transcriptomic data sets, we uncover the potential distribution of split burpitide precursor peptides in Streptophyta. Metabolomic analysis of target plants confirms our bioinformatic predictions of new cyclopeptide alkaloids from both known and new sources.

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Nettoor Veettil, Vajid, e Vijaya Chitra. "LANTIBIOTICS OF MILK ISOLATES: A SHORT REVIEW ON CHARACTERIZATION AND POTENTIAL APPLICATIONS". Journal of microbiology, biotechnology and food sciences 11, n. 4 (1 febbraio 2022): e3702. http://dx.doi.org/10.55251/jmbfs.3702.

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Milk, due to its high nutritional content, is an excellent medium for supporting growth of diverse group of microorganisms, many of which produce beneficial compounds like bacteriocins. Class I bacteriocins, called lantibiotics, are ribosomally synthesized, post-translationally modified peptides containing unusual amino acids, such as dehydrated and lanthionine residues with antibacterial activities. Bacterial strains isolated from milk and dairy products produce a range of lantibiotics which can employed for development of food preservatives, flavor enhancers and as alternate treatment strategies for multi drug resistant bacterial pathogens. The diverse category of lantibiotics from milk isolates include well characterized prototypes like nisin to newer peptides yet to be studied. In this review, details of most prominent lantibiotics obtained from milk isolates have been presented with special focus on applications of these lantibiotics in therapeutics and food.

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Vries, Reinder H., Jakob H. Viel, Ruben Oudshoorn, Oscar P. Kuipers e Gerard Roelfes. "Selective Modification of Ribosomally Synthesized and Post‐Translationally Modified Peptides (RiPPs) through Diels–Alder Cycloadditions on Dehydroalanine Residues". Chemistry – A European Journal 25, n. 55 (9 settembre 2019): 12698–702. http://dx.doi.org/10.1002/chem.201902907.

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33

Bartholomae, Maike, Andrius Buivydas, Jakob H. Viel, Manuel Montalbán-López e Oscar P. Kuipers. "Major gene-regulatory mechanisms operating in ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthesis". Molecular Microbiology 106, n. 2 (5 settembre 2017): 186–206. http://dx.doi.org/10.1111/mmi.13764.

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Stafford, Jillian L., Veronica K. Montoya, Jeffrey J. Bierman e Mark C. Walker. "Assessing the Impact of the Leader Peptide in Protease Inhibition by the Microviridin Family of RiPPs". Biomedicines 12, n. 12 (18 dicembre 2024): 2873. https://doi.org/10.3390/biomedicines12122873.

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Abstract (sommario):

Background: Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing class of natural products biosynthesized from a genetically encoded precursor peptide. RiPPs have attracted attention for the ability to generate and screen libraries of these compounds for useful biological activities. To facilitate this screening, it is useful to be able to do so with the leader peptide still present. We assessed the suitability of the microviridin family for these screening experiments by determining their activity with the leader peptide still present. Methods: Modified precursor peptides with the leader present were heterologously expressed in Escherichia coli. Their ability to inhibit elastase was tested with a fluorogenic substrate. HPLC was used to monitor degradation of the modified precursor peptides by elastase. SDS-PAGE was used to determine the ability of immobilized modified precursor peptide to pull down elastase. Results: We found that the fully modified precursor peptide of microviridin B can inhibit the serine protease elastase with a low nanomolar IC50, and that the fully modified precursor with an N-terminal His-tag can mediate interactions between elastase and Ni-NTA resin, all indicating leader peptide removal is not necessary for microviridins to bind their target proteases. Additionally, we found that a bicyclic variant was able to inhibit elastase with the leader peptide still present, although with a roughly 100-fold higher IC50 and being subject to hydrolysis by elastase. Conclusions: These results open a pathway to screening libraries of microviridin variants for improved protease inhibition or other characteristics that can serve as, or as inspirations for, new pharmaceuticals.

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Hug, Joachim J., Nicolas A. Frank, Christine Walt, Petra Šenica, Fabian Panter e Rolf Müller. "Genome-Guided Discovery of the First Myxobacterial Biarylitide Myxarylin Reveals Distinct C–N Biaryl Crosslinking in RiPP Biosynthesis". Molecules 26, n. 24 (10 dicembre 2021): 7483. http://dx.doi.org/10.3390/molecules26247483.

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Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a structurally diverse group of natural products. They feature a wide range of intriguing post-translational modifications, as exemplified by the biarylitides. These are a family of cyclic tripeptides found in Planomonospora, carrying a biaryl linkage between two aromatic amino acids. Recent genomic analyses revealed that the minimal biosynthetic prerequisite of biarylitide biosynthesis consists of only one ribosomally synthesized pentapeptide precursor as the substrate and a modifying cytochrome-P450-dependent enzyme. In silico analyses revealed that minimal biarylitide RiPP clusters are widespread among natural product producers across phylogenetic borders, including myxobacteria. We report here the genome-guided discovery of the first myxobacterial biarylitide MeYLH, termed Myxarylin, from Pyxidicoccus fallax An d48. Myxarylin was found to be an N-methylated tripeptide that surprisingly exhibits a C–N biaryl crosslink. In contrast to Myxarylin, previously isolated biarylitides are N-acetylated tripeptides that feature a C–C biaryl crosslink. Furthermore, the formation of Myxarylin was confirmed by the heterologous expression of the identified biosynthetic genes in Myxococcus xanthus DK1622. These findings expand the structural and biosynthetic scope of biarylitide-type RiPPs and emphasize the distinct biochemistry found in the myxobacterial realm.

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Hu, Gang-Ao, Yue Song, Shi-Yi Liu, Wen-Chao Yu, Yan-Lei Yu, Jian-Wei Chen, Hong Wang e Bin Wei. "Exploring the Diversity and Specificity of Secondary Biosynthetic Potential in Rhodococcus". Marine Drugs 22, n. 9 (6 settembre 2024): 409. http://dx.doi.org/10.3390/md22090409.

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The actinomycete genus Rhodococcus is known for its diverse biosynthetic enzymes, with potential in pollutant degradation, chemical biocatalysis, and natural product exploration. Comparative genomics have analyzed the distribution patterns of non-ribosomal peptide synthetases (NRPSs) in Rhodococcus. The diversity and specificity of its secondary metabolism offer valuable insights for exploring natural products, yet remain understudied. In the present study, we analyzed the distribution patterns of biosynthetic gene clusters (BGCs) in the most comprehensive Rhodococcus genome data to date. The results show that 86.5% of the gene cluster families (GCFs) are only distributed in a specific phylogenomic-clade of Rhodococcus, with the most predominant types of gene clusters being NRPS and ribosomally synthesized and post-translationally modified peptides (RiPPs). In-depth mining of RiPP gene clusters revealed that Rhodococcus encodes many clade-specific novel RiPPs, with thirteen core peptides showing antibacterial potential. High-throughput elicitor screening (HiTES) and non-targeted metabolomics revealed that a marine-derived Rhodococcus strain produces a large number of new aurachin-like compounds when exposed to specific elicitors. The present study highlights the diversity and specificity of secondary biosynthetic potential in Rhodococcus, and provides valuable information for the targeted exploration of novel natural products from Rhodococcus, especially for phylogenomic-clade-specific metabolites.

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Xu, Kuang, Sijia Guo, Wei Zhang, Zixin Deng, Qi Zhang e Wei Ding. "Genome Mining and Biological Engineering of Type III Borosins from Bacteria". International Journal of Molecular Sciences 25, n. 17 (29 agosto 2024): 9350. http://dx.doi.org/10.3390/ijms25179350.

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Borosins are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) with α-N-methylated backbones. Although the first mature compound of borosin was reported in 1997, the biosynthetic pathway was elucidated 20 years later. Until this work, borosins have been able to be categorized into 11 types based on the features of their protein structure and core peptides. Type III borosins were reported only in fungi initially. In order to explore the sources and potential of type III borosins, a precise genome mining work of type III borosins was conducted in bacteria and KchMA’s self-methylation activity was validated by biochemical experiment. Furthermore, a commercial protease and AI-assisted rational design was employed to engineer KchMA for the capacity to produce various N-methylated peptides. Our work demonstrates that type III borosins are abundant not only in eukaryotes but also in bacteria and have immense potential as a tool for synthetic biology.

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Yang, Xiao, e Wilfred A. van der Donk. "Ribosomally Synthesized and Post-Translationally Modified Peptide Natural Products: New Insights into the Role of Leader and Core Peptides during Biosynthesis". Chemistry - A European Journal 19, n. 24 (10 maggio 2013): 7662–77. http://dx.doi.org/10.1002/chem.201300401.

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Huo, Liujie, Xiling Zhao, Jeella Z. Acedo, Paola Estrada, Satish K. Nair e Wilfred A. Donk. "Characterization of a Dehydratase and Methyltransferase in the Biosynthesis of Ribosomally Synthesized and Post‐translationally Modified Peptides in Lachnospiraceae". ChemBioChem 21, n. 1-2 (4 novembre 2019): 190–99. http://dx.doi.org/10.1002/cbic.201900483.

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40

Lethbridge, Benjamin J., Robert E. Asenstorfer, Laura S. Bailey, Brenda T. Breil, Jodie V. Johnson, Graham P. Jones, Victor Rumjanek, James J. Sims, Max E. Tate e Eric W. Triplett. "Post translational modifications of Trifolitoxin: a blue fluorescent peptide antibiotic". Journal of Antibiotics 75, n. 3 (12 gennaio 2022): 125–35. http://dx.doi.org/10.1038/s41429-021-00497-0.

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Abstract (sommario):

AbstractTrifolitoxin (TFX, C41H63N15O15S) is a selective, ribosomally-synthesized, post-translationally modified, peptide antibiotic, produced by Rhizobium leguminosarum bv. trifolii T24. TFX specifically inhibits α-proteobacteria, including the plant symbiont Rhizobium spp., the plant pathogen Agrobacterium spp. and the animal pathogen Brucella abortus. TFX-producing strains prevent legume root nodulation by TFX-sensitive rhizobia. TFX has been isolated as a pair of geometric isomers, TFX1 and TFX2, which are derived from the biologically inactive primary amino acid sequence: Asp-Ile-Gly-Gly-Ser-Arg-Gln-Gly-Cys-Val-Ala. Gly-Cys is present as a thiazoline ring and the Arg-Gln-Gly sequence is extensively modified to a UV absorbing, blue fluorescent chromophore. The chromophore consists of a conjugated, 5-membered heterocyclic ring and side chain of modified glutamine.

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41

Arnison, Paul G., Mervyn J. Bibb, Gabriele Bierbaum, Albert A. Bowers, Tim S. Bugni, Grzegorz Bulaj, Julio A. Camarero et al. "Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature". Nat. Prod. Rep. 30, n. 1 (2013): 108–60. http://dx.doi.org/10.1039/c2np20085f.

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42

Ortega, Manuel A., e Wilfred A. van der Donk. "New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products". Cell Chemical Biology 23, n. 1 (gennaio 2016): 31–44. http://dx.doi.org/10.1016/j.chembiol.2015.11.012.

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43

Adam, Sebastian, Andreas Klein, Frank Surup e Jesko Koehnke. "The structure of CgnJ, a domain of unknown function protein from the crocagin gene cluster". Acta Crystallographica Section F Structural Biology Communications 75, n. 3 (21 febbraio 2019): 205–11. http://dx.doi.org/10.1107/s2053230x19000712.

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Natural products often contain interesting new chemical entities that are introduced into the structure of a compound by the enzymatic machinery of the producing organism. The recently described crocagins are novel polycyclic peptides which belong to the class of ribosomally synthesized and post-translationally modified peptide natural products. They have been shown to bind to the conserved prokaryotic carbon-storage regulator Ain vitro. In efforts to understand crocagin biosynthesis, the putative biosynthetic genes were expressed and purified. Here, the first crystal structure of a protein from the crocagin-biosynthetic gene cluster, CgnJ, a domain of unknown function protein, is reported. Possible functions of this protein were explored by structural and sequence homology analyses. Even though the sequence homology to proteins in the Protein Data Bank is low, the protein shows significant structural homology to a protein with known function within the competency system ofBacillus subtilis, ComJ, leading to the hypothesis of a similar role of the protein within the producing organism.

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Roblero-Mejía, Dora Onely, Carlos García-Ausencio, Romina Rodríguez-Sanoja, Fernando Guzmán-Chávez e Sergio Sánchez. "Embleporicin: A Novel Class I Lanthipeptide from the Actinobacteria Embleya sp. NF3". Antibiotics 13, n. 12 (5 dicembre 2024): 1179. https://doi.org/10.3390/antibiotics13121179.

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Genome mining has emerged as a revolutionary tool for discovering new ribosomally synthesized and post-translationally modified peptides (RiPPs) in various genomes. Recently, these approaches have been used to detect and explore unique environments as sources of RiPP-producing microorganisms, particularly focusing on endophytic microorganisms found in medicinal plants. Some endophytic actinobacteria, especially strains of Streptomyces, are notable examples of peptide producers, as specific biosynthetic clusters encode them. To uncover the genetic potential of these organisms, we analyzed the genome of the endophytic actinobacterium Embleya sp. NF3 using genome mining and bioinformatics tools. Our analysis led to the identification of a putative class I lanthipeptide. We cloned the core biosynthetic genes of this putative lanthipeptide, named embleporicin, and expressed them in vitro using a cell-free protein system (CFPS). The resulting product demonstrated antimicrobial activity against Micrococcus luteus ATCC 9341. This represents the first RiPP reported in the genus Embleya and the first actinobacterial lanthipeptide produced through cell-free technology.

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Poorinmohammad, Naghmeh, Reyhaneh Bagheban-Shemirani e Javad Hamedi. "Genome mining for ribosomally synthesised and post-translationally modified peptides (RiPPs) reveals undiscovered bioactive potentials of actinobacteria". Antonie van Leeuwenhoek 112, n. 10 (24 maggio 2019): 1477–99. http://dx.doi.org/10.1007/s10482-019-01276-6.

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46

Chekan, Jonathan R., Lisa S. Mydy, Michael A. Pasquale e Roland D. Kersten. "Plant peptides – redefining an area of ribosomally synthesized and post-translationally modified peptides". Natural Product Reports, 2024. http://dx.doi.org/10.1039/d3np00042g.

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Abstract (sommario):

Plant peptide natural products are ribosomally synthesized and post-translationally modified peptides (RiPPs). We review structure, biosynthesis, and bioactivity of plant RiPPs and define burpitides, a recent addition to plant RiPP classes.

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47

Liu, Cheng Li, Zi Jie Wang, Jing Shi, Zhang Yuan Yan, Guo Dong Zhang, Rui Hua Jiao, Ren Xiang Tan e Hui Ming Ge. "P450‐Modified Multicyclic Cyclophane‐Containing Ribosomally Synthesized and Post‐Translationally Modified Peptides". Angewandte Chemie International Edition, 10 dicembre 2023. http://dx.doi.org/10.1002/anie.202314046.

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Abstract (sommario):

Cyclic peptides with cyclophane‐linkers represent an attractive compound type due to the fine‐tuned rigid three‐dimensional structures and unusual biophysical features. Cytochrome P450 enzymes are capable of catalyzing not only the C‐C and C‐O oxidative coupling reactions found in vancomycin and other nonribosomal peptides (NRPs), but they also exhibit novel catalytic activities to generate cyclic ribosomally synthesized and post‐translationally modified peptides (RiPPs) through cyclophane linkage. To discover more P450‐modified multicyclic RiPPs, we set out to find cryptic and unknown P450‐modified RiPP biosynthetic gene clusters (BGCs) through genome mining. Synergized bioinformatic analysis reveals that P450‐modified RiPP BGCs are broadly distributed in bacteria and can be classified into 11 classes. Focusing on two classes of P450‐modified RiPP BGCs where precursor peptides contain multiple conserved aromatic amino acid residues, we characterized 11 novel P450‐modified multicyclic RiPPs with different cyclophane‐linkers through heterologous expression. Further mutation of the key ring‐forming residues and combinatorial biosynthesis study revealed the order of bond formation and the specificity of P450s. This study reveals the functional diversity of P450 enzymes involved in the cyclophane‐containing RiPPs and indicates that P450 enzymes are promising tools for rapidly obtaining structurally diverse cyclic peptide derivatives.

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Liu, Cheng Li, Zi Jie Wang, Jing Shi, Zhang Yuan Yan, Guo Dong Zhang, Rui Hua Jiao, Ren Xiang Tan e Hui Ming Ge. "P450‐Modified Multicyclic Cyclophane‐Containing Ribosomally Synthesized and Post‐Translationally Modified Peptides". Angewandte Chemie, 10 dicembre 2023. http://dx.doi.org/10.1002/ange.202314046.

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Abstract (sommario):

Cyclic peptides with cyclophane‐linkers represent an attractive compound type due to the fine‐tuned rigid three‐dimensional structures and unusual biophysical features. Cytochrome P450 enzymes are capable of catalyzing not only the C‐C and C‐O oxidative coupling reactions found in vancomycin and other nonribosomal peptides (NRPs), but they also exhibit novel catalytic activities to generate cyclic ribosomally synthesized and post‐translationally modified peptides (RiPPs) through cyclophane linkage. To discover more P450‐modified multicyclic RiPPs, we set out to find cryptic and unknown P450‐modified RiPP biosynthetic gene clusters (BGCs) through genome mining. Synergized bioinformatic analysis reveals that P450‐modified RiPP BGCs are broadly distributed in bacteria and can be classified into 11 classes. Focusing on two classes of P450‐modified RiPP BGCs where precursor peptides contain multiple conserved aromatic amino acid residues, we characterized 11 novel P450‐modified multicyclic RiPPs with different cyclophane‐linkers through heterologous expression. Further mutation of the key ring‐forming residues and combinatorial biosynthesis study revealed the order of bond formation and the specificity of P450s. This study reveals the functional diversity of P450 enzymes involved in the cyclophane‐containing RiPPs and indicates that P450 enzymes are promising tools for rapidly obtaining structurally diverse cyclic peptide derivatives.

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49

Mi, Xuenan, Emily Desormeaux, Tung Le, Wilfred A. van der Donk e Diwakar Shukla. "Sequence Controlled Secondary Structure Is Important for the Site-selectivity of Lanthipeptide Cyclization". Chemical Science, 2023. http://dx.doi.org/10.1039/d2sc06546k.

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Abstract (sommario):

Lanthipeptides are ribosomally synthesized and post-translationally modified peptides that are generated from precursor peptides through a dehydration and cyclization process. ProcM, a class II lanthipeptide synthetase, demonstrates high substrate tolerance....

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Saad, Hamada, Thomas Majer, Keshab Bhattarai, Sarah Lampe, Dinh T. Nguyen, Markus Kramer, Jan Straetener, Heike Broetz-Oesterhelt, Douglas A. Mitchell e Harald Gross. "Bioinformatics-Guided Discovery of Biaryl-Linked Lasso Peptides". Chemical Science, 2023. http://dx.doi.org/10.1039/d3sc02380j.

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Abstract (sommario):

Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that feature an isopeptide bond and a distinct lariat fold. A growing number of secondary modifications have...

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