A ribosomally synthesized and post-translationally modified peptide containing a β-amino acid and a macrocyclic motif

Abstract Ribosomally synthesized and post-translationally modified peptides (RiPPs) are structurally complex naturally occurring metabolites across all three domains of life. Despite the structural diversity of RiPPs that stems from the extensive post-translational modifications, only α-amino acid residues have been found in known RiPPs. Here we report discovery of a new 27-mer peptide, kintamdin, using comprehensive MS and NMR structural elucidation and genomic analysis together with computational modelling. The peptide features a β-amino acid residue and a new thioether macrocyclic ring. Heterologous expression and gene inactivation allowed the identification of the minimal biosynthetic gene cluster (BGC). The gene products in kin BGC share low homologues compared to other known RiPP pathways, further rendering the novelty of kintamdin. Biochemical analysis indicated that KinO mediate di-methylation reaction to yield kintamidn. Finally, the occurrence of the kin-like BGCs in Gram-positive bacteria suggested the biological importance of this new group of RiPPs.

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MAPRes: Mining association patterns among preferred amino acid residues in the vicinity of amino acids targeted for post-translational modifications

PROTEOMICS ◽

10.1002/pmic.200700657 ◽

2008 ◽

Vol 8 (10) ◽

pp. 1954-1958 ◽

Cited By ~ 6

Author(s):

Ishtiaq Ahmad ◽

Wajahat M. Qazi ◽

Ahmed Khurshid ◽

Munir Ahmad ◽

Daniel C. Hoessli ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Amino Acid Residues ◽

Association Patterns ◽

Post Translational Modifications

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Characterization of the Ohmyungsamycin Biosynthetic Pathway and Generation of Derivatives with Improved Antituberculosis Activity

Biomolecules ◽

10.3390/biom9110672 ◽

2019 ◽

Vol 9 (11) ◽

pp. 672 ◽

Cited By ~ 5

Author(s):

Eunji Kim ◽

Yern-Hyerk Shin ◽

Tae Ho Kim ◽

Woong Sub Byun ◽

Jinsheng Cui ◽

...

Keyword(s):

Amino Acid ◽

Draft Genome ◽

Biosynthetic Gene Cluster ◽

Antituberculosis Activity ◽

Amino Acid Residues ◽

Acid Modification ◽

Streptomyces Sp ◽

P450 Gene ◽

Draft Genome Sequencing

The cyclic depsipeptides ohmyungsamycin (OMS) A (1) and B (2), isolated from the marine-derived Streptomyces sp. SNJ042, contain two non-proteinogenic amino acid residues, β-hydroxy-l-phenylalanine (β-hydroxy-l-Phe) and 4-methoxy-l-tryptophan (4-methoxy-l-Trp). Draft genome sequencing of Streptomyces sp. SNJ042 revealed the OMS biosynthetic gene cluster consisting of a nonribosomal peptide synthetase (NRPS) gene and three genes for amino acid modification. By gene inactivation and analysis of the accumulated products, we found that OhmL, encoding a P450 gene, is an l-Phe β-hydroxylase. Furthermore, OhmK, encoding a Trp 2,3-dioxygenase homolog, and OhmJ, encoding an O-methyltransferase, are suggested to be involved in hydroxylation and O-methylation reactions, respectively, in the biosynthesis of 4-methoxy-l-Trp. In addition, the antiproliferative and antituberculosis activities of the OMS derivatives dehydroxy-OMS A (4) and demethoxy-OMS A (6) obtained from the mutant strains were evaluated in vitro. Interestingly, dehydroxy-OMS A (4) displayed significantly improved antituberculosis activity and decreased cytotoxicity compared to wild-type OMS A.

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Discovery of Gene Cluster for Mycosporine-Like Amino Acid Biosynthesis from Actinomycetales Microorganisms and Production of a Novel Mycosporine-Like Amino Acid by Heterologous Expression

Applied and Environmental Microbiology ◽

10.1128/aem.00727-14 ◽

2014 ◽

Vol 80 (16) ◽

pp. 5028-5036 ◽

Cited By ~ 39

Author(s):

Kiyoko T. Miyamoto ◽

Mamoru Komatsu ◽

Haruo Ikeda

Keyword(s):

Amino Acid ◽

Gene Cluster ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Dependent Manner ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Gram Positive ◽

Content Type ◽

Gram Positive Bacteria

ABSTRACTMycosporines and mycosporine-like amino acids (MAAs), including shinorine (mycosporine-glycine-serine) and porphyra-334 (mycosporine-glycine-threonine), are UV-absorbing compounds produced by cyanobacteria, fungi, and marine micro- and macroalgae. These MAAs have the ability to protect these organisms from damage by environmental UV radiation. Although no reports have described the production of MAAs and the corresponding genes involved in MAA biosynthesis from Gram-positive bacteria to date, genome mining of the Gram-positive bacterial database revealed that two microorganisms belonging to the orderActinomycetales,Actinosynnema mirumDSM 43827 andPseudonocardiasp. strain P1, possess a gene cluster homologous to the biosynthetic gene clusters identified from cyanobacteria. When the two strains were grown in liquid culture,Pseudonocardiasp. accumulated a very small amount of MAA-like compound in a medium-dependent manner, whereasA. mirumdid not produce MAAs under any culture conditions, indicating that the biosynthetic gene cluster ofA. mirumwas in a cryptic state in this microorganism. In order to characterize these biosynthetic gene clusters, each biosynthetic gene cluster was heterologously expressed in an engineered host,Streptomyces avermitilisSUKA22. Since the resultant transformants carrying the entire biosynthetic gene cluster controlled by an alternative promoter produced mainly shinorine, this is the first confirmation of a biosynthetic gene cluster for MAA from Gram-positive bacteria. Furthermore,S. avermitilisSUKA22 transformants carrying the biosynthetic gene cluster for MAA ofA. mirumaccumulated not only shinorine and porphyra-334 but also a novel MAA. Structure elucidation revealed that the novel MAA is mycosporine-glycine-alanine, which substitutesl-alanine for thel-serine of shinorine.

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Biosynthesis of the β-Methylarginine Residue of Peptidyl Nucleoside Arginomycin in Streptomyces arginensis NRRL 15941

Applied and Environmental Microbiology ◽

10.1128/aem.01172-14 ◽

2014 ◽

Vol 80 (16) ◽

pp. 5021-5027 ◽

Cited By ~ 11

Author(s):

Jun Feng ◽

Jun Wu ◽

Jie Gao ◽

Zhigui Xia ◽

Zixin Deng ◽

...

Keyword(s):

Amino Acid ◽

Biosynthetic Pathway ◽

Biosynthetic Gene Cluster ◽

Open Reading Frames ◽

Enzymatic Conversion ◽

Content Type ◽

Gram Positive Bacteria ◽

Adenosyl Methionine ◽

Bacteria And Fungi ◽

Reading Frames

ABSTRACTThe peptidyl nucleoside arginomycin is active against Gram-positive bacteria and fungi but displays much lower toxicity to mice than its analog blasticidin S. It features a rare amino acid, β-methylarginine, which is attached to the deoxyhexose moiety via a 4′-aminoacyl bond. We here report cloning of the complete biosynthetic gene cluster for arginomycin fromStreptomyces arginensisNRRL 15941. Among the 14 putative essential open reading frames,argM, encoding an aspartate aminotransferase (AAT), and adjacentargN, encoding anS-adenosyl methionine (SAM)-dependent methyltransferase, are coupled to catalyze arginine and yield β-methylarginine inEscherichia coli. Purified ArgM can transfer the α-amino group ofl-arginine to α-ketoglutaric acid to give glutamate and thereby convertsl-arginine to 5-guanidino-2-oxopentanoic acid, which is methylated at the C-3 position by ArgN to form 5-guanidino-3-methyl-2-oxopentanoic acid. Iteratively, ArgM specifically catalyzes transamination from the donorl-aspartate to the resulting 5-guanidino-3-methyl-2-oxopentanoic acid, generating β-methylarginine. The complete and concise biosynthetic pathway for the rare and bioactive amino acid revealed by this study may pave the way for the production of β-methylarginine either by enzymatic conversion or by engineered living cells.

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Pentaminomycins C–E: Cyclic Pentapeptides as Autophagy Inducers from a Mealworm Beetle Gut Bacterium

Microorganisms ◽

10.3390/microorganisms8091390 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1390 ◽

Cited By ~ 2

Author(s):

Sunghoon Hwang ◽

Ly Thi Huong Luu Le ◽

Shin-Il Jo ◽

Jongheon Shin ◽

Min Jae Lee ◽

...

Keyword(s):

Amino Acid ◽

2D Nmr ◽

Biosynthetic Gene Cluster ◽

Amino Acid Residues ◽

Structural Variations ◽

Nonribosomal Peptide ◽

Peptide Synthetase ◽

Nrps Module ◽

Mealworm Beetle

Pentaminomycins C–E (1–3) were isolated from the culture of the Streptomyces sp. GG23 strain from the guts of the mealworm beetle, Tenebrio molitor. The structures of the pentaminomycins were determined to be cyclic pentapeptides containing a modified amino acid, N5-hydroxyarginine, based on 1D and 2D NMR and mass spectroscopic analyses. The absolute configurations of the amino acid residues were assigned using Marfey’s method and bioinformatics analysis of their nonribosomal peptide biosynthetic gene cluster (BGC). Detailed analysis of the BGC enabled us to propose that the structural variations in 1–3 originate from the low specificity of the adenylation domain in the nonribosomal peptide synthetase (NRPS) module 1, and indicate that macrocyclization can be catalyzed noncanonically by penicillin binding protein (PBP)-type TE. Furthermore, pentaminomycins C and D (1 and 2) showed significant autophagy-inducing activities and were cytoprotective against oxidative stress in vitro.

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Mutagenesis of NosM Leader Peptide Reveals Important Elements in Nosiheptide Biosynthesis

Applied and Environmental Microbiology ◽

10.1128/aem.02880-16 ◽

2016 ◽

Vol 83 (4) ◽

Cited By ~ 3

Author(s):

Liang Jin ◽

Xuri Wu ◽

Yanjiu Xue ◽

Yue Jin ◽

Shuzhen Wang ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Gene Cluster ◽

Genetic Manipulation ◽

Fold Increase ◽

Biosynthetic Gene Cluster ◽

Leader Peptide ◽

Amino Acid Residues ◽

Precursor Peptide

ABSTRACT Nosiheptide, a typical member of the ribosomally synthesized and posttranslationally modified peptides (RiPPs), exhibits potent activity against multidrug-resistant Gram-positive bacterial pathogens. The precursor peptide of nosiheptide (NosM) is comprised of a leader peptide with 37 amino acids and a core peptide containing 13 amino acids. To pinpoint elements in the leader peptide that are essential for nosiheptide biosynthesis, a collection of mutants with unique sequence features, including N- and C-terminal motifs, peptide length, and specific sites in the leader peptide, was generated by mutagenesis in vivo. The effects of various mutants on nosiheptide biosynthesis were evaluated. In addition to the necessity of a conserved motif LEIS box, native length and the N-terminal 12 amino acid residues were indispensable, and single-site substitutions of these 12 amino acid residues resulted in changes ranging from a greater-than-5-fold decrease to a 2-fold increase of nosiheptide production, depending on the sites and substituted residues. Moreover, although the C-terminal motif is not conservative, significant effects of this portion on nosiheptide production were also evident. Taken together, the present results further highlight the importance of the leader peptide in nosiheptide biosynthesis, and provide new insights into the diversity and specificity of leader peptides in the biosynthesis of various RiPPs. IMPORTANCE As a representative thiopeptide, nosiheptide exhibits excellent antibacterial activity. Although the biosynthetic gene cluster and several modification steps have been revealed, the presence and roles of the leader peptide within the precursor peptide of the nosiheptide gene cluster remain elusive. Thus, identification of specific elements in the leader peptide can significantly facilitate the genetic manipulation of the gene cluster for increasing nosiheptide production or generating diverse analogues. Given the complexity of the biosynthetic process, the instability of the leader peptide, and the unavailability of intermediates, cocrystallization of intermediates, leader peptide, and modification enzymes is currently not feasible. Therefore, a mutagenesis approach was used to construct a series of leader peptide mutants to uncover a number of crucial and characteristic elements affecting nosiheptide biosynthesis, which moves a considerable distance toward a thorough understanding of the biosynthetic machinery for thiopeptides.

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Comparison of Predicted Amino Acid Sequences of Allatotropin/Allatostatin Receptors from Solitary to Eusocial Bee Species (Hymenoptera, Apoidea)

Journal of Apicultural Science ◽

10.2478/jas-2019-0021 ◽

2019 ◽

Vol 63 (2) ◽

pp. 267-279

Author(s):

Huipeng Yang ◽

Jie Wu

Keyword(s):

Amino Acid ◽

Juvenile Hormone ◽

Amino Acid Sequences ◽

Amino Acid Residues ◽

Post Translational Modification ◽

Post Translational Modifications ◽

Specific Amino Acid ◽

Hormone Synthesis ◽

Evolution Of Eusociality ◽

Coupling Characteristics

AbstractAn increasingly amount of evidence supports that the evolution of eusociality is accompanies by shifts in ancient molecular and physiological pathways. The juvenile hormone, one of the most important hormones in the post-embryonic development of insects, attracts the most attention in the context of social organization. Allatoregulatory neuropeptides (Allatotropin, Allatostatin-A and Allatostatin-C) are known to regulate juvenile hormone synthesis and release in insects. In order to clarify the transitions of juvenile hormone synthesis involved in eusocial evolution, the substitutions of amino acid residues and the complexity of post-translational modifications in allatoregulatory neuropeptide receptors were characterized. Both allatotropin and allatostatin receptors are identified in all examined bee species regardless if they are solitary or eusocial. Although the amino acid sequences are highly conserved, phylogenetic results are consistent with the eusocial status. The abundance of predicted post-translational modifications correlates with social complexity except for that in allatostatin-C receptors. Even though the consequences of these specific amino acid substitutions and various post-translational modification complexity have not been studied, they likely contribute to the localizing, binding and coupling characteristics of the receptor groups.

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Effects of Modifications on the Immunosuppressive Properties of Cyclolinopeptide A and its Analogs in Animal Experimental Models

10.20944/preprints202103.0500.v1 ◽

2021 ◽

Author(s):

Michał Zimecki ◽

Krzysztof Kaczmarek

Keyword(s):

Amino Acid ◽

Biological Activities ◽

Peptide Bond ◽

Mechanisms Of Action ◽

Experimental Models ◽

Amino Acid Residues ◽

Modified Peptides ◽

Immunosuppressive Potency

The consequences of manipulations in structure and amino acid composition of native cyclolinopeptide A (CLA) from linen seeds and its linear precursor on their biological activities and mechanisms of action are reviewed. The modifications included truncation of the peptide chain, replacement of amino acid residues with proteinogenic or non-proteinogenic ones, modifications of peptide bond, and others. The studies revealed changes in the immunosuppressive potency of these analogs investigated in a number of in vitro and in vivo experimental models, predominantly in rodents, as well as differences in their postulated mechanism of action. The modified peptides were compared with cyclosporine A and parent CLA. Some of the synthesized and investigated peptides show potential therapeutic usefulness.

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Mutually exclusive locales for N-linked glycans and disorder in glycoproteins

10.1101/443143 ◽

2018 ◽

Author(s):

Alvina Singh ◽

Indu Kumari ◽

Dharma Pally ◽

Shyamili Goutham ◽

Sujasha Ghosh ◽

...

Keyword(s):

Amino Acid ◽

Protein Stability ◽

Amino Acid Residue ◽

Tertiary Structure ◽

Amino Acid Residues ◽

Mutual Exclusivity ◽

Post Translational Modifications ◽

Phylogenetic Conservation ◽

And Function ◽

Disordered Regions

AbstractSeveral post-translational modifications of proteins lie within regions of disorder, stretches of amino acid residues that exhibit a dynamic tertiary structure and resist crystallization. Such localization has been proposed to expand the binding versatility of the disordered regions, and hence, the repertoire of interacting partners for the proteins. However, investigating a dataset of 500 human N-linked glycoproteins, we observed that the sites of N-linked glycosylations, or N-glycosites, lay predominantly within the regions of predicted order rather than their unstructured counterparts. This mutual exclusivity between disordered stretches and N-glycosites could not be reconciled merely through asymmetry in distribution of asparagines, serines or threonines residues, which comprise the minimum-required signature for conjugation by N-linked glycans, but rather by a contextual enrichment of these residues next to each other within the ordered portions. In fact, N-glycosite neighborhoods and disordered stretches showed distinct sets of enriched residues suggesting their individualized roles in protein phenotype. N-glycosite neighborhood residues also showed higher phylogenetic conservation than disordered stretches within amniote orthologs of glycoproteins. However, a universal search for residue-combinations that are putatively domain-constitutive ranked the disordered regions higher than the N-glycosite neighborhoods. We propose that amino acid residue-combinations bias the permissivity for N-glycoconjugation within ordered regions, so as to balance the tradeoff between the evolution of protein stability, and function, contributed by the N-linked glycans and disordered regions respectively.

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Structural Analysis and Characterization of Lacticin Q, a Novel Bacteriocin Belonging to a New Family of Unmodified Bacteriocins of Gram-Positive Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.02286-06 ◽

2007 ◽

Vol 73 (9) ◽

pp. 2871-2877 ◽

Cited By ~ 89

Author(s):

Koji Fujita ◽

Shiro Ichimasa ◽

Takeshi Zendo ◽

Shoko Koga ◽

Fuminori Yoneyama ◽

...

Keyword(s):

Amino Acid ◽

Dna Sequences ◽

High Performance ◽

Hypothetical Protein ◽

Exchange Chromatography ◽

Amino Acid Residues ◽

Gram Positive ◽

Gram Positive Bacteria ◽

Methionine Residue ◽

New Family

ABSTRACT Lactococcus lactis QU 5 isolated from corn produces a novel bacteriocin, termed lacticin Q. By acetone precipitation, cation-exchange chromatography, and reverse-phase high-performance liquid chromatography, lacticin Q was purified from the culture supernatant of this organism, and its molecular mass was determined to be 5,926.50 Da by mass spectrometry. Subsequent analyses of amino acid and DNA sequences revealed that lacticin Q comprised 53 amino acid residues and that its N-terminal methionine residue was formylated. In contrast to most bacteriocins produced by gram-positive bacteria, lacticin Q had no N-terminal extensions such as leader or signal sequences. It showed 66% and 48% identity to AucA, a hypothetical protein from Corynebacterium jeikeium plasmid pA501, and aureocin A53, a bacteriocin from Staphylococcus aureus A53, respectively. The characteristics of lacticin Q were determined and compared to those of nisin A. Similar to nisin A, lacticin Q exhibited antibacterial activity against various gram-positive bacteria. Lacticin Q was very stable against heat treatment and changes in pH; in particular, it was stable at alkaline pH values, while nisin A was inactivated. Moreover, lacticin Q induced ATP efflux from a Listeria sp. strain in a shorter time and at a lower concentration than nisin A, indicating that the former affected indicator cells in a different manner from that of the latter. The results described here clarified the fact that lacticin Q belongs to a new family of class II bacteriocins and that it can be employed as an alternative to or in combination with nisin A.

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