The anti-staphylococcal lipolanthines are ribosomally synthesized lipopeptides

Wiebach, Vincent; Mainz, Andi; Siegert, Mary‐Ann J.; Jungmann, Natalia A.; Lesquame, Guillaume; Tirat, Sophie; Dreux-Zigha, Assia; Aszodi, J.; Beller, Dominique Le; Süssmuth, Roderich D.

doi:10.1038/s41589-018-0068-6

Cited by 103 publications

(154 citation statements)

References 33 publications

Supporting

Mentioning

141

Contrasting

Unclassified

Order By: Relevance

“…For example, some class I, II, and III lanthipeptide BGCs contain a YcaO family protein (PF02624), members of which catalyze modification to the amide backbone [63]. Moreover, a number of BGCs for all four classes of lanthipeptides encode polyketide or fatty acid biosynthetic machinery, as in the recently reported class III lipolanthine [56], or non-ribosomal peptide biosynthetic machinery. Enzymes from other families, such as radical SAM (PF04055), cytochrome P450 (PF00067), and ketoglutarate-dependent oxygenases (PF03171), are present in lanthipeptide BGCs and may catalyze the installation of additional secondary modifications.…”

Section: Resultsmentioning

confidence: 98%

“…Enzymes that are among the most abundant in one class of lanthipeptide BGCs are generally also present in the other classes, if at lower abundance ( Supplementary Table S10 and Figure S8, Additional File 1). For example, flavoprotein family enzymes, which have been shown to catalyze oxidative decarboxylation of the C-terminus of some lanthipeptides (LanDs) [53][54][55][56][57], halogenation of amino acid side chains [55], and oxidation of the sulfur in lanthionine crosslinks [58], are among the most abundant enzymes in class I BGCs but are present in class II and III BGCs as well. Likewise, NAD(P)Hdependent FMN reductase family enzymes, such as those that catalyze the reduction of dehydro amino acid side chains to form D-amino acid residues (LanJ B s) [59,60], are among the most common tailoring enzymes in class II BGCs and are present in class I and III BGCs.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family

Walker

Mitchell

Donk

2020

Preprint

View full text Add to dashboard Cite

BackgroundLanthipeptides belong to the ribosomally synthesized and post-translationally modified peptide group of natural products and have a variety of biological activities ranging from antibiotics to antinociceptives. These peptides are cyclized through thioether crosslinks and can bear other secondary post-translational modifications. While lanthipeptide biosynthetic gene clusters can be identified by the presence of characteristic enzymes involved in the post-translational modification of these peptides, locating the precursor peptides encoded within these clusters is challenging due to their short length and high sequence variability, which limits the high-throughput exploration of lanthipeptide precursor peptides. To address this challenge, we enhanced the predictive capabilities of Rapid ORF Description & Evaluation Online (RODEO) to identify all known classes of lanthipeptides. ResultsUsing RODEO, we mined over 100,000 bacterial and archaeal genomes in the RefSeq database. We identified nearly 8,500 lanthipeptide precursor peptides. These precursor peptides were identified in a broad range of bacterial phyla as well as the Euryarchaeota phylum of archaea. Bacteroidetes were found to encode a large number of these biosynthetic gene clusters, despite making up a relatively small portion of the genomes in this dataset. While a number of these precursor peptides are similar to those of previously characterized lanthipeptides, even more were not, including potential antibiotics. Additionally, examination of the biosynthetic gene clusters revealed enzymes that install secondary post-translational modifications are more widespread than initially thought. ConclusionLanthipeptide biosynthetic gene clusters are more widely distributed and the precursor peptides encoded within these clusters are more diverse than previously appreciated, demonstrating that the lanthipeptide sequence-function space remains largely underexplored.

show abstract

Section: Resultsmentioning

confidence: 98%

Section: Resultsmentioning

confidence: 99%

Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family

Walker

Mitchell

Donk

2020

Preprint

View full text Add to dashboard Cite

show abstract

“…6). 34 . The study presented here renews great interest in flavoproteins, as their catalytic mechanisms have not been fully appreciated in various biochemical processes, particularly those involving additional non-redox reactions [35][36][37] .…”

Section: Resultsmentioning

confidence: 99%

LanD-like Flavoprotein-Catalyzed Aminovinyl-Cysteine Formation through Oxidative Decarboxylation and Cyclization of a Peptide at the C-Terminus

Liu

Qiu

et al. 2020

Preprint

View full text Add to dashboard Cite

Aminovinyl-cysteine residues arise from processing the C-terminal L-Cys and an internal L-Ser/L-Thr or L-Cys of a peptide. Formation of these nonproteinogenic amino acids, which occur in a macrocyclic ring of diverse ribosomally synthesized lanthipeptides and non-lanthipeptides, remains poorly understood. Here, we report that LanD-like flavoproteins in the biosynthesis of distinct non-lanthipeptides share an unexpected dual activity for aminovinylcysteine formation. Each flavoprotein catalyzes oxidative decarboxylation of the C-terminal L-Cys and couples the resulting enethiol nucleophile with the internal residue to afford a thioether linkage for peptide cyclization. The cyclization step, which largely depends on proximity effect by positioning the enethiol intermediate with a bent conformation at the active site, can be substrate-dependent, proceeding inefficiently through nucleophilic substitution for an unmodified peptide or efficiently through Michael addition for a dehydrated/dethiolated peptide. Uncovering this unusual flavin-dependent paradigm for thioether residue formation advances the understanding in the biosynthesis of aminovinyl-cysteine-containing RiPPs and renews interest in flavoproteins, particularly those involved in non-redox transformations. LanD-like flavoproteins activity, which is flexible in peptide substrate and amenable for evolution by engineering, can be combined with different post-translational modifications for structural diversity, thereby holding promise for peptide macrocyclization/functionalization in drug development by chemoenzymatic or synthetic biology approaches.

show abstract

“…B. das antibakterielle Nisin oder das antivirale Labyrinthopeptin . Das gemeinsame Strukturmerkmal ist der post‐translationale Aufbau der Thioether‐enthaltenden Aminosäuren (Methyl)lanthionin ((Me)Lan), (Methyl)labionin ((Me)Lab) und das kürzlich gefundene Avionin (Avi, Abbildung a) . Die Lanthipeptide können zudem, aufgrund ihrer modifizierenden Enzyme, in vier Klassen unterteilt werden .…”

Section: Introductionunclassified

Eine amphipathische alpha‐Helix lenkt die Modifizierung ribosomal‐synthetisierter Lipolanthine

et al. 2020

Self Cite

View full text Add to dashboard Cite

Die stark anti‐Gram‐positiven Lipolanthine repräsentieren eine neue Gruppe von lipidierten, ribosomal synthetisierten und post‐translational modifizierten Peptiden (RiPPS). Sie sind bicyclische Octapeptide mit einem zentralen quaternären Kohlenstoffatom in der Aminosäure Avionin, die durch die Klasse‐III Lanthipeptidsynthetase MicKC und die Cystein‐Decarboxylase MicD synthetisiert werden. Genome‐Mining eröffnete eine weit gefächerte und unerwartete biosynthetische Diversität an Lipolanthin‐Genclustern, die Elemente der RiPP‐, Polyketid‐ und der nicht‐ribosomalen Peptidbiosynthese kombiniert. Durch NMR‐Spektroskopie konnten wir zeigen, dass ein (θxx)θxxθxxθ (θ=L, I, V, M oder T)‐Motiv, das konserviert im Leader‐Peptid der Klasse‐III und ‐IV Lanthipeptide vorliegt, eine amphipatische α‐Helix in MicA bildet. Dies hat einen Einfluss auf die enzymatische Prozessierung des Peptidsubstrats. Unsere Ergebnisse liefern allgemeine Regeln für die Substratauswahl und die enzymatische Regulation während der Lipolanthin‐Reifung. Diese Erkenntnisse werden zukünftige Untersuchungen hinsichtlich der Konstruktion neuer Lanthipeptid‐Grundgerüste mit antibakteriellem Potential erleichtern.

show abstract

The anti-staphylococcal lipolanthines are ribosomally synthesized lipopeptides

Cited by 103 publications

References 33 publications

Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family

Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family

LanD-like Flavoprotein-Catalyzed Aminovinyl-Cysteine Formation through Oxidative Decarboxylation and Cyclization of a Peptide at the C-Terminus

Eine amphipathische alpha‐Helix lenkt die Modifizierung ribosomal‐synthetisierter Lipolanthine

Contact Info

Product

Resources

About