Cyclic Lipopeptide Production by Plant-Associated Pseudomonas spp.: Diversity, Activity, Biosynthesis, and Regulation

Cyclic lipopeptides (CLPs) are versatile molecules produced by a variety of bacterial genera, including plant-associated Pseudomonas spp. CLPs are composed of a fatty acid tail linked to a short oligopeptide, which is cyclized to form a lactone ring between two amino acids in the peptide chain. CLPs are very diverse both structurally and in terms of their biological activity. The structural diversity is due to differences in the length and composition of the fatty acid tail and to variations in the number, type, and configuration of the amino acids in the peptide moiety. CLPs have received considerable attention for their antimicrobial, cytotoxic, and surfactant properties. For plant-pathogenic Pseudomonas spp., CLPs constitute important virulence factors, and pore formation, followed by cell lysis, is their main mode of action. For the antagonistic Pseudomonas sp., CLPs play a key role in antimicrobial activity, motility, and biofilm formation. CLPs are produced via nonribosomal synthesis on large, multifunctional peptide synthetases. Both the structural organization of the CLP synthetic templates and the presence of specific domains and signature sequences within peptide synthetase genes will be described for both pathogenic and antagonistic Pseudomonas spp. Finally, the role of various genes and regulatory mechanisms in CLP production by Pseudomonas spp., including two-component regulation and quorum sensing, will be discussed in detail.

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Aminoacyl chain translocation catalysed by a type II thioesterase domain in an unusual non-ribosomal peptide synthetase

Nature Communications ◽

10.1038/s41467-021-27512-0 ◽

2022 ◽

Vol 13 (1) ◽

Author(s):

Shan Wang ◽

William D. G. Brittain ◽

Qian Zhang ◽

Zhou Lu ◽

Ming Him Tong ◽

...

Keyword(s):

Chain Transfer ◽

Acyl Chain ◽

Structural Diversity ◽

Type Ii ◽

Diverse Range ◽

Translocation Event ◽

Peptide Synthetases ◽

Peptide Synthetase ◽

Biosynthetic Engineering

AbstractNon-Ribosomal Peptide Synthetases (NRPSs) assemble a diverse range of natural products with important applications in both medicine and agriculture. They consist of several multienzyme subunits that must interact with each other in a highly controlled manner to facilitate efficient chain transfer, thus ensuring biosynthetic fidelity. Several mechanisms for chain transfer are known for NRPSs, promoting structural diversity. Herein, we report the first biochemically characterized example of a type II thioesterase (TEII) domain capable of catalysing aminoacyl chain transfer between thiolation (T) domains on two separate NRPS subunits responsible for installation of a dehydrobutyrine moiety. Biochemical dissection of this process reveals the central role of the TEII-catalysed chain translocation event and expands the enzymatic scope of TEII domains beyond canonical (amino)acyl chain hydrolysis. The apparent co-evolution of the TEII domain with the NRPS subunits highlights a unique feature of this enzymatic cassette, which will undoubtedly find utility in biosynthetic engineering efforts.

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Daptomycin biosynthesis in Streptomyces roseosporus: cloning and analysis of the gene cluster and revision of peptide stereochemistry

Microbiology ◽

10.1099/mic.0.27757-0 ◽

2005 ◽

Vol 151 (5) ◽

pp. 1507-1523 ◽

Cited By ~ 217

Author(s):

Vivian Miao ◽

Marie-Françoise Coëffet-LeGal ◽

Paul Brian ◽

Renee Brost ◽

Julia Penn ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Gene Cluster ◽

Binding Pocket ◽

Biosynthetic Gene Cluster ◽

Streptomyces Roseosporus ◽

Cyclic Lipopeptide ◽

Peptide Synthetase ◽

Amino Acid Binding ◽

Condensation Domain

Daptomycin is a 13 amino acid, cyclic lipopeptide produced by a non-ribosomal peptide synthetase (NRPS) mechanism in Streptomyces roseosporus. A 128 kb region of S. roseosporus DNA was cloned and verified by heterologous expression in Streptomyces lividans to contain the daptomycin biosynthetic gene cluster (dpt). The cloned region was completely sequenced and three genes (dptA, dptBC, dptD) encoding the three subunits of an NRPS were identified. The catalytic domains in the subunits, predicted to couple five, six or two amino acids, respectively, included a novel activation domain and amino-acid-binding pocket for incorporating the unusual amino acid l-kynurenine (Kyn), three types of condensation domains and an extra epimerase domain (E-domain) in the second module. Novel genes (dptE, dptF) whose products likely work in conjunction with a unique condensation domain to acylate the first amino acid, as well as other genes (dptI, dptJ) probably involved in supply of the non-proteinogenic amino acids l-3-methylglutamic acid and Kyn, were located next to the NRPS genes. The unexpected E-domain suggested that daptomycin would have d-Asn, rather than l-Asn, as originally assigned, and this was confirmed by comparing stereospecific synthetic peptides and the natural product both chemically and microbiologically.

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Massetolide A Biosynthesis in Pseudomonas fluorescens

Journal of Bacteriology ◽

10.1128/jb.01563-07 ◽

2007 ◽

Vol 190 (8) ◽

pp. 2777-2789 ◽

Cited By ~ 105

Author(s):

I. de Bruijn ◽

M. J. D. de Kock ◽

P. de Waard ◽

T. A. van Beek ◽

J. M. Raaijmakers

Keyword(s):

In Silico Analysis ◽

Gene Clusters ◽

Site Directed Mutagenesis ◽

Pcr Analysis ◽

Exponential Growth Phase ◽

Swarming Motility ◽

Acylhomoserine Lactone ◽

Cyclic Lipopeptide ◽

Peptide Moiety ◽

Peptide Synthetase

ABSTRACT Massetolide A is a cyclic lipopeptide (CLP) antibiotic produced by various Pseudomonas strains from diverse environments. Cloning, sequencing, site-directed mutagenesis, and complementation showed that massetolide A biosynthesis in P. fluorescens SS101 is governed by three nonribosomal peptide synthetase (NRPS) genes, designated massA, massB, and massC, spanning approximately 30 kb. Prediction of the nature and configuration of the amino acids by in silico analysis of adenylation and condensation domains of the NRPSs was consistent with the chemically determined structure of the peptide moiety of massetolide A. Structural analysis of massetolide A derivatives produced by SS101 indicated that most of the variations in the peptide moiety occur at amino acid positions 4 and 9. Regions flanking the mass genes contained several genes found in other Pseudomonas CLP biosynthesis clusters, which encode LuxR-type transcriptional regulators, ABC transporters, and an RND-like outer membrane protein. In contrast to most Pseudomonas CLP gene clusters known to date, the mass genes are not physically linked but are organized in two separate clusters, with massA disconnected from massB and massC. Quantitative real-time PCR analysis indicated that transcription of massC is strongly reduced when massB is mutated, suggesting that these two genes function in an operon, whereas transcription of massA is independent of massBC and vice versa. Massetolide A is produced in the early exponential growth phase, and biosynthesis appears not to be regulated by N-acylhomoserine lactone-based quorum sensing. Massetolide A production is essential in swarming motility of P. fluorescens SS101 and plays an important role in biofilm formation.

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Substrate Specificity of the Nonribosomal Peptide Synthetase PvdD from Pseudomonas aeruginosa

Journal of Bacteriology ◽

10.1128/jb.185.9.2848-2855.2003 ◽

2003 ◽

Vol 185 (9) ◽

pp. 2848-2855 ◽

Cited By ~ 40

Author(s):

David F. Ackerley ◽

Tom T. Caradoc-Davies ◽

Iain L. Lamont

Keyword(s):

Amino Acids ◽

Pseudomonas Aeruginosa ◽

Substrate Specificity ◽

Three Dimensional ◽

Protein Product ◽

Synthetase Activity ◽

Nonribosomal Peptide ◽

Peptide Synthetases ◽

Three Dimensional Modeling ◽

Peptide Synthetase

ABSTRACT Pseudomonas aeruginosa PAO1 secretes a siderophore, pyoverdinePAO, which contains a short peptide attached to a dihydroxyquinoline moiety. Synthesis of this peptide is thought to be catalyzed by nonribosomal peptide synthetases, one of which is encoded by the pvdD gene. The first module of pvdD was overexpressed in Escherichia coli, and the protein product was purified. l-Threonine, one of the amino acid residues in pyoverdinePAO, was an effective substrate for the recombinant protein in ATP-PPi exchange assays, showing that PvdD has peptide synthetase activity. Other amino acids, including d-threonine, l-serine, and l-allo-threonine, were not effective substrates, indicating that PvdD has a high degree of substrate specificity. A three-dimensional modeling approach enabled us to identify amino acids that are likely to be critical in determining the substrate specificity of PvdD and to explore the likely basis of the high substrate selectivity. The approach described here may be useful for analysis of other peptide synthetases.

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Bio-organometallic Peptide Conjugates: Recent Advances in Their Synthesis and Prospects for Biomedical Application

Current Organic Chemistry ◽

10.2174/1385272824666200309093938 ◽

2020 ◽

Vol 24 (21) ◽

pp. 2508-2523

Author(s):

Johana Gómez ◽

Diego Sierra ◽

Constanza Cárdenas ◽

Fanny Guzmán

Keyword(s):

Amino Acids ◽

Biomedical Application ◽

Structural Diversity ◽

Biological Properties ◽

Therapeutic Agents ◽

Organometallic Complexes ◽

Chemical Behavior ◽

Metal Compounds ◽

Bioorganometallic Chemistry ◽

Pharmacological Control

One area of organometallic chemistry that has attracted great interest in recent years is the syntheses, characterization and study of organometallic complexes conjugated to biomolecules with different steric and electronic properties as potential therapeutic agents against cancer and malaria, as antibiotics and as radiopharmaceuticals. This minireview focuses on the unique structural diversity that has recently been discovered in α- amino acids and the reactions of metallocene complexes with peptides having different chemical behavior and potential medical applications. Replacing α-amino acids with metallocene fragments is an effective way of selectively influencing the physicochemical, structural, electrochemical and biological properties of the peptides. Consequently, research in the field of bioorganometallic chemistry offers the opportunity to develop bioactive metal compounds as an innovative and promising approach in the search for pharmacological control of different diseases.

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Meroterpenoids: A Comprehensive Update Insight on Structural Diversity and Biology

Biomolecules ◽

10.3390/biom11070957 ◽

2021 ◽

Vol 11 (7) ◽

pp. 957

Author(s):

Mamona Nazir ◽

Muhammad Saleem ◽

Muhammad Imran Tousif ◽

Muhammad Aijaz Anwar ◽

Frank Surup ◽

...

Keyword(s):

Amino Acids ◽

Secondary Metabolites ◽

Biological Effects ◽

Structural Diversity ◽

Chemical Diversity ◽

Biosynthetic Pathways ◽

Natural Sources ◽

Hybrid Compounds ◽

Anti Inflammatory

Meroterpenoids are secondary metabolites formed due to mixed biosynthetic pathways which are produced in part from a terpenoid co-substrate. These mixed biosynthetically hybrid compounds are widely produced by bacteria, algae, plants, and animals. Notably amazing chemical diversity is generated among meroterpenoids via a combination of terpenoid scaffolds with polyketides, alkaloids, phenols, and amino acids. This review deals with the isolation, chemical diversity, and biological effects of 452 new meroterpenoids reported from natural sources from January 2016 to December 2020. Most of the meroterpenoids possess antimicrobial, cytotoxic, antioxidant, anti-inflammatory, antiviral, enzyme inhibitory, and immunosupressive effects.

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Association of Human Plasma Metabolomics with Delayed Dark Adaptation in Age-Related Macular Degeneration

Metabolites ◽

10.3390/metabo11030183 ◽

2021 ◽

Vol 11 (3) ◽

pp. 183

Author(s):

Kevin M Mendez ◽

Janice Kim ◽

Inês Laíns ◽

Archana Nigalye ◽

Raviv Katz ◽

...

Keyword(s):

Amino Acids ◽

Fatty Acid ◽

Macular Degeneration ◽

Dark Adaptation ◽

Ultra Performance Liquid Chromatography ◽

Cross Sectional Study ◽

Age Related Macular Degeneration ◽

Cross Sectional ◽

Age Related ◽

Vitreoretinal Disease

The purpose of this study was to analyze the association between plasma metabolite levels and dark adaptation (DA) in age-related macular degeneration (AMD). This was a cross-sectional study including patients with AMD (early, intermediate, and late) and control subjects older than 50 years without any vitreoretinal disease. Fasting blood samples were collected and used for metabolomic profiling with ultra-performance liquid chromatography–mass spectrometry (LC-MS). Patients were also tested with the AdaptDx (MacuLogix, Middletown, PA, USA) DA extended protocol (20 min). Two measures of dark adaptation were calculated and used: rod-intercept time (RIT) and area under the dark adaptation curve (AUDAC). Associations between dark adaption and metabolite levels were tested using multilevel mixed-effects linear modelling, adjusting for age, gender, body mass index (BMI), smoking, race, AMD stage, and Age-Related Eye Disease Study (AREDS) formulation supplementation. We included a total of 71 subjects: 53 with AMD (13 early AMD, 31 intermediate AMD, and 9 late AMD) and 18 controls. Our results revealed that fatty acid-related lipids and amino acids related to glutamate and leucine, isoleucine and valine metabolism were associated with RIT (p < 0.01). Similar results were found when AUDAC was used as the outcome. Fatty acid-related lipids and amino acids are associated with DA, thus suggesting that oxidative stress and mitochondrial dysfunction likely play a role in AMD and visual impairment in this condition.

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EFFECTS OF HYPOGLYCIN A ON THE METABOLISM OF AMINO ACIDS BY LIVER SLICES

Canadian Journal of Biochemistry ◽

10.1139/o64-015 ◽

1964 ◽

Vol 42 (1) ◽

pp. 139-142 ◽

Cited By ~ 6

Author(s):

S. J. Patrick ◽

L. C. Stewart

Keyword(s):

Amino Acids ◽

Fatty Acids ◽

Fatty Acid ◽

Glutamic Acid ◽

Rat Liver ◽

Inhibitory Effects ◽

Liver Slices

The effects of hypoglycin A on the metabolism of L-leucine-C14, L-alanine-C14, and L-glutamic-acid-C14 by rat liver slices have been investigated. Hypoglycin exerted markedly inhibitory effects on the conversion of leucine-C14 to fatty acid, cholesterol, and CO2. Conversion of alanine-C14 and glutamic acid-C14 to fatty acids was also inhibited by hypoglycin. No effects of hypoglycin on the conversion of C14-amino acids into protein or glycogen were demonstrated.

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Nutritional Analysis and Quality Evaluation in Muscle of Crucifix Crab Charybdis feriatus From Three Wild Populations

Journal of Food Research ◽

10.5539/jfr.v3n2p27 ◽

2014 ◽

Vol 3 (2) ◽

pp. 27 ◽

Cited By ~ 2

Author(s):

Jian-xue Lu ◽

Yang-yang Gong ◽

Yan-qing Huang ◽

Hong-yu Ma ◽

Xiong Zou ◽

...

Keyword(s):

Amino Acids ◽

Fatty Acid ◽

Unsaturated Fatty Acids ◽

Fatty Acid Content ◽

Total Content ◽

Essential Amino Acids ◽

Maturation Stage ◽

Wild Populations ◽

Nutritional Analysis ◽

Significant Difference

Three wild populations of crucifix crab Charybdis feriatus were sampled and muscle was analyzed for proximate composition, amino acid and fatty acid composition, aimed to quantify and compare the nutritional quality from three different locations in China. Results showed that crude protein content in muscle of female crucifix crab C. feriatus from Zhoushan (ZS) and Xiapu (XP) (84.84%-88.35%) were significantly higher than that of crucifix crab C. feriatus from Qionghai (QH) (74.33%), while there was no significant difference in terms of crude fat content (3.82%-4.07%). The highest content of ash was found in muscle of crucifix crab C. feriatus from QH (5.36%). The muscle of crucifix crab C. feriatus from ZS and XP had significantly higher contents of total amino acids, essential amino acids, non-essential amino acids and delicious amino acids than those of QH group (P < 0.05). The total saturated and unsaturated fatty acid content in the muscle of crucifix crab C. feriatus from three wild populations showed significant difference (P < 0.05). The ZS group had highest content of poly-unsaturated fatty acids (33.64%) and total content of EPA and DHA (22.85%) as well, followed by XP and QH group (P < 0.05). Overall, the differences in chemical composition in muscle of C. feriatus from different locations could be attributed to environmental variables and maturation stage.

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The Contribution of Syringopeptin and Syringomycin to Virulence of Pseudomonas syringae pv. syringae strain B301D on the Basis of sypA and syrB1 Biosynthesis Mutant Analysis

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2001.14.3.336 ◽

2001 ◽

Vol 14 (3) ◽

pp. 336-348 ◽

Cited By ~ 83

Author(s):

Brenda K. Scholz-Schroeder ◽

Michael L. Hutchison ◽

Ingeborg Grgurina ◽

Dennis C. Gross

Keyword(s):

Pseudomonas Syringae ◽

High Performance ◽

Sweet Cherry ◽

Peptide Structure ◽

Acid Activation ◽

Virulence Determinants ◽

Amino Acid Activation ◽

Peptide Synthetases ◽

Peptide Synthetase ◽

Peptide Biosynthesis

Sequencing of an approximately 3.9-kb fragment downstream of the syrD gene of Pseudomonas syringae pv. syringae strain B301D revealed that this region, designated sypA, codes for a peptide synthetase, a multifunctional enzyme involved in the thiotemplate mechanism of peptide biosynthesis. The translated protein sequence encompasses a complete amino acid activation module containing the conserved domains characteristic of peptide synthetases. Analysis of the substrate specificity region of this module indicates that it incorporates 2,3-dehydroaminobutyric acid into the syringopeptin peptide structure. Bioassay and high performance liquid chromatography data confirmed that disruption of the sypA gene in strain B301D resulted in the loss of syringopeptin production. The contribution of syringopeptin and syringomycin to the virulence of P. syringae pv. syringae strain B301D was examined in immature sweet cherry with sypA and syrB1 synthetase mutants defective in the production of the two toxins, respectively. Syringopeptin (sypA) and syringomycin (syrB1) mutants were reduced in virulence 59 and 26%, respectively, compared with the parental strain in cherry, whereas the syringopeptin-syringomycin double mutant was reduced 76% in virulence. These data demonstrate that syringopeptin and syringomycin are major virulence determinants of P. syringae pv. syringae.

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