scholarly journals A noncanonical vacuolar sugar transferase required for biosynthesis of antimicrobial defense compounds in oat

2019 ◽  
Vol 116 (52) ◽  
pp. 27105-27114 ◽  
Author(s):  
Anastasia Orme ◽  
Thomas Louveau ◽  
Michael J. Stephenson ◽  
Ingo Appelhagen ◽  
Rachel Melton ◽  
...  
Keyword(s):  
Natural Products ◽  
Agronomic Traits ◽  
Glycosyl Hydrolase ◽  
Critical Role ◽  
Large Family ◽  
Biosynthetic Gene Cluster ◽  
Uridine Diphosphate ◽  
Sugar Chain ◽  
Defense Compounds ◽  
Antimicrobial Defense

Plants produce an array of natural products with important ecological functions. These compounds are often decorated with oligosaccharide groups that influence bioactivity, but the biosynthesis of such sugar chains is not well understood. Triterpene glycosides (saponins) are a large family of plant natural products that determine important agronomic traits, as exemplified by avenacins, antimicrobial defense compounds produced by oats. Avenacins have a branched trisaccharide moiety consisting ofl-arabinose linked to 2d-glucose molecules that is critical for antifungal activity. Plant natural product glycosylation is usually performed by uridine diphosphate-dependent glycosyltransferases (UGTs). We previously characterized the arabinosyltransferase that initiates the avenacin sugar chain; however, the enzymes that add the 2 remainingd-glucose molecules have remained elusive. Here we characterize the enzymes that catalyze these last 2 glucosylation steps. AsUGT91G16 is a classical cytosolic UGT that adds a 1,2-linkedd-glucose molecule tol-arabinose. Unexpectedly, the enzyme that adds the final 1,4-linkedd-glucose (AsTG1) is not a UGT, but rather a sugar transferase belonging to Glycosyl Hydrolase family 1 (GH1). Unlike classical UGTs, AsTG1 is vacuolar. Analysis of oat mutants reveals thatAsTG1corresponds toSad3, a previously uncharacterized locus shown by mutation to be required for avenacin biosynthesis.AsTG1andAsUGT91G16form part of the avenacin biosynthetic gene cluster. Our demonstration that a vacuolar transglucosidase family member plays a critical role in triterpene biosynthesis highlights the importance of considering other classes of carbohydrate-active enzymes in addition to UGTs as candidates when elucidating pathways for the biosynthesis of glycosylated natural products in plants.

scholarly journals Identification, heterologous production and bioactivity of lentinulin A and dendrothelin A, two natural variants of backbone N-methylated peptide macrocycle omphalotin A

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Emmanuel Matabaro ◽  
Hannelore Kaspar ◽  
Paul Dahlin ◽  
Daniel L. V. Bader ◽  
Claudia E. Murar ◽  
...  
Keyword(s):  
Natural Products ◽  
Lentinula Edodes ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Precursor Protein ◽  
Fungal Genome ◽  
Homologous Gene ◽  
C Terminus ◽  
Natural Variants ◽  
Recombinant Peptides

AbstractBackbone N-methylation and macrocyclization improve the pharmacological properties of peptides by enhancing their proteolytic stability, membrane permeability and target selectivity. Borosins are backbone N-methylated peptide macrocycles derived from a precursor protein which contains a peptide α-N-methyltransferase domain autocatalytically modifying the core peptide located at its C-terminus. Founding members of borosins are the omphalotins from the mushroom Omphalotus olearius (omphalotins A-I) with nine out of 12 L-amino acids being backbone N-methylated. The omphalotin biosynthetic gene cluster codes for the precursor protein OphMA, the protease prolyloligopeptidase OphP and other proteins that are likely to be involved in other post-translational modifications of the peptide. Mining of available fungal genome sequences revealed the existence of highly homologous gene clusters in the basidiomycetes Lentinula edodes and Dendrothele bispora. The respective borosins, referred to as lentinulins and dendrothelins are naturally produced by L. edodes and D. bispora as shown by analysis of respective mycelial extracts. We produced all three homologous peptide natural products by coexpression of OphMA hybrid proteins and OphP in the yeast Pichia pastoris. The recombinant peptides differ in their nematotoxic activity against the plant pathogen Meloidogyne incognita. Our findings pave the way for the production of borosin peptide natural products and their potential application as novel biopharmaceuticals and biopesticides.

scholarly journals mSphere of Influence: Synthetic Biology of Natural Product Biosynthesis

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Mark C. Walker
Keyword(s):  
Natural Products ◽  
Synthetic Biology ◽  
Natural Product ◽  
Gene Cluster ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Natural Product Biosynthesis ◽  
Antibiotic Compounds ◽  
Approaches To Study

ABSTRACT Mark Walker studies the biosynthesis and engineering of bacterial natural products with the long-term goal of identifying new antibiotic compounds. In this mSphere of Influence, he reflects on how “Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A” by K. Yamanaka, K. A. Reynolds, R. D. Kersten, K. S. Ryan, et al. (Proc Natl Acad Sci USA 111:1957–1962, 2014, https://doi.org/10.1073/pnas.1319584111) impacted his thinking on using synthetic biology approaches to study natural product biosynthesis.

scholarly journals Solvent Derived Artifacts in Natural Products Chemistry

2009 ◽  
Vol 4 (3) ◽  
pp. 1934578X0900400 ◽  
Author(s):  
Federica Maltese ◽  
Frank van der Kooy ◽  
Robert Verpoorte
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Chemical Reactions ◽  
Critical Role ◽  
Total Yield ◽  
Purification Method ◽  
Active Compounds ◽  
Natural Product Chemistry ◽  
Extraction And Purification ◽  
Product Chemistry

Solvents play an important and critical role in natural product chemistry. They are mainly used during the extraction and purification of metabolites from a biological matrix. To a lesser extent, solvents are also used as reagents or catalysts to perform chemical reactions. This review focuses on the most important classes of solvents, including alcohols, halogen-containing solvents, esters, ethers, acids and bases. The chemical reactions associated with the use of these solvents to form the so-called “artifacts” are discussed and the most common contaminants found in these solvents are also reviewed. The formation of artifacts and the use of contaminated solvents mainly leads to the formation of new compounds, loss of activity of active compounds, formation of active compounds from inactive ones (false positives), loss in total yield of important compounds during isolation, formation of toxic compounds and difficulty in reproducing an extraction or purification method. Finally, the need for stability studies of purified natural products is emphasized, as this is a common overlooked aspect in natural product chemistry.

Genome-Wide Analysis of Phospholipase D Gene Family and Profiling of Phospholipids under Abiotic Stresses in Brassica napus

2019 ◽  
Vol 60 (7) ◽  
pp. 1556-1566 ◽  
Author(s):  
Shaoping Lu ◽  
Tarig Fadlalla ◽  
Shan Tang ◽  
Long Li ◽  
Usman Ali ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Stress Tolerance ◽  
Abiotic Stresses ◽  
Gene Expression Analysis ◽  
Agronomic Traits ◽  
Membrane Lipids ◽  
Protein Structures ◽  
Large Family ◽  
Membrane Phospholipids ◽  
Genome Wide

Abstract Oil crop Brassica napus is subjected to environmental stresses such as drought, cold and salt. Phospholipase Ds (PLDs) have vital roles in regulation of plant growth, development and stress tolerance. In this study, 32 BnaPLD genes were identified and classified into six subgroups depending on the conserved protein structures. High similarity in gene and protein structures exists between BnaPLDs and AtPLDs. Gene expression analysis showed that BnaPLDα1s and BnaPLDδs had higher expression than other PLDs. BnaPLDα1 and BnaPLDδ were significantly induced by abiotic stresses including dehydration, NaCl, abscisic acid (ABA) and 4�C. Lipidomic analysis showed that the content of main membrane phospholipids decreased gradually under stresses, except phosphatidylglycerol increased under the treatment of ABA and phosphatidylethanolamine increased under 4�C. Correspondingly, their product of phosphatidic acid increased often with a transient peak at 8 h. The plant height of mutants of PLDα1 was significantly reduced. Agronomic traits such as yield, seed number, silique number and branches were significantly impaired in PLDα1 mutants. These results indicate that there is a large family of PLD genes in B. napus, especially BnaPLDα1s and BnaPLDδs may play important roles in membrane lipids remodeling and maintaining of the growth and stress tolerance of B. napus.

scholarly journals Identification and Characterization of Circular Intronic RNAs Derived from Insulin Gene

2020 ◽  
Vol 21 (12) ◽  
pp. 4302 ◽  
Author(s):  
Debojyoti Das ◽  
Aniruddha Das ◽  
Mousumi Sahu ◽  
Smruti Sambhav Mishra ◽  
Shaheerah Khan ◽  
...  
Keyword(s):  
Rna Binding ◽  
Cell Function ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Large Family ◽  
Normal Diet ◽  
Circular Rnas ◽  
Sequencing Data ◽  
Reverse Transcription Pcr ◽  
Β Cell Function

Circular RNAs (circRNAs) are a large family of noncoding RNAs that have emerged as novel regulators of gene expression. However, little is known about the function of circRNAs in pancreatic β-cells. Here, transcriptomic analysis of mice pancreatic islet RNA-sequencing data identified 77 differentially expressed circRNAs between mice fed with a normal diet and a high-fat diet. Surprisingly, multiple circRNAs were derived from the intron 2 of the preproinsulin 2 (Ins2) gene and are termed as circular intronic (ci)-Ins2. The expression of ci-Ins2 transcripts in mouse pancreatic islets, and βTC6 cells were confirmed by reverse transcription PCR, DNA sequencing, and RNase R treatment experiments. The level of ci-Ins2 was altered in βTC6 cells upon exposure to elevated levels of palmitate and glucose. Computational analysis predicted the interaction of several RNA-binding proteins with ci-Ins2 and their flanking region, suggesting their role in the ci-Ins2 function or biogenesis. Additionally, bioinformatics analysis predicted the association of several microRNAs with ci-Ins2. Gene ontology and pathway analysis of genes targeted by miRNAs associated with ci-Ins2 suggested the regulation of several key biological processes. Together, our findings indicate that differential expression of circRNAs, especially ci-Ins2 transcripts, may regulate β-cell function and may play a critical role in the development of diabetes.

scholarly journals MicroRNA Regulation of the Small Rho GTPase Regulators—Complexities and Opportunities in Targeting Cancer Metastasis

Cancers ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1092 ◽  
Author(s):  
Brock A. Humphries ◽  
Zhishan Wang ◽  
Chengfeng Yang
Keyword(s):  
Transcriptional Activation ◽  
Rho Gtpases ◽  
Cancer Metastasis ◽  
Rho Gtpase ◽  
Critical Role ◽  
Large Family ◽  
Actin Dynamics ◽  
Guanine Nucleotide ◽  
Nucleotide Exchange ◽  
Guanine Nucleotide Exchange

The small Rho GTPases regulate important cellular processes that affect cancer metastasis, such as cell survival and proliferation, actin dynamics, adhesion, migration, invasion and transcriptional activation. The Rho GTPases function as molecular switches cycling between an active GTP-bound and inactive guanosine diphosphate (GDP)-bound conformation. It is known that Rho GTPase activities are mainly regulated by guanine nucleotide exchange factors (RhoGEFs), GTPase-activating proteins (RhoGAPs), GDP dissociation inhibitors (RhoGDIs) and guanine nucleotide exchange modifiers (GEMs). These Rho GTPase regulators are often dysregulated in cancer; however, the underlying mechanisms are not well understood. MicroRNAs (miRNAs), a large family of small non-coding RNAs that negatively regulate protein-coding gene expression, have been shown to play important roles in cancer metastasis. Recent studies showed that miRNAs are capable of directly targeting RhoGAPs, RhoGEFs, and RhoGDIs, and regulate the activities of Rho GTPases. This not only provides new evidence for the critical role of miRNA dysregulation in cancer metastasis, it also reveals novel mechanisms for Rho GTPase regulation. This review summarizes recent exciting findings showing that miRNAs play important roles in regulating Rho GTPase regulators (RhoGEFs, RhoGAPs, RhoGDIs), thus affecting Rho GTPase activities and cancer metastasis. The potential opportunities and challenges for targeting miRNAs and Rho GTPase regulators in treating cancer metastasis are also discussed. A comprehensive list of the currently validated miRNA-targeting of small Rho GTPase regulators is presented as a reference resource.

scholarly journals Tracking Down Biotransformation to the Genetic Level: Identification of a Highly Flexible Glycosyltransferase from Saccharothrix espanaensis

2013 ◽  
Vol 79 (17) ◽  
pp. 5224-5232 ◽  
Author(s):  
Tina Strobel ◽  
Yvonne Schmidt ◽  
Anton Linnenbrink ◽  
Andriy Luzhetskyy ◽  
Marta Luzhetska ◽  
...  
Keyword(s):  
Natural Products ◽  
Phenolic Compounds ◽  
Natural Product ◽  
Defense Mechanism ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Gene Encoding ◽  
Content Type ◽  
Genetic Level ◽  
Level Identification

ABSTRACTSaccharothrix espanaensisis a member of the orderActinomycetales. The genome of the strain has been sequenced recently, revealing 106 glycosyltransferase genes. In this paper, we report the detection of a glycosyltransferase fromSaccharothrix espanaensiswhich is able to rhamnosylate different phenolic compounds targeting different positions of the molecules. The gene encoding the flexible glycosyltransferase is not located close to a natural product biosynthetic gene cluster. Therefore, the native function of this enzyme might be not the biosynthesis of a secondary metabolite but the glycosylation of internal and external natural products as part of a defense mechanism.

scholarly journals Biosynthesis and molecular engineering of templated natural products

2016 ◽  
Vol 4 (4) ◽  
pp. 553-575 ◽  
Author(s):  
Ming Chen ◽  
Jingyu Liu ◽  
Panpan Duan ◽  
Mulin Li ◽  
Wen Liu
Keyword(s):  
Natural Products ◽  
Critical Role ◽  
Structural Complexity ◽  
Limited Range ◽  
Molecular Engineering ◽  
First Century ◽  
Design Development ◽  
Post Translational Modifications ◽  
Development And Utilization ◽  
Living Organisms

Abstract Bioactive small molecules that are produced by living organisms, often referred to as natural products (NPs), historically play a critical role in the context of both medicinal chemistry and chemical biology. How nature creates these chemical entities with stunning structural complexity and diversity using a limited range of simple substrates has not been fully understood. Focusing on two types of NPs that share a highly evolvable ‘template’-biosynthetic logic, we here provide specific examples to highlight the conceptual and technological leaps in NP biosynthesis and witness the area of progress since the beginning of the twenty-first century. The biosynthesis of polyketides, non-ribosomal peptides and their hybrids that share an assembly-line enzymology of modular multifunctional proteins exemplifies an extended ‘central dogma’ that correlates the genotype of catalysts with the chemotype of products; in parallel, post-translational modifications of ribosomally synthesized peptides involve a number of unusual biochemical mechanisms for molecular maturation. Understanding the biosynthetic processes of these templated NPs would largely facilitate the design, development and utilization of compatible biosynthetic machineries to address the challenge that often arises from structural complexity to the accessibility and efficiency of current chemical synthesis.

scholarly journals A Deep Learning Genome-Mining Strategy Improves Biosynthetic Gene Cluster Prediction

2018 ◽  
Author(s):  
Geoffrey D. Hannigan ◽  
David Prihoda ◽  
Andrej Palicka ◽  
Jindrich Soukup ◽  
Ondrej Klempir ◽  
...  
Keyword(s):  
Natural Products ◽  
Deep Learning ◽  
Learning Strategy ◽  
Genome Mining ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Antimicrobial Drugs ◽  
Drug Candidates ◽  
Significant Step

AbstractNatural products represent a rich reservoir of small molecule drug candidates utilized as antimicrobial drugs, anticancer therapies, and immunomodulatory agents. These molecules are microbial secondary metabolites synthesized by co-localized genes termed Biosynthetic Gene Clusters (BGCs). The increase in full microbial genomes and similar resources has led to development of BGC prediction algorithms, although their precision and ability to identify novel BGC classes could be improved. Here we present a deep learning strategy (DeepBGC) that offers more accurate BGC identification and an improved ability to extrapolate and identify novel BGC classes compared to existing tools. We supplemented this with downstream random forest classifiers that accurately predicted BGC product classes and potential chemical activity. Application of DeepBGC to bacterial genomes uncovered previously undetectable BGCs that may code for natural products with novel biologic activities. The improved accuracy and classification ability of DeepBGC represents a significant step forward forin-silicoBGC identification.

scholarly journals Characterization of FtsH Essentiality in Streptococcus mutans via Genetic Suppression

2021 ◽  
Vol 12 ◽  
Author(s):  
Yaqi Wang ◽  
Wei Cao ◽  
Justin Merritt ◽  
Zhoujie Xie ◽  
Hao Liu
Keyword(s):  
Gene Cluster ◽  
Streptococcus Mutans ◽  
Response Regulator ◽  
Critical Role ◽  
Acid Stress ◽  
Biosynthetic Gene Cluster ◽  
Oral Microbiome ◽  
Regulatory Function ◽  
Biosynthetic Gene ◽  
Gene Encoding

FtsH belongs to the AAA+ ATP-dependent family of proteases, which participate in diverse cellular processes and are ubiquitous among bacteria, chloroplasts, and mitochondria. FtsH is poorly characterized in most organisms, especially compared to other major housekeeping proteases. In the current study, we examined the source of FtsH essentiality in the human oral microbiome species Streptococcus mutans, one of the primary etiological agents of dental caries. By creating a conditionally lethal ftsH mutant, we were able to identify a secondary suppressor missense mutation in the vicR gene, encoding the response regulator of the essential VicRK two-component system (TCS). Transcriptomic analysis of the vicR (G195R) mutant revealed significantly reduced expression of 46 genes, many of which were located within the genomic island Tnsmu2, which harbors the mutanobactin biosynthetic gene cluster. In agreement with the transcriptomic data, deletion of the mutanobactin biosynthetic gene cluster suppressed ftsH essentiality in S. mutans. We also explored the role of FtsH in S. mutans physiology and demonstrated its critical role in stress tolerance, especially acid stress. The presented results reveal the first insights within S. mutans for the pleiotropic regulatory function of this poorly understood global regulator.

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