Structure, properties, and biological functions of nonribosomal lipopeptides from pseudomonads

2020 ◽  
Vol 37 (1) ◽  
pp. 29-54 ◽  
Author(s):  
Sebastian Götze ◽  
Pierre Stallforth
Keyword(s):  
Natural Product ◽  
Ecological Niches ◽  
Product Class ◽  
Biological Functions ◽  
Metabolic Diversity ◽  
Wide Range ◽  
Structure Properties

Bacteria of the genus Pseudomonas display a fascinating metabolic diversity. In this review, we focus our attention on the natural product class of nonribosomal lipopeptides, which help pseudomonads to colonize a wide range of ecological niches.

scholarly journals New Deoxyenhygrolides from Plesiocystis pacifica Provide Insights into Butenolide Core Biosynthesis

Marine Drugs ◽  
2022 ◽  
Vol 20 (1) ◽  
pp. 72
Author(s):  
Joachim J. Hug ◽  
Louise Kjaerulff ◽  
Ronald Garcia ◽  
Rolf Müller
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Benzyl Alcohol ◽  
In Silico ◽  
Structure Elucidation ◽  
Product Class ◽  
Biological Functions ◽  
Biosynthetic Genes

Marine myxobacteria present a virtually unexploited reservoir for the discovery of natural products with diverse biological functions and novel chemical scaffolds. We report here the isolation and structure elucidation of eight new deoxyenhygrolides (1–8) from the marine myxobacterium Plesiocystis pacifica DSM 14875T. The herein described deoxyenhygrolides C–J (1–8) feature a butenolide core with an ethyl residue at C-3 of the γ-lactone in contrast to the previously described derivatives, deoxyenhygrolides A and B, which feature an isobutyl residue at this position. The butenolide core is 2,4-substituted with a benzyl (1, 2 and 7), benzoyl (3 and 4) or benzyl alcohol (5, 6 and 8) moiety in the 2-position and a benzylidene (1–6) or benzylic hemiketal (7 and 8) in the 4-position. The description of these new deoxyenhygrolide derivatives, alongside genomic in silico investigation regarding putative biosynthetic genes, provides some new puzzle pieces on how this natural product class might be formed by marine myxobacteria.

The untapped potential of plant sesterterpenoids: chemistry, biological activities and biosynthesis

2021 ◽  
Author(s):  
Kai Guo ◽  
Yan Liu ◽  
Sheng-Hong Li
Keyword(s):  
Natural Product ◽  
Biological Activities ◽  
Product Class

An overall coverage of plant sesterterpenoids including the distribution, chemistry, biological activities, biosynthesis and evolution is provided, highlighting the untapped potential of this enigmatic but promising natural product class in plants.

scholarly journals Leeches as the intermediate host for strigeid trematodes: genetic diversity and taxonomy of the genera Australapatemon Sudarikov, 1959 and Cotylurus Szidat, 1928

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ewa Pyrka ◽  
Gerard Kanarek ◽  
Grzegorz Zaleśny ◽  
Joanna Hildebrand
Keyword(s):  
Intermediate Host ◽  
Life Cycles ◽  
Coi Gene ◽  
Small Rivers ◽  
Ecological Niches ◽  
Its2 Region ◽  
28S Rrna ◽  
Intermediate Hosts ◽  
Internal Transcribed Spacer Region ◽  
Wide Range

Abstract Background Leeches (Hirudinida) play a significant role as intermediate hosts in the circulation of trematodes in the aquatic environment. However, species richness and the molecular diversity and phylogeny of larval stages of strigeid trematodes (tetracotyle) occurring in this group of aquatic invertebrates remain poorly understood. Here, we report our use of recently obtained sequences of several molecular markers to analyse some aspects of the ecology, taxonomy and phylogeny of the genera Australapatemon and Cotylurus, which utilise leeches as intermediate hosts. Methods From April 2017 to September 2018, 153 leeches were collected from several sampling stations in small rivers with slow-flowing waters and related drainage canals located in three regions of Poland. The distinctive forms of tetracotyle metacercariae collected from leeches supplemented with adult Strigeidae specimens sampled from a wide range of water birds were analysed using the 28S rDNA partial gene, the second internal transcribed spacer region (ITS2) region and the cytochrome c oxidase (COI) fragment. Results Among investigated leeches, metacercariae of the tetracotyle type were detected in the parenchyma and musculature of 62 specimens (prevalence 40.5%) with a mean intensity reaching 19.9 individuals. The taxonomic generic affiliation of metacercariae derived from the leeches revealed the occurrence of two strigeid genera: Australapatemon Sudarikov, 1959 and Cotylurus Szidat, 1928. Phylogenetic reconstructions based on the partial 28S rRNA gene, ITS2 region and partial COI gene confirmed the separation of the Australapatemon and Cotylurus clades. Taking currently available molecular data and our results into consideration, recently sequenced tetracotyle of Australapatemon represents most probably Au. minor; however, unclear phylogenetic relationships between Au. burti and Au. minor reduce the reliability of this conclusion. On the other hand, on the basis of the obtained sequences, supplemented with previously published data, the metacercariae of Cotylurus detected in leeches were identified as two species: C. strigeoides Dubois, 1958 and C. syrius Dubois, 1934. This is the first record of C. syrius from the intermediate host. Conclusions The results of this study suggest the separation of ecological niches and life cycles between C. cornutus (Rudolphi, 1808) and C. strigeoides/C. syrius, with potential serious evolutionary consequences for a wide range of host–parasite relationships. Moreover, phylogenetic analyses corroborated the polyphyletic character of C. syrius, the unclear status of C. cornutus and the separate position of Cotylurus raabei Bezubik, 1958 within Cotylurus. The data demonstrate the inconsistent taxonomic status of the sequenced tetracotyle of Australapatemon, resulting, in our opinion, from the limited availability of fully reliable, comparative sequences of related taxa in GenBank.

scholarly journals Shape Neutral Analysis of Graph-based Data-structures

2018 ◽  
Vol 18 (3-4) ◽  
pp. 470-483 ◽  
Author(s):  
GREGORY J. DUCK ◽  
JOXAN JAFFAR ◽  
ROLAND H. C. YAP
Keyword(s):  
Data Structure ◽  
Data Structures ◽  
Program Analysis ◽  
Constraint Handling ◽  
C Programs ◽  
Wide Range ◽  
Target Program ◽  
Target Data ◽  
Structure Graph ◽  
Structure Properties

AbstractMalformed data-structures can lead to runtime errors such as arbitrary memory access or corruption. Despite this, reasoning over data-structure properties for low-level heap manipulating programs remains challenging. In this paper we present a constraint-based program analysis that checks data-structure integrity, w.r.t. given target data-structure properties, as the heap is manipulated by the program. Our approach is to automatically generate a solver for properties using the type definitions from the target program. The generated solver is implemented using a Constraint Handling Rules (CHR) extension of built-in heap, integer and equality solvers. A key property of our program analysis is that the target data-structure properties are shape neutral, i.e., the analysis does not check for properties relating to a given data-structure graph shape, such as doubly-linked-lists versus trees. Nevertheless, the analysis can detect errors in a wide range of data-structure manipulating programs, including those that use lists, trees, DAGs, graphs, etc. We present an implementation that uses the Satisfiability Modulo Constraint Handling Rules (SMCHR) system. Experimental results show that our approach works well for real-world C programs.

scholarly journals Adaptation limits ecological diversification and promotes ecological tinkering during the competition for substitutable resources

2018 ◽  
Vol 115 (44) ◽  
pp. E10407-E10416 ◽  
Author(s):  
Benjamin H. Good ◽  
Stephen Martis ◽  
Oskar Hallatschek
Keyword(s):  
Evolutionary Dynamics ◽  
Competitive Exclusion ◽  
Directional Selection ◽  
Ecological Niches ◽  
Ecological Diversification ◽  
Effective Competition ◽  
Uptake Rates ◽  
Wide Range ◽  
Dynamical Features ◽  
Adaptation Limits

Microbial communities can evade competitive exclusion by diversifying into distinct ecological niches. This spontaneous diversification often occurs amid a backdrop of directional selection on other microbial traits, where competitive exclusion would normally apply. Yet despite their empirical relevance, little is known about how diversification and directional selection combine to determine the ecological and evolutionary dynamics within a community. To address this gap, we introduce a simple, empirically motivated model of eco-evolutionary feedback based on the competition for substitutable resources. Individuals acquire heritable mutations that alter resource uptake rates, either by shifting metabolic effort between resources or by increasing the overall growth rate. While these constitutively beneficial mutations are trivially favored to invade, we show that the accumulated fitness differences can dramatically influence the ecological structure and evolutionary dynamics that emerge within the community. Competition between ecological diversification and ongoing fitness evolution leads to a state of diversification–selection balance, in which the number of extant ecotypes can be pinned below the maximum capacity of the ecosystem, while the ecotype frequencies and genealogies are constantly in flux. Interestingly, we find that fitness differences generate emergent selection pressures to shift metabolic effort toward resources with lower effective competition, even in saturated ecosystems. We argue that similar dynamical features should emerge in a wide range of models with a mixture of directional and diversifying selection.

scholarly journals New Pharmacological Opportunities for Betulinic Acid

Planta Medica ◽  
2017 ◽  
Vol 84 (01) ◽  
pp. 8-19 ◽  
Author(s):  
José Ríos ◽  
Salvador Máñez
Keyword(s):  
Metabolic Syndrome ◽  
Natural Product ◽  
Betulinic Acid ◽  
Therapeutic Potential ◽  
Present Review ◽  
Antitumor Effects ◽  
Pharmacological Activities ◽  
Naturally Occurring ◽  
Wide Range ◽  
Birch Trees

AbstractBetulinic acid is a naturally occurring pentacyclic lupane-type triterpenoid usually isolated from birch trees, but present in many other botanical sources. It is found in different plant organs, both as a free aglycon and as glycosyl derivatives. A wide range of pharmacological activities has been described for this triterpenoid, including antiviral and antitumor effects. In addition, several other interesting properties have been identified in the fields of immunity and metabolism, namely antidiabetic, antihyperlipidemic, and anti-inflammatory activities. Taken together, these latter three properties make betulinic acid a highly interesting prospect for treating metabolic syndrome. The present review focuses on the therapeutic potential of this agent, along with several of its semisynthetic derivatives, which could open new frontiers in the use of natural product-based medicines.

scholarly journals Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species

2021 ◽  
Vol 17 (2) ◽  
pp. e1008767
Author(s):  
Zutan Li ◽  
Hangjin Jiang ◽  
Lingpeng Kong ◽  
Yuanyuan Chen ◽  
Kun Lang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Prediction Accuracy ◽  
Cross Validation ◽  
Biological Processes ◽  
Biological Functions ◽  
Learning Framework ◽  
Wide Range ◽  
Genomic Scale ◽  
Downstream Gene Expression ◽  
Fold Cross Validation

N6-methyladenine (6mA) is an important DNA modification form associated with a wide range of biological processes. Identifying accurately 6mA sites on a genomic scale is crucial for under-standing of 6mA’s biological functions. However, the existing experimental techniques for detecting 6mA sites are cost-ineffective, which implies the great need of developing new computational methods for this problem. In this paper, we developed, without requiring any prior knowledge of 6mA and manually crafted sequence features, a deep learning framework named Deep6mA to identify DNA 6mA sites, and its performance is superior to other DNA 6mA prediction tools. Specifically, the 5-fold cross-validation on a benchmark dataset of rice gives the sensitivity and specificity of Deep6mA as 92.96% and 95.06%, respectively, and the overall prediction accuracy is 94%. Importantly, we find that the sequences with 6mA sites share similar patterns across different species. The model trained with rice data predicts well the 6mA sites of other three species: Arabidopsis thaliana, Fragaria vesca and Rosa chinensis with a prediction accuracy over 90%. In addition, we find that (1) 6mA tends to occur at GAGG motifs, which means the sequence near the 6mA site may be conservative; (2) 6mA is enriched in the TATA box of the promoter, which may be the main source of its regulating downstream gene expression.

Characterization of proteins with Siaα2-3/6Gal-linked glycans from bovine milk and role of their glycans against influenza A virus

2018 ◽  
Vol 9 (10) ◽  
pp. 5198-5208 ◽  
Author(s):  
Hanjie Yu ◽  
Yaogang Zhong ◽  
Zhiwei Zhang ◽  
Xiawei Liu ◽  
Kun Zhang ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Bovine Milk ◽  
Milk Proteins ◽  
Biological Functions ◽  
Wide Range ◽  
Range Of Functions ◽  
Bovine Milk Proteins

The bovine milk proteins have a wide range of functions, but the role of the attached glycans in their biological functions has not been fully understood yet.

Botanical Identity of Seasonal Flowering Plants Available and Maintained in the Home Gardens of District Nainital, Uttarakhand

2016 ◽  
Vol 23 (2) ◽  
pp. 89-102
Author(s):  
Kuldeep Negi ◽  
Vandana Tiwari ◽  
Puran Mehta ◽  
Rajni Rawat ◽  
Saraswati Ojha ◽  
...  
Keyword(s):  
Economic Status ◽  
Plant Genetic Resources ◽  
Geographical Area ◽  
Flowering Plants ◽  
Home Gardens ◽  
Flowering Plant ◽  
Ecological Niches ◽  
Wide Range ◽  
Seasonal Flowering ◽  
Flowering Plant Species

Uttarakhand is a store house of plant genetic resources of several crop groups including ornamentals and seasonal flowering plant species. A wide range of seasonal flowering plants are being grown in the region because of its various and favourable agro-geo climatic zones. Ornamental plant enhances aesthetic value of our environment. There are 8 developmental blocks and 1082 villages in district Nainital of Uttarakhand. Nainital district, is a part of Kumaun region of Uttarakhand. It lies between 29?0.1' to 29?36' 21'' N latitude and 78?50' 53'' to 80?06' E longitude. More than 7.62 lakh population reside in 4064 km2 of geographical area of district Nainital. The district falls under sub-tropical to temperate zones. During the course of field survey (2013-2015), we came across wide range of seasonal flowering plants mostly belong to exotic origin being grown in the home gardens of natives of the region situated in different agro-ecological niches. The present study highlighted a total of 150 seasonal flowering plants with 120 genera belonging to 50 families. These were arranged alphabetically with botanical names followed by vernacular and trade name, family, origin or native place, nature, season with appropriate remarks of variation in shape, size and colour, method of propagation with economic status.

scholarly journals Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia

2020 ◽  
Vol 295 (44) ◽  
pp. 14826-14839
Author(s):  
Serina L. Robinson ◽  
Barbara R. Terlouw ◽  
Megan D. Smith ◽  
Sacha J. Pidot ◽  
Timothy P. Stinear ◽  
...  
Keyword(s):  
Machine Learning ◽  
Natural Product ◽  
Global Analysis ◽  
Gene Clusters ◽  
Divergent Evolution ◽  
Acid Activation ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Predictive Tool ◽  
Wide Range

Enzymes that cleave ATP to activate carboxylic acids play essential roles in primary and secondary metabolism in all domains of life. Class I adenylate-forming enzymes share a conserved structural fold but act on a wide range of substrates to catalyze reactions involved in bioluminescence, nonribosomal peptide biosynthesis, fatty acid activation, and β-lactone formation. Despite their metabolic importance, the substrates and functions of the vast majority of adenylate-forming enzymes are unknown without tools available to accurately predict them. Given the crucial roles of adenylate-forming enzymes in biosynthesis, this also severely limits our ability to predict natural product structures from biosynthetic gene clusters. Here we used machine learning to predict adenylate-forming enzyme function and substrate specificity from protein sequences. We built a web-based predictive tool and used it to comprehensively map the biochemical diversity of adenylate-forming enzymes across >50,000 candidate biosynthetic gene clusters in bacterial, fungal, and plant genomes. Ancestral phylogenetic reconstruction and sequence similarity networking of enzymes from these clusters suggested divergent evolution of the adenylate-forming superfamily from a core enzyme scaffold most related to contemporary CoA ligases toward more specialized functions including β-lactone synthetases. Our classifier predicted β-lactone synthetases in uncharacterized biosynthetic gene clusters conserved in >90 different strains of Nocardia. To test our prediction, we purified a candidate β-lactone synthetase from Nocardia brasiliensis and reconstituted the biosynthetic pathway in vitro to link the gene cluster to the β-lactone natural product, nocardiolactone. We anticipate that our machine learning approach will aid in functional classification of enzymes and advance natural product discovery.

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