Origin and Evolution of Fusidane-Type Antibiotics Biosynthetic Pathway through Multiple Horizontal Gene Transfers

Abstract Fusidane-type antibiotics represented by fusidic acid, helvolic acid, and cephalosporin P1 have very similar core structures, but they are produced by fungi belonging to different taxonomic groups. The origin and evolution of fusidane-type antibiotics biosynthetic gene clusters (BGCs) in different antibiotics producing strains remained an enigma. In this study, we investigated the distribution and evolution of the fusidane BGCs in 1,284 fungal genomes. We identified 12 helvolic acid BGCs, 4 fusidic acid BGCs, and 1 cephalosporin P1 BGC in Pezizomycotina fungi. Phylogenetic analyses indicated six horizontal gene transfer (HGT) events in the evolutionary trajectory of the BGCs, including 1) three transfers across Eurotiomycetes and Sordariomycetes classes; 2) one transfer between genera under Sordariomycetes class; and 3) two transfers within Aspergillus genus under Eurotiomycetes classes. Finally, we proposed that the ancestor of fusidane BGCs would be originated from the Zoopagomycota by ancient HGT events according to the phylogenetic trees of key enzymes in fusidane BGCs (OSC and P450 genes). Our results extensively clarify the evolutionary trajectory of fusidane BGCs by HGT among distantly related fungi and provide new insights into the evolutionary mechanisms of metabolic pathways in fungi.

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Expanding magnetic organelle biogenesis in the domain Bacteria

Microbiome ◽

10.1186/s40168-020-00931-9 ◽

2020 ◽

Vol 8 (1) ◽

Author(s):

Wei Lin ◽

Wensi Zhang ◽

Greig A. Paterson ◽

Qiyun Zhu ◽

Xiang Zhao ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Biological Significance ◽

Gene Clusters ◽

Magnetic Sensors ◽

Evolutionary Origin ◽

Phylogenomic Analysis ◽

Organelle Biogenesis ◽

Taxonomic Distribution ◽

Origin And Evolution ◽

Bacterial Phyla

Abstract Background The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Magnetosomes, as nano-sized magnetic sensors in MTB, facilitate cell navigation along the local geomagnetic field, a behaviour referred to as magnetotaxis or microbial magnetoreception. Recent discovery of novel MTB outside the traditionally recognized taxonomic lineages suggests that MTB diversity across the domain Bacteria are considerably underestimated, which limits understanding of the taxonomic distribution and evolutionary origin of magnetosome organelle biogenesis. Results Here, we perform the most comprehensive metagenomic analysis available of MTB communities and reconstruct metagenome-assembled MTB genomes from diverse ecosystems. Discovery of MTB in acidic peatland soils suggests widespread MTB occurrence in waterlogged soils in addition to subaqueous sediments and water bodies. A total of 168 MTB draft genomes have been reconstructed, which represent nearly a 3-fold increase over the number currently available and more than double the known MTB species at the genome level. Phylogenomic analysis reveals that these genomes belong to 13 Bacterial phyla, six of which were previously not known to include MTB. These findings indicate a much wider taxonomic distribution of magnetosome organelle biogenesis across the domain Bacteria than previously thought. Comparative genome analysis reveals a vast diversity of magnetosome gene clusters involved in magnetosomal biogenesis in terms of gene content and synteny residing in distinct taxonomic lineages. Phylogenetic analyses of core magnetosome proteins in this largest available and taxonomically diverse dataset support an unexpectedly early evolutionary origin of magnetosome biomineralization, likely ancestral to the origin of the domain Bacteria. Conclusions These findings expand the taxonomic and phylogenetic diversity of MTB across the domain Bacteria and shed new light on the origin and evolution of microbial magnetoreception. Potential biogenesis of the magnetosome organelle in the close descendants of the last bacterial common ancestor has important implications for our understanding of the evolutionary history of bacterial cellular complexity and emphasizes the biological significance of the magnetosome organelle.

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Genome sequence of bioactive streptomycete isolated from mangrove forest in East Malaysia, Streptomyces monashensis MUSC 1JT

Progress in Drug Discovery & Biomedical Science ◽

10.36877/pddbs.a0000045 ◽

2019 ◽

Vol 2 (1) ◽

Author(s):

Hooi-Leng Ser ◽

Jodi Woan-Fei Law ◽

Wen-Si Tan ◽

Wai-Fong Yin ◽

Kok-Gan Chan ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Gene Clusters ◽

Pharmaceutical Products ◽

Neuroprotective Agents ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Colon Cancer Cell Lines ◽

East Malaysia ◽

Streptomyces Olivaceoviridis ◽

Bioactive Potential

Members of Streptomyces are known to be prolific producers of bioactive compounds, including antibacterials, antioxidants, neuroprotective agents as well as immunomodulatory compounds. Isolated from East Malaysia, Streptomyces monashensis MUSC 1JT (=DSM 103626T =MCCC 1K03221T) was initially described as a novel streptomycete using a polyphasic approach. Based on phylogenetic analyses, the closely strains related to MUSC 1JT were identified as Streptomyces corchorusii DSM 40340T (98.7 %), Streptomyces olivaceoviridis NBRC 3066T (98.7 %), Streptomyces canarius NBRC 13431T (98.6 %), and Streptomyces coacervatus AS-0823T (98.4 %). Seven day fermentative extracts of MUSC 1JT exhibited potent antioxidant activity and significant cytotoxic activity against colon cancer cell lines, thus the strain was selected for whole genome sequencing. The genome size of MUSC 1JT is described to be 10.3 Mbps with G + C content of 71.50%. Based on antiSMASH analysis, the strain possessess great genomic potential, having fifty nine biosynthetic gene clusters related to production of secondary metabolites and antibiotics. Therefore, these results serve a foundation for further in-depth investigation to harness its bioactive potential for the development of highly valuable pharmaceutical products.

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Evolutionary trajectory of phytoalexin biosynthetic gene clusters in rice

The Plant Journal ◽

10.1111/tpj.13200 ◽

2016 ◽

Vol 87 (3) ◽

pp. 293-304 ◽

Cited By ~ 31

Author(s):

Koji Miyamoto ◽

Masahiro Fujita ◽

Matthew R. Shenton ◽

Shota Akashi ◽

Chizu Sugawara ◽

...

Keyword(s):

Gene Clusters ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Evolutionary Trajectory

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A short guide to phylogeny reconstruction

Plant Soil and Environment ◽

10.17221/2194-pse ◽

2008 ◽

Vol 53 (No. 10) ◽

pp. 442-446 ◽

Cited By ~ 5

Author(s):

E. Michu

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Dna Sequences ◽

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Amino Acid Sequences ◽

Short Introduction ◽

Closely Related Species ◽

Origin And Evolution ◽

Anatomical Characters

This review is a short introduction to phylogenetic analysis. Phylogenetic analysis allows comprehensive understanding of the origin and evolution of species. Generally, it is possible to construct the phylogenetic trees according to different features and characters (e.g. morphological and anatomical characters, RAPD patterns, FISH patterns, sequences of DNA/RNA and amino acid sequences). The DNA sequences are preferable for phylogenetic analyses of closely related species. On the other hand, the amino acid sequences are used for phylogenetic analyses of more distant relationships. The sequences can be analysed using many computer programs. The methods most often used for phylogenetic analyses are neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference.

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BGDMdocker: a Docker workflow for analysis and visualization pan-genome and biosynthetic gene clusters of bacterial

10.1101/098392 ◽

2017 ◽

Cited By ~ 1

Author(s):

Gong Cheng ◽

Quan Lu ◽

Zongshan Zhou ◽

Ling Ma ◽

Guocai Zhang ◽

...

Keyword(s):

Gene Cluster ◽

Phylogenetic Trees ◽

Rapid Development ◽

Bacterial Genome ◽

Gene Clusters ◽

Supplementary Information ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Pan Genome ◽

Link Type

ABSTRACTMotivationAt present Docker technology has received increasing level of attention throughout the bioinformatics community. However, its implementation details have not yet been mastered by most biologists and applied widely in biological researches. In order to popularizing this technology in the bioinformatics and sufficiently use plenty of public resources of bioinformatics tools (Dockerfile and image of scommunity, officially and privately) in Docker Hub Registry and other Docker sources based on Docker, we introduced full and accurate instance of a bioinformatics workflow based on Docker to analyse and visualize pan-genome and biosynthetic gene clusters of a bacteria in this article, provided the solutions for mining bioinformatics big data from various public biology databases. You could be guided step-by-step through the workflow process from docker file to build up your own images and run an container fast creating an workflow.ResultsWe presented a BGDMdocker (bacterial genome data mining docker-based) workflow based on docker. The workflow consists of three integrated toolkits, Prokka v1.11, panX, and antiSMASH3.0. The dependencies were all written in Dockerfile, to build docker image and run container for analysing pan-genome of total 44 Bacillus amyloliquefaciens strains, which were retrieved from public? database. The pan-genome totally includes 172,432 gene, 2,306 Core gene cluster. The visualized pan-genomic data such as alignment, phylogenetic trees, maps mutations within that cluster to the branches of the tree, infers loss and gain of genes on the core-genome phylogeny for each gene cluster were presented. Besides, 997 known (MIBiG database) and 553 unknown (antiSMASH-predicted clusters and Pfam database) genes of biosynthesis gene clusters types and orthologous groups were mined in all strains. This workflow could also be used for other species pan-genome analysis and visualization. The display of visual data can completely duplicated as well as done in this paper. All result data and relevant tools and files can be downloaded from our website with no need to register. The pan-genome and biosynthetic gene clusters analysis and visualization can be fully reusable immediately in different computing platforms (Linux, Windows, Mac and deployed in the cloud), achieved cross platform deployment flexibility, rapid development integrated software package.Availability and implementationBGDMdocker is available at http://42.96.173.25/bapgd/ and the source code under GPL license is available at https://github.com/cgwyx/debian_prokka_panx_antismash_biodocker.Contactchenggongwyx@foxmail.comSupplementary informationSupplementary data are available at biorxiv online.

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Phylogenetic relationships of the Helmeted Woodpecker (Dryocopus galeatus): A case of interspecific mimicry?

10.1101/023663 ◽

2015 ◽

Author(s):

Brett W. Benz ◽

Mark B. Robbins ◽

Kevin J. Zimmer

Keyword(s):

Atlantic Forest ◽

Phylogenetic Analyses ◽

Evolutionary Game ◽

Field Studies ◽

Plumage Coloration ◽

Evolutionary Mechanisms ◽

Behavioral Studies ◽

Social Costs And Benefits ◽

Taxonomic Groups ◽

Behavioral Mimicry

Examples of phenotypic convergence in plumage coloration have been reported in a wide diversity of avian taxonomic groups, yet the underlying evolutionary mechanisms driving this phenomenon have received little scientific inquiry. Herein, we document a striking new case of plumage convergence in the Helmeted Woodpecker (Dryocopus galeatus) and explore the possibility of visual mimicry among Atlantic Forest woodpeckers. Our multi-locus phylogenetic analyses unequivocally placeD. galeatuswithinCeleus, indicating the former has subsequently converged in appearance upon the distantly related and syntopicDryocopus lineatus, to which it bears a remarkable resemblance in plumage coloration and pattern. Although details of the Helmeted Woodpecker’s ecology and natural history are only now beginning to emerge, its smaller size and submissive behavior are consistent with predictions derived from evolutionary game theory models and the interspecific social dominance mimicry hypothesis (ISDM). Moreover, estimates of avian visual acuity suggest that size-related mimetic deception is plausible at distances ecologically relevant toCeleusandDryocopusforaging behavior. In light of our results, we recommend taxonomic transfer ofD. galeatustoCeleusand emphasize the need for detailed behavioral studies that examine the social costs and benefits of plumage convergence to explicitly test for ISDM and other forms of mimicry in these Atlantic Forest woodpecker communities. Future field studies examining potential cases of competitive mimicry should also take into account the mimic’s acoustic behavior, particularly in the presence of putative model species and other heterospecific competitors, as any discontinuity between morphological and behavioral mimicry would likely preclude the possibility of deception.

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Molecular evidence for hybridization in the aquatic plant Limosella on sub-Antarctic Marion Island

Antarctic Science ◽

10.1017/s0954102021000079 ◽

2021 ◽

pp. 1-9

Author(s):

John H. Chau ◽

Michelle Greve ◽

Bettine Jansen van Vuuren

Keyword(s):

Phylogenetic Trees ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Variability ◽

Molecular Evidence ◽

Marion Island ◽

Specific Sequence ◽

Nuclear Locus ◽

Species Specific ◽

Taxonomic Groups

Abstract DNA sequence data have become a crucial tool in assessing the relationship between morphological variation and genetic and taxonomic groups, including in the Antarctic biota. Morphologically distinct populations of submersed aquatic vascular plants were observed on sub-Antarctic Marion Island, potentially representing the two species of such plants listed in the island's flora, Limosella australis R.Br. (Scrophulariaceae) and Ranunculus moseleyi Hook.f. (Ranunculaceae). To confirm their taxonomic identity, we sequenced a nuclear locus (internal transcribed spacer; ITS) and two plastid loci (trnL-trnF, rps16) from three specimens collected on Marion Island and compared the sequences with those in public sequence databases. For all three loci, sequences from the Marion Island specimens were nearly identical despite morphological dissimilarity, and phylogenetic analyses resolved them to a position in Limosella. In phylogenetic trees and comparisons of species-specific sequence polymorphisms, the Marion Island specimens were closest to a clade comprising Limosella aquatica L., L. curdieana F.Muell. and L. major Diels for ITS and closest to L. australis for the plastid loci. Cytonuclear discordance suggests a history of hybridization or introgression, which may have consequences for morphological variability and ecological adaptation.

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Expanding the Natural Products Heterologous Expression Repertoire in the Model Cyanobacterium Anabaena sp. Strain PCC 7120: Production of Pendolmycin and Teleocidin B-4

10.26434/chemrxiv.11316098.v1 ◽

2019 ◽

Cited By ~ 1

Author(s):

Patrick Videau ◽

Kaitlyn Wells ◽

Arun Singh ◽

Jessie Eiting ◽

Philip Proteau ◽

...

Keyword(s):

Natural Products ◽

Genome Mining ◽

Gene Clusters ◽

Combinatorial Biosynthesis ◽

Test Case ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Cyanobacterium Anabaena ◽

Anabaena Sp ◽

Pcc 7120

Cyanobacteria are prolific producers of natural products and genome mining has shown that many orphan biosynthetic gene clusters can be found in sequenced cyanobacterial genomes. New tools and methodologies are required to investigate these biosynthetic gene clusters and here we present the use of <i>Anabaena </i>sp. strain PCC 7120 as a host for combinatorial biosynthesis of natural products using the indolactam natural products (lyngbyatoxin A, pendolmycin, and teleocidin B-4) as a test case. We were able to successfully produce all three compounds using codon optimized genes from Actinobacteria. We also introduce a new plasmid backbone based on the native <i>Anabaena</i>7120 plasmid pCC7120ζ and show that production of teleocidin B-4 can be accomplished using a two-plasmid system, which can be introduced by co-conjugation.

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