The gill-associated symbiont microbiome is a main source of woody-plant polysaccharide hydrolase genes and secondary metabolite gene clusters inNeoteredo reynei, a unique shipworm from south Atlantic mangroves

AbstractTeredinidae is a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract ofNeoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the symbiotic gammaproteobacterial community of gills of differentN. reyneispecimens, indicating closely related bacterial types are shared, while intestine and digestive glands presented related, and more diverse microbiomes that did not overlap with gills. Annotation of assembled metagenomic contigs revealed that the symbiotic community ofN. reyneigills was a hotspot of woody-polysaccharides degrading hydrolase genes, and Biosynthetic Gene Clusters (BGCs), while in contrast, the digestive tract microbiomes seems to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbioticTeredinibacterstrains from the gills, a representative ofTeredinibacter turnerae“clade I” strain, and a yet to be cultivatedTeredinibactersp. type. TheseTeredinibactergenomes, as well as unbinned gill-derived gammaproteobacteria contigs, code for novelty including an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Multivariate analyzes have shown that the secondary metabolome encoded on the genomes ofTeredinibacterrepresentatives, including the genomes binned fromN. reyneigill’s metagenomes, stand out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results grouped here add to the growing characterization of shipworm symbiotic microbiomes and indicate that theN. reyneigill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.

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Identification and Characterization of the Asperthecin Gene Cluster of Aspergillus nidulans

Applied and Environmental Microbiology ◽

10.1128/aem.01743-08 ◽

2008 ◽

Vol 74 (24) ◽

pp. 7607-7612 ◽

Cited By ~ 116

Author(s):

Edyta Szewczyk ◽

Yi-Ming Chiang ◽

C. Elizabeth Oakley ◽

Ashley D. Davidson ◽

Clay C. C. Wang ◽

...

Keyword(s):

Secondary Metabolite ◽

Polyketide Synthase ◽

Gene Clusters ◽

Laboratory Culture ◽

Culture Conditions ◽

Type I ◽

Genes Encoding ◽

Identification And Characterization ◽

Normal Laboratory

ABSTRACT The sequencing of Aspergillus genomes has revealed that the products of a large number of secondary metabolism pathways have not yet been identified. This is probably because many secondary metabolite gene clusters are not expressed under normal laboratory culture conditions. It is, therefore, important to discover conditions or regulatory factors that can induce the expression of these genes. We report that the deletion of sumO, the gene that encodes the small ubiquitin-like protein SUMO in A. nidulans, caused a dramatic increase in the production of the secondary metabolite asperthecin and a decrease in the synthesis of austinol/dehydroaustinol and sterigmatocystin. The overproduction of asperthecin in the sumO deletion mutant has allowed us, through a series of targeted deletions, to identify the genes required for asperthecin synthesis. The asperthecin biosynthesis genes are clustered and include genes encoding an iterative type I polyketide synthase, a hydrolase, and a monooxygenase. The identification of these genes allows us to propose a biosynthetic pathway for asperthecin.

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Identification and Characterization of Biosynthetic Gene Clusters from Halophilic Marine Fungus Eurotium rubrum

10.20944/preprints202002.0388.v1 ◽

2020 ◽

Author(s):

Obul Reddy Bandapali ◽

Frederik Teilfeldt Hansen ◽

Alisha Parveen ◽

Pradeep Phule ◽

Emmagouni Sharath Kumar Goud ◽

...

Keyword(s):

Polyketide Synthase ◽

Gene Clusters ◽

Marine Fungus ◽

Type I ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Peptide Synthetase ◽

Future Drug ◽

Identification And Characterization

Eurotium rubrum is a halophilic marine ascomycete, which can bear the hypersalinities of the Red Sea and proliferate, while most living entities cannot bear this condition. Recently, a 26.2 Mb assembled genome of this fungus had become available. Marine fungi are fascinating organisms capable of harboring several biosynthetic gene clusters (BGCs), which enables them to produce several natural compounds with antibiotic and anticancerous properties. Understanding the BGCs are critically important for the development of biotechnological applications and the discovery of future drugs. There is no knowledge available on the BGCs of this halophilic marine ascomycete. Herein, we set out to explore and characterize BGCs and the corresponding genes from E. rubrum using bioinformatic methods. We deciphered 36 BGCs in the genome of E. rubrum. These 36 BGCs can be grouped into four non-ribosomal peptide synthetase (NRPS) clusters, eight NRPS-like (NRPSL) BGCs, eight type I polyketide synthase (T1PKS), 11 terpene BGCs including one β-lactone cluster, four hybrid BGCs, and two siderophore BGCs. This study is an example of marine genomics application into potential future drug-like compound discovery.

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Characterization of class 1 integrons carrying blaVIM-2 and blaVIM-4 gene cassette in Pseudomonas aeruginosa isolated in the University Clinical Hospital of Bialystok (northeastern Poland)

10.26226/morressier.56d6be75d462b80296c9763a ◽

2016 ◽

Author(s):

Pawel Sacha

Keyword(s):

Pseudomonas Aeruginosa ◽

Gene Cassette ◽

Clinical Hospital ◽

Class 1 Integrons ◽

Class 1 ◽

Northeastern Poland ◽

The University

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Characterization of the ribosomal RNA gene clusters in Halobacterium cutirubrum.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(20)71184-1 ◽

1985 ◽

Vol 260 (2) ◽

pp. 899-906

Author(s):

I Hui ◽

P P Dennis

Keyword(s):

Ribosomal Rna ◽

Gene Clusters ◽

Ribosomal Rna Gene

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Proteins encoded by the DpnI restriction gene cassette. Hyperproduction and characterization of the DpnI endonuclease.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)68093-7 ◽

1988 ◽

Vol 263 (29) ◽

pp. 14696-14702

Author(s):

A G de la Campa ◽

S S Springhorn ◽

P Kale ◽

S A Lacks

Keyword(s):

Gene Cassette

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Identification and Characterization of Inorganic Pyrophosphatase and PAP Phosphatase from Thermococcus onnurineus NA1

Journal of Bacteriology ◽

10.1128/jb.01699-08 ◽

2009 ◽

Vol 191 (10) ◽

pp. 3415-3419 ◽

Cited By ~ 4

Author(s):

Hyun Sook Lee ◽

Yun Jae Kim ◽

Jung-Hyun Lee ◽

Sung Gyun Kang

Keyword(s):

Gene Clusters ◽

Inorganic Pyrophosphatase ◽

Thermococcus Onnurineus Na1 ◽

First Report ◽

Activation System ◽

Sulfate Activation ◽

Pyrococcus Abyssi ◽

Identification And Characterization ◽

Hypothetical Genes

ABSTRACT Two hypothetical genes were functionally verified to be a pyrophosphatase and a PAP phosphatase in Thermococcus onnurineus NA1. This is the first report of the pyrophosphatases and the PAP phosphatases being organized in the gene clusters of the sulfate activation system only in T. onnurineus NA1 and “Pyrococcus abyssi.”

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Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese

Microorganisms ◽

10.3390/microorganisms9081612 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1612

Author(s):

Werner Ruppitsch ◽

Andjela Nisic ◽

Patrick Hyden ◽

Adriana Cabal ◽

Jasmin Sucher ◽

...

Keyword(s):

Genetic Diversity ◽

Safety Evaluation ◽

Gene Clusters ◽

Northern Region ◽

Genomic Diversity ◽

High Genetic Diversity ◽

Pathogenic Factors ◽

Flavor Development ◽

Genomic Characterization

In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank.

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Karyotype Characterization of Nine Periwinkle Species (Gastropoda, Littorinidae)

Genes ◽

10.3390/genes9110517 ◽

2018 ◽

Vol 9 (11) ◽

pp. 517 ◽

Cited By ~ 3

Author(s):

Daniel García-Souto ◽

Sandra Alonso-Rubido ◽

Diana Costa ◽

José Eirín-López ◽

Emilio Rolán-Álvarez ◽

...

Keyword(s):

Dna Sequences ◽

Chromosome Numbers ◽

Gene Clusters ◽

Chromosomal Mapping ◽

Closely Related Species ◽

Submetacentric Chromosome ◽

The Family ◽

Littorina Arcana

Periwinkles of the family Littorinidae (Children, 1834) are common members of seashore littoral communities worldwide. Although the family is composed of more than 200 species belonging to 18 genera, chromosome numbers have been described in only eleven of them. A molecular cytogenetic analysis of nine periwinkle species, the rough periwinkles Littorina arcana, L. saxatilis, and L. compressa, the flat periwinkles L. obtusata and L. fabalis, the common periwinkle L. littorea, the mangrove periwinkle Littoraria angulifera, the beaded periwinkle Cenchritis muricatus, and the small periwinkle Melarhaphe neritoides was performed. All species showed diploid chromosome numbers of 2n = 34, and karyotypes were mostly composed of metacentric and submetacentric chromosome pairs. None of the periwinkle species showed chromosomal differences between male and female specimens. The chromosomal mapping of major and minor rDNA and H3 histone gene clusters by fluorescent in situ hybridization demonstrated that the patterns of distribution of these DNA sequences were conserved among closely related species and differed among less related ones. All signals occupied separated loci on different chromosome pairs without any evidence of co-localization in any of the species.

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Aromatic Polyketides from a Symbiotic Strain Aspergillus fumigatus D and Characterization of Their Biosynthetic Gene D8.t287

Marine Drugs ◽

10.3390/md18060324 ◽

2020 ◽

Vol 18 (6) ◽

pp. 324

Author(s):

Yi Hua ◽

Rui Pan ◽

Xuelian Bai ◽

Bin Wei ◽

Jianwei Chen ◽

...

Keyword(s):

Aspergillus Fumigatus ◽

Polyketide Synthase ◽

Gene Knockout ◽

Gene Clusters ◽

Inhibitory Effect ◽

Genomic Feature ◽

Biosynthetic Gene ◽

Aromatic Polyketides ◽

Staphyloccocus Aureus ◽

Coastal Plant

The chemical investigation of one symbiotic strain, Aspergillus fumigatus D, from the coastal plant Edgeworthia chrysantha Lindl led to the isolation of eight compounds (1–8), which were respectively identified as rubrofusarin B (1), alternariol 9-O-methyl ether (2), fonsecinone D (3), asperpyrone A (4), asperpyrone D (5), fonsecinone B (6), fonsecinone A (7), and aurasperone A (8) by a combination of spectroscopic methods (1D NMR and ESI-MS) as well as by comparison with the literature data. An antimicrobial assay showed that these aromatic polyketides exhibited no remarkable inhibitory effect on Escherichia coli, Staphyloccocus aureus and Candida albicans. The genomic feature of strain D was analyzed, as well as its biosynthetic gene clusters, using antibiotics and Secondary Metabolite Analysis Shell 5.1.2 (antiSMASH). Plausible biosynthetic pathways for dimeric naphtho-γ-pyrones 3–8 were first proposed in this work. A non-reducing polyketide synthase (PKS) gene D8.t287 responsible for the biosynthesis of these aromatic polyketides 1–8 was identified and characterized by target gene knockout experiment and UPLC-MS analysis.

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