Biosynthetic gene profiling and genomic potential of the novel photosynthetic marine bacterium Roseibaca domitiana
Shifting the bioprospecting targets toward underexplored bacterial groups combined with genome mining studies contributes to avoiding the rediscovery of known compounds by revealing novel, promising biosynthetic gene clusters (BGCs). With the aim of determining the biosynthetic potential of a novel...
Published in: | Frontiers in Microbiology |
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ftdoajarticles:oai:doaj.org/article:367534367030413e91f3a586243b9cd9 2023-11-05T03:33:53+01:00 Biosynthetic gene profiling and genomic potential of the novel photosynthetic marine bacterium Roseibaca domitiana Giuliano Gattoni Fabiana Di Costanzo Rafael R. de la Haba Ana B. Fernández Shaday Guerrero-Flores Nelly Selem-Mojica Antonio Ventosa Paulina Corral 2023-09-01T00:00:00Z https://doi.org/10.3389/fmicb.2023.1238779 https://doaj.org/article/367534367030413e91f3a586243b9cd9 EN eng Frontiers Media S.A. https://www.frontiersin.org/articles/10.3389/fmicb.2023.1238779/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2023.1238779 https://doaj.org/article/367534367030413e91f3a586243b9cd9 Frontiers in Microbiology, Vol 14 (2023) biosynthetic profiling photosynthetic bacteria bacteriochlorophyll genome mining Roseibaca biosynthetic gene cluster (BGC) Microbiology QR1-502 article 2023 ftdoajarticles https://doi.org/10.3389/fmicb.2023.1238779 2023-10-08T00:36:46Z Shifting the bioprospecting targets toward underexplored bacterial groups combined with genome mining studies contributes to avoiding the rediscovery of known compounds by revealing novel, promising biosynthetic gene clusters (BGCs). With the aim of determining the biosynthetic potential of a novel marine bacterium, strain V10T, isolated from the Domitian littoral in Italy, a comparative phylogenomic mining study was performed across related photosynthetic bacterial groups from an evolutionary perspective. Studies on polyphasic and taxogenomics showed that this bacterium constitutes a new species, designated Roseibaca domitiana sp. nov. To date, this genus has only one other validly described species, which was isolated from a hypersaline Antarctic lake. The genomic evolutionary study linked to BGC diversity revealed that there is a close relationship between the phylogenetic distance of the members of the photosynthetic genera Roseibaca, Roseinatronobacter, and Rhodobaca and their BGC profiles, whose conservation pattern allows discriminating between these genera. On the contrary, the rest of the species related to Roseibaca domitiana exhibited an individual species pattern unrelated to genome size or source of isolation. This study showed that photosynthetic strains possess a streamlined content of BGCs, of which 94.34% of the clusters with biotechnological interest (NRPS, PKS, RRE, and RiPP) are completely new. Among these stand out T1PKS, exclusive of R. domitiana V10T, and RRE, highly conserved only in R. domitiana V10T and R. ekhonensis, both categories of BGCs involved in the synthesis of plant growth-promoting compounds and antitumoral compounds, respectively. In all cases, with very low homology with already patented molecules. Our findings reveal the high biosynthetic potential of infrequently cultured bacterial groups, suggesting the need to redirect attention to microbial minorities as a novel and vast source of bioactive compounds still to be exploited. Article in Journal/Newspaper Antarc* Antarctic Directory of Open Access Journals: DOAJ Articles Frontiers in Microbiology 14 |
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Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
biosynthetic profiling photosynthetic bacteria bacteriochlorophyll genome mining Roseibaca biosynthetic gene cluster (BGC) Microbiology QR1-502 |
spellingShingle |
biosynthetic profiling photosynthetic bacteria bacteriochlorophyll genome mining Roseibaca biosynthetic gene cluster (BGC) Microbiology QR1-502 Giuliano Gattoni Fabiana Di Costanzo Rafael R. de la Haba Ana B. Fernández Shaday Guerrero-Flores Nelly Selem-Mojica Antonio Ventosa Paulina Corral Biosynthetic gene profiling and genomic potential of the novel photosynthetic marine bacterium Roseibaca domitiana |
topic_facet |
biosynthetic profiling photosynthetic bacteria bacteriochlorophyll genome mining Roseibaca biosynthetic gene cluster (BGC) Microbiology QR1-502 |
description |
Shifting the bioprospecting targets toward underexplored bacterial groups combined with genome mining studies contributes to avoiding the rediscovery of known compounds by revealing novel, promising biosynthetic gene clusters (BGCs). With the aim of determining the biosynthetic potential of a novel marine bacterium, strain V10T, isolated from the Domitian littoral in Italy, a comparative phylogenomic mining study was performed across related photosynthetic bacterial groups from an evolutionary perspective. Studies on polyphasic and taxogenomics showed that this bacterium constitutes a new species, designated Roseibaca domitiana sp. nov. To date, this genus has only one other validly described species, which was isolated from a hypersaline Antarctic lake. The genomic evolutionary study linked to BGC diversity revealed that there is a close relationship between the phylogenetic distance of the members of the photosynthetic genera Roseibaca, Roseinatronobacter, and Rhodobaca and their BGC profiles, whose conservation pattern allows discriminating between these genera. On the contrary, the rest of the species related to Roseibaca domitiana exhibited an individual species pattern unrelated to genome size or source of isolation. This study showed that photosynthetic strains possess a streamlined content of BGCs, of which 94.34% of the clusters with biotechnological interest (NRPS, PKS, RRE, and RiPP) are completely new. Among these stand out T1PKS, exclusive of R. domitiana V10T, and RRE, highly conserved only in R. domitiana V10T and R. ekhonensis, both categories of BGCs involved in the synthesis of plant growth-promoting compounds and antitumoral compounds, respectively. In all cases, with very low homology with already patented molecules. Our findings reveal the high biosynthetic potential of infrequently cultured bacterial groups, suggesting the need to redirect attention to microbial minorities as a novel and vast source of bioactive compounds still to be exploited. |
format |
Article in Journal/Newspaper |
author |
Giuliano Gattoni Fabiana Di Costanzo Rafael R. de la Haba Ana B. Fernández Shaday Guerrero-Flores Nelly Selem-Mojica Antonio Ventosa Paulina Corral |
author_facet |
Giuliano Gattoni Fabiana Di Costanzo Rafael R. de la Haba Ana B. Fernández Shaday Guerrero-Flores Nelly Selem-Mojica Antonio Ventosa Paulina Corral |
author_sort |
Giuliano Gattoni |
title |
Biosynthetic gene profiling and genomic potential of the novel photosynthetic marine bacterium Roseibaca domitiana |
title_short |
Biosynthetic gene profiling and genomic potential of the novel photosynthetic marine bacterium Roseibaca domitiana |
title_full |
Biosynthetic gene profiling and genomic potential of the novel photosynthetic marine bacterium Roseibaca domitiana |
title_fullStr |
Biosynthetic gene profiling and genomic potential of the novel photosynthetic marine bacterium Roseibaca domitiana |
title_full_unstemmed |
Biosynthetic gene profiling and genomic potential of the novel photosynthetic marine bacterium Roseibaca domitiana |
title_sort |
biosynthetic gene profiling and genomic potential of the novel photosynthetic marine bacterium roseibaca domitiana |
publisher |
Frontiers Media S.A. |
publishDate |
2023 |
url |
https://doi.org/10.3389/fmicb.2023.1238779 https://doaj.org/article/367534367030413e91f3a586243b9cd9 |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
Frontiers in Microbiology, Vol 14 (2023) |
op_relation |
https://www.frontiersin.org/articles/10.3389/fmicb.2023.1238779/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2023.1238779 https://doaj.org/article/367534367030413e91f3a586243b9cd9 |
op_doi |
https://doi.org/10.3389/fmicb.2023.1238779 |
container_title |
Frontiers in Microbiology |
container_volume |
14 |
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1781701818482425856 |