Biology subjects

Lautru, S.

Publications and source records attributed to Lautru, S..

6 recordsLinked to original sources

bioRxiv2026

Effect of gene cluster relocation to the central chromosomal compartment on its expression in Streptomyces

Streptomyces bacteria are renowned for their intricate life cycle and prolific production of specialized metabolites, including antibiotics. Their linear chromosome is spatially compartmentalized: the central region contains highly conserved and expressed genes, while the terminal regions harbor less conserved, poorly expressed sequences, often rich in specialized metabolite biosynthetic gene clusters. To investigate the relationship between genome architecture and gene expression, we relocated the congocidine antibiotic biosynthetic gene cluster (CGC) from its native terminal position to the central compartment in Streptomyces ambofaciens. This relocation enhanced CGC transcription compared to its original terminal location, both in antisense orientation during exponential growth and in sense orientation after metabolic differentiation, resulting in 50% increase in congocidine production. At the 3D-level, transcription-induced domains formed at both the relocated and native CGC sites, creating sharp boundaries at a larger scale. Notably, the formation of such a boundary in the central compartment during the early stationary phase did not disrupt interarm contacts or affect neighboring gene expression. These results indicate that relocating a terminal cluster to the central chromosomal compartment provides a more favorable environment for transcription without altering chromosome compaction in the stationary phase, offering a promising strategy to enhance antibiotic production in the native host. Key points- Central relocation of a gene cluster enhanced its transcription while preserving chromosome compaction. - A transcription-induced domain formed at the new locus without altering neighboring gene expression. - This strategy increased antibiotic yield by 50% in the native host.

microbiology↗

bioRxiv2025

Identification of the negamycin split biosynthetic gene cluster in Kitasatospora purpeofusca ATCC21470

Negamycin is a ribosome-targeting antibiotic with activity against Gram-positive and Gram-negative bacteria including ESKAPE pathogens. Furthermore, it promotes premature stop codon readthrough. Its therapeutic potential is limited by low natural production and synthetic complexity. To enable scalable biosynthesis, we identified and characterized its genetic basis in Kitasatospora purpeofusca ATCC 21470. Two distant chromosomal regions, neg1 and neg2, were found to be essential. Deletion of neg1, involved in nitrite provision for N-N bond formation, reduced production to [~]10%, while deletion of neg2, which directs {beta}-lysine generation and scaffold assembly, abolished it completely. Isotope-labeling experiments confirmed nitrite incorporation. Transcriptomic and proteomic analyses further supported the involvement of both regions. The heterologous expression of neg1 along with the neg2 region in Streptomyces albidoflavus reconstituted negamycin biosynthesis, confirming the unusual involvement of two distant gene clusters in the biosynthesis, and provides a foundation for biotechnological production and further development of this promising antibiotic. SIGNIFICANCEThe rapid rise of antimicrobial resistance (AMR), particularly among Gram-negative ESKAPE pathogens, represents one of the most urgent global health threats. Despite this, the discovery and development of new antibiotics have stagnated. Addressing this challenge requires the exploration of natural products with novel mechanisms of action, alongside the development of scalable production strategies. Negamycin has emerged as a compelling candidate in this regard, characterized by an unusual mechanism of action and therapeutic potential extending beyond traditional antibacterial use. However, its development has been constrained by low production yields in the native producer. In this study, we identify and characterize the biosynthetic genes responsible for negamycin production, providing a foundation for pathway engineering, yield optimization, and the rational design of new analogs.

microbiology↗

bioRxiv2024

Root associated Streptomyces produce galbonolides to modulate plant immunity and promote rhizosphere colonisation

The rhizosphere, which serves as the primary interface between plant roots and the soil, constitutes an ecological niche for a huge diversity of microbial communities. Currently, there is little knowledge on the nature and the function of the different metabolites released by rhizospheric microbes to facilitate colonization of this highly competitive environment. Here, we demonstrate how the production of galbonolides, a group of polyene macrolides that inhibit plant and fungal Inositol Phosphorylceramide Synthase (IPCS), empowers the rhizospheric Streptomyces strain AgN23, to thrive in the rhizosphere by triggering the plants defence mechanisms. Metabolomic analysis of AgN23-inoculated Arabidopsis roots revealed a strong induction in the production of an indole alkaloid, camalexin, which is a major phytoalexin in Arabidopsis. By using a plant mutant compromised in camalexin synthesis, we show that camalexin production is necessary for the successful colonization of the rhizosphere by AgN23. Conversely, hindering galbonolides biosynthesis in AgN23 knock-out mutant resulted in loss of inhibition of IPCS, a deficiency in plant defence activation, notably the production of camalexin, and a strongly reduced development of the mutant bacteria in the rhizosphere. Together, our results identified galbonolides as important metabolites mediating rhizosphere colonisation by Streptomyces. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/576418v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1ec39f3org.highwire.dtl.DTLVardef@1d0a14eorg.highwire.dtl.DTLVardef@e1f61org.highwire.dtl.DTLVardef@12e487e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO Model summarizing the mode of action of galbonolides in stimulating plant defence to support AgN23 colonization of the rhizosphere. Galbonolides secretion by Streptomyces sp. AgN23 trigger Inositol Phosphoceramide Synthase (IPCS) inhibition in Arabidopsis root cells (orange arrow). The resulting raise in Ceramide precursors of the IPCS may result in the different defence responses associated to AgN23: Hypersensitive Responses (HR), Salicylic Acid (SA) signalling, nuclear Ca2+ influx, defence gene expression and camalexin biosynthesis. This production of camalexin (blue arrow) exert a positive effect on AgN23 growth in the rhizosphere, presumably by restricting the growth of bacterial and fungal competitors sensitive to this phytoalexin. In addition, galbonolides secretion in the rhizosphere may also directly interfere with fungal competitors of AgN23. C_FIG

microbiology↗

bioRxiv2024

SYNTERUPTOR: mining genomic islands for non-classical specialised metabolite gene clusters

Microbial specialised metabolite biosynthetic gene clusters (SMBGCs) are a formidable source of natural products of pharmaceutical interest. With the multiplication of genomic data available, very efficient bioinformatic tools for automatic SMBGC detection have been developed. Nevertheless, most of these tools identify SMBGCs based on sequence similarity with enzymes typically involved in specialised metabolism and thus may miss SMBGCs coding for under characterised enzymes. Here we present SYNTERUPTOR (https://bioi2.i2bc.paris-saclay.fr/synteruptor), a program that identifies genomic islands, known to be enriched in SMBGCs, in the genomes of closely related species. With this tool, we identified a SMBGC in the genome of Streptomyces ambofaciens ATCC23877, undetected by earlier versions of antiSMASH, and experimentally demonstrated that it directs the biosynthesis of two metabolites, one of which was identified as sphydrofuran. SYNTERUPTOR is also a valuable resource for the delineation of individual SMBGCs within antiSMASH regions that may encompass multiple clusters, and for refining the boundaries of these SMBGCs.

bioinformatics↗

bioRxiv2023

Phage-mediated dispersal of multicellular bacteria

Streptomyces are renowned for their prolific production of specialized metabolites with applications in medicine and agriculture. These multicellular bacteria present a sophisticated developmental cycle, and play a key role in soil ecology. Little is known about Streptomyces-phage interactions and the impact of phages on Streptomyces physiology. In this study, we investigated the conditions governing the expression and production of Samy, a prophage found in Streptomyces ambofaciens ATCC 23877. This siphoprophage is produced simultaneously with the activation of other mobile genetic elements. We show that Samy production increases bacterial dispersal under in vitro stress conditions. Altogether, we unveiled a new property of a bacteriophage infection that it is closely linked to the multicellular community life of Streptomyces bacteria. Graphical summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/549817v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@126b3fcorg.highwire.dtl.DTLVardef@1f26808org.highwire.dtl.DTLVardef@18bfdcforg.highwire.dtl.DTLVardef@1c44be3_HPS_FORMAT_FIGEXP M_FIG C_FIG IMPORTANCEStreptomyces are multicellular bacteria producing valuable metabolites, including antibiotics, with applications in medicine and agriculture. In this study, we characterized a novel temperate phage, named Samy, and its impact on bacteria physiology. Remarkably, the presence and production of Samy increases bacterial dispersal under in vitro stress conditions. This constitutes an emerging property associated with bacteriophage infection that might enhance the spread of the species. Our study reveals a new aspect of bacteriophage infection in the context of multicellular aggregate dynamics.

microbiology↗

bioRxiv2020

Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation

Streptomyces are among the most prolific bacterial producers of specialized metabolites, including antibiotics. The linear chromosome is partitioned into a central region harboring core genes and two extremities enriched in specialized metabolite biosynthetic gene clusters (SMBGCs). The molecular mechanisms governing structure and function of these compartmentalized genomes remain mostly unknown. Here we show that in exponential phase, chromosome structure correlates with genetic compartmentalization: conserved, large and highly transcribed genes form boundaries that segment the central part of the chromosome into domains, whereas the terminal ends are transcriptionally, largely quiescent compartments with different structural features. Onset of metabolic differentiation is accompanied by remodeling of chromosome architecture from an open to a rather closed conformation, in which the SMBGCs are expressed forming new boundaries. Altogether, our results reveal that S. ambofaciens linear chromosome is partitioned into structurally distinct entities, indicating a link between chromosome folding, gene expression and genome evolution.

microbiology↗