Roles of LuxR-family regulators in the biosynthesis of secondary metabolites in Actinobacteria

Li, Zhangqun; Li, Xiaofang; Xia, Haiyang

doi:10.1007/s11274-022-03414-1

Cited by 7 publications

(5 citation statements)

References 88 publications

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“…An assortment of sigma factors present in a genome is a proxy of physiological and developmental characteristics, primarily since accessory sigma factors (such as ECF) usually activate the transcription of specific gene sets in response to environmental signals [80]. Selfsame, this bacterium possesses proteins involved in the Lux operon, which regulates the expression of different genes involved in virulence factor expression, exoenzyme secretion, biofilm formation, motility, oxidative stress response, cellulase synthesis, carbon metabolism, RNA processing, sugar transport, and vitamin and biosynthesis of secondary metabolites [81].…”

Section: Discussionmentioning

confidence: 99%

“…In Actinobacteriota, LuxR regulators are associated with different domains, and such combinations of domains result in modulation of the expression of different genes, including genes for the biosynthesis of secondary metabolites [81, 89]. Moreover, the specific combination of the LuxR+domain is dependent on the environmental origin of the bacterium, with a positive correlation between the number of LuxR proteins and the association with plants [89].…”

Section: Discussionmentioning

confidence: 99%

“…Selfsame, this bacterium possesses proteins involved in the Lux operon, which regulates the expression of different genes involved in virulence factor expression, exoenzyme secretion, biofilm formation, motility, oxidative stress response, cellulase synthesis, carbon metabolism, RNA processing, sugar transport, and vitamin and biosynthesis of secondary metabolites [81]. Some core proteins allow Solirubrobacter to resist different types of environmental stresses, such as oxidative, osmotic, or temperature shock.…”

Section: Discussionmentioning

confidence: 99%

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Unraveling the Genomic and Environmental Diversity of the UbiquitousSolirubrobacter

Jara-Servín,

Mejia,

Romero

et al. 2023

Preprint

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2.AbstractSolirubrobacter, a genus within the Actinobacteriota phylum, is commonly found in soils and rhizospheres yet remains unexplored despite its widespread presence and diversity, as revealed through metagenomic studies. Previously recognized as a prevalent soil bacterium, our study delved into phylogenomics, pangenomics, environmental diversity, and bacterial interactions ofSolirubrobacter. Analyzing the limited genomic sequences available for this genus, we uncovered a pangenome consisting of 19,645 protein families, with 2,644 constituting a strict core genome. While reported isolates do not exhibit motility, we intriguingly discovered the presence of flagellin genes, albeit with an incomplete flagellum assembly pathway. Our examination of 16S ribosomal genes unveiled a considerable diversity (3,166 operational taxonomic units OTUs) ofSolirubrobacterin Mexican soils, and co-occurrence network analysis indicated its extensive connectivity with other bacterial taxa. Through phylogenomic analysis, we delved into the relatedness of sequenced strains and notably dismissed ASM999324v1 as a member of this genus. Our investigation extended to the metagenomic diversity ofSolirubrobacteracross various environments, affirming its pervasive presence in rhizospheres and certain soils. This broader pangenomic view revealed genes linked to transcription, signal transduction, defense mechanisms, and carbohydrate metabolism, highlightingSolirubrobacter’sadaptability. We observed thatSolirubrobacter’sprevalence in rhizospheres is geographically indiscriminate, prompting intriguing questions about its potential interactions with plants and the biotic and abiotic determinants of its soil occurrence. Given its richness and diversity,Solirubrobactermight be a versatile yet overlooked keystone species in its environments, meriting further recognition and study.3.Impact statementThis study explored the enigmatic world ofSolirubrobacter, a widespread microbe commonly found in soils and plants across various regions. Despite its prevalence, little is known about its genetic diversity and functionality and how it thrives in diverse environments. Our research unveils the genetic secrets ofSolirubrobacter, shedding light on its adaptability and ecological interactors and roles. We showed thatSolirubrobacterenvironmental prevalence makes it a good candidate for studying the genetic basis of being a successful microbe associated with soil and plants.4.Data summaryData, scripts and statistical analysis available in GitHub:https://github.com/genomica-fciencias-unam/SolirubrobacterSequences, phylogenetic analysis, raw data structures:https://doi.org/10.6084/m9.figshare.2444652116S rRNA gene raw data:https://www.ncbi.nlm.nih.gov/sra/PRJNA603586https://www.ncbi.nlm.nih.gov/sra/PRJNA603590Shotgun metagenomes:https://www.ncbi.nlm.nih.gov/bioproject/603603All supporting data, code, and protocols are within the article, supplementary files, and described repositories.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Unraveling the Genomic and Environmental Diversity of the UbiquitousSolirubrobacter

Jara-Servín,

Mejia,

Romero

et al. 2023

Preprint

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“…In addition, several large SARPs have specific domain architectures, which include an N-terminal SARP domain and half of a C-terminal that is homologous to guanylate cyclases and LAL regulators (large ATP-binding regulators of the LuxR family) ( Li et al, 2022 ). The C-terminal half includes the ATP/GTP binding domain that is characteristic of these protein families but lacks the signature sequence at the N-terminus of guanylate cyclases or the LuxR-type helix-turn-helix (HTH) motif for DNA binding present at the C-terminus of LAL regulators ( Barreales et al, 2018 ).…”

Section: The Functional Domain Organization and Classification Of Sarpsmentioning

confidence: 99%

“…The pimR gene, which encodes the SARP-LAL regulator, and the pimM gene, which encodes the PAS-LuxR regulator, are located in the pimaricin BGC in S. natalensis . PimR binds the promoter of pimM and activates its transcription, and in turn, PimM activates the transcription of biosynthetic genes in the pimaricin BGC ( Santos-Aberturas et al, 2012 ; Li et al, 2022 ). The PimR-binding site contains three heptameric direct repeats separated by four nucleotide spacers that do not overlap the-35 promoter box ( Tanaka et al, 2007 ; Santos-Aberturas et al, 2012 ).…”

Section: The Regulatory Function Of Sarps In Secondary Metabolismmentioning

confidence: 99%

The roles of SARP family regulators involved in secondary metabolism in Streptomyces

Yan,

Xia

2024

Front. Microbiol.

Self Cite

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Streptomyces species are best known for their ability to produce abundant secondary metabolites with versatile bioactivities and industrial importance. These metabolites are usually biosynthesized through metabolic pathways encoded by cluster-situated genes. These genes are also known as biosynthetic gene clusters (BGCs) of secondary metabolites. The expression of BGCs is intricately controlled by pyramidal transcriptional regulatory cascades, which include various regulators. Streptomyces antibiotic regulatory proteins (SARPs), a genus-specific family of regulators, are widely distributed and play important roles in regulating the biosynthesis of secondary metabolites in Streptomyces. Over the past decade, the biological functions of SARPs have been extensively investigated. Here, we summarized the recent advances in characterizing the roles of SARPs involved in Streptomyces secondary metabolism from the following three aspects. First, the classification and domain organization of SARPs were summarized according to their size variation. Second, we presented a detailed description of the regulatory mechanisms and modes of action of SARPs involved in secondary metabolism. Finally, the biotechnological application of SARPs was illustrated by improving the production of target secondary metabolites and discovering novel bioactive natural products. This review will help researchers to comprehensively understand the roles of SARPs in secondary metabolite biosynthesis in Streptomyces, which will contribute to building a solid foundation for their future application in synthetic biology.

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Insights into the roles of biochar pores toward alleviating antibiotic resistance genes accumulation in biofiltration systems

Wei,

Zheng,

Han

et al. 2024

Bioresource Technology

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Roles of LuxR-family regulators in the biosynthesis of secondary metabolites in Actinobacteria

Cited by 7 publications

References 88 publications

Unraveling the Genomic and Environmental Diversity of the UbiquitousSolirubrobacter

Unraveling the Genomic and Environmental Diversity of the UbiquitousSolirubrobacter

The roles of SARP family regulators involved in secondary metabolism in Streptomyces

Insights into the roles of biochar pores toward alleviating antibiotic resistance genes accumulation in biofiltration systems

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