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Current Opinion in Microbiology Apr 2024Streptomyces are a large genus of multicellular bacteria best known for their prolific production of bioactive natural products. In addition, they play key roles in the... (Review)
Review
Streptomyces are a large genus of multicellular bacteria best known for their prolific production of bioactive natural products. In addition, they play key roles in the mineralisation of insoluble resources, such as chitin and cellulose. Because of their multicellular mode of growth, colonies of interconnected hyphae extend over a large area that may experience different conditions in different parts of the colony. Here, we argue that within-colony phenotypic heterogeneity can allow colonies to simultaneously respond to divergent inputs from resources or competitors that are spatially and temporally dynamic. We discuss causal drivers of heterogeneity, including competitors, precursor availability, metabolic diversity and division of labour, that facilitate divergent phenotypes within Streptomyces colonies. We discuss the adaptive causes and consequences of within-colony heterogeneity, highlight current knowledge (gaps) and outline key questions for future studies.
Topics: Streptomyces; Phenotype
PubMed: 38447313
DOI: 10.1016/j.mib.2024.102448 -
Biotechnology and Applied Biochemistry Aug 2023Actinomycetes are a distinct group of filamentous bacteria. The Streptomyces genus within this group has been extensively studied over the years, with substantial... (Review)
Review
Actinomycetes are a distinct group of filamentous bacteria. The Streptomyces genus within this group has been extensively studied over the years, with substantial contributions to society and science. This genus is known for its antimicrobial production, as well as antitumor, biopesticide, and immunomodulatory properties. Therefore, the extraordinary plasticity of the Streptomyces genus has inspired new research techniques. The newest way of exploring Streptomyces has comprised the discovery of new natural metabolites and the application of emerging tools such as CRISPR technology in drug discovery. In this narrative review, we explore relevant published literature concerning the ongoing novelties of the Streptomyces genus.
Topics: Streptomyces; Biotechnology; Anti-Infective Agents; Actinobacteria
PubMed: 36924211
DOI: 10.1002/bab.2455 -
Canadian Journal of Microbiology Jun 2024have a uniquely complex developmental life cycle that involves the coordination of morphological differentiation with the production of numerous bioactive specialized... (Review)
Review
have a uniquely complex developmental life cycle that involves the coordination of morphological differentiation with the production of numerous bioactive specialized metabolites. The majority of spp. are soil-dwelling saprophytes, while plant pathogenicity is a rare attribute among members of this genus Phytopathogenic are responsible for economically important diseases such as common scab, which affects potato and other root crops. Following the acquisition of genes encoding virulence factors, pathogens are expected to have specifically adapted their regulatory pathways to enable transition from a primarily saprophytic to a pathogenic lifestyle. Investigations of the regulation of pathogenesis have primarily focused on and the principal pathogenicity determinant thaxtomin A. The coordination of growth and thaxtomin A production in this species is controlled in a hierarchical manner by cluster-situated regulators, pleiotropic regulators, signalling and plant-derived molecules, and nutrients. Although the majority of phytopathogenic produce thaxtomins, many also produce additional virulence factors, and there are scab-causing pathogens that do not produce thaxtomins. The development of effective control strategies for common scab and other plant diseases requires a more in-depth understanding of the genetic and environmental factors that modulate the plant pathogenic lifestyle of these organisms.
Topics: Streptomyces; Plant Diseases; Virulence; Virulence Factors; Gene Expression Regulation, Bacterial; Bacterial Proteins; Plants; Solanum tuberosum; Indoles; Piperazines
PubMed: 38190652
DOI: 10.1139/cjm-2023-0171 -
Environmental Microbiome Mar 2024The complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the...
BACKGROUND
The complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the seeds is still relatively unexplored and no studies have been conducted with olive trees so far. In this study, we aimed to characterize the bacterial, fungal and archaeal communities present in seeds of ten olive genotypes growing in the same orchard through amplicon sequencing to test whether the olive genotype is a major driver in shaping the seed microbial community, and to identify the origin of the latter. Therefore, we have developed a methodology for obtaining samples from the olive seed's endosphere under sterile conditions.
RESULTS
A diverse microbiota was uncovered in olive seeds, the plant genotype being an important factor influencing the structure and composition of the microbial communities. The most abundant bacterial phylum was Actinobacteria, accounting for an average relative abundance of 41%. At genus level, Streptomyces stood out because of its potential influence on community structure. Within the fungal community, Basidiomycota and Ascomycota were the most abundant phyla, including the genera Malassezia, Cladosporium, and Mycosphaerella. The shared microbiome was composed of four bacterial (Stenotrophomonas, Streptomyces, Promicromonospora and Acidipropionibacterium) and three fungal (Malassezia, Cladosporium and Mycosphaerella) genera. Furthermore, a comparison between findings obtained here and earlier results from the root endosphere of the same trees indicated that genera such as Streptomyces and Malassezia were present in both olive compartments.
CONCLUSIONS
This study provides the first insights into the composition of the olive seed microbiota. The highly abundant fungal genus Malassezia and the bacterial genus Streptomyces reflect a unique signature of the olive seed microbiota. The genotype clearly shaped the composition of the seed's microbial community, although a shared microbiome was found. We identified genera that may translocate from the roots to the seeds, as they were present in both organs of the same trees. These findings set the stage for future research into potential vertical transmission of olive endophytes and the role of specific microbial taxa in seed germination, development, and seedling survival.
PubMed: 38491515
DOI: 10.1186/s40793-024-00560-x -
Trends in Genetics : TIG Nov 2023Streptomyces are prolific producers of specialized metabolites with applications in medicine and agriculture. Remarkably, these bacteria possess a large linear... (Review)
Review
Streptomyces are prolific producers of specialized metabolites with applications in medicine and agriculture. Remarkably, these bacteria possess a large linear chromosome that is genetically compartmentalized: core genes are grouped in the central part, while the ends are populated by poorly conserved genes including antibiotic biosynthetic gene clusters. The genome is highly unstable and exhibits distinct evolutionary rates along the chromosome. Recent chromosome conformation capture (3C) and comparative genomics studies have shed new light on the interplay between genome dynamics in space and time. Here, we review insights that illustrate how the balance between chance (random genome variations) and necessity (structural and functional constraints) may have led to the emergence of spatial structuring of the Streptomyces chromosome.
PubMed: 37679290
DOI: 10.1016/j.tig.2023.07.008 -
Journal of Agricultural and Food... Jan 2024Sustainable agriculture is increasingly linked to biological pesticides as alternatives to agro-chemicals. species suppress plant diseases through their unique traits... (Review)
Review
Sustainable agriculture is increasingly linked to biological pesticides as alternatives to agro-chemicals. species suppress plant diseases through their unique traits and numerous metabolites. Although many strains have been developed into commercial products, their roles in the biocontrol of phytopathogens and mechanisms of functional metabolite synthesis remain poorly understood. In this review, biocontrol of plant diseases by is summarized on the basis of classification of fungal and bacterial diseases and secondary metabolites produced by that act on phytopathogenic microorganisms are discussed. The associated non-ribosomal peptide synthetases and polyketide synthetases responsible for biosynthesis of these secondary metabolites are also investigated, and advances in fermentation of are described. Finally, the need to develop precise and effective biocontrol methods for plant diseases is highlighted.
Topics: Streptomyces; Agriculture; Fermentation; Biological Control Agents; Plant Diseases
PubMed: 38230633
DOI: 10.1021/acs.jafc.3c08265 -
Biomolecules Apr 2024In recent years, CRISPR-Cas toolboxes for editing have rapidly accelerated natural product discovery and engineering. However, Cas efficiencies are oftentimes...
In recent years, CRISPR-Cas toolboxes for editing have rapidly accelerated natural product discovery and engineering. However, Cas efficiencies are oftentimes strain-dependent, and the commonly used Cas9 (SpCas9) is notorious for having high levels of off-target toxicity effects. Thus, a variety of Cas proteins is required for greater flexibility of genetic manipulation within a wider range of strains. This study explored the first use of sp. Cas12j, a hypercompact Cas12 subfamily, for genome editing in and its potential in activating silent biosynthetic gene clusters (BGCs) to enhance natural product synthesis. While the editing efficiencies of Cas12j were not as high as previously reported efficiencies of Cas12a and Cas9, Cas12j exhibited higher transformation efficiencies compared to SpCas9. Furthermore, Cas12j demonstrated significantly improved editing efficiencies compared to Cas12a in activating BGCs in sp. A34053, a strain wherein both SpCas9 and Cas12a faced limitations in accessing the genome. Overall, this study expanded the repertoire of Cas proteins for genome editing in actinomycetes and highlighted not only the potential of recently characterized Cas12j in but also the importance of having an extensive genetic toolbox for improving the editing success of these beneficial microbes.
Topics: Streptomyces; Gene Editing; CRISPR-Cas Systems; Acidaminococcus; CRISPR-Associated Protein 9; Multigene Family; Bacterial Proteins; CRISPR-Associated Proteins; Genome, Bacterial
PubMed: 38672502
DOI: 10.3390/biom14040486 -
Scientific Reports Nov 2023Despite the rising interest in bacteriophages, little is known about their infection cycle and lifestyle in a multicellular host. Even in the model system Streptomyces,...
Despite the rising interest in bacteriophages, little is known about their infection cycle and lifestyle in a multicellular host. Even in the model system Streptomyces, only a small number of phages have been sequenced and well characterized so far. Here, we report the complete characterization and genome sequences of Streptomyces phages Vanseggelen and Verabelle isolated using Streptomyces coelicolor as a host. A wide range of Streptomyces strains could be infected by both phages, but neither of the two phages was able to infect members of the closely related sister genus Kitasatospora. The phages Vanseggelen and Verabelle have a double-stranded DNA genome with lengths of 48,720 and 48,126 bp, respectively. Both phage genomes contain 72 putative genes, and the presence of an integrase encoding protein indicates a lysogenic lifestyle. Characterization of the phages revealed their stability over a wide range of temperatures (30-45 °C) and pH values (4-10). In conclusion, Streptomyces phage Vanseggelen and Streptomyces phage Verabelle are newly isolated phages that can be classified as new species in the genus Camvirus, within the subfamily Arquattrovirinae.
Topics: Bacteriophages; Streptomyces; Genome, Viral; DNA, Viral; Siphoviridae; Phylogeny
PubMed: 37978256
DOI: 10.1038/s41598-023-47634-3 -
Microbial Cell Factories Jul 2023Streptomyces are well known for their potential to produce various pharmaceutically active compounds, the commercial development of which is often limited by the low...
BACKGROUND
Streptomyces are well known for their potential to produce various pharmaceutically active compounds, the commercial development of which is often limited by the low productivity and purity of the desired compounds expressed by natural producers. Well-characterized promoters are crucial for driving the expression of target genes and improving the production of metabolites of interest.
RESULTS
A strong constitutive promoter, stnYp, was identified in Streptomyces flocculus CGMCC4.1223 and was characterized by its effective activation of silent biosynthetic genes and high efficiency of heterologous gene expression. The promoter stnYp showed the highest activity in model strains of four Streptomyces species compared with the three frequently used constitutive promoters ermEp*, kasOp*, and SP44. The promoter stnYp could efficiently activate the indigoidine biosynthetic gene cluster in S. albus J1074, which is thought to be silent under routine laboratory conditions. Moreover, stnYp was found suitable for heterologous gene expression in different Streptomyces hosts. Compared with the promoters ermEp*, kasOp*, and SP44, stnYp conferred the highest production level of diverse metabolites in various heterologous hosts, including the agricultural-bactericide aureonuclemycin and the antitumor compound YM-216391, with an approximately 1.4 - 11.6-fold enhancement of the yields. Furthermore, the purity of tylosin A was greatly improved by overexpressing rate-limiting genes through stnYp in the industrial strain. Further, the yield of tylosin A was significantly elevated to 10.30 ± 0.12 g/L, approximately 1.7-fold higher than that of the original strain.
CONCLUSIONS
The promoter stnYp is a reliable, well-defined promoter with strong activity and broad suitability. The findings of this study can expand promoter diversity, facilitate genetic manipulation, and promote metabolic engineering in multiple Streptomyces species.
Topics: Tylosin; Biological Products; Streptomyces; Promoter Regions, Genetic; Multigene Family
PubMed: 37443029
DOI: 10.1186/s12934-023-02136-9 -
International Journal of Systematic and... Sep 2023Two novel actinobacterial strains, designated RB6PN23 and K1PA1, were isolated from peat swamp soil samples in Thailand and characterized using a polyphasic taxonomic...
Two novel actinobacterial strains, designated RB6PN23 and K1PA1, were isolated from peat swamp soil samples in Thailand and characterized using a polyphasic taxonomic approach. The strains were filamentous Gram-stain-positive bacteria containing -diaminopimelic acid in their whole-cell hydrolysates. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strain RB6PN23 was most closely related to (99.1 % sequence similarity) and (98.5%), while strain K1PA1 showed 98.8 and 98.7% sequence similarities to and , respectively. However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were below the species-level thresholds (95-96 % ANI and 70 % dDDH). The genomes of strains RB6PN23 and K1PA1 were estimated to be 7.88 Mbp and 7.39 Mbp in size, respectively, with DNA G+C contents of 70.2 and 73.2 mol%. Moreover, strains RB6PN23 and K1PA1 encode 37 and 24 putative biosynthetic gene clusters, respectively, and analysis revealed that these new species have a high potential to produce unique natural products. Genotypic and phenotypic characteristics confirmed that strains RB6PN23 and K1PA1 represented two novel species in the genus . The names proposed for these strains are sp. nov. (type strain RB6PN23=TBRC 17040=NBRC 116113) and sp. nov. (type strain K1PA1=TBRC 17041=NBRC 116114). Additionally, a giant linear polyene compound, neotetrafibricin A, exhibiting antifungal activity in strain RB6PN23, was identified through HPLC and quadrupole time-of-flight MS analysis. The crude extract from the culture broth of strain RB6PN23 exhibited strong antifungal activity against , and . This finding suggests that strain RB6PN23 could be a promising candidate for biological control of fungal diseases.
PubMed: 37768174
DOI: 10.1099/ijsem.0.006063