Molecular genetic analysis of determinants defining synthesis of 2,4-diacetylphloroglucinol by Pseudomonas brassicacearum BIM B-446 bacteria

Mandryk-Litvinkovich, M. N.; Muratova, A. A.; Nosonova, T. L.; Evdokimova, O. V.; Валентович, Л. Н.; Титок, М. А.; Коломиец, Э. И.

doi:10.1134/s0003683817010124

Cited by 11 publications

(3 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We also noticed that genes of COG1545 that were largely absent in most Kitasatospora strains but were quite abundant in the other two genera. It has been reported that proteins of COG1545 were involved in synthesis of 2,4-Diacetylphloroglucinol, a low-molecular weight polyketide antibiotic produced by Pseudomonas brassicacearum strains ( Mandryk-Litvinkovich et al, 2017 ), suggesting another obvious difference between genera. Nevertheless, more experimental evidences, both morphologically (e.g., morphological characteristics revealed by transmission electron microscopy) and biochemically, were needed to verified these differences, especially between Kitasatospora and Streptomyces .…”

Section: Discussionmentioning

confidence: 99%

Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces

Wang

Sun

et al. 2021

Front. Microbiol.

View full text Add to dashboard Cite

While the genus Streptomyces (family Streptomycetaceae) has been studied as a model for bacterial secondary metabolism and genetics, its close relatives have been less studied. The genus Kitasatospora is the second largest genus in the family Streptomycetaceae. However, its taxonomic position within the family remains under debate and the secondary metabolic potential remains largely unclear. Here, we performed systematic comparative genomic and phylogenomic analyses of Kitasatospora. Firstly, the three genera within the family Streptomycetaceae (Kitasatospora, Streptomyces, and Streptacidiphilus) showed common genomic features, including high G + C contents, high secondary metabolic potentials, and high recombination frequencies. Secondly, phylogenomic and comparative genomic analyses revealed phylogenetic distinctions and genome content differences among these three genera, supporting Kitasatospora as a separate genus within the family. Lastly, the pan-genome analysis revealed extensive genetic diversity within the genus Kitasatospora, while functional annotation and genome content comparison suggested genomic differentiation among lineages. This study provided new insights into genomic characteristics of the genus Kitasatospora, and also uncovered its previously underestimated and complex secondary metabolism.

show abstract

Section: Discussionmentioning

confidence: 99%

Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces

Wang

Sun

et al. 2021

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

“…Strain SC5 DAPG biosynthesis cluster ( phlACBDE and phlHGF ) presents high identity to the functional DAPG biosynthesis gene cluster of P. thivervalensis PITR2 (~99% identity; Keel et al, 1996 ; Molina et al, 2003 ), and other studied biocontrol Pseudomonas strains such as P. kilonensis F113 (~93% identity; Redondo-Nieto et al, 2013 ; Vacheron et al, 2018 ), P. brassicacearum BIM B-446 (~93% identity; Mandryk-Litvinkovich et al, 2017 ), P. brassicacearum 3Re2-7 (~93% identity; Nelkner et al, 2019 ), P. brassicacearum LBUM300 (~93% identity; Lanteigne et al, 2012 ; Novinscak et al, 2016 ), among others. Moreover, BLAST analysis revealed that the hcnABC gene cluster of P. thivervalensis SC5 also presented high identity to the functional hcnABC genes of several HCN-producing Pseudomonas , including P. thivervalensis PITR2 (~99% identity; Ramette et al, 2003 ), P. brassicacearum 3Re2-7 (~92% identity; Nelkner et al, 2019 ) and P. brassicacearum LBUM300 (~92% identity; Lanteigne et al, 2012 ; Novinscak et al, 2016 ).…”

Section: Resultsmentioning

confidence: 99%

Genomic Analysis of the 1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Pseudomonas thivervalensis SC5 Reveals Its Multifaceted Roles in Soil and in Beneficial Interactions With Plants

et al. 2021

View full text Add to dashboard Cite

Beneficial 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing bacteria promote plant growth and stress resistance, constituting a sustainable alternative to the excessive use of chemicals in agriculture. In this work, the increased plant growth promotion activity of the ACC deaminase-producing Pseudomonas thivervalensis SC5, its ability to limit the growth of phytopathogens, and the genomics behind these important properties are described in detail. P. thivervalensis SC5 displayed several active plant growth promotion traits and significantly increased cucumber plant growth and resistance against salt stress (100mmol/L NaCl) under greenhouse conditions. Strain SC5 also limited the in vitro growth of the pathogens Botrytis cinerea and Pseudomonas syringae DC3000 indicating active biological control activities. Comprehensive analysis revealed that P. thivervalensis SC5 genome is rich in genetic elements involved in nutrient acquisition (N, P, S, and Fe); osmotic stress tolerance (e.g., glycine-betaine, trehalose, and ectoine biosynthesis); motility, chemotaxis and attachment to plant tissues; root exudate metabolism including the modulation of plant phenolics (e.g., hydroxycinnamic acids), lignin, and flavonoids (e.g., quercetin); resistance against plant defenses (e.g., reactive oxygens species-ROS); plant hormone modulation (e.g., ethylene, auxins, cytokinins, and salicylic acid), and bacterial and fungal phytopathogen antagonistic traits (e.g., 2,4-diacetylphloroglucinol, HCN, a fragin-like non ribosomal peptide, bacteriocins, a lantipeptide, and quorum-quenching activities), bringing detailed insights into the action of this versatile plant-growth-promoting bacterium. Ultimately, the combination of both increased plant growth promotion/protection and biological control abilities makes P. thivervalensis SC5 a prime candidate for its development as a biofertilizer/biostimulant/biocontrol product. The genomic analysis of this bacterium brings new insights into the functioning of Pseudomonas and their role in beneficial plant-microbe interactions.

show abstract

“…phlABC-DEF with percentage similarity. Phl genes were reported for its biocontrol activity [29] making it a significant product in tandem with antibiotics. Anti-SMASH software showed that phl gene cluster sequence showed 75% similarity with bacteria BGC0000281 and 62% with another bacteria BGC0000280 as shown in Fig.…”

Section: Mining Secondary Metabolitementioning

confidence: 99%

An Approach to In Silico Dissection of Bacterial Intelligence Through Selective Genomic Tools

2018

View full text Add to dashboard Cite

All the genetic potential and the intelligence a bacteria can showcase in a given environment are embedded in its genome. In this study, we have presented systematic guidelines to understand a bacterial genome with the relevant set of in silico tools using a novel bacteria as an example. This study presents a multi-dimensional approach from genome annotation to tracing genes and their network of metabolism operating in an organism. It also shows how the sequence can be used to mine the enzymes and construction of its 3-dimensional structure so that its functional behavior can be predicted and compared. The discriminating algorithm allows analysis of the promoter region and provides the insight in the regulation of genes in spite of the similarity in its sequences. The ecological niche specific bacterial behavior and adapted altered physiology can be understood through the presence of secondary metabolite, antibiotic resistance genes, and viral genes; and it helps in the valorization of genetic information for developing new biological application/processes. This study provides an in silico work plan and necessary steps for genome analysis of novel bacteria without any rigorous wet lab experiments.

show abstract

Molecular genetic analysis of determinants defining synthesis of 2,4-diacetylphloroglucinol by Pseudomonas brassicacearum BIM B-446 bacteria

Cited by 11 publications

References 23 publications

Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces

Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces

Genomic Analysis of the 1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Pseudomonas thivervalensis SC5 Reveals Its Multifaceted Roles in Soil and in Beneficial Interactions With Plants

An Approach to In Silico Dissection of Bacterial Intelligence Through Selective Genomic Tools

Contact Info

Product

Resources

About