Species-Wide Genome Mining of Pseudomonas putida for Potential Secondary Metabolites and Drug-Like Natural Products Characterization

Aiman, Sara; Shehroz, Muhammad; Munir, Mehwish; Gul, Sahib; Shah, Mohibullah; Khan, Asifullah

doi:10.4172/jpb.1000460

Cited by 11 publications

(8 citation statements)

References 61 publications

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“…In contrast, the P. putida group was demonstrated to host CLP producers from different families [ 30 , 31 ]. CLP production is widespread within the P. putida group and different type strains (i.e., P. capeferrum , P. entomophila , and P. soli ) and many non-type strains (e.g., RW10S2, PCL1445, BW11M1, 250J, COR5, COW10, COR19, COR51; Table S7 ) were formerly characterized as producers of CLPs from the Viscosin (WLIP producers), Putisolvin, Entolysin, and Xantholysin families [ 30 , 31 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 ]. Among the 16 type strains of the newly described species, four were previously described as CLP producers: two WLIP producers, P. fakonensis COW40 and P. xanthosomae COR54; and two xantholysin producers, P. maumuensis COW77 and P. muyukensis COW39 ( Table S6 ) [ 30 , 31 ].…”

Section: Resultsmentioning

confidence: 99%

The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas putida Group

et al. 2021

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The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of Pseudomonas are well known to represent only a small fraction of this diversity and the number of available Pseudomonas genome sequences is increasing rapidly. Consequently, new Pseudomonas species are regularly reported and the number of species within the genus is constantly evolving. In this study, whole genome sequencing enabled us to define 43 new Pseudomonas species and provide an update of the Pseudomonas evolutionary and taxonomic relationships. Phylogenies based on the rpoD gene and whole genome sequences, including, respectively, 316 and 313 type strains of Pseudomonas, revealed sixteen groups of Pseudomonas and, together with the distribution of cyclic lipopeptide biosynthesis gene clusters, enabled the partitioning of the P. putida group into fifteen subgroups. Pairwise average nucleotide identities were calculated between type strains and a selection of 60 genomes of non-type strains of Pseudomonas. Forty-one strains were incorrectly assigned at the species level and among these, 19 strains were shown to represent an additional 13 new Pseudomonas species that remain to be formally classified. This work pinpoints the importance of correct taxonomic assignment and phylogenetic classification in order to perform integrative studies linking genetic diversity, lifestyle, and metabolic potential of Pseudomonas spp.

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Section: Resultsmentioning

confidence: 99%

The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas putida Group

et al. 2021

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“…This corresponds with its known induction profile in camphor-grown P. putida ATCC 17453 as an activity that only commences expression in late trophophase when the majority of the C10 bicyclic terpenoid has been consumed and the activity levels of the DKCMOs have fallen by >90% [21]. Because high levels of Fred are characteristic of idiophase, it is possible that rather than acting to supply FNR to the DKCMOs, the enzyme serves a role in the biosynthesis of secondary metabolites such as the polyketides, arylpolyenes, phenazines, acyl-homoserine lactones and rhamnolipids known to be produced in idiophase by a number of other P. putida species [42,43]. Such a role for Fred is also consistent with the almost identical induction profile for the enzyme when P. putida ATCC 17453 is grown on an equivalent minimal medium containing 10 mM succinate as the sole carbon source (Figure S3).…”

Section: Resultsmentioning

confidence: 99%

Conferring the Metabolic Self-Sufficiency of the CAM Plasmid of Pseudomonas putida ATCC 17453: The Key Role of Putidaredoxin Reductase

Willetts

2019

Microorganisms

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The relative importance of camphor (CAM) plasmid-coded putidaredoxin reductase (PdR) and the chromosome-coded flavin reductases Frp1, Frp2 and Fred for supplying reduced FMN (FNR) to the enantiocomplementary 2,5- and 3,6-diketocamphane monooxygenases (DKCMOs) that are essential for the growth of Pseudomonas putida ATCC 17453 on (rac)-camphor was examined. By undertaking studies in the time window prior to the induction of Fred, and selectively inhibiting Frp1 and 2 with Zn2+, it was confirmed that PdR could serve as the sole active supplier of FNR to the DKCMOs. This establishes for the first time that the CAM plasmid can function as an autonomous extrachromosomal genetic element able to express all the enzymes and redox factors necessary to ensure entry of the C10 bicyclic terpene into the central pathways of metabolism via isobutyryl-CoA.

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“…Further, the absence of any detectible titre of Fred until 180–210 min, at which point the residual ( rac )-camphor in the medium has fallen to barely detectible levels and the culture was progressing from late log into stationary phase growth, reinforces the proposal [ 8 ] that Fred plays no significant role in trophophasic growth and is more likely to be induced specifically to support one or more aspects of secondary metabolism in P. putida NCIMB 10007. It is known that strains of P. putida initiate the synthesis of a suite of novel secondary metabolites on entering idiophase [ 36 ] and a recent survey of 58 strains revealed biosynthetic gene clusters for a wide range of nonribosomal peptides, polyketides and bacteriocins [ 37 ].…”

Section: Discussionmentioning

confidence: 99%

Regulation of Camphor Metabolism: Induction and Repression of Relevant Monooxygenases in Pseudomonas putida NCIMB 10007

2018

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For the first time, the differential rates of synthesis of all the key monooxygenases involved in the catabolism by Pseudomonas putida NCIMB 10007 of bicyclic (rac)-camphor to ∆2,5-3,4,4-trimethylpimelyl-CoA, the first aliphatic pathway intermediate, have been determined to help establish the relevant induction profile of each of the oxygen-dependent enzymes. The efficacy of both relevant substrates and pathway metabolites as inducers has been established. Further, inhibitors with characterised functionality have been used to indicate that the pertinent regulatory controls operate at the level of transcription of the corresponding genes.

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Species-Wide Genome Mining of Pseudomonas putida for Potential Secondary Metabolites and Drug-Like Natural Products Characterization

Cited by 11 publications

References 61 publications

The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas putida Group

The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas putida Group

Conferring the Metabolic Self-Sufficiency of the CAM Plasmid of Pseudomonas putida ATCC 17453: The Key Role of Putidaredoxin Reductase

Regulation of Camphor Metabolism: Induction and Repression of Relevant Monooxygenases in Pseudomonas putida NCIMB 10007

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