The Combined Use of Proteomics and Transcriptomics Reveals a Complex Secondary Metabolite Network in <i>Peperomia obtusifolia</i>

Batista, Andrea N. L.; Santos-Pinto, José Roberto Aparecido dos; Batista, João M.; Souza-Moreira, Tatiana M.; Santoni, Mariana Marchi; Zanelli, Cleslei Fernando; Kato, Massuo Jorge; López, Silvia N.; Palma, Mário Sérgio; Furlan, Maysa

doi:10.1021/acs.jnatprod.6b00827

Cited by 15 publications

(10 citation statements)

References 36 publications

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“…The present results are in accordance with those recently published for transcriptomes for the Piperaceae species Piper nigrum and Peperomia obtusifolia, which were assembled using Illumina HiSeq 2000 and 2500 platforms, respectively. 12,19 Sequence homology searches were conducted for the transcript functional annotation. Therefore, all transcripts were submitted to BLASTX 20 searches against the NCBI non-redundant (Nr) protein database, and 148,113 (68%) transcripts had significant similarity with an E (expect) value less than 1e −5 ( Table 2).…”

Section: Resultsmentioning

confidence: 99%

“…12 By using the BLASTN 20 web tool from NCBI, it was possible to verify that the transcripts from both species present a high degree of similarity ( Figure S5, Supplementary Information). Thus, apart from catalyzing the formation of (S)-tocopherols, these enzymes may also be responsible for the non-stereoselective cyclization that yields the racemic chromane and chromene moieties.…”

Section: Candidate Genes Involved In Benzopyran Biosynthesismentioning

confidence: 99%

“…Because orsellinic acid is commonly found in sordariomycetes and eurotiomycetes, these results suggest that orsellinic acid-derived benzopyrans may be formed by the combination of biosynthetic efforts from the host plant and endophytic fungi. 12 Some studies have already been performed in Piper gaudichaudianum aimed at elucidating the biosynthesis of gaudichaudianic acid (1) (Figure 2), 10 which is the major prenylated chromene isolated from this species and described as a potent trypanocidal compound against the Y-strain of Trypanosoma cruzi. 13 Interestingly, trypanocidal assays indicated that the (+)-enantiomer was more active than its antipode and that the enantiomer mixtures showed a synergistic effect, with the racemic mixture being the most active.…”

Section: Introductionmentioning

confidence: 99%

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Biosynthetic Insights into p-Hydroxybenzoic Acid-Derived Benzopyrans in Piper gaudichaudianum

Batista¹,

Batista²,

Souza-Moreira³

et al. 2017

J. Braz. Chem. Soc.

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Piper gaudichaudianum Kunth (Piperaceae) accumulates gaudichaudianic acid, a prenylated benzopyran, as its major component. Interestingly, this trypanocidal compound occurs as a racemic mixture. Herein, transcriptomic investigations of Piper gaudichaudianum using the RNAseq approach are reported, and from the analysis of the transcripts expressed it was possible to propose a complete biosynthetic pathway for the production of gaudichaudianic acid, including the steps that originate its precursor, p-hydroxybenzoic acid. Peperomia obtusifolia (L.) A. Dietr. (Piperaceae) also accumulates racemic benzopyrans, however, its chromanes originate from the polyketide pathway, while the chromenes from Piper derives from the shikimate pathway. Recent transcriptomic and proteomic studies of the former species did not identify polyketide synthases involved in the production of the benzopyran moiety, but revealed the expression of tocopherol cyclase, which may be responsible for the cyclization of the 3,4-dihydro-2H-pyran ring. The analysis of the enzymes involved in the secondary metabolism of Piper gaudichaudianum and the comparison with the data previously obtained from Peperomia obtusifolia can provide valuable information on how these compounds are biosynthesized.Keywords: Piperaceae, chromene, transcriptome, RNA-seq, de novo assembly, biosynthesis IntroductionChromanes and chromenes, which are secondary metabolites commonly found in some species from Piper and Peperomia genera (Piperaceae), are characterized by the presence of a benzopyran ring with various levels of oxidation. [1][2][3] This nucleus is considered a privileged structure that is very common in bioactive natural products, such as coumarins, flavones, tocopherols (vitamin E) and tetrahydrocannabinoids. 4,5 The benzopyran moieties, 2H-chromenes and chromanes, isolated from Piper gaudichaudianum and Peperomia obtusifolia, respectively, have been demonstrated as potent trypanocidal compounds. 6,7 Curiously, both classes of compounds occur as racemic mixtures in these species, though their formation follows two distinct biosynthetic routes. 6,8,9 In Piper gaudichaudianum, chromenes originate from the shikimate pathway and use p-hydroxybenzoic acid (p-HBA) as a precursor. 10 In the case of Peperomia obtusifolia, chromanes are formed through the polyketide pathway and use orsellinic acid as a precursor. 1,11 Additionally, the formation of both classes of metabolites involves the condensation of an aromatic unit (p-HBA or orsellinic acid) and an isoprene unit (dimethylallyl pyrophosphate, isopentenyl pyrophosphate or geranyl pyrophosphate), followed by cyclization that gives rise to the benzopyran ring. During cyclization, the carbon atom at C-2 becomes a stereogenic center and, different from other benzopyrans such as vitamin E, both enantiomers are biosynthesized (Figure 1). Thus, the study of the proteins and genes possibly responsible for the biosynthesis of benzopyrans in these species, as well as the comparison between them, may provide new insights into how...

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Section: Resultsmentioning

confidence: 99%

Section: Candidate Genes Involved In Benzopyran Biosynthesismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Biosynthetic Insights into p-Hydroxybenzoic Acid-Derived Benzopyrans in Piper gaudichaudianum

Batista¹,

Batista²,

Souza-Moreira³

et al. 2017

J. Braz. Chem. Soc.

Self Cite

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“…As shown for a few examples in Tables 2-4 which consist in a sampling of recently reported works on natural compounds, this "Systematism" is already used by a few groups who catalogued the chemical compounds in a given organ of a given plant (Batista et al, 2017;Sendker et al, 2017;Ma et al, 2018;Sharma et al, 2018), in a fungus (Chang et al, 2017), or in a microorganism (McMullin et al, 2017;Verastegui-Omana et al, 2017). In such cases, an idea of the possible diversity of those sources is given.…”

Section: At the Development Stage: Systematic Inventories Of Natural mentioning

confidence: 99%

Unraveling Plant Natural Chemical Diversity for Drug Discovery Purposes

Lautie

Russo

Ducrot³

2020

Front. Pharmacol.

141

114

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The screening and testing of extracts against a variety of pharmacological targets in order to benefit from the immense natural chemical diversity is a concern in many laboratories worldwide. And several successes have been recorded in finding new actives in natural products, some of which have become new drugs or new sources of inspiration for drugs. But in view of the vast amount of research on the subject, it is surprising that not more drug candidates were found. In our view, it is fundamental to reflect upon the approaches of such drug discovery programs and the technical processes that are used, along with their inherent difficulties and biases. Based on an extensive survey of recent publications, we discuss the origin and the variety of natural chemical diversity as well as the strategies to having the potential to embrace this diversity. It seemed to us that some of the difficulties of the area could be related with the technical approaches that are used, so the present review begins with synthetizing some of the more used discovery strategies, exemplifying some key points, in order to address some of their limitations. It appears that one of the challenges of natural product-based drug discovery programs should be an easier access to renewable sources of plant-derived products. Maximizing the use of the data together with the exploration of chemical diversity while working on reasonable supply of natural product-based entities could be a way to answer this challenge. We suggested alternative ways to access and explore part of this chemical diversity with in vitro cultures. We also reinforced how important it was organizing and making available this worldwide knowledge in an "inventory" of natural products and their sources. And finally, we focused on strategies based on synthetic biology and syntheses that allow reaching industrial scale supply. Approaches based on the opportunities lying in untapped natural plant chemical diversity are also considered.

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“…Several TFs were also identified that link flavonoid, caffeine, and theanine biosyntheses. A transcriptomic and proteomic shot-gun approach was used with the ornamental plant Peperomia obtusifolia L. to study the production of benzopyrans derived from orsellinic acid, a phenolic acid usually found in fungi [65]. The analyses led to the identification of both the mevalonate and methylerythritol pathways as being active in the leaves, and showed that terpenoid biosynthesis was the pathway with the highest number of enzymes identified.…”

Section: Importance Of -Omics For the Study Of Plant Secondary Metmentioning

confidence: 99%

Agrobiotechnology Goes Wild: Ancient Local Varieties as Sources of Bioactives

Berni

Cantini

Romi

et al. 2018

IJMS

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The identification and use of species that have best adapted to their growth territory is of paramount importance to preserve biodiversity while promoting sustainable agricultural practices. Parameters including resistance to natural conditions (biotic and abiotic risk factors), biomass and fruit productivity, and phytochemical content with nutraceutical potential, could be used as quantitative markers of the adaptability of plants to wild environments characterized by minimal human impact. Ancient varieties, which are plant varieties growing in regional territories and not destined for market distribution, are a source of unique genetic characters derived from many years of adaptation to the original territory. These plants are often more resistant to biotic and abiotic stresses. In addition, these varieties have a high phytochemical (also known as bioactives) content considered health-beneficial. Notably, the content of these compounds is often lower in commercial cultivars. The use of selected territorial varieties according to the cultivation area represents an opportunity in the agricultural sector in terms of biodiversity preservation, environmental sustainability, and valorization of the final products. Our survey highlights the nutraceutical potential of ancient local varieties and stresses the importance of holistic studies (-omics) to investigate their physiology and secondary metabolism.

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The Combined Use of Proteomics and Transcriptomics Reveals a Complex Secondary Metabolite Network in Peperomia obtusifolia

Cited by 15 publications

References 36 publications

Biosynthetic Insights into p-Hydroxybenzoic Acid-Derived Benzopyrans in Piper gaudichaudianum

Biosynthetic Insights into p-Hydroxybenzoic Acid-Derived Benzopyrans in Piper gaudichaudianum

Unraveling Plant Natural Chemical Diversity for Drug Discovery Purposes

Agrobiotechnology Goes Wild: Ancient Local Varieties as Sources of Bioactives

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