Evolutionary Implications and Physicochemical Analyses of Selected Proteins of Type III Polyketide Synthase Family

Mallika, V.; Sivakumar, Krishnankutty C.; Soniya, E. V.

doi:10.4137/ebo.s6854

Cited by 15 publications

(11 citation statements)

References 57 publications

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“…Date palm has only 9 and A. thaliana has 5 PKSs based on chalcone synthases and chalcone synthases like-proteins that deposited in the NCBI database. All of these PKSs were localized intracellular in the cytoplasma to build a polyketide product as been reported by (Mallika et al 2011)…”

Section: Protein Mining For Pkssupporting

confidence: 55%

PKS-A Clade of Oil Palm Might Play Role During Defense AgainstGanoderma boninenseInfection

Tanjung¹,

Aditama²,

Utomo³

et al. 2020

Preprint

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SPolyketide synthase (PKS) is an essential catalyzing enzyme in the polyketide (PK) biosynthesis pathway of bacteria, fungi and plants which have diverse beneficial functions such as antibiotic and antiparasitic. This study was aimed to identify specific plant type III PKSs in the African oil palm, Elaeis guineensis, and predict its biosynthesized metabolites as plant defense compounds against the most threatening fungal pathogen, Ganoderma boninense that causing the basal stem rot disease. We used the oil palm protein database to detect the presence of type III PKS domains using the HMMER version V3.1b2. An artificial inoculation was made on oil palm root tissues and RNA sequencing was performed to obtain the transcriptome profile after 7 days exposure to G. boninense. Among 40,421 proteins, we identified 38 of which containing type III PKS domains. Signal peptide signature motifs were absence in all PKSs suggesting their intracellular functions during the polyketide biosynthesis. A molecular phylogeny analysis reflected the relationships among these PKSs that clustered into PKS-A, -B and -C clades. Most of the PKS-A members were up-regulated after G. boninense infection, indicating their essential role in the biosynthesis of PK products which might needed for defense.

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Section: Protein Mining For Pkssupporting

confidence: 55%

PKS-A Clade of Oil Palm Might Play Role During Defense AgainstGanoderma boninenseInfection

Tanjung¹,

Aditama²,

Utomo³

et al. 2020

Preprint

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“…This indicates significant site-specific selective constraints for most members of the Arabidopsis pectin lyase family. This led to group-specific functional evolution after diversification [46] , [47] . Moreover, critical amino acid residues responsible of functional divergence were predicted based on site-specific profiles, in combination with suitable cut-off values derived from the posterior probability of each comparison.…”

Section: Resultsmentioning

confidence: 99%

The Pectin Lyases in Arabidopsis thaliana: Evolution, Selection and Expression Profiles

Cao

2012

PLoS ONE

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Pectin lyases are a group of enzymes that are thought to contribute to many biological processes, such as the degradation of pectin. However, until this study, no comprehensive study incorporating phylogeny, chromosomal location, gene duplication, gene organization, functional divergence, adaptive evolution, expression profiling and functional networks has been reported for Arabidopsis. Sixty-seven pectin lyase genes have been identified, and most of them possess signal sequences targeting the secretory pathway. Phylogenetic analyses identified five gene groups with considerable conservation among groups. Pectin lyase genes were non-randomly distributed across chromosomes and clustering was evident. Functional divergence and adaptive evolution analyses suggested that purifying selection was the main force driving pectin lyase evolution, although some critical sites responsible for functional divergence might be the consequence of positive selection. A stigma- and receptacle-specific expression promoter was identified, and it had increased expression in response to wounding. Two hundred and eighty-eight interactions were identified by functional network analyses, and most of these were involved in cellular metabolism, cellular transport and localization, and stimulus responses. This investigation contributes to an improved understanding of the complexity of the Arabidopsis pectin lyase gene family.

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“…In higher plants, the CHS-type shows >80% similarity with chalcone synthases and >70% similarity with non-chalcone synthases, or STS- and CTAS-types [30].…”

Section: Resultsmentioning

confidence: 99%

“…Type III PKS is a class of enzymes that catalyzes the synthesis of polyketides, such as CHS, BUS, and STS. In higher plants, the CHS-type shows >80% similarity with chalcone synthases and >70% similarity with non-chalcone synthases, or STS- and CTAS-types [30] .…”

Section: Resultsmentioning

confidence: 99%

De Novo Sequencing of Hypericum perforatum Transcriptome to Identify Potential Genes Involved in the Biosynthesis of Active Metabolites

Wang

Hua

et al. 2012

PLoS ONE

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Background Hypericum perforatum L. (St. John’s wort) is a medicinal plant with pharmacological properties that are antidepressant, anti-inflammatory, antiviral, anti-cancer, and antibacterial. Its major active metabolites are hypericins, hyperforins, and melatonin. However, little genetic information is available for this species, especially that concerning the biosynthetic pathways for active ingredients.Methodology/Principal FindingsUsing de novo transcriptome analysis, we obtained 59,184 unigenes covering the entire life cycle of these plants. In all, 40,813 unigenes (68.86%) were annotated and 2,359 were assigned to secondary metabolic pathways. Among them, 260 unigenes are involved in the production of hypericin, hyperforin, and melatonin. Another 2,291 unigenes are classified as potential Type III polyketide synthase. Our BlastX search against the AGRIS database reveals 1,772 unigenes that are homologous to 47 known Arabidopsis transcription factor families. Further analysis shows that 10.61% (6,277) of these unigenes contain 7,643 SSRs.ConclusionWe have identified a set of putative genes involved in several secondary metabolism pathways, especially those related to the synthesis of its active ingredients. Our results will serve as an important platform for public information about gene expression, genomics, and functional genomics in H. perforatum.

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Evolutionary Implications and Physicochemical Analyses of Selected Proteins of Type III Polyketide Synthase Family

Cited by 15 publications

References 57 publications

PKS-A Clade of Oil Palm Might Play Role During Defense AgainstGanoderma boninenseInfection

PKS-A Clade of Oil Palm Might Play Role During Defense AgainstGanoderma boninenseInfection

The Pectin Lyases in Arabidopsis thaliana: Evolution, Selection and Expression Profiles

De Novo Sequencing of Hypericum perforatum Transcriptome to Identify Potential Genes Involved in the Biosynthesis of Active Metabolites

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