Protein replenishment in pitcher fluids of Nepenthes × ventrata revealed by quantitative proteomics (SWATH-MS) informed by transcriptomics

Zakaria, Wan Nor Adibah Wan; Aizat, Wan Mohd; Goh, Hoe-Han; Noor, Normah Mohd

doi:10.1007/s10265-019-01130-w

Cited by 13 publications

(24 citation statements)

References 55 publications

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“…5) already showed high expression levels on D0. This corroborates findings that most of the endogenous secreted proteins already present in pitcher fluids before opening with certain proteins continuously replenished or induced by prey 15,34,37,46 . In comparison, there was no clear trend in the expression of transporters on D0 (Fig.…”

Section: Discussionsupporting

confidence: 89%

“…Therefore, the transcriptomic analysis provides an alternative to studying the functional genomics of tropical pitcher plants. This reference transcriptome of N. ampullaria pitchers based on the previous RNA-seq experiment 38 is by far one of the most comprehensive reports comparable to N. mirabilis 16 , N. www.nature.com/scientificreports www.nature.com/scientificreports/ rafflesiana 15 , N. x ventrata 37,41 , and N. khasiana 6 . Only 5.3% single-copy orthologs were missing based on BUSCO analysis and 31.4% of 158,756 unigenes were functionally annotated, in which 76% were annotated to plants compared to 62% for N. rafflesiana 15 .…”

Section: Discussionmentioning

confidence: 86%

“…None have investigated the effect of protein loss in the trapping organ apart from a recent report of N. x ventrata pitcher fluid profiling 37 , which is limited by a lack of control samples after 3 days of pitcher opening to discern the effect of pitcher longevity from protein depletion. The study shows that pitchers can respond to the loss of endogenous proteins by continuous secretion of certain proteins, such as aspartic proteinases, neprosin, a serine carboxypeptidase, a β-1,3-glucanase, a PR protein, and a TLP 37 . This is consistent with increased fluid protein content in newly opened N. alata pitchers 50 .…”

Section: Discussionmentioning

confidence: 99%

“…To investigate the effect of endogenous protein depletion on the regulation of protein secretion, we profiled the known secreted proteins and transporters. Based on previous reports on pitcher fluid protein profiling 2,15,16,37 , we identified the homologous unigenes encoding secreted proteins, namely aspartic protease (Nep), neprosin (Npr), cysteine protease, serine carboxypeptidase (SCP), purple acid phosphatase (PAP), S-like ribonuclease (RNase), α-glucosidase, β-1,3-glucanase, galactosidase, endonuclease (Endo), GDSL esterase/lipase, peroxidase (Prx), chitinase (Chit), pathogenesis-related (PR) protein, thaumatin-like protein (TLP), and desiccation-related protein (DRP) (Fig. 5).…”

Section: Transcriptional Regulation Of Pitcher Fluid Proteins and Tramentioning

confidence: 99%

“…Despite recent studies on the prey-induced secretion of digestive enzymes 23,24 , molecular data on the regulation of endogenous protein secretion and replenishment are still lacking to elucidate the molecular and physiological roots of plant carnivory mechanisms. Recently, we reported that certain proteins were replenished even without prey induction in the pitcher fluids of Nepenthes x ventrata within three days of pitcher opening 37 , which indicates molecular regulation of protein secretion in the pitchers in response to protein loss. In the current study, we performed detailed downstream transcriptomic analyses on the RNA-sequencing (RNA-seq) data from previously reported experiment 38 to identify transcriptome-wide pitcher response to endogenous protein loss during early pitcher opening.…”

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confidence: 95%

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Transcriptome-wide shift from photosynthesis and energy metabolism upon endogenous fluid protein depletion in young Nepenthes ampullaria pitchers

Goh

Baharin

Salleh

et al. 2020

Sci Rep

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faris 'imadi Mohd Salleh, Rishiesvari Ravee, Wan nor Adibah Wan Zakaria & normah Mohd noor carnivorous pitcher plants produce specialised pitcher organs containing secretory glands, which secrete acidic fluids with hydrolytic enzymes for prey digestion and nutrient absorption. The content of pitcher fluids has been the focus of many fluid protein profiling studies. These studies suggest an evolutionary convergence of a conserved group of similar enzymes in diverse families of pitcher plants. A recent study showed that endogenous proteins were replenished in the pitcher fluid, which indicates a feedback mechanism in protein secretion. This poses an interesting question on the physiological effect of plant protein loss. However, there is no study to date that describes the pitcher response to endogenous protein depletion. To address this gap of knowledge, we previously performed a comparative RNA-sequencing experiment of newly opened pitchers (D0) against pitchers after 3 days of opening (D3C) and pitchers with filtered endogenous proteins (>10 kDa) upon pitcher opening (D3L). Nepenthes ampullaria was chosen as a model study species due to their abundance and unique feeding behaviour on leaf litters. The analysis of unigenes with top 1% abundance found protein translation and stress response to be overrepresented in D0, compared to cell wall related, transport, and signalling for D3L. Differentially expressed gene (DEG) analysis identified DEGs with functional enrichment in protein regulation, secondary metabolism, intracellular trafficking, secretion, and vesicular transport. the transcriptomic landscape of the pitcher dramatically shifted towards intracellular transport and defence response at the expense of energy metabolism and photosynthesis upon endogenous protein depletion. This is supported by secretome, transportome, and transcription factor analysis with RT-qPCR validation based on independent samples. This study provides the first glimpse into the molecular responses of pitchers to protein loss with implications to future cost/benefit analysis of carnivorous pitcher plant energetics and resource allocation for adaptation in stochastic environments.Carnivorous plants are commonly found in habitats deprived of nutrients, especially nitrogen and phosphorus. To qualify as carnivorous, a plant must have at least one adaptation for active attraction, capture, digestion, and clear nutritional benefit from carnivory 1 . The convergent evolution of passive pitfall traps resulted in carnivorous pitcher plants of diverse orders and families, including Nepenthaceae (Caryophyllales), Cephalotaceae (Oxalidales), and Sarraceniaceae (Ericales) at distant geographical locations but sharing similar digestive fluid proteins 2-4 . A species-rich monotypic group of tropical pitcher plants from genus Nepenthes develop attractive pitchers of diverse shapes and sizes 5 . Recently, two highly conserved leaf developmental regulatory genes, ASYMMETRIC LEAVES1 (AS1) and REVOLUTA (REV), have been shown to be key in pitcher developme...

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Section: Discussionsupporting

confidence: 89%