The Hevea brasiliensis AP2/ERF superfamily: from ethylene signalling to latex harvesting and physiological disease response

Putranto, Riza Arief; Montoro, Pascal

doi:10.22302/ppbbi.jur.mp.v84i1.201

Cited by 3 publications

(5 citation statements)

References 30 publications

(45 reference statements)

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“…These DEGs and DAPs were significantly enriched in 28 KEGG pathways, which were mainly related to energy metabolism, carbohydrate metabolism, lipid metabolism, ROS scavenging, PCD, and signal transduction/information processing (Figure 2c; Table S4). Thus, it can be concluded that TPD affects energy, carbohydrate, and lipid metabolism, as well as ROS scavenging, PCD, and signal transduction/ information processing, which is consistent with the physiological parameters of latex from healthy and TPD-affected trees and in agreement with previous studies (Chen et al, 2003;de Fa€ y, 2011;Li et al, 2010Li et al, , 2016Peng et al, 2011;Putranto & Montoro, 2016;Venkatachalam et al, 2009;Zhang et al, 2017). Notably, the correlation between DEGs and DAPs was very poor (r = 0.024 in T2_H and r = 0.104 in T4_H), indicating that the protein abundance in the latex of TPD-affected trees may be significantly affected by post-translational modifications and splicing events (Pandey & Mann, 2000).…”

Section: Discussionsupporting

confidence: 92%

“…TPD seriously affects the NR yield and quality of rubber trees (Putranto & Montoro, 2016;Zhang et al, 2017). Previous studies investigated the molecular mechanisms of TPD using suppression subtractive hybridization and transcriptome sequencing analysis (Li et al, 2010(Li et al, , 2016Liu et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

“…HbEREBP1 belongs to the APETALA2/ethylene response factor (AP2/ERF) superfamily, whose members are critical in plant ET signal transduction. Several AP2/ERF members are highly accumulated in laticifers and produced in response to ET stimulation (Nie et al., 2016; Putranto & Montoro, 2016). In the present study, both RNA‐seq and RT‐qPCR assays showed no expression differences of HbEREBP1 in the latex between TPD‐affected trees and healthy trees, suggesting that HbEREBP1 may not be involved in HbFPS1 downregulation in TPD‐affected trees.…”

Section: Discussionmentioning

confidence: 99%

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Downregulation of HbFPS1 affects rubber biosynthesis of Hevea brasiliensis suffering from tapping panel dryness

et al. 2023

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SUMMARY Tapping panel dryness (TPD) is a century‐old problem that has plagued the natural rubber production of Hevea brasiliensis. TPD may result from self‐protective mechanisms of H. brasiliensis in response to stresses such as excessive hormone stimulation and mechanical wounding (bark tapping). It has been hypothesized that TPD impairs rubber biosynthesis; however, the underlying mechanisms remain poorly understood. In the present study, we firstly verified that TPD‐affected rubber trees exhibited lower rubber biosynthesis activity and greater rubber molecular weight compared to healthy rubber trees. We then demonstrated that HbFPS1, a key gene of rubber biosynthesis, and its expression products were downregulated in the latex of TPD‐affected rubber trees, as revealed by transcriptome sequencing and iTRAQ‐based proteome analysis. We further discovered that the farnesyl diphosphate synthase HbFPS1 could be recruited to small rubber particles by HbSRPP1 through protein–protein interactions to catalyze farnesyl diphosphate (FPP) synthesis and facilitate rubber biosynthesis initiation. FPP content in the latex of TPD‐affected rubber trees was significantly decreased with the downregulation of HbFPS1, ultimately resulting in abnormal development of rubber particles, decreased rubber biosynthesis activity, and increased rubber molecular weight. Upstream regulator assays indicated that a novel regulator, MYB2‐like, may be an important regulator of downregulation of HbFPS1 in the latex of TPD‐affected rubber trees. Our findings not only provide new directions for studying the molecular events involved in rubber biosynthesis and TPD syndrome and contribute to rubber management strategies, but also broaden our knowledge of plant isoprenoid metabolism and its regulatory networks.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Downregulation of HbFPS1 affects rubber biosynthesis of Hevea brasiliensis suffering from tapping panel dryness

et al. 2023

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“…Arabidopsis thaliana (L.) Heynh is an important and well-described model plant for molecular biology due to its advantages of short life cycle (6 weeks) and small genome size (~125Mb) with five chromosomes (Initiative, 2000). The in silico comparative analysis between H. brasiliensis and A. thaliana have successfully identified important gene families such as the APETALA2/ETHYLENE RESPONSE FACTORS (AP2/ERF) superfamily (Duan et al, 2010;Putranto et al, 2015a;Putranto et al, 2015b;Putranto and Montoro, 2016), Calcium-Dependent Protein Kinase (CDPK) family (Xiao et al, 2017), Abscisic acid (ABA) receptor gene family (Guo et al, 2017), Glucose-6-Phospate Dehydrogenase (G6PDH) family (Long et al, 2016), Sucrose synthase gene family (Xiao et al, 2014), Metacaspase family (Liu et al, 2016), Aquaporin family (Zou et al, 2015), ABC transporter family (Zhiyi et al, 2015), Small Rubber Particle (SRPP) gene family (Lau et al, 2016) and Protease Inhibitors (PI) family (Martiansyah et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

In silico Identification and Comparative Analysis of Hevea brasiliensis COBRA Gene Family

Putranto¹,

Martiansyah²,

Saptari³

2017

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In this paper, the H. brasiliensis COBRA gene family, alleged to be involved in laticifer differentiation, was identified from the public rubber tree genome of Reyan 7-33-97 clone. A comparative analysis was carried out against A. thaliana genomic database. This analysis has resulted to the in silico validation of thirteen putative genes encoding glycophosphatidylinositol anchors (GPI) proteins harbored by nine Hevea genomic scaffolds. The sequence’s similarity of HbCOBL against AtCOBL genes were ranged from the threshold 50 to 81.58% covering 151 to 458 amino acid residues, respectively. Three partial and ten full-length protein sequences of HbCOBL genes were annotated. The partial protein sequences ranged from 89 to 184 amino acid residues as opposed to the full-length proteins ranging from 160 to 471 amino acid residues. Two types of COBRA domains (pfam04833 and cl04787) were found among HbCOBL genes. Phylogenetic analysis has clustered two subfamilies. Nine HbCOBL genes (HbCOBL-B, HbCOBL-J, HbCOBL-C, HbCOBL-H, HbCOBL-F, HbCOBL-I, HbCOBL-M, HBCOBL-A, and HbCOBL-N) were clustered as COBRA gene subfamily-I. By contrast, four genes (HbCOBL-O, HbCOBL-P, HbCOBL-E, and HbCOBL-L) were clustered as COBRA gene subfamily-II. The HbCOB subfamily-II was marked by the addition of 203 residues in C-terminal which is different with Arabidopsis. The gene HbCOBL-C was the putative ortholog to AtCOB carrying the unique COBRA domain cl04787 with 74 amino acid residues. Taken together, these results showed that Hevea and Arabidopsis COBRA genes might share similar functions while differ in gene structure.

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“…Identifikasi gen spesifik dan fungsinya membantu kita dalam memahami perkembangan evolusi molekuler gen dan protein serta lebih jauh lagi dapat mengenali perbedaan morfologi ataupun fenotipe tanaman (Sharma & Suresh, 2015). Analisis in silico komparatif A. thaliana dan H. brasiliensis telah berhasil mengidentifikasi beberapa famili gen penting seperti superfamili APETALA2/ETHYLENE RESPONSE FACTORS (AP2/ERF) (Duan et al, 2010;Putranto & Montoro, 2016;Putranto et al, 2015a;Putranto et al, 2015b) famili CalciumDependent Protein Kinase (CDPK) (Xiao et al, 2017), famili reseptor asam absisat (ABA) (Guo et al, 2017), famili Glucose-6-Phosphate Dehydrogenase (G6PDH) , famili Metacaspase , famili Aquaporin (Zou et al, 2015), dan famili ABC Transporter (Zhiyi et al, 2015). Di sisi lain, studi komparatif sejenis juga telah berhasil dilakukan pada spesies lain seperti Oryza vs Shorgum untuk identifikasi dan analisis filogenetik gen transporter Ca 2+ (Goel et al, 2011) dan gen siDof pada tanaman millet (Setaria italica) ( Zhang et al, 2017).…”

Section: Pendahuluanunclassified

Identifikasi famili gen putatif penyandi protease inhibitor dengan pendekatan in silico komparatif pada genom Hevea brasiliensis Muell. Arg (Identification of putative gene family encoding protease inhibitors by in silico comparative analysis in Hevea brasiliensis Muell. Arg genome)

Martiansyah¹,

Putranto²,

Khumaida³

2017

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Protease inhibitors (PIs) are small proteins that form complexes with proteases and inhibits their proteolytic activity. Its potential application as an antimicrobial agent has been studied. Most of PIs' molecule size is around 8-22 kDa depending on their protein families.To date, on the basis of sequence homologies of inhibitor domains, PIs have been classified into 48 families in all organisms. In plant, more than 13 families of PIs have been identified but they were not widely identified in the rubber tree (Hevea brasiliensis Muell.Arg). In the present study, 40 putative HbPI genes, designated as HbPI01 to HbPI36, were identified from whole-genome sequence of rubber tree clone Reyan 7-33-97 using 7453 scaffolds available online in NCBI with the accession code: LVXX01000000. Multiple sequence alignment using MUSCLE algorithm discovered seven conserved motifs (Motifs I-VII) among HbPIs. Phylogenetic analysis of 50 and 36 PI amino acid residues of 32 scaffolds containing putative PI genes from Arabidopsis thaliana and H. brasiliensis showed three clusters (families): LTP-I, SERPIN and LTP-II. LTP-I has 23 putative HbPI genes (HbPI05 to HbPI27) and 12 AtPI genes. SERPIN, a family member of serine protease inhibitor group, has 11 putative HbPI genes (HbPI01 to HbPI04 and HbPI28 to HbPI34) and 22 AtPI genes. LTP-II has 2 putative HbPI genes (HbPI35 to HbPI36) and 16 AtPI genes. In conclusion, this work provides valuable information for further functional characterization of HbPI genes in H. brasiliensis.[Key words: protease inhibitor, genome-wide, scaffold, in silico, Hevea brasiliensis]. AbstrakProtease inhibitor (PI) merupakan protein yang membentuk kompleks dengan protease dan menghambat aktivitas proteolitik dari enzim tersebut. Potensi penggunaan protease inhibitor sebagai agensia antimikroba telah diketahui. Kebanyakan PI memiliki ukuran molekul sekitar 8-22 kDa bergantung pada familinya. Saat ini, PI dapat diklasifikasikan menjadi 48 famili di seluruh organisme berdasarkan kemiripan sekuen dari domain inhibitornya. Pada tanaman, lebih dari 13 famili PI telah diketahui tetapi pada tanaman karet (Hevea brasiliensis Muell.Arg) belum diidentifikasi. Pada penelitian ini, sebanyak 40 gen putatif penyandi PI (HbPI01 hingga HbPI36) telah berhasil diidentifikasi dari 7453 scaffold genom utuh tanaman karet klon Reyan 7-33-97 yang tersedia secara daring dengan kode aksesi LVXX01000000. Penjajaran sekuen menggunakan algoritma MUSCLE memper-lihatkan tujuh konservasi motif (Motif I-VIII) pada famili gen putatif HbPIs. Analisis pohon filogenetik dari tanaman Arabidopsis thaliana dan H. brasiliensis sebanyak 50 dan 36 sekuen residu asam amino dari 32 scaffold yang mengandung gen putatif PI menunjukkan adanya tiga klaster besar, yaitu famili LTP-I, SERPIN dan LTP-II. LTP-I terdiri dari 23 gen putatif HbPI (HbPI05 hingga HbPI27) dan 12 gen AtPI. SERPIN yang merupakan anggota kelas protease inhibitor serin terdiri dari 11 gen putatif HbPI (HbPI01hingga HbPI04 dan HbPI28 hingga HbPI34) dan 22 gen AtPI. LTP-II terdiri dari 2 gen putatif HbPI (HbPI35 hingga HbPI36) dan 16 gen AtPIs. Penelitian ini menghasilkan informasi penting untuk melakukan karakterisasi fungsional lebih mendalam pada gen HbPI tanaman karet ke depannya.[Kata kunci: protease inhibitor, genome-wide,scaffold, in silico, Hevea brasiliensis].

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The Hevea brasiliensis AP2/ERF superfamily: from ethylene signalling to latex harvesting and physiological disease response

Abstract: Abstrak Etilen merupakan hormon yang dikenal karena perannya dalam proses penyadapan lateks di tanaman karet (Hevea brasiliensis)

Cited by 3 publications

References 30 publications

Downregulation of HbFPS1 affects rubber biosynthesis of Hevea brasiliensis suffering from tapping panel dryness

Downregulation of HbFPS1 affects rubber biosynthesis of Hevea brasiliensis suffering from tapping panel dryness

In silico Identification and Comparative Analysis of Hevea brasiliensis COBRA Gene Family

Identifikasi famili gen putatif penyandi protease inhibitor dengan pendekatan in silico komparatif pada genom Hevea brasiliensis Muell. Arg (Identification of putative gene family encoding protease inhibitors by in silico comparative analysis in Hevea brasiliensis Muell. Arg genome)

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