Search for Triterpene Synthase in the NCBI Database

Mohammad Basyuni

1,2

, Rahmah Hayati

, Yuntha Bimantara

, Arif Nuryawan

, Etti Sartina Siregar

and Sumaiyah

Department of Forestry, Faculty of Forestry, Universitas Sumatera Utara, Jl. Tri Dharma Ujung No. 1 Medan 20155,

North Sumatra, Indonesia

Mangrove and Bio-Resources Group, Center of Excellence for Natural Resources-Based Technology, Universitas

Sumatera Utara, Medan 20155, North Sumatra, Indonesia

Faculty of Mathematics and Natural Sciences, Universitas Sumatera Utara, Medan 20155, North Sumatra, Indonesia

Faculty of Pharmacy, Universitas Sumatera Utara, Medan 20155, North Sumatra, Indonesia

Keywords: -amyrin, lupeol, database, oxidosqualene, triterpene synthase

Abstract: Triterpenes are common chemical components of higher plants. The present work reports on triterpene

synthase through a search for National Center for Biotechnology Information (NCBI) databases

(https://www.ncbi.nlm.nih.gov/). To generate a amount of valued data, the main term triterpene synthase

was implemented. Results detected in 22 databases for triterpene synthase. All triterpene synthase databases

are composed of literature, genes, proteins, genomes and chemical properties. No data on genetics is

surprising. Bookshelf, MeSH (Medical Subject Headings), National Medicine Library (NML), PubMed, and

PubMed Central were discussed in the literature. Gene consisted of Gene, Gene Expression Omnibus (GEO)

DataSets, GEO Profiles, HomoloGene, and PopSet. Proteins included Conserved Domains, Identical Groups

of Proteins, Proteins, Clusters of Proteins, Sparcle, and Structure. Genomes associated in Nucleotide and

Probe. There were 98 nucleotides of plant triterpene synthases, which Arabidopsis thaliana were

predominant with 29 triterpene synthases. BioSystems, PubChem BioAssay, PubChem Compound and

PubChem Substance depicted the chemical property. The present study delivers crucial data regarding

biotechnology of triterpene synthases.

1 INTRODUCTION

Triterpenes are common chemical constituents of

higher plants. In the plant kingdom, triterpenes

along with phytosterols are biosynthesized by the

enzyme oxidosqualene cyclases (OCSs) from a

sustained precursor 2,3-oxidosqualene. 2,3-

Oxidosqualene occurs in triterpene or phytosterol

synthases at the branching point of the isoprenoid

pathway (Augustin et al., 2011). It is important to

note that more than hundreds of triterpenes are

engaged in the cyclicisation of 2,3-oxidosqualene to

generate mono- and multi-functional synthesis of

triterpene. (such as -amyrin synthesis, lupeol

synthesis or mix products of -amyrin, lupeol, and

-amyrin) (Basyuni et al. 2006, 2017a; Shibuya et

al., 2007 ).

The synthesis of triterpene was cloned and

abundantly described. Triterpene synthase for its

biological and physiological operations is also

extensively investigated (Basyuni et al., 2009,

2012a,b; Sheng and Sun, 2011; Lambert et al.,

2011). For instance, triterpene synthase's

physiological and molecular reactions to abiotic

stress such as salinity (Basyuni et al., 2009,

2012a,b). Salinity increased triterpene synthesis

genes against salt concentration in mangroves

(Basyuni et al., 2009, 2012a,b); the significance of

pentacyclic triterpenes as a multi-target technique

for metabolic and vascular disease prevention and

therapy (Sheng and Sun, 2011)

Although big numbers of research have been well

documented in triterpene synthases (Yu et al., 2009;

Agustin et al., 2011; Sawai and Saito, 2011; Moses

et al., 2014; Thimmappa et al., 2014; Isah et al.,

2016), limited work concentrated on biotechnology

data from all accessible databases in triterpene

syntheses. Here we report another technique to

collect useful data needed in latest biotechnology-

related science studies through a preferred search

engine. Therefore, the aim of this research was to

Basyuni, M., Hayati, R., Bimantara, Y., Nuryawan, A., Siregar, E. and Sumaiyah, .

Search for Triterpene Synthase in the NCBI Database.

DOI: 10.5220/0008386600080011

In Proceedings of the International Conference on Natural Resources and Technology (ICONART 2019), pages 8-11

ISBN: 978-989-758-404-6

explain the implementation of the National Center

for Biotechnology Information (NCBI) database

search to gain more insight into a lot of useful data

about updated triterpene synthesis biotechnology.

2 MATERIALS AND METHOD

The search engine for NCBI databases

(https:/www.ncbi.nlm.nih.gov/) was used to produce

many precious triterpene synthase data

biotechnologies. As stated previously on January 19,

2019, data bases were obtained by typing triterpene

synthase for all database searches. All databases

composed of triterpene synthase literature, genes,

protein, genomes and chemical properties were

performed using the Search button. Bookshelf,

MeSH (Medical Subject Headings), NLM (National

Medicine Library) catalogue, PubMed, PubMed

Central, EST, Gene, GEO datasets, PopSet, Identical

Protein Groups, Protein, Sparde, Structure,

Assembly, BioProject, BioSample, Genome, GSS,

Nucleotide, Probe, SRA, Taxonomy, Biosystems

and PubChem BioAssay were included in the data

variables.

3 RESULT AND DISCUSSION

Table 1 illustrates the NCBI literature on triterpene

synthase. Four biographies stored in countless

numbers. The internet NCBI literature provides

internet libraries and free access to bookshelf data

(eight books and reports). The title of books was five

with a total of eight items.

Table 1: Literature source of NCBI database for plant

triterpene synthase

Literature

Total

Description

Bookshelf

Books and reports

NLM

Books, journals and more in

the NLM

Catalog

PubMed

1126

Collections abstract/ citations

of science and medicine

PubMed

Central

2857

Full-text journal articles

Furthermore, one NLM catalog reported as

known Plant isoprenoids: methods and protocols. In

the database, there were 1126 Pubmed, which within

five years consist of 2014 (99 documents), 2015

(114), 2016 (91), 2017 (88), and 2017 with 88

publications. Meanwhile, there was 2857 PubMed

Central documentation in the triterpene synthase,

with NIH grants of 474 documents (Table 1). The

PubMed database includes quotes from different

topics in triterpene synthase, many links to open

access papers from triterpene synthase reports.

Table 2: Genes source of NCBI database for plant

triterpene synthase

Gene

Sum

Definition

Gene

Collected gene loci data

Geo Data Sets

Functional genomic studies

Geo Profiles

728

Gene expression and profiles of

molecular abundance

HomoloGene

Homologous gene sets for the

organism chosen

PopSet

Sets of sequences from research

in phylogenetics and population

UniGene

Expressed transcript clusters

Facts on both gene sources and health are

presented in Table 2. This information includes

genes associated with Arabidopsis thaliana than

consisting of 9 genes, and they are three genes of

pentacyclic triterpene synthase (1,3, and 7), two

lupeol synthases (1 and 2), marneral synthase 1,

baruol synthase 1, camelliol C synthase 1, and

terpenoid cyclase family protein. It is important to

recognize that this research did not detect the OMIM

(Online Mendelian Inheritance in Man) (Table 2).

Table 3: Proteins source NCBI database for plant

triterpene synthase

Proteins

Number

Explanation

Conserved

Domains

Protein domains preserved

Identical Protein

Groups

Sequences of protein

grouped by identity

Protein

304

Protein sequences

Protein Clusters

Sequence-based clusters of

proteins

Sparcle

Functional protein

categorization by domain

architecture

Structure

Biomolecular structures

experimentally determined

Regarding with protein for triterpene synthase

observed in the database, two conserved protein

domains were found. Both are the enzymes of

Isoprenoid Biosynthesis, Class 1 and Trans IPPS

HH: Trans-Isoprenyl Diphosphate Synthases, head-

to-head as displayed in Table 3. There were 17

identical protein groups. These groups are

pentacyclic triterpene synthase 1 with 582 amino

Search for Triterpene Synthase in the NCBI Database

acid protein from A. thaliana (Mayer et al., 1999),

putative pentacyclic triterpene synthase 3 with 760

aa protein from A. thaliana (Tabata et al., 2000),

Putative pentacyclic triterpene synthase 7 with 706

aa protein from A. thaliana (Salanaubat et al., 2000),

thalianol synthase 1 with 758 aa protein from A.

thaliana (Tabata et al., 2000), pentacyclic triterpene

synthase 1 with 766 aa protein from A. thaliana

(Mayer et al., 1999), Putative pentacyclic triterpene

synthase 7 with 761 aa protein from A. thaliana.

Furthermore, taraxerol synthase (771 aa protein)

and germanicol synthase (759 aa protein), both are

from Rhizophora stylosa (Basyuni et al., 2007a),

low-quality protein putative pentacyclic triterpene

synthase 7 with 760 aa protein from A. lyrata subsp.

Lyrata (Hu et al., 2011), pentacyclic triterpene

synthase with 683 aa protein from A. thaliana (),

several multifunctional triterpene synthases from

Kandelia candel (Basyuni et al., 2006), R. stylosa

(Basyuni et al., 2007a), Costus speciosus (Kawano

et al., 2002), and Genlisea aurea (Leushkin et al.,

2013), pentacyclic triterpene synthase from A.

thaliana with 763 aa protein (Husselstein–Muller et

al., 2001), and three triterpene synthases from

Eugenia uniflora.

There were 304 proteins of triterpene synthase,

which 169 proteins belong plant. The top organisms

were A. thaliana (63), Panax quinquefolius (8),

Botryococcus braunii (8), P. ginseng (6), P.

notoginseng (6), Lycopodium clavatum (6), Lotus

japonicus (5), Ocimum basilicum (5), R. stylosa (4),

B. gymnorhiza (4), Pisum sativum (4), Malus

domestica (4). One protein cluster from Arabidopsis.

In this study, nine sparcles and sixteen structures

proteins were described (Table 3).

Recently, triterpene synthase protein modeling

has been characterized from mangrove trees

(Basyuni et al. 2018). In addition to protein from

NCBI database, another source from KEGG, with

search term: triterpene synthase found three entries:

ath: AT3G29255, putative pentacyclic triterpene

synthase 7, and ath:AT4G15340, K15823 arabdiol

synthase PEN1, pentacyclic triterpene synthase 1,

ath:At5G36150, K16205 tirucalldienol synthase,

PEN3; putative pentacyclic triterpene synthase 3.

In the enzyme database, search term of OSC

resulted of 5 hits, they were dammarenediol II

synthase (Tansakul et al., 2006), lanosterol synthase

(Suzuki et al., 2006), cycloartenol synthase such as

KcCAS and RsCAS (Basyuni et al., 2007b), -

amyrin synthase such as BgbAS (Basyuni et al.,

2007a), and -amyrin synthase such as mixed

amyrin synthase KcMS (Basyuni et at., 2007a).

These results implied a diversity of OSC genes in

the plant kingdom.

Nucleotide base sequences for genomes consisted

of 98 nucleotides and TaqMan probe (22) as shown

in Table 4. The top organisms for nucleotides were

A. thaliana (29), P. quinquefolius (8), P.

notoginseng (6), L. japonicus (5), M. domestica (5),

Ocimum basilicum (5), E. uniflora (3), Monteverdia

ilicifolia (3), P. ginseng (3), Lycopodium clavatum

(3), Medicago truncatula (2), P. sativum (2), R.

stylosa (2), B. gymnorhiza (2), Eleutherococcus

senticosus (2), Bupleurum kaoi (2), and Centella

asiatica (2).

Table 4: Genome source of triterpene synthase

Genomes

Total

Explanation

Nucleotide

RNA and DNA sequences

Probe

Probes and primers based on

sequences

Variation of the triterpene synthase chemical

features was shown in Table 5. There have been 120

molecular pathways linked to genes, proteins, and

chemicals. Online screening works are accessible for

one hundred and three bioactivities. One compound

from PubChem and one substance from PubChem in

the database.

Table 5: Chemicals source NCBI database for Plant and

triterpene synthase

Chemicals

Amount

Information

BioSystems

120

Molecular pathways associated

with genes, proteins and

chemicals

PubChem

BioAssay

103

Studies of bioactivity screening

PubChem

Compound

Chemical data with constructions,

understanding and connections

PubChem

Substance

Substance deposited and chemical

data

4 CONCLUSIONS

The online NCBI discusses numerous data on

triterpene synthase from biology and biotechnology.

The current research urged biotechnology scientists

to use the NCBI search engine to obtain more

advantages. The current research also provides

important information on triterpene synthase

biotechnology.

ICONART 2019 - International Conference on Natural Resources and Technology

ACKNOWLEDGMENTS

This research was in part funded by World Class

Research from Directorate for Research and

Community Service, Ministry of Research,

Technology and Higher Education, the Republic of

Indonesia.

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Search for Triterpene Synthase in the NCBI Database