NCBI Database on Cycloartenol Synthase

Mohammad Basyuni

1,2

, Rahmah Hayati

, Yuntha Bimantara

, Rizka Amelia

, Sumaiyah

, Era

Yusraini

, and Hirosuke Oku

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

Sumatera 20155, Indonesia

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

Sumatera Utara, Medan North Sumatera 20155, Indonesia.

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

Faculty of Agriculture, Universitas Sumatera Utara, Medan 20155, Indonesia

Molecular Biotechnology Group, Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara,

Okinawa 903-0213, Japan

Keywords: Abiotic stress, cycloartenol, isoprenoid, oxidosqualene

Abstract: Cycloartenol synthase (EC 5.4.99.8) is a cycloartenol-converting enzyme. The current research describes

the search of cycloartenol synthase databases from the National Center for Biotechnology Information

(NCBI). A amount of precious information was generated by NCBI database search

(https:/www.ncbi.nlm.nih.gov/). Results discovered in 22 cycloartenol synthase databases. All literature,

genes, genetics, protein, genomes, and chemical features of cycloartenol synthase databases. Bookshelf,

MeSH (Medical Subject Headings) and PubMed Central were discussed in the literature. Gene was made up

of profiles from Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet, and UniGene. Data on

genetics such as MedGen was available for cycloartenol synthase. Proteins characteristic comprised

Conserved Domains, Identical groups of proteins, clusters of proteins, sparcle, and structure. Nucleotide and

sample were engaged in genomes. BioSystems, PubChem BioAssay, PubChem Compound, and PubChem

Substance are the chemical properties. The present work affords vital information in term biotechnology of

cycloartenol synthase.

1 INTRODUCTION

Phytosterol including cycloartenol is ordinary

chemical constituents in higher plants (Augustin et

al., 2011; Uddin et al., 2015). Phytosterols serve as

chemotaxonomy markers also have been shown

(Koch et al., 2011). Many phylogenetic analyses

have been suggested that plant oxidosqualene

cyclases (OSCs) are generally evolutionarily

derived from cycloartenol synthase (Zhang et al.,

2003; Basyuni et al., 2007a,b). More than

thousands different OSC genes together with

cycloartenol have been reported from plant

kingdom, which are expanded from a shared 2,3-

oxidosqualene substrate via OSCs, they separate in

the cyclization of this intermediacy into each of

phytosterol of cycloartenol and lanosterol or a

diversity of triterpenes (Augustin et al., 2011). In

plantae, cycloartenol synthase (CAS) along with

lanosterol synthase (LAS), family member of OSC

are accountable for biosynthesis of phytosterol,

and more OSCs are committed for triterpene

synthesis (Thimmappa et al., 2014).

Lanosterol and cycloartenol are significant

elements of the membrane and can provide

substrates for hormones of sterols (Bloch 1983).

Our previous studies have shown that membrane

lipids (triterpenoids and phytosterols) have an

evident role in mangrove modification to salinity

stress (Oku et al., 2003; Basyuni et al., 2009,

2012a,b), Saccharomyces cerevisiae, GIL77,

modulated the salt tolerance of lanosterol synthase

deficient (Inafuku et al., 2018). Even though a

significant number of studies in cycloartenol

synthases have been well documented (Agustin et

al., 2011; Xue et al., 2012; Gas-Pascual et al.,

2014; Moses et al., 2014; Thimmappa et al., 2014;),

Limited work concentrated on biotechnology data

from all accessible databases in cycloartenol

synthases. Here we report an alternative technique

Basyuni, M., Hayati, R., Bimantara, Y., Amelia, R., Sumaiyah, S., Yusraini, E. and Oku, H.

NCBI Database on Cycloartenol Synthase.

DOI: 10.5220/0008386800160019

In Proceedings of the International Conference on Natural Resources and Technology (ICONART 2019), pages 16-19

ISBN: 978-989-758-404-6

to collect useful data needed in latest

biotechnology-related science studies on

cycloartenol synthase through a preferred search

engine. Therefore, the aim of this research was to

explain the implementation of the National Center

for Biotechnology Information (NCBI) databases

(GQuery) search to gain more deepful information

on updated cycloartenol synthesis biotechnology.

2 MATERIALS AND METHODE

The search engine for NCBI databases

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

produce a amount of useful rubber plant data

biotechnology. As stated previously on September

19, 2018, data bases were obtained by writing

Hevea brasiliensis in all database searches. All

databases composed of literature, health, genes,

protein, genomes, and chemical properties were

featured. Cycloartenol synthase (GQuery) was

performed. The bookshelf, MeSH (Medical

Subject Headings), NLM (National Medicine

Library) Catalog, 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 the data variables.

3 RESULTS AND DISCUSSIONS

Table 1 demonstrates the literature on cycloartenol

synthase available in the NCBI. Four biographies

stored in countless numbers. The web NCBI

literature provides internet libraries and free access

to bookshelf data (two reports and books), 2 MeSH

(Medical Subject Headings), namely cycloartenol

synthase [Supplementary Concept] and 3-beta-(2-

(diethylamino) ethoxy) androst-5-en-17-one [

Additional Concept], ontology used to index

PubMed papers.

Table 1: Literature source NCBI database for

cycloartenol synthase

Literature

Total

Information

Bookshelf

Reports and books

Mesh

Medical topic in the

collections of the NLM

PubMed

312

Scientific and medical

abstracts/quotations

PubMed

Central

584

Articles in full-text journals

Furthermore, 87 Pubmed and 232 PubMed Central

documentations were stored as called the plant

cycloartenol synthase (Table 1). The PubMed

database includes quotes derived different topics in

many connections to reports of full-text papers on

rubber plants open access.

Table 2: Genes source NCBI database for cycloartenol

synthase

Health

Amount

Explanation

Gene

242

Gathered data about the gene

loci

GEO Profiles

116

Gene profile and molecular

abundance patterns

HomoloGene

Homologous gene sets for

chosen organisms

PopSet

Sets of phylogenetic and

population studies sequences

UniGene

Groups of transcripts

conveyed

Table 3: Genetics source NCBI database for cycloartenol

synthase

Genetics

Total

Information

MedGen

Literature and connections in

medical genetics

Table 4: Proteins source NCBI database for cycloartenol

synthase

Proteins

Number

Explanation

Conserved

Domains

Preserved protein domains

Identical

Protein

Groups

723

Sequences of proteins

classified by similarity

Protein

976

Sequences of proteins

Protein

Clusters

Sequence of protein clusters

based on similarity

Structure

Experimentally determined

biomolecular structures

Table 5: Genomes source NCBI database for Plant and

cycloartenol synthase

Genomes

Number

Description

Nucleotide

1583

RNA and DNA sequences

Probe

Biomolecular structures

experimentally determined

Information on genes sources is displayed in

Table 2. This data is as well as genes associated to

cycloartenol synthase than consisting of 242 genes

with top organisms are Rosa chinensis (15), Malus

domestica (14), Camellia sinensis (11), Zea mays

(10), Pyrus x bretschneideri (10), Gossypium

hirsutum (10), G. raimondii (10), Vitis vinifera

(10), Aegilops tauschii (8), Arachis hypogaea (8),

NCBI Database on Cycloartenol Synthase

Brachypodium distachyon (7), Phoenix dactylifera

(7), Nicotiana tabacum (7), and all other taxa.

Table 2 shows there is 116 GEO profiles, one

homologene, three popset, and 66 uniges. It is

important to note that top organisms for unigene

are Malus domestica (5), Zea mays (5), Panicum

virgatum (4), Brassica napus (3), Arabidopsis

thaliana (3), Citrus sinensis (3), Medicago

truncatula (3), Vitis vinifera (3), Triticum aestivum

(3), and Pinus taeda (3). The three popsets are

Nicotiana tabacum cycloartenol synthase (CAS1)

mRNA, complete cds, Bacillariophyta cycloartenol

synthase gene, partial cds, and Avena cycloartenol

synthase gene, complete cds.

Table 3 shows one genetics information on

medical genetics literature and links. On the other

hand, Table 4 depicts protein source from NCBI

database for there are five sources for protein that

consists of one conserved domain, 723 identical

protein groups, 976 proteins, 17 protein clusters,

and two structures. The conserved domains

comprise C-terminal domain of squalene-hopene

cyclase. EC:5.4.99.17 registered as squalene-

hopene cyclase, in bacteria activates the cyclisation

of squalene into hopene. This response is partly

cationic cyclisation cascade, to be similar to a

critical level in cholesterol biosynthesis. The C-

terminal half of the molecule belongs to this family

(Marchler-Bauer et al., 2016).

The same protein groups combined from 13

invertebrates, 437 plants and fungi, and 26

prokaryotes. It is interesting to note that 976

proteins are consisting of animals (2), plants (797),

fungi (1), protists (85), bacteria (90) and archaea

(1). Top organism for plants are 51 Oryza sativa

(International Rice Genome Sequencing Project,

2005), 46 Vitis vinifera (Roach et al., 2018) and

46 Zea mays (Soderlund et al., 2009), 21 Medicago

truncatula (Young et al., 2011), and 20

Arabidopsis thaliana (Corey et al., 1993).

The two structures of cycloartenol are structure

of human OSC in complex with Ro 48-8071

[Isomerase, EC: 5.4.99.7] and Human OSC

structure in lanosterol complex [Isomerase, EC:

5.4.99.7].

Table 5 displays 1583 nucleotides that

comprising of Animals(6), Plants(1,294), Fungi(1),

Protists(111), Bacteria(171), Archaea(1). The top

plant species as following Oryza sativa (55),

Malus domestica (45), Zea mays (43), Glycine

max (27), Vitis vinifera (27), and all other taxa

(1097). There are 92 probes in the cycloartenol

synthase. Table 6 describes the chemical source of

the NCBI database that consists of 10234

Biosystems, 107 PubChem bioassay, 22 PubChem

compound, and 58 PubChem substance.

Table 6: Chemicals source NCBI database for

cycloartenol synthase

Chemicals

Total

Information

BioSystems

10234

Molecular pathways

associated to genes, proteins

and chemicals

PubChem

BioAssay

107

Bioactivity screening

PubChem

Compound

Chemical data with systems,

experience and relationships

PubChem

Substance

Substance stored and

chemical data

Protein modeling of cycloartenol synthase from

mangrove trees has recently been defined (Basyuni

et al. 2018). The protein modeling for KcCAS in

Kandelia candel and RsCAS of Rhizophora stylosa

cycloartenol synthases was analyzed by Pyre2

showed homolous results with lightly divergent in

sequence similarity. By disparity, the Swiss model

for KcCAS had marginally greater sequence

homology (47.3%) and differentiated Qmean

(0.70) from RsCAS.

4 CONCLUSIONS

The web NCBI defines multiple biological and

biotechnology data on cycloartenol synthase. The

current work motivated scientists in the field of

biotechnology to obtain more advantages using the

NCBI search engine. The present study also

delivers crucial data regarding biotechnology of

triterpene synthases.

ACKNOWLEDGMENTS

This work was in part assisted by an International

Research Collaboration and Scientific Publication

Grant 2019 from Universitas Sumatera Utara.

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NCBI Database on Cycloartenol Synthase