Plant Polyprenol Reductase in the 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, North

Sumatra 20155, Indonesia

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

Sumatera Utara, Medan North Sumatra 20155, Indonesia

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

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

Keywords: Biotechnology, gene, plasma membrane, polyprenol reductase,

Abstract: Chemical constituents such as polyprenols and dolichols are known to generate higher plants. The present

document discusses the database search (https:/www.ncbi.nlm.nih.gov/) or GQuery on plant polyprenol

reductase from the National Center for Biotechnology Information (NCBI). A amount of useful data was

searched for NCBI databases. Results developed for plant polyprenol reductase in 10 databases. All

polyprenol reductase plant databases consisting of source literature, genes, genetics, protein, genomes, and

chemical characteristics. It is noteworthy that plant polyprenol reductase has complete information. The

literature comprised of PubMed and PubMed Central. Gene consisted of Gene, GEO Profiles, and UniGene.

Genetics data was available for plant polyprenol reductases such as dbGap and MedGen. Proteins feature

contained four protein sequences. Genomes encompassed one BioSample and 365 Nucleotides. The

chemicals property denoted 3392 BioSystems. The present study affords indispensable information

concerning biotechnology of plant polyprenol reductase.

1 INTRODUCTION

Higher plants are well known to produce short to

lengthy polyisoprenoids, which are classified into

polyprenol and dolichol (Sagami et al., 2018). The

occurrence of polyisoprenoids in the tropical,

subtropical and temperate areas was outlined in

different plant organs (Skorupins-Tudek et al., 2008;

Surmacz and Swiezewska, 2011; Basyuni et al.,

2016, 2017 Arifiyanto et al., 2017; Basyuni and

Wati, 2017). These reports demonstrated the

extensive distribution in the plant kingdom of

polyisoprenoids. In plant leaves, polyprenols are

defined and minor dolichols are identified

(Skorupins-Tudek et al., 2008; Surmacz and

Swiezewska, 2011; Arifiyanto et al., 2017; Basyuni

and Wati, 2017). Otherwise, dolichols in plant roots,

yeast and animal tissues were identified extensively

(Grabińska. and Palamarczyk 2002; Ishiguro et al.,

2014; Basyuni et al., 2016, 2017; Sagami et al.,

2018). By contrast to these studies, it is noteworthy

that the primary structure of polyisoprenoids in

mangroves and coastal plant leaves and roots was

dolichols (Basyuni et al., 2016, 2017).

The presence of adequate dolichols in these

plants leaves suggests that the polyprenol reductase

enzyme worked (Basyuni et al., 2018a,b,c). It has

also been reported the presence of polyprenol

reductase enzyme in Arabidopsis thaliana (Jozwiak

et al., 2015) and other higher plants (Basyuni and

Wati, 2018). This enzyme connected with the

SRD5A3 protein in animals has been revealed to

catalyze the final step in the dolichol biosynthetic of

polyprenol converted to dolichols (Rosenwald et al.,

1993; Cantagrel et al., 2010; Gründahl et al., 2012;

Sagami et al., 2018). Limited work focused on the

biotechnology data investigated from all earlier

accessible NCBI databases in the plant polyprenol

reductase. Here, through a search engine, we report a

quick and simple technique to collect useful data

needed in latest biotechnology-related science

studies. The aim of this research is to describe the

implementation of the National Center for

Biotechnology Information (NCBI) databases in

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

Plant Polyprenol Reductase in the Database.

DOI: 10.5220/0008386700120015

In Proceedings of the International Conference on Natural Resources and Technology (ICONART 2019), pages 12-15

ISBN: 978-989-758-404-6

order to obtain more insight into useful data on

updated biotechnology on polyprenol reductase in

plants.

2 MATERIAL AND METHOD

The online search engine for NCBI databases

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

produce useful data about polyprenol reductase in

the plant. As stated previously on 19 February 2018,

databases were accessed by typing plant and

polyprenol reductase in all NCBI databases. The

characteristic was all databases made using GQuery

that consisted of the literature, genes, protein,

genomes and chemical characteristics of plant

polyprenol reductase. The considerations for data

included the PubMed, PubMed Central, GEO (Gene

Expression Omnibus) profiles, UniGene, dbGaP

(database of Genotypes and Phenotypes), MedGen,

Protein, Assembly, BioCollections, BioSamples,

Clone, GSS (Genome Survey Sequences),

Nucleotide, and BioSystems.

3 RESULTS AND DISCUSSION

The search for plant polyprenol reductase led ten

databases for plant polyprenol reductase in the NCBI

database. Table 1 demonstrates the literature on

plant polyprenol reductase available in the NCBI.

Two biographies deposited with countless figures.

The online NCBI literature provides online libraries

and free access to two PubMed papers consisting of

science and medical abstracts / citations and 23

PubMed Central articles.

Table 1: Literature source NCBI database for plant and

polyprenol reductase

Literature

Number

Description

PubMed

Abstracts/quotations from

science and medicine

PubMed Central

Articles in full-text journals

Information on sources of genes is shown in

Table 2. This information includes plant-related

polyprenol reductase genes than consisting of one

gene, namely TNF receptor-associated factor 6

[Harpegnathos saltator (Jerdon's jumping ant)].

Table 2 shows 20 GEO profiles and three unigenes.

Arabidopsis thaliana species dominated the Geo

profiles. The Geo profiles are AT1G72590-Red light

effect on the root, AT2G16530-Diurnal and

circadian-regulated genes (II), AT1G72590-

Necrosis- and ethylene-inducing peptide effect on

dicots, AT1G72590-Leaf Response to Aphid

Feeding, AT1G72590-MicroRNA miR159a

overexpression effect on flower, AT1G72590-

MicroRNA miR319a overexpression effect on the

leaf, AT1G72590-Vier F-Box VFB triple mutant

seedlings, AT1G72590-Chitin oligomer chitooctaose

effect on seedlings, the effect of AT1G72590-

MicroRNA miR156b and miR164b on floral apex,

AT1G72590- MicroRNA miR164b and miR172a on

vegetative apex, DFG10-Saponin treatment effect:

time course, AT2G16530-Indole acetic acid

treatment time course (AG), AT1G72590- the

impact of salt stress on mannitol-producing M6PR

transgenic plant with salt tolerance: leaf,

AT1G72590-Indole acetic acid treatment time

course (ATH1), AT1G72590- mRNA cap-binding

protein ABH1 mutant response to abscisic acid,

AT1G72590-Salt stress effect on multiple

genotypes: leaf, LOC4336740-Cytokinin effect on

rice roots and leaves: time course, AT1G72590

Ozone impact on double-null mutant leaves of G-

protein: time span, AT1G72590-Pollinated pistils:

time span, and AT1G72590-Indole acetic acid

therapy: time span and time span (Table 2).

The UniGene consisted of 3 clusters of expressed

transcripts. They are Putative polyprenol reductase 2

(AT2G16530), represented by 11 ESTs from 5

cDNA libraries. This gene corresponds to 2

reference sequences (different isoforms) (Joswiak et

al., 2015). The 2

UniGene was Probable polyprenol

reductase 2-like, Soybean protein-encoding gene

LOC100814660. Displayed by 13 ESTs from 8

cDNA libraries and Transcribed locus, moderately

similar to XP_003537828.1 predicted: probable

polyprenol reductase 2-like Glycine max. This

unigene was represented by Lotus japonicus putative

protein-coding gene and represented by 4 ESTs from

3 cDNA libraries.

Table 2: Genes source NCBI database for plant polyprenol

reductase

Genes

Total

Information

Gene

Collected gene loci data

GEO

Profiles

Gene expression and profiles of

molecular abundance

UniGene

Expressed transcript clusters

Furthermore, the genetics source NCBI database

comprises of 8 dbGaP and 2 MedGen. The study of

the database of Genotypes and Phenotypes consist of

phs000287.v6.p1 Cardiovascular Health Study

(CHS) Cohort, phs000280.v5.p1 Atherosclerosis

Plant Polyprenol Reductase in the Database

Risk in Communities (ARIC) Cohort,

phs000209.v13.p3 Multi-Ethnic Study of

Atherosclerosis (MESA) Cohort, phs001496.v1.p1

A genomic approach to the prescription of warfarin

in Hispanics of the Admixed Caribbean,

phs000007.v30.p11 Framingham Cohort,

phs000309.v3.p2 The CARDIA-GENEVA Study,

phs000090.v5.p1 GENEVA: The Atherosclerosis

Risk in Communities (ARIC) Study, and

phs000547.v1.p1 A Study of the Genome-Wide

Association in SUCCESS Trial Breast Cancer

Patients. Regarding with protein for plant polyprenol

reductase observed in the database, 55 proteins were

recorded.

The biological and pharmacological function of

polyisoprenoids especially dolichols have been well

documented (Tao et al., 2016; Illian et al., 2018; Sari

et al., 2018). Furthermore, the role of dolichols for

the clinical and biochemical phenotypes in dolichol-

linked Congenital disorders of glycosylation (CDG)

has been described (Buczkowska et al., 2015).

Table 3: Genetics source NCBI database for plant and

polyprenol reductase

Genetics

Number

Explanation

dbGaP

Genotype/phenotype

interaction studies

MedGen

Medicinal genetics

literature and links

Table 4: Protein source NCBI database and plant

polyprenol reductase

Proteins

Number

Description

Protein

Protein sequence

Table 5: Genomes source NCBI database for plant

polyprenol reductase

Genomes

Number

Information

Assembly

Information on assembly of

genomes

BioCollections

149

Museum, herbarium and other

collections of biorepository

BioSample

Information of of materials

from biological sources

Clone

cDNA and genomic clones

GSS

Genome search sequences

Nucleotide

266

RNA and DNA sequences

The MedGene has two kinds of Glycyrrhetinic

acid product and High-Selenium Brassica juncea

(Table 3). Table 4 shows 55 protein sequences that

consist of 39 eudicots and 16 monocots. The top

plant species for protein sequence in the plant

polyprenol reductases are Noccaea caerulescens

(12), Vitis vinifera (6), Arachis ipaensis (6), Ananas

comosus (5), Dendrobium catenatum (5), and

Dichanthelium oligosanthes (3), and others (18).

Furthermore, it has been shown from Table 5;

there are 266 nucleotides from plant polyprenol

reductase, which classified from molecular type as

227 from genomic/RNA and only 22 from mRNA.

While from the sources database of nucleotide are

derived from INSDC (International Nucleotide

Sequence Database Collaboration)/Genbank (109)

and RefSeq (157). The mRNA molecule type of

plant polyprenol reductase is derived from Arachis

ipaensis (6), Ananas comosus (5), Dendrobium

catenatum (4), Arachis duranensis (2). Juglans regia

(2), and all other taxa (3).

Recently three predicted polyprenol reductases

from K. obovata had been described (Basyuni et al.,

2018a,b,c) to add previous information on

polyprenol reductase from A. thaliana (Jozwiak et

al., 2015). The position of predicted polyprenol

reductase K. obovata existed together with Ricinus

communis and Iopoea nil (Basyuni et al., 2018b,c;

Basyuni and Wati, 2018). Polyprenol reductase also

occurred in yeast Saccharomyces cerevisiae

(Szkopinska et al., 2006).

Table 6: Chemicals source NCBI database for plant and

polyprenol reductase

Chemicals

Total

Explanation

BioSystems

3392

Gene, protein and chemicals

linked molecular pathways

No variation of chemical features of the plant

polyprenol reductase as was displayed in Table 5, in

this report only BioSystems were detected.

Biosystems contained two types, conserved

biosystems (135) and organism-specific biosystems

(3257). According to a record type, 3,359 pathways,

28 structural complexes, five working sets.

Concerning to source name consisting of GO (135)

and KEGG (3,255). The BioAssays comprised

BioAssays via Actives (3,255) and BioAssays via

Target (157).

ICONART 2019 - International Conference on Natural Resources and Technology

4 CONCLUSIONS

The web NCBI supplied countless data on plant

polyprenol reductase in biology and biotechnology.

The current research encouraged researchers in the

field of biotechnology to obtain more advantages

using the NCBI search engine. The present study

also delivers crucial data regarding biotechnology of

plant polyprenol reductase.

ACKNOWLEDGMENTS

World Class Research asissted this work from

Directorate for Research and Community Service,

Ministry of Research, Technology and Higher

Education, the Republic of Indonesia.

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