Information on Polyprenol Reductase Enzyme in the NCBI Online

Mohammad Basyuni

1,2

, Yuntha Bimantara

, Rahmah Hayati

, Jayusman

, Rizka Amelia

, Irma Deni

Arif Nuryawan

1,2

, Sumaiyah

2,4

and Etti Sartina Siregar

2,5

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

Sumatera 20155, Indonesia

Center of Excellence for Mangrove, Universitas Sumatera Utara, Medan, North Sumatera 20155, Indonesia

Balai Besar Penelitian Dan Pengembangan Bioteknologi dan Pemuliaan Tanaman Hutan, Yogyakarta 55582, Indonesia

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

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

ameliarizka0@gmail.com, irma.deni31@gmail.com, arif5@usu.ac.id, sumaiyah7777@gmail.com, ettisartina@yahoo.com

Keywords: Gene, Plasma Membrane, Polyprenol Reductase.

Abstract: Polyprenol reductase an enzyme is necessary to convert polyprenol to dolichol in the last phase of dolichol

biosynthesis. The present work reports search result of National Center for Biotechnology Information

(NCBI) databases on polyprenol reductase. To produce some useful data, the search for NCBI databases

(https:/www.ncbi.nlm.nih.gov/) was used. Results detected in 16 databases for polyprenol reductase. The

databases of the polyprenol reductase consist of literature, health, genomes, genes, protein, and chemical

features. The literature contained 16 bookshelves, 1 MeSH (Medical Subject Headings), 16 PubMed, and 58

PubMed Central. Health comprised 3532 Clincar documents, 163 dbGap, 899 GTR, 257 MedGen, 3 OMIM

(Online Mendelian Inheritance in Man database). Gene involves of 681 Genes, 303 GEO profiles, 1

HomoloGene, and 20 UniGenes. Proteins properties contained 933 Identical Protein Groups, 1,208 Proteins,

and 4 Protein Clusters. Genomes included 37,135 nucleotides, which are derived from 34,821 bacteria,

1,151 animals, 603 plants, 340 archaea, 141 fungi, and 7 viruses. The chemicals property represented 3648

BioSystems and five bioactivity screening studies. The present data provides indispensable information

about biotechnology of polyprenol reductase enzyme.

1 INTRODUCTION

Polyprenol reductase is an enzyme that stimulates

the reduction of polyprenols into dolichols in the

dolichol biosynthesis (Rosenwald et al., 1993;

Quellhorst Jr et al. 1997; Sagami et al. 2018). The

occurrence of polyprenol reductase has been

described as various organisms. In the plant

kingdom, for example, has been described in

Arabidopsis thaliana (Jozwiak et al., 2015),

Kandelia obovata leaves (Basyuni et al., 2018a,b,c),

spinach leaves (Sakaihara et al., 2000). Polyprenol

reductase has been shown in Haloferax volcani, a

halophilic archeon (Naparstek et al., 2012),

mammalian (Dsouzaschorey et al., 1994), yeasts

(Tateyama and Sagami, 2001; Szkapinska et al.,

2006), hamster (Chaves et al., 2015), and human

(Cantegral et al., 2010).

The biological and pharmacological activity of

polyprenol reductase has been described, such as

prostate cancer prevention (Nacusi and Tindall,

2011; Schmidt and Tindall, 2011). Polyprenol

reductase has been shown to play a role in

congenital disorders of glycosylation (CDG)

(Gründahl et al., 2012) and genetic defects of

dolichol metabolism in dolichol-related CDGs for

clinical and biochemical phenotypes (Buczkowska et

al., 2015).

In this context, it is essential to understand

further the polyprenol reductase enzyme relating

biotechnology from all databases available. Here we

report a brief review via a search engine to gather

useful data in biotechnology-related science studies.

Therefore, the present study aimed to report the use

of the databases of the National Center for

Biotechnology Information (NCBI) search to obtain

more insight on updated biotechnology related to

polyprenol reductase enzyme.

104

Basyuni, M., Bimantara, Y., Hayati, R., Jayusman, ., Amelia, R., Deni, I., Nuryawan, A., Sumaiyah, . and Siregar, E.

Information on Polyprenol Reductase Enzyme in the NCBI Online.

DOI: 10.5220/0008525901040107

In Proceedings of the International Conference on Natural Resources and Technology (ICONART 2019), pages 104-107

ISBN: 978-989-758-404-6

2 MATERIALS AND METHOD

The material of this work applied databases of

polyprenol reductase that were used to produce some

valuable information biotechnology can be

conducted using NCBI databases search engine

online (https://www.ncbi.nlm.nih.gov/). The

material was derived from typing on all database

search as mentioned earlier on January 22, 2019.

Information features include the Bookshelf, MeSH

(Medical Subject Headings), NLM (National Library

of Medicine) Catalog, PubMed, PubMed Central,

Clinvar, a database of Genotypes and Phenotypes

(dbGap), Genetic Testing Registry (GTR). MedGen,

Online Mendelian Inheritance in Man (OMIM),

BioSample, Clone, database of human genomic

structural variation (dbVar), Genome, GSS (Genome

Survey Sequences), Nucleotide, Probe, EST, Gene,

Gene Expression Omnibus (GEO) Profiles,

HomoloGene, UniGene, Identical Protein Groups,

Protein, Protein Clusters, Biosystems, and PubChem

BioAssay.

3 RESULT AND DISCUSSION

The exploration for the polyprenol reductase enzyme

showed sixteen databases in the NCBI database.

Table 1 depicts the literature available in the NCBI

concerning polyprenol reductase. Four biographies,

namely bookshelf, MeSH, PubMed, and PubMed

Central with a number of deposited documents. The

online NCBI literature provides online libraries and

free access to bookshelf data (sixteen books and

reports). MeSH contained one ontology used for

Pubmed indexing. PubMed covered the publication

year 1990-2018.

Table 1: Literature source NCBI database for polyprenol

Reductase.

Literature

Sum

Information

Bookshelf

Books and reports

MeSH

The ontology used to

index Pubmed

PubMed

Abstracts/quotations

from science and

medicine

PubMed Central

Full-text journal

articles

Table 2: Health source NCBI database for polyprenol

reductase.

Health

Total

Definition

Clinvar

3532

variations in human clinical

importance

dbGap

163

genotype/phenotype interaction

issues

GTR

899

genetic testing registry

MedGen

257

Medical genetics literature and links

OMIM

online mendelian inheritance in man

Information on health sources is displayed in

Table 2. This data is including 3,532 ClinVar

relating to individual variations of clinical

significance, 163 dbGap, 899 GTR, 257 MedGen. It

is important to mention that this research (Table 2)

identified the OMIM (Online Mendelian Inheritance

in Man). The OMIM consisted of Steroid 5-alpha-

reductase 3, SRD5A3, Steroid 5-alpha-reductase 1,

SRD5A1, and Congenital disorder of glycosylation

(CDG), CDG1Q as previously was reported

((Gründahl et al., 2012; Buczkowska et al., 2015).

Table 3: Genomes source NCBI database for polyprenol

reductase.

Genomes

Number

Explanation

BioSample

302

descriptions of materials from

biological sources

Clone

genomic and cDNA clones

dbVar

21,375

studies of structural genome

variation

Genome

organizational genome

sequencing projects

GSS

1,514

genome project sequences

Nucleotide

37,135

DNA and RNA sequences

Probe

samples and primers based on

sequences

Furthermore, genome source for polyprenol

reductase enzyme namely 302 BioSample, 12 clones

of genomic and cDNA, 21,375 trials of structural

genome variability, 4 projects of genome sequencing,

1514 GSS, 37,135 DNA and RNA sequences, and

18 Probes. It is intersting that from 37,135

nucleotides in the databases comprised of 1,151

animals, 603 plants, 141 fungi, 78 protists, 34,821

bacteria, 340 archea, and 7 viruses while the

molecular type contained 36,192 DNA/RNA and

851 mRNA.

The Genes collection consisted of 1 Expressed

sequence tag (EST), 681 information about gene

loci, 303 gene expressions, one homologene, and 20

Unigenes as depicted in Table 4. Table 5 shows the

protein source for 933 identical protein groups,

1,208 protein, and 4 protein clusters. Four protein

Information on Polyprenol Reductase Enzyme in the NCBI Online

105

clusters are 3-oxo-5-alpha-steroid 4-dehydrogenase,

C-terminal domain containing Embryophyte protein

(Accession: PLN03164), 3-oxo-5-alpha-steroid 4-

dehydrogenase family protein conserved in

Arabidopsis thaliana (Accession: CLSN2912717),

probable polyprenol reductase 1-like conserved in

BOP clade, and probable polyprenol reductase 2-like

conserved in Glycine max (Accession:

CLSN2960920).

Table 4: Genes source NCBI database for polyprenol

Reductase.

Genes

Number

Definition

EST

expressed sequence tag sequences

Gene

681

collected gene loci data

GEO Profiles

303

gene expression and profiles of

molecular abundance

HomoloGene

homologous gene

UniGene

sets of expressed transcripts for

chosen organisms

Table 5: Proteins source NCBI database for polyprenol

reductase.

Proteins

Number

Explanation

Identical Protein

Groups

933

identity grouped protein

sequences

Protein

1,208

protein sequences

Protein Clusters

Sequence of protein clusters

based on similarity

Table 6: Chemicals source NCBI database for polyprenol

reductase.

Chemicals

Amount

Information

BioSystems

3,648

gene, protein and chemicals

linked molecular pathways

PubChem

BioAssay

screening of bioactivity

The biological activities have been well

documented (Nacusi and Tindall, 2011; Schmidt and

Tindall, 2011Buczkowska et al., 2015; Tao et al.,

2016). Polyprenol reductase has been reported to

play an essential role in CDG (Gründahl et al., 2012)

and the clinical and biochemical phenotypes in

dolichol-concerning CDG (Buczkowska et al., 2015).

Probable polyprenol reductases from K. obovata

had been reported (Basyuni et al., 2018a,b,c) to

different previous data on polyprenol reductase from

A. thaliana (Jozwiak et al., 2015). The position of

predicted polyprenol reductase from K. obovata sit

together with Ricinus communis and Iopoea nil

(Basyuni et al., 2018b,c; Basyuni and Wati, 2018).

Variation of chemical features of the polyprenol

reductase as was displayed in Table 6, in this report

only BioSystems and PubChem BioAssay were

detected. Biosystems contained two types, conserved

biosystems (206) and organism-specific biosystems

(3442). According to a record type, 3,608 pathways,

28 structural complexes, 12 functional sets. Relating

to source name consisting of BioCyc (2), GO (196)

and KEGG (3,337). Whereas the source of databases

derived from INSDC/GenBank was 24,798 and

RefSeq was 12,331. The PubChem BioAssays

comprised 5 bioactivities screening studies (Table

6). These five Assays are Upregulation of NADH-

cytochrome b5 reductase expression in Candida

albicans SC5314 at 200 uM after 24 hrs by MALDI-

TOF MS, Upregulation of Glutathione reductase

expression in Candida albicans SC5314 at 200 uM

after 24 hrs by MALDI-TOF MS, Upregulation of

Mitochondrial 2-enoyl thioester reductase

expression in Candida albicans SC5314 at 200 uM

after 24 hrs by MALDI-TOF MS, Upregulation of

Aldose reductase expression in Candida albicans

SC5314 at 200 uM after 24 hrs by MALDI-TOF

MS, and Inhibition of 5alpha-reductase in human

epidermis assessed as inhibition of [14C]testosterone

to DHT after 24 hrs.

4 CONCLUSIONS

The NCBI online discusses different data about

polyprenol reductase enzyme in biology and

biotechnology. The current study also delivers

important data regarding biotechnology of

polyprenol reductase.

ACKNOWLEDGMENTS

This work was in part assisted 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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