Protein Induced as Salinity Stress in Elaeis guineensis Jacq.

Dolly Sojuangan Siregar

, Mohammad Basyuni

and Rahmah Hayati

Department of Agrotechnology, Faculty of Agriculture, Universitas Samudra, Meurandeh, Langsa City, Aceh, Indonesia

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

20155, Indonesia

Graduate School of Agrotechnology, Faculty of Agriculture, Universitas Sumatera Utara, Jl. Dr. A Sofyan No. 3 Medan, North

Sumatera 20155, Indonesia

Keywords: Oil Palm, Plasma Membrane, Salinity.

Abstract: Palm oil plants (Elaeis guineensis) are oil-producing plants grown in the tropics. Palm oil is sensitive to low

temperatures but high tolerance to salinity stress and drought. The present work evaluates of the bioinformatics on

the NCBI database as well as expected the physicochemical of protein salinity. There is three protein salinity induced

from E. guineensis deposited in NCBI. Length of genes was between 525 to 633 bp. The same Molecular weight at

X1 and X2 was 5945.24, but it is different from X3 which was 18052.17. Chloroplast transit peptide ranged from

0.142 and 0.445. Reactive oxygen species (ROS) plays a crucial role in promoting mitochondrial peptide targets in

plants induced by salinity, ranging from 0.022 to 0.110. These results d variations and roles of different physical and

chemical characteristics of amino acids in protein due to salinity stress in oil palm plants.

1 INTRODUCTION

Salinity is a major problem that affects the world's

agricultural output and ecosystems. In latest decades,

elevated soil salinity has transformed global farming

barriers (Rengasamy, 2006; Munns and Tester, 2008).

About 50% of the world's land will become salt by the

21st century (Mahajan and Tuteja 2005).

One of the most notable concerns of osmotic stress

in plants is the production of high quantities of reactive

oxygen species (ROS), followed by oxidative damage,

e.g. protein, lipid, pigment, and DNA degradation. (Das

and Roychoudhury 2014).

Palm oil (Elaeis guineensis) is susceptible to low

temperatures but has a high tolerance to salt stress and

drought (Cao et al., 2011). By identifying and validating

genes associated with salinity stress responses in oil

palm, it will help through molecular breeding.

The first sensory mechanism that senses salt

stimulation is two elements that are seen during salinity

stress circumstances, namely hyperosmotic stress and

Na+ ion toxicity. As a result of salinity stress, plants

produce Ca

+ and ROS which are secondary

messengers. The main organ of the plant that feels the

salinity stress is the root. Plasma membranes and

cytoplasmic proteins, G proteins, Ca2 + binding

proteins, phosphoproteins and ethylene receptors

intermediate the process. (Ghosh and Xu 2014).

At present, it is indispensable to recognize the nature

of the mechanism of salt adaptation in oil palm plants to

advance future oil palm varieties that are tolerant of

salinity. The discovery of salt-tolerant genes will help

breeders select parent species (germplasm) and

progenies using marker aid. The results of the

physiological and multi-OMICS analysis may deliver

responses to the subsequent major questions:

1. Are some existing oil palm varieties adaptive to salt

stress?

2. What is the mechanism for the adaptation of salt

stress to oil palm plants?

3. Are there differences between sporogenous tissue

in roots and leaves during salt stress?

4. Does the oil palm salinity gene affect the

phenotype?

5. What is related to the modification of

posttranslational salinity tolerance in oil palm

plants?

The present study, therefore, evaluates of the

bioinformatics on the NCBI database as well as

expected the physicochemical of protein salinity from

E. guineensis.

112

Siregar, D., Basyuni, M. and Hayati, R.

Protein Induced as Salinity Stress in Elaeis guineensis Jacq..

DOI: 10.5220/0008526301120115

In Proceedings of the International Conference on Natural Resources and Technology (ICONART 2019), pages 112-115

ISBN: 978-989-758-404-6

2 MATERIAL AND METHOD

2.1 Materials

Three salinity genes on oil palm acquired from NCBI.

The DNA and amino acid references used in the

research follow:

1. XM_019850660.1 GI: 1130661850 Salt stress-

induced hydrophobic peptide ESI3-like [E.

guineensis]; NCBI Reference Sequence:

XP_019706219.1

2. XM_019846899.1 GI: 1130626415 Salt stress-

induced hydrophobic peptide ESI3-like [E.

guineensis]; NCBI Reference Sequence:

XP_019702458.1

3. JZ142439.1 GI: 527498159 EgFLSTP6 E.

guineensis cDNA similar to salt tolerance protein

6, mRNA sequence 525 bp linear mRNA

2.2 Physicochemical Features of the

Salinity Protein of Oil Palm

Online Protparam (web.expasy.org/protparam/) has

been used to control the composition,

physicochemical features of oil palm plants ' protein

salinity. The calculated factors are the length of

genes/bp, molecular weight, theoretical isoelectric

values points, a total number of atoms, total

negatively charged residues, total number of

positively charged residues, instability coefficient,

aliphatic index, and grand mean of hydropathicity as

prior described (Basyuni et al., 2017)

2.3 Peptide Transfer and Subcellular

Localization of Protein-induced

Salinity Proteins in Oil Palm Plants

Peptide predictions transit through the online P1.1

target server (www.cbs.dtu.dk/services/targetp/).

Peptide chloroplast transit, mitochondrial target

peptide, the signal peptide of the secretory pathway,

reliability indicator were found. Online PSORT

(predictive tool for subcellular localization of

proteins) (psort.hgc.jp/form.html) is used to analyze

the subcellular of protein dehydration which is

induced by salinity stress in oil palm plants as earlier

shown (Basyuni and Wati, 2017).

2.4 Phylogenetic Analysis of Protein-

induced Salinity in Oil Palm

Locus numbers of the sequence of the physical and

chemical characteristic of oil palm protein induced

salinity used this investigation in this manner:

E.guineensis XM_019850660, XM_019846899, and

JZ142439.1. Phylogenetic analysis of amino acid

arrangement from of protein-induced salinity in oil

palm was carried out with CLUSTAL W ver. 1.83

(Thompson et al., 1994) of the DNA Data Bank of

Japan (Mishima, Shizuoka, Japan) accompanied by

depicting with TreeView, ver. 1.6.6 (Page, 1996)

according to a neighbor-joining method. Bootstrap

analysis with 1000 repetitions was used to weigh the

strong point of the knots in the tree (Felsenstein.

1995).

3 RESULT

3.1. Physicochemical Characteristics of

the Protein Induced Salinity in E.

guineensis

The physicochemical activities of a protein are

analyzed by the similar properties of the amino acids

in it. Each protein molecule contains of a long chain

of amino acid residues and is connected by peptide

bonds. Table 1 showed the several parameters of

physicochemical protein induced salinity in

E.guineensis. Length of genes between 525 to 633 bp.

The same Molecular weight at X1 and X2 is 5945.24,

but it is different from X3 which is 18052.17.

Theoretical isoelectric points values at X1 and X2 are

almost close to 4.65 and 4.0 but different from X3

which is 8.69. The total number of atoms at X1 and

X2 is almost close to 8.64 and 8.71 three times

different from X3 which is 2478.

The total number of negatively charged residues

X1 and X2 which are 3 and 4 are different from X3

which is 11. The total number of positively charged

residues on X1 and X2 is the same, namely 1, but

different from X3, namely 14, Instability coefficient

at X1, X2 and X3 between 27.15 and 31.66. Aliphatic

indexes at X1 and X2 are 162.42 and 165.93 but are

low at X3 which is 60.18. The hydrophobicity is a

significant stabilization force in protein folding.

Grand average of hydropathicity on X1 and X2 is

1.604 and 1.491 while X3 is -0.443. Despite the

availability of thousands of stress associated ESTs of

in E. guineensis (Low et al., 2008), quantitative gene

expression analysis of these genes is only recently

attempted for the identification of candidate

genes/factors that are contributing to salinity

tolerance. With the advent of the qPCR technique, it

is easier to quantify each gene and establish its

relevance under the given stress situations.

Protein Induced as Salinity Stress in Elaeis guineensis Jacq.

113

Table 1: Physicochemical characteristic of the protein

induced salinity in E.guineensis.

Variant

Length of

genes/bp

630

633

525

Molecular weight

5945.24

18052.17

Theoretical

isoelectric points

values

4.65

4.00

8.69

Total number of

atoms

864

871

2478

Total number of

negatively

charged residues

Total number of

positively charged

residues

Instability

coefficient

27.15

31.66

27.54

Aliphatic index

162.41

165.93

60.18

Grand average of

hydropathicity

1.604

1.491

-0.443

3.2. Potential Transfer of Peptide and

Subcellular Location

The potential for a prospective transfer peptide in E.

guineensis is shown in Table 2. Four reliability

factors were identified: chloroplast transit peptide,

mitochondrial target peptide, secretory path signal

peptide, and prediction of reliability. Chloroplast

transit peptide ranges from 0.142 and 0.445. ROS

plays a crucial role in promoting mitochondrial

peptide targets in plants that are gripped by salinity

(Huang et al., 2016), ranging from 0.022 to 0.110.

The signal peptide of the secretory pathway can be

found in terminal N and terminal C of protein and

most cases stored in mature proteins with values

ranging from 0.154 and 0.670. Reliability of X1, X2

and X3 predictions ranges between 3 and 5. These

indicated that ROS-scavenging enzymes played

crucial roles in salinity tolerance mechanism (Joseph

et al., 2011).

Table 2: The promising of potential transit peptide induced

salinity in E. guineensis.

Varian

Reliability

Chloroplast

transit peptide

Mitochondrial

target peptide

Signal

peptide of

secretory

pathway

Reliabilit

predictio

0.142

0.022

0.670

0.445

0.076

0.154

0.291

0.110

0.170

Table 3 shows the subcellular location of protein-

induced salinity in E. guineensis. There are two (2)

variants (X1, X2) were located in the vacuole (Vac),

Plasma (Plas), and extracellular (Extr). One variant

(X1) in Endoplasmic Reticulum (ER), Golgi (Golg).

One variant (X3) were located in Mitochondrial (Mito),

Cytoplasm (Cyto), Nucleolus (Nucl) and Chloroplast

(Chlo).

Table 3: Subcellular localization of protein-induced salinity

in E.guineensis.

Vac

Pla

Golg

Extr

Mito

Cyt

Chl

Note: Vac: Vacuole, ER: Endoplasmic Reticulum, Plas: Plasma

Golg: Golgi, Extr: Extracellular, Mito: Mitochondrial, Cyto

Cytoplasm, Nucl: Nucleolus, Chlo: Chloroplast, nd: not

detected

Figure 1: Phylogenetic tree among observed genes.

Figure 1 illustrates the phylogenetic among the

gene observed. There are three branches

representative by each gene. To further understand

the genes, several additional genes related to salinity

from E. guineensis are needed.

4 CONCLUSIONS

These findings stated differences and roles in salt-

induced amino acids in oil palm of various physical

XP 019706219.1

XP 019702458.1

JZ142439.1

0.1

ICONART 2019 - International Conference on Natural Resources and Technology

114

and chemical features. The promising prospective

transit peptide, subcellular location of protein genes

owing to the stress of salinity in E. guineensis.

ACKNOWLEDGEMENTS

This research was partially endorsed by a Penelitian

Strategis Nasional Institusi (PSN Institusi 2019)

(PSN Institusi 2019) from the Directorate for

Research and Community Service, Ministry of

Research, Technology and Higher Education,

Republic of Indonesia.

REFERENCES

Basyuni, M., Wasilah, M., and Sumardi. 2017.

Bioinformatics study of the mangrove actin genes

Journal of Physics Conference Series 801, 012013

Basyuni, M. and Wati, R., 2017. Bioinformatics analysis of

the oxidosqualene cyclase gene and the amino acid

sequence in mangrove plants. In Journal of Physics:

Conference Series 801, 012011.

Cao, H. X., Sun, C. X., Shao, H. B., and Lei, X. T. 2011.

Effects of low temperature and drought on the

physiological and growth changes in oil palm seedlings.

African Journal of Biotechnology, 10(14), 2630-2637.

Das K, and Roychoudhury A. 2014. Reactive oxygen

species (ROS) and response of antioxidants as ROS-

scavengers during environmental stress in plants.

Frontiers in Environmental Science 2:53.

Felsenstein, J., 1985. Confidence limits on phylogenies: an

approach using the bootstrap. Evolution, 39(4), pp.783-

791.

Ghosh, D. and Xu, J., 2014. Abiotic stress responses in

plant roots: a proteomics perspective. Frontiers in Plant

Science 5, 6.

Huang, S., Van Aken, O., Schwarzländer, M., Belt, K. and

Millar, A.H., 2016. The roles of mitochondrial reactive

oxygen species in cellular signaling and stress response

in plants. Plant physiology, 171(3), 1551-1559.

Joseph, B., Jini, D. and Sujatha, S., 2011. Development of

salt stress-tolerant plants by gene manipulation of

antioxidant enzymes. Asian Journal of Agricultural

Research, 5(1), 17-27.

Low, E.T.L., Alias, H., Boon, S.H., Shariff, E.M., Tan,

C.Y.A., Ooi, L.C., Cheah, S.C., Raha, A.R., Wan, K.L.

and Singh, R., 2008. Oil palm (Elaeis guineensis Jacq.)

tissue culture ESTs: identifying genes associated with

callogenesis and embryogenesis. BMC Plant Biology,

8(1), p.62.

Mahajan S, and Tuteja N. 2005. Cold, salinity and drought

stress: an overview. Archives of Biochemistry and

Biophysics 444,139-158.

Munns, R. and Tester, M., 2008. Mechanisms of salinity

tolerance. Annual Review of Plant Biology 59, 651-681.

Page, R.D., 1996. Tree View: An application to display

phylogenetic trees on personal computers.

Bioinformatics, 12(4), pp.357-358.

Rengasamy, P., 2006. World salinization with emphasis on

Australia. Journal of Experimental Botany, 57(5),

1017-1023.

Thompson, J.D., Higgins, D.G. and Gibson, T.J., 1994.

CLUSTAL W: improving the sensitivity of progressive

multiple sequence alignment through sequence

weighting, position-specific gap penalties and weight

matrix choice. Nucleic acids research, 22(22), pp.4673-

4680.

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