NUCLEOTIDE POLYMORPHISM OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) FROM KELAMPAYAN

NUCLEOTIDE POLYMORPHISM OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) FROM KELAMPAYAN

(N eolamarckia cadamba)

Ling Siaw Ching

Bachelor of Science with Honours

QK

898

N83 2013

1..755 2013

pusat Khidmat Maldumat Akademi\;

UNIVERS111

Nucleotide Polymorphism of UDP-Glucose Dehydrogenase (UDPGDH) From Kelampayan (Neolamarckia cadamba)

Ling Siaw Ching

A project submitted in partial fulfilment of the requirement for the degree of Bachelor of Science with Honours

(Resource B iotechno 10gy)

Department of Molecular Biology Faculty of Resource Science and Technology

Universiti Malaysia Sarawak 2013

ACKNOWLEDGEMENTS

I would like to express my sincere gratefulness to God for giving me wisdom and strength in completing my project. Deepest appreciation to my supervisor and co-supervisor: Dr.

Ho Wei Seng and Dr. Pang Shek Ling, for giving me support and guidance throughout this project. I am grateful as they always put in a lot of effort in order to help me in any way they could to ensure my project can be done smoothly. Greatest appreciation to my family whose gave me full support in the completion of this project. I am also grateful to all the master students for their guidance and sharing of their experience with me. Lastly, I would like to thank my fellow friends for their help, encouragement and support throughout the completion of my final year project.

I

DECLARATION

I hereby declare that this project entitled "Nucleotide Polymorphism of UDP­

Glucose Dehydrogenase (UDPGDH) From Kelampayan (Neolamarckia cadamba)" is a record of an original work done by me and is my own effort under the supervision of Dr.

Ho Wei Seng and that no part has been plagiarized without citations. The results embodied in this thesis have not been submitted to any other University or Institute for the award of any degree or diploma.

Ling Siaw Ching

Resource Biotechnology Programme Department of Molecular Biology

Faculty of Resource Science and Technology Universiti Malaysia Sarawak

II

....

Pusat Khidmat Maklumat AkademBL

Acknowledgements Declaration

Table of Contents List of Abbreviations List of Tables

List of Figures Abstract

1.0 Introduction

2.0 Literature Review 3

T ABLE OF CONTENTS

II

III

v

VII VIII

IX

2.1 Neolamarckia cadamba (Roxb.) Bosser 3

2.2 UDP-Glucose Dehydrogenase gene 5

2.3 Cell Wall and Wood Formation 7

2.4 Single Nucleotide Polymorphism (SNP) 11

3.0 Materials and Method 13

3.1 Plant Materials 13

3.2 DNA Extraction 13

3.3 Agarose Gel Electrophoresis 13

3.4 DNA Quantification 14

3.5 Primer Design 14

3.6 Polymerase Chain Reaction (PCR) 15

3.7 PCR Product Purification 16

3.8 DNA Sequencing~and Data Analysis 16

I III

17

,..

4.0 Results and Discussions

4.1 Plant materials ₁₇

4.2 DNA Extraction and Purification ₁₈

4.3 Agarose Gel Electrophoresis ₁₉

4.4 DNA Quantification ₁₉

4.5 Primer Design 20

4.6 Optimization of Polymerase Chain Reaction 22

4.7 PCR Product Purification 25

4.8 DNA Sequencing and Data Analysis 26

5.0 Conclusions and Recommendations 35

References 36

Appendix A 38

Appendix B 40

IV

,..

CAPS

cDNA

CIA

CTAB

DBH

DNA

EDTA

GPS

IUBMB

PCR

RFLP

SNP

UDP-Api

LIST OF ABBREVIATIONS

Cleaved Amplified Polymorphic Sequences

Complementary DNA

Chloroform-Isoamyl Alcohol

Cetyltrimethylammonium Bromide

Diameter at Breast Height

distilled deionized water

Deoxyribonucleic acid

Ethylenediamine tetraacetic acid

Global Positioning System

International Union of Biochemistry and Molecular Biology

Polymerase Chain Reaction

Restriction Fragment Length Polymorphism

Single Nucleotide Polymorphism

Annealing Temperature

Melting Temperature

UDP-Apiose

v

UDP-Ara UDP-Arabinose

UDP-GaIA UDP-Galacturonic acid

UDP-G1c Uridine Diphosphate Glucose

UDPGDH UDP-Glucose Dehydrogenase

UDP-Xyl UDP-xylose

UV Ultraviolet

VI

LIST OF TABLES

Table Page

3.1 DBH and GPS reading for five Kelampayan trees 17 4.1 Absorbance reading at A2so, A260 and A23o, absorbance value and DNA 20

concentration of sample I to 5.

4.2 Primers designed to amplify the UDP-glucose dehydrogenase gene 22

4.3 peR Profile 23

4.4 BLASTn output for amplified partial UDPGDH DNA 26

4.5 The position of SNP and InDels 27

4.6 Possible recognition and cutting site of restriction enzymes in partial 31 UDP-glucose dehydrogenase gene

VII

r ^I

I

LIST OF FIGURES

Figure Page

2.1 Neolamarckia cadamba flowers 4

2.2 Neolamarckia cadamba fruits 4

2.3 Pathway for production of hemicellulose precursor through oxidation 6 of UDP-Glucose

2.4 Three-dimensional structure of a secondary cell wall 9 2.5 Structural model of cellulose microfibril with hemicellulose, pectic 9

substance proteins and lipids

2.6 Role of hemicellulose and pectin in the structural organization of 10 cellulose microfibrils

4.1 Optimization of annealing temperature 24

4.2 PCR products 24

4.3 Purified PCR products 25

4.4 Alignment of partial UDP-glucose dehydrogenase gene from five 28 Kelampayan trees using CLC Free Workbench 6.0

4.5 Electrophoragram shows the overlapping of two peaks 32 4.6 Positions of restriction enzymes for SNP site

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VIII

NUCLEOTIDE POLYMORPHISM OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) FROM KELAMPAYAN (Neolamarckia cadamba)

LING SlAW CHING

Resource Biotechnology

Faculty of Resource Science and Technology Universiti Malaysia Sarawak

ABSTRACT

Neolamarckia cadamba (Roxb.) Bosser, also known as Kelampayan, is a medium to large sized, fast growing tree that is belongs to the family of Rubiaceae./Kelampayan is used for industrial plantation and reforestation.

It gives the best raw materials for plywood industry as well as pulp and paper industry. UDP-glucose dehydrogenase is an enzyme that catalyzes the conversion of UDP-gIucose to UDP-glucuronate, which acts as a key precursor for the synthesis of hemicellulose and pectin in a multistep non-reversible reaction.

Hemicellulose and pectin are the important components for cell wall formation. The main objective of this study was to identify nucleotide polymorphisms caused by single nucleotide polymorphisms (SNP) in UDP­

glucose dehydrogenase gene in Kelampayan. In order to do this, DNA extracted from five Kelampayan trees were first subjected to polymerase chain reaction to obtain the desired UDPGDH sequence. BLASTn analysis was then performed to search for sequence homology. Five UDPGDH sequences were aligned using CLC Free Workbench 6.0 for SNP detection. A total of 3 SNP and 3 InDels had been detected in partial UDP-glucose dehydrogenase sequence. Apart from that, five restriction enzymes which include BssKl.

PspGl, StyD41 and MspJI were also detected for three SNP sites.

Keywords: Neolamarckia cadamba. UDP-glucose dehydrogenase gene (UDPGDH), Single Nucleotide Polymorphism (SNP).

ABSTRAK

Neolamarckia cadamba (Roxb.) Bosser. juga dekenali sebagai Kelampayan. adalah pokok yang bersaiz sederhana ke saiz besar, pokok cepal lumbuh yang lergolong dalam keluarga Rubiaceae. Kelampayan digunakan unluk per/adangan induslri dan penanaman semula hulan. la memberi bahan-bahan menlah yang terbaik bagi induslri papan lapis serla pulpa dan induslri kerlas. UDP-glukosa dehidrogenase merupakan enzim yang memangkinkan penukaran UDP-glukosa kepada UDP-glucuronale. yang berlindak sebagai pelopor ulama unluk sinlesis hemiselulosa dan peklin dalam salu lindak balas bukan berbalik berperingkal.

Hemiselulosa dan peklin adalah komponen penling unluk pembenlukan dinding sel. Objektijulama kajian in;

adalah untuk mengenal pasli polimorfisme nukleolida yang disebabkan oleh polimorfisme nukleolida tunggal (SNP) dalam UDP-glukosa dehidrogenase gen di Kelampayan. Kajian ini bermula dengan pengekslrakkan DNA daripada lima pokok Kelampayan. Selerusnya, DNA yang diekslrak itu lerlak/uk kepada lindak balas berantai polymerase unluk mendapalkan urulan UDPGDH yang dikehendaki. Analisis BLASTn kemudian dilakukan un/uk mencari urulan homology yang terdapat di NCB!. Ini diikuti oleh pengesanan SNP melalui pengajaran urutan dengan menggunakan CLC Free Workbench 6.0. Hasil kajian ini menunjukkan seramai 3 SNP dan 3 InDels sepanjang urutan UDP-glukosa dehidrogenase. Selain daripada itu, lima enzim penyekatan yang termasuk BssKl, PspGI, StyD41 dan MspJI juga dikesan di tiga posisi SNP.

kunci: Neolamarckia cadamba, UDP-glukosa dehidrogenase (UDPGDH). polimorfisme nukleotida tunggal (SNP)

IX

1.0 INTRODUCTION

Neolamarckia cadamba (Roxb.) Bosser, also known as Kelampayan, is a medium to large sized, fast growing tree that is belongs to the family of Rubiaceae. Due to the fast growing properties, ability to grow in different types of soil and the absence of serious pests and diseases Kelampayan is used for industrial plantation and reforestation (Krisnawati et al., 2011 ). Apart from that, Kelampayan is increasingly important as it gives the best raw material for plywood industry as well as pulp and paper industry. The various uses of this tree make it even more attractive to be used in reforestation programmes.

Genetic improvement of Kelampayan is necessary to enhance their economic traits such as the wood quality. The most significant step of plant breeding is the selection of the plants with desirable characteristics. The conventional method of plant selection is based on the phenotypic marker or morphological marker such as the plant height is taken into account. However, this method does not give the correct picture of genetic make-up of the plant as most of the traits are controlled by many genes and influences by environmental factors. In some cases, particular genes does not expressed if environment is not suitable.

Moreover, conventional methods are time consuming and labour requiring (Jehan and Lakhanpaul, 2006).

Although another two set of markers, called biochemical marker and DNA marker, have overcome the limitations of phenotypic marker, their uses are also restricted. For biochemical marker, secondary metabolites which are used as the marker are a product of a complex and long pathway and thus require the study of many genes. DNA markers, such as Restriction Fragment Length Polymorphism (RFLP), requires large amount of DNA and are time consuming (Jehan and Lakhanpaul, 2006).

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To overcome those problems, a new approach which is Single Nucleotide Polymorphism (SNP) is utilised to increase the selection efficiency and to reduce the time and costs associated with measuring wood properties. Single nucleotide polymorphisms (SNPs) are a type of polymorphism involving variation of a single base pair. It is the DNA sequence in which the purine or pyrimidine base such as cytosine of a single nucleotide has been replaced by another base.

During photosynthesis, plant cells produce carbohydrates by the fixation of carbon dioxide. These carbohydrates will be transported to other non photosynthetic cells in the roots, reproductive structures and developing organs. Therefore, sucrose transport is essential for the distribution of carbohydrates in plants. Sucrose cleavage is crucial for the allocation of the carbon sources to plants. In sucrose metabolism, sucrose is broken down by sucrose synthase into fructose and uridine diphosphate glucose (UDP-glucose) (Koch, 2004). The product of cleavage, UDP-glucose, will then be catalysed by UDP-glucose dehydrogenase to form UDP-glucuronate, which is crucial for wood formation (Koch, 2004). Therefore, UDP-glucose dehydrogenase is very important in the synthesis of UDP­

glucuronate and subsequently the wood formation.

The objective of this study was to design a pair of primer for amplifying UDP­

glucose dehydrogenase gene. Besides that, the sequence polymorphism of the UDP­

glucose dehydrogenase gene of five selected Kelampayan trees as well as the possible restriction enzymes at SNP site was determined.

2

I

2.0 LITERATURE REVIEW

2.1 Neolamarckia cadamba (Roxb.) Bosser

Neoiamarckia cadamba, also known as Kelampayan, is a medium to large sized, fast growing tree that belongs to the family of Rubiaceae. It is a deciduous tree with a broad umbrella-shaped crown and straight cylindrical bole (Krisnawati et ai., 2011). The tree is able to attain a height of 45 m and a stem diameter of about 100 to 160 cm (Krisnawati et ai., 2011). It is naturally distributed from India and Nepal, through Thailand and Indo­

China and east-ward in the Malaysian Archipelago to Papua New Guinea. However, it has been introduced to Africa and Central America. According to Joker (2000), "Kelampayan is found in areas below 1 000 m altitude or in an area where there is more than 1500 mm of rain/year". Nevertheless, Kelampayan can also survive in an area with minimum rain of 200 mm per year.

Kelampayan starts to flowering when the tree reaches 4 to 5 years old. The flowers of Kelampayan are orange in colour, small in size and have a sphere shape (Figure 2.1).

The fruits are characterized by small capsules which packed closely to form a fleshy, yellow or orange coloured infructescence containing approximately 8,000 seeds (Figure 2.2) whereas the seeds are trigonal or irregular shaped which dispersed through wind, rain, flood or river (Joker, 2000).

The wood of Kelampayan is classified as a lightweight hardwood which gives the best raw materials for plywood industries. The wood is white to creamy white, no characteristic odour, straight-grained and fine to medium textured (Sankar, 2012). The wood density is in the range of 290-560 kg/m³ at 15% moisture content (Krisnawati et ai., 011). The wood of Kelampayan is moderately strong, works easily under tools and is

3

suitable for making plywood, light construction materials, flooring, paper and pulp, boxes and crates, tea-chests, packing cases, shuttering, ceiling boards, toys, wooden shoes, furniture, yokes, carvings, matches, chopsticks and pencils (Krisnawati et ai., 2011).

Other than that, it is also reported that the bark and leaves of the tree have various medicinal uses such as curing ulcer, fever, vomiting, urinary retention, inflammation of eyes, cough, diarrhoea, burning sensation (Huang, 2012).

Figure 2.1 Neolamarckia cadamba flowers (Source:

http://naturemagnificent.blogspot.coml2011_07_01_archive.html).

Figure 2.2 Neolamarckia cadamba fruits (Source:

http://tO.gstatic.comlimages?q=tbn:ANd9GcTQh_lcRTBKZrpOS12ugevBgQliliDm7y13MIVD83SyXhvaOF wYK).

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Posat Kbidmat·Makiumat AkademDc

2.2 UDP-Glucose Dehydrogenase gene

UDP-glucose dehydrogenase gene is very important as it encodes for an enzyme known as UDP-glucose dehydrogenase. UDP-glucose dehydrogenase catalyzes the conversion of UDP-glucose to UDP-glucuronate, which acts as a key precursor for the synthesis of hemicellulose and pectin in a multistep non-reversible reaction. Hemicellulose and pectin are the important components for cell waIf formation (Johansson, 2003).

UDP-glucose + 2 NAD+ --.~ UDP-glucuronate + 2 NADH

UDP-glucose dehydrogenase plays a significant role in supplying UDP-sugars to cell wall and glycoprotein synthesis. It was reported to be the possible marker for secondary cell wall formation. The highest expression of UDP-glucose dehydrogenase is mainly found in the xylem and maturing leaves where the cell wall reinforced to its final size. UDP-glucose dehydrogenase are synthesized in the Goigi bodies and then transported to the cell wall. This has proved the roles of the enzymes in cell wall synthesis as many of the cell wall components are synthesized in the Golgi bodies (Johansson, 2003).

UDP-glucose dehydrogenase uses UDP-glucose as a substrate. It oxidises the C6 carbon of UDP-glucose from an alcohol to carbonic group on a two fold oxidation reaction with no release of intermediates (Klinghammer and Tenhaken, 2007). The product, UDP­

glucuronate, is regarded as a central biosynthetic intermediate of many matrix polysaccharide precursors as many of the hemicellulose sugar precursors, such as UDP­

arabinose (UDP-Ara), UDP-xylose (UDP-Xyl), UDP-galacturonic acid (UDP-GaIA), IDP-Apiose (UDP-Api) and methylated derivatives thereof are derived from it (Figure

5

2.3) (Seitz, 2000). In other word, UDP-glucuronate is the key precursor of Hemicellulose and pectin synthesis for cell wall formation and therefore, the biochemical pathway is very important for the synthesis of cell wan materials.

GICr-p • Inottol-1-P Glc-1-P Inositol

! !

UDP-Glc GlcUA

2 NAQ+

~

!

2

NAOH1

II UDP-GrcUA

1 ----­

UDP-GaIUA UDPrXYI UDP-Api UDP-Ara

Hemicellulose + pectic polymers

Figure 2.3 Pathway for production of hemicellulose precursor through oxidation ofUDP-Glc (Source:

Tenhaken and Thulke, 1996).

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2.3 Cell Wall and Wood Formation

Almost all plant cells are enclosed by a strong but often flexible cell wall. Cell wall is a complex network of polysaccharides that surround and provide mechanical support as well as protection to the plant cells. It also possesses important roles in cell-cell recognition, defence responses and the maintenance of suitable environmental conditions (Seitz et al., 2000). Cell walls are divided into two types; namely primary cell wall and secondary cell wall.

Both primary and secondary cell walls contain cellulose, hemicellulose and pectin, but in different proportion. Primary cell wall is made up of approximately 30% of cellulose and more than 60% of matrix polysaccharides, which are hemicellulose and pectin. On the other hand, secondary cell walls of woody tissue are composed of 40-50% cellulose, 25­

35% lignin, and 25% hemicellulose (xylan, glucuronoxylan, arabinoxylan, or glucomannan) (plomion et al., 2001).

The macromolecular organization of the secondary wall of the cells from tree xylem is in large part responsible for the mechanical and physiological properties of wood.

Wood is considered as the fifth most important product of the world trade (Plomion et al., 2001). It is crucial to have a proper wood formation as timber possess the economic and commercial values. Wood or secondary xylem is manufactured by a succession of five major steps, which includes cell division, cell expansion (elongation and radial enlargement), cell wall thickening (involving cellulose, hemicellulose, cell wall proteins, and lignin biosynthesis and deposition), programmed cell death, and heartwood formation (plomion et ai., 2001).

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During the formation of primary cell wall, the cells located on the xylem side of the cambium will divides. Then, the derivative cells expand longitudinally and radially to reach their final size. When the expansion of primary cell wall is completed, secondary cell wall begins to form inside the primary cell wall (Plomion et aI., 2001). Formation of secondary cell wall is driven by the expression of several genes involved in the biosynthesis and assembly of four major compounds namely polysaccharides (cellulose and hemicellulose), lignin, cell wall protein and pectin (Plomion et aI., 2001). At this stage, maturation of cells occurs. The lignin is deposited and the amorphic cellulose matrix swells transversely. Then, the cellulose crystalline and the microfibrils shrink longitudinally.

Finally, the cellular process is ceased and the cell is death. Wood is then formed.

Secondary cell wall is divided into several layers, namely S I, S2 and S3 (Figure 2.4).

Each of these layers is made up of cellulose microfibrils, arranged in ordered, parallel arrangement. Hemicellulose and lignin are present in each of these layers (Figure 2.5). The thickness of these three layers are different, with SI the thinnest followed by S3 and S2 which is the most important layers of the cell wall that provides mechanical support.

Hemicellulose is important in wood formation as it influence the assembly of cellulose microfibrils by altering the cellulose ribbon formation and consequently affecting the crystal structure (Figure 2.6) (Ruel et at., 2006). Without the interaction of hemicellulose, the cellulose microfibrils are unorganised and loose which is the factor that decreases the quality of wood (Ruel et aI., 2006).

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lumen

cellulose

Transverse section of a tracheid

. middle lamella

Figure 2.4 Three-dimensional structure of a secondary cell wall. (Source: Plomion et al., 2001 ).

Amorphous

i

proteins lipids

Crystolline orron~menl

Flcure 2.5 Structural model of cellulose microfibril with hemicellulose, pectic substance proteins and lipids.

(Source: http://www.uky.eduJ-dhildibiochemlllB/\ectlIB.html).

9

A Celuloee nicrOllH'il

B

Fipre 2.6 Role of hemicellulose and pectin in the structural organization of cellulose microfibrils. (Source:

http://www.uky.edul-dhild/biochemllIB/lectllB.html).

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2.4 Single Nucleotide Polymorphism (SNP)

Single-nucleotide polymorphisms (SNPs) are the variations in DNA sequences that occur when a single nucleotide (A, T, C, or 0) in the genome sequence differs between two individual DNA samples (Cull is, 2004). Single nucleotide polymorphisms (SNPs) are used

as genetic markers that can be mined from sequence data and are useful as a tool for marker-assisted selection in plants.

Single Nucleotide Polymorphisms (SNPs) are highly abundant in most of the living organisms. A variant in the genome will only be considered as SNP if it has an abundance of 1% or greater (Jehan and Lakhanpaul, 2006). According to Duran et ai., (2009), there are three forms of SNPs, namely transitions (Crr or O/A), transversions (C/O, AIT, CIA or T/G) and small insertions-deletions (InDels). Transition substitution is the replacement of

purine with other purine or pyrimidine with other pyrimidine whereas transversion substitution involves the replacement of purine to pyrimidine and vice versa (Pratik, 2007).

SNPs may occur in the coding region, non-coding region and the intergenic regions of the genome. SNP wiII not affect the function of the cells if it does not cause a change in the protein structure. Based on the genetic mapping, SNPs provide a valuable marker for the study of agronomic traits in plant species (Chagne et ai., 2007).

Single base substitutions in the coding region are divided into two types, which are synonymous and non-synonymous. Synonymous, also known as silent mutation refers to the nucleotide substitution that leads to the same polypeptide sequences. On the other hand, non synonymous is defined by the nucleotide substitution that leads to a different polypeptide sequences (Xu, 2010).

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SNPs are used routinely in crop breeding programmes. By applying single nucleotide polymorphisms (SNP) genotyping, selective breeding of plants with desirable

traits can be very efficiency by allowing the traits to be selected and identified before growing the plants to maturity. Besides that, SNPs can be used as marker to choose for trees with good phenotypic traits based on their DNA sequences. This is important to breed the plants with good quality wood.

o

.1 Plant Materials

iMer bark tissue of Kelampayan was extracted from five Kelampayan trees at Kota Slmarahan areas by Tchin .

.2 DNA Extraction

J~l Chemicals and Reagents

The reagents used in DNA extraction were liquid nitrogen, CT AB extraction buffer (100 mM Tris-Cl pH 8.0; 1.4 M NaCI; 20 mM EDT A; 2% CT AB; 1 % polyvinylpyrrolidone ); 2% (v/v) ~-mercaptoethanol], chloroform/isoamyl alcohol (24: 1 v/v), isopropanol, 70% ethanol, TE buffer and sterile distilled deionized water (ddH20) .

.2.2 DNA Isolation Protocol and Purification

D A isolation had been done by using the modified CT AB method from Doyle and Doyle (1990). Total genomic DNA of five Kelampayan trees was extracted. The isolated DNA

was

Agarose Gel Electrophoresis

Aprose gel electrophoresis was carried out to detect whether the genomic DNA was _=ssfully isolated from the inner bark of Kelampayan. 0.8% of agarose gel was

~ by adding 0.4g of agarose powder to 50 ml of 1 x T AE buffer. Then, 2 III of

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