Selectable Markers & Markers for Screening 6-SMG... ·  · 2010-02-16Selectable Markers & Markers for Screening Guo-qing Song & David Douches 1 CSS451 2010. ... Nitrilase 0 Cyanamide

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Selectable Markers & Markers for Screening

1Guo-qing Song & David DouchesCSS451 2010

Ch 15

Gene Clone and DNA Analysis in Agriculture

Chapter 15

Gene Clone and DNA Analysis in Agriculture

Chapter 15 3 p341-344 Chapter 15.3 p341 344

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Selectable markers &Markers for screening

• A selectable marker will protect the organism from a selective agent that would normally kill it or prevent its growth. In most applications, only one in a several million

billi ll ill t k DNA R th th h ki i l ll i ti tor billion cells will take up DNA. Rather than checking every single cell, scientists use a selective agent to kill all cells that do not contain the foreign DNA, leaving only the desired ones.

• Antibiotics are the most common selective agents. In bacteria, antibiotics are used almost exclusively. In plants, antibiotics that kill the chloroplast are often used as well, y p palthough tolerance to salts and growth-inhibiting hormones is becoming more popular.

• A marker for screening will make cells containing the gene look different. There are three types of screening commonly used:G fl t t i (GFP) k ll l d UV li ht A i li d• Green fluorescent protein (GFP) makes cells glow green under UV light. A specialized microscope is required to see individual cells. Yellow and red versions are also available, so scientists can look at multiple genes at once. It is commonly used to measure gene expression.

• GUS assay (using β-glucuronidase) is an excellent method for detecting a single cell by staining it blue without using any complicated equipment. The drawback is that the cells are killed in the process. It is particularly common in plant science.

• Blue/white screening is used in bacteria. The lacZ gene makes cells turn blue in special media (e.g. X-gal). A colony of cells with the gene can be seen with the naked eye.

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Literature

Miki, B., McHugh, S. Selectable Marker Genes in Transgenic Plants - Applications, Alternatives and Biosafety. Journal of Biotechnology. 2004. 107(3): 193-232.

Hare, P., Chua, N. Excision of Selectable Marker Genes from Transgenic Plants. Nature Biotechnology 2002 20(6): 575-580Nature Biotechnology. 2002. 20(6): 575 580.

Goldstein et al. A Review - Human Safety and Genetically Modified Plants - A Review of Antibiotic Resistance Markers and Future Transformation Selection Technologies. Journal of Applied Microbiology. 2005. 99: 7-23.

Ramessar, K., Peremarti, A., Gomez-Galera, S., Naqvi, S., Moralejo, M., Munoz, P., Capell, T., Christou, P. Biosafety and Risk Assessment Framework for Selectable Marker Genes in Transgenic Crop Plants: A Case of the Science Not Supporting the Politics Transgenic Research 2007 16(3): 261-280the Politics. Transgenic Research. 2007. 16(3): 261 280.

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LacZ gene

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Selectable MarkersSelectable Markers

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Selectable Markers

•• About About 50 50 selectable marker genesselectable marker genes

•• Six negative SMG: Six negative SMG: codAcodA, , aux2aux2, , tms2tms2, , Six negative SMG Six negative SMG codAcodA, , aux2aux2, , tms2tms2, , dhlAdhlA, , CYP105ACYP105A, and , and cuecue

•• nptIInptII, , hpthpt, and , and barbar contribute to production of contribute to production of pp pp ppover 95% transgenic plantsover 95% transgenic plants

•• pmipmi (the (the E. coliE. coli manmanA): mannoseA): mannose--dependent SMGdependent SMG

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Miki & McHugh,J. Biotech. 2004, 107: 193-232

Marker genes listed in US field test notifications and release

Enzyme Number of records

permits for the years 2001 and 2002 (data extracted from ISB, 2003)

Enzyme Number of records in 2001 and 2002

Neomycin phosphotransferase II (NPT II) 949Hygromycin B phosphotransferase (hpt) 65Hygromycin B phosphotransferase (hpt) 65Phosphinothricin N-acetyltransferase (PAT) 3275-Enolpyruvylshikimate-3-phosphate (EPSP) synthase 507

93.8%

Acetolactate synthase or acetohydroxyacid synthase 5Nitrilase 0Cyanamide hydratase 2Cyanamide hydratase 2Glucuronidase (GUS) 91Luciferase 4

8Green fluorescent protein (GFP) 20

Miki & McHugh,J. Biotech. 2004, 107: 193-232

NPT II—Kanamycin (Km) resistance

• NPT II = neomycin phosphotransferase II • Normally, plant cells are sensitive to Km.

Km inhibit p t in nth i nd p t in t n l ti n • Km inhibits protein synthesis and protein translocation across membranes.

• Expression of the NPTII in plant cells results in p f psynthesis of NPTII enzyme

• The enzyme detoxifies Km by phosphorylation

ATP ADP

Km

ATP ADP

NPTII enzymeKm-PO4

(U bl t di t l t th)NPTII enzyme(Disrupts plant growth)

(Unable to disrupts plant growth)

Km-resistant

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Km-sensitive

Example 1: Km-selection

Dose experiment on Km-resistance

Km=0 (mg/L)

Km=10 Km=20

Km=30 Km=50 Km=100

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Example 1: Km-selection

Km= 0 mg/L Km= 25 mg/LNonNon--transformed transformed ExplantsExplants

Km 0 mg/L Km 25 mg/L

Transformed Transformed ExplantsExplants

InoculationInoculationInoculationInoculation Selection & RegenerationSelection & RegenerationSelection & RegenerationSelection & Regeneration

11Song and Sink. Plant Cell Reports (2004)

Bar-Phosphinothricin (PPT) resistance

• PPT normally acts to inhibit glutamine synthetase, causing a fatal accumulation of ammonia

• PAT belongs to the family of acetyltransferases It detoxifies PPT byPAT belongs to the family of acetyltransferases. It detoxifies PPT by catalysing the addition of an acetyl group to the free amino group

ATP, NH3 ADP, PI

Glutamate Glutamine

Glutamine Synthase

Non-trangenic

Rapid accumulation of ammonia which lead to death of the plant

Glutamine Synthase

Inhibiting GSto death of the plant cellPPT

Trangenic PATAcetyl PPT

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Acetyl-PPT

Example 2: PPT-selection

2 wk, 5 mg/L ppt

PPT = 0.2 mg/L

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Chl h l d Chlorophenol red assay

2 wk, 5 mg/L ppt

14WT Transgenic

L18 L25L21 L22 L28

Song et al. Acta Horticulturae 738: 397-408 (2007)

Example 2: PPT-resistance

PPT=7500 ppm, 1 week

NT L18

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Song et al. JASHS. (2008)

Example 2: PPT-resistance

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Hpt, hph or aphIV-Hygromycin (Hyg) B resistance

The hygromycin phosphotransferase (denoted hpt, hph or aphIV) gene was originally derived from Escherichia coli. p ) g g yThe gene codes for hygromycin phosphotransferase (HPT), which detoxifies the aminocyclitol antibiotic hygromycin B. A large number of plants have been transformed with the hpt gene and hygromycin B has proved very effective in hpt gene and hygromycin B has proved very effective in the selection of a wide range of plants, including monocotyledonous.

Most plants exhibit higher sensitivity to hygromycin B than to kanamycin, for instance cereals. Likewise, the hpt gene is used widely in selection of transformed mammalian cells.

Like kanamycin and other aminoglycoside antibiotics, hygromycin B inhibits protein synthesis by interfering with mRNA translation and causing mistranslocation of mRNA.

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Example 3: Hyg-selection

HygHyg--Selection (50 mg/L)Selection (50 mg/L) HygHyg--Selection &Selection &HygHyg Selection (50 mg/L)Selection (50 mg/L) HygHyg Selection & Selection & RegenerationRegeneration(50 mg/L)(50 mg/L)

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NPTII, HPT, and BarNPTII, HPT, and BarNPTII, HPT, and BarNPTII, HPT, and Bar

K i 50 /L Gl f i t 5 /L H i 50 /LKanamycin=50 mg/LTimentin=250mg/L

Glufosinate =5 mg/LTimentin=250mg/L

Hygromycin=50 mg/LTimentin=250mg/L

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Friendly SMGFriendly SMGFriendly SMGFriendly SMG

Advantages: The PositechTM by Syngenta

Non toxicRapid and efficient

maize, rice, wheat, barley, cassava, sugar beet, watermelon, tomato, squash, cabbage, sunflower, oilseed rape, sweet

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Trait stackingAddress public concern

, p ,orange, almond, papaya, and apple

MannoseATP

mannose-6-phosphate phosphate deficiency

PMI1

mannitol-1-phosphate

M6PR2

NADPH

fructose-6-phosphate

PMIPase3

mannitol

PO4

metabolism

1 – PMI, phosphomannose isomerase activity is low in some

Mtd4

fructoseNADH

plants, and apparently absent in others, grasses like wheat, rice, corn, and sorghum. Gene for this enzyme is also known as manA.2 – M6PR, mannose-6-phosphate reductase, is present in some

metabolism2 M6PR, mannose 6 phosphate reductase, is present in some higher plant families3 – non-specific phosphatases, Pases, are present in nearly all higher plants. This releases phosphate otherwise sequestered in

d it l h h t

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mannose and mannitol phosphate4 – Mtd, mannitol dehydrogenase, is present in nearly all higher plants

Other SMG

Isopentyl transferasesHistidine kinase homologueHistidine kinase homologueHairy root-inducing genes

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Markers for ScreeningMarkers for Screening

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GUS: beta-glucuronidase

5-bromo-4-chloro-indolyl glucuronide ( -gluc): Colorless

4-methyl-umbelliferyl-beta-D-glucuronide ( -gluc)

X

+ X -Gluc 37C + Gluc+ O2

Beta-glucuronidaseThe GUS histochemical X

Hydrolysis of the X-Gluc substrate by the GUS enzyme

Dimerization of the Gluc product by reaction with O2

histochemical staining assay

Gluc 37C + Gluc+Beta-glucuronidase

+ -Gluc + Gluc+

Hydrolysis of the X-Gluc substrate by the GUS enzyme

Fluorescent of the released fluorescent product

Fluorogenic staining

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Ruijter et al., 2003, Plant Biology, 5:103-115

y ym f p

The GUS Histochemical Staining Assay

Blueberry Blueberry Blueberry Blueberry Sweetpotato Sweetpotato Sweetpotato Sweetpotato

WTWTWTWTStemStemStemStem

Celery Celery Celery Celery

WTWTWTWT

WTWTWTWTStemStemStemStemWTWTWTWTWTWTWTWT

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WTWTWTWT

Song GQ & Sink KC. Plant Cell, Tissue and Organ Culture 88: 193-200 (2007)

The GUS Histochemical Staining Assay

Rice Rice Rice Rice

Evaluation of different promotersEvaluation of different promotersEvaluation of different promotersEvaluation of different promoters

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Luciferase (LUC)

A conditional non-selectable marker gene

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Firefly Luciferase (ff-LUC)

In the absence of CoA the protein is inactivated by complex is inactivated by complex formation with oxyluciferin and the reaction is non-enzymatic (the “so-called” flash reaction)

Oxyluciferin+O2, ATP

Oxyluciferin-AMP + PPi + CO2

Oxyluciferin- Oxyluciferin+CoA AMP + PPi + CO2In the presence of CoA the

luciferase protein is rapidly released from the complex, resulting in an enzymatic reaction

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Green Fluorescent Protein (GFP)

The great advantage of GFP as a non-conditional reporter is the direct visualization of GFP in living cells in real time without invasive procedures such as the application or penetration of cells with

b t t d d t th t diff ithi substrate and products that may diffuse within or among cells. Both considerations provide a significant improvement over GUS and LUC as reporter genes

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reporter genes.

GFP

In 1994 GFP was cloned. Now GFP is found in laboratories all over the world where it is used in every conceivable plant and animal. The GFP gene can be introduced into organisms and maintained in their genome th h b di l l i j ti ith through breeding, or local injection with a viral vector which can be used to introduce the gene.

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Green Fluorescent Protein (GFP)

The GFP is composed of 238 amino acids originally isolated from the acids, originally isolated from the jellyfish Aequorea victoria that fluoresces green when exposed to blue lightlight.

Martin Chalfie, Osamu Shimomura and Roger Y. Tsien were awarded the 2008 Nobel Prize in Chemistry on 10 December Nobel Prize in Chemistry on 10 December 2008 for their discovery and development of the green fluorescent protein.

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protein.

GFP

O2

Fluorescent of GFP

Formation of the chromophone requires molecular oxygen

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Ruijter et al., 2003, Plant Biology, 5:103-115

GFP

A Transgenic embryoid of Valencia sweet orange; bar = 200 μm A Transgenic embryoid of Valencia sweet orange; bar = 200 μm. B Transgenic plant of Valencia sweet orange in the greenhouse. C GFP expression in shoot tip of a transgenic Valencia plant; bar = 1 mm

33Guo et al., Plant Cell Rep. 2005, 24: 482-486

M k f St t iMarker-free Strategies

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Concerns about the SMG

Although no adverse biosafety effects have been reported for the marker genes that have been p gadopted for widespread use, biosafety concerns should help direct which markers will be chosen for future crop development. Common sense di t t th t k f i i t dictates that marker genes conferring resistance to significant therapeutic antibiotics could not be used.

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Marker-free Strategies

f f k 1. Co-transformation and segregation of marker genes

2 Transposon-mediated repositioning of genes2. Transposon mediated repositioning of genes

3. Intrachromosomal homologous recombination to remove SMG

4. Site-specific recombinase-mediated excision of marker genes

36Miki & McHugh. J. Biotech. 2004, 193-232

Co-transformation

Co-transformationPositive selection

Co transformation

Segregation

None T-DNA

g g

None T DNA

PCR

SMG-free transformants

Marker-free Strategies

1. Co-transformation and segregation of marker genes

• Co-transformation with separate plasmids in one or two bAgrobacterium strains

• Co-transformation with single plasmids carrying multiple T-DNA regions

An advantage of Agrobacterium-mediated co-transformation technologies over biolistic transformation is that the co-

regions

transformation genes often integrate into differernt loci in plant genome.

38Miki & McHugh. J. Biotech. 2004, 193-232

Marker-free Strategies

4. Site-specific recombinase-mediated excision of marker genes

)• The Cre-LoxP System (bacteriophage)

• The FLP-FRT System (yeast)The FLP-FRT System (yeast)

• The R-RS System

The FLP–FRT system derived from the Saccharomycescerevisiae 2 plasmid

Cre, FLP and R are the recombinases, and l

The R–RS system from Zygosaccharomyces rouxii

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loxP, FRT and RS are the recombination sites.

Marker-free Strategies

Figure 1. Recognition sites for recombinases shown to function in plants share a similar design.All comprise palindromes, which flank the six to eight innermost base pairs. Each recombinase binding element (RBE) is bound by a single recombinase subunit. Cleavage of the sites occurs at the borders between the RBEs and the core sequence The core element is the site of strand exchange and confers

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between the RBEs and the core sequence. The core element is the site of strand exchange and confers directionality on the recombination site. Recombination requires two recombinase recognition sites bound by four identical recombinase subunits.

Peter D. Hare & Nam-Hai Chua. Nature Biotechnology 20, 575 - 580 (2002) Excision of selectable marker genes from transgenic plants

Marker-free StrategiesIntegration

Selection with SMG

LoxpFRTRS

LoxpFRTRS

nptIIhptbar

CreFlpR

SMGLB RB

Ind TGXX

Targetgene

SMG Ind TG

Excision of SMG

XX

SMGLB RB

Ind TG

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Experiment 6: Histochemical GUS assay

Objective:j

To get familiar with using the gusA as a screening marker

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