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How Transgenic plant is used in
      Agricultural Field
     转基因植物在农业生产中的应用
             Dr. Hongmei Cheng
                         程红梅
    Biotechnology Research Institute, CAAS




                  chenghm@caas.net.cn,
             Tel:82106125, Crop institue buliding 401
Biotechnology Research Institute was founded in 1986
BRI-CAAS

  Permanent staff: 112
  Academician: 1
  Professor: 26
  Associate Professor: 32
  Assistant Professor: 24
  PhD and Master Students
  >150
Organizations-Departments and labs
Research Departments: 2
Department of Plant Biotechnology and Molecular Biology
Department of Molecular Microbiology
Laboratories: 8
Laboratory of Plant Genetic Engineering
Laboratory of molecular biology for plant stress tolerance
Laboratory of plant metabolic engineering
Laboratory of plant functional genomics
Laboratory of gene expression and molecular farming
Laboratory of biosafety assessment of GMOs
Laboratory of genetic engineering for agro-microorganisms
Laboratory of genetic engineering for environmental-
       microorganisms
Organizations-Research Centers


Research Centers:
1. Research Center for Crop Molecular Designing
2. Research Center for Microorganism Genetic Engineering

3. Research Center for Biosafety Assessment of GMOs
4. Key laboratory for Crop Molecular Biology, Ministry of
   Agriculture
Engineering Center
1. Center for Biotechnology Products
Remarkable Achievements
Insect Resistance

         Transgenic Bt cotton
           resistant to ball worm
         1.   Commercialized since 1998
         2.   In 2007, more than 70% cotton
              are transgenic, Accumulated
              acreage: 2.4 million ha.
         3.    Accumulated benefit since
              1998: >126 billion RMB
Molecular Farming and Bioreactor



Without signal peptide   With signal peptide targeting
                             to extracellular space


   Phytase Expression Vectors                            Efficiency corn transformation system




Phytase corn in greenhouse                               Molecular Screen and enzymatic activity assay
Producing phytase by transgenic corn


                        1. Used as feed additive
                           to increase the
                           efficiency use of
                           phosphorus and
                           proteinsmetal ions
                           bioavailability

                        2. Highly expressed lines
                            have been obtained

                        3. Biosafety assessment
                            of transgenic corn
Phytase corn in field       completed
What is Biotechnology?
               How about some definitions

General Definition
   The application of technology to improve
    a biological organism


Detailed Definition
     The application of the technology to modify the
     biological function of an organism by adding genes
     from another organism
These definitions imply biotechnology
           is needed because:

•Nature has a rich source of variation


• Here we see bean has many
  seedcoat colors and patterns
  in nature


     But we know nature does not have
     all of the traits we need
But nature does not contain all the
         genetic variation man desires


•Fruits with vaccines




•Grains with improved nutrition
Central Dogma of Molecular Genetics

(The guiding principle that controls trait expression)



         Protein                             Trait
                                        (or phenotype)
                     Translation

                                                   Seed shape

DNA                      RNA
         Transcription
(gene)
                                   Plant height
In General, Plant Biotechnology Techniques
           Fall Into Two Classes

Gene Manipulation
  • Identify a gene from another species which controls
    a trait of interest
  • Or modify an existing gene (create a new allele)

Gene Introduction
  • Introduces that gene into an organism
  • Technique called transformation
  • Forms transgenic organisms
Genes Are Cloned Based On:

Similarity to known genes
 Homology cloning (mouse clone used to obtain human gene)


Protein sequence
 Complementary genetics (predicting gene sequence
    from protein)

Chromosomal location
 Map-based cloning (using genetic approach)
Homology Cloning

                          Clones transferred
                               to filter



Human clone
                                               Mouse probe
  library
                                               added to filter




               Hot-spots are human
              homologs to mouse gene
Complementary Genetics

1. Protein sequence is related to gene sequence
   NH3+-Met-Asp-Gly--------------Trp-Ser-Lys-COO-
        ATG GAT-GCT              TGG-AGT-AAA
              C   C                    C   G
                  A                  TCT
                  G                    C
                                       A
                                       G

2. The genetic code information is used to design PCR primers
   Forward primer: 5’-ATGGAT/CGCN-3’
   Reverse primer: 5’-T/CTTNC/GT/ACCA-3’

  Notes: T/C = a mixture of T and C at this position;
         N = a mixture of all four nucleotides
         Reverse primer is the reverse complement of the gene sequence
Complementary Genetics
                      (cont.)
3. Use PCR to amplify gene fragment
   a. template DNA is melted (94C)
      3’                             5’
      5’                             3’



      3’                             5’

      5’                             3’


   b. primers anneal to complementary site in melted DNA (55C)
          3’                              5’

          5’                              3’


   c. two copies of the template DNA made (72C)
     3’                              5’

     5’                              3’
Complementary Genetics
                  (cont.)
4. Gene fragment used to screen library

                             Clones transferred
                                  to filter



  Human clone
    library                                          PCR fragment
                                                  probe added to filter




                Hot-spots are human gene
                       of interest
Map-based Cloning
                                           Gene Marker
1. Use genetic techniques to
find marker near gene

                                          Gene/Marker
2. Find cosegregating marker


3. Discover overlapping clones
   (or contig) that contains the marker   Gene/Marker



                                          Gene/Marker
4. Find ORFs on contig


5. Prove one ORF is the gene by      Mutant + ORF = Wild type?
   transformation or mutant analysis Yes? ORF = Gene
Gene Manipulation

• It is now routine to isolate genes

• But the target gene must be carefully chosen

• Target gene is chosen based on desired phenotype

Function:
  Glyphosate (RoundUp) resistance
       EPSP synthase enzyme
  Increased Vitamin A content
       Vitamin A biosynthetic pathway enzymes
Introducing the Gene or
          Developing Transgenics

Steps

1. Create transformation cassette


2. Introduce and select for transformants
Transformation Cassettes

Contains

1. Gene of interest
     • The coding region and its controlling elements

2. Selectable marker
     • Distinguishes transformed/untransformed plants

3. Insertion sequences
     • Aids Agrobacterium insertion
Gene of Interest
          Promoter    TP            Coding Region



Promoter Region
  • Controls when, where and how much the gene is expressed
      ex.: CaMV35S (constitutive; on always)
           Glutelin 1 (only in rice endosperm during seed development)

Transit Peptide
  • Targets protein to correct organelle
      ex.: RbCS (RUBISCO small subunit; choloroplast target

Coding Region
  • Encodes protein product
      ex.: EPSP
           -carotene genes
Selectable Marker
           Promoter              Coding Region



Promoter Region
  • Normally constitutive
     ex.: CaMV35s (Cauliflower Mosaic Virus 35S RNA promoter

Coding Region
  • Gene that breaks down a toxic compound;
  non-transgenic plants die
     ex.: nptII [kanamycin (bacterial antibiotic) resistance]
          aphIV [hygromycin (bacterial antibiotic) resistance]
          Bar [glufosinate (herbicide) resistance]
Effect of Selectable Marker

Non-transgenic = Lacks Kan or Bar Gene

  Plant dies in presence
  of selective compound    X
                               Transgenic = Has Kan or Bar Gene

                                 Plant grows in presence
                                 of selective compound
Insertion Sequences

             TL                            TR




Required for proper gene insertions
 • Used for Agrobacterium-transformation
    ex.: Right and Left borders of T-DNA
Let’s Build A Complex Cassette
               pB19hpc (Golden Rice Cassette)



     TL     aphIV         35S Gt1       psy    35S rbcS       crtl    TR


T-DNA       Hygromycin          Phytoene           Phytoene          T-DNA
Border       Resistance         Synthase          Desaturase         Border



Insertion    Selectable             Gene of        Gene of           Insertion
Sequence      Marker                Interest       Interest          Sequence
Delivering the Gene
                to the Plant
• Transformation cassettes are developed in the lab

• They are then introduced into a plant

• Two major delivery methods

    • Agrobacterium

                                   Tissue culture
    • Gene Gun                     required to generate
                                   transgenic plants
Plant Tissue Culture
    A Requirement for Transgenic Development




                  Callus
                  grows
A plant part               Shoots
 Is cultured               develop      Shoots are rooted;
                                     plant grows to maturity
Agrobacterium
             A natural DNA delivery system

• A plant pathogen found in nature
• Infects many plant species
• Delivers DNA that encodes for plant hormones
• DNA incorporates into plant chromosome
• Hormone genes expressed and galls form at infection site

                  Gall on
                   stem


                               Gall on
                                leaf
But Nature’s Agrobacterium
               Has Problems
Infected tissues cannot be regenerated (via tissue culture)
into new plants
Why?
   • Phytohormone balance incorrect regeneration
Solution? Transferred DNA (T-DNA) modified by
    • Removing phytohormone genes
    • Retaining essential transfer sequences
    • Adding cloning site for gene of interest
The Gene Gun
• DNA vector is coated onto gold or tungsten particles

• Particles are accelerated at high speeds by the gun

• Particles enter plant tissue

• DNA enters the nucleus and
  incorporates into chromosome

• Integration process unknown
Transformation Steps

Prepare tissue for transformation
   • Tissue must be capable of developing into normal plants
   • Leaf, germinating seed, immature embryos

Introduce DNA
   • Agrobacterium or gene gun

Culture plant tissue
   • Develop shoots
   • Root the shoots

Field test the plants
   • Multiple sites, multiple years
The Lab Steps
Lab Testing The Transgenics

Insect Resistance          Cold Tolerance




 Transgene=                  Transgene=
Bt-toxin protein       CBF transcription factors
The Next Test Is The Field
     Herbicide Resistance


                             Non-transgenics




           Transgenics
Final Test
  Consumer Acceptance

  RoundUp Ready Corn




Before                After
The Organization of the CBF
Transcriptional Activator Protein
Encoding Genes in Tomato
Plant Responses to Cold
 Cold-acclimating, freezing tolerant
 Non-acclimating, freezing intolerant
 Non-acclimating, chilling intolerant



    Presume the differences due to
    regulation of cold induced genes
Cold acclimation and freezing tolerance in Arabidopsis thaliana
                2 days -5oC; 4 days recovery at 20oC
          No acclimation                   4 days ~ 2 oC
Arabidopsis Genes
 Cold – regulated genes
  - COR
    - 1st identified low temp. induced genes
Function of COR15a
Two classifications
  –LEA II proteins
  –Novel hydrophilic proteins
  • Involves the stabilization of membranes
  • Decrease the propensity of membranes to from
  hexagonal II phase lipids in response to freezing
COR Genes
Promoter elements
  – C-repeat/Drought responsive element
    (CRT/DRE)
Promoter elements of COR Genes:
   – C-repeat/Drought responsive element
   (CRT/DRE)
COR genes was accomplished by overexpressing the
Arabidopsis transcriptional activator CBF1 (CRT/DRE binding
factor 1)

CBF1 binds to CRT/DRE DNA regulatory element present in
the promoters of the COR genes

CBF1 resulted in a greater increase in freezing tolerance than
did expressing COR15a alone.
CBF1 pathway might control one set of cold-acclimation
response
        CBF1 has a mass of 24 kDa, has AP2 domain in
Stockinger:
Arabidopsis, tobacco, and other plants proteins.
         have demonstrated that Ap2 domain includes a
Ohme-takagi
DNA-binding region.

CBF1is a transcriptional activator that can activate
CRT/DRE-containing genes and was a probable regulator of
COR gene expression in Arabidposis

CBF1 appears to be an important regulator of the cold-
acclimation response, controlling the level of COR gene
expression.
CRT/DRE Sequences

COR15a     ATTTCATGGCCGACCTGCTTTTT
           ACTTGTTGGCCGACATACATTTG
           CAAAATAAACCGACAAGGTTGCA
COR15b     ACTTGATGGCCGACCTCTTTTTT
           TGTGGCATACCGACTTCTAGATG
COR78      AAGATCAAGCCGACACAGACACG
           GATATACTACCGACATGAGTTCC
           AATATCATACCGACATCAGTTTG
           AGACATGGACCGACTACTAATAA
RD29b      AAACGTGGACCGACTAAAACTAA
KIN1       AAATAGCTACCGACATAAGGCAA
           ACTACTGATCCGACATCAAAACC
COR6.6     AAAAAGCTACCGACATAAGCCAA
COR47       ATTCATCTACCGACTTCAAGAAA
            CAATCAAAGCCGACCATTCAGCT
            CCCACATGACCGACATCTTATGC
            TAGCTTTAGCCGACGTGTCTAAT
ERD10/LTI45 ACCGACCGACCGACGTAAAAGAA
            ATTCATCCACCGACCGACCGACG
CBF Gene Family
 Binds CRT/DRE element
 Transcription activators
 Plays a regulatory role
  – Overexpression induces COR genes
CBF Gene Family
CBF is a member of a small gene family encoding three closely
related transcriptional activator.

CBF1, CBF2 and CBF3 are physically linked n direct repeat
on chromosome 4 near molecular markers PG11 and m600(-71cM)
Like CBF1, both CBF2 and CBF3 proteins can activate
expression of reporter genes in yeast that contain the CRT/DRE as
an upstream activator sequence, indicating that these two family
member are also transcriptional activators.
CBF1
  1     32 44 47              106                       213


          NLS       AP2 Domain      Activation Domain




“Zip-Code”
to get protein
into nucleus

                 Binds to CRT/DRE
                                    “Flips the switch”
                                    Causing Gene Activation
COR Gene Activation by CBF

                      Activation Domain

                      DNA Binding Domain




                             COR GENE
CR

CR




          CR



                    TA
                      TA
  T/

  T/




            T/
    DR

    DR




              DR
      E

      E




                E
Thomashow 2001
Proposed Regulatory
          Mechanism
• Warm temperature



                     COR
Proposed Regulatory
             Mechanism
• Cold temperature


   CBF     CBF
                      COR
Proposed Regulatory
             Mechanism
• Cold temperature


   CBF     CBF
                     COR
Project Overview
Most plants possess CBFs
– Based on BLASTs of different crop species


Tomato
– Cultivated species, TA491
– Cold tolerance wild species, LA407
Chromosomal Location of the 6 Arabidopsis CBFs




At1g12610
DREB1F                                                    CBF4
                                                         DREB1D
                                                        At5g51990
At1g63030         CBF1         CBF3       CBF2
 DREB1E          DREB1B      DREB1A      DREB1C
                At4g25490   At4g25480   At4g25470




            1                                       4               5
CBF Signature Sequences
AtCBF1:        PKKPAGRKKFRETRHP   FADSAWR
AtCBF2:        PKKPAGRKKFRETRHP   FADSAWR
AtCBF3:        PKKPAGRKKFRETRHP   FADSAWR
AtCBF4:        PKKRAGRKKFRETRHP   FADSAWR
AtCBF5:        PKKRAGRRIFKETRHP   FSDSAWR
AtCBF6:        PKKRAGRRVFKETRHP   FADSAWR

LeCBF1:        PKKPAGRKKFRETRHP   FSDSAWR
LeCBF2:        PKKPAGRKKFRETRHP   FADSVWR

GmCBF1:        PKKRAGRKKFRETRHP   FADSAWR
GmCBF2:        PKKRAGRKKFRETRHP   FADSASR
GmCBF3:        PKKRAGRRVFKETRHP   FADSRWR

MtCBF3:        PKKRAGRKKFKETRHP   FADSAWR
MtCBF2:        PKKRAGRKKFKETRHP   FADSAWR
MtCBF1:        PKKRAGRRVFKETRHP   FADSAWR

HvCBF1:        PKRPAGRTKFHETRHP   FADSAWR
HvCBF3:       PAKRPAGRTKFRETRHP   FADSAWL

Consensus:     PKKPAGRKKFRETRHP   FADSAWR
                  R   Rx K         S
Objectives
• Estimate CBF gene copy number
• Clone all family members,
• Sequence all CBFs in Tomato, and analyze
  it, include upstream and downstream
  sequence
• Determine expression in response to:
  • Low temperature
  • Drought
Lambda Phage Clone




 Phage Genomic clone:


Le3
Lambda Phage Clone



Phage Genomic subclones and sequence:


•   Isolate le3DNA from the phage plate
• Digest the DNA with NotI or Xba I enzymes
• Subclone them into NotI or XbaI cut pGEM11Z
• Get the physics map of Le3 19kb fragment
•   Sequence clones
•   Design primers to do the primer walk
Sequence analysis:
• Alignment sequence data using Sequencher software
• Detect the CBF loci from the sequence, find the open
reading frame
• Protein sequence alignment of AtCBF and LeCBF
23/CHENG4/M13R.phd.1
21/CHENG3/M13R.phd.1
    03/cheng3/E10.phd.1
           43/CHENG3/ES173.phd.1
              46/CHENG8/ES176.phd.1
                  44/CHENG3/ES204.phd.1
                             30/CHENG8/M13F.phd.1
                          31/CHENG3/ES184.phd.1
                          14/CHENG3/ES155.phd.1
                                   31/CHENG3/E7.phd.1
                                    43/CHENG3/ES203.phd.1
                                                   29/CHENG7/M13R.phd.1
                                                         30/CHENG3/ES183.phd.1
                                                            01/cheng3/E8.phd.1
                                                                  28/CHENG7/M13F.phd.1
                                                                       42/CHENG3/ES172.phd.1
                                                                             26/CHENG6/M13F.phd.1
                                                                                   15/CHENG3/ES156.phd.1
                                                                                           22/CHENG4/M13F.phd.1
                                                                                             20/CHENG3/M13F.phd.1
                                                                                               44/CHENG6/ES174.phd.1
                                                                                                               07_CHENG2_E23
                                                                                                               22/CHEN2/M13F.phd.1
                                                                                                               34/CHENG6/ES187.phd.1
                                                                                                                            02/cheng2/E9.phd.1
                                                                                                                             19/CHENG2/ES163.phd.1
                                                                                                                                             06_CHENG2_E22
                                                                                                                                           28/CHENG2/ES181.phd.1
                                                                                                                                                     27/CHENG2/E3.phd.1
                                                                                                                                                        05/cheng2/E12.phd.1


1    188    363    585       866   1,038   1,234        1,585      1,939   2,183   2,446       2,775   3,021        3,349         3,686    3,953   4,241    4,506     4,905
CCAAAAGGGAAGTATCAAAGTACAGAAAAAAACTAAAAATATGCCAAGTTAGACGCACGGAAGATTTGGAAGTTGAAACTTAACTTTTCTTAAACCCACAGCCCCACTCCAGCTGTCATATAAAACAGCTGCCCCACTCTATTTTTTAATAACAGCCTGTCTACTT
ATCACCACCCTCTAACTCCGTGTTCTTTGGTCTCAACTATATATAGAAATCAAACTTTTCACATTTTACCATAACAATTAAACTCTCTAACATCATAAATATCACTAGTTAAAGAAAGAAACAAAAATATAAATCGATATGTTTTATTCGGACCCACGTATAGAAT
CTTGTTCATCGTTTTCTGACAGTATTAGAGCCAATCATTCTGACGAGGAAGTTATTTTAGCTTCAAATAATCCGAAGAAGCCAGCTGGCAGAAAGAAGTTTCGAGAAACTCGACATCCAGTGTACAGGGGAGTGAGGAAGAGGAATTCTGGAAAATGGGTTTGTGA
AGTCAGAGAACCAAATAAGAAGACGAGGATTTGGCTTGGTACTTTTCCTACTGCTGAAATGGCGGCTAGAGCTCATGATGTGGCGGCTATAGCATTAAGAGGACGTTCAGCTTGTTTGAATTTTGCTGACTCTGCTTGGAGGCTGCCTACTCCAGATTCCTCTGAC
ACTAAGGATATTCAAAAGGCGGCCGCTCAGGCCGCCGAAATCTTCCGACCTTTAAAGTCGGAGGAAGAAGAATCAGTGGTTAAAGATCAATCTACTACTCCAGATGATATGTTTTTTATGGATGAGGAAGCGTTATTCTGCATGCCGGGTTTACTTACGAATATGG
CGGAAGGATTAATGGTACCTCCACCTCAATGTACTGAAATGGGAGATCATGTGGAAGCTGATGATATGCCTTTATGGAGCTATTCTATATAATAAGTAAGTATAATGAGAGGAGTAACAATGCTAAGAGTGAAGTTTATTAGTTTCGTGCTTAATATTTGGATATG
GTACGAATTAGTGTATAAGTATTGTAATTTGTAATGATCATGTAGATATTACTAGTATTGCTATATACTATTATAACAAAATGGTTGAAGCTAAATGAGAATCATTGGCGTATATAAGACTATTGTGTGTTTTATGACAGTTAGTCTTAGAGTTTTTTCTCATGGT
TGAATTTGGTTAAGAAGCTGTTAAATGCGTTGTTCCACCAGCTTCGGAAAAACAACAGACACATACTCTAAAAAAAGCATAAAGCATTTGCTTCTGGTTTAAGCAACTGAGTGAAAAAGTAGATTTGTGGAGTATTTTTTCAAGCCGATTACTATGTCACAATCAA
TCAAAGAACATTGCTTATATCATAATTTTTATAAATTTTCAAAAATAAATATATCTATATATACATATAATTATTTTTTTAAAAGTTTAACATGTACACATGTTTCTCAATTTTACACGTGTGTCCGCCTATGATACAAATTTTATTAGTAATGACAATTGTAGAA
CTTTCTAGAATGAAATAACAATGGAGACAATTCAAATAGTTTGGAGATATATATATGTCTCAACATTGTGGTACTAATCCAATTCCAAGCATATCGATGCTGGAAATGATGCACGTGGTCCACGCGTATAATTTCCCGCGTGAGAAAATGAAAAGTAATTTATTGG
AGTTGCAATAATTGATGATATAATTAACCGTCAAAAGCGTGTGTTGAGTTTTAATCAGTTATAAATTGGTACTTAGTTCACTTGTGACTTCATACATATACATATAATCATTTCAAAGGTCAATTTTCAAACTCATCTTTCAATTGGATCAAGTAGGGGGCGGCTA
TATATATATATATATATTGGCCTAAGAATAGAACGGCAACTTACCCTTCACCTTCCACTATCTTTTCAAAGATTCTCAATAATCAGTAGTATGATAATGAACAATGCTAAATGATCAACAAAATTTAATCAGAAATTTTAAAAAAATTGTAACGTCTCTTTTATTT
TAATATAATTTTTTTTATTTTAATAAAAGAATAAAAATATAAAAAAATATCATTTTAATCAAATTCTGATCAAATTTGCTGACCATAAGAATTTTTTCATTTATTAATTAGTTTTATTCTTCATTATACTATCGTACTTATAAAAATCTCTTTCATTATGAAACTT
TACATATTTACCTTTTATTTGAATAGATTATCCTAAAATTGGTCAAAAATATCTTTGTCATTATGGAACTCAAACTTCACTTTTAGGGTTGGGGTACTTATAAATATAATAGTTTGGAATAAAATTATAAATCTAATAAAATATACTTGGGTTTATATCTAGTCTC
CTAAAATAGAAATAACACACACTCTCTCTCACACACACACACACTCCCCTTTTCATTCCCTTCATATTTTGTTACTCCTATTATTTTTAACTATTCTATTCTAGTCTAATTTCTCCTCTACAAAGCTTGAATCTCTAGATATAGTTATTGTCCTCAGTTATGTTAT
TTTCTCATTTCAAGTATTTTCAGCTACTTCCCAACATTAGAAAAGTCCATAAAATATAAATAATAATATATAAACATAAAATAAAATTAAAAATTTATTATATATAAAAAATAGTAATTTTTTTTTGGAATGAAACTTAACCAAACTCATAAAATATGCTAATTAA
TTAATAAGGGATATATAGGTAAATATGTATGTATGGAAGAGACATTTTAATCTTAAAAAAATAATTTTCTTCTCTGTTTCATTTTTTTAAGAAGCAGAACTTTTAGATTCTTCCCAACAACAGAACAACTGCTTCTTACTTTTTGCAAACACTTGATTTTTCAAAA
AGAAAAAACATACTTTTTTCTAGGAAAAAAAAACGCTTTTGGCCTTCCAATGAATCCAATTCTAATTCAATCTTAACAAATTTAGGGTATAATCAGAAAAAAAAATATTTTTTCTTAATTTATTAAAAGTGACCAGTAAAAATGGAAATTAGATTAGAAAATATTT
GTCGAATAAATAGAGACGAAGAGAGTTTAAAAAAGAAGTTGATGAATGCTGACCTTTTCCTTTGACAACTATTGGTTCAATGAATCTCCAAAGATTTATCTCTCAATTTTAAAAAATTGGTGATGACGAGATAGATGGTATAAAATAGATGCAACAAGAATAATTT
TTTTTATTTTTTTTAATGTTATCATATTGAAATGACAAAGATTGGTCAGTATATATTCCAAAAAGGAAGTAAAGAGGAAAAGTTTTACAAGTCACAAGTTGCCACACGAGTTGTACGCAAATCCACTTGTCCCATAAAACAAAACAGCTGGGCTTACGCTTTTATA
ATCCAGCCTGTATCCTTTAATTATCACTCCGTGTTCTCTTCTCCTTTCACTATCATACTCTACTTTCCACTATAAATATATGTAACCAACACATAACACTTCTTTAACTCAACAATTATACAAATACTTTCTATTTTTAGCTCTCAACAACAATGAATATCTTTGA
AACCTATTATTCAGACTCGTTAATTTTAACCGAATCATCTTCTTCTTCATCGTCATCGTCGTTTTCTGAAGAGGAAGTTATTTTAGCTTCGAATAACCCGAAAAAGCCAGCTGGCAGGAAGAAGTTTCGAGAAACACGGCATCCGATATACAGGGGAATCAGGAAG
AGGAATTCAGGAAAATGGGTTTGTGAAGTCAGAGAACCAAATAAGAAGACAAGGATTTGGCTTGGTACTTTTCCTACGGCTGAAATGGCGGCTAGAGCTCATGACGTGGCGGCTTTAGCATTAAGAGGCCGTTCTGCTTGTTTGAATTTCTCTGATTCTGCTTGGA
GGCTGCCTATCCCTGCTTCCTCCAACTCTAAAGATATTCAAAAGGCGGCCGCTCAGGCCGTCGAAATCTTCCGATCGGAAGAAGTTTCAGGAGAATCTCCTGAAACGTCAGAAAATGTGCAAGAGAGTAGTGACTTCGTGGATGAGGAGGCGATCTTTTTCATGCC
AGGATTACTTGCAAATATGGCAGAAGGACTTATGCTACCTCCACCTCAATGTGCAGAAATGGGAGATCATTGTGTGGAAACTGATGCCTACATGATAACTTTATGGAATTATTCTATCTAAAATAGTAGTACAATTTATCAAATTACTAGGATTTAGAAGATTTTG
TTAGTTTTTGGTATTCAGTATTTAGATACTAAGAATGTATATTATTAGTATTTTTATTTTGGCCAAATACATGAACATGAACAGAAACTTGTTGGGTTTTTTTACTCAGGTACCTCAACTACATCATTTTTCTATTGATTATTGAACTACACATAATTTGTTTCTT
TAAAACACTGTTGGTTGATTTTGATCGACTTTTTTATTATAAATGTCTTCAATAATGTTCGAATTGTAATAATTTTGATTAAATGAATGAAGACAAACCGTGTTAATCTTAATTGTTTTCTAATGTGTTCAAATGACTTAAGTAAAACACAATTATTCTTGAACAT
TTTCACTATCAATTGGATTAATGAGTTGTGGAACAACATATCTATTCTCTATCAATAATCTTCACAAATCTGGTTCCACATCAGACAACAGTGTTTGTTTAAACAGAACAAATTATGGGGATTCAATGGTTCAATAGGAAAATGACGTAGTAAAGGAATCTGAAAA
TAAAAAAATCGAACAAATTTAGGGATCTGCTTATTGTACCGAACCATGTAGGTAGATAGTAGTGCCACCAAATAATGACACGTGTCAATGGGATGACTTGGTTTTGGCAGTAGTGAGAAGTAAAGATTAGCGTTGCAAATTTCAAGCCGTCATATTTGAATAAATG
AAGTGTGGAGTGATATGACAATGTTCAATATTTTTTGCCATTCCGAGTATTGAAGAATTACAATTTCTAACTTATTTTTCGTAATTACTGAGTATCTAAATGTTAATTTTATGAATCCAATCTAAGCAAAGTTATCTGATATTGAAAAAACTTGTTTACTTAAAAA
CTAAGAAAACTAAAAATATATAATCCCTTCGTTCAAAAATAATGAAGGGGTGCTCAATATGAGTCAACCATATTCAAATTAAAGTTTCAATTTCAATTCCAAAGTTATTTGTCTCAACATTGAAAAATTTCAGTATTATGAAATTACAAAATAAATAAGATATAAC
TTTTTCATGTTTATAAACACTTTAAAACTGTAATATATAAAATATGAGTAATGAGTAGAGTGAAATATAGGAAAGTTTCCAAATATAGCTTTTAGCCTATCGTTATCTATCTAGAATGCCATTTATTGTACTACTGCCTCCTCTTTGTACGCACTATTTTGACTTG
TTCTTTTCCTTCATTCGTGTACAATTTTATTTTTCCACAAAGTTTTCGTAGGTTTAGGTTAAGATAGTTAGAATTTCTTATAAATTATTTAGTTTCTTGATTCTAATTTAAGTAACACAGTTCTAATAAATACTATACGAAGTATTATAAAATAAAAAAATAAAAT
TTATGATTTAAAACATAATATTTGTGTGACTATAGAAGTTATGTTAGTAAATAAGTATAACATTAGTTTCTATTGGTGAATATAACAAGCAATTATTTTAGGGACAGATTAACAATGCATTCCATGTCTAAGTCCAATTCTTTTTTCCCAATAATACTTATTTCCT
TTAATTTTAAAAAAAATCTCCTCTTTTTATTCTGTTTAAAAAAAATATGATTTTTTTTTTGCTAGCAACTTTTCACGTGACATGTTTAAGGCCATAATATTAAAGTGTAGTTTTATACATTTGACATAACTTTAAATTAACACTACATGATCAAAAAAATTATTTT
TTAAAACTTCGTGTCAAGTTAAACTAAACCAATTTTTATAAAACGGATGAAGTATTAAATTAGATGCACACTTTATTAATCACGTGAATATAACTAGCCTAATGAGCAAGAAGACTTGTTGAAGTCAATATATATTTCATGTGGACCTTAGACAAAAATAGTTTAT
TACTCTTTTATATTTCAATTTACGAAATCTTAAAATTTAATATATTTGTAAACAATATACAAAAATACTTATAAGTTATAACAATTAATATTTTAAAAATATTTAAAATATAAAATTTAATAATCAAAAATATATTTATTTAAATTTTAAAATTAAAAATATATCA
CGTATATTGAGATCGAGAACCCAGTACAAATATTGTAGATGAGATCTATTCCTTTTAGTTAGGAAGGAAGGAAGAAGGATAGGCAAAAAGTAGAAAGTTTGCCACATCAGCAGAAAGGCTACACGAATTATACACACTTGAGACTATAAAACAGCTGTCTACTTAT
CACTATCCAACTCCGTGTAATACCGAACTTTTTTAAATTCAACACTTCACTTATCATATGTTTTATATATATGCATTGAGAAAATCCAATTTCATAATTCACCACAAACCCAAAAACGTCCATCCATCGTACACTACTATATTTTACTCTCTCGTCAAAATAGTAT
TATCATATCATGGATATCTTTGAATCCTATTATTCAAATTCTTTCGTTGAATCATTATTATCATCGTCATTATCAATATCTGATACTAATAATCTCAATCACTACTCCCCTAATGAGGAAGTTATTATTTTAGCTTCGAATAACCCGAAAAAGCCAGCTGGCAGGA
AGAAGTTTCGAGAAACTCGACATCCAGTATACAGGGGAATCAGGAAGAGGAATTCAGGAAAATGGGTTTGTGAAGTCAGAGAACCAAATAAGAAGACAAGGATTTGGCTTGGTACTTTTCCTACGGCTGAAATGGCGGCTAGAGCTCATGACGTGGCGGCTATAGC
ATTAAGAGGCCGTTCTGCTTGTTTGAATTTCGCTGATTCAGTTTGGAGGTTGCCTATACCTGCTTCCTCCAACTCTAAAGATATTCAAAAGGCGGCCGCTGAGGCCGCCGAAATCTTTCGATCGGAAGAAGTTTCAGGAGAATCTCCTGAAACGTCAGAAAATGTG
CAAGAGAGTAGTGACTTCGTGGATGAGGAAGCGCTGTTTTCCATGCCAGGATTACTTGCAAATATGGCAGAAGGACTCATGCTACCTCCTCCCCAATGTTTAGAGATCGGAGACCATTACGTTGAATTAGCTGATGTGCACGCTTATATGCCTTTATGGAATTATT
CTATATAATTACAAGATTTTAATAGTCAGTATTTTAATGGTACAAATCATGTATAGGTAAATGCGTAGTAACAATATTTGAATGAAACAAAGTGAACAAGTTCATCTAATTTATCAACAGCTATATTTCATCTATCCTTAGAATTTTCAATATATTTTATATTTTG
TAGATTTAGAATTAATAACGTATAACTAATATATTGTGGTTCTTAGACTGTATTGAATAAGCGGGGAGGACATTGTCAATATGAAGAGTTTGTGGAATTTATTTTCATTATTTGTTATTTTTTTTATTTTAAAGGGAAAAGACATAAAAAGAAATTTTGAATTTGG
TTCGAAAACTAACTTTAGTATTTTAACTATACGGGCGTTTAAATATTTCTCTTAACATCTTCAAAATGAATTAAAAACCACCCTGAGATTACTATTCCTTTCTCACTTGTCACATCATAGCCATGTAAGTGCCACAACAACATATCAGTATCATGTCGTTAGTTAT
TTTCATCATTTTTCTTTAGCATTTCTTTAAAATTAATTTACACTAATTAATTAATTCAAATTGCATTTTCTAAAATTAAAATTAAAAATGTCGACACATTTTTATTTTACCCCGTACCCAACTCCCACCCACCCCCTTACTTCTTTCTTCTTCCTTCTTCTTCACC
ATTTCTAACTCTCAATGTTCATTTTCCCCTCTCCATATTTTTCAACTACTTCCACCATCCAAACTCCTTTCATCGTAACACTCAAATCACCGCCGAAGCTCCATTATATATATATATATATATATTAGAAGATAAACATATAGAAACATGTAGTTAAAGGAAAGAA
ATAAAAACAATTTACTTCTAAGAAGACGA
 Tomato Genomic Clone Le-3
                            (~19kb)

                  LeCBF3            LeCBF1          LeCBF2
 Right                                                             Left



          4.4kb            3.2kb            3.1kb            8kb

                    NotI             NotI            NotI




                           CBF1        CBF3           CBF2

                            2.7kb           2kb
Protein sequence alignment of LeCBF1.2.3
LeCBF1   MNIFETYYSDSLILTESSSSSSSS--------SFSEEEVILASNNPKKPAGRKKFRETRH 52
LeCBF2   MDIFESYYSNSFVESLLSSSLSISDTNNLNHYSPNEEVIILASNNPKKPAGRKKFRETRH 60
LeCBF3   -----MFYSDPRIESCSSFSDSIR-------ANHSDEEVILASNNPKKPAGRKKFRETRH 48
               :**:. : :    * * *       . .:* :*********************
               AP2 Domain
LeCBF1   PIYRGIRKRNSGKWVCEVREPNKKTRIWLGTFPTAEMAARAHDVAALALRGRSACLNFSD 112
LeCBF2   PVYRGIRKRNSGKWVCEVREPNKKTRIWLGTFPTAEMAARAHDVAAIALRGRSACLNFAD 120
LeCBF3   PVYRGVRKRNSGKWVCEVREPNKKTRIWLGTFPTAEMAARAHDVAAIALRGRSACLNFAD 108
         *:***:****************************************:***********:*


LeCBF1   SAWRLPIPASSNSKDIQKAAAQAVEIFRSEEVSGESPETSENVQESSD--FVDEEAIFFM 170
LeCBF2   SVWRLPIPASSNSKDIQKAAAEAAEIFRSEEVSGESPETSENVQESSD--FVDEEALFSM 178
LeCBF3   SAWRLPTPDSSDTKDIQKAAAQAAEIFRPLKSEEEESVVKDQSTTPDDMFFMDEEALFCM 168
         *.**** * **::********:*.****. : . *.. ..::     ..*   *:****:* *


LeCBF1   PGLLANMAEGLMLPPPQCAEMGDHCVETD---AYMITLWNYSI 210
LeCBF2   PGLLANMAEGLMLPPPQCLEIGDHYVELADVHAYMP-LWNYSI 220
LeCBF3   PGLLTNMAEGLMVPPPQCTEMGDHVEADD-----MP-LWSYSI 205
         ****:*******:***** *:***          *   **.***
Protein sequence alignment of AtCBF and LeCBF
AtCBF4   MNPFYSTFPDSFLSI-SDHRSPVS--------DSSECSPKLASSCPKKRAGRKKFRETRH 51
AtCBF5   MNPFYSTFPDSFLSI-SDHRSPVS--------DSSECSPKLASSCPKKRAGRKKFRETRH 51
AtCBF1   MNSF-SAFSEMFG---SDYEP-----------QGGDYCPTLATSCPKKPAGRKKFRETRH 45
AtCBF2   MNSF-SAFSEMFG---SDYESPVS--------SGGDYSPKLATSCPKKPAGRKKFRETRH 48
AtCBF3   MNSF-SAFSEMFG---SDYESSVS--------SGGDYIPTLASSCPKKPAGRKKFRETRH 48
LeCBF1   MNIFETYYSDSLILTESSSSSSSS--------SFSEEEVILASNNPKKPAGRKKFRETRH 52
LeCBF2   MDIFESYYSNSFVESLLSSSLSISDTNNLNHYSPNEEVIILASNNPKKPAGRKKFRETRH 60
LeCBF3   -----MFYSDPRIESCSSFSDSIR-------ANHSDEEVILASNNPKKPAGRKKFRETRH 48
AtCBF6   ---------------------------------MNNDDIILAEMRPKKRAGRRVFKETRH 27
                                           .:   **   *** ***: *:****


AtCBF4   PIYRGVRQRNSGKWVCEVREPNKKSRIWLGTFPTVEMAARAHDVAALALRGRSACLNFAD 111
AtCBF5   PIYRGVRQRNSGKWVCEVREPNKKSRIWLGTFPTVEMAARAHDVAALALRGRSACLNFAD 111
AtCBF1   PIYRGVRQRNSGKWVSEVREPNKKTRIWLGTFQTAEMAARAHDVAALALRGRSACLNFAD 105
AtCBF2   PIYRGVRQRNSGKWVCELREPNKKTRIWLGTFQTAEMAARAHDVAAIALRGRSACLNFAD 108
AtCBF3   PIYRGVRRRNSGKWVCEVREPNKKTRIWLGTFQTAEMAARAHDVAALALRGRSACLNFAD 108
LeCBF1   PIYRGIRKRNSGKWVCEVREPNKKTRIWLGTFPTAEMAARAHDVAALALRGRSACLNFSD 112
LeCBF2   PVYRGIRKRNSGKWVCEVREPNKKTRIWLGTFPTAEMAARAHDVAAIALRGRSACLNFAD 120
LeCBF3   PVYRGVRKRNSGKWVCEVREPNKKTRIWLGTFPTAEMAARAHDVAAIALRGRSACLNFAD 108
AtCBF6   PVYRGIRRRNGDKWVCEVREPTHQRRIWLGTYPTADMAARAHDVAVLALRGRSACLNFAD 87
         *:***:*:**..***.*:***.:: ******: *.:*********.:***********:*
AtCBF4   SAWRLRIPETTCPKEIQKAASEAAMAFQNETTT---EGS-KTAAEAEEAAGEGVREGERR 167
AtCBF5   SAWRLRIPETTCPKEIQKAASEAAMAFQNETTT---EGS-KTAAEAEEAAGEGVREGERR 167
AtCBF1   SAWRLRIPESTCAKDIQKAAAEAALAFQDETCD---TTTTDHGLDMEETMVEAIYTPE-- 160
AtCBF2   SAWRLRIPESTCAKEIQKAAAEAALNFQDEMCH---MTTDAHGLDMEETLVEAIYTPE-- 163
AtCBF3   SAWRLRIPESTCAKDIQKAAAEAALAFQDEMCD---ATT-DHGFDMEETLVEAIYTAE-- 162
LeCBF1   SAWRLPIPASSNSKDIQKAAAQAVEIFRSEEVS---GESPETSENVQE------------ 157
LeCBF2   SVWRLPIPASSNSKDIQKAAAEAAEIFRSEEVS---GESPETSENVQE------------ 165
LeCBF3   SAWRLPTPDSSDTKDIQKAAAQAAEIFRPLKSE---EEESVVKDQSTT------------ 153
AtCBF6   SAWRLPVPESNDPDVIRRVAAEAAEMFRPVDLESGITVLPCAGDDVDLGFGSGSGSGSGS 147
         *.***   * :. .. *::.*::*.   *:             :


AtCBF4   AEEQNGGVFYMDDEALLGMPNFFENMAEGMLLPPPE---VGWNHN-DFDGVGD----VSL 219
AtCBF5   AEEQNGGVFYMDDEALLGMPNFFENMAEGMLLPPPE---VGWNHN-DFDGVGD----VSL 219
AtCBF1   ---QSEGAFYMDEETMFGMPTLLDNMAEGMLLPPPS---VQWNHNYDGEGDGD----VSL 210
AtCBF2   ---QSQDAFYMDEEAMLGMSSLLDNMAEGMLLPSPS---VQWNYNFDVEGDDD----VSL 213
AtCBF3   ---QSENAFYMHDEAMFEMPSLLANMAEGMLLPLPS---VQWNHNHEVDGDDDD---VSL 213
LeCBF1   ----SSD--FVDEEAIFFMPGLLANMAEGLMLPPPQ---CAEMGDHCVETD---AYMITL 205
LeCBF2   ----SSD--FVDEEALFSMPGLLANMAEGLMLPPPQ---CLEIGDHYVELADVHAYMP-L 215
LeCBF3   ----PDDMFFMDEEALFCMPGLLTNMAEGLMVPPPQ---CTEMGDHVEADD-----MP-L 200
AtCBF6   EERNSSSYGFGDYEEVS---TTMMRLAEGPLMSPPRSYMEDMTPTNVYTEEEMCYEDMSL 204
                 .   : . * :    : .:*** ::. *                       *
Drought        Nacl(250mm)        ABA(100µm)
             McM      1 2 4 6 8 24      1 2 4 8 16 24    1 2 4 8 16 24 (hours)

3’ LeCBF1.
3’ LeCBF2
3’ LeCBF3
  Le25
  eIF4A


                cold 4ºC (24hL)       cold 4ºC(16hL/D)       Control
             0 .25 .5 1 2 4 8 24 7d    0 1 2 4 8 16 24   0 1 2 4 8 16 24 (hours)
3’ LeCBF1

3’ LeCBF2
3’ LeCBF3
  eIF4A
Tomato CBF Genes Expression Pattern Under Different Stress
  The expression of LeCBF1 and LeCBF2 under various stress treatments was investigated
  using RNA Gel Blot analysis
  LeCBF1 but not LeCBF2 was found to be cold-responsive



                                      Drought        Nacl(250m )
                                                              m         ABA(100µm)
                           McM     1 2 4 6 8 24      1 2 4 8 16 24    1 2 4 8 16 24 (hours)

              3’ LeCBF1.
              3’ LeCBF2
                 Le25
                eLF4A

                              cold 4ºC(24hL)       cold 4ºC(16hL/D)       Control
                           0 .25 .5 1 2 4 824 7d    0 1 2 4 8 1624    0 1 2 4 8 16 24 (hours)
             3’ LeCBF1

              3’ LeCBF2
                eLF4A
Thank You!

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