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Identification and analysis of the cis-regulatory element for the AID-mediated somatic hypermutation and application of this process for the artificial protein evolution in chicken B-cell line DT40 [Elektronische Ressource] / Vera Batrak

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Published 01 January 2009
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TECHNISCHE UNIVERSITÄT MÜNCHEN

Lehrstuhl für Entwicklungsgenetik





Identification and analysis of the cis-regulatory element for the AID-
mediated somatic hypermutation and application of this process for the
artificial protein evolution in chicken B-cell line DT40


Vera Batrak



Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für
Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung
des akademischen Grades eines
Doktors der Naturwissenschaften
genehmigten Dissertation.

Vorsitzender: Univ.- Prof. Dr. S. Scherer
Prüfer der Dissertation:
1. Univ.- Prof. Dr. W. Wurst
2. Univ.- Prof. Dr. M. J. Atkinson


Die Dissertation wurde am 23.06.2009 bei der Technischen Universität München
eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung,
Landnutzung und Umwelt am 27.10.2009 angenommen.
SUMMARY

Somatic hypermutation (SHM) is one of three mechanisms of immunoglobulin (Ig)
gene diversification at the post-V(D)J-recombination stage. Depending on species SHM is
responsible for antibody repertoire production and/or affinity maturation of germinal centre B
lymphocytes. The diversification process involves introducing non-template mutations into
6 the Ig gene at a rate which is 10 higher than the spontaneous mutation rate in somatic cells.
SHM is initiated by activation-induced cytidine deaminase (AID), an enzyme that deaminates
cytosine residues in transcription-dependent manner and completed by error-prone repair of
the resulted uracils.
SHM is specific for the Ig locus; other transcribed genes of B-cells do not undergo
mutations at such a high rate. When mistargeted, hypermutation represents a threat to genome
integrity and was shown to be associated with a number of B-cell lymphomas. Although there
have been identified a number of factors including cis- and trans- regulatory elements which
seem to play a role in recruiting of the SHM to the Ig locus, unambiguous element responsible
for the SHM targeting has not been identified and mechanisms of this process remain unclear.
The present study describes the generation of a reporter for somatic hypermutation
which allowed deletion analysis of the Ig light chain (IgL) locus of the DT40 B-cell line in
order to identify a cis-regulatory element responsible for activation of the hypermutation.
Deletion of this element, extending for 9.8 kb from the IgL transcription start site towards the
next downstream locus, named DIVAC for diversification activator, abolished hypermutation.
It was also shown that DIVAC is able to act over a distance in both directions, which allowed
suggesting of a model for the action of this element.
Also the study describes the generation of a second type of a hypermutation vector
which allowed biotechnological exploitation of the somatic hypermutation. Use of this vector
and the DT40 cell line allowed the specific and efficient mutation of a transgene placed within
the Ig locus. This strategy permits optimization of in situ directed protein evolution based on
hypermutation. This artificial evolution system has a number of advantages compared to the
known methods of in vitro and in situ directed evolution and can be applied for optimization
of any gene whose phenotype can be screened in DT40 cells. Using the described system it
was possible to optimize both green and red fluorescent proteins and generate variants with
higher fluorescent intensity and spectrally shifted emissions.
ii
ZUSAMENFASSUNG

Die Somatische Hypermutation (SHM) ist einer von drei Mechanismen des
Rearrangements der Immunoglobulin(Ig)-Gene, die im Anschluss an die V(D)J
Rekombination stattfindet und, je nach Spezies, entweder für das Antikörperrepertoire
und/oder für Reifung von Antikörper-Affinität verantwortlich ist. Durch die SHM werden
6Zufallsmutationen in das Ig Gen eingeführt, wobei die Mutationshäufigkeit um bis zu 10 -
fach höher ist als die spontane Mutationsrate in somatischen Zellen. SHM wird während der
Transkription durch Deaminierung von Cytosin durch das Enzym Aktivierungsinduzierte
Cytidin Deaminase (AID) ausgelöst und durch eine fehlerhafte DNA-Reparatur des daraus
resultierenden Uracils abgeschlossen.
SHM ist spezifisch für den Ig Locus, während andere transkribierte Gene in B-Zellen
nicht eine solche hohe Mutationshäufigkeit zeigen. Bei fehlerhafter unspezifischer Aktivität
von AID stellt die SHM aber eine Gefahr für die Integrität des Genoms und wird mit
verschiedenen B-Zell Lymphomen in Zusammenhang gebracht. Es ist noch weitgehend
unklar, welche Mechanismen dazu führen, dass SHM auf den Ig-locus beschränkt ist.
In dieser Arbeit ist die Entwicklung eines Reporterkonstrukts zum Nachweis der SHM
beschrieben, das erlaubte eine Deletionsanalyse des Ig-Leichtkettenlocus der DT40 B-
Zelllinie durchzuführen. Dabei wurde das cis-regulatorisches Element (DIVAC,
Diversification Activator) entdeckt, das für die Auslösung von SHM verantwortlich ist. Bei
Deletion von DIVAC konnte keine SHM mehr nachgewiesen werden. Des weiteren wurde
auch bestimmt, über welche genomischen Distanzen DIVAC seine Funktion entfalten kann.
Diese Ergebnisse erlaubten die Erstellung eines Modells zur Funktionsweise von DIVAC
während der SHM.
Darüberhinaus wird in dieser Arbeit auch die Entwicklung eines Vektors beschrieben,
der eine biotechnologische Anwendung der SHM möglich macht. Der Vektor ist für die
Zellinie DT40 konstruiert und ermöglicht ein beliebiges Transgen spezifisch und effizient im
Ig Locus durch SHM zu mutieren. Das daraus resultierende System der künstlichen in situ
Proteinevolution hat eine Reihe von Vorteilen zu bereits etablierten Methoden, Proteine in
vitro oder in situ artifiziel zu verändern. SHM kann zur Optimierung eines jeden Proteins
angewendet werden, dessen Phänotyp in der DT40 Zellinie erkennbar ist. Im Rahmen dieser
Arbeit war es daher möglich, grün und rot fluoreszierende Proteine zu optimieren, wobei
sowohl Varianten mit erhöhter Fluoreszensintensität als auch mit Verschiebung des
Emissionsspektrums entwickelt wurden.

iii
ABBREVIATIONS

AID Activation Induced Cytidine Deaminase
APOBEC-1 Apolipoprotein B RNA Editing Catalytic Polypeptide 1
BDT Big Dye Terminator
BSR Blasticidine S Resistance gene
C region Immunoglobulin Constant region
CIP Calf Intestine Phosphatase
CSR Class Switch Recombination
D region Immunoglobulin Diversity region
DMSO Dimethyl Sulfoxide
dNTP Deoxynucleotide Triple Phosphate
DSB Double Strand Break
EDTA Ethylene di-Amine Tetra Acetic Acid
EF Elongation Factor
FACS Fluorescence Activated Cell Sorting
FBS Fetal Bovine Serum
FRET Fluorescence Resonance Energy Transfer
FSC Forward Scatter
EtBr Ethidium Bromide
GC Gene Conversion
GFP Green Fluorescent Protein
GPT Guanine Phosphoribosyl Transferase
4-HT 4-Hydroxy Tamoxifen
Ig Immunoglobulin
IgL Immunoglobulin Light Chain
IRES Internal Ribosome Entry Site
J region Immunoglobulin Joining region
LB Luria Broth
MAR Matrix Attachment Region
MMR Mismatch Repair
NHEJ Nonhomologues End Joining
PBS Phosphate Buffer Saline
PCR Polymerase Chain Reaction
pKS (+) pBluescript vector
Pol Polymerase
Puro Puromycin
RFP Red Fluorescent Protein
RSV Rous Sarcoma Virus
S region Switch region
SDS Sodium Dodecyl Sulphate
SHM Somatic Hypermutation
sIgM Surface Immunoglobulin M
SSB Single Strand Break
TAE Tris Acetic Acid ETDA
TE Tris EDTA
TLS Trans Lesion Synthesis
UNG Uracil DNA Glycosylase
V region Immunoglobulin Variable region
2YT 2 x Yeast Extract Tryptone
iv
TABLE OF CONTENTS
SUMMARY II
ZUZAMMENFASSUNG III
ABBREVIATIONS IV
TABLE OF CONTENTS V
INTRODUCTION
I. Evolution of the immune system 1
II. Immunoglobulin repertoire generation in gnathostomata 3
1. V(D)J recombination 3
2. Post-V(D)J remodeling of the immunoglobulin gene 4
a. Gene conversion 4
b. Somatic hypermutation 5
c. Class switch recombination 6
III. B- lymphocytes development 8
1. Mouse and human 8
2. Gallus gallus and other species with post-V(D)J-Ig repertoire formation 9
IV. Chicken B-cell line DT40 10
1. Unique characteristics of DT40 10
2. Elimination of gene conversion in DT40. Cross talk between gene conversion
and somatic hypermutation 11
V. Molecular mechanism of somatic hypermutation 13
1. First phase: cytidine deamination by AID 13
2. Processing the AID-generated mismatches 14
a. Uracil excision by UNG 15
b. Mismatch repair 16
c. Translesion synthesis 17
d. Triggering of the translesion synthesis by PCNA 19
VI. Ig locus specificity of somatic hypermutation 20
1. Cis-acting DNA elements 20
2. Trans-acting factors 22
3. Chromatin structure 22
4. Cell cycle restriction 23
5. Subcellular localization 24
VII. Application of the somatic hypermutation and gene conversion for biotechnology 24
v
1. Green and red fluorescent proteins as objects for the directed protein
evolution in vitro 25
2. Using of in situ directed protein evolution based on hypermutation 26

OBJECTIVES 29

MATERIALS AND METHODS

I. Materials 30
1. Equipment 30
2. Experimental kits 30
3. Enzymes 30
4. DNA size marker 31
5. Plasmids 31
6. Bacterial strain 31
7. Mammalian cell line 31
8. Media 31
9. Oligonucleotides 32
II. Methods 34
1. Polymerase Chain Reaction (PCR) 34
2. Analysis of DNA by electrophoresis 34
3. Restriction enzyme digestion 34
4. Purification and gel purification of DNA 34
5. DNA ligation 35
6. Culture of E.coli 35
7. E.coli DH5α competent cell preparation 35
8. Transformation 36
9. Colony PCR 36
10. Plasmid preparation 36
11. Determination of DNA and RNA concentration 36
12. Basic cell culture techniques 37
13. Thawing of DT40 cells 37
14. Freezing down of DT40 cells 37
15. Transfection 37
16. Identifying Targeted Events by PCR 38
17. Subcloning of DT40 cells 38
18. Drug resistance marker recycling 38
19. Flow cytometry 39
20. Fluorescence Activated Cell Sorting (FACS) 39
21. Genomic DNA isolation 39
22. Total RNA isolation 40
23. First strand cDNA synthesis 40
24. Fluorescent spectra measurement in DT40 40

vi
RESULTS
I. Application of somatic hypermutation for artificial protein evolution 41
1. Improvement of the artificial evolution system and application for
optimization of the GFP proteins 41
a. Analysis of the mutations responsible for the increase of the eGFP
brightness 41
b. Construction of a vector pHypermut2 for improvement of the artificial
evolution system 42
c. Confirmation of the new GFP phenotypes 46
d. Development of chimeric GFP variants for an additional
increase of brightness 47
e. Spectral properties of the brightest GFP variants 49
2. Application of the advanced artificial evolution system for optimization of the
RFP proteins 50
1. EqFP615 and strategy for its improvement by somatic hypermutation 50
2. Generation of the RFP variants with increased fluorescence and far-red
shifted emission spectrum 52
3. Spectral characteristics of the new RFP variants 57
4. Analysis of the mutations responsible for the RFP improvement 58
5. Confirmation of the new RFP phenotypes 60
II. Identification and characterization of a cis-acting diversification activator
necessary for the AID mediated hypermutation 63
1. Construction of a GFP2 - reporter for somatic hypermutation activity 63
2. Identification of a cis-regulatory element for the somatic hypermutation 65
3. Distance of the bidirectional effect of the cis-regulatory element
for hypermutation 70

DISCUSSION
I. Application of the somatic hypermutation for artificial protein evolution 77
II Identification of a cis-acting diversification activator both necessary
and sufficient for the AID mediated hypermutation 84
REFERENCES 87
PUBLICATION LIST 102
ACKNOWLEDGEMENTS 104
LEBENSLAUF 106
vii
INTRODUCTION

I. Evolution of the immune system
The major part of the earth biomass consists of microorganisms, many of which are
pathogens capable of causing life-threating infections to other organisms. The first host
response to infection is innate immunity, which is based on the recognition of specific
pathogen-associated molecular patterns (PAMPs) by germ-line encoded Toll-like receptors
[1]. Some of the innate immunity pathways are conserved between plants and animals that are
divided by billions of years of evolution [2].
In addition to the PAMPs-recognition system, vertebrates have evolved an adaptive
immunity which is triggered by innate defense mechanisms and mediated primarily by
specialized white blood cells (lymphocytes). There are two classes of lymphocytes: T-cells,
responsible for the cell-mediated immune response, and B-cells which mediate humoral
immunity. Lymphocytes perform antigen-specific recognition using receptors expressed on
their surface, T-cell receptors (TCRs) and B-cell receptors (BCRs, antibodies or
immunoglobulins (Igs)). All receptors produced by an individual lymphocyte have the same
antigen-biding site recognizing a specific epitope of the antigen [3]. The recognition is
achieved in different manner: while BCRs are capable to interact with antigens directly, TCRs
recognize a processed form of antigen, presented on the surface of the specialized cells by
Major Histocompatibility Complex (MHC)-encoded proteins.
While the T-cell receptor has a dimeric configuration, the immunoglobulin is a
tetramer of two light and two heavy polypeptide chains encoded by different loci: light chains
fall into the lambda (λ) and kappa (κ) families and heavy chains form a single family. Each Ig
or TCR polypeptide consists of a terminal variable region contributing to the antigen
recognition and a constant region that serves structural, signaling and effector functions.
Antigen receptor genes exist in the germline in a “split” configuration and are assembled
somatically during B- and T-lymphocytes development by site-specific recombination.
Multiple C regions, each with specialized effector function, are encoded in the heavy chain
locus. The Variable (V) region is encoded by Variable (V), Joining (J) (in heavy chain also
Diversity (D)) gene segments which are assembled by V(D)J recombination, a process, which
can be found in all jawed vertebrates (gnathostomata), beginning with cartilaginous fish [4-7].
Evolutionary appearance of RAG1 and RAG2 recombinases coincides with V(D)J
rearrangements [8, 9]. As these recombinases are able to catalyze transposition, it was
suggested that during evolution the diversification of germ-line antigen receptors may have
1 developed by germline insertion of a transposable element into an ancestral receptor gene,
probably containing an Ig-like V-domain [10, 11] soon after the evolutionary divergence of
jawed and jawless vertebrates [12-14].
As BCRs and TCRs possess sequence conservation and use the same recombination
machinery, it is speculated that they may have derived from a common “primordial” receptor
[15, 16]. While configuration and diversification mechanisms of TCRs have been maintained
during evolution, those for BCRs underwent significant changes [16-18]. While all TCRs
described to date have a translocon configuration (each cluster containing individual V, (D), J,
and C as the repeating unit) (Figure 1), Ig genes have either cluster configuration (repeating
unit contains all the gene segments necessary for expression of the receptor) as in
cartilaginous fish, or translocon configuration as in mammals and amphibians, or a
combination of the two as in bony fish. In addition to the functional V-segments, the Ig loci of
farm animals and birds were shown to contain non-functional pseudo (ψ)-genes. Birds
represent an extreme in the evolution of the translocon configuration: while both light and
heavy chain loci contain multiple V regions, all but one of them is a pseudo-gene (Figure 1).
Conflicting with the theory linking the appearance of adaptive immunity to the RAG –
transposon invasion [18] is a recent study of lamprey and hagfish, the only survived groups of
jawless vertebrates (agnatha). This investigation revealed that these animals lacking RAG1/2
are nevertheless capable of an adaptive immune response using a recombinatorial mechanism
of receptor gene generation. This process uses a previously unknown class of non-Ig receptor
molecules called variable lymphocyte receptors, VLRs [19, 20].











2
Figure 1. The organization of antigen receptor genes depicted using rectangles to indicate the
individual variable region gene segments (blue, V, green, D; and yellow, J) or the constant region
genes (violet). Pseudo-genes of chicken are depicted in light blue. Taken from [18].

As only lamprey, hagfish and jawed vertebrates survived from the early vertebrate
radiation, it is not clear whether the agnathan VLRs were the precursors of vertebrate
immune receptors or if the rearranging VLRs and Igs/TCRs developed independently from
“primordial” receptors during convergent evolution [15, 20].
Unlike TCRs, B-cell receptors undergo additional diversification following V(D)J
recombination, including gene conversion, somatic hypermutation and class switch
recombination. It is known that somatic hypermutation was found already in cartilaginous fish
(sharks) [15, 16, 21-23], class switch recombination appears in a primitive form in
amphibians [24, 25]. Dogfish (cartilaginous fish) was found also to have a structural and
functional homolog of the protein AID (Activation Induced Deaminase), necessary for
initiation of the post-V(D)J-recombination diversification processes (Section V) [26].

II. Immunoglobulin repertoire generation in gnathostomata
Diversification of the Ig receptor gene allowed jawed vertebrates to generate a
lymphocyte receptor repertoire of sufficient diversity for recognition the antigenic component
of many potential pathogens or toxins.
In the mice and humans the primary Ig repertoire is achieved by V(D)J recombination
within the light and heavy chains separately while in farm animals and birds primary diversity
is mediated by post-V(D)J remodeling that includs gene conversion and somatic
hypermutation. After antigen stimulation, the affinity maturation of Ig gene in most species is
achieved by somatic hypermutation (in rare cases accompanied by gene conversion) and the
effector function of immunoglobulin can be changed by class switch recombination.

II.1. V(D)J recombination
In order to assemble the complete receptor molecule early in lymphocyte development
(Section III) germline-encoded segments of the Ig gene are somatically recombined in
different permutations within individual lymphocytes (Figure 2) [4, 5, 27]. V(D)J
recombination is mediated by lymphocyte–specific recombinases RAG1 and RAG2 using
special signal sequences flanking the individual segments [8]. This recombinatorial joining of
3