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DNA.While we think ofgenomic DNA as a stable geneticblueprint,the lymphocyte cell lineage does not retain an in-tact copy ofthis blueprint.Genomic rearrangement is an es-sential feature oflymphocyte differentiation,and no othervertebrate cell type has been shown to undergo this process.This chapter first describes the detailed organization of the immunoglobulin genes,the process ofIg-gene rearrange-ment,and the mechanisms by which the dynamic im-munoglobulin genetic system generates more than 10
8
different antigenic specificities.Then it describes the mecha-nism ofclass switching,the role ofdifferential RNA process-ing in the expression ofimmunoglobulin genes,and theregulation ofIg-gene transcription.The chapter concludeswith the application ofour knowledge ofthe molecular
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PolyadenylationRNA splicing(A)
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LL
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Genetic Model Compatible with Ig Structure
I
Multigene Organization of Ig Genes
I
Variable-Region Gene Rearrangements
I
Mechanism of Variable-Region DNARearrangements
I
Generation of Antibody Diversity
I
Class Switching among Constant-Region Genes
I
Expression of Ig Genes
I
Synthesis, Assembly, and Secretion of Immunoglobulins
I
Regulation of Ig-Gene Transcription
I
Antibody Genes and Antibody Engineering
Organization andExpression of ImmunoglobulinGenes
O
      
the vertebrate immune system is its ability torespond to an apparently limitless array offor-eign antigens.As immunoglobulin (Ig) sequence data accu-mulated,virtually every antibody molecule studied wasfound to contain a unique amino acid sequence in its vari-able region but only one ofa limited number ofinvariant se-quences in its constant region.The genetic basis for thiscombination ofconstancy and tremendous variation in asingle protein molecule lies in the organization ofthe im-munoglobulin genes.In germ-line DNA,multiple gene segments encode por-tions ofa single immunoglobulin heavy or light chain.Thesegene segments are carried in the germ cells but cannot betranscribed and translated into complete chains until they are rearranged into functional genes.During B-cell matura-tion in the bone marrow,certain ofthese gene segments arerandomly shuffled by a dynamic genetic system capable of generating more than 10
6
combinations.Subsequentprocesses increase the diversity ofthe repertoire ofantibody binding sites to a very large number that exceeds 10
6
by atleast two or three orders ofmagnitude.The processes ofB-cell development are carefully regulated:the maturation ofaprogenitor B cell progresses through an ordered sequence of Ig-gene rearrangements,coupled with modifications to thegene that contribute to the diversity ofthe final product.By the end ofthis process,a mature,immunocompetent B cellwill contain coding sequences for one functional heavy-chain variable-region and one light-chain variable-region.The individual B cell is thus antigenically committed to aspecific epitope.After antigenic stimulation ofa mature Bcell in peripheral lymphoid organs,further rearrangementofconstant-region gene segments can generate changes inthe isotype expressed,which produce changes in the biolog-ical effector functions ofthe immunoglobulin moleculewithout changing its specificity.Thus,mature B cells containchromosomal DNA that is no longer identical to germ-line
Kappa Light-Chain Gene Rearrangement
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biology ofimmunoglobulin genes to the engineering ofanti-body molecules for therapeutic and research applications.Chapter 11 covers in detail the entire process ofB-cell devel-opment from the first gene rearrangements in progenitor Bcells to final differentiation into memory B cells and anti-body-secreting plasma cells.Figure 5-1 outlines the sequen-tial stages in B-cell development,many ofwhich result fromcritical rearrangements.
Genetic Model Compatiblewith Ig Structure
The results ofthe immunoglobulin-sequencing studies de-scribed in Chapter 4 revealed a number offeatures of immunoglobulin structure that were difficult to reconcilewith classic genetic models.Any viable model ofthe
106
PART II
Generation of B-Cell and T-Cell Responses
VISUALIZING CONCEPTS
FIGURE
5
-
1
Overview of B-cell development. The events thatoccur during maturation in the bone marrow do not require anti-gen, whereas activation and differentiation of mature B cells in pe-ripheral lymphoid organs require antigen. The labels mIgM andmIgD refer to membrane-associated Igs. IgG, IgA, and IgE are se-creted immunoglobulins.
Lymphoid cellPartial heavy-chain gene rearrangementHematopoietic stem cellPro-B cellComplete heavy-chain gene rearrangementPre-B cellLight-chain gene rearrangementImmature B cellChange in RNA processing
PeripherallymphoidorgansBonemarrow 
Mature B cell Antigen stimulation Activated B cellDifferentiationIgM-secreting plasma cellsClass switchingMemory B cellsof variousisotypesPlasma cellssecreting variousisotypesNoneIg EXPRESSEDCELLNoneNone
µ
Heavy chain + surrogate light chainmIgMmIgM + mIgDIgMIgGIgAIgE
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immunoglobulin genes had to account for the followingproperties ofantibodies:
I
The vast diversity ofantibody specificities
I
The presence in Ig heavy and light chains ofa variableregion at the amino-terminal end and a constant regionat the carboxyl-terminal end
I
The existence ofisotypes with the same antigenicspecificity,which result from the association ofa givenvariable region with different heavy-chain constantregions
Germ-Line and Somatic-Variation ModelsContended To Explain Antibody Diversity
For several decades,immunologists sought to imagine a ge-netic mechanism that could explain the tremendous diversity ofantibody structure.Two different sets oftheories emerged.The
germ-line theories
maintained that the genome con-tributed by the germ cells,egg and sperm,contains a largerepertoire ofimmunoglobulin genes;thus,these theories in-voked no special genetic mechanisms to account for anti-body diversity.They argued that the immense survival valueofthe immune system justified the dedication ofa significantfraction ofthe genome to the coding ofantibodies.In con-trast,the
somatic-variation theories
maintained that thegenome contains a relatively small number ofimmunoglob-ulin genes,from which a large number ofantibody specifici-ties are generated in the somatic cells by mutation orrecombination.As the amino acid sequences ofmore and more im-munoglobulins were determined,it became clear that theremust be mechanisms not only for generating antibody diver-sity but also for maintaining constancy.Whether diversity was generated by germ-line or by somatic mechanisms,aparadox remained:How could stability be maintained in theconstant (C) region while some kind ofdiversifying mecha-nism generated the variable (V) region?Neither the germ-line nor the somatic-variation propo-nents could offer a reasonable explanation for this centralfeature ofimmunoglobulin structure.Germ-line proponentsfound it difficult to account for an evolutionary mechanismthat could generate diversity in the variable part ofthe many heavy- and light-chain genes while preserving the constantregion ofeach unchanged.Somatic-variation proponentsfound it difficult to conceive ofa mechanism that could di-versify the variable region ofa single heavy- or light-chaingene in the somatic cells without allowing alteration in theamino acid sequence encoded by the constant region.A third structural feature requiring an explanationemerged when amino acid sequencing ofthe humanmyeloma protein called Ti1 revealed that identical variable-region sequences were associated with both
and
heavy-chain constant regions.A similar phenomenon was observedin rabbits by C.Todd,who found that a particular allotypicmarker in the heavy-chain variable region could be associ-ated with
,
,and
heavy-chain constant regions.Consid-erable additional evidence has confirmed that a singlevariable-region sequence,defining a particular antigenicspecificity,can be associated with multiple heavy-chainconstant-region sequences;in other words,different classes,or isotypes,ofantibody (e.g.,IgG,IgM) can be expressedwith identical variable-region sequences.
Dreyer and Bennett Proposedthe Two-Gene Model
In an attempt to develop a genetic model consistent with theknown findings about the structure ofimmunoglobulins,W.Dreyer and J.Bennett suggested,in their classic theoreticalpaper of1965,that two separate genes encode a single im-munoglobulin heavy or light chain,one gene for the V region(variable region) and the other for the C region (constant re-gion).They suggested that these two genes must somehowcome together at the DNA level to form a continuous mes-sage that can be transcribed and translated into a single Igheavy or light chain.Moreover,they proposed that hundredsor thousands ofV-region genes were carried in the germ line,whereas only single copies ofC-region class and subclassgenes need exist.The strength ofthis type ofrecombinational model(which combined elements ofthe germ-line and somatic-variation theories) was that it could account for those im-munoglobulins in which a single V region was combinedwith various C regions.By postulating a single constant-region gene for each immunoglobulin class and subclass,themodel also could account for the conservation ofnecessary biological effector functions while allowing for evolutionary diversification ofvariable-region genes.At first,support for the Dreyer and Bennett hypothesiswas indirect.Early studies ofDNA hybridization kinetics us-ing a radioactive constant-region DNA probe indicated thatthe probe hybridized with only one or two genes,confirmingthe model’s prediction that only one or two copies ofeachconstant-region class and subclass gene existed.However,in-direct evidence was not enough to overcome stubborn resis-tance in the scientific community to the hypothesis ofDreyerand Bennet.The suggestion that two genes encoded a singlepolypeptide contradicted the existing one gene–onepolypeptide principle and was without precedent in any known biological system.As so often is the case in science,theoretical and intellec-tual understanding ofIg-gene organization progressed aheadofthe available methodology.Although the Dreyer and Ben-nett model provided a theoretical framework for reconcilingthe dilemma between Ig-sequence data and gene organiza-tion,actual validation oftheir hypothesis had to wait for sev-eral major technological advances in the field ofmolecularbiology.
Organization and Expression of Immunoglobulin Genes
CHAPTER
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