Lewin Benjamin (ed.) Genes IX

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'196

€

Toll,

which

is related

to mammalian

ILI

recep-

tor, triggers

the

pathway

in Drosophila

that

con-

trols

dorsal-ventral

development.

This leads

activation

of the transcription

factor

dorsal,

member

of the Rel

family,

which is

relared

to the

mammalian

factor

NF-rB. The

pathway

innate

immunity

parallel

to the Toll

pathway,

with

similar components.

fact,

one of the

first

indications

of the nature

of innate

immunity

flies

was the discovery

of the

transcription

fac-

tor Dif

(dorsal-related

immunity

factor),

which

activated

by one of

the

pathways.

Flies

have no

system

of adaptive

immunity,

but

are resistant

to microbial

infections.

This

because

their innate immune

systems

trigger

synthesis

potent

antimicrobial peptides.

Seven

distinct

peptides

have

been

identified

Drosophila,

where

they

are synthesized

the

fat body

(the

equivalent

organ

ro rhe liver).

Two

of the

peptides

are

antifungal,

and five

act largely

bacteria. The

general

mode

of action is

kill

the target

organism

permeabilizing

irs

membrane.

AII of

these

peptides

are coded by

genes

whose

promoters

respond

to transcrip-

tion factors

the Rel family. ; ri,,rrilr ,1,;

sum-

marizes

the

components

of the innate pathways

Drosophila.

TWo innate

response pathways

function

Drosophila;

one responds

principally

to fungi,

whereas

the

other responds principally

gram-negative

bacteria.

Gram-positive

bacte-

ria may

be able

to trigger

both

pathways.

i..

ri::

outlines

the steps in

each

path-

way. Fungi

and

gram-positive

bacteria

activate

proteolytic

cascade that

generates

pepticles

that

activate a TLR. This

is the

NF-rB-like

path-

way. The dToll receptor

activates

the transcrip-

tion factor Dif

relative

NF-rB), leading

ultimately

to activation

of the

antifungal

pep-

tide

drosomycin.

Gram-negative

bacteria trig-

ger

pathway

via

a different

receptor

that

activates

the transcription

factor

Relish, Iead-

ing

production

of the

bactericidal

peptide

attacin.

This

pathway

called the Imd

path-

way after one

its

components,

protein

that

has

"death

domain" related

those found

in the

pathways

for

apoptosis.

The key

agents in responding

to the bacte-

ria are

proteins

called

PGRPs

because of

their

high

affinities for bacterial peptidoglycans.

There

are

two types of

these

proteins.

PGRP-SAs

are

short extracellular

proteins.

They

probably

func-

tion

by activating

the

proteases

that trigger

the

Toll

pathway.

PGRP-LCs

are transmembrane

proteins

with an

extracellular

PGRP domain.

Their

exact role has

to be determined.

i:,i,;,ri'i

'',

Innate immunity is triggered by PAMPs.

In flies,

they cause

the

production

peptides

that acti-

vate

Totll.ike receptors. The receptors lead to a

pathway

that activates

a transcription

factor ofthe Re[ famity. Tar-

get genes

for this factor inctude bactericidal and antifun-

gal" peptides.

The

peptides

act by

permeabiLizing

the

membrane

of the

pathogenic

organism.

rri'i,ili,ir: .r

:,il

One of the

Drosophilo

jnnate

immunity

pathways

closely

related to the

mammaUan

pathway

for

activating NF-rB; the other

has components

retated

those of apoptosis

pathways.

Fungi

Gram-positive Gram-negative

J"r'r*

:;tciJ;;rcidar

and

urosomvctn

peplloes

23.21

Innate Immunity Utitizes Conserved

Signating

Pathways

The innate immune

response is highly con-

served. Mice that

are resistant to septic shock

when they are treated with

LPS have mutations

the

Toll-like receptor

TLR4. A human

homolog

of the

Toll receptor can activate

some

immune-response

genes,

suggesting

that the

pathway

of innate

immunity may also

function

in man.

The

pathway

downstream of

the TLRs

generally

similar

all cases,

typically

lead-

ing to activation of the transcription

factor NF-

rB. We

not

yet

know whether the upstream

pathway

conserved,

and in

particular

whether

the PAMPs function by

generating

ligands that

in turn activate the

TLRs or whether they

might

interact directly with them.

The

pathway

upstream of the

TLRs is different in mammals

and flies, because the

pathogens

directly activate

mammalian TLRs.

the case of

LPS, the

pathogen

binds

to the surface

protein

CDl4;

this enables CDI4 to activate

TLR4, triggering

the innate response

pathway.

There

are

-20

receptors in the TLR class in the human

genome,

which

gives

some

indication of how many

pathogens

can trigger the

innate response.

Plants have extensive defense mechanisms,

among which are

pathways

analogous

to the

innate response in

animals.

The same

principle

applies that PAMPs are the

motifs that identify

the infecting agent as a

pathogen.

The

proteins

that respond to the

pathogens

are coded

by a

class

genes

called the disease resistance

genes.

Many

of these

genes

code for receptors that

share a

property

with the TLR class of animal

receptors: The extracellular domain

has

motif

called the leucine-rich region

(LLR).

The

response mechanism is different from animal

cells, and is directed to activating a

mitogen-

activated

protein

kinoset

(MAPK)

cascade.

Many

different

pathogens

activate the same cas-

cade, which suggests that a variety of

pathogen-

receptor interactions

converge at or before

the

activation of the first MAPK.

Sum

mary

Immunoglobulins

and T cell receptors are

pro-

teins that

play

analogous functions in the roles

of B

cells and T cells in the immune system. An

Ig or TCR

protein

generated

rearrange-

ment of DNA in

a single

lymphocyte;

exposure

to an antigen recognized

by the

TCR leads

to clonal expansion to

generate

many cells that

have the

same specificity as the original cell.

il:::,ffi

,,1":li:iii11ffiffJ u;:H,

:i:H;

CHAPTER 23 Immune

Djversitv

creating

a large repertoire

of cells of different

specificities.

Each immunoglobulin

protein

is a tetramer

containing

two identical

light

chains

and two

identical heavy

chains. A

TCR is

a dimer con-

taining two different

chains.

Each

polypeptide

chain

is expressed

from a

gene

created by link-

ing one of many

V segments via D segments

and J segments

to one of a

few

C segments.

L chains

(either

l,) have the

general

struc-

ture

V-J-C, Ig

chains

have the structure V-D-

J-C.

TCR cr and

have components

like Ig L

chains, and

TCR 6 and

are

Ig H chains.

Each type of chain

coded by a

large

clus-

ter of

genes

separated

from the cluster of D,

J, and C segments.

The

numbers

of each type

of segment and

their organization are different

for each type of chain,

but the

principle

and

mechanism

of recombination appear to be the

same.

The same

nonamer and heptamer con-

sensus sequences

are involved

each

recom-

bination;

the reaction always involves

joining

of a consensus with

23 bp spacing to a consen-

sus

with l2 bp spacing.

The

cleavage

reaction

is catalyzed by

the RAGI and RAG2

proteins,

and the

joining

reaction is catalyzed by the same

NHEJ

pathway

that

repairs double-strand breaks

in cells. The mechanism of

action

of the

RAG

proteins

is related to the action of site-specific

recombination catalyzed by resolvases.

Considerable diversity

generated

join-

ing different

D, and J segments to a C seg-

ment; however,

additional variations are

introduced

the

form of changes at the

junc-

tions between segments

during the recombina-

tion

process.

Changes are also induced

immunoglobulin

genes

by somatic mutation,

which requires the

actions of cytidine

deaminase

and uracil

glycosylase.

Mutations induced

cytidine deaminase

probably

lead

removal

of uracil by uracil

glycosylase,

followed

by the

induction of mutations at the sites where bases

are mlsslng.

Allelic exclusion ensures that a

given

lym-

phocyte

synthesizes

only a single Ig or TCR. A

productive

rearrangement inhibits the occur-

rence

further rearrangements. The use

the

V region

fixed by

the first

productive

rearrangement, but B cells switch

use of Cs

genes

from the initial

chain to one of the H

chains coded

farther downstream. This

process

involves a different type of recombination in

which

the

sequences

between the

VDJ

region

and the

new

gene

are deleted. More than

one switch occurs in Cs

gene

usage. Class

switching requires the same cytidine

deami-

nase

that is required

for somatic

mutation,

but

its role is not knonm.

an earlier

stage of Ig

pro-

duction, switches

occur from

synthesis

of a

membrane-bound

version

the

protein

to a

secreted version. These

switches

are accom-

plished

by alternative

splicing

of the transcript.

Innate

immunity is

a response

triggered by

receptors whose

specificity is

predefined

for

cer-

tain common motifs found

bacteria and other

infective

agents. The receptor

that

triggers the

pathway

is typically

a member

of the Toll-like

class, and the

pathway

resembles

the

pathway

triggered

by Toll receptors

during

embryonic

development. The

pathway

culminates in acti-

vation of transcription factors

that

cause

genes

to be expressed whose

products

inactivate

the

infective agent,

typically by

permeabilizing

its

membrane.

References

Immunogtobutin

Genes Are Assembled

from Their Parts in

Lymphocytes

Reviews

AIt, F.

W.,

Blackwell,

T. I(., and

Yancopoulos,

(1987).

Development

of the

primary

antibody

repertoire. Science 2)8, lO7

9-1087 .

Blackwell, T. I(. and Alr,

F. W.

(1989).

Mechanism

and developmental

program

of immunoglob-

ulin

gene

rearrangement

in mammals. Annu.

Rev. Genet. 23, 605-636.

Hood, L., I(ronenberg, M.,

and Hunkapiller, T.

(1985).

cell antigen receptors

and the

immunoglobulin

supergene family.

Cell 40,

225-229.

Tonegawa, S.

(1983).

Somatic

generation

of anti-

body diversity. Nature

302, 575-581.

Yancopoulos, G. D. andAlr,

F. W

(1986).

Regula-

tion

of the assembly and expression

of vari-

able-region

genes.

Annu. Rev.

Immunol. 4,

)39-368.

Rese

rc h

Hozumi, N. andTonegawa,

(1976).

Evidence for

somatic

rearrangement

immunoglobulin

genes

coding for variable

and constant

regions. Proc. Natl Acad

Sci. USA73,

1628-3632.

Light

Chains Are Assembled

by a Singte

Recombination

Max, E. E.,

Seidman, J. G., and Leder, P.

(L979).

Sequences oI five

potential

recombination

sites encoded close

to an immunoslobulin r

Resea rc h

constant region

gene.

Proc. Natl. Acad. Sci USA

76,3450-)454.

Immune Recombination Uses

Two Types

of Consensus Sequence

R esea

Lewis,

S., Gifford,

A., and Baltimore,

(1985).

DNA

elements are asymmetrically

joined

dur-

ing the site-specific

recombination of kappa

immunoglobulin

genes.

Science

228,

677-685.

Attetic Exclusion

Is Triggered

Productive Rearrangement

Review

Storb, U.

(1987\.

Transgenic mice with

immunoglobulin

genes.

Annu

Rev. Immunol. 5,

t5t-t7 4.

The

RAG

Proteins Catatyze

Breakage

and Reunion

Reviews

Gellert, M.

(1992).

Molecular

analysis of VDJ

recombination

Annu. Rev. Genet.26,

425-446.

J eggo, P. A.

(

I 998

DNA breakag

e and

repair. Adv.

Genet )8,185-218.

Schatz,

G., Oettinger,

A., and Schlissel, M. S.

11992).

VDJ

recombination:

molecular biology

and

regulation. Annu. Rev.

Immunol. lO,

)59-)83

Resea rc h

Agrawal,

A.,

Eastman,

M., and Schatz,

D. G.

(

1998). Transposition

mediated by

RAGI and

RAG2 and its implications

for the evolution

the

immune system. Nature

)94,

7 44-7 5I .

Hiom, K., Melek, M., and Gellert,

(I998).

DNA

transposition

by the

RAGI and RAG2

pro-

teins: a

possible

source of oncogenic

transloca-

tions. Cell 94,

463-470.

Ma, Y., Pannicke, U., Schwarz,

I(., and Lieber, M.

\2002).

Hairpin opening

and overhang

pro-

cessing by an Artemis/DNA-dependent

protein

kinase

complex

nonhomologous

end

join-

ing and

V(D)J recombination.

Cell

108,

78t-794.

Melek, M. and

Gellert,

(2000).

RAGI/2-mediated

resolution

of transposition

intermediates:

two

pathways

and

possible consequences

. Cell l0l,

625-6)).

Qiu,

X., I(ale, S. B.,

Yarnell Schultz,

H., and

Roth, D. B.

(200I).

Separation-of-function

mutants

reveal critical

roles for

RAG2 in both

the cleavage and

joining

steps

of V(D)J

recom-

bination.

Mol.

Cell

77-87 .

Roth, D. B.,

Menetski, J.

P.,

Nakajima,

P. B.,

Bosma, M. J., and

Gellert,

(1992).

V D J

recombination:

broken

DNA molecules

with

covalently

sealed

(hairpin) coding ends

SCID

mouse thymocytes.

Cell

70, 983-991.

References

60s

Schatz,

G. and Baltimore,

(1988).

Stable

expression of

immunoglobulin

gene

V(D)J

recombinase

activity by

gene

transfer

into

lT3

fibroblasts.

Cell 5), I07-I15.

Schatz, D. G.,

Oettinger,

M. A., and Baltimore, D.

(1989).

The V(D)J recombination

activating

gene,

RAG- I .

Cell 59,

I03

5-l 048.

Tsai,

L., Drejer, A. H.,

and

Drejer, A. H.

(2002).

Evidence

of a critical architectural

function for

the RAG

proteins

in end

processing, protec-

tion, and

joining

V(D)J

recombination.

Genes Dev. 16, 19)4-1949.

Yarnell Schultz, H., Landree, M. A.,

Qiu,

X.,

I(ale, S. B., and Roth, D. B.

(2001).

Joining-

deficient RAGI mutants block V(D)J recombi-

nation in vitro

and

hairpin

opening in

vitro.

Mol

Cell

7,65-75.

Switching 0ccurs by a Novel

Recombi nation Reaction

Honjo, T, I(inoshita,

I(., and Muramatsu, M.

(2002)

. Molecular mechanism of class switch

recombination: linkage with

somatic

hyper-

mutation. Annu Rev. Immunol.20, 165-196.

Li,

2., Woo, C. J., Iglesias-Ussel, M. D., Ronai, D.,

and Scharff, M. D.

(2004).

The

generation

antibody

diversity through somatic hypermu-

tation and class switch recombination.

Genes

Dev. ),8, l-ll.

Resea rc h

Bransteitter, R

Pham, P., Scharff, M. D., and

Goodman, M F.

(2003).

Activation-induced

cytidine

deaminase deaminates deoxycytidine

single-stranded DNA but requires

the

action of RNase. Proc Natl Acad.

Sci. US,4 100.

4to2-4107.

Gu,

H.,

Zot,Y. R., and Rajewsky, K.

(I993).

Inde-

pendent

control of immunoglobulin

switch

recombination

at individual

switch regions

evidenced

through Cre-loxP-mediated

gene

targeting.

Cell

7), I 155-l

164.

Iwasato, T.,

Shimizu, A., Honjo, T.,

and

Yamagishi,

(I990).

Circular DNA is

excised by

immunoglobulin

class switch recombination.

Cell 62, 14)-149.

I(inoshita,

I(., Tashiro,

J., Tomita, S., Lee,

C. G.,

and Honjo, T.

(1998).

Target

specificity of

immunoglobulin

class

switch recombination is

not

determined by nucleotide

sequences of

S regions. Immunity

9, 849-858.

Manis, J. P.,

Gu,

Y.,

Lansford, R.,

Sonoda, E., Fer-

rini,

R., Davidson,

L., Rajewsky, I(.,

and Alt,

F. W.

(1998).

I(u70 is required

for late B cell

development

and immunoglobulin

heavy

chain

class switching.

J. Exp. Med. 187,

2081-2089.

Matsuoka,

M., Yoshida,

I(., Maeda, T.,

Usuda, S.,

and

Sakano, H.

(1990).

Switch circular DNA

formed in

cytokine-treated mouse

spleno-

cytes: evidence

for intramolecular

DNA dele-

CHAPTER 23 Immune

Diversitv

tion in immunoglobuiin class switching. Cel/

62, t35-t42.

Muramatsu, M., I(noshita, I(., Fagarasan,

S.,

Yamada,

S., Shinkai,

Y., and Honjo, T.

(2000).

Class switch recombination and hypermuta-

tion require activation-induced cytidine

deaminase

(AID),

potential

RNA editing

enzyme. Cell lO2, 55j-56).

Pham, P., Bransteitter, R., Petruska,

J., and Good-

man, M. F.

(2003).

Processive

AID-catalysed

cytosine deamination on single-standed DNA

simulates somatic hypermutation.

Nature

424,

I 03-l 07.

Revy, P., Muto, T., Levy, Y., Geissmann, F., Plebani,

A., Sanal,

O.,

Catalan,

N.,

Forveille, M.,

Dufourcq-Labelouse, R.,

Gennery, A., Tezcan,

I., Ersoy, F., I(ayserili, H.,Ugazio, A.

G.,

Brousse,

N.,

Muramatsu, M.,

Notarangelo,

L. D., I(noshita, K.,

and

Honjo,

(2000).

Activation-induced

cytidine deaminase

(AID)

deficiency causes the autosomal recessive

form

of the Hyper-IgM syndrome

(HIGM2).

Cell lO2, 565-575.

Rolink, A., Melchers, F., and Andersson,

(19961

The

SCID but

not

the

RAG-2

gene product

required for

mu-S epsilon heavy

chain class

switching.

Immunity 5,

)19-)30.

von Schwedler, U., Jack, H. M., and

Wabl,

(1990).

Circular DNA is a

product

of the

immunoglobulin

class switch rearrangement.

Nature 345,452-456.

Xu, L., Gorham, B., Li, S. C., Bottaro, A., Alt,

F. W.,

and

Rothman, P.

(19931.

Replacement

germ-line

epsilon

promoter

gene

targeting

alters control of immunoglobulin heavy

chain

class switching. Proc. Natl. Acad

Sci. USA 90,

3705-3709.

Somatic Mutation

Generates

Additional

Diversity in Mouse

and

Human

Being

Reviews

French,

D. L., Laskov R., and Scharff,

M. D.

(

I 989). The role

of somatic hypermutation

the

generation

o{ antibody diversity.

Science

244, tt52-tt57.

I(ocks, C. and Rajewsky, K.

(1989).

Stable

expres-

sion and somatic hypermutation

of antibody

regions in

B-cell developmental

pathways.

Annu. Rev. Immunol.T, 5)7-559.

Resea

rch

I(m, S., Davis, M.,

Sinn,

E.,

Patten, P., and Hood,

(

l98l

)

. Antibody diversity:

somatic hypermu-

tation of rearranged

genes.

Cell

22,

573-581.

Somatic Mutation Is Induced

by Cytidine

Deaminase

and UraciI Glycosytase

Reviews

Honjo,

T., Ifinoshita, I(., and Muramatsu,

(2002\

. Molecular mechanism

class switch

Reviews

606

recombination:

Iinkage

with

somatic hyper-

mutation.

Annu. Rev.

Immunol.20,

165-196.

I(inoshita,

I(. and Honjo,

(200I).

Linking

class-

switch recombination

with somatic

hypermu-

tation. Nal. Rev. Mol.

Cell Biol 2,

49)-50).

Li,2., Woo,

C J., Iglesias-Ussel,

D., Ronai, D.,

and

Scharff, M. D.

(2004).

The

generation

antibody diversity

through

somatic hypermu-

tation and

class switch recombination.

Genes

Dev.18,

l-ll.

Resea rc h

Noia, J. and Neuberger,

(2002).

Altering

the

pathway

of immunoglobulin

hypermutation

inhibiting

uracil-DNA glycosylase.

Nature

4t9,43-48.

Muramatsu,

M., I(noshita,

I(., Fagarasan,

S.,

Yamada, S.,

Shinkai, Y., and

Honjo, T.

(2000).

Class switch recombination

and hypermuta-

tion require activation-induced

cytidine

deaminase

(AID),

potential

RNA

editing

enzyme.

Cell

102,

553-563.

Peters, A.

and Storb,

(19961

Somaric hypermu-

tation of immunoglobulin genes

is linked

transcription initiation.

Immunity

4, 57-65.

Revy,

P., Muto, T., Levy,

Y., Geissmann,

F., Plebani,

A., Sanal,

O., Catalan,

N.,

Forveille,

M.,

Dufourcq-Labelouse,

R.,

Gennery, A., Tezcan,

I., Ersoy,

F., I(ayserili,

H., Ugazio,

A. G.,

Brousse,

N.,

Muramatsu,

M., Notarangelo,

L. D., ICnoshita,

I(.,

and Honjo, T.

(2000).

Activation-induced

cytidine deaminase

(AID)

deficiency causes

the autosomal recessive

form

of the Hyper-IgM

syndrome

(HIGM2).

Cell 102, 565-575.

Avian

Immunoglobulins

Are Assembled

from Pseudogenes

Reynaud, C. A., Anquez,

V.,

Grimal, H., and Weill,

J. C.

(1987).

A hyperconversion

mechanism

generates

the chicken

light chain

preimmune

repertoire.

Cell

48,

37 9-388.

Sale, J. E.,

Calandrini, D. M., Takata,

M., Takeda,

S.,

and

Neuberger, M.

(2001).

Ablation of

XRCC2/3

transforms immunoglobulin

gene

conversion into somatic hypermutation.

N6ture 412.921-926.

B Ce[[ Memory A[lows

a Rapid

Secondary

Response

Review

Rajewsky, K.

(

1996)

. Clonal selection

and learning

in the antibody system.

Nature 381,751-758.

Ce[[ Receptors Are Retated

Immunogtobutins

Reviews

Davis, M. M.

(1990).

T-cell

receptor

gene

diversity

and selection. Annu Rey. Biochem.

59,

475-496.

Resea rc h

I(ronenberg, M.,

Siu, G.,

Hood, L. E., and Shastri,

(1986).

The molecular

genetics

of the T-cell

antigen receptor and

T-cell

antigen

recogni-

tion. Annu Rev. Immunol. 4, 529-591.

Marrack, P

and

I(appler, J.

(1987lt.

The

T-cell

receptor.

Science

238, lO7)-1079.

Raulet, D. H.

(1989).

The structure, function, and

molecular

genetics

of the

gamma/delta

T-cell

receptor. Annu. Rev.

Immunol. T, 175-207.

The T Cett Receptor

Functions

Conjunction

with the

MHC

Review

Goldrath, A. W and Bevan,

(1999).

Selecting

and maintaining a diverse

cell

repertoire.

Nature 402,255-262.

The Major

Histocompatibitity

Locus

Codes for Many Genes

ofthe Immune

System

Reviews

Flavell, R. A., AIIen, H., Burkly,

L. C., Sherman,

D. H.,

Waneck,

G. L., and Widera,

(1986).

Molecular

biology

of the

H-2 histocompatibil-

ity

complex. Science

23j,

437-443.

I(umnovics, A., Takada, T., and

Lindahl, I(. F.

(2003).

Genomic

organization of the

mam-

malian MHC. Annu. Rev.

Immunol.2l,

629-657.

Steinmetz,

and

Hood, L.

(1983).

Genes of the

MHC complex

in mouse and

man.

Science

222,

727-7)2.

Resea

rch

I(aufman,

J. et al.

(19991.

The chicken

B locus is a

minimal essential

maj or histocompatibility

complex. Nature

401, 923-925.

Innate Immunitv Utilizes

Conserved

Signating

Pathways

Reviews

Aderem, A. and Ulevitch,

R. J.

(2000).

Toll-like

receptors in the

induction of the

innate

immune response. Nature

406,

82-7 87.

Dangl,

L. and

Jones,

(2001). Plant

pathogens

and

integrated

defence

responses

to infection. Nature

4ll,826-83).

Hoffmann, J. A., Kafatos,

F. C., Janeway, C.

4.,

and Ezekowitz,

R. A.

(19991

. Phylogenetic

perspectives

innate immunity.

Science 284,

l3l3-1318.

Janeway, C. A. and

Medzhitov

(2002).

Innate

immune recognition.

Annu. Rev.

Immunol.20,

t97-2t6.

Resea

rc h

Asai, T., Tena, G.,

Plotnikova, J., Willmann,

M. R.,

Chiu. W. L, Gomez-Gomez,L.,

Boller,

T.,

Ausubel, F. M.,

and Sheen, J.

(2002).

MAP

kinase

signalling

cascade

in Arabidopsis

innate

immunity.

Nature 415,

97 7

-98).

References 607

Hoffmann,

J. A.

(2003).

The immune response

Drosophila.

Nature

426,

JJ-)8.

Ip, Y. T., Reach, M., Engstrom, Y., Kadalayil, L.,

Cai,

H.,

Gonzdlez-Crespo, S.,

Tatei, K.,

and

Levine, M.

(1993).

Dif, a dorsal-related

gene

that mediates an immune response in

Drosophila.

Cell

7 5, 7 53-7 63.

Lemaitre, B.,

Nicolas,

E., Michaut, L., Reichhart,

J. M., and Hoffmann,

(1996).

The

dorsoventral regulatory

gene

cassette spAtzle/

Toll/cactus

controls the

potent

antifungal

response in Drosophila adults.

Cell

86,

973-983.

Medzhitov R., Preston-Hurlburt, P.,

and Janeway,

(1997).

A human homologue

of the

Drosophila Toll

protein

signals activation of

adaptive immunity.

Nature )88, 394-)97.

Poltorak, A., He,

X.,

Smirnova,

I., Liu, M. Y., Huf-

fel, C. V.,

Du, X., Birdwell, D., Alejos, E., Silva,

M., Galanos, C.,

Freudenberg, M., Ricciardi-

Castagnoli,

P., Layton, B., and Beutler, B.

(1998).

Defective LPS signaling in C3H/HeJ

and C57BL/

IOScCr mice: mutations in Tlr4

gelre.

Science

282, 2085-2088.

Rutschmann, S., Jung,

A. C., Hetru,

C.,

Reichhart,

M.. Hoffmann.

A.. and Ferrandon. D.

(2000).

The Rel

protein

DIF mediates

the anti-

fungal but not the antibacterial

host

defense

in Drosophila. Immunity 12, 569-580.

Williams, M. J.,

Rodriguez. A., Kimbrell,

A.,

and

Eldon, E. D.

(L997\.

The l8-wheeler

mutation

reveals complex antibacterial

gene

regulation

in Drosophila host defense. EMBO J. 16,

6t20-6130.

608

CHAPTER 23

Immune Diversitv

Promoters

and

Enhancers

CHAPTER

OUTLINE

Introduction

Eukaryotic

RNA Polymerases

Consist

Many

Subunits

RNA

polymerase

synthesizes rRNA in

the nucteolus.

RNA

potymerase

II synthesizes

mRNA in the nucleoplasm.

RNA

potymerase

III

synthesizes smatl RNAs in

the

nucteoo[asm.

A[[

eukaryotic RNA

potymerases

have

-12

subunits and are

aggregates

>500

kD.

Some subunits are common

to a[[ three RNA

polymerases.

The

largest subunit in

RNA

potymerase

has a CTD

(carboxy-terminaI

domain)

consisting of multiple repeats

of a heptamer.

Promoter Etements

Are Defined

by Mutations

and

Footprinting

Promoters

are defined by their

abil.ity to cause transcription

of an attached

sequence in an

appropriate test system in

vitro or in vivo.

RNA Polymerase I Has

a Bipartite Promoter

The

RNA

polymerase

promoter

consists

of a core

promoter

and an upstream

control etement

(UPE).

The factor

UBFl wraps DNA

around a

protein

structure to

bring the core and

UPE

into

proximity.

SL1 includes

the

factor

TBP

that

is involved in

initiation by

a[[ three RNA

potymerases.

RNA

potymerase

binds to the

UBFl-SL1 comptex at the core

promoter.

RNA

Potymerase

III

Uses Both Downstream

and Upstream

Promoters

RNA

potymerase

III has

two types of

promoters.

InternaI

promoters

have

short consensus

sequences located

within the transcription

unit and cause initiation

to occur

a fixed djstance

upstream.

Upstream

promoters

contajn three short consensus

sequences upstream

of the startpoint that are bound

transcription factors.

TFInB Is

the Commitment Factor for Po[

III Promoters

TFruA and TFxIC

bind to the

consensus sequences and

enabte TFgB

to bind at the startpoint.

TFuB

has TBP as one

subunit and enabtes RNA

potymerase

to bind.

The Startpoint

for

RNA

Polymerase II

RNA

potymerase

II requires

general

transcription

factors

(catted

TF11X) to initjate transcription.

RNA

potymerase

promoters

have

a short

conserved

sequence

Py2CAPy5

(the

initiator InR) at the startpoint.

The

TATA

box

a common

component of

RNA

potymerase

oromoters and consists

of an A-T-rich octamer

located

-25

bp upstream ofthe startpoint.

The DPE is a common component

of RNA

potymerase

pro-

moters that do

not

contain

a TATA box.

core

promoter

for RNA

potymerase

II inctudes the

InR

and

either a

TATA box or a DPE.

TBP Is

a Universal

Factor

TBP is a component of

the

positioning

factor that is

required for each type

of RNA

potymerase

to bind its

promorer.

The factor

for

RNA

potymerase

is TF11D, which consists

TBP and 11

TAFs, with a tota[ mass

-800

kD.

TBP Binds

DNA in

an Unusual

Way

TBP binds to the

TATA box

the

minor

groove

DNA.

It forms a saddle around

the

DNA

and

bends

-80'.

Some

of the

TAFs resemble histones and

may form a struc-

ture resembting a

histone octamer.

The BasaI Apparatus

Assembtes at

the Promoter

Binding of

TFnD to the

TATA box is the

first step in

initiation.

0ther transcription

factors bind to

the comptex

defined

order, extending

the length ofthe

protected

region on DNA.

When RNA

potymerase

II binds to

the comptex,

'it

initiates

transcription.

Initiation

Is Fotlowed by

Promoter Ctearance

TFuE and TFnH are

required to

mett DNA to a[[ow

potymerase

movemenr.

Phosphorytation

of the CTD

may be required

for etongation

to begin.

Further

phosphorylation

of the

CTD

is required at some

pro-

moters to end abort'ive

initiation.

The CTD may coordinate

processing

of RNA

with

transcriotion.

Continued on

poge

609

?Ed

?rlI/3|

i21tg{

A Connection

between

Transcription

and Reoair

Transcribed

genes

are

preferentialty

repaired when DNA damage occurs.

TFnH

provides

the Link to a

complex

reparr

enzymes.

Mutations in

the

XPD

component of

TFnH

cause three types of

human

diseases

Short

Sequence

Etements Bind Activators

Short conserved seouence elements are

dispersed

the

region

preceding

the

startooi

nt.

The upstream etements increase

the

fre-

quency

of initiation.

The factors

that bind to them to stimulate

transcriotion

are catled activators.

Promoter

Construction Is Ftexibte

but

Context Can

Be Important

No individuaI upstream

e[ement

essen-

tial for

promoter

function,

atthough one or

more etements must be

present

for

effi-

cient

initiation.

Some e[ements are recoqnized

muttipte

factors,

and the factor that is

used at any

particular promoter

may

be determined

by the context of

the other

factors

that

are

bound.

En hancers

Contain

BidirectionaI

Elements

That Assist Initiation

enhancer activates the nearest

pro-

moter

it,

and can be any

distance

either uostream or downstream of the

pr0m0Ier.

UAS

(upstream

activator

sequence)

yeast

behaves

[ike an enhancer but works

onty upstream of the

promoter.

Similar

sequence etements are found in

enhancers

and oromoters.

Enhancers

form comolexes

of activators

that interact

directty or indirectty with

the

promoter.

Enhancers Contain the Same Elements

That Are Found at Promoters

Enhancers are

made

ofthe same short

sequence etements that are

found in

Dr0mote15.

The

density of sequence components is

greater

the enhancer than in the

promoter.

Enhancers

Work by

Increasing

the

Concentration of Activators Near the

Promoter

Enhancers usualty work onty in

crs config-

uration with a target

promoter.

Enhancers

can be

made

to work in

trans

configuration by tinking the DNA that

con-

tains the target

promoter

to the DNA that

contains the enhancer

via

protein

bridge

or by catenating the two

motecules.

The

principle

that an enhancer works in

any situation

which it is constrained

be in the same

proximity

as the

promoter.

Gene Expression

Associated with

Demethytation

at the 5' end of the

gene

necessary for

transcription.

CpG

Is[ands Are

Regu[atory Targets

CpG

islands

surround the

promoters

constitutive[y expressed

genes

where they

are unmethylated.

CpG

istands

also are

found

at the

promot-

ers of some tissue-regulated

genes.

There

are

-29,000

CpG islands in

the

numan

genome.

Methytation of a CpG island

prevents

acti-

vation of a

promoter

wjthjn it.

Repression is caused by

proteins

that bind

to methytated CpG doubLets.

Summarv

Introduction

Initiation

of transcription requires

the enzyme

RNA

polymerase

and transcription factors.

Any

protein

that is needed

for the initiation

of tran-

scription,

but which is not itself

part

of RNA

polymerase,

defined as a transcription

factor.

Many

transcription factors

act by recognizing

cis-acting

sites on DNA. Binding

to DNA, how-

ever, is not

the only means

of action for

a tran-

scription

factor. A factor

may recognize

another

factor,

or may recognize

RNA

polymerase,

may

incorporated

into

an initiation

complex

only in the

presence

of several

other

proteins.

The ultimate

test for membership

of the tran-

scription

apparatus

is functional:

protein

must

needed for

transcription to occur

at a spe-

cific

promoter

or set of

promoters.

significant difference between

the tran-

scription of eukaryotic and

prokaryotic

mRNAs

that

initiation

at a eukaryotic

promoter

involves alarge number

factors

that

bind to

a variety

of cli-acting elements. The

promoter

is defined as

the

region

containing all

these bind-

ing

sites, that is, all the binding

sites that

can

support transcription at the normal

efficiency

and

with the

proper

control. Thus

the major

feature

defining the

promoter

for

a eukaryotic

mRNA is the location

of binding sites for

tran-

scription factors. RNA

polymerase

itself

binds

610

CHAPTER

Promoters

and Enhancers