kelompok 8 genome organization and gene expression

8/17/2019 Kelompok 8 Genome Organization and Gene Expression

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Genom Organizationand Gene Expression

KELOMPOK 8Aisirotul Maisah 4411413006

Firman Heru K 4411413011

Alfiani Umi Farkha 441141301

Pu!i Hanani 441141303"iti Alfath 441141303


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• The nuclear genom contains most of the generequired for the plant’s physiological functions.

• The rst plant genome to be fully sequenced,in 2000 was that of a small dicotyledonousangiosperm called thale cress or Arabidopsisthaliana

•

The genom of A. thaliana is made up of onlyabout 1! million base pairs "1! #bp$ whichare distributed o%er %e chromosome

• &ithin its nuclear genome, A. thaliana holds

some 2!.'00 protein(coding genes and almostanother 000 genes that are eitherpseudogenes "nonfunctional genes$ or parts oftransposon.


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The nuclear genome is pac)aged

into chromatin

• The nuclear genom consists of *+A moleculesthat are wrapped around histone proteins toform beadli)e structure called nucleosomes.

•

*+A and histone, together with other proteinsthat bind to the *+A, are reered to aschromatin.

• Two types of chromatin can be distinguished -

euchromatin and heterochromatin• eterochromatin is usually more tightly

pac)aged and thus appears dar)er than the lesscondensed euchromatin


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• #ost genes that are acti%ely transcribed in a

plant are located within the euchromaticregions of a chromosome, while many geneslocated in heterochromatic regions are nottranscribed( these genes are inacti%e or silent

• /ompared with euchromatin, heterochromatinis relati%ely gene poor. eterochromaticregions include the centromeres, se%eral so(called )nobs, and the regions immmadiatelyadacent to the telomers, or chromosomeends, )nown as the subtelomeric

• eterochromatic structure often consist ofhighly repetiti%e *+A sequence, or tandemrepeats - bloc)s of nucleotide motifs of about10 to 10 bp that are repeatd o%er and o%er


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• A second class of repeats is the

dispered repeats. ne types ofdispersed repeats is )nown as simplesequence repeats " 334$ ormicrosatellites

• These repeats consist of sequencemotifs as short as two nucleotidesthat are repeated hundreds or e%en

thousands of times.• Another dominant group of dispersed

repeat found in heterochromatin is the

5umping genes6 or transposons


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/entromeres, telomeres, and nucleolarorgani7ers contain repetiti%e sequence

• The most prominent structural landmar) onchromosomes are centromeres, telomeres, andnucleolar organi7ers.

• /entomers are constrictions of the chromosomeswhere sister chromatids adhere to each other andwhere spindle bers attach during cell di%ision

• The attachment of bers to the centromeres ismediated by the )inetochore, a protein comple8

surrounding the centromere• /entromere consist of highly repetiti%e *+A

regions and inacti%e transposable elements


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• Telomeres are sequence located at the ends of eachchromosome. Telomeres act as caps on the chromosome endsand pre%ents loss of *+A during *+A replication

• The *+A molecules that ma)e up ribosomes "r4+A$ aretranscribed from nucleolar organizer (NO) regions. 9ecauseribosomes are needed for translation, it is not surprising that+os contain hundreds of repeated copies of each r4+A gene

• *epending on the plants species, one or se%eral nucleolarorgani7ers are presents within the genome

• *ue to their repetiti%e nature and their high :/ content, +oscan be seen through a light microscope and thus can ser%e as

chromosome(specic mar)ers• The r*+A of the nucleolar organi7er, along with proteins that

transcripts for assembly into ribosomes, forms a prominentnuclear structure called the nucleolus


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Transposons are mobile sequencewithin the genome

• ne dominant type of repetiti%e *+A within theheterochromatic regions of the genome is the transposon.

• Transposon or transposable elements are alson )nown as5umping genes6 because some of them ha%e the ability toinsert a copy of themsel%es in a new location within genome

• There are two large classes of transposons - theretroelements or retrotransposon and the *+A transposons

• These two classes are distinguished by their mode ofreplication and insertion into a new location

•

4etransposons ma)e an 4+A copy of themsel%es, which isthen reser%e(transcribed into *+A before it is insertedelsewhere in the genom


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• *+A transposons, by contrast, mo%e from one position toanother using a cut(and(paste mechanism cataly7ed by anen7yme that is encoded within the transposon sequence

• This en7ymes, transposase, splices out the transposon and

insertsit elsewhere in the genome, in most cases )eepingthe total transposon copy number the same

• Transposition into a gene can result in mutations. ;f atransposon lands within a coding region, the gene may beinacti%ated. ;nsertion od a transposon close to a gene can

also alter that gene’s e8pression pattern


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•


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• 9oth types of polyploidy can result fromincomplete meiosis during gametogenesis.*uring meiosis, the chromosomes of a diploidgerm cell undergo *+A replication followed by

two rounds of di%ision

• ;f chromosome duplication is not followed by cellde%ision during meiosis, diploid gametes result

• &ithin a species or in a self(fertili7ing indi%idual,if a diploid egg is fertili7ed by diploid sperm, theresulting 7ygote contains four copies of eachchromosome and is said to be autotetraploid


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Allopolyploids usually form in one of

two ways -

1.A haploid sperm from one speciesand a haploid egg from anotherspecies may form a diploid

interspecies hybrid

2.*iploid gametes from two dierentspecies may oin to form a tetraploid

7ygote.


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• *iploid interspecies hybrids occur naturally, but they arefrequently sterile because their chromosome cannot pair

properly during prophase 1 of meiosis

• The lac) of fertility in interspecies hybrids is in star)

contast to the phenomenon )nown as hybrid %igor orheterosis - the increase %igor often obser%ed in the

ospring of crosses between two inbred %arieties of thesame plants species

• eterosis can contributed to larger plants, greater

biomass, and higher yields in agricultural crops•


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3ome of the genetic changes that ha%e beenobser%ed in newly formed allopolyploids compared

with their parent species are the following -

• 4estructing of the chromosome,including loss of *+A sequence

• /hanges in epigenetic modications

• /hanges in gene transcriptionalacti%ity

• Acti%ation of pre%iously dormanttransposable elements through lossof gene silencing


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•


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Plant #$to%lasmi& 'enomes (

Mito&hon)ria an) #hloro%lasts

• *n a))ition to the nu&lear +enome, %lant &ells &ontain

t-o a))itional +enome, -hi&h the$ share -ith animal

&ells, an) the &hloro%last +enome.

• #$to%lasmi& +enome are %ro/a/l$ the eolutionar$remnants the +enomes of /a&terial &ells that -ere

en+ulfe) /$ another &ell.

• "he en)os$m/ioti& theor$, %ostulates that the ori+inal

mito&hon)rion -as an o$+en2usin+ /a&terium that

-as a/sor/e) /$ another %rokar$oti& or+anism.


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• "-o main lines of ei)en&e are often &ite) in su%%ort

of the en)o&$m/ioti& theor$ (

1. oth mito&hon)ria an) &hloro%lasts are en&lose) /$

an outer an) an inner mem/rane, an) the inner

mem/rane is &ontinuous -ith a))itional mem/rane2

/oun) &om%artments insi)e the or+anelle.

. oth or+anella +enomes sho- seuen&e similarit$ to

%ro&ar$oti& +enomes.

•. "he or+anelar +enomes, like those of %ro&ar$otes are

not en&lose) in a nu&lear enelo%e an) are &alle)nucleoids.


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• Or+anellar +enomes &onsist mostl$ of linear

&hromosomes.

– For man$ $ears or+anelar &hromosomes ha) /een thou+htto &ontain a +enome2si5e) 7A mole&ule in &ir&ular form,

similar to the &ir&ular %lasmi)s of /a&teria.

– Most of the 7A in /oth %lant mito&hon)ria an)

&hloro%lasts is foun) in linear mole&ules that m$ &ontainmore than one &o%$ of the +enome.

– Or+anelar +enomes are &om%le in stru&ture an) the$

usuall$ &onsist of multi%le &o%ies of the +enome on the

same 7A mole&ul


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• Or+anellar +eneti&s )o not o/e$ Men)elian la-s.

– "he +eneti&s of or+anellar +ene are +oerne) /$ t-o

%rin&i%les that )istin+uish them from Men)elian +eneti&s.1. oth mito&hon)ria an) %lasti) +enerall$ sho- uniparental

inheritance seual offs%rin+ ia %ollen an) e++s9 onl$

inherit or+anelles from one %arent9. Amon+ the

'$mnos%erms from %aternal %arent, for An+is%erms frommaternal %arent.

. oth &hloro%lasts an) mito&hon)ria &an segregate

vegetatively e+etatie &ell as o%%ose) to a +amete9 &an

+ie rise to another e+etatie &ell ia mitosis that is+eneti&all$ )ifferent.

–.Or+anellar +eneti&s )o not o/e$ Men)elian la-s, /ut usuall$

sho- uni%arental inheritan&e an) e+etatie se+ra+ation.


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"rans&ri%tional :e+ulation of 7u&lear 'ene

E%ression.

• "he %ath from +ene to %rotein is a multiste% %ro&ess

&atal$5e) /$ man$ en5$mes.

• Ea&h ste% is su/!e&t to re+ulation /$ the %lant to &ontrol

the amount of %rotein that is %ro)u&e) /$ ea&h +ene. – :e+ulation of the first ste%, trans&ri%tion, )etermines

-hen an) -hether an m:7A is ma)e.

– "his leel of re+ulation, -hi&h is referre) to as

transcriptional regulation, in&lu)es the &ontrol oftran&ri%tion initiation, maintenan&e, an) termination.


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– "he net leel in the re+ulation of +ene e%ression,

kno-n as posttranscriptional regulation, o&&urs after

trans&ri%tion in&lu)es &ontrols on m:7A sta/ilit$,translation effi&ien&$ an) )e+ra)ation.

– Finall$, protein stability %osttranslational re+ulation9

%la$s an im%ortant role in the oerall a&tiit$ of a +ene

or its %ro)u&t.


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• :7A %ol$merase ** /in)s to the %romoter re+ion of most

%rotein2&o)in+ +enes.

– 'ene trans&ri%tion is fa&ilitate) /$ an en5$me &alle) :7A %ol$merase, -hi&h /in)s to the 7A to the 7A to /e

trans&ri/e) an) makes an m:7A trans&ri%t &om%lementar$

to the 7A seuen&e.

–

"he re+ion of the +ene that /in)s :7A %ol$merase is&alle) the promotor.

– "he stru&ture of the eukar$oti& %romoter into t-o %art (

1. Core promoter or minimum promoter, &onsistin+ of the

minimum u%stream seuen&e reuire) for +enee%ression.

2. Regulatory sequence, -hi&h &ontrol the a&tiit$ of the

&ore %romoter.


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• *n a))ition to :7A %ol$merase an) the +eneral trans&ri%tion

fa&tors, most +enes, es%e&iall$ those that %la$ im%ortant roles

in )eelo%ment, reuire s%e&ifi& trans&ri%tion fa&tors alsooften &alle) +ene re+ulator$ %roteins9 for :7A %ol$merase to

/e&ome a&tie.

• "hese re+ulator$ %roteins /in) to the 7A an) /e&ome %art of

the trans&ri%tion initiation &om%le.


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E%i+eneti& mo)ifi&ations hel% )etermine +ene

a&tiit$

• "rans&ri%tion &an /e initiate) onl$ if the 7A is a&&essi/le to

the :7A %ol$merase an) other reuire) /in)in+ %rotein.

• "o make the 7A a&&essi/le, its %a&ka+in+ has to /e

;looseene)


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• E%i+eneti& mo)ifi&ations, su&h us meth$lation of 7A an)

meth$lation an) a&et$lation of histone %roteins, hel% the

)etermine +ene a&tiit$.


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Posttrans&ri%tional :e+ulation of 7u&lear 'ene

E%ression

• An or+anism often %ro)u&e)s m:7A in res%onse to a s%e&ifi&

situation. *n or)er to remain useful as a s%e&ifi& res%one to a

s%e&ifi& situation, in)ii)ual m:7As must hae a finite

lifetime.

• :7A sta/ilit$ &an /e influen&e) /$ cis2elements.

– One me&hanism /$ -hi&h m:7A sta/ilit$ is re+ulate)

)e%ents on the %resen&e of &ertain seuen&e -ithin the

m:7A mole&ule it sel, &alle) &is2elements.

– "hese &is2elements &an /e /oun) /$ :7A2/in)in+ %roteins, -hi&h ma$ either sta/ili5e the m:7A or %romote

its )e+ra)ation /$ nu&lease.


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• 7on&o)in+ :7As re+ulate m:7A a&tiit$ ia the :7A

interferen&e :7Ai9 %ath-a$.

–

Another me&hanism for re+ulatin+ m:7A sta/ilit$ is theRNA Interference (RNAi path!ay.

– "he :7Ai %ath-a$ is a set of &ellular rea&tions to the

%resen&e of )ou/le2stran)e) :7A )s:7A9 mole&ules.

– :e&all that m:7A is usuall$ a sin+le2stran)e) mole&ule

ss:7A9.

– *n %lant &ells, )s:7A usuall$ o&&ur as a result of one of

three t$%es of eents


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1. "he %resen&e of mi&ro:7As mi:7As9, -hi&h are inole)

innormal )eelo%mental %ro&esses.


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. "he %ro)u&tion of short interferin+ :7As si:7As9, -hi&h

silen&e &ertain +enes


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3. "he intro)u&tion of forei+n :7As, either /$ iral infe&tion or

ia transformation /$ forei+n +ene


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Posttranslational re+ulation )etermines the life

s%an of %roteins

• As -e hae seen, m:7A sta/ilit$ %la$s an im%ortant

role in the a/ilit$ of the +ene to %ro)u&e a fun&tional

%rotein. >e turn net to the sta/ilit$ of %roteins an the

me&hanisms that re+ulate a %rotein=s life s%an.• "he &$to%lasmi& %ath-a$s of %rotein turnoer

inoles the A"P2)e%en)ent formation of a &oalent

/on) /et-een the %rotein that is to /e )e+ra)e) an) a

small, ?62amino a&i) %ol$%e%ti)e &alle) u/iuitin.


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• U/iuitination is initiate) -hen the u/iuitin

a&tiatin+ en5$me E19 &atal$5es the A"P )e%en)ent

a)en$l$lation of the # terminus of u/iuitin. "hea)en$l$late) u/iuitin is then transferre) to a

&$steine resi)ue on a se&on) en5$me, the u/iuitin

&on!u+atin+ en5$me E9. Proteins )estine) for

)e+ra)ation are /oun) /$ a thir) t$%e of %rotein, a

u/iuitin li+ase E39


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"ools for @tu)$in+ 'ene Fun&tion

• *n)ii)uals that &ontain s%e&ifi& &han+es in

their 7A seuen&e are &alle) mutants. "he

anal$sis of mutants is an etremel$ %o-erful

tool that &an hel% s&ientists infer the fun&tionof a +ene or ma% its lo&ation on the

&hromosoms.


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Mutant anal$sis &an hel% to elu&i)ate +ene

fun&tion

• "he use of mutants for +ene i)entifi&ation

relies on the a/ilit$ to )istin+uish a mutant

from a normal in)ii)ual, so the &han+e in the

mutant=s nu&leoti)e seuen&e must result in analtere) %henot$%e.


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• "here are seeral -a$s to ma% a mutation to

its &hromosome an) ultimatel$ &lone theaffe&te) +ene, e%lain a metho) &alle) ma%

/ase) &lonin+, -hi&h uses &rosses /et-een a

mutant an) a -il) t$%e %alnt an) +eneti&anal$sis of the offs%rin+ to narro- )o-n the

lo&ation of the mutation to a short se+ment of

the &hromosome, -hi&h is then seuen&e).


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Mole&ular te&hniues &an measure the

a&tiit$ of +enes

• On&e a +ene of interest has /een i)entifie), s&ientists

are usuall$ intereste) in -here an) -hen the +ene is

e%resse).

• For eam%le, a +ene ma$ /e e%resse) onl$ inre%ro)u&tie tissues, or onl$ * e+etatie ones.

• All mi&roarra$ te&hniues use a soli) su%%ort, su&h as

a +lass sli)e, onto -hi&h 7A seuen&es are s%otte)

that are re%resentatie of sin+le +enes of a +ien

s%e&ies.


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:ene fusions can introduse reporter

genes

• A gene fusions is an articialconstruct that combines part of thegene of interest with another gene

that produces a readily detectableprotein

• A gene’s e8pression is regulated by

transcription factors that ne(tune itsacti%ity and allow it to be trancsribedonly where and when its needed.


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:enetic modication of crop plants

• ;n contrast to classical selecti%ebreeding, bioengineering allows thetransfer of specic gene ora gened

between spiceis that cannot becrossed succesfully


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• 9iotechnological tools circum%entthis problem by allowing insertion ofonly the desired genes into the

recipient plant, most often either byAgrobacterium(mediatedtransformation or by biolistics.

•


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There are three essesntial dierences between:#s and con%entionally bred %arieties of crops

• :ene transfer into :#s occurs in thelaboratory and does not require crossbreeding

• The donor genes of :#s can be deri%ed fromany organism, not ust those with which therecipient can be succesfully crossed

• :#s may carry gene constructs that are theproduct of splicing a %ariety of geneticcomponents together to produce genes withaltogether new functions "for e8ample, thepromoter(:=< fusion genes we describedearlier

T f i t t


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Transgenes can confer resistance toherbicides or plant pets

• Any gene articially tranferred into anorganism is referred to as atransgene

•


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• Another commonly used transgeneencodes an inseticidal to8in from thsoil bacterium Bacillus thuringiensis

"9t$

: ti ll di d i


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:enetically modied organisms are

contro%ersial

• The de%elopment of :#s has notbeen greeted with uni%ersalenthusiasm and support . ;n spite of

their enoumous humanitarianpotential, many indi%iduals, as wellas the go%ernment of some

countries, loo) on :#s withsuspicion and cocern.


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kelompok 8 genome organization and gene expression

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