Prokaryotic chromosome structure

PACKING OF DNA

1. PROKARYOTIC CHROMOSOME
STRUCTURE
Dr. Esther Shoba R
Assistant Professor
Kristu Jayanti College

5. Theterm“prokaryote”means“primitivenucleus”.Cellin
prokaryoteshavenonucleus.Theprokaryoticchromosomeis
dispersedwithinthecellandisnotenclosedbyaseparate
membrane.
MuchoftheinformationaboutthestructureofDNAhascome
fromstudiesofprokaryotes,becausetheyarelesscomplex
(geneticallyandbiochemically)thaneukaryotes.
Prokaryotesaremonoploid=theyhaveonlyonesetofgenes
(onecopyofthegenome).
Inmostvirusesandprokaryotes,thesinglesetofgenesis
storedinasinglechromosome(singlemoleculeeitherRNAor
DNA).
ThesmallestknownRNAviruseshaveonlythreegenes.
ThesmallestknownDNAviruseshaveonly9to11genes.

6. Thebacterialchromosomemustbetightlypackedtofitinto
thesmallvolumeofthebacterialcell.Thecontourlengthof
thecircularDNAmoleculepresentinthechromosomeofthe
bacteriumEscherichiacoliisabout1500µm.BecauseanE.
colicellhasadiameterofonly1to2µm,thelargeDNA
moleculemustexistinahighlycondensed(foldedorcoiled)
configuration.
CompactingtheDNAinvolvessupercoiling,orfurthertwisting
thetwistedchromosome.
Thechromosome'sfiftyorsoDNAdomainsareheldtogether
byascaffoldofRNAandprotein,andtheentirenucleoidis
attachedtothecellmembrane.
Thismembraneattachmentaidsinthesegregationofthe
chromosomes aftertheyreplicateinpreparationforcell
division.
Bacterialackthehistoneproteinsthatarefoundboundto
DNAandthatformanucleosomsofeukaryoticchromosomes.

7. DNAmoleculeinanE.colichromosomeisorganizedinto50–100
domainsorloops.
Replicationofthecircularchromosomebeginsatasinglepoint,
calledOriC,andproceedsinbothdirectionsaroundcircle,untilthe
tworeplicationforksmeetup.
Theresultsistwoidenticalloops.Replicationtakesapproximately
fortyminutes.
In1997FBlattnerandcolleaguespublishedthesequenceof
4,639,221basepairsoftheK-12laboratorystrain.E.coliis
estimatedtohave4,279genes.
ManysetsofgenesontheE.colichromosomeareorganizedinto
operons.
Anoperonisasetoffunctionallyrelatedgenesthatarecontrolledby
asinglepromoterandthatarealltranscribedatthesametime.
Itisalsoquitecommonforbacterialspeciestopossessextra
chromosomalgeneticelementscalledplasmids.Thesearesmall,
circularDNAmoleculeswhich,whenpresent,varyinumberfrom
onetoaboutthirtyidenticalcopiespercell.
Plasmidsincludethefertilityfactor,aswellasplasmidsthatcarry
drug-resistancegenes.

13. WHAT HELPS CONDENSATION AND ORGANISATION
•NUCLEOIDASSOCIATEDPROTEINS
•NAPsarehighlyabundantandconstituteasignificant
proportionoftheproteincomponentofnucleoid
•NAPsinduceandstabilizebendsinDNA,thusaidinDNA
condensationbyreducingthepersistencelength.NAPs
condenseDNAbybridging,wrapping,andbunchingthatcould
occurbetweennearbyDNAsegmentsordistantDNAsegments
ofthechromosome.

14. •AnothermechanismbywhichNAPsparticipatein
chromosomecompactionisbyconstrainingnegative
supercoilsinDNAthuscontributingtothetopological
organizationofthechromosome.
•Thereareatleast12NAPsidentifiedinE.coli,themost
extensivelystudiedofwhichareHU,IHF,H-NS,andFis.
TheirabundanceandDNAbindingpropertiesandeffecton
DNAcondensationandorganizationaresummarizedinthe
tablesbelow

18. HU
•Histone-likeproteinfromE.colistrainU93(HU)isan
evolutionarilyconservedproteininbacteria.HUexistsinE.
coliashomo-andheterodimersoftwosubunitsHUαandHUβ
sharing69%aminoacididentity.
•HUisanon-sequencespecificDNAbindingprotein.Itbinds
withlow-affinitytoanylinearDNA.However,itpreferentially
bindswithhigh-affinitytoastructurallydistortedDNA.
•ExamplesofdistortedDNAsubstratesincludecruciform
DNA,bulgedDNA,dsDNAcontainingasingle-stranded
breaksuchasnicks,gaps,orforks.

19. •Furthermore,HUspecificallybindsandstabilizesaprotein-
mediatedDNAloop.
•InthestructurallyspecificDNAbindingmode,HUrecognizesa
commonstructuralmotifdefinedbybendsorkinkscreatedby
distortion,whereasitbindstoalinearDNAbylockingthe
phosphatebackbone.
•Whilethehigh-affinitystructurally-specificbindingisrequired
forspecializedfunctionsofHUsuchassite-specific
recombination,DNArepair,DNAreplicationinitiation,and
generegulation,itappearsthatthelow-affinitygeneralbinding
isinvolvedinDNAcondensation
•oneHUdimerevery~150bpofthechromosomalDNAbased
ontheestimatedabundanceof30,000HUdimerspercell
(4600000bp/30,000)

20. IHF –INTEGRATION HOST FACTOR
•Integrationhostfactor(IHF)isstructurallyalmostidenticalto
HUbutbehavesdifferentlyfromHUinmanyaspects.
•UnlikeHU,whichpreferentiallybindstoastructuralmotif
regardlessofthesequence,IHFpreferentiallybindstoa
specificDNAsequenceeventhoughthespecificityarises
throughthesequence-dependentDNAstructureand
deformability.
•ThespecificbindingofIHFatcognatesitesbendsDNAsharply
by>160-degree.

21. Anoccurrenceofthecognatesequencemotifisabout3000inthe
E.coligenome.
TheestimatedabundanceofIHFinthegrowthphaseisabout
6000dimerspercell.
AssumingthatoneIHFdimerbindstoasinglemotifandnucleoid
containsmorethanonegenomeequivalentduringtheexponential
growthphase,mostoftheIHFmoleculeswouldoccupyspecific
sitesinthegenomeandlikelyonlycondenseDNAbyinducing
sharpbending.