RNA Metabolism and Gene Expression in Archaea

276 Pages·2017·7.68 MB·English

by  Béatrice Clouet-d'Orval (eds.)

Nucleic Acids and Molecular Biology 32
Béatrice Clouet-d’Orval Editor
RNA
Metabolism
and Gene
Expression in
Archaea
Nucleic Acids and Molecular Biology
Volume 32
Serieseditor
AllenW.Nicholson
Philadelphia,PA19122,USA
Moreinformationaboutthisseriesathttp://www.springer.com/series/881
Be´atrice Clouet-d’Orval
Editor
RNA Metabolism and Gene
Expression in Archaea
Editor
Be´atriceClouet-d’Orval
LaboratoiredeMicrobiologieetdeGe´ne´tique
Mole´culaires(LMGM),CentredeBiologieInte´grative(CBI)
Universite´deToulouse,CNRS
Toulouse,France
ISSN0933-1891 ISSN1869-2486 (electronic)
NucleicAcidsandMolecularBiology
ISBN978-3-319-65794-3 ISBN978-3-319-65795-0 (eBook)
DOI10.1007/978-3-319-65795-0
LibraryofCongressControlNumber:2017957625
©SpringerInternationalPublishingAG2017
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Outline and Synopsis
AlthoughmanyreviewsandbookssurveymanyaspectsofRNAinBacteriaandin
Eukarya, no book has so far attempted to provide a panoramic view of enzymes,
machines,andpathwaysthatsynthetize,modify,anddegradeRNAinArchaea,the
thirddomainoflife.
The early studies of C.R Woese of microbial phylogeny based on rRNA
sequences yielded the remarkable finding that the prokaryotic world was not
monophyletic but separated into two distinct domains: Archaea and Bacteria.
This major advance during the last part of the twentieth century opened a novel
vision of the living world. The universal tree predicted that the Archaea were
specific relatives of the Eukarya, to the exclusion of the Bacteria. Astonishingly,
geneticinformationprocessingsystemsintheArchaeaareoftencloselyrelatedto
theircounterpartsineukaryotes(translation,transcription,replication,DNArecom-
bination,andrepair)evenifArchaeahaveabacteria-likecellularstructure.Archaea
arenow consideredasmodelswithanemphasisonstudying themolecularmech-
anisms that universally conserve the evolutionary history of life and for the
emergence of new technologies. With the advent of whole genome sequencing, a
promisingwaytotakeadvantageofthesesimilaritiesistoanalyzetheevolutionof
cellular systems through phylogenomic approaches. Over the years, our vision of
archaeal microorganisms has evolved from exotic microbial extremophiles to
organismsofgeneralimportancethatareusedtoelucidatefundamentalbiological
questions. More recently, a newly discovered deep-sea archaeon named Loki
suggests eukaryotes evolved directly from archaea rather than representing a
separate branch of life. In consideration of this fundamental finding, Archaea are
now renowned to be important model microorganisms for the study of molecular
mechanisms that are conserved between Eukarya and Archaea. In particular,
ArchaeaandEukaryasharemanyRNAbiologyaspectswhichareatthecenterof
cellularregulationpathways.Majorexamplesarethe3Dstructuresofthearchaeal
RNA polymerase and archaeal exosome which resemble eukaryal RNA polymer-
asesandRNA-degradingexosomecomplexes,respectively.Moreover,mostofthe
archaeal tRNA and rRNA modifications rely on RNP guide machineries
orthologoustotheeukaryalC/D andH/ACA RNPcomplexes. Thishighlights the
v
vi OutlineandSynopsis
advantage of an archaeal model to gain further mechanistic and evolutionary
information of fundamental processes across the three domains of life. Neverthe-
less, for over a decade, numerous signaling pathways have been described in
Eukarya and Bacteria in which RNA processing regulates gene expression. In
Archaea, these processes have been overlooked. Molecular mechanisms of RNA
maturation and decay and posttranscriptional control of gene expression are far
fromunderstood.
Given that the RNA field is moving very fast, it is time to cover many of the
excitingandsometimesoverlookeddevelopmentsinthefieldthatrevealoriginality
ofthearchaealsystemandilluminatethefascinatingbiologythatsetsthestagefor
RNA. Therefore, this volume of Nucleic Acid and Molecular Biology provides a
reviewofourknowledgeondifferentaspectsofRNAbiologyinarchaealcellsfrom
synthesistodegradationthroughmodification,maturation,andregulatoryfunction
aswellasdefensesystemincludingevolutionaryconsiderationsofthoseprocesses.
However,thefieldofarchaealvirologywillnotbediscussedinthisbooksinceto
datethereisnoevidenceontheexistenceofarchaealRNAvirusesoranyregulatory
RNAmoleculesinvolvedintheviruslifecycles.
Thistaskisachievedby11chaptersthatcollectivelysummarizerecentadvances
inourunderstandingofRNAmetabolismatalllevels.
Contents
1 AGlobalCharacterisationoftheArchaealTranscription
Machinery. .. . . . . . .. . . . . . .. . . . . .. . . . . . .. . . . . . .. . . . . .. . 1
KatherineSmollett,FabianBlombach,ThomasFouqueau,
andFinnWerner
2 TranscriptionFactor-MediatedGeneRegulationinArchaea. . . . . 27
ElizabethA.Karr,CatherineE.Isom,VyTrinh,andEvelinePeeters
3 TranslationRegulation:TheArchaea-EukaryalConnection. . . . . 71
DarioBenelli,AnnaLaTeana,andPaolaLondei
4 AnOverviewofRibonucleaseRepertoireandRNAProcessing
PathwaysinArchaea. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
DuyKhanhPhung,MarieBouvier,andBe´atriceClouet-d’Orval
5 TheArchaealExosome:DegradationandTailingatthe30-End
ofRNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
ElenaEvguenieva-Hackenberg,SusannGauernack,andGabriele
Klug
6 LifeandDeathofRibosomesinArchaea. . . . . . . . . . . . . . . . . . . . 129
Se´bastienFerreira-Cerca
7 StructureandFunctionofArchaealRibonucleaseP. . . . . . . . . . . . 159
MakotoKimura,KosukeOshima,XuzhuGao,DanJiang,
TakashiNakashima,andToshifumiUeda
8 FunctionandBiosynthesisoftheUniversaltRNAModification
N6-Threonylcarbamoyl-Adenosine. . . . . . . . . . . . . . . . . . . . . . . . . 177
AdelinePichard-Kostuch,Marie-ClaireDaugeron,PatrickForterre,
andTamaraBasta
9 EvolutionofC/DBoxsRNAs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
VanessaTrippandLennartRandau
vii
viii Contents
10 DiverseFunctionsofSmallRNAs(sRNAs)inHalophilicArchaea:
FromNon-codingRegulatorysRNAstoMicroprotein-Encoding
sRNAs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
JanaKliemtandJ€orgSoppa
11 CRISPRandSalty:CRISPR-CasSystemsinHaloarchaea. . . . . . . 243
Lisa-KatharinaMaier,OmerS.Alkhnbashi,RolfBackofen,
andAnitaMarchfelder
Chapter 1
A Global Characterisation of the Archaeal
Transcription Machinery
KatherineSmollett,FabianBlombach,ThomasFouqueau,
andFinnWerner
Abstract Archaeaemployaeukaryote-liketranscriptionapparatustotranscribea
bacteria-like genome; while the RNA polymerase, basal factors and promoter
elements mirror the eukaryotic RNA polymerase II system, archaeal genomes are
densely packed with genes organised into multicistronic transcription units. The
molecular mechanisms of archaeal transcription have been studied and
characterised in great detail in vitro, but until recently relatively little was known
about its global characteristics. In this chapter we discuss an integrated view of
transcription from the molecular to the global level. Systems biology approaches
haveprovidedcompellinginsightsintopromoterandterminatorDNAelements,the
genome-wide distribution of transcription initiation- and elongation factors and
RNA polymerase, the archaeal transcriptome and chromatinorganisation. Overall
theseanalysesilluminatetranscriptionfromagenome-wideperspectiveandserve
as a resource for the community. In addition, Big Data can often validate mecha-
nistic models based on biochemical and structural information, and generate new
workinghypothesesthatcanbethoroughlytestedanddissectedinvitro.Thisisan
excitingtimetostudygeneexpressioninthearchaeasinceweareatthebrinkofa
comprehensiveyetdetailedunderstandingoftranscription.
1.1 Introduction
Archaeaareprokaryotesandassuchsharemanypropertieswithbacteriaincluding
circular genomes, densely packed with genes organised into operons. However,
their transcription machinery is closely related to that of RNA polymerase II, the
enzymeresponsibleformRNAtranscriptionineukaryotes(Fig.1.1).Thissimilar-
ity extends from the RNA polymerase (RNAP) subunit composition, via general
transcription factors required for initiation, to their cognate promoter elements
(Fig. 1.1a, b) (Werner and Grohmann 2011). In essence, archaeal transcription
K.Smollett(cid:129)F.Blombach(cid:129)T.Fouqueau(cid:129)F.Werner(*)
InstituteofStructuralandMolecularBiology,DivisionofBiosciences,UniversityCollege
London,GowerStreet,LondonWC1E6BT,UK
e-mail:[email protected]
©SpringerInternationalPublishingAG2017 1
B.Clouet-d’Orval(ed.),RNAMetabolismandGeneExpressioninArchaea,
NucleicAcidsandMolecularBiology32,DOI10.1007/978-3-319-65795-0_1