SELENOPROTEINS : methods and protocols

335 Pages·2017·7.842 MB·English

Methods in
Molecular Biology 1661
Laurent Chavatte Editor
Seleno-
proteins
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Selenoproteins
Methods and Protocols
Edited by
Laurent Chavatte
Centre International de Recherche en Infectiologie, CIRI, Lyon, France
INSERM U1111, Lyon, France
CNRS/ENS/UCBL1 UMR5308, Lyon, France
Laboratoire de Chimie Analytique Bio-Inorganique et Environnement, LCABIE
CNRS/Univ Pau & Pays Adour, Institut des Sciences
Analytiques et de Physico-Chimie Pour l'Environnement
et Les Matériaux, UMR5254, Pau, France
Editor
LaurentChavatte
CentreInternationaldeRecherche
enInfectiologie,CIRI
Lyon,France
INSERMU1111
Lyon,France
CNRS/ENS/UCBL1UMR5308
Lyon,France
LaboratoiredeChimieAnalytique
Bio-InorganiqueetEnvironnement,LCABIE
CNRS/UnivPau&PaysAdour,InstitutdesSciences
AnalytiquesetdePhysico-ChimiePourl’Environnement
etLesMate´riaux,UMR5254
Pau,France
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-7257-9 ISBN978-1-4939-7258-6 (eBook)
DOI10.1007/978-1-4939-7258-6
LibraryofCongressControlNumber:2017950666
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Preface
Selenium (Se) was discovered in 1817 by John Jacob Berzelius, a Swedish chemist who
nameditafterthegoddessofthemoonSelene,sincethiselementhadmanysimilaritieswith
Tellurium (“tellus” meaning earth in Latin), found at the same period. For more than
hundred years, selenium was viewed as a toxic element. It is only rather recently (in the
1950s)thatseleniumhasbeenrecognizedasanessentialnutrientformammals.Seleniumis
implicated in many facets of human health and diseases, including cancer prevention,
cardiovascular function, immunity, and brain function [1–3]. Selenium is incorporated in
asmallbutvitalgroupofproteins,theselenoproteins,intheformofarareaminoacid,the
selenocysteine (Sec). Often located in the catalytic site of enzymes, selenocysteine is a key
component of oxido-reduction reactions. Twenty-five selenoprotein genes have been dis-
coveredsofarinhuman[4,5],andaunifiednomenclaturehasbeenrecentlyproposed[6]
(see Table 1). Selenoproteins are mostly involved in redox homeostasis and signaling,
antioxidant defense, and selenoprotein biosynthesis, although about one third of the
selenoproteome remains without precise function (for review see Ref. 7). Remarkably, in
the1990sseleniumhasamendedthegeneticcodedecipheredinthe1960ssinceselenocys-
teineisencodedbyaUGAcodoninselenoproteinmRNAs,whichisotherwisereadasastop
codon in other cellular mRNAs. In this regard, cells have evolved a unique and complex
mechanismforUGArecodingasselenocysteinethatisregulatedatmanylevels,givingrise
to a prioritized synthesis of selenoproteins. This noncanonical translational pathway for
selenoproteinbiosynthesisreliesontwopivotalRNAmolecules,namelytheselenocysteine-
tRNA[Ser]Sec (Fig. 1) and the SElenoCysteine Insertion Sequence (SECIS) within seleno-
proteinmRNA(Fig.2),andtheirproteininteractingpartners(asreviewedin[2,3,8–12]).
Due to the low levels of selenium in the body and complex biosynthesis, research on
selenoproteins has been particularly challenging. Therefore, selenoproteins offer a
fascinating playground in a broad range of fields in biology, including bioinformatics,
genetics, RNA structure, translational control, biophysics, enzymology, animal models,
and human health and diseases. This book aims at providing an update on state-of-the-art
methodologiestostudythesevariousaspectsofselenoproteinbiology.
v
vi Preface
Table1
List of the human selenoprotein genes identified to date, using the unified nomenclature
Genename Proteinname Synonyms
DIO1 Iodothyroninedeiodinase1 D1
DIO2 Iodothyroninedeiodinase2 D2
DIO3 Iodothyroninedeiodinase3 D3
GPX1 Glutathioneperoxidase1 Glutathioneperoxidase1
GPX2 Glutathioneperoxidase2 Glutathioneperoxidase2
GPX3 Glutathioneperoxidase3 Glutathioneperoxidase3
GPX4 Glutathioneperoxidase4 Glutathioneperoxidase4
GPX6 Glutathioneperoxidase6 Glutathioneperoxidase6
MSRB1 MethioninesulfoxidereductaseB1 SelR,SelX,SEPX1
SELENOF SelenoproteinF Selenoprotein15,Sel15,Sep15
SELENOH SelenoproteinH SelH
SELENOI SelenoproteinI SelI
SELENOK SelenoproteinK SelK
SELENOM SelenoproteinM SelM
SELENON SelenoproteinN SelN
SELENOO SelenoproteinO SelO
SELENOP SelenoproteinN SelP,SEPP1,SEPP,SeP
SELENOS SelenoproteinS SelS,SEPS1,VIMP
SELENOT SelenoproteinT SelT
SELENOV SelenoproteinV SelV
SELENOW SelenoproteinW SelW
SEPHS2 Selenophosphate2 Selenide,waterdikinase2,SPS2
TXNRD1 Thioredoxinreductase1 TR1,TRXR1
TXNRD2 Thioredoxinreductase3 TR3,TRXR2,mitochondrial
thioredoxinreductase
TXNRD3 Thioredoxinreductase3 TR2,TRXR3,TGR
Preface vii
a A 3’ b
C
C
G
5’
G C
1 tRNA[Ser]Sec
C G Acceptor
C G 70 arm
C G
SerRS
5a G C
5b G U 67b
A U
5c 67a
U U TψC-arm
6 66 Ser-tRNA[Ser]Sec
D-arm AG CC A C C 6U0 Um 1A
U 10 U A
G G A C U C C G U G G
50 A U ψ C PSTK
G C U G G G G G
U 20 U A GC A4 74 6l
G U 46a U CA 4 6k Variable
C G 46b G U G4 6Cj 46i arm pSer-tRNA[Ser]Sec
A U 46c4 6d C G SEPHS2
Anticodon 30 GG CC 40 46e 4U6f A 46g 46h H2SePO3- HSe-
arm C A SepSecS
U 6A 2Pi
i
5U A
mcm C
Sec-tRNA[Ser]Sec
5U
mcm m
Fig.1Structure and aminoacylation of Sec-tRNA[Ser]Sec. (a) Cloverleaf structure of the two isoforms of the
tRNA[Ser]Sec differing from modification at position U34 between 5U and 5U . (b) The aminoacylation
mcm mcm m
of tRNA[Ser]Sec necessitates four enzymes instead of one for other tRNAs, including seryl-tRNA synthetase
(SerRS), the phosphoseryl-tRNA kinase (PSKT), Sec synthase (SepSecS, also referred to as SLA/LP), and
selenophosphate 2 synthetase (SEPHS2), which generates selenophosphate (H SePO (cid:1)) from selenide
2 3
(HSe(cid:1))
viii Preface
SECIS element
a
100-3000nt
Sec
Start Stop
5’ Cap AUG UGA UAA/G AAAAAA-3’
Selenoprotein mRNA
0-1500nt
EFsec
b A SBP2
n
EFsec Sec-tRNA[Ser]Sec
eL30
SBP2
P A
E
AUG UGA UAA/G
Cap
Ribosomes
Fig.2Mechanismforselenoproteinbiosynthesisineukaryotes.(a)Schematicrepresentationofaselenopro-
tein mRNA with its different cis-acting features: the SECIS element located in the 30UTR and the UGA-
selenocysteine codon present in frame in the Open Reading Frame (ORF). (b) Representation of the trans-
acting factors needed for the efficient recoding of UGA as selenocysteine. Essential factors include the
ribosomes, the Sec-tRNA[Ser]Sec, a dedicated elongation factor EFsec, and a SECIS binding protein SBP2 (or
SECIBP2).Accessoryand/orregulatoryproteinshavealsobeendescribed(forreviewseeRefs.8–12)
Pau,France LaurentChavatte
References
1. Rayman MP (2012) Selenium and human health. Lancet 379(9822):1256–1268. doi:10.1016/
S0140-6736(11)61452-9.S0140–6736(11)61452–9[pii]
2.PappLV,LuJ,HolmgrenA,KhannaKK(2007)Fromseleniumtoselenoproteins:synthesis,identity,
andtheirroleinhumanhealth.AntioxidRedoxSignal9(7):775–806
3.HatfieldDL,GladyshevVN(2002)Howseleniumhasalteredourunderstandingofthegeneticcode.
MolCellBiol22(11):3565–3576
4. Lobanov AV, Hatfield DL, Gladyshev VN (2009) Eukaryotic selenoproteins and selenoproteomes.
BiochimBiophysActa1790(11):1424–1428.doi:10.1016/j.bbagen.2009.05.014.S0304–4165(09)
00148–2[pii]
5. Kryukov GV, Castellano S, Novoselov SV, Lobanov AV, Zehtab O, Guigo R, Gladyshev VN (2003)
Characterizationofmammalianselenoproteomes.Science300(5624):1439–1443
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Chavatte L, Conrad M, Copeland PR, Diamond AM, Driscoll DM, Ferreiro A, Flohe L, Green FR,
GuigoR,HandyDE,HatfieldDL,HeskethJ,HoffmannPR,HolmgrenA,HondalRJ,HowardMT,
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G,SchmidtEE,SchomburgL,SchweizerU,SimonovicM,SundeRA,TsujiPA,TweedieS,UrsiniF,
Preface ix
WhangerPD,ZhangY(2016)SelenoproteinGeneNomenclature.TheJournalofbiologicalchemistry
291(46):24,036–24,040
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Contents
Preface ..................................................................... v
Contributors................................................................. xiii
PART I BIOINFORMATIC TOOLS FOR SELENOPROTEIN IDENTIFICATION
AND EVOLUTION
1 SECISearch3andSeblastian:In-SilicoToolstoPredictSECIS
ElementsandSelenoproteins............................................. 3
MarcoMariotti
2 Selenoprofiles:AComputationalPipelineforAnnotation
ofSelenoproteins ....................................................... 17
DidacSantesmasses,MarcoMariotti,andRodericGuigo´
3 SelGenAmic:AnAlgorithmforSelenoproteinGeneAssembly................ 29
LiangJiangandQiongLiu
PART II SELENOPROTEIN BIOSYNTHESIS
4 SelenocysteinetRNA[Ser]Sec,theCentralComponentofSelenoprotein
Biosynthesis:Isolation,Identification,Modification,andSequencing.......... 43
BradleyA.Carlson,ByeongJaeLee,PetraA.Tsuji,
PaulR.Copeland,UlrichSchweizer,VadimN.Gladyshev,
andDolphL.Hatfield
5 IdentificationandCharacterizationofProteinsthatBind
0
toSelenoprotein3 UTRs................................................ 61
EricM.CockmanandDonnaM.Driscoll
6 SpecificChemicalApproachesforStudyingMammalianRibosomes
ComplexedwithLigandsInvolvedinSelenoproteinSynthesis................ 73
OlgaKossinova,AlexeyMalygin,AlainKrol,andGalinaKarpova
7 InVitroTranslationAssaysforSelenocysteineInsertion ..................... 93
MarkH.PinkertonandPaulR.Copeland
8 StudyingSelenoproteinmRNATranslationUsingRNA-Seq
andRibosomeProfiling.................................................. 103
BrianK.Dalley,LisaBaird,andMichaelT.Howard
9 ModificationofSelenoproteinmRNAsbyCapTri-methylation............... 125
Anne-SophieGribling-Burrer,GilbertEriani,andChristineAllmang
PART III SELENOPROTEIN DETECTION AND QUANTIFICATION
10 TotalSeleniumQuantificationinBiologicalSamples
byInductivelyCoupledPlasmaMassSpectrometry(ICP-MS)................ 145
Ve´roniqueVacchinaandJeanDumont
xi