Extracellular Nucleic Acids

237 Pages·2010·1.84 MB·English

by  Wen-Chi Chiang

Nucleic Acids and Molecular Biology
25
Series Editors
Hans J. Gross, Janusz M. Bujnicki
Yo Kikuchi Elena Y. Rykova (Eds.)
l
Extracellular Nucleic Acids
Editors
YoKikuchi ElenaY.Rykova
DepartmentofEnvironmental InstituteofChemicalBiology
andLifeSciences andFundamentalMedicine,
ToyohashiUniversityofTechnology LavrentjevaProspect,8
441-8580Toyohashi-city,Aichi 630090Novosibirsk
Japan Russia
[email protected] [email protected]
SeriesEditors
HansJ.Gross JanuszM.Bujnicki
Institutfu¨rBiochemie InternationalInstituteofMolecular
Biozentrum andCellBiology
AmHubland LaboratoryofBioinformaticsand
97074Wu¨rzburg ProteinEngineering
Germany Trojdena4
02-109Warsaw
Poland
ISSN0933-1891 e-ISSN1869-2486
ISBN978-3-642-12616-1 e-ISBN978-3-642-12617-8
DOI10.1007/978-3-642-12617-8
SpringerHeidelbergDordrechtLondonNewYork
LibraryofCongressControlNumber:2010931462
#Springer-VerlagBerlinHeidelberg2010
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Preface
Nucleic acids have a wide variety of functions in the main systems of life, gene
maintenance,andexpression,andthereforenucleicacidsasfunctionalformshave
beenbelievedtoexistonlyinsidecells.Extracellularnucleicacidshavelongbeen
known, but these nucleic acids were initially presumed to be derived from cells
lysed by natural cell death or viruses and considered to be of limited importance.
However, these extracellular nucleic acids have recently emerged as important
players in the fields of medical and environmental microbiology. In recent years,
extracellular nucleic acids have been shown to be involved in not only microbial
evolutionasgeneticelementsbuttoalsohavestructuralrolesinbacterialcommu-
nities,suchasbiofilms.Circulatingnucleicacidshavebeenfoundinhumanblood
innormalandpathologicstates.Moreover,theyareexpectedtobethelowinvasive
markersfordiagnosisofseveraldiseases.Extracellularnucleicacidshaveattracted
attentionasactivemodulatorsoftheimmunesysteminhigherorganisms.
ThisvolumeoftheNucleicAcidsandMolecularBiologyseriesisdevotedtothe
extracellular nucleic acids, which are found in different biological fluids in the
highestorganismsandintheextracellularmilieuofbacterialcommunities.Appli-
cationsofthephenomenaarealsoimportanttopicsforconsideration.
Recently, characterization and the role of extracellular DNA of the bacterium
PseudomonasaeruginosawereclearlydescribedbyTolker-Nielsenandcolleagues.
ChiangandTolker-Nielsenbeginthisvolumebydescribingnewrolesofextracel-
lularDNAinbacterialbiofilmformation.
ExtracellularDNAsintheenvironmentarethoughttobeusedasgeneticdonors
in natural transformation of several organisms. The following two chapters are
relatedtoevolutionandmicrobialecology.LangandBeattyintroducedextracellu-
larDNAspackedinvirus-likeparticles.TaniandNasudiscussextracellularDNAs
andmicrobialdiversityfromaglobalviewpoint.
Extracellular DNAs of high molecular weight seem to be more stable than
previouslyimagined. Kaneko andItayadescribe anew technique for introduction
of large DNAs from lysed cells into other species mimicking horizontal gene
transfer in nature. Chapter 5 by Kikuchi also presents technology-oriented topics.
v
vi Preface
Thephysiologyandbiotechnologyofamarinebacteriumaredescribed.Inaddition
to the extracellular DNA, analysis of extracellular RNAs of this organism is
described. A newly developed method for production of RNA drugs using this
bacteriumisalsopresented.
One of the current hot topics in biology, systemic RNA interference, in which
some RNAs interfere with gene expression, is strongly related to the subject of
extracellular RNAs. Timmons reviews these topics and leads to the following
chaptersforhigherorganisms.
Extracellularnucleicacidscirculatinginthehumanbloodwerefirstconsidered
tobeproductsofcelldegradation.Lateron,concentrationandcompositionofthe
circulating nucleic acids were found to be significantly changed in the blood of
patients with different pathologies, including cancer, compared with healthy sub-
jects.Rykovaetal.reviewtherecentprogressintheinvestigationofthecirculating
DNAandRNAasmarkersofcancerandotherdisorders,suchasdiabetes,trauma,
stroke, myocardial infarction, complications in transplantation, etc. Development
of the low invasive diagnostics of pregnancy-associated and fetal disorders based
on the circulating DNA and RNA markers is described by Tsang and Lo. Tewari
and Mitchell discuss the assessment of microRNAs as a promising approach
for cancer diagnostics. Questions are brought up, which remain to be resolved
to develop robust assays for the pathologies diagnosis and prognosis relevant for
clinicaluse.
GahanandStrounpresentdatahighlightingappearanceofextracellularnucleic
acidsinthehumanbloodandindicatingtheirimportantbiologicalrolesinnormal
andpathologicstatesoftheorganism.Thechapterprovidesevidencethatcirculat-
ing nucleic acids can play signaling roles under normal conditions and become
causative factors in the disease development. One of the important properties of
nucleic acids and their metabolites is their potential to be active modulators of
theimmunesystem,which isdetailed intwochapters.Koyamaetal.describethe
recognition and immune response of “nonself” nucleic acids during infection and
“self”nucleicacidsinautoimmunedisorders.Someclinicalapplicationsofnucleic
acidsthatutilizetheirimmunogenicpotentialareillustrated.KlinmanandKlaschik
give the detailed description of the gene expression regulation by unmethylated
CpG DNA triggered by Toll-like receptor 9 (TLR9). Synergistic modulation of
geneexpressionbyTLR9andTLR3ligandsisalsodiscussed.
This volume covers almost all current fields related to extracellular nucleic
acids, including the fields of basic biology, ecology, and medical sciences. These
are currently emerging fields of study. The reviews presented in this book will
provide readers current knowledge into these exciting fields and also stimulate
discussiontoaddressnewfrontiers.
Toyohashi,Japan YoKikuchi
Novosibirsk,Russia ElenaY.Rykova
Contents
1 ExtracellularDNAasMatrixComponentinMicrobialBiofilms ..... 1
Wen-ChiChiangandTimTolker-Nielsen
2 GeneTransferAgentsandDefectiveBacteriophagesasSources
ofExtracellularProkaryoticDNA ...................................... 15
AndrewS.LangandJ.ThomasBeatty
3 RolesofExtracellularDNAinBacterialEcosystem .................. 25
KatsujiTaniandMasaoNasu
4 StableExtracellularDNA:ANovelSubstrateforGenetic
EngineeringthatMimicsHorizontalGeneTransferinNature ...... 39
ShinyaKanekoandMitsuhiroItaya
5 ExtracellularNucleicAcidsoftheMarinePhototrophicBacterium
RhodovulumsulfidophilumandRelatedBacteria:Physiology
andBiotechnology ....................................................... 55
YoKikuchi
6 SystemicRNAiinC.elegansfromtheViewpointofRNA
asExtracellularSignals ................................................. 69
LisaTimmons
7 CirculatingNucleicAcidsinHealthandDisease ...................... 93
E.Y.Rykova,P.P.Laktionov,andV.V.Vlassov
8 CirculatingMicroRNAsinCancer .................................... 129
PatrickS.MitchellandMuneeshTewari
9 BiologyandDiagnosticApplicationsofCell-FreeFetalNucleic
AcidsinMaternalPlasma .............................................. 147
JasonC.H.TsangandY.M.DennisLo
vii
viii Contents
10 TheBiologyofCirculatingNucleicAcidsinPlasma
andSerum(CNAPS) .................................................... 167
P.B.GahanandM.Stroun
11 ModulationandRegulationofGeneExpressionbyCpG
Oligonucleotides ......................................................... 191
DennisKlinmanandSvenKlaschik
12 ImmuneRecognitionofNucleicAcidsandTheirMetabolites ...... 209
ShoheiKoyama,ShizuoAkira,andKenJ.Ishii
Index .......................................................................... 229
Contributors
Shizuo Akira Laboratory of Host Defense, WPI Immunology Frontier Research
Center,OsakaUniversity,3-1Yamada-oka,Suita,Osaka565-0871,Japan
J. Thomas Beatty Department of Microbiology and Immunology, University of
BritishColumbia,Vancouver,BC,V6T1Z3,Canada
Wen-Chi Chiang Department of International Health, Immunology and Micro-
biology, FacultyofHealth Sciences,UniversityofCopenhagen,Blegdamsvej 3B,
2200Copenhagen,Denmark
P.B. Gahan King’s College London, Anatomy and Human Sciences, London
Bridge,LondonSE11UL,UK
KenJ.Ishii LaboratoryofVaccineScience,WPIImmunologyFrontierResearch
Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan,
[email protected]; Laboratory of Adjuvant Innovation, National
Institute of Biomedical Innovation, 7-6-8 Asagi Saito, Ibaraki, Osaka 567-0085,
Japan
Mitsuhiro Itaya Institute for Advanced Biosciences, Keio University,
Nipponkoku,Tsuruoka-shi,Yamagata997-0017,Japan
Shinya Kaneko Graduate School of Bioscience and Biotechnology, Department
of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku,
Yokohama-shi,Kanagawa226-8501,Japan
Yo Kikuchi Department of Environmental and Life Sciences, Toyohashi
University of Technology, 1-1 Hibarigaoka, Tempaku-cho 441-8580 Toyohashi,
Japan,[email protected]
ix
x Contributors
SvenKlaschik CancerandInflammationProgram,NationalCancerInstitute,NCI
inFrederick,Frederick,MD21702,USA
Dennis Klinman Laboratory of Experimental Immunology, National Cancer
InstituteatFrederick,Frederick,MD21702-1201,USA
Shohei Koyama Department of Respiratory Medicine, Tohoku University
Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai-city, Miyagi
980-8575,Japan
P.P. Laktionov Institute of Chemical Biology and Fundamental Medicine, SB
RAS,8,LavrentjevaProsp.,Novosibirsk630090,Russia
AndrewS.Lang DepartmentofBiology,MemorialUniversityofNewfoundland,
St.John’s,NLA1B3X9,Canada,[email protected]
Y.M. Dennish Lo Li Ka Shing Institute of Health Sciences and Department of
Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales
Hospital,Shatin,NewTerritories,HongKongSAR,China,[email protected]
PatrickS.Mitchell HumanBiologyDivision,FredHutchinsonCancerResearch
Center, 1100 Fairview Avenue North, Mailstop D4-100, Seattle, WA 98109,
USA; Molecular and Cellular Biology Program, University of Washington,
Seattle,WA,USA
Masao Nasu Department of Environmental Science and Microbiology, Graduate
School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita,
Osaka,565-0871,Japan,[email protected]
Elena Y. Rykova Institute of Chemical Biology and Fundamental Medicine,
Siberian Division of the Russian Academy of Sciences, Lavrentiev Prosp., 8,
Novosibirsk630090,Russia,[email protected]
M. Stroun OncoXL, Eclosion, 14m chemin des Aulx, 1228 Plan-les-Ouates,
Geneva,Switzerland,[email protected]
Katsuji Tani Department of Environmental Science and Microbiology, Faculty
of Pharmaceutical Sciences, Osaka-ohtani University, 3-11-1 Nishikiori-kita,
Tondabayashi,Osaka584-0854,Japan
Muneesh Tewari Human Biology Division, Fred Hutchinson Cancer Research
Center,1100FairviewAvenueNorth,MailstopD4-100,Seattle,WA98109USA,
[email protected]; Clinical Research Division, Fred Hutchinson Cancer
Research Center, Seattle, WA, USA; Public Health Sciences Division, Fred
HutchinsonCancerResearchCenter,Seattle,WA,USA