Table Of ContentAna Lúcia Leitão · Francisco J. Enguita
Editors
Non-coding
RNAs and
Inter-kingdom
Communication
Non-coding RNAs and Inter-kingdom
Communication
ú ã
Ana L cia Leit o Francisco J. Enguita
(cid:129)
Editors
Non-coding RNAs
and Inter-kingdom
Communication
123
Editors
Ana Lúcia Leitão Francisco J.Enguita
Universidade NovadeLisboa Universidade deLisboa
Caparica Lisbon
Portugal Portugal
ISBN978-3-319-39494-7 ISBN978-3-319-39496-1 (eBook)
DOI 10.1007/978-3-319-39496-1
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Preface
More than 60 years ago, in 1954, James Watson and the Russian Physicist George
Gamow founded the “RNA Tie club”, a scientific club of selected gentlemen
members with the main objective of sharing their ideas and findings not yet mature
enough to be published in scientific journals. Brainstorming sessions gave rise to
many seminal concepts in cell biology, which were further demonstrated by labo-
ratoryexperiences.Gamow postulated the concept ofa “genetic code” based onthe
existence of triplets of bases (codons) that will translate the DNA language into
proteinaminoacids.Furthermore,inthelast1950s,anotherillustratedmemberofthe
club, Francis Crick, enunciated the “adaptor theory” based on an intermediate
molecule (transfer-RNA) that would be the physical link between nucleic acids and
proteins. These ideas were later described in an essential Crick’s article, which is
consideredbymanyauthorsastheembryoniccoreoftheconceptoftheRNAworld.
The RNA world stands on the idea that RNA molecules were the first precursors
ofthelivingcells,beingtheoriginoftheevolutionofallbiologicalmacromolecules.
Several arguments clearly support the theory that the primitive cells could be built
over processing units based on RNA molecules, including the existence of catalytic
RNA molecules. However, for long time the chemical and structural similarities
between DNA and RNA, catalogued RNA as a short-life accessory player in cell
physiology. Moreover, the paradigm of the reduced stability of RNA vs DNA
prevented for a long time the consideration of RNA as a precursor molecule. In
consequence, RNA must be placed at the root of the molecular tree of life.
Thecentraldogmaofbiologyholdsthatgeneticinformationnormallyflowsfrom
DNAtoRNAandtoproteins.Asaconsequenceithasbeengenerallyassumedthat
genescodeforproteins,andthatproteinsfulfilnotonlymoststructuralandcatalytic
but also most regulatory functions in cells. This is essentially true in prokaryotic
organisms whose genomes are almost entirely composed of closely packed protein
coding sequences. However, this is not the case in higher organisms in which pro-
teomes and their coding sequences occupy only a tiny fraction of the genome.
Around 97–98 % of the transcriptional output of the human genome is non-protein
codingRNA(ncRNA).RNAisanidealmoleculetoregulatebiologicalnetworksdue
v
vi Preface
itssequenceinformationandstructuralplasticity.TheintrinsicrelevanceofncRNAs
intheregulationofgenomicoutputhasbeenrapidlyunveilingduringthelastdecade.
Nevertheless,functionalelementsintheprimarysequenceofthemajorityofncRNAs
thatdetermine their regulatoryroleremainunknown.The dominance ofncRNAs in
the genomic output of the higher organisms suggests that they are not simply
occasionaltranscriptswithidiosyncraticfunctions,butratherthattheymayconstitute
anextensiveunrecognizedregulatorynetworkwithinhigherorganisms.Thefactthat
noncoding RNAs constitute the majority of the transcription of the genomes of
humans and other complex organisms suggests that a second tier of genetic output
andanetworkofparallelRNA-mediatedinteractionshasevolvedintheseorganisms,
which may enable the integration and coordination of sophisticated suites of gene
expression required for differentiation and development.
Recent evidences also pointed out to the pivotal role of ncRNAs in the
cell-to-cell communication phenomenon, suggesting a transversal role of ncRNA
molecules as modulators in organism interaction. There is a common and central
biological language represented by functional RNA molecules. Within a complex
multi-cellular organism, cells are able to secrete ncRNAs that can travel using the
circulating biofluids to reach distant targets where they will exert their regulatory
actions functioning as slow genetic hormones. In pathological conditions such as
cancer, experimental evidences suggested the use of ncRNAs by tumour cells to
preparetheirtissueniche before ametastatic colonization. Different organisms can
alsotakeadvantageofncRNAsfortheirfunctionalassociations.Thisisnotonlythe
caseoftheparasiticassociationsbetweeninfectiousagentssuchasviruses,bacteria
and fungi that can hijack the host defenses using ncRNAs, but also this phe-
nomenon can be observed in mutualistic and symbiotic interactions.
The present book is a compilation of selected biological topics where ncRNAs
are mediators of inter-kingdom communication. The book is divided in two main
sectionscoveringtheroleofncRNAsinbacterialandviralinteractionwithdifferent
hosts and the modulatory effect of ncRNAs in the interactions between eukaryotic
organisms.
This overall project would not be possible without the involvement and the
passion of all the contributing authors, but also without the help and collaboration
oftheanonymousreviewerswhosesuggestionsandcriticismswereessentialforthe
consecution of the work that you have now in your hands. Our most sincere
acknowledgements to all of them… we are in debt with you.
Caparica, Portugal Ana Lúcia Leitão
Lisbon, Portugal Francisco J. Enguita
Contents
Part I Non-coding RNAs in Bacterial and Viral Interactions
with Different Hosts
1 The Roles of MicroRNAs and PiRNAs in Virus-Host
Interactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Anh T. Tran
2 Microbial Manipulation Host Dark Matter . . . . . . . . . . . . . . . . . . 27
Samantha Barichievy, Loretta Magagula, Youtaro Shibayama
and Musa M. Mhlanga
3 Interplays Between Gut Microbiota and Gene Expression
Regulation by miRNAs: Towards a Symbiotic Vision of Host
and Guest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Antonella Celluzzi and Andrea Masotti
4 Azotobacter vinelandii Small RNAs: Their Roles
in the Formation of Cysts and Other Processes. . . . . . . . . . . . . . . 67
Miguel Castañeda, Liliana López-Pliego and Guadalupe Espín
5 Streptomyces Bacteria: Specialized Metabolism, Inter-species
Interations and Non-coding RNAs . . . . . . . . . . . . . . . . . . . . . . . . 83
Matthew J. Moody, Stephanie E. Jones, David A. Crisante
and Marie A. Elliot
6 Role of Small RNAs in Wolbachia-Mosquito Interactions. . . . . . . . 103
Sassan Asgari
7 Uptake and Reaction of C. elegans to Environmental RNAs. . . . . . 117
Ahmed Waqas and Ge Shan
vii
viii Contents
Part II Non-coding RNAs and Interactions Between
Eukaryotic Organisms
8 Rapid Evolution of Mosquito Anti-viral ncRNA Pathway
Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Corey L. Campbell, Laura B. Dickson and William C. Black IV
9 Differential Expression of Toxoplasma gondii MicroRNAs
in Murine and Human Hosts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Müşerref Duygu Saçar Demirci, Caner Bağcı and Jens Allmer
10 Hypothetical Plant-Mammal Small RNA Communication:
Packaging and Stoichiometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
Kenneth W. Witwer
11 Different Types of Small RNAs in Protozoa. . . . . . . . . . . . . . . . . . 177
Ling-Ling Zheng, Jian-You Liao, Yan-Zi Wen, Geoff Hide,
Liang-Hu Qu and Zhao-Rong Lun
12 Function of Non-coding RNA in Toxoplasma gondii Infection. . . . . 197
Mariana Matrajt
13 MicroRNAs of Filarial Nematodes: A New Frontier
in Host-Pathogen Interactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Lucienne Tritten and Timothy G. Geary
14 Human Fungal Infections: Emerging Role of Small Non-coding
RNAs as Modulators of Host-pathogen Interactions. . . . . . . . . . . . 225
Ana Lúcia Leitão, Marina C. Costa and Francisco J. Enguita
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
Part I
Non-coding RNAs in Bacterial
and Viral Interactions
with Different Hosts
Chapter 1
The Roles of MicroRNAs and PiRNAs
in Virus-Host Interactions
Anh T. Tran
Abstract MicroRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) are two
groups of small non-coding RNAs with different functional roles. miRNAs are
post-transcriptionalregulatorsofgeneexpressioninaplethoraofcriticalprocesses
in multicellular eukaryotes. Therefore, it comes as no surprise that viral pathogens
have evolved ways to subvert the miRNA network. It is increasingly evident that
miRNAs have functional roles in viral replication as well as their potential
employment by host cells to combat viral infection. A number of viruses are now
known to encode for miRNAs, predominantly in DNA viruses such as her-
pesviruses. Although virus-encoded miRNAs have been reported in retroviruses
such as HIV-1, their functional significance is under debate. This controversy also
extendstoRNAvirusesandtheirabilitytoexpressmiRNAs.Identificationoftarget
genesforsomeoftheseviralmiRNAssuggeststheymayfunctionintheregulation
of lytic and latent viral replication and in restricting antiviral responses. Viruses
have also evolved the ability to downregulate or upregulate the expression of
specific cellular miRNAs to enhance their replication. I will also briefly review
evidencethatdemonstratetheroleofpiRNAsinsilencingtransposableelementsto
maintain germline genome integrity. This chapter provides an overview of our
current understanding of the complex relationship between viruses and cellular
miRNA and piRNA machineries.
1.1 miRNA and piRNA Biogenesis and Function
1.1.1 miRNAs
miRNAs are noncoding RNAs *21–23 nucleotide (nt) in length that
post-transcriptionally regulate the expression of a plethora of eukaryotic genes.
A.T.Tran(&)
DevelopmentalandStemCellBiology,PeterGilganCentreforResearchandLearning,
TheHospitalforSickChildren,686BayStreet,M5G0A4,Toronto,ON18-9410,Canada
e-mail:Anh_T.Tran@outlook.com
©SpringerInternationalPublishingSwitzerland2016 3
A.L.LeitãoandF.J.Enguita(eds.),Non-codingRNAsandInter-kingdom
Communication,DOI10.1007/978-3-319-39496-1_1
