Flavivirus 3' UTR

The Flavivirus positive-oriented, single-stranded RNA genome has a length of 10,000 - 11,000 bases. The genus includes human pathogens like Zika virus, West-Nile virus, Dengue virus, Yellow Fever virus and other.{{Cite web|title=International Committee on Taxonomy of Viruses (ICTV)|url=https://ictv.global/taxonomy|access-date=2020-08-14|website=talk.ictvonline.org|language=en}}

The 3' UTR ranges between 400 and 700 nucleotides in length.{{Cite journal|last1=Ng|first1=Wy|last2=Soto-Acosta|first2=Ruben|last3=Bradrick|first3=Shelton|last4=Garcia-Blanco|first4=Mariano|last5=Ooi|first5=Eng|date=2017-06-06|title=The 5′ and 3′ Untranslated Regions of the Flaviviral Genome|journal=Viruses|language=en|volume=9|issue=6|pages=137|doi=10.3390/v9060137|issn=1999-4915|pmc=5490814|pmid=28587300|doi-access=free}} Its RNA secondary structure is known to be necessary for the viral replication during infection. In contrast to the structurally conserved 5' UTR of flaviviruses, individual structural elements differ between different viruses, which is associated with the host-adaptation. Flaviviruses are therefore classified into four different groups: Mosquito-borne flaviviruses (MBFV), tick-borne flaviviruses (TBFV), insect-specific flaviviruses (ISFV) and those with no known vector (NKV).{{Cite journal|last1=Kuno|first1=Goro|last2=Chang|first2=Gwong-Jen J.|last3=Tsuchiya|first3=K. Richard|last4=Karabatsos|first4=Nick|last5=Cropp|first5=C. Bruce|date=1998-01-01|title=Phylogeny of the Genus Flavivirus|journal=Journal of Virology|language=en|volume=72|issue=1|pages=73–83|doi=10.1128/JVI.72.1.73-83.1998|pmid=9420202|pmc=109351|issn=1098-5514|doi-access=free}}{{Cite journal|last1=Gaunt|first1=Michael W.|last2=Sall|first2=Amadou A.|last3=Lamballerie|first3=Xavier de|last4=Falconar|first4=Andrew K. I.|last5=Dzhivanian|first5=Tatyana I.|last6=Gould|first6=Ernest A.|date=2001-08-01|title=Phylogenetic relationships of flaviviruses correlate with their epidemiology, disease association and biogeography|journal=Journal of General Virology|language=en|volume=82|issue=8|pages=1867–1876|doi=10.1099/0022-1317-82-8-1867|pmid=11457992|issn=0022-1317|doi-access=free}}

Across all groups, three RNA secondary structure elements are conserved within the 3' UTR: the dumbbell element (DB), cis-acting replication element (CRE) and the exoribonuclease-resistant RNA elements (xrRNA). Further, unique elements have been observed for specific groups as well.{{citation needed|date=October 2022}}

The 3' UTR of flavivirus - and sometimes even a small part of the 3' end of the coding region - is also called subgenomic flavivirus RNA (sfRNA).{{Cite journal|last1=Bidet|first1=Katell|last2=Garcia-Blanco|first2=Mariano A.|date=2014-09-01|title=Flaviviral RNAs: weapons and targets in the war between virus and host|url=https://portlandpress.com/biochemj/article/462/2/215/47699/Flaviviral-RNAs-weapons-and-targets-in-the-war|journal=Biochemical Journal|language=en|volume=462|issue=2|pages=215–230|doi=10.1042/BJ20140456|pmid=25102029|issn=0264-6021}} It has been shown that sfRNA is implied in many different pathways that comprises both, host defenses and viral infection.{{Cite journal|last1=Chang|first1=Ruey-Yi|last2=Hsu|first2=Ta-Wen|last3=Chen|first3=Yen-Lin|last4=Liu|first4=Shu-Fan|last5=Tsai|first5=Yi-Jer|last6=Lin|first6=Yun-Tong|last7=Chen|first7=Yi-Shiuan|last8=Fan|first8=Yi-Hsin|date=2013-09-01|title=Japanese encephalitis virus non-coding RNA inhibits activation of interferon by blocking nuclear translocation of interferon regulatory factor 3|url=https://linkinghub.elsevier.com/retrieve/pii/S0378113513002423|journal=Veterinary Microbiology|language=en|volume=166|issue=1–2|pages=11–21|doi=10.1016/j.vetmic.2013.04.026|pmid=23755934}}{{Cite journal|last1=Moon|first1=S. L.|last2=Anderson|first2=J. R.|last3=Kumagai|first3=Y.|last4=Wilusz|first4=C. J.|last5=Akira|first5=S.|last6=Khromykh|first6=A. A.|last7=Wilusz|first7=J.|date=2012-11-01|title=A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability|journal=RNA|language=en|volume=18|issue=11|pages=2029–2040|doi=10.1261/rna.034330.112|issn=1355-8382|pmc=3479393|pmid=23006624}}{{Cite journal|last1=Clarke|first1=B.D.|last2=Roby|first2=J.A.|last3=Slonchak|first3=A.|last4=Khromykh|first4=A.A.|date=2015-08-01|title=Functional non-coding RNAs derived from the flavivirus 3′ untranslated region|url=https://linkinghub.elsevier.com/retrieve/pii/S0168170215000519|journal=Virus Research|language=en|volume=206|pages=53–61|doi=10.1016/j.virusres.2015.01.026|pmid=25660582}} SfRNA is produced by incomplete degradation of the viral genome by the host cell (via XRN1).{{Cite journal|last1=Chapman|first1=E. G.|last2=Costantino|first2=D. A.|last3=Rabe|first3=J. L.|last4=Moon|first4=S. L.|last5=Wilusz|first5=J.|last6=Nix|first6=J. C.|last7=Kieft|first7=J. S.|date=2014-04-18|title=The Structural Basis of Pathogenic Subgenomic Flavivirus RNA (sfRNA) Production|url= |journal=Science|language=en|volume=344|issue=6181|pages=307–310|doi=10.1126/science.1250897|issn=0036-8075|pmc=4163914|pmid=24744377|bibcode=2014Sci...344..307C}} Local RNA secondary structures (xrRNA elements) in the 3' UTR and long-range RNA-RNA interactions between 5' UTR and 3' UTR of flaviviruses stall XRN1 and causes the undigested fragment of the genome.{{citation needed|date=October 2022}}

The exoribonuclease-resistant RNA elements (xrRNA) are described throughout all groups of flaviviruses. Usually, each virus harbors two xrRNAs, xrRNA1 and xrRNA2, in the beginning of the 3' UTR.{{Cite journal|last1=Pijlman|first1=Gorben P.|last2=Funk|first2=Anneke|last3=Kondratieva|first3=Natasha|last4=Leung|first4=Jason|last5=Torres|first5=Shessy|last6=van der Aa|first6=Lieke|last7=Liu|first7=Wen Jun|last8=Palmenberg|first8=Ann C.|last9=Shi|first9=Pei-Yong|last10=Hall|first10=Roy A.|last11=Khromykh|first11=Alexander A.|date=2008-12-11|title=A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity|journal=Cell Host & Microbe|volume=4|issue=6|pages=579–591|doi=10.1016/j.chom.2008.10.007|issn=1934-6069|pmid=19064258|doi-access=free}} The formation of these stem-loops, especially xrRNA1, is vital to ensure resistance against XRN1 activity.{{Cite journal|last1=Moon|first1=Stephanie L.|last2=Anderson|first2=John R.|last3=Kumagai|first3=Yutaro|last4=Wilusz|first4=Carol J.|last5=Akira|first5=Shizuo|last6=Khromykh|first6=Alexander A.|last7=Wilusz|first7=Jeffrey|date=2012-11-01|title=A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability|journal=RNA|volume=18|issue=11|pages=2029–2040|doi=10.1261/rna.034330.112|issn=1469-9001|pmc=3479393|pmid=23006624}} The Y-shaped stem-loop is also termed SL II and SL IV, respectively. In order to function as xrRNA, the sequence downstream is needed as well, since the upper loop region forms a pseudoknot (PK) with the single-stranded region directly downstream to its respective hairpin. In some species, the region downstream also forms a small hairpin. In such cases, the PK interactions takes place between the two loop regions. Conserved formation of these structures were observed in mammalian cells but not in mosquito cells, suggesting this region has varying functions in different hosts.{{Cite journal|last1=Villordo|first1=Sergio M.|last2=Filomatori|first2=Claudia V.|last3=Sánchez-Vargas|first3=Irma|last4=Blair|first4=Carol D.|last5=Gamarnik|first5=Andrea V.|date=2015-01-30|editor-last=Nagy|editor-first=Peter D.|title=Dengue Virus RNA Structure Specialization Facilitates Host Adaptation|journal=PLOS Pathogens|language=en|volume=11|issue=1|pages=e1004604|doi=10.1371/journal.ppat.1004604|issn=1553-7374|pmc=4311971|pmid=25635835 |doi-access=free }}{{Cite journal|last1=Ng|first1=Wy Ching|last2=Soto-Acosta|first2=Ruben|last3=Bradrick|first3=Shelton S.|last4=Garcia-Blanco|first4=Mariano A.|last5=Ooi|first5=Eng Eong|date=2017-06-06|title=The 5′ and 3′ Untranslated Regions of the Flaviviral Genome|journal=Viruses|volume=9|issue=6|page=137|doi=10.3390/v9060137|issn=1999-4915|pmc=5490814|pmid=28587300|doi-access=free}} In plant-viruses, xrRNA elements have been observed as well, showing some similarities to flaviviral xrRNAs.{{Cite journal|last1=Iwakawa|first1=Hiro-oki|last2=Mizumoto|first2=Hiroyuki|last3=Nagano|first3=Hideaki|last4=Imoto|first4=Yuka|last5=Takigawa|first5=Kazuma|last6=Sarawaneeyaruk|first6=Siriruk|last7=Kaido|first7=Masanori|last8=Mise|first8=Kazuyuki|last9=Okuno|first9=Tetsuro|date=2008-10-15|title=A Viral Noncoding RNA Generated by cis-Element-Mediated Protection against 5′→3′ RNA Decay Represses both Cap-Independent and Cap-Dependent Translation|url= |journal=Journal of Virology|language=en|volume=82|issue=20|pages=10162–10174|doi=10.1128/JVI.01027-08|issn=0022-538X|pmc=2566255|pmid=18701589}}{{Cite journal|last1=Steckelberg|first1=Anna-Lena|last2=Akiyama|first2=Benjamin M.|last3=Costantino|first3=David A.|last4=Sit|first4=Tim L.|last5=Nix|first5=Jay C.|last6=Kieft|first6=Jeffrey S.|date=2018-06-19|title=A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure|journal=Proceedings of the National Academy of Sciences|language=en|volume=115|issue=25|pages=6404–6409|doi=10.1073/pnas.1802429115|issn=0027-8424|pmc=6016793|pmid=29866852|bibcode=2018PNAS..115.6404S |doi-access=free}} However, plant-virus xrRNA and flaviviral xrRNA are distinguishable by their underlying three-dimensional folds.{{Cite journal|last1=Steckelberg|first1=Anna-Lena|last2=Vicens|first2=Quentin|last3=Costantino|first3=David A.|last4=Nix|first4=Jay C.|last5=Kieft|first5=Jeffrey S.|date=2020-05-01|title=The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold|journal=bioRxiv|language=en|doi=10.1101/2020.04.30.070631|s2cid=218530297|doi-access=free}} It has been reported that xrRNAs block the progression of 5' to 3' exoribonuclease producing subgenomic RNAs. xrRNA elements can be found in some of the deadliest viruses in agriculture including, potato leafroll virus (PLRV), leading responsible virus for worldwide potato yield loss, maize chlorotic mottle virus (MCMV), responsible for 90% maize/corn yield loss in sub-Saharan Africa, and maize yellow dwarf virus-RMV (MYDV- RMV), formerly BYDV-RMV.

The dumbbell element (DB) are important for viral RNA synthesis.{{Cite journal|last1=Sztuba-Solinska|first1=Joanna|last2=Teramoto|first2=Tadahisa|last3=Rausch|first3=Jason W.|last4=Shapiro|first4=Bruce A.|last5=Padmanabhan|first5=Radhakrishnan|last6=Le Grice|first6=Stuart F. J.|date=2013-05-01|title=Structural complexity of Dengue virus untranslated regions: cis-acting RNA motifs and pseudoknot interactions modulating functionality of the viral genome|journal=Nucleic Acids Research|volume=41|issue=9|pages=5075–5089|doi=10.1093/nar/gkt203|issn=1362-4962|pmc=3643606|pmid=23531545}} Via the formation of additional pseudoknots, the loop regions of DB pairs with a complementary motif further downstream of the respective DB element.{{Cite journal|last1=Shi|first1=P. Y.|last2=Brinton|first2=M. A.|last3=Veal|first3=J. M.|last4=Zhong|first4=Y. Y.|last5=Wilson|first5=W. D.|date=1996-04-02|title=Evidence for the existence of a pseudoknot structure at the 3' terminus of the flavivirus genomic RNA|url=https://www.ncbi.nlm.nih.gov/pubmed/8672458|journal=Biochemistry|volume=35|issue=13|pages=4222–4230|doi=10.1021/bi952398v|issn=0006-2960|pmid=8672458}}{{Cite journal|last1=Olsthoorn|first1=R. C.|last2=Bol|first2=J. F.|date=2001-10-01|title=Sequence comparison and secondary structure analysis of the 3' noncoding region of flavivirus genomes reveals multiple pseudoknots|journal=RNA|volume=7|issue=10|pages=1370–1377|issn=1355-8382|pmc=1370180|pmid=11680841}} The DB elements also expose conserved sequences (CS) and repeated conserved sequences (RCS).{{Cite journal|last1=Hahn|first1=C. S.|last2=Hahn|first2=Y. S.|last3=Rice|first3=C. M.|last4=Lee|first4=E.|author5-link=Lynn Dalgarno|last5=Dalgarno|first5=L.|last6=Strauss|first6=E. G.|last7=Strauss|first7=J. H.|date=1987-11-05|title=Conserved elements in the 3' untranslated region of flavivirus RNAs and potential cyclization sequences|url=https://www.ncbi.nlm.nih.gov/pubmed/2828633|journal=Journal of Molecular Biology|volume=198|issue=1|pages=33–41|doi=10.1016/0022-2836(87)90455-4|issn=0022-2836|pmid=2828633|doi-access=free}} Further, the DB elements are also playing a role in viral translation, as deletion of both elements reduced viral translation levels.{{Cite journal|last1=Romero|first1=T. A.|last2=Tumban|first2=E.|last3=Jun|first3=J.|last4=Lott|first4=W. B.|last5=Hanley|first5=K. A.|date=2006-11-01|title=Secondary structure of dengue virus type 4 3' untranslated region: impact of deletion and substitution mutations|journal=Journal of General Virology|language=en|volume=87|issue=11|pages=3291–3296|doi=10.1099/vir.0.82182-0|pmid=17030863|issn=0022-1317|doi-access=free}}{{Cite journal|last1=Manzano|first1=Mark|last2=Reichert|first2=Erin D.|last3=Polo|first3=Stephanie|last4=Falgout|first4=Barry|last5=Kasprzak|first5=Wojciech|last6=Shapiro|first6=Bruce A.|last7=Padmanabhan|first7=Radhakrishnan|date=2011-06-24|title=Identification of Cis -Acting Elements in the 3′-Untranslated Region of the Dengue Virus Type 2 RNA That Modulate Translation and Replication|journal=Journal of Biological Chemistry|language=en|volume=286|issue=25|pages=22521–22534|doi=10.1074/jbc.M111.234302|issn=0021-9258|pmc=3121397|pmid=21515677|doi-access=free}}

There is evidence that pseudoknot-forming stem-loops (SL-PK) are encoded by dual-host insect-specific flaviviruses and classical insect-specific flaviviruses{{cite journal| author=Slonchak A, Parry R, Pullinger B, Sng JDJ, Wang X, Buck TF | display-authors=etal| title=Structural analysis of 3'UTRs in insect flaviviruses reveals novel determinants of sfRNA biogenesis and provides new insights into flavivirus evolution. | journal=Nat Commun | year= 2022 | volume= 13 | issue= 1 | pages= 1279 | pmid=35277507 | doi=10.1038/s41467-022-28977-3 | pmc= 8917146| bibcode=2022NatCo..13.1279S| s2cid=247407895}} but while short stem-loops are present in the genomes of all mosquito-borne flaviviruses, they are not involved in pseudoknot interactions for which structural is available.{{cite journal| author=Funk A, Truong K, Nagasaki T, Torres S, Floden N, Balmori Melian E | display-authors=etal| title=RNA structures required for production of subgenomic flavivirus RNA. | journal=J Virol | year= 2010 | volume= 84 | issue= 21 | pages= 11407–17 | pmid=20719943 | doi=10.1128/JVI.01159-10 | pmc=2953152 }}{{cite journal| author=Chapman EG, Moon SL, Wilusz J, Kieft JS| title=RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA. | journal=eLife | year= 2014 | volume= 3 | issue= | pages= e01892 | pmid=24692447 | doi=10.7554/eLife.01892 | pmc=3968743 | doi-access=free }} It is thought that SL-PK might stabilise xrRNAs or confer additional XRN1 resistance as abolishing the SL-PK of various viruses reduces the production of sfRNAs.

The cis-acting replication element (CRE) structure is structurally conserved among known flaviviruses. It consists of a small hairpin (sHP) and a larger structural element (3'SL). Mutations of sHP are shown to be lethal for Dengue virus in mosquito cells.{{Cite journal|last1=Villordo|first1=Sergio M.|last2=Gamarnik|first2=Andrea V.|date=2013-08-01|title=Differential RNA sequence requirement for dengue virus replication in mosquito and mammalian cells|journal=Journal of Virology|volume=87|issue=16|pages=9365–9372|doi=10.1128/JVI.00567-13|issn=1098-5514|pmc=3754043|pmid=23760236}} CRE is highly involved in the 5'-3' UTR interaction of flaviviruses.{{Cite journal|last1=Fernández-Sanlés|first1=Alba|last2=Ríos-Marco|first2=Pablo|last3=Romero-López|first3=Cristina|last4=Berzal-Herranz|first4=Alfredo|date=2017-04-03|title=Functional Information Stored in the Conserved Structural RNA Domains of Flavivirus Genomes|journal=Frontiers in Microbiology|volume=8|page=546|doi=10.3389/fmicb.2017.00546|issn=1664-302X|pmc=5376627|pmid=28421048|doi-access=free}} Regions of sHP are interacting with the SLB element and the cHP in the 5' UTR, whereas the 3'SL harbors a sequence that can interact with SLB, to further stabilize this long-range RNA-RNA interaction.

In ISFV, structural alignments of the 3' UTR revealed that many species harbor three to four repeats of two highly conserved elements, termed Ra and Rb.{{Cite journal|last1=Hoshino|first1=Keita|last2=Isawa|first2=Haruhiko|last3=Tsuda|first3=Yoshio|last4=Yano|first4=Kazuhiko|last5=Sasaki|first5=Toshinori|last6=Yuda|first6=Masao|last7=Takasaki|first7=Tomohiko|last8=Kobayashi|first8=Mutsuo|last9=Sawabe|first9=Kyoko|date=2007-03-01|title=Genetic characterization of a new insect flavivirus isolated from Culex pipiens mosquito in Japan|journal=Virology|language=en|volume=359|issue=2|pages=405–414|doi=10.1016/j.virol.2006.09.039|pmid=17070886|doi-access=free}}{{Cite journal|last1=Ochsenreiter|first1=Roman|last2=Hofacker|first2=Ivo|last3=Wolfinger|first3=Michael|date=2019-03-24|title=Functional RNA Structures in the 3′UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses|journal=Viruses|language=en|volume=11|issue=3|pages=298|doi=10.3390/v11030298|issn=1999-4915|pmc=6466055|pmid=30909641|doi-access=free}} These elements show variable loop regions and low sequence conservation in the Ra element. However, strong structure conservation and the occurrence of multiple copies may hint towards a possible functional importance of these elements.

In different studies, a short stem-loop, named SL6 has been observed in at least TBEV, LGTV and OHFV.{{Citation|last1=Gritsun|first1=T.S.|title=Origin and Evolution of 3′Utr of Flaviviruses: Long Direct Repeats as A Basis for the Formation of Secondary Structures and Their Significance for Virus Transmission|date=2006|url=https://linkinghub.elsevier.com/retrieve/pii/S0065352706690052|journal=Advances in Virus Research|volume=69|pages=203–248|publisher=Elsevier|language=en|doi=10.1016/s0065-3527(06)69005-2|isbn=978-0-12-373712-0|access-date=2020-08-27|last2=Gould|first2=E.A.|pmid=17222695}}{{Cite journal|last1=Gritsun|first1=Dmitri J.|last2=Jones|first2=Ian M.|last3=Gould|first3=Ernest A.|last4=Gritsun|first4=Tamara S.|date=2014-03-19|editor-last=Donlin|editor-first=Maureen J.|title=Molecular Archaeology of Flaviviridae Untranslated Regions: Duplicated RNA Structures in the Replication Enhancer of Flaviviruses and Pestiviruses Emerged via Convergent Evolution|journal=PLOS ONE|language=en|volume=9|issue=3|pages=e92056|doi=10.1371/journal.pone.0092056|issn=1932-6203|pmc=3960163|pmid=24647143|bibcode=2014PLoSO...992056G|doi-access=free}} SL6 shows a high heterogeneity among different tick-borne flaviviruses, but is structurally conserved supported by multiple covariation.

{{Navbox

| name = hide the gallery

| title = Gallery of Flavivirus 3' UTR RNA structures

| titlestyle = background:#e7dcc3

| state = autocollapse

| list1 = {{Gallery

| Image:RF03547.svg|Flavi_xrRNA Secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF03547 RF03547]

| Image:RF03541.svg|Flavi_ISFV_xrRNA Secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF03541 RF03541]

| Image:RF03542.svg|Flavi_ISFV_repeat_Ra_Rb Secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF03542 RF03542]

| Image:RF03544.svg|Flavi_ISFV_repeat_Ra Secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF03544 RF03544]

| Image:RF03543.svg|Flavi_ISFV_repeat_Rb Secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF03543 RF03543]

| Image:RF03545.svg|Flavi_ISFV_CRE Secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF03545 RF03545]

| Image:RF03539.svg|Flavi_NKV_xrRNA Secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF03539 RF03539]

| Image:RF03540.svg|Flavi_NKV_CRE Secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF03540 RF03540]

| Image:RF03538.svg|Flavi_TBFV_CRE Secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF03538 RF03538]

| Image:RF03537.svg|Flavi_TBFV_SL6 Secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF03537 RF03537]

| Image:RF03536.svg|Flavi_TBFV_xrRNA Secondary structure taken from the [http://rfam.org Rfam] database. Family [http://rfam.org/family/RF03536 RF03536]

}}

}}

Category:Non-coding RNA

Category:Flaviviridae