TY - JOUR

T1 - Untranslated Regions of a Segmented Kindia Tick Virus Genome Are Highly Conserved and Contain Multiple Regulatory Elements for Viral Replication

AU - Tsishevskaya, Anastasia A.

AU - Alkhireenko, Daria A.

AU - Bayandin, Roman B.

AU - Kartashov, Mikhail Yu

AU - Ternovoi, Vladimir A.

AU - Gladysheva, Anastasia V.

N1 - Whole-genome sequencing of Kindia tick virus was performed within the framework of the Order of the Government of the Russian Federation of 14 November 2020, No. 2985-r, on Russian–Guinean scientific and technical cooperation in the field of epidemiology, prevention, and monitoring of bacterial and viral infections in the Republic of Guinea. Analysis of untranslated regions was supported by the Ministry of Science and Higher Education of the Russian Federation (agreement No. 075-15-2021-1355 of 12 October 2021) as part of the implementation of certain activities of the Federal Scientific and Technical Program for the Development of Synchrotron and Neutron Research and Research Infrastructure for 2019–2027.

PY - 2024/2

Y1 - 2024/2

N2 - Novel segmented tick-borne RNA viruses belonging to the group of Jingmenviruses (JMVs) are widespread across Africa, Asia, Europe, and America. In this work, we obtained whole-genome sequences of two Kindia tick virus (KITV) isolates and performed modeling and the functional annotation of the secondary structure of 5′ and 3′ UTRs from JMV and KITV viruses. UTRs of various KITV segments are characterized by the following points: (1) the polyadenylated 3′ UTR; (2) 5′ DAR and 3′ DAR motifs; (3) a highly conserved 5′-CACAG-3′ pentanucleotide; (4) a binding site of the La protein; (5) multiple UAG sites providing interactions with the MSI1 protein; (6) three homologous sequences in the 5′ UTR and 3′ UTR of segment 2; (7) the segment 2 3′ UTR of a KITV/2017/1 isolate, which comprises two consecutive 40 nucleotide repeats forming a Y-3 structure; (8) a 35-nucleotide deletion in the second repeat of the segment 2 3′ UTR of KITV/2018/1 and KITV/2018/2 isolates, leading to a modification of the Y-3 structure; (9) two pseudoknots in the segment 2 3′ UTR; (10) the 5′ UTR and 3′ UTR being represented by patterns of conserved motifs; (11) the 5′-CAAGUG-3′ sequence occurring in early UTR hairpins. Thus, we identified regulatory elements in the UTRs of KITV, which are characteristic of orthoflaviviruses. This suggests that they hold functional significance for the replication of JMVs and the evolutionary similarity between orthoflaviviruses and segmented flavi-like viruses.

AB - Novel segmented tick-borne RNA viruses belonging to the group of Jingmenviruses (JMVs) are widespread across Africa, Asia, Europe, and America. In this work, we obtained whole-genome sequences of two Kindia tick virus (KITV) isolates and performed modeling and the functional annotation of the secondary structure of 5′ and 3′ UTRs from JMV and KITV viruses. UTRs of various KITV segments are characterized by the following points: (1) the polyadenylated 3′ UTR; (2) 5′ DAR and 3′ DAR motifs; (3) a highly conserved 5′-CACAG-3′ pentanucleotide; (4) a binding site of the La protein; (5) multiple UAG sites providing interactions with the MSI1 protein; (6) three homologous sequences in the 5′ UTR and 3′ UTR of segment 2; (7) the segment 2 3′ UTR of a KITV/2017/1 isolate, which comprises two consecutive 40 nucleotide repeats forming a Y-3 structure; (8) a 35-nucleotide deletion in the second repeat of the segment 2 3′ UTR of KITV/2018/1 and KITV/2018/2 isolates, leading to a modification of the Y-3 structure; (9) two pseudoknots in the segment 2 3′ UTR; (10) the 5′ UTR and 3′ UTR being represented by patterns of conserved motifs; (11) the 5′-CAAGUG-3′ sequence occurring in early UTR hairpins. Thus, we identified regulatory elements in the UTRs of KITV, which are characteristic of orthoflaviviruses. This suggests that they hold functional significance for the replication of JMVs and the evolutionary similarity between orthoflaviviruses and segmented flavi-like viruses.

KW - Flaviviridae

KW - Jingmenvirus group

KW - Kindia tick virus

KW - RNA structure

KW - flavi-like virus

KW - ixodid ticks

KW - orthoflavivirus

KW - phylogenetics

KW - segmented virus

KW - untranslated region

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85187295904&origin=inward&txGid=892e8ce9f24cf40b88a838f974300d5a

UR - https://www.webofscience.com/wos/woscc/full-record/WOS:001172667600001

UR - https://www.mendeley.com/catalogue/a15ce707-6f80-3eab-87e8-3c44d6acd8ca/

U2 - 10.3390/microorganisms12020239

DO - 10.3390/microorganisms12020239

M3 - Article

C2 - 38399643

VL - 12

JO - Microorganisms

JF - Microorganisms

SN - 2076-2607

IS - 2

M1 - 239

ER -