Phylogenetic study on structural elements of HIV-1 poly(A) region. 1. PolyA and DSE hairpins
Genome of human immunodeficiency virus type 1 (HIV-1) is highly heterogeneous. The aim of this work was a phylogenetic study on structural elements of the HIV-1 poly(A) region, in particular polyA and DSE hairpins which compose a core poly(A) site. Methods. The secondary structure of the HIV-1 core...
Saved in:
| Published in: | Вiopolymers and Cell |
|---|---|
| Date: | 2013 |
| Main Authors: | , , , |
| Format: | Article |
| Language: | English |
| Published: |
Інститут молекулярної біології і генетики НАН України
2013
|
| Subjects: | |
| Online Access: | https://nasplib.isofts.kiev.ua/handle/123456789/153248 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Journal Title: | Digital Library of Periodicals of National Academy of Sciences of Ukraine |
| Cite this: | Phylogenetic study on structural elements of HIV-1 poly(A) region. 1. PolyA and DSE hairpins / M.I. Zarudnaya, A.L. Potyahaylo, I.M. Kolomiets, D.M. Hovorun // Вiopolymers and Cell. — 2013. — Т. 29, №. 6. — С. 454-462. — Бібліогр.: 18 назв. — англ. |
Institution
Digital Library of Periodicals of National Academy of Sciences of Ukraine| id |
nasplib_isofts_kiev_ua-123456789-153248 |
|---|---|
| record_format |
dspace |
| spelling |
Zarudnaya, M.I. Potyahaylo, A.L. Kolomiets, I.M. Hovorun, D.M. 2019-06-13T16:21:49Z 2019-06-13T16:21:49Z 2013 Phylogenetic study on structural elements of HIV-1 poly(A) region. 1. PolyA and DSE hairpins / M.I. Zarudnaya, A.L. Potyahaylo, I.M. Kolomiets, D.M. Hovorun // Вiopolymers and Cell. — 2013. — Т. 29, №. 6. — С. 454-462. — Бібліогр.: 18 назв. — англ. 0233-7657 DOI: http://dx.doi.org/10.7124/bc.00083F https://nasplib.isofts.kiev.ua/handle/123456789/153248 577.21.5 Genome of human immunodeficiency virus type 1 (HIV-1) is highly heterogeneous. The aim of this work was a phylogenetic study on structural elements of the HIV-1 poly(A) region, in particular polyA and DSE hairpins which compose a core poly(A) site. Methods. The secondary structure of the HIV-1 core poly(A) site has been predicted by the UNAFold program. Results. The structure of the polyA and DSE hairpins has been analysed in 1679 HIV-1 genomes of group M and 18 genomes of simian immunodeficiency virus SIVcpzPtt. We found 244 and 171 different sequences for the HIV-1 polyA and DSE hairpins, respectively. However 70 % of the HIV-1 isolates studied contain one of 7 variants of the polyA hairpin which occur with a frequency 5 % (main variants) and 79 % of the isolates contain one of 7 main variants of the DSE hairpin. We also revealed subtype and country specific mutations in these hairpins. We found that the SIV polyA hairpin most closely resembles that found in HIV-1 genomes of B/C subtypes. Conclusions. The results of our large-scale phylogenetic study support some structural models of the HIV-1 5' UTR, in particular the tertiary interaction between the polyA hairpin and the matrix region in HIV-1 gRNA. Possibly, the DSE hairpin appeared in the course of viral evolution of the HIV-1 group M. An exposure of the U/GU-rich element in the apical loop of DSE hairpin could significantly increase the efficiency of pre-mRNA polyadenylation in this HIV-1 group. Геном вірусу імунодефіциту людини (ВІЛ-1) надзвичайно гетерогенний. Мета. Провести філогенетичний аналіз структурних елементів області полі(А) ВІЛ-1, зокрема, шпильок поліA і DSE, які складають основний сайт полі(А). Методи. Передбачення вторинної структури основного полі(А)-сайта здійснювали за допомогою програми UNAFold. Результати. Структуру шпильок поліA і DSE проаналізовано для 1679 геномів ВІЛ-1 групи M та 18 геномів вірусу імунодефіциту мавп SIVcpzPtt: у геномах ВІЛ-1 виявлено 244 і 171 різна послідовність шпильок поліA і DSE відповідно. Однак 70 % вивчених геномів містили один із семи варіантів шпильки поліA, які зустрічалися з частотою 5 % (основні варіанти), і 79 % ізолятів вміщують один із семи основних варіантів шпильки DSE. Виявлено також специфічні для певного субтипу або країни мутації зазначених шпильок. Встановлено, що шпилька поліA з геному SIVcpzPtt дуже схожа на таку з геному ВІЛ-1 субтипів B і C. Висновки. Результати наших широкомасштабних досліджень підтримують деякі структурні моделі 5' нетрансльованої ділянки геному ВІЛ-1, зокрема, третинну взаємодію між шпилькою поліA і областю гена матриксного білка. Шпилька DSE, можливо, утворилася у процесі еволюції ВІЛ-1 групи М. Експонування U/GU-збагаченого елемента в апікальній петлі цієї шпильки могло значно підвищити ефективність поліаденілювання про-мРНК у ВІЛ-1 цієї групи. Геном ВИЧ-1 чрезвычайно гетерогенен. Цель. Провести филогенетический анализ структурных элементов области (поли)А ВИЧ-1, в частности, шпилек полиА и DSE, составляющих основной поли(А)-сайт. Методы. Вторичная структура основного поли(А)-сайта предсказана с помощью программы UNA Fold. Результаты. Структура шпилек полиА и DSE проанализирована в 1679 геномах ВИЧ-1 группы M и 18 геномах вируса иммунодефицита обезьян SIVcpzPtt: в геномах ВИЧ-1 выявлены соответственно 244 и 171 различная последовательность шпилек полиА и DSE. Однако 70 % изученных геномов содержат один из семи вариантов шпильки полиА, встречающихся с частотой 5 % (основные варианты) и 79 % изолятов содержат один из семи основных вариантов шпильки DSE. Обнаружены также варианты шпилек, специфические для определенного субтипа или страны. Выявлено, что шпилька полиА в геноме SIVcpzPtt наиболее близка по структуре таковой в геноме ВИЧ-1 субтипов В и С. Выводы. Результаты наших широкомасштабных исследований свидетельствуют в пользу некоторых структурных моделей 5' нетранслируемой области генома ВИЧ-1, в частности, наличия третичного взаимодействия между шпилькой полиА и участком в гене матриксного белка. Шпилька DSE, возможно, образовалась в процессе эволюции ВИЧ-1 группы М. Экспонирование U/GU- богатого элемента в апикальной петле шпильки DSE могло значи- тельно повысить эффективность полиаденилирования про- мРНК в ВИЧ-1 данной группы. en Інститут молекулярної біології і генетики НАН України Вiopolymers and Cell Structure and Function of Biopolymers Phylogenetic study on structural elements of HIV-1 poly(A) region. 1. PolyA and DSE hairpins Філогенетичний аналіз структурних елементів в області полі(А) ВІЛ-1. 1. Шпильки поліA та DSE Филогенетический анализ структурных элементов в области поли(А) ВИЧ-1. 1. Шпильки полиA и DSE Article published earlier |
| institution |
Digital Library of Periodicals of National Academy of Sciences of Ukraine |
| collection |
DSpace DC |
| title |
Phylogenetic study on structural elements of HIV-1 poly(A) region. 1. PolyA and DSE hairpins |
| spellingShingle |
Phylogenetic study on structural elements of HIV-1 poly(A) region. 1. PolyA and DSE hairpins Zarudnaya, M.I. Potyahaylo, A.L. Kolomiets, I.M. Hovorun, D.M. Structure and Function of Biopolymers |
| title_short |
Phylogenetic study on structural elements of HIV-1 poly(A) region. 1. PolyA and DSE hairpins |
| title_full |
Phylogenetic study on structural elements of HIV-1 poly(A) region. 1. PolyA and DSE hairpins |
| title_fullStr |
Phylogenetic study on structural elements of HIV-1 poly(A) region. 1. PolyA and DSE hairpins |
| title_full_unstemmed |
Phylogenetic study on structural elements of HIV-1 poly(A) region. 1. PolyA and DSE hairpins |
| title_sort |
phylogenetic study on structural elements of hiv-1 poly(a) region. 1. polya and dse hairpins |
| author |
Zarudnaya, M.I. Potyahaylo, A.L. Kolomiets, I.M. Hovorun, D.M. |
| author_facet |
Zarudnaya, M.I. Potyahaylo, A.L. Kolomiets, I.M. Hovorun, D.M. |
| topic |
Structure and Function of Biopolymers |
| topic_facet |
Structure and Function of Biopolymers |
| publishDate |
2013 |
| language |
English |
| container_title |
Вiopolymers and Cell |
| publisher |
Інститут молекулярної біології і генетики НАН України |
| format |
Article |
| title_alt |
Філогенетичний аналіз структурних елементів в області полі(А) ВІЛ-1. 1. Шпильки поліA та DSE Филогенетический анализ структурных элементов в области поли(А) ВИЧ-1. 1. Шпильки полиA и DSE |
| description |
Genome of human immunodeficiency virus type 1 (HIV-1) is highly heterogeneous. The aim of this work was a phylogenetic study on structural elements of the HIV-1 poly(A) region, in particular polyA and DSE hairpins which compose a core poly(A) site. Methods. The secondary structure of the HIV-1 core poly(A) site has been predicted by the UNAFold program. Results. The structure of the polyA and DSE hairpins has been analysed in 1679 HIV-1 genomes of group M and 18 genomes of simian immunodeficiency virus SIVcpzPtt. We found 244 and 171 different sequences for the HIV-1 polyA and DSE hairpins, respectively. However 70 % of the HIV-1 isolates studied contain one of 7 variants of the polyA hairpin which occur with a frequency 5 % (main variants) and 79 % of the isolates contain one of 7 main variants of the DSE hairpin. We also revealed subtype and country specific mutations in these hairpins. We found that the SIV polyA hairpin most closely resembles that found in HIV-1 genomes of B/C subtypes. Conclusions. The results of our large-scale phylogenetic study support some structural models of the HIV-1 5' UTR, in particular the tertiary interaction between the polyA hairpin and the matrix region in HIV-1 gRNA. Possibly, the DSE hairpin appeared in the course of viral evolution of the HIV-1 group M. An exposure of the U/GU-rich element in the apical loop of DSE hairpin could significantly increase the efficiency of pre-mRNA polyadenylation in this HIV-1 group.
Геном вірусу імунодефіциту людини (ВІЛ-1) надзвичайно гетерогенний. Мета. Провести філогенетичний аналіз структурних елементів області полі(А) ВІЛ-1, зокрема, шпильок поліA і DSE, які складають основний сайт полі(А). Методи. Передбачення вторинної структури основного полі(А)-сайта здійснювали за допомогою програми UNAFold. Результати. Структуру шпильок поліA і DSE проаналізовано для 1679 геномів ВІЛ-1 групи M та 18 геномів вірусу імунодефіциту мавп SIVcpzPtt: у геномах ВІЛ-1 виявлено 244 і 171 різна послідовність шпильок поліA і DSE відповідно. Однак 70 % вивчених геномів містили один із семи варіантів шпильки поліA, які зустрічалися з частотою 5 % (основні варіанти), і 79 % ізолятів вміщують один із семи основних варіантів шпильки DSE. Виявлено також специфічні для певного субтипу або країни мутації зазначених шпильок. Встановлено, що шпилька поліA з геному SIVcpzPtt дуже схожа на таку з геному ВІЛ-1 субтипів B і C. Висновки. Результати наших широкомасштабних досліджень підтримують деякі структурні моделі 5' нетрансльованої ділянки геному ВІЛ-1, зокрема, третинну взаємодію між шпилькою поліA і областю гена матриксного білка. Шпилька DSE, можливо, утворилася у процесі еволюції ВІЛ-1 групи М. Експонування U/GU-збагаченого елемента в апікальній петлі цієї шпильки могло значно підвищити ефективність поліаденілювання про-мРНК у ВІЛ-1 цієї групи.
Геном ВИЧ-1 чрезвычайно гетерогенен. Цель. Провести филогенетический анализ структурных элементов области (поли)А ВИЧ-1, в частности, шпилек полиА и DSE, составляющих основной поли(А)-сайт. Методы. Вторичная структура основного поли(А)-сайта предсказана с помощью программы UNA Fold. Результаты. Структура шпилек полиА и DSE проанализирована в 1679 геномах ВИЧ-1 группы M и 18 геномах вируса иммунодефицита обезьян SIVcpzPtt: в геномах ВИЧ-1 выявлены соответственно 244 и 171 различная последовательность шпилек полиА и DSE. Однако 70 % изученных геномов содержат один из семи вариантов шпильки полиА, встречающихся с частотой 5 % (основные варианты) и 79 % изолятов содержат один из семи основных вариантов шпильки DSE. Обнаружены также варианты шпилек, специфические для определенного субтипа или страны. Выявлено, что шпилька полиА в геноме SIVcpzPtt наиболее близка по структуре таковой в геноме ВИЧ-1 субтипов В и С. Выводы. Результаты наших широкомасштабных исследований свидетельствуют в пользу некоторых структурных моделей 5' нетранслируемой области генома ВИЧ-1, в частности, наличия третичного взаимодействия между шпилькой полиА и участком в гене матриксного белка. Шпилька DSE, возможно, образовалась в процессе эволюции ВИЧ-1 группы М. Экспонирование U/GU- богатого элемента в апикальной петле шпильки DSE могло значи- тельно повысить эффективность полиаденилирования про- мРНК в ВИЧ-1 данной группы.
|
| issn |
0233-7657 |
| url |
https://nasplib.isofts.kiev.ua/handle/123456789/153248 |
| citation_txt |
Phylogenetic study on structural elements of HIV-1 poly(A) region. 1. PolyA and DSE hairpins / M.I. Zarudnaya, A.L. Potyahaylo, I.M. Kolomiets, D.M. Hovorun // Вiopolymers and Cell. — 2013. — Т. 29, №. 6. — С. 454-462. — Бібліогр.: 18 назв. — англ. |
| work_keys_str_mv |
AT zarudnayami phylogeneticstudyonstructuralelementsofhiv1polyaregion1polyaanddsehairpins AT potyahayloal phylogeneticstudyonstructuralelementsofhiv1polyaregion1polyaanddsehairpins AT kolomietsim phylogeneticstudyonstructuralelementsofhiv1polyaregion1polyaanddsehairpins AT hovorundm phylogeneticstudyonstructuralelementsofhiv1polyaregion1polyaanddsehairpins AT zarudnayami fílogenetičniianalízstrukturnihelementívvoblastípolíavíl11špilʹkipolíatadse AT potyahayloal fílogenetičniianalízstrukturnihelementívvoblastípolíavíl11špilʹkipolíatadse AT kolomietsim fílogenetičniianalízstrukturnihelementívvoblastípolíavíl11špilʹkipolíatadse AT hovorundm fílogenetičniianalízstrukturnihelementívvoblastípolíavíl11špilʹkipolíatadse AT zarudnayami filogenetičeskiianalizstrukturnyhélementovvoblastipoliavič11špilʹkipoliaidse AT potyahayloal filogenetičeskiianalizstrukturnyhélementovvoblastipoliavič11špilʹkipoliaidse AT kolomietsim filogenetičeskiianalizstrukturnyhélementovvoblastipoliavič11špilʹkipoliaidse AT hovorundm filogenetičeskiianalizstrukturnyhélementovvoblastipoliavič11špilʹkipoliaidse |
| first_indexed |
2025-11-27T00:44:36Z |
| last_indexed |
2025-11-27T00:44:36Z |
| _version_ |
1850783634718457856 |
| fulltext |
STRUCTURE AND FUNCTION OF BIOPOLYMERS
UDC 577.21.5
Phylogenetic study on structural elements of HIV-1
poly(A) region. 1. PolyA and DSE hairpins
M. I. Zarudnaya, A. L. Potyahaylo, I. M. Kolomiets, D. M. Hovorun
Institute of Molecular Biology and Genetics, NAS of Ukraine
150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
m.i.zarudna@imbg.org.ua
Genome of human immunodeficiency virus type 1 (HIV-1) is highly heterogeneous. Aim. A phylogenetic study on
structural elements of the HIV-1 poly(A) region, in particular polyA and DSE hairpins which compose a core
poly(A) site. Methods. The secondary structure of the HIV-1 core poly(A) site has been pre- dicted by the UNAFold
program. Results. The structure of the polyA and DSE hairpins has been analysed in 1679 HIV-1 genomes of
group M and 18 genomes of simian immunodeficiency virus SIVcpzPtt. We found 244 and 171 different
sequences for the HIV-1 polyA and DSE hairpins, respectively. However 70 % of the HIV-1 isolates studied
contain one of 7 variants of the polyA hairpin which occur with a frequency �5 % (main variants) and 79 % of the
isolates contain one of 7 main variants of the DSE hairpin. We also revealed subtype and country specific
mutations in these hairpins. We found that the SIV polyA hairpin most closely resembles that found in HIV-1
genomes of B/C subtypes. Conclusions. The results of our large-scale phylogenetic study support some
structural models of the HIV-1 5' UTR, in particular the tertiary interaction between the polyA hairpin and the
matrix region in HIV-1 gRNA. Possibly, the DSE hairpin appeared in the course of viral evolution of the HIV-1
group M. An exposure of the U/GU-rich element in the apical loop of DSE hairpin could significantly increase
the efficiency of pre-mRNA polyadenylation in this HIV-1 group.
Keywords: HIV-1, SIVcpzPtt, poly(A) region, secondary structure, polyA hairpin, DSE hairpin.
Introduction. Polyadenylation of the pre-mRNAs in
mammals and their viruses depends on at least two se-
quence elements: the poly(A) signal (most often the
AAUAAA hexamer) and the U/GU-rich downstream
sequence element (DSE). These elements compose the
core poly(A) site. Multiple protein factors assemble on-
to this site, in particular, the cleavage and polyadeny-
lation specificity factor (CPSF) binds to the AAUAAA
hexamer and the cleavage stimulation factor (CstF)
binds to the U/GU-rich DSE [1, 2]. The efficiency of po-
lyadenylation process can be modulated by upstream se-
quence elements (USEs) or/and auxiliary downstream
sequence elements (AuxDSEs) [3]. In the HIV-1 retro-
virus, the identical sequences encompassing AAUAAA
and DSE are present at both the 5' and 3' ends of the
HIV-1 pre-mRNA and a strict regulation is needed to re-
press the premature polyadenylation at the 5' end of the
transcript and stimulate the reaction at the 3' end. In par-
ticular, usage of the 3' poly(A) site is promoted by the
USEs that are present exclusively at the 3' end of the
transcript [4].
In HIV-1 pre-mRNA, the AAUAAA hexamer is
partly occluded by base pairing in the upper part of the
polyA hairpin [5], the stability of which is delicately ba-
lanced to allow the regulation of polyadenylation reac-
tion at the both ends [6]. Two putative DSEs, UGUGU
and GUUGUGU, are located 6 and 19 nt downstream
of the cleavage site, respectively. Recently we have first
presented a structural model for the core poly(A) site at
the 3' end of the HIV-1 pre-mRNA [7] (Fig 1). The tracts
interacting with the polyadenylation factors as well as
other functionally important elements are indicated in
this figure. The other elements are functional at the 5'
end of HIV-1 genomic RNA (gRNA), inasmuch as they
454
ISSN 0233–7657. Biopolymers and Cell. 2013. Vol. 29. N 6. P. 454–462 doi: 10.7124/bc.00083F
� Institute of Molecular Biology and Genetics, NAS of Ukraine, 2013
455
PHYLOGENETIC STUDY ON STRUCTURAL ELEMENTS OF HIV-1 POLY(A) REGION
are located in the long terminal repeats of proviral DNA
they are also duplicated at the 3' end of the transcript.
HIV-1 genome is highly heterogeneous. The aim of
this work was a large-scale phylogenetic study on the
structural elements of the HIV-1 poly(A) region. First we
investigated how mutations in the polyA and DSE hair-
pins affect their secondary structure and also compared
the structure of these elements in HIV-1 pre-mRNAs
and pre-mRNAs of simian immunodeficiency virus of
chimpanzee Pan troglodytes troglodytes (SIVcpzPtt).
Materials and methods. The sequences encompas-
sing the complete poly(A) region in HIV-1 and SIV ge-
nomes have been extracted from the Entrez Nucleotide
database of NCBI. We have examined all HIV-1 geno-
mic sequences presented in this database by the end of
2010 and all corresponding genomic sequences from
SIVcpzPtt and SIVgor (gorilla) presented by the end of
2012. The secondary structure of the poly(A) site has
been predicted by the UNAFold program [11]. The ba-
se changes in sequences of HIV-1 and SIV pre-mRNAs
were determined as compared to RefSec (the HXB2 iso-
late, GenBank accession number K03455). Nucleotide
numbering starts with 1 at the first nucleotide of each in-
dividual structural element.
Results and discussion. PolyA hairpin. We have ana-
lysed the structure of elements of the HIV-1 core poly(A)
site for 1679 HIV-1 pre-mRNAs of group M (isolated
from 997 patients) and found 244 different sequences for
the polyA hairpin. These sequences contained up to ele-
ven base changes in comparison with the RefSec. The
polyA hairpins with the combination of base changes oc-
curring with a frequency � 5 % (the main variants, pA1–
pA7) are shown in Fig. 2. Their distribution by subtypes
A–C, and CRF01_AE, comprising large sub pools, is gi-
ven in Table 1. The total data on other subtypes and CRFs
comprising small subpools are listed in the last column.
All main variants of the polyA hairpin have identi-
cal upper part with a partly occluded AAUAAA hexa-
mer, while their stems contain different small defects
(bulges and internal loops). As seen in Table 1, some po-
lyA hairpin variants, for example pA1 (without muta-
tions) and pA2 (with the C39U base substitution) occur
in HIV-1 isolates of several subtypes with different
frequencies, while other variants occur mainly in HIV-
1 isolates of certain subtypes. In HIV-1 isolates of sub-
types D, F and G, the variants pA1 and pA2 are the most
frequent. It is of interest to note that none of the base
changes occurring in the main variants of polyA hair-
pin of subtype C isolates (pA4 and pA7) was found in
the main variants of CRF01_AE (pA5 and pA6).
Depending on the subtype, 52–84 % of HIV-1 isola-
tes contain one of main variants of the polyA hairpin
(Table 1). However, within a certain subtype their oc-
currence may be country specific. For example, the po-
lyA hairpin with the double mutation U38C + C39U
(pA4) occurs often in HIV-1 isolates of subtype C from
the African countries: Mozambique (35 %), South Af-
rica (47 %), Tanzania (54 %), and Zambia (72 %) and
rarely in Indian HIV-1 isolates (3 %). On the contrary,
the variant with the four base changes (pA7) occurs fre-
quently (55 %) in subtype C isolates from India and ra-
rely or is absent in the African countries. Some polyA
hairpins occurring with a frequency < 5 % in the HIV-1
isolates studied, though not presented in Table 1, are ra-
ther frequent in certain countries, for example, the hair-
pin with base changes C36A + U37C + U43C (pA8,
Fig. 2) was found in 10 % of subtype A isolates from
Tanzania. In general 70 % of all HIV-1 isolates studied
have one of the 7 main variants of the polyA hairpin.
What are the peculiarities of the polyA hairpin formed
in the rest of HIV-1 isolates? Table 2 is given to illust-
rate this issue. It shows the base changes in the polyA
hairpin for 26 HIV-1 isolates of subtype C from Mozam-
bique, which comprise half of the whole pool of these
isolates. As many as 54 % of HIV-1 isolates presented
A-U
A-U
C-G
U-A
C-G
U
C-G
G-C
A-U
A-U
C
U-A
U-A
C-G
G-U
U-A
C-G
A-U
C-G
C-G
U-A
G-C
C-G
C-G
G-U
U-AU G
U
U
C C
U G
U
G
U
U
G
U
A U
A G
A C
U C
G UC 1
2
3
9650
9600
Fig. 1. The 3' core poly(A) site of HIV-1 HXB2 pre-mRNA (RefSec).
Nucleotide positions are numbered as in the HXB2 genome. The AAU
AAA hexamer and the U/GU-rich signals are shadowed. The motifs
which are functional at the 5' end of HIV-1 genome: 1 – involved in
the long distance interaction with the matrix coding region [8]; 2 – the
5' strand of U5-AUG duplex [9]; 3 – a primer activation signal (PAS)
regulating the initiation of reverse transcription [10]
in Table 2 have one of the main polyA hairpin variants
such as pA4 (42 %), pA2 (8 %) and pA7 (4 %). The
polyA hairpins in the rest of isolates can be considered
as these three main variants with one or two base chan-
ges which occur with different frequencies in the HIV-
1 isolates studied.
For example, A32G (GenBank acc. no. AM076852)
occurs with a frequency below the error of sequencing
and submission of HIV-1 genomic sequence into Gen
Bank (0.5 % [12]), while A44G (AM076846) is very
frequent in HIV-1 isolates of subtype CRF01_AE but is
random in isolates of subtype C. Precisely rare and ran-
dom base changes lead to a great variety in sequences of
the polyA hairpin. The rare and random mutations pre-
sented in Table 2 did not affect greatly the overall struc-
ture of the polyA hairpin, except for G31A (AM076874).
This base change occurs singly or in the combination
with different mutations with a frequency of 2.1 % in
the HIV-1 isolates studied. In most cases, it results in
two alternative conformations of the hairpin with the
456
ZARUDNAYA M. I. ET AL.
pA2
-18.5
pA3
-16.5
pA4
-18.5
pA5
-18.1
pA6
-18.1
pA7
-20.6
pA8
A-U
A-U
C-G
U-A
C-G
G-C
A-U
A C
U-A
U-A
C-G
G-C
U-A
C-G
A-U
C C-G U
A U
A G
A C
U C
G UC
U
A
C G
pA9
-14.8 -14.9
A-U
A-U
C-G
U-A
C-G
G-C
A-U
A-U
U-G
U-A
C-G
G-C
U-A
C-G
A-U
C C-G U
A U
A G
A C
U C
G UC
U
A
C G
pA10
-18.8
G, kcal/molÄ
pA1
1
10
20
30
40
-18.5
A-U
A-U
C-G
U-A
C-G
U
C-G
G-C
A-U
A-U
C
U-A
U-A
C-G
G-U
U-A
C-G
A-U
C C-G U
A U
A G
A C
U C
G UC
A-U
A-U
C-G
U-A
C-G
U
C-G
G-C
A-U
C
A
U-A
U-A
C-G
G-U
U-A
C-G
A-U
C C-G U
A U
A G
A C
U C
G UC
A
A-U
A-U
C-G
U-A
C-G
U
C-G
G-C
A-U
C
A-U
U-A
U-A
C-G
G-U
U-A
C-G
A-U
C C-G U
A U
A G
A C
U C
G UC
A-U
A-U
C-G
U-A
C-G
U
C-G
G-C
A-U
A-U
A A
U-A
U-A
C-G
G U
U G
C-G
A-U
C C-G U
A U
A G
A C
U C
G UC
A-U
A-U
C-G
U-A
C-G
U
C-G
G-C
A-U
A-U
A G
U-A
U-A
C-G
G U
U G
C-G
A-U
C C-G U
A U
A G
A C
U C
G UC
A-U
A-U
C-G
U-A
C-G
U
C-G
G-C
A-U
C
A-U
U-G
U-A
C-G
G-C
U-A
C-G
A-U
C C-G U
A U
A G
A C
U C
G UC
A-U
A-U
C-G
U-A
C-G
U
C-G
G-C
U
A-U
A-U
U-A
U-A
C-G
G-U
U-A
C-G
A-U
C C-G U
A U
A G
A C
U C
G UC
A A
A G
U C
A-U
A-U
C-G
U-A
C-G
U
C-G
G-C
A-U
C
A-U
U-G
U-A
C-G
G-C
U-A
C-G
A-U
C C-G U
C
U
U
C
A
C
C U
G-U
U-A
U-A
C-G
G-U
C-G
G-C
A-U
C
A-U
U-G
U-A
C-G
G-C
U-A
C-G
A-U
C C-G U
CU
C
A
A
U
A
A A
Fig. 2. Optimal structures of polyA hairpin variants in HIV-1 and SIVcpzPtt pre-mRNAs. The base changes as compared to RefSec are squared,
insertions and deletions are indicated by triangle and spot, respectively. The AAUAAA hexamer is shadowed. pA1–pA7 – main variants of the
polyA hairpin in HIV-1 isolates of group M; pA8 – rather frequent variant in subtype A isolates from Tanzania; pA9 – variant with the G31A base
change; pA10 – polyA hairpin variant in SIVcpzPtt isolates
Variant Base changes
Subtype
A B C CRF01_AE Others
Number of HIV-1 isolates (number of patients)
141 (122) 645 (258) 291 (234) 162 (61) 440 (322)
pA1 No 17 50 2 0 42
pA2 C39U 32 27 8 0 10
pA3 U38C + C39A 0 6 1 0 0.4
pA4 U38C + C39U 3 1 40 0 8
pA5 10_11ins A + C39A + A44G 0 0.1 0 46 1
pA6 10_11ins A + C39G + A44G 0 0 0 6 0
pA7 U38C + C39U + A40G + U43C 0 0.1 15 0 2
Total – 52 84 67 52 63
Table 1
Occurrence of polyA hairpin variants in HIV-1 isolates of different subtypes (%)
same free energy and complete exposure of the AAUA
AA hexamer in one of these conformations (for examp-
le, see pA9 in Fig. 2).
As seen in Table 2, the double mutation U38C +
+ C39U (both as the pA4 variant and in combination
with other base changes) is prevailing among the HIV-
1 isolates from Mozambique (77 %). The availability of
a certain motif containing one or several frequent base
changes in combination with rare and/or random muta-
tions is also characteristic of the polyA hairpins in HIV-
1 isolates of other subtypes. It is also a peculiarity of
other structural elements in the HIV-1 polyA region.
457
PHYLOGENETIC STUDY ON STRUCTURAL ELEMENTS OF HIV-1 POLY(A) REGION
Accession
number
Patient
Base changes in polyA hairpin
PolyA
hairpin
Position
7 10 31 32 36 37 38 39 40 43 44
AM076840 PG174 A10G U38A C39U
AM076842 PG174 A10G U38A C39U
AM076844 PG81 U38C C39U pA4
AM076846 PG56 U38C C39U A44G
AM076848 PG5 U38C C39U pA4
AM076850 PG5 U38C C39U pA4
AM076852 PG6 A32G C39U
AM076854 PG184 U38C C39U pA4
AM076856 PG196 U38C C39U pA4
AM076858 PG182 U38C C39U A40G
AM076860 PG182 U38C C39U A40G
AM076862 PG188 U38C C39U pA4
AM076864 PG189 C36U U38C C39U A40G U43C
AM076866 PG203 U38C C39U A40G
AM076868 PG215 C39U pA2
AM076870 PG224 U38C C39U pA4
AM076872 PG227 U38C C39U A40G U43C pA7
AM076874 PG227 G31A U38C C39U A40G U43C
AM076876 PG227 U7C C36U U38C C39U A40G U43C
AM076878 PG230 C36A U37C C39U
AM076880 PG231 U38C C39U pA4
AM076882 PG177 C39U pA2
AM076884 PG178 U38C C39U pA4
AM076886 PG217 U38C C39U pA4
AM076888 PG218 C36U U38C C39U
AM076891 PG36 U38C C39U pA4
Table 2
Base changes in polyA hairpin of HIV-1 subtype C isolates from Mozambique
In general the base changes which led to significant
alterations in the polyA hairpin structure occurred only
in 4 % of all HIV-1 genomes studied. The structures of
the polyA region in the HIV-1 isolates studied are presen-
ted in our database CESSHIV-1 which is currently avai-
lable online at http://www.cesshiv1.org. Base change fre-
quency at each position of the polyA hairpin is presen-
ted in Suppl. information (Table S1). Rather frequent mu-
tations in this element are an insertion between positions
10, 11 and base changes at positions 37–40, 43, and 44.
HIV-1 gRNA contains several strong binding sites
for multifunctional virion infectivity factor (Vif) inclu-
ding the polyA hairpin [13]. In particular, Vif-RNA
interaction is important for viral particle assembly. Vif
specifically binds to the stem of polyA hairpin, however
structural and sequence determinants of this binding
458
ZARUDNAYA M. I. ET AL.
5 10 15 20 25 30
0
20
40
60
80
100
120
1220
1240
5 10 15 20 25 30
0
10
20
30
N
u
m
b
er
ÄG kcal/mol
A
N
u
m
b
er
ÄG kcal/mol
B
Fig. 3. Free energy distribution of HIV-1 polyA hairpin variants: A – all 1863 polyA hairpins; B – 286 HIV-1 polyA hairpins with different
sequences (see Section PolyA hairpin)
are not defined. Various defects in the stem of polyA
hairpin (Fig. 2) can modulate its binding to Vif.
Base changes in the AAUAAA hexamer and the
neighbouring GCUUGCC tract occur with a frequency
below the error level, except for a position 28 in the po-
lyA hairpin at which mutations occur with a frequency
of 0.7 %. We have also shown high conservation of the
sequence GGCAAGC in the matrix region of HIV-1
gRNA for a large pool of HIV-1 isolates. Thus, our data
support a statement about the long distance interaction
between the GCUUGCC and GGCAAGC sequences
important for the tertiary structure of the 5' untranslated
region of HIV-1 gRNA [8].
As mentioned in Introduction, a balanced stability
of the polyA hairpin is crucial for HIV-1 replication [6,
14]. Both destabilization and stabilization of the wild
type hairpin inhibits polyadenylation of HIV-1 pre-
mRNA at the 3' end of the transcript. Stabilization of
this hairpin by 10.4 kcal/mol blocked the access of po-
lyadenylation factors to the hexamer and led to comp-
lete loss of polyadenylation at the 3' end of HIV-1 pre-
mRNA [6, 14]. Destabilization by 8.5 kcal/mol increa-
sed the efficiency of premature polyadenylation at the
5' end of HIV-1 transcript from 5–10 % to 30–40 %
[14], that affects less severely polyadenylation at the 3'
end than stabilization of the polyA hairpin. It was
459
PHYLOGENETIC STUDY ON STRUCTURAL ELEMENTS OF HIV-1 POLY(A) REGION
G, kcal/molÄ
1 1
10
10
20 20
U U
G G
U U
U G
C-G
U-A
G-C
C-G
C-G
G-U
G U-A A
U
C C
U
U U
G G
U U
U G
C-G
U-A
C-G
C-G
G-U
G U-A A
C
U
C
U
A
C
U U
G A
U U
U G
C-G
U-A
G-C
C-G
C-G
G-U
G U-A A
U
C C
U
U U
G U
U U
U G
C-G
U-A
G-C
C-G
C-G
G-U
G U-A A
U
C C
U
G U
U U
G A
U-G
C-G
U-A
G-C
C-G
C-G
G-U
G U-A A
U
C C
U
C
U
C
U
A
C
G U
U U
G A
U-G
C-G
U-A
C-G
C-G
G-U
G U-A A
C
U
C
U
A
C
U U
G G
U U
C-G
U-A
C-G
C-G
G-U
G U-A A
U U
A G
U U
U G
C-G
U-A
G-C
C-G
C-G
G-U
G U-A A
U
C C
U
DSE1 DSE2 DSE3 DSE4 DSE5
U A
A G
U U
U C
C-G
U-A
G-C
C-G
C-G
G-U
U-A
U G-U C
U
C C
U
A U
A U
U
C-G
U
C-G
U-A
C-G
C-G
G-U
U-A
U G-U C
C
U
C
U
A
C
U A
A G
U U
U C
C-G
U-A
C-G
C-G
G-U
U-A
U G-U C
C
U
C
U
A
U
DSE6 DSE7 DSE8 DSE 1SIV DSE 2SIV DSE 3SIV
-5.4 -2.2 -5.4 -5.4 -5.4 -6.5 -3.3 -2.4 -4.0 -2.6 -6.5
Fig. 4. Optimal structures of DSE hairpin variants in HIV-1 and SIVcpzPtt pre-mRNAs. The base changes as compared to RefSec are squared, de-
letions are indicated by spot. The U/GU-rich DSE signal is shadowed. DSE1–DSE7 – main variants of the DSE hairpin in HIV-1 isolates of group
M (for DSE2 a suboptimal structure with free energy difference of –0.9 kcal/mol is shown); DSE8 – frequent variant in subtype D isolates;
DSE
SIV
1–DSE
SIV
3 – DSE-like hairpin variants in SIVcpzPtt isolates
Variant Base changes
Subtype
A B C CRF01_AE Others
Number of HIV-1 isolates (number of patients)
141 (122) 645 (258) 291 (234) 162 (61) 440 (322)
DSE1 RS 30.5 76.0 65.3 0 58.6
DSE2 G6A 3.5 7.3 6.5 0 7.7
DSE3 G10A 0 2.2 5.5 0 1.8
DSE4 G15A 36.9 0.5 1.0 0 3.9
DSE5 G15U 7.1 0.1 0.7 0 3.6
DSE6 U12G + G13U + G15A + U16G 0 0 0 43.8 0.9
DSE7 G6A + U12G + G13U + G15A + U16G 0 0 0 13.6 0
Total – 78 86 79 57 76
Table 3
Occurrence of DSE hairpin variants in HIV-1 isolates of different subtypes (%)
shown by the method of virus evolution that HIV-1 mu-
tants with stabilized or destabilized polyA hairpin have
improved their replication capacity via drifting towards
a hairpin of thermodynamic stability that is close to the
value of the wild type hairpin [15].
Free energy distribution of the HIV-1 polyA hairpins
is presented in Fig. 3, A. Here we have analysed the HIV-
1 genomes which contain both the complete poly(A) re-
gion (see Materials and methods) and incomplete regions
encompassing a polyA hairpin sequence (see CESSHIV-
1 database). In sum we have analyzed 1863 genomes
(from 1072 patients) which contain 286 different sequen-
ces of the polyA hairpin. For two patients with multiple
identical sequences of the polyA hairpin, we considered
for analysis only one intrapatient sequence.
The major peak in Fig. 3, A, corresponds to the HIV-
1 isolates containing the polyA hairpins with free ener-
gy (dG) of –18.5 kcal/mol. The main variants of the po-
lyA hairpin pA1, pA2 and pA4 make a major contribu-
tion to this peak (92 %), while other main variants cont-
ribute to minor peaks at –16.5, –18.1 and –20.6 kcal/mol.
The minor peak at –12.8 kcal/mol corresponds mostly
to the polyA hairpins with the base change G31A and
double mutation G31A + C39U.
Free energy distribution of the 286 HIV-1 polyA hair-
pins with different sequences is shown in Fig. 3, B. In ge-
neral both distributions are similar. The main peak in Fig.
3, B, also corresponds to –18.5 kcal/mol. A maximal num-
ber of different sequences of the polyA hairpin (29 ones)
contribute to this peak. Both distributions are skewed,
in particular the number of HIV-1 isolates with the polyA
hairpins with dG > –18.5 kcal/mol (26.9 %) significantly
exceeds that with dG < –18.5 kcal/mol (6.5 %).
Free energy distributions of the HIV-1 polyA hair-
pins for different subtypes (A, B, C, D, G, CRF01_AE
and CRF02_AG) are similar to those presented in Fig.
3, A. All distributions are skewed and have the maxi-
mum at –18.5 kcal/mol, except that the plot for CRF01_
AE has a maximum at –18.1 kcal/mol. Thus, a free ener-
gy of the polyA hairpin lies within the range of –10.9 �
� –20.9 kcal/mol in most HIV-1 isolates (98.5 %), and
the polyA hairpin with dG of –18.5 kcal/mol is found in
66.6 % isolates.
To gain insight into the evolution of frequent muta-
tions in HIV-1 polyA hairpin we studied a structure of
the core poly(A) site in 18 isolates of SIVcpzPtt that is
an ancestor of HIV-1 group M [16]. Similarity of the po-
lyA hairpin in SIVcpzPtt and HIV-1 was first reported
by Berkhout et al. [5]. The SIV polyA hairpin presented
in their article possesses the upper part identical to that
in HIV-1 HXB2 genome and a stem with two bulges 0�
� 2 and 0 � 1. In our study we found 14 different sequ-
ences of the SIV polyA hairpin, including the sequences
identical to the HIV-1 polyA hairpin variants pA1, pA2
and pA4. All SIV isolates have the polyA hairpin with the
common upper part, except for three isolates in which
the apical loop is elongated by 2 nucleotides (nt) thus
exposing 5 nt instead of 4 nt of the AAUAAA hexamer.
The combination of base changes 35_36insA +
+ C39del + A40G + U43C can be considered as a fre-
quent motif of the SIV polyA hairpin (Supplementary
information, Table S2). Three SIV isolates have the po-
lyA hairpin containing exclusively this motif (pA10,
Fig. 2). The double mutation 35_36insA + C39del was
found in three HIV-1 polyA hairpins (two isolates of
subtype C and one of subtype B) and A40G + U43C is a
constituent of the combination of base changes in the
HIV-1 polyA variant pA7 specific for subtype C isolates.
DSE hairpin. The variants of HIV-1 DSE hairpin
with combinations of base changes occurring with a
frequency � 5 % (the main variants, DSE1-DSE7) are
shown in Fig. 4. Their distribution by subtype is given
in Table 3. The variants DSE1-DSE3 are found in HIV-1
isolates of different subtypes, while the variants DSE4–
DSE7 occur predominantly in HIV-1 isolates of certain
subtype. HIV-1 isolates of subtypes D, F and G com-
monly have the DSE hairpin without mutations (DSE1),
except that the variant with the base changes G6A +
+ U16del + G17del (DSE8, Fig. 4) occurs rather fre-
quently in HIV-1 isolates of subtype D (19 %). About
80 % of the HIV-1 isolates studied have one of the main
DSE hairpin variants.
The apical loop is the most variable region of the
DSE hairpin (Supplementary information, Table S3).
In the U/GU-rich tract, frequent base changes occur at
positions 12, 13, 15 and 16. The combination of these
four base changes, which is specific for CRF01_AE,
does not impair DSE signal (DSE6, Fig. 4). According
to our description of the mammalian DSE region [17],
it is composed of certain U/GU-rich pentamers (in par-
ticular the GUUGU, UGUGU or GUGUU tracts) which
are located at different distances from each other. All the-
460
ZARUDNAYA M. I. ET AL.
se pentamers are found in the apical loop of the main va-
riants of the DSE hairpin as single or overlapping tracts.
In DSE5, the GUUGU pentamer overlaps the UGUUU
tract which is a U-rich (URE) DSE signal of the type «a
four out of five base URE» [18]. In some HIV-1 isolates
of CRF01_AE, the mutations at positions 12 and/or 13
impair DSE signal by preventing a complete exposure of
the U/GU-rich tract, which can decrease an efficiency
of the polyadenylation process. It concerns mainly the
group of 46 HIV-1 isolates from 3 patients, which pos-
sess the DSE hairpin with a combination of base chan-
ges G6A + C8U + U12del + G15C + U16A + 17G18.
The sequences of both strands of the DSE hairpin
stem are well conserved. The rather frequent base chan-
ge G6A destabilizes the hairpin and leads to partial oc-
clusion of the U/GU-rich tract in the optimal structure;
however this tract is completely exposed in a the subop-
timal structure with close free energy (DSE2, Fig. 4).
Rare mutations (4 %) occur at position 17 (deletion and
G17A base change) and between positions 17 and 18
(insertion). The deletion occurs in 39 % of HIV-1 isola-
tes of subtype D and does not affect DSE signal exposu-
re (DSE8, Fig. 4). The insertion 17G18 in combina-
tions with some base changes impairs DSE signal ex-
posure, mainly in the above mentioned group of 46 iso-
lates of CRF01_AE.
The 5' strand of the DSE hairpin together with two
neighboring residues (tract 2 in Fig. 1) correspond to
the 5' strand of the U5-AUG duplex formed at the 5' end
of HIV-1 gRNA. The mutation G6A in the DSE hairpin
corresponds to G9651A in HXB2 genome resulting in a
G-U to A-U base pair substitution in the duplex. We have
shown that the 3' strand of this duplex is also well con-
served in a large pool of HIV-1 isolates, which supports
the formation of the U5-AUG duplex. The conservation
of tract 3 encompassing PAS signal supports its func-
tional importance, including tRNA3
Lys-PAS interaction.
In the SIV isolates studied, we have not found a hair-
pin similar to the HIV-1 DSE hairpin as distinct from
the polyA hairpin occurred in both HIV-1 and SIV. How-
ever a hairpin with the bottom duplex like in the HIV-1
DSE hairpin (frequently with an additional base pair
G-U) was found in almost all SIV isolates (DSESIV1-
DSESIV3, Fig. 4). The main difference between the
HIV-1 DSE hairpin and its SIV analogue is the absence
of the U/GU-rich tract in the DSESIV apical loop. Only
one SIV hairpin has such tract but not completely ex-
posed (DSESIV2, Fig. 4). Probably, SIV isolates use
UGUGU signal just downstream of the polyA hairpin
(Fig. 1) that is partly occluded.
The strains of HIV-1 are classified into four groups:
M, N, O and P which are of chimpanzee or gorilla ori-
gin [16]. We have not found any DSE hairpin exposing
the U/GU-rich tract in either HIV-1 groups N, O and P
(36 isolates) or SIV from gorilla (5 isolates). We hy-
pothesize that the U/GU-rich tract exposed in the apical
loop of DSE hairpin has been acquired in HIV-1 group
M in the course of evolution. At present it is poorly un-
derstood why only group M, but not other HIV-1 groups,
resulted in a global pandemic [16]. An effective DSE
may be one of the features that makes group M much
more prevalent than groups N, O and P.
Ì. ². Çàðóäíà, À. Ë. Ïîòÿãàéëî, I. M. Êîëî쳺öü, Ä. M. Ãîâîðóí
Ô³ëîãåíåòè÷íèé àíàë³ç ñòðóêòóðíèõ åëåìåíò³â â îáëàñò³ ïîë³(À)
²Ë-1. 1. Øïèëüêè ïîë³A òà DSE
Ðåçþìå
Ãåíîì â³ðóñó ³ìóíîäåô³öèòó ëþäèíè (²Ë-1) íàäçâè÷àéíî ãåòåðî-
ãåííèé. Ìåòà. Ïðîâåñòè ô³ëîãåíåòè÷íèé àíàë³ç ñòðóêòóðíèõ åëå-
ìåíò³â îáëàñò³ ïîë³(À) ²Ë-1, çîêðåìà, øïèëüîê ïîë³A ³ DSE, ÿê³
ñêëàäàþòü îñíîâíèé ñàéò ïîë³(À). Ìåòîäè. Ïåðåäáà÷åííÿ âòî-
ðèííî¿ ñòðóêòóðè îñíîâíîãî ïîë³(À)-ñàéòà çä³éñíþâàëè çà äîïî-
ìîãîþ ïðîãðàìè UNAFold. Ðåçóëüòàòè. Ñòðóêòóðó øïèëüîê ïî-
ë³A ³ DSE ïðîàíàë³çîâàíî äëÿ 1679 ãåíîì³â ²Ë-1 ãðóïè M òà 18 ãå-
íîì³â â³ðóñó ³ìóíîäåô³öèòó ìàâï SIVcpzPtt: ó ãåíîìàõ ²Ë-1 âèÿâ-
ëåíî 244 ³ 171 ð³çíà ïîñë³äîâí³ñòü øïèëüîê ïîë³A ³ DSE â³äïîâ³äíî.
Îäíàê 70 % âèâ÷åíèõ ãåíîì³â ì³ñòèëè îäèí ³ç ñåìè âàð³àíò³â øïè-
ëüêè ïîë³A, ÿê³ çóñòð³÷àëèñÿ ç ÷àñòîòîþ �5 % (îñíîâí³ âàð³àíòè), ³
79 % ³çîëÿò³â ì³ñòÿòü îäèí ³ç ñåìè îñíîâíèõ âàð³àíò³â øïèëüêè
DSE. Âèÿâëåíî òàêîæ ñïåöèô³÷í³ äëÿ ïåâíîãî ñóáòèïó àáî êðà¿íè
ìóòàö³¿ çàçíà÷åíèõ øïèëüîê. Âñòàíîâëåíî, ùî øïèëüêà ïîë³A ç ãå-
íîìó SIVcpzPtt äóæå ñõîæà íà òàêó ç ãåíîìó ²Ë-1 ñóáòèï³â B ³ C.
Âèñíîâêè. Ðåçóëüòàòè íàøèõ øèðîêîìàñøòàáíèõ äîñë³äæåíü
ï³äòðèìóþòü äåÿê³ ñòðóêòóðí³ ìîäåë³ 5' íåòðàíñëüîâàíî¿ ä³ëÿí-
êè ãåíîìó ²Ë-1, çîêðåìà, òðåòèííó âçàºìîä³þ ì³æ øïèëüêîþ ïî-
ë³A ³ îáëàñòþ ãåíà ìàòðèêñíîãî á³ëêà. Øïèëüêà DSE, ìîæëèâî,
óòâîðèëàñÿ ó ïðîöåñ³ åâîëþö³¿ ²Ë-1 ãðóïè Ì. Åêñïîíóâàííÿ U/
GU-çáàãà÷åíîãî åëåìåíòà â àï³êàëüí³é ïåòë³ ö³º¿ øïèëüêè ìîãëî
çíà÷íî ï³äâèùèòè åôåêòèâí³ñòü ïîë³àäåí³ëþâàííÿ ïðî-ìÐÍÊ ó
²Ë-1 ö³º¿ ãðóïè.
Êëþ÷îâ³ ñëîâà: ²Ë-1, SIVcpzPtt, îáëàñòü ïîë³(À), âòîðèííà
ñòðóêòóðà, øïèëüêà ïîë³À, øïèëüêà DSE.
Ì. È. Çàðóäíàÿ, À. Ë. Ïîòÿãàéëî, È. Í. Êîëîìèåö, Ä. Í. Ãîâîðóí
Ôèëîãåíåòè÷åñêèé àíàëèç ñòðóêòóðíûõ ýëåìåíòîâ â îáëàñòè
ïîëè(À) ÂÈ×-1. 1. Øïèëüêè ïîëèA è DSE
Ðåçþìå
Ãåíîì ÂÈ×-1 ÷ðåçâû÷àéíî ãåòåðîãåíåí. Öåëü. Ïðîâåñòè ôèëîãå-
íåòè÷åñêèé àíàëèç ñòðóêòóðíûõ ýëåìåíòîâ îáëàñòè (ïîëè)À ÂÈ×-
461
PHYLOGENETIC STUDY ON STRUCTURAL ELEMENTS OF HIV-1 POLY(A) REGION
462
ZARUDNAYA M. I. ET AL.
1, â ÷àñòíîñòè, øïèëåê ïîëèÀ è DSE, ñîñòàâëÿþùèõ îñíîâíîé ïî-
ëè(À)-ñàéò. Ìåòîäû. Âòîðè÷íàÿ ñòðóêòóðà îñíîâíîãî ïîëè(À)-
ñàéòà ïðåäñêàçàíà ñ ïîìîùüþ ïðîãðàììû UNA Fold. Ðåçóëüòà-
òû. Ñòðóêòóðà øïèëåê ïîëèÀ è DSE ïðîàíàëèçèðîâàíà â 1679 ãå-
íîìàõ ÂÈ×-1 ãðóïïû M è 18 ãåíîìàõ âèðóñà èììóíîäåôèöèòà îáå-
çüÿí SIVcpzPtt: â ãåíîìàõ ÂÈ×-1 âûÿâëåíû ñîîòâåòñòâåííî 244 è
171 ðàçëè÷íàÿ ïîñëåäîâàòåëüíîñòü øïèëåê ïîëèÀ è DSE. Îäíàêî
70 % èçó÷åííûõ ãåíîìîâ ñîäåðæàò îäèí èç ñåìè âàðèàíòîâ øïèëü-
êè ïîëèÀ, âñòðå÷àþùèõñÿ ñ ÷àñòîòîé �5 % (îñíîâíûå âàðèàíòû)
è 79 % èçîëÿòîâ ñîäåðæàò îäèí èç ñåìè îñíîâíûõ âàðèàíòîâ
øïèëüêè DSE. Îáíàðóæåíû òàêæå âàðèàíòû øïèëåê, ñïåöèôè-
÷åñêèå äëÿ îïðåäåëåííîãî ñóáòèïà èëè ñòðàíû. Âûÿâëåíî, ÷òî
øïèëüêà ïîëèÀ â ãåíîìå SIVcpzPtt íàèáîëåå áëèçêà ïî ñòðóêòóðå
òàêîâîé â ãåíîìå ÂÈ×-1 ñóáòèïîâ  è Ñ. Âûâîäû. Ðåçóëüòàòû íà-
øèõ øèðîêîìàñøòàáíûõ èññëåäîâàíèé ñâèäåòåëüñòâóþò â ïîëüçó
íåêîòîðûõ ñòðóêòóðíûõ ìîäåëåé 5' íåòðàíñëèðóåìîé îáëàñòè
ãåíîìà ÂÈ×-1, â ÷àñòíîñòè, íàëè÷èÿ òðåòè÷íîãî âçàèìîäåéñò-
âèÿ ìåæäó øïèëüêîé ïîëèÀ è ó÷àñòêîì â ãåíå ìàòðèêñíîãî áåëêà.
Øïèëüêà DSE, âîçìîæíî, îáðàçîâàëàñü â ïðîöåññå ýâîëþöèè ÂÈ×-1
ãðóïïû Ì. Ýêñïîíèðîâàíèå U/GU- áîãàòîãî ýëåìåíòà â àïèêàëü-
íîé ïåòëå øïèëüêè DSE ìîãëî çíà÷è òåëüíî ïîâûñèòü ýôôåêòèâ-
íîñòü ïîëèàäåíèëèðîâàíèÿ ïðî-ìÐÍÊ â ÂÈ×-1 äàííîé ãðóïïû.
Êëþ÷åâûå ñëîâà: ÂÈ×-1, SIVcpzPtt, îáëàñòü ïîëè(À), âòîðè÷-
íàÿ ñòðóêòóðà, øïèëüêà ïîëèÀ, øïèëüêà DSE.
REFERENCES
1. Zarudnaya M. I. mRNA polyadenylation. 1. 3'-end formation
of vertebrates' mRNAs // Biopolym. Cell.–2001.–17, N 2.–
P. 93–108.
2. Chan S., Choi E. A., Shi Y. Pre-mRNA 3'-end processing comp-
lex assembly and function // Wiley Interdiscip. Rev. RNA.–
2011.–2, N 3.–P. 321–335.
3. Zarudnaya M. I., Potyahaylo A. L., Kolomiets I. M., Hovorun D. Ì.
Auxiliary elements of mammalian pre-mRNAs polyadenylation
signals // Biopolym. Cell.–2002.–18, N 6.–P. 500–517.
4. Valsamakis A., Zeichner S., Carswell S., Alwine J. C. The human
immunodeficiency virus type 1 polyadenylylation signal: a 3' long
terminal repeat element upstream of the AAUAAA necessary for
efficient polyadenylylation // Proc. Natl Acad. Sci. USA.–1991.–
88, N 6.–P. 2108–2112.
5. Berkhout B., Klaver B., Das A. T. A conserved hairpin structure
predicted for the poly(A) signal of human and simian immuno-
deficiency viruses // Virology.–1995.–207, N 1.–P. 276–281.
6. Klasens B. I., Thiesen M., Virtanen A., Berkhout B. The ability of
the HIV-1 AAUAAA signal to bind polyadenylation factors is
controlled by local RNA structure // Nucleic Acids Res.–1999.–
27, N 2.–P. 446–454.
7. Zarudnaya M. I., Potyahaylo A. L., Otenko V. V., Kolomiets I. N.,
Hovorun D. Ì. The secondary structure of ñore poly(A) signal
of human immunodeficiency virus pre-mRNA // Reports of the
Nat. Acad. Sci. of Ukraine.–2011.–N 4.–P. 170–176.
8. Paillart J. C., Skripkin E., Ehresmann B., Ehresmann C., Mar-
quet R. In vitro evidence for a long range pseudoknot in the 5'-
untranslated and matrix coding regions of HIV-1 genomic RNA
// J. Biol. Chem.–2002.–277, N 8.–P. 5995–6004.
9. Abbink T. E., Berkhout B. A novel long distance base-pairing in-
teraction in human immunodeficiency virus type 1 RNA occlu-
des the Gag start codon // J. Biol. Chem.–2003.–278, N 13.–
P. 11601–11611.
10. Ooms M., Cupac D., Abbink T. E., Huthoff H., Berkhout B. The
availability of the primer activation signal (PAS) affects the
efficiency of HIV-1 reverse transcription initiation // Nucleic
Acids Res.–2007.–35, N 5.–P. 1649–1659.
11. Markham N. R., Zuker M. UNAFold: software for nucleic acid
folding and hybridization // Methods Mol. Biol.–2008.–453.–
P. 3–31.
12. Yuan Y., Kerwood D. J., Paoletti A. C., Shubsda M. F., Borer P.
N. Stem of SL1 RNA in HIV-1: structure and nucleocapsid pro-
tein binding for a 1 x 3 internal loop // Biochemistry.–2003.–42,
N 18.–P. 5259–5269.
13. Henriet S., Richer D., Bernacchi S., Decroly E., Vigne R., Ehres-
mann B., Ehresmann C., Paillart J. C., Marquet R. Cooperative
and specific binding of Vif to the 5' region of HIV-1 genomic
RNA // J. Mol. Biol.–2005.–354, N 1.–P. 55–72.
14. Das A. T., Klaver B., Berkhout B. A hairpin structure in the R re-
gion of the human immunodeficiency virus type 1 RNA genome
is instrumental in polyadenylation site selection // J. Virol.–
1999.–73, N 1.–P. 81–91.
15. Berkhout B. HIV-1 as RNA evolution machine // RNA Biol.–
2011.–8, N 2.–P. 225–229.
16. Sharp P. M., Hahn B. H. Origins of HIV and the AIDS pandemic
// Cold Spring Harb. Perspect. Med.–2011.–1, N 1.–a006841.
17. Zarudnaya M. I., Kolomiets I. M., Potyahaylo A. L., Hovorun D.
M. Downstream elements of mammalian pre-mRNA polyadeny-
lation signals: primary, secondary and higher-order structures //
Nucleic Acids Res.–2003.–31, N 5.–P. 1375–1386.
18. Chou Z.-F., Chen F., Wilusz J. Sequence and position require-
ments for uridylate-rich downstream elements of polyadenyla-
tion signals // Nucleic Acids Res.–1994.–22, N 13.–P. 2525–
2531.
Received 18.06.13
|