Розподіл шпилькових структур у плазмідах збудника сибірської виразки
Однією з важливих біологічних функцій шпилькових структур є захист РНК-транскриптів від деградувальної дії різних факторів, а також регуляція транскрипції за рахунок їхнього формування у термінаторах транскрипції. Проведено пошук та визначено розподіли термодинамічно стабільних досконалих і недоскон...
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Інститут молекулярної біології і генетики НАН України
2008
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Лиманська, О.Ю. Лиманський, О.П. 2019-06-21T05:35:31Z 2019-06-21T05:35:31Z 2008 Розподіл шпилькових структур у плазмідах збудника сибірської виразки / О.Ю. Лиманська, О.П. Лиманський // Біополімери і клітина. — 2008. — Т. 24, № 6. — С. 463-469. — Бібліогр.: 24 назв. — укр., англ. 0233-7657 DOI: http://dx.doi.org/10.7124/bc.0007BE https://nasplib.isofts.kiev.ua/handle/123456789/157884 577.2:573.6:616-0227 Однією з важливих біологічних функцій шпилькових структур є захист РНК-транскриптів від деградувальної дії різних факторів, а також регуляція транскрипції за рахунок їхнього формування у термінаторах транскрипції. Проведено пошук та визначено розподіли термодинамічно стабільних досконалих і недосконалих інвертованих повторів у плазмідах рХО1 і рХО2 патогенних штамів Bacillus anthracis. Аналіз послідовностей плазмід рХО1 і рХО2 B. anthracis виявив, що перша містить 176 інвертованих послідовностей з енергією від –30,6 до –10,0 ккал/моль, а друга – 57 шпильок з енергією від –27,2 до –10,0 ккал/моль. Представлено фізичні карти плазмід рХО1 і рХО2 з локалізованими шпильковими структурами. Показано, що останні на фізичних картах плазмід рХО1 і рХО2 розташовані в ділянці регуляторних генів або в елементах з невизначеною функцією. An important biological function of hairpin-loop structures is the defense of RNA transcripts from degradation by different factors as well as the transcription regulation due to their formation in transcription terminators. The patterns of thermodynamically stable perfect and imperfect inverted repeats were determined for pXO1 and pXO2 plasmids of pathogenic Bacillus anthracis strains. A sequence analysis of these plasmids has shown the plasmid pXO1 contains 176 inverted repeats, the energy of which varies from –30.6 kcal/mol to –10.0 kcal/mol, and the plasmid pXO2 of B. anthracis contains 57 inverted sequences with energy from –27.2 kcal/mol to –10.0 kcal/mol. Physical maps of the pXO1 and pXO2 plasmids with located hairpins are presented. These hairpin-loop structures are shown to be localized in the sites of regulatory genes or the elements encoding proteins of unknown function. Одной из важных биологических функций шпилечных структур является защита РНК-транскриптов от деградирующего дей- ствия разных факторов, а также регуляция транскрипции за счет их формирования в терминаторах транскрипции. Проведен поиск и определены распределения термодинамически стабильных совершенных и несовершенных инвертированных повторов в плазмидах рХО1 и рХО2 патогенных штаммов Bacillus anthracis. Анализ последовательностей плазмид рХО1 и рХО2 B. anthracis выявил, что первая содержит 176 инвертированных последовательностей с энергией от –30,6 до –10,0 ккал/моль, а вторая – 57 шпилек с энергией от –27,2 до –10,0 ккал/моль. Представлены физические карты плазмид рХО1 и рХО2 с локализованными шпилечными структурами. Показано, что последние на физических картах плазмид рХО1 и рХО2 локализованы в области регуляторных генов или в элементах с неопределенной функцией. uk Інститут молекулярної біології і генетики НАН України Біополімери і клітина Структура та функції біополімерів Розподіл шпилькових структур у плазмідах збудника сибірської виразки Pаспределение шпилечных структур в плазмидах возбудителя сибирской язвы Distribution of hairpin-loop structures in plasmids of anthrax infectious agent Article published earlier |
| institution |
Digital Library of Periodicals of National Academy of Sciences of Ukraine |
| collection |
DSpace DC |
| title |
Розподіл шпилькових структур у плазмідах збудника сибірської виразки |
| spellingShingle |
Розподіл шпилькових структур у плазмідах збудника сибірської виразки Лиманська, О.Ю. Лиманський, О.П. Структура та функції біополімерів |
| title_short |
Розподіл шпилькових структур у плазмідах збудника сибірської виразки |
| title_full |
Розподіл шпилькових структур у плазмідах збудника сибірської виразки |
| title_fullStr |
Розподіл шпилькових структур у плазмідах збудника сибірської виразки |
| title_full_unstemmed |
Розподіл шпилькових структур у плазмідах збудника сибірської виразки |
| title_sort |
розподіл шпилькових структур у плазмідах збудника сибірської виразки |
| author |
Лиманська, О.Ю. Лиманський, О.П. |
| author_facet |
Лиманська, О.Ю. Лиманський, О.П. |
| topic |
Структура та функції біополімерів |
| topic_facet |
Структура та функції біополімерів |
| publishDate |
2008 |
| language |
Ukrainian |
| container_title |
Біополімери і клітина |
| publisher |
Інститут молекулярної біології і генетики НАН України |
| format |
Article |
| title_alt |
Pаспределение шпилечных структур в плазмидах возбудителя сибирской язвы Distribution of hairpin-loop structures in plasmids of anthrax infectious agent |
| description |
Однією з важливих біологічних функцій шпилькових структур є захист РНК-транскриптів від деградувальної дії різних факторів, а також регуляція транскрипції за рахунок їхнього формування у термінаторах транскрипції. Проведено пошук та визначено розподіли термодинамічно стабільних досконалих і недосконалих інвертованих повторів у плазмідах рХО1 і рХО2 патогенних штамів Bacillus anthracis. Аналіз послідовностей плазмід рХО1 і рХО2 B. anthracis виявив, що перша містить 176 інвертованих послідовностей з енергією від –30,6 до –10,0 ккал/моль, а друга – 57 шпильок з енергією від –27,2 до –10,0 ккал/моль. Представлено фізичні карти плазмід рХО1 і рХО2 з локалізованими шпильковими структурами. Показано, що останні на фізичних картах плазмід рХО1 і рХО2 розташовані в ділянці регуляторних генів або в елементах з невизначеною функцією.
An important biological function of hairpin-loop structures is the defense of RNA transcripts from degradation by different factors as well as the transcription regulation due to their formation in transcription terminators. The patterns of thermodynamically stable perfect and imperfect inverted repeats were determined for pXO1 and pXO2 plasmids of pathogenic Bacillus anthracis strains. A sequence analysis of these plasmids has shown the plasmid pXO1 contains 176 inverted repeats, the energy of which varies from –30.6 kcal/mol to –10.0 kcal/mol, and the plasmid pXO2 of B. anthracis contains 57 inverted sequences with energy from –27.2 kcal/mol to –10.0 kcal/mol. Physical maps of the pXO1 and pXO2 plasmids with located hairpins are presented. These hairpin-loop structures are shown to be localized in the sites of regulatory genes or the elements encoding proteins of unknown function.
Одной из важных биологических функций шпилечных структур является защита РНК-транскриптов от деградирующего дей- ствия разных факторов, а также регуляция транскрипции за счет их формирования в терминаторах транскрипции. Проведен поиск и определены распределения термодинамически стабильных совершенных и несовершенных инвертированных повторов в плазмидах рХО1 и рХО2 патогенных штаммов Bacillus anthracis. Анализ последовательностей плазмид рХО1 и рХО2 B. anthracis выявил, что первая содержит 176 инвертированных последовательностей с энергией от –30,6 до –10,0 ккал/моль, а вторая – 57 шпилек с энергией от –27,2 до –10,0 ккал/моль. Представлены физические карты плазмид рХО1 и рХО2 с локализованными шпилечными структурами. Показано, что последние на физических картах плазмид рХО1 и рХО2 локализованы в области регуляторных генов или в элементах с неопределенной функцией.
|
| issn |
0233-7657 |
| url |
https://nasplib.isofts.kiev.ua/handle/123456789/157884 |
| citation_txt |
Розподіл шпилькових структур у плазмідах збудника сибірської виразки / О.Ю. Лиманська, О.П. Лиманський // Біополімери і клітина. — 2008. — Т. 24, № 6. — С. 463-469. — Бібліогр.: 24 назв. — укр., англ. |
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Distribution of hairpin-loop structures in plasmids of
anthrax infectious agent
O. Yu. Limanskaya1,2, A. P. Limanskii1
1 I.I. Mechnikov Institute of Microbiology and Immunology of Academy of Medical Sciences of Ukraine
14 Pushkinska Str., Kharkiv, 61057 Ukraine
2 National Research Centre “Institute for Experimental and Clinical Veterinary Medicine”
83 Pushkinska Str., Kharkiv, 61023 Ukraine
olga.limanskaya@mail.ru
An important biological function of hairpin-loop structures is the defense of RNA transcripts from
degradation by different factors as well as the transcription regulation due to their formation in
transcription terminators. The patterns of thermodynamically stable perfect and imperfect inverted repeats
were determined for pXO1 and pXO2 plasmids of pathogenic Bacillus anthracis strains. A sequence
analysis of these plasmids has shown the plasmid pXO1 contains 176 inverted repeats, the energy of which
varies from –30.6 kcal/mol to –10.0 kcal/mol, and the plasmid pXO2 of B. anthracis contains 57 inverted
sequences with energy from –27.2 kcal/mol to –10.0 kcal/mol. Physical maps of the pXO1 and pXO2
plasmids with located hairpins are presented. These hairpin-loop structures are shown to be localized in the
sites of regulatory genes or the elements encoding proteins of unknown function.
Keywords: Bacillus ànthracis, hairpin-loop structure, inverted repeat, cruciform structure.
Introduction. At present, the intensive efforts of scientists
are aimed at the development of efficient approaches
to analyze so called genetic texts, i.e. nucleotide
sequences of genomes. A computer analysis is of
special importance for studying DNA text due to the
possibility to establish certain functions of different
DNA fragments: search for structural genes,
regulatory sites, etc. The accuracy of current computer
methods in determ ining genes of a known nucleotide
sequence is not higher than 70% [1].
Be ing a new branch of sci ence, genomics is still de -
scrip tive and de vel op ing along with tech ni cal prog ress.
The se quenc ing of genomes has deep ened and ex tended
our un der stand ing of ge netic in for ma tion. At pres ent,
the most im por tant parts of ge nome are con sid ered to be
exome (com pris ing only 1% of ge nome), introme,
methylome, transcriptome (a set of all RNA tran scripts
in one or a pop u la tion of cells), and variome (to tal ge -
netic vari a tions, char ac ter iz ing the spe cies, or a sum of
single nucleotide polymorphisms) [2, 3].
463
ISSN 1993-6842. Biopolymers and cell. 2008. vol. 24. N 6. Translated from Ukrainian
© O. Yu. LIMANSKAYA, A. P. LIMANSKII, 2008
In eukaryotes and prokaryotes the con ser va tive
frac tions of ge nome, non-cod ing pro teins, have very
im por tant func tions, namely, they are a source of both
sense and antisense non-cod ing RNAs of dif fer ent
vari ants of introns, com pris ing introme (some times
introns may func tion as exons, and vice versa). The
data on introme of mi cro or gan isms would al low to
iden tify bi o log i cally sig nif i cant prop er ties, reg u lated
by introns.
Func tions of var i ous genes are known to de pend on
many fac tors, how ever, the to tal num ber of el e men tary
reg u la tory fac tors is thought to be con sid er ably smaller
than the to tal num ber of genes. An in sig nif i cant part of
el e men tary fac tors (com pared to the to tal num ber of
genes) may be suf fi cient to reg u late a con sid er able
num ber of genes. Ge nome se quences of eukaryotes and
prokaryotes con tain a huge amount of in for ma tion re -
lated to their mo lec u lar ge net ics. While sci en tists are
de vel op ing ap proaches to ob tain this in for ma tion and
solve var i ous prob lems of genomics, much at ten tion is
given to search of re peats, since they com prise a large
part of ge nome. In par tic u lar, hu man ge nome con tains
over 50% of re peats, some classes of which play a vi tal
struc tural and functional role. Still, search for repeats is
a highly challenging endeavor.
Ba cil lus anthracis is a large rod-shaped,
Gram-pos i tive, an aer o bic bac te rium, which is an eti o -
log i cal agent of an thrax, a dan ger ous and of ten fa tal
dis ease of both hu mans and an i mals. Along with
B. thuringiensis, B. ce reus, and B. mycoides, it be -
longs to B. ce reus ge nus. These closely-re lated bac te -
ria are an i mal (B. anthracis and B. ce reus) and in sect
patho gens (B. thuringiensis). B. anthracis dif fers from
the rest of the ge nus mem bers by the pres ence of
megaplasmids pXO1 and pXO2, cod ing the syn the sis
of tox ins and cap sules, re spec tively, and pro vid ing for
vir u lence of the bac te rium. There are some known iso -
lates of B. anthracis with one or two plasmids ab sent.
Be sides, there is a pos si bil ity of plasmid trans fer
among re lated spe cies or nat u ral loss of the pXO1
plasmid [4]. There are also data on the suc cess ful
trans fer of the pXO1 plasmid into other bac te ria and
ex pres sion of the tox ins genes, such as lef and cya, in
heterologous sys tems [5]. The ab sence of one of
plasmids re sults in the loss of patho genic prop er ties of
B. anthracis strain [6].
The pos si bil ity of form ing hair pin-loop struc tures
at tracted at ten tion due to their ca pa bil ity to reg u late a
sta bil ity of mi cro or gan ism’s mRNAs [7, 8]. In [9] we
de ter mined the dis tri bu tion of ther mo dy nam i cally sta -
ble per fect in verted re peats for two iso lates of slow
grow ing My co bac te rium tu ber cu lo sis with com plete
ge nome (H37Rv and CDC1551). Re gard less of a high
level of homology (over 90%) of genomes of these my -
co bac te ria iso lates they dif fer in vir u lence level,
namely, H37Rv is a lab o ra tory strain, while clin i cal iso -
late CDC1551 is highly vir u lent. We proved both iso -
lates to have eight long in verted re peats of 48-62 nu -
cleo tides, six of which co in cide com pletely. At the
same time in the CDC1551 ge nome (con trary to
H37Rv) there is a highly sta ble hair pin of 58 nu cleo -
tides at 5'-end of DNA tem plate chain [9]. It was sup -
posed that lo cal iza tion of highly sta ble hair pin,
DG=-53.9 kcal/mol at 5'-end of DNA of the CDC1551
iso late may re sult in dif fer ent de gree of RNA tran -
scripts sta bil ity or dif fer ent level of tran scrip tion ter mi -
na tion ef fi ciency in the CDC1551 strain com pared to
the H37Rv iso late, which, in its turn, may be one of the
rea sons of dif fer ent vir u lence of the strains, regardless
of similarity in physical maps of their genomes.
The in verted re peats may also serve as rec og ni tion
sites for recombinases. The pres ence of in verted re peats
may tes tify to the prob a bil ity of DNA se quences trans -
fer among re peats due to the tran scrip tion or re com bi -
na tion [10]. An im por tant bi o log i cal func tion of hair -
pins is the pro tec tion of RNA tran scripts of plasmids,
de ter min ing vir u lence of B. anthracis, from deg ra da -
tion by dif fer ent fac tors. We used com puter anal y sis to
char ac ter ize ther mo dy nam i cally sta ble per fect and mis -
matched in verted re peats, form ing hair pin-loop struc -
tures, or hair pins which may ap pear in the pXO1 and
pXO2 plasmids of B. anthracis patho genic strains, and
presented the physical maps of plasmids with located
hairpins.
Ma te ri als and Meth ods. Iso lates of pXO2 plasmid
(num ber AE 011191 (NC 003981), 94829 bp) and
pXO1 plasmid (num ber AF 065504, 181654 bp) with
com plete ge nome were used. Oligo soft ware (ver sion
3.4) was used to search for per fect in verted re peats and
de ter mine their ther mo dy namic char ac ter is tics [11].
RNA 2 soft ware of GeneBee was used to search for mis -
matched re peats and de ter mine their pa ram e ters [12].
464
LIMANSKAYA O. Yu., LIMANSKII A. P.
Since soft ware, used in this work, al lows an a lyz ing se -
quences, not ex ceed ing 15000 bp, the com plete se -
quences of pXO1 and pXO2 plasmids, ob tained from
GenBank da ta base, were cut in frag ments of 14000 bp.
Re sults and Dis cus sion. Re peats may be di rect and
in verted, per fect (com plete co in ci dence of their se -
quences) or im per fect (con tain ing mis matches). In -
verted re peats in RNA and DNA mol e cules may be in
two dif fer ent conformational states – ei ther as sin gle- or
dou ble-stranded he lix, or in the form of hair pin-loop
struc ture, con sist ing of a dou ble-stranded stem and sin -
gle-stranded loop. Ear lier it was shown that un der phys -
i o log i cal con di tions the superhelical DNA with in -
verted re peats (pal in dromes) may form hair pins as
frag ments of cru ci form struc ture with the stem length
not less 7 bp and the loop not ex ceed ing 4-5 bp in
[13-15]. We have used these pa ram e ters to de ter mine
ther mo dy nam i cally sta ble per fect in verted re peats in
the se quences of pXO1 (Ta ble 1) and pXO2 plasmids
of the patho genic strain A2012 B. anthracis (Table 2).
The com puter anal y sis re vealed that the pXO1
plasmid con tains 67 hair pin-loop struc tures with the
loop not ex ceed ing 5 nu cleo tides (Fig.1). The free en -
ergy (-DG) of 11 hair pins is over 20 kcal/mol (Ta ble 1).
It is note wor thy that the pXO1 plasmid has four per fect
in verted re peats with high val ues of -DG (over 20
kcal/mol) and the loop of 8-13 nu cleo tides (po si tions 5,
11, 12, 27 in Ta ble 1). We be lieve that this fact is in fa -
vor of the in vivo ex is tence of hair pins with loops of
8-13 nucleotides.
For con ve nience, the pal in dromes, po ten tially ca pa -
ble of form ing hair pins due to interstranded com ple men -
tary pair ing of nu cleo tides in sin gle-stranded DNA and
RNA, may be di vided into long and short re peats (over
45 nu cleo tides and less than 45 nu cleo tides, re spec -
tively). The pXO1 plasmid may con tain 17 long pal in -
dromes of 45-66 nu cleo tides with DG rang ing from -30.6
to -20.7 kcal/mol, and 10 short pal in dromes of 31-43 nu -
cleo tides with DG from -20.5 to -30.6 kcal/mol (Ta ble 1).
It should be noted that the ma jor ity of hair pin struc tures
on the phys i cal map of the pXO1 plasmid is lo cated ei -
ther in the area of reg u la tory genes or in the el e ments of
un known func tion (Fig.1, b). This fact proves the well
known lit er a ture data on the pres ence of cru ci form struc -
tures in the reg u la tory frag ments, in many tran scrip tion
ter mi na tors, in par tic u lar [16].
465
DISTRIBUTION OF HAIRPIN-LOOP STRUCTURES IN PLASMIDS OF ANTHRAX INFECTIOUS AGENT
Stem
length, b.p.
Loop length,
b.p.
Free energy,
kcal/mol
Position on plasmid
18 12 –21,5 24754–24801
20 8 –23,9 24990–25038
19 4 –22,9 26110–26131
18 4 –28,3 26553–26592
21 10 –20,7 42014–42065
25 12 –22,5 48010–48071
24 18 –30,6 55825–55890
19 3 –21,9 60528–60568
20 7 –28 63955–64001
13 5 –22,9 71398–71428
20 5 –30,5 72274–72318
21 8 –29,8 100450–10049
23 5 –25 105993–10604
16 5 –21,7 109971–11000
22 3 –21 114805–114851
20 13 –29,7 120940–120991
24 8 –21,2 121312–121367
24 4 –24,3 136336–136387
19 4 –21,7 137579–137620
22 3 –25,3 146102–146148
25 3 –21,4 148426–148478
18 4 –23 153484–153522
18 3 –25 159742–159782
20 3 –20,5 162053–162095
14 4 –21 169071–169102
17 17 –24,1 172043–172093
18 9 –29,3 179421–179465
Table 1
Thermodynamically stable hairpin-loop structures potentially
formed by inverted repeats for pXO1 plasmid of pathogenic
strain Bacillus anthracis
Note. Perfect hairpins are shown in bold
The pXO2 plasmid may con tain 25 hair pin struc -
tures with the loop up to 5 nu cleo tides (Fig.2). Be sides,
there are two long per fect in verted re peats with the loop
ex ceed ing 5 nu cleo tides and -DG over 20 kcal/mol (po -
si tions 4, 5 in Table 2).
Con trary to the pXO1 plasmid, the pXO2 plasmid
con tains nei ther long pal in dromes with the loop up to 5
nu cleo tides, nor a sin gle per fect short pal in drome with
-DG over 20 kcal/mol (Ta ble 2). Fig.2, b shows a phys i -
cal map of the pXO2 plasmid with po si tions of hair pin
struc tures found. It should be noted that func tions of the
ma jor ity of genes of the pXO2 plasmid are yet to be de -
ter mined, and the data ob tained can be an a lyzed there -
af ter. Ac cord ing to the re sults, the per fect and mis -
matched in verted re peats are highly sta ble ge netic el e -
ments for both plasmids. The anal y sis of po ten tially
prob a ble sec ond ary struc tures al lows the sup po si tion
on the bi o log i cal func tion of men tioned hair pins be ing
the pro tec tion of RNA tran scripts of plasmids, caus ing
virulence of bacteria, from degrading by different
factors.
As shown in [18-20], the in verted re peats form cru -
ci form struc tures in neg a tively superhelical DNA both
in vivo and in vi tro. There are spe cific bio chem i cal [21]
and bio phys i cal meth ods to de tect hair pin struc tures in
vi tro. While mo lec u lar bi o log i cal meth ods, based on
cut ting a hair pin loop with a nuclease (spe cific for sin -
gle-stranded DNA), al low de ter min ing the se quence
and lo cat ing the in verted re peat on the ge nome, mod ern
meth ods of nanobiotechnology, first of all scan ning
probe mi cros copy, en able di rect visualization of a
hairpin structure [22].
466
LIMANSKAYA O. Yu., LIMANSKII A. P.
Stem length,
b.p.
Loop
length, b.p.
Free energy,
kcal/mol
Position on
plasmid
20 9 –20,0 13585–13634
17 4 –24,3 29190–29227
22 7 –27,2 37712–37762
20 6 –21,2 44958–45003
20 11 –27,1 48478–48528
20 8 –22,4 59914–59961
Table 2
Thermodynamically stable hairpin-loop structures, potentially
formed by inverted repeats, for pXO2 plasmid of pathogenic
strain Bacillus anthracis
Note. Perfect hairpins are shown in bold.
Fig.1 Histogram of distribution of possible hairpin-loop structures
on pXO1 plasmid (181654 bp) of anthrax agent (a) and physical
map of pXO1 plasmid of Bacillus anthracis [17] (b). Figures show
positions of known genes of toxins, elements IS1623, and expected
positions of 143 open reading frames. Encoding genes: lef -
endopeptidase of lethal factor, cya - calmodulin-sensitive adenylate
cyclase; pagA - protective antigen; topo I - topoisomerase I;
gerXA, ger XB - development of spores; atxA - positive
transregulator of expression of antrax toxin gene; pagR -
transcriptional repressor. Arrows indicate positions of
thermodynamically stable perfect and mismatched hairpin
structures; asterisks show hairpin structures, where the loop
exceeds 12 nucleotides; hairpins with the free energy over: 1 - 10; 2
- 15; 3 - 20: 4 - 25; 5 - 30 kcal/mol
RNA mol e cules are known as the most la bile
macromolecules pres ent in cells. The level of mRNA
is reg u lated at the stages of syn the sis and deg ra da tion.
The sta bil ity of mRNA is de ter mined by the com bi na -
tion of trans- and cis-fac tors, the for mer in clud ing
exo- and endoribonucleases, and the lat ter be ing di -
vided into two classes – sta bi liz ers and destabilizers.
Destabilizing el e ments pro vide bind ing of nu cleases
and ini ti a tion of deg ra da tion pro cesses, while sta bi liz -
ers pre vent deg ra da tion of mRNA, block ing the ac tion
of dif fer ent nu cleases. One of the pos si ble mech a -
nisms of mRNA sta bi li za tion is re lated to the for ma -
tion of non-ca non i cal (hair pin) struc ture at 3'- or
5'-end of mRNA. For in stance, the for ma tion of such
hair pin at 5'-end sta bi lizes mRNA of Esch e richia coli
through pre ven tion of in ter ac tion be tween 5'-end of
mRNA and RNAse E [23].
Be sides, hair pin struc tures may of ten ap pear in -
side the in ner tran scrip tion ter mi na tors i.e. spe cific
frag ments of DNA tem plate, where an elon ga tion
com plex of RNA poly mer ase – DNA tem plate – RNA
trascript stops and usu ally dis so ci ates. Though it is
true that many bac te ria (an thrax agent among them)
sel dom con tain clas sic tran scrip tion ter mi na tors, it
may be sup posed that hair pin-loop struc tures found
are formed to pro vide reg u la tion at the level of tran -
scrip tion.
Thus, the anal y sis of se quences of the pXO1 and
pXO2 plasmids of B. anthracis al lowed to pro pose the
phys i cal maps of plasmids with lo cated per fect and
mis matched in verted re peats, po ten tially ca pa ble of
form ing ther mo dy nam i cally sta ble hair pin-loop struc -
tures. The length of highly sta ble hair pins ranges from
66 to 19 nu cleo tides, their free en ergy be ing -30.6 to
-10.3 kcal/mol.
The ma jor ity of hair pins, de fined at the phys i cal
maps of pXO1 and pXO2 plasmids, are lo cated ei ther
in the area of pos i tive trans-reg u la tors or in the el e -
ments of un known func tion. We sup pose that the lo ca -
tion of hair pin struc tures in the ge nome of pXO1 and
pXO2 plasmids is not ran dom; sim i lar to long
homopurine tracts, po ten tially ca pa ble of form ing tri -
plexes, they may be sit u ated within pro mot ers and
ter mi na tors of tran scrip tion as well as near “hot” spots
of re com bi na tion [24].
The work was sup ported by grants of AMS 47/2002
and AMS 72/2007, the Acad emy of Med i cal Sci ences
of Ukraine.
467
DISTRIBUTION OF HAIRPIN-LOOP STRUCTURES IN PLASMIDS OF ANTHRAX INFECTIOUS AGENT
Fig.2 Histogram of distribution of possible hairpin-loop structures
on pXO2 plasmid (94829 bp) of anthrax agent (a) and physical map
of pXO2 plasmid of B. anthracis (number AF188935, 96231
nucleotides long) (b). Location of known virulent genes (capA,
capB, capC, capD, cape, topB) and positive trans-regulators (acpA,
acpB) is presented in the inner circle.
Arrows indicate positions of potentially perfect and mismatched
hairpin structures, the loop of which does not exceed 12
nucleotides. Other symbols: - mismatched and perfect hairpins,
free energy of about 10 kcal/mol, the loop up to 8 nucleotides; -
perfect hairpins, free energy over 10 kcal/mol; - perfect hairpins,
free energy over 20 kcal/mol; - mismatched hairpins, free energy
over 10 kcal/mol; - mismatched hairpins, free energy over 20
kcal/mol
Î. Þ. Ëè ìà íñüêà, Î. Ï. Ëè ìà íñüêèé
Ðîç ïîä³ë øïèëü êî âèõ ñòðóê òóð ó ïëàçì³äàõ çáóä íè êà
ñèá³ðñüêî¿ âè ðàç êè
Ðå çþ ìå
Îäí³ºþ ç âàæ ëè âèõ á³îëîã³÷íèõ ôóíêö³é øïèëü êî âèõ ñòðóê òóð º
çà õèñò ÐÍÊ-òðàíñ êðèïò³â â³ä äåã ðà äó âàëü íî¿ ä³¿ ð³çíèõ ôàê -
òîð³â, à òà êîæ ðå ãó ëÿö³ÿ òðàíñ êðèïö³¿ çà ðà õó íîê ¿õíüî ãî ôîð -
ìó âàí íÿ ó òåðì³íà òî ðàõ òðàíñ êðèïö³¿. Ïðî âå äå íî ïî øóê òà
âèç íà ÷å íî ðîç ïîä³ëè òåð ìî äè íàì³÷íî ñòàá³ëüíèõ äîñ êî íà ëèõ ³
íå äîñ êî íà ëèõ ³íâåð òî âà íèõ ïî âòîð³â ó ïëàçì³äàõ ðÕÎ1 ³ ðÕÎ2
ïà òî ãåí íèõ øòàì³â Bacillus anthracis. Àíàë³ç ïîñë³äîâ íîñ òåé
ïëàçì³ä ðÕÎ1 ³ ðÕÎ2 B. anthracis âè ÿ âèâ, ùî ïåð øà ì³ñòèòü 176
³íâåð òî âà íèõ ïîñë³äîâ íîñ òåé ç åíåð㳺þ â³ä –30,6 äî –10,0
êêàë/ìîëü, à äðó ãà – 57 øïèëü îê ç åíåð㳺þ â³ä –27,2 äî –10,0
êêàë/ìîëü. Ïðåä ñòàâ ëå íî ô³çè÷í³ êàð òè ïëàçì³ä ðÕÎ1 ³ ðÕÎ2 ç
ëî êàë³çî âà íè ìè øïèëü êî âè ìè ñòðóê òó ðà ìè. Ïî êà çà íî, ùî
îñòàíí³ íà ô³çè÷ íèõ êàð òàõ ïëàçì³ä ðÕÎ1 ³ ðÕÎ2 ðîç òà øî âàí³
â ä³ëÿíö³ ðå ãó ëÿ òîð íèõ ãåí³â àáî â åëå ìåí òàõ ç íå âèç íà ÷å íîþ
ôóíêö³ºþ.
Êëþ ÷îâ³ ñëî âà: Bacillus ànthracis, øïèëü êî âà ñòðóê òó ðà,
³íâåð òî âà íèé ïî âòîð, õðåñ òî ïîä³áíà ñòðóê òó ðà.
Î. Þ. Ëè ìàí ñêàÿ, À. Ï. Ëè ìàí ñêèé
Pàñ ïðå äå ëå íèå øïè ëå÷ íûõ ñòðóê òóð â ïëàç ìè äàõ âîç áó äè òå ëÿ
ñè áèð ñêîé ÿçâû
Ðå çþ ìå
Îäíîé èç âàæ íûõ áè î ëî ãè ÷åñ êèõ ôóíê öèé øïè ëå÷ íûõ ñòðóê òóð
ÿâ ëÿ åò ñÿ çà ùè òà ÐÍÊ-òðàíñ êðèï òîâ îò äåã ðà äè ðó þ ùå ãî äåé-
ñòâèÿ ðàç íûõ ôàê òî ðîâ, à òàê æå ðå ãó ëÿ öèÿ òðàíñ êðèï öèè çà
ñ÷åò èõ ôîð ìè ðî âà íèÿ â òåð ìè íà òî ðàõ òðàíñ êðèï öèè. Ïðî âå -
äåí ïî èñê è îïðå äå ëå íû ðàñ ïðå äå ëå íèÿ òåð ìî äè íà ìè ÷åñ êè ñòà -
áèëü íûõ ñî âåð øåí íûõ è íå ñî âåð øåí íûõ èí âåð òè ðî âàí íûõ
ïî âòî ðîâ â ïëàç ìè äàõ ðÕÎ1 è ðÕÎ2 ïà òî ãåí íûõ øòàì ìîâ
Bacillus anthracis. Àíàëèç ïî ñëå äî âà òåëü íîñ òåé ïëàç ìèä ðÕÎ1
è ðÕÎ2 B. anthracis âû ÿ âèë, ÷òî ïåðâàÿ ñî äåð æèò 176 èí âåð òè -
ðî âàí íûõ ïî ñëå äî âà òåëü íîñ òåé ñ ýíåð ãè åé îò –30,6 äî
–10,0 êêàë/ìîëü, à âòîðàÿ – 57 øïè ëåê ñ ýíåð ãè åé îò –27,2 äî
–10,0 êêàë/ìîëü. Ïðåä ñòàâ ëå íû ôè çè ÷åñ êèå êàð òû ïëàç ìèä
ðÕÎ1 è ðÕÎ2 ñ ëî êà ëè çî âàí íû ìè øïè ëå÷ íû ìè ñòðóê òó ðà ìè.
Ïî êà çà íî, ÷òî ïîñëåäíèå íà ôè çè ÷åñ êèõ êàð òàõ ïëàç ìèä ðÕÎ1
è ðÕÎ2 ëî êà ëè çî âà íû â îá ëàñ òè ðå ãó ëÿ òîð íûõ ãå íîâ èëè â ýëå -
ìåí òàõ ñ íå îïðå äå ëåí íîé ôóíêöèåé.
Êëþ ÷å âûå ñëî âà: Bacillus ànthracis, øïè ëå÷ íàÿ ñòðóê òó ðà,
èí âåð òè ðî âàí íûé ïî âòîð, êðåñ òî îá ðàç íàÿ ñòðóê òó ðà.
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DISTRIBUTION OF HAIRPIN-LOOP STRUCTURES IN PLASMIDS OF ANTHRAX INFECTIOUS AGENT
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