Научная статья на тему 'Polymorphism of the dtxR gene in the currently existing strains of Сorynebacterium diphtheriae'

Polymorphism of the dtxR gene in the currently existing strains of Сorynebacterium diphtheriae Текст научной статьи по специальности «Биологические науки»

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Ключевые слова
diphtheria / Corynebacterium diphtheriae / dtxR / multilocus sequence typing / metalloregulatory proteins / дифтерия / Corynebacterium diphtheriae / dtxR / мультилокусное сиквенс-типирование / металлорегуляторные белки

Аннотация научной статьи по биологическим наукам, автор научной работы — Chagina I.A., Perevarova Yu.S., Perevarov V.V., Chaplin A.V., Borisova O.Yu.

The pathogenic mechanism used by Corynebacterium diphtheriae is attributed to the ability of the diphtheria toxin to disrupt protein synthesis in human cells. Diphtheria toxin production is regulated by the DtxR protein. The latter is involved in the ironmediated repression of the toxin gene and coordinates activities of other genes essential for the survival of C. diphtheriae. The DtxR-encoding gene occurs in both toxigenic and non-toxigenic strains; therefore it can be used to analyze the population structure of the species. In our work we have studied 45 strains of C. diphtheriae isolated in the Russian Federation in 2010–2015. These strains were analyzed to reveal that gene dtxR is a highly conservative region of С. diphtheriae genome that can be found in all members of the studied species. The majority of the discovered polymorphisms were synonymous (16 of 18 single nucleotide polymorphisms identified). In spite of the low phylogenetic signal, the allelic variant of dtxR was associated with the strain’s phenotype (biovar, toxigenicity). The obtained data indicate the presence of aggressive negative selection aimed to maintain the existing protein sequence in the population. Based on the results, we recommend dtxR polymerase chain reaction as an additional technique for pathogen identification, which is especially relevant considering the increasing prevalence of the disease associated with non-toxigenic C. diphtheriae strains.

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ПОЛИМОРФИЗМ ГЕНА DTXR У СОВРЕМЕННЫХ ШТАММОВ СORYNEBACTERIUM DIPHTHERIAE

Считается, что патогенез Corynebacterium diphtheriae основан на воздействии дифтерийного токсина на синтез белка в клетках человека. Регуляция синтеза токсина находится под контролем белка DtxR. Данный белок осуществляет железоопосредованную репрессию гена дифтерийного токсина, а также координирует работу множества других генов, необходимых для нормальной жизнедеятельности C. diphtheriae. Ген, кодирующий DtxR, можно использовать для анализа популяционной структуры вида, так как он присутствует в геноме как токсигенных, так и нетоксигенных штаммов. В работе было изучено 45 штаммов C. diphtheriae, выделенных на территории Российской Федерации в 2010– 2015 гг. Анализ этих штаммов показал, что ген dtxR обнаруживается у всех представителей вида и является высококонсервативным участком генома С. diphtheriae. Большинство выявленных полиморфизмов были синонимичны (16 из 18 однонуклеотидных замен). Несмотря на низкий уровень филогенетического сигнала, аллельный вариант dtxR был ассоциирован с биологическими признаками штамма (биовар, токсигенность). Полученные данные свидетельствуют о высокой активности отрицательного отбора, направленного на поддержание в популяции существующей последовательности белка, и позволяют рекомендовать наработку фрагментов гена dtxR методом полимеразной цепной реакции в качестве дополнительного метода идентификации возбудителя, что особенно актуально в условиях растущего числа заболеваний, ассоциированных с нетоксигенными штаммами C. diphtheriae.

Текст научной работы на тему «Polymorphism of the dtxR gene in the currently existing strains of Сorynebacterium diphtheriae»

POLYMORPHISM OF THE DTXR GENE IN THE CURRENTLY EXISTING STRAINS OF СORYNEBACTERIUM DIPHTHERIAE

Chagina IA1, Perevarova YuS2, Perevarov VV2, Chaplin AV2 Borisova OYu1>2, Kafarskaia LI2, Afanas'ev SS1, Aleshkin VA1

1G. N. Gabrichevsky Research Institute for Epidemiology and Microbiology, Moscow, Russia 2Plrogov Russian National Research Medical University, Moscow, Russia

The pathogenic mechanism used by Corynebacterium diphtheriae is attributed to the ability of the diphtheria toxin to disrupt protein synthesis in human cells. Diphtheria toxin production is regulated by the DtxR protein. The latter is involved in the iron-mediated repression of the toxin gene and coordinates activities of other genes essential for the survival of C. diphtheriae. The DtxR-encoding gene occurs in both toxigenic and non-toxigenic strains; therefore it can be used to analyze the population structure of the species. In our work we have studied 45 strains of C. diphtheriae isolated in the Russian Federation in 2010-2015. These strains were analyzed to reveal that gene dtxR is a highly conservative region of С. diphtheriae genome that can be found in all members of the studied species. The majority of the discovered polymorphisms were synonymous (16 of 18 single nucleotide polymorphisms identified). In spite of the low phylogenetic signal, the allelic variant of dtxR was associated with the strain's phenotype (biovar, toxigenicity). The obtained data indicate the presence of aggressive negative selection aimed to maintain the existing protein sequence in the population. Based on the results, we recommend dtxR polymerase chain reaction as an additional technique for pathogen identification, which is especially relevant considering the increasing prevalence of the disease associated with non-toxigenic C. diphtheriae strains.

Keywords: diphtheria, Corynebacterium diphtheriae, dtxR, multilocus sequence typing, metalloregulatory proteins

Funding: this study was conducted as part of two projects: The Study of the Role of Microbial Communities in Human Oropharynx and Blood in Diphtheria, Pertussis and Other Infectious Inflammatory Diseases (Project ID А16-116021550311-2) and The Development of Molecular-Genetic Methods for Laboratory Diagnosis of Diphtheria and Pertussis (Project ID АААА-А16-116101810127-7) supported by the Sectoral Research Program of the Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (Problem-oriented Research in Epidemiological Surveillance of Infectious and Parasitic Diseases in 2016-2020).

[23 Correspondence should be addressed: Andrei Chaplin

ul. Ostrovityanova, d. 1, Moscow, Russia, 117997; okolomedik@gmail.com

Received: 02.02.2017 Accepted: 18.02.2017

ПОЛИМОРФИЗМ ГЕНА DTXR У СОВРЕМЕННЫХ ШТАММОВ СORYNEBACTERIUM DIPHTHERIAE

И. А. Чагина1, Ю. С. Переварова2, В. В. Переваров2, А. В. Чаплин2 н, О. Ю. Борисова1,2, Л. И. Кафарская2, С. С. Афанасьев1, В. А. Алешкин1

1 Московский научно-исследовательский институт эпидемиологии и микробиологии имени Г. Н. Габричевского, Москва

2 Российский национальный исследовательский медицинский университет имени Н. И. Пирогова, Москва

Считается, что патогенез Corynebacterium diphtheriae основан на воздействии дифтерийного токсина на синтез белка в клетках человека. Регуляция синтеза токсина находится под контролем белка DtxR. Данный белок осуществляет железоопосредованную репрессию гена дифтерийного токсина, а также координирует работу множества других генов, необходимых для нормальной жизнедеятельности C. diphtheriae. Ген, кодирующий DtxR, можно использовать для анализа популяционной структуры вида, так как он присутствует в геноме как токсигенных, так и нетоксигенных штаммов. В работе было изучено 45 штаммов C. diphtheriae, выделенных на территории Российской Федерации в 20102015 гг. Анализ этих штаммов показал, что ген dtxR обнаруживается у всех представителей вида и является высококонсервативным участком генома С. diphtheriae. Большинство выявленных полиморфизмов были синонимичны (16 из 18 однонуклеотидных замен). Несмотря на низкий уровень филогенетического сигнала, аллельный вариант dtxR был ассоциирован с биологическими признаками штамма (биовар, токсигенность). Полученные данные свидетельствуют о высокой активности отрицательного отбора, направленного на поддержание в популяции существующей последовательности белка, и позволяют рекомендовать наработку фрагментов гена dtxR методом полимеразной цепной реакции в качестве дополнительного метода идентификации возбудителя, что особенно актуально в условиях растущего числа заболеваний, ассоциированных с нетоксигенными штаммами C. diphtheriae.

Ключевые слова: дифтерия, Corynebacterium diphtheriae, dtxR, мультилокусное сиквенс-типирование, металлорегуляторные белки

Финансирование: исследование выполнено в рамках Отраслевой научно-исследовательской программы Роспотребнадзора на 2016-2020 гг. «Проблемно-ориентированные научные исследования в области эпидемиологического надзора за инфекционными и паразитарными болезнями» по проектам № А16-116021550311-2 «Изучение роли микробиоценозов ротоглотки и крови человека при дифтерии, коклюше и других инфекционно-вос-палительных заболеваниях» и № АААА-А16-116101810127-7 «Разработка молекулярно-генетических методов лабораторной диагностики дифтерии и коклюша».

[>3 Для корреспонденции: Чаплин Андрей Викторович

ул. Островитянова, д. 1, г Москва, 117997; okolomedik@gmail.com

Статья получена: 02.02.2017 Статья принята к печати: 18.02.2017

In spite of successful vaccination strategies, sporadic cases of diphtheria still occur, and the infection remains a serious health issue. Virulence of Corynebacterium diphtheriae is associated with its ability to produce a diphtheria toxin encoded by the tox gene [1]. Its pathogenic mechanism is based on ADP ribosylation of the elongation factor 2 that disrupts protein synthesis in human cells [2]. It should be noted that the presence of the tox gene in the C. diphtheriae genome does not necessarily confer toxigenicity. There are nontoxigenic tox-bearing strains (NTTB strains) that have lost their ability to synthesize a fully functional toxin following a series of mutations [3, 4].

Although tox is a part of the phage genome, iron-mediated regulation of toxin expression is exerted by the iron-sensing regulator DtxR, the product of the chromosomal gene dtxR. Thus, tox transcription directly depends on iron homeostasis, as low iron levels trigger tox expression followed by synthesis of the diphtheria toxin [5].

The dtxR gene is present in both toxigenic and nontoxigenic strains [6] meaning that it has functions other than regulation of diphtheria toxin synthesis. The DtxR regulon is reported to contain 20 more loci, including genes responsible for iron metabolism. To date, the DtxR protein of C. diphtheriae is known to regulate siderophore synthesis, a high-affinity transport system (ciuABCDEFG) and transcription of 3 loci involved in heme-monooxygenase (hmuO) activity [1, 7]. DtxR may also have a role in regulating bacterial virulence [7].

Microorganisms need large amounts of iron which is not so easy to acquire. However, iron excess stimulates production of toxic reactive oxygen species. Mammals have developed a mechanism of nonspecific defense against infections that relies on reducing the levels of unbound iron by specific iron-binding proteins [8, 9].

Therefore, survival and dissemination of the pathogen in the host depends on its ability to acquire different metal ions from protein complexes. For that, the pathogen employs various uptake mechanisms. Gene expression is controlled by metalloregulatory proteins - highly conserved transcriptional regulators [10, 11]. Once they bind to a specific metal ion, these regulators change their conformation and trigger or repress binding of the active site to the gene operator [12].

DtxR is a typical example of a metalloregulatory protein. Crystallography demonstrates that in its inactive state DtxR is a monomer that consists of two domains. A large conserved N-terminal domain contains two binding sites for iron ions and a helix-turn-helix motif that can bind to DNA; a smaller, less conserved C-terminal domain resembles the SH3 domain of eukaryotes. Ferrous ions bind to the binding sites rendering the repressor active. Once it is activated, dimerization occurs [13].

The two DtxR domains are linked by a proline-rich peptide segment. When the repressor is inactive, this segment binds to the SH3-resembling domain resulting in the formation of a prolylpeptide-SH3 complex (Pr-SH3) and stabilizing the repressor in its inactive state. After ferrous ions bind to the N-terminal domain triggering DtxR activation, the Pr-SH3 complex dissociates and the proline segment stabilizes helical segments of the N-terminal domain, which leads to dimerization of two protein subunits [14].

Considering the role of DtxR in C. diphtheriae survival, the dtxR gene must be studied to evaluate the pathogenic potential of C. diphtheriae, elucidate dynamics of circulating strains and assess feasibility of dtxR as a target for the PCR-based diagnosis of diphtheria or other infections associated with nontoxigenic C. diphtheria strains. The aim of this work was to identify genetic polymorphisms of DtxR and to

analyze the population structure of C. diphtheriae strains circulating in Russia.

METHODS

We studied genotypic characteristics of 45 strains of C. diphtheriae (bv. gravis and bv. mitis) isolated in 2010-2015. The study was conducted at the Reference center for Measles, Parotitis, Rubella, Pertussis, and Diphtheria of Gabrichevsky Moscow Research Institute of Epidemiology and Microbiology. C. diphtheriae strains were obtained from bacterial laboratories of the institutions for disease prevention and centers for hygiene and epidemiology located in 14 different regions of Russia, where the strains had been isolated for diagnostic or preventive screening or for the purpose of epidemiological research. The following collection strains were used: C. diphtheriae (State Research Center for Applied Microbiology & Biotechnology, Obolensk, Russia) and C. diphtheriae PW 8 (Therapeutic Products Regulatory Research Center, Moscow, Russia). Besides, the following strains were used as PCR negative control, 1 strain per species: C. ulcerans, C. pseudotuberculosis, C. amycolatum, C. glucuronolyticum, C. xerosis, C. afermentans subsp. afermentans, C. afermentans subsp. lipophiium, C. coyleae, C. pseudodiphtheriticum, C. macifaciens, C. simulans, and C. durum from the collection of Gabrichevsky Research Institute.

The strains were isolated following the guidelines of the Laboratory Diagnosis of Diphtheria manual (Guidelines 4.2.698-98 and 4.2.3065-13). The isolates were seeded onto the solid tellurite blood agar base containing 2 % agar (Microgen, Russia), 10 % bovine blood (LeiTran, Russia), and 0.02 % potassium tellurite (State Research Center for Applied Microbiology & Biotechnology, Russia). Then the cultures were thermostated for 24-48 h at 37 °C. Morphological, toxigenic and biochemical profiles of the grown cultures were prepared according to Guidelines 4.2.698-98 and 4.2.3065-13 mentioned above using the biochemical test system DS-DIPH-CORYNE (Diagnostic Systems, Russia).

Chromosomal DNA was extracted by boiling from a freshly grown 24-hour old C. diphtheriae culture. A culture sample was picked up with a sterile loop and suspended in 100 pl of deionized water, incubated for 20 min at 95 °C and centrifuged. The supernatant was used for the PCR assay.

PCR amplification of the dtxR gene of C. diphtheriae was performed using a pair of primers to cover the entire region of the studied gene: a previously proposed F1 5'-GGGACTACAACGCAACAAGAA-3' [15] and R1 5'-TCATCTAATTTCGCCGCCTTTA-3' designed by the PerlPrimer application, v1.1.21 [16]. Specificity of primers was checked using BLASTn by comparing their sequences to similar sequences of other Corynebacterium species obtained from the NCBI Nucleotide database.

The reaction mix contained a PCR buffer with 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 mM MgCl2, 0.2 pM of each primer, 200 pM of each dNTP, 1 pL of the DNA solution, and 1 unit/50 pL Taq DNA polymerase (Fermentas, Lithuania). Amplification was performed in the Tertsik amplifier (DNA Technology, Russia) operated in the automatic mode The amplified fragments were analyzed by 1.5 % agarose gel electrophoresis. Sequencing of the obtained fragments was performed by Evrogen, Russia.

C. diphtheriae strains were genotyped by multilocus sequence typing (MLST) according to the international protocol [17] using fragments of sequences of 7 housekeeping genes, namely atpA (encodes the a-subunit of ATP synthase),

dnaE (encodes the a-subunit of the DNA polymerase III holoenzyme), dnaK (encodes the Hsp70 chaperone), fusA (encodes elongation factor G), leuA (encodes 2-isopropylmalate synthase), odhA (encodes components Е1 and Е2 of the 2-oxoglutarate dehydrogenase complex), and rpoB (encodes the p-subunit of RNA-polymerase). Allelic profiles were identified for each strain.

The obtained sequences were compared to the nucleotide sequences published in GenBank. The sequence of the dtxR gene of C. diphtheriae PW8 was used as a reference (Genbank NC_016789.1).

Nucleotide sequences were aligned using the MUSCLE algorithm [18]. Polymorphisms were mapped to the protein structure based on the PDB data. Queries to the NCBI Nucleotide database were run using BLASTn. To identify alleles of the housekeeping genes, the PubMLST software was used. To estimate selection pressure on the dtxR gene, we applied the Nei-Gojobori method and calculated the Ka/Ks ratio, where Ka is the number of nonsynonymous substitutions per site and Ks is the number of synonymous substitutions per site [19]. Fisher's exact test was performed on contingency tables using the AS159 algorithm [20] and R 3.3.2. Phylogenetic trees were reconstructed by neighbor-joining based on the comparison of dtxR nucleotide sequences and included sequences of C. diphtheriae PW8, C. diphtheriae NCTC 13129 and C. diphtheriae 178-01 (Genbank NC_016789.1, BX248353.1 and NZ_JZUJ01000001.1). Evolutionary distances were computed using the Maximum Composite Likelihood method [21] and scaled as units of substitutions per site. Evolutionary analysis was performed by MEGA7 v.7.0.21 [22]

RESULTS

PCR amplification revealed the presence of the dtxR gene in all studied toxigenic and nontoxigenic strains of C. diphtheriae. Besides, PCR results came out negative for all allied species.

The samples of 45 C. diphtheriae strains were sequenced and the obtained sequences were compared to the dtxR

sequences retrieved from GenBank revealing polymorphisms at 18 positions: 66, 126, 225, 273, 358, 402, 440, 474, 504,507, 516, 558, 564, 579, 639, 640, 654 and 685 (Table 1).

The majority of substitutions relative to the reference sequence were synonymous. Specifically, the most frequent single nucleotide substitution at position 273 of the dtxR gene did not affect the protein sequence. This substitution was observed in 14 strains.

Polymorphisms at positions 440 and 640 that resulted in A147V and L2141substitutions, respectively, seemed to have no significant effect on the DtxR function. According to the 3D protein structure published in PDB (ID 2QQ9), amino acid at position 147 is found in the unstructured proline-rich (Pr) region. Since this segment participates in protein dimerization, we cannot rule out a possible effect of the amino acid substitution on DtxR activation. It appears that substitution of leucine for isoleucine at position 214 of the C-terminal domain does not have any effect on protein folding because these amino acids have similar properties. Thus, nonsynonymous substitutions are very likely to produce no effect on the DtxR function.

Many of the identified sequence variants are well known and were described previously by other researchers. However, we were able to identify a new single nucleotide polymorphism at position 358 that also has no effect on the amino acid sequence. A nucleotide query to the NCBI Nucleotide database performed by BLASTn returned no results.

We observed various combinations of polymorphisms in the dtxR gene relative to the reference sequence. Based on the discovered combinations of nucleotide sequences, C. diphtheriae isolates were distributed into several groups (Table 2).

More than a half (55 %) of identified nucleotide sequences differed from the reference sequence. It should be noted that the new substitution at position 358 was observed in one strain only (group 5) that had the least number of substitutions compared to the reference sequence, including nonsynonymous polymorphisms.

Based on the alignment of dtxR sequences, we constructed a phylogenetic tree (see the Figure).

Table 1. Frequency of nucleotide substitutions In the dtxR gene of the studied strains of C. diphtheriae relative to the strain PW8

Position of nucleotide In the dtxR gene Nucleotide substitution Encoded amino acid Amino acid substitution Number of strains

66 A-T 22 - 5

126 C-T 42 - 5

225 T-C 75 - 6

273 C-T 91 - 14

358 T-C 120 - 1

402 T-A 134 - 1

440 C-T 147 Alanine (A) - Valine (V) 6

474 C-T 158 - 6

504 T-A 168 - 6

507 C-T 169 - 6

516 T-C 172 - 6

558 C-T 186 - 2

564 T-A 188 - 6

579 C-T 193 - 2

639 C-T 213 - 4

640 C-A 214 Leucine (L) - Isoleucine (I) 2

654 T-C 218 - 2

685 C-T 229 - 1

Group of strains Number of strains (n = 45) Position of nucleotide In dtxR nucleotide sequence

66 126 225 273 358 402 440 474 504 507 516 558 564 579 639 640 654 685

1 20 (44 %) * * * * * * * * * * * * * * * * * *

2 5 (11 %) * T * * * * * * * * * * * * * * * *

3 9 (20 %) * * * T * * * * * * * * * * * * * *

4 5 (11 %) * * С T * * * * * * * * * * T * * *

5 1 (2 %) * * С * С A T T A T C T A T T A C T

6 1 (2 %) T * * * * * T T A T C T A T T A C *

7 4 (9 %) T * * * * * T T A T C * A * * * * *

Reference strain PW8 - A С T С T T С С T С T С T С С С T С

Note. * — a match with the reference; T, A — polymorphism with amino acid substitution.

Table 2. Combinations of polymorphisms of the dtxR gene in C. diphtheriae strains

The branching order is an approximation to some extent, due to the similarity of the analyzed sequences and hence a weak phylogenetic signal. The tree in the dendrogram is not rooted due to the lack of possibility to select an appropriate outgroup.

We also analyzed correlations between group composition and toxigenicity, biovars and sequence types (ST) determined by MLST (Table 3). Profiles of NTTB strains were previously described in [23].

Based on the distribution of toxigenic and nontoxigenic strains of different biovars with regard to the allelic variants of dtxR, Fisher's exact test was performed. The test was performed on 2 x 7 contingency tables to examine the association between a biovar type and the allelic variant of dtxR (p = 0.00078) and on 3 x 7 contingency tables to examine the association between toxigenicity and the allelic variant of dtxR (p = 2.8-10-9). The obtained results prompt us to conclude that the associations between a biovar type/toxigenicity and the allelic variant of dtxR are not accidental and implicate a phylogenetic signal — a sum of associations between the allelic variant of the gene and biological characteristics of the strains. Distribution of sequence types was nonuniform, identical sequence types were rarely found in one group.

To assess selection pressure on the dtxR gene, we calculated the Ka/Ks ratio (0.0526). The obtained value (Ka/Ks < 1) indicates a strong negative selection, i.e., selection pressure is aimed at maintaining the current protein sequence [24].

DISCUSSION

Our study confirmed the essential role of DtxR in the viability of toxigenic and nontoxigenic strains of C. diphtheriae. The observed polymorphisms provide new information of the variability of its strains in Russia. dtxR-related nucleotide and amino-acid substitutions were studied previously under various conditions with regard to diphtheria dissemination [25-27]. This work was conducted against the background of sporadic incidence. We performed a comprehensive analysis of nucleotide sequences and assessed their correlation with strain toxigenicity, biovars and sequence types. This approach allowed us to better understand the structure of the population of currently circulating C. diphtheriae strains.

The hypothesis about the significant effect of horizontal gene transfer on the structure of C. diphtheriae population was discussed earlier [17]. There are works describing transfer mechanisms for genes conferring antibiotic resistance [28] and virulence [29]. Components of the DtxR regulon may vary in

different strains of C. diphtheriae due to the loss, acquisition, or partial deletion of genes responsible for iron provision and hence tox expression [1, 30]. The discovered correlation between a sequence type and the allelic variant of dtxR proves the idea that homologous recombination in C. diphtheriae does not completely block the phylogenetic signal [17]. At the same time, the analysis of the population structure did not reveal any direct correlation between a biovar and the dtxR allele meaning that there is no phylogenetic basis for such classification, which is mainly determined by the frequency of horizontal gene transfer [31].

Less than a half (45 %) of the studied sequences were found to be identical to the reference sequence. Of 13 polymorphisms, only 1 was identified as new (position 358), but it did not affect the amino acid sequence. The most frequent was the synonymous polymorphism at position 273 observed in 14 strains. Our work demonstrates that Russian strains carry a smaller range of variants of the primary DtxR structure [26, 27].

It should be noted that although dtxR affects bacterial resistance to oxidative stress, under normal conditions it is not a critical gene for C. diphtheria [32], as was proved in the experiment with the mutant DtxR-defective strain [33]. However, we did not observe any significant changes in the studied sequences that could result in the synthesis of

The phylogenetic tree of C. diphtheriae strains based on the dtxR gene sequences

The tree is scaled to 0.1 substitutions per 200 b. p.; branch lengths correspond to the evolutionary distances used to construct the tree. Sequences within groups are identical.

Table 3. Group composition according to polymorphism combinations in the dtxR gene of C. diphtheriae strains

Group Number of substitutions in dtxR relative to strain PW8 Number of strains Biovar (number of strains) Toxigenicity (number of strains) Sequence type

1 - 20 mitis (18), gravis (2) notoxigenic (15) *

NTTB strains (3) 76

toxigenic (2) 5, 46

2 1 5 mitis NTTB strains 40

3 1 9 gravis (1), mitis (8) toxigenic (8) 25

notoxigenic (1) 123

4 3 5 mitis toxigenic 28, 67

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5 15 1 mitis notoxigenic -

6 12 1 gravis toxigenic 8

7 7 4 gravis toxigenic 8

Note. * — MLST non performed,--ST not found in the database.

a functionally inactive protein. There were two nucleotide polymorphisms that did result in amino acid substitutions, but the analysis of PDB data showed that those substitutions did not affect protein folding. Perhaps, functionally important polymorphisms of the dtxR gene may impair strain adaptation to the mammalian host limiting distribution of alleles that lead to the synthesis of the defective protein among the C. diphtheriae population. The value of the Ka/Ks ratio proved that DtxR is controlled by the stabilizing selection.

The pathogenic potential of C. diphtheriae does not always depend on strain's ability to produce the diphtheria toxin. For example, nontoxigenic strains of C. diphtheriae are becoming an increasing source of severe infection causing endocarditis [34], arthritis [35] and osteomyelitis [36]. Nontoxigenic strains are especially dangerous for patients with compromised immunity [37, 38]. This necessitates a more comprehensive approach to C. diphtheriae identification as currently existing methods are aimed at detecting toxigenic strains only.

Our findings confirmed the presence of the dtxR gene in both toxigenic and nontoxigenic strains of C. diphtheriae proving the feasibility of PCR-based identification proposed earlier [39]. Sequencing demonstrated that polymorphisms occurred mainly in the C-terminal domain of DtxR [15]. However, nucleotide substitutions were also observed in other gene regions (positions 66, 126, 225, 273, and 358). One

of such substitutions (position 126) was found in 5 strains (group 2) in the region corresponding to the primer that had been proposed earlier for PCR- dtxR [15, 39]. The pair of primers used in this study proved their high specificity confirmed by zero false-positive results. This, PCR-based identification of C. diphtheriae is a promising technique for the diagnosis of diphtheria and infections associated with nontoxigenic strains.

CONCLUSIONS

We analyzed the structure of C. diphtheriae population based on the allelic variants of the dtxR gene. The analysis revealed that 55 % of strains had sequences different from the reference sequence. The majority of the discovered polymorphisms were synonymous. The absence of wild strains with defective DtxR and a high similarity of the analyzed nucleotide sequences indicate a strong negative selection aimed to maintain the currently existing repressor sequence.

Homologous recombination attenuates the phylogenetic signal but does not block it completely. We discovered associations between the allelic variants of dtxR and toxigenicity/ biovar type. The obtained results allow us to conclude that dtxR represents a conserved sequence. We recommend PCR-dtxR as an accurate method for identification of toxigenic and nontoxigenic strains of C. diphtheriae.

References

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6. Dinu S, Damian M, Badell E, Dragomirescu CC, Guiso N. New diphtheria toxin repressor types depicted in a Romanian collection of Corynebacterium diphtheriae isolates. J Basic Microbiol. 2014 Oct; 54 (10): 1136-9.

7. Yellaboina S, Ranjan S, Chakhaiyar P, Hasnain SE, Ranjan A. Prediction of DtxR regulon: identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae. BMC Microbiol. 2004 Sep 24; 4: 38.

8. Agranoff DD, Krishna S. Metal ion homeostasis and intracellular parasitism. Mol Microbiol. 1998 May; 28 (3): 403-12.

9. Valko M, Morris H, Cronin MT. Metals, Toxicity and Oxidative Stress. Curr Med Chem. 2005; 12 (10): 1161-208.

10. Rolerson E, Swick A, Newlon L, Palmer C, Pan Y, Keeshan B, et al. The SloR/Dlg metalloregulator modulates Streptococcus mutans virulence gene expression. J Bacteriol. 2006 Jul; 188 (14): 5033-44.

11. Reyes-Caballero H,Campanello GC, GiedrocDP. Metalloregulatory proteins: metal selectivity and allosteric switching. Biophys Chem. 2011 Jul; 156 (2-3): 103-14.

12. Krebs JE, Goldstein ES, Kilpatrick ST. Lewin's Genes XI. 11th ed.

Burlington: Jones & Bartlett Learning; 2014.

13. D'Aquino JA, Ringe D. Mechanism of metal ion activation of the diphtheria toxin repressor DtxR. AIP Conf Proc. 2006; 851: 196-8.

14. Bhattacharya N, Yi M, Zhou HX, Logan TM. Backbone Dynamics in an Intramolecular Prolylpeptide-SH3 Complex from the Diphtheria Toxin Repressor, DtxR. J Mol Biol. 2007 Dec 7; 374 (4): 977-92.

15. Nakao H, Mazurova IK, Glushkevich T, Popovic T. Analysis of heterogeneity of Corynebacterium diphtheriae toxin gene, tox, and its regulatory element, dtxR, by direct sequencing. Res Microbiol. 1997 Jan; 148 (1): 45-54.

16. Marshall OJ. PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics. 2004 Oct 12; 20 (15): 2471-2.

17. Bolt F, Cassiday P, Tondella ML, DeZoysa A, Efstratiou A, Sing A, et al. Multilocus Sequence Typing Identifies Evidence for Recombination and Two Distinct Lineages of Corynebacterium diphtheriae. J Clin Microbiol. 2010 Nov; 48 (11): 4177-85.

18. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004 Mar 19; 32 (5): 1792-7.

19. Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986 Sep; 3 (5): 418-26.

20. Patefield WM. Algorithm AS 159: An Efficient Method of Generating Random R x C Tables with Given Row and Column Totals. J R Stat Soc Ser C Appl Stat. 1981; 30 (1): 91-7.

21. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A. 2004 Jul 27; 101 (30): 11030-5.

22. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016 Jul; 33 (7): 1870-4.

23. Borisova ОYu, Chagina IA, Chaplin AV, Kombarova SYu, Kafarskaya LI, Aleshkin VA. [Specificities of the structure of the tox gene encoding diphtheria toxin of Сorynebacterium diphtheriaе strains isolated in Russia in 2010-2015]. Infektsionnye bolezni. 2015; 13 (3): 12-7. Russian.

24. Yang Z, Bielawski JP. Statistical methods for detecting molecular adaptation. Trends Ecol Evol. 2000 Dec 1;15(12):496-503.

25. Kombarova SIu, Mazurova IK, Mel'nikov VG, Kostiu-kova NN, Volkovoj KI, Borisova OIu, et al. [Genetic structure of Corynebacterium diphtheriae strains isolated in Russia during epidemics of various intensity]. Zh Mikrobiol Epidemiol Immunobiol. 2001 May-Jun; (3): 3-8. Russian.

26. De Zoysa A, Efstratiou A, Hawkey PM. Molecular characterization of diphtheria toxin repressor (dtxR) genes present in nontoxigenic Corynebacterium diphtheriae strains isolated in the United Kingdom. J Clin Microbiol. 2005 Jan; 43 (1): 223-8.

27. Kombarova SIu, Borisova OIu, Mel'nikov VG, Gubina NI, Loseva LV, Mazurova IK. [Polymorphism of tox and dtxR genes in

circulating strains of Corynebacterium diphtheriae]. Zh Mikrobiol Epidemiol Immunobiol. 2009 Jan-Feb; (1): 7-11. Russian.

28. Serwold-Davis TM, Groman N, Rabin M. Transformation of Corynebacterium diphtheriae, Corynebacterium ulcerans, Corynebacterium glutamicum, and Escherichia coli with the C. diphtheriae plasmid pNG2. Proc Natl Acad Sci U S A. 1987 Jul; 84 (14): 4964-8.

29. Sangal V, Blom J, Sutcliffe IC, von Hunolstein C, Burkovski A, Hoskisson PA. Adherence and invasive properties of Corynebacterium diphtheriae strains correlates with the predicted membrane-associated and secreted proteome. BMC Genomics. 2015 Oct 9; 16: 765.

30. Drazek ES, Hammack CA, Schmitt MP. Corynebacterium diphtheriae genes required for acquisition of iron from haemin and haemoglobin are homologous to ABC haemin transporters. Mol Microbiol. 2000 Apr; 36 (1): 68-84.

31. Sangal V, Burkovski A, Hunt AC, Edwards B, Blom J, Hoskisson PA. A lack of genetic basis for biovar differentiation in clinically important Corynebacterium diphtheriae from whole genome sequencing. Infect Genet Evol. 2014 Jan; 21: 54-7.

32. Oram DM, Avdalovic A, Holmes RK. Construction and characterization of transposon insertion mutations in Corynebacterium diphtheriae that affect expression of the diphtheria toxin repressor (DtxR). J Bacteriol. 2002 Oct; 184 (20): 5723-32.

33. Boyd JM, Hall KC, Murphy JR. DNA sequences and characterization of dtxR alleles from Corynebacterium diphtheriae PW8(-), 1030(-), and C7hm723(-). J Bacteriol. 1992 Feb; 174 (4): 1268-72.

34. Muttaiyah S, Best EJ, Freeman JT, Taylor SL, Morris AJ, Roberts SA. Corynebacterium diphtheriae endocarditis: A case series and review of the treatment approach. Int J Infect Dis. 2011 Sep; 15 (9): e584-8.

35. Barakett V, Morel G, Lesage D, Petit JC. Septic arthritis due to a nontoxigenic strain of Corynebacterium diphtheriae subspecies mitis. Clin Infect Dis. 1993 Sep; 17 (3): 520-1.

36. Farfour E, Badell E, Zasada A, Hotzel H, Tomaso H, Guillot S, et al. Characterization and comparison of invasive Corynebacterium diphtheriae isolates from France and Poland. J Clin Microbiol. 2012 Jan; 50 (1): 173-5.

37. Lake JA, Ehrhardt MJ, Suchi M, Chun RH, Willoughby RE. A Case of Necrotizing Epiglottitis Due to Nontoxigenic Corynebacterium diphtheriae. Pediatrics. 2015 Jul; 136 (1): e242-5.

38. WojewodaCM, Koval CE, Wilson DA, Chakos MH, Harrington SM. Bloodstream Infection Caused by Nontoxigenic Corynebacterium diphtheriae in an Immunocompromised Host in the United States. J Clin Microbiol. 2012 Jun; 50 (6): 2170-2.

39. Pimenta FP, Matias GA, Pereira GA, Camello TC, Alves GB, Rosa AC, et al. A PCR for dtxR gene: Application to diagnosis of non-toxigenic and toxigenic Corynebacterium diphtheriae. Mol Cell Probes. 2008 Jun; 22 (3): 189-92.

Литература

1. Trost E, Blom J, Soares S de C, Huang IH, Al-Dilaimi A, Schröder J, et al. Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia. J Bacteriol. 2012 Jun; 194 (12): 3199-215.

2. Deng Q, Barbieri JT. Molecular Mechanisms of the Cytotoxicity of ADP-Ribosylating Toxins. Annu Rev Microbiol. 2008; 62 (1): 271-88.

3. Комбарова С. Ю., Борисова О. Ю., Мельников В. Г., Наумов Л. С., Нарвская О. В., Мокроусов И. В. и др. Наблюдение за циркуляцией штаммов Corynebacterium diphtheriae, различающихся по признаку токсигенности. Мед. альманах. 2009; (2): 108-11.

4. Мельников В. Г., Комбарова С. Ю., Борисова О. Ю., Воло-жанцев Н. В., Веревкин В. В., Волковой К. И. и др. Характеристика нетоксигенных штаммов Corynebacterium diphtheriae,

несущих ген дифтерийного токсина. Журн. микробиол., эпи-демиол. и иммунобиол. 2004; (1): 3-7.

5. Merchant AT, Spatafora GA. A role for the DtxR family of metalloregulators in gram-positive pathogenesis. Mol Oral Microbiol. 2014 Feb; 29 (1): 1-10.

6. Dinu S, Damian M, Badell E, Dragomirescu CC, Guiso N. New diphtheria toxin repressor types depicted in a Romanian collection of Corynebacterium diphtheriae isolates. J Basic Microbiol. 2014 Oct; 54 (10): 1136-9.

7. Yellaboina S, Ranjan S, Chakhaiyar P, Hasnain SE, Ranjan A. Prediction of DtxR regulon: identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae. BMC Microbiol. 2004 Sep 24; 4: 38.

8. Agranoff DD, Krishna S. Metal ion homeostasis and intracellular parasitism. Mol Microbiol. 1998 May; 28 (3): 403-12.

9. Valko M, Morris H, Cronin MT. Metals, Toxicity and Oxidative Stress. Curr Med Chem. 2005; 12 (10): 1161-208.

10. Rolerson E, Swick A, Newlon L, Palmer C, Pan Y, Keeshan B, et al. The SloR/Dlg metalloregulator modulates Streptococcus mutans virulence gene expression. J Bacteriol. 2006 Jul; 188 (14): 5033-44.

11. Reyes-Caballero H, Campanello GC, Giedroc DP. Metalloregulatory proteins: metal selectivity and allosteric switching. Biophys Chem. 2011 Jul; 156 (2-3): 103-14.

12. Krebs JE, Goldstein ES, Kilpatrick ST. Lewin's Genes XI. 11th ed. Burlington: Jones & Bartlett Learning; 2014.

13. D'Aquino JA, Ringe D. Mechanism of metal ion activation of the diphtheria toxin repressor DtxR. AIP Conf Proc. 2006; 851: 196-8.

14. Bhattacharya N, Yi M, Zhou HX, Logan TM. Backbone Dynamics in an Intramolecular Prolylpeptide-SH3 Complex from the Diphtheria Toxin Repressor, DtxR. J Mol Biol. 2007 Dec 7; 374 (4): 977-92.

15. Nakao H, Mazurova IK, Glushkevich T, Popovic T. Analysis of heterogeneity of Corynebacterium diphtheriae toxin gene, tox, and its regulatory element, dtxR, by direct sequencing. Res Microbiol. 1997 Jan; 148 (1): 45-54.

16. Marshall OJ. PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics. 2004 Oct 12; 20 (15): 2471-2.

17. Bolt F, Cassiday P, Tondella ML, DeZoysa A, Efstratiou A, Sing A, et al. Multilocus Sequence Typing Identifies Evidence for Recombination and Two Distinct Lineages of Corynebacterium diphtheriae. J Clin Microbiol. 2010 Nov; 48 (11): 4177-85.

18. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004 Mar 19; 32 (5): 1792-7.

19. Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986 Sep; 3 (5): 418-26.

20. Patefield WM. Algorithm AS 159: An Efficient Method of Generating Random R x C Tables with Given Row and Column Totals. J R Stat Soc Ser C Appl Stat. 1981; 30 (1): 91-7.

21. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A. 2004 Jul 27; 101 (30): 11030-5.

22. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016 Jul; 33 (7): 1870-4.

23. Борисова О. Ю., Чагина И. А., Чаплин А. В., Комбаро-ва С. Ю., Кафарская Л. И., Алешкин В. А. Особенности структуры гена tox, кодирующего дифтерийный токсин штаммов Corynebacterium diphtheriae, выделенных в России в 2010-2015 гг. Инфек. бол. 2015; 13 (3): 12-7.

24. Yang Z, Bielawski JP. Statistical methods for detecting molecular adaptation. Trends Ecol Evol. 2000 Dec 1;15(12):496-503.

25. Комбарова С. Ю., Мазурова И. К., Мельников В. Г., Костюкова Н. Н., Волкова К. И., Борисова О. Ю. и др. Генетическая структура штаммов Corynebacterium diphtheriae, выделенных в России при разной интенсивности эпидемического процесса дифтерии. Журн. микробиол., эпидемиол. и иммунобиол. 2001; (3): 3-8.

26. De Zoysa A, Efstratiou A, Hawkey PM. Molecular characterization of diphtheria toxin repressor (dtxR) genes present in nontoxigenic

Corynebacterium diphtheriae strains isolated in the United Kingdom. J Clin Microbiol. 2005 Jan; 43 (1): 223-8.

27. Комбарова С. Ю., Борисова О. Ю., Мельников В. Г., Губина Н. И., Лосева Л. В., Мазурова И. К. Полиморфизм генов tox и dtxR у циркулирующих штаммов Corynebacterium diphtheriae. Журн. микробиол., эпидемиол. и иммунобиол. 2009; (1): 7-11.

28. Serwold-Davis TM, Groman N, Rabin M. Transformation of Corynebacterium diphtheriae, Corynebacterium ulcerans, Corynebacterium glutamicum, and Escherichia coli with the C. diphtheriae plasmid pNG2. Proc Natl Acad Sci U S A. 1987 Jul; 84 (14): 4964-8.

29. Sangal V, Blom J, Sutcliffe IC, von Hunolstein C, Burkovski A, Hoskisson PA. Adherence and invasive properties of Corynebacterium diphtheriae strains correlates with the predicted membrane-associated and secreted proteome. BMC Genomics. 2015 Oct 9; 16: 765.

30. Drazek ES, Hammack CA, Schmitt MP. Corynebacterium diphtheriae genes required for acquisition of iron from haemin and haemoglobin are homologous to ABC haemin transporters. Mol Microbiol. 2000 Apr; 36 (1): 68-84.

31. Sangal V, Burkovski A, Hunt AC, Edwards B, Blom J, Hoskisson PA. A lack of genetic basis for biovar differentiation in clinically important Corynebacterium diphtheriae from whole genome sequencing. Infect Genet Evol. 2014 Jan; 21: 54-7.

32. Oram DM, Avdalovic A, Holmes RK. Construction and characterization of transposon insertion mutations in Corynebacterium diphtheriae that affect expression of the diphtheria toxin repressor (DtxR). J Bacteriol. 2002 Oct; 184 (20): 5723-32.

33. Boyd JM, Hall KC, Murphy JR. DNA sequences and characterization of dtxR alleles from Corynebacterium diphtheriae PW8(-), 1030(-), and C7hm723(-). J Bacteriol. 1992 Feb; 174 (4): 1268-72.

34. Muttaiyah S, Best EJ, Freeman JT, Taylor SL, Morris AJ, Roberts SA. Corynebacterium diphtheriae endocarditis: A case series and review of the treatment approach. Int J Infect Dis. 2011 Sep; 15 (9): e584-8.

35. Barakett V, Morel G, Lesage D, Petit JC. Septic arthritis due to a nontoxigenic strain of Corynebacterium diphtheriae subspecies mitis. Clin Infect Dis. 1993 Sep; 17 (3): 520-1.

36. Farfour E, Badell E, Zasada A, Hotzel H, Tomaso H, Guillot S, et al. Characterization and comparison of invasive Corynebacterium diphtheriae isolates from France and Poland. J Clin Microbiol. 2012 Jan; 50 (1): 173-5.

37. Lake JA, Ehrhardt MJ, Suchi M, Chun RH, Willoughby RE. A Case of Necrotizing Epiglottitis Due to Nontoxigenic Corynebacterium diphtheriae. Pediatrics. 2015 Jul; 136 (1): e242-5.

38. WojewodaCM, Koval CE, Wilson DA, Chakos MH, Harrington SM. Bloodstream Infection Caused by Nontoxigenic Corynebacterium diphtheriae in an Immunocompromised Host in the United States. J Clin Microbiol. 2012 Jun; 50 (6): 2170-2.

39. Pimenta FP, Matias GA, Pereira GA, Camello TC, Alves GB, Rosa AC, et al. A PCR for dtxR gene: Application to diagnosis of non-toxigenic and toxigenic Corynebacterium diphtheriae. Mol Cell Probes. 2008 Jun; 22 (3): 189-92.

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