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Tyakht AV, Manolov AI, Kanygina AV, Ischenko DS, Kovarsky BA, Popenko AS, Pavlenko AV, Elizarova AV, Rakitina DV, Baikova JP, Ladygina VG, Kostryukova ES, Karpova IY, Semashko TA, Larin AK, Grigoryeva TV, Sinyagina MN, Malanin SY, Shcherbakov PL, Kharitonova AY, Khalif IL, Shapina MV, Maev IV, Andreev DN, Belousova EA, Buzunova YM, Alexeev DG, Govorun VM. Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn's disease discovered using metagenomic and genomic analyses. BMC Genomics 2018; 19:968. [PMID: 30587114 PMCID: PMC6307143 DOI: 10.1186/s12864-018-5306-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/23/2018] [Indexed: 12/12/2022] Open
Abstract
Background Crohn’s disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated. Methods We performed a metagenomic study investigating the gut microbiota of patients with Crohn’s disease. A metagenomic reconstruction of the consensus genome content of the species was used to assess the genetic variability. Results The abnormal shifts in the microbial community structures in Crohn’s disease were heterogeneous among the patients. The metagenomic data suggested the existence of multiple E. coli strains within individual patients. We discovered that the genetic diversity of the species was high and that only a few samples manifested similarity to the adherent-invasive varieties. The other species demonstrated genetic diversity comparable to that observed in the healthy subjects. Our results were supported by a comparison of the sequenced genomes of isolates from the same microbiota samples and a meta-analysis of published gut metagenomes. Conclusions The genomic diversity of Crohn’s disease-associated E. coli within and among the patients paves the way towards an understanding of the microbial mechanisms underlying the onset and progression of the Crohn’s disease and the development of new strategies for the prevention and treatment of this disease. Electronic supplementary material The online version of this article (10.1186/s12864-018-5306-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander V Tyakht
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700. .,ITMO University, 49 Kronverkskiy pr, Saint-Petersburg, Russian Federation, 197101.
| | - Alexander I Manolov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Alexandra V Kanygina
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Dmitry S Ischenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Boris A Kovarsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Anna S Popenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Alexander V Pavlenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Anna V Elizarova
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Daria V Rakitina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Julia P Baikova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Valentina G Ladygina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Elena S Kostryukova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Irina Y Karpova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Tatyana A Semashko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Andrei K Larin
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Tatyana V Grigoryeva
- Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation, 420008
| | - Mariya N Sinyagina
- Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation, 420008
| | - Sergei Y Malanin
- Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation, 420008
| | - Petr L Shcherbakov
- Moscow Clinical Scientific Center, 86 Shosse Entuziastov St., Moscow, Russian Federation, 111123
| | - Anastasiya Y Kharitonova
- Clinical and Research Institute of Emergency Children's Surgery and Trauma, 22 Bolshaya Polyanka St., Moscow, Russian Federation, 119180
| | - Igor L Khalif
- State Scientific Center of Coloproctology, 2 Salam Adil St., Moscow, Russian Federation, 123423
| | - Marina V Shapina
- State Scientific Center of Coloproctology, 2 Salam Adil St., Moscow, Russian Federation, 123423
| | - Igor V Maev
- Moscow State University of Medicine and Dentistry, Build. 6, 20 Delegatskaya St., Moscow, Russian Federation, 127473
| | - Dmitriy N Andreev
- Moscow State University of Medicine and Dentistry, Build. 6, 20 Delegatskaya St., Moscow, Russian Federation, 127473
| | - Elena A Belousova
- Moscow Regional Research and Clinical Institute, 61/2 Shchepkina str, Moscow, Russian Federation, 129110
| | - Yulia M Buzunova
- Moscow Regional Research and Clinical Institute, 61/2 Shchepkina str, Moscow, Russian Federation, 129110
| | - Dmitry G Alexeev
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Vadim M Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700.,M.M. Shemyakin - Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, Russian Federation, 117997
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2
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Snezhkina AV, Krasnov GS, Zhikrivetskaya SO, Karpova IY, Fedorova MS, Nyushko KM, Belyakov MM, Gnuchev NV, Sidorov DV, Alekseev BY, Melnikova NV, Kudryavtseva AV. [Overexpression of microRNAs miR-9, -98, and -199 Correlates with the Downregulation of HK2 Expression in Colorectal Cancer]. Mol Biol (Mosk) 2018; 52:220-230. [PMID: 29695690 DOI: 10.7868/s0026898418020052] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/12/2016] [Indexed: 11/23/2022]
Abstract
Glycolysis activation is one of the main features of energy metabolism in cancer cells that is associated with the increase in glycolytic enzyme synthesis, primarily, hexokinases (HKs), in many types of tumors. Conversely, in colorectal cancer (CRC) the decrease in the expression of HK2 gene, which encodes one of the key rate-limiting enzyme of glycolysis, was revealed, thus, the study of the mechanisms of its inhibition in CRC is of particular interest. To search for potential microRNAs, inhibiting the expression of HK2 in CRC, we have performed the analysis of data from "The Cancer Genome Atlas" (TCGA) and five microRNA-mRNA target interaction databases (TargetScan, DIANA microT, mirSVR (miRanda), PicTar, and miRTarBase) using original CrossHub software. Seven microRNAs containing binding site on mRNA HK2, which expression is negatively correlated with HK2 expression, were selected for further analysis. The expression levels of these microRNAs and mRNA HK2 were estimated by quantitative PCR on a set of CRC samples. It has been shown, that the expression of three microRNAs (miR-9-5p, -98-5p, and -199-5p) was increased and correlated negatively with mRNA level of HK2 gene. Thus, downregulation of HK2 gene may be caused by its negative regulation through microRNAs miR-9-5p, -98-5p, and -199-5p.
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Affiliation(s)
- A V Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - G S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - S O Zhikrivetskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - I Y Karpova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - M S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - K M Nyushko
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, 125284 Russia
| | - M M Belyakov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, 125284 Russia
| | - N V Gnuchev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - D V Sidorov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, 125284 Russia
| | - B Y Alekseev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, 125284 Russia
| | - N V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - A V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, 125284 Russia.,
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3
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Rakitina DV, Manolov AI, Kanygina AV, Garushyants SK, Baikova JP, Alexeev DG, Ladygina VG, Kostryukova ES, Larin AK, Semashko TA, Karpova IY, Babenko VV, Ismagilova RK, Malanin SY, Gelfand MS, Ilina EN, Gorodnichev RB, Lisitsyna ES, Aleshkin GI, Scherbakov PL, Khalif IL, Shapina MV, Maev IV, Andreev DN, Govorun VM. Genome analysis of E. coli isolated from Crohn's disease patients. BMC Genomics 2017; 18:544. [PMID: 28724357 PMCID: PMC5517970 DOI: 10.1186/s12864-017-3917-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/02/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn's disease (CD). The phylogeny of E. coli isolated from Crohn's disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related. RESULTS We performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains. CDEC was shown to belong to A, B1, B2 and D phylogenetic groups. The plasmid and several operons from the reference CD-associated E. coli strain LF82 were demonstrated to be more often present in CDEC genomes belonging to different phylogenetic groups than in genomes of commensal strains. The operons include carbon-source induced invasion GimA island, prophage I, iron uptake operons I and II, capsular assembly pathogenetic island IV and propanediol and galactitol utilization operons. CONCLUSIONS Our findings suggest that CDEC are phylogenetically diverse. However, some strains isolated from independent sources possess highly similar chromosome or plasmids. Though no CD-specific genes or functional domains were present in all CD-associated strains, some genes and operons are more often found in the genomes of CDEC than in commensal E. coli. They are principally linked to gut colonization and utilization of propanediol and other sugar alcohols.
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Affiliation(s)
- Daria V. Rakitina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Alexander I. Manolov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | | | - Sofya K. Garushyants
- Skolkovo Institute of Science and Technology, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Julia P. Baikova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry G. Alexeev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute for Physics and Technology, Moscow, Russia
| | - Valentina G. Ladygina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Elena S. Kostryukova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Andrei K. Larin
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Tatiana A. Semashko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Irina Y. Karpova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vladislav V. Babenko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Ruzilya K. Ismagilova
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Fundamental Medicine and Biology of Kazan Federal University, Kazan, Russia
| | - Sergei Y. Malanin
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Fundamental Medicine and Biology of Kazan Federal University, Kazan, Russia
| | - Mikhail S. Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Elena N. Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Roman B. Gorodnichev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Eugenia S. Lisitsyna
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Gennady I. Aleshkin
- The Gamaleya Research Institute for Epidemiology and Microbiology of the Russian Academy of Medical Science, Moscow, Russia
| | - Petr L. Scherbakov
- Central Scientific Institute of Gastroenterology, Moscow Clinical Research Centre, Moscow, Russia
| | - Igor L. Khalif
- State Scientific Center of Coloproctology, Ministry of Health of Russian Federation, Moscow, Russia
| | - Marina V. Shapina
- State Scientific Center of Coloproctology, Ministry of Health of Russian Federation, Moscow, Russia
| | - Igor V. Maev
- Moscow State University of Medicine and Dentistry named after A.I. Evdokimov, Ministry of Health of Russian Federation, Moscow, Russia
| | - Dmitry N. Andreev
- Moscow State University of Medicine and Dentistry named after A.I. Evdokimov, Ministry of Health of Russian Federation, Moscow, Russia
| | - Vadim M. Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute for Physics and Technology, Moscow, Russia
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4
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Kudryavtseva AV, Fedorova MS, Zhavoronkov A, Moskalev AA, Zasedatelev AS, Dmitriev AA, Sadritdinova AF, Karpova IY, Nyushko KM, Kalinin DV, Volchenko NN, Melnikova NV, Klimina KM, Sidorov DV, Popov AY, Nasedkina TV, Kaprin AD, Alekseev BY, Krasnov GS, Snezhkina AV. Effect of lentivirus-mediated shRNA inactivation of HK1, HK2, and HK3 genes in colorectal cancer and melanoma cells. BMC Genet 2016; 17:156. [PMID: 28105937 PMCID: PMC5249010 DOI: 10.1186/s12863-016-0459-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background The switch from oxidative phosphorylation to glycolysis in proliferating cancer cells, even under aerobic conditions, has been shown first in 1926 by Otto Warburg. Today this phenomenon is known as the “Warburg effect” and recognized as a hallmark of cancer. The metabolic shift to glycolysis is associated with the alterations in signaling pathways involved in energy metabolism, including glucose uptake and fermentation, and regulation of mitochondrial functions. Hexokinases (HKs), which catalyze the first step of glycolysis, have been identified to play a role in tumorigenesis of human colorectal cancer (CRC) and melanoma. However, the mechanism of action of HKs in the promotion of tumor growth remains unclear. Results The purpose of the present study was to investigate the effect of silencing of hexokinase genes (HK1, HK2, and HK3) in colorectal cancer (HT-29, SW 480, HCT-15, RKO, and HCT 116) and melanoma (MDA-MB-435S and SK-MEL-28) cell lines using short hairpin RNA (shRNA) lentiviral vectors. shRNA lentiviral plasmid vectors pLSLP-HK1, pLSLP-HK2, and pLSLP-HK3 were constructed and then transfected separately or co-transfected into the cells. HK2 inactivation was associated with increased expression of HK1 in colorectal cancer cell lines pointing to the compensation effect. Simultaneous attenuation of HK1 and HK2 levels led to decreased cell viability. Co-transfection with shRNA vectors against HK1, HK2, and HK3 mRNAs resulted in a rapid cell death via apoptosis. Conclusions We have demonstrated that simultaneous inactivation of HK1 and HK2 was sufficient to decrease proliferation and viability of melanoma and colorectal cancer cells. Our results suggest that HK1 and HK2 could be the key therapeutic targets for reducing aerobic glycolysis in examined cancers.
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Affiliation(s)
- Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia. .,National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia.
| | - Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alex Zhavoronkov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University Eastern Campus, Baltimore, Maryland, USA
| | - Alexey A Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexander S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,N.N. Blokhin Russian Cancer Research Center, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Asiya F Sadritdinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Irina Y Karpova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kirill M Nyushko
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Nadezhda N Volchenko
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kseniya M Klimina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V Sidorov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Tatiana V Nasedkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,N.N. Blokhin Russian Cancer Research Center, Moscow, Russia
| | - Andrey D Kaprin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Boris Y Alekseev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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5
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Ikryannikova LN, Ischenko DS, Lominadze GG, Kanygina AV, Karpova IY, Kostryukova ES, Mayansky NA, Skvortsov VS, Ilina EN, Govorun VM. The mystery of the fourth clone: comparative genomic analysis of four non-typeable Streptococcus pneumoniae strains with different susceptibilities to optochin. Eur J Clin Microbiol Infect Dis 2015; 35:119-30. [PMID: 26563895 DOI: 10.1007/s10096-015-2516-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/26/2015] [Indexed: 11/25/2022]
Abstract
Optochin-resistant pneumococci can be rarely caught in clinical microbiology laboratories because of the routine identification of all such strains as viridans group non-pneumococci. We were lucky to find four non-typeable Streptococcus pneumoniae clones demonstrating the different susceptibilities to optochin: one of them (Spn_13856) was resistant to optochin, while the other three (Spn_1719, Spn_27, and Spn_2298) were susceptible. Whole genome nucleotide sequences of these strains were compared to reveal the differences between the optochin-resistant and optochin-susceptible strains. Two adjacent genes coding maltose O-acetyltransferase and uridine phosphorylase which were presented in the genomes of all optochin-susceptible strains and missed in the optochin-resistant strain were revealed. Non-synonymous substitutions in 14 protein-coding genes were discovered, including the Ala49Ser mutation in the C-subunit of the F0 part of the ATP synthase rotor usually associated with pneumococcal optochin resistance. Modeling of a process of optochin interaction with the F0 part of the ATP synthase rotor indicates that the complex of optochin with "domain C" composed by wild-type C-subunits is more stable than the same complex composed of Ala49Ser mutant C-subunits.
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Affiliation(s)
- L N Ikryannikova
- Research Institute of Physical-Chemical Medicine, Ministry of Public Health of Russian Federation, 119992, Malaya Pirogovskaya str., 1a, Moscow, Russia.
| | - D S Ischenko
- Research Institute of Physical-Chemical Medicine, Ministry of Public Health of Russian Federation, 119992, Malaya Pirogovskaya str., 1a, Moscow, Russia
| | - G G Lominadze
- Federal State Budgetary Institute "Scientific Center of Children Health" of RAMS, Moscow, Russia
| | - A V Kanygina
- Research Institute of Physical-Chemical Medicine, Ministry of Public Health of Russian Federation, 119992, Malaya Pirogovskaya str., 1a, Moscow, Russia
| | - I Y Karpova
- Research Institute of Physical-Chemical Medicine, Ministry of Public Health of Russian Federation, 119992, Malaya Pirogovskaya str., 1a, Moscow, Russia
| | - E S Kostryukova
- Research Institute of Physical-Chemical Medicine, Ministry of Public Health of Russian Federation, 119992, Malaya Pirogovskaya str., 1a, Moscow, Russia
| | - N A Mayansky
- Federal State Budgetary Institute "Scientific Center of Children Health" of RAMS, Moscow, Russia
| | - V S Skvortsov
- Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121, Russia
| | - E N Ilina
- Research Institute of Physical-Chemical Medicine, Ministry of Public Health of Russian Federation, 119992, Malaya Pirogovskaya str., 1a, Moscow, Russia
| | - V M Govorun
- Research Institute of Physical-Chemical Medicine, Ministry of Public Health of Russian Federation, 119992, Malaya Pirogovskaya str., 1a, Moscow, Russia
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Podgorny OV, Polina NF, Babenko VV, Karpova IY, Kostryukova ES, Govorun VM, Lazarev VN. Isolation of single Chlamydia-infected cells using laser microdissection. J Microbiol Methods 2015; 109:123-8. [DOI: 10.1016/j.mimet.2014.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 12/12/2014] [Accepted: 12/23/2014] [Indexed: 11/15/2022]
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7
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Chernyaeva EN, Shulgina MV, Rotkevich MS, Dobrynin PV, Simonov SA, Shitikov EA, Ischenko DS, Karpova IY, Kostryukova ES, Ilina EN, Govorun VM, Zhuravlev VY, Manicheva OA, Yablonsky PK, Isaeva YD, Nosova EY, Mokrousov IV, Vyazovaya AA, Narvskaya OV, Lapidus AL, O'Brien SJ. Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology. BMC Genomics 2014; 15:308. [PMID: 24767249 PMCID: PMC4234438 DOI: 10.1186/1471-2164-15-308] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 04/15/2014] [Indexed: 11/10/2022] Open
Abstract
Background Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome. Description Here we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes. Conclusions Implementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains.
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Affiliation(s)
- Ekaterina N Chernyaeva
- St, Petersburg State University, Theodosius Dobzhansky Center for Genome Bioinformatics, 41 Sredniy prospect, St, Petersburg, Russia.
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Tyakht AV, Kostryukova ES, Popenko AS, Belenikin MS, Pavlenko AV, Larin AK, Karpova IY, Selezneva OV, Semashko TA, Ospanova EA, Babenko VV, Maev IV, Cheremushkin SV, Kucheryavyy YA, Shcherbakov PL, Grinevich VB, Efimov OI, Sas EI, Abdulkhakov RA, Abdulkhakov SR, Lyalyukova EA, Livzan MA, Vlassov VV, Sagdeev RZ, Tsukanov VV, Osipenko MF, Kozlova IV, Tkachev AV, Sergienko VI, Alexeev DG, Govorun VM. Human gut microbiota community structures in urban and rural populations in Russia. Nat Commun 2014; 4:2469. [PMID: 24036685 PMCID: PMC3778515 DOI: 10.1038/ncomms3469] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 08/20/2013] [Indexed: 02/06/2023] Open
Abstract
The microbial community of the human gut has a crucial role in sustaining host homeostasis. High-throughput DNA sequencing has delineated the structural and functional configurations of gut metagenomes in world populations. The microbiota of the Russian population is of particular interest to researchers, because Russia encompasses a uniquely wide range of environmental conditions and ethnogeographical cohorts. Here we conduct a shotgun metagenomic analysis of gut microbiota samples from 96 healthy Russian adult subjects, which reveals novel microbial community structures. The communities from several rural regions display similarities within each region and are dominated by the bacterial taxa associated with the healthy gut. Functional analysis shows that the metabolic pathways exhibiting differential abundance in the novel types are primarily associated with the trade-off between the Bacteroidetes and Firmicutes phyla. The specific signatures of the Russian gut microbiota are likely linked to the host diet, cultural habits and socioeconomic status.
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Affiliation(s)
- Alexander V Tyakht
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
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9
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Shitikov EA, Bespyatykh JA, Ischenko DS, Alexeev DG, Karpova IY, Kostryukova ES, Isaeva YD, Nosova EY, Mokrousov IV, Vyazovaya AA, Narvskaya OV, Vishnevsky BI, Otten TF, Zhuravlev VY, Yablonsky PK, Ilina EN, Govorun VM. Unusual large-scale chromosomal rearrangements in Mycobacterium tuberculosis Beijing B0/W148 cluster isolates. PLoS One 2014; 9:e84971. [PMID: 24416324 PMCID: PMC3885621 DOI: 10.1371/journal.pone.0084971] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 11/28/2013] [Indexed: 11/18/2022] Open
Abstract
The Mycobacterium tuberculosis (MTB) Beijing family isolates are geographically widespread, and there are examples of Beijing isolates that are hypervirulent and associated with drug resistance. One-fourth of Beijing genotype isolates found in Russia belong to the B0/W148 group. The aim of the present study was to investigate features of these endemic strains on a genomic level. Four Russian clinical isolates of this group were sequenced, and the data obtained was compared with published sequences of various MTB strain genomes, including genome of strain W-148 of the same B0/W148 group. The comparison of the W-148 and H37Rv genomes revealed two independent inversions of large segments of the chromosome. The same inversions were found in one of the studied strains after deep sequencing using both the fragment and mate-paired libraries. Additionally, inversions were confirmed by RFLP hybridization analysis. The discovered rearrangements were verified by PCR in all four newly sequenced strains in the study and in four additional strains of the same Beijing B0/W148 group. The other 32 MTB strains from different phylogenetic lineages were tested and revealed no inversions. We suggest that the initial largest inversion changed the orientation of the three megabase (Mb) segment of the chromosome, and the second one occurred in the previously inverted region and partly restored the orientation of the 2.1 Mb inner segment of the region. This is another remarkable example of genomic rearrangements in the MTB in addition to the recently published of large-scale duplications. The described cases suggest that large-scale genomic rearrangements in the currently circulating MTB isolates may occur more frequently than previously considered, and we hope that further studies will help to determine the exact mechanism of such events.
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MESH Headings
- Antitubercular Agents/therapeutic use
- China/epidemiology
- Chromosome Inversion
- Chromosome Mapping
- Chromosomes, Bacterial
- DNA, Bacterial/classification
- DNA, Bacterial/genetics
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Genome, Bacterial
- High-Throughput Nucleotide Sequencing
- Humans
- Mycobacterium tuberculosis/classification
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Phylogeny
- Russia/epidemiology
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/epidemiology
- Tuberculosis, Pulmonary/microbiology
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Affiliation(s)
- Egor A. Shitikov
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
- * E-mail:
| | - Julia A. Bespyatykh
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
| | - Dmitry S. Ischenko
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Dmitry G. Alexeev
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Irina Y. Karpova
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
| | | | - Yulia D. Isaeva
- Moscow Scientific-Practical Center of Treatment of Tuberculosis of Moscow Healthcare, Moscow, Russian Federation
| | - Elena Y. Nosova
- Moscow Scientific-Practical Center of Treatment of Tuberculosis of Moscow Healthcare, Moscow, Russian Federation
| | - Igor V. Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Anna A. Vyazovaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Olga V. Narvskaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Boris I. Vishnevsky
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Tatiana F. Otten
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Valery Y. Zhuravlev
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Peter K. Yablonsky
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Elena N. Ilina
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
| | - Vadim M. Govorun
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
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Tyakht AV, Popenko AS, Belenikin MS, Altukhov IA, Pavlenko AV, Kostryukova ES, Selezneva OV, Larin AK, Karpova IY, Alexeev DG. MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads. Source Code Biol Med 2012; 7:13. [PMID: 23216677 PMCID: PMC3599743 DOI: 10.1186/1751-0473-7-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 11/27/2012] [Indexed: 11/10/2022]
Abstract
MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies, including long reads (such as Sanger and 454 sequencing) and next-generation (including SOLiD and Illumina). It is the first metagenomic web service that is capable of processing SOLiD color-space reads, to authors’ knowledge. The web service allows phylogenetic and functional profiling of metagenomic samples using coverage depth resulting from the alignment of the reads to the catalogue of reference sequences which are built into the pipeline and contain prevalent microbial genomes and genes of human gut microbiota. The obtained metagenomic composition vectors are processed by the statistical analysis and visualization module containing methods for clustering, dimension reduction and group comparison. Additionally, the MALINA database includes vectors of bacterial and functional composition for human gut microbiota samples from a large number of existing studies allowing their comparative analysis together with user samples, namely datasets from Russian Metagenome project, MetaHIT and Human Microbiome Project (downloaded from
http://hmpdacc.org). MALINA is made freely available on the web at
http://malina.metagenome.ru. The website is implemented in JavaScript (using Ext JS), Microsoft .NET Framework, MS SQL, Python, with all major browsers supported.
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Affiliation(s)
- Alexander V Tyakht
- Research Institute of Physico-Chemical Medicine of Russian Federal Medico-Biological Agency (RIPCM), Malaya Pirogovskaya 1a, Moscow, 119435, Russia.
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