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Averina OV, Kovtun AS, Mavletova DA, Ziganshin RH, Danilenko VN, Mihaylova D, Blazheva D, Slavchev A, Brazkova M, Ibrahim SA, Krastanov A. Oxidative Stress Response of Probiotic Strain Bifidobacterium longum subsp. longum GT15. Foods 2023; 12:3356. [PMID: 37761064 PMCID: PMC10530004 DOI: 10.3390/foods12183356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
Bifidobacterium is a predominant and important genus in the bacterial population of the human gut microbiota. Despite the increasing number of studies on the beneficial functionality of bifidobacteria for human health, knowledge about their antioxidant potential is still insufficient. Several in vivo and in vitro studies of Bifidobacterium strains and their cellular components have shown good antioxidant capacity that provided a certain protection of their own and the host's cells. Our work presents the data of transcriptomic, proteomic, and metabolomic analyses of the growing and stationary culture of the probiotic strain B. longum subsp. longum GT15 after exposure to hydrogen peroxide for 2 h and oxygen for 2 and 4 h. The results of the analysis of the sequenced genome of B. longum GT15 showed the presence of 16 gene-encoding proteins with known antioxidant functions. The results of the full transcriptomic analysis demonstrated a more than two-fold increase of levels of transcripts for eleven genes, encoding proteins with antioxidant functions. Proteomic data analysis showed an increased level of more than two times for glutaredoxin and thioredoxin after the exposure to oxygen, which indicates that the thioredoxin-dependent antioxidant system may be the major redox homeostasis system in B. longum bacteria. We also found that the levels of proteins presumably involved in global stress, amino acid metabolism, nucleotide and carbohydrate metabolism, and transport had significantly increased in response to oxidative stress. The metabolic fingerprint analysis also showed good discrimination between cells responding to oxidative stress and the untreated controls. Our results provide a greater understanding of the mechanism of oxidative stress response in B. longum and the factors that contribute to its survival in functional food products.
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Affiliation(s)
- Olga V. Averina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.K.); (D.A.M.); (V.N.D.)
| | - Aleksey S. Kovtun
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.K.); (D.A.M.); (V.N.D.)
| | - Dilara A. Mavletova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.K.); (D.A.M.); (V.N.D.)
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia;
| | - Valery N. Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.K.); (D.A.M.); (V.N.D.)
| | - Dasha Mihaylova
- Department of Biotechnology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.M.); (A.K.)
| | - Denica Blazheva
- Department of Microbiology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.B.); (A.S.)
| | - Aleksandar Slavchev
- Department of Microbiology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.B.); (A.S.)
| | - Mariya Brazkova
- Department of Biotechnology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.M.); (A.K.)
| | - Salam A. Ibrahim
- Food Microbiology and Biotechnology Laboratory, Food and Nutritional Science Program, North Carolina A&T State University, Greensboro, NC 27411-1064, USA;
| | - Albert Krastanov
- Department of Biotechnology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.M.); (A.K.)
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2
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Reyes-Castillo PA, González-Vázquez R, Torres-Maravilla E, Bautista-Hernández JI, Zúñiga-León E, Leyte-Lugo M, Mateos-Sánchez L, Mendoza-Pérez F, Gutiérrez-Nava MA, Reyes-Pavón D, Azaola-Espinosa A, Mayorga-Reyes L. Bifidobacterium longum LBUX23 Isolated from Feces of a Newborn; Potential Probiotic Properties and Genomic Characterization. Microorganisms 2023; 11:1648. [PMID: 37512821 PMCID: PMC10385183 DOI: 10.3390/microorganisms11071648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/17/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Bifidobacterium longum is considered a microorganism with probiotic potential, which has been extensively studied, but these probiotic effects are strain dependent. This work aims to characterize the probiotic potential, based on the biochemical and genomic functionality, of B. longum LBUX23, isolated from neonates' feces. B. longum LBUX23 contains one circular genome of 2,287,838 bp with a G+C content of 60.05%, no plasmids, no CRISPR-Cas operon, possesses 56 tRNAs, 9 rRNAs, 1 tmRNA and 1776 coding sequences (CDSs). It has chromosomally encoded resistance genes to ampicillin and dicloxacillin, non-hemolytic activity, and moderate inhibition of Escherichia coli ATCC 25922 and to some emergent pathogen's clinical strains. B. longum LBUX23 was able to utilize lactose, sucrose, fructooligosaccharides (FOS), and lactulose. The maximum peak of bacterial growth was observed in sucrose and FOS at 6 h; in lactose and lactulose, it was shown at 8 h. B. longum LBUX23 can survive in gastrointestinal conditions (pH 4 to 7). A decrease in survival (96.5 and 93.8%) was observed at pH 3 and 3.5 during 120 min. argC, argH, and dapA genes could be involved in this tolerance. B. longum LBUX23 can also survive under primary and secondary glyco- or tauro-conjugated bile salts, and a mixture of bile salts due to the high extracellular bile salt hydrolase (BSH) activity (67.3 %), in taurocholic acid followed by taurodeoxycholic acid (48.5%), glycocholic acid (47.1%), oxgall (44.3%), and glycodeoxycholic acid (29.7%) probably due to the presence of the cbh and gnlE genes which form an operon (start: 119573 and end: 123812). Low BSH activity was determined intracellularly (<7%), particularly in glycocholic acid; no intracellular activity was shown. B. longum LBUX23 showed antioxidant effects in DPPH radical, mainly in intact cells (27.4%). In the case of hydroxyl radical scavenging capacity, cell debris showed the highest reduction (72.5%). In the cell-free extract, superoxide anion radical scavenging capacity was higher (90.5%). The genome of B. longum LBUX23 contains PNPOx, AhpC, Bcp, trxA, and trxB genes, which could be involved in this activity. Regarding adherence, it showed adherence up to 5% to Caco-2 cells. B. longum LBUX23 showed in vitro potential probiotic properties, mainly in BSH activity and antioxidant capacity, which indicates that it could be a good candidate for antioxidant or anti-cholesterol tests using in vivo models.
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Affiliation(s)
- Pedro A Reyes-Castillo
- Doctorado en Ciencias Biologicas y de la Salud, Universidad Autonoma Metropolitana, Unidad Xochimilco, Ciudad de Mexico 04960, Mexico
| | - Raquel González-Vázquez
- Laboratorio de Biotecnologia, Departamento de Sistemas Biologicos, CONAHCYT-Universidad Autónoma Metropolitana, Unidad Xochimilco, Ciudad de Mexico 04960, Mexico
| | - Edgar Torres-Maravilla
- Facultad de Medicina Mexicali, Universidad Autonoma de Baja California, Mexicali 21000, Mexico
| | - Jessica I Bautista-Hernández
- Laboratorio de Biotecnologia, Departamento de Sistemas Biologicos, Universidad Autonoma Metropolitana, Unidad Xochimilco, Ciudad de Mexico 04960, Mexico
| | - Eduardo Zúñiga-León
- Centro de Investigación en Recursos Bioticos, Facultad de Ciencias, Universidad Autonoma del Estado de Mexico, Carretera Toluca-Ixtlahuaca Km 14.5, San Cayetano, Toluca 50295, Mexico
| | - Martha Leyte-Lugo
- Laboratorio de Biotecnologia, Departamento de Sistemas Biologicos, CONAHCYT-Universidad Autónoma Metropolitana, Unidad Xochimilco, Ciudad de Mexico 04960, Mexico
| | - Leovigildo Mateos-Sánchez
- Unidad de Cuidados Intensivos de Neonatos, Unidad Medica de Alta Especialidad, Hospital Gineco Obstetricia No. 4 "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social, Ciudad de Mexico 01090, Mexico
| | - Felipe Mendoza-Pérez
- Laboratorio de Biotecnologia, Departamento de Sistemas Biologicos, Universidad Autonoma Metropolitana, Unidad Xochimilco, Ciudad de Mexico 04960, Mexico
| | - María Angélica Gutiérrez-Nava
- Laboratorio de Ecologia Microbiana, Departamento de Sistemas Biologicos, Universidad Autonoma Metropolitana, Unidad Xochimilco, Ciudad de Mexico 04960, Mexico
| | - Diana Reyes-Pavón
- Facultad de Medicina Mexicali, Universidad Autonoma de Baja California, Mexicali 21000, Mexico
| | - Alejandro Azaola-Espinosa
- Laboratorio de Biotecnologia, Departamento de Sistemas Biologicos, Universidad Autonoma Metropolitana, Unidad Xochimilco, Ciudad de Mexico 04960, Mexico
| | - Lino Mayorga-Reyes
- Laboratorio de Biotecnologia, Departamento de Sistemas Biologicos, Universidad Autonoma Metropolitana, Unidad Xochimilco, Ciudad de Mexico 04960, Mexico
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Danilenko VN, Alekseeva MG, Koshenko TA, Kovtun AS, Nezametdinova VZ. Species-Forming PFNA Operon of Bifidobacteria: Modules of Sensor Proteins Pkb2 and FN3, Structure and Distribution among Different Species and Strains of Bifidobacteria in Human Intestinal Microbiome. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422090071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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4
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Nezametdinova VZ, Yunes RA, Dukhinova MS, Alekseeva MG, Danilenko VN. The Role of the PFNA Operon of Bifidobacteria in the Recognition of Host's Immune Signals: Prospects for the Use of the FN3 Protein in the Treatment of COVID-19. Int J Mol Sci 2021; 22:ijms22179219. [PMID: 34502130 PMCID: PMC8430577 DOI: 10.3390/ijms22179219] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
Bifidobacteria are some of the major agents that shaped the immune system of many members of the animal kingdom during their evolution. Over recent years, the question of concrete mechanisms underlying the immunomodulatory properties of bifidobacteria has been addressed in both animal and human studies. A possible candidate for this role has been discovered recently. The PFNA cluster, consisting of five core genes, pkb2, fn3, aaa-atp, duf58, tgm, has been found in all gut-dwelling autochthonous bifidobacterial species of humans. The sensory region of the species-specific serine-threonine protein kinase (PKB2), the transmembrane region of the microbial transglutaminase (TGM), and the type-III fibronectin domain-containing protein (FN3) encoded by the I gene imply that the PFNA cluster might be implicated in the interaction between bacteria and the host immune system. Moreover, the FN3 protein encoded by one of the genes making up the PFNA cluster, contains domains and motifs of cytokine receptors capable of selectively binding TNF-α. The PFNA cluster could play an important role for sensing signals of the immune system. Among the practical implications of this finding is the creation of anti-inflammatory drugs aimed at alleviating cytokine storms, one of the dire consequences resulting from SARS-CoV-2 infection.
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Affiliation(s)
- Venera Z. Nezametdinova
- Laboratory of Bacterial Genetics, The Vavilov Institute of General Genetics, 117971 Moscow, Russia; (V.Z.N.); (R.A.Y.); (M.G.A.)
| | - Roman A. Yunes
- Laboratory of Bacterial Genetics, The Vavilov Institute of General Genetics, 117971 Moscow, Russia; (V.Z.N.); (R.A.Y.); (M.G.A.)
| | - Marina S. Dukhinova
- International Institute ‘Solution Chemistry of Advanced Materials and Technologies’, ITMO University, 197101 Saint-Petersburg, Russia;
| | - Maria G. Alekseeva
- Laboratory of Bacterial Genetics, The Vavilov Institute of General Genetics, 117971 Moscow, Russia; (V.Z.N.); (R.A.Y.); (M.G.A.)
| | - Valery N. Danilenko
- Laboratory of Bacterial Genetics, The Vavilov Institute of General Genetics, 117971 Moscow, Russia; (V.Z.N.); (R.A.Y.); (M.G.A.)
- Correspondence:
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5
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The Putative Antidepressant Mechanisms of Probiotic Bacteria: Relevant Genes and Proteins. Nutrients 2021; 13:nu13051591. [PMID: 34068669 PMCID: PMC8150869 DOI: 10.3390/nu13051591] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023] Open
Abstract
Probiotic bacteria are widely accepted as therapeutic agents against inflammatory bowel diseases for their immunostimulating effects. In the last decade, more evidence has emerged supporting the positive effects of probiotics on the course of neurodegenerative and psychiatric diseases. This brief review summarizes the data from clinical studies of probiotics possessing antidepressant properties and focuses on the potential genes and proteins underlying these mechanisms. Data from small-sample placebo-controlled pilot studies indicate that certain strains of bacteria can significantly reduce the symptoms of depression, especially in depressed patients. Despite the disparity between studies attempting to pinpoint the bacterial putative genes and proteins accounting for these mechanisms, they ultimately show that bacteria are a potential source of metabiotics—microbial metabolites or structural components. Since the constituents of cells—namely, secreted proteins, peptides and cell wall components—are most likely to be entangled in the gut–brain axis, they can serve as starting point in the search for probiotics with concrete properties.
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6
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Veselovsky VA, Dyachkova MS, Menyaylo EA, Polyaeva PS, Olekhnovich EI, Shitikov EA, Bespiatykh DA, Semashko TA, Kasianov AS, Ilina EN, Danilenko VN, Klimina KM. Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors. Front Immunol 2020; 11:595877. [PMID: 33304352 PMCID: PMC7701253 DOI: 10.3389/fimmu.2020.595877] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/20/2020] [Indexed: 01/14/2023] Open
Abstract
As permanent residents of the normal gut microbiota, bifidobacteria have evolved to adapt to the host’s immune response whose priority is to eliminate pathogenic agents. The mechanisms that ensure the survival of commensals during inflammation and maintain the stability of the core component of the normal gut microbiota in such conditions remain poorly understood. We propose a new in vitro approach to study the mechanisms of resistance to immune response factors based on high-throughput sequencing followed by transcriptome analysis. This approach allowed us to detect differentially expressed genes associated with inflammation. In this study, we demonstrated that the presence of the pro-inflammatory cytokines IL-6 and TNFα to the growth medium of the B. longum subsp. longum GT15 strain changes the latter’s growth rate insignificantly while affecting the expression of certain genes. We identified these genes and performed a COG and a KEGG pathway enrichment analysis. Using phylogenetic profiling we predicted the operons of genes whose expression was triggered by the cytokines TNFα and IL-6 in vitro. By mapping the transcription start points, we experimentally validated the predicted operons. Thus, in this study, we predicted the genes involved in a putative signaling pathway underlying the mechanisms of resistance to inflammatory factors in bifidobacteria. Since bifidobacteria are a major component of the human intestinal microbiota exhibiting pronounced anti-inflammatory properties, this study is of great practical and scientific relevance.
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Affiliation(s)
- Vladimir A Veselovsky
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Marina S Dyachkova
- Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Egor A Menyaylo
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Polina S Polyaeva
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Evgenii I Olekhnovich
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Egor A Shitikov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry A Bespiatykh
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Tatiana A Semashko
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Artem S Kasianov
- Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia.,Laboratory of Plant Genomics, The Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Valeriy N Danilenko
- Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Faculty of Ecology, International Institute for Strategic Development of Sectoral Economics Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
| | - Ksenia M Klimina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.,Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
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7
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Dyakov IN, Mavletova DA, Chernyshova IN, Snegireva NA, Gavrilova MV, Bushkova KK, Dyachkova MS, Alekseeva MG, Danilenko VN. FN3 protein fragment containing two type III fibronectin domains from B. longum GT15 binds to human tumor necrosis factor alpha in vitro. Anaerobe 2020; 65:102247. [PMID: 32771620 PMCID: PMC7409735 DOI: 10.1016/j.anaerobe.2020.102247] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 07/09/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022]
Abstract
Most species of the genus Bifidobacterium contain the gene cluster PFNA, which is presumably involved in the species-specific communication between bacteria and their hosts. The gene cluster PFNA consists of five genes including fn3, which codes for a protein containing two fibronectin type III domains. Each fibronectin domain contains sites similar to cytokine-binding sites of human receptors. Based on this finding we assumed that this protein would bind specifically to human cytokines in vitro. We cloned a fragment of the fn3 gene (1503 bp; 501 aa) containing two fibronectin domains, from the strain B. longum subsp. longum GT15. After cloning the fragment into the expression vector pET16b and expressing it in E. coli, the protein product was purified to a homogenous state for further analysis. Using the immunoferment method, we tested the purified fragment's ability to bind the following human cytokines: IL-1β, IL-6, IL-10, TNFα. We developed a sandwich ELISA system to detect any specific interactions between the purified protein and any of the studied cytokines. We found that the purified protein fragment only binds to TNFα.
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Affiliation(s)
- Ilya N Dyakov
- I.I, Mechnikov Research Institute for Vaccines and Sera, Malyj Kazennyj Per., 5, Moscow, Russia, 105064
| | - Dilara A Mavletova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina St., 3, Moscow, Russia, 119991
| | - Irina N Chernyshova
- I.I, Mechnikov Research Institute for Vaccines and Sera, Malyj Kazennyj Per., 5, Moscow, Russia, 105064
| | - Nadezda A Snegireva
- I.I, Mechnikov Research Institute for Vaccines and Sera, Malyj Kazennyj Per., 5, Moscow, Russia, 105064
| | - Marina V Gavrilova
- I.I, Mechnikov Research Institute for Vaccines and Sera, Malyj Kazennyj Per., 5, Moscow, Russia, 105064
| | - Kristina K Bushkova
- I.I, Mechnikov Research Institute for Vaccines and Sera, Malyj Kazennyj Per., 5, Moscow, Russia, 105064
| | - Marina S Dyachkova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina St., 3, Moscow, Russia, 119991
| | - Maria G Alekseeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina St., 3, Moscow, Russia, 119991
| | - Valery N Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina St., 3, Moscow, Russia, 119991; Peoples' Friendship University of Russia (RUDN University), Faculty of Ecology, International Institute for Strategic Development of Sectoral Economics, Miklukho-Maklaya St., 6, Moscow, Russia, 117198; Pharmabiotics Limited Liability Company, Bolshoy Boulevard, 42, Bldg. 1, 1238, Moscow, Russia, 121205.
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8
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Zakharevich NV, Nezametdinova VZ, Averina OV, Chekalina MS, Alekseeva MG, Danilenko VN. Complete Genome Sequence of Bifidobacterium angulatum GT102: Potential Genes and Systems of Communication with Host. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Kudryavtseva AV, Lukyanova EN, Kalinin DV, Zaretsky AR, Pokrovsky AV, Golovyuk AL, Fedorova MS, Pudova EA, Kharitonov SL, Pavlov VS, Kobelyatskaya AA, Melnikova NV, Dmitriev AA, Polyakov AP, Alekseev BY, Kiseleva MV, Kaprin AD, Krasnov GS, Snezhkina AV. Mutational load in carotid body tumor. BMC Med Genomics 2019; 12:39. [PMID: 30871634 PMCID: PMC6416835 DOI: 10.1186/s12920-019-0483-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Carotid body tumor (CBT) is a rare neoplasm arising from paraganglion located near the bifurcation of the carotid artery. There is great intra-tumor heterogeneity, and CBT development could be associated with both germline and somatic allelic variants. Studies on the molecular genetics of CBT are limited, and the molecular mechanisms of its pathogenesis are not fully understood. This work is focused on the estimation of mutational load (ML) in CBT. Methods Using the NextSeq 500 platform, we performed exome sequencing of tumors with matched lymph node tissues and peripheral blood obtained from six patients with CBT. To obtain reliable results in tumors with low ML, we developed and successfully applied a complex approach for the analysis of sequencing data. ML was evaluated as the number of somatic variants per megabase (Mb) of the target regions covered by the Illumina TruSeq Exome Library Prep Kit. Results The ML in CBT varied in the range of 0.09–0.28/Mb. Additionally, we identified several pathogenic/likely pathogenic somatic and germline allelic variants across six patients studied (including TP53 variants). Conclusions Using the developed approach, we estimated the ML in CBT, which is much lower than in common malignant tumors. Identified variants in known paraganglioma/pheochromocytoma-causative genes and novel genes could be associated with the pathogenesis of CBT. The obtained results expand our knowledge of the mutation process in CBT as well as the biology of tumor development.
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Affiliation(s)
- Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Elena N Lukyanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V Kalinin
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrew R Zaretsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anatoly V Pokrovsky
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexander L Golovyuk
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena A Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey L Kharitonov
- 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
| | - Vladislav S Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey P Polyakov
- 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
| | - Marina V Kiseleva
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey D Kaprin
- 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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10
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Sharma V, Mobeen F, Prakash T. Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics. Genes (Basel) 2018; 9:genes9100477. [PMID: 30275399 PMCID: PMC6210967 DOI: 10.3390/genes9100477] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 09/10/2018] [Indexed: 12/15/2022] Open
Abstract
Members of the genus Bifidobacterium are found in a wide-range of habitats and are used as important probiotics. Thus, exploration of their functional traits at the genus level is of utmost significance. Besides, this genus has been demonstrated to exhibit an open pan-genome based on the limited number of genomes used in earlier studies. However, the number of genomes is a crucial factor for pan-genome calculations. We have analyzed the pan-genome of a comparatively larger dataset of 215 members of the genus Bifidobacterium belonging to different habitats, which revealed an open nature. The pan-genome for the 56 probiotic and human-gut strains of this genus, was also found to be open. The accessory- and unique-components of this pan-genome were found to be under the operation of Darwinian selection pressure. Further, their genome-size variation was predicted to be attributed to the abundance of certain functions carried by genomic islands, which are facilitated by insertion elements and prophages. In silico functional and host-microbe interaction analyses of their core-genome revealed significant genomic factors for niche-specific adaptations and probiotic traits. The core survival traits include stress tolerance, biofilm formation, nutrient transport, and Sec-secretion system, whereas the core probiotic traits are imparted by the factors involved in carbohydrate- and protein-metabolism and host-immunomodulations.
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Affiliation(s)
- Vikas Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005, India.
| | - Fauzul Mobeen
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005, India.
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005, India.
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Nezametdinova VZ, Mavletova DA, Alekseeva MG, Chekalina MS, Zakharevich NV, Danilenko VN. Species-specific serine-threonine protein kinase Pkb2 of Bifidobacterium longum subsp. longum: Genetic environment and substrate specificity. Anaerobe 2018. [PMID: 29534913 DOI: 10.1016/j.anaerobe.2018.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The objective of this study was to determine for phosphorylated substrates of the species-specific serine-threonine protein kinase (STPK) Pkb2 from Bifidobacterium longum subsp. longum GT15. Two approaches were employed: analyses of phosphorylated membrane vesicles protein spectra following kinase reactions and analyses of the genes surrounding pkb2. A bioinformatics analysis of the genes surrounding pkb2 found a species-specific gene cluster PFNA in the genomes of 34 different bifidobacterial species. The identified cluster consisted of 5-8 genes depending on the species. The first five genes are characteristic for all considered species. These are the following genes encoding serine-threonine protein kinase (pkb2), fibronectin type III domain-containing protein (fn3), AAA-ATPase (aaa-atp), hypothetical protein with DUF58 domain (duf58) and transglutaminase (tgm). The sixth (protein phosphatase, prpC), seventh (hypothetical protein, BLGT_RS02790), and eighth (FHA domain-containing protein, fha) genes are included in this cluster, but they are not found in all species. The operon organization of the PFNA gene cluster was confirmed with transcriptional analysis. AAA-ATPase, which is encoded by a gene of the PFNA gene cluster, was found to be a substrate of the STPK Pkb2. Fourteen AAA-ATPase sites (seven serine, six threonine, and one tyrosine) phosphorylated by STPK Pkb2 were revealed. Analysis of the spectra of phosphorylated membrane vesicles proteins allowed us to identify eleven proteins that were considered as possible Pkb2 substrates. They belong to several functional classes: proteins involved in transcription and translation; proteins of the F1-domain of the FoF1-ATPase; ABC-transporters; molecular chaperone GroEL; and glutamine synthase, GlnA1. All identified proteins were considered moonlighting proteins. Three out of 11 proteins (glutamine synthetase GlnA1 and FoF1-ATPase alpha and beta subunits) were selected for further in vitro phosphorylation assays and were shown to be phosphorylated by Pkb2. Four phosphorylated substrates of the species-specific STPK Pkb2 from B. longum subsp. longum GT15 were identified for the first time. They included the moonlighting protein glutamine synthase GlnA, FoF1-ATPase alpha and beta subunits, and the chaperone MoxR family of AAA-ATPase. The ability of bifidobacterial STPK to phosphorylate the substrate on serine, threonine, and tyrosine residues was shown for the first time.
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Affiliation(s)
- V Z Nezametdinova
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation.
| | - D A Mavletova
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
| | - M G Alekseeva
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
| | - M S Chekalina
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
| | - N V Zakharevich
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
| | - V N Danilenko
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
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Ates O. Systems Biology of Microbial Exopolysaccharides Production. Front Bioeng Biotechnol 2015; 3:200. [PMID: 26734603 PMCID: PMC4683990 DOI: 10.3389/fbioe.2015.00200] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/30/2015] [Indexed: 11/23/2022] Open
Abstract
Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.
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Affiliation(s)
- Ozlem Ates
- Department of Medical Services and Techniques, Nisantasi University, Istanbul, Turkey
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Draft Genome Sequences of Bifidobacterium angulatum GT102 and Bifidobacterium adolescentis 150: Focusing on the Genes Potentially Involved in the Gut-Brain Axis. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00709-15. [PMID: 26139716 PMCID: PMC4490845 DOI: 10.1128/genomea.00709-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The draft genome sequences of Bifidobacterium angulatum GT102 and Bifidobacterium adolescentis 150 strains isolated from the human intestinal microbiota are reported. Both strains are able to produce gamma-aminobutyric acid (GABA). Detailed genomes analysis will help to understand the role of GABA in the functioning of gut-brain axis.
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