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Simcox BS, Rohde KH. Orphan response regulator NnaR is critical for nitrate and nitrite assimilation in Mycobacterium abscessus. Front Cell Infect Microbiol 2024; 14:1411333. [PMID: 38854658 PMCID: PMC11162112 DOI: 10.3389/fcimb.2024.1411333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/10/2024] [Indexed: 06/11/2024] Open
Abstract
Mycobacterium abscessus (Mab) is an opportunistic pathogen afflicting individuals with underlying lung disease such as Cystic Fibrosis (CF) or immunodeficiencies. Current treatment strategies for Mab infections are limited by its inherent antibiotic resistance and limited drug access to Mab in its in vivo niches resulting in poor cure rates of 30-50%. Mab's ability to survive within macrophages, granulomas and the mucus laden airways of the CF lung requires adaptation via transcriptional remodeling to counteract stresses like hypoxia, increased levels of nitrate, nitrite, and reactive nitrogen intermediates. Mycobacterium tuberculosis (Mtb) is known to coordinate hypoxic adaptation via induction of respiratory nitrate assimilation through the nitrate reductase narGHJI. Mab, on the other hand, does not encode a respiratory nitrate reductase. In addition, our recent study of the transcriptional responses of Mab to hypoxia revealed marked down-regulation of a locus containing putative nitrate assimilation genes, including the orphan response regulator nnaR (nitrate/nitrite assimilation regulator). These putative nitrate assimilation genes, narK3 (nitrate/nitrite transporter), nirBD (nitrite reductase), nnaR, and sirB (ferrochelatase) are arranged contiguously while nasN (assimilatory nitrate reductase identified in this work) is encoded in a different locus. Absence of a respiratory nitrate reductase in Mab and down-regulation of nitrogen metabolism genes in hypoxia suggest interplay between hypoxia adaptation and nitrate assimilation are distinct from what was previously documented in Mtb. The mechanisms used by Mab to fine-tune the transcriptional regulation of nitrogen metabolism in the context of stresses e.g. hypoxia, particularly the role of NnaR, remain poorly understood. To evaluate the role of NnaR in nitrate metabolism we constructed a Mab nnaR knockout strain (MabΔnnaR ) and complement (MabΔnnaR+C ) to investigate transcriptional regulation and phenotypes. qRT-PCR revealed NnaR is necessary for regulating nitrate and nitrite reductases along with a putative nitrate transporter. Loss of NnaR compromised the ability of Mab to assimilate nitrate or nitrite as sole nitrogen sources highlighting its necessity. This work provides the first insights into the role of Mab NnaR setting a foundation for future work investigating NnaR's contribution to pathogenesis.
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Affiliation(s)
| | - Kyle H. Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
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Ensinck D, Gerhardt ECM, Rollan L, Huergo LF, Gramajo H, Diacovich L. The PII protein interacts with the Amt ammonium transport and modulates nitrate/nitrite assimilation in mycobacteria. Front Microbiol 2024; 15:1366111. [PMID: 38591044 PMCID: PMC11001197 DOI: 10.3389/fmicb.2024.1366111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/04/2024] [Indexed: 04/10/2024] Open
Abstract
PII proteins are signal transduction proteins that belong to a widely distributed family of proteins involved in the modulation of different metabolisms in bacteria. These proteins are homotrimers carrying a flexible loop, named T-loop, which changes its conformation due to the recognition of diverse key metabolites, ADP, ATP, and 2-oxoglutarate. PII proteins interact with different partners to primarily regulate a set of nitrogen pathways. In some organisms, PII proteins can also control carbon metabolism by interacting with the biotin carboxyl carrier protein (BCCP), a key component of the acetyl-CoA carboxylase (ACC) enzyme complex, inhibiting its activity with the consequent reduction of fatty acid biosynthesis. Most bacteria contain at least two PII proteins, named GlnB and GlnK, with different regulatory roles. In mycobacteria, only one PII protein was identified, and the three-dimensional structure was solved, however, its physiological role is unknown. In this study we purified the Mycobacterium tuberculosis (M. tb) PII protein, named GlnB, and showed that it weakly interacts with the AccA3 protein, the α subunit shared by the three different, and essential, Acyl-CoA carboxylase complexes (ACCase 4, 5, and 6) present in M. tb. A M. smegmatis deletion mutant, ∆MsPII, exhibited a growth deficiency on nitrate and nitrite as unique nitrogen sources, and accumulated nitrite in the culture supernatant. In addition, M. tb PII protein was able to interact with the C-terminal domain of the ammonium transporter Amt establishing the ancestral role for this PII protein as a GlnK functioning protein.
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Affiliation(s)
- Delfina Ensinck
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Edileusa C. M. Gerhardt
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Lara Rollan
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Luciano F. Huergo
- Setor Litoral, Federal University of Paraná, Universidade Federal do Paraná (UFPR), Matinhos, Paraná, Brazil
- Graduated Program in Sciences-Biochemistry, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Hugo Gramajo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lautaro Diacovich
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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3
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Gladysh NS, Bogdanova AS, Kovalev MA, Krasnov GS, Volodin VV, Shuvalova AI, Ivanov NV, Popchenko MI, Samoilova AD, Polyakova AN, Dmitriev AA, Melnikova NV, Karpov DS, Bolsheva NL, Fedorova MS, Kudryavtseva AV. Culturable Bacterial Endophytes of Wild White Poplar ( Populus alba L.) Roots: A First Insight into Their Plant Growth-Stimulating and Bioaugmentation Potential. BIOLOGY 2023; 12:1519. [PMID: 38132345 PMCID: PMC10740426 DOI: 10.3390/biology12121519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/06/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
The white poplar (Populus alba L.) has good potential for a green economy and phytoremediation. Bioaugmentation using endophytic bacteria can be considered as a safe strategy to increase poplar productivity and its resistance to toxic urban conditions. The aim of our work was to find the most promising strains of bacterial endophytes to enhance the growth of white poplar in unfavorable environmental conditions. To this end, for the first time, we performed whole-genome sequencing of 14 bacterial strains isolated from the tissues of the roots of white poplar in different geographical locations. We then performed a bioinformatics search to identify genes that may be useful for poplar growth and resistance to environmental pollutants and pathogens. Almost all endophytic bacteria obtained from white poplar roots are new strains of known species belonging to the genera Bacillus, Corynebacterium, Kocuria, Micrococcus, Peribacillus, Pseudomonas, and Staphylococcus. The genomes of the strains contain genes involved in the enhanced metabolism of nitrogen, phosphorus, and metals, the synthesis of valuable secondary metabolites, and the detoxification of heavy metals and organic pollutants. All the strains are able to grow on media without nitrogen sources, which indicates their ability to fix atmospheric nitrogen. It is concluded that the strains belonging to the genus Pseudomonas and bacteria of the species Kocuria rosea have the best poplar growth-stimulating and bioaugmentation potential, and the roots of white poplar are a valuable source for isolation of endophytic bacteria for possible application in ecobiotechnology.
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Affiliation(s)
- Natalya S. Gladysh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - Alina S. Bogdanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, 127434 Moscow, Russia
| | - Maxim A. Kovalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Vsevolod V. Volodin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Anastasia I. Shuvalova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - Nikita V. Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, 127434 Moscow, Russia
| | - Mikhail I. Popchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Institute of Geography, Russian Academy of Sciences, Staromonetny Pereulok, 29/4, 119017 Moscow, Russia
| | - Aleksandra D. Samoilova
- Faculty of Soil Science, Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia; (A.D.S.); (A.N.P.)
| | - Aleksandra N. Polyakova
- Faculty of Soil Science, Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia; (A.D.S.); (A.N.P.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Dmitry S. Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - Maria S. Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
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4
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Li J, Nian Y, Liu J, Yang M, Jin Y, Kang X, Xu H, Shang Z, Lin W. Identification of a Potential Antimycobacterial Drug Sensitizer Targeting a Flavin-Independent Methylenetetrahydrofolate Reductase. ACS OMEGA 2023; 8:38406-38417. [PMID: 37867661 PMCID: PMC10586308 DOI: 10.1021/acsomega.3c05021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023]
Abstract
The increasing antibiotic resistance of Mycobacterium tuberculosis and pathogenic nontuberculosis mycobacteria highlights the urgent need for new prevention and treatment strategies. Recently, the cocrystal structure of a Mycobacterium smegmatis flavin-independent 5,10-methylenetetrahydrofolate reductase (MsmMTHFR) that binds with a reduced nicotinamide adenine dinucleotide (NADH) has been well-determined, providing a structural basis for the screening of antimycobacterial leads targeting MsmMTHFR, a new enzyme involved in tetrahydrofolic acid (THF) biosynthesis. In this study, we identified compound AB131 as a promising candidate that fits well into the NADH binding pocket of MsmMTHFR through virtual screening. We discovered that AB131 and its derivatives (13 and 14) can sensitize the antimycobacterial activity of the antitubercular drug para-aminosalicyclic acid (PAS) by 2-5-fold against various species of mycobacteria. Although the compounds themselves do not exhibit any antimycobacterial activity, the high binding affinity of AB131 with MsmMTHFR or Rv2172c was evaluated by microscale thermophoresis analysis. Additionally, we predicted and validated the key residues (V115, V117, P118, and R163) of MsmMTHFR that are involved in the interaction with AB131 by using molecular docking and mutagenesis analysis. These findings offer a potential exploitable target for developing potent and specific antimycobacterial drug sensitizers.
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Affiliation(s)
- Jiacong Li
- Department
of Pathogen Biology, School of Medicine & Holistic Integrative
Medicine, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
- School
of Pharmacy, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237 Shanghai, China
| | - Yong Nian
- School
of Pharmacy, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
| | - Jian Liu
- School
of Pharmacy, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
| | - Mingxia Yang
- Department
of Pathogen Biology, School of Medicine & Holistic Integrative
Medicine, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
- The
Center for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Yuanling Jin
- Department
of Pathogen Biology, School of Medicine & Holistic Integrative
Medicine, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
| | - Xiaoman Kang
- CAS
Key Laboratory of Synthetic Biology, Centre
of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, 200032 Shanghai, China
| | - Haodong Xu
- School
of Pharmacy, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
| | - Zhuo Shang
- School of
Pharmaceutical Sciences, Shandong University, 250100 Jinan, China
| | - Wei Lin
- Department
of Pathogen Biology, School of Medicine & Holistic Integrative
Medicine, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
- School
of Pharmacy, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237 Shanghai, China
- Jiangsu
Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, 210023 Nanjing, China
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5
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Hamada MA, Soliman ERS. Characterization and genomics identification of key genes involved in denitrification-DNRA-nitrification pathway of plant growth-promoting rhizobacteria (Serratia marcescens OK482790). BMC Microbiol 2023; 23:210. [PMID: 37543572 PMCID: PMC10403818 DOI: 10.1186/s12866-023-02941-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/11/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND A wide variety of microorganisms, including bacteria, live in the rhizosphere zone of plants and have an impact on plant development both favorably and adversely. The beneficial outcome is due to the presence of rhizobacteria that promote plant growth (PGPR). RESULTS In this study, a bacterial strain was isolated from lupin rhizosphere and identified genetically as Serratia marcescens (OK482790). Several biochemically and genetically characteristics were confirmed in vitro and in vivo to determine the OK482790 strain ability to be PGPR. The in vitro results revealed production of different lytic enzymes (protease, lipase, cellulase, and catalase), antimicrobial compounds (hydrogen cyanide, and siderophores), ammonia, nitrite, and nitrate and its ability to reduce nitrate to nitrite. In silico and in vitro screening proposed possible denitrification-DNRA-nitrification pathway for OK482790 strain. The genome screening indicated the presence of nitrite and nitrate genes encoding Nar membrane bound sensor proteins (NarK, NarQ and NarX). Nitrate and nitrite reductase encoding genes (NarI, NarJ, NarH, NarG and NapC/NirT) and (NirB, NirC, and NirD) are also found in addition to nitroreductases (NTR) and several oxidoreductases. In vivo results on wheat seedlings confirmed that seedlings growth was significantly improved by soil inoculation of OK482790 strain. CONCLUSIONS This study provides evidence for participation of S. marcescens OK482790 in nitrogen cycling via the denitrification-DNRA-nitrification pathway and for its ability to produce several enzymes and compounds that support the beneficial role of plant-microbe interactions to sustain plant growth and development for a safer environment.
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Affiliation(s)
- Marwa A Hamada
- Botany and Microbiology Department, Faculty of Science, Helwan University, Helwan, Egypt
| | - Elham R S Soliman
- Botany and Microbiology Department, Faculty of Science, Helwan University, Helwan, Egypt.
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Wang M, Ryan KS. Reductases Produce Nitric Oxide in an Alternative Pathway to Form the Diazeniumdiolate Group of l-Alanosine. J Am Chem Soc 2023. [PMID: 37478476 DOI: 10.1021/jacs.3c04447] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
l-Alanosine is a diazeniumdiolate (N-nitrosohydroxylamine) antibiotic that inhibits MTAP-deficient tumor cells by blocking de novo adenine biosynthesis. Previous work revealed the early steps in the biosynthesis of l-alanosine. In the present study, we used genome mining to discover two new l-alanosine-producing strains that lack the aspartate-nitrosuccinate pathway genes found in the original l-alanosine producer. Instead, nitrate is reduced with a unique set of nitrate-nitrite reductases. These enzymes are typically used as part of the nitrogen cycle for denitrification or assimilation, and our report here shows how enzymes from the nitrogen cycle can be repurposed for the biosynthesis of specialized metabolites. The widespread distribution of nitric-oxide-producing reductases also indicates a potential for the discovery of new nitric-oxide-derived natural products.
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Affiliation(s)
- Menghua Wang
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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Lycus P, Einsle O, Zhang L. Structural biology of proteins involved in nitrogen cycling. Curr Opin Chem Biol 2023; 74:102278. [PMID: 36889028 DOI: 10.1016/j.cbpa.2023.102278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 03/08/2023]
Abstract
Microbial metabolic processes drive the global nitrogen cycle through sophisticated and often unique metalloenzymes that facilitate difficult redox reactions at ambient temperature and pressure. Understanding the intricacies of these biological nitrogen transformations requires a detailed knowledge that arises from the combination of a multitude of powerful analytical techniques and functional assays. Recent developments in spectroscopy and structural biology have provided new, powerful tools for addressing existing and emerging questions, which have gained urgency due to the global environmental implications of these fundamental reactions. The present review focuses on the recent contributions of the wider area of structural biology to understanding nitrogen metabolism, opening new avenues for biotechnological applications to better manage and balance the challenges of the global nitrogen cycle.
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Affiliation(s)
- Pawel Lycus
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany; Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.
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Fu D, Zhang L, Li H, Li F, Yue Z, Li Y, Cai Q. Effects of the nitrogen form ratios on photosynthetic productivity of poplar under condition of phenolic acids. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2022; 25:1189-1198. [PMID: 36368337 DOI: 10.1080/15226514.2022.2144795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phenolic acids can reduce nitrogen utilization rate of poplar, which seriously restrict the productivity of poplar plantation. In this study, three phenolic acid concentrations (T0, T1, and T2) and three ratios of nitrogen forms (NH4+-N to NO3--were 1:3, 1:7, and 1:14) were chosen for orthogonal experiment on poplar (Populus × euramericana "Neva") seedlings to study the effects of the nitrogen form ratios on photosynthetic productivity of poplar under environment of phenolic acids. Results showed that photosynthetic physiology parameters were influenced by both phenolic acid concentration and nitrogen form ratio. The order of net photosynthetic rate (PN) values obtained from 9 treatments were T1-1:3, T0-1:3, T2-1:3, T0-1:7, T1-1:7, T0-1:14, T2-1:7, T1-1:14, and T2-1:14 (from high to low). Under environment of phenolic acids, when poplar were treated with NH4+-N to NO3--N ratio of 1:14, the major limitation factor of photosynthesis was non stomatal factor. When poplar were treated with NH4+-N to NO3-N ratio of 1:3, the major limitation factor of photosynthesis changed to stomatal factor. The leaf nitrogen content and total biomass were obviously positively related with PN (p < 0.05). Phenolic acid inhibited photosynthetic productivity of poplar in a major way and this effect decreased with increase of the content of NH4+-N.
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Affiliation(s)
- Degang Fu
- College of agriculture and forestry science, Linyi University, Lin'yi, China
- Shandong Provincial Forestry Protection and Development Service Center, Ji'nan, Shandong province, China
| | - Liudong Zhang
- Shandong Provincial Forestry Protection and Development Service Center, Ji'nan, Shandong province, China
| | - Hui Li
- College of agriculture and forestry science, Linyi University, Lin'yi, China
| | - Feng Li
- State-owned Yishan Forest Farm of Yishui County, Yi'shui, Shandong, China
| | - Zongjie Yue
- State-owned Shenxian Forest Management Center o Shenxian County, Shenxian, Shandong, China
| | - Yaobin Li
- State-owned Donming Forest Farm of Shandong Province, Dong'ming, Shandong, China
| | - Qicheng Cai
- State-owned Yishan Forest Farm of Yishui County, Yi'shui, Shandong, China
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9
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Iyanagi T. Roles of Ferredoxin-NADP + Oxidoreductase and Flavodoxin in NAD(P)H-Dependent Electron Transfer Systems. Antioxidants (Basel) 2022; 11:2143. [PMID: 36358515 PMCID: PMC9687028 DOI: 10.3390/antiox11112143] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 07/21/2023] Open
Abstract
Distinct isoforms of FAD-containing ferredoxin-NADP+ oxidoreductase (FNR) and ferredoxin (Fd) are involved in photosynthetic and non-photosynthetic electron transfer systems. The FNR (FAD)-Fd [2Fe-2S] redox pair complex switches between one- and two-electron transfer reactions in steps involving FAD semiquinone intermediates. In cyanobacteria and some algae, one-electron carrier Fd serves as a substitute for low-potential FMN-containing flavodoxin (Fld) during growth under low-iron conditions. This complex evolves into the covalent FNR (FAD)-Fld (FMN) pair, which participates in a wide variety of NAD(P)H-dependent metabolic pathways as an electron donor, including bacterial sulfite reductase, cytochrome P450 BM3, plant or mammalian cytochrome P450 reductase and nitric oxide synthase isoforms. These electron transfer systems share the conserved Ser-Glu/Asp pair in the active site of the FAD module. In addition to physiological electron acceptors, the NAD(P)H-dependent diflavin reductase family catalyzes a one-electron reduction of artificial electron acceptors such as quinone-containing anticancer drugs. Conversely, NAD(P)H: quinone oxidoreductase (NQO1), which shares a Fld-like active site, functions as a typical two-electron transfer antioxidant enzyme, and the NQO1 and UDP-glucuronosyltransfease/sulfotransferase pairs function as an antioxidant detoxification system. In this review, the roles of the plant FNR-Fd and FNR-Fld complex pairs were compared to those of the diflavin reductase (FAD-FMN) family. In the final section, evolutionary aspects of NAD(P)H-dependent multi-domain electron transfer systems are discussed.
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Affiliation(s)
- Takashi Iyanagi
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Akoh 678-1297, Hyogo, Japan
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10
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Lee MH. Harness the functions of gut microbiome in tumorigenesis for cancer treatment. Cancer Commun (Lond) 2021; 41:937-967. [PMID: 34355542 PMCID: PMC8504147 DOI: 10.1002/cac2.12200] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/16/2021] [Indexed: 11/08/2022] Open
Abstract
It has been shown that gut microbiota dysbiosis leads to physiological changes and links to a number of diseases, including cancers. Thus, many cancer categories and treatment regimens should be investigated in the context of the microbiome. Owing to the availability of metagenome sequencing and multiomics studies, analyses of species characterization, host genetic changes, and metabolic profile of gut microbiota have become feasible, which has facilitated an exponential knowledge gain about microbiota composition, taxonomic alterations, and host interactions during tumorigenesis. However, the complexity of the gut microbiota, with a plethora of uncharacterized host‐microbe, microbe‐microbe, and environmental interactions, still contributes to the challenge of advancing our knowledge of the microbiota‐cancer interactions. These interactions manifest in signaling relay, metabolism, immunity, tumor development, genetic instability, sensitivity to cancer chemotherapy and immunotherapy. This review summarizes current studies/molecular mechanisms regarding the association between the gut microbiota and the development of cancers, which provides insights into the therapeutic strategies that could be harnessed for cancer diagnosis, treatment, or prevention.
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Affiliation(s)
- Mong-Hong Lee
- Research Institute of Gastroenterology, Sun Yat-sen University, Guangzhou, Guangdong, 510020, P. R. China.,Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510020, P. R. China
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11
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Tan W, Shao ZH, Zhao GP. In vitro Nitrate Reductase Activity Assay of Mycolicibacterium smegmatis Crude Extract. Bio Protoc 2021; 11:e4098. [PMID: 34395734 DOI: 10.21769/bioprotoc.4098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 11/02/2022] Open
Abstract
Nitrate is one of the major inorganic nitrogen sources for microorganisms. Many bacterial and archaeal lineages can express cytoplasmic assimilatory nitrate reductase (NAS), which catalyzes the rate-limiting reduction of nitrate to nitrite in the nitrate assimilation pathway. Here, we present a detailed protocol for measuring in vitro nitrate reductase (NaR) activity of NAS enzymes from Mycolicibacterium smegmatis crude extract using both physiological and non-physiological electron donors.
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Affiliation(s)
- Wei Tan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China.,CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhi-Hui Shao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Guo-Ping Zhao
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China.,CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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12
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Eltarahony M, Ibrahim A, El-shall H, Ibrahim E, Althobaiti F, Fayad E. Antibacterial, Antifungal and Antibiofilm Activities of Silver Nanoparticles Supported by Crude Bioactive Metabolites of Bionanofactories Isolated from Lake Mariout. Molecules 2021; 26:3027. [PMID: 34069487 PMCID: PMC8161313 DOI: 10.3390/molecules26103027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/24/2022] Open
Abstract
Lake Mariout is one of the polluted coastal marine ecosystems in Egypt which is considered to be a reservoir of serious effluents from different anthropogenic activities. Such selective pressure enforces indigenous microbial populations to acquire new advantageous themes. Thus, in this study, two Streptomyces strains were screened, from Lake Mariout's sediment for bioreduction of 5 mM AgNO3. Both strains were identified molecularly; their biochemical and physiological characterization revealed their ability to secrete bioactive metabolites with antagonistic activity. The cultural and incubation conditions influencing AgNPs productivity were evaluated. Subsequently, the physicochemical properties of the biofabricated AgNPs were pursued. UV-Vis spectroscopy detected surface plasmon resonance at range 458-422 nm. XRD indicated crystalline, pure, face-centered cubic AgNPs; EDX demonstrated strong silver signal at 3.5 keV. Besides, FT-IR and TGA analysis unveiled self-stabilization and functionalization of AgNPs by bioorganic molecules. However, electron microscopy micrographs depicted numerous uniform spherical AgNPs (1.17-13.3 nm). Potent bactericidal and fungicide activity were recorded by zone of inhibition assay at 50 μg/mL. Further, the antibiofilm activity was exerted in a dose-dependent manner. Moreover, the conjugation of AgNPs with the crude bioactive metabolites of both bionanofactories ameliorated the antimicrobial potency, reflecting a synergistic efficiency versus examined pathogens (free-living and biofilm).
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Affiliation(s)
- Marwa Eltarahony
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Alexandria, Egypt; (H.E.-s.); (E.I.)
| | - Amany Ibrahim
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Hadeel El-shall
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Alexandria, Egypt; (H.E.-s.); (E.I.)
| | - Eman Ibrahim
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Alexandria, Egypt; (H.E.-s.); (E.I.)
| | - Fayez Althobaiti
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (F.A.); (E.F.)
| | - Eman Fayad
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (F.A.); (E.F.)
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13
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Yang W, Chen CH, Jia M, Xing X, Gao L, Tsai HT, Zhang Z, Liu Z, Zeng B, Yeung SCJ, Lee MH, Cheng C. Tumor-Associated Microbiota in Esophageal Squamous Cell Carcinoma. Front Cell Dev Biol 2021; 9:641270. [PMID: 33681225 PMCID: PMC7930383 DOI: 10.3389/fcell.2021.641270] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/26/2021] [Indexed: 12/24/2022] Open
Abstract
Important evidence indicates the microbiota plays a key role in esophageal squamous cell carcinoma (ESCC). The esophageal microbiota was prospectively investigated in 18 patients with ESCC and 11 patients with physiological normal (PN) esophagus by 16S rRNA gene profiling, using next-generation sequencing. The microbiota composition in tumor tissues of ESCC patients were significantly different from that of patients with PN tissues. The ESCC microbiota was characterized by reduced microbial diversity, by decreased abundance of Bacteroidetes, Fusobacteria, and Spirochaetes. Employing these taxa into a microbial dysbiosis index demonstrated that dysbiosis microbiota had good capacity to discriminate between ESCC and PN esophagus. Functional analysis characterized that ESCC microbiota had altered nitrate reductase and nitrite reductase functions compared with PN group. These results suggest that specific microbes and the microbiota may drive or mitigate ESCC carcinogenesis, and this study will facilitate assigning causal roles in ESCC development to certain microbes and microbiota.
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Affiliation(s)
- Weixiong Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chang-Han Chen
- Department of Applied Chemistry, and Graduate Institute of Biomedicine and Biomedical Technology, National Chi Nan University, Nantou County, Taiwan
| | - Minghan Jia
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiangbin Xing
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lu Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hsin-Ting Tsai
- Department of Applied Chemistry, and Graduate Institute of Biomedicine and Biomedical Technology, National Chi Nan University, Nantou County, Taiwan
| | - Zhanfei Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhenguo Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Bo Zeng
- Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Sai-Ching Jim Yeung
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mong-Hong Lee
- Guangdong Research Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chao Cheng
- Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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14
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Mycobacterium smegmatis does not display functional redundancy in nitrate reductase enzymes. PLoS One 2021; 16:e0245745. [PMID: 33471823 PMCID: PMC7816997 DOI: 10.1371/journal.pone.0245745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/06/2021] [Indexed: 12/04/2022] Open
Abstract
Reduction of nitrate to nitrite in bacteria is an essential step in the nitrogen cycle, catalysed by a variety of nitrate reductase (NR) enzymes. The soil dweller, Mycobacterium smegmatis is able to assimilate nitrate and herein we set out to confirm the genetic basis for this by probing NR activity in mutants defective for putative nitrate reductase (NR) encoding genes. In addition to the annotated narB and narGHJI, bioinformatics identified three other putative NR-encoding genes: MSMEG_4206, MSMEG_2237 and MSMEG_6816. To assess the relative contribution of each, the corresponding gene loci were deleted using two-step allelic replacement, individually and in combination. The resulting strains were tested for their ability to assimilate nitrate and reduce nitrate under aerobic and anaerobic conditions, using nitrate assimilation and modified Griess assays. We demonstrated that narB, narGHJI, MSMEG_2237 and MSMEG_6816 were individually dispensable for nitrate assimilation and for nitrate reductase activity under aerobic and anaerobic conditions. Only deletion of MSMEG_4206 resulted in significant reduction in nitrate assimilation under aerobic conditions. These data confirm that in M. smegmatis, narB, narGHJI, MSMEG_2237 and MSMEG_6816 are not required for nitrate reduction as MSMEG_4206 serves as the sole assimilatory NR.
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15
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Lu Y, Li X, Chen Y, Wang Y, Zhu G, Zeng RJ. The indispensable role of assimilation in methane driven nitrate removal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:141089. [PMID: 32745852 DOI: 10.1016/j.scitotenv.2020.141089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 05/27/2023]
Abstract
Methane is a greenhouse gas that can be released from sludge anaerobic fermentation in wastewater treatment plants. Methane is also an alternative additional carbon source for deep nitrate removal of secondary effluent. A sequencing experiment was conducted to study the efficacy of nitrate removal with methane as the sole carbon source. The maximum nitrate removal rate was 17.2 mg-N·L-1·d-1. Nitrate removal was confirmed to arise via two pathways: aerobic methane oxidation coupled to denitrification (AME-D) contributed to 55% of the nitrate removal with the rest stemming from assimilation by methanotrophs. Additional study revealed that nitrate assimilated by methanotrophs was used for the synthesis of proteins, resulting in a protein content of 52.2% dry weight. Metagenomic sequencing revealed a high abundance of nitrate assimilation and glutamine synthetase genes, which were primarily provided by methanotrophs (mainly Methylomonas). Assimilatory nitrate removal by methanotrophs has a high potential for advanced nitrogen removal and for alleviating methane emissions. The nitrogen-rich biomass produced by nitrate absorption could also be used as a biofertilizer for nitrogen recycling.
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Affiliation(s)
- Yongze Lu
- School of Energy and Environment, Southeast University, Nanjing, Jiangsu 210096, China; State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu 210096, China.
| | - Xin Li
- School of Energy and Environment, Southeast University, Nanjing, Jiangsu 210096, China; State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu 210096, China.
| | - Yue Chen
- School of Energy and Environment, Southeast University, Nanjing, Jiangsu 210096, China; State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu 210096, China.
| | - Yongzhen Wang
- School of Energy and Environment, Southeast University, Nanjing, Jiangsu 210096, China; State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu 210096, China.
| | - Guangcan Zhu
- School of Energy and Environment, Southeast University, Nanjing, Jiangsu 210096, China; State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu 210096, China.
| | - Raymond Jianxiong Zeng
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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16
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Yamada H, Chikamatsu K, Aono A, Murata K, Miyazaki N, Kayama Y, Bhatt A, Fujiwara N, Maeda S, Mitarai S. Fundamental Cell Morphologies Examined With Cryo-TEM of the Species in the Novel Five Genera Robustly Correlate With New Classification in Family Mycobacteriaceae. Front Microbiol 2020; 11:562395. [PMID: 33304323 PMCID: PMC7701246 DOI: 10.3389/fmicb.2020.562395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/12/2020] [Indexed: 11/25/2022] Open
Abstract
A recent study proposed the novel classification of the family Mycobacteriaceae based on the genome analysis of core proteins in 150 Mycobacterium species. The results from these analyses supported the existence of five distinct monophyletic groups within the genus Mycobacterium. That is, Mycobacterium has been divided into two novel genera for rapid grower Mycobacteroides and Mycolicibacterium, and into three genera for slow grower Mycolicibacter, Mycolicibacillus, and an emended genus Mycobacterium, which include all the major human pathogens. Here, cryo-TEM examinations of 1,816 cells of 31 species (34 strains) belonging to the five novel genera were performed. The fundamental morphological properties of every single cell, such as cell diameter, cell length, cell perimeter, cell circularity, and aspect ratio were measured and compared between these genera. In 50 comparisons on the five parameters between any two genera, only five comparisons showed “non-significant” differences. That is, there are non-significant differences between slow grower genus Mycolicibacillus and genus Mycobacterium in average cell diameter (p = 0.15), between rapid grower genus Mycobacteroides and slow grower genus Mycobacterium in average cell length (p > 0.24), between genus Mycobacteroides and genus Mycobacterium (p > 0.68) and between genus Mycolicibacter and genus Mycolicibacillus (p > 0.11) in average cell perimeter, and between genus Mycolicibacterium and genus Mycobacterium in circularity (p > 0.73). The other 45 comparisons showed significant differences between the genera. Genus Mycobacteroides showed the longest average cell diameter, whereas the genus Mycolicibacter showed the shortest average diameter. Genus Mycolicibacterium showed the most extended average cell length, perimeter, and aspect ratio, whereas the genus Mycolicibacillus showed the shortest average cell length, perimeter, and aspect ratio. Genus Mycolicibacillus showed the highest average cell circularity, whereas genus Mycobacterium showed the lowest average cell circularity. These fundamental morphological data strongly support the new classification in the family Mycobacteriaceae, and this classification is rational and effective in the study of the members of the family Mycobacteriaceae. Because both the genus Mycolicibacterium and the genus Mycobacterium contain many species and showed larger significant standard deviations in every parameter, these genera may be divided into novel genera which show common genotype and phenotypes in morphology and pathogenicity.
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Affiliation(s)
- Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Kinuyo Chikamatsu
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Akio Aono
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Kazuyoshi Murata
- Supportive Center for Brain Research, National Institute for Physiological Science, Okazaki, Japan
| | - Naoyuki Miyazaki
- Supportive Center for Brain Research, National Institute for Physiological Science, Okazaki, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | | | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Nagatoshi Fujiwara
- Department of Food and Nutrition, Faculty of Contemporary Human Life Science, Tezukayama University, Nara, Japan
| | - Shinji Maeda
- Department of Pharmacy, Faculty of Pharmaceutical Science, Hokkaido University of Science, Sapporo, Japan
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan.,Department of Basic Mycobacteriology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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