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Mahadi WSW, Wong CMVL, Rodrigues KF, Teoh CP, Lindang HU, Budiman C. Complete genome sequence data of an Antarctic bacterium Arthrobacter sp. EM1 from the freshwater lake of the King George Island. Data Brief 2024; 52:109841. [PMID: 38146304 PMCID: PMC10749255 DOI: 10.1016/j.dib.2023.109841] [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: 05/20/2023] [Revised: 10/31/2023] [Accepted: 11/16/2023] [Indexed: 12/27/2023] Open
Abstract
Arthrobacter sp. EM1 is a cold-adapted bacterium isolated from the Antarctic region, which was known to exhibit mannan-degrading activity. Accordingly, this strain not only promises a cell factory for mannan-degrading enzymes, widely used in industry but also serves as a model organism to decipher its cold adaptation mechanism. Accordingly, whole genome sequencing of the EM1 strain was performed via Single Molecule Real Time sequencing under the PacBio platform, followed by genome HGAP de novo assembly and genome annotation through Rapid Annotation System Technology (RAST) server. The chromosome of this strain is 3,885,750 bp in size with a GC content of 65.8. The annotation predicted a total of 3607 protein-coding genes and 65 RNA genes, which were classified under 398 subsystems. The subsystem with the highest number of genes is carbohydrate metabolism (397 genes), which includes two genes encoding mannan-degrading enzymes (endoglucanase and α-mannosidase). This confirmed that the EM1 strain is able to produce cold-adapted mannan degrading enzymes. The complete genome sequence data have been submitted to the National Center for Biotechnology Information (NCBI) and have been deposited at GenBank (Bioproject ID Accession Number: PRJNA963062; Biosample ID Accession Number: SAMN34434776; GenBank: CP124836.1; https://www.ncbi.nlm.nih.gov/nuccore/CP124836).
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Affiliation(s)
- Wan Shuhaida Wan Mahadi
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah 88400, Malaysia
| | | | - Kenneth Francis Rodrigues
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah 88400, Malaysia
| | - Chui Peng Teoh
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah 88400, Malaysia
| | - Herman Umbau Lindang
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah 88400, Malaysia
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching–Kota Samarahan Expressway, Kota Samarahan, Sarawak 94300, Malaysia
| | - Cahyo Budiman
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah 88400, Malaysia
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El-Sabeh A, Mlesnita AM, Munteanu IT, Honceriu I, Kallabi F, Boiangiu RS, Mihasan M. Characterisation of the Paenarthrobacter nicotinovorans ATCC 49919 genome and identification of several strains harbouring a highly syntenic nic-genes cluster. BMC Genomics 2023; 24:536. [PMID: 37697273 PMCID: PMC10494377 DOI: 10.1186/s12864-023-09644-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/01/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Paenarthrobacter nicotinovorans ATCC 49919 uses the pyridine-pathway to degrade nicotine and could provide a renewable source of precursors from nicotine-containing waste as well as a model for studying the molecular evolution of catabolic pathways and their spread by horizontal gene transfer via soil bacterial plasmids. RESULTS In the present study, the strain was sequenced using the Illumina NovaSeq 6000 and Oxford Nanopore Technology (ONT) MinION platforms. Following hybrid assembly with Unicycler, the complete genome sequence of the strain was obtained and used as reference for whole-genome-based phylogeny analyses. A total of 64 related genomes were analysed; five Arthrobacter strains showed both digital DNA-DNA hybridization and average nucleotide identity values over the species threshold when compared to P. nicotinovorans ATCC 49919. Five plasmids and two contigs belonging to Arthrobacter and Paenarthrobacter strains were shown to be virtually identical with the pAO1 plasmid of Paenarthrobacter nicotinovorans ATCC 49919. Moreover, a highly syntenic nic-genes cluster was identified on five plasmids, one contig and three chromosomes. The nic-genes cluster contains two major locally collinear blocks that appear to form a putative catabolic transposon. Although the origins of the nic-genes cluster and the putative transposon still elude us, we hypothesise here that the ATCC 49919 strain most probably evolved from Paenarthrobacter sp. YJN-D or a very closely related strain by acquiring the pAO1 megaplasmid and the nicotine degradation pathway. CONCLUSIONS The data presented here offers another snapshot into the evolution of plasmids harboured by Arthrobacter and Paenarthrobacter species and their role in the spread of metabolic traits by horizontal gene transfer among related soil bacteria.
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Affiliation(s)
- Amada El-Sabeh
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania
| | | | | | - Iasmina Honceriu
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania
| | - Fakhri Kallabi
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Marius Mihasan
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania.
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Ghorbel S, Aldilami M, Zouari-Mechichi H, Mechichi T, AlSherif EA. Isolation and characterization of a plant growth‑promoting rhizobacterium strain MD36 that promotes barley seedlings and growth under heavy metals stress. 3 Biotech 2023; 13:145. [PMID: 37124983 PMCID: PMC10140241 DOI: 10.1007/s13205-023-03566-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/15/2023] [Indexed: 05/02/2023] Open
Abstract
Plant growth, promoting, bacteria, (PGPB) can improve plant germination and growth in heavy metal-contaminated land and enhance heavy metal removal efficiency. In this study, we isolated PGPR bacterial strains which can withstand heavy metal pollution and tested their ability to improve barley germination under heavy metal stress. Out of 16 multi-resistant heavy metal isolates, strain MD36 was identified by 16S rRNA sequencing and shared close relation to different species of the genus Glutamicibacter. The new isolated strain showed other important PGPR activities, mainly IAA production and salt tolerance. The effect of adding the strain MD36 to barley grains under heavy metal stress enhanced their germination up to 100%, while the percentage of germination ranged between 0 and 20% for non-inoculated grains. In addition, in these conditions, MD36 can significantly enhance barley growth by reducing the heavy metal effect. This study strongly recommends the use of MD36 as seed coatings trials in the field to enhance growth and yield in soils contaminated with heavy metals, as well as in bioremediation of HM-contaminated salt-containing soils and water.
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Affiliation(s)
- Sofiane Ghorbel
- Jeddah, College of Science and Arts at Khulais, Biology Department, University of Jeddah, Jeddah, Saudi Arabia
- Plant Physiology and Functional Genomics Research Unit, Institute of Biotechnology, University of Sfax, 3038 Sfax, Tunisia
| | - Mohammad Aldilami
- Jeddah, College of Science and Arts at Khulais, Biology Department, University of Jeddah, Jeddah, Saudi Arabia
| | - Hela Zouari-Mechichi
- Laboratory of Biochemistry and Enzymatic Engineering of Lipases, National School of Engineers of Sfax, University of Sfax, 3038 Sfax, Tunisia
| | - Tahar Mechichi
- Laboratory of Biochemistry and Enzymatic Engineering of Lipases, National School of Engineers of Sfax, University of Sfax, 3038 Sfax, Tunisia
| | - Emad Ali AlSherif
- Jeddah, College of Science and Arts at Khulais, Biology Department, University of Jeddah, Jeddah, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni‒Suef, 62521 Egypt
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Potential of growth-promoting bacteria in maize (Zea mays L.) varies according to soil moisture. Microbiol Res 2023; 271:127352. [PMID: 36907073 DOI: 10.1016/j.micres.2023.127352] [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: 11/19/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Climate change has caused irregularities in water distribution, which affect the soil drying-wetting cycle and the development of economically important agricultural crops. Therefore, the use of plant growth-promoting bacteria (PGPB) emerges as an efficient strategy to mitigate negative impacts on crop yield. We hypothesized that the use of PGPB (in consortium or not) had potential to promote maize (Zea mays L.) growth under a soil moisture gradient in both non-sterile and sterile soils. Thirty PGPB strains were characterized for direct plant growth-promotion and drought tolerance induction mechanisms and were used in two independent experiments. Four soil water contents were used to simulate a severe drought (30% of field capacity [FC]), moderate drought (50% of FC), no drought (80% of FC) and, finally, a water gradient comprising the three mentioned soil water contents (80%, 50%, and 30% of FC). Two bacteria strains (BS28-7 Arthrobacter sp. and BS43 Streptomyces alboflavus), in addition to three consortia (BC2, BC4 and BCV) stood out in maize growth performance in experiment 1 and were used in experiment 2. Overall, under moderate drought, inoculation with BS43 surpassed the control treatment in root dry mass and nutrient uptake. Considering the water gradient treatment (80-50-30% of FC), the greatest total biomass was found in the uninoculated treatment when compared to BS28-7, BC2, and BCV. The greatest development of Z. mays L. was only observed under constant water stress conditions in the presence of PGPB. This is the first report that demonstrated the negative effect of individual inoculation of Arthrobacter sp. and the consortium of this strain with Streptomyces alboflavus on the growth of Z. mays L. based on a soil moisture gradient; however, future studies are needed for further validation.
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Hernández-Fernández G, Galán B, Carmona M, Castro L, García JL. Transcriptional response of the xerotolerant Arthrobacter sp. Helios strain to PEG-induced drought stress. Front Microbiol 2022; 13:1009068. [PMID: 36312951 PMCID: PMC9608346 DOI: 10.3389/fmicb.2022.1009068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
A new bacterial strain has been isolated from the microbiome of solar panels and classified as Arthrobacter sp. Helios according to its 16S rDNA, positioning it in the “Arthrobacter citreus group.” The isolated strain is highly tolerant to desiccation, UV radiation and to the presence of metals and metalloids, while it is motile and capable of growing in a variety of carbon sources. These characteristics, together with observation that Arthrobacter sp. Helios seems to be permanently prepared to handle the desiccation stress, make it very versatile and give it a great potential to use it as a biotechnological chassis. The new strain genome has been sequenced and its analysis revealed that it is extremely well poised to respond to environmental stresses. We have analyzed the transcriptional response of this strain to PEG6000-mediated arid stress to investigate the desiccation resistance mechanism. Most of the induced genes participate in cellular homeostasis such as ion and osmolyte transport and iron scavenging. Moreover, the greatest induction has been found in a gene cluster responsible for biogenic amine catabolism, suggesting their involvement in the desiccation resistance mechanism in this bacterium.
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Affiliation(s)
- Gabriel Hernández-Fernández
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
| | - Beatriz Galán
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
| | - Manuel Carmona
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
| | - Laura Castro
- Department of Chemical and Materials Engineering, Complutense University of Madrid, Madrid, Spain
| | - José Luis García
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
- *Correspondence: José Luis García,
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The Novel Monooxygenase Gene dipD in the dip Gene Cluster of Alcaligenes faecalis JQ135 Is Essential for the Initial Catabolism of Dipicolinic Acid. Appl Environ Microbiol 2022; 88:e0036022. [PMID: 35766505 PMCID: PMC9317849 DOI: 10.1128/aem.00360-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Dipicolinic acid (DPA), an essential pyridine derivative biosynthesized in Bacillus spores, constitutes a major proportion of global biomass carbon pool. Alcaligenes faecalis strain JQ135 could catabolize DPA through the "3HDPA (3-hydroxydipicolinic acid) pathway." However, the genes involved in this 3HDPA pathway are still unknown. In this study, a dip gene cluster responsible for DPA degradation was cloned from strain JQ135. The expression of dip genes was induced by DPA and negatively regulated by DipR. A novel monooxygenase gene, dipD, was crucial for the initial hydroxylation of DPA into 3HDPA and proposed to encode the key catalytic component of the multicomponent DPA monooxygenase. The heme binding protein gene dipF, ferredoxin reductase gene dipG, and ferredoxin genes dipJ/dipK/dipL were also involved in the DPA hydroxylation and proposed to encode other components of the multicomponent DPA monooxygenase. The 18O2 stable isotope labeling experiments confirmed that the oxygen atom in the hydroxyl group of 3HDPA came from dioxygen molecule rather than water. The protein sequence of DipD exhibits no significant sequence similarities with known oxygenases, suggesting that DipD was a new member of oxygenase family. Moreover, bioinformatic survey suggested that the dip gene cluster was widely distributed in many Alpha-, Beta-, and Gammaproteobacteria, including soil bacteria, aquatic bacteria, and pathogens. This study provides new molecular insights into the catabolism of DPA in bacteria. IMPORTANCE Dipicolinic acid (DPA) is a natural pyridine derivative that serves as an essential component of the Bacillus spore. DPA accounts for 5 to 15% of the dry weight of spores. Due to the huge number of spores in the environment, DPA is also considered to be an important component of the global biomass carbon pool. DPA could be decomposed by microorganisms and enter the global carbon cycling; however, the underlying molecular mechanisms are rarely studied. In this study, a DPA catabolic gene cluster (dip) was cloned and found to be widespread in Alpha-, Beta-, and Gammaproteobacteria. The genes responsible for the initial hydroxylation of DPA to 3-hydroxyl-dipicolinic acid were investigated in Alcaligenes faecalis strain JQ135. The present study opens a door to elucidate the mechanism of DPA degradation and its possible role in DPA-based carbon biotransformation on earth.
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Bacterial Diversity and Community Structure in the Rhizosphere of Four Halophytes. Curr Microbiol 2021; 78:2720-2732. [PMID: 34023980 DOI: 10.1007/s00284-021-02536-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/05/2021] [Indexed: 10/21/2022]
Abstract
The study of the rhizosphere microbial community in salinized soils aids in the elucidation of new and important microbial functional groups, which is of great importance in vegetation restoration and ecological reconstruction of salinized soil. The rhizosphere soil bacterial diversity and community structures of four halophytes, including Kalidium foliatum, Lycium ruthenicum, Karelinia caspia and Phragmites australis, typically distributed in the saline-alkaline land of Southern Xinjiang, China, were studied using an Illumina paired-end sequence platform. The study aims to reveal the alpha diversity, species composition, abundance and the differences of rhizosphere bacteria among the four halophytes, explore their correlation with environmental factors. The results showed that the highest bacterial species diversity was associated with P. communis, followed by K. foliatum, K. caspia, and L. ruthenicum. The species richness was the lowest for L. ruthenicum, while the others showed no significant difference. Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes were the most dominant phyla. And Bacillus and Halomonas were the most common dominant genera. The bacterial communities associated with K. foliatum and K. caspia were similar, while that of L. ruthenicum was significantly different from other halophytes. Soil total nitrogen and total phosphorus, soil organic matter, soil water content, electronic conductivity and pH were identified as the key factors affecting bacterial abundance associated with the assayed halophytes. These results indicate that the four halophytes evaluated in the present study have a similar rhizosphere bacterial community structure due to their being in the same region. However, the bacterial abundance is different among the plant species, and soil properties are the important factors driving the structures of bacterial communities.
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Christakis CA, Daskalogiannis G, Chatzaki A, Markakis EA, Mermigka G, Sagia A, Rizzo GF, Catara V, Lagkouvardos I, Studholme DJ, Sarris PF. Endophytic Bacterial Isolates From Halophytes Demonstrate Phytopathogen Biocontrol and Plant Growth Promotion Under High Salinity. Front Microbiol 2021; 12:681567. [PMID: 34017321 PMCID: PMC8129196 DOI: 10.3389/fmicb.2021.681567] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/07/2021] [Indexed: 01/22/2023] Open
Abstract
Halophytic endophytes potentially contribute to the host's adaptation to adverse environments, improving its tolerance against various biotic and abiotic stresses. Here, we identified the culturable endophytic bacteria of three crop wild relative (CWR) halophytes: Cakile maritima, Matthiola tricuspidata, and Crithmum maritimum. In the present study, the potential of these isolates to improve crop adaptations to various stresses was investigated, using both in vitro and in-planta approaches. Endophytic isolates were identified by their 16S rRNA gene sequence and evaluated for their ability to: grow in vitro in high levels of NaCl; inhibit the growth of the economically important phytopathogens Verticillium dahliae, Ralstonia solanacearum, and Clavibacter michiganensis and the human pathogen Aspergillus fumigatus; provide salt tolerance in-planta; and provide growth promoting effect in-planta. Genomes of selected isolates were sequenced. In total, 115 endophytic isolates were identified. At least 16 isolates demonstrated growth under increased salinity, plant growth promotion and phytopathogen antagonistic activity. Three showed in-planta suppression of Verticillium growth. Furthermore, representatives of three novel species were identified: two Pseudomonas species and one Arthrobacter. This study provides proof-of-concept that the endophytes from CWR halophytes can be used as "bio-inoculants," for the enhancement of growth and stress tolerance in crops, including the high-salinity stress.
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Affiliation(s)
- Christos A Christakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
| | | | - Anastasia Chatzaki
- Laboratory of Mycology, Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization DIMITRA, Heraklion, Greece
| | - Emmanouil A Markakis
- Laboratory of Mycology, Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization DIMITRA, Heraklion, Greece
| | - Glykeria Mermigka
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
| | - Angeliki Sagia
- Department of Biology, University of Crete, Heraklion, Greece
| | - Giulio Flavio Rizzo
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Ilias Lagkouvardos
- ZIEL-Institute for Food and Health, Technical University of Munich, Freising, Germany
| | | | - Panagiotis F Sarris
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece.,Department of Biology, University of Crete, Heraklion, Greece.,Biosciences, University of Exeter, Exeter, United Kingdom
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Oyewusi HA, Wahab RA, Huyop F. Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria. Mol Biol Rep 2021; 48:2687-2701. [PMID: 33650078 DOI: 10.1007/s11033-021-06239-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/16/2021] [Indexed: 12/11/2022]
Abstract
An integral approach to decoding both culturable and uncultured microorganisms' metabolic activity involves the whole genome sequencing (WGS) of individual/complex microbial communities. WGS of culturable microbes, amplicon sequencing, metagenomics, and single-cell genome analysis are selective techniques integrating genetic information and biochemical mechanisms. These approaches transform microbial biotechnology into a quick and high-throughput culture-independent evaluation and exploit pollutant-degrading microbes. They are windows into enzyme regulatory bioremediation pathways (i.e., dehalogenase) and the complete bioremediation process of organohalide pollutants. While the genome sequencing technique is gaining the scientific community's interest, it is still in its infancy in the field of pollutant bioremediation. The techniques are becoming increasingly helpful in unraveling and predicting the enzyme structure and explore metabolic and biodegradation capabilities.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia.
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, PMB 5351, Ado Ekiti, Ekiti State, Nigeria.
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia.
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Wong RR, Lim ZS, Shaharuddin NA, Zulkharnain A, Gomez-Fuentes C, Ahmad SA. Diesel in Antarctica and a Bibliometric Study on Its Indigenous Microorganisms as Remediation Agent. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18041512. [PMID: 33562609 PMCID: PMC7915771 DOI: 10.3390/ijerph18041512] [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] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/03/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Diesel acts as a main energy source to complement human activities in Antarctica. However, the increased expedition in Antarctica has threatened the environment as well as its living organisms. While more efforts on the use of renewable energy are being done, most activities in Antarctica still depend heavily on the use of diesel. Diesel contaminants in their natural state are known to be persistent, complex and toxic. The low temperature in Antarctica worsens these issues, making pollutants more significantly toxic to their environment and indigenous organisms. A bibliometric analysis had demonstrated a gradual increase in the number of studies on the microbial hydrocarbon remediation in Antarctica over the year. It was also found that these studies were dominated by those that used bacteria as remediating agents, whereas very little focus was given on fungi and microalgae. This review presents a summary of the collective and past understanding to the current findings of Antarctic microbial enzymatic degradation of hydrocarbons as well as its genotypic adaptation to the extreme low temperature.
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Affiliation(s)
- Rasidnie Razin Wong
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
| | - Zheng Syuen Lim
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, Shibaura Institute of Technology, College of Systems Engineering and Science, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan;
| | - Claudio Gomez-Fuentes
- Department of Chemical Engineering, Universidad de Magallanes, Avda. Bulnes, Punta Arenas, Región de Magallanes y Antártica Chilena 01855, Chile;
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes, Punta Arenas, Región de Magallanes y Antártica Chilena 01855, Chile
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes, Punta Arenas, Región de Magallanes y Antártica Chilena 01855, Chile
- National Antarctic Research Centre, Universiti Malaya B303 Level 3, Block B, IPS Building, Kuala Lumpur 50603, Malaysia
- Correspondence:
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Differential Effects of Homologous Transcriptional Regulators NicR2A, NicR2B1, and NicR2B2 and Endogenous Ectopic Strong Promoters on Nicotine Metabolism in Pseudomonas sp. Strain JY-Q. Appl Environ Microbiol 2021; 87:AEM.02457-20. [PMID: 33187996 DOI: 10.1128/aem.02457-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/04/2020] [Indexed: 01/27/2023] Open
Abstract
Nicotine is a toxic environmental pollutant that widely exists in tobacco wastes. As a natural nicotine-degrading strain, Pseudomonas sp. strain JY-Q still has difficulties degrading high concentrations of nicotine. In this study, we investigated the effect of two homologous transcriptional regulators and endogenous ectopic strong promoters on the efficiency of nicotine degradation. Comparative genomics analysis showed that two homologous transcriptional regulators, namely, NicR2A and NicR2Bs (NicR2B1 plus NicR2B2), can repress nicotine degradation gene expression. When both nicR2A and nicR2Bs were deleted, the resulting mutant JY-Q ΔnicR2A ΔnicR2B1 ΔnicR2B2 (QΔABs) exhibits a 17% higher nicotine degradation efficiency than wild-type JY-Q. Transcriptome sequencing (RNA-seq) analysis showed that the transcription levels (fragments per kilobase per million [FPKM] value) of six genes were higher than those of the other genes in JY-Q. Based on the genetic organization of these genes, three putative promoters, PRS28250 , PRS09985 , and PRS24685 , were identified. Their promoter activities were evaluated by comparing their expression levels using reverse transcriptase quantitative PCR (RT-qPCR). We found that the transcription levels of RS28250, RS09985, and RS24685 were respectively 16.8, 2.6, and 1.6 times higher than that of hspB2, encoding 6-hydroxy-3-succinylpyridine hydroxylase, which is involved in nicotine degradation. Thus, two strong endogenous promoters, namely, PRS28250 and PRS09985 , were selected to replace the original promoters of nic2 gene clusters. The effect of the endogenous ectopic promoter was also related to the position of target gene clusters. When the promoter PRS28250 replaced the promoter of hspB2, the resultant mutant QΔABs-ΔPhspB2 ::PRS28250 exhibited nicotine-degrading efficiency 69% higher than that of JY-Q. This research suggests a feasible strategy to enhance strains' capacity for nicotine degradation by removal of repressing regulatory proteins and replacing the target promoter with strong endogenous ectopic promoters.IMPORTANCE This study evaluated the differential effects of homologous NicR2A and NicR2Bs and endogenous ectopic strong promoters on nicotine metabolism in Pseudomonas sp. strain JY-Q. Based on our differential analysis, a feasible strategy is presented to modify wild-type (WT) strain JY-Q by removing repressing regulatory proteins NicR2A and NicR2Bs and replacing the target promoter with strong endogenous ectopic promoters. The resulting mutants exhibited high tolerance and degradation of nicotine. These findings should be beneficial for improving the pollutant-degrading capacity of natural strains through genomic modification.
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An X, Cheng Y, Miao L, Chen X, Zang H, Li C. Characterization and genome functional analysis of an efficient nitrile-degrading bacterium, Rhodococcus rhodochrous BX2, to lay the foundation for potential bioaugmentation for remediation of nitrile-contaminated environments. JOURNAL OF HAZARDOUS MATERIALS 2020; 389:121906. [PMID: 31874764 DOI: 10.1016/j.jhazmat.2019.121906] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 06/10/2023]
Abstract
Nitriles are a class of extremely toxic chemicals with extensive applications, and these compounds pose potential risks to humans and ecosystems. The activated sludge isolate Rhodococcus rhodochrous BX2 efficiently metabolizes aliphatic nitriles. However, the molecular underpinnings of the degradation mechanism of aliphatic nitriles by BX2 remain unknown, and the metabolic fate of aliphatic nitriles also has not been elucidated. Here, strain BX2 was capable of completely mineralizing three aliphatic nitriles. Bioinformatic analysis yielded a deeper insight into the genetic basis of BX2 for efficient degradation of aliphatic nitriles and adaptation to harsh environments. Transcriptional, enzyme activity and metabolite analyses confirmed that the intracellular inducible nitrile hydratase/amidase pathway is the preferred metabolic pathway. Our findings provide an in-depth understanding of the environmental fate of aliphatic nitriles and, most importantly, offer a new perspective on the potential applications of the genus Rhodococcus in bioremediation and the development of degradation enzyme resources.
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Affiliation(s)
- Xuejiao An
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Yi Cheng
- College of Science, China Agricultural University, Beijing 100083, PR China
| | - Lei Miao
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Xi Chen
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Hailian Zang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
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13
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Santos RG, Hurtado R, Gomes LGR, Profeta R, Rifici C, Attili AR, Spier SJ, Mazzullo G, Morais-Rodrigues F, Gomide ACP, Brenig B, Gala-García A, Cuteri V, Castro TLDP, Ghosh P, Seyffert N, Azevedo V. Complete genome analysis of Glutamicibacter creatinolyticus from mare abscess and comparative genomics provide insight of diversity and adaptation for Glutamicibacter. Gene 2020; 741:144566. [PMID: 32171826 DOI: 10.1016/j.gene.2020.144566] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/02/2019] [Accepted: 03/08/2020] [Indexed: 10/24/2022]
Abstract
Bacteria of the genusGlutamicibacterare considered ubiquitous because they can be found in soil, water and air. They have already been isolated from different habitats, including different types of soil, clinical samples, cheese and plants. Glutamicibacter creatinolyticus is a Gram-positive bacterium important to various biotechnological processes, however, as a pathogen it is associated to urinary tract infections and bacteremia. Recently,Glutamicibacter creatinolyticusLGCM 259 was isolated from a mare, which displayed several diffuse subcutaneous nodules with heavy vascularization. In this study, sequencing, genomic analysis ofG. creatinolyticusLGCM 259 and comparative analyseswere performedamong 4representatives of different members of genusfromdifferent habitats, available in the NCBI database. The LGCM 259 strain's genome carries important factors of bacterial virulence that are essential in cell viability, virulence, and pathogenicity. Genomic islands were predicted for 4 members of genusGlutamicibacter,showing ahigh number of GEIs,which may reflect a high interspecific diversity and a possible adaptive mechanism responsible for the survival of each species in its specific niche. Furthermore,G. creatinolyticusLGCM 259 sharessyntenicregions, albeit with a considerable loss of genes, in relation to the other species. In addition,G. creatinolyticusLGCM 259 presentsresistancegenes to 6 differentclasses ofantibiotics and heavy metals, such as: copper, arsenic, chromium and cobalt-zinc-cadmium.Comparative genomicsanalysescouldcontribute to the identification of mobile genetic elements particular to the speciesG. creatinolyticuscompared to other members of genus. The presence of specific regions inG. creatinolyticuscould be indicative of their rolesin host adaptation, virulence, and the characterization ofastrain that affects animals.
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Affiliation(s)
- Roselane Gonçalves Santos
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Raquel Hurtado
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Lucas Gabriel Rodrigues Gomes
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rodrigo Profeta
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Claudia Rifici
- Department of Veterinary Science, University of Messina (Italy), Polo Universitario, dell'Annunziata, 98168 Messina, ME, Italy
| | - Anna Rita Attili
- School of Biosciences and Veterinary Medicine, University of Camerino (Italy), Via Circonvallazione 93/95, 62024 Matelica, MC, Italy.
| | - Sharon J Spier
- Department of Veterinary Medicine and Epidemiology, University of California, Davis, CA, USA.
| | - Giuseppe Mazzullo
- Department of Veterinary Science, University of Messina (Italy), Polo Universitario, dell'Annunziata, 98168 Messina, ME, Italy.
| | - Francielly Morais-Rodrigues
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Anne Cybelle Pinto Gomide
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, Göttingen, Germany.
| | - Alfonso Gala-García
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Institute of Biological Sciences, Federal University of Para, PA, Brazil
| | - Vincenzo Cuteri
- School of Biosciences and Veterinary Medicine, University of Camerino (Italy), Via Circonvallazione 93/95, 62024 Matelica, MC, Italy.
| | - Thiago Luiz de Paula Castro
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Núbia Seyffert
- Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil
| | - Vasco Azevedo
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
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14
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Brandsch R, Mihasan M. A soil bacterial catabolic pathway on the move: Transfer of nicotine catabolic genes between Arthrobacter genus megaplasmids and invasion by mobile elements. J Biosci 2020. [DOI: 10.1007/s12038-020-00030-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Xia Z, Yu M, Yao J, Feng Z, Li D, Liu T, Cheng G, He D, Li X. Functional analysis of the agnH gene involved in nicotine-degradation pathways in Agrobacterium tumefaciens strain SCUEC1. FEMS Microbiol Lett 2020; 367:5775478. [DOI: 10.1093/femsle/fnaa040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/28/2020] [Indexed: 01/11/2023] Open
Abstract
ABSTRACT
Agrobacterium tumefaciens strain SCUEC1 is a nicotine-degrading bacterium, which has been recently isolated from the tobacco waste-contaminated field soil. However, the mechanism for nicotine degradation in this strain remains unclear. Here, we analyze the function and biological properties of the agnH gene in the strain SCUEC1. The overexpression of the AgnH protein was detected by SDS-PAGE analysis, and functional insight of the AgnH protein was carried out with monitoring the changes of maleic acid into fumaric acid by high performance liquid chromatography (HPLC). Moreover, the effects of temperature, pH and metal ions on the enzymatic activities of the AgnH protein were also analyzed. The results demonstrated that the agnH gene was successfully ligated to the plasmid pET28a. The optimal condition for the enzymatic activities for the AgnH, approximately 28.0 kDa, was determined as 37 °C, pH 8.0 and 25 µM Mg2+. Conclusively, the agnH gene fulfils an important role in the conversion of maleic acid into fumaric acid involved in nicotine-degradation pathways in Agrobacterium tumefaciens strain SCUEC1.
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Affiliation(s)
- Zhenzhen Xia
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China & Key Laboratory for the State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
| | - Mengfei Yu
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China & Key Laboratory for the State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
| | - Jiacheng Yao
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China & Key Laboratory for the State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
| | - Zhe Feng
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China & Key Laboratory for the State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
| | - Dinghua Li
- Hunan Beye Biotechnology Ltd, 23 Kaiyuan East Road, Changsha County, Changsha, 410139, Hunan, China
| | - Tao Liu
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China & Key Laboratory for the State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
| | - Guojun Cheng
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China & Key Laboratory for the State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
| | - Donglan He
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China & Key Laboratory for the State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
| | - Xiaohua Li
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China & Key Laboratory for the State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, 182 Minzu Avenue, Wuhan, 430074, Hubei, China
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16
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Brandsch R, Mihasan M. A soil bacterial catabolic pathway on the move: Transfer of nicotine catabolic genes between Arthrobacter genus megaplasmids and invasion by mobile elements. J Biosci 2020; 45:58. [PMID: 32345784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The 165,137 bp plasmid pAO1 of Paenarthrobacter nicotinovorans carries the genes of a nicotine catabolic pathway. The genes are organized into several gene modules responsible for the catabolism of L- and D-nicotine to nicotine blue, alpha-ketoglutarate and succinate. Various modules of these genes have been shown to be present in gram-positive (Gram?) soil bacteria. The presence of the identical pAO1 nic-genes on the 288,370 bp plasmid pZXY21 of Arthrobacter sp. ZXY2 (96 percent to 100 percent at the nucleotide level) permitted the identification of the limits of this DNA fragment. At the 5' end of the nic-genes are located the ORFs of two predicted integrases of the tyrosine recombinase family with conserved R, H, R and Y catalytic residues and that of a small transposase with a predicted leucine zipper motive. They are related to Tn554A, Tn554B and Tn554C of Staphylococcus aureus and suggest that the entire nic-genes DNA fragment represents a large catabolic transposon. Surprisingly the nic-genes on pZXY21 were found to be interspersed by mobile elements encoding transposases of various IS families. Insertion of these IS elements disrupts nicotine degradation and divide the nic-genes DNA into potentially new transposons. This finding may illustrate how nicotine catabolic genes can be mobilized and spread by horizontal gene transfer to other soil bacteria.
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Affiliation(s)
- Roderich Brandsch
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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17
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Guo X, Xie C, Wang L, Li Q, Wang Y. Biodegradation of persistent environmental pollutants by Arthrobacter sp. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:8429-8443. [PMID: 30706270 DOI: 10.1007/s11356-019-04358-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 01/23/2019] [Indexed: 05/17/2023]
Abstract
Persistent environmental pollutants are a growing problem around the world. The effective control of the pollutants is of great significance for human health. Some microbes, especially Arthrobacter, can degrade pollutants into nontoxic substances in various ways. Here, we review the biological properties of Arthrobacter adapting to a variety of environmental stresses, including starvation, hypertonic and hypotonic condition, oxidative stress, heavy metal stress, and low-temperature stress. Furthermore, we categorized the Arthrobacter species that can degrade triazines, organophosphorus, alkaloids, benzene, and its derivatives. Metabolic pathways behind the various biodegradation processes are further discussed. This review will be a helpful reference for comprehensive utilization of Arthrobacter species to tackle environmental pollutants.
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Affiliation(s)
- Xiaohong Guo
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Chengyun Xie
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Lijuan Wang
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Qinfan Li
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Yan Wang
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China.
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18
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Romaniuk K, Golec P, Dziewit L. Insight Into the Diversity and Possible Role of Plasmids in the Adaptation of Psychrotolerant and Metalotolerant Arthrobacter spp. to Extreme Antarctic Environments. Front Microbiol 2018; 9:3144. [PMID: 30619210 PMCID: PMC6305408 DOI: 10.3389/fmicb.2018.03144] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/04/2018] [Indexed: 11/13/2022] Open
Abstract
Arthrobacter spp. are coryneform Gram-positive aerobic bacteria, belonging to the class Actinobacteria. Representatives of this genus have mainly been isolated from soil, mud, sludge or sewage, and are usually mesophiles. In recent years, the presence of Arthrobacter spp. was also confirmed in various extreme, including permanently cold, environments. In this study, 36 psychrotolerant and metalotolerant Arthrobacter strains isolated from petroleum-contaminated soil from the King George Island (Antarctica), were screened for the presence of plasmids. The identified replicons were thoroughly characterized in order to assess their diversity and role in the adaptation of Arthrobacter spp. to harsh Antarctic conditions. The screening process identified 11 different plasmids, ranging in size from 8.4 to 90.6 kb. A thorough genomic analysis of these replicons detected the presence of numerous genes encoding proteins that potentially perform roles in adaptive processes such as (i) protection against ultraviolet (UV) radiation, (ii) resistance to heavy metals, (iii) transport and metabolism of organic compounds, (iv) sulfur metabolism, and (v) protection against exogenous DNA. Moreover, 10 of the plasmids carry genetic modules enabling conjugal transfer, which may facilitate their spread among bacteria in Antarctic soil. In addition, transposable elements were identified within the analyzed plasmids. Some of these elements carry passenger genes, which suggests that these replicons may be actively changing, and novel genetic modules of adaptive value could be acquired by transposition events. A comparative genomic analysis of plasmids identified in this study and other available Arthrobacter plasmids was performed. This showed only limited similarities between plasmids of Antarctic Arthrobacter strains and replicons of other, mostly mesophilic, isolates. This indicates that the plasmids identified in this study are novel and unique replicons. In addition, a thorough meta-analysis of 247 plasmids of psychrotolerant bacteria was performed, revealing the important role of these replicons in the adaptation of their hosts to extreme environments.
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Affiliation(s)
- Krzysztof Romaniuk
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Piotr Golec
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
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19
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Ren L, Jia Y, Zhang R, Lin Z, Zhen Z, Hu H, Yan Y. Insight Into Metabolic Versatility of an Aromatic Compounds-Degrading Arthrobacter sp. YC-RL1. Front Microbiol 2018; 9:2438. [PMID: 30364317 PMCID: PMC6193132 DOI: 10.3389/fmicb.2018.02438] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/24/2018] [Indexed: 01/11/2023] Open
Abstract
The genus Arthrobacter is ubiquitously distributed in different natural environments. Many xenobiotic-degrading Arthrobacter strains have been isolated and described; however, few have been systematically characterized with regard to multiple interrelated metabolic pathways and the genes that encode them. In this study, the biodegradability of seven aromatic compounds by Arthrobacter sp. YC-RL1 was investigated. Strain YC-RL1 could efficiently degrade p-xylene (PX), naphthalene, phenanthrene, biphenyl, p-nitrophenol (PNP), and bisphenol A (BPA) under both separated and mixed conditions. Based on the detected metabolic intermediates, metabolic pathways of naphthalene, biphenyl, PNP, and BPA were proposed, which indicated that strain YC-RL1 harbors systematic metabolic pathways toward aromatic compounds. Further, genomic analysis uncovered part of genes involved in the proposed pathways. Both intradiol and extradiol ring-cleavage dioxygenase genes were identified in the genome of strain YC-RL1. Meanwhile, gene clusters predicted to encode the degradation of biphenyl (bph), para-substituted phenols (npd) and protocatechuate (pca) were identified, and bphA1A2BCD was proposed to be a novel biphenyl-degrading gene cluster. The complete metabolic pathway of biphenyl was deduced via intermediates and functional gene analysis (bph and pca gene clusters). One of the these genes encoding ring-cleavage dioxygenase in bph gene cluster, a predicted 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) gene, was cloned and its activity was confirmed by heterologous expression. This work systematically illuminated the metabolic versatility of aromatic compounds in strain YC-RL1 via the combination of metabolites identification, genomics analysis and laboratory experiments. These results suggested that strain YC-RL1 might be a promising candidate for the bioremediation of aromatic compounds pollution sites.
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Affiliation(s)
- Lei Ren
- Agricultural College, Guangdong Ocean University, Zhanjiang, China.,Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Jia
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Zhang
- Agricultural College, Guangdong Ocean University, Zhanjiang, China.,Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, China
| | - Zhong Lin
- Agricultural College, Guangdong Ocean University, Zhanjiang, China.,Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang, China
| | - Zhen Zhen
- Agricultural College, Guangdong Ocean University, Zhanjiang, China
| | - Hanqiao Hu
- Agricultural College, Guangdong Ocean University, Zhanjiang, China
| | - Yanchun Yan
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
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20
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Ruan A, Gao Y, Fang C, Xu Y. Isolation and characterization of a novel nicotinophilic bacterium,Arthrobactersp. aRF‐1 and its metabolic pathway. Biotechnol Appl Biochem 2018; 65:848-856. [DOI: 10.1002/bab.1682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 06/14/2018] [Accepted: 06/16/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Aidong Ruan
- State Key Laboratory of Hydrology‐Water Resources and Hydraulic EngineeringHohai University Nanjing 210098 People's Republic of China
| | - Yuan Gao
- State Key Laboratory of Hydrology‐Water Resources and Hydraulic EngineeringHohai University Nanjing 210098 People's Republic of China
| | - Chao Fang
- State Key Laboratory of Hydrology‐Water Resources and Hydraulic EngineeringHohai University Nanjing 210098 People's Republic of China
| | - Yaofei Xu
- State Key Laboratory of Hydrology‐Water Resources and Hydraulic EngineeringHohai University Nanjing 210098 People's Republic of China
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21
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Ang TF, Maiangwa J, Salleh AB, Normi YM, Leow TC. Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications. Molecules 2018; 23:E1100. [PMID: 29735886 PMCID: PMC6100074 DOI: 10.3390/molecules23051100] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/07/2018] [Accepted: 04/09/2018] [Indexed: 11/16/2022] Open
Abstract
The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.
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Affiliation(s)
- Thiau-Fu Ang
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Jonathan Maiangwa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Yahaya M Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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22
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Bacterial community structure associated with the rhizosphere soils and roots of Stellera chamaejasme L. along a Tibetan elevation gradient. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1336-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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23
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Comparative transcriptomic and proteomic analysis of Arthrobacter sp. CGMCC 3584 responding to dissolved oxygen for cAMP production. Sci Rep 2018; 8:1246. [PMID: 29352122 PMCID: PMC5775200 DOI: 10.1038/s41598-017-18889-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 12/18/2017] [Indexed: 01/09/2023] Open
Abstract
Arthrobacter sp. CGMCC 3584 is able to produce high yields of extracellular cyclic adenosine monophosphate (cAMP), which plays a vital role in the field of treatment of disease and animal food, during aerobic fermentation. However, the molecular basis of cAMP production in Arthrobacter species is rarely explored. Here, for the first time, we report the comparative transcriptomic and proteomic study of Arthrobacter cells to elucidate the higher productivity of cAMP under high oxygen supply. We finally obtained 14.1% and 19.3% of the Arthrobacter genome genes which were up-regulated and down-regulated notably, respectively, with high oxygen supply, and identified 54 differently expressed proteins. Our results revealed that high oxygen supply had two major effects on metabolism: inhibition of glycolysis, pyruvate metabolism, nitrogen metabolism, and amino acid metabolism (histidine, branched-chain amino acids and glutamate metabolism); enhancement of the tricarboxylic acid cycle and purine metabolism. We also found that regulation of adenylate cyclase and phosphodiesterase was not significant under high oxygen supply, suggesting efficient cAMP export might be important in cAMP production. These findings may contribute to further understanding of capacities of Arthrobacter species and would be highly useful in genetic regulation for desirable production.
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Niu H, Yang W, Zhuang K, Chen X, Chen Y, Liu D, Wu J, Zhu C, Ying H. Screening of promoters from Arthrobacter sp. CGMCC 3584 using a green fluorescent protein reporter system. World J Microbiol Biotechnol 2017; 33:208. [DOI: 10.1007/s11274-017-2375-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 10/29/2017] [Indexed: 11/29/2022]
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Li J, Qian S, Xiong L, Zhu C, Shu M, Wang J, Jiao Y, He H, Zhang F, Linhardt RJ, Zhong W. Comparative Genomics Reveals Specific Genetic Architectures in Nicotine Metabolism of Pseudomonas sp. JY-Q. Front Microbiol 2017; 8:2085. [PMID: 29163390 PMCID: PMC5674928 DOI: 10.3389/fmicb.2017.02085] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/11/2017] [Indexed: 12/21/2022] Open
Abstract
Microbial degradation of nicotine is an important process to control nicotine residues in the aqueous environment. In this study, a high active nicotine degradation strain named Pseudomonas sp. JY-Q was isolated from tobacco waste extract (TWE). This strain could completely degrade 5.0 g l−1 nicotine in 24 h under optimal culture conditions, and it showed some tolerance even at higher concentrations (10.0 g l−1) of nicotine. The complete genome of JY-Q was sequenced to understand the mechanism by which JY-Q could degrade nicotine and tolerate such high nicotine concentrations. Comparative genomic analysis indicated that JY-Q degrades nicotine through putative novel mechanisms. Two candidate gene cluster duplications located separately at distant loci were predicted to be responsible for nicotine degradation. These two nicotine (Nic) degradation-related loci (AA098_21325—AA098_21340, AA098_03885—AA098_03900) exhibit nearly completely consistent gene organization and component synteny. The nicotinic acid (NA) degradation gene cluster (AA098_17770–AA098_17790) and Nic-like clusters were both predicted to be flanked by mobile genetic elements (MGE). Furthermore, we analyzed the regions of genomic plasticity (RGP) in the JY-Q strain and found a dynamic genome carrying a type VI secretion system (T6SS) that promotes nicotine metabolism and tolerance based on transcriptomics and used in silico methods to identify the T6SS effector protein. Thus, a novel nicotine degradation mechanism was elucidated for Pseudomonas sp. JY-Q, suggesting its potential application in the bioremediation of nicotine-contaminated environments, such as TWEs.
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Affiliation(s)
- Jun Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Shulan Qian
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Lie Xiong
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Chengyun Zhu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Ming Shu
- Technology Center, China Tobacco Zhejiang Industrial Co., Ltd., Hangzhou, China
| | - Jie Wang
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yang Jiao
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Houlong He
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Fuming Zhang
- Departments of Chemical and Biological Engineering, Biological Science, Chemistry and Chemical Biology and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Robert J Linhardt
- Departments of Chemical and Biological Engineering, Biological Science, Chemistry and Chemical Biology and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Weihong Zhong
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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Wang H, Zhi XY, Qiu J, Shi L, Lu Z. Characterization of a Novel Nicotine Degradation Gene Cluster ndp in Sphingomonas melonis TY and Its Evolutionary Analysis. Front Microbiol 2017; 8:337. [PMID: 28337179 PMCID: PMC5343071 DOI: 10.3389/fmicb.2017.00337] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/17/2017] [Indexed: 11/13/2022] Open
Abstract
Sphingomonas melonis TY utilizes nicotine as a sole source of carbon, nitrogen, and energy through a variant of the pyridine and pyrrolidine pathways (VPP). A 31-kb novel nicotine-degrading gene cluster, ndp, in strain TY exhibited a different genetic organization with the vpp cluster in strains Ochrobactrum rhizosphaerae SJY1 and Agrobacterium tumefaciens S33. Genes in vpp were separated by a 20-kb interval sequence, while genes in ndp were localized together. Half of the homolog genes were in different locus in ndp and vpp. Moreover, there was a gene encoding putative transporter of nicotine or other critical metabolite in ndp. Among the putative nicotine-degrading related genes, the nicotine hydroxylase, 6-hydroxy-L-nicotine oxidase, 6-hydroxypseudooxynicotine oxidase, and 6-hydroxy-3-succinyl-pyridine monooxygenase responsible for catalyzing the transformation of nicotine to 2, 5-dihydropyridine in the initial four steps of the VPP were characterized. Hydroxylation at C6 of the pyridine ring and dehydrogenation at the C2–C3 bond of the pyrrolidine ring were the key common reactions in the VPP, pyrrolidine and pyridine pathways. Besides, VPP and pyrrolidine pathway shared the same latter part of metabolic pathway. After analysis of metabolic genes in the pyridine, pyrrolidine, and VPP pathways, we found that both the evolutionary features and metabolic mechanisms of the VPP were more similar to the pyrrolidine pathway. The linked ndpHFEG genes shared by the VPP and pyrrolidine pathways indicated that these two pathways might share the same origin, but variants were observed in some bacteria. And we speculated that the pyridine pathway was distributed in Gram-positive bacteria and the VPP and pyrrolidine pathways were distributed in Gram-negative bacteria by using comprehensive homologs searching and phylogenetic tree construction.
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Affiliation(s)
- Haixia Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University Kunming, China
| | - Jiguo Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University Nanjing, China
| | - Longxiang Shi
- Institution of System Engineering, College of Computer Science and Technology, Zhejiang University Hangzhou, China
| | - Zhenmei Lu
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
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Hiraoka S, Machiyama A, Ijichi M, Inoue K, Oshima K, Hattori M, Yoshizawa S, Kogure K, Iwasaki W. Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami. BMC Genomics 2016; 17:53. [PMID: 26764021 PMCID: PMC4712596 DOI: 10.1186/s12864-016-2380-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Great East Japan Earthquake of 2011 triggered large tsunami waves, which flooded broad areas of land along the Pacific coast of eastern Japan and changed the soil environment drastically. However, the microbial characteristics of tsunami-affected soil at the genomic level remain largely unknown. In this study, we isolated microbes from a soil sample using general low-nutrient and seawater-based media to investigate microbial characteristics in tsunami-affected soil. RESULTS As expected, a greater proportion of strains isolated from the tsunami-affected soil than the unaffected soil grew in the seawater-based medium. Cultivable strains in both the general low-nutrient and seawater-based media were distributed in the genus Arthrobacter. Most importantly, whole-genome sequencing of four of the isolated Arthrobacter strains revealed independent losses of siderophore-synthesis genes from their genomes. Siderophores are low-molecular-weight, iron-chelating compounds that are secreted for iron uptake; thus, the loss of siderophore-synthesis genes indicates that these strains have adapted to environments with high-iron concentrations. Indeed, chemical analysis confirmed the investigated soil samples to be rich in iron, and culture experiments confirmed weak cultivability of some of these strains in iron-limited media. Furthermore, metagenomic analyses demonstrated over-representation of denitrification-related genes in the tsunami-affected soil sample, as well as the presence of pathogenic and marine-living genera and genes related to salt-tolerance. CONCLUSIONS Collectively, the present results would provide an example of microbial characteristics of soil disturbed by the tsunami, which may give an insight into microbial adaptation to drastic environmental changes. Further analyses on microbial ecology after a tsunami are envisioned to develop a deeper understanding of the recovery processes of terrestrial microbial ecosystems.
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Affiliation(s)
- Satoshi Hiraoka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, 277-8568, Japan.
| | - Asako Machiyama
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, 113-0032, Japan.
| | - Minoru Ijichi
- Atmosphere and Ocean Research Institute, the University of Tokyo, Chiba, 277-8564, Japan.
| | - Kentaro Inoue
- Atmosphere and Ocean Research Institute, the University of Tokyo, Chiba, 277-8564, Japan.
| | - Kenshiro Oshima
- Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.
| | - Masahira Hattori
- Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, the University of Tokyo, Chiba, 277-8564, Japan.
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute, the University of Tokyo, Chiba, 277-8564, Japan.
| | - Wataru Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, 277-8568, Japan.
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, 113-0032, Japan.
- Atmosphere and Ocean Research Institute, the University of Tokyo, Chiba, 277-8564, Japan.
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