1
|
Bacterial degradation of mixed-PAHs and expression of PAH-catabolic genes. World J Microbiol Biotechnol 2023; 39:47. [DOI: 10.1007/s11274-022-03489-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
|
2
|
The structure-function relationship of bacterial transcriptional regulators as a target for enhanced biodegradation of aromatic hydrocarbons. Microbiol Res 2022; 262:127087. [DOI: 10.1016/j.micres.2022.127087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/20/2022]
|
3
|
A Review of Pyrene Bioremediation Using Mycobacterium Strains in a Different Matrix. FERMENTATION 2022. [DOI: 10.3390/fermentation8060260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Polycyclic aromatic hydrocarbons are compounds with 2 or more benzene rings, and 16 of them have been classified as priority pollutants. Among them, pyrene has been found in higher concentrations than recommended, posing a threat to the ecosystem. Many bacterial strains have been identified as pyrene degraders. Most of them belong to Gram-positive strains such as Mycobacterium sp. and Rhodococcus sp. These strains were enriched and isolated from several sites contaminated with petroleum products, such as fuel stations. The bioremediation of pyrene via Mycobacterium strains is the main objective of this review. The scattered data on the degradation efficiency, formation of pyrene metabolites, bio-toxicity of pyrene and its metabolites, and proposed degradation pathways were collected in this work. The study revealed that most of the Mycobacterium strains were capable of degrading pyrene efficiently. The main metabolites of pyrene were 4,5-dihydroxy pyrene, phenanthrene-4,5-dicarboxylate, phthalic acid, and pyrene-4,5-dihydrodiol. Some metabolites showed positive results for the Ames mutagenicity prediction test, such as 1,2-phenanthrenedicarboxylic acid, 1-hydroxypyrene, 4,5-dihydropyrene, 4-phenanthrene-carboxylic acid, 3,4-dihydroxyphenanthrene, monohydroxy pyrene, and 9,10-phenanthrenequinone. However, 4-phenanthrol showed positive results for experimental and prediction tests. This study may contribute to enhancing the bioremediation of pyrene in a different matrix.
Collapse
|
4
|
Imam A, Kumar Suman S, Kanaujia PK, Ray A. Biological machinery for polycyclic aromatic hydrocarbons degradation: A review. BIORESOURCE TECHNOLOGY 2022; 343:126121. [PMID: 34653630 DOI: 10.1016/j.biortech.2021.126121] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 06/13/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are hazardous environmental pollutants with widespread and well-recognized health concerns. Amidst more than a hundred known PAHs, 16 are categorized as priority pollutants. Use of widely diverse biological machinery comprising bacteria, fungi, and algae harnessed from contaminated sites has emerged as an ecologically safe and sustainable approach for PAH degradation. The potential of these biological systems has been thoroughly examined to maximize the degradation of specific PAHs by understanding their detailed biochemical pathways, enzymatic system, and gene organization. Recent advancements in microbial genetic engineering and metabolomics using modern analytical tools have facilitated the bioremediation of such xenobiotics. This review explores the role of microbes, their biochemical pathways, genetic regulation of metabolic pathways, and the effect of biosurfactants against the backdrop of PAH substrate structures.
Collapse
Affiliation(s)
- Arfin Imam
- Analytical Sciences Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun 248005, Uttarakhand, India; Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun 248005, Uttarakhand, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
| | - Sunil Kumar Suman
- Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun 248005, Uttarakhand, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
| | - Pankaj K Kanaujia
- Analytical Sciences Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun 248005, Uttarakhand, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
| | - Anjan Ray
- Analytical Sciences Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun 248005, Uttarakhand, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India.
| |
Collapse
|
5
|
Cárdenas Espinosa MJ, Schmidgall T, Wagner G, Kappelmeyer U, Schreiber S, Heipieper HJ, Eberlein C. An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene. PLoS One 2021; 16:e0260002. [PMID: 34780548 PMCID: PMC8592408 DOI: 10.1371/journal.pone.0260002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/30/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial degradation of xenobiotic compounds is an intense field of research already for decades. Lately, this research is complemented by downstream applications including Next Generation Sequencing (NGS), RT-PCR, qPCR, and RNA-seq. For most of these molecular applications, high-quality RNA is a fundamental necessity. However, during the degradation of aromatic substrates, phenolic or polyphenolic compounds such as polycatechols are formed and interact irreversibly with nucleic acids, making RNA extraction from these sources a major challenge. Therefore, we established a method for total RNA extraction from the aromatic degrading Pseudomonas capeferrum TDA1 based on RNAzol® RT, glycogen and a final cleaning step. It yields a high-quality RNA from cells grown on TDA1 and on phenol compared to standard assays conducted in the study. To our knowledge, this is the first report tackling the problem of polyphenolic compound interference with total RNA isolation in bacteria. It might be considered as a guideline to improve total RNA extraction from other bacterial species.
Collapse
Affiliation(s)
| | - Tabea Schmidgall
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Georg Wagner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Uwe Kappelmeyer
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stephan Schreiber
- Department Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hermann J. Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Christian Eberlein
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| |
Collapse
|
6
|
Akbari A, David C, Rahim AA, Ghoshal S. Salt selected for hydrocarbon-degrading bacteria and enhanced hydrocarbon biodegradation in slurry bioreactors. WATER RESEARCH 2021; 202:117424. [PMID: 34332190 DOI: 10.1016/j.watres.2021.117424] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/12/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Hydrocarbon and salt contamination of surface and groundwater resources often co-occur from oil production activities. However, salt is often considered as a potential inhibitor of microbial activity. The feasibility of microbiome-based biotechnologies to treat the hydrocarbon contamination is contingent on the ability of the indigenous community to adapt to saline conditions. Here, we demonstrate enhanced hydrocarbon biodegradation in soil slurries under saline conditions of up to ~1 M (5%) compared to non-saline systems and the underlying causes. The mineralization extent of hexadecane was enhanced by salinity in the absence of nutrients. Salinity, similar to nutrients, enhanced the mineralization but through ecological selection. Microbial community analysis indicated a significant enrichment of Actinobacteria phylum and an increase in the absolute abundance of the hydrocarbon-degrading Dietzia genus, but a decrease in the total population size with salinity. Moreover, the in situ expression of alkane hydroxylases genes of Dietzia was generally increased with salinity. The data demonstrate that indigenous halotolerant hydrocarbon degraders were enriched, and their hydrocarbon degradation genes upregulated under saline conditions. These findings have positive implications for engineered biotreatment approaches for hydrocarbons in saline environments such as those affected with produced waters and oil sands tailing ponds.
Collapse
Affiliation(s)
- Ali Akbari
- Department of Civil Engineering, McGill University, Montreal, Quebec H3A 0C3, Canada
| | - Carolyn David
- Department of Civil Engineering, McGill University, Montreal, Quebec H3A 0C3, Canada
| | - Arshath Abdul Rahim
- Department of Civil Engineering, McGill University, Montreal, Quebec H3A 0C3, Canada
| | - Subhasis Ghoshal
- Department of Civil Engineering, McGill University, Montreal, Quebec H3A 0C3, Canada.
| |
Collapse
|
7
|
S, Singh SK, Haritash AK. Evolutionary Relationship of Polycyclic Aromatic Hydrocarbons Degrading Bacteria with Strains Isolated from Petroleum Contaminated Soil Based on 16S rRNA Diversity. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1825003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Sakshi
- Department of Environmental Engineering, Delhi Technological University, Shahbad Daulatpur, Delhi, India
| | - S. K. Singh
- Department of Environmental Engineering, Delhi Technological University, Shahbad Daulatpur, Delhi, India
| | - A. K. Haritash
- Department of Environmental Engineering, Delhi Technological University, Shahbad Daulatpur, Delhi, India
| |
Collapse
|
8
|
Ebrahimi V, Eyvazi S, Montazersaheb S, Yazdani P, Hejazi MA, Tarhriz V, Hejazi MS. Polycyclic Aromatic Hydrocarbons Degradation by Aquatic Bacteria Isolated from Khazar Sea, the World’s Largest Lake. PHARMACEUTICAL SCIENCES 2020. [DOI: 10.34172/ps.2020.28] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background: Aquatic microorganisms have an important role in the bioremediation of environmental pollutants. Polycyclic Aromatic Hydrocarbons (PAHs) are described as dangerous pollutants that can bind covalently to the nucleic acids, causing mutations. Therefore, they have carcinogenic and toxic properties. Also, are involved in diseases such as asthma, lung dysfunction, and chronic bronchitis. This study aimed to isolate and characterize aquatic bio-degrading bacteria from the world’s largest lake, Khazar, with the ability to use PAHs as only carbon source. Methods: Samples were taken from the estuary of Siah Rud River (Mazandaran province, Iran) and Fereydunkenar beach leading to isolation of twenty-three bacteria on marine agar and sea water media. The isolates were cultured on separate ONR7a medium, each supplemented with only one PAH; as the sole carbon source; including naphthalene, phenanthrene, and anthracene. Results: Eleven bacterial isolates were able to grow on supplemented media: TBZ-E1, TBZ-E2, TBZ-E3, TBZ-S12, TBZ-S16, TBZ-E20, TBZ-SF2, TBZ-F1, TBZ-F2, TBZ-F3 and TBZ2. These isolates belong to Alteromonas, Marivivens, Pseudoalteromonas, Vibrio, Shewanella, Photobacterium, Mycobacterium and Pseudomonas genera. The qualitative analysis showed that the consortium of isolates TBZ-F1, TBZ-F2, TBZ-F3, TBZ-SF2, and TBZ2 displayed the highest degradation rate for phenanthrene and naphthalene. Naphthalene, phenanthrene, and anthracene were potently degraded by TBZ2 and TBZ-SF2 and accordingly were subjected to measure degradation potential of mentioned PAHs. Conclusion: The bacterial isolates of Caspian lake have a critical duty in biodegradation of PAHs. These isolates are representative samples of the bacterial population of this lake, participating in the purification process of this habitat.
Collapse
Affiliation(s)
- Vida Ebrahimi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shirin Eyvazi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soheila Montazersaheb
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parivar Yazdani
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Amin Hejazi
- Branch for the Northwest and West Region, Agriculture Biotechnology Research Institute of Iran (ABRII), Tabriz, Iran
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Saeid Hejazi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
9
|
Liang Z, Li G, Mai B, An T. Biodegradation of typical BFRs 2,4,6-tribromophenol by an indigenous strain Bacillus sp. GZT isolated from e-waste dismantling area through functional heterologous expression. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134159. [PMID: 31491624 DOI: 10.1016/j.scitotenv.2019.134159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/22/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Legacy wastewater contaminants from e-waste dismantling process such as 2,4,6-tribromophenol (TBP), one of the most widely used brominated flame retardants (BFRs), have raised concern owing to their toxicity and recalcitrance. Our previously isolated Bacillus sp. GZT from river sludge in e-waste dismantling area is a good candidate for bioremediation of BFRs contaminated sites considering its remarkable degradability of TBP and its intermediates. However, there exists a new challenge because bio-degrader cannot produce enough biomass or metabolic activity to cleanup TBP in practice complex environment. Here, we heterologously expressed and functionally characterized the genes and enzymes responsible for TBP degradation to examine the feasibility of enhancing the ability of this microorganism to detoxify TBP. Results demonstrated that five recombinant strains containing functional genes, designated tbpA, tbpB, tbpC, tbpD, and tbpE, become more tolerant toward a wide range of brominated compounds than the nontransgenic strain. Cytochrome P450 reductase encoded by tbpA gene could greatly increase efficiency to remove TBP (98.8%), as compared to wild-type strain GZT (93.2%). Its debromination intermediates 2,4-dibromophenol, 2,6-dibromo-4-methylphenol and 2-bromophenol were significantly metabolized by halophenol dehalogenases encoded by tbpB, tbpC, and tbpD, respectively. Finally, under the function of tbpE gene encoding enzyme, further debrominated product (phenol) was dramatically detoxified. To reduce the risk of these xenobiotics, the expression of these genes can be induced and significantly up-regulated during exposure to them. These results open broad scope for future study in developing genetic engineering technologies for more efficient remediation wastewater of e-waste recycling sites contaminated with TBP, which would certainly be important steps to lower TBP exposures and prevent potential health effects.
Collapse
Affiliation(s)
- Zhishu Liang
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Guiying Li
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
| | - Bixian Mai
- State Key Laboratory of Organic Geochemistry, Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Taicheng An
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| |
Collapse
|
10
|
Wang X, Wan G, Shi L, Gao X, Zhang X, Li X, Zhao J, Sha B, Huang Z. Direct micro-electric stimulation alters phenanthrene-degrading metabolic activities of Pseudomonas sp. strain DGYH-12 in modified bioelectrochemical system. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:31449-31462. [PMID: 31478172 PMCID: PMC6828628 DOI: 10.1007/s11356-019-05670-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/03/2019] [Indexed: 05/23/2023]
Abstract
Bioelectrochemical systems (BESs) have great potential for treating wastewater containing polycyclic aromatic hydrocarbons (PAHs); however, detailed data on cell physiological activities in PAH biodegradation pathways stimulated by BESs are still lacking. In this paper, a novel BES device was assembled to promote the growth of Pseudomonas sp. DGYH-12 in phenanthrene (PHE) degradation. The results showed that in the micro-electric field (0.2 V), cell growth rate and PHE degradation efficiency were 22% and 27.2% higher than biological control without electric stimulation (BC), respectively. The extracellular polymeric substance (EPS) concentration in BES (39.38 mg L-1) was higher than control (33.36 mg L-1); moreover, the membrane permeability and ATPase activities were also enhanced and there existing phthalic acid and salicylic acid metabolic pathways in the strain. The degradation genes nahAc, pcaH, and xylE expression levels were upregulated by micro-electric stimulation. This is the first study to analyze the physiological and metabolic effect of micro-electric stimulation on a PHE-degrading strain in detail and systematically.
Collapse
Affiliation(s)
- Xingbiao Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Guilong Wan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Liuyang Shi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Xiaolong Gao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Xiaoxia Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Xiaoguang Li
- Binzhou Engineering Technology Research Center for High Salt Wastewater Treatment (chips) of Befar Group, Binzhou, Shandong Province, 256602, People's Republic of China
| | - Jianfang Zhao
- Binzhou Engineering Technology Research Center for High Salt Wastewater Treatment (chips) of Befar Group, Binzhou, Shandong Province, 256602, People's Republic of China
| | - Beibei Sha
- Binzhou Engineering Technology Research Center for High Salt Wastewater Treatment (chips) of Befar Group, Binzhou, Shandong Province, 256602, People's Republic of China
| | - Zhiyong Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
| |
Collapse
|
11
|
Tao Y, Li H, Gu J, Shi H, Han S, Jiao Y, Zhong G, Zhang Q, Akindolie MS, Lin Y, Chen Z, Zhang Y. Metabolism of diethyl phthalate (DEP) and identification of degradation intermediates by Pseudomonas sp. DNE-S1. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 173:411-418. [PMID: 30798184 DOI: 10.1016/j.ecoenv.2019.02.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/04/2019] [Accepted: 02/16/2019] [Indexed: 06/09/2023]
Abstract
A Pseudomonas sp. DNE-S1 (GenBank accession number MF803832), able to degrade DEP in a wide range of acid-base conditions, was isolated from landfill soil. The growth kinetics of DNE-S1 on DEP followed the inhibition model. Fe3+ could promote the degradation ability of DNE-S1 to DEP probably by over-expression of the gene phthalate dihydrodiol dehydrogenase (ophB) and phthalate dioxygenase ferredoxin reductase (ophA4). The degradation rate of DEP (500 mg L-1 at 12 h) increased by 14.5% in the presence of Fe3+. Cu2+, Zn2+, and Mn2+ showed an inhibiting effect on the degradation performance of the strain and could alter the cellular morphology, surface area and volume of DNE-S1. Three degradation intermediates, namely ethyl methyl phthalate (EMP), dimethyl phthalate (DMP), and phthalic acid (PA), were detected in the biodegradation of DEP, and the biochemical pathway of DEP degradation was proposed. This study provides new information on the biochemical pathways and the responsible genes involved in DEP degradation.
Collapse
Affiliation(s)
- Yue Tao
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Hanxu Li
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Jidong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, Special Administrative Region
| | - Hongtao Shi
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Siyue Han
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Yaqi Jiao
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Guanyu Zhong
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Qi Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Modupe S Akindolie
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Yulong Lin
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, No. 18, Liaohe West Road, Jinzhou New District, Dalian, Liaoning Province, PR China
| | - Ying Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China.
| |
Collapse
|
12
|
Abdelhaleem HAR, Zein HS, Azeiz A, Sharaf AN, Abdelhadi AA. Identification and characterization of novel bacterial polyaromatic hydrocarbon-degrading enzymes as potential tools for cleaning up hydrocarbon pollutants from different environmental sources. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2019; 67:108-116. [PMID: 30807915 DOI: 10.1016/j.etap.2019.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/06/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are recalcitrant hazardous environmental contaminants. Various strategies, including chemical and physical like oxidation, fixation, leaching, and electrokinetic or biological-based techniques are used for remediation of polluted sites. Bioremediation of PAHs, via PAH-degrading endophytic and rhizospheric microbes, represent a time-/cost-effective way for ecorestoration. Four bacterial strains were isolated from contaminated soil on MSM supplemented with anthracene, alpha-naphthalene or catechol as sole carbon sources. These isolates were identified with 16S rRNA as Bacillus anthracis, B. cereus, B. mojavensis and B. subtilis. The degradation efficiency on the selected aromatic compounds was tested by HPLC analysis. B. subtilis showed the highest degradation efficiency of anthracene (99%) after five days of incubation. B. subtilis showed the highest catechol 1, 2 dioxygenase activity in MSM supplemented with anthracene. The enzyme was purified by gel filtration chromatography and characterized (70 kD, Km 2.7 μg and Vmax 178U/mg protein). The catechol 1,2 dioxygenase gene from the identified four bacterial strains were isolated and submitted to GenBank (accession numbers MG255165-MG255168). The gene expression level of catechol 1,2 dioxygenase was upregulated 23.2-fold during the 72 h of incubation period. Furthermore, B. subtilis is a promising strain to be used in bioremediation of aromatic compounds-contaminated environments.
Collapse
Affiliation(s)
- Heba A R Abdelhaleem
- College of Biotechnology, Misr University for Science and Technology (MUST), 6(th) October City, Egypt
| | - Haggag S Zein
- Department of Genetics Faculty of Agriculture, Cairo University, PO Box 12613 Giza, Egypt
| | - Abdel Azeiz
- College of Biotechnology, Misr University for Science and Technology (MUST), 6(th) October City, Egypt
| | - Ahmed N Sharaf
- Department of Genetics Faculty of Agriculture, Cairo University, PO Box 12613 Giza, Egypt
| | - Abdelhadi A Abdelhadi
- Department of Genetics Faculty of Agriculture, Cairo University, PO Box 12613 Giza, Egypt.
| |
Collapse
|
13
|
Isolation, cloning and characterization of an azoreductase and the effect of salinity on its expression in a halophilic bacterium. Int J Biol Macromol 2019; 123:1062-1069. [DOI: 10.1016/j.ijbiomac.2018.11.175] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/18/2018] [Accepted: 11/18/2018] [Indexed: 11/17/2022]
|
14
|
Draft Genome Sequence of Mycobacterium parafortuitum Strain P7335. Microbiol Resour Announc 2018; 7:MRA00950-18. [PMID: 30533921 PMCID: PMC6256513 DOI: 10.1128/mra.00950-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 07/25/2018] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium parafortuitum is a rapidly growing nontuberculous mycobacterium, initially isolated from soil in Japan. The 6,175,772-bp draft genome sequence of M. parafortuitum strain P7335 exhibits a G+C content of 68.4%, 5,783 protein-coding genes, and 66 predicted RNA genes, including 59 tRNA genes, 6 rRNA operons, and 1 transfer-messenger RNA. Mycobacterium parafortuitum is a rapidly growing nontuberculous mycobacterium, initially isolated from soil in Japan. The 6,175,772-bp draft genome sequence of M. parafortuitum strain P7335 exhibits a G+C content of 68.4%, 5,783 protein-coding genes, and 66 predicted RNA genes, including 59 tRNA genes, 6 rRNA operons, and 1 transfer-messenger RNA.
Collapse
|
15
|
Selection and validation of reference genes for gene expression studies in Klebsiella pneumoniae using Reverse Transcription Quantitative real-time PCR. Sci Rep 2018; 8:9001. [PMID: 29899556 PMCID: PMC5998039 DOI: 10.1038/s41598-018-27420-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/23/2018] [Indexed: 12/27/2022] Open
Abstract
For reliable results, Reverse Transcription Quantitative real-time Polymerase Chain Reaction (RT-qPCR) analyses depend on stably expressed reference genes for data normalization purposes. Klebsiella pneumoniae is an opportunistic Gram-negative bacterium that has become a serious threat worldwide. Unfortunately, there is no consensus for an ideal reference gene for RT-qPCR data normalization on K. pneumoniae. In this study, the expression profile of eleven candidate reference genes was assessed in K. pneumoniae cells submitted to various experimental conditions, and the expression stability of these candidate genes was evaluated using statistical algorithms BestKeeper, NormFinder, geNorm, Delta CT and RefFinder. The statistical analyses ranked recA, rho, proC and rpoD as the most suitable reference genes for accurate RT-qPCR data normalization in K. pneumoniae. The reliability of the proposed reference genes was validated by normalizing the relative expression of iron-regulated genes in K. pneumoniae cells submitted to iron-replete and iron-limited conditions. This work emphasizes that the stable expression of any potential reference candidate gene must be validated in each physiological condition or experimental treatment under study.
Collapse
|
16
|
Feng NX, Yu J, Mo CH, Zhao HM, Li YW, Wu BX, Cai QY, Li H, Zhou DM, Wong MH. Biodegradation of di-n-butyl phthalate (DBP) by a novel endophytic Bacillus megaterium strain YJB3. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 616-617:117-127. [PMID: 29112835 DOI: 10.1016/j.scitotenv.2017.10.298] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/27/2017] [Accepted: 10/29/2017] [Indexed: 05/10/2023]
Abstract
Phthalic acid esters (PAEs) are a group of recalcitrant and hazardous organic compounds that pose a great threat to both ecosystem and human beings. A novel endophytic strain YJB3 that could utilize a wide range of PAEs as the sole carbon and energy sources for cell growth was isolated from Canna indica root tissue. It was identified as Bacillus megaterium based on morphological characteristics and 16S rDNA sequence homology analysis. The degradation capability of the strain YJB3 was investigated by incubation in mineral salt medium containing di-n-butyl-phthalate (DBP), one of important PAEs under different environmental conditions, showing 82.5% of the DBP removal in 5days of incubation under the optimum conditions (acetate 1.2g·L-1, inocula 1.8%, and temperature 34.2°C) achieved by two-step sequential optimization technologies. The DBP metabolites including mono-butyl phthalate (MBP), phthalic acid (PA), protocatechuic acid (PCA), etc. were determined by GC-MS. The PCA catabolic genes responsible for the aromatic ring cleavage of PCA in the strain YJB3 were excavated by whole-genome sequencing. Thus, a degradation pathway of DBP by the strain YJB3 was proposed that MBP was formed, followed by PA, and then the intermediates were further utilized till complete degradation. To our knowledge, this is the first study to show the biodegradation of PAEs using endophyte. The results in the present study suggest that the strain YJB3 is greatly promising to act as a competent inoculum in removal of PAEs in both soils and crops.
Collapse
Affiliation(s)
- Nai-Xian Feng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, PR China
| | - Jiao Yu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, PR China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, PR China.
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, PR China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, PR China
| | - Bing-Xiao Wu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, PR China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, PR China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, PR China
| | - Dong-Mei Zhou
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, PR China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Ming-Hung Wong
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, PR China; Consortium on Health, Environment, Education and Research (CHEER), Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong, PR China
| |
Collapse
|
17
|
In silico characterization of a novel dehalogenase (DehHX) from the halophile Pseudomonas halophila HX isolated from Tuz Gölü Lake, Turkey: insights into a hypersaline-adapted dehalogenase. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1266-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
|
18
|
Anabestani A, Izadpanah K, Abbà S, Galetto L, Ghorbani A, Palmano S, Siampour M, Veratti F, Marzachì C. Identification of putative effector genes and their transcripts in three strains related to 'Candidatus Phytoplasma aurantifolia'. Microbiol Res 2017; 199:57-66. [PMID: 28454710 DOI: 10.1016/j.micres.2017.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/22/2017] [Accepted: 03/04/2017] [Indexed: 11/25/2022]
Abstract
Molecular mechanisms underlying phytoplasma interactions with host plants are largely unknown. In this study attempts were made to identify effectors of three phytoplasma strains related to 'Ca. P. aurantifolia', crotalaria phyllody (CrP), faba bean phyllody (FBP), and witches' broom disease of lime (WBDL), using information from draft genome of peanut witches' broom phytoplasma. Seven putative effectors were identified in WBDL genome (SAP11, SAP21, Eff64, Eff115, Eff197, Eff211 and EffSAP67), five (SAP11, SAP21, Eff64, Eff99 and Eff197) in CrP and two (SAP11, Eff64) in FBP. No homologs to Eff64, Eff197 and Eff211 in phytoplasmas of other phylogenetic groups were found. SAP11 and Eff64 homologs of 'Ca. P. aurantifolia' strains shared at least 95.9% identity and were detected in the three phytoplasmas, supporting their role within the group. Five of the putative effectors (SAP11, SAP21, Eff64, Eff115, and Eff99) were transcribed from total RNA extracts of periwinkle plants infected with these phytoplasmas. Transcription profiles of selected putative effectors of CrP, FBP and WBDL indicated that SAP11 transcripts were the most abundant in the three phytoplasmas. SAP21 transcript levels were comparable to those of SAP11 for CrP and not measurable for the other phytoplasmas. Eff64 had the lowest transcription level irrespective of sampling date and phytoplasma isolate. Eff115 transcript levels were the highest in WBDL infected plants. This work reports the first sequence information for 14 putative effectors in three strains related to 'Ca. P. aurantifolia', and offers novel insight into the transcription profile of five of them during infection of periwinkle.
Collapse
Affiliation(s)
- Ameneh Anabestani
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, I-10135, Torino, Italy; Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Keramat Izadpanah
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Simona Abbà
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, I-10135, Torino, Italy
| | - Luciana Galetto
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, I-10135, Torino, Italy
| | - Abozar Ghorbani
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Sabrina Palmano
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, I-10135, Torino, Italy
| | - Majid Siampour
- Department of Plant Protection, Shahrekord University, Shahrekord, Iran
| | - Flavio Veratti
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, I-10135, Torino, Italy
| | - Cristina Marzachì
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, I-10135, Torino, Italy.
| |
Collapse
|
19
|
Kwak Y, Li QX, Shin JH. Draft genome sequence of Mycobacterium rufum JS14(T), a polycyclic-aromatic-hydrocarbon-degrading bacterium from petroleum-contaminated soil in Hawaii. Stand Genomic Sci 2016; 11:47. [PMID: 27486485 PMCID: PMC4969647 DOI: 10.1186/s40793-016-0167-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/13/2016] [Indexed: 11/10/2022] Open
Abstract
Mycobacterium rufum JS14T (=ATCC BAA-1377T, CIP 109273T, JCM 16372T, DSM 45406T), a type strain of the species Mycobacterium rufum sp. . belonging to the family Mycobacteriaceae, was isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soil in Hilo (HI, USA) because it harbors the capability of degrading PAH. Here, we describe the first genome sequence of strain JS14T, with brief phenotypic characteristics. The genome is composed of 6,176,413 bp with 69.25 % G + C content and contains 5810 protein-coding genes with 54 RNA genes. The genome information on M. rufum JS14T will provide a better understanding of the complexity of bacterial catabolic pathways for degradation of specific chemicals.
Collapse
Affiliation(s)
- Yunyoung Kwak
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 702-701 Republic of Korea
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822 USA
| | - Jae-Ho Shin
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 702-701 Republic of Korea
| |
Collapse
|
20
|
Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments. World J Microbiol Biotechnol 2016; 32:135. [PMID: 27344438 DOI: 10.1007/s11274-016-2081-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.
Collapse
|
21
|
Characterization of PAS domains in Frankia and selected Actinobacteria and their possible interaction with other co-domains for environmental adaptation. Symbiosis 2016. [DOI: 10.1007/s13199-016-0413-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
22
|
Guo M, Gong Z, Allinson G, Tai P, Miao R, Li X, Jia C, Zhuang J. Variations in the bioavailability of polycyclic aromatic hydrocarbons in industrial and agricultural soils after bioremediation. CHEMOSPHERE 2016; 144:1513-20. [PMID: 26498099 DOI: 10.1016/j.chemosphere.2015.10.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 10/01/2015] [Accepted: 10/07/2015] [Indexed: 05/15/2023]
Abstract
The aim of this study was to demonstrate the variations in bioavailability remaining in industrial and agricultural soils contaminated by polycyclic aromatic hydrocarbons (PAHs) after bioremediation. After inoculation of Mycobacterium sp. and Mucor sp., PAH biodegradation was tested on a manufactured gas plant (MGP) soil and an agricultural soil. PAH bioavailability was assessed before and after biodegradation using solid-phase extraction (Tenax-TA extraction) and solid-phase micro-extraction (SPME) to represent bioaccessibility and chemical activity of PAHs, respectively. Only 3- and 4-ring PAHs were noticeably biodegradable in the MGP soil. PAH biodegradation in the agricultural soil was different from that in the MGP soil. The rapidly desorbing fractions (F(rap)) extracted by Tenax-TA and the freely dissolved concentrations of 3- and 4-ring PAHs determined by SPME from the MGP soil decreased after 30 days biodegradation; those values of the 5- and 6-ring PAHs changed to a lesser degree. For the agricultural soil, the F(rap) values of the 3- and 4-ring PAHs also decreased after the biodegradation experiment. The Tenax-TA extraction and the SPME have the potential to assess variations in the bioavailability of PAHs and the degree of biodegradation in contaminated MGP soils. In addition, Tenax-TA extraction is more sensitive than SPME when used in the agricultural soil.
Collapse
Affiliation(s)
- Meixia Guo
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Zongqiang Gong
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China.
| | - Graeme Allinson
- School of Applied Sciences, RMIT University, Melbourne, Victoria, 3001, Australia; Centre for Environmental Sustainability and Remediation (EnSuRE), RMIT University, Melbourne, Victoria, 3001, Australia
| | - Peidong Tai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China
| | - Renhui Miao
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xiaojun Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China
| | - Chunyun Jia
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China
| | - Jie Zhuang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China
| |
Collapse
|
23
|
Longang A, Buck C, Kirkwood KM. Halotolerance and effect of salt on hydrophobicity in hydrocarbon-degrading bacteria. ENVIRONMENTAL TECHNOLOGY 2015; 37:1133-1140. [PMID: 26915518 DOI: 10.1080/09593330.2015.1102333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Hydrocarbon-contaminated environments often also experience co-contamination with elevated levels of salt. This paper investigates the occurrence of halotolerance among several hydrocarbon-degrading bacteria, as an initial assessment of the importance of salt contamination to bioremediation strategies. Halotolerance was common, but not ubiquitous, among the 12 hydrocarbon-degrading bacteria tested, with many strains growing at up to 75 or 100 g NaCl L(-1) in rich medium. Greater sensitivity to elevated salt concentrations was observed among aromatics degraders compared to saturates degraders, and in defined medium compared to rich medium. Observed effects of high salt concentrations included increased lag times and decreased maximum growth. Many strains exhibited flocculation at elevated salt concentrations, but this did not correlate to any patterns in cell surface hydrophobicity, measured using the Bacterial Adhesion to Hydrocarbon assay. The occurrence of halotolerance in hydrocarbon-degrading bacteria suggests the potential for native microorganisms to contribute to the bioremediation of oil and salt co-contaminated sites, and indicates the need for a better understanding of the relationship between halotolerance and hydrocarbon biodegradation capabilities.
Collapse
Affiliation(s)
- Adégilns Longang
- a Department of Chemical and Biological Engineering , University of Ottawa, Ottawa , ON , Canada
| | - Chris Buck
- a Department of Chemical and Biological Engineering , University of Ottawa, Ottawa , ON , Canada
| | - Kathlyn M Kirkwood
- a Department of Chemical and Biological Engineering , University of Ottawa, Ottawa , ON , Canada
| |
Collapse
|
24
|
Li F, Zhu L, Wang L, Zhan Y. Gene expression of an arthrobacter in surfactant-enhanced biodegradation of a hydrophobic organic compound. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:3698-3704. [PMID: 25680000 DOI: 10.1021/es504673j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Surfactants can affect the biodegradation process and the fate of hydrophobic organic compounds (HOCs) in the environment. Previous studies have shown that surfactants can enhance the biodegradation of HOCs by increasing cell surface hydrophobicity (CSH) and membrane fluidity. In this study, we took this work one step further by investigating the expression levels of three genes of Arthrobacter sp. SA02 in the biodegradation of phenanthrene as a typical HOC at different concentrations of sodium dodecyl benzenesulfonate (SDBS), which is a widely used surfactant. The Δ9 fatty acid desaturase gene codes for Δ9 fatty acid desaturase, which can convert saturated fatty acid to its unsaturated form. The ring-hydroxylating dioxygenase (RHDase) and the 1-hydroxyl-2-naphthoate dioxygenase (1H2Nase) genes code for the RHDase and 1H2Nase enzymes, respectively, which play a key role in decomposing doubly hydroxylated aromatic compounds. The results show that these three genes were upregulated in the presence of SDBS. On the basis of the genetic and physiological changes, we proposed a pathway that links the gene expression with the physiological phenomena, including CSH, membrane fluidity, and intracellular degradation. This study advances our understanding of the surfactant-enhanced biodegradation of HOCs at the gene level, and the proposed pathway should be further validated in the future.
Collapse
Affiliation(s)
- Feng Li
- †Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- ‡Zhejiang Provincial Key Laboratory of Organic Pollution Process Control, Hangzhou 310058, China
- §Department of Environmental Science and Engineering, Xiangtan University, Xiangtan 411105, China
| | - Lizhong Zhu
- †Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- ‡Zhejiang Provincial Key Laboratory of Organic Pollution Process Control, Hangzhou 310058, China
| | - Lingwen Wang
- †Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- ‡Zhejiang Provincial Key Laboratory of Organic Pollution Process Control, Hangzhou 310058, China
| | - Yu Zhan
- †Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- ‡Zhejiang Provincial Key Laboratory of Organic Pollution Process Control, Hangzhou 310058, China
| |
Collapse
|
25
|
Rienksma RA, Suarez-Diez M, Mollenkopf HJ, Dolganov GM, Dorhoi A, Schoolnik GK, Martins Dos Santos VA, Kaufmann SH, Schaap PJ, Gengenbacher M. Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing. BMC Genomics 2015; 16:34. [PMID: 25649146 PMCID: PMC4334782 DOI: 10.1186/s12864-014-1197-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/22/2014] [Indexed: 02/06/2023] Open
Abstract
Background The human pathogen Mycobacterium tuberculosis has the capacity to escape eradication by professional phagocytes. During infection, M. tuberculosis resists the harsh environment of phagosomes and actively manipulates macrophages and dendritic cells to ensure prolonged intracellular survival. In contrast to other intracellular pathogens, it has remained difficult to capture the transcriptome of mycobacteria during infection due to an unfavorable host-to-pathogen ratio. Results We infected the human macrophage-like cell line THP-1 with the attenuated M. tuberculosis surrogate M. bovis Bacillus Calmette–Guérin (M. bovis BCG). Mycobacterial RNA was up to 1000-fold underrepresented in total RNA preparations of infected host cells. We employed microbial enrichment combined with specific ribosomal RNA depletion to simultaneously analyze the transcriptional responses of host and pathogen during infection by dual RNA sequencing. Our results confirm that mycobacterial pathways for cholesterol degradation and iron acquisition are upregulated during infection. In addition, genes involved in the methylcitrate cycle, aspartate metabolism and recycling of mycolic acids were induced. In response to M. bovis BCG infection, host cells upregulated de novo cholesterol biosynthesis presumably to compensate for the loss of this metabolite by bacterial catabolism. Conclusions Dual RNA sequencing allows simultaneous capture of the global transcriptome of host and pathogen, during infection. However, mycobacteria remained problematic due to their relatively low number per host cell resulting in an unfavorable bacterium-to-host RNA ratio. Here, we use a strategy that combines enrichment for bacterial transcripts and dual RNA sequencing to provide the most comprehensive transcriptome of intracellular mycobacteria to date. The knowledge acquired into the pathogen and host pathways regulated during infection may contribute to a solid basis for the deployment of novel intervention strategies to tackle infection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-014-1197-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rienk A Rienksma
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, 6703, HB, Wageningen, the Netherlands.
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, 6703, HB, Wageningen, the Netherlands.
| | - Hans-Joachim Mollenkopf
- Core Facility Microarray/Genomics, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.
| | - Gregory M Dolganov
- Department of Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5124, USA.
| | - Anca Dorhoi
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.
| | - Gary K Schoolnik
- Department of Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5124, USA.
| | - Vitor Ap Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, 6703, HB, Wageningen, the Netherlands. .,LifeGlimmer GmbH, Markelstrasse 38, 12163, Berlin, Germany.
| | - Stefan He Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, 6703, HB, Wageningen, the Netherlands.
| | - Martin Gengenbacher
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany. .,Present address: Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, 117545, Singapore.
| |
Collapse
|
26
|
Decreasing global transcript levels over time suggest that phytoplasma cells enter stationary phase during plant and insect colonization. Appl Environ Microbiol 2015; 81:2591-602. [PMID: 25636844 DOI: 10.1128/aem.03096-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To highlight different transcriptional behaviors of the phytoplasma in the plant and animal host, expression of 14 genes of "Candidatus Phytoplasma asteris," chrysanthemum yellows strain, was investigated at different times following the infection of a plant host (Arabidopsis thaliana) and two insect vector species (Macrosteles quadripunctulatus and Euscelidius variegatus). Target genes were selected among those encoding antigenic membrane proteins, membrane transporters, secreted proteins, and general enzymes. Transcripts were detected for all analyzed genes in the three hosts; in particular, those encoding the antigenic membrane protein Amp, elements of the mechanosensitive channel, and two of the four secreted proteins (SAP54 and TENGU) were highly accumulated, suggesting that they play important roles in phytoplasma physiology during the infection cycle. Most transcripts were present at higher abundance in the plant host than in the insect hosts. Generally, transcript levels of the selected genes decreased significantly during infection of A. thaliana and M. quadripunctulatus but were more constant in E. variegatus. Such decreases may be explained by the fact that only a fraction of the phytoplasma population was transcribing, while the remaining part was aging to a stationary phase. This strategy might improve long-term survival, thereby increasing the likelihood that the pathogen may be acquired by a vector and/or inoculated to a healthy plant.
Collapse
|
27
|
Yang Y, Wang J, Liao J, Xie S, Huang Y. Distribution of naphthalene dioxygenase genes in crude oil-contaminated soils. MICROBIAL ECOLOGY 2014; 68:785-793. [PMID: 25008984 DOI: 10.1007/s00248-014-0457-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 06/27/2014] [Indexed: 06/03/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are one of the major pollutants in soils in oil exploring areas. Biodegradation is the major process for natural elimination of PAHs from contaminated soils. Functional genes can be used as biomarkers to assess the biodegradation potential of indigenous microbial populations. However, little is known about the distribution of PAH-degrading genes in the environment. The links between environmental parameters and the distribution of PAH metabolic genes remain essentially unclear. The present study investigated the abundance and diversity of naphthalene dioxygenase genes in the oil-contaminated soils in the Shengli Oil Field (China). Spatial variations in the density and diversity of naphthalene dioxygenase genes occurred in this area. Four different sequence genotypes were observed in the contaminated soils, with the predominance of novel PAH-degrading genes. Pearson's correlation analysis illustrated that gene abundance had positive correlations with the levels of total organic carbon and aromatic hydrocarbons, while gene diversity showed a negative correlation with the level of polar aromatics. This work could provide some new insights toward the distribution of PAH metabolic genes and PAH biodegradation potential in oil-contaminated ecosystems.
Collapse
Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | | | | | | | | |
Collapse
|
28
|
Alarico S, Costa M, Sousa MS, Maranha A, Lourenço EC, Faria TQ, Ventura MR, Empadinhas N. Mycobacterium hassiacum recovers from nitrogen starvation with up-regulation of a novel glucosylglycerate hydrolase and depletion of the accumulated glucosylglycerate. Sci Rep 2014; 4:6766. [PMID: 25341489 PMCID: PMC5381378 DOI: 10.1038/srep06766] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/17/2014] [Indexed: 01/24/2023] Open
Abstract
Some microorganisms accumulate glucosylglycerate (GG) during growth under nitrogen deprivation. However, the molecular mechanisms underlying the role of GG and the regulation of its levels in the nitrogen stress response are elusive. Since GG is required for biosynthesis of mycobacterial methylglucose lipopolysaccharides (MGLP) we examined the molecular mechanisms linking replenishment of assimilable nitrogen to nitrogen-starved M. hassiacum with depletion of GG accumulated during nitrogen deficiency. To probe the involvement of a newly identified glycoside hydrolase in GG depletion, we produced the mycobacterial enzyme recombinantly and confirmed the specific hydrolysis of GG (GG hydrolase, GgH) in vitro. We have also observed a pronounced up-regulation of GgH mRNA in response to the nitrogen shock, which positively correlates with GG depletion in vivo and growth stimulation, implicating GgH in the recovery process. Since GgH orthologs seem to be absent from most slowly-growing mycobacteria including M. tuberculosis, the disclosure of the GgH function allows reconfiguration of the MGLP pathway in rapidly-growing species and accommodation of this possible regulatory step. This new link between GG metabolism, MGLP biosynthesis and recovery from nitrogen stress furthers our knowledge on the mycobacterial strategies to endure a frequent stress faced in some environments and during long-term infection.
Collapse
Affiliation(s)
- Susana Alarico
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Mafalda Costa
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Marta S Sousa
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Ana Maranha
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Eva C Lourenço
- ITQB - Instituto de Tecnologia Química e Biológica, Oeiras, Portugal
| | - Tiago Q Faria
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - M Rita Ventura
- ITQB - Instituto de Tecnologia Química e Biológica, Oeiras, Portugal
| | - Nuno Empadinhas
- 1] CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal [2] III/UC - Institute for Interdisciplinary Research, University of Coimbra, Portugal
| |
Collapse
|
29
|
Vandera E, Samiotaki M, Parapouli M, Panayotou G, Koukkou AI. Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 on phenanthrene, phthalate and glucose. J Proteomics 2014; 113:73-89. [PMID: 25257624 DOI: 10.1016/j.jprot.2014.08.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 07/18/2014] [Accepted: 08/22/2014] [Indexed: 10/24/2022]
Abstract
UNLABELLED In the present study, by applying comparative quantitative proteomics, we investigated the metabolic adaptation of Arthrobacter phenanthrenivorans Sphe3 when using phenanthrene, phthalate, glucose or glucose plus phenanthrene as sole carbon and energy sources. More than a third of the total Sphe3 proteins, with function prediction within the genome, were identified with confidence. Proteomic analysis data and annotated genomic information coincide, allowing us to clarify the phenanthrene catabolic pathway. We confirmed the implication of several proteins in aromatic substrate degradation by identifying those mediating the initial ring-hydroxylation and ring cleavage of phenanthrene to phthalate, phthalate degradation, as well as ortho- and meta-protocatechuate catabolism. Repression of catabolic genes by glucose was observed by both proteomic and transcriptional analyses. The presence of aromatic substrates resulted in changes in the abundance of proteins involved in substrate and amino acid metabolism, stress response, detoxification and membrane and cell wall metabolism. Uptake and transport associated proteins differ in the substrates used, indicating the use of different uptake mechanisms for transport of each compound in the Sphe3 cells. Our results also suggest the activation of a glyoxylate shunt in the presence of aromatic compounds, based on the up-regulation of the key enzymes of this pathway. BIOLOGICAL SIGNIFICANCE A. phenanthrenivorans Sphe3, isolated from a creosote contaminated soil in Greece, can grow on phenanthrene as the sole source of carbon and energy. To explore the phenanthrene catabolic pathway by determining the key proteins involved in this pathway, as well as the global changes in proteins due to the adaptive response of Sphe3 cells grown on different substrates, we applied a gel-free quantitative proteomic analysis using nanoLC-MS/MS. To our knowledge this is the first study of comparative global proteomic changes occurring in the Sphe3 cells under exposure in different nutritional environments. The extended proteomic changes observed in Sphe3 grown on different substrates provide an insight in the complex interactions occurring in the presence of aromatic compounds and could serve as a basis for further investigations intended to elucidate the general regulatory mechanism by which Sphe3 adapts to such xenobiotic environments. This may light the way for more efficient engineering of bacteria towards more effective bioremediation applications.
Collapse
Affiliation(s)
- Elpiniki Vandera
- Sector of Organic Chemistry and Biochemistry, University of Ioannina, Greece
| | - Martina Samiotaki
- Biomedical Sciences Research Center "Alexander Fleming", Vari, Athens, Greece.
| | - Maria Parapouli
- Sector of Organic Chemistry and Biochemistry, University of Ioannina, Greece
| | - George Panayotou
- Biomedical Sciences Research Center "Alexander Fleming", Vari, Athens, Greece
| | - Anna Irini Koukkou
- Sector of Organic Chemistry and Biochemistry, University of Ioannina, Greece.
| |
Collapse
|
30
|
Badejo AC, Chung WH, Kim NS, Chai JC, Lee YS, Jung KH, Kim HJ, Chai YG. Energy metabolism in Mycobacterium gilvum PYR-GCK: insights from transcript expression analyses following two states of induction. PLoS One 2014; 9:e99464. [PMID: 24927157 PMCID: PMC4057218 DOI: 10.1371/journal.pone.0099464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/14/2014] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium gilvum PYR-GCK, a pyrene degrading bacterium, has been the subject of functional studies aimed at elucidating mechanisms related to its outstanding pollutant bioremediation/biodegradation activities. Several studies have investigated energy production and conservation in Mycobacterium, however, they all focused on the pathogenic strains using their various hosts as induction sources. To gain greater insight into Mycobacterium energy metabolism, mRNA expression studies focused on respiratory functions were performed under two different conditions using the toxic pollutant pyrene as a test substrate and glucose as a control substrate. This was done using two transcriptomic techniques: global transcriptomic RNA-sequencing and quantitative Real-Time PCR. Growth in the presence of pyrene resulted in upregulated expression of genes associated with limited oxygen or anaerobiosis in M. gilvum PYR-GCK. Upregulated genes included succinate dehydrogenases, nitrite reductase and various electron donors including formate dehydrogenases, fumarate reductases and NADH dehydrogenases. Oxidative phosphorylation genes (with respiratory chain complexes I, III -V) were expressed at low levels compared to the genes coding for the second molecular complex in the bacterial respiratory chain (fumarate reductase); which is highly functional during microaerophilic or anaerobic bacterial growth. This study reveals a molecular adaptation to a hypoxic mode of respiration during aerobic pyrene degradation. This is likely the result of a cellular oxygen shortage resulting from exhaustion of the oxygenase enzymes required for these degradation activities in M. gilvum PYR-GCK.
Collapse
Affiliation(s)
| | - Won Hyong Chung
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Nam Shin Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Jin Choul Chai
- Department of Molecular and Life Science, Hanyang University, Ansan, Korea
| | - Young Seek Lee
- Department of Molecular and Life Science, Hanyang University, Ansan, Korea
| | - Kyoung Hwa Jung
- Department of Molecular and Life Science, Hanyang University, Ansan, Korea
| | - Hyo Joon Kim
- Department of Molecular and Life Science, Hanyang University, Ansan, Korea
- * E-mail: (HJK); (YGC)
| | - Young Gyu Chai
- Department of Molecular and Life Science, Hanyang University, Ansan, Korea
- Department of Nanobiotechnology, Hanyang University, Seoul, Korea
- * E-mail: (HJK); (YGC)
| |
Collapse
|
31
|
Elango V, Urbano M, Lemelle KR, Pardue JH. Biodegradation of MC252 oil in oil:sand aggregates in a coastal headland beach environment. Front Microbiol 2014; 5:161. [PMID: 24782849 PMCID: PMC3989593 DOI: 10.3389/fmicb.2014.00161] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/25/2014] [Indexed: 12/30/2022] Open
Abstract
Unique oil:sand aggregates, termed surface residue balls (SRBs), were formed on coastal headland beaches along the northern Gulf of Mexico as emulsified MC252 crude oil mixed with sand following the Deepwater Horizon spill event. The objective of this study is to assess the biodegradation potential of crude oil components in these aggregates using multiple lines of evidence on a heavily-impacted coastal headland beach in Louisiana, USA. SRBs were sampled over a 19-month period on the supratidal beach environment with reasonable control over and knowledge of the residence time of the aggregates on the beach surface. Polycyclic aromatic hydrocarbons (PAHs) and alkane concentration ratios were measured including PAH/C30-hopane, C2/C3 phenanthrenes, C2/C3 dibenzothiophenes and alkane/C30-hopane and demonstrated that biodegradation was occurring in SRBs in the supratidal. These biodegradation reactions occurred over time frames relevant to the coastal processes moving SRBs off the beach. In contrast, submerged oil mat samples from the intertidal did not demonstrate chemical changes consistent with biodegradation. Review and analysis of additional biogeochemical parameters suggested the existence of a moisture and nutrient-limited biodegradation regime on the supratidal beach environment. At this location, SRBs possess moisture contents <2% and molar C:N ratios from 131–323, well outside of optimal values for biodegradation in the literature. Despite these limitations, biodegradation of PAHs and alkanes proceeded at relevant rates (2–8 year−1) due in part to the presence of degrading populations, i.e., Mycobacterium sp., adapted to these conditions. For submerged oil mat samples in the intertidal, an oxygen and salinity-impacted regime is proposed that severely limits biodegradation of alkanes and PAHs in this environment. These results support the hypothesis that SRBs deposited at different locations on the beach have different biogeochemical characteristics (e.g., moisture, salinity, terminal electron acceptors, nutrient, and oil composition) due, in part, to their location on the landscape.
Collapse
Affiliation(s)
- Vijaikrishnah Elango
- Department of Civil and Environmental Engineering, Louisiana State University Baton Rouge, LA, USA
| | - Marilany Urbano
- Department of Civil and Environmental Engineering, Louisiana State University Baton Rouge, LA, USA
| | - Kendall R Lemelle
- Department of Civil and Environmental Engineering, Louisiana State University Baton Rouge, LA, USA
| | - John H Pardue
- Department of Civil and Environmental Engineering, Louisiana State University Baton Rouge, LA, USA
| |
Collapse
|
32
|
Suppressor analysis reveals a role for SecY in the SecA2-dependent protein export pathway of Mycobacteria. J Bacteriol 2013; 195:4456-65. [PMID: 23913320 DOI: 10.1128/jb.00630-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
All bacteria use the conserved Sec pathway to transport proteins across the cytoplasmic membrane, with the SecA ATPase playing a central role in the process. Mycobacteria are part of a small group of bacteria that have two SecA proteins: the canonical SecA (SecA1) and a second, specialized SecA (SecA2). The SecA2-dependent pathway exports a small subset of proteins and is required for Mycobacterium tuberculosis virulence. The mechanism by which SecA2 drives export of proteins across the cytoplasmic membrane remains poorly understood. Here we performed suppressor analysis on a dominant negative secA2 mutant (secA2 K129R) of the model mycobacterium Mycobacterium smegmatis to better understand the pathway used by SecA2 to export proteins. Two extragenic suppressor mutations were identified as mapping to the promoter region of secY, which encodes the central component of the canonical Sec export channel. These suppressor mutations increased secY expression, and this effect was sufficient to alleviate the secA2 K129R phenotype. We also discovered that the level of SecY protein was greatly diminished in the secA2 K129R mutant, but at least partially restored in the suppressors. Furthermore, the level of SecY in a suppressor strongly correlated with the degree of suppression. Our findings reveal a detrimental effect of SecA2 K129R on SecY, arguing for an integrated system in which SecA2 works with SecY and the canonical Sec translocase to export proteins.
Collapse
|