1
|
Zahra I, DeVine L, Cole R, Malik HA, Wu J, Wen J, Hedfi A, Liaqat A, Ijaz R, Ramzan U, Shakoori AR, Shakoori FR, Betenbaugh MJ. Insights into the differential proteome landscape of a newly isolated Paramecium multimicronucleatum in response to cadmium stress. J Proteomics 2024; 300:105178. [PMID: 38636824 DOI: 10.1016/j.jprot.2024.105178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/01/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]
Abstract
Employing microbial systems for the bioremediation of contaminated waters represent a potential option, however, limited understanding of the underlying mechanisms hampers the implication of microbial-mediated bioremediation. The omics tools offer a promising approach to explore the molecular basis of the bioremediation process. Here, a mass spectrometry-based quantitative proteome profiling approach was conducted to explore the differential protein levels in cadmium-treated Paramecium multimicronucleatum. The Proteome Discoverer software was used to identify and quantify differentially abundant proteins. The proteome profiling generated 7,416 peptide spectral matches, yielding 2824 total peptides, corresponding to 989 proteins. The analysis revealed that 29 proteins exhibited significant (p ≤ 0.05) differential levels, including a higher abundance of 6 proteins and reduced levels of 23 proteins in Cd2+ treated samples. These differentially abundant proteins were associated with stress response, energy metabolism, protein degradation, cell growth, and hormone processing. Briefly, a comprehensive proteome profile in response to cadmium stress of a newly isolated Paramecium has been established that will be useful in future studies identifying critical proteins involved in the bioremediation of metals in ciliates. SIGNIFICANCE: Ciliates are considered a good biological indicator of chemical pollution and relatively sensitive to heavy metal contamination. A prominent ciliate, Paramecium is a promising candidate for the bioremediation of polluted water. The proteins related to metal resistance in Paramecium species are still largely unknown and need further exploration. In order to identify and reveal the proteins related to metal resistance in Paramecia, we have reported differential protein abundance in Paramecium multimicronucleatum in response to cadmium stress. The proteins found in our study play essential roles during stress response, hormone processing, protein degradation, energy metabolism, and cell growth. It seems likely that Paramecia are not a simple sponge for metals but they could also transform them into less toxic derivatives or by detoxification by protein binding. This data will be helpful in future studies to identify critical proteins along with their detailed mechanisms involved in the bioremediation and detoxification of metal ions in Paramecium species.
Collapse
Affiliation(s)
- Itrat Zahra
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Lauren DeVine
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Robert Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Hafiza Aroosa Malik
- Bioenergy Research Center, Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan.
| | - Jinke Wu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Junneng Wen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Amor Hedfi
- Department of Biology, College of Sciences, Taif University, POBox 11099, Taif 21944, Saudi Arabia.
| | - Ayesha Liaqat
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Roohi Ijaz
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Uzma Ramzan
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Abdul Rauf Shakoori
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Farah Rauf Shakoori
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
2
|
Huang M, Liu W, Qin C, Xu Y, Zhou X, Wen Q, Ma W, Huang Y, Chen X. Copper Resistance Mechanism and Copper Response Genes in Corynebacterium crenatum. Microorganisms 2024; 12:951. [PMID: 38792781 PMCID: PMC11124244 DOI: 10.3390/microorganisms12050951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Heavy metal resistance mechanisms and heavy metal response genes are crucial for microbial utilization in heavy metal remediation. Here, Corynebacterium crenatum was proven to possess good tolerance in resistance to copper. Then, the transcriptomic responses to copper stress were investigated, and the vital pathways and genes involved in copper resistance of C. crenatum were determined. Based on transcriptome analysis results, a total of nine significantly upregulated DEGs related to metal ion transport were selected for further study. Among them, GY20_RS0100790 and GY20_RS0110535 belong to transcription factors, and GY20_RS0110270, GY20_RS0100790, and GY20_RS0110545 belong to copper-binding peptides. The two transcription factors were studied for the function of regulatory gene expression. The three copper-binding peptides were displayed on the C. crenatum surface for a copper adsorption test. Furthermore, the nine related metal ion transport genes were deleted to investigate the effect on growth in copper stress. This investigation provided the basis for utilizing C. crenatum in copper bioremediation.
Collapse
Affiliation(s)
- Mingzhu Huang
- National R&D Center of Freshwater Fish Processing, Jiangxi Normal University, Nanchang 330022, China; (M.H.); (W.L.); (Y.H.)
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China; (C.Q.); (Y.X.); (X.Z.); (Q.W.); (W.M.)
| | - Wenxin Liu
- National R&D Center of Freshwater Fish Processing, Jiangxi Normal University, Nanchang 330022, China; (M.H.); (W.L.); (Y.H.)
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China; (C.Q.); (Y.X.); (X.Z.); (Q.W.); (W.M.)
| | - Chunyan Qin
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China; (C.Q.); (Y.X.); (X.Z.); (Q.W.); (W.M.)
| | - Yang Xu
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China; (C.Q.); (Y.X.); (X.Z.); (Q.W.); (W.M.)
| | - Xu Zhou
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China; (C.Q.); (Y.X.); (X.Z.); (Q.W.); (W.M.)
| | - Qunwei Wen
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China; (C.Q.); (Y.X.); (X.Z.); (Q.W.); (W.M.)
| | - Wenbin Ma
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China; (C.Q.); (Y.X.); (X.Z.); (Q.W.); (W.M.)
| | - Yanzi Huang
- National R&D Center of Freshwater Fish Processing, Jiangxi Normal University, Nanchang 330022, China; (M.H.); (W.L.); (Y.H.)
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China; (C.Q.); (Y.X.); (X.Z.); (Q.W.); (W.M.)
| | - Xuelan Chen
- National R&D Center of Freshwater Fish Processing, Jiangxi Normal University, Nanchang 330022, China; (M.H.); (W.L.); (Y.H.)
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China; (C.Q.); (Y.X.); (X.Z.); (Q.W.); (W.M.)
| |
Collapse
|
3
|
Kumari S, Ali A, Kumar M. Nucleotide-induced ClpC oligomerization and its non-preferential association with ClpP isoforms of pathogenic Leptospira. Int J Biol Macromol 2024; 266:131371. [PMID: 38580013 DOI: 10.1016/j.ijbiomac.2024.131371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/15/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Bacterial caseinolytic protease-chaperone complexes participate in the elimination of misfolded and aggregated protein substrates. The spirochete Leptospira interrogans possess a set of Clp-chaperones (ClpX, ClpA, and ClpC), which may associate functionally with two different isoforms of LinClpP (ClpP1 and ClpP2). The L. interrogans ClpC (LinClpC) belongs to class-I chaperone with two active ATPase domains separated by a middle domain. Using the size exclusion chromatography, ANS dye binding, and dynamic light scattering analysis, the LinClpC is suggested to undergo nucleotide-induced oligomerization. LinClpC associates with either pure LinClpP1 or LinClpP2 isoforms non-preferentially and with equal affinity. Regardless, pure LinClpP isoforms cannot constitute an active protease complex with LinClpC. Interestingly, the heterocomplex LinClpP1P2 in association with LinClpC forms a functional proteolytic machinery and degrade β-casein or FITC-casein in an energy-independent manner. Adding either ATP or ATPγS further fosters the LinClpCP1P2 complex protease activity by nurturing the functional oligomerization of LinClpC. The antibiotic, acyldepsipeptides (ADEP1) display a higher activatory role on LinClpP1P2 protease activity than LinClpC. Altogether, this work illustrates an in-depth study of hetero-tetradecamer LinClpP1P2 association with its cognate ATPase and unveils a new insight into the structural reorganization of LinClpP1P2 in the presence of chaperone, LinClpC to gain protease activity.
Collapse
Affiliation(s)
- Surbhi Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Arfan Ali
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Khanapara, Assam 781022, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| |
Collapse
|
4
|
Huang M, Zhu L, Feng L, Zhan L, Zhao Y, Chen X. Reforming Nitrate Metabolism for Enhancing L-Arginine Production in Corynebacterium crenatum Under Oxygen Limitation. Front Microbiol 2022; 13:834311. [PMID: 35356524 PMCID: PMC8959459 DOI: 10.3389/fmicb.2022.834311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
Various amino acids are widely manufactured using engineered bacteria. It is crucial to keep the dissolved oxygen at a certain level during fermentation, but accompanied by many disadvantages, such as high energy consumption, reactive oxygen species, and risk of phage infections. Thus, anaerobic production of amino acids is worth attempting. Nitrate respiration systems use nitrate as an electron acceptor under anoxic conditions, which is different from the metabolism of fermentation and can produce energy efficiently. Herein, we engineered Corynebacterium crenatum to enhance L-arginine production under anaerobic conditions through strengthening nitrate respiration and reforming nitrogen flux. The construction of mutant strain produced up to 3.84 g/L L-arginine under oxygen limitation with nitrate, and this value was 131.33% higher than that produced by the control strain under limited concentrations of oxygen without nitrate. Results could provide fundamental information for improving L-arginine production by metabolic engineering of C. crenatum under oxygen limitation.
Collapse
Affiliation(s)
- Mingzhu Huang
- Department of Life Science, Jiangxi Normal University, Nanchang, China.,National R&D Center for Freshwater Fish Processing, Nanchang, China
| | - Lingfeng Zhu
- Department of Life Science, Jiangxi Normal University, Nanchang, China
| | - Lin Feng
- Department of Life Science, Jiangxi Normal University, Nanchang, China
| | - Li Zhan
- Department of Life Science, Jiangxi Normal University, Nanchang, China
| | - Yue Zhao
- Department of Life Science, Jiangxi Normal University, Nanchang, China
| | - Xuelan Chen
- Department of Life Science, Jiangxi Normal University, Nanchang, China.,National R&D Center for Freshwater Fish Processing, Nanchang, China.,Key Laboratory of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal University, Nanchang, China
| |
Collapse
|