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Mittal P, Sinha AK, Pandiyan A, Kumari L, Ray MK, Pavankumar TL. A type II toxin-antitoxin system is responsible for the cell death at low temperature in Pseudomonas syringae Lz4W lacking RNase R. J Biol Chem 2024; 300:107600. [PMID: 39059490 DOI: 10.1016/j.jbc.2024.107600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/17/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
RNase R (encoded by the rnr gene) is a highly processive 3' → 5' exoribonuclease essential for the growth of the psychrotrophic bacterium Pseudomonas syringae Lz4W at low temperature. The cell death of a rnr deletion mutant at low temperature has been previously attributed to processing defects in 16S rRNA, defective ribosomal assembly, and inefficient protein synthesis. We recently showed that RNase R is required to protect P. syringae Lz4W from DNA damage and oxidative stress, independent of its exoribonuclease activity. Here, we show that the processing defect in 16S rRNA does not cause cell death of the rnr mutant of P. syringae at low temperature. Our results demonstrate that the rnr mutant of P. syringae Lz4W, complemented with a RNase R deficient in exoribonuclease function (RNase RD284A), is defective in 16S rRNA processing but can grow at 4 °C. This suggested that the processing defect in ribosomal RNAs is not a cause of the cold sensitivity of the rnr mutant. We further show that the rnr mutant accumulates copies of the indigenous plasmid pLz4W that bears a type II toxin-antitoxin (TA) system (P. syringae antitoxin-P. syringae toxin). This phenotype was rescued by overexpressing antitoxin psA in the rnr mutant, suggesting that activation of the type II TA system leads to cold sensitivity of the rnr mutant of P. syringae Lz4W. Here, we report a previously unknown functional relationship between the cold sensitivity of the rnr mutant and a type II TA system in P. syringae Lz4W.
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Affiliation(s)
- Pragya Mittal
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India; Celtic Renewables Ltd, Edinburgh Napier University, Edinburgh, UK.
| | - Anurag K Sinha
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India; National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Apuratha Pandiyan
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Leela Kumari
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Malay K Ray
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Theetha L Pavankumar
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India; Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA; Department of Molecular and Cellular Biology, University of California, Davis, California, USA.
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Rahman MA, Heme UH, Parvez MAK. In silico functional annotation of hypothetical proteins from the Bacillus paralicheniformis strain Bac84 reveals proteins with biotechnological potentials and adaptational functions to extreme environments. PLoS One 2022; 17:e0276085. [PMID: 36228026 PMCID: PMC9560612 DOI: 10.1371/journal.pone.0276085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/28/2022] [Indexed: 11/26/2022] Open
Abstract
Members of the Bacillus genus are industrial cell factories due to their capacity to secrete significant quantities of biomolecules with industrial applications. The Bacillus paralicheniformis strain Bac84 was isolated from the Red Sea and it shares a close evolutionary relationship with Bacillus licheniformis. However, a significant number of proteins in its genome are annotated as functionally uncharacterized hypothetical proteins. Investigating these proteins' functions may help us better understand how bacteria survive extreme environmental conditions and to find novel targets for biotechnological applications. Therefore, the purpose of our research was to functionally annotate the hypothetical proteins from the genome of B. paralicheniformis strain Bac84. We employed a structured in-silico approach incorporating numerous bioinformatics tools and databases for functional annotation, physicochemical characterization, subcellular localization, protein-protein interactions, and three-dimensional structure determination. Sequences of 414 hypothetical proteins were evaluated and we were able to successfully attribute a function to 37 hypothetical proteins. Moreover, we performed receiver operating characteristic analysis to assess the performance of various tools used in this present study. We identified 12 proteins having significant adaptational roles to unfavorable environments such as sporulation, formation of biofilm, motility, regulation of transcription, etc. Additionally, 8 proteins were predicted with biotechnological potentials such as coenzyme A biosynthesis, phenylalanine biosynthesis, rare-sugars biosynthesis, antibiotic biosynthesis, bioremediation, and others. Evaluation of the performance of the tools showed an accuracy of 98% which represented the rationality of the tools used. This work shows that this annotation strategy will make the functional characterization of unknown proteins easier and can find the target for further investigation. The knowledge of these hypothetical proteins' potential functions aids B. paralicheniformis strain Bac84 in effectively creating a new biotechnological target. In addition, the results may also facilitate a better understanding of the survival mechanisms in harsh environmental conditions.
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Affiliation(s)
- Md. Atikur Rahman
- Institute of Microbiology, Friedrich Schiller University Jena, Thuringia, Germany
| | - Uzma Habiba Heme
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Thuringia, Germany
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Ijaq J, Chandra D, Ray MK, Jagannadham MV. Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation. Front Genet 2022; 13:825269. [PMID: 35360867 PMCID: PMC8963723 DOI: 10.3389/fgene.2022.825269] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/07/2022] [Indexed: 11/28/2022] Open
Abstract
Exploring the molecular mechanisms behind bacterial adaptation to extreme temperatures has potential biotechnological applications. In the present study, Pseudomonas sp. Lz4W, a Gram-negative psychrophilic bacterium adapted to survive in Antarctica, was selected to decipher the molecular mechanism underlying the cold adaptation. Proteome analysis of the isolates grown at 4°C was performed to identify the proteins and pathways that are responsible for the adaptation. However, many proteins from the expressed proteome were found to be hypothetical proteins (HPs), whose function is unknown. Investigating the functional roles of these proteins may provide additional information in the biological understanding of the bacterial cold adaptation. Thus, our study aimed to assign functions to these HPs and understand their role at the molecular level. We used a structured insilico workflow combining different bioinformatics tools and databases for functional annotation. Pseudomonas sp. Lz4W genome (CP017432, version 1) contains 4493 genes and 4412 coding sequences (CDS), of which 743 CDS were annotated as HPs. Of these, from the proteome analysis, 61 HPs were found to be expressed consistently at the protein level. The amino acid sequences of these 61 HPs were submitted to our workflow and we could successfully assign a function to 18 HPs. Most of these proteins were predicted to be involved in biological mechanisms of cold adaptations such as peptidoglycan metabolism, cell wall organization, ATP hydrolysis, outer membrane fluidity, catalysis, and others. This study provided a better understanding of the functional significance of HPs in cold adaptation of Pseudomonas sp. Lz4W. Our approach emphasizes the importance of addressing the “hypothetical protein problem” for a thorough understanding of mechanisms at the cellular level, as well as, provided the assessment of integrating proteomics methods with various annotation and curation approaches to characterize hypothetical or uncharacterized protein data. The MS proteomics data generated from this study has been deposited to the ProteomeXchange through PRIDE with the dataset identifier–PXD029741.
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Affiliation(s)
- Johny Ijaq
- Metabolomics Facility, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Deepika Chandra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Malay Kumar Ray
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - M. V. Jagannadham
- Metabolomics Facility, School of Life Sciences, University of Hyderabad, Hyderabad, India
- *Correspondence: M. V. Jagannadham,
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Pavankumar TL, Mittal P, Hallsworth JE. Molecular insights into the ecology of a psychrotolerant
Pseudomonas syringae. Environ Microbiol 2020; 23:3665-3681. [DOI: 10.1111/1462-2920.15304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Theetha L. Pavankumar
- Department of Microbiology and Molecular Genetics, Briggs Hall, One Shields Avenue University of California Davis CA USA
| | - Pragya Mittal
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine University of Edinburgh Crewe Road South, Edinburgh, EH42XU, Scotland UK
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological Sciences Queen's University Belfast 19 Chlorine Gardens, Belfast, BT9 5DL Northern Ireland UK
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Di Venere M, Viglio S, Sassera D, Fumagalli M, Bardoni A, Salvini R, Cagnone M, Iadarola P. Do the complementarities of electrokinetic and chromatographic procedures represent the "Swiss knife" in proteomic investigation? An overview of the literature in the past decade. Electrophoresis 2017; 38:1538-1550. [PMID: 28130906 DOI: 10.1002/elps.201600504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/11/2017] [Accepted: 01/11/2017] [Indexed: 12/21/2022]
Abstract
This report reviews the literature of the past decade dealing with the combination of electrokinetic and chromatographic strategies in the proteomic field. Aim of this article is to highlight how the application of complementary techniques may contribute to substantially improve protein identification. Several studies here considered demonstrate that exploring the combination of these approaches can be a strategy to enrich the extent of proteomic information achieved from a sample. The coupling of "top-down" and "bottom-up" proteomics may result in the generation of a hybrid analytical tool, very efficient not only for large-scale profiling of complex proteomes but also for studying specific subproteomes. The range of applications described, while evidencing a continuous boost in the imagination of researchers for developing new combinations of methods for protein separation, also underlines the adaptability of these techniques to a wide variety of samples. This report points out the general usefulness of combining different procedures for proteomic analysis, an approach that allows researchers to go deeper in the proteome of samples under investigation.
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Affiliation(s)
- Monica Di Venere
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Davide Sassera
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Marco Fumagalli
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Anna Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Maddalena Cagnone
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Paolo Iadarola
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
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Ghobakhlou AF, Johnston A, Harris L, Antoun H, Laberge S. Microarray transcriptional profiling of Arctic Mesorhizobium strain N33 at low temperature provides insights into cold adaption strategies. BMC Genomics 2015; 16:383. [PMID: 25975821 PMCID: PMC4432818 DOI: 10.1186/s12864-015-1611-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 05/01/2015] [Indexed: 11/29/2022] Open
Abstract
Background Arctic Mesorhizobium strain N33 was isolated from nodules of the legume Oxytropis arctobia in Canada’s eastern Arctic. This symbiotic bacterium can grow at temperatures ranging from 0 to 30 °C, fix nitrogen at 10 °C, and is one of the best known cold-adapted rhizobia. Despite the economic potential of this bacterium for northern regions, the key molecular mechanisms of its cold adaptation remain poorly understood. Results Using a microarray printed with 5760 Arctic Mesorhizobium genomic clones, we performed a partial transcriptome analysis of strain N33 grown under eight different temperature conditions, including both sustained and transient cold treatments, compared with cells grown at room temperature. Cells treated under constant (4 and 10 °C) low temperatures expressed a prominent number of induced genes distinct from cells treated to short-term cold-exposure (<60 min), but exhibited an intermediate expression profile when exposed to a prolonged cold exposure (240 min). The most prominent up-regulated genes encode proteins involved in metabolite transport, transcription regulation, protein turnover, oxidoreductase activity, cryoprotection (mannitol, polyamines), fatty acid metabolism, and membrane fluidity. The main categories of genes affected in N33 during cold treatment are sugar transport and protein translocation, lipid biosynthesis, and NADH oxidoreductase (quinone) activity. Some genes were significantly down-regulated and classified in secretion, energy production and conversion, amino acid transport, cell motility, cell envelope and outer membrane biogenesis functions. This might suggest growth cessation or reduction, which is an important strategy to adjust cellular function and save energy under cold stress conditions. Conclusion Our analysis revealed a complex series of changes associated with cold exposure adaptation and constant growth at low temperatures. Moreover, it highlighted some of the strategies and different physiological states that Mesorhizobium strain N33 has developed to adapt to the cold environment of the Canadian high Arctic and has revealed candidate genes potentially involved in cold adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1611-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abdollah-Fardin Ghobakhlou
- Graduate Programs in Agri-Food Microbiology, Faculty of Agriculture and Food Sciences, Laval University, Quebec City, Quebec, G1V 0A6, Canada.
| | - Anne Johnston
- Eastern Cereal & Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, K1A 0C6, Canada.
| | - Linda Harris
- Eastern Cereal & Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, K1A 0C6, Canada.
| | - Hani Antoun
- Department of Soils and Agri-Food Engineering, Laval University, Quebec City, Quebec, G1V 0A6, Canada.
| | - Serge Laberge
- Soils and Crops Research Development Center, Agriculture and Agri-Food Canada, Quebec City, Quebec, G1V 2 J3, Canada.
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Li B, Wang L, Ibrahim M, Ge M, Wang Y, Mannan S, Asif M, Sun G. Membrane protein profiling of Acidovorax avenae subsp. avenae under various growth conditions. Arch Microbiol 2015; 197:673-82. [PMID: 25763989 DOI: 10.1007/s00203-015-1100-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 02/01/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
Abstract
Membrane proteins (MPs) of plant pathogenic bacteria have been reported to be able to regulate many essential cellular processes associated with plant disease. The aim of the current study was to examine and compare the expression of MPs of the rice bacterial pathogen Acidovorax avenae subsp. avenae strain RS-1 under Luria-Bertani (LB) medium, M9 medium, in vivo rice plant conditions and leaf extract (LE) medium mimicking in vivo plant condition. Proteomic analysis identified 95, 72, 75, and 87 MPs under LB, in vivo, M9 and LE conditions, respectively. Among them, six proteins were shared under all tested growth conditions designated as abundant class of proteins. Twenty-six and 21 proteins were expressed uniquely under in vivo versus LB medium and LE versus M9 medium, respectively, with 17 proteins common among these uniquely induced proteins. Moreover, most of the shared proteins are mainly related to energy metabolism, transport of small molecules, protein synthesis and secretion as well as virulence such as NADH, OmpA, secretion proteins. Therefore, the result of this study not only suggests that it may be an alternate method to analyze the in vivo expression of proteins by using LE medium to mimic plant conditions, but also reveals that the two sets of differentially expressed MPs, in particular the common MPs between them, might be important in energy metabolism, stress response and virulence of A. avenae subsp. avenae strain RS-1.
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Affiliation(s)
- Bin Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China,
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Nunn BL, Slattery KV, Cameron KA, Timmins-Schiffman E, Junge K. Proteomics of Colwellia psychrerythraea at subzero temperatures - a life with limited movement, flexible membranes and vital DNA repair. Environ Microbiol 2015; 17:2319-35. [PMID: 25471130 DOI: 10.1111/1462-2920.12691] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 10/23/2014] [Accepted: 10/23/2014] [Indexed: 11/27/2022]
Abstract
The mechanisms that allow psychrophilic bacteria to remain metabolically active at subzero temperatures result from form and function of their proteins. We present first proteomic evidence of physiological changes of the marine psychrophile Colwellia psychrerythraea 34H (Cp34H) after exposure to subzero temperatures (-1, and -10°C in ice) through 8 weeks. Protein abundance was compared between different treatments to understand the effects of temperature and time, independently and jointly, within cells transitioning to, and being maintained in ice. Parallel [3H]-leucine and [3H]-thymidine incubations indicated active protein and DNA synthesis to -10°C. Mass spectrometry-based proteomics identified 1763 proteins across four experimental treatments. Proteins involved in osmolyte regulation and polymer secretion were found constitutively present across all treatments, suggesting that they are required for metabolic success below 0°C. Differentially abundant protein groups indicated a reallocation of resources from DNA binding to DNA repair and from motility to chemo-taxis and sensing. Changes to iron and nitrogen metabolism, cellular membrane structures, and protein synthesis and folding were also revealed. By elucidating vital strategies during life in ice, this study provides novel insight into the extensive molecular adaptations that occur in cold-adapted marine organisms to sustain cellular function in their habitat.
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Affiliation(s)
- Brook L Nunn
- Department of Genome Sciences, University of Washington, Box 355065, Seattle, WA, 98195, USA
| | - Krystal V Slattery
- Applied Physics Laboratory, Polar Science Center, University of Washington, Box 355640, Seattle, WA, 98195, USA
| | - Karen A Cameron
- Applied Physics Laboratory, Polar Science Center, University of Washington, Box 355640, Seattle, WA, 98195, USA
| | - Emma Timmins-Schiffman
- Department of Genome Sciences, University of Washington, Box 355065, Seattle, WA, 98195, USA
| | - Karen Junge
- Applied Physics Laboratory, Polar Science Center, University of Washington, Box 355640, Seattle, WA, 98195, USA
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A new enabling proteomics methodology to investigate membrane associated proteins from parasitic nematodes: case study using ivermectin resistant and ivermectin susceptible isolates of Caenorhabditis elegans and Haemonchus contortus. Vet Parasitol 2014; 207:266-75. [PMID: 25537855 DOI: 10.1016/j.vetpar.2014.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 11/23/2014] [Accepted: 12/06/2014] [Indexed: 01/06/2023]
Abstract
The mechanisms involved in anthelmintic resistance (AR) are complex but a greater understanding of AR management is essential for effective and sustainable control of parasitic helminth worms in livestock. Current tests to measure AR are time consuming and can be technically problematic, gold standard diagnostics are therefore urgently required to assist in combatting the threat from drug resistant parasites. For anthelmintics such as ivermectin (IVM), target proteins may be present in the cellular membrane. As proteins usually act in complexes and not in isolation, AR may develop and be measurable in the target associated proteins present in the parasite membrane. The model nematode Caenorhabditis elegans was used to develop a sub-proteomic assay to measure protein expression differences, between IVM resistant and IVM susceptible isolates in the presence and absence of drug challenge. Evaluation of detergents including CHAPS, ASB-14, C7BzO, Triton ×100 and TBP (tributyl phosphine) determined optimal conditions for the resolution of membrane proteins in Two Dimensional Gel Electrophoresis (2DE). These sub-proteomic methodologies were then translated and evaluated using IVM-susceptible and IVM-resistant Haemonchus contortus; a pathogenic blood feeding parasitic nematode which is of global importance in livestock health, welfare and productivity. We have demonstrated the successful resolution of membrane associated proteins from both C. elegans and H. contortus isolates, using a combination of CHAPS and the zwitterionic amphiphilic surfactant ASB-14 to further support the detection of markers for AR.
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Moreno R, Rojo F. Features of pseudomonads growing at low temperatures: another facet of their versatility. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:417-426. [PMID: 25646532 DOI: 10.1111/1758-2229.12150] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pseudomonads are a diverse and ecologically successful group of γ-proteobacteria present in many environments (terrestrial, freshwater and marine), either free living or associated with plants or animals. Their success is at least partly based on their ability to grow over a wide range of temperatures, their capacity to withstand different kinds of stress and their great metabolic versatility. Although the optimal growth temperature of pseudomonads is usually close to 25–30°C, many strains can also grow between 5°C and 10°C, and some of them even close to 0°C. Such low temperatures strongly affect the physicochemical properties of macromolecules, forcing cells to evolve traits that optimize growth and help them withstand cold-induced stresses such as increased levels of reactive oxygen species, reduced membrane fluidity and enzyme activity, cold-induced protein denaturation and the greater stability of DNA and RNA secondary structures. This review gathers the information available on the strategies used by pseudomonads to adapt to low temperature growth, and briefly describes some of the biotechnological applications that might benefit from cold-adapted bacterial strains and enzymes, e.g., biotransformation or bioremediation processes to be performed at low temperatures.
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Masoudzadeh N, Alidoust L, Samie N, Hajfarajollah H, Sharafi H, Modiri S, Zahiri HS, Vali H, Noghabi KA. Distinctive protein expression patterns of the strain Brevundimonas sp. ZF12 isolated from the aqueous zone containing high levels of radiation to cadmium-induced stress. J Biotechnol 2014; 186:49-57. [PMID: 24997353 DOI: 10.1016/j.jbiotec.2014.05.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/16/2014] [Accepted: 05/21/2014] [Indexed: 11/18/2022]
Abstract
In the current study, different protein expression profiles in a strain Brevundimonas sp. ZF12, isolated from the aqueous zone containing high levels of radiation, were characterized following exposure to cadmium (II) using a proteomic strategy. In order to gain a deeper understanding of the cellular events that allow this strain to survive and undergo cadmium adaptation and sorption, the strain was tested under three experimental conditions of 5, 10 and 30 ppm cadmium (II) ions stress. Two-dimensional polyacrylamide gel electrophoresis and mass spectrometry were used to identify the differentially expressed proteins under cadmium (II) stress. 20 differentially expressed spots were successfully identified by MS/MS analysis. These proteins are involved in DNA repair and protection, amino acid metabolism, nucleotide metabolism, energy homeostasis, oxidative stress response, redox homeostasis, protein folding and heat-shock response. The results obviously indicate that the ZF12 strain tends to endure the cadmium (II) stress conditions by modification in many aspects of its cellular physiology and metabolism.
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Affiliation(s)
- Nasrin Masoudzadeh
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Leila Alidoust
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Nima Samie
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Hamidreza Hajfarajollah
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Hakimeh Sharafi
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Sima Modiri
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Hossein Shahbani Zahiri
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Hojatollah Vali
- Facility for Electron Microscopy Research, McGill University, 3640 Street, Montreal, Canada
| | - Kambiz Akbari Noghabi
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran.
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García-Descalzo L, García-López E, Alcázar A, Baquero F, Cid C. Proteomic analysis of the adaptation to warming in the Antarctic bacteria Shewanella frigidimarina. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2229-40. [PMID: 25149826 DOI: 10.1016/j.bbapap.2014.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 08/06/2014] [Accepted: 08/11/2014] [Indexed: 12/27/2022]
Abstract
Antarctica is subjected to extremely variable conditions, but the importance of the temperature increase in cold adapted bacteria is still unknown. To study the molecular adaptation to warming of Antarctic bacteria, cultures of Shewanella frigidimarina were incubated at temperatures ranging from 0°C to 30°C, emulating the most extreme conditions that this strain could tolerate. A proteomic approach was developed to identify the soluble proteins obtained from cells growing at 4°C, 20°C and 28°C. The most drastic effect when bacteria were grown at 28°C was the accumulation of heat shock proteins as well as other proteins related to stress, redox homeostasis or protein synthesis and degradation, and the decrease of enzymes and components of the cell envelope. Furthermore, two main responses in the adaptation to warm temperature were detected: the presence of diverse isoforms in some differentially expressed proteins, and the composition of chaperone interaction networks at the limits of growth temperature. The abundance changes of proteins suggest that warming induces a stress situation in S. frigidimarina forcing cells to reorganize their molecular networks as an adaptive response to these environmental conditions.
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Affiliation(s)
| | - Eva García-López
- Centro de Astrobiologia (CSIC-INTA), 28850 Torrejón de Ardoz, Spain
| | - Alberto Alcázar
- Department of Investigation, Hospital Ramon y Cajal, 28034 Madrid, Spain
| | - Fernando Baquero
- Centro de Astrobiologia (CSIC-INTA), 28850 Torrejón de Ardoz, Spain; Department of Microbiology, Hospital Ramon y Cajal, 28034 Madrid, Spain
| | - Cristina Cid
- Centro de Astrobiologia (CSIC-INTA), 28850 Torrejón de Ardoz, Spain.
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Ibrahim M, Tao Z, Hussain A, Chunlan Y, Ilyas M, Waheed A, Yuan F, Li B, Xie GL. Deciphering the role of Burkholderia cenocepacia membrane proteins in antimicrobial properties of chitosan. Arch Microbiol 2013; 196:9-16. [PMID: 24213809 DOI: 10.1007/s00203-013-0936-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/09/2013] [Accepted: 10/24/2013] [Indexed: 10/26/2022]
Abstract
Chitosan, a versatile derivative of chitin, is widely used as an antimicrobial agent either alone or mixed with other natural polymers. Burkholderia cenocepacia is a multidrug-resistant bacteria and difficult to eradicate. Our previous studies shown that chitosan had strong antibacterial activity against B. cenocepacia. In the current study, we have investigated the molecular aspects for the susceptibility of B. cenocepacia in response to chitosan antibacterial activity. We have conducted RNA expression analysis of drug efflux system by RT-PCR, membrane protein profiling by SDS-PAGE, and by LC-MS/MS analysis following the validation of selected membrane proteins by real-time PCR analysis. By RT-PCR analysis, it was found that orf3, orf9, and orf13 were expressed at detectable levels, which were similar to control, while rest of the orf did not express. Moreover, shotgun proteomics analysis revealed 21 proteins in chitosan-treated cells and 16 proteins in control. Among them 4 proteins were detected as shared proteins under control and chitosan-treated cells and 17 proteins as uniquely identified proteins under chitosan-treated cells. Among the catalog of uniquely identified proteins, there were proteins involved in electron transport chain and ATP synthase, metabolism of carbohydrates and adaptation to atypical conditions proteins which indicate that utilization and pattern of chitosan is diverse which might be responsible for its antibacterial effects on bacteria. Moreover, our results showed that RND drug efflux system, which display the ability to transport a variety of structurally unrelated drugs from a cell and consequently are capable of conferring resistance to a diverse range of chemotherapeutic agents, was not determined to play its role in response to chitosan. It might be lipopolysaccharides interaction with chitosan resulted in the destabilization of membrane protein to membrane lyses to cell death. Membrane proteome analysis were also validated by RT-qPCR analysis, which corroborated our results that of membrane proteins.
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Affiliation(s)
- Muhammad Ibrahim
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, 388 Yuhangtang Road, Hangzhou, 310058, People's Republic of China
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Rovoli M, Gortzi O, Lalas S, Kontopidis G. β-Lactoglobulin improves liposome’s encapsulation properties for vitamin E delivery. J Liposome Res 2013; 24:74-81. [DOI: 10.3109/08982104.2013.839701] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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15
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Feller G. Psychrophilic enzymes: from folding to function and biotechnology. SCIENTIFICA 2013; 2013:512840. [PMID: 24278781 PMCID: PMC3820357 DOI: 10.1155/2013/512840] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/06/2012] [Indexed: 05/10/2023]
Abstract
Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry, University of Liège, B6a, 4000 Liège, Belgium
- *Georges Feller:
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