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Ruiz-Blas F, Muñoz-Hisado V, Garcia-Lopez E, Moreno A, Bartolomé M, Leunda M, Martinez-Alonso E, Alcázar A, Cid C. The hidden microbial ecosystem in the perennial ice from a Pyrenean ice cave. Front Microbiol 2023; 14:1110091. [PMID: 36778858 PMCID: PMC9909108 DOI: 10.3389/fmicb.2023.1110091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023] Open
Abstract
Over the last years, perennial ice deposits located within caves have awakened interest as places to study microbial communities since they represent unique cryospheric archives of climate change. Since the beginning of the twentieth century, the temperature has gradually increased, and it is estimated that by the end of this century the increase in average temperature could be around 4.0°C. In this context of global warming the ice deposits of the Pyrenean caves are undergoing a significant regression. Among this type of caves, that on the Cotiella Massif in the Southern Pyrenees is one of the southernmost studied in Europe. These types of caves house microbial communities which have so far been barely explored, and therefore their study is necessary. In this work, the microbial communities of the Pyrenean ice cave A294 were identified using metabarcoding techniques. In addition, research work was carried out to analyze how the age and composition of the ice affect the composition of the bacterial and microeukaryotic populations. Finally, the in vivo effect of climate change on the cellular machinery that allow microorganisms to live with increasing temperatures has been studied using proteomic techniques.
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Affiliation(s)
- Fátima Ruiz-Blas
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
- Section Geomicrobiology, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | | | | | - Ana Moreno
- Departamento de Procesos Geoambientales y Cambio Global, Instituto Pirenaico de Ecología - CSIC, Zaragoza, Spain
| | - Miguel Bartolomé
- Departamento de Procesos Geoambientales y Cambio Global, Instituto Pirenaico de Ecología - CSIC, Zaragoza, Spain
- Institut für Geologie und Mineralogie, Universität zu Köln, Köln, Germany
| | - Maria Leunda
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
- Swiss Federal Research Institute for Forest, Snow and Landscape Research WSL, Zurich, Switzerland
- Department of Plant Biology and Ecology, University of the Basque Country, Leioa, Spain
| | - Emma Martinez-Alonso
- Department of Investigation, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Ramón y Cajal, Madrid, Spain
| | - Alberto Alcázar
- Department of Investigation, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Ramón y Cajal, Madrid, Spain
| | - Cristina Cid
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
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Calvanese M, Colarusso A, Lauro C, Parrilli E, Tutino ML. Soluble Recombinant Protein Production in Pseudoalteromonas haloplanktis TAC125: The Case Study of the Full-Length Human CDKL5 Protein. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2406:219-232. [PMID: 35089560 DOI: 10.1007/978-1-0716-1859-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 is an unconventional protein production host displaying a notable proficiency in the soluble production of difficult proteins, especially of human origin. Furthermore, the accumulation of recombinant products in insoluble aggregates has never been observed in this bacterium, indicating that its cellular physicochemical conditions and/or folding processes are rather different from those observed in mesophilic bacteria. The ability of this cell factory was challenged by producing a human protein, the cyclin-dependent kinase-like 5 (hCDKL5) in the bacterium cytoplasm at 0 °C. Human CDKL5 is a serine/threonine protein kinase characterized by the absence of a defined structure for the last two/third of its sequence, one of the largest intrinsically disordered regions so far observed in a human protein. This large unstructured domain makes difficult its production in most of the conventional hosts since the recombinant product accumulates as insoluble aggregates and/or is heavily proteolyzed. As the full-length hCDKL5 production is of great interest both for basic science and as protein drug for an enzyme replacement therapy, its production in the Antarctic bacterium was tested by combining the use of a regulated psychrophilic gene expression system with the use of a defined growth medium optimized for the host growth at subzero temperature. This is the first report of soluble and full-length recombinant production of hCDKL5 protein in a bacterium.
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Affiliation(s)
- Marzia Calvanese
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
| | - Andrea Colarusso
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
| | - Concetta Lauro
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy.
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Soluble Recombinant Protein Production in Pseudoalteromonas haloplanktis TAC125: The Case Study of the Full-Length Human CDKL5 Protein. Methods Mol Biol 2022. [PMID: 35089560 DOI: 10.1007/978-1-0716-1859-2_132406:219-232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 is an unconventional protein production host displaying a notable proficiency in the soluble production of difficult proteins, especially of human origin. Furthermore, the accumulation of recombinant products in insoluble aggregates has never been observed in this bacterium, indicating that its cellular physicochemical conditions and/or folding processes are rather different from those observed in mesophilic bacteria. The ability of this cell factory was challenged by producing a human protein, the cyclin-dependent kinase-like 5 (hCDKL5) in the bacterium cytoplasm at 0 °C. Human CDKL5 is a serine/threonine protein kinase characterized by the absence of a defined structure for the last two/third of its sequence, one of the largest intrinsically disordered regions so far observed in a human protein. This large unstructured domain makes difficult its production in most of the conventional hosts since the recombinant product accumulates as insoluble aggregates and/or is heavily proteolyzed. As the full-length hCDKL5 production is of great interest both for basic science and as protein drug for an enzyme replacement therapy, its production in the Antarctic bacterium was tested by combining the use of a regulated psychrophilic gene expression system with the use of a defined growth medium optimized for the host growth at subzero temperature. This is the first report of soluble and full-length recombinant production of hCDKL5 protein in a bacterium.
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Colarusso A, Lauro C, Calvanese M, Parrilli E, Tutino ML. Improvement of Pseudoalteromonas haloplanktis TAC125 as a Cell Factory: IPTG-Inducible Plasmid Construction and Strain Engineering. Microorganisms 2020; 8:microorganisms8101466. [PMID: 32987756 PMCID: PMC7598627 DOI: 10.3390/microorganisms8101466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023] Open
Abstract
Our group has used the marine bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) as a platform for the successful recombinant production of “difficult” proteins, including eukaryotic proteins, at low temperatures. However, there is still room for improvement both in the refinement of PhTAC125 expression plasmids and in the bacterium’s intrinsic ability to accumulate and handle heterologous products. Here, we present an integrated approach of plasmid design and strain engineering finalized to increment the recombinant expression and optimize the inducer uptake in PhTAC125. To this aim, we developed the IPTG-inducible plasmid pP79 and an engineered PhTAC125 strain called KrPL LacY+. This mutant was designed to express the E. coli lactose permease and to produce only a truncated version of the endogenous Lon protease through an integration-deletion strategy. In the wild-type strain, pP79 assured a significantly better production of two reporters in comparison to the most recent expression vector employed in PhTAC125. Nevertheless, the use of KrPL LacY+ was crucial to achieving satisfying production levels using reasonable IPTG concentrations, even at 0 °C. Both the wild-type and the mutant recombinant strains are characterized by an average graded response upon IPTG induction and they will find different future applications depending on the desired levels of expression.
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Söderberg JJ, Grgic M, Hjerde E, Haugen P. Aliivibrio wodanis as a production host: development of genetic tools for expression of cold-active enzymes. Microb Cell Fact 2019; 18:197. [PMID: 31711487 PMCID: PMC6844050 DOI: 10.1186/s12934-019-1247-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/31/2019] [Indexed: 01/16/2023] Open
Abstract
Background Heterologous production of cold-adapted proteins currently represents one of the greatest bottlenecks in the ongoing bioprospecting efforts to find new enzymes from low-temperature environments, such as, the polar oceans that represent essentially untapped resources in this respect. In mesophilic expression hosts such as Escherichia coli, cold-adapted enzymes often form inactive aggregates. Therefore it is necessary to develop new low-temperature expression systems, including identification of new host organisms and complementary genetic tools. Psychrophilic bacteria, including Pseudoalteromonas haloplanktis, Shewanella and Rhodococcus erythropolis have all been explored as candidates for such applications. However to date none of these have found widespread use as efficient expression systems, or are commercially available. In the present work we explored the use of the sub-Arctic bacterium Aliivibrio wodanis as a potential host for heterologous expression of cold-active enzymes. Results We tested 12 bacterial strains, as well as available vectors, promoters and reporter systems. We used RNA-sequencing to determine the most highly expressed genes and their intrinsic promoters in A. wodanis. In addition we examined a novel 5′-fusion to stimulate protein production and solubility. Finally we tested production of a set of “difficult-to-produce” enzymes originating from various bacteria and one Archaea. Our results show that cold-adapted enzymes can be produced in soluble and active form, even in cases when protein production failed in E. coli due to the formation of inclusion bodies. Moreover, we identified a 60-bp/20-aa fragment from the 5′-end of the AW0309160_00174 gene that stimulates expression of Green Fluorescent Protein and improves production of cold-active enzymes when used as a 5′-fusion. A 25-aa peptide from the same protein enhanced secretion of a 25-aa-sfGFP fusion. Conclusions Our results indicate the use of A. wodanis and associated genetic tools for low-temperature protein production and indicate that A. wodanis represents an interesting platform for further development of a protein production system that can promote further cold-enzyme discoveries.
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Affiliation(s)
- Jenny Johansson Söderberg
- Department of Chemistry and Center for Bioinformatics (SfB) and The Norwegian Structural Biology Centre (NorStruct), Faculty of Science and Technology, UiT -The Arctic University of Norway, 9037, Tromsø, Norway
| | - Miriam Grgic
- Department of Chemistry and Center for Bioinformatics (SfB) and The Norwegian Structural Biology Centre (NorStruct), Faculty of Science and Technology, UiT -The Arctic University of Norway, 9037, Tromsø, Norway
| | - Erik Hjerde
- Department of Chemistry and Center for Bioinformatics (SfB) and The Norwegian Structural Biology Centre (NorStruct), Faculty of Science and Technology, UiT -The Arctic University of Norway, 9037, Tromsø, Norway
| | - Peik Haugen
- Department of Chemistry and Center for Bioinformatics (SfB) and The Norwegian Structural Biology Centre (NorStruct), Faculty of Science and Technology, UiT -The Arctic University of Norway, 9037, Tromsø, Norway.
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New insights on Pseudoalteromonas haloplanktis TAC125 genome organization and benchmarks of genome assembly applications using next and third generation sequencing technologies. Sci Rep 2019; 9:16444. [PMID: 31712730 PMCID: PMC6848147 DOI: 10.1038/s41598-019-52832-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
Pseudoalteromonas haloplanktis TAC125 is among the most commonly studied bacteria adapted to cold environments. Aside from its ecological relevance, P. haloplanktis has a potential use for biotechnological applications. Due to its importance, we decided to take advantage of next generation sequencing (Illumina) and third generation sequencing (PacBio and Oxford Nanopore) technologies to resequence its genome. The availability of a reference genome, obtained using whole genome shotgun sequencing, allowed us to study and compare the results obtained by the different technologies and draw useful conclusions for future de novo genome assembly projects. We found that assembly polishing using Illumina reads is needed to achieve a consensus accuracy over 99.9% when using Oxford Nanopore sequencing, but not in PacBio sequencing. However, the dependency of consensus accuracy on coverage is lower in Oxford Nanopore than in PacBio, suggesting that a cost-effective solution might be the use of low coverage Oxford Nanopore sequencing together with Illumina reads. Despite the differences in consensus accuracy, all sequencing technologies revealed the presence of a large plasmid, pMEGA, which was undiscovered until now. Among the most interesting features of pMEGA is the presence of a putative error-prone polymerase regulated through the SOS response. Aside from the characterization of the newly discovered plasmid, we confirmed the sequence of the small plasmid pMtBL and uncovered the presence of a potential partitioning system. Crucially, this study shows that the combination of next and third generation sequencing technologies give us an unprecedented opportunity to characterize our bacterial model organisms at a very detailed level.
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Parrilli E, Tedesco P, Fondi M, Tutino ML, Lo Giudice A, de Pascale D, Fani R. The art of adapting to extreme environments: The model system Pseudoalteromonas. Phys Life Rev 2019; 36:137-161. [PMID: 31072789 DOI: 10.1016/j.plrev.2019.04.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/02/2019] [Indexed: 01/10/2023]
Abstract
Extremophilic microbes have adapted to thrive in ecological niches characterized by harsh chemical/physical conditions such as, for example, very low/high temperature. Living organisms inhabiting these environments have developed peculiar mechanisms to cope with extreme conditions, in such a way that they mark the chemical-physical boundaries of life on Earth. Studying such mechanisms is stimulating from a basic research viewpoint and because of biotechnological applications. Pseudoalteromonas species are a group of marine gamma-proteobacteria frequently isolated from a range of extreme environments, including cold habitats and deep-sea sediments. Since deep-sea floors constitute almost 60% of the Earth's surface and cold temperatures represent the most common of the extreme conditions, the genus Pseudoalteromonas can be considered one of the most important model systems for studying microbial adaptation. Particularly, among all Pseudoalteromonas representatives, P. haloplanktis TAC125 has recently gained a central role. This bacterium was isolated from seawater sampled along the Antarctic ice-shell and is considered one of the model organisms of cold-adapted bacteria. It is capable of thriving in a wide temperature range and it has been suggested as an alternative host for the soluble overproduction of heterologous proteins, given its ability to rapidly multiply at low temperatures. In this review, we will present an overview of the recent advances in the characterization of Pseudoalteromonas strains and, more importantly, in the understanding of their evolutionary and chemical-physical strategies to face such a broad array of extreme conditions. A particular attention will be given to systems-biology approaches in the study of the above-mentioned topics, as genome-scale datasets (e.g. genomics, proteomics, phenomics) are beginning to expand for this group of organisms. In this context, a specific section dedicated to P. haloplanktis TAC125 will be presented to address the recent efforts in the elucidation of the metabolic rewiring of the organisms in its natural environment (Antarctica).
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Affiliation(s)
- Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario M. S. Angelo, Via Cintia, 80126 Napoli, Italy
| | - Pietro Tedesco
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Marco Fondi
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, ViaMadonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario M. S. Angelo, Via Cintia, 80126 Napoli, Italy
| | | | - Donatella de Pascale
- Institute of Protein Biochemistry, CNR, Napoli, Italy, Stazione Zoologica "Anthon Dorn", Villa Comunale, I-80121 Napoli, Italy
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, ViaMadonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy.
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Deng Y, Wang Y, Xia Y, Zhang AN, Zhao Y, Zhang T. Genomic resolution of bacterial populations in saccharin and cyclamate degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 658:357-366. [PMID: 30579193 DOI: 10.1016/j.scitotenv.2018.12.162] [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: 10/16/2018] [Revised: 12/10/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
The benefits of extensive artificial sweeteners use come at a cost of their ubiquitous occurrence in the aquatic environment. Biodegradation is crucial for the removal of artificial sweeteners in the environment, yet comprehensive characterizations of the degradation consortia that degrade these compounds have not been initiated. Here, we performed metagenomic analysis of microbial communities fulfilling complete mineralization of two typical artificial sweeteners, i.e. saccharin and cyclamate. Genome-resolved metagenomics enabled the recovery and metabolic characterization of total 23 population genomes from 8 phyla in the two consortia, most of which represented novel species. The saccharin-degrading consortia was notably dominated by a betaproteobacterial genome from the family Rhodocyclaceae, accounting for 15.5% of total sequences. For the cyclamate enrichment, 28.1% of the total sequences were assigned to three similarly abundant Alphaproteobacteria population genomes belonging to the family Sphingomonadaceae and Methylobacteriaceae. The metabolic potential of these population genomes were examined to potentially identify the roles of these populations in biodegradation of artificial sweeteners, and focusing on the energy and nutrient metabolisms.
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Affiliation(s)
- Yu Deng
- Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China; Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, China
| | - Yulin Wang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, China
| | - Yu Xia
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, China
| | - An Ni Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, China
| | - Yuehao Zhao
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, China
| | - Tong Zhang
- Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China; Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, China.
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Taboada H, Meneses N, Dunn MF, Vargas-Lagunas C, Buchs N, Castro-Mondragón JA, Heller M, Encarnación S. Proteins in the periplasmic space and outer membrane vesicles of Rhizobium etli CE3 grown in minimal medium are largely distinct and change with growth phase. MICROBIOLOGY-SGM 2018; 165:638-650. [PMID: 30358529 DOI: 10.1099/mic.0.000720] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Rhizobium etli CE3 grown in succinate-ammonium minimal medium (MM) excreted outer membrane vesicles (OMVs) with diameters of 40 to 100 nm. Proteins from the OMVs and the periplasmic space were isolated from 6 and 24 h cultures and identified by proteome analysis. A total of 770 proteins were identified: 73.8 and 21.3 % of these occurred only in the periplasm and OMVs, respectively, and only 4.9 % were found in both locations. The majority of proteins found in either location were present only at 6 or 24 h: in the periplasm and OMVs, only 24 and 9 % of proteins, respectively, were present at both sampling times, indicating a time-dependent differential sorting of proteins into the two compartments. The OMVs contained proteins with physiologically varied roles, including Rhizobium adhering proteins (Rap), polysaccharidases, polysaccharide export proteins, auto-aggregation and adherence proteins, glycosyl transferases, peptidoglycan binding and cross-linking enzymes, potential cell wall-modifying enzymes, porins, multidrug efflux RND family proteins, ABC transporter proteins and heat shock proteins. As expected, proteins with known periplasmic localizations (phosphatases, phosphodiesterases, pyrophosphatases) were found only in the periplasm, along with numerous proteins involved in amino acid and carbohydrate metabolism and transport. Nearly one-quarter of the proteins present in the OMVs were also found in our previous analysis of the R. etli total exproteome of MM-grown cells, indicating that these nanoparticles are an important mechanism for protein excretion in this species.
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Affiliation(s)
- Hermenegildo Taboada
- 1Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C. P. 62210, México
| | - Niurka Meneses
- 1Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C. P. 62210, México.,3Faculty of Science, Department of Chemistry and Biochemistry, University of Bern, 3010 Bern, Switzerland.,2Mass Spectrometry and Proteomics Laboratory, Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | - Michael F Dunn
- 1Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C. P. 62210, México
| | - Carmen Vargas-Lagunas
- 1Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C. P. 62210, México
| | - Natasha Buchs
- 2Mass Spectrometry and Proteomics Laboratory, Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | - Jaime A Castro-Mondragón
- 4Aix Marseille University, INSERM, TAGC, Theory and Approaches of Genomic Complexity, UMR_S 1090, Marseille, France
| | - Manfred Heller
- 2Mass Spectrometry and Proteomics Laboratory, Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | - Sergio Encarnación
- 1Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C. P. 62210, México
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Huang X, Duan X, Li J, Niu J, Yuan S, Wang X, Lambert N, Li X, Xu J, Gong Z, Yan S, Xie L, Xie J. The Synergistic Effect of Exogenous Glutamine and Rifampicin Against Mycobacterium Persisters. Front Microbiol 2018; 9:1625. [PMID: 30079057 PMCID: PMC6062616 DOI: 10.3389/fmicb.2018.01625] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 06/28/2018] [Indexed: 12/22/2022] Open
Abstract
Persisters, stochastic dormant variants of normal bacteria cell, represent a significant portion of the survivors upon exposure to antibiotics and other environmental stresses, which contributes substantially to high level antibiotics tolerance. Glutamine is a crucial component of the Mycobacteria nitrogen pool that is indispensable for survival upon stresses. To study whether a synergistic effect exists between glutamine and antibiotics against Mycobacterial persisters, the efficacy of rifampicin alone or together with exogenous glutamine upon Mycobacterium smegmatis mc2 155 persisters was monitored. The result showed that glutamine decreases M. smegmatis tolerance to rifampicin upon starvation. The reactive oxygen species level of the strains treated with rifampicin and glutamine increased. The synergism of glutamine and rifampicin to kill persisters might derive from altering the oxidative phosphorylation and TCA cycle, as both evidenced by both ATP level increase and transcriptome change. Glutamine might represent a synergistic agent of rifampicin to kill Mycobacteria persisters.
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Affiliation(s)
- Xue Huang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Xiangke Duan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Jiang Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Jingjing Niu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Siqi Yuan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Xiaoyu Wang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Nzungize Lambert
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Xue Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Junqi Xu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Zhen Gong
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Shuangquan Yan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
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Mocali S, Chiellini C, Fabiani A, Decuzzi S, de Pascale D, Parrilli E, Tutino ML, Perrin E, Bosi E, Fondi M, Lo Giudice A, Fani R. Ecology of cold environments: new insights of bacterial metabolic adaptation through an integrated genomic-phenomic approach. Sci Rep 2017; 7:839. [PMID: 28404986 PMCID: PMC5429795 DOI: 10.1038/s41598-017-00876-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/01/2017] [Indexed: 12/26/2022] Open
Abstract
Cold environments dominate Earth's biosphere, hosting complex microbial communities with the ability to thrive at low temperatures. However, the underlying molecular mechanisms and the metabolic pathways involved in bacterial cold-adaptation mechanisms are still not fully understood. Herein, we assessed the metabolic features of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125), a model organism for cold-adaptation, at both 4 °C and 15 °C, by integrating genomic and phenomic (high-throughput phenotyping) data and comparing the obtained results to the taxonomically related Antarctic bacterium Pseudoalteromonas sp. TB41 (PspTB41). Although the genome size of PspTB41 is considerably larger than PhTAC125, the higher number of genes did not reflect any higher metabolic versatility at 4 °C as compared to PhTAC125. Remarkably, protein S-thiolation regulated by glutathione and glutathionylspermidine appeared to be a new possible mechanism for cold adaptation in PhTAC125. More in general, this study represents an example of how 'multi-omic' information might potentially contribute in filling the gap between genotypic and phenotypic features related to cold-adaptation mechanisms in bacteria.
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Affiliation(s)
- Stefano Mocali
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy.
| | - Carolina Chiellini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy.,Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Arturo Fabiani
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy
| | - Silvia Decuzzi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy.,Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Donatella de Pascale
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples 'Federico II', Complesso Universitario, Monte Sant'Angelo, Via Cinthia 4, 80126, Naples, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples 'Federico II', Complesso Universitario, Monte Sant'Angelo, Via Cinthia 4, 80126, Naples, Italy
| | - Elena Perrin
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Emanuele Bosi
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Marco Fondi
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Angelina Lo Giudice
- Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Spianata San Raineri 86, 98122, Messina, Italy.,Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontrès 31, 98166, Messina, Italy
| | - Renato Fani
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
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Fondi M, Bosi E, Presta L, Natoli D, Fani R. Modelling microbial metabolic rewiring during growth in a complex medium. BMC Genomics 2016; 17:970. [PMID: 27881075 PMCID: PMC5121958 DOI: 10.1186/s12864-016-3311-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 11/17/2016] [Indexed: 11/21/2022] Open
Abstract
Background In their natural environment, bacteria face a wide range of environmental conditions that change over time and that impose continuous rearrangements at all the cellular levels (e.g. gene expression, metabolism). When facing a nutritionally rich environment, for example, microbes first use the preferred compound(s) and only later start metabolizing the other one(s). A systemic re-organization of the overall microbial metabolic network in response to a variation in the composition/concentration of the surrounding nutrients has been suggested, although the range and the entity of such modifications in organisms other than a few model microbes has been scarcely described up to now. Results We used multi-step constraint-based metabolic modelling to simulate the growth in a complex medium over several time steps of the Antarctic model organism Pseudoalteromonas haloplanktis TAC125. As each of these phases is characterized by a specific set of amino acids to be used as carbon and energy source our modelling framework describes the major consequences of nutrients switching at the system level. The model predicts that a deep metabolic reprogramming might be required to achieve optimal biomass production in different stages of growth (different medium composition), with at least half of the cellular metabolic network involved (more than 50% of the metabolic genes). Additionally, we show that our modelling framework is able to capture metabolic functional association and/or common regulatory features of the genes embedded in our reconstruction (e.g. the presence of common regulatory motifs). Finally, to explore the possibility of a sub-optimal biomass objective function (i.e. that cells use resources in alternative metabolic processes at the expense of optimal growth) we have implemented a MOMA-based approach (called nutritional-MOMA) and compared the outcomes with those obtained with Flux Balance Analysis (FBA). Growth simulations under this scenario revealed the deep impact of choosing among alternative objective functions on the resulting predictions of fluxes distribution. Conclusions Here we provide a time-resolved, systems-level scheme of PhTAC125 metabolic re-wiring as a consequence of carbon source switching in a nutritionally complex medium. Our analyses suggest the presence of a potential efficient metabolic reprogramming machinery to continuously and promptly adapt to this nutritionally changing environment, consistent with adaptation to fast growth in a fairly, but probably inconstant and highly competitive, environment. Also, we show i) how functional partnership and co-regulation features can be predicted by integrating multi-step constraint-based metabolic modelling with fed-batch growth data and ii) that performing simulations under a sub-optimal objective function may lead to different flux distributions in respect to canonical FBA. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3311-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019, Sesto F.no, Italy.
| | - Emanuele Bosi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019, Sesto F.no, Italy
| | - Luana Presta
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019, Sesto F.no, Italy
| | - Diletta Natoli
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019, Sesto F.no, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019, Sesto F.no, Italy
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Fondi M, Maida I, Perrin E, Mellera A, Mocali S, Parrilli E, Tutino ML, Liò P, Fani R. Genome-scale metabolic reconstruction and constraint-based modelling of the Antarctic bacteriumPseudoalteromonas haloplanktis TAC125. Environ Microbiol 2014; 17:751-66. [DOI: 10.1111/1462-2920.12513] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 05/13/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Marco Fondi
- Laboratory of Microbial and Molecular Evolution; Department of Biology; University of Florence; Via Madonna del Piano 6, Sesto Fiorentino Florence 50019 Italy
- ComBo; Florence Computational Biology Group; University of Florence; Via Madonna del Piano 6, Sesto Fiorentino Florence 50019 Italy
| | - Isabel Maida
- Laboratory of Microbial and Molecular Evolution; Department of Biology; University of Florence; Via Madonna del Piano 6, Sesto Fiorentino Florence 50019 Italy
| | - Elena Perrin
- Laboratory of Microbial and Molecular Evolution; Department of Biology; University of Florence; Via Madonna del Piano 6, Sesto Fiorentino Florence 50019 Italy
| | - Alessandra Mellera
- Laboratory of Microbial and Molecular Evolution; Department of Biology; University of Florence; Via Madonna del Piano 6, Sesto Fiorentino Florence 50019 Italy
- ComBo; Florence Computational Biology Group; University of Florence; Via Madonna del Piano 6, Sesto Fiorentino Florence 50019 Italy
| | - Stefano Mocali
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura; Centro di Ricerca per l'Agrobiologia e la Pedologia (CRA-ABP); Firenze Italy
| | | | - Maria Luisa Tutino
- Department of Chemical Sciences; University of Naples Federico II; Naples Italy
| | - Pietro Liò
- Computer Laboratory; Cambridge University; Cambridge UK
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution; Department of Biology; University of Florence; Via Madonna del Piano 6, Sesto Fiorentino Florence 50019 Italy
- ComBo; Florence Computational Biology Group; University of Florence; Via Madonna del Piano 6, Sesto Fiorentino Florence 50019 Italy
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Giordano D, Coppola D, Russo R, Tinajero-Trejo M, di Prisco G, Lauro F, Ascenzi P, Verde C. The globins of cold-adapted Pseudoalteromonas haloplanktis TAC125: from the structure to the physiological functions. Adv Microb Physiol 2014; 63:329-89. [PMID: 24054800 DOI: 10.1016/b978-0-12-407693-8.00008-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Evolution allowed Antarctic microorganisms to grow successfully under extreme conditions (low temperature and high O2 content), through a variety of structural and physiological adjustments in their genomes and development of programmed responses to strong oxidative and nitrosative stress. The availability of genomic sequences from an increasing number of cold-adapted species is providing insights to understand the molecular mechanisms underlying crucial physiological processes in polar organisms. The genome of Pseudoalteromonas haloplanktis TAC125 contains multiple genes encoding three distinct truncated globins exhibiting the 2/2 α-helical fold. One of these globins has been extensively characterised by spectroscopic analysis, kinetic measurements and computer simulation. The results indicate unique adaptive structural properties that enhance the overall flexibility of the protein, so that the structure appears to be resistant to pressure-induced stress. Recent results on a genomic mutant strain highlight the involvement of the cold-adapted globin in the protection against the stress induced by high O2 concentration. Moreover, the protein was shown to catalyse peroxynitrite isomerisation in vitro. In this review, we first summarise how cold temperatures affect the physiology of microorganisms and focus on the molecular mechanisms of cold adaptation revealed by recent biochemical and genetic studies. Next, since only in a very few cases the physiological role of truncated globins has been demonstrated, we also discuss the structural and functional features of the cold-adapted globin in an attempt to put into perspective what has been learnt about these proteins and their potential role in the biology of cold-adapted microorganisms.
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Slattery M, Ankisetty S, Corrales J, Marsh-Hunkin KE, Gochfeld DJ, Willett KL, Rimoldi JM. Marine proteomics: a critical assessment of an emerging technology. JOURNAL OF NATURAL PRODUCTS 2012; 75:1833-1877. [PMID: 23009278 DOI: 10.1021/np300366a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.
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Affiliation(s)
- Marc Slattery
- Department of Pharmacognosy, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, USA.
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Ritter A, Com E, Bazire A, Goncalves MDS, Delage L, Pennec GL, Pineau C, Dreanno C, Compère C, Dufour A. Proteomic studies highlight outer-membrane proteins related to biofilm development in the marine bacterium Pseudoalteromonas sp. D41. Proteomics 2012; 12:3180-92. [DOI: 10.1002/pmic.201100644] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Revised: 07/27/2012] [Accepted: 08/04/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Andrés Ritter
- Laboratoire de Biotechnologie et Chimie Marines; Université de Bretagne-Sud (UEB), IUEM; Lorient France
- IFREMER; Service Interfaces et Capteurs; Plouzané France
| | - Emmanuelle Com
- Proteomics Core Facility BIOGENOUEST; IRSET - Inserm U1085; Campus de Beaulieu; Rennes France
| | - Alexis Bazire
- Laboratoire de Biotechnologie et Chimie Marines; Université de Bretagne-Sud (UEB), IUEM; Lorient France
| | | | - Ludovic Delage
- CNRS, UPMC; UMR 7139 Végétaux Marins et Biomolécules; Station Biologique; Roscoff France
| | - Gaël Le Pennec
- Laboratoire de Biotechnologie et Chimie Marines; Université de Bretagne-Sud (UEB), IUEM; Lorient France
| | - Charles Pineau
- Proteomics Core Facility BIOGENOUEST; IRSET - Inserm U1085; Campus de Beaulieu; Rennes France
| | | | | | - Alain Dufour
- Laboratoire de Biotechnologie et Chimie Marines; Université de Bretagne-Sud (UEB), IUEM; Lorient France
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Tang K, Jiao N, Liu K, Zhang Y, Li S. Distribution and functions of TonB-dependent transporters in marine bacteria and environments: implications for dissolved organic matter utilization. PLoS One 2012; 7:e41204. [PMID: 22829928 PMCID: PMC3400609 DOI: 10.1371/journal.pone.0041204] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 06/18/2012] [Indexed: 11/18/2022] Open
Abstract
Background Bacteria play critical roles in marine nutrient cycles by incorporating and redistributing dissolved organic matter (DOM) and inorganic nutrients in the ocean. TonB-dependent transporter (TBDT) proteins allow Gram-negative bacteria to take up scarce resources from nutrient-limiting environments as well as siderophores, heme, vitamin B12, and recently identified carbohydrates. Thus, the characterization of TBDT distribution and functions is essential to better understand the contribution TBDT to DOM assimilation and its consequences on nutrient cycling in the environment. Methodology/Principal Findings This study presents the distribution of encoded known and putative TBDT proteins in the genomes of microorganisms and from the Global Ocean Survey data. Using a Lek clustering algorithm and substrate specificities, the TBDT sequences were mainly classified into the following three groups: (1) DOM transporters; (2) Siderophores/Vitamins transporters; and (3) Heme/Hemophores/Iron(heme)-binding protein transporters. Diverse TBDTs were found in the genomes of oligotroph Citromicrobium bathyomarinum JL354 and Citromicrobium sp JLT1363 and were highly expressed in the stationary phase of bacterial growth. The results show that the Gammaproteobacteria and the Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria accounted for the majority of the TBDT gene pool in marine surface waters. Conclusions/Significance The results of this study confirm the ecological importance of TBDTs in DOM assimilation for bacteria in marine environments owing to a wide range of substrate utilization potential in the ubiquitous Gammaproteobacteria and CFB group bacteria.
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Affiliation(s)
- Kai Tang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, China.
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Predicted protein subcellular localization in dominant surface ocean bacterioplankton. Appl Environ Microbiol 2012; 78:6550-7. [PMID: 22773648 DOI: 10.1128/aem.01406-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria consume dissolved organic matter (DOM) through hydrolysis, transport and intracellular metabolism, and these activities occur in distinct subcellular localizations. Bacterial protein subcellular localizations for several major marine bacterial groups were predicted using genomic, metagenomic and metatranscriptomic data sets following modification of MetaP software for use with partial gene sequences. The most distinct pattern of subcellular localization was found for Bacteroidetes, whose genomes were substantially enriched with outer membrane and extracellular proteins but depleted of inner membrane proteins compared with five other taxa (SAR11, Roseobacter, Synechococcus, Prochlorococcus, oligotrophic marine Gammaproteobacteria). When subcellular localization patterns were compared between genes and transcripts, three taxa had expression biased toward proteins localized to cell locations outside of the cytosol (SAR11, Roseobacter, and Synechococcus), as expected based on the importance of carbon and nutrient acquisition in an oligotrophic ocean, but two taxa did not (oligotrophic marine Gammaproteobacteria and Bacteroidetes). Diel variations in the fraction and putative gene functions of transcripts encoding inner membrane and periplasmic proteins compared to cytoplasmic proteins suggest a close coupling of photosynthetic extracellular release and bacterial consumption, providing insights into interactions between phytoplankton, bacteria, and DOM.
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Identification of cold-inducible inner membrane proteins of the psychrotrophic bacterium, Shewanella livingstonensis Ac10, by proteomic analysis. Extremophiles 2012; 16:227-36. [DOI: 10.1007/s00792-011-0422-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 12/13/2011] [Indexed: 11/27/2022]
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