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Gutiérrez MC, Cáceres A, Herruzo-Ruiz AM, Siles JA, Vázquez F, Alhama J, Michán C, Martín MA. Assessment of nitrification process in a sequencing batch reactor: Modelling and genomic approach. Environ Res 2024; 246:118035. [PMID: 38199477 DOI: 10.1016/j.envres.2023.118035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Nitrification of ammoniacal nitrogen (N-NH4+) to nitrate (N-NO3-) was investigated in a lab-scale sequencing batch reactor (SBR) to evaluate its efficiency. During the nitrification process the removal of N-NH4+ reached 96%, resulting in 73% formation of N-NO3-. A lineal correlation (r2 = 0.9978) was obtained between the concentration of volatile suspended solids (VSS) and the maximal N-NO3- concentration at the end of each batch cycle under stationary state. The bacterial taxons in the initial inoculum were identified, revealing a complex diverse community mainly in the two major bacterial phyla Proteobacteria and Actinobacteria. The FAPROTAX algorithm predicted the presence in the inoculum of taxa involved in relevant processes of the nitrogen metabolism, highlighting the bacterial genera Nitrospira and Nitrosomonas that are both involved in the nitrification process. A kinetic model was formulated for predicting and validating the transformation of N-NH4+, N-NO2- and N-NO3- and the removal of organic and inorganic carbon (TOC and IC, respectively). The results showed how the increase in biomass concentration slowed down the transformation to oxidised forms of nitrogen and increased denitrification in the settling and filling stages under free aeration conditions.
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Affiliation(s)
- M C Gutiérrez
- Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Campus de Excelencia Internacional Agroalimentario ceiA3, University of Cordoba, Campus Universitario de Rabanales, Carretera N-IV, km 396, edificio Marie Curie, 14071, Córdoba, Spain
| | - A Cáceres
- Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Campus de Excelencia Internacional Agroalimentario ceiA3, University of Cordoba, Campus Universitario de Rabanales, Carretera N-IV, km 396, edificio Marie Curie, 14071, Córdoba, Spain
| | - A M Herruzo-Ruiz
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Excelencia Internacional Agroalimentario ceiA3, edificio Severo Ochoa, 14071, Córdoba, Spain
| | - J A Siles
- Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Campus de Excelencia Internacional Agroalimentario ceiA3, University of Cordoba, Campus Universitario de Rabanales, Carretera N-IV, km 396, edificio Marie Curie, 14071, Córdoba, Spain
| | - F Vázquez
- Department of Electrical Engineering and Automation, University of Cordoba, Cordoba, 14071, Spain
| | - J Alhama
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Excelencia Internacional Agroalimentario ceiA3, edificio Severo Ochoa, 14071, Córdoba, Spain
| | - C Michán
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Excelencia Internacional Agroalimentario ceiA3, edificio Severo Ochoa, 14071, Córdoba, Spain
| | - M A Martín
- Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Campus de Excelencia Internacional Agroalimentario ceiA3, University of Cordoba, Campus Universitario de Rabanales, Carretera N-IV, km 396, edificio Marie Curie, 14071, Córdoba, Spain.
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Michán‐Doña A, Vázquez‐Borrego MC, Michán C. Are there any completely sterile organs or tissues in the human body? Is there any sacred place? Microb Biotechnol 2024; 17:e14442. [PMID: 38465728 PMCID: PMC10926192 DOI: 10.1111/1751-7915.14442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/12/2024] Open
Abstract
The human microbiome comprises an ample set of organisms that inhabit and interact within the human body, contributing both positively and negatively to our health. In recent years, several research groups have described the presence of microorganisms in organs or tissues traditionally considered as 'sterile' under healthy and pathological conditions. In this sense, microorganisms have been detected in several types of cancer, including those in 'sterile' organs. But how can the presence of microorganisms be detected? In most studies, 16S and internal transcribed spacer (ITS) ribosomal DNA (rDNA) sequencing has led to the identification of prokaryotes and fungi. However, a major limitation of this technique is that it cannot distinguish between living and dead organisms. RNA-based methods have been proposed to overcome this limitation, as the shorter half-life of the RNA would identify only the transcriptionally active microorganisms, although perhaps not all the viable ones. In this sense, metaproteomic techniques or the search for molecular metabolic signatures could be interesting alternatives for the identification of living microorganisms. In summary, new technological advances are challenging the notion of 'sterile' organs in our body. However, to date, evidence for a structured living microbiome in most of these organs is scarce or non-existent. The implementation of new technological approaches will be necessary to fully understand the importance of the microbiome in these organs, which could pave the way for the development of a wide range of new therapeutic strategies.
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Affiliation(s)
- Alfredo Michán‐Doña
- Departamento de MedicinaHospital Universitario de JerezJerez de la FronteraSpain
- Biomedical Research and Innovation Institute of Cadiz (INiBICA)CádizSpain
| | - Mari C. Vázquez‐Borrego
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC)CórdobaSpain
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3Universidad de CórdobaCórdobaSpain
| | - Carmen Michán
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC)CórdobaSpain
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3Universidad de CórdobaCórdobaSpain
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Casares-Jimenez M, Garcia-Garcia T, Suárez-Cárdenas JM, Perez-Jimenez AB, Martín MA, Caballero-Gómez J, Michán C, Corona-Mata D, Risalde MA, Perez-Valero I, Guerra R, Garcia-Bocanegra I, Rivero A, Rivero-Juarez A, Garrido JJ. Correlation of hepatitis E and rat hepatitis E viruses urban wastewater monitoring and clinical cases. Sci Total Environ 2024; 908:168203. [PMID: 37914110 DOI: 10.1016/j.scitotenv.2023.168203] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/19/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Wastewater pathogen monitoring is useful for surveillance of enteric pathogens. Information about the presence of Paslahepevirus balayani (HEV) and emergent Rocahepevirus ratti (RHEV) in untreated water and their correlation with clinical cases is scarce. Aim To longitudinally monitor HEV and RHEV in wastewater and to evaluate their possible correlation with human cases. METHODS This study was carried out in the city of Cordoba (southern Spain) from March 2021 to March 2023. HEV and RHEV occurrence were evaluated by PCR in three sample types: i) sera from patients with acute hepatitis attended at the reference hospital, ii) liver and faeces from urban rodents, and iii) grab sewage samples collected weekly from the municipal wastewater treatment plant. RESULTS We analysed 106 untreated wastewater samples, 304 individuals with acute hepatitis, and 20 rodents. HEV and RHEV were detected in only one (0.9 %) and almost all samples (94.3 %) of wastewater samples, respectively. A total of 22 cases of acute HEV infection (7.2 %) and two cases of RHEV (0.7 %) were detected from all acute hepatitis cases observed. Only RHEV was found in rodents, with a positive frequency of 55 %. The presence of HEV in wastewater coincided with the detection of one case in which the same HEV genotype was isolated. A concentration of HEV clinical cases between June and July of 2022 was observed but not detected in water. Both RHEV clinical cases were detected in summer 2022, but no correlation was found with wastewater detection. CONCLUSIONS Our study shows that there is no correlation between clinical cases and wastewater detection of HEV or RHEV.
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Affiliation(s)
- Maria Casares-Jimenez
- Unit of Infectious Diseases, Hospital Universitario Reina Sofia, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba (UCO), Cordoba, Spain
| | - Transito Garcia-Garcia
- Grupo de Inmunogenómica y Patogénesis Molecular, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - José M Suárez-Cárdenas
- Grupo de Inmunogenómica y Patogénesis Molecular, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Grupo GA-14, Córdoba, Spain
| | - Ana B Perez-Jimenez
- Clinical Microbiology Unit, Hospital Universitario Reina Sofía, Córdoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - María A Martín
- Departamento de Química Inorgánica e Ingeniería Química, Universidad de Córdoba, Córdoba, Spain
| | - Javier Caballero-Gómez
- Unit of Infectious Diseases, Hospital Universitario Reina Sofia, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba (UCO), Cordoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain; Departamento Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad Animal, 14014 Córdoba, Spain
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
| | - Diana Corona-Mata
- Unit of Infectious Diseases, Hospital Universitario Reina Sofia, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba (UCO), Cordoba, Spain
| | - María A Risalde
- CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain; Departamento de Anatomía y Anatomía Patológica Comparadas y Toxicología, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad Animal, 14014 Córdoba, Spain
| | - Ignacio Perez-Valero
- Unit of Infectious Diseases, Hospital Universitario Reina Sofia, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba (UCO), Cordoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Ignacio Garcia-Bocanegra
- CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain; Departamento Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad Animal, 14014 Córdoba, Spain
| | - Antonio Rivero
- Unit of Infectious Diseases, Hospital Universitario Reina Sofia, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba (UCO), Cordoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Antonio Rivero-Juarez
- Unit of Infectious Diseases, Hospital Universitario Reina Sofia, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba (UCO), Cordoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain.
| | - Juan J Garrido
- Grupo de Inmunogenómica y Patogénesis Molecular, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Grupo GA-14, Córdoba, Spain
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Valenzuela-Molina F, Bura FI, Vázquez-Borrego MC, Granados-Rodríguez M, Rufián-Andujar B, Rufián-Peña S, Casado-Adam Á, Sánchez-Hidalgo JM, Rodríguez-Ortiz L, Ortega-Salas R, Martínez-López A, Michán C, Alhama J, Arjona-Sánchez Á, Romero-Ruiz A. Intraoperative oxygen tension and redox homeostasis in Pseudomyxoma peritonei: A short case series. Front Oncol 2023; 13:1076500. [PMID: 36776312 PMCID: PMC9909963 DOI: 10.3389/fonc.2023.1076500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
Introduction Pseudomyxoma peritonei (PMP) is a rare malignant disease characterized by a massive multifocal accumulation of mucin within the peritoneal cavity. The current treatment option is based on complete cytoreductive surgery combined with hyperthermic intraperitoneal chemotherapy. However, the recurrence is frequent with subsequent progression and death. To date, most of the studies published in PMP are related to histological and genomic analyses. Thus, the need for further studies unveiling the underlying PMP molecular mechanisms is urgent. In this regard, hypoxia and oxidative stress have been extensively related to tumoral pathologies, although their contribution to PMP has not been elucidated. Methods In this manuscript, we have evaluated, for the first time, the intratumoral real-time oxygen microtension (pO2mt) in the tumor (soft and hard mucin) and surrounding healthy tissue from five PMP patients during surgery. In addition, we measured hypoxia (Hypoxia Inducible Factor-1a; HIF-1α) and oxidative stress (catalase; CAT) markers in soft and hard mucin from the same five PMP patient samples and in five control samples. Results The results showed low intratumoral oxygen levels, which were associated with increased HIF-1α protein levels, suggesting the presence of a hypoxic environment in these tumors. We also found a significant reduction in CAT activity levels in soft and hard mucin compared with healthy tissue samples. Discussion In conclusion, our study provides the first evidence of low intratumoral oxygen levels in PMP patients associated with hypoxia and oxidative stress markers. However, further investigation is required to understand the potential role of oxidative stress in PMP in order to find new therapeutic strategies.
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Affiliation(s)
- Francisca Valenzuela-Molina
- Surgical Oncology Unit, Department of Surgery, Reina Sofia University Hospital, Cordoba, Spain,GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - Florina I. Bura
- GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - Mari C. Vázquez-Borrego
- GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain,*Correspondence: Álvaro Arjona Sánchez, ; Mari C. Vázquez Borrego,
| | - Melissa Granados-Rodríguez
- GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - Blanca Rufián-Andujar
- Surgical Oncology Unit, Department of Surgery, Reina Sofia University Hospital, Cordoba, Spain,GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - Sebastián Rufián-Peña
- Surgical Oncology Unit, Department of Surgery, Reina Sofia University Hospital, Cordoba, Spain,GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - Ángela Casado-Adam
- Surgical Oncology Unit, Department of Surgery, Reina Sofia University Hospital, Cordoba, Spain,GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - Juan Manuel Sánchez-Hidalgo
- Surgical Oncology Unit, Department of Surgery, Reina Sofia University Hospital, Cordoba, Spain,GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - Lidia Rodríguez-Ortiz
- Surgical Oncology Unit, Department of Surgery, Reina Sofia University Hospital, Cordoba, Spain,GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - Rosa Ortega-Salas
- GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain,Pathology Unit, Reina Sofia University Hospital, Cordoba, Spain
| | - Ana Martínez-López
- GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain,Pathology Unit, Reina Sofia University Hospital, Cordoba, Spain
| | - Carmen Michán
- GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - José Alhama
- GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - Álvaro Arjona-Sánchez
- Surgical Oncology Unit, Department of Surgery, Reina Sofia University Hospital, Cordoba, Spain,GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain,*Correspondence: Álvaro Arjona Sánchez, ; Mari C. Vázquez Borrego,
| | - Antonio Romero-Ruiz
- GE09 Research in peritoneal and retroperitoneal oncological surgery, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
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Michán C. Picturing natural microbiomes: Matrix-assisted laser desorption/ionization mass spectrometry imaging for unravelling the architecture of environmental microbial communities. Environ Microbiol 2023; 25:135-136. [PMID: 36239226 PMCID: PMC10092596 DOI: 10.1111/1462-2920.16247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 01/25/2023]
Affiliation(s)
- Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Córdoba, Spain
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Abstract
Importance of viruses for biotechnological processes.
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Affiliation(s)
- Carmen Michán
- Departamento de Bioquímica y Biología MolecularUniversidad de CórdobaCampus de Excelencia Internacional Agroalimentario CeiA3Campus de RabanalesEdificio Severo OchoaCórdobaE‐14071Spain
| | - Alfredo Michán‐Doña
- Departamento de MedicinaHospital Universitario de JerezJerezSpain
- Biomedical Research and Innovation Institute of Cadiz (INiBICA)CádizSpain
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Alhama J, Maestre JP, Martín MÁ, Michán C. Monitoring COVID-19 through SARS-CoV-2 quantification in wastewater: progress, challenges and prospects. Microb Biotechnol 2021; 15:1719-1728. [PMID: 34905659 PMCID: PMC9151337 DOI: 10.1111/1751-7915.13989] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/13/2022] Open
Abstract
Wastewater‐Based Epidemiology (WBE) is widely used to monitor the progression of the current SARS‐CoV‐2 pandemic at local levels. In this review, we address the different approaches to the steps needed for this surveillance: sampling wastewaters (WWs), concentrating the virus from the samples and quantifying them by qPCR, focusing on the main limitations of the methodologies used. Factors that can influence SARS‐CoV‐2 monitoring in WWs include: (i) physical parameters as temperature that can hamper the detection in warm seasons and tropical regions, (ii) sampling methodologies and timetables, being composite samples and Moore swabs the less variable and more sensitive approaches, (iii) virus concentration methodologies that need to be feasible and practicable in simpler laboratories and (iv) detection methodologies that should tend to use faster and cost‐effective procedures. The efficiency of WW treatments and the use of WWs for SARS‐CoV‐2 variants detection are also addressed. Furthermore, we discuss the need for the development of common standardized protocols, although these must be versatile enough to comprise variations among target communities. WBE screening of risk populations will allow for the prediction of future outbreaks, thus alerting authorities to implement early action measurements.
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Affiliation(s)
- José Alhama
- Department of Biochemistry and Molecular Biology, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, Córdoba, 14071, Spain
| | - Juan P Maestre
- Department of Civil, Architectural, and Environmental Engineering, The University of Texas at Austin, 301 E. Dean Keeton St., Stop C1786, Austin, TX, 78712, USA
| | - M Ángeles Martín
- Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Universidad de Córdoba, Institute of Fine Chemistry and Nanochemistry (IUNAN), Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Marie Curie, Córdoba, 14071, Spain
| | - Carmen Michán
- Department of Biochemistry and Molecular Biology, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, Córdoba, 14071, Spain
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Márquez P, Herruzo-Ruiz AM, Siles JA, Alhama J, Michán C, Martín MA. Influence of packing material on the biofiltration of butyric acid: A comparative study from a physico-chemical, olfactometric and microbiological perspective. J Environ Manage 2021; 294:113044. [PMID: 34130131 DOI: 10.1016/j.jenvman.2021.113044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/10/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
The influence of bed material on the odor removal performance of a biofilter was studied. A compost-wood biofilter and a wood biofilter were treated with a gaseous stream contaminated with butyric acid and comparatively evaluated at pilot scale using olfactometric, physico-chemical and microbiological approaches. The variables analyzed in both biofilters were correlated with specific families of their microbiota composition. In addition to a higher nutrients content (nitrogen and phosphorus), the compost-wood biofilter registered maximum values in number of aerobic microorganisms (3.6·108 CFU/g) and in aerobic microbiological activity (≈40 mg O2/g VS of cumulative oxygen demand at 20 h). This may explain the higher performance of this biofilter compared to the wood biofilter, withstanding odor loads of up to 1450 ouE/m2·s with odor removal efficiencies close to 100%. The analysis of the microbial community showed that Actinobacteria, particularly the mostly aerobic Microbacteriaceae family, might play an important role in butyric acid degradation and hence reduce odor impact. The multidisciplinary analysis carried out in this work could be a very useful strategy for the optimal design of biofiltration operations.
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Affiliation(s)
- P Márquez
- Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Universidad de Córdoba, Campus Universitario de Rabanales, Carretera N-IV, Km 396, Edificio Marie Curie, 14071, Córdoba, Spain
| | - A M Herruzo-Ruiz
- Department of Biochemistry and Molecular Biology, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, 14071, Córdoba, Spain
| | - J A Siles
- Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Universidad de Córdoba, Campus Universitario de Rabanales, Carretera N-IV, Km 396, Edificio Marie Curie, 14071, Córdoba, Spain
| | - J Alhama
- Department of Biochemistry and Molecular Biology, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, 14071, Córdoba, Spain
| | - C Michán
- Department of Biochemistry and Molecular Biology, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, 14071, Córdoba, Spain
| | - M A Martín
- Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Universidad de Córdoba, Campus Universitario de Rabanales, Carretera N-IV, Km 396, Edificio Marie Curie, 14071, Córdoba, Spain.
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Herruzo-Ruiz AM, Fuentes-Almagro CA, Jiménez-Pastor JM, Pérez-Rosa VM, Blasco J, Michán C, Alhama J. Meta-omic evaluation of bacterial microbial community structure and activity for the environmental assessment of soils: overcoming protein extraction pitfalls. Environ Microbiol 2021; 23:4706-4725. [PMID: 34258847 DOI: 10.1111/1462-2920.15673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/08/2021] [Accepted: 07/11/2021] [Indexed: 11/27/2022]
Abstract
Microorganisms play unique, essential and integral roles in the biosphere. This work aims to assess the utility of soil's metaomics for environmental diagnosis. Doñana National Park (DNP) was selected as a natural lab since it contains a strictly protected core that is surrounded by numerous threats of pollution. Culture-independent high-throughput molecular tools were used to evaluate the alterations of the global structure and metabolic activities of the microbiome. 16S rRNA sequencing shows lower bacterial abundance and diversity in areas historically exposed to contamination that surround DNP. For metaproteomics, an innovative post-alkaline protein extraction protocol was developed. After NaOH treatment, successive washing with Tris-HCl buffer supplemented with glycerol was essential to eliminate interferences. Starting from soils with different physicochemical characteristics, the method renders proteins with a remarkable resolution on SDS-PAGE gels. The proteins extracted were analysed by using an in-house database constructed from the rRNA data. LC-MS/MS analysis identified 2182 non-redundant proteins with 135 showing significant differences in relative abundance in the soils around DNP. Relevant global biological processes were altered in response to the environmental changes, such as protective and antioxidant mechanisms, translation, folding and homeostasis of proteins, membrane transport and aerobic respiratory metabolism.
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Affiliation(s)
- Ana M Herruzo-Ruiz
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| | | | - José M Jiménez-Pastor
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| | - Víctor M Pérez-Rosa
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| | - Julián Blasco
- Department of Ecology and Coastal Management, ICMAN-CSIC, Campus Rio San Pedro, Puerto Real, E-11510, Spain
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| | - José Alhama
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
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10
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Michán C, Blasco J, Alhama J. High-throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments. Microb Biotechnol 2021; 14:870-885. [PMID: 33559398 PMCID: PMC8085945 DOI: 10.1111/1751-7915.13763] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
Aquatic environments are the recipients of many sources of environmental stress that trigger both local and global changes. To evaluate the associated risks to organisms and ecosystems more sensitive and accurate strategies are required. The analysis of the microbiome is one of the most promising candidates for environmental diagnosis of aquatic systems. Culture-independent interconnected meta-omic approaches are being increasing used to fill the gaps that classical microbial approaches cannot resolve. Here, we provide a prospective view of the increasing application of these high-throughput molecular technologies to evaluate the structure and functional activity of microbial communities in response to changes and disturbances in the environment, mostly of anthropogenic origin. Some relevant topics are reviewed, such as: (i) the use of microorganisms for water quality assessment, highlighting the incidence of antimicrobial resistance as an increasingly serious threat to global public health; (ii) the crucial role of microorganisms and their complex relationships with the ongoing climate change, and other stress threats; (iii) the responses of the environmental microbiome to extreme pollution conditions, such as acid mine drainage or oil spills. Moreover, protists and viruses, due to their huge impacts on the structure of microbial communities, are emerging candidates for the assessment of aquatic environmental health.
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Affiliation(s)
- Carmen Michán
- Departamento de Bioquímica y Biología MolecularCampus de Excelencia Internacional Agroalimentario CeiA3Universidad de CórdobaCampus de Rabanales, Edificio Severo OchoaCórdobaE‐14071Spain
| | - Julián Blasco
- Department of Ecology and Coastal ManagementICMAN‐CSICCampus Rio San PedroPuerto Real (Cádiz)E‐11510Spain
| | - José Alhama
- Departamento de Bioquímica y Biología MolecularCampus de Excelencia Internacional Agroalimentario CeiA3Universidad de CórdobaCampus de Rabanales, Edificio Severo OchoaCórdobaE‐14071Spain
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11
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Reyes J, Toledo M, Michán C, Siles JA, Alhama J, Martín MA. Biofiltration of butyric acid: Monitoring odor abatement and microbial communities. Environ Res 2020; 190:110057. [PMID: 32805248 DOI: 10.1016/j.envres.2020.110057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/10/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
The objective of this study is to evaluate comparatively the odor removal efficacy of two biofilters operated under different conditions and to identify taxonomically the microbial communities responsible for butyric acid degradation. Both biofiltration systems, which were filled with non-inoculated wood chips and exposed to gas streams containing butyric acid, were evaluated under different operational conditions (gas airflow and temperature) from the physical-chemical, microbiological and olfactometric points of view. The physical-chemical characterization showed the acidification of the packing material and the accumulation of butyric acid during the biofiltration process (<60 days). The removal efficacy was found to be 98-100% during the first 20 days of operation, even at high odor concentration. Changes in the operational temperature increased the odor load factor from 400 to 1400 ouE/m2·s, which led to the reduction of microbiota in the packing material, and a drastic drop of the odor removal efficacy. However, the progressive increase in gas airflow improved the biodegradation efficacy of butyric acid up to 88% with odor loadings as high as 33,000 ouE/m3, while a linear relationship between odor inlet load and removal capacity was also found. The analysis of the microbial community showed that Proteobacteria was the most abundant phylum along the biofiltration time (58-92%) and regardless of the operational conditions. Finally, principal component analysis applied to the physical-chemical and microbiological data set revealed significant differences between the two biofilters under study.
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Affiliation(s)
- J Reyes
- Chemical Engineering Department, University of Cordoba, Campus Universitario de Rabanales, Ctra. N-IV, Km 396, Building Marie Curie (C-3), 14071, Córdoba, Spain
| | - M Toledo
- Chemical Engineering Department, University of Cordoba, Campus Universitario de Rabanales, Ctra. N-IV, Km 396, Building Marie Curie (C-3), 14071, Córdoba, Spain
| | - C Michán
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus Universitario de Rabanales, Ctra. N-IV, Km 396, Building Severo Ochoa, 14071, Córdoba, Spain
| | - J A Siles
- Chemical Engineering Department, University of Cordoba, Campus Universitario de Rabanales, Ctra. N-IV, Km 396, Building Marie Curie (C-3), 14071, Córdoba, Spain
| | - J Alhama
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus Universitario de Rabanales, Ctra. N-IV, Km 396, Building Severo Ochoa, 14071, Córdoba, Spain
| | - M A Martín
- Chemical Engineering Department, University of Cordoba, Campus Universitario de Rabanales, Ctra. N-IV, Km 396, Building Marie Curie (C-3), 14071, Córdoba, Spain.
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12
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Ruiz-Castilla FJ, Bieber J, Caro G, Michán C, Sychrova H, Ramos J. Regulation and activity of CaTrk1, CaAcu1 and CaHak1, the three plasma membrane potassium transporters in Candida albicans. Biochim Biophys Acta Biomembr 2020; 1863:183486. [PMID: 33069635 DOI: 10.1016/j.bbamem.2020.183486] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/25/2020] [Accepted: 10/02/2020] [Indexed: 11/16/2022]
Abstract
Wild-type cells of Candida albicans, the most common human fungal pathogen, are able to grow at very low micromolar concentrations of potassium in the external milieu. One of the reasons behind that behaviour is the existence of three different types of K+ transporters in their plasma membrane: Trk1, Acu1 and Hak1. This work shows that the transporters are very differently regulated at the transcriptional level upon exposure to saline stress, pH alterations or K+ starvation. We propose that different transporters take the lead in the diverse environmental conditions, Trk1 being the "house-keeping" one, and Acu1/Hak1 dominating upon K+ limiting conditions. Heterologous expression of the genes coding for the three transporters in a Saccharomyces cerevisiae strain lacking its endogenous potassium transporters showed that all of them mediated cation transport but with very different efficiencies. Moreover, expression of the transporters in S. cerevisiae also affected other physiological characteristics such as sodium and lithium tolerance, membrane potential or intracellular pH, being, in general, CaTrk1 the most effective in keeping these parameters close to the usual wild-type physiological levels.
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Affiliation(s)
| | - Jan Bieber
- Laboratory of Membrane Transport, Institute of Physiology, Czech Academy of Sciences, 142 20 Prague 4, Czech Republic
| | - Gabriel Caro
- Department of Microbiology, University of Córdoba, 14071 Córdoba, Spain
| | - Carmen Michán
- Department of Biochemistry and Molecular Biology, Campus de Excelencia Internacional Agroalimentario CeiA3, University of Córdoba, 14071 Córdoba, Spain
| | - Hana Sychrova
- Laboratory of Membrane Transport, Institute of Physiology, Czech Academy of Sciences, 142 20 Prague 4, Czech Republic
| | - José Ramos
- Department of Microbiology, University of Córdoba, 14071 Córdoba, Spain.
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13
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Siles JA, Michán C. Bacteria, archae, fungi and viruses: it takes a community to eliminate waste. Microb Biotechnol 2020; 13:892-894. [PMID: 31701639 PMCID: PMC7264746 DOI: 10.1111/1751-7915.13503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 11/28/2022] Open
Abstract
Importance of the microbiota communities for improving the efficiency in Waste Water Treatment Plants.
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Affiliation(s)
- José Angel Siles
- Departamento de Química Inorgánica e Ingeniería QuímicaUniversidad de CórdobaCampus Universitario de Rabanales, edificio Marie Curie C‐3, planta baja14071CórdobaSpain
| | - Carmen Michán
- Departamento de Bioquímica y Biología MolecularUniversidad de Córdoba Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa C‐6, 2ª Planta14071CórdobaSpain
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14
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Bejaoui S, Michán C, Telahigue K, Nechi S, Cafsi ME, Soudani N, Blasco J, Costa PM, Alhama J. Metal body burden and tissue oxidative status in the bivalve Venerupis decussata from Tunisian coastal lagoons. Mar Environ Res 2020; 159:105000. [PMID: 32662434 DOI: 10.1016/j.marenvres.2020.105000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
Coastal transitional waters are exposed to many anthropogenic threats. This study aims to assess the trace metals' pollution status of transitional waters by evaluating its biological effects in the clam Venerupis decussata. Among the studied sites along the Tunisian littoral, South Tunis and Boughrara were the most impacted, since clams from these two lagoons presented significant differences in: (i) trace metal contents, (ii) in-cell hydrogen peroxide, (iii) enzymatic and non-enzymatic defenses, (iv) damage to lipids and proteins, and (v) protein post-translational modifications. These changes related to evident histopathological traits. PCA showed a clear separation between the digestive gland and gills tissues and illustrated an impact gradient in Tunisian coastal lagoons. Water temperature was revealed as an added natural stressor that, when concurring with high pollution, may jeopardize an ecosystem's health and contribute to the accumulation of hazardous metals in organisms.
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Affiliation(s)
- Safa Bejaoui
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain; Laboratory of Ecology, Biology and Physiology of Aquatic Organisms, Biology Department, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain
| | - Khaoula Telahigue
- Anatomy and Cytology Service, CHU Mohamed Taher Maamouri Hospital, University Tunis El Manar, Tunis, Tunisia
| | - Salwa Nechi
- Anatomy and Cytology Service, CHU Mohamed Taher Maamouri Hospital, University Tunis El Manar, Tunis, Tunisia
| | - Mhamed El Cafsi
- Laboratory of Ecology, Biology and Physiology of Aquatic Organisms, Biology Department, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Nejla Soudani
- Laboratory of Ecology, Biology and Physiology of Aquatic Organisms, Biology Department, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Julián Blasco
- Dpt. Ecology and Coastal Management, ICMAN-CSIC, Campus Rio San Pedro, E-11510, Puerto Real (Cadiz), Spain
| | - Pedro M Costa
- UCIBIO - Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - José Alhama
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain.
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15
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Huertas MJ, Michán C. Paving the way for the production of secretory proteins by yeast cell factories. Microb Biotechnol 2019; 12:1095-1096. [PMID: 30735012 PMCID: PMC6801135 DOI: 10.1111/1751-7915.13342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 11/06/2018] [Indexed: 01/23/2023] Open
Affiliation(s)
- Maria José Huertas
- Instituto de Bioquímica Vegetal y FotosíntesisUniversidad de Sevilla‐CSICAmérico Vespucio 4941092SevillaSpain
| | - Carmen Michán
- Departamento de Bioquímica y Biología MolecularCampus de Excelencia Internacional Agroalimentario CeiA3Universidad de CórdobaEdificio Severo Ochoa C‐6, 2Planta14071CórdobaSpain
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16
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Ramos-Moreno L, Ramos J, Michán C. Overlapping responses between salt and oxidative stress in Debaryomyces hansenii. World J Microbiol Biotechnol 2019; 35:170. [PMID: 31673816 DOI: 10.1007/s11274-019-2753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 11/26/2022]
Abstract
Debaryomyces hansenii is a halotolerant yeast of importance in basic and applied research. Previous reports hinted about possible links between saline and oxidative stress responses in this yeast. The aim of this work was to study that hypothesis at different molecular levels, investigating after oxidative and saline stress: (i) transcription of seven genes related to oxidative and/or saline responses, (ii) activity of two main anti-oxidative enzymes, (iii) existence of common metabolic intermediates, and (iv) generation of damages to biomolecules as lipids and proteins. Our results showed how expression of genes related to oxidative stress was induced by exposure to NaCl and KCl, and, vice versa, transcription of some genes related to osmotic/salt stress responses was regulated by H2O2. Moreover, and contrary to S. cerevisiae, in D. hansenii HOG1 and MSN2 genes were modulated by stress at their transcriptional level. At the enzymatic level, saline stress also induced antioxidative enzymatic defenses as catalase and glutathione reductase. Furthermore, we demonstrated that both stresses are connected by the generation of intracellular ROS, and that hydrogen peroxide can affect the accumulation of in-cell sodium. On the other hand, no significant alterations in lipid oxidation or total glutathione content were observed upon exposure to both stresses tested. The results described in this work could help to understand the responses to both stressors, and to improve the biotechnological potential of D. hansenni.
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Affiliation(s)
- Laura Ramos-Moreno
- Departamento de Microbiología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, 14071, Córdoba, España, Spain
| | - José Ramos
- Departamento de Microbiología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, 14071, Córdoba, España, Spain
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, 14071, Córdoba, España, Spain.
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17
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Michán C, Chicano-Gálvez E, Fuentes-Almagro CA, Alhama J. Redox and global interconnected proteome changes in mice exposed to complex environmental hazards surrounding Doñana National Park. Environ Pollut 2019; 252:427-439. [PMID: 31158671 DOI: 10.1016/j.envpol.2019.05.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/30/2019] [Accepted: 05/16/2019] [Indexed: 06/09/2023]
Abstract
Natural environments are receiving an increasing number of contaminants. Therefore, the evaluation and identification of early responses to pollution in these complex habitats is an urgent and challenging task. Doñana National Park (DNP, SW Spain) has been widely used as a model area for environmental studies because, despite its strictly protected core, it is surrounded by numerous threat sources from agricultural, mining and industrial activities. Since many pollutants often induce oxidative stress, redox proteomics was used to detect redox-based variations within the proteome of Mus spretus mice captured in DNP and the surrounding areas. Functional analysis showed that most differentially oxidized proteins are involved in the maintenance of homeostasis, by eliciting mechanisms to respond to toxic substances and oxidative stress, such as antioxidant and biotransformation processes, immune and inflammatory responses, and blood coagulation. Furthermore, changes in the overall protein abundance were also analysed by label-free quantitative proteomics. The upregulation of phase I and II biotransformation enzymes in mice from Lucio del Palacio may be an alert for organic pollution in the area located at the heart of DNP. Metabolic processes involved in protein turnover (proteolysis, amino acid catabolism, new protein biosynthesis and folding) were activated in response to oxidative damage to these biomolecules. Consequently, aerobic respiratory metabolism increased to address the greater ATP demands. Alterations of cholesterol metabolism that could cause hepatic steatosis were also detected. The proteomic detection of globally altered metabolic and physiological processes offers a complete view of the main biological changes caused by environmental pollution in complex habitats.
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Affiliation(s)
- Carmen Michán
- Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | | | | | - José Alhama
- Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain.
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18
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Alhama J, Fuentes-Almagro CA, Abril N, Michán C. Alterations in oxidative responses and post-translational modification caused by p,p´-DDE in Mus spretus testes reveal Cys oxidation status in proteins related to cell-redox homeostasis and male fertility. Sci Total Environ 2018; 636:656-669. [PMID: 29723838 DOI: 10.1016/j.scitotenv.2018.04.305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
The major derivate of DDT, 1,1-dichloro-2,2-bis (p-chlorophenyl) ethylene (p,p´-DDE), is a persistent pollutant previously associated with oxidative stress. Additionally, p,p´-DDE has been linked to several metabolic alterations related to sexual function in rodents. In this study, we analysed the effects of a non-lethal p,p´-DDE dose to Mus spretus mice in testes, focusing on oxidative damage to biomolecules, defence mechanisms against oxidative stress and post-translational protein modifications. No increase in lipid or DNA oxidation was observed, although antioxidative enzymatic defences and redox status of glutathione were altered in several ways. Global protein carbonylation and phosphorylation were significantly reduced in testes from p,p´-DDE-exposed mice; however, the total redox state of Cys thiols did not exhibit a defined pattern. We analysed the reversible redox state of specific Cys residues in detail with differential isotopic labelling and a shotgun labelling-based MS/MS proteomic approach for identification and quantification of altered peptides. Our results show that Cys residues are significantly affected by p,p´-DDE in several proteins related to oxidative stress and/or male fertility, particularly those participating in fertilization, sperm capacitation and blood coagulation. These molecular changes could explain the sexual abnormalities previously described in p,p´-DDE exposed organisms.
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Affiliation(s)
- José Alhama
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - Carlos A Fuentes-Almagro
- Servicio Central de Apoyo a la Investigación (SCAI), Unidad de Proteómica, Universidad de Córdoba, Campus de Rabanales, Edificio Ramón y Cajal, E-14071 Córdoba, Spain
| | - Nieves Abril
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain.
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19
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Ramos J, Melero Y, Ramos-Moreno L, Michán C, Cabezas L. Debaryomyces hansenii Strains from Valle De Los Pedroches Iberian Dry Meat Products: Isolation, Identification, Characterization, and Selection for Starter Cultures. J Microbiol Biotechnol 2017; 27:1576-1585. [DOI: 10.4014/jmb.1704.04045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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20
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Prista C, Michán C, Miranda IM, Ramos J. The halotolerant Debaryomyces hansenii, the Cinderella of non-conventional yeasts. Yeast 2016; 33:523-533. [PMID: 27279567 DOI: 10.1002/yea.3177] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/10/2016] [Accepted: 05/10/2016] [Indexed: 11/10/2022] Open
Abstract
Debaryomyces hansenii is a halotolerant yeast with a high biotechnological potential, particularly in the food industry. However, research in this yeast is limited by its molecular peculiarities. In this review we summarize the state of the art of research in this microorganisms, describing both pros and cons. We discuss (i) its halotolerance, (ii) the molecular factors involved in saline and osmotic stress, (iii) its high gene density and ambiguous CUG decoding, and (iv) its biotechnological and medical interests. We trust that all the bottlenecks in its study will soon be overcome and D. hansenii will become a fundamental organism for food biotechnological processes. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Catarina Prista
- LEAF - Research Centre Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, 1649-003, Portugal
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Isabel M Miranda
- Department of Microbiology, Faculty of Medicine, University of Porto, Porto, Portugal.,CINTESIS - Centre for Health Technology and Services Research, Faculty of Medicine of the University of Porto, Portugal
| | - José Ramos
- Departamento de Microbiología, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain.
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21
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Abril N, Chicano-Gálvez E, Michán C, Pueyo C, López-Barea J. iTRAQ analysis of hepatic proteins in free-living Mus spretus mice to assess the contamination status of areas surrounding Doñana National Park (SW Spain). Sci Total Environ 2015; 523:16-27. [PMID: 25847312 DOI: 10.1016/j.scitotenv.2015.03.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 03/26/2015] [Accepted: 03/26/2015] [Indexed: 05/22/2023]
Abstract
This work aims to develop and integrate new -omics tools that would be applicable to different ecosystem types for a technological updating of environmental evaluations. We used a 2nd-generation (iTRAQ-8plex) proteomic approach to identify/quantify proteins differentially expressed in the liver of free-living Mus spretus mice from Doñana National Park or its proximities. Mass spectrometry was performed in an LTQ Orbitrap system for iTRAQ reporter ion quantitation and protein identification using a Mus musculus database as reference. A prior IEF step improved the separation of the complex peptide mixture. Over 2000 identified proteins were altered, of which 118 changed by ≥2.5-fold in mice from at least two problem sites. Part of the results obtained with the iTRAQ analysis was confirmed by Western blot. Over 75% of the 118 proteins were upregulated in animals captured at polluted sites and only 16 proteins were downregulated. Upregulated proteins were involved in stress response; cell proliferation and apoptosis; signal transduction; metastasis or tumour suppression; xenobiotic export or vesicular trafficking; and metabolism. The downregulated proteins, all potentially harmful, were classified as oncoproteins and proteins favouring genome instability. The iTRAQ results presented here demonstrated that the survival of hepatic cells is compromised in animals living at polluted sites, which showed deep alterations in metabolism and the signalling pathways. The identified proteins may be useful as biomarkers of environmental pollution and provide insight about the metabolic pathways and/or physiological processes affected by pollutants in DNP and its surrounding areas.
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Affiliation(s)
- Nieves Abril
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence (ceiA3-UCO), University of Córdoba, Severo Ochoa Building, Rabanales Campus, 14071 Córdoba, Spain
| | - Eduardo Chicano-Gálvez
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence (ceiA3-UCO), University of Córdoba, Severo Ochoa Building, Rabanales Campus, 14071 Córdoba, Spain
| | - Carmen Michán
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence (ceiA3-UCO), University of Córdoba, Severo Ochoa Building, Rabanales Campus, 14071 Córdoba, Spain
| | - Carmen Pueyo
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence (ceiA3-UCO), University of Córdoba, Severo Ochoa Building, Rabanales Campus, 14071 Córdoba, Spain
| | - Juan López-Barea
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence (ceiA3-UCO), University of Córdoba, Severo Ochoa Building, Rabanales Campus, 14071 Córdoba, Spain.
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Affiliation(s)
- M José Huertas
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Isla de la Cartuja, Universidad de Sevilla-CSICAv. Américo Vespucio 49, 41092, Seville, Spain
| | - Carmen Michán
- Campus de Rabanales, Department of Biochemistry and Molecular Biology, Universidad de CórdobaEdificio Severo Ochoa C-6, 2a Planta, 14071, Córdoba, Spain
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Affiliation(s)
- M José Huertas
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Isla de la Cartuja, Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, 41092 Seville, Spain
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Michán C, Martínez JL, Alvarez MC, Turk M, Sychrova H, Ramos J. Salt and oxidative stress tolerance in Debaryomyces hansenii and Debaryomyces fabryi. FEMS Yeast Res 2012; 13:180-8. [PMID: 23122272 DOI: 10.1111/1567-1364.12020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 09/24/2012] [Accepted: 10/30/2012] [Indexed: 11/28/2022] Open
Abstract
We report the characterization of five strains belonging to the halotolerant highly related Debaryomyces hansenii/fabryi species. The analysis performed consisted in studying tolerance properties, membrane characteristics, and cation incell amounts. We have specifically investigated (1) tolerance to different chemicals, (2) tolerance to osmotic and salt stress, (3) tolerance and response to oxidative stress, (4) reactive oxygen species (ROS) content, (5) relative membrane potential, (6) cell volume, (7) K(+) and Na(+) ion content, and (8) membrane fluidity. Unexpectedly, no direct relationship was found between one particular strain, Na(+) content and its tolerance to NaCl or between its ROS content and its tolerance to H(2)O(2). Results show that, although in general, human origin D. fabryi strains were more resistant to oxidative stress and presented shorter doubling times and smaller cell volume than food isolated D. hansenii ones, strains belonging to the same species can be significantly different. Debaryomyces fabryi CBS1793 strain highlighted for its extremely tolerant behavior when exposed to the diverse stress factors studied.
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Affiliation(s)
- Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
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Molina-Santiago C, Udaondo Z, Marin A, García-Salamanca A, Michán C, Daniels C, Molina L, Ramos JL. Evolution of antibiotic resistance, catabolic pathways and niche colonization. Microb Biotechnol 2012; 5:452-4. [PMID: 22676058 PMCID: PMC3815322 DOI: 10.1111/j.1751-7915.2012.00335.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Carlos Molina-Santiago
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, Granada, Spain
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Affiliation(s)
- Carmen Michán
- Universidad de Córdoba, Campus de Rabanales, Department of Biochemistry and Molecular Biology, Edificio Severo Ochoa C-6, 2aPlanta, 14071, Córdoba, Spain
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Vargas P, Felipe A, Michán C, Gallegos MT. Induction of Pseudomonas syringae pv. tomato DC3000 MexAB-OprM multidrug efflux pump by flavonoids is mediated by the repressor PmeR. Mol Plant Microbe Interact 2011; 24:1207-19. [PMID: 21649511 DOI: 10.1094/mpmi-03-11-0077] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In this study, we have analyzed the expression of the Pseudomonas syringae pv. tomato DC3000 mexAB-oprM efflux pump operon and of the regulatory gene pmeR, and we have investigated the role of the PmeR protein on transcription from both promoters. We demonstrate that mexAB-oprM and pmeR are expressed in vivo at a relatively high and moderate basal level, respectively, which, in both cases, increases in the presence of different flavonoids and other compounds, such as butyl and methylparaben. We show that PmeR is the local repressor of the mexAB-oprM promoter and is able to regulate its own expression. The mechanism for this regulation includes binding to a pseudopalindromic operator site which overlaps both mexAB-oprM and pmeR promoters. We have also proven that flavonoids are able to interact with PmeR and induce a conformational change that interferes with the DNA binding ability of PmeR, thereby modulating mexAB-oprM and pmeR expression. Finally, we demonstrate by in vivo experiments that the PmeR/MexAB-OprM system contributes to the colonization of tomato plants. These results provide new insight into a transcriptional regulator and a transport system that play essential roles in the ability of P. syringae pv. tomato DC3000 to resist the action of flavonoids produced by the host.
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Affiliation(s)
- Paola Vargas
- Department of Soil Microbiology and Symbiotic System, Estación Experimental del Zaidin, Granada, Spain
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Daniels C, Michán C, Ramos JL. Cold is cool, the human microbiota and taking multiple SIPs. Microb Biotechnol 2011; 4:554-7. [PMID: 21848612 PMCID: PMC3819006 DOI: 10.1111/j.1751-7915.2011.00287.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- Craig Daniels
- Structural Proteomics in Toronto, UHN and University of Toronto, Banting and Best Department of Medical Research, Toronto, Ontario, Canada
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Daniels C, Ramos J, Molina‐Santiago C, Michán C. Directed evolution, natural products for cancer chemotherapy, and micro-biosensing robots. Microb Biotechnol 2011; 4:314-7. [PMID: 21518297 PMCID: PMC3818989 DOI: 10.1111/j.1751-7915.2011.00267.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Craig Daniels
- Structural Proteomics in Toronto, UHN and University of Toronto, Banting and Best Department of Medical Research; C.H. Best Institute 112 College Street, M5G 1L6, Toronto, Ontario, Canada
| | - Juan‐Luis Ramos
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, E‐18008 Granada, Spain
| | - Carlos Molina‐Santiago
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, E‐18008 Granada, Spain
| | - Carmen Michán
- Universidad de Córdoba, Campus de Rabanales, Dept. of Biochemistry and Molecular Biology, Edificio Severo Ochoa C‐6, 2Planta, 14071, Córdoba, Spain
- *E‐mail ; Tel. (+34) 957 218082; Fax (+34) 957 218688
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Daniels C, Michán C, Ramos JL. New molecular tools for enhancing methane production, explaining thermodynamically limited lifestyles and other important biotechnological issues. Microb Biotechnol 2011; 2:533-6. [PMID: 21255285 PMCID: PMC3815360 DOI: 10.1111/j.1751-7915.2009.00134.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Craig Daniels
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental Protection, C/ Prof. Albareda, 1, E-18008 Granada, Spain
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Abstract
In the following highlight we refer to a number of new advances in the field of Biotechnology that address issues relating to the synthesis of new antibiotics, new biocatalysts and matrices in biofilms.
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Affiliation(s)
- Craig Daniels
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Dept. of Environmental Protection, C/ Prof. Albareda, 1, E-18008 Granada, Spain
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Michán C, Daniels C, Fernández M, Solano J, De La Campa AM, Ramos JL. Sugar (ribose), spice (peroxidase) and all things nice (laccase hair-dyes). Microb Biotechnol 2011; 3:131-3. [PMID: 21255315 PMCID: PMC3836576 DOI: 10.1111/j.1751-7915.2010.00167.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Carmen Michán
- Universidad de Córdoba, Campus de Rabanales, Department. of Biochemistry and Molecular Biology, Edificio Severo Ochoa C-6, 2a Planta, 14071, Córdoba, Spain
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Affiliation(s)
- Craig Daniels
- Structural Proteomics in Toronto, UHN and University of Toronto, Banting and Best Department of Medical Research, C.H. Best Institute 112 College Street, M5G 1L6, Toronto, Ontario, Canada
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Daniels C, Krell T, Michán C, Ramos JL. Struggling to get a universal meningococcal vaccine and novel uses for bacterial toxins in cancer treatment. Microb Biotechnol 2011; 3:359-61. [PMID: 21255335 PMCID: PMC3815803 DOI: 10.1111/j.1751-7915.2010.00195.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Craig Daniels
- Structural Proteomics in Toronto, UHN and University of Toronto, Banting and Best Department of Medical Research, C.H. Best Institute, 112 College Street, M5G 1L6, Toronto, Ontario, Canada
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Michán C, Daniels C, Ramos J. New molecular techniques for pathogen analysis, in silico
determination of RND efflux pump substrate specificity, shotgun proteomic monitoring of bioremediation and yeast bio-applications. Microb Biotechnol 2010. [PMCID: PMC3815337 DOI: 10.1111/j.1751-7915.2010.00225.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Carmen Michán
- Universidad de Córdoba, Campus de Rabanales, Dept. of Biochemistry and Molecular Biology, Edificio Severo Ochoa C‐6, 2 Planta, 14071, Córdoba, Spain
| | - Craig Daniels
- Structural Proteomics in Toronto, UHN and University of Toronto, Banting and Best Department of Medical Research, C.H. Best Institute 112 College Street, M5G 1L6, Toronto, Ontario, Canada
| | - Juan‐Luis Ramos
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, E‐18008 Granada, Spain
- *E‐mail ; Tel. (+34) 958 181608; Fax (+34) 958 135740
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Affiliation(s)
- Craig Daniels
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental Protection, C/ Prof. Albareda, 1, E-18008 Granada, Spain
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Michán C, Pueyo C. Growth phase-dependent variations in transcript profiles for thioredoxin- and glutathione-dependent redox systems followed by budding and hyphal Candida albicans cultures. FEMS Yeast Res 2009; 9:1078-90. [PMID: 19702871 DOI: 10.1111/j.1567-1364.2009.00558.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We report the absolute transcription profiles of 24 genes coding for putative thioredoxin (Trx)- and glutathione (GSH)-dependent redox system components, accompanying the Candida albicans batch culture growth, under either yeast or hyphal conditions. All mRNAs investigated (plus the housekeeping ACT1) displayed significant alterations in their steady-state copy number. Collectively, these quantifications show that: (1) the most abundant mRNAs during active growth coded for putative thiol peroxidases (TSA1, PRX1, AHP11 and AHP12) and for donor thioredoxin Trx1p, i.e. those five mRNAs represented >74% of all transcript molecules quantified in a late exponential phase; (2) the transcripts under study differed between budding and hyphal cells not only in their abundance but also in their profiles throughout the growth stages; (3) mRNA amounts for four GSH-transferase putative genes (GTT12, GTT13, GTT14 and GST3) increased in the stationary phase in yeast but not under filamentous conditions. Hydrogen peroxide resistance, plus GSH, GSSG and reactive oxygen species contents, throughout yeast and hyphal growth, were also studied, and the differences observed were related to the transcript profiles.
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Affiliation(s)
- Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, 14071 Córdoba, Spain.
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Michán C, Ramos JL, Daniels C. Twenty one important things you should know. Microb Biotechnol 2009; 2:397-400. [PMID: 21255270 PMCID: PMC3815899 DOI: 10.1111/j.1751-7915.2009.00128.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Carmen Michán
- Universidad de Córdoba, Campus de Rabanales, Dept. of Biochemistry and Molecular Biology, Edificio Severo Ochoa C-6, 2a Planta, 14071, Córdoba, Spain
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Michán C, Monje-Casas F, Pueyo C. Transcript copy number of genes for DNA repair and translesion synthesis in yeast: contribution of transcription rate and mRNA stability to the steady-state level of each mRNA along with growth in glucose-fermentative medium. DNA Repair (Amst) 2005; 4:469-78. [PMID: 15725627 DOI: 10.1016/j.dnarep.2004.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2004] [Revised: 12/02/2004] [Accepted: 12/06/2004] [Indexed: 11/24/2022]
Abstract
We quantitated the copy number of mRNAs (NTG1, NTG2, OGG1, APN1, APN2, MSH2, MSH6, REV3, RAD30) encoding different DNA repair enzymes and translesion-synthesis polymerases in yeast. Quantitations reported examine how the steady-state number of each transcript is modulated in association with the growth in glucose-fermentative medium, and evaluate the respective contribution of the rate of mRNA degradation and transcription initiation to the specific mRNA level profile of each gene. Each transcript displayed a unique growth-related profile, therefore altering the relative abundance of mRNAs coding for proteins with similar functions, as cells proceed from exponential to stationary phase. Nonetheless, as general trend, they exhibited maximal levels when cells proliferate rapidly and minimal values when cells cease proliferation. We found that previous calculations on the stability of the investigated mRNAs might be biased, in particular regarding those that respond to heat shock stress. Overall, the mRNAs experienced drastic increments in their stabilities in response to gradual depletion of essential nutrients in the culture. However, differences among the mRNA stability profiles suggest a dynamic modulation rather than a passive process. As general rule, the investigated genes were much more frequently transcribed during the fermentative growth than later during the diauxic arrest and the stationary phase, this finding conciliating low steady-state levels with increased mRNA stabilities. Interestingly, while the rate at which each gene is transcribed appeared as the only determinant of the number of mRNA copies at the exponential growth, later, when cell growth is arrested, the rate of mRNA degradation becomes also a key factor for gene expression. In short, our results raise the question of how important the respective contribution of transcription and mRNA stability mechanisms is for the steady-state profile of a given transcript, and how this contribution may change in response to nutrient-availability.
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Affiliation(s)
- Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, edificio Severo Ochoa, planta 2a, Carretera Madrid-Cádiz Km 396-a, Universidad de Córdoba, 14071-Córdoba, Spain
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Abstract
Rob is regarded as a constitutively expressed protein, although little is known about how rob gene is regulated. We show here by reverse transcription-PCR that the transcriptional levels of rob are strongly down-regulated in response to the superoxide-generating agent paraquat (PQ). Repression reached a maximum of 20-fold after 10 min exposure at 10 microM PQ. The magnitude of rob repression was comparable to that of induction quantified for the most sensitive SoxS targets. beta-Galactosidase expression with the rob2::lacZ transcriptional fusion indicates that down-regulation of rob expression takes place, at least in part, at the level of transcription initiation. Moreover, ca. 50% of the rob mRNA was degraded in <1 min after the addition of rifampin to inhibit transcription. This intrinsic short half-life, which is of obvious benefit for a rapid down-regulation after transcription ceases, was unaffected by the addition of PQ. No repression was observed in a soxR-null strain, indicating that the rob transcript level might be negatively modulated by the intracellular amounts of SoxS protein. Gel retardation assays support the idea that in vivo SoxS would block rob transcription directly.
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Affiliation(s)
- Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales edificio C-6, Carretera Madrid-Cádiz KM 396-a, Universidad de Córdoba, 14071 Córdoba, Spain
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Abstract
By multiplex reverse transcription-PCR, we demonstrate that the SoxRS response, which protects cells against superoxide toxicity, is triggered also by hydrogen peroxide. SoxR-dependent inductions of 7. 3-, 7.6-, 4.6-, 2.2-, and 2.6-fold were quantified for soxS, micF, sodA, inaA, and fpr transcripts, respectively. This finding suggests an extensive and tight connectivity between different regulatory pathways in the Escherichia coli response to oxidative stress.
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Affiliation(s)
- M Manchado
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, 14071 Córdoba, Spain
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Michán C, Manchado M, Dorado G, Pueyo C. In vivo transcription of the Escherichia coli oxyR regulon as a function of growth phase and in response to oxidative stress. J Bacteriol 1999; 181:2759-64. [PMID: 10217765 PMCID: PMC93716 DOI: 10.1128/jb.181.9.2759-2764.1999] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Simultaneous expression of seven genes in Escherichia coli was measured by a reverse transcription-multiplex PCR fluorescence procedure. Genes studied were (i) oxyR (transcriptional regulator); (ii) katG, dps, gorA, and ahpCF (controlled by OxyR); (iii) sodA (controlled by SoxRS); and (iv) trxA (not related to OxyR or SoxRS). Except for trxA, transcription of all genes was activated during the course of growth of wild-type bacteria, though notable variations were observed with respect to both the time and extent of activation. Whereas oxyR, katG, dps, and gorA were activated during exponential growth, ahpCF and sodA were stimulated in stationary phase. Maximal induction ranged from 4.6- to 86.5-fold, for gorA and dps, respectively. Treatment with H2O2 stimulated expression of the genes (katG, dps, ahpCF, and gorA) previously identified as members of the OxyR regulon, except for oxyR itself. Induction by H2O2 was a remarkably rapid and reversible process that took place in an OxyR-dependent and sigmaS-independent manner. NaCl induced expression of the genes controlled by OxyR, including the oxyR locus. This transcriptional up-regulation was preserved in a strain with the DeltaoxyR::kan mutation, but it was abolished (ahpCF) or significantly reduced (oxyR and dps) in a strain with the rpoS::Tn10 mutation, potentially reflecting positive transcriptional regulation of the oxyR regulon by sigmaS. Expression of trxA was not increased either by H2O2 stress or by a shift to high-osmolarity conditions.
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Affiliation(s)
- C Michán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, 14071 Córdoba, Spain
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Salto R, Delgado A, Michán C, Marqués S, Ramos JL. Modulation of the function of the signal receptor domain of XylR, a member of a family of prokaryotic enhancer-like positive regulators. J Bacteriol 1998; 180:600-4. [PMID: 9457863 PMCID: PMC106927 DOI: 10.1128/jb.180.3.600-604.1998] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The XylR protein controls expression from the Pseudomonas putida TOL plasmid upper pathway operon promoter (Pu) in response to aromatic effectors. XylR-dependent stimulation of transcription from a Pu::lacZ fusion shows different induction kinetics with different effectors. With toluene, activation followed a hyperbolic curve with an apparent K of 0.95 mM and a maximum beta-galactosidase activity of 2,550 Miller units. With o-nitrotoluene, in contrast, activation followed a sigmoidal curve with an apparent K of 0.55 mM and a Hill coefficient of 2.65. m-Nitrotoluene kept the XylR regulator in an inactive transcriptional form. Therefore, upon binding of an effector, the substituent on the aromatic ring leads to productive or unproductive XylR forms. The different transcriptional states of the XylR regulator are substantiated by XylR mutants. XylRE172K is a mutant regulator that is able to stimulate transcription from the Pu promoter in the presence of m-nitrotoluene; however, its response to m-aminotoluene was negligible, in contrast with the wild-type regulator. These results illustrate the importance of the electrostatic interactions in effector recognition and in the stabilization of productive and unproductive forms by the regulator upon aromatic binding. XylRD135N and XylRD135Q are mutant regulators that are able to stimulate transcription from Pu in the absence of effectors, whereas substitution of Glu for Asp135 in XylRD135E resulted in a mutant whose ability to recognize effectors was severely impaired. Therefore, the conformation of mutant XylRD135Q as well as XylRD135N seemed to mimic that of the wild-type regulator when effector binding occurred, whereas mutant XylRD135E seemed to be blocked in a conformation similar to that of wild-type XylR and XylRE172K upon binding to an inhibitor molecule such as m-nitrotoluene or m-aminotoluene.
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Affiliation(s)
- R Salto
- Department of Biochemistry, Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
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Michán C, Delgado A, Haïdour A, Lucchesi G, Ramos JL. In vivo construction of a hybrid pathway for metabolism of 4-nitrotoluene in Pseudomonas fluorescens. J Bacteriol 1997; 179:3036-8. [PMID: 9139924 PMCID: PMC179070 DOI: 10.1128/jb.179.9.3036-3038.1997] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Pseudomonas fluorescens 410PR grows on 4-nitrobenzoate but does not metabolize 4-nitrotoluene. The TOL pWW0 delta pm plasmid converts 4-nitrotoluene into 4-nitrobenzoate through its upper pathway, but it does not metabolize 4-nitrobenzoate. P. fluorescens 410PR(pWW0 delta pm) transconjugants were isolated and found to be able to grow on 4-nitrotoluene. This phenotype was stable after growth for at least 300 generations without any selective pressure. P. fluorescens 410PR(pWW0 delta pm) converted 4-nitrotoluene into 4-nitrobenzoate via 4-nitrobenzylalcohol and 4-nitrobenzaldehyde. 4-Nitrobenzoate was metabolized via 4-hydroxylaminobenzoate and finally yielded NH4+ and 3,4-dihydroxybenzoate, which was mineralized.
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Affiliation(s)
- C Michán
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Biochemistry and Molecular and Cellular Biology of Plants, Granada, Spain.
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Abstract
At least twenty-seven proteins belong to the XylS/AraC family of prokaryote transcriptional regulators. All members of this family except CelD and TetD are positive transcriptional factors. Three subgroups were distinguished within the family in accordance with the Needleman and Wunsch algorithm. Multiple alignment of these proteins revealed that they shared a high degree of sequence homology at their C-terminal end, where a characteristic conserved motif, whose consensus sequence is I-DIA--GF-S--YF--F---G-TPS--R (where - means any aminoacid), was found. Within the homologous C-terminal region, but outside the above consensus motif, a putative DNA-binding domain organized as a helix-turn-helix motif was located in all regulators. For regulators recognizing chemical signals, the non-homologous N-terminal region of these regulators is presumed to contain binding sites for activator molecules that confer specificity.
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Affiliation(s)
- M T Gallegos
- Consejo Superior de Investigaciones Científicas, Department of Plant Biochemistry, Granada, Spain
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Michán C, Kessler B, de Lorenzo V, Timmis KN, Ramos JL. XylS domain interactions can be deduced from intraallelic dominance in double mutants of Pseudomonas putida. Mol Gen Genet 1992; 235:406-12. [PMID: 1465113 DOI: 10.1007/bf00279387] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The XylS protein is the positive regulator of the TOL plasmid-encoded meta-cleavage pathway for the metabolism of alkylbenzoates in Pseudomonas putida. This protein is activated by a variety of benzoate analogues. To elucidate the functional domains of the regulator and their interactions, several fusions of the XylS C-terminus to MS2 polymerase and of the N-terminus to beta-galactosidase were constructed but all are inactive. In addition, 15 double mutant xylS genes were constructed in vitro by fusing parts of various mutant genes to produce mutant regulators exhibiting C-terminal and N-terminal amino acid substitutions. The phenotypic properties of the parental single mutant genes, and those of the double mutant genes, suggest that the C-terminal region is involved in binding to DNA sequences at the promoter of the meta-cleavage pathway operon, and that the benzoate effector binding pocket includes critical residues present at both the N-terminal and C-terminal ends of the protein. The intraallelic dominance of the Ile229 (Ser229-->Ile) and Val274 (Asp274-->Val) substitutions over the N-terminal His41 (Arg41-->His) substitution, and the intraallelic dominance of Thr45 (Arg45-->Thr) over Ile229 and Val274, support the proposal that these two regions of the regulator interact functionally. Combination of the Leu88 (Trp88-->Leu) and Arg256 (Pro256-->Arg) substitutions did not suppress the semiconstitutive phenotype conferred by Leu88, but resulted in a protein with altered ability to recognize benzoates. In contrast, the Leu88 semiconstitutive phenotype was suppressed by Val288 (Asp288-->Val), and the double mutant was susceptible to activation by benzoates.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- C Michán
- C.S.I.C., Estación Experimental del Zaidín, Granada, Spain
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