1
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Padilla-Vaca F, de la Mora J, García-Contreras R, Ramírez-Prado JH, Vicente-Gómez M, Vargas-Gasca F, Anaya-Velázquez F, Páramo-Pérez I, Rangel-Serrano Á, Cuéllar-Mata P, Vargas-Maya NI, Franco B. Theoretical study of ArcB and its dimerization, interaction with anaerobic metabolites, and activation of ArcA. PeerJ 2023; 11:e16309. [PMID: 37849831 PMCID: PMC10578306 DOI: 10.7717/peerj.16309] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
The complex metabolism of Escherichia coli has been extensively studied, including its response to oxygen availability. The ArcA/B two-component system (TCS) is the key regulator for the transition between these two environmental conditions and has been thoroughly characterized using genetic and biochemical approaches. Still, to date, limited structural data is available. The breakthrough provided by AlphaFold2 in 2021 has brought a reliable tool to the scientific community for assessing the structural features of complex proteins. In this report, we analyzed the structural aspects of the ArcA/B TCS using AlphaFold2 models. The models are consistent with the experimentally determined structures of ArcB kinase. The predicted structure of the dimeric form of ArcB is consistent with the extensive genetic and biochemical data available regarding mechanistic signal perception and regulation. The predicted interaction of the dimeric form of ArcB with its cognate response regulator (ArcA) is also consistent with both the forward and reverse phosphotransfer mechanisms. The ArcB model was used to detect putative binding cavities to anaerobic metabolites, encouraging testing of these predictions experimentally. Finally, the highly accurate models of other ArcB homologs suggest that different experimental approaches are needed to determine signal perception in kinases lacking the PAS domain. Overall, ArcB is a kinase with features that need further testing, especially in determining its crystal structure under different conditions.
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Affiliation(s)
| | - Javier de la Mora
- Genética Molecular, Instituto de Fisiología Celular, Mexico City, Mexico City, México
| | | | | | | | | | | | | | | | | | | | - Bernardo Franco
- Biology, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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2
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Padilla-Vaca F, de la Mora J, García-Contreras R, Ramírez-Prado JH, Alva-Murillo N, Fonseca-Yepez S, Serna-Gutiérrez I, Moreno-Galván CL, Montufar-Rodríguez JM, Vicente-Gómez M, Rangel-Serrano Á, Vargas-Maya NI, Franco B. Two-Component System Sensor Kinases from Asgardian Archaea May Be Witnesses to Eukaryotic Cell Evolution. Molecules 2023; 28:5042. [PMID: 37446705 DOI: 10.3390/molecules28135042] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
The signal transduction paradigm in bacteria involves two-component systems (TCSs). Asgardarchaeota are archaea that may have originated the current eukaryotic lifeforms. Most research on these archaea has focused on eukaryotic-like features, such as genes involved in phagocytosis, cytoskeleton structure, and vesicle trafficking. However, little attention has been given to specific prokaryotic features. Here, the sequence and predicted structural features of TCS sensor kinases analyzed from two metagenome assemblies and a genomic assembly from cultured Asgardian archaea are presented. The homology of the sensor kinases suggests the grouping of Lokiarchaeum closer to bacterial homologs. In contrast, one group from a Lokiarchaeum and a meta-genome assembly from Candidatus Heimdallarchaeum suggest the presence of a set of kinases separated from the typical bacterial TCS sensor kinases. AtoS and ArcB homologs were found in meta-genome assemblies along with defined domains for other well-characterized sensor kinases, suggesting the close link between these organisms and bacteria that may have resulted in the metabolic link to the establishment of symbiosis. Several kinases are predicted to be cytoplasmic; some contain several PAS domains. The data shown here suggest that TCS kinases in Asgardian bacteria are witnesses to the transition from bacteria to eukaryotic organisms.
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Affiliation(s)
- Felipe Padilla-Vaca
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Javier de la Mora
- Departamento de Genética Molecular, Instituto de Fisiologia Celular, Universidad Nacional Autonoma de Mexico, Circuito Exterior s/n, Mexico City 04510, Mexico
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | | | - Nayeli Alva-Murillo
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Sofia Fonseca-Yepez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Isaac Serna-Gutiérrez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Carolina Lisette Moreno-Galván
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - José Manolo Montufar-Rodríguez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Marcos Vicente-Gómez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Ángeles Rangel-Serrano
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Naurú Idalia Vargas-Maya
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Bernardo Franco
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
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3
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Vargas-Maya NI, Olmedo-Monfil V, Ramírez-Prado JH, Reyes-Cortés R, Padilla-Vaca F, Franco B. Catalases in the pathogenesis of Sporothrix schenckii research. PeerJ 2022; 10:e14478. [PMID: 36523453 PMCID: PMC9745942 DOI: 10.7717/peerj.14478] [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: 09/08/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Pathogenic fungal infection success depends on the ability to escape the immune response. Most strategies for fungal infection control are focused on the inhibition of virulence factors and increasing the effectiveness of antifungal drugs. Nevertheless, little attention has been focused on their physiological resistance to the host immune system. Hints may be found in pathogenic fungi that also inhabit the soil. In nature, the saprophyte lifestyle of fungi is also associated with predators that can induce oxidative stress upon cell damage. The natural sources of nutrients for fungi are linked to cellulose degradation, which in turn generates reactive oxygen species (ROS). Overall, the antioxidant arsenal needed to thrive both in free-living and pathogenic lifestyles in fungi is fundamental for success. In this review, we present recent findings regarding catalases and oxidative stress in fungi and how these can be in close relationship with pathogenesis. Additionally, special focus is placed on catalases of Sporothrix schenckii as a pathogenic model with a dual lifestyle. It is assumed that catalase expression is activated upon exposure to H2O2, but there are reports where this is not always the case. Additionally, it may be relevant to consider the role of catalases in S. schenckii survival in the saprophytic lifestyle and why their study can assess their involvement in the survival and therefore, in the virulence phenotype of different species of Sporothrix and when each of the three catalases are required. Also, studying antioxidant mechanisms in other isolates of pathogenic and free-living fungi may be linked to the virulence phenotype and be potential therapeutic and diagnostic targets. Thus, the rationale for this review to place focus on fungal catalases and their role in pathogenesis in addition to counteracting the effect of immune system reactive oxygen species. Fungi that thrive in soil and have mammal hosts could shed light on the importance of these enzymes in the two types of lifestyles. We look forward to encouraging more research in a myriad of areas on catalase biology with a focus on basic and applied objectives and placing these enzymes as virulence determinants.
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Affiliation(s)
| | | | | | - Ruth Reyes-Cortés
- Biology Department, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Felipe Padilla-Vaca
- Biology Department, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Bernardo Franco
- Biology Department, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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4
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Duarte-Velázquez I, de la Mora J, Ramírez-Prado JH, Aguillón-Bárcenas A, Tornero-Gutiérrez F, Cordero-Loreto E, Anaya-Velázquez F, Páramo-Pérez I, Rangel-Serrano Á, Muñoz-Carranza SR, Romero-González OE, Cardoso-Reyes LR, Rodríguez-Ojeda RA, Mora-Montes HM, Vargas-Maya NI, Padilla-Vaca F, Franco B. Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships. PeerJ 2022; 10:e13772. [PMID: 35880217 PMCID: PMC9308461 DOI: 10.7717/peerj.13772] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/01/2022] [Indexed: 01/17/2023] Open
Abstract
Organisms need mechanisms to perceive the environment and respond accordingly to environmental changes or the presence of hazards. Transcription factors (TFs) are required for cells to respond to the environment by controlling the expression of genes needed. Escherichia coli has been the model bacterium for many decades, and still, there are features embedded in its genome that remain unstudied. To date, 58 TFs remain poorly characterized, although their binding sites have been experimentally determined. This study showed that these TFs have sequence variation at the third codon position G+C content but maintain the same Codon Adaptation Index (CAI) trend as annotated functional transcription factors. Most of these transcription factors are in areas of the genome where abundant repetitive and mobile elements are present. Sequence divergence points to groups with distinctive sequence signatures but maintaining the same type of DNA binding domain. Finally, the analysis of the promoter sequences of the 58 TFs showed A+T rich regions that agree with the features of horizontally transferred genes. The findings reported here pave the way for future research of these TFs that may uncover their role as spare factors in case of lose-of-function mutations in core TFs and trace back their evolutionary history.
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Affiliation(s)
- Isabel Duarte-Velázquez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Javier de la Mora
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autonoma de Mexico, Mexico City, México
| | | | - Alondra Aguillón-Bárcenas
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Fátima Tornero-Gutiérrez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Eugenia Cordero-Loreto
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Fernando Anaya-Velázquez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Itzel Páramo-Pérez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Ángeles Rangel-Serrano
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | | | | | - Luis Rafael Cardoso-Reyes
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | | | - Héctor Manuel Mora-Montes
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Naurú Idalia Vargas-Maya
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Felipe Padilla-Vaca
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Bernardo Franco
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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5
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Romero-García AG, Prado-Rúbio OA, Contreras-Zarazúa G, Ramírez-Márquez C, Ramírez-Prado JH, Segovia-Hernández JG. Simultaneous Design and Controllability Optimization for the Reaction Zone for Furfural Bioproduction. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c02261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
| | - Oscar Andrés Prado-Rúbio
- Departamento de Ingeniería Química, Universidad Nacional de Colombia, Km 9 vía al Aeropuerto La Nubia, Campus La Nubia, Bloque L, Manizales, Caldas, 170001 Colombia
| | | | - César Ramírez-Márquez
- Chemical Engineering Department, University of Guanajuato, Campus Guanajuato, Gto., México, 36005
| | - Jorge Humberto Ramírez-Prado
- Centro de Investigación Científica de Yucatán, A. C., Unidad de Biotecnología, Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP 97200, Mérida, Yucatán, México
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6
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Leal-Alvarado DA, Estrella-Maldonado H, Sáenz-Carbonell L, Ramírez-Prado JH, Zapata-Pérez O, Santamaría JM. Genes coding for transporters showed a rapid and sharp increase in their expression in response to lead, in the aquatic fern (Salvinia minima Baker). Ecotoxicol Environ Saf 2018; 147:1056-1064. [PMID: 29976008 DOI: 10.1016/j.ecoenv.2017.09.046] [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: 05/22/2017] [Revised: 09/08/2017] [Accepted: 09/16/2017] [Indexed: 05/27/2023]
Abstract
Salvinia minima was assessed for its ability to accumulate lead (Pb) by exposing it to concentrations of 40µM Pb(NO3)2 during 24h. At the same time, the expression levels were quantified, of four genes coding for transporters: SmABCC (ABCC-MRP), SmATPase (ATPase-P3A), SmNhaD (Type-Na+/H+) and SmABCG (ABCG-WBC). In the absence of lead, S. minima had very low expression of those genes, when plants were exposed to the metal however, those genes showed a rapid (in just three hours or less) and sharp increase (up to 60 times) in their expression, particularly the SmNhaD (Type-Na+/H+) gene. This sharp increase in expression levels of the genes studied, occurred at the same time that the plant accumulated the highest content of lead in its tissues. The first two genes, are apparently implicated in detoxification and lead accumulation mechanisms, while the other two genes are apparently involved in maintaining cell balance (homeostatic control) and membrane integrity. Our results confirmed that S. minima is efficient for phytoremediation of water bodies contaminated by lead, as it is efficient in accumulating this metal in its tissues (bioconcentration factor; BCF) values greater than 1000, in short times of exposure. More importantly, our data on the expression profiles of four genes coding for transporters, represent a first sight scenario of the molecular basis for understanding the different mechanism of detoxification, apparently present in this aquatic fern.
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Affiliation(s)
- D A Leal-Alvarado
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán, Mexico
| | - H Estrella-Maldonado
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán, Mexico
| | - L Sáenz-Carbonell
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán, Mexico
| | - J H Ramírez-Prado
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán, Mexico
| | - Omar Zapata-Pérez
- Centro de Investigación y de Estudios Avanzados Unidad Mérida, Km. 6 Antigua Carretera a Progreso Apdo. Postal 73, Cordemex, 97310 Mérida, Yucatán, Mexico
| | - J M Santamaría
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán, Mexico.
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Leal-Alvarado DA, Martínez-Hernández A, Calderón-Vázquez CL, Uh-Ramos D, Fuentes G, Ramírez-Prado JH, Sáenz-Carbonell L, Santamaría JM. Identification of up-regulated genes from the metal-hyperaccumulator aquatic fern Salvinia minima Baker, in response to lead exposure. Aquat Toxicol 2017; 193:86-96. [PMID: 29053962 DOI: 10.1016/j.aquatox.2017.10.006] [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: 08/04/2017] [Revised: 10/10/2017] [Accepted: 10/12/2017] [Indexed: 06/07/2023]
Abstract
Lead (Pb) is one of the most serious environmental pollutants. The aquatic fern Salvinia minima Baker is capable to hyper-accumulate Pb in their tissues. However, the molecular mechanisms involved in its Pb accumulation and tolerance capacity are not fully understood. In order to investigate the molecular mechanisms that are activated by S. minima in response to Pb, we constructed a suppression subtractive hybridization library (SSH) in response to an exposure to 40μM of Pb(NO3)2 for 12h. 365 lead-related differentially expressed sequences tags (ESTs) were isolated and sequenced. Among these ESTs, 143 unique cDNA (97 were registered at the GenBank and 46 ESTs were not registered, because they did not meet the GenBank conditions). Those ESTs were identified and classified into 3 groups according to Blast2GO. In terms of metabolic pathways, they were grouped into 29 KEGG pathways. Among the ESTs, we identified some that might be part of the mechanism that this fern may have to deal with this metal, including abiotic-stress-related transcription factors, some that might be involved in tolerance mechanisms such as ROS scavenging, membrane protection, and those of cell homeostasis recovery. To validate the SSH library, 4 genes were randomly selected from the library and analyzed by qRT-PCR. These 4 genes were transcriptionally up-regulated in response to lead in at least one of the two tested tissues (roots and leaves). The present library is one of the few genomics approaches to study the response to metal stress in an aquatic fern, representing novel molecular information and tools to understand the molecular physiology of its Pb tolerance and hyperaccumulation capacity. Further research is required to elucidate the functions of the lead-induced genes that remain classified as unknown, to perhaps reveal novel molecular mechanisms of Pb tolerance and accumulation capacity in aquatic plants.
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Affiliation(s)
- Daniel A Leal-Alvarado
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200, Mérida, Yucatán, Mexico
| | - A Martínez-Hernández
- Colegio de Posgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Champotón, Campeche, C. P. 24450, Mexico
| | - C L Calderón-Vázquez
- Instituto Politécnico Nacional-CIIDIR, SINALOA, Boulevard Juan de Dios Bátiz Paredes #250, Colonia San Joachin, Guasave, Sinaloa, Mexico
| | - D Uh-Ramos
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200, Mérida, Yucatán, Mexico
| | - G Fuentes
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200, Mérida, Yucatán, Mexico
| | - J H Ramírez-Prado
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200, Mérida, Yucatán, Mexico
| | - L Sáenz-Carbonell
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200, Mérida, Yucatán, Mexico
| | - J M Santamaría
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200, Mérida, Yucatán, Mexico.
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Quiroz-Ramírez JJ, Sánchez-Ramírez E, Hernández S, Ramírez-Prado JH, Segovia-Hernández JG. Multiobjective Stochastic Optimization Approach Applied to a Hybrid Process Production–Separation in the Production of Biobutanol. Ind Eng Chem Res 2017. [DOI: 10.1021/acs.iecr.6b04230] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Juan José Quiroz-Ramírez
- Universidad de Guanajuato, Campus Guanajuato, Departamento
de Ingeniería Química, Noria Alta s/n, 36050, Guanajuato, Gto. México
| | - Eduardo Sánchez-Ramírez
- Universidad de Guanajuato, Campus Guanajuato, Departamento
de Ingeniería Química, Noria Alta s/n, 36050, Guanajuato, Gto. México
| | - Salvador Hernández
- Universidad de Guanajuato, Campus Guanajuato, Departamento
de Ingeniería Química, Noria Alta s/n, 36050, Guanajuato, Gto. México
| | - Jorge Humberto Ramírez-Prado
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Biotecnología,
Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP 97200, Mérida, Yucatán México
| | - Juan Gabriel Segovia-Hernández
- Universidad de Guanajuato, Campus Guanajuato, Departamento
de Ingeniería Química, Noria Alta s/n, 36050, Guanajuato, Gto. México
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Marfil-Santana MD, O'Connor-Sánchez A, Ramírez-Prado JH, De Los Santos-Briones C, López-Aguiar LK, Rojas-Herrera R, Lago-Lestón A, Prieto-Davó A. A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products. J Microbiol 2016; 54:774-781. [PMID: 27796931 DOI: 10.1007/s12275-016-6092-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/27/2016] [Accepted: 08/26/2016] [Indexed: 11/30/2022]
Abstract
The need for new antibiotics has sparked a search for the microbes that might potentially produce them. Current sequencing technologies allow us to explore the biotechnological potential of microbial communities in diverse environments without the need for cultivation, benefitting natural product discovery in diverse ways. A relatively recent method to search for the possible production of novel compounds includes studying the diverse genes belonging to polyketide synthase pathways (PKS), as these complex enzymes are an important source of novel therapeutics. In order to explore the biotechnological potential of the microbial community from the largest underground aquifer in the world located in the Yucatan, we used a polyphasic approach in which a simple, non-computationally intensive method was coupled with direct amplification of environmental DNA to assess the diversity and novelty of PKS type I ketosynthase (KS) domains. Our results suggest that the bioinformatic method proposed can indeed be used to assess the novelty of KS enzymes; nevertheless, this in silico study did not identify some of the KS diversity due to primer bias and stringency criteria outlined by the metagenomics pipeline. Therefore, additionally implementing a method involving the direct cloning of KS domains enhanced our results. Compared to other freshwater environments, the aquifer was characterized by considerably less diversity in relation to known ketosynthase domains; however, the metagenome included a family of KS type I domains phylogenetically related, but not identical, to those found in the curamycin pathway, as well as an outstanding number of thiolases. Over all, this first look into the microbial community found in this large Yucatan aquifer and other fresh water free living microbial communities highlights the potential of these previously overlooked environments as a source of novel natural products.
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Affiliation(s)
- Miguel David Marfil-Santana
- Center for Scientific Investigation of Yucatan (CICY), Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, C.P. 97200, Mexico
| | - Aileen O'Connor-Sánchez
- Center for Scientific Investigation of Yucatan (CICY), Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, C.P. 97200, Mexico
| | - Jorge Humberto Ramírez-Prado
- Center for Scientific Investigation of Yucatan (CICY), Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, C.P. 97200, Mexico
| | - Cesar De Los Santos-Briones
- Center for Scientific Investigation of Yucatan (CICY), Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, C.P. 97200, Mexico
| | - Lluvia Korynthia López-Aguiar
- School of Chemistry, National Autonomous University of Mexico (UNAM), Campus Sisal, Puerto de Abrigo s/n Municipio de Hunucmá, Sisal, Yucatan, C.P. 97356, Mexico
| | - Rafael Rojas-Herrera
- School of Chemical Engeneering, Autonomous University of Yucatan (UADY), Periférico Norte Kilometro 33.5, Chuburná de Hidalgo Inn, Mérida, Yucatán, C.P. 97203, Mexico
| | - Asunción Lago-Lestón
- Post Graduate Studies and Research Center of Ensenada (CICESE), Ensenada, Baja California, C.P. 22860, Mexico
| | - Alejandra Prieto-Davó
- School of Chemistry, National Autonomous University of Mexico (UNAM), Campus Sisal, Puerto de Abrigo s/n Municipio de Hunucmá, Sisal, Yucatan, C.P. 97356, Mexico.
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Ramírez-Prado JH, Martínez-Márquez EI, Olmedo-Alvarez G. cry1Aa Lacks Stability Elements at Its 5′-UTR but Integrity of Its Transcription Terminator Is Critical to Prevent Decay of Its Transcript. Curr Microbiol 2006; 53:23-9. [PMID: 16775783 DOI: 10.1007/s00284-005-5178-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 06/22/2005] [Accepted: 11/14/2005] [Indexed: 10/24/2022]
Abstract
We analyzed the influence of the 5' and 3' untranslated regions of the Bacillus thuringiensis cry1Aa on its mRNA stability. Although the cry1Aa gene has a stable transcript (8 min), its 5' UTR did not provide stability to the reporter gene uidA. Stability of cry1Aa could be increased to 40 min by addition of an SP82 stability element at the 5' UTR, suggesting that once the 5' and 3' ends were protected initiation of decay could be effectively blocked. We generated mutations in the transcription terminator and found that changes that reduced the stability of the stem, a larger loop, or elimination of the U-trail sharply decreased the half-life of the transcript. Therefore, unlike some stable bacterial transcripts, cry1Aa lacks special features at the end 5' to prevent decay, but its terminator is the main determinant of its stability.
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