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Velazquez D, Sigala JC, Martínez LM, Gaytán P, Gosset G, Lara AR. Glucose transport engineering allows mimicking fed-batch performance in batch mode and selection of superior producer strains. Microb Cell Fact 2022; 21:183. [PMID: 36071458 PMCID: PMC9450411 DOI: 10.1186/s12934-022-01906-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/26/2022] Open
Abstract
Background Fed-batch mode is the standard culture technology for industrial bioprocesses. Nevertheless, most of the early-stage cell and process development is carried out in batch cultures, which can bias the initial selection of expression systems. Cell engineering can provide an alternative to fed-batch cultures for high-throughput screening and host selection. We have previously reported a library of Escherichia coli strains with single and multiple deletions of genes involved in glucose transport. Compared to their wild type (W3110), the mutant strains displayed lower glucose uptake, growth and aerobic acetate production rates. Therefore, when cultured in batch mode, such mutants may perform similar to W3110 cultured in fed-batch mode. To test that hypothesis, we evaluated the constitutive expression of the green fluorescence protein (GFP) in batch cultures in microbioreactors using a semi defined medium supplemented with 10 or 20 g/L glucose + 0.4 g yeast extract/g glucose. Results The mutant strains cultured in batch mode displayed a fast-growth phase (growth rate between 0.40 and 0.60 h−1) followed by a slow-growth phase (growth rate between 0.05 and 0.15 h−1), similar to typical fed-batch cultures. The phase of slow growth is most probably caused by depletion of key amino acids. Three mutants attained the highest GFP fluorescence. Particularly, a mutant named WHIC (ΔptsHIcrr, ΔmglABC), reached a GFP fluorescence up to 14-fold greater than that of W3110. Strain WHIC was cultured in 2 L bioreactors in batch mode with 100 g/L glucose + 50 g/L yeast extract. These cultures were compared with exponentially fed-batch cultures of W3110 maintaining the same slow-growth of WHIC (0.05 h−1) and using the same total amount of glucose and yeast extract than in WHIC cultures. The WHIC strain produced approx. 450 mg/L GFP, while W3110 only 220 mg/L. Conclusion The combination of cell engineering and high throughput screening allowed the selection of a particular mutant that mimics fed-batch behavior in batch cultures. Moreover, the amount of GFP produced by the strain WHIC was substantially higher than that of W3110 under both, batch and fed-batch schemes. Therefore, our results represent a valuable technology for accelerated bioprocess development. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01906-1.
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Affiliation(s)
- Daniela Velazquez
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Vasco de Quiroga 4871, 05348, Mexico City, Mexico
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Vasco de Quiroga 4871, 05348, Mexico City, Mexico
| | - Luz María Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Paul Gaytán
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Vasco de Quiroga 4871, 05348, Mexico City, Mexico.
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Roldán‐Salgado A, Muslinkina L, Pletnev S, Pletneva N, Pletnev V, Gaytán P. A novel violet fluorescent protein contains a unique oxidized tyrosine as the simplest chromophore ever reported in fluorescent proteins. Protein Sci 2022; 31:688-700. [PMID: 34936154 PMCID: PMC8862416 DOI: 10.1002/pro.4265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 12/14/2022]
Abstract
We describe an engineered violet fluorescent protein from the lancelet Branchiostoma floridae (bfVFP). This is the first example of a GFP-like fluorescent protein with a stable fluorescent chromophore lacking an imidazolinone ring; instead, it consists of oxidized tyrosine 68 flanked by glycine 67 and alanine 69. bfVFP contains the simplest chromophore reported in fluorescent proteins and was generated from the yellow protein lanFP10A2 by two synergetic mutations, S148H and C166I. The chromophore structure was confirmed crystallographically and by high-resolution mass spectrometry. The photophysical characteristics of bfVFP (323/430 nm, quantum yield 0.33, and Ec 14,300 M-1 cm-1 ) make it potentially useful for multicolor experiments to expand the excitation range of available FP biomarkers and Förster resonance energy transfer with blue and cyan fluorescent protein acceptors.
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Affiliation(s)
| | - Liya Muslinkina
- Structural Biology Section, Research Technologies BranchNational Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaMarylandUSA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - Nadya Pletneva
- Shemyakin‐Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
| | - Vladimir Pletnev
- Shemyakin‐Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
| | - Paul Gaytán
- Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
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3
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Cesa-Luna C, Baez A, Aguayo-Acosta A, Llano-Villarreal RC, Juárez-González VR, Gaytán P, Bustillos-Cristales MDR, Rivera-Urbalejo A, Muñoz-Rojas J, Quintero-Hernández V. Growth inhibition of pathogenic microorganisms by Pseudomonas protegens EMM-1 and partial characterization of inhibitory substances. PLoS One 2020; 15:e0240545. [PMID: 33057351 PMCID: PMC7561207 DOI: 10.1371/journal.pone.0240545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 04/08/2020] [Accepted: 09/28/2020] [Indexed: 11/18/2022] Open
Abstract
The bacterial strain, EMM-1, was isolated from the rhizosphere of red maize ("Rojo Criollo") and identified as Pseudomonas protegens EMM-1 based on phylogenetic analysis of 16S rDNA, rpoB, rpoD, and gyrB gene sequences. We uncovered genes involved in the production of antimicrobial compounds like 2,4-diacetylphloroglucinol (2,4-DAPG), pyoluteorin, and lectin-like bacteriocins. These antimicrobial compounds are also produced by other fluorescent pseudomonads alike P. protegens. Double-layer agar assay showed that P. protegens EMM-1 inhibited the growth of several multidrug-resistant (MDR) bacteria, especially clinical isolates of the genera Klebsiella and β-hemolytic Streptococcus. This strain also displayed inhibitory effects against diverse fungi, such as Aspergillus, Botrytis, and Fusarium. Besides, a crude extract of inhibitory substances secreted into agar was obtained after the cold-leaching process, and physicochemical characterization was performed. The partially purified inhibitory substances produced by P. protegens EMM-1 inhibited the growth of Streptococcus sp. and Microbacterium sp., but no inhibitory effect was noted for other bacterial or fungal strains. The molecular weight determined after ultrafiltration was between 3 and 10 kDa. The inhibitory activity was thermally stable up to 60°C (but completely lost at 100°C), and the inhibitory activity remained active in a wide pH range (from 3 to 9). After treatment with a protease from Bacillus licheniformis, the inhibitory activity was decreased by 90%, suggesting the presence of proteic natural compounds. All these findings suggested that P. protegens EMM-1 is a potential source of antimicrobials to be used against pathogens for humans and plants.
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Affiliation(s)
- Catherine Cesa-Luna
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
| | - Antonino Baez
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
| | - Alberto Aguayo-Acosta
- Department of Microbiology and Immunology, Biological Sciences Faculty, Universidad Autónoma de Nuevo León, Ciudad Universitaria, San Nicolás de la Garza, Nuevo León, México
| | - Roberto Carlos Llano-Villarreal
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
| | - Víctor Rivelino Juárez-González
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Paul Gaytán
- Unidad de Síntesis y Secuenciación de ADN, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - María del Rocío Bustillos-Cristales
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
| | - América Rivera-Urbalejo
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
- Facultad de Estomatología, BUAP, Puebla, Pue., México
| | - Jesús Muñoz-Rojas
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
| | - Verónica Quintero-Hernández
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
- CONACYT–ESMG, LEMM, CICM, IC-BUAP, Puebla, Pue., México
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4
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Navarro-González SS, Ramírez-Trujillo JA, Peña-Chora G, Gaytán P, Roldán-Salgado A, Corzo G, Lina-García LP, Hernández-Velázquez VM, Suárez-Rodríguez R. Enhanced Tolerance against a Fungal Pathogen and Insect Resistance in Transgenic Tobacco Plants Overexpressing an Endochitinase Gene from Serratia marcescens. Int J Mol Sci 2019; 20:E3482. [PMID: 31315176 PMCID: PMC6679225 DOI: 10.3390/ijms20143482] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/11/2019] [Accepted: 07/14/2019] [Indexed: 11/16/2022] Open
Abstract
In this study we cloned a chitinase gene (SmchiC), from Serratia marcescens isolated from the corpse of a Diatraea magnifactella lepidopteran, which is an important sugarcane pest. The chitinase gene SmchiC amplified from the S. marcescens genome was cloned into the transformation vector p2X35SChiC and used to transform tobacco (Nicotiana tabacum L. cv Petit Havana SR1). The resistance of these transgenic plants to the necrotrophic fungus Botrytis cinerea and to the pest Spodoptera frugiperda was evaluated: both the activity of chitinase as well as the resistance against B. cinerea and S. frugiperda was significantly higher in transgenic plants compared to the wild-type.
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Affiliation(s)
- Samantha Sarai Navarro-González
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos 62209, Mexico
| | - José Augusto Ramírez-Trujillo
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos 62209, Mexico
| | - Guadalupe Peña-Chora
- Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos 62209, Mexico
| | - Paul Gaytán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Abigail Roldán-Salgado
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Gerardo Corzo
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Laura Patricia Lina-García
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos 62209, Mexico
| | - Víctor Manuel Hernández-Velázquez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos 62209, Mexico
| | - Ramón Suárez-Rodríguez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos 62209, Mexico.
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5
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Muslinkina L, Roldán-Salgado A, Gaytán P, Juárez-González VR, Rudiño E, Pletneva N, Pletnev V, Dauter Z, Pletnev S. Structural Factors Enabling Successful GFP-Like Proteins with Alanine as the Third Chromophore-Forming Residue. J Mol Biol 2019; 431:1397-1408. [PMID: 30797856 DOI: 10.1016/j.jmb.2019.02.013] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/05/2019] [Accepted: 02/15/2019] [Indexed: 11/18/2022]
Abstract
GFP-like proteins from lancelets (lanFPs) is a new and least studied group that already generated several outstanding biomarkers (mNeonGreen is the brightest FP to date) and has some unique features. Here, we report the study of four homologous lanFPs with GYG and GYA chromophores. Until recently, it was accepted that the third chromophore-forming residue in GFP-like proteins should be glycine, and efforts to replace it were in vain. Now, we have the first structure of a fluorescent protein with a successfully matured chromophore that has alanine as the third chromophore-forming residue. Consideration of the protein structures revealed two alternative routes of posttranslational transformation, resulting in either chromophore maturation or hydrolysis of GYG/GYA tripeptide. Both transformations are catalyzed by the same set of catalytic residues, Arg88 and Glu35-Wat-Glu211 cluster, whereas the residues in positions 62 and 102 shift the equilibrium between chromophore maturation and hydrolysis.
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Affiliation(s)
- Liya Muslinkina
- Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, IL 60439, USA
| | - Abigail Roldán-Salgado
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Paul Gaytán
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Víctor R Juárez-González
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Enrique Rudiño
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Nadya Pletneva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Vladimir Pletnev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA
| | - Sergei Pletnev
- Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, IL 60439, USA.
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6
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Fragoso-Jiménez JC, Baert J, Nguyen TM, Liu W, Sassi H, Goormaghtigh F, Van Melderen L, Gaytán P, Hernández-Chávez G, Martinez A, Delvigne F, Gosset G. Growth-dependent recombinant product formation kinetics can be reproduced through engineering of glucose transport and is prone to phenotypic heterogeneity. Microb Cell Fact 2019; 18:26. [PMID: 30710996 PMCID: PMC6359759 DOI: 10.1186/s12934-019-1073-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 06/28/2018] [Accepted: 01/23/2019] [Indexed: 12/31/2022] Open
Abstract
Background Escherichia coli W3110 and a group of six isogenic derivatives, each displaying distinct specific rates of glucose consumption were characterized to determine levels of GFP production and population heterogeneity. These strains have single or combinatory deletions in genes encoding phosphoenolpyruvate:sugar phosphotransferase system (PTS) permeases as PtsG and ManX, as well as common components EI, Hpr protein and EIIA, also the non-PTS Mgl galactose/glucose ABC transporter. They have been transformed for expressing GFP based on a lac-based expression vector, which is subject to bistability. Results These strains displayed specific glucose consumption and growth rates ranging from 1.75 to 0.45 g/g h and 0.54 to 0.16 h−1, respectively. The rate of acetate production was strongly reduced in all mutant strains when compared with W3110/pV21. In bioreactor cultures, wild type W3110/pV21 produced 50.51 mg/L GFP, whereas strains WG/pV21 with inactive PTS IICBGlc and WGM/pV21 with the additional inactivation of PTS IIABMan showed the highest titers of GFP, corresponding to 342 and 438 mg/L, respectively. Moreover, we showed experimentally that bistable expression systems, as lac-based ones, induce strong phenotypic segregation among microbial populations. Conclusions We have demonstrated that reduction on glucose consumption rate in E. coli leads to an improvement of GFP production. Furthermore, from the perspective of phenotypic heterogeneity, we observed in this case that heterogeneous systems are also the ones leading to the highest performance. This observation suggests reconsidering the generally accepted proposition stating that phenotypic heterogeneity is generally unwanted in bioprocess applications.![]() Electronic supplementary material The online version of this article (10.1186/s12934-019-1073-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Carlos Fragoso-Jiménez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Jonathan Baert
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Thai Minh Nguyen
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Wenzheng Liu
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Hosni Sassi
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Frédéric Goormaghtigh
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Paul Gaytán
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Georgina Hernández-Chávez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Frank Delvigne
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium.
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
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7
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Diupotex M, Martínez-Salazar MB, Escalona-Montaño AR, Zamora-Chimal J, Salaiza-Suazo N, Ruiz-Remigio A, Roldán-Salgado A, Aguirre-García MM, Martínez-Calvillo S, Gaytán P, Becker I. The mKate fluorescent protein expressed by Leishmania mexicana modifies the parasite immunopathogenicity in BALB/c mice. Parasite Immunol 2019; 41:e12608. [PMID: 30500992 DOI: 10.1111/pim.12608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 09/05/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 11/27/2022]
Abstract
Parasites have been engineered to express fluorescent reporter proteins, yet the impact of red fluorescent proteins on Leishmania infections remains largely unknown. We analysed the infection outcome of Leishmania mexicana parasites engineered for the constitutive expression of mKate protein and evaluated their immunogenicity in BALB/c mice. Infection of BALB/c mice with mKate transfected L. mexicana (LmexmKate ) parasites caused enlarged lesion sizes, leading to ulceration, and containing more parasites, as compared to LmexWT . The mKate protein showed immunogenic properties inducing antibody production against the mKate protein, as well as enhancing antibody production against the parasite. The augmented lesion sizes and ulcers, together with the more elevated antibody production, were related to an enhanced number of TNF-α and IL-1β producing cells in the infected tissues. We conclude that mKate red fluorescent protein is an immunogenic protein, capable of modifying disease evolution of L. mexicana.
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Affiliation(s)
- Mariana Diupotex
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Hospital General de México, Ciudad de México, México
| | - María Berenice Martínez-Salazar
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Hospital General de México, Ciudad de México, México
| | - Alma Reyna Escalona-Montaño
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Hospital General de México, Ciudad de México, México
| | - Jaime Zamora-Chimal
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Hospital General de México, Ciudad de México, México
| | - Norma Salaiza-Suazo
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Hospital General de México, Ciudad de México, México
| | - Adriana Ruiz-Remigio
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Hospital General de México, Ciudad de México, México
| | | | - María Magdalena Aguirre-García
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Hospital General de México, Ciudad de México, México
| | - Santiago Martínez-Calvillo
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, México
| | - Paul Gaytán
- Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Ingeborg Becker
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Hospital General de México, Ciudad de México, México
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8
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Gaytán P, Roldán-Salgado A, Yáñez JA, Morales-Arrieta S, Juárez-González VR. CiPerGenesis, A Mutagenesis Approach that Produces Small Libraries of Circularly Permuted Proteins Randomly Opened at a Focused Region: Testing on the Green Fluorescent Protein. ACS Comb Sci 2018; 20:400-413. [PMID: 29812897 DOI: 10.1021/acscombsci.7b00152] [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] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Circularly permuted proteins (cpPs) represent a novel type of mutant proteins with original termini that are covalently linked through a peptide connector and opened at any other place of the polypeptide backbone to create new ends. cpPs are finding wide applications in biotechnology because their properties may be quite different from those of the parental protein. However, the actual challenge for the creation of successful cpPs is to identify those peptide bonds that can be broken to create new termini and ensure functional and well-folded cpPs. Herein, we describe CiPerGenesis, a combinatorial mutagenesis approach that uses two oligonucleotide libraries to amplify a circularized gene by PCR, starting and ending from a focused target region. This approach creates small libraries of circularly permuted genes that are easily cloned in the correct direction and frame using two different restriction sites encoded in the oligonucleotides. Once expressed, the protein libraries exhibit a unique sequence diversity, comprising cpPs that exhibit ordinary breakpoints between adjacent amino acids localized at the target region as well as cpPs with new termini containing user-defined truncations and repeats of some amino acids. CiPerGenesis was tested at the lid region G134-H148 of green fluorescent protein (GFP), revealing that the most fluorescent variants were those starting at Leu141 and ending at amino acids Tyr145, Tyr143, Glu142, Leu141, Lys140, and H139. Purification and biochemical characterization of some variants suggested a differential expression, solubility and maturation extent of the mutant proteins as the likely cause for the variability in fluorescence intensity observed in colonies.
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Affiliation(s)
- Paul Gaytán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Abigail Roldán-Salgado
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Jorge A. Yáñez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Sandra Morales-Arrieta
- Departamento de Ingeniería en Biotecnología, Universidad Politécnica del Estado de Morelos, Boulevard Cuauhnáhuac No. 566, Col. Lomas del Texcal, Jiutepec, Morelos 62550, México
| | - Víctor R. Juárez-González
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
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9
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García G, Ramos F, Martínez-Hernández F, Hernández L, Yáñez J, Gaytán P. A new subtype of Entamoeba gingivalis: "E. gingivalis ST2, kamaktli variant". Parasitol Res 2018; 117:1277-1284. [PMID: 29429011 PMCID: PMC5978907 DOI: 10.1007/s00436-018-5798-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 11/10/2017] [Accepted: 01/31/2018] [Indexed: 11/24/2022]
Abstract
Entamoeba gingivalis is a protozoan that resides in the oral cavity. Using molecular biology techniques, we identified a novel organism that shares the same ecological niche as E. gingivalis. To differentiate this organism from E. gingivalis, we named it “kamaktli variant.” By sequencing the 18S-ITS1-5.8S-ITS2 rRNA region, we demonstrated that kamaktli variant is 89% identical to E. gingivalis. To elucidate the relationship between kamaktli variant and E. gingivalis, we performed a phylogenetic analysis. Both taxa clustered in the same clade with high support, indicating that the amoebas are closely related (98/99/1.00, maximum parsimony/maximum likelihood/MrBayes, respectively). Given this information, we propose that these molecular differences between kamaktli variant and E. gingivalis ST1 are sufficient to distinguish them as independent subtypes, and we name the new subtype “E. gingivalis ST2, kamaktli variant.”
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Affiliation(s)
- Gabriela García
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad 3000, Cd. Universitaria Coyoacán, CP.04510, Ciudad de México, Mexico.
| | - Fernando Ramos
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad 3000, Cd. Universitaria Coyoacán, CP.04510, Ciudad de México, Mexico
| | - Fernando Martínez-Hernández
- Departamento de Ecología de Agentes Patógenos, Hospital General Dr. Manuel Gea González, Calzada de Tlalpan 4800, Tlalpan, CP.14080, Ciudad de México, Mexico
| | - Lilian Hernández
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad 3000, Cd. Universitaria Coyoacán, CP.04510, Ciudad de México, Mexico
| | - Jorge Yáñez
- Unidad de Síntesis y Secuenciación de DNA, Instituto de Biotecnología, UNAM, Av. Universidad 2001, CP.14000, Cuernavaca, Morelos, Mexico
| | - Paul Gaytán
- Unidad de Síntesis y Secuenciación de DNA, Instituto de Biotecnología, UNAM, Av. Universidad 2001, CP.14000, Cuernavaca, Morelos, Mexico
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Llamas-Guillén BA, Pastor N, López-Herrera G, González-Serrano ME, Valenzuela-Vázquez L, Bravo-Adame ME, Villanueva-Cabello TM, Gaytán P, Yañez J, Martinez-Duncker I, Ruiz-Fernández M, Veillette A, Espinosa-Padilla SE, Cruz-Munoz ME. Two novel mutations in ZAP70 gene that result in human immunodeficiency. Clin Immunol 2017; 183:278-284. [PMID: 28912049 DOI: 10.1016/j.clim.2017.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/23/2017] [Accepted: 09/09/2017] [Indexed: 11/28/2022]
Affiliation(s)
| | - Nina Pastor
- Cell Dynamics Research Center-IICBA, Autonomous University of Morelos State, Mexico
| | | | | | | | | | | | - Paul Gaytán
- Biotechnology Institute, Autonomous National University of México, Mexico
| | - Jorge Yañez
- Biotechnology Institute, Autonomous National University of México, Mexico
| | | | | | | | | | - Mario Ernesto Cruz-Munoz
- School of Medicine, Autonomous University of Morelos State, Mexico; Diagnostic and Molecular Medicine Unit "Dr. Ruy Pérez Tamayo", Morelos Children Hospital, Mexico.
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Cárcamo E, Roldán-Salgado A, Osuna J, Bello-Sanmartin I, Yáñez JA, Saab-Rincón G, Viadiu H, Gaytán P. Spiked Genes: A Method to Introduce Random Point Nucleotide Mutations Evenly throughout an Entire Gene Using a Complete Set of Spiked Oligonucleotides for the Assembly. ACS Omega 2017; 2:3183-3191. [PMID: 30023688 PMCID: PMC6044943 DOI: 10.1021/acsomega.7b00508] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/21/2017] [Indexed: 06/08/2023]
Abstract
In vitro mutagenesis methods have revolutionized biological research and the biotechnology industry. In this study, we describe a mutagenesis method based on synthesizing a gene using a complete set of forward and reverse spiked oligonucleotides that have been modified to introduce a low ratio of mutant nucleotides at each position. This novel mutagenesis scheme named "Spiked Genes" yields a library of clones with an enhanced mutation distribution due to its unbiased nucleotide incorporation. Using the far-red fluorescent protein emKate as a model, we demonstrated that Spiked Genes yields richer libraries than those obtained via enzymatic methods. We obtained a library without bias toward any nucleotide or base pair and with even mutations, transitions, and transversion frequencies. Compared with enzymatic methods, the proposed synthetic approach for the creation of gene libraries represents an improved strategy for screening protein variants and does not require a starting template.
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Affiliation(s)
- Edson Cárcamo
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Abigail Roldán-Salgado
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Joel Osuna
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Iván Bello-Sanmartin
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Jorge A. Yáñez
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Gloria Saab-Rincón
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Héctor Viadiu
- Instituto
de Química, Universidad Nacional
Autónoma de México, Circuito Exterior, Ciudad Universitaria, Ciudad
de Mexico 04510, México
| | - Paul Gaytán
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
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Rodríguez-Mejía JL, Roldán-Salgado A, Osuna J, Merino E, Gaytán P. A Codon Deletion at the Beginning of Green Fluorescent Protein Genes Enhances Protein Expression. J Mol Microbiol Biotechnol 2016; 27:1-10. [PMID: 27820932 DOI: 10.1159/000448786] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recombinant protein expression is one of the key issues in protein engineering and biotechnology. Among the different models for assessing protein production and structure-function studies, green fluorescent protein (GFP) is one of the preferred models because of its importance as a reporter in cellular and molecular studies. In this research we analyze the effect of codon deletions near the amino terminus of different GFP proteins on fluorescence. Our study includes Gly4 deletions in the enhanced GFP (EGFP), the red-shifted GFP and the red-shifted EGFP. The Gly4 deletion mutants and their corresponding wild-type counterparts were transcribed under the control of the T7 or Trc promoters and their expression patterns were analyzed. Different fluorescent outcomes were observed depending on the type of fluorescent gene versions. In silico analysis of the RNA secondary structures near the ribosome binding site revealed a direct relationship between their minimum free energy and GFP production. Integrative analysis of these results, including SDS-PAGE analysis, led us to conclude that the fluorescence improvement of cells expressing different versions of GFPs with Gly4 deleted is due to an enhancement of the accessibility of the ribosome binding site by reducing the stability of the RNA secondary structures at their mRNA leader regions.
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Roldán-Salgado A, Sánchez-Barreto C, Gaytán P. LanFP10-A, first functional fluorescent protein whose chromophore contains the elusive mutation G67A. Gene 2016; 592:281-90. [PMID: 27418528 DOI: 10.1016/j.gene.2016.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 04/22/2016] [Revised: 07/04/2016] [Accepted: 07/09/2016] [Indexed: 01/18/2023]
Abstract
Since Green Fluorescent Protein (GFP) was first successfully expressed in heterologous systems in 1994, many genes encoding other natural autofluorescent proteins (AFPs) have been cloned and subsequently modified by protein engineering to improve their physicochemical properties. Throughout this twenty-two-year period, glycine 67 (Gly67) has been regarded as the only amino acid in the entire protein family that is essential for the formation of the different reported chromophores. In this work, we demonstrate that a synthetic gene encoding LanFP10-A, a natural protein encoded in the genome of the lancelet Branchiostoma floridae containing the G67A mutation, produces a heterologous, functional yellow fluorescent protein when expressed in E. coli. In contrast to LanFP10-A, LanFP6-A, a second GFP-like protein found in the lancelet genome that also contains the natural G67A mutation, was non-fluorescent.
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Affiliation(s)
- Abigail Roldán-Salgado
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Celidee Sánchez-Barreto
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Paul Gaytán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico.
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14
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Tejerizo GT, Bañuelos LA, Cervantes L, Gaytán P, Pistorio M, Romero D, Brom S. Development of molecular tools to monitor conjugative transfer in rhizobia. J Microbiol Methods 2015; 117:155-63. [PMID: 26272377 DOI: 10.1016/j.mimet.2015.08.005] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 01/26/2023]
Abstract
Evolution of bacterial populations has been extensively driven by horizontal transfer events. Conjugative plasmid transfer is considered the principal contributor to gene exchange among bacteria. Several conjugative and mobilizable plasmids have been identified in rhizobia, and two major molecular mechanisms that regulate their transfer have been described, under laboratory conditions. The knowledge of rhizobial plasmid transfer regulation in natural environments is very poor. In this work we developed molecular tools to easily monitor the conjugative plasmid transfer in rhizobia by flow cytometry (FC) or microscopy. 24 cassettes were constructed by combining a variety of promotors, fluorescent proteins and antibiotic resistance genes, and used to tag plasmids and chromosome of donor strains. We were able to detect plasmid transfer after conversion of non-fluorescent recipients into fluorescent transconjugants. Flow cytometry (FC) was optimized to count donor, recipient and transconjugant strains to determine conjugative transfer frequencies. Results were similar, when determined either by FC or by viable counts. Our constructions also allowed the visualization of transconjugants in crosses performed on bean roots. The tools presented here may also be used for other purposes, such as analysis of transcriptional fusions or single-cell tagging. Application of the system will allow the survey of how different environmental conditions or other regulators modulate plasmid transfer in rhizobia.
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Affiliation(s)
- Gonzalo Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata-CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.
| | - Luis Alfredo Bañuelos
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Laura Cervantes
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Paul Gaytán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata-CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - David Romero
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
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15
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Noda-García L, Juárez-Vázquez AL, Ávila-Arcos MC, Verduzco-Castro EA, Montero-Morán G, Gaytán P, Carrillo-Tripp M, Barona-Gómez F. Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα)₈ isomerase evolutionary intermediates from a diverse metagenome. BMC Evol Biol 2015; 15:107. [PMID: 26058375 PMCID: PMC4462073 DOI: 10.1186/s12862-015-0378-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 12/19/2014] [Accepted: 05/11/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Current sequence-based approaches to identify enzyme functional shifts, such as enzyme promiscuity, have proven to be highly dependent on a priori functional knowledge, hampering our ability to reconstruct evolutionary history behind these mechanisms. Hidden Markov Model (HMM) profiles, broadly used to classify enzyme families, can be useful to distinguish between closely related enzyme families with different specificities. The (βα)8-isomerase HisA/PriA enzyme family, involved in L-histidine (HisA, mono-substrate) biosynthesis in most bacteria and plants, but also in L-tryptophan (HisA/TrpF or PriA, dual-substrate) biosynthesis in most Actinobacteria, has been used as model system to explore evolutionary hypotheses and therefore has a considerable amount of evolutionary, functional and structural knowledge available. We searched for functional evolutionary intermediates between the HisA and PriA enzyme families in order to understand the functional divergence between these families. RESULTS We constructed a HMM profile that correctly classifies sequences of unknown function into the HisA and PriA enzyme sub-families. Using this HMM profile, we mined a large metagenome to identify plausible evolutionary intermediate sequences between HisA and PriA. These sequences were used to perform phylogenetic reconstructions and to identify functionally conserved amino acids. Biochemical characterization of one selected enzyme (CAM1) with a mutation within the functionally essential N-terminus phosphate-binding site, namely, an alanine instead of a glycine in HisA or a serine in PriA, showed that this evolutionary intermediate has dual-substrate specificity. Moreover, site-directed mutagenesis of this alanine residue, either backwards into a glycine or forward into a serine, revealed the robustness of this enzyme. None of these mutations, presumably upon functionally essential amino acids, significantly abolished its enzyme activities. A truncated version of this enzyme (CAM2) predicted to adopt a (βα)6-fold, and thus entirely lacking a C-terminus phosphate-binding site, was identified and shown to have HisA activity. CONCLUSION As expected, reconstruction of the evolution of PriA from HisA with HMM profiles suggest that functional shifts involve mutations in evolutionarily intermediate enzymes of otherwise functionally essential residues or motifs. These results are in agreement with a link between promiscuous enzymes and intragenic epistasis. HMM provides a convenient approach for gaining insights into these evolutionary processes.
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Affiliation(s)
- Lianet Noda-García
- Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México. .,Current Addresses: Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.
| | - Ana L Juárez-Vázquez
- Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México.
| | - María C Ávila-Arcos
- Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México. .,Current Addresses: Department of Genetics, Stanford University, Stanford, CA, USA.
| | - Ernesto A Verduzco-Castro
- Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México.
| | - Gabriela Montero-Morán
- Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México. .,Current Addresses: División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí, México.
| | - Paul Gaytán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 2001, CP 62250, Cuernavaca, México.
| | - Mauricio Carrillo-Tripp
- Biomolecular Diversity Laboratories, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México.
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México.
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16
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García G, Ramos F, Pérez RG, Yañez J, Estrada MS, Mendoza LH, Martinez-Hernandez F, Gaytán P. Molecular epidemiology and genetic diversity of Entamoeba species in a chelonian collection. J Med Microbiol 2013; 63:271-283. [PMID: 24194557 DOI: 10.1099/jmm.0.061820-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [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: 11/18/2022] Open
Abstract
Veterinary medicine has focused recently on reptiles, due to the existence of captive collections in zoos and an increase in the acquisition of reptiles as pets. The protozoan parasite, Entamoeba can cause amoebiasis in various animal species and humans. Although amoebiasis disease is remarkably rare in most species of chelonians and crocodiles, these species may serve as Entamoeba species carriers that transmit parasites to susceptible reptile species, such as snakes and lizards, which can become sick and die. In this study, we identified the Entamoeba species in a population of healthy (disease-free) chelonians, and evaluated their diversity through the amplification and sequencing of a small subunit rDNA region. Using this procedure, three Entamoeba species were identified: Entamoeba invadens in 4.76 % of chelonians, Entamoeba moshkovskii in 3.96 % and Entamoeba terrapinae in 50 %. We did not detect mixed Entamoeba infections. Comparative analysis of the amplified region allowed us to determine the intra-species variations. The E. invadens and E. moshkovskii strains isolated in this study did not exhibit marked differences with respect to the sequences reported in GenBank. The analysis of the E. terrapinae isolates revealed three different subgroups (A, B and C). Although subgroups A and C were very similar, subgroup B showed a relatively marked difference with respect to subgroups A and C (Fst = 0.984 and Fst = 1.000, respectively; 10-14 % nucleotide variation, as determined by blast) and with respect to the sequences reported in GenBank. These results suggested that E. terrapinae subgroup B may be either in a process of speciation or belong to a different lineage. However, additional research is necessary to support this statement conclusively.
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Affiliation(s)
- Gabriela García
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad 3000, Colonia Copilco Universidad, Delegación Coyoacan, México DF, CP 04510, México
| | - Fernando Ramos
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad 3000, Colonia Copilco Universidad, Delegación Coyoacan, México DF, CP 04510, México
| | - Rodrigo Gutiérrez Pérez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad 3000, Colonia Copilco Universidad, Delegación Coyoacan, México DF, CP 04510, México
| | - Jorge Yañez
- Unidad de Síntesis y Secuenciación de DNA, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Cuernavaca Morelos, CP 62210, México
| | - Mónica Salmerón Estrada
- Herpetario de la Facultad de Ciencias, Universidad Nacional Autónoma de México, Av. Universidad 3000, Colonia Copilco Universidad, Delegación Coyoacan, México DF, CP 04510, México
| | - Lilian Hernández Mendoza
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad 3000, Colonia Copilco Universidad, Delegación Coyoacan, México DF, CP 04510, México
| | - Fernando Martinez-Hernandez
- Departamento de Ecología de Agentes Patógenos, Hospital General Doctor Manuel Gea González, Calz de Tlalpan 4800, Tlalpan, México DF, CP 14000, México
| | - Paul Gaytán
- Unidad de Síntesis y Secuenciación de DNA, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Cuernavaca Morelos, CP 62210, México
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Gaytán P, Roldán-Salgado A. Elimination of redundant and stop codons during the chemical synthesis of degenerate oligonucleotides. Combinatorial testing on the chromophore region of the red fluorescent protein mKate. ACS Synth Biol 2013; 2:453-62. [PMID: 23654278 DOI: 10.1021/sb3001326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 11/29/2022]
Abstract
Although some strategies have been reported for the elimination of stop and redundant codons during the chemical synthesis of degenerate oligonucleotides, incorporating an expensive cocktail of 20 trimer-phosphoramidites is currently a commonly employed and straightforward approach. As an alternative option, we describe here a cheaper strategy based on standard monomer-phosphoramidites and a simplified resin-splitting procedure. The accurate division of the resin, containing the growing oligonucleotide, into four columns represents the key step in this approach. The synthesis of the degenerate codon NDT in column 1, loaded with 60% of the resin, produces 12 codons, while a degenerate codon VMA in column 2, loaded with 30% of the resin, produces 6 codons. Codons ATG and TGG, independently synthesized in columns 3 and 4, respectively, and loaded with 5% each, completes the 20 different codons. The experimental frequency of each mutant codon in the library was assessed by randomizing 12 contiguous codons that encode for amino acids located in the chromophore region of the enhanced red fluorescent protein mKate-S158A. Furthermore, randomization of three contiguous codons that encode for the amino acids Phe62, Met63, and Tyr64, which are equivalent to Phe64, Ser65, and Tyr66 in GFP, gave rise to some red and golden yellow fluorescent mutants displaying interesting phenotypes and spectroscopic properties. The absorption and emission spectra of two of these mutants also suggested that the complete maturation of the red and golden yellow chromophores in mKate proceeds via the formation of a green-type chromophore and a cyan-type chromophore, respectively.
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Affiliation(s)
- Paul Gaytán
- Instituto de Biotecnología-Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México.
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Noda-García L, Camacho-Zarco AR, Medina-Ruíz S, Gaytán P, Carrillo-Tripp M, Fülöp V, Barona-Gómez F. Evolution of substrate specificity in a recipient's enzyme following horizontal gene transfer. Mol Biol Evol 2013; 30:2024-34. [PMID: 23800623 DOI: 10.1093/molbev/mst115] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Despite the prominent role of horizontal gene transfer (HGT) in shaping bacterial metabolism, little is known about the impact of HGT on the evolution of enzyme function. Specifically, what is the influence of a recently acquired gene on the function of an existing gene? For example, certain members of the genus Corynebacterium have horizontally acquired a whole l-tryptophan biosynthetic operon, whereas in certain closely related actinobacteria, for example, Mycobacterium, the trpF gene is missing. In Mycobacterium, the function of the trpF gene is performed by a dual-substrate (βα)8 phosphoribosyl isomerase (priA gene) also involved in l-histidine (hisA gene) biosynthesis. We investigated the effect of a HGT-acquired TrpF enzyme upon PriA's substrate specificity in Corynebacterium through comparative genomics and phylogenetic reconstructions. After comprehensive in vivo and enzyme kinetic analyses of selected PriA homologs, a novel (βα)8 isomerase subfamily with a specialized function in l-histidine biosynthesis, termed subHisA, was confirmed. X-ray crystallography was used to reveal active-site mutations in subHisA important for narrowing of substrate specificity, which when mutated to the naturally occurring amino acid in PriA led to gain of function. Moreover, in silico molecular dynamic analyses demonstrated that the narrowing of substrate specificity of subHisA is concomitant with loss of ancestral protein conformational states. Our results show the importance of HGT in shaping enzyme evolution and metabolism.
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Affiliation(s)
- Lianet Noda-García
- Evolution of Metabolic Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Cinvestav-IPN, Irapuato, México
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Gaytán P, López-Bustos E, Güereca L. Repetitive use of polyacrylamide gels for the analysis and purification of oligonucleotides. Anal Biochem 2013; 439:62-4. [PMID: 23603299 DOI: 10.1016/j.ab.2013.03.037] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/23/2013] [Accepted: 03/27/2013] [Indexed: 11/30/2022]
Abstract
The repetitive use of polyacrylamide slab gels for the analysis of oligonucleotides by ultraviolet (UV) shadowing across the complete electrophoresis cassette is addressed. Visualization of the samples is possible by preparing the gel between a quartz plate and a highly sensitive glass fluorescent plate whose preparation is described here. Within a working day, gels can be reloaded up to five times with no detriment to the resolution of the oligonucleotide bands. Taking advantage of this detection approach, we also devised a strategy to reuse gels in the purification of oligonucleotides, combining electroelution and subsequent concentration of the samples using centrifugal filter units.
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Affiliation(s)
- Paul Gaytán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62250, Mexico.
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20
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Osuna J, Flores H, Gaytán P. A reporter system that discriminates EF-hand-sensor motifs from signal-modulators at the single-motif level. FEBS Lett 2012; 586:3398-403. [DOI: 10.1016/j.febslet.2012.07.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 07/07/2012] [Accepted: 07/17/2012] [Indexed: 01/25/2023]
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Gaytán P, Contreras-Zambrano C, Ortiz-Alvarado M, Morales-Pablos A, Yáñez J. TrimerDimer: an oligonucleotide-based saturation mutagenesis approach that removes redundant and stop codons. Nucleic Acids Res 2009; 37:e125. [PMID: 19783828 PMCID: PMC2764442 DOI: 10.1093/nar/gkp602] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [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] [Indexed: 11/14/2022] Open
Abstract
9-fluorenylmethoxycarbonyl (Fmoc) and 4,4'-dimethoxytrityl (DMTr) are orthogonal hydroxyl protecting groups that have been used in conjunction to assemble oligonucleotide libraries whose variants contain wild-type and mutant codons randomly interspersed throughout a focused DNA region. Fmoc is labile to organic bases and stable to weak acids, whereas DMTr behaves oppositely. Based on these chemical characteristics, we have now devised TrimerDimer, a novel codon-based saturation mutagenesis approach that removes redundant and stop codons during the assembly of degenerate oligonucleotides. In this approach, five DMTr-protected trinucleotide phosphoramidites (dTGG, dATG, dTTT, dTAT and dTGC) and five Fmoc-protected dinucleotide phosphoramidites (dAA, dTT, dAT, dGC and dCG) react simultaneously with a starting oligonucleotide growing on a solid support. The Fmoc group is then removed and the incorporated dimers react with a mixture of three DMTr-protected monomer phosphoramidites (dC, dA and dG) to produce 15 trinucleotides: dCAA, dAAA, dGAA, dCTT, dATT, dGTT, dCAT, dAAT, dGAT, dCGC, dAGC, dGGC, dCCG, dACG and dGCG. After one mutagenic cycle, 20 codons are generated encoding the 20 natural amino acids. TrimerDimer was tested by randomizing the four contiguous codons that encode amino acids L64-G67 of an engineered, nonfluorescent GFP protein. Sequencing of 89 nonfluorescent mutant clones and isolation of two fluorescent mutants confirmed the principle.
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Affiliation(s)
- Paul Gaytán
- Instituto de Biotecnología-Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México.
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22
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Flores-Ramírez G, Rivera M, Morales-Pablos A, Osuna J, Soberón X, Gaytán P. The effect of amino acid deletions and substitutions in the longest loop of GFP. BMC Chem Biol 2007; 7:1. [PMID: 17594481 PMCID: PMC1919350 DOI: 10.1186/1472-6769-7-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Accepted: 06/26/2007] [Indexed: 11/12/2022]
Abstract
Background The effect of single and multiple amino acid substitutions in the green fluorescent protein (GFP) from Aequorea victoria has been extensively explored, yielding several proteins of diverse spectral properties. However, the role of amino acid deletions in this protein -as with most proteins- is still unknown, due to the technical difficulties involved in generating combinatorial in-phase amino acid deletions on a target region. Results In this study, the region I129-L142 of superglo GFP (sgGFP), corresponding to the longest loop of the protein and located far away from the central chromophore, was subjected to a random amino acid deletion approach, employing an in-house recently developed mutagenesis method termed Codon-Based Random Deletion (COBARDE). Only two mutants out of 16384 possible variant proteins retained fluorescence: sgGFP-Δ I129 and sgGFP-Δ D130. Interestingly, both mutants were thermosensitive and at 30°C sgGFP-Δ D130 was more fluorescent than the parent protein. In contrast with deletions, substitutions of single amino acids from residues F131 to L142 were well tolerated. The substitution analysis revealed a particular importance of residues F131, G135, I137, L138, H140 and L142 for the stability of the protein. Conclusion The behavior of GFP variants with both amino acid deletions and substitutions demonstrate that this loop is playing an important structural role in GFP folding. Some of the amino acids which tolerated any substitution but no deletion are simply acting as "spacers" to localize important residues in the protein structure.
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Affiliation(s)
- Gabriela Flores-Ramírez
- Departamento de Ingeniería Celular y Biocatálisis. Instituto de Biotecnología, Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México
| | - Manuel Rivera
- Departamento de Ingeniería Celular y Biocatálisis. Instituto de Biotecnología, Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México
| | - Alfredo Morales-Pablos
- Departamento de Ingeniería Celular y Biocatálisis. Instituto de Biotecnología, Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México
| | - Joel Osuna
- Departamento de Ingeniería Celular y Biocatálisis. Instituto de Biotecnología, Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México
| | - Xavier Soberón
- Departamento de Ingeniería Celular y Biocatálisis. Instituto de Biotecnología, Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México
| | - Paul Gaytán
- Departamento de Ingeniería Celular y Biocatálisis. Instituto de Biotecnología, Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México
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Aguilar-Díaz H, Bobes RJ, Carrero JC, Camacho-Carranza R, Cervantes C, Cevallos MA, Dávila G, Rodríguez-Dorantes M, Escobedo G, Fernández JL, Fragoso G, Gaytán P, Garciarubio A, González VM, González L, José MV, Jiménez L, Laclette JP, Landa A, Larralde C, Morales-Montor J, Morett E, Ostoa-Saloma P, Sciutto E, Santamaría RI, Soberón X, de la Torre P, Valdés V, Yánez J. The genome project of Taenia solium. Parasitol Int 2005; 55 Suppl:S127-30. [PMID: 16337432 DOI: 10.1016/j.parint.2005.11.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [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: 11/17/2022]
Abstract
We have constituted a consortium of key laboratories at the National Autonomous University of Mexico to carry out a genomic project for Taenia solium. This project will provide powerful resources for the study of taeniasis/cysticercosis, and, in conjunction with the Echinococcus granulosus and Echinococcus multilocularis genome project of expressed sequence tags (ESTs), will mark the advent of genomics for cestode parasites. Our project is planned in two consecutive stages. The first stage is being carried out to determine some basic parameters of the T. solium genome. Afterwards, we will evaluate the best strategy for the second stage, a full blown genome project. We have estimated the T. solium genome size by two different approaches: cytofluorometry on isolated cyton nuclei, as well as a probabilistic calculation based on approximately 2000 sequenced genomic clones, approximately 3000 ESTs, resulting in size estimates of 270 and 251 Mb, respectively. In terms of sequencing, our goal for the first stage is to characterize several thousand EST's (from adult worm and cysticerci cDNA libraries) and genomic clones. Results obtained so far from about 16,000 sequenced ESTs from the adult stage, show that only about 40% of the T. solium coding sequences have a previously sequenced homologue. Many of the best hits are found with mammalian genes, especially with humans. However, 1.5% of the hits lack homologues in humans, making these genes immediate candidates for investigation on pharmaco-therapy, diagnostics and vaccination. Most T. solium ESTs are related to gene regulation, and signal transduction. Other important functions are housekeeping, metabolism, cell division, cytoskeleton, proteases, vacuolar transport, hormone response, and extracellular matrix activities. Preliminary results also suggest that the genome of T. solium is not highly repetitive.
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Affiliation(s)
- Hugo Aguilar-Díaz
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico
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Gaytán P, Yáñez J, Grande R, Morett E, Soberón X. Improving random mutagenesis by purification of the oligonucleotide variants. Comb Chem High Throughput Screen 2005; 8:537-44. [PMID: 16178813 DOI: 10.2174/1386207054867355] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An oligonucleotide-based mutagenesis method is presented where, contrary to most classical mutagenic approaches, preselection of the variants is performed at the oligonucleotide level to avoid cloning of non-desired sequences. The method relies on the generation of differentially phosphate-protected oligonucleotides. Protection of the phosphates is accomplished by substoichiometric incorporation of an Fmoc-protected and n-propyl-protected trinucleotide phosphoramidite during ordinary oligonucleotide assembly. Instead of the alkali-labile beta-cyanoethyl group introduced in ordinary assembly, the trinucleotide introduces the alkali-stable n-propyl group. As a result, single mutants carry three ionic phosphates less than the wild-type sequence, double mutants carry six ionic phosphates less and so on. This difference in ionic ratio enables separation of the variants by conventional polyacrilamide gel electrophoresis. In the exemplified library described herein, two sub-populations containing mainly triple and quadruple mutants were selected out of five possible sub-populations.
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Affiliation(s)
- P Gaytán
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México.
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25
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Yáñez J, Argüello M, Osuna J, Soberón X, Gaytán P. Combinatorial codon-based amino acid substitutions. Nucleic Acids Res 2004; 32:e158. [PMID: 15537836 PMCID: PMC534637 DOI: 10.1093/nar/gnh156] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [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: 09/28/2004] [Revised: 10/22/2004] [Accepted: 10/22/2004] [Indexed: 11/14/2022] Open
Abstract
Twenty Fmoc-protected trinucleotide phosphoramidites representing a complete set of codons for the natural amino acids were chemically synthesized for the first time. A pool of these reagents was incorporated into oligonucleotides at substoichiometric levels to generate two libraries of variants that randomly carry either few or many codon replacements on a region encoding nine amino acids of the bacterial enzyme TEM-1 beta-lactamase. Assembly of the libraries was performed in a completely automated mode through a simple modification of ordinary protocols. This technology eliminates codon redundancy, stop codons and enables complete exploration of sequence space for single, double and triple mutations throughout a protein region spanning several residues. Sequence analysis of many non-selected clones revealed a good incorporation of the trinucleotides, producing combinations of mutations quite different from those obtained using conventional degenerate oligonucleotides. Ceftazidime-selection experiments yielded several never before reported variants containing novel amino acid combinations in the beta-lactamase omega loop region.
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Affiliation(s)
- Jorge Yáñez
- Instituto de Biotecnología/UNAM, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México
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26
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Osuna J, Yáñez J, Soberón X, Gaytán P. Protein evolution by codon-based random deletions. Nucleic Acids Res 2004; 32:e136. [PMID: 15459282 PMCID: PMC521680 DOI: 10.1093/nar/gnh135] [Citation(s) in RCA: 19] [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] [Received: 08/13/2004] [Revised: 09/10/2004] [Accepted: 09/15/2004] [Indexed: 11/14/2022] Open
Abstract
A method to delete in-phase codons throughout a defined target region of a gene has been developed. This approach, named the codon-based random deletion (COBARDE) method, is able to delete complete codons in a random and combinatorial mode. Robustness, automation and fine-tuning of the mutagenesis rate are essential characteristics of the method, which is based on the assembly of oligonucleotides and on the use of two transient orthogonal protecting groups during the chemical synthesis. The performance of the method for protein function evolution was demonstrated by changing the substrate specificity of TEM-1 beta-lactamase. Functional ceftazidime-resistant beta-lactamase variants containing several deleted residues inside the catalytically important omega-loop region were found. The results show that the COBARDE method is a useful new molecular tool to access previously unexplorable sequence space.
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Affiliation(s)
- Joel Osuna
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología/UNAM, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México
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Abstract
Four known and nine new ceftazidime-resistance beta-lactamases were generated by a novel, contaminating codon-based mutagenesis approach. In this method, wild-type codons are spiked with a set of mutant codons during oligonucleotide synthesis, generating random combinatorial libraries of primers that contain few codon replacements per variant. Mutant codons are assembled by tandem addition of a diluted mixture of five Fmoc-dimer amidites to the growing oligo and a mixture of four DMTr-monomer amidites to generate 20 trinucleotides that encode a set of 18 amino acids. Wild-type codons are assembled with conventional chemistry and the whole process takes place in only one synthesis column, making its automation feasible. The random and binomial behavior of this approach was tested in the polylinker region of plasmid pUC19 by the synthesis of three oligonucleotide libraries mutagenized at different rates and cloned as mutagenic cassettes. Additionally, the method was biologically assessed by mutating six contiguous codons that encode amino acids 237-243 (ABL numbering) of the TEM(pUC19) beta-lactamase, which is functionally equivalent to the clinically important TEM-1 beta-lactamase. The best ceftazidime-recognizing variant was a triple mutant, R164H:E240K: R241A, displaying a 333-fold higher resistance than the wild-type enzyme.
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Affiliation(s)
- Paul Gaytán
- Instituto de Biotecnología/UNAM, Ap. Postal 510-3, Cuernavaca, Morelos 62250, México.
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Gaytán P, Yáñez J, Sánchez F, Soberón X. Orthogonal combinatorial mutagenesis: a codon-level combinatorial mutagenesis method useful for low multiplicity and amino acid-scanning protocols. Nucleic Acids Res 2001; 29:E9. [PMID: 11160911 PMCID: PMC30410 DOI: 10.1093/nar/29.3.e9] [Citation(s) in RCA: 16] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe here a method to generate combinatorial libraries of oligonucleotides mutated at the codon-level, with control of the mutagenesis rate so as to create predictable binomial distributions of mutants. The method allows enrichment of the libraries with single, double or larger multiplicity of amino acid replacements by appropriate choice of the mutagenesis rate, depending on the concentration of synthetic precursors. The method makes use of two sets of deoxynucleoside-phosphoramidites bearing orthogonal protecting groups [4,4'-dimethoxytrityl (DMT) and 9-fluorenylmethoxycarbonyl (Fmoc)] in the 5' hydroxyl. These phosphoramidites are divergently combined during automated synthesis in such a way that wild-type codons are assembled with commercial DMT-deoxynucleoside-methyl-phosphoramidites while mutant codons are assembled with Fmoc-deoxynucleoside-methyl-phosphoramidites in an NNG/C fashion in a single synthesis column. This method is easily automated and suitable for low mutagenesis rates and large windows, such as those required for directed evolution and alanine scanning. Through the assembly of three oligonucleotide libraries at different mutagenesis rates, followed by cloning at the polylinker region of plasmid pUC18 and sequencing of 129 clones, we concluded that the method performs essentially as intended.
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Affiliation(s)
- P Gaytán
- Unidad de Síntesis and Departamento de Reconocimiento Molecular y Bioestructura, Instituto de Biotecnología/UNAM Ap. Postal 510-3 Cuernavaca, Morelos 62250, México
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29
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Gaytán P, Yañez J, Sánchez F, Mackie H, Soberón X. Combination of DMT-mononucleotide and Fmoc-trinucleotide phosphoramidites in oligonucleotide synthesis affords an automatable codon-level mutagenesis method. Chem Biol 1998; 5:519-27. [PMID: 9751646 DOI: 10.1016/s1074-5521(98)90007-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Synthetic DNA has been used to introduce variability into protein-coding regions. In protocols that produce a few mutations per gene, the sampling of amino-acid sequence space is limited by the bias imposed by the genetic code. It has long been apparent that the incorporation of trinucleotides in the synthetic regime would circumvent this problem and significantly enhance the usefulness of the technique. RESULTS A new method is described for the creation of codon-level degenerate oligodeoxyribonucleotides that combines conventional dimethoxytrityl (DMT) mononucleoside phosphoramidite chemistry with 9-fluorenylmethoxycarbonyl (Fmoc) trinucleotide phosphoramidites (whose synthesis is reported in the paper). The substoichiometric use of these Fmoc-trinucleotides in an automatable, solid-phase synthesis procedure afforded DNA fragments comprising the wild-type sequence and a controllable distribution of mutants within two- and three-codon stretches of DNA, within the multiple cloning site of the conventional cloning vector pUC19. CONCLUSIONS DMT and Fmoc are compatible protecting groups in conventional oligonucleotide synthesis methods, resulting in controllable levels of codon-based mutagenesis.
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Affiliation(s)
- P Gaytán
- Department of Molecular Recognition and Biostructure, Instituto de Biotecnología/UNAM, Cuernavaca, Mor. México
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