1
|
Murga-Garrido SM, Ulloa-Pérez EJ, Díaz-Benítez CE, Orbe-Orihuela YC, Cornejo-Granados F, Ochoa-Leyva A, Sanchez-Flores A, Cruz M, Castañeda-Márquez AC, Plett-Torres T, Burguete García AI, Lagunas-Martínez A. Virulence Factors of the Gut Microbiome Are Associated with BMI and Metabolic Blood Parameters in Children with Obesity. Microbiol Spectr 2023; 11:e0338222. [PMID: 36786619 PMCID: PMC10101034 DOI: 10.1128/spectrum.03382-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/29/2023] [Indexed: 02/15/2023] Open
Abstract
The development of metabolic diseases is linked to the gut microbiota. A cross-sectional study involving 45 children (6 to 12 years old) was conducted to investigate the relationship between gut microbiota and childhood obesity. Anthropometric and metabolic measurements, food-frequency questionnaires (FFQs), and feces samples were obtained. Using the body mass index (BMI) z-score, we categorized each participant as normal weight (NW), or overweight and obese (OWOB). We determined 2 dietary profiles: one with complex carbohydrates and proteins (pattern 1), and the other with saturated fat and simple carbohydrates (pattern 2). The microbial taxonomic diversity and metabolic capacity were determined using shotgun metagenomics. We found differences between both BMI groups diversity. Taxa contributing to this difference, included Eubacterium sp., Faecalibacterium prausnitzii, Dialister, Monoglobus pectinilyticus, Bifidobacterium pseudocatenulatum, Intestinibacter bartlettii, Bacteroides intestinalis, Bacteroides uniformis, and Methanobrevibacter smithii. Metabolic capacity differences found between NW and OWOB, included the amino acid biosynthesis pathway, the cofactor, carrier, and vitamin biosynthesis pathway, the nucleoside and nucleotide biosynthesis and degradation pathways, the carbohydrate-sugar degradation pathway, and the amine and polyamine biosynthesis pathway. We found significant associations between taxa such as Ruminococcus, Mitsuokella multacida, Klebsiella variicola, and Citrobacter spp., metabolic pathways with the anthropometric, metabolic, and dietary data. We also found the microbiome's lipooligosaccharide (LOS) category as differentially abundant between BMI groups. Metabolic variations emerge during childhood as a result of complex nutritional and microbial interactions, which should be explained in order to prevent metabolic illnesses in adolescence and maturity. IMPORTANCE The alteration of gut microbiome composition has been commonly observed in diseases involving inflammation, such as obesity and metabolic impairment. Inflammatory host response in the gut can be a consequence of dietary driven dysbiosis. This response is conducive to blooms of particular bacterial species, adequate to survive in an inflammatory environment by means of genetical capability of utilizing alternative nutrients. Understanding the genomic and metabolic contribution of microbiota to inflammation, including virulence factor prevalence and functional potential, will contribute to identifying modifiable early life exposures and preventive strategies associated with obesity risk in childhood.
Collapse
Affiliation(s)
- S. M. Murga-Garrido
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
- PECEM (MD/PhD), Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - E. J. Ulloa-Pérez
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - C. E. Díaz-Benítez
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Y. C. Orbe-Orihuela
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - F. Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - A. Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - A. Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - M. Cruz
- Unidad de Investigación Médica en Bioquímica, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - A. C. Castañeda-Márquez
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - T. Plett-Torres
- PECEM (MD/PhD), Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - A. I. Burguete García
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - A. Lagunas-Martínez
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| |
Collapse
|
2
|
Arrieta O, Molina-Romero C, Cornejo-Granados F, Marquina-Castillo B, Avilés-Salas A, López-Leal G, Cardona AF, Ortega-Gómez A, Orozco-Morales M, Ochoa-Leyva A, Hernandez-Pando R. Clinical and pathological characteristics associated with the presence of the IS6110 Mycobacterim tuberculosis transposon in neoplastic cells from non-small cell lung cancer patients. Sci Rep 2022; 12:2210. [PMID: 35140255 PMCID: PMC8828834 DOI: 10.1038/s41598-022-05749-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 01/17/2022] [Indexed: 12/27/2022] Open
Abstract
Lung cancer (LC) and pulmonary tuberculosis (TB) are the deadliest neoplastic and bacterial infectious diseases worldwide, respectively. Clinicians and pathologists have long discussed the co-existence of LC and TB, and several epidemiologic studies have presented evidence indicating that TB could be associated with the development of LC, particularly adenocarcinoma. Nonetheless, this data remains controversial, and the mechanism which could underlie the association remains largely unexplored. Some bioinformatic studies have shown that human cancer biopsies have a very high frequency of bacterial DNA integration; since Mycobacterium Tuberculosis (MTb) is an intracellular pathogen, it could play an active role in the cellular transformation. Our group performed an exploratory study in a cohort of 88 LC patients treated at the Instituto Nacional de Cancelorogía (INCan) of Mexico City to evaluate the presence of MTb DNA in LC tissue specimens. For the first time, our results show the presence of the MTb IS6110 transposon in 40.9% (n = 36/88) of patients with lung adenocarcinomas. Additionally, through in-situ PCR we identified the presence of IS6110 in the nuclei of tumor cells. Furthermore, shotgun sequencing from two samples identified traces of MTb genomes present in tumor tissue, suggesting that similar Mtb strains could be infecting both patients.
Collapse
Affiliation(s)
- Oscar Arrieta
- Thoracic Oncology Unit and Laboratory of Personalized Medicine, Instituto Nacional de Cancerología (INCan), San Fernando #22, Section XVI, Tlalpan, 14080, Mexico City, Mexico.
| | - Camilo Molina-Romero
- Thoracic Oncology Unit and Laboratory of Personalized Medicine, Instituto Nacional de Cancerología (INCan), San Fernando #22, Section XVI, Tlalpan, 14080, Mexico City, Mexico
| | - Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, Mexico
| | - Brenda Marquina-Castillo
- Experimental Pathology Laboratory, Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | - Gamaliel López-Leal
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, Mexico
| | - Andrés F Cardona
- Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia.,Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (FOX-G/ONCOLGroup), Universidad El Bosque, Bogotá, Colombia
| | - Alette Ortega-Gómez
- Translational Medicine Laboratory, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Mario Orozco-Morales
- Thoracic Oncology Unit and Laboratory of Personalized Medicine, Instituto Nacional de Cancerología (INCan), San Fernando #22, Section XVI, Tlalpan, 14080, Mexico City, Mexico
| | - Adrián Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, Mexico
| | - Rogelio Hernandez-Pando
- Experimental Pathology Laboratory, Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.
| |
Collapse
|
3
|
Gomez-Fuentes S, Hernández-de la Fuente S, Morales-Ruiz V, López-Recinos D, Guevara-Salinas A, Parada-Colin MC, Espitia C, Ochoa-Leyva A, Sánchez F, Villalobos N, Arce-Sillas A, Hernández M, Mora SI, Fragoso G, Sciutto E, Adalid-Peralta L. A novel, sequencing-free strategy for the functional characterization of Taenia solium proteomic fingerprint. PLoS Negl Trop Dis 2021; 15:e0009104. [PMID: 33600419 PMCID: PMC7924735 DOI: 10.1371/journal.pntd.0009104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/04/2020] [Revised: 03/02/2021] [Accepted: 01/04/2021] [Indexed: 12/18/2022] Open
Abstract
The flatworm Taenia solium causes human and pig cysticercosis. When cysticerci are established in the human central nervous system, they cause neurocysticercosis, a potentially fatal disease. Neurocysticercosis is a persisting public health problem in rural regions of Mexico and other developing countries of Latin America, Asia, and Africa, where the infection is endemic. The great variability observed in the phenotypic and genotypic traits of cysticerci result in a great heterogeneity in the patterns of molecules secreted by them within their host. This work is aimed to identify and characterize cysticercal secretion proteins of T. solium cysticerci obtained from 5 naturally infected pigs from Guerrero, Mexico, using 2D-PAGE proteomic analysis. The isoelectric point (IP) and molecular weight (MW) of the spots were identified using the software ImageMaster 2D Platinum v.7.0. Since most secreted proteins are impossible to identify by mass spectrometry (MS) due to their low concentration in the sample, a novel strategy to predict their sequence was applied. In total, 108 conserved and 186 differential proteins were identified in five cysticercus cultures. Interestingly, we predicted the sequence of 14 proteins that were common in four out of five cysticercus cultures, which could be used to design vaccines or diagnostic methods for neurocysticercosis. A functional characterization of all sequences was performed using the algorithms SecretomeP, SignalP, and BlastKOALA. We found a possible link between signal transduction pathways in parasite cells and human cancer due to deregulation in signal transduction pathways. Bioinformatics analysis also demonstrated that the parasite release proteins by an exosome-like mechanism, which could be of biological interest.
Collapse
Affiliation(s)
- Sandra Gomez-Fuentes
- Unidad Periférica de Neuroinflamación para el estudio de patologías neurológicas del Instituto de Investigaciones Biomédicas en el Instituto Nacional de Neurología y Neurocirugía, México, México
| | - Sarah Hernández-de la Fuente
- Unidad Periférica de Neuroinflamación para el estudio de patologías neurológicas del Instituto de Investigaciones Biomédicas en el Instituto Nacional de Neurología y Neurocirugía, México, México
| | - Valeria Morales-Ruiz
- Unidad Periférica de Neuroinflamación para el estudio de patologías neurológicas del Instituto de Investigaciones Biomédicas en el Instituto Nacional de Neurología y Neurocirugía, México, México
| | - Dina López-Recinos
- Unidad Periférica de Neuroinflamación para el estudio de patologías neurológicas del Instituto de Investigaciones Biomédicas en el Instituto Nacional de Neurología y Neurocirugía, México, México
| | - Adrián Guevara-Salinas
- Unidad Periférica de Neuroinflamación para el estudio de patologías neurológicas del Instituto de Investigaciones Biomédicas en el Instituto Nacional de Neurología y Neurocirugía, México, México
| | - María Cristina Parada-Colin
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, México
| | - Clara Espitia
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, México
| | - Adrián Ochoa-Leyva
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Chamilpa, Cuernavaca, Morelos
| | - Filiberto Sánchez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Chamilpa, Cuernavaca, Morelos
| | - Nelly Villalobos
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Universidad Nacional Autónoma de México, México, México
| | - Asiel Arce-Sillas
- Unidad Periférica de Neuroinflamación para el estudio de patologías neurológicas del Instituto de Investigaciones Biomédicas en el Instituto Nacional de Neurología y Neurocirugía, México, México
| | - Marisela Hernández
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, México
| | - Silvia Ivonne Mora
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, México
| | - Gladis Fragoso
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, México
| | - Edda Sciutto
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, México
| | - Laura Adalid-Peralta
- Unidad Periférica de Neuroinflamación para el estudio de patologías neurológicas del Instituto de Investigaciones Biomédicas en el Instituto Nacional de Neurología y Neurocirugía, México, México
- Instituto Nacional de Neurología y Neurocirugía, La Fama, México, México
| |
Collapse
|
4
|
Calderón de la Barca AM, Castillo-Fimbres RS, Mejía-León ME, Quihui-Cota L, Ochoa-Leyva A, Aguayo-Patrón SV. Enteric parasitic infection disturbs bacterial structure in Mexican children with autoantibodies for type 1 diabetes and/or celiac disease. Gut Pathog 2020; 12:37. [PMID: 32788927 PMCID: PMC7418185 DOI: 10.1186/s13099-020-00376-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/05/2020] [Indexed: 01/04/2023] Open
Abstract
Background Intestinal bacterial dysbiosis and increased gut permeability are associated with higher risk of developing type 1 diabetes (T1D) or celiac disease (CD). There is a lack of information on parasitism involved in gut disturbance of predisposed children. We evaluated the effect of enteropathogenic parasites (Cryptosporidium spp., Cyclospora spp. G. lamblia, and Blastocystis spp.) on the bacterial structure of feces from children with autoantibodies for T1D or CD. Participants included 37 children under 18 years of age, from whom stools were analyzed for enteric parasites by qPCR and 22/37 for bacterial profile by sequencing the V3–V4 region of the 16s rRNA gene. Dietary, clinical, and socioeconomic data was recorded. Results Pathogens parasitized 28/37 participants, Cryptosporidium spp. was the most prevalent (62.2%), followed by both Cyclospora cayetanensis and Blastocystis spp (37.8%). There were no dietary differences (p > 0.05) attributable to parasitism. Co-infected participants with Cryptosporidium and Cyclospora did not differ (p = 0.064) from non-infected participants in bacterial alpha phylogenetic diversity. The same parasites’ co-infection was associated with a decreased abundance of the Ruminococaceae (p = 0.04) and Verrucomicrobioceae families, of the Akkermansia genus (p = 0.009). There was a lower Firmicutes/Bacteroidetes ratio (p = 0.02) in infected than in uninfected participants. Conclusions Cryptosporidium and Cyclospora affected the bacterial structure at family and genus levels, decreasing the ratio between Firmicutes and Bacteroidetes in children with auto-antibodies for T1D or CD, which could increase the risk of illness onset.
Collapse
Affiliation(s)
- Ana M Calderón de la Barca
- Dept. Nutrición, Centro de Investigación en Alimentación y Desarrollo, A.C., Astiazarán Rojas No. 46, Hermosillo, 83304 Sonora Mexico
| | - Reyna S Castillo-Fimbres
- Dept. Nutrición, Centro de Investigación en Alimentación y Desarrollo, A.C., Astiazarán Rojas No. 46, Hermosillo, 83304 Sonora Mexico
| | - María Esther Mejía-León
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Dr. Humberto Torres Sanginés S/N Centro Cívico, Mexicali, 21000 B.C. Mexico
| | - Luis Quihui-Cota
- Dept. Nutrición, Centro de Investigación en Alimentación y Desarrollo, A.C., Astiazarán Rojas No. 46, Hermosillo, 83304 Sonora Mexico
| | - Adrián Ochoa-Leyva
- Dept. Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, 62210 Morelos Mexico
| | - Sandra V Aguayo-Patrón
- Dept. Nutrición, Centro de Investigación en Alimentación y Desarrollo, A.C., Astiazarán Rojas No. 46, Hermosillo, 83304 Sonora Mexico.,Universidad del Valle de México, Hermosillo, Son. Mexico
| |
Collapse
|
5
|
Zatarain-Barrón ZL, Ramos-Espinosa O, Marquina-Castillo B, Barrios-Payán J, Cornejo-Granados F, Maya-Lucas O, López-Leal G, Molina-Romero C, Anthony RM, Ochoa-Leyva A, De La Rosa-Velázquez IA, Rebollar-Vega RG, Warren RM, Mata-Espinosa DA, Hernández-Pando R, van Soolingen D. Evidence for the Effect of Vaccination on Host-Pathogen Interactions in a Murine Model of Pulmonary Tuberculosis by Mycobacterium tuberculosis. Front Immunol 2020; 11:930. [PMID: 32508826 PMCID: PMC7248268 DOI: 10.3389/fimmu.2020.00930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/11/2019] [Accepted: 04/21/2020] [Indexed: 12/18/2022] Open
Abstract
The global control of Tuberculosis remains elusive, and Bacillus Calmette-Guérin (BCG) -the most widely used vaccine in history-has proven insufficient for reversing this epidemic. Several authors have suggested that the mass presence of vaccinated hosts might have affected the Mycobacterium tuberculosis (MTB) population structure, and this could in turn be reflected in a prevalence of strains with higher ability to circumvent BCG-induced immunity, such as the recent Beijing genotype. The effect of vaccination on vaccine-escape variants has been well-documented in several bacterial pathogens; however the effect of the interaction between MTB strains and vaccinated hosts has never been previously described. In this study we show for the first time the interaction between MTB Beijing-genotype strains and BCG-vaccinated hosts. Using a well-controlled murine model of progressive pulmonary tuberculosis, we vaccinated BALB/c mice with two different sub-strains of BCG (BCG-Phipps and BCG-Vietnam). Following vaccination, the mice were infected with either one of three selected MTB strains. Strains were selected based on lineage, and included two Beijing-family clinical isolates (strains 46 and 48) and a well-characterized laboratory strain (H37Rv). Two months after infection, mice were euthanized and the bacteria extracted from their lungs. We characterized the genomic composite of the bacteria before and after exposure to vaccinated hosts, and also characterized the local response to the bacteria by sequencing the lung transcriptome in animals during the infection. Results from this study show that the interaction within the lungs of the vaccinated hosts results in the selection of higher-virulence bacteria, specifically for the Beijing genotype strains 46 and 48. After exposure to the BCG-induced immune response, strains 46 and 48 acquire genomic mutations associated with several virulence factors. As a result, the bacteria collected from these vaccinated hosts have an increased ability for immune evasion, as shown in both the host transcriptome and the histopathology studies, and replicates far more efficiently compared to bacteria collected from unvaccinated hosts or to the original-stock strain. Further research is warranted to ascertain the pathways associated with the genomic alterations. However, our results highlight novel host-pathogen interactions induced by exposure of MTB to BCG vaccinated hosts.
Collapse
Affiliation(s)
- Zyanya Lucia Zatarain-Barrón
- Experimental Pathology Laboratory, Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Octavio Ramos-Espinosa
- Experimental Pathology Laboratory, Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Brenda Marquina-Castillo
- Experimental Pathology Laboratory, Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Jorge Barrios-Payán
- Experimental Pathology Laboratory, Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Otoniel Maya-Lucas
- Department of Genetics and Molecular Biology, Centro de Investigaciones y de Estudios Avanzados (CINVESTAV), Mexico City, Mexico
| | - Gamaliel López-Leal
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Camilo Molina-Romero
- Experimental Pathology Laboratory, Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Richard M Anthony
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Adrián Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Inti Alberto De La Rosa-Velázquez
- Genomics Laboratory, Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México - Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Rosa Gloria Rebollar-Vega
- Genomics Laboratory, Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México - Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Robin M Warren
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, MRC Centre for Molecular and Cellular Biology, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Dulce Adriana Mata-Espinosa
- Experimental Pathology Laboratory, Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Rogelio Hernández-Pando
- Experimental Pathology Laboratory, Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| |
Collapse
|
6
|
Cornejo-Granados F, Calderón de la Barca AM, Torres N, Martínez-Romero E, Torres J, López-Vidal Y, Soberón X, Partida-Martínez LP, Pinto-Cardoso S, Alcaraz LD, Pardo-López L, Canizales-Quinteros S, Puente JL, Ochoa-Leyva A. Microbiome-MX 2018: microbiota and microbiome opportunities in Mexico, a megadiverse country. Res Microbiol 2019; 170:235-241. [PMID: 30922683 DOI: 10.1016/j.resmic.2019.03.001] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 02/13/2019] [Accepted: 03/12/2019] [Indexed: 11/29/2022]
Abstract
A weekly conference series paired with lectures entitled "Microbiome-MX: exploring the Microbiota and Microbiome Research in Mexico" was organized to provide a multidisciplinary overview of the most recent research done in Mexico using high-throughput sequencing. Scientists and postgraduate students from several disciplines such as microbiology, bioinformatics, virology, immunology, nutrition, and medical genomics gathered to discuss state of the art in each of their respective subjects of expertise, as well as advances, applications and new opportunities on microbiota/microbiome research. In particular, high-throughput sequencing is a crucial tool to understand the challenges of a megadiverse developing country as Mexico, and moreover to know the scientific capital and capabilities available for collaboration. The conference series addressed three main topics important for Mexico: i) the complex role of microbiota in health and prevalent diseases such as obesity, diabetes, inflammatory bowel disease, tuberculosis, HIV, autoimmune diseases and gastric cancer; ii) the use of local, traditional and prehispanic products as pre/probiotics to modulate the microbiota and improve human health; and iii) the impact of the microbiota in shaping the biodiversity of economically important terrestrial and marine ecosystems. Herein, we summarize the contributions that Mexican microbiota/microbiome research is making to the global trends, describing the highlights of the conferences and lectures, rather than a review of the state-of-the-art of this research. This meeting report also presents the efforts of a multidisciplinary group of scientist to encourage collaborations and bringing this research field closer for younger generations.
Collapse
Affiliation(s)
- Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico.
| | - Ana María Calderón de la Barca
- Departamento de Nutrición Humana, Centro de Investigación en Alimentación y Desarrollo, A.C. Astiazarán Rosas No. 46. Col. La Victoria, Hermosillo, 83304, Sonora, Mexico.
| | - Nimbe Torres
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán Vasco de Quiroga No 15, Ciudad de México, 14080, Cd de México, Mexico.
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico.
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Instituto Mexicano del Seguro Social, Cd de México, Mexico.
| | - Yolanda López-Vidal
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Cd. México, Mexico.
| | - Xavier Soberón
- Instituto Nacional de Medicina Genómica, Cd. México, Mexico.
| | - Laila P Partida-Martínez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato, 36824, Mexico.
| | - Sandra Pinto-Cardoso
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4501, Colonia Sección XVI, Ciudad de México, C.P, 14080, Mexico.
| | - Luis David Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Ciudad de México, Mexico; Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de México, Mexico.
| | - Liliana Pardo-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico.
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Cd de México, Mexico.
| | - José Luis Puente
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico.
| | - Adrián Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico.
| |
Collapse
|
7
|
Astudillo-Melgar F, Ochoa-Leyva A, Utrilla J, Huerta-Beristain G. Bacterial Diversity and Population Dynamics During the Fermentation of Palm Wine From Guerrero Mexico. Front Microbiol 2019; 10:531. [PMID: 30967846 PMCID: PMC6440455 DOI: 10.3389/fmicb.2019.00531] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 12/07/2018] [Accepted: 03/01/2019] [Indexed: 01/09/2023] Open
Abstract
Palm wine is obtained by fermentation of palm tree sap. In the Pacific coast of Mexico, palm wine is called Tuba and it is consumed as a traditional fermented beverage. Tuba has empirical applications such as an auxiliary in gastrointestinal diseases and a good source of nutrients. In the present study, a next-generation sequencing of the V3-V4 regions of the 16S rRNA gene was employed to analyze bacterial diversity and population dynamics during the fermentation process of Tuba, both in laboratory controlled conditions and in commercial samples from local vendors. Taxonomic identification showed that Fructobacillus was the main genus in all the samples, following by Leuconostoc, Gluconacetobacter, Sphingomonas, and Vibrio. Alpha diversity analysis demonstrated variability between all the samples. Beta diversity clustered the bacterial population according to the collection origin of the sample. Metabolic functional profile inference showed that the members of the bacterial communities may present the vitamin, antibiotic and antioxidant biosynthesis genes. Additionally, we further investigated the correlation between the predominant genera and some composition parameters of this beverage. This study provides the basis of the bacterial community composition and functionality of the fermented beverage.
Collapse
Affiliation(s)
- Fernando Astudillo-Melgar
- Laboratorio de Investigación en Biotecnología, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Adrián Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - José Utrilla
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gerardo Huerta-Beristain
- Laboratorio de Investigación en Biotecnología, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
| |
Collapse
|
8
|
Cervantes-Echeverría M, Equihua-Medina E, Cornejo-Granados F, Hernández-Reyna A, Sánchez F, López-Contreras BE, Canizales-Quinteros S, Ochoa-Leyva A. Whole-genome of Mexican-crAssphage isolated from the human gut microbiome. BMC Res Notes 2018; 11:902. [PMID: 30558657 PMCID: PMC6296078 DOI: 10.1186/s13104-018-4010-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/12/2018] [Indexed: 11/22/2022] Open
Abstract
Objectives crAssphage is a newly found phage described as the most abundant virus in the human gut microbiome. The majority of the crAssphage proteins are unknown in sequences databases, and its pathogenicity and epidemiology in humans are yet unclear. Hence, being one of the most abundant phages in the human gut microbiome more investigation at the genomic level is necessary to improve our understanding, especially in the Latin American population. Data description In this article, we provide the whole genome of a crAssphage isolated from the human gut microbiome of the Mexican population, which was named Mexican-crAssphage. The genome consists of 96,283 bp, G+C content of 29.24% and 87 coding sequences. Notably, we did not find any transfer RNA genes in the genome sequence. We also sequenced viral-like enriched particles from 28 fecal samples, and we detected the presence of the Mexican-crAssphage genome in 8 samples (28.5%). To our knowledge, our data is the first whole genome report of the crAssphage isolated from the Latin American Population and provides valuable information for the experimental characterization of the most abundant human gut bacteriophage. The whole genome shotgun project of the Mexican-crAssphage is available at DDBJ/ENA/GenBank under the GenBank MK069403.
Collapse
Affiliation(s)
- Melany Cervantes-Echeverría
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Edgar Equihua-Medina
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Abigail Hernández-Reyna
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Filiberto Sánchez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Blanca Estela López-Contreras
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Adrián Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico.
| |
Collapse
|
9
|
Cornejo-Granados F, Hurtado-Ramírez JM, Hernández-Pando R, Ochoa-Leyva A. Secret-AAR: a web server to assess the antigenic density of proteins and homology search against bacterial and parasite secretome proteins. Genomics 2018; 111:1514-1516. [PMID: 30316740 DOI: 10.1016/j.ygeno.2018.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 07/25/2018] [Revised: 10/10/2018] [Accepted: 10/10/2018] [Indexed: 12/13/2022]
Abstract
The secretome refers to all the Excreted/Secreted (ES) proteins of a cell, and these are involved in critical biological processes, such as cell-cell communication, and host immune responses. Recently, we introduced the Abundance of Antigenic Aegions (AAR) value to assess the protein antigenic density and to evaluate the antigenic potential of secretomes. Here, to facilitate the AAR calculation, we implemented it as a user-friendly webserver. We extended the webserver capabilities implementing a sequence-based tool for searching homologous proteins across secretomes, including experimental and predicted secretomes of Mycobacterium tuberculosis and Taenia solium. Additionally, twelve secretomes of helminths, five of Mycobacterium and two of Gram-negative bacteria are also available. Our webserver is a useful tool for researchers working on immunoinformatics and reverse vaccinology, aiming at discovering candidate proteins for new vaccines or diagnostic tests, and it can be used to prioritize the experimental analysis of proteins for druggability assays. The Secret-AAR web server is available at http://microbiomics.ibt.unam.mx/tools/aar/.
Collapse
Affiliation(s)
- Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Juan Manuel Hurtado-Ramírez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Rogelio Hernández-Pando
- Experimental Pathology Section, National Institute of Medical Sciences and Nutrition "Salvador Zubirán", Mexico City 14000, Mexico
| | - Adrián Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico.
| |
Collapse
|
10
|
López-Contreras BE, Morán-Ramos S, Villarruel-Vázquez R, Macías-Kauffer L, Villamil-Ramírez H, León-Mimila P, Vega-Badillo J, Sánchez-Muñoz F, Llanos-Moreno LE, Canizalez-Román A, Del Río-Navarro B, Ibarra-González I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA, Canizales-Quinteros S. Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits. Pediatr Obes 2018; 13:381-388. [PMID: 29388394 DOI: 10.1111/ijpo.12262] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 10/25/2017] [Accepted: 10/31/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND Childhood obesity is a serious public health problem in Mexico. Adult gut microbiota composition has been linked to obesity, but few studies have addressed the role of gut microbiota in childhood obesity. OBJECTIVES The aim of this study is to compare gut microbiota composition in obese and normal-weight children and to associate gut microbiota profiles with amino acid serum levels and obesity-related metabolic traits. METHODS Microbial taxa relative abundance was determined by 16S rRNA sequencing in 67 normal-weight and 71 obese children aged 6-12 years. Serum amino acid levels were measured by mass spectrometry. Associations between microbiota composition, metabolic parameters and amino acid serum levels were tested. RESULTS No significant differences in phyla abundances or Firmicutes/Bacteroidetes ratios were observed between normal-weight and obese children. However, Bacteroides eggerthii abundance was significantly higher in obese children and correlated positively with body fat percentage and negatively with insoluble fibre intake. Additionally, Bacteroides plebeius and unclassified Christensenellaceae abundances were significantly higher in normal-weight children. Abundance of both these species correlated negatively with phenylalanine serum levels, a metabolite also found to be associated with obesity in Mexican children. CONCLUSIONS The study identified bacterial species associated with obesity, metabolic complications and amino acid serum levels in Mexican children.
Collapse
Affiliation(s)
- B E López-Contreras
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - S Morán-Ramos
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.,Consejo Nacional de Ciencia y Tecnología (CONACYT), Mexico City, Mexico
| | - R Villarruel-Vázquez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - L Macías-Kauffer
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - H Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - P León-Mimila
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - J Vega-Badillo
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - F Sánchez-Muñoz
- Departamento de Inmunología, Instituto Nacional de Cardiología 'Ignacio Chávez', Mexico City, Mexico
| | - L E Llanos-Moreno
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - A Canizalez-Román
- CIASaP, Facultad de Medicina, Universidad Autónoma de Sinaloa, Culiacán, Mexico
| | | | - I Ibarra-González
- Instituto de Investigaciones Biomédicas, UNAM/Instituto Nacional de Pediatría, Mexico City, Mexico.,Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - M Vela-Amieva
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - T Villarreal-Molina
- Laboratorio de Genómica de Enfermedades Cardiovasculares, INMEGEN, Mexico City, Mexico
| | - A Ochoa-Leyva
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.,Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - C A Aguilar-Salinas
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición, Mexico City, Mexico
| | - S Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| |
Collapse
|
11
|
Bobes RJ, Navarrete-Perea J, Ochoa-Leyva A, Anaya VH, Hernández M, Cervantes-Torres J, Estrada K, Sánchez-Lopez F, Soberón X, Rosas G, Nunes CM, García-Varela M, Sotelo-Mundo RR, López-Zavala AA, Gevorkian G, Acero G, Laclette JP, Fragoso G, Sciutto E. Experimental and Theoretical Approaches To Investigate the Immunogenicity of Taenia solium-Derived KE7 Antigen. Infect Immun 2017; 85:e00395-17. [PMID: 28923896 PMCID: PMC5695116 DOI: 10.1128/iai.00395-17] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/11/2017] [Indexed: 11/20/2022] Open
Abstract
Taenia solium cysticercosis, a parasitic disease that affects human health in various regions of the world, is preventable by vaccination. Both the 97-amino-acid-long KETc7 peptide and its carboxyl-terminal, 18-amino-acid-long sequence (GK-1) are found in Taenia crassiceps Both peptides have proven protective capacity against cysticercosis and are part of the highly conserved, cestode-native, 264-amino-acid long protein KE7. KE7 belongs to a ubiquitously distributed family of proteins associated with membrane processes and may participate in several vital cell pathways. The aim of this study was to identify the T. solium KE7 (TsKE7) full-length protein and to determine its immunogenic properties. Recombinant TsKE7 (rTsKE7) was expressed in Escherichia coli Rosetta2 cells and used to obtain mouse polyclonal antibodies. Anti-rTsKE7 antibodies detected the expected native protein among the 350 spots developed from T. solium cyst vesicular fluid in a mass spectrometry-coupled immune proteomic analysis. These antibodies were then used to screen a phage-displayed 7-random-peptide library to map B-cell epitopes. The recognized phages displayed 9 peptides, with the consensus motif Y(F/Y)PS sequence, which includes YYYPS (named GK-1M, for being a GK-1 mimotope), exactly matching a part of GK-1. GK-1M was recognized by 58% of serum samples from cysticercotic pigs with 100% specificity but induced weak protection against murine cysticercosis. In silico analysis revealed a universal T-cell epitope(s) in native TsKE7 potentially capable of stimulating cytotoxic T lymphocytes and helper T lymphocytes under different major histocompatibility complex class I and class II mouse haplotypes. Altogether, these results provide a rationale for the efficacy of the KETc7, rTsKE7, and GK-1 peptides as vaccines.
Collapse
Affiliation(s)
- Raúl J Bobes
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - José Navarrete-Perea
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
- Instituto Nacional de Medicina Genómica, México City, México
| | - Adrián Ochoa-Leyva
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Víctor Hugo Anaya
- Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, México
| | - Marisela Hernández
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | | | - Karel Estrada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Filiberto Sánchez-Lopez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Xavier Soberón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Instituto Nacional de Medicina Genómica, México City, México
| | - Gabriela Rosas
- Facultad de Medicina, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Cáris Maroni Nunes
- UNESP, Universidade Estadual Paulista, Department of Animal Health and Production, Araçatuba, SP, Brazil
| | - Martín García-Varela
- Instituto de Biología, Universidad Nacional Autónoma de México, México City, México
| | - Rogerio Rafael Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora, México
| | - Alonso Alexis López-Zavala
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora, México
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
| | - Goar Gevorkian
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Gonzalo Acero
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Juan P Laclette
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Gladis Fragoso
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Edda Sciutto
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| |
Collapse
|
12
|
Cornejo-Granados F, Zatarain-Barrón ZL, Cantu-Robles VA, Mendoza-Vargas A, Molina-Romero C, Sánchez F, Del Pozo-Yauner L, Hernández-Pando R, Ochoa-Leyva A. Secretome Prediction of Two M. tuberculosis Clinical Isolates Reveals Their High Antigenic Density and Potential Drug Targets. Front Microbiol 2017; 8:128. [PMID: 28223967 PMCID: PMC5293778 DOI: 10.3389/fmicb.2017.00128] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 11/01/2016] [Accepted: 01/18/2017] [Indexed: 12/15/2022] Open
Abstract
The Excreted/Secreted (ES) proteins play important roles during Mycobacterium tuberculosis invasion, virulence, and survival inside the host and they are a major source of immunogenic proteins. However, the molecular complexity of the bacillus cell wall has made difficult the experimental isolation of the total bacterial ES proteins. Here, we reported the genomes of two Beijing genotype M. tuberculosis clinical isolates obtained from patients from Vietnam (isolate 46) and South Africa (isolate 48). We developed a bioinformatics pipeline to predict their secretomes and observed that ~12% of the genome-encoded proteins are ES, being PE, PE-PGRS, and PPE the most abundant protein domains. Additionally, the Gene Ontology, KEGG pathways and Enzyme Classes annotations supported the expected functions for the secretomes. The ~70% of an experimental secretome compiled from literature was contained in our predicted secretomes, while only the 34–41% of the experimental secretome was contained in the two previously reported secretomes for H37Rv. These results suggest that our bioinformatics pipeline is better to predict a more complete set of ES proteins in M. tuberculosis genomes. The predicted ES proteins showed a significant higher antigenic density measured by Abundance of Antigenic Regions (AAR) value than the non-ES proteins and also compared to random constructed secretomes. Additionally, we predicted the secretomes for H37Rv, H37Ra, and two M. bovis BCG genomes. The antigenic density for BGG and for isolates 46 and 48 was higher than the observed for H37Rv and H37Ra secretomes. In addition, two sets of immunogenic proteins previously reported in patients with tuberculosis also showed a high antigenic density. Interestingly, mice infected with isolate 46 showed a significant lower survival rate than the ones infected with isolate 48 and both survival rates were lower than the one previously reported for the H37Rv in the same murine model. Finally, after a druggability analysis of the secretomes, we found potential drug targets such as cytochrome P450, thiol peroxidase, the Ag85C, and Ribonucleoside Reductase in the secreted proteins that could be used as drug targets for novel treatments against Tuberculosis.
Collapse
Affiliation(s)
- Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Zyanya L Zatarain-Barrón
- Experimental Pathology Laboratory, Department of Pathology, National Institute of Medical Science and Nutrition "Salvador Zubirán" Mexico City, Mexico
| | - Vito A Cantu-Robles
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | | | | | - Filiberto Sánchez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Luis Del Pozo-Yauner
- Laboratorio de Estructura de Proteínas, National Institute of Genomic Medicine Mexico City, Mexico
| | - Rogelio Hernández-Pando
- Experimental Pathology Laboratory, Department of Pathology, National Institute of Medical Science and Nutrition "Salvador Zubirán" Mexico City, Mexico
| | - Adrián Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| |
Collapse
|
13
|
Gomez S, Adalid-Peralta L, Palafox-Fonseca H, Cantu-Robles VA, Soberón X, Sciutto E, Fragoso G, Bobes RJ, Laclette JP, Yauner LDP, Ochoa-Leyva A. Erratum: Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR). Sci Rep 2015; 5:12385. [PMID: 26373697 PMCID: PMC4570980 DOI: 10.1038/srep12385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
14
|
Bikel S, Valdez-Lara A, Cornejo-Granados F, Rico K, Canizales-Quinteros S, Soberón X, Del Pozo-Yauner L, Ochoa-Leyva A. Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome. Comput Struct Biotechnol J 2015; 13:390-401. [PMID: 26137199 PMCID: PMC4484546 DOI: 10.1016/j.csbj.2015.06.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 02/07/2023] Open
Abstract
The advances in experimental methods and the development of high performance bioinformatic tools have substantially improved our understanding of microbial communities associated with human niches. Many studies have documented that changes in microbial abundance and composition of the human microbiome is associated with human health and diseased state. The majority of research on human microbiome is typically focused in the analysis of one level of biological information, i.e., metagenomics or metatranscriptomics. In this review, we describe some of the different experimental and bioinformatic strategies applied to analyze the 16S rRNA gene profiling and shotgun sequencing data of the human microbiome. We also discuss how some of the recent insights in the combination of metagenomics, metatranscriptomics and viromics can provide more detailed description on the interactions between microorganisms and viruses in oral and gut microbiomes. Recent studies on viromics have begun to gain importance due to the potential involvement of viruses in microbial dysbiosis. In addition, metatranscriptomic combined with metagenomic analysis have shown that a substantial fraction of microbial transcripts can be differentially regulated relative to their microbial genomic abundances. Thus, understanding the molecular interactions in the microbiome using the combination of metagenomics, metatranscriptomics and viromics is one of the main challenges towards a system level understanding of human microbiome.
Collapse
Affiliation(s)
- Shirley Bikel
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico
| | - Alejandra Valdez-Lara
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico
| | - Fernanda Cornejo-Granados
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico
| | - Karina Rico
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico
| | - Xavier Soberón
- Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F., Mexico
| | | | - Adrián Ochoa-Leyva
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico
| |
Collapse
|
15
|
Gomez S, Adalid-Peralta L, Palafox-Fonseca H, Cantu-Robles VA, Soberón X, Sciutto E, Fragoso G, Bobes RJ, Laclette JP, Yauner LDP, Ochoa-Leyva A. Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR). Sci Rep 2015; 5:9683. [PMID: 25989346 PMCID: PMC4437048 DOI: 10.1038/srep09683] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [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: 10/29/2014] [Accepted: 03/16/2015] [Indexed: 11/09/2022] Open
Abstract
Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest.
Collapse
Affiliation(s)
- Sandra Gomez
- Instituto Nacional de Neurología y Neurocirugía, México, D.F., C.P. 14269, México
| | - Laura Adalid-Peralta
- 1] Instituto Nacional de Neurología y Neurocirugía, México, D.F., C.P. 14269, México [2] Unidad Periférica del Instituto de Investigaciones Biomédicas en el Instituto Nacional de Neurología y Neurocirugía, México, D.F., C.P. 14269, México
| | | | - Vito Adrian Cantu-Robles
- Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610, México
| | - Xavier Soberón
- 1] Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610, México [2] Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos, C.P. 62210, México
| | - Edda Sciutto
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F., C.P. 04510, México
| | - Gladis Fragoso
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F., C.P. 04510, México
| | - Raúl J Bobes
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F., C.P. 04510, México
| | - Juan P Laclette
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F., C.P. 04510, México
| | - Luis del Pozo Yauner
- Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610, México
| | - Adrián Ochoa-Leyva
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica (INMEGEN), Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan México, D.F. C.P. 14610, México
| |
Collapse
|
16
|
del Pozo-Yauner L, Wall JS, González Andrade M, Sánchez-López R, Rodríguez-Ambriz SL, Pérez Carreón JI, Ochoa-Leyva A, Fernández-Velasco DA. The N-terminal strand modulates immunoglobulin light chain fibrillogenesis. Biochem Biophys Res Commun 2013; 443:495-9. [PMID: 24321098 DOI: 10.1016/j.bbrc.2013.11.123] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 11/27/2013] [Indexed: 12/20/2022]
Abstract
It has been suggested that the N-terminal strand of the light chain variable domain (V(L)) protects the molecule from aggregation by hindering spurious intermolecular contacts. We evaluated the impact of mutations in the N-terminal strand on the thermodynamic stability and kinetic of fibrillogenesis of the V(L) protein 6aJL2. Mutations in this strand destabilized the protein in a position-dependent manner, accelerating the fibrillogenesis by shortening the lag time; an effect that correlated with the extent of destabilization. In contrast, the effect on the kinetics of fibril elongation, as assessed in seeding experiments was of different nature, as it was not directly dependant on the degree of destabilization. This finding suggests different factors drive the nucleation-dependent and elongation phases of light chain fibrillogenesis. Finally, taking advantage of the dependence of the Trp fluorescence upon environment, four single Trp substitutions were made in the N-terminal strand, and changes in solvent exposure during aggregation were evaluated by acrylamide-quenching. The results suggest that the N-terminal strand is buried in the fibrillar state of 6aJL2 protein. This finding suggest a possible explanation for the modulating effect exerted by the mutations in this strand on the aggregation behavior of 6aJL2 protein.
Collapse
Affiliation(s)
- Luis del Pozo-Yauner
- Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610, Mexico.
| | - Jonathan S Wall
- Departments of Radiology and Medicine, The University of Tennessee Medical Center, 1924 Alcoa Highway, Knoxville, TN, USA
| | - Martín González Andrade
- Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610, Mexico
| | - Rosana Sánchez-López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Col. Chamilpa Cuernavaca, Morelos C.P. 62210, Mexico
| | - Sandra L Rodríguez-Ambriz
- Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Calle CEPROBI No. 8, Col. San Isidro, Yautepec, Morelos C.P. 62731, Mexico
| | - Julio I Pérez Carreón
- Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610, Mexico
| | - Adrián Ochoa-Leyva
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica (INMEGEN), Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan México, D.F. C.P. 14610, Mexico
| | - D Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Interior, Ciudad Universitaria, Av. Universidad 3000, México, D.F. C.P. 04510, Mexico
| |
Collapse
|
17
|
Lara-González S, Estrella-Hernández P, Ochoa-Leyva A, Del Carmen Portillo-Téllez M, Caro-Gómez LA, Figueroa-Angulo EE, Salgado-Lugo H, Miranda Ozuna JFT, Ortega-López J, Arroyo R, Brieba LG, Benítez-Cardoza CG. Structural and thermodynamic folding characterization of triosephosphate isomerases from Trichomonas vaginalis reveals the role of destabilizing mutations following gene duplication. Proteins 2013; 82:22-33. [PMID: 23733417 DOI: 10.1002/prot.24333] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [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: 10/07/2012] [Revised: 05/01/2013] [Accepted: 05/03/2013] [Indexed: 11/07/2022]
Abstract
We report the structures and thermodynamic analysis of the unfolding of two triosephosphate isomerases (TvTIM1 and TvTIM2) from Trichomonas vaginalis. Both isoforms differ by the character of four amino acids: E/Q 18, I/V 24, I/V 45, and P/A 239. Despite the high sequence and structural similarities between both isoforms, they display substantial differences in their stabilities. TvTIM1 (E18, I24, I45, and P239) is more stable and less dissociable than TvTIM2 (Q18, V24, V45, and A239). We postulate that the identities of residues 24 and 45 are responsible for the differences in monomer stability and dimer dissociability, respectively. The structural difference between both amino acids is one methyl group. In TvTIMs, residue 24 is involved in packing α-helix 1 against α-helix 2 of each monomer and residue 45 is located at the center of the dimer interface forming a "ball and socket" interplay with a hydrophobic cavity. The mutation of valine at position 45 for an alanine in TvTIM2 produces a protein that migrates as a monomer by gel filtration. A comparison with known TIM structures indicates that this kind of interplay is a conserved feature that stabilizes dimeric TIM structures. In addition, TvTIMs are located in the cytoplasm and in the membrane. As TvTIM2 is an easily dissociable dimer, the dual localization of TvTIMs may be related to the acquisition of a moonlighting activity of monomeric TvTIM2. To our knowledge, this is the simplest example of how a single amino acid substitution can provide alternative function to a TIM barrel protein.
Collapse
Affiliation(s)
- Samuel Lara-González
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, San Luis Potosí, San Luis Potosí, México, CP 78216
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Ochoa-Leyva A, Montero-Morán G, Saab-Rincón G, Brieba LG, Soberón X. Alternative splice variants in TIM barrel proteins from human genome correlate with the structural and evolutionary modularity of this versatile protein fold. PLoS One 2013; 8:e70582. [PMID: 23950966 PMCID: PMC3741200 DOI: 10.1371/journal.pone.0070582] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 06/20/2013] [Indexed: 12/20/2022] Open
Abstract
After the surprisingly low number of genes identified in the human genome, alternative splicing emerged as a major mechanism to generate protein diversity in higher eukaryotes. However, it is still not known if its prevalence along the genome evolution has contributed to the overall functional protein diversity or if it simply reflects splicing noise. The (βα)8 barrel or TIM barrel is one of the most frequent, versatile, and ancient fold encountered among enzymes. Here, we analyze the structural modifications present in TIM barrel proteins from the human genome product of alternative splicing events. We found that 87% of all splicing events involved deletions; most of these events resulted in protein fragments that corresponded to the (βα)2, (βα)4, (βα)5, (βα)6, and (βα)7 subdomains of TIM barrels. Because approximately 7% of all the splicing events involved internal β-strand substitutions, we decided, based on the genomic data, to design β-strand and α-helix substitutions in a well-studied TIM barrel enzyme. The biochemical characterization of one of the chimeric variants suggests that some of the splice variants in the human genome with β-strand substitutions may be evolving novel functions via either the oligomeric state or substrate specificity. We provide results of how the splice variants represent subdomains that correlate with the independently folding and evolving structural units previously reported. This work is the first to observe a link between the structural features of the barrel and a recurrent genetic mechanism. Our results suggest that it is reasonable to expect that a sizeable fraction of splice variants found in the human genome represent structurally viable functional proteins. Our data provide additional support for the hypothesis of the origin of the TIM barrel fold through the assembly of smaller subdomains. We suggest a model of how nature explores new proteins through alternative splicing as a mechanism to diversify the proteins encoded in the human genome.
Collapse
Affiliation(s)
- Adrián Ochoa-Leyva
- Instituto Nacional de Medicina Genómica (INMEGEN), México City, México
- * E-mail: (AOL); (XS)
| | - Gabriela Montero-Morán
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Gloria Saab-Rincón
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Xavier Soberón
- Instituto Nacional de Medicina Genómica (INMEGEN), México City, México
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (AOL); (XS)
| |
Collapse
|
19
|
Ochoa-Leyva A, Barona-Gómez F, Saab-Rincón G, Verdel-Aranda K, Sánchez F, Soberón X. Exploring the Structure-Function Loop Adaptability of a (β/α)(8)-Barrel Enzyme through Loop Swapping and Hinge Variability. J Mol Biol 2011; 411:143-57. [PMID: 21635898 DOI: 10.1016/j.jmb.2011.05.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 03/31/2011] [Accepted: 05/18/2011] [Indexed: 11/26/2022]
Abstract
Evolution of proteins involves sequence changes that are frequently localized at loop regions, revealing their important role in natural evolution. However, the development of strategies to understand and imitate such events constitutes a challenge to design novel enzymes in the laboratory. In this study, we show how to adapt loop swapping as semiautonomous units of functional groups in an enzyme with the (β/α)(8)-barrel and how this functional adaptation can be measured in vivo. To mimic the natural mechanism providing loop variability in antibodies, we developed an overlap PCR strategy. This includes introduction of sequence diversity at two hinge residues, which connect the new loops with the rest of the protein scaffold, and we demonstrate that this is necessary for a successful exploration of functional sequence space. This design allowed us to explore the sequence requirements to functional adaptation of each loop replacement that may not be sampled otherwise. Libraries generated following this strategy were evaluated in terms of their folding competence and their functional proficiency, an observation that was formalized as a Structure-Function Loop Adaptability value. Molecular details about the function and structure of some variants were obtained by enzyme kinetics and circular dichroism. This strategy yields functional variants that retain the original activity at higher frequencies, suggesting a new strategy for protein engineering that incorporates a more divergent sequence exploration beyond that limited to point mutations. We discuss how this approach may provide insights into the mechanism of enzyme evolution and function.
Collapse
Affiliation(s)
- Adrián Ochoa-Leyva
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, C.P. 62210, México
| | | | | | | | | | | |
Collapse
|
20
|
Ochoa-Leyva A, Soberón X, Sánchez F, Argüello M, Montero-Morán G, Saab-Rincón G. Protein design through systematic catalytic loop exchange in the (beta/alpha)8 fold. J Mol Biol 2009; 387:949-64. [PMID: 19233201 DOI: 10.1016/j.jmb.2009.02.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2008] [Revised: 02/02/2009] [Accepted: 02/10/2009] [Indexed: 11/19/2022]
Abstract
Protein engineering by directed evolution has proven effective in achieving various functional modifications, but the well-established protocols for the introduction of variability, typically limited to random point mutations, seriously restrict the scope of the approach. In an attempt to overcome this limitation, we sought to explore variant libraries with richer diversity at regions recognized as functionally important through an exchange of natural components, thus combining design with combinatorial diversity. With this approach, we expected to maintain interactions important for protein stability while directing the introduction of variability to areas important for catalysis. Our strategy consisted in loop exchange over a (beta/alpha)(8) fold. Phosphoribosylanthranilate isomerase was chosen as scaffold, and we investigated its tolerance to loop exchange by fusing variant libraries to the chloramphenicol acetyl transferase coding gene as an in vivo folding reporter. We replaced loops 2, 4, and 6 of phosphoribosylanthranilate isomerase with loops of varied types and sizes from enzymes sharing the same fold. To allow for a better structural fit, saturation mutagenesis was adopted at two amino acid positions preceding the exchanged loop. Our results showed that 30% to 90% of the generated mutants in the different libraries were folded. Some variants were selected for further characterization after removal of chloramphenicol acetyl transferase gene, and their stability was studied by circular dichroism and fluorescence spectroscopy. The sequences of 545 clones show that the introduction of variability at "hinges" connecting the loops with the scaffold exhibited a noticeable effect on the appearance of folded proteins. Also, we observed that each position accepted foreign loops of different sizes and sequences. We believe our work provides the basis of a general method of exchanging variably sized loops within the (beta/alpha)(8) fold, affording a novel starting point for the screening of novel activities as well as modest diversions from an original activity.
Collapse
Affiliation(s)
- Adrián Ochoa-Leyva
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca, Morelos 62271, México
| | | | | | | | | | | |
Collapse
|
21
|
Wright H, Noda-García L, Ochoa-Leyva A, Hodgson DA, Fülöp V, Barona-Gómez F. The structure/function relationship of a dual-substrate (betaalpha)8-isomerase. Biochem Biophys Res Commun 2007; 365:16-21. [PMID: 17967415 DOI: 10.1016/j.bbrc.2007.10.101] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 10/17/2007] [Indexed: 11/25/2022]
Abstract
Two structures of phosphoribosyl isomerase A (PriA) from Streptomyces coelicolor, involved in both histidine and tryptophan biosynthesis, were solved at 1.8A resolution. A closed conformer was obtained, which represents the first complete structure of PriA, revealing hitherto unnoticed molecular interactions and the occurrence of conformational changes. Inspection of these conformers, including ligand-docking simulations, allowed identification of residues involved in substrate recognition, chemical catalysis and conformational changes. These predictions were validated by mutagenesis and functional analysis. Arg19 and Ser81 were shown to play critical roles within the carboxyl and amino phosphate-binding sites, respectively; the catalytic residues Asp11 and Asp130 are responsible for both activities; and Thr166 and Asp171, which make an unusual contact, are likely to elicit the conformational changes needed for adopting the active site architectures. This represents the first report of the structure/function relationship of this (betaalpha)8-isomerase.
Collapse
Affiliation(s)
- Helena Wright
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | | | | | | | | | | |
Collapse
|
22
|
Wright H, Noda-García L, Ochoa-Leyva A, Hodgson DA, Barona-Gómez F, Fülöp V. Structural studies of the dual-substrate TIM-barrel phosphoribosyl isomerase A. Acta Crystallogr A 2007. [DOI: 10.1107/s0108767307097231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|