1
|
Tenorio-Salgado S, Villalpando-Aguilar JL, Hernandez-Guerrero R, Poot-Hernández AC, Perez-Rueda E. Exploring the enzymatic repertoires of Bacteria and Archaea and their associations with metabolic maps. Braz J Microbiol 2024:10.1007/s42770-024-01462-3. [PMID: 39052173 DOI: 10.1007/s42770-024-01462-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/11/2024] [Indexed: 07/27/2024] Open
Abstract
The evolution, survival, and adaptation of microbes are consequences of gene duplication, acquisition, and divergence in response to environmental challenges. In this context, enzymes play a central role in the evolution of organisms, because they are fundamental in cell metabolism. Here, we analyzed the enzymatic repertoire in 6,467 microbial genomes, including their abundances, and their associations with metabolic maps. We found that the enzymes follow a power-law distribution, in relation to the genome sizes. Therefore, we evaluated the total proportion enzymatic classes in relation to the genomes, identifying a descending-order proportion: transferases (EC:2.-), hydrolases (EC:3.-), oxidoreductases (EC:1.-), ligases (EC:6.-), lyases (EC:4.-), isomerases (EC:5.-), and translocases (EC:7-.). In addition, we identified a preferential use of enzymatic classes in metabolism pathways for xenobiotics, cofactors and vitamins, carbohydrates, amino acids, glycans, and energy. Therefore, this analysis provides clues about the functional constraints associated with the enzymatic repertoire of functions in Bacteria and Archaea.
Collapse
Affiliation(s)
- Silvia Tenorio-Salgado
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Yucatán, México
- Tecnológico Nacional de México, Instituto Tecnológico de Mérida, Av. Tecnológico km. 4.5, 97118, Merida, Yucatan, Mexico
| | - José Luis Villalpando-Aguilar
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Yucatán, México
- Facultad Ciencias de la Salud, Universidad Vizcaya de las Américas, Prolongación Allende, Campeche, 24035, Campeche, Mexico
| | - Rafael Hernandez-Guerrero
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Yucatán, México
| | - Augusto César Poot-Hernández
- Unidad de Bioinformática y Manejo de la Información. Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Yucatán, México.
| |
Collapse
|
2
|
Yang X, Liu P, Yu H, Ling M, Ma M, Wang Q, Tang X, Shen Z, Zhang Y. Comparative analysis of the intestinal flora of BmNPV-resistant and BmNPV-sensitive silkworm varieties. Microb Pathog 2024; 191:106649. [PMID: 38636568 DOI: 10.1016/j.micpath.2024.106649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Bombyx mori nucleopolyhedrovirus (BmNPV) is a very common and infectious virus that affects silkworms and hinders silk production. To investigate the intestinal flora of BmNPV-resistant and BmNPV-sensitive silkworm varieties, 16 S rDNA high-throughput sequencing was performed. The results of the cluster analysis showed that the intestinal flora of the resistant silkworm variety was more abundant than that of the sensitive silkworm variety. This was found even when infection with BmNPV caused a sharp decline in the number of intestinal floral species in both resistant and sensitive silkworm varieties. The abundances of the intestinal flora, including Aureimonas, Ileibacterium, Peptostreptococcus, Pseudomonas, Enterococcus, and Halomonas, in the resistant variety were considerably greater after infection with BmNPV than those in the sensitive variety. After infection with BmNPV, four kinds of important intestinal bacteria, namely, f_Saccharimonadaceae, Peptostreptococcus, Aureirmonas, and f_Rhizobiaceae, were found in the resistant silkworm variety. In the sensitive silkworm variety, only Faecalibaculum was an important intestinal bacterium. The differential or important bacteria mentioned above might be involved in immunoreaction or antiviral activities, especially in the intestines of BmNPV-resistant silkworms. By conducting a functional enrichment analysis, we found that BmNPV infection did not change the abundance of important functional components of the intestinal flora in resistant or sensitive silkworm varieties. However, some functional factors, such as the biosynthesis, transport, and catabolism of secondary metabolites (e.g., terpenoids and polyketides) and lipid transport and metabolism, were more important in the resistant silkworm variety than in the sensitive variety; thus, these factors may increase the resistance of the host to BmNPV. To summarize, we found significant differences in the composition, abundance, and function of the intestinal flora between resistant and sensitive silkworm varieties, especially after infection with BmNPV, which might be closely related to the resistance of resistant silkworm varieties to BmNPV.
Collapse
Affiliation(s)
- Xu Yang
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China.
| | - Pai Liu
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China.
| | - Haodong Yu
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China.
| | - Min Ling
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China.
| | - Mingzhen Ma
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China.
| | - Qiang Wang
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu Province, China.
| | - Xudong Tang
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu Province, China.
| | - Zhongyuan Shen
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu Province, China.
| | - Yiling Zhang
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu Province, China.
| |
Collapse
|
3
|
Poot-Hernandez AC, Rodriguez-Vazquez K, Perez-Rueda E. Identifying similarities at metabolic pathways with a strategy of Enzymatic Step Sequences. MethodsX 2023; 10:102118. [PMID: 36970029 PMCID: PMC10034429 DOI: 10.1016/j.mex.2023.102118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
An easy and fast strategy to compare functionally the metabolic maps is described. The KEGG metabolic maps are transformed into linear Enzymatic Step Sequences (ESS) using the Breadth First Search (BFS) algorithm. To do this, the KGML files are retrieved, and directed graph representations are created; where the nodes represent enzymes or enzymatic complexes, and the edges represent a compound, that is the 'product' from one reaction and a 'substrate' for the next. Then, a set of initialization nodes are selected, and used as the root for the construction of the BFS tree. This tree is used as a guide to the construction of the ESS. From each leaf (terminal node), the path is traced backwards until it reaches the root metabolic map and with two or fewer neighbors in the graph. In a second step, the ESS are compared with a Dynamic Programing algorithm, considering an "ad hoc" substitution matrix, and minimizing the global score. The dissimilarity values between two EC numbers ranged from 0 to 1, where 0 indicates similar EC numbers, and 1 indicates different EC numbers. Finally, the alignment is evaluated by using the normalized entropy-based function, considering a threshold of ≤ 0.27 as significant.•The KEGG metabolic maps are transformed into linear Enzymatic Step Sequences (ESS) using the Breadth First Search (BFS) algorithm.•Nodes represent enzymes or enzymatic complexes, and the edges represent a compound, that is 'product' from one reaction and a 'substrate' for the next.•The ESS are compared with a Dynamic Programing algorithm, considering an "ad hoc" substitution matrix, and minimizing the global score.
Collapse
Affiliation(s)
- Augusto Cesar Poot-Hernandez
- Unidad de Bioinformática y Manejo de la Información. Instituto de Fisiología Celular. Universidad Nacional Autónoma de México, Ciudad Universitaria, México, Mexico
| | - Katya Rodriguez-Vazquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, Mexico
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán. Mérida, Yucatán. Mexico
| |
Collapse
|
4
|
Abernathy BE, Schoenfuss TC, Bailey AS, Gallaher DD. Polylactose Exhibits Prebiotic Activity and Reduces Adiposity and Nonalcoholic Fatty Liver Disease in Rats Fed a High-Fat Diet. J Nutr 2020; 151:352-360. [PMID: 33382431 PMCID: PMC8096245 DOI: 10.1093/jn/nxaa376] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/23/2020] [Accepted: 11/03/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Prebiotic dietary fibers change the intestinal microbiome favorably and provide a health benefit to the host. OBJECTIVES Polylactose is a novel fiber, synthesized by extrusion of lactose. We evaluated its prebiotic activity by determining its fermentability, effect on the microbiota, and effects on adiposity and liver lipids in a diet-induced obesity animal model. METHODS Male Wistar rats (4-5 wk old) were fed normal-fat (NF, 25% fat energy) or high-fat (HF, 51% fat energy) diets containing different fibers (6% fiber of interest and 3% cellulose, by weight), including cellulose (NFC and HFC, negative and positive controls, respectively), polylactose (HFPL), lactose matched to residual lactose in the HFPL diet, and 2 established prebiotic fibers: polydextrose (HFPD) and fructooligosaccharide (HFFOS). After 10 wk of feeding, organs were harvested and cecal contents collected. RESULTS HFPL animals had greater cecum weight (3 times greater than HFC) and lower cecal pH (∼1 pH unit lower than HFC) than all other groups, suggesting that polylactose is more fermentable than other prebiotic fibers (HFPD, HFFOS; P < 0.05). HFPL animals also had increased taxonomic abundance of the probiotic species Bifidobacterium in the cecum relative to all other groups (P < 0.05). Epididymal fat pad weight was significantly decreased in the HFPL group (29% decrease compared with HFC) compared with all other HF groups (P < 0.05) and did not differ from the NFC group. Liver lipids and cholesterol were reduced in HFPL animals when compared with HFC animals (P < 0.05). CONCLUSIONS Polylactose is a fermentable fiber that elicits a beneficial change in the gut microbiota as well as reducing adiposity in rats fed HF diets. These effects of polylactose were greater than those of 2 established prebiotics, fructooligosaccharide and polydextrose, suggesting that polylactose is a potent prebiotic.
Collapse
Affiliation(s)
- Breann E Abernathy
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA
| | - Tonya C Schoenfuss
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA
| | - Allison S Bailey
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA
| | | |
Collapse
|
5
|
Identification of functional signatures in the metabolism of the three cellular domains of life. PLoS One 2019; 14:e0217083. [PMID: 31136618 PMCID: PMC6538242 DOI: 10.1371/journal.pone.0217083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/04/2019] [Indexed: 11/19/2022] Open
Abstract
In order to identify common and specific enzymatic activities associated with the metabolism of the three cellular domains of life, the conservation and variations between the enzyme contents of Bacteria, Archaea, and Eukarya organisms were evaluated. To this end, the content of enzymes belonging to a particular pathway and their abundance and distribution in 1507 organisms that have been annotated and deposited in the KEGG database were assessed. In addition, we evaluated the consecutive enzymatic reaction pairs obtained from metabolic pathway reactions and transformed into sequences of enzymatic reactions, with catalytic activities encoded in the Enzyme Commission numbers, which are linked by a substrate. Both analyses are complementary: the first considers individual reactions associated with each organism and metabolic map, and the second evaluates the functional associations between pairs of consecutive reactions. From these comparisons, we found a set of five enzymatic reactions that were widely distributed in all the organisms and considered here as universal to Bacteria, Archaea, and Eukarya; whereas 132 pairs out of 3151 reactions were identified as significant, only 5 of them were found to be widely distributed in all the taxonomic divisions. However, these universal reactions are not widely distributed along the metabolic maps, suggesting their dispensability to all metabolic processes. Finally, we found that universal reactions are also associated with ancestral domains, such as those related to phosphorus-containing groups with a phosphate group as acceptor or those related to the ribulose-phosphate binding barrel, triosephosphate isomerase, and D-ribose-5-phosphate isomerase (RpiA) lid domain, among others. Therefore, we consider that this analysis provides clues about the functional constraints associated with the repertoire of enzymatic functions per organism.
Collapse
|
6
|
Pittol M, Scully E, Miller D, Durso L, Mariana Fiuza L, Valiati VH. Bacterial Community of the Rice Floodwater Using Cultivation-Independent Approaches. Int J Microbiol 2018; 2018:6280484. [PMID: 29666650 PMCID: PMC5831270 DOI: 10.1155/2018/6280484] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 12/09/2017] [Accepted: 12/26/2017] [Indexed: 11/17/2022] Open
Abstract
In agricultural systems, interactions between plants and microorganisms are important to maintaining production and profitability. In this study, bacterial communities in floodwaters of rice fields were monitored during the vegetative and reproductive stages of rice plant development using 16S amplicon sequencing. The study was conducted in the south of Brazil, during the crop years 2011/12 and 2012/13. Comparative analyses showed strong differences between the communities of floodwaters associated with the two developmental stages. During the vegetative stage, 1551 operational taxonomic units (OTUs) were detected, while less than half that number (603) were identified in the reproductive stage. The higher bacterial richness observed in floodwater collected during the vegetative stage may have been favored by the higher concentration of nutrients, such as potassium, due to rhizodeposition and fertilizer application. Eighteen bacterial phyla were identified in both samples. Both communities were dominated by Gammaproteobacteria. In the vegetative stage, Alphaproteobacteria and Betaproteobacteria were more abundant and, in contrast, Bacilli and Clostridia were the more dominant classes in the reproductive stage. The major bacterial taxa identified have been previously identified as important colonizers of rice fields. The richness and composition of bacterial communities over cultivation time may contribute to the sustainability of the crop.
Collapse
Affiliation(s)
- Michele Pittol
- Programa de Pós-Graduação em Biologia, Universidade do Vale do Rio dos Sinos (UNISINOS), 950 Unisinos Avenue, São Leopoldo, RS, Brazil
| | - Erin Scully
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Center for Grain and Animal Health Research, Stored Product Insect and Engineering Research Unit (SPIERU), 1515 College Ave., Manhattan, KS, USA
| | - Daniel Miller
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Agroecosystem Management Research Unit (AMRU), 251 Filley Hall, UNL East Campus, Lincoln, NE, USA
| | - Lisa Durso
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Agroecosystem Management Research Unit (AMRU), 251 Filley Hall, UNL East Campus, Lincoln, NE, USA
| | - Lidia Mariana Fiuza
- Programa de Pós-Graduação em Biologia, Universidade do Vale do Rio dos Sinos (UNISINOS), 950 Unisinos Avenue, São Leopoldo, RS, Brazil
| | - Victor Hugo Valiati
- Programa de Pós-Graduação em Biologia, Universidade do Vale do Rio dos Sinos (UNISINOS), 950 Unisinos Avenue, São Leopoldo, RS, Brazil
| |
Collapse
|
7
|
Nourdin-Galindo G, Sánchez P, Molina CF, Espinoza-Rojas DA, Oliver C, Ruiz P, Vargas-Chacoff L, Cárcamo JG, Figueroa JE, Mancilla M, Maracaja-Coutinho V, Yañez AJ. Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups. Front Cell Infect Microbiol 2017; 7:459. [PMID: 29164068 PMCID: PMC5671498 DOI: 10.3389/fcimb.2017.00459] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/16/2017] [Indexed: 11/13/2022] Open
Abstract
Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these genes could be directly associated with inter-genogroup differences in pathogenesis and host-pathogen interactions, information that could be useful in designing novel strategies for diagnosing and controlling P. salmonis infection.
Collapse
Affiliation(s)
- Guillermo Nourdin-Galindo
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Laboratory of Integrative Bioinformatics, Facultad de Ciencias, Centro de Genómica y Bioinformática, Universidad Mayor, Santiago, Chile
| | - Patricio Sánchez
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Centro FONDAP, Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - Cristian F Molina
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,AUSTRAL-omics, Universidad Austral de Chile, Valdivia, Chile
| | - Daniela A Espinoza-Rojas
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Laboratory of Integrative Bioinformatics, Facultad de Ciencias, Centro de Genómica y Bioinformática, Universidad Mayor, Santiago, Chile
| | - Cristian Oliver
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Centro FONDAP, Interdisciplinary Center for Aquaculture Research, Concepción, Chile.,Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Viña del Mar, Chile
| | - Pamela Ruiz
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Centro FONDAP, Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - Luis Vargas-Chacoff
- Facultad de Ciencias, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan G Cárcamo
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Centro FONDAP, Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - Jaime E Figueroa
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Centro FONDAP, Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - Marcos Mancilla
- Laboratorio de Diagnóstico y Biotecnología, ADL Diagnostic Chile SpA., Puerto Montt, Chile
| | - Vinicius Maracaja-Coutinho
- Laboratory of Integrative Bioinformatics, Facultad de Ciencias, Centro de Genómica y Bioinformática, Universidad Mayor, Santiago, Chile.,Laboratory of Integrative Bioinformatics, Instituto Vandique, João Pessoa, Brazil.,Beagle Bioinformatics, Santiago, Chile
| | - Alejandro J Yañez
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Centro FONDAP, Interdisciplinary Center for Aquaculture Research, Concepción, Chile.,AUSTRAL-omics, Universidad Austral de Chile, Valdivia, Chile
| |
Collapse
|
8
|
Rivera-Gómez N, Martínez-Núñez MA, Pastor N, Rodriguez-Vazquez K, Perez-Rueda E. Dissecting the protein architecture of DNA-binding transcription factors in bacteria and archaea. MICROBIOLOGY-SGM 2017; 163:1167-1178. [PMID: 28777072 DOI: 10.1099/mic.0.000504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene regulation at the transcriptional level is a central process in all organisms where DNA-binding transcription factors play a fundamental role. This class of proteins binds specifically at DNA sequences, activating or repressing gene expression as a function of the cell's metabolic status, operator context and ligand-binding status, among other factors, through the DNA-binding domain (DBD). In addition, TFs may contain partner domains (PaDos), which are involved in ligand binding and protein-protein interactions. In this work, we systematically evaluated the distribution, abundance and domain organization of DNA-binding TFs in 799 non-redundant bacterial and archaeal genomes. We found that the distributions of the DBDs and their corresponding PaDos correlated with the size of the genome. We also identified specific combinations between the DBDs and their corresponding PaDos. Within each class of DBDs there are differences in the actual angle formed at the dimerization interface, responding to the presence/absence of ligands and/or crystallization conditions, setting the orientation of the resulting helices and wings facing the DNA. Our results highlight the importance of PaDos as central elements that enhance the diversity of regulatory functions in all bacterial and archaeal organisms, and our results also demonstrate the role of PaDos in sensing diverse signal compounds. The highly specific interactions between DBDs and PaDos observed in this work, together with our structural analysis highlighting the difficulty in predicting both inter-domain geometry and quaternary structure, suggest that these systems appeared once and evolved with diverse duplication events in all the analysed organisms.
Collapse
Affiliation(s)
- Nancy Rivera-Gómez
- Centro de Investigaciones en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Mario Alberto Martínez-Núñez
- Laboratorio de Estudios Ecogenómicos, Facultad de Ciencias, Unidad Académica de Ciencias y Tecnología de Yucatán, Universidad Nacional Autónoma de México, Mérida, Yucatán, México
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, IICBA. Universidad Autónoma del Estado de Morelos Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos 62209, México
| | - Katya Rodriguez-Vazquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización. Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas. Ciudad Universitaria, Universidad Nacional Autónoma de México, México, D.F, México
| | - Ernesto Perez-Rueda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.,Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Mérida, Yucatán, México
| |
Collapse
|