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Herrera-Morandé A, Vallejos-Baccelliere G, Cea PA, Zamora RA, Cid D, Maturana P, González-Ordenes F, Castro-Fernández V, Guixé V. Kinetic characterization and phylogenetic analysis of human ADP-dependent glucokinase reveal new insights into its regulatory properties. Arch Biochem Biophys 2023; 741:109602. [PMID: 37084804 DOI: 10.1016/j.abb.2023.109602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 04/23/2023]
Abstract
Although ADP-dependent sugar kinases were first described in archaea, at present, the presence of an ADP-dependent glucokinase (ADP-GK) in mammals is well documented. This enzyme is mainly expressed in hematopoietic lineages and tumor tissues, although its role has remained elusive. Here, we report a detailed kinetic characterization of the human ADP-dependent glucokinase (hADP-GK), addressing the influence of a putative signal peptide for endoplasmic reticulum (ER) destination by characterizing a truncated form. The truncated form revealed no significant impact on the kinetic parameters, showing only a slight increase in the Vmax value, higher metal promiscuity, and the same nucleotide specificity as the full-length enzyme. hADP-GK presents an ordered sequential kinetic mechanism in which MgADP is the first substrate to bind and AMP is the last product released, being the same mechanism described for archaeal ADP-dependent sugar kinases, in agreement with the protein topology. Substrate inhibition by glucose was observed due to sugar binding to nonproductive species. Although Mg2+ is an essential component for kinase activity, it also behaves as a partial mixed-type inhibitor for hADP-GK, mainly by decreasing the MgADP affinity. Regarding its distribution, phylogenetic analysis shows that ADP-GK´s are present in a wide diversity of eukaryotic organisms although it is not ubiquitous. Eukaryotic ADP-GKs sequences cluster into two main groups, showing differences in the highly conserved sugar-binding motif reported for archaeal enzymes [NX(N)XD] where a cysteine residue is found instead of asparagine in a significant number of enzymes. Site directed mutagenesis of the cysteine residue by asparagine produces a 6-fold decrease in Vmax, suggesting a role for this residue in the catalytic process, probably by facilitating the proper orientation of the substrate to be phosphorylated.
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Affiliation(s)
- Alejandra Herrera-Morandé
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| | - Gabriel Vallejos-Baccelliere
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| | - Pablo A Cea
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ricardo A Zamora
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Dixon Cid
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Pablo Maturana
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Felipe González-Ordenes
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Víctor Castro-Fernández
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Victoria Guixé
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
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Kobayashi S, Maldonado JE, Gaete A, Araya I, Aguado-Norese C, Cumplido N, Díaz S, Espinoza A, Fernández E, Gajardo F, González-Ordenes F, Hauyon K, Maldonado P, Maldonado R, Pochet I, Riveros A, Sandoval P, Sepúlveda-González A, Stuardo C, Tapia-Reyes P, Thornton C, Undurraga S, Varas M, Valdivieso C, Gutiérrez RA, Orellana A, Montecino M, Maass A, González M, Allende ML, Hodar C, Irles P. DNA sequencing in the classroom: complete genome sequence of two earwig (Dermaptera; Insecta) species. Biol Res 2023; 56:6. [PMID: 36797803 PMCID: PMC9935246 DOI: 10.1186/s40659-023-00414-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/16/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Despite representing the largest fraction of animal life, the number of insect species whose genome has been sequenced is barely in the hundreds. The order Dermaptera (the earwigs) suffers from a lack of genomic information despite its unique position as one of the basally derived insect groups and its importance in agroecosystems. As part of a national educational and outreach program in genomics, a plan was formulated to engage the participation of high school students in a genome sequencing project. Students from twelve schools across Chile were instructed to capture earwig specimens in their geographical area, to identify them and to provide material for genome sequencing to be carried out by themselves in their schools. RESULTS The school students collected specimens from two cosmopolitan earwig species: Euborellia annulipes (Fam. Anisolabididae) and Forficula auricularia (Fam. Forficulidae). Genomic DNA was extracted and, with the help of scientific teams that traveled to the schools, was sequenced using nanopore sequencers. The sequence data obtained for both species was assembled and annotated. We obtained genome sizes of 1.18 Gb (F. auricularia) and 0.94 Gb (E. annulipes) with the number of predicted protein coding genes being 31,800 and 40,000, respectively. Our analysis showed that we were able to capture a high percentage (≥ 93%) of conserved proteins indicating genomes that are useful for comparative and functional analysis. We were also able to characterize structural elements such as repetitive sequences and non-coding RNA genes. Finally, functional categories of genes that are overrepresented in each species suggest important differences in the process underlying the formation of germ cells, and modes of reproduction between them, features that are one of the distinguishing biological properties that characterize these two distant families of Dermaptera. CONCLUSIONS This work represents an unprecedented instance where the scientific and lay community have come together to collaborate in a genome sequencing project. The versatility and accessibility of nanopore sequencers was key to the success of the initiative. We were able to obtain full genome sequences of two important and widely distributed species of insects which had not been analyzed at this level previously. The data made available by the project should illuminate future studies on the Dermaptera.
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Affiliation(s)
- Sanae Kobayashi
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466Facultad de Ciencias, Universidad de Chile, 7800003 Santiago, Chile
| | - Jonathan E. Maldonado
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.412179.80000 0001 2191 5013Facultad de Química y Biología, Universidad de Santiago de Chile, 9170022 Santiago, Chile
| | - Alexis Gaete
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466INTA, Universidad de Chile, 7830490 Santiago, Chile
| | - Ingrid Araya
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.512263.1Advanced Center for Chronic Diseases (ACCDiS), Sergio Livingstone 1007, 8380494 Independencia, Santiago Chile
| | - Constanza Aguado-Norese
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466INTA, Universidad de Chile, 7830490 Santiago, Chile
| | - Nicolás Cumplido
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466Facultad de Ciencias, Universidad de Chile, 7800003 Santiago, Chile
| | - Sebastián Díaz
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466Facultad de Ciencias, Universidad de Chile, 7800003 Santiago, Chile
| | - Alonso Espinoza
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.412848.30000 0001 2156 804XFacultad de Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andres Bello, Santiago, Chile
| | - Edelmira Fernández
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466Facultad de Ciencias, Universidad de Chile, 7800003 Santiago, Chile
| | - Felipe Gajardo
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466Facultad de Ciencias, Universidad de Chile, 7800003 Santiago, Chile
| | - Felipe González-Ordenes
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466Facultad de Ciencias, Universidad de Chile, 7800003 Santiago, Chile
| | - Khantati Hauyon
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466INTA, Universidad de Chile, 7830490 Santiago, Chile
| | - Piedad Maldonado
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466Facultad de Ciencias, Universidad de Chile, 7800003 Santiago, Chile
| | - Rodrigo Maldonado
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.412848.30000 0001 2156 804XFacultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Isabel Pochet
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.7870.80000 0001 2157 0406Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Aníbal Riveros
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.424112.00000 0001 0943 9683ANID-Millennium Science Initiative Program—Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - Paula Sandoval
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.7870.80000 0001 2157 0406Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ailynne Sepúlveda-González
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466INTA, Universidad de Chile, 7830490 Santiago, Chile
| | - Camila Stuardo
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466INTA, Universidad de Chile, 7830490 Santiago, Chile
| | - Patricio Tapia-Reyes
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.7870.80000 0001 2157 0406Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carolina Thornton
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.7870.80000 0001 2157 0406Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Soledad Undurraga
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.412199.60000 0004 0487 8785Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Macarena Varas
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466Facultad de Ciencias, Universidad de Chile, 7800003 Santiago, Chile
| | - Camilo Valdivieso
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466Facultad de Ciencias, Universidad de Chile, 7800003 Santiago, Chile
| | | | - Rodrigo A. Gutiérrez
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.7870.80000 0001 2157 0406Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ariel Orellana
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.412848.30000 0001 2156 804XFacultad de Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andres Bello, Santiago, Chile
| | - Martín Montecino
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.412848.30000 0001 2156 804XFacultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Alejandro Maass
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466Departamento de Ingeniería Matemática, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466INTA, Universidad de Chile, 7830490 Santiago, Chile
| | - Miguel L. Allende
- Millennium Institute Center for Genome Regulation, 7800003 Santiago, Chile ,grid.443909.30000 0004 0385 4466Facultad de Ciencias, Universidad de Chile, 7800003 Santiago, Chile
| | - Christian Hodar
- Millennium Institute Center for Genome Regulation, 7800003, Santiago, Chile. .,INTA, Universidad de Chile, 7830490, Santiago, Chile.
| | - Paula Irles
- Institute of Agri-food, Animal and Environmental Sciences, Universidad de O´Higgins, Rancagua, Chile.
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