Identification and Characterization of Dmct: A Cation Transporter in Yarrowia lipolytica Involved in Metal Tolerance
Abstract
:1. Introduction
2. Materials and Methods
2.1. In Silico Analysis
2.2. Microorganisms and Growth Conditions
2.3. Construction of Δdmct Strain
2.4. Reintegration of the DMCT Gene
2.5. Phenotypic Characterization
2.6. Intracellular Accumulation of Cations
2.7. Statistical Analysis
3. Results
3.1. In Silico Yl-Dmct Protein Analysis
3.2. In Silico Yl-Dmct Analysis: Cellular Location, Phylogenetic Analysis, and Three-Dimensional Modeling
3.3. In Silico Analysis of Putative Binding Sites for Transcription Factors in the Promoter Region from the Yl-DMCT Gene
3.4. Δdmct and Rdmct Strains’ Phenotypic Characterization
3.5. Cell and Colony Morphological Characteristics
3.6. Intracellular Accumulation of Divalent Metal Cations and Cell Wall Integrity
3.7. Identification of Putative Genes That Participate in the Transport of Metals as a Possible Compensatory Response to Dmct Deletion
4. Discussion
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Protein * | Function | Organism | Length (Aa) | % Complete Gene Similarity | % CDF Domain Similarity |
---|---|---|---|---|---|
YlDmct | Hypothetical transport of metal divalent cations (This studio) | Y. lipolytica | 555 | 100 | 100 |
Cot1 | Transport of metal cations in vacuole, resistance to cobalt and rhodium, response to stress | S. cerevisiae | 439 | 22.67 | 18.67 |
Zcr1 | Resistance to zinc and cadmium | S. cerevisiae | 442 | 21.07 | 19.41 |
Mmt1p | Zinc transport | S. cerevisiae | 510 | 19.28 | 23.44 |
Zrg17 | Zinc transport in endoplasmic reticulum | Z. rouxii | 634 | 21.14 | 24.24 |
Msc2 | Zinc homeostasis, zinc influx to the endoplasmic reticulum | S. cerevisiae | 725 | 19.12 | 19.88 |
Mitochondrial metal transporter | Iron accumulation in mitochondria | S. cerevisiae | 510 | 19.85 | 23.44 |
Cobalt toxicity protein | Zinc vacuolar transport and cobalt and rhodium resistance | S. cerevisiae | 439 | 19.01 | 18.67 |
Cation diffusion facilitator family transporter | Iron, copper, zinc and cadmium transport | C. albicans | 616 | 44.30 | 56.77 |
Metal cation transporter | Copper, zinc and cadmium ion efflux | C. albicans | 626 | 20.73 | 20.56 |
Zinc/cadmium resistance protein | Copper, zinc and cadmium efflux | L. elongisporus | 474 | 23.20 | 20.70 |
Mitochondrial protein with role in iron accumulation | Iron accumulation | S. stipitis | 430 | 21.73 | 22.73 |
Zinc/cadmium resistance protein | Copper, zinc and cadmium efflux | K. phaffii | 459 | 19.93 | 19.76 |
Homologous | Cation | Organism | Location | Accesion Number * | Aa ** | Identity (%) |
---|---|---|---|---|---|---|
Zrt3 | Fe2+/Zn2+ | S. c. | Vacuole/ Lysosome | P34240 | 503 | 13 |
Fth1 | Fe2+ | S. c. | P38310 | 465 | 14 | |
C. g. | Q6FJK8 | 435 | 15 | |||
Fet5 | Fe2+ | S. c. | P43561 | 622 | 14 | |
C. g. | A0A0W0DZF1 | 621 | 13 | |||
Cot1 | Fe2+/Zn2+ | S. c. | P32798 | 439 | 16 | |
Zrc1 | Fe2+/Zn2+ | S. c. | P20107 | 442 | 13 | |
Smf3 | Fe2+ | S. c. | Q12078 | 473 | 15 | |
C. a. | Q5ACZ8 | 514 | 14 | |||
Ctr2 | Cu2+ | S. c. | P38865 | 189 | 9 | |
Ccc2 | Fe2+/Cu2+ | S. c. | Golgi apparatus | P38995 | 1004 | 13 |
C. a. | Q5AG51 | 1204 | 11 | |||
Hmx1 | Fe2+ | S. c. | P32339 | 317 | 13 | |
Fet3 | Cu2+ | S. c. | P38993 | 636 | 14 | |
C. g. | Q96WT3 | 635 | 15 |
Trancription Factor | Binding Site | Function | Genes That Regulate | Functional Homologous Predicted in Y. lipolytica | Reference |
---|---|---|---|---|---|
Stb5p | −679, −531, −407, −389, −256, −103 | Involved in the transcription of transmembrane transporters. | ZRT3 | YALI0A10637p/Q6CHB0 YALI0C15202p/Q6CBV4 YALI0F03630p/B5RSK6 YALI0F16599p/Q6C1G1 YALI0D12628p/Q6C9A9 YALI0C22990p/Q6CB01 YALI0B06853p/Q6CFH8 | [57] |
Aft2p | −961 | In the absence of iron, which is responsible for the transcription of genes, products mobilize copper. | FTH1, FET5, FET3, SMF3 | No significant similarity found in genome | [58] |
Yap1p | −882 | Related to cadmium tolerance, is involved in the transcription of genes that respond to ionic detoxification, besides the expression of ferredoxin and ferredoxin reductase proteins. | ZRT1, FTH1, FET5, FET3, COT1, ZRC1, SMF3. CTR2, CCC2, HMX1 | YALI0F03388p/Q6C317 YALI0D09757p/Q6C9N3 YALI0B13200p/Q6CET1 YALI0F27445p/Q6C065 | [59] |
Cup2p | −919 | Activates the transcription of metallothionein proteins when the cell is in an environment that presents excess metals. | FET3 | CRF1/P45815 YALI0E31669p/Q6C3W4 | [60] |
Nrg1p | −791, −773, −738, −729, −728, −718, −647, −646, −605, −604, −588, −559, −349, −348, −81 | Related to the response to stress due to pH changes | FET3 | YALI0C12364p/Q6CC55 YALI0E07942p/Q6C6N4 YALI0D23749p/Q6C809 YALI0D18678p/Q6C8L5 YALI0B21582p/F2Z5Y0 YALI0A16841p/Q6CGR7 YALI0C05995p/Q6CCW4 YALI0F21923p/Q6C0T4 YALI0F22649p/Q6C0Q3 | [61] |
Skn7p | −531, −27 | Responsible for regulating genes involved in the antioxidant cellular response. | ZRT3, HMX1 | YALI0D14520p/Q6C937 YALI0D04785p/Q6CA95 YALI0C21340p/Q6CB75 YALI0E13948p/Q6C5Z0 | [62] |
Msn2p | −854, −791, −773, −738, −729, −718, −646, −604, −560, −559, −348, −300, −104, −81, | Responsible for regulating genes involved in the antioxidant cellular response. | FET3, ZRC1, CTR2, CCC2, HMX1 | No significant similarity found in genome | [63] |
Msn4p | −791, −773, −738, −729, −718, −646, −604, −559, −348, −81 | Responsible for regulating genes involved in the antioxidant cellular response. | FET3, CCC2, HMX1 | YALI0C13750p/Q6CC08 | [63] |
Chr | Gene (Locus Tag/ID) | Similar to | Possible Function | Functional Domains |
---|---|---|---|---|
A | YALI_A11605g/Q6CH77 | MSF transporter | Transport of small molecules by the gradient | MSF superfamily |
YALI_A14883g/Q6CGY6 | Ferrichrome-type siderophore transporter | Iron homeostasis | MSF superfamily | |
B | YALI0_B06094g/Q6CFK7 | RdgB Ca2+ transporter | Metal binding and calcium transport | DDHD superfamily |
YALI0_B17864g/Q6CE78 | High-affinity potassium absorption transporter | Potassium transport | 2a38euk superfamily | |
YALI0_B19250g/Q6CE20 | Ferrichrome-type siderophore transporter | Iron homeostasis | MSF superfamily | |
C | YALI0_C02541g/Q6CD98 | MSF transporter | Unknown specificity | MSF superfamily |
YALI0_C04411g/Q6CD22 | SMF1/E protein | Divalent and trivalent metal transporter | SLC5-6-like_sbd superfamily | |
YALI0_C06105g/Q6CCV9 | MSF transporter | Unknown specificity | MSF superfamily | |
YALI0_C09823g/Q6CCF5 | MSF transporter | Anion-cation simporter | MSF superfamily | |
YALI0_C10311g/Q6CCD6 | High-affinity potassium transporter | Potassium transport | K-Trans superfamily | |
YALI0_C10670g/Q6CCC4 | MSF transporter | Unknown specificity | MSF superfamily | |
YALI0_C12254g/Q6CC58 | Iron transporter in mitochondria MMT2 | Transport of divalent cation metals | SelP_N superfamily, FieF domain | |
YALI0_C16225g/Q6CBR6 | MSF transporter | Unknown specificity | MSF superfamily | |
YALI0_C17105g/Q6CBM9 | MSF transporter | Unknown specificity | MSF superfamily | |
YALI0_C18051g/Q6CBK3 | YCFI metal resistance protein | Vacuolar transport with increased tolerance to metals | MRP_assoc_pro superfamily | |
D | YALI0_D00319g/Q6CAS6 | Divalent cation transporter ALR1 | Divalent cation transport | Alr1p-like superfamily |
YALI0_D20064g/Q6C8F6 | MSF transporter | Unknown specificity | MSF superfamily | |
YALI0_D24651g/Q6C7X0 | MSF transporter | Unknown specificity | MSF superfamily | |
YALI0_D26818g/Q6C7M8 | SMF2 carrier protein | Manganese transport | Nramp domain | |
E | YALI0_E00748g/Q6C7H7 | Zrt2 transporter | Zinc transporter | Zip superfamily |
YALI0_E00462g/Q6C7J0 | Alr1 transporter | Divalent cations transport | Alr1p-like superfamily | |
YALI0_E11473g/Q6C691 | HAK1 transporter | Potassium transport | K-Trans superfamily | |
YALI0_E14234g/Q6C5X7 | YBT1 transporter | Involved with Ca2+ and metal resistance | MRP_assoc_pro superfamily | |
F | YALI0_F19118g/Q6C155 | Ferrichrome-type siderophore transporter | Iron homeostasis | MSF superfamily |
YALI0_F20922g/Q6C0X7 | Ferrichrome-type siderophore transporter | Iron homeostasis | MSF superfamily | |
YALI0_F27709g/Q6C053 | Ferrichrome-type siderophore transporter | Iron homeostasis | MSF superfamily | |
YALI0_F29711g/Q6BZZ0 | MSF transporter | Unknown specificity | MSF superfamily |
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González-Lozano, K.J.; Aréchiga-Carvajal, E.T.; Jiménez-Salas, Z.; Valdez-Rodríguez, D.M.; León-Ramírez, C.G.; Ruiz-Herrera, J.; Adame-Rodríguez, J.M.; López-Cabanillas-Lomelí, M.; Campos-Góngora, E. Identification and Characterization of Dmct: A Cation Transporter in Yarrowia lipolytica Involved in Metal Tolerance. J. Fungi 2023, 9, 600. https://doi.org/10.3390/jof9060600
González-Lozano KJ, Aréchiga-Carvajal ET, Jiménez-Salas Z, Valdez-Rodríguez DM, León-Ramírez CG, Ruiz-Herrera J, Adame-Rodríguez JM, López-Cabanillas-Lomelí M, Campos-Góngora E. Identification and Characterization of Dmct: A Cation Transporter in Yarrowia lipolytica Involved in Metal Tolerance. Journal of Fungi. 2023; 9(6):600. https://doi.org/10.3390/jof9060600
Chicago/Turabian StyleGonzález-Lozano, Katia Jamileth, Elva Teresa Aréchiga-Carvajal, Zacarías Jiménez-Salas, Debany Marlen Valdez-Rodríguez, Claudia Geraldine León-Ramírez, José Ruiz-Herrera, Juan Manuel Adame-Rodríguez, Manuel López-Cabanillas-Lomelí, and Eduardo Campos-Góngora. 2023. "Identification and Characterization of Dmct: A Cation Transporter in Yarrowia lipolytica Involved in Metal Tolerance" Journal of Fungi 9, no. 6: 600. https://doi.org/10.3390/jof9060600