Use of bioinformatics characterization of molybdenum transport genes in Ipomoea trifida and Ipomoea triloba

Luís Gustavo Gomes Lobo, Carolina Cabral da Silva, Silvia Graciele Hülse de Souza, Tiago Benedito dos Santos

Article ID: 10845
Vol 8, Issue 1, 2025


Abstract


Molybdenum (Mo) is considered and described as an essential element for living organisms’ development. Until now, no studies have been performed on genes involved in the Mo transporter in ancestral Ipomoea species. This study aimed to identify potential Mo genes in Ipomoea trifida and I. triloba genomes using bioinformatics tools. We identified four Mo transporter genes, two in I. trifida and two in I. triloba. Based on the RNA-seq datasets, we observed that Mo genes are expressed (in silico) and present different mechanisms between the tissues analyzed. The information generated in this study fills missing gaps in the literature on the Mo gene in an important agronomic crop.


Keywords


gene expression; in silico; molybdate; motif signature; phylogeny

Full Text:

PDF


References


1.

1.         Melo RAC, Amaro GB, da Silva GO, et al. Root production and quality attributes of sweetpotato genotypes in Brasília-DF, Brazil, during two cropping seasons. Colloquium Agrariae. 2020; 16(2): 90-95.

2.

2.         Muñoz-Rodríguez P, Carruthers T, Wells T, et al. The research behind a taxonomic monograph: a case study from Ipomoea (Convolvulaceae). Kew Bulletin. 2024; 79(4): 897-914.

3.

3.         Ugent D, Peterson LW. Archaeological Remains of Potato and Sweet Potato in Peru. Economic Botany. 1982; 36(2): 182-192.

4.

4.         Mitchell TC, Williams BRM, Wood JRI, et al. How the temperate world was colonised by bindweeds: biogeography of the Convolvuleae (Convolvulaceae). BMC Evolutionary Biology. 2016; 16(1).

5.

5.         de Castro Vendrame LP, Melo RAC, da Silva GO, et al. Sweet potato (Ipomoea batatas L. Lam.) cultivation and potentialities. In Varieties and Landraces: Cultural Practices and Traditional Uses (pp. 245-259). 2023. Academic Press.

6.

6.         Alam MK. A comprehensive review of sweet potato (Ipomoea batatas [L.] Lam): Revisiting the associated health benefits. Trends in Food Science & Technology. 2021; 115: 512-529.

7.

7.         Austin DF. The taxonomy, evolution and genetic diversity of sweet potatoes and related wild species. In: Exploration, maintenance, and utilization of sweetpotato genetic resources. International Potato Center; 1988.

8.

8.         Khan MIR, Nazir F, Maheshwari C, et al. Mineral nutrients in plants under changing environments: A road to future food and nutrition security. The plant genome. 2023; 16(4): e20362.

9.

9.         Akhtar K, Ain NU, Prasad PV, et al. Physiological, molecular, and environmental insights into plant nitrogen uptake, and metabolism under abiotic stresses. The plant genome. 2024; 17(2): e20461.  

10.

10.     Wang Q, Li S, Li J, et al. The utilization and roles of nitrogen in plants. Forests. 2024; 15(7): 1191. doi: 10.3390/f15071191

11.

11.     Ge M, Zhong R, Sadeghnezhad E, et al. Genome-wide identification and expression analysis of magnesium transporter gene family in grape (Vitis vinifera). BMC Plant Biology. 2022; 22(1): 217.

12.

12.     Li G, Yang D, Hu Y, et al. Genome-wide identification and expression analysis of nitrate transporter (NRT) gene family in Eucalyptus grandis. Genes. 2024; 15(7): 930.

13.

13.     Omari Alzahrani F. Ammonium Transporter 1 (AMT1) Gene Family in Pomegranate: Genome-Wide Analysis and Expression Profiles in Response to Salt Stress. Current Issues in Molecular Biology. 2025; 47(1): 59.

14.

14.     Li H, Bao C, Xing H, et al. Genome-Wide Identification and Expression Assessment for the Phosphate Transporter 2 Gene Family Within Sweet Potato Under Phosphorus Deficiency Stress. International Journal of Molecular Sciences. 2025; 26(6): 2681.

15.

15.     Liu X, Li J, Luo D, et al. Genome-wide characterization of the NRT1 family members under cold stress in Coconut (Cocos nucifera L.). Scientia Horticulturae. 2025; 341, 113959.

16.

16.     Vatansever R, Filiz E, Ozyigit II. In silico identification and comparative analysis of molybdenum (Mo) transporter genes in plants. Brazilian Journal of Botany. 2015; 39(1): 87-99.

17.

17.     Huang XY, Hu DW, Zhao FJ. Molybdenum: More than an essential element. Verbruggen N, ed. Journal of Experimental Botany. 2021; 73(6): 1766-1774.

18.

18.     Leimkühler S. The biosynthesis of the molybdenum cofactors in Escherichia coli. Environmental microbiology, 2020; 22(6): 2007-2026.

19.

19.     Bittner F. Molybdenum metabolism in plants and crosstalk to iron. Frontiers in Plant Science. 2014; 5.

20.

20.     Hippler FWR, Boaretto RM, Dovis VL, et al. Revisiting nutrient management for Citrus production: to what extent does molybdenum affect nitrogen assimilation of trees? Scientia Horticulturae. 2017; 225: 462-470.

21.

21.     Mendel RR, Oliphant KD. The Final Step in Molybdenum Cofactor Biosynthesis—A Historical View. Molecules. 2024; 29(18): 4458.

22.

22.     Rana M, Bhantana P, Imran M, et al. Molybdenum potential vital role in plants metabolism for optimizing the growth and development. Annals of Environmental Science and Toxicology. 2020; 4(1): 032-044.

23.

23.     Mayr SJ, Mendel RR, Schwarz G. Molybdenum cofactor biology, evolution and deficiency. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research. 2021; 1868(1): 118883.

24.

24.     Tejada-Jiménez M, Chamizo-Ampudia A, Galván A, et al. Molybdenum metabolism in plants. Metallomics. 2013; 5(9): 1191.

25.

25.     Arnon DI, Stout PR. Molybdenum as an essential element for higher plants. Plant Physiology. 1939; 14(3): 599-602.

26.

26.     Bavaresco LG, Silva SAF, de Souza SGH, et al. Molybdenum (Mo) transporter genes in Panicoideae species: a genome-wide evolution study. Journal of Crop Science and Biotechnology. 2022; 25(3): 277-287.

27.

27.     Tejada JM, Chamiso AA, Llamas A, et al. Roles of molybdenum in plants and improvement of its acquisition and use efficiency. In: Hossain MA, Kamiya T, Burritt DJ, et al. (editors). Plant micronutrient use efficiency. Molecular and genomic perspectives in crop plants. Academic Press; 2018.

28.

28.     Giovannuzzi S. Chapter 10—Molybdenum Enzymes; In: Supuran CT, Donald WABT-M (editors). Academic Press: Warsaw, Poland; 2024. pp. 557–580.

29.

29.     Gil-Díez P, Tejada-Jiménez M, León-Mediavilla J, et al. MtMOT1.2 Is Responsible for Molybdate Supply to Medicago Truncatula Nodules. Plant, Cell & Environment. 2019; 42, 310-320.

30.

30.     Hu D, Li M, Zhao, FJ, et al. The Vacuolar Molybdate Transporter OsMOT1;2 Controls Molybdenum Remobilization in Rice. Frontiers in Plant Science. 2022; 13: 863816.

31.

31.     Roychoudhury A, Chakraborty S. Cobalt and molybdenum transport in plants. In Metal and Nutrient Transporters in Abiotic Stress. Academic Press; 2021. pp. 199-211.

32.

32.     Zhao Q, Su X, Wang Y, et al. Structural Analysis of Molybdate Binding Protein ModA from Klebsiella Pneumoniae. Biochemical and Biophysical Research Communications. 2023; 681: 41-46.

33.

33.     Wang Z, Hong Y, Guo Z, et al. Natural variation in a molybdate transporter confers salt tolerance in tomato. Plant Physiology. 2025; 197(2): kiaf004.

34.

34.     Minner-Meinen R, Weber JN, Kistner S, et al. Physiological importance of molybdate transporter family 1 in feeding the molybdenum cofactor biosynthesis pathway in Arabidopsis thaliana. Molecules. 2022; 27(10): 3158.

35.

35.     Altschul S. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research. 1997; 25(17): 3389-3402.

36.

36.     Wilkins MR, Gasteiger E. Bairoch A, et al. Protein identification and analysis tools in the ExPASy server. Methods in Molecular Biology. 1999; 112: 531-52.

37.

37.     Chou KC, Shen HB. Plant-mPLoc: A Top-Down Strategy to Augment the Power for Predicting Plant Protein Subcellular Localization. Newbigin E, ed. PLoS ONE. 2010; 5(6): e11335.

38.

38.     Hu B, Jin J, Guo AY, et al. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 2014; 31(8): 1296-1297.

39.

39.     Bailey TL, Johnson J, Grant CE, et al. The MEME Suite. Nucleic Acids Research. 2015; 43(W1): W39-W49.

40.

40.     Nielsen H, Krogh A. Prediction of signal peptides and signal anchors by a hidden Markov model. In: Proceedings of the International Conference on Intelligent Systems for Molecular Biology; 1998.

41.

41.     Chao J, Li Z, Sun Y, et al. MG2C: a user-friendly online tool for drawing genetic maps. Molecular Horticulture. 2021; 1(1).

42.

42.     Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular Biology and Evolution. 2016; 33(7): 1870-1874.

43.

43.     Huang Z, Zhong XJ, He J, et al. Genome-Wide Identification, Characterization, and Stress-Responsive Expression Profiling of Genes Encoding LEA (Late Embryogenesis Abundant) Proteins in Moso Bamboo (Phyllostachys edulis). Imai R, ed. PLOS ONE. 2016; 11(11): e0165953.

44.

44.     Chen C, Chen H, Zhang Y, et al. TBtools, a toolkit for biologists integrating various HTS-data handling tools with a user-friendly interface. Molecular Plant. 2020; 13(8): 1194-1202.

45.

45.     Kumar A, Singh B, Raigond P, et al. Phytic acid: Blessing in disguise, a prime compound required for both plant and human nutrition. Food Research International. 2021; 142: 110193.

46.

46.     Gasber A, Klaumann S, Trentmann O, et al. Identification of an Arabidopsis solute carrier critical for intracellular transport and inter‐organ allocation of molybdate. Plant Biology. 2011; 13(5): 710-718.

47.

47.     Ishikawa S, Hayashi S, Tanikawa H, et al. Tonoplast-Localized OsMOT1; 2 Participates in Interorgan Molybdate Distribution in Rice. Plant and Cell Physiology. 2021; 62(5): 913-921.

48.

48.     Baxter I, Muthukumar B, Park HC, et al. Variation in Molybdenum Content Across Broadly Distributed Populations of Arabidopsis thaliana Is Controlled by a Mitochondrial Molybdenum Transporter (MOT1). Bergelson J, ed. PLoS Genetics. 2008; 4(2): e1000004.

49.

49.     Rogozin IB, Wolf YI, Sorokin AV, et al. Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Current Biology. 2003; 13(17): 1512-1517.

50.

50.     Rogozin IB. Analysis of evolution of exon-intron structure of eukaryotic genes. Briefings in Bioinformatics. 2005; 6(2): 118-134.

51.

51.     Tejada-Jiménez M, Llamas Á, Sanz-Luque E, et al. A high-affinity molybdate transporter in eukaryotes. Proceedings of the National Academy of Sciences. 2007; 104(50): 20126-20130.

52.

52.     Compton ELR, Karinou E, Naismith JH, et al. Low Resolution Structure of a Bacterial SLC26 Transporter Reveals Dimeric Stoichiometry and Mobile Intracellular Domains. Journal of Biological Chemistry. 2011; 286(30): 27058-27067.

53.

53.     Freeling M. Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition. Annual Review of Plant Biology. 2009; 60(1): 433-453.

54.

54.     Blanc G, Wolfe KH. Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes. The Plant Cell. 2004; 16(7): 1667-1678.

55.

55.     Papp B, Pál C, Hurst LD. Dosage sensitivity and the evolution of gene families in yeast. Nature. 2003; 424(6945): 194-197.

56.

56.     Li BZ, Merrick M, Li SM, et al. Molecular basis and regulation of ammonium transporter in rice. Rice Science. 2009; 16(4): 314-322.

57.

57.     De Smet R, Van de Peer Y. Redundancy and rewiring of genetic networks following genome-wide duplication events. Current Opinion in Plant Biology. 2012; 15(2): 168-176.

58.

58.     Smith AL, Hodkinson TR, Villellas J, et al. Global gene flow releases invasive plants from environmental constraints on genetic diversity. Proceedings of the National Academy of Sciences. 2020; 117(8): 4218-4227.

59.

59.     Wu S, Lau KH, Cao Q, et al. Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nature Communications. 2018; 9(1).

60.

60.     Rashid M, Guangyuan H, Guangxiao Y, et al. AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots. Evolutionary Bioinformatics. 2012; 8.

61.

61.     Fernie AR, Tohge T. The Genetics of Plant Metabolism. Annual Review of Genetics. 2017; 51(1): 287-310.




DOI: https://doi.org/10.24294/th10845

Refbacks

  • There are currently no refbacks.


License URL: https://creativecommons.org/licenses/by/4.0/

This site is licensed under a Creative Commons Attribution 4.0 International License.