Insights into Microprotein A novel tool to unravel crop improvement

N Premalatha; A T Hemavathy; K Mahadevan; D Kavithamani; S Kavitha; V V Geetha; M K Mathivathana; S M Samyuktha

doi:10.14719/pst.6416

Authors

N Premalatha Department of Cotton, Tamil Nadu Agricultural University, Coimbatore 641 006, Tamil Nadu, India https://orcid.org/0000-0001-9527-7843
A T Hemavathy Department of Pulses, Tamil Nadu Agricultural University, Coimbatore 641 006, Tamil Nadu, India https://orcid.org/0000-0002-7312-3779
K Mahadevan Department of Pulses, Tamil Nadu Agricultural University, Coimbatore 641 006, Tamil Nadu, India https://orcid.org/0000-0001-5425-6827
D Kavithamani Department of Millets, Tamil Nadu Agricultural University, Coimbatore 641 006, Tamil Nadu, India https://orcid.org/0000-0003-0350-4266
S Kavitha Department of Millets, Tamil Nadu Agricultural University, Coimbatore 641 006, Tamil Nadu, India https://orcid.org/0000-0002-7045-4062
V V Geetha Krishi Vigyan Kendra, Tamil Nadu Agricultural University, Tindivanam 604 001, Tamil Nadu, India https://orcid.org/0000-0002-7964-5631
M K Mathivathana College of Agricultural Technology, Theni 625 531, Tamil Nadu, India https://orcid.org/0009-0002-5626-8949
S M Samyuktha Department of Genetics and Plant Breeding, Dhanalakshmi Srinivasan Agriculture College, Perambalur 606 302, Tamil Nadu, India https://orcid.org/0000-0002-4048-1182

DOI:

https://doi.org/10.14719/pst.6416

Keywords:

Gene regulation , Microprotein, MiP Finder, Protein-protein interaction

Abstract

Small regulatory proteins with a size range of 5 to 20 kilodaltons (kDa) are known as microproteins (miPs). They are connected to bigger, frequently multi-domain proteins and typically include a single protein domain. Through their interactions with other proteins, these microproteins modify the post-translational gene expression level. Numerous microproteins that are essential for controlling transcription factor activity have been discovered in both plants and animals in recent years. Microproteins are necessary for several phases of plant development, such as seed germination, seedling growth, stomatal regulation, root formation, pigment synthesis, blooming and floral development. Certain microproteins viz., viral protein U (Vpu) microProtein, negatively regulates the K+ ion channel TASK1 in humans, LITTLE ZIPPER proteins found in arabidopsis which regulate transcription factor and mitochondrial microprotein BRAWNI are conserved only among vertebrates are exclusive to a given species, whilst others have evolved to be conserved since they first appeared early in evolutionary history. Food security is being challenged by the cumulative consequences of climate change and unsustainable agricultural methods, which increases the need for sustainable and innovative solutions since microproteins are essential regulators of several physiological processes in plants. They are excellent candidates for creating synthetic miPs that can be employed to support plant stress resilience leading to increased productivity. Understanding the microproteins' regulatory mechanisms is a crucial step in developing microproteins into useful biotechnological tools for crop bioengineering. There is a theory that target proteins and microproteins have similar evolutionary histories. Microproteins work at the molecular level by obstructing the assembly of higher-order protein complexes. Their potential for biotechnological applications is further enhanced by their ability to function as dominant regulators in a focused and precise manner. In addition to exploring the processes of microproteins and their functional roles in plant biology, this study intends to provide the groundwork for future investigations by helping scientists identify, characterize and map these proteins.

Downloads

Download data is not yet available.

References

Harshitha BS, Manjunath KK, Bhargavi HA. Mysterious microproteins as a novel tool for crop improvement: A review. The Pharma Innov J. 2023;12(1):2317?22. https://doi.org/10.22271/tpi.2023.v12.i1z.18331.

Staub D, Wenkel S. Cross-species genome-wide identification of evolutionary conserved MicroProteins. Genome Biol Evolution. 2017;9:777–89. doi: 10.1093/gbe/evx041.

Saroha A, Kotiyal A, Nanoemulsion R. A futuristic approach to disease elimination for food safety. Ann Phytomed. 2023;12(1):180?86. DOI:10.54085/ap.2023.12.1.50.

Makde DM, Baheti PJ, Thote L. Green synthesis of zinc oxide nanoparticles (Zno-Nps) Ailanthus excelsa Roxb. stem bark extract and its antibacterial activity. Ann Phytomed. 2022;11(2):743?47. DOI: 10.54085/ap.2022.11.2.90.

Dang R. Role of antinutrient metabolites of plant on production of secondary metabolites and human health. Ann Phytomed. 2018;7(1):1?4. DOI:10.21276/AP.2018.7.1.1

Benezra R, Davis RL, Lockshon D, Turner DL, Weintraub H. The protein Id: a negative regulator of helix-loop-helix DNA binding proteins. Cell. 1990;61:49–59. DOI: 10.1016/0092-8674(90)90214-y

Wenkel S, Emery J, Hou BH, Evans MMS, Barton MK. A feedback regulatory module formed by LITTLE ZIPPER and HD-ZIPIII genes. Plant Cell. 2007;19:3379–90. https://doi.org/10.1105/tpc.107.055772

Fesenko I, Shabalina SA, Mamaeva A, Knyazev A, Glushkevich A, Lyapina I, et al. A vast pool of line age specific microproteins encoded by long noncoding RNAs in plants. Nucleic Acids Res. 2021;49(18):10328?46. DOI: 10.1093/nar/gkab816

Mohideen AP. Green synthesis of silver nanoparticles (AgNPs) using of Laurus nobilis L. leaf extracts and evaluating its antiarthritic activity by in vitro protein denaturation and membrane stabilization assays. Ann Phytomed. 2022;10(2):67?71. DOI: http://dx.doi.org/10.21276/ap.2021.10.2.9

Eguen T, Straub D, Graeff M, Wenkel S. Micro proteins: small size - big impact. Trends Plant Sci. 2015;20:477–82. https://doi.org/10.1016/j.tplants.2015.05.011

Graeff M, Straub, D, Eguen T, Dolde U, Rodrigues V, Brandt R, Wenkel S. MicroProtein-mediated recruitment of CONSTANS into a TOPLESS trimeric complex represses flowering in arabidopsis. PLoS Genetics. 2016;12:1005959. https://doi.org/10.1371/journal.pgen.1005959

Bhati KK, Dolde U, Wenkel S. Micro proteins expanding functions and novel modes of regulation. Mol Plant Biol. 2021;14:705–07. DOI: 10.1016/j.molp.2021.01.006

Wu Q, Zhong S, Shi H. MicroProteins: dynamic and accurate regulation of protein activity. J Integr Plant Biol. 2022;64:812–20. https://doi.org/10.1111/jipb.13229

Hsu K, Seharaseyon J, Dong P, Bour S, Marba E. Mutual functional destruction of HIV-1 Vpu and host TASK-1 channel. Mol Cell. 2004;14:259–67. https://doi.org/10.1016/S1097-2765(04)00183-2

Ahrens CH, Wade JT, Champion MM, Langer JD. A practical guide to small protein discovery and characterization using mass spectrometry. J Bacteriol. 2022;204:e0035321. DOI: 10.1128/JB.00353-21

Bhati KK, Blaakmeer A, Paredes EB, Dolde U, Eguen T, Hong S, et al. Approaches to identify and characterize micro proteins and their potential uses in biotechnology. Cell Mol Life Sci. 2018;75:2529–36. DOI: 10.1007/s00018-018-2818-8

Donnelly DP, Rawlins CM, DeHart CJ, Fornelli L, Schachner LF, Lin Z, et al. Best practices and benchmarks for intact protein analysis for top-down mass spectrometry. Nat Methods. 2019;16:587–94. DOIhttps://doi.org/10.1038/s41592-019-0457-0.

Kaulich PT, Cassidy L, Weidenbach K, Schmitz RA, Tholey. Complementarity of different SDS-PAGE gel staining methods for the identification of short open reading frame-encoded peptides. Proteomics. 2020;20. DOI: 10.1002/pmic.202000084

Zabret J, Bohn S, Schuller SK, Arnolds O, Langer JD. Structural insights into photosystem II assembly. Nat Plant. 2021;7:524–38. DOI: 10.1038/s41477-021-00895-0

Tian H, Wang X, Guo H, Cheng Y, Hou C, Chen JG, Wang S. NTL8 regulates trichome formation in Arabidopsis by directly activating R3 MYB genes TRY and TCL1. Plant Physiol. 2017a;174:2363–75. https://doi.org/10.1104/pp.17.00510

Olexiouk V, Crappe J, Verbruggen S, Verhegen K, Martens L, Menschaert G. sORFs.org: a repository of small ORFs identified by ribosome profiling. Nucleic Acids Res. 2016;44:324–29. DOI: 10.1093/nar/gkx1130

Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Benfey PN, et al. Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. Plant Cell. 2014;2746–60. https://doi.org/10.1105/tpc.114.125617.

Dolde U, Rodrigues V, Straub D, Bhati KK, Choi S, Yang SW, Wenkel S. Synthetic MicroProteins: versatile tools for posttranslational regulation of target proteins. Plant Physio. 2018;176:3136–45. https://doi.org/10.1104/pp.17.01743

Floyd SK, Ryan JG, Conway SJ, Brenner E, Burris KP, Burris JN, et al. Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor. Mol Phylogenetics Evolution. 2014;81:159–73. https://doi.org/10.1016/j.ympev.2014.06.017

Zhang W, Ning G, Lv H, Liao L, Bao M. Single MYB-type transcription factor AtCAPRICE, a new efficient tool to engineer the production of anthocyanin in tobacco. Biochem Biophys Res Commun. 2009b; 388:742–47. DOI: 10.1016/j.bbrc.2009.08.092

Tominaga R, Iwata M, Sano R, Inoue K, Okada K, Wada T. Arabidopsis CAPRICE-LIKE MYB 3 (CPL3) controls endoreduplication and flowering development in addition to trichome and root hair formation. Development. 2008;135:1335–45. DOI: 10.1242/dev.017947

Bollier N, Sicard A, Leblond J, Latrasse D, Gonzalez N, At-MINI. zinc FINGER2 and Sl-INHIBITOR of meristem activity, a conserved missing link in the regulation of floral meristem termination in Arabidopsis and tomato. Plant Cell. 2018;30;83–100. https://doi.org/10.1105/tpc.17.00653

Schnittger A, Jurgens G, Hu lskamp M. Tissue layer and organ specificity of trichome formation are regulated by GLABRA1 and TRIPTYCHON in Arabidopsis. Development. 1998;125:2283–89. DOI: 10.1242/dev.125.12.2283

Tian T, Liu Y, Yan H, You Q, Yi X. AgriGO v2.0: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2017b;45 W122–W129. https://doi.org/10.1093/nar/gkx382

Wada T, Tachibana T, Shimura Y, Okada K. Epidermal cell differentiation in Arabidopsis determined by a Myb homolog. CPC Sci. 1997;277:1113–16. DOI: 10.1126/science.277.5329.1113

Canales C, Grigg S, Tsiantis M. The formation and patterning of leaves: recent advances. Planta. 2005;221:752–56. DOI: 10.1007/s00425-005-1549-x

Brandt R, Xie Y, Musielak T, Graeff M, Stierhof YD, Huang H, et al. Control of stem cell homeostasis via interlocking microRNA and microProtein feedback loops. Mech Develop. 2013;130:25–33. http://dx.doi.org/10.1016/j.mod.2012.06.007

Zhu HF, Fitzsimmons K, Khandelwal A, Kranz RG. CPC, a single-repeat R3 MYB, is a negative regulator of anthocyanin biosynthesis in Arabidopsis. Mol Plant. 2009;2:790–802. DOI: 10.1093/mp/ssp030

Wada T, Tominaga-Wada R. CAPRICE family genes control flowering time through both promoting and repressing CONSTANS and FLOWERING LOCUS T expression. Plant Sci. 2015;241:260–65. https://doi.org/10.1016/j.plantsci.2015.10.015

Wada T, Kurata T, Tominaga R, Koshino- Kimura Y, Tachibana T, Goto K, et al. Role of a positive regulator of root hair development, CAPRICE, in Arabidopsis root epidermal cell differentiation. Develop. 2002;129:5409–19. ttps://doi.org/10.1242/dev.00111

Chory J, Chatterjee M, Cook RK, Elich T, Fankhauser C, Li J. From seed germination to flowering, light controls plant development via phytochrome. Proceed of the Nat Acad of Sci. 1996;93(22):12066?71. DOI: 10.1073/pnas.93.22.12066

Bhati KK, Blaakmeer A, Paredes EB, Dolde U, Eguen T, Hong S, Rodrigues V. Approaches to identify and characterize microProteins and their potential uses in biotechnology. Cellular and Mol Life Sci. 2018;75:2529–36. doi: 10.1007/s00018-018-2818-8.

Seo PJ, Hong SY, Ryu JY, Jeong EY, Kim SG, Baldwin IT, Park CM. Targeted inactivation of transcription factors by overexpression of their truncated forms in plants. Plant J Cell Mol Biol. 2012;72(1):16272.https://doi.org/10.1111/j.1365-313X.2012.05069.x