Role of food derived microRNAs in regulating bioactivity of endogenously synthesized microRNAs.
Sarita Jena, M.V. Sc & PhD
Assistant Professor. Department of Veterinary Biochemistry, IVSA&H, Campus 4, SOA Deemed to be University Bharatpur, Khordha, Odisha, Pin Code-751003
Contact No: 7873186773
Email ID: saritajenabiswal@gmail.com
Abstract
MicroRNA (miRNA), a small regulating non-coding RNA (18-22 nucleotides) being endogenous in nature is now showing its action as a dietary factor since 2012. This short form of RNA is synthesized from miRNA containing genes following a linear pathway of biogenesis in a cell. Endogenous miRNAs are found in plasma, urine, saliva and other body fluids and they have been proven to be associated with many metabolic diseases such as obesity, diabetes, cancer as well as infectious diseases. In 2012, first bioactive role of microRNA as a dietary ingredient has been evidenced in rice although some other studies denied the theory of bioactivity of dietary plant miRNAs. But food of animal origin like cow milk enriched in miR-29b/200c became popular in subsequent year to prove its nutritional significance by justifying the key properties such as accessibility, stability, absorbability and bioactivity. Further studies following controlled experimental procedures in subsequent years had validated both plant and animal derived micro-RNAs, may compensate the bioactive action of endogenous miRNAs. In 2015, dietary miRNA database (http://sbbi.unl.edu/dmd/) was built. Recently the finding of SIDT1, an RNA transporter expressed in the mammalian stomach may validate the absorbability property of dietary miRNA. Here this short manuscript would focus on the key properties of various animal and plant derived miRNAs, thereby discriminate the roles of exogenous miRNAs from endogenous miRNAs to compensate the requirements in fulfilling its regulatory actions.
Introduction
MicroRNA (miRNA) is a short processed functional noncoding endogenous RNA transcript (18-22 nucleotides) that post transcriptionally regulates the gene expression. This short form of RNA is synthesized from microRNA containing genes following endogenous biogenesis pathway. For human beings, endogenous miRNAs are found in plasma, urine, saliva, other body fluids and they have been proven to be associated with many metabolic diseases such as obesity, diabetes, cancers as well as infectious diseases. MicroRNAs also have dietary significance. Food nutrients are categorised into macro nutrients (Carbohydrate, proteins and fat) and micronutrients (vitamins and minerals) essential for energy production, tissue repair and regulation of metabolism. MicroRNA as a food ingredient is in the preliminary stage or in controversy to prove itself by justifying its nutrient properties.
Food derived micro-RNA
Expressed micro-RNAs in various foods of plant and animal origin are called food derived micro-RNA. These are of approximately of 18-22 nucleotides. These micro RNAs circulates in various biological fluids in miRNA vesicles of 20 to 5000 nm in diameter or conjugated with RNA binding proteins and high-density lipoproteins (HDL).
History of food derived microRNA
First miRNA was discovered in 1993 for the gene lin-4, then second microRNA was identified in 2002 for the gene Let-7. In the same year role of miRNAs in cancer was published. In 2004 Prognostic values of miRNA was published. Presence of miRNA in plants (Arabidopsis spp) were first reported in 2002. Plant miRNA a novel functional component of food and make a critical contribution to maintaining and shaping of body was revealed in 2012. Then in 2014 dietary role of microRNA in cow milk was published. In 2015 dietary microRNA database was built. In the same year, future research had been put forth to better address absorption, tissue distribution, function of dietary plant and animal derived microRNAs in the context of human health and disease. In 2021, it is shown that transporters of miRNA such as SIDT1 (systemic RNA interference defective protein 1 transmembrane family member1) are expressed in the gastric pit cells of the stomach (Li J et al.,2019; Chen Q et al.,2021)
Occurrence of dietary miRNA
About 15 dietary species including plant and animal have been curated in dietary microRNA database such as human, chicken, cow, pig, salmon, Rice, wheat, soyabean, tomato, corn, apple, orange, banana, grape etc. (http://sbbi.unl.edu/dmd/). Due to its gene regulating actions, beneficial health effects in targeting diseases, its wide spread occurrence in various food, exogenous microRNAs and its compensative bioactive actions for endogenous microRNAs can become the recent topic of discussion.
Endogenous microRNA biogenesis
In the nucleus, DNA containing miRNA cluster transcribes primary microRNA (pri-miRNA) that contains appox. 80 nucleotide RNA stem loop structures using RNA polymerase II enzyme. Then nuclear RNAase III, Drosha crops the stem loop to release a small hairpin shaped RNA of about 60 nucleotides in length. The site of action of Drosha is about either 11 bp from basal junction or approx. 22bp away from the apical junction. Hairpin structure has 3’ hydroxyl and 5’ phosphate groups with two nucleotide overhangs at its 3’ end, also known as pre-miRNA (precursor miRNA). Then pre-miRNA comes to cytoplasm through nuclear pore complex. Inside cytoplasm another RNAase III enzyme Dicer cleaves the pre-miRNA about 21-25 nucleotides from 3’end or 22 nucleotides from 5’end. Cleavage by Dicer yield imperfect RNA duplex with 5p and 3p strand. With the help of Argonaut protein either 5p or 3p strand loaded into microRNA RISC, interacts with m-RNA via their seed sequence about first 2-8 nucleotides starting at 5’end of any mature strand. Then AGO proteins cleave the extensively complementarity target mRNAs and repress the translation. Then miRNA comes to circulation crossing cell membrane via exocytosis and empty RISC undergo autophagy or ubiquitin proteosome system of degradation. It is natural the biogenesis pathway of miRNA is more or less same in different species, the cross-species regulation of miRNA for better health needs to be addressed further. Types of Cross species regulation of gene expression through miRNA include food ingestion, microbial interaction, parasitic interactions among each other. Dietary significance of miRNAs still be in debate to prove its nutritive value and cross species gene regulation.
Properties of food derived miRNA
miRNAs are widely found in eukaryotic cells as well as different plant and animal food sources. By defining the properties like accessibility, stability, absorbability and bioactivity miRNAs are showing their dietary significance. Accessibility/abundance in food can be measured by quantitative reverse transcription polymerase chain reaction (qRT-PCR), Northern blotting, In situ hybridisation, Sanger sequencing, Next generation sequencing etc. The units of expression to measure miRNA are copies, molar concentration (ng/mL or fmol/Kg), reads (reads/million). In nutrition stability of food ingredient means it would take part in uptake, circulation and utilization in the human/animal body in their original molecular form that means stable enough in a hostile environment such as pH, temperature, RNAase activity and phagocytosis. In cellular system, for a specific miRNA, besides sufficient uptake and stability, its bioactivity highly depends on its absorbability means it must pass the GI tract to reach at the cell. Bioactivity is the final determining property to consider dietary miRNA as a functional food ingredient when it binds to the target m-RNA and inhibits its action (Li J et al., 2019).
Evidence of complementary effect of dietary micro-RNA
Plant derived miRNA
miRNA MIR168a from rice (Oryza sativa; osa-MIR168a) is detectable in human and animal sera, and osa-MIR168a decreases the expression of LDL receptor adapter protein mRNA, thereby inhibiting LDL receptor expression in mouse liver. This increases the LDL cholesterol level. In HepG2 cells miR-27a decreases the expression of LDLRAP1 and increases the LDL level which may lead to atherosclerosis. Therefore, dietary osa-MIR168a may complement the actions of microRNA-27a in development of atherosclerosis (Zang L et al., 2012; Alvarez LM et al.,2015).
Dietary plant MIR156 downregulates wint10b, cyclin D1 proteins indicates its negative effect on intestinal cell proliferation in IPEC-J2 cells (Li M et al., 2019). This microRNA may compensate the effect of mir-124-3p which also down regulates the expression of cyclin D1 (Xue Y et al., 2024)
Animal derived miRNA
Baier SR et al. 2014 states miRNAs in milk are bioactive food compounds that regulate human genes. Most of the bovine miRNA sequences are similar to the human miRNA sequences. Only endogenous expression level of miRNA may not always compensate for the exogenous micro-RNA. For example, dietary cow milk miR-29b and 200c increase the expression level of endogenous microRNAs when mice provided with miR-29b/200c sufficient diet compared to deficient diet. Mir-29b directly target many inhibitors of osteogenesis like HDAC4, TGF-BETA3, PTEN and indirectly increases the expression of RUNX2 to promote osteoblast differentiation (Baier SR et al, 2014; Li Z et al, 2019; Xia T et al, 2020). Apart from osteogenesis, MicroRNA mimic of 29b represses the protein level of B2R, CCND-1, MMP-2. MMP-9 in immortalised human early-pregnancy extravillous trophoblast cell line HTR-8/SVneo. These proteins promote the migration and invasion of extravillous trophoblasts during placenta formation in pregnancy (Wang L and Li Y, 2020).
Bovine Milk miR-200c decreases cancer risk by targeting the transcription factor zinc finger E-box binding homeobox 1 (ZEB1). miR-200c–dependent loss of ZEB1 induces E-cadherin expression, thereby limiting epithelial to- mesenchymal transition, a key event in metastasis. (Baier SR et al, 2014).
MiR-144 and miR-451 often acts as a tumor suppressor gene in cancers and modulates multiple pathways by targeting different downstream mRNAs. miR-144/451 gene deletion results in elevated 14-3-3ζ level, a cytoplasmic adaptor protein which sequesters the transcription factor Foxo3 to cytoplasm, thus, dampens the expression of Foxo3 directly-transcribed anti-oxidant genes, catalase (cat) and glutathione peroxidases 1 (gpx1). Dietary blood meal to those mice partially decreased the expression level of 14-3-3ζ. Both MiR-144 and 451 are located in the chromosomal region 17q11.2 (Wang W et al., 2017)
Reasons of controversy in defining nutrient properties of dietary miRNA
- Present in very low quantities
- Loss in cooking
- Apart from dietary miRNA other sources of miRNAs are circulating in biological fluids
- Absorption site of exogenous miRNAs
- Less evidence of bioactive roles of exogenous miRNAs
Conclusion
Although experiments in dietary microRNAs arise lot of controversies it is worthwhile to check the dietary miRNAs effect on endogenous bioactivity of miRNAs which may increase the clarity in understanding regarding their nutritional properties.
References
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