Role of microRNA in Phosphorus Deficiency

Presented By:Kunj Bihari Gupta

M.Phil-Ph.D (1st sem)Center for Biosciences

School of Basic and Applied SciencesCentral University of Punjab

IntroductionWhat are MicroRNAs (miRs)? – MicroRNAs are a class of 21-24 nucleotides long, single stranded, endogenous, non-coding RNAs involved in PTGS in all eukaryotes . Transcribed from genomic DNA mainly by RNA poly II. Nascent transcript known as pri-miR, then pre-miR and finally form mature miR. Generate dsRNA with the target mRNA which is chopped by different nucleases.

Brief HistoryFirst miR lin-4 was discovered in 1993 by

Victor Ambros in C. elegansRegulate lin-14 protein.In 2000 second miR (let-7) characterized in C. elegansTotal 24,521 miRs discovered so far.

MicroRNA Database. (2013). (http://www.mirbase.org/)

Nomenclature of microRNAAccording to standard nomenclature system,

name of any MicroRNA is written as mir-123.miR = MicroRNA (mature form).mir = Precursor MicroRNA.Number indicates order of discovery.Annotated with an additional lower case

letter e.g.- miR-123a & miR-123b, if deference in only one or two nucleotides.

Additional dash-number suffix e.g., miR-123-1 & miR-123-2, if produce same miR but transcribed from different places in the genome of same organism.

When two miRs originate from opposite arms of the same mir, then they are denoted with a -3p or -5p suffix.

When relative expression levels are known, then an asterisk (*) are use to differentiate e.g.- miR-123 (more) and miR-123*(less).

Species specific miR are denoted as below - hsa = Homo sapiens (Human)oar = Ovis aries (Sheep)ath = Arabidopsis thaliana (model plant)d = Drosophila

microRNA BiogenesisGenomic

DNA

Pri-miRNA

Pre-miRNA

Mature-miRNA

Transcription (Poly II)

Drosa+DGCR8 complex

Pre-miRNAIn Side Cytoplasm

In Side Nucleus

Exportin- 5

Dicer

Nephew k.p. et al., 2010

Although the miRNA is only 24 nucleotides long,But its 5' and 3' ends seem to have distinct roles-• miRNAs can regulate their targets simply by strong pairing with so-called seed sequence that consist of just seven or eight bases complementary to the miRNA 5' end.•miRNA 3' ends provide an additional measure of regulatory control by permitting the function of target sites that have only limited complementarity to the miRNA 5' end.

miRNA targeting to Gene Silencing

Sun et al., 2010

miR can regulate gene expression in two ways:-

1. Indirect- activating/deactivating regulatory elements.

2. Direct- making double stranded transcript by binding to regulating genes.

Regulation of miRNA miRNA is regulated by transcription factors (TFs) which bind to few kb to more than 50 kb upstream of the miRNA genes.

Very few exact TF binding sites have been identified experimentally.

Important Web Sites regarding Micro RNA

• miRBase: http://www.mirbase.org/ • Diana Lab: http://diana.cslab.ece.ntua.gr/ • MicroCosm: http://www.ebi.ac.uk/enrightsrv/microcosm/• miRNAminer: http://groups.csail.mit.edu/pag/mirnaminer• miRviewer: http://people.csail.mit.edu/akiezun/miRviewer• Patrocles: http://www.patrocles.org/ • microRBase: http://microrna.sanger.ac.uk/ • PicTar: http://pictar.mdc-berlin.de/ • TargetRank: http://hollywood.mit.edu/targetrank• TargetScanS: http://www.targetscan.org/

Plant StressWhen plants are subjected to other than ideal

growing conditions, then it considered to be under stress.

Plants are sessile hence cannot escape from stress.

Stress may trigger a wide range of plant responses:-

- Altered gene expression- Cellular metabolism- Changes in growth rates and crop yield, etc.

Stress Biotic – Imposed by another living organism Abiotic – Arising from an excess or deficit in

the physical and chemical environment.

ABIOTIC STRESSESEnvironmental, non-biological

•Temperature (high / low)•Water (high / low)•Salt•Radiation•Chemical•Nutrition deficiency

BIOTIC STRESSESCaused by living organisms

•Fungi•Bacteria•Insects•Herbivores•Other plants/competition

Phosphorus (P)Function: Stimulates early growth and root

formation, hastens maturity, promotes seed production and makes plants hardy.

Symptoms: Small root growth, spindly stalk, delayed maturity, purplish discoloration of leaves, dying of tips of older leaves, and poor fruit and seed development.

Phosphate starvation responses

Nilssona L et al., 2010

Gene involved in Phosphate HomeostasisUbiquitin-conjugating E2 enzyme (UBC24).Phosphate starvation responsive (PHR1,

PHR2).Phosphate transporter genes (Pht1.8 &

Pht1.9).PHO1,PHO2 gene. etc.

Nilssona L et al., 2010

microRNA involved in Phosphate Homeostasis

RootShoot

Hsieh Li-Ching et al., 2009

Out of many miR, miR399 are most studied.

Which is strongly induced upon P starvation.

It is a family of nearly similar 6 different miR

named as miR399a, miR399b miR399c,

miR399d, miR399e, miR399f in case of

Arabidopsis.

The target for this miR is PHO2 gene.

Binds to the 5’ UTR of PHO2 transcripts.

ConclusionPlants are sessile in nature so, continuously

exposed to different stress.

It is interesting to know the role of miRNAs,

involved in the regulation of plant abiotic stress.

To find out stress-responsive miRNAs,

smallRNA libraries were created and sequenced

with pooled RNAs from plants treated with

different abiotic stresses

miR399 are most studied in P starvation

state.

This miR down regulate the PHO2 gene

transcripts.

Expression of this miR is also tightly

regulated by an transcription factor MYB-2 in

Arabidopsis.

Sun et al., 2010

ReferencesBaek, D., Park, H. C., Kim, M. C.& Yun, D.-J. (2013). The role of Arabidopsis MYB2

in miR399f-mediated phosphate-starvation response. Plant Signaling & Behavior 8(3): 234-238.

Bartel, D. P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2): 281-297.

Fujii, H., Chiou, T.-J., Lin, S.-I., Aung, K.& Zhu, J.-K. (2005). A miRNA Involved in Phosphate-Starvation Response in Arabidopsis. Current Biology 15(22): 2038-2043.

Großhans, H., & Filipowicz, W. (2008). Molecular biology: the expanding world of small RNAs. Nature 451(7177): 414-416.

Krol, J., Loedige, I. & Filipowicz, W. (2010). The widespread regulation of microRNA biogenesis, function and decay. Nature Reviews Genetics 11(9): 597-610.

MicroRNA Database. (2013).page.<http://www.mirbase.org>. Accessed 2013 Nov 07.

Sun, W., Julie Li, Y.-S., Huang, H.-D., Shyy, J. Y.& Chien, S. (2010). microRNA: a master regulator of cellular processes for bioengineering systems. Annual Review Of Biomedical Engineering12(1):21-27.

Sunkar, R. & Zhu, J.-K. (2004). Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. The Plant Cell Online 16(8): 2001-2019.

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