Farzana BIBI, Muhammad DIN, Muhammad Younas Khan BAROZAI

Bioinformatics profiling and characterization of potential microRNAs and their targets in the genus Coffea

MicroRNAs (miRNAs) are a class of noncoding small endogenous RNAs with lengths of 18 to 26 nucleotides that have beenshown to regulate gene expression at posttranscriptional levels by targeting mRNAs for degradation or by inhibiting protein translation.Although thousands of miRNAs have been identified in many species, limited miRNAs have been reported in the genus Coffea, amember of the family Rubiaceae that is endemic to tropical Asia and South Africa. The genus Coffea, whose seeds are known as coffeebeans, is used to make coffee. In this study, we identified 51 potential genus Coffea miRNAs, belonging to 51 families, using a well-definedcomparative genome-based computational approach in genus Coffea expressed sequences tags. These identified miRNAs potentiallytarget 150 protein-coding genes, which can act as transcription factors and take part in multiple biological and metabolic processes,hypothetical proteins, signal transduction, transporters, growth and development, stress-related processes, structural constituents, anddisease-related processes. The results of this research may contribute to the understanding of the miRNA-mediated life processes in thegenus Coffea.

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Akter A, Islam MM, Mondal SI, Mahmud Z, Jewel NA, Ferdous S, Amin MR, Rahman MM (2014). Computational identification of miRNA and targets from expressed sequence tags of coffee (Coffea arabica). Saudi J Biol Sci 21: 3-12.
Ali SH, Barozai MYK, Din M, Aziz AN (2016). A review on the sorghum for biofuel and microRNAs. Pure Appl Biol 5: 1064- 1100.
Allen E, Xie Z, Gustafson AM, Carrington JC (2005). microRNAdirected phasing during trans-acting siRNA biogenesis in plants. Cell 121: 207-221.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990). Basic local alignment search tool. J Mol Biol 215: 403-410.
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
Ambros V (2004). The functions of animal microRNAs. Nature 431: 350-355.
Baloch IA, Barozai MYK, Din M (2015a). Identification and characterization of 25 microRNAs and their targeted proteins in apricot (Prunus armeniaca L.). J Anim Plant Sci 25: 1466- 1476.
Baloch IA, Barozai MYK, Din M, Achakzai AKK (2015b). Computational identification of 18 microRNAs and their targets in three species of rose. Pak J Bot 47: 1281-1285.
Barozai MYK (2012a). Identification and characterization of the microRNAs and their targets in Salmo salar. Gene 499: 163- 168.
Barozai MYK (2012b). In-silico identification of microRNAs and their targets in fibre and oil producing plant Flax (Linum usitatissimum L.). Pak J Bot 44: 1357-1362.
Barozai MYK (2012c). The novel 172 sheep (Ovis aries) microRNAs and their targets. Mol Biol Rep 39: 6259-6266.
Barozai MYK (2013). Identification of microRNAs and their targets in Artemisia annua L. Pak J Bot 45: 461-465.
Barozai MYK, Baloch IA, Din M (2011a). Identification of microRNAs and their targets in Helianthus. Mol Biol Rep 39: 2523-2532.
Barozai MYK, Baloch IA, Din M (2011b). Computational identification of microRNAs and their targets in two species of evergreen spruce tree (Picea). Proc Wrld Acad Sci E 75: 413- 418.
Barozai MYK, Din M (2017). Initial screening of plant most conserved microRNAs targeting infectious viruses: HBV and HCV. In: 2017 14th International Bhurban Conference on Applied Sciences and Technology; 2017. New York, NY, USA: IEEE.
Barozai MYK, Din M, Baloch IA (2011c). Identification of microRNAs in ecological model plant Mimulus. J Biophys Chem 2: 322-331.
Barozai MYK, Din M, Baloch IA (2013a). Structural and functional based identification of the bean (Phaseolus) microRNAs and their targets from expressed sequence tags. J Struct Funct Genom 14: 11-18.
Barozai MYK, Husnain T (2011). Identification of biotic and abiotic stress up-regulated ESTs in Gossypium arboretum. Mol Biol Rep 39: 1011-1018.
Barozai MYK, Irfan M, Yousaf R, Ali I, Qaisar U, Maqbool A, Zahoor M, Rashid B, Hussnain T, Riazuddin S (2008). Identification of microRNAs in cotton. Plant Physiol Biochem 46: 739-751.
Barozai MYK, Kakar S, Sarangzai AM (2013b). Profiling the carrot (Daucus carota L.) microRNAs and their targets. Pak J Bot 45: 353-358.
Barozai MYK, Shah SQ, Din M, Muhammad, R (2014). Codon usage bias and RNA secondary structures analysis for virus resistant genes in Arabidopsis thaliana and Oryza sativa. Pure Appl Biol 3: 81-91.
Barozai MYK, Wahid AH (2012). In-silico identification and characterization of cumulative abiotic stress responding genes in potato (Solanum tuberosum L.). Pak J Bot 44: 57-69.
Bartel DP (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
Crooks GE, Hon G, Chandonia JM, Brenner SE (2004). WebLogo: a sequence logo generator. Genome Res 14: 1188-1190.
Dai X, Zhao PX (2011). psRNATarget: a plant small RNA target analysis server. Nucl Acids Res 39: 155-159.
Din M, Barozai MYK (2014a). Profiling and characterization of eggplant (Solanum melongena L.) microRNAs and their targets. Mol Biol Rep 41: 889-894.
Din M, Barozai MYK (2014b). Profiling microRNAs and their targets in an important fleshy fruit: tomato (Solanum lycopersicum L.). Gene 535: 198-203.
Din M, Barozai MYK, Baloch IA (2014). Identification and functional analysis of new conserved microRNAs and their targets in potato (Solanum tuberosum L.). Turk J Bot 38: 1199-1213.
Din M, Barozai MYK, Baloch IA (2016). Profiling and annotation of microRNAs and their putative target genes in chilli (Capsicum annuum L.) using ESTs. Gene Reps 5: 62-69.
Favero DS, Jacques CN, Iwase A, Le KN, Zhao J, Sugimoto K, Neff MM (2016). Suppressor of phytochrome b represses genes associated with auxin signaling to modulate hypocotyl growth. Plant Physiol 171: 2701-2716.
Ferrazzano GF, Amato I, Ingenito A, De Natale A, Pollio A (2009). Anti-cariogenic effects of polyphenols from plant stimulant beverages (cocoa, coffee, tea). Fitoterapia 80: 255-262.
Floyd SK, Bowman JL (2004). Gene regulation: ancient microRNA target sequences in plants. Nature 428: 485-486.
Frazier TP, Xie F, Freistaedter A, Burklew CE, Zhang B (2010). Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta 232: 1289- 1308.
Friedman J, Waller GR (1983). Caffeine hazards and their prevention in germinating seeds of coffee (Coffea arabica L.). J Chem Ecol 9: 1099-1106.
Ghani A, Din M, Baloch IA, Barozai MYK (2013). Identification of microRNA in 12 plant species of Fabaceae. Pure Appl Bio 2: 104-115.
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008). MiRBase: tools for microRNA genomics. Nucl Acids Res 36: 154-158.
Jin H, Martin C (1999). Multifunctionality and diversity within the plant MYB-gene family. Plant Mol Biol 41: 577-585.
Jin WB, Li NN, Zhang B, Wu FL, Li WJ, Guo AG, Deng ZY (2008). Identification and verification of microRNA in wheat (Triticum aestivum). J Plant Res 121: 351-355.
Jones-Rhoades MW, Bartel DP (2004). Computational identification of plant microRNAs and their targets, including a stressinduced miRNA. Mol Cell 14: 787-799.
Jones-Rhoades MW, Bartel DP, Bartel B (2006). MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57: 19-53.
Kim YS, Kim SG, Lee M, Lee I, Park HY, Seo PJ, Jung JH, Kwon EJ, Suh SW, Paek KH et al. (2008). HD-ZIP III activity is modulated by competitive inhibitors via a feedback loop in Arabidopsis shoot apical meristem development. Plant Cell 20: 920-933.
Kruger J, Rehmsmeier M (2006). RNAhybrid: microRNA target prediction easy, fast and flexible. Nucl Acids Res 34: 451-454.
Lakshmi K, Kalaivani A (2016). Expression of caffeic acid o-methyltransferase gene involved in lignin biosynthesis of sugarcane. J Sugarcane Res 5: 78-82.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R et al. (2007). ClustalW and ClustalX version 2. Bioinformatics 23: 2947-2948.
Loss-Morais G, Ferreira DC, Margis R, Alves-Ferreira M, Corrêa RL (2014). Identification of novel and conserved microRNAs in Coffea canephora and Coffea arabica. Gen Mol Biol 37: 671- 682.
Mithoe SC, Ludwig C, Pel MJ, Cucinotta M, Casartelli A, Mbengue M, Sklenar J, Derbyshire P, Robatzek S, Pieterse CM et al. (2016). Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase. EMBO Rep 17: 441-454.
Rebijith KB, Asokan R, Ranjitha HH, Krishna V, Nirmalbabu K (2013). In silico mining of novel microRNAs from coffee (Coffea arabica) using expressed sequence tags. J Hort Sci Biotech 88: 325-337.
Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005). Specific effects of microRNAs on the plant transcriptome. Dev Cell 8: 517-527.
Shah SQ, Barozai MYK, Din M, Baloch IA, Wahid HA (2016). RNA secondary structure analysis for abiotic stress resistant and housekeeping genes in Arabidopsis thaliana and Oryza sativa. Pure Appl Biol 5: 476-482.
Sunkar R, Jagadeeswaran G (2008). In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol 8: 37.
Swartz JR (2016). Control of metabolic flux in cell-free biosynthetic systems. US Patent 20: 115-558.
Talukdar G, Inoue R, Yoshida T, Ishimoto T, Yaku K, Nakagawa T, Mori H (2017). Novel role of serine racemase in anti-apoptosis and metabolism. Biochim Biophys Acta 1861: 3378-3387.
Wahid HA, Barozai MYK, Din M (2016). Functional characterization of fifteen hundred transcripts from Ziarat juniper (Juniperus excelsa M.Bieb). Adv Life Sci 4: 20-26.
Wang J, Yang X, Xu H, Chi X, Zhang M, Hou X (2012). Identification and characterization of microRNAs and their target genes in Brassica oleracea. Gene 505: 300-308.
Xie F, Frazier TP, Zhang B (2010). Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta 232: 417-434.
Xie FL, Huang SQ, Guo K, Xiang AL, Zhu YY, Nie L, Yang ZM (2007). Computational identification of novel microRNAs and targets in Brassica napus. FEBS Lett 581: 1464-1474.
Zhang BH, Pan XP, Cannon CH, Cobb GP, Anderson TA (2006a). Conservation and divergence of plant microRNA genes. Plant J 46: 243-259.
Zhang BH, Pan XP, Cox SB, Cobb GP, Anderson TA (2006b). Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci 63: 246-254.
Zhang BH, Pan XP, Stellwag EJ (2008). Identification of soybean microRNAs and their targets. Planta 229: 161-182.
Zhang BH, Wang QL, Pan XP (2007a). MicroRNAs and their regulatory roles in animals and plants. J Cell Physiol 210: 279- 289.
Zhang BH, Wang QL, Wang KB, Pan XP, Liu F, Guo TL, Cobb GP, Anderson TA (2007b). Identification of cotton microRNAs and their targets. Gene 397: 26-37.
Zuker M (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucl Acids Res 31: 3406-3415.