A.S.N. Reddy

A.S.N. ReddyProfessor
Office: Biology Building - Room Number 420
Phone: 970-491-5773
Website: http://wp.natsci.colostate.edu/reddylab
Education: Ph.D., Jawaharlal Nehru University
Email: Anireddy.Reddy@ColoState.EDU

One of the fundamental questions in plant biology is how plants sense and respond to environmental (abiotic and biotic) and hormonal signals that regulate diverse cellular processes and various aspects of plant growth and development.  Our group has been studying i) calcium-mediated signal transduction mechanisms with emphasis on calcium sensors and their target proteins, ii) mechanisms that regulate basic and alternative splicing of pre-messenger RNAs in response to stresses, iii) disease resistance, iv) cell wall degrading enzymes for biofuel production and iv) synthetic signal transduction circuits in plants.  We use molecular, cell biological, genetic, biochemical, bioinformatics and computational tools to accomplish our research goals.  Arabidopsis, maize, potato and Miscanthus are used in our research.  Studies on computational aspects of alternative splicing and protein-protein interactions are being done in collaboration with Asa Ben-Hur in the Department of Computer Science at CSU  (http://www.cs.colostate.edu/~asa/projects.html). In signaling research, our work is focused on calcium/calmodulin-mediated signal transduction mechanisms in plant growth and development, and in plant responses to pathogens and abiotic stresses.  Calcium is a key messenger in transducing diverse signals in plants.   We have been particularly interested in calcium sensors and downstream targets of calcium sensors in understanding diverse cellular and physiological processes regulated by calcium.  Using bioinformatics tools we have extensively characterized several gene families involved in calcium signaling.  In a comprehensive screen for calmodulin interacting proteins, we identified over 100 calmodulin-binding proteins ranging from transcription factors to molecular motors.  During the last twenty years we have been studying the function of several of these calmodulin-binding proteins in plant growth and development, and plant responses to various biotic and abiotic stresses.   Our group has extensively characterized function and regulation a novel calcium/calmodulin-regulated microtubule motor protein involved in cell morphogenesis and cell division.  We have identified several calmodulin target proteins that play a central role in plant disease resistance and abiotic stress responses and elucidated signaling pathways involving these proteins.  Additionally, we demonstrated a critical role for a pollen-specific calmodulin-binding protein in pollen germination.  We have generated and tested chimeric motors and receptors by combining modular domains from plant and animal proteins for potential applications in synthetic biology and nanobiotechnolgy. In gene regulation area, our focus is on precursor-mRNA splicing.  Alternative splicing of pre-mRNAs is emerging as an important step in regulating transcriptome complexity and eventually proteome diversity.  More recently, it has become evident that alternative splicing is coupled to nonsense-mediated decay to regulate the abundance of transcripts through a mechanism called regulated unproductive splicing and translation (RUST).  Our group has been studying spliceosomal proteins, identified several putative splicing regulators, called serine/arginine-rich (SR) proteins, and analyzed their functions using a variety of genetic, biochemical and cell biological approaches.  By studying alternative splicing of Arabidopsis SR genes, we have demonstrated extensive alternative splicing (generation of over 90 splice variants from 15 genes) of this family of genes.  Furthermore, out studies have demonstrated that stresses have rapid and dramatic effect on alternative splicing, suggesting rapid reprogramming of gene expression at the splicing level.  Recent studies suggest that plants can rapidly alter their transcriptome complexity in response to stresses by regulating alternative splicing of master splicing regulators. Our current focus is on genome-scale analyses of targets of calmodulin-regulated transcription factors and stress-regulated alternative splicing in various mutants, using high-throughput next generation sequencing technologies (ChIP-seq, RNA-seq and RIP-seq) and computational tools. A thorough understanding of mechanisms by which plants respond to stresses will pave the way to engineer plants that are capable of growing well under adverse environmental conditions.  In addition to these projects, we are also working on developing transformation tools in Miscanthus, a potential energy crop, and cloning and expression of cell wall degrading enzymes from fungal species with an ultimate goal to use them in the production of ethanol from lignocellulose. For additional details on our ongoing research projects please visit our website at http://lamar.colostate.edu/~reddy

Selected Publications

Ling, Y., Serrano, N., Gao, G., Atia, M. Mokhtar, M., Woo, Y.H., Bazin, J., Veluchamy, A., Behamud, M., Crespi, M., Gehring, C., Reddy, A.S.N. and Mahfouz, M.M. (2018) Thermopriming triggers splicing memory in Arabidopsis. J. Expt. Bot. 69: 2659-2675.  

Gao Y, Xi F, Zhang H, Liu X, Wang H, Zhao L, Reddy A, Gu L (2018), Single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) in plants: The status of the bioinformatics tools to unravel the transcriptome complexity. Current Bioinformatics (in press)

Albaqami, M. and Reddy, A.S.N. (2018) Development of an in vitro pre-mRNA splicing assay using plant nuclear extract. Plant Methods 14, pages 1-12.

Ullah, F., Hamilton, M., Reddy, A.S. Ben-Hur, A (2018) Exploring the relationship between intron retention and chromatin accessibility in plants. BMC Genomics, 19, Pages 1-11.

Sergei A Filichkin, Mike Hamilton, Palitha D Dharmawardhana, Sunil K Singh, Christopher Sullivan, Asa Ben-Hur, Anireddy SN Reddy and Pankaj Jaiswal (2018) Abiotic stresses modulate landscape of poplar transcriptome via alternative splicing, differential intron retention, and isoform ratio switching. Frontiers in Plant Science 9, pages 1-17.

Salah E. Abdel-Ghany, S.E., Day, I., Heuberger, A.L., Broeckling, C.D. and Reddy, A.S.N. (2016) Production of Phloroglucinol, a Platform Chemical, in Arabidopsis using a Bacterial Gene. Scientific Reports. 6:38483: Pages 1-14

Salah E. Abdel-Ghany*, Michael Hamilton*, Jennifer L. Jacobi, Peter Ngam, Nicholas Devitt, Faye Schilkey, Asa Ben-Hur, Anireddy S.N. Reddy (2016) A survey of the sorghum transcriptome using single-molecule long reads. (*joint first authors) Nature Communications 7:11706, Pages 1-11. DOI: 10.1038/ncomms11706

K. V.S.K. Prasad*, Amira A.E. Abdel-Hameed*, Denghui Xing, and Anireddy S.N. Reddy (2016) Global gene expression analysis using RNA-seq uncovered a new role for SR1/CAMTA3 transcription factor in salt stress. Scientific Reports 6:27021: pages 1-15 (*joint first authors)

D. Xing, Y.Wang, Michael Hamilton, Asa Ben-Hur and A.S.N. Reddy (2015) Transcriptome-wide identification of RNA targets of Arabidopsis serine/arginine protein 45 (SR45) uncovers the unexpected roles of this RNA binding protein in RNA processing. Plant Cell 27:3294-3308.

Salah E. Abdel-Ghany, Maxim Golovkin, and A.S.N. Reddy (2015) Engineering of Plants for the Production of Commercially Important Products: Approaches and Accomplishments. In: Plant Biology and Biotechnolgy. Vol. II: Plant Genomics and Biotechnology, Springer Publisher.

Saiprasad G. Palusa and A.S.N. Reddy (2015) Differential Recruitment of Splice Variants from SR Pre-mRNAs to Polysomes During Development and in Response to Stresses. Plant and Cell Physiology. 56: 421-427.

Sergei A. Filichkin, Jason S. Cumbie, J., Palitha Dharmawadhana, Pankaj Jaiswal, Jeff H. Chang, Saiprasad G. Palusa, A.S.N. Reddy, Molly Megraw, Todd C. Mockler (2015) Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis. Mol. Plant 8:207-227.

Shin, S., Golovkin, M. and Reddy. A.S.N (2014) A pollen-specific calmodulin-binding protein, NPG1, interacts with putative pectate lyases. Scientific Reports 4:5263. doi: 10.1038/srep05263.

Palusa, S. G. and Reddy, A.S.N. (2013) Analysis of RNA-protein Interactions Using Electrophoretic Mobility Shift Assay (Gel Shift Assay).  Bio-Protocols Nov. 20, 2013

Reddy, A.S.N., Marquez, Y., Kalyna, M. and Barta, A. (2013)  Complexity of the alternative splicing landscape in plants.  Plant Cell. 25: 3657-3683.  Featured in “IN BRIEF” section of Plant Cell.

Abdel-Ghany, S.E., Day, I., Heuberger, A.L., Broeckling, C.D. and Reddy, A.S.N.(2013) Metabolic engineering of Arabidopsis for butanetriol production using bacterial genes. Metabolic Engineering 20: 109-120.

Lazzaro, M.D., Marom, E.Y.,  Reddy, A.S.N. (2013) Polarized cell growth, organelle motility, and cytoskeletal organization in conifer pollen tube tips are regulated by KCBP, the calmodulin binding kinesin.  Planta 238:587-597.

Helena Celesnik, Gul S. Ali, Faith M. Robison and Anireddy S.N. Reddy (2013) Arabidopsis thaliana VOZ (Vascular plant One-Zinc finger) transcription factors are required for proper regulation of flowering time.  Biology Open 2: 421-431. Featured on cover page.

K. Laluk, K.V.S.K. Prasad, T. Savchenko, H. Celesnik, K. Dehesh, M. Levy, T. Mitchell-Olds, A.S.N. Reddy (2012) The calmodulin-binding transcription factor SIGNAL RESPONSIVE1 is a novel regulator of glucosinolate metabolism and herbivory tolerance in Arabidopsis. Plant Cell Physiol. 53: 2008-2015

Julie Thomas, Saiprasad G. Palusa, K.V.S.K. Prasad, Gul Shad Ali, Giridara-Kumar Surabhi, Asa Ben-Hur, Salah E. Abdel-Ghany and Anireddy S. N. Reddy (2012) Identification of an intronic splicing regulatory element involved in autoregulation of alternative splicing of the SCL33 pre-mRNA. Plant Journal 72: 935-946.

Irene S. Day, Maxim Golovkin, Saiprasad Goud Palusa, Alicia Link, Gul Shad Ali, Julie Thomas, Dale N. Richardson, and Anireddy S.N. Reddy(2012) Interactions of SR45, an SR-like protein, with spliceosomal proteins and an intronic sequence: Insights into regulated splicing.  Plant Journal  71, 936–947.

M.F. Rogers, J. Thomas, A.S.N. Reddy, and A. Ben-Hur (2012). SpliceGrapher: Detecting patterns of alternativesplicing from RNA-seq data in the context of gene models and EST data. Genome Biology, 13, R4. Designated as "Highly Accessed" article

Cheung, A and Reddy, A.S.N. (2012) Nuclear Architecture and Dynamics:  Territories, Nuclear Bodies and Nucleocytoplasmic Trafficking. Plant Physiol. 158: 23-25.

Reddy, A.S.N., Rogers, M., Richardson, D., Hamilton, M. and Ben-Hur, A.  (2012) Deciphering the plant splicing code: Experimental and computational approaches for predicting alternative splicing and splicing regulatory elements. Front. Plant Sci. 3:18. doi: 10.3389/fpls.2012.00018

Reddy, A.S.N., Day, I.S, Janett Göhring, Andrea Barta (2012) Localization and dynamics of plant splicing regulators.  Plant Physiol.  158: 67-77.

Reddy, A.S.N., Ali, G.S., Celesnik, H. and Day, I.S. (2011) Coping with stresses:  Roles of calcium- and calcium/calmodulin-regulated gene expression. Plant Cell  23: 2010-2032

Dale N. Richardson, Mark F. Rogers, Adam Labadorf, Asa Ben-Hur, Hui Guo, Andrew H. Patersonand Anireddy S.N. Reddy (2011) Comparative Analysis of Serine/Arginine-Rich Proteins Across 27 Eukaryotes: Insights into Sub-family Classification and Extent of Alternative Splicing. PLoS ONE  6:e24542, Pages 1-16.

M. Hamilton, A.S.N. Reddy, and A. Ben-Hur. Kernel methods for Calmodulin binding and binding site prediction (2011) In: Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine Pages 381-386, ACM New York, NY, USA

Reddy, A.S.N., Ben-Hur, A. and Day, I.S.  (2011) Experimental and computational approaches for the study of calmodulin interactions.  Phytochemistry, 72:1007-1019

Reddy, A.S.N., and Ali,  G.S (2011) Plant SR proteins:  Roles in pre-mRNA splicing, plant development and stress responses.  Advanced Review, Wiley Interdisciplinary Reviews (WIREs) RNA. In press

Reddy, A.S.N. and Day, I (2011) Microtubule motor proteins in the eukaryotic green lineage: Functions and regulation. In The Plant Cytoskeleton, Advances in Plant Biology 2, Springer. Pages 119-141.

Reddy, A.S.N. and Day, I.S. (2011) Calcium signaling in plants. Indian J. Agric. Biochem.  24, 1-16.

Irene S. Day. and Reddy, A. S.N. (2011) Elucidation of calcium signaling components and networks,  In Coding and Decoding of Calcium Signals in Plants. Ed. S. Luan, Springer (In press).

Barta, A.,  Kalyna, A., Reddy A.S.N.  (2010) Implementing a Rational and Consistent Nomenclature for Serine/Arginine-Rich Protein Splicing Factors (SR Proteins) in Plants.  Plant Cell 22: 2926-2929.

Labadorf, A., Link, A., Rogers, M., Thomas, J., Reddy, A.S.N. and Ben-Hur, A.  Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtiiBMC Genomics 11, 114 (2010) Designated as "Highly Accessed Article".  Chlamydomonas Alternative Splicing web site: http://combi.cs.colostate.edu/as/chlamy/chlamy.CL01777/chlamy.CL01777.html

Palusa, S. G. and Reddy, A.S.N. (2010) Extensive coupling of alternative splicing of pre-mRNAs of SR genes with nonsense-mediated decay.  New Phytologist 185: 83-89.

Yang, T., Ali, G.S., Yang, L., Du, L., Reddy, A.S.N. and Poovaiah (2010) Calcium/calmodulin-regulated receptor-like kinase, CRLK, interacts with MEKK1 in plants.  Plant Signaling and Behavior.  8, 991-994.

Maia V. Vinogradova, Galina G. Malanina, A. S.N. Reddy, Robert J. FlettericK (2009) Structure of the complex of a mitotic kinesin with its calcium binding regulator.  Proc. Natl. Acad. Sci.  106, 8175-8179

Liqun Du, Gul S. Ali, Kayla A. Simons, Jingguo Hou, Tianbao Yang, A.S.N. Reddy and B. W. Poovaiah (2009) Ca2+/calmodulin Regulates Salicylic Acid-mediated Plant Immunity. Nature 457: 1154-1158. Featured under “Leading Edge” section of Cell.

Edited a Book on “Nuclear Pre-mRNA Processing in Plants” (Eds. A.S.N. Reddy and M. Golovkin) 2008 - published by Springer-Verlag.

Maia V. Vinogradova, Galina G. Malanina, V. S. Reddy, A.S.N. Reddy, R. J. Fletterick (2008) Structural dynamics of the microtubule binding and regulatory elements in the kinesin-like calmodulin binding protein. J Struc. Biol. 163:76-83 Featured on cover.

Ali, G.S., and Reddy, A.S.N (2008). PAMP-Triggered Immunity: Early events in the activation of flagellin sensitive2 . Plant Signaling &Behavior. 3:423-426

S. Schindler, K. Szafranski1, M. Hiller, G. S Ali, S. G. Palusa, Rolf Backofen, M. Platzer, A. S.N. Reddy (2008) Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding gene. BMC Genomics 10: 9:159; pages 1-11.

Ali, G.S., Hanumappa, M., Prasad, K.V.S.K. and Reddy, A.S.N (2008). Analyses of in vivo interactions and mobility of two spliceosomal proteins using FRAP and BiFC. PLoS ONE 6;3(4):e1953; pages 1-13.

Reddy, A.S.N (2007) Alternative Splicing of pre-mRNAs in plants in the genomic era Ann. Rev. Plant Biology 58: 267-294.

Palusa, S.G., Ali, G.S. and Reddy, A.S.N. (2007) Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins and its regulation by hormones and stresses. Plant J. 49: 1091-1107.

Day, I. and Reddy, A.S.N (2007) Proteomic Approaches to Construct Calcium Signaling Networks in Plants. In: Plant Proteomics: Technologies, Strategies, and Applications. Wiley Publisher; pages 645-657

Ali, G.S., Prasad, K.V.S.K., Day, I. and Reddy, A.S.N (2007). Ligand-dependent changes in the mobility of FLAGELLIN SENSITIVE2, an Arabidopsis receptor-like kinase. Plant Cell Physiol. 48: 1601-1611.

Ali, G.S., Palusa, S.G., Golovkin, M., Prasad, J., Manley, J. and Reddy, A.S.N (2007). A plant-specific splicing factor Regulates Multiple Developmental Processes PLoS ONE, 5: e471, Pages 1-13.

Ali, G. S. and Reddy, A.S. N. (2006) ATP, phosphorylation and transcription regulate the mobility of plant splicing factors. J. Cell Sci. 119: 3527-3538. (Featured on cover)

Richardson, D., Simmons, M., Reddy, A.S.N. (2006) Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes. BMC Genomics 7: 1-37. (designated as a highly accessed article)

Reddy, A.S.N. (2004) Plant serine/arginine-rich proteins and their role in pre-mRNA splicing. Trends in Plant Science 9: 541-547.

Vaka S. Reddy, Irene S. Day, Tyler Thomas and Reddy, A.S.N. (2004) KIC, a Novel Ca2+-Binding Protein with One EF-Hand Motif, Interacts with a Microtubule Motor Protein and Regulates Trichome Morphogenesis. Plant Cell 16: 185-200.

Vaka S. Reddy, and Reddy, A.S.N. (2004)Developmental and cell-specific expression of ZWICHEL is regulated by the intron and exon sequences of its upstream protein-coding gene. Plant Mol. Biol. 54: 273-293.

Ali, G.S., Golovkin, M., and Reddy, A.S.N. (2003). Nuclear localization and in vivo dynamics of a plant-specific serine/arginine-rich protein. Plant. J. 36: 883-893.

Golovkin, M. and Reddy, A.S.N (2003) A calmodulin-binding protein from Arabidopsis has an essential role in pollen germination. Proc. Natl. Acad. Sci. USA. 100: 10558-10663.

Irene S. Day Gul Shad Ali, Vaka S. Reddy and A.S.N. Reddy (2002) Analysis of EF-hand-containing proteins in Arabidopsis. Genome Biology 3: Research0056.1-0056.24.

Reddy, A.S.N. and Day, I (2001) Kinesins in the Arabidopsis genome: A comparative among analysis among eukaryotes. BMC Genomics 2:2.1-2.13.

Narasimhulu, S.B. and Reddy, A.S.N. (1998) Characterization of microtubule binding domains in the Arabidopsis kinesin-like calmodulin binding protein. Plant Cell 10: 957-965.

Bowser, J. and Reddy, A.S.N. (1997) Localization of a kinesin-like calmodulin-binding protein in dividing cells of Arabidopsis and tobacco. Plant J. 12: 1429-1438.

Golovkin, M. and Reddy, A.S.N. (1996) Structure and expression of a plant U1 snRNP 70K gene: Alternative splicing of U1 snRNP pre-mRNAs produces two different transcripts. Plant Cell 8: 1421-1435.

Reddy, A.S.N., Safadi, F., Narasimhulu, S.B., Golovkin, M. and Hu, X (1996) A novel plant calmodulin-binding protein with a kinesin heavy chain motor domain. J. Biol. Chem. 271: 7052-7060.