Generic placeholder image

Current Bioinformatics

Editor-in-Chief

ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

Research Article

HSEAT: A Tool for Plant Heat Shock Element Analysis, Motif Identification and Analysis

Author(s): Sarah Rizwan Qazi, Noor ul Haq, Shakeel Ahmad and Samina N. Shakeel*

Volume 15, Issue 3, 2020

Page: [196 - 203] Pages: 8

DOI: 10.2174/1574893614666190102151956

Price: $65

Abstract

Background: Previous methods used to discover cis-regulatory motifs in promoter region of plant genes possess very limited performance, especially for analysis of novel and rare motifs. Different plant genes have differential expression under different environmental or experimental conditions and modular regulation of cis-regulatory sequences in promoter regions of the same or different genes. It has previously been revealed that Heat Shock Proteins (HSPs) creation is correlated with plant tolerance under heat and other stress conditions. Regulation of these HSP genes is controlled by interactions between heat shock factors (HSFs) with cis-acting motifs present in the promoter region of the genes. Differential expression of these HSP genes is because of their unique promoter architecture, cis-acting sequences and their interaction with HSFs.

Objective: A versatile promoter analysis tool was proposed for identification and analysis of promoters of HSPs.

Methods: Heat Shock Element Analysis Tool (HSEAT) has been implemented in java programming language using pattern recognition approach. This tool has build-in MS access database for storing different motifs.

Results: HSEAT has been designed to detect different types of Heat Shock Elements (HSEs) in promoter regions of plant HSPs with integration of complete analysis of plant promoters to the tool. HSEAT is user-friendly, interactive application to discover various types of HSEs e.g. TTC Rich Types, Gap Types and Prefect HSE as well as STRE in HSPs. Here we examined and evaluated some known HSP promoters from different plants using this tool with already available tools.

Conclusion: HSEAT has extensive potential to explore conserved or semi-conserved motifs or potential binding sites of different transcription factors for other stress regulating genes. This tool can be found at https://sourceforge.net/projects/heast/.

Keywords: Heat shock element, heat shock proteins, plants, stress, motifs, transcription.

Graphical Abstract
[1]
Chauhan H, Khurana N, Agarwal P, Khurana P. Heat shock factors in rice (Oryza sativa L.): genome-wide expression analysis during reproductive development and abiotic stress. Mol Genet Genomics 2011; 286(2): 171-87.
[http://dx.doi.org/10.1007/s00438-011-0638-8] [PMID: 21792744]
[2]
Li J, Zhang J, Jia H, et al. The Populus trichocarpa PtHSP17.8 involved in heat and salt stress tolerances. Plant Cell Rep 2016; 35(8): 1587-99.
[http://dx.doi.org/10.1007/s00299-016-1973-3] [PMID: 27021382]
[3]
Guo M, Liu JH, Ma X, Luo DX, Gong ZH, Lu MH. The plant Heat Stress Transcription Factors (HSFs): structure, regulation, and function in response to abiotic stresses. Front Plant Sci 2016; 7: 114.
[http://dx.doi.org/10.3389/fpls.2016.00114] [PMID: 26904076]
[4]
Burke JJ, Oliver MJ. Isolation of Arabidopsis mutants lacking components of acquired thermotolerance. Plant Physiol 2000; 123(2): 575-88.
[http://dx.doi.org/10.1104/pp.123.2.575] [PMID: 10859187]
[5]
SchAffl F, PrAndl R, Reindl A. Regulation of the heat-shock response. Plant Physiol 1998; 117(4): 1135-41.
[http://dx.doi.org/10.1104/pp.117.4.1135] [PMID: 9701569]
[6]
Haq NU, Ammar M, Bano A, Luthe DS, Heckathorn SA, Shakeel SN. Molecular characterization of Chenopodium album chloroplast small heat shock protein and its expression in response to different abiotic stresses. Plant Mol Biol Report 2013; 31(6): 1230-41.
[http://dx.doi.org/10.1007/s11105-013-0588-x]
[7]
Haq NU, Raza S, Luthe DS, Heckathorn SA, Shakeel SN. A dual role for the chloroplast small heat shock protein of Chenopodium album including protection from both heat and metal stress. Plant Mol Biol Report 2013; 31(2): 398-408.
[http://dx.doi.org/10.1007/s11105-012-0516-5]
[8]
Nover L, Bharti K, DAring P, Mishra SK, Ganguli A, Scharf KD. Arabidopsis and the heat stress transcription factor world: how many heat stress transcription factors do we need? Cell Stress Chaperones 2001; 6(3): 177-89.
[http://dx.doi.org/10.1379/1466-1268(2001)0060177:AATHST2.0.CO;2] [PMID: 11599559]
[9]
Guo L, Chen S, Liu K, et al. Isolation of heat shock factor HsfA1a-binding sites in vivo revealed variations of heat shock elements in Arabidopsis thaliana. Plant Cell Physiol 2008; 49(9): 1306-15.
[http://dx.doi.org/10.1093/pcp/pcn105] [PMID: 18641404]
[10]
Scharf K-D, Siddique M, Vierling E. The expanding family of Arabidopsis thaliana small heat stress proteins and a new family of proteins containing α-crystallin domains (Acd proteins). Cell Stress Chaperones 2001; 6(3): 225-37.
[http://dx.doi.org/10.1379/1466-1268(2001)0060225:TEFOAT2.0.CO;2] [PMID: 11599564]
[11]
Busch W, Wunderlich M, SchAffl F. Identification of novel heat shock factor-dependent genes and biochemical pathways in Arabidopsis thaliana. Plant J 2005; 41(1): 1-14.
[http://dx.doi.org/10.1111/j.1365-313X.2004.02272.x] [PMID: 15610345]
[12]
Sakurai H, Takemori Y. Interaction between heat shock transcription factors (HSFs) and divergent binding sequences: binding specificities of yeast HSFs and human HSF1. J Biol Chem 2007; 282(18): 13334-41.
[http://dx.doi.org/10.1074/jbc.M611801200] [PMID: 17347150]
[13]
Bonner JJ, Ballou C, Fackenthal DL. Interactions between DNA-bound trimers of the yeast heat shock factor. Mol Cell Biol 1994; 14(1): 501-8.
[http://dx.doi.org/10.1128/MCB.14.1.501] [PMID: 8264619]
[14]
Amin J, Ananthan J, Voellmy R. Key features of heat shock regulatory elements. Mol Cell Biol 1988; 8(9): 3761-9.
[http://dx.doi.org/10.1128/MCB.8.9.3761] [PMID: 3146692]
[15]
Topol J, Ruden DM, Parker CS. Sequences required for in vitro transcriptional activation of a Drosophila hsp 70 gene. Cell 1985; 42(2): 527-37.
[http://dx.doi.org/10.1016/0092-8674(85)90110-2] [PMID: 4028160]
[16]
Xiao H, Perisic O, Lis JT. Cooperative binding of Drosophila heat shock factor to arrays of a conserved 5 bp unit. Cell 1991; 64(3): 585-93.
[http://dx.doi.org/10.1016/0092-8674(91)90242-Q] [PMID: 1899357]
[17]
Shakeel S, Haq NU, Heckathorn SA, Hamilton EW, Luthe DS. Ecotypic variation in chloroplast small heat-shock proteins and related thermotolerance in Chenopodium album. Plant Physiol Biochem 2011; 49(8): 898-908.
[http://dx.doi.org/10.1016/j.plaphy.2011.05.002] [PMID: 21684754]
[18]
Santoro N, Johansson N, Thiele DJ. Heat shock element architecture is an important determinant in the temperature and transactivation domain requirements for heat shock transcription factor. Mol Cell Biol 1998; 18(11): 6340-52.
[http://dx.doi.org/10.1128/MCB.18.11.6340] [PMID: 9774650]
[19]
Haralampidis K, Milioni D, Rigas S, Hatzopoulos P. Combinatorial interaction of cis elements specifies the expression of the Arabidopsis AtHsp90-1 gene. Plant Physiol 2002; 129(3): 1138-49.
[http://dx.doi.org/10.1104/pp.004044] [PMID: 12114568]
[20]
Siderius MH, Mager WH. General stress response: In search of a common denominator. In: Hohmann S, Mager WH, Eds. . Yeast stress and responses. Austin, Texas, Mol Biol Intelligence Units, RG., Landes Company. 1997; pp. 213-30.
[21]
Xiao H, Lis JT. Germline transformation used to define key features of heat-shock response elements. Science 1988; 239(4844): 1139-42.
[http://dx.doi.org/10.1126/science.3125608] [PMID: 3125608]
[22]
Yabe N, Takahashi T, Komeda Y. Analysis of tissue-specific expression of Arabidopsis thaliana HSP90-family gene HSP81. Plant Cell Physiol 1994; 35(8): 1207-19.
[http://dx.doi.org/10.1093/oxfordjournals.pcp.a078715] [PMID: 7697294]
[23]
Marrs K, Sinibaldi R. Deletion analysis of the maize hsp82, hsp81, and hsp17. 9 promoters in maize and transgenic tobacco: contributions of individual heat shock elements and recognition by distinct protein factors during both heat shock and development. Maydica 1997; 42(2): 211-26.
[24]
Rieping M, SchAffl F. Synergistic effect of upstream sequences, CCAAT box elements, and HSE sequences for enhanced expression of chimaeric heat shock genes in transgenic tobacco. Mol Gen Genet 1992; 231(2): 226-32.
[http://dx.doi.org/10.1007/BF00279795] [PMID: 1736093]
[25]
Chinn AM, Comai L. The heat shock cognate 80 gene of tomato is flanked by matrix attachment regions. Plant Mol Biol 1996; 32(5): 959-68.
[http://dx.doi.org/10.1007/BF00020492] [PMID: 8980546]
[26]
Bailey TL, Williams N, Misleh C, Li WW. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 2006; 34(Suppl. 2): W369-73.
[http://dx.doi.org/10.1093/nar/gkl198] [PMID: 16845028]
[27]
Sharov AA, Ko MS. Exhaustive search for over-represented DNA sequence motifs with CisFinder. DNA Res 2009; 16(5): 261-73.
[http://dx.doi.org/10.1093/dnares/dsp014] [PMID: 19740934]
[28]
Fu Y, Frith MC, Haverty PM, Weng Z. MotifViz: an analysis and visualization tool for motif discovery. Nucleic Acids Res 2004; 32(Suppl. 2): W420-3.
[http://dx.doi.org/10.1093/nar/gkh426] [PMID: 15215422]
[29]
Klepper K, Drabløs F. MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis. BMC Bioinformatics 2013; 14(1): 9.
[http://dx.doi.org/10.1186/1471-2105-14-9] [PMID: 23323883]
[30]
MacIsaac KD, Fraenkel E. Practical strategies for discovering regulatory DNA sequence motifs. PLOS Comput Biol 2006; 2(4) e36
[http://dx.doi.org/10.1371/journal.pcbi.0020036] [PMID: 16683017]
[31]
Tran NTL, Huang C-H. A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data. Biol Direct 2014; 9(1): 4.
[http://dx.doi.org/10.1186/1745-6150-9-4] [PMID: 24555784]
[32]
Mahony S, Benos PV. STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 2007; 35(Suppl. 2): W253-8.
[http://dx.doi.org/10.1093/nar/gkm272] [PMID: 17478497]
[33]
Hertz GZ, Stormo GD. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999; 15(7-8): 563-77.
[http://dx.doi.org/10.1093/bioinformatics/15.7.563] [PMID: 10487864]
[34]
Thompson K. Programming techniques: regular expression search algorithm. Commun ACM 1968; 11(6): 419-22.
[http://dx.doi.org/10.1145/363347.363387]
[35]
PrliŽØ A, Yates A, Bliven SE, et al. BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics 2012; 28(20): 2693-5.
[http://dx.doi.org/10.1093/bioinformatics/bts494] [PMID: 22877863]
[36]
Osteryoung KW, Sundberg H, Vierling E. Poly(A) tail length of a heat shock protein RNA is increased by severe heat stress, but intron splicing is unaffected. Mol Gen Genet 1993; 239(3): 323-33.
[http://dx.doi.org/10.1007/BF00276930] [PMID: 8391109]
[37]
Okumura T, Makiguchi H, Makita Y, Yamashita R, Nakai K. Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. Nucleic Acids Res 2007; 35(Suppl. 2): W227-31.
[http://dx.doi.org/10.1093/nar/gkm362] [PMID: 17537821]
[38]
Rombauts S, Déhais P, Van Montagu M, Rouzé P. PlantCARE, a plant cis-acting regulatory element database. Nucleic Acids Res 1999; 27(1): 295-6.
[http://dx.doi.org/10.1093/nar/27.1.295] [PMID: 9847207]
[39]
van Helden J. Regulatory sequence analysis tools. Nucleic Acids Res 2003; 31(13): 3593-6.

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy