Sequence Characterization, Expression, and Evolutionary Analysis of Heat Shock Transcription Factors in Apple

doi:10.7668/hbnxb.2017.02.012

Abstract

Abstract: To extensively understand the sequence feature and evolution of heat shock transcription factors (Hsf)in the genome of apple,fifty MdHsf genes were identified using bioinformatics methods at the whole-genome level of apple,and a series of analysis including sequence characterization,phylogenetic relationship,gene expression and selective pressure of MdHsf genes were further performed.Phylogenetic relationship and sequence characterization analysis showed that,like the model species Arabidopsis and rice,50 MdHsf genes were divided into three subfamilies A,B and C.Additionally,at least two genes were found in the same end clades in the phylogenetic tree,indicating that the lineage-specific amplification had happened during evolutionary processes of apple Hsf gene family.Although the intron numbers and sizes of MdHsf genes were relatively divergent,the conserved motifs and domains of MdHsf proteins were highly conserved because of functional constraints.Based on EST data,72% of the 50 genes (except 14 genes such as MdHsfA2a and MdHsfA3a/b/c)had transcription activities.Selective pressure signatures demonstrated that no positive selection site was identified in the cleaned codon alignments for 36 MdHsf genes based on site-specific model,suggesting that this protein family was controlled by purifying selection.However,branch-site model had identified a total of five positively selected sites in the d and e clade of the phylogenetic tree,i.e.28R,30L,35D,51M and 67V.28R and 30L were included in the Hsf domains,while 35D,51M and 67V were not mapped on the region of Hsf domains,suggesting that purifying selection was the main evolutionary dynamics of functional conservation Hsf domains except for 28R and 30L.In conclusion,various Hsfs existed in apple genome,and the conserved motifs and functional domains were conserved.The majority of them had transcription activity,and the evolution of this family was dominated by purifying selection.

Key words: Apple, Heat shock transcription factors (Hsf), Expression, Evolution

CLC Number:

Q78
S661.03

ZHANG Guojun, WANG Tingting, HU Lizong, LI Shufen, GAO Wujun. Sequence Characterization, Expression, and Evolutionary Analysis of Heat Shock Transcription Factors in Apple[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2017, 32(2): 71-80. doi: 10.7668/hbnxb.2017.02.012.

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References

[1] Åkerfelt M, Morimoto R I, Sistonen L. Heat shock factors:integrators of cell stress, development and lifespan[J]. Nat Rev Mol Cell Bio, 2010, 11(8):545-555.
[2] Ohama N, Sato H, Shinozaki K, et al. Transcriptional regulatory network of plant heat stress response[J]. Trends Plant Sci, 2016, 22(1):53-65.
[3] Wiederrecht G,Seto D,Parker C S.Isolation of the gene encoding the S.cerevisiae heatshock transcription factor[J]. Cell,1988,54(6):841-853.
[4] Clos J,Westwood J T,Becker P B,et al.Molecular cloning and expression of a heaxameric drosophila heat stress factor subject to negative regulation[J].Cell,1990,63(5):1085-1097.
[5] Fujimoto M, Hayashida N, Katoh, et al. A novel mouse HSF3 has a potential to activate nonclassical heat-shock genes during heat shock[J]. Mol Biol Cell, 2010, 21(1):106-116.
[6] Rabindran S K,Giorgi G,Clos J,et al.Molecular cloning and expression of a human heat shock factor,HSF1[J].Proc Natl Acad Sci USA,1991,88(16):6906-6910.
[7] Scharf K D,Rose S,Zott W,et al.Three tomato genes code for heat stress transcription factors with a region of remarkable homology to the DNA-binding domain of the yeast HSF[J].EMBO J,1990,9(13):4495-4501.
[8] Hü bel A,Sch ffl F. Arabidopsis heat shock factor:isolation and characterization of the gene and the recombinant protein[J].Plant Mol Biol,1994,26(1):353-362.
[9] Yamanouchi U,Yano M,Lin H,et al.A rice spotted leaf gene, Spl7,encodes a heat stress transcription factor protein[J].Proc Natl Acad Sci USA,2002,99(11):7530-7535.
[10] Guo J,Wu J,Ji Q,et al.Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis[J].J Genetics Genomics,2008,35(2):105-118.
[11] Chauhan H,Khurana N,Agarwal P,et al.Heat shock factors in rice(Oryza sativa L.):genome-wide expression analysis during reproductive development and abiotic stress[J].Mol Genet Genomics,2011,286(2):171-187.
[12] Lin Y X,Jiang H Y,Chu Z X,et al.Genome-wide identification,classification and analysis of heat shock transcription factor family in maize[J].BMC Genomics,2011,12(1):76.
[13] Scharf K D,Berberich T,Ebersberger I,et al.The plant heat stress transcription factor(Hsf)family:structure,function and evolution[J].Biochimica et Biophysica Acta 2012,1819(2):104-119.
[14] Song X,Liu G,Duan W,et al.Genome-wide identification,classification and expression analysis of the heat shock transcription factor family in Chinese cabbage[J].Mol Genet Genomics,2014,289(4):541-551.
[15] Huang Y,Li M Y,Wang F,et al.Heat shock factors in carrot:genome-wide identification,classification,and expression profiles response to abiotic stress[J].Mol Biol Rep,2015,42(5):893-905.
[16] Liu Z W, Wu Z J, Li X H, et al. Identification, classification, and expression profiles of heat shock transcription factors in tea plant (Camellia sinensis) under temperature stress[J]. Gene, 2016, 576(1):52-59.
[17] Guo M, Liu J H, Ma X, et al. The plant heat stress transcription factors (HSFs):structure, regulation, and function in response to abiotic stresses[J]. Front Plant Sci, 2016, 7(273):114.
[18] Raxwal V. Structural and functional diversity of plant heat shock factors[J]. Plant Stress, 2012, 6:89-96.
[19] Velasco R,Zharkikh A,Affourtit J,et al.The genome of the domesticated apple(Malus domestica Borkh.)[J].Nature Genetics,2010,42(10):833-839.
[20] Giorno F,Guerriero G,Baric S,et al.Heat shock transcriptional factors in Malus domestica:identification,classification and expression analysis[J].BMC Genomics,2012,13(1):639.
[21] Edgar R C.MUSCLE:multiple sequence alignment with high accuracy and high throughput[J].Nucl Acids Res,2004,32(5):1792-1797.
[22] Tamura K, Stecher G, Peterson D, et al. MEGA6:Molecular evolutionary genetics analysis version 6.0[J]. Mol Biol Evol, 2013, 30(12):2725-2729.
[23] Thompson J D,Gibson T J,Plewniak F,et al.The CLUSTAL_X windows interface:flexible strategies for multiple sequence alignment aided by quality analysis tools[J].Nucleic Acids Res,1997,25(25):4876-4882.
[24] Castresana J.Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis[J].Mol Biol Evol,2000,17(4):540-552.
[25] Suyama M,Torrents D,Bork P.PAL2NAL:robust conversion of protein sequence alignments into the corresponding codon alignments[J].Nucleic Acids Res,2006,34:609-612.
[26] Page R D.TreeView:an application to display phylogenetic trees on personal computers[J].Comput Appl Biosci,1996,12(4):357-358.
[27] Yang Z.PAML4:phylogenetic analysis by maximum likelihood[J].Mol Biol Evol,2007,24(8):1586-1591.
[28] Arnold K,Bordoli L,Kopp J,et al.The SWISS-MODEL workspace:a web-based environment for protein structure homology modelling[J].Bioinformatics,2006,22(2):195-201.
[29] Yang Z,Wong W S,Nielsen R.Bayes empirical Bayes inference of amino acid sites under positive selection[J].Mol Biol Evol,2005,22(4):1107-1118.
[30] Zhang J,Nielsen R,Yang Z.Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level[J].Mol Biol Evol,2005,22(12):2472-2479.
[31] Wang F,Dong Q,Jiang H,et al.Genome-wide analysis of the heat shock transcription factors in Populus trichocarpa and Medicago truncatula[J].Mol Biol Rep,2012,39(2):1877-1886.
[32] Chung E,Kim K M,Lee J H.Genome-wide analysis and molecular characterization of heat shock transcription factor family in Glycine max[J].J Genet Genomics,2013,40(3):127-135.

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