期刊论文详细信息
BMC Evolutionary Biology
Convergent evolution of heat-inducibility during subfunctionalization of the Hsp70 gene family
Thomas U Berendonk1  Martin Schlegel2  Sascha Krenek2 
[1] Institute of Hydrobiology, Technische Universität Dresden, Dresden, 01062, Germany;Molecular Evolution and Animal Systematics, University of Leipzig, Leipzig, 04103, Germany
关键词: Temperature stress;    RT-qPCR;    Paramecium;    Molecular chaperones;    Heat-shock proteins;    Heat-inducibility;    Gene duplication;    DnaK;    Convergent evolution;    Ciliate;   
Others  :  1129780
DOI  :  10.1186/1471-2148-13-49
 received in 2012-10-11, accepted in 2013-02-18,  发布年份 2013
PDF
【 摘 要 】

Background

Heat-shock proteins of the 70 kDa family (Hsp70s) are essential chaperones required for key cellular functions. In eukaryotes, four subfamilies can be distinguished according to their function and localisation in different cellular compartments: cytosol, endoplasmic reticulum, mitochondria and chloroplasts. Generally, multiple cytosol-type Hsp70s can be found in metazoans that show either constitutive expression and/or stress-inducibility, arguing for the evolution of different tasks and functions. Information about the hsp70 copy number and diversity in microbial eukaryotes is, however, scarce, and detailed knowledge about the differential gene expression in most protists is lacking. Therefore, we have characterised the Hsp70 gene family of Paramecium caudatum to gain insight into the evolution and differential heat stress response of the distinct family members in protists and to investigate the diversification of eukaryotic hsp70s focusing on the evolution of heat-inducibility.

Results

Eleven putative hsp70 genes could be detected in P. caudatum comprising homologs of three major Hsp70-subfamilies. Phylogenetic analyses revealed five evolutionarily distinct Hsp70-groups, each with a closer relationship to orthologous sequences of Paramecium tetraurelia than to another P. caudatum Hsp70-group. These highly diverse, paralogous groups resulted from duplications preceding Paramecium speciation, underwent divergent evolution and were subject to purifying selection. Heat-shock treatments were performed to test for differential expression patterns among the five Hsp70-groups as well as for a functional conservation within Paramecium. These treatments induced exceptionally high mRNA up-regulations in one cytosolic group with a low basal expression, indicative for the major heat inducible hsp70s. All other groups showed comparatively high basal expression levels and moderate heat-inducibility, signifying constitutively expressed genes. Comparative EST analyses for P. tetraurelia hsp70s unveiled a corresponding expression pattern, which supports a functionally conserved evolution of the Hsp70 gene family in Paramecium.

Conclusions

Our analyses suggest an independent evolution of the heat-inducible cytosol-type hsp70s in Paramecium and in its close relative Tetrahymena, as well as within higher eukaryotes. This result indicates convergent evolution during hsp70 subfunctionalization and implies that heat-inducibility evolved several times during the course of eukaryotic evolution.

【 授权许可】

   
2013 Krenek et al.; licensee BioMed Central Ltd.

【 预 览 】
附件列表
Files Size Format View
20150226111235555.pdf 708KB PDF download
Figure 4. 22KB Image download
Figure 3. 45KB Image download
Figure 2. 95KB Image download
Figure 1. 142KB Image download
【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】
  • [1]Schlesinger MJ, Ashburner M, Tissieres A: Heat shock, from bacteria to man. Cold Spring Harbour: Cold Spring Harbour Laboratory Press; 1982.
  • [2]Ritossa F: A new puffing pattern induced by temperature shock and DNP in Drosophila. Experientia 1962, 18(12):571-573.
  • [3]Boorstein WR, Craig EA: Transcriptional regulation of Ssa3, an Hsp70 gene from Saccharomyces cerevisiae. Mol Cell Biol 1990, 10(6):3262-3267.
  • [4]Mayer MP, Bukau B: Hsp70 chaperones: Cellular functions and molecular mechanism. Cell Mol Life Sci 2005, 62(6):670-684.
  • [5]Nover L: Heat shock response. Boca Raton, FL: CRC Press; 1991.
  • [6]Pirkkala L, Nykanen P, Sistonen L: Roles of the heat shock transcription factors in regulation of the heat shock response and beyond. FASEB J 2001, 15(7):1118-1131.
  • [7]Bukau B, Weissman J, Horwich A: Molecular chaperones and protein quality control. Cell 2006, 125(3):443-451.
  • [8]Daugaard M, Rohde M, Jaattela M: The heat shock protein 70 family: Highly homologous proteins with overlapping and distinct functions. FEBS Lett 2007, 581(19):3702-3710.
  • [9]Hartl FU: Molecular chaperones in cellular protein folding. Nature 1996, 381(6583):571-580.
  • [10]Borchiellini C, Boury-Esnault N, Vacelet J, Le Parco Y: Phylogenetic analysis of the Hsp70 sequences reveals the monophyly of metazoa and specific phylogenetic relationships between animals and fungi. Mol Biol Evol 1998, 15(6):647-655.
  • [11]Boorstein WR, Ziegelhoffer T, Craig EA: Molecular evolution of the Hsp70 multigene family. J Mol Evol 1994, 38(1):1-17.
  • [12]Gupta RS, Golding GB: Evolution of Hsp70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes. J Mol Evol 1993, 37(6):573-582.
  • [13]Gupta RS, Singh B: Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus. Curr Biol 1994, 4(12):1104-1114.
  • [14]Fraga J, Montalvo AM, De Doncker S, Dujardin JC, Van der Auwera G: Phylogeny of Leishmania species based on the heat-shock protein 70 gene. Infect Genet Evol 2010, 10(2):238-245.
  • [15]Simpson AGB, Gill EE, Callahan HA, Litaker RW, Roger AJ: Early evolution within kinetoplastids (Euglenozoa), and the late emergence of trypanosomatids. Protist 2004, 155(4):407-422.
  • [16]Budin K, Philippe H: New insights into the phylogeny of eukaryotes based on ciliate Hsp70 sequences. Mol Biol Evol 1998, 15(8):943-956.
  • [17]Hori M, Tomikawa I, Przybos E, Fujishima M: Comparison of the evolutionary distances among syngens and sibling species of Paramecium. Mol Phyl Evol 2006, 38(3):697-704.
  • [18]Gething MJ, Sambrook J: Protein folding in the cell. Nature 1992, 355(6355):33-45.
  • [19]Tavaria M, Gabriele T, Kola I, Anderson RL: A hitchhiker's guide to the human Hsp70 family. Cell Stress Chaperon 1996, 1(1):23-28.
  • [20]Nikolaidis N, Nei M: Concerted and nonconcerted evolution of the Hsp70 gene superfamily in two sibling species of nematodes. Mol Biol Evol 2004, 21(3):498-505.
  • [21]Bettencourt BR, Feder ME: Hsp70 duplication in the Drosophila melanogaster species group: How and when did two become five? Mol Biol Evol 2001, 18(7):1272-1282.
  • [22]Kudla G, Helwak A, Lipinski L: Gene conversion and GC-content evolution in mammalian Hsp70. Mol Biol Evol 2004, 21(7):1438-1444.
  • [23]Martin AP, Burg TM: Perils of paralogy: Using HSP70 genes for inferring organismal phylogenies. Syst Biol 2002, 51(4):570-587.
  • [24]Karlin S, Brocchieri L: Heat shock protein 70 family: Multiple sequence comparisons, function, and evolution. J Mol Evol 1998, 47(5):565-577.
  • [25]Becker J, Craig EA: Heat-shock proteins as molecular chaperones. Eur J Biochem 1994, 219(1–2):11-23.
  • [26]Feder ME, Hofmann GE: Heat-shock proteins, molecular chaperones, and the stress response: Evolutionary and ecological physiology. Annu Rev Physiol 1999, 61:243-282.
  • [27]Genevaux P, Georgopoulos C, Kelley WL: The Hsp70 chaperone machines of Escherichia coli: a paradigm for the repartition of chaperone functions. Mol Microbiol 2007, 66(4):840-857.
  • [28]Matsumoto R, Akama K, Rakwal R, Iwahashi H: The stress response against denatured proteins in the deletion of cytosolic chaperones SSA1/2 is different from heat-shock response in Saccharomyces cerevisiae. BMC Genomics 2005., 6
  • [29]Park HO, Craig EA: Positive and negative regulation of basal expression of a yeast HSP70 gene. Mol Cell Biol 1989, 9(5):2025-2033.
  • [30]Eisen JA, Coyne RS, Wu M, Wu DY, Thiagarajan M, Wortman JR, Badger JH, Ren QH, Amedeo P, Jones KM: Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol 2006, 4(9):1620-1642.
  • [31]Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Segurens B, Daubin V, Anthouard V, Aiach N: Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 2006, 444(7116):171-178.
  • [32]Feng LF, Chang Y, Yuan DX, Miao W: Expression analysis of 5 hsp70 genes in Tetrahymena thermophila [Article in Chinese]. Dongwuxue Yanjiu 2011, 32(3):267-276.
  • [33]Sigrist CJA, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P: PROSITE: A documented database using patterns and profiles as motif descriptors. Brief Bioinform 2002, 3(3):265-274.
  • [34]Dingwall C, Laskey RA: Nuclear targeting sequences - a consensus? Trends Biochem Sci 1991, 16(12):478-481.
  • [35]Rensing SA, Maier UG: Phylogenetic analysis of the stress-70 protein family. J Mol Evol 1994, 39(1):80-86.
  • [36]Blackburn EH, Karrer KM: Genomic reorganization in ciliated protozoans. Annu Rev Genet 1986, 20:501-521.
  • [37]Sung W, Tucker AE, Doak TG, Choi E, Thomas WK, Lynch M: Extraordinary genome stability in the ciliate Paramecium tetraurelia. Proc Natl Acad Sci USA 2012, 109(47):19339-19344.
  • [38]Arnaiz O, Cain S, Cohen J, Sperling L: ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res 2007, 35:D439-D444.
  • [39]Nei M, Gojobori T: Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986, 3(5):418-426.
  • [40]Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002, 3(7):research0034–-research0034.11.
  • [41]Santacruz H, Vriz S, Angelier N: Molecular characterization of a heat shock cognate cDNA of zebrafish, hsc70, and developmental expression of the corresponding transcripts. Dev Genet 1997, 21(3):223-233.
  • [42]Hill JK, Thomas CD, Huntley B: Climate and habitat availability determine 20th century changes in a butterfly's range margin. Proc R Soc Lond Ser B-Biol Sci 1999, 266(1425):1197-1206.
  • [43]Goldbaum O, Richter-Landsberg C: Stress proteins in oligodendrocytes: differential effects of heat shock and oxidative stress. J Neurochem 2001, 78(6):1233-1242.
  • [44]Fangue NA: Intraspecific variation in thermal tolerance and heat shock protein gene expression in common killifish, Fundulus heteroclitus. J Exp Biol 2006, 209(15):2859-2872.
  • [45]Yu T, Barchetta S, Pucciarelli S, La Terza A, Miceli C: A novel robust heat-inducible promoter for heterologous gene expression in Tetrahymena thermophila. Protist 2012, 163(2):284-295.
  • [46]Hori M, Fujishima M: The endosymbiotic bacterium Holospora obtusa enhances heat-shock gene expression of the host Paramecium caudatum. J Eukaryot Microbiol 2003, 50(4):293-298.
  • [47]Chang SC, Wooden SK, Nakaki T, Kim YK, Lin AY, Kung L, Attenello JW, Lee AS: Rat gene encoding the 78-kDa glucose-regulated protein Grp78 - Its regulatory sequences and the effect of protein glycosylation on its expression. Proc Natl Acad Sci USA 1987, 84(3):680-684.
  • [48]Tillman JB, Mote PL, Walford RL, Spindler SR: Structure and regulation of the mouse GRP78 (BiP) promoter by glucose and calcium ionophore. Gene 1995, 158(2):225-229.
  • [49]Schröder HC, Hassanein HMA, Lauenroth S, Koziol C, Mohamed T, Lacorn M, Steinhart H, Batel R, Müller WEG: Induction of DNA strand breaks and expression of HSP70 and GRP78 homolog by cadmium in the marine sponge Suberites domuncula. Arch Environ Contam Toxicol 1999, 36(1):47-55.
  • [50]Aoki T, Koike T, Nakano T, Shibahara K, Kondo S, Kikuchi H, Honjo T: Induction of Bip mRNA upon programmed cell death of differentiated PC12 cells as well as rat sympathetic neurons. J Biochem 1997, 121(1):122-127.
  • [51]Kozutsumi Y, Segal M, Normington K, Gething MJ, Sambrook J: The presence of malfolded proteins in the endoplasmic reticulum signals the induction of glucose-regulated proteins. Nature 1988, 332(6163):462-464.
  • [52]Hori M, Fujii K, Fujishima M: Micronucleus-specific bacterium Holospora elegans irreversibly enhances stress gene expression of the host Paramecium caudatum. J Eukaryot Microbiol 2008, 55(6):515-521.
  • [53]Craig EA, Gambill BD, Nelson RJ: Heat shock proteins: Molecular chaperones of protein biogenesis. Microbiol Rev 1993, 57(2):402-414.
  • [54]Okamoto K, Brinker A, Paschen SA, Moarefi I, Hayer-Hartl M, Neupert W, Brunner M: The protein import motor of mitochondria: a targeted molecular ratchet driving unfolding and translocation. EMBO J 2002, 21(14):3659-3671.
  • [55]Kabani M, Martineau CN: Multiple hsp70 isoforms in the eukaryotic cytosol: mere redundancy or functional specificity? Curr Genomics 2008, 9(5):338-248.
  • [56]Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Badger JH: Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biol 2011, 12(10):R100.
  • [57]Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM: Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol 2006, 4(9):e286.
  • [58]van Hoek MJ, Hogeweg P: Metabolic adaptation after whole genome duplication. Mol Biol Evol 2009, 26(11):2441-2453.
  • [59]Fokin S: Morphological and molecular investigations of Paramecium schewiakoffi sp. nov. (Ciliophora, Oligohymenophorea) and current status of distribution and taxonomy of Paramecium spp. Eur J Protistol 2004, 40(3):225-243.
  • [60]Parfrey LW, Lahr DJG, Knoll AH, Katz LA: Estimating the timing of early eukaryotic diversification with multigene molecular clocks. Proc Natl Acad Sci USA 2011, 108(33):13624-13629.
  • [61]Wright ADG, Lynn DH: Maximum ages of ciliate lineages estimated using a small subunit rRNA molecular clock: Crown eukaryotes date back to the paleoproterozoic. Arch Protistenkd 1997, 148(4):329-341.
  • [62]Sonneborn TM: Methods in Paramecium research. In Methods in Cell Physiology. Edited by Prescott DM. New York: Academic Press; 1970:241-339.
  • [63]Krenek S, Berendonk TU, Petzoldt T: Thermal performance curves of Paramecium caudatum: A model selection approach. Eur J Protistol 2011, 47(2):124-137.
  • [64]Bailey MJ, Lilley AK, Thompson IP, Rainey PB, Ellis RJ: Site directed chromosomal marking of a fluorescent pseudomonad isolated from the phytosphere of sugar beet; Stability and potential for marker gene transfer. Mol Ecol 1995, 4(6):755-763.
  • [65]Chomczynski P, Sacchi N: Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 1987, 162(1):156-159.
  • [66]Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28(10):2731-2739.
  • [67]Padidam M, Sawyer S, Fauquet CM: Possible emergence of new geminiviruses by frequent recombination. Virology 1999, 265(2):218-225.
  • [68]Sawyer SA: A computer package for the statistical detection of gene conversion. Louis: Distributed by the author, Department of Mathematics, Washington University in St; 2007. available at http://www.math.wustl.edu/ webcite~sawyer/geneconv/
  • [69]Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P: RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 2010, 26(19):2462-2463.
  • [70]Zdobnov EM, Apweiler R: InterProScan–an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17(9):847-848.
  • [71]Schneider TD, Stephens RM: Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 1990, 18(20):6097-6100.
  • [72]Roshan U, Livesay DR: Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics 2006, 22(22):2715-2721.
  • [73]Darriba D, Taboada GL, Doallo R, Posada D: ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 2011, 27(8):1164-1165.
  • [74]Le SQ, Gascuel O: An improved general amino acid replacement matrix. Mol Biol Evol 2008, 25(7):1307-1320.
  • [75]Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22(21):2688-2690.
  • [76]Stamatakis A, Hoover P, Rougemont J: A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 2008, 57(5):758-771.
  • [77]Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19(12):1572-1574.
  • [78]Miller MA, Pfeiffer W, Schwartz T: The CIPRES science gateway: a community resource for phylogenetic analyses. In Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery. Salt Lake City, Utah: ACM; 2011:1-8.
  • [79]Krenek S, Petzoldt T, Berendonk TU: Coping with temperature at the warm edge - Patterns of thermal adaptation in the microbial eukaryote Paramecium caudatum. PLoS One 2012, 7(3):e30598.
  • [80]Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, Lightfoot S, Menzel W, Granzow M, Ragg T: The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol 2006, 7:3.
  • [81]Pfaffl MW, Horgan GW, Dempfle L: Relative expression software tool (REST©) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 2002, 30(9):e36.
  • [82]Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999, 41:95-98.
  文献评价指标  
  下载次数:68次 浏览次数:34次