RNA-Seq-Based Comparative Transcriptome Analysis Highlights New Features of the Heat-Stress Response in the Extremophilic Bacterium Deinococcus radiodurans.
Xue, Dong; Liu, Wenzheng; Chen, Yunet al.
2019 • In International Journal of Molecular Sciences, 20 (22)
[en] Deinococcus radiodurans is best known for its extraordinary resistance to diverse environmental stress factors, such as ionizing radiation, ultraviolet (UV) irradiation, desiccation, oxidation, and high temperatures. The heat response of this bacterium is considered to be due to a classical, stress-induced regulatory system that is characterized by extensive transcriptional reprogramming. In this study, we investigated the key functional genes involved in heat stress that were expressed and accumulated in cells (R48) following heat treatment at 48 degrees C for 2 h. Considering that protein degradation is a time-consuming bioprocess, we predicted that to maintain cellular homeostasis, the expression of the key functional proteins would be significantly decreased in cells (RH) that had partly recovered from heat stress relative to their expression in cells (R30) grown under control conditions. Comparative transcriptomics identified 15 genes that were significantly downregulated in RH relative to R30, seven of which had previously been characterized to be heat shock proteins. Among these genes, three hypothetical genes (dr_0127, dr_1083, and dr_1325) are highly likely to be involved in response to heat stress. Survival analysis of mutant strains lacking DR_0127 (a DNA-binding protein), DR_1325 (an endopeptidase-like protein), and DR_1083 (a hypothetical protein) showed a reduction in heat tolerance compared to the wild-type strain. These results suggest that DR_0127, DR_1083, and DR_1325 might play roles in the heat stress response. Overall, the results of this study provide deeper insights into the transcriptional regulation of the heat response in D. radiodurans.
RNA-Seq-Based Comparative Transcriptome Analysis Highlights New Features of the Heat-Stress Response in the Extremophilic Bacterium Deinococcus radiodurans.
Publication date :
2019
Journal title :
International Journal of Molecular Sciences
ISSN :
1661-6596
eISSN :
1422-0067
Publisher :
Multidisciplinary Digital Publishing Institute (MDPI), Switzerland
Mattimore, V.; Battista, J.R. Radioresistance of Deinococcus radiodurans: Functions necessary to survive ionizing radiation are also necessary to survive prolonged desiccation. J. Bacteriol. 1996, 178, 633–637. [CrossRef] [PubMed]
Wang, P.; Schellhorn, H.E. Induction of resistance to hydrogen peroxide and radiation in Deinococcus radiodurans. Can. J. Microbiol. 1995, 41, 170–176. [CrossRef] [PubMed]
Bauermeister, A.; Moeller, R.; Reitz, G.; Sommer, S.; Rettberg, P. Effect of relative humidity on Deinococcus radiodurans’ resistance to prolonged desiccation, heat, ionizing, germicidal, and environmentally relevant UV radiation. Microb. Ecol. 2011, 61, 715–722. [CrossRef]
Slade, D.; Radman, M. Oxidative stress resistance in Deinococcus radiodurans. Microbiol. Mol. Biol. Rev. 2011, 75, 133–191. [CrossRef]
Blasius, M.; Sommer, S.; Hübscher, U. Deinococcus radiodurans: What belongs to the survival kit? Crit. Rev. Biochem. Mol. Biol. 2008, 43, 221–238. [CrossRef]
Harada, K.; Oda, S. Induction of thermotolerance by split-dose hyperthermia at 52◦C in Deinococcus radiodurans. Agric. Biol. Chem. 1988, 52, 2391–2396.
Schmid, A.K.; Lidstrom, M.E. Involvement of two putative alternative sigma factors in stress response of the radioresistant bacterium Deinococcus radiodurans. J. Bacteriol. 2002, 184, 6182–6189. [CrossRef]
Schmid, A.K.; Howell, H.A.; Battista, J.R.; Peterson, S.N.; Lidstrom, M.E. Global transcriptional and proteomic analysis of the Sig1 heat shock regulon of Deinococcus radiodurans. J. Bacteriol. 2005, 187, 3339–3351. [CrossRef]
Schmid, A.K.; Howell, H.A.; Battista, J.R.; Peterson, S.N.; Lidstrom, M.E. HspR is a global negative regulator of heat shock gene expression in Deinococcus radiodurans. Mol. Microbiol. 2005, 55, 1579–1590. [CrossRef] [PubMed]
Schmid, A.K.; Lipton, M.S.; Mottaz, H.; Monroe, M.E.; Smith, R.D.; Lidstrom, M.E. Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans. J. Proteome Res. 2005, 4, 709–718. [CrossRef] [PubMed]
Bauermeister, A.; Hahn, C.; Rettberg, P.; Reitz, G.; Moeller, R. Roles of DNA repair and membrane integrity in heat resistance of Deinococcus radiodurans. Arch. Microbiol. 2012, 194, 959–966. [CrossRef]
Bepperling, A.; Alte, F.; Kriehuber, T.; Braun, N.; Weinkauf, S.; Groll, M.; Haslbeck, M.; Buchner, J. Alternative bacterial two-component small heat shock protein systems. Proc. Natl. Acad. Sci. USA 2012, 109, 20407–20412. [CrossRef]
Meyer, L.; Coste, G.; Sommer, S.; Oberto, J.; Confalonieri, F.; Servant, P.; Pasternak, C. DdrI, a cAMP receptor protein family member, acts as a major regulator for adaptation of Deinococcus radiodurans to various stresses. J. Bacteriol. 2018, 13, e00129-18. [CrossRef]
Lesley, S.A.; Graziano, J.; Cho, C.Y.; Knuth, M.W.; Klock, H.E. Gene expression response to misfolded protein as a screen for soluble recombinant protein. Protein Eng. 2002, 15, 153–160. [CrossRef]
Lim, B.; Gross, C.A. Cellular response to heat shock and cold shock. In Bacterial Stress Responses; ASM Press: Washington, DC, USA, 2011; pp. 93–114.
Ventura, M.; Canchaya, C.; Zhang, Z.; Bernini, V.; Fitzgerald, G.F.; Van Sinderen, D. How high G+C Gram-positive bacteria and in particular bifidobacteria cope with heat stress: Protein players and regulators. FEMS Microbiol. Rev. 2006, 30, 734–759. [CrossRef]
Arsène, F.; Tomoyasu, T. The heat shock response of Escherichia coli. Int. J. Food 2000, 55, 3–9. [CrossRef]
Chastanet, A.; Fert, J.; Msadek, T. Comparative genomics reveal novel heat shock regulatory mechanisms in Staphylococcus aureus and other Gram-positive bacteria. Mol. Microbiol. 2003, 47, 1061–1073. [CrossRef]
Wick, L.M.; Egli, T. Molecular components of physiological stress responses in Escherichia coli. Adv. Biochem. Eng. Biotechnol. 2004, 89, 1–45. [PubMed]
Gunasekera, T.S.; Csonka, L.N.; Paliy, O. Genome-wide transcriptional responses of Escherichia coli K-12 to continuous osmotic and heat stresses. J. Bacteriol. 2008, 190, 3712–3720. [CrossRef] [PubMed]
Anderson, K.L.; Roberts, C.; Disz, T.; Vonstein, V.; Hwang, K.; Overbeek, R.; Olson, P.D.; Projan, S.J.; Dunman, P.M. Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover. J. Bacteriol. 2006, 188, 6739–6756. [CrossRef] [PubMed]
Ye, Y.; Zhang, L.; Hao, F.; Zhang, J.; Wang, Y.; Tang, H. Global metabolomic responses of Escherichia coli to heat stress. J. Proteome Res. 2012, 11, 2559–2566. [CrossRef] [PubMed]
Chowdhury Paul, S.; Jain, P.; Mitra, J.; Dutta, S.; Bhattacharya, P.; Bal, B.; Bhattacharyya, D.; Das Gupta, S.; Pal, S. Induction of Cr(VI) reduction activity in an Anoxybacillus strain under heat stress: A biochemical and proteomic study. FEMS Microbiol. Lett. 2012, 331, 70–80. [CrossRef] [PubMed]
Chan, K.-G.; Priya, K.; Chang, C.-Y.; Abdul Rahman, A.Y.; Tee, K.K.; Yin, W.-F. Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures. PeerJ 2016, 4, e2223. [CrossRef]
Gomide, A.C.P.; de Sá, P.G.; Cavalcante, A.L.Q.; de Jesus Sousa, T.; Gomes, L.G.R.; Ramos, R.T.J.; Azevedo, V.; Silva, A.; Folador, A.R.C. Heat shock stress: Profile of differential expression in Corynebacterium pseudotuberculosis biovar Equi. Gene 2018, 645, 124–130. [CrossRef]
Tsai, C.-H.; Liao, R.; Chou, B.; Contreras, L.M. Transcriptional analysis of Deinococcus radiodurans reveals novel small RNAs that are differentially expressed under ionizing radiation. Appl. Environ. Microbiol. 2015, 81, 1754–1764. [CrossRef]
Tanaka, M.; Earl, A.M.; Howell, H.A.; Park, M.J.; Eisen, J.A.; Peterson, S.N.; Battista, J.R. Analysis of Deinococcus radiodurans’s transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics 2004, 168, 21–33. [CrossRef]
Liu, Y.; Zhou, J.; Omelchenko, M.V.; Beliaev, A.S.; Venkateswaran, A.; Stair, J.; Wu, L.; Thompson, D.K.; Xu, D.; Rogozin, I.B.; et al. Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc. Natl. Acad. Sci. USA 2003, 100, 4191–4196. [CrossRef] [PubMed]
Wang, Z.; Gerstein, M.; Snyder, M. RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10, 57–63. [CrossRef] [PubMed]
López-Leal, G.; Tabche, M.L.; Castillo-Ramírez, S.; Mendoza-Vargas, A.; Ramírez-Romero, M.A.; Dávila, G. RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock. BMC Genom. 2014, 15, 770. [CrossRef] [PubMed]
Wang, J.; Chen, L.; Huang, S.; Liu, J.; Ren, X.; Tian, X.; Qiao, J.; Zhang, W. RNA-seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803. Biotechnol. Biofuels 2012, 5, 89. [CrossRef] [PubMed]
Lindquist, S. The heat-shock response. Annu. Rev. Biochem. 1986, 55, 1151–1191. [CrossRef] [PubMed]
Guyot, S.; Pottier, L.; Ferret, E.; Gal, L.; Gervais, P. Physiological responses of Escherichia coli exposed to different heat-stress kinetics. Arch. Microbiol. 2010, 8, 651–661. [CrossRef]
Bruhn-Olszewska, B.; Szczepaniak, P.; Matuszewska, E.; Kuczyńska-Wiśnik, D.; Stojowska-Swędrzyńska, K.; Moruno Algara, M.; Laskowska, E. Physiologically distinct subpopulations formed in Escherichia coli cultures in response to heat shock. Microbiol. Res. 2018, 209, 33–42. [CrossRef]
Baneyx, F.; Mujacic, M. Recombinant protein folding and misfolding in Escherichia coli. Nat. Biotechnol. 2004, 11, 1399. [CrossRef]
Parsell, D.A.; Lindquist, S. The function of heat-Shock proteins in stress tolerance: degradation and reactivation of damaged proteins. Annu. Rev. Genet. 1993, 1, 437–496. [CrossRef]
Schumann, W. Regulation of bacterial heat shock stimulons. Cell Stress Chaperones 2016, 21, 959–968. [CrossRef]
Kuroda, A.; Nomura, K.; Ohtomo, R.; Kato, J.; Ikeda, T.; Takiguchi, N.; Ohtake, H.; Kornberg, A. Role of inorganic polyphosphate in promoting ribosomal protein degradation by the Lon protease in E. coli. Science 2001, 293, 705–708. [CrossRef] [PubMed]
Servant, P.; Jolivet, E.; Bentchikou, E.; Mennecier, S.; Bailone, A.; Sommer, S. The ClpPX protease is required for radioresistance and regulates cell division after γ-irradiation in Deinococcus radiodurans. Mol. Microbiol. 2007, 66, 1231–1239. [CrossRef] [PubMed]
Matuszewska, M.; Kuczyńska-Wiśnik, D.; Laskowska, E.; Liberek, K. The small heat shock protein IbpA of Escherichia coli cooperates with IbpB in stabilization of thermally aggregated proteins in a disaggregation competent state. J. Biol. Chem. 2005, 280, 12292–12298. [CrossRef] [PubMed]
Kuczyńska-Wiśnik, D.; Kȩdzierska, S.; Matuszewska, E.; Lund, P.; Taylor, A.; Lipińska, B.; Laskowska, E. The Escherichia coli small heat-shock proteins IbpA and IbpB prevent the aggregation of endogenous proteins denatured in vivo during extreme heat shock. Microbiology 2002, 148, 1757–1765. [CrossRef] [PubMed]
Singh, H.; Appukuttan, D.; Lim, S. Hsp20, a small heat shock protein of Deinococcus radiodurans, confers tolerance to hydrogen peroxide in Escherichia coli. J. Microbiol. Biotechnol. 2014, 24, 1118–1122. [CrossRef]
Azam, T.A.; Ishihama, A. Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J. Biol. Chem. 1999, 274, 33105–33113. [CrossRef]
Browning, D.F.; Grainger, D.C.; Busby, S.J.W. Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression. Curr. Opin. Microbiol. 2010, 13, 773–780. [CrossRef]
Langmead, B.; Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012, 4, 357–359. [CrossRef]
Kim, D.; Pertea, G.; Trapnell, C.; Pimentel, H.; Kelley, R.; Salzberg, S.L. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013, 14, R36. [CrossRef]
Trapnell, C.; Roberts, A.; Goff, L.; Pertea, G.; Kim, D.; Kelley, D.R.; Pimentel, H.; Salzberg, S.L.; Rinn, J.L.; Pachter, L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 2012, 7, 562–578. [CrossRef] [PubMed]
Boyle, E.I.; Weng, S.; Gollub, J.; Jin, H.; Botstein, D.; Cherry, J.M.; Sherlock, G. GO::TermFinder—Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 2004, 20, 3710–3715. [CrossRef] [PubMed]
Sheng, D.; Gao, G.; Tian, B.; Xu, Z.; Zheng, Z.; Hua, Y. RecX is involved in antioxidant mechanisms of the radioresistant bacterium Deinococcus radiodurans. FEMS Microbiol. Lett. 2005, 244, 251–257. [CrossRef] [PubMed]