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Protein & Peptide Letters

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ISSN (Print): 0929-8665
ISSN (Online): 1875-5305

Research Article

Phosphorylation Regulation of a Histone-like HU Protein from Deinococcus radiodurans

Author(s): Jinfeng Hou, Jingli Dai, Zijing Chen, Yudong Wang, Jiajia Cao, Jing Hu, Shumai Ye, Yuejin Hua and Ye Zhao*

Volume 29, Issue 10, 2022

Published on: 07 October, 2022

Page: [891 - 899] Pages: 9

DOI: 10.2174/0929866529666220819121911

open access plus

Abstract

Background: Histone-like proteins are small molecular weight DNA-binding proteins that are widely distributed in prokaryotes. These proteins have multiple functions in cellular structures and processes, including the morphological stability of the nucleoid, DNA compactness, DNA replication, and DNA repair. Deinococcus radiodurans, an extremophilic microorganism, has extraordinary DNA repair capability and encodes an essential histone-like protein, DrHU.

Objective: We aim to investigate the phosphorylation regulation role of a histone-like HU protein from Deinococcus radiodurans.

Methods: LC-MS/MS analysis was used to determine the phosphorylation site of endogenous DrHU. The predicted structure of DrHU-DNA was obtained from homology modeling (Swissmodel) using Staphylococcus aureus HU-DNA structure (PDB ID: 4QJU) as the starting model. Two types of mutant proteins T37E and T37A were generated to explore their DNA binding affinity. Complemented-knockout strategy was used to generate the ΔDrHU/pk-T37A and ΔDrHU/pk-T37E strains for growth curves and phenotypical analyses.

Results and Discussion: The phosphorylation site Thr37, which is present in most bacterial HU proteins, is located at the putative protein-DNA interaction interface of DrHU. Compared to the wild-type protein, one in which this threonine is replaced by glutamate to mimic a permanent state of phosphorylation (T37E) showed enhanced double-stranded DNA binding but a weakened protective effect against hydroxyl radical cleavage. Complementation of T37E in a DrHU-knockout strain caused growth defects and sensitized the cells to UV radiation and oxidative stress.

Conclusions: Phosphorylation modulates the DNA-binding capabilities of the histone-like HU protein from D. radiodurans, which contributes to the environmental adaptation of this organism.

Keywords: Nucleoid-association protein, histone-like protein, deinococcus, phosphorylation, DNA binding, DrHU.

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[1]
Carabetta, V.J. Addressing the possibility of a histone-like code in bacteria. J. Proteome Res., 2021, 20(1), 27-37.
[http://dx.doi.org/10.1021/acs.jproteome.0c00442] [PMID: 32962352]
[2]
Stojkova, P.; Spidlova, P.; Stulik, J. Nucleoid-associated protein HU: A lilliputian in gene regulation of bacterial virulence. Front. Cell. Infect. Microbiol., 2019, 9, 159.
[http://dx.doi.org/10.3389/fcimb.2019.00159] [PMID: 31134164]
[3]
Grove, A. Functional evolution of bacterial histone-like HU proteins. Curr. Issues Mol. Biol., 2011, 13(1), 1-12.
[PMID: 20484776]
[4]
Ferrándiz, M.J.; Carreño, D.; Ayora, S.; de la Campa, A.G. HU of streptococcus pneumoniae is essential for the preservation of DNA supercoiling. Front. Microbiol., 2018, 9, 493.
[http://dx.doi.org/10.3389/fmicb.2018.00493] [PMID: 29662473]
[5]
Li, S.; Waters, R. Escherichia coli strains lacking protein HU are UV sensitive due to a role for HU in homologous recombination. J. Bacteriol., 1998, 180(15), 3750-3756.
[http://dx.doi.org/10.1128/JB.180.15.3750-3756.1998] [PMID: 9683467]
[6]
Conforte, V.P.; Malamud, F.; Yaryura, P.M.; Toum Terrones, L.; Torres, P.S.; De Pino, V.; Chazarreta, C.N.; Gudesblat, G.E.; Castagnaro, A.P.; Marano, R. M.; Vojnov, A.A. The histone-like protein HupB influences biofilm formation and virulence in Xanthomonas citri ssp. citri through the regulation of flagellar biosynthesis. Mol. Plant Pathol., 2019, 20(4), 589-598.
[http://dx.doi.org/10.1111/mpp.12777] [PMID: 30537413]
[7]
Oberto, J.; Nabti, S.; Jooste, V.; Mignot, H.; Rouviere-Yaniv, J. The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction. PLoS One, 2009, 4(2), e4367.
[http://dx.doi.org/10.1371/journal.pone.0004367] [PMID: 19194530]
[8]
Mangan, M.W.; Lucchini, S.; Ó Cróinín, T.; Fitzgerald, S.; Hinton, J.C.D.; Dorman, C.J. Nucleoid-associated protein Hu controls three regulons that coordinate virulence, response to stress and general physiology in Salmonella enterica serovar typhimurium. Microbiology (Reading); , 2011, pp. 1075-1087.
[http://dx.doi.org/10.1099/mic.0.046359-0]
[9]
Stojkova, P.; Spidlova, P.; Lenco, J.; Rehulkova, H.; Kratka, L.; Stulik, J. HU protein is involved in intracellular growth and full virulence of Francisella tularensis. Virulence, 2018, 9(1), 754-770.
[http://dx.doi.org/10.1080/21505594.2018.1441588] [PMID: 29473442]
[10]
Dorman, C.J.; Deighan, P. Regulation of gene expression by histone-like proteins in bacteria. Curr. Opin. Genet. Dev., 2003, 13(2), 179-184.
[http://dx.doi.org/10.1016/S0959-437X(03)00025-X] [PMID: 12672495]
[11]
Preobrajenskaya, O.; Boullard, A.; Boubrik, F.; Schnarr, M.; Rouvière-Yaniv, J. The protein HU can displace the LexA repressor from its DNA-binding sites. Mol. Microbiol., 1994, 13(3), 459-467.
[http://dx.doi.org/10.1111/j.1365-2958.1994.tb00440.x] [PMID: 7997162]
[12]
Kamashev, D.; Rouviere-Yaniv, J. The histone-like protein HU binds specifically to DNA recombination and repair intermediates. EMBO J., 2000, 19(23), 6527-6535.
[http://dx.doi.org/10.1093/emboj/19.23.6527] [PMID: 11101525]
[13]
Mukherjee, A.; Sokunbi, A.O.; Grove, A. DNA protection by histone-like protein HU from the Hyperthermophilic Eubacterium thermotoga maritima. Nucleic Acids Res., 2008, 36(12), 3956-3968.
[http://dx.doi.org/10.1093/nar/gkn348] [PMID: 18515342]
[14]
Mukherjee, A.; Bhattacharyya, G.; Grove, A. The C-terminal domain of HU-related histone-like protein Hlp from Mycobacterium smegmatis mediates DNA end-joining. Biochemistry, 2008, 47(33), 8744-8753.
[http://dx.doi.org/10.1021/bi800010s] [PMID: 18656956]
[15]
Hołówka, J.; Trojanowski, D.; Ginda, K.; Wojtaś, B.; Gielniewski, B.; Jakimowicz, D.; Zakrzewska-Czerwińska, J. HupB is a bacterial nucleoid-associated protein with an indispensable eukaryotic-like tail. MBio, 2017, 8(6), e01272-e17.
[http://dx.doi.org/10.1128/mBio.01272-17] [PMID: 29114022]
[16]
Ghosh, S.; Padmanabhan, B.; Anand, C.; Nagaraja, V. Lysine acetylation of the mycobacterium tuberculosis HU protein modulates its DNA binding and genome organization. Mol. Microbiol., 2016, 100(4), 577-588.
[http://dx.doi.org/10.1111/mmi.13339] [PMID: 26817737]
[17]
Kim, D.H. Im, H.; Jee, J. G.; Jang, S. B.; Yoon, H. J.; Kwon, A. R.; Kang, S. M.; Lee, B. J. B-arm flexibility of Hu from Staphylococcus aureus dictates the DNA-binding and recognition mechanism., Acta. Crystallogr. D Biol. Crystallogr., 2014, 12(2014), 3273-3289.
[18]
Rice, P.A.; Yang, S.; Mizuuchi, K.; Nash, H.A. Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn. Cell, 1996, 87(7), 1295-1306.
[http://dx.doi.org/10.1016/S0092-8674(00)81824-3] [PMID: 8980235]
[19]
Swinger, K.K.; Lemberg, K.M.; Zhang, Y.; Rice, P.A. Flexible DNA bending in HU-DNA cocrystal structures. EMBO J., 2003, 22(14), 3749-3760.
[http://dx.doi.org/10.1093/emboj/cdg351] [PMID: 12853489]
[20]
Guo, F.; Adhya, S. Spiral structure of Escherichia coli HUalphabeta provides foundation for DNA supercoiling. Proc. Natl. Acad. Sci. USA, 2007, 104(11), 4309-4314.
[http://dx.doi.org/10.1073/pnas.0611686104] [PMID: 17360520]
[21]
Grove, A.; Saavedra, T.C. The role of surface-exposed lysines in wrapping DNA about the bacterial histone-like protein HU. Biochemistry, 2002, 41(24), 7597-7603.
[http://dx.doi.org/10.1021/bi016095e] [PMID: 12056890]
[22]
Bhowmick, T.; Ghosh, S.; Dixit, K.; Ganesan, V.; Ramagopal, U.A.; Dey, D.; Sarma, S.P.; Ramakumar, S.; Nagaraja, V. Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with structure-based inhibitors. Nat. Commun., 2014, 5(1), 4124.
[http://dx.doi.org/10.1038/ncomms5124] [PMID: 24916461]
[23]
Saitoh, F.; Kawamura, S.; Yamasaki, N.; Tanaka, I.; Kimura, M. Arginine-55 in the beta-arm is essential for the activity of DNA-binding protein HU from Bacillus stearothermophilus. Biosci. Biotechnol. Biochem., 1999, 63(12), 2232-2235.
[http://dx.doi.org/10.1271/bbb.63.2232] [PMID: 10664859]
[24]
Chen, Z.; Tang, Y.; Hua, Y.; Zhao, Y. Structural features and functional implications of proteins enabling the robustness of Deinococcus radiodurans. Comput. Struct. Biotechnol. J., 2020, 18, 2810-2817.
[http://dx.doi.org/10.1016/j.csbj.2020.09.036] [PMID: 33133422]
[25]
Lim, S.; Jung, J.H.; Blanchard, L.; de Groot, A. Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species. FEMS Microbiol. Rev., 2019, 43(1), 19-52.
[http://dx.doi.org/10.1093/femsre/fuy037] [PMID: 30339218]
[26]
Daly, M.J. A new perspective on radiation resistance based on Deinococcus radiodurans. Nat. Rev. Microbiol., 2009, 7(3), 237-245.
[http://dx.doi.org/10.1038/nrmicro2073] [PMID: 19172147]
[27]
Bouthier de la Tour, C.; Blanchard, L.; Dulermo, R.; Ludanyi, M.; Devigne, A.; Armengaud, J.; Sommer, S.; de Groot, A. The abundant and essential HU proteins in Deinococcus deserti and Deinococcus radiodurans are translated from leaderless mRNA. Microbiology, 2015, 161(12), 2410-2422.
[http://dx.doi.org/10.1099/mic.0.000186] [PMID: 26385459]
[28]
Nguyen, H.H.; de la Tour, C.B.; Toueille, M.; Vannier, F.; Sommer, S.; Servant, P. The essential histone-like protein HU plays a major role in Deinococcus radiodurans nucleoid compaction. Mol. Microbiol., 2009, 73(2), 240-252.
[http://dx.doi.org/10.1111/j.1365-2958.2009.06766.x] [PMID: 19570109]
[29]
Ghosh, S.; Grove, A. The Deinococcus radiodurans-encoded HU protein has two DNA-binding domains. Biochemistry, 2006, 45(6), 1723-1733.
[http://dx.doi.org/10.1021/bi0514010] [PMID: 16460019]
[30]
Ghosh, S.; Grove, A. Histone-like protein HU from Deinococcus radiodurans binds preferentially to four-way DNA junctions. J. Mol. Biol., 2004, 337(3), 561-571.
[http://dx.doi.org/10.1016/j.jmb.2004.02.010] [PMID: 15019777]
[31]
Chen, S.W.; Banneville, A.S.; Teulon, J.M.; Timmins, J.; Pellequer, J.L. Nanoscale surface structures of DNA bound to Deinococcus radiodurans HU unveiled by atomic force microscopy. Nanoscale, 2020, 12(44), 22628-22638.
[http://dx.doi.org/10.1039/D0NR05320A] [PMID: 33150905]
[32]
Taylor, B.C.; Young, N.L. Combinations of histone post-translational modifications. Biochem. J., 2021, 478(3), 511-532.
[http://dx.doi.org/10.1042/BCJ20200170] [PMID: 33567070]
[33]
Zhou, C.; Dai, J.; Lu, H.; Chen, Z.; Guo, M.; He, Y.; Gao, K.; Ge, T.; Jin, J.; Wang, L.; Tian, B.; Hua, Y.; Zhao, Y. Succinylome analysis reveals the involvement of lysine succinylation in the extreme resistance of Deinococcus radiodurans. Proteomics, 2019, 19(20), e1900158.
[http://dx.doi.org/10.1002/pmic.201900158] [PMID: 31487437]
[34]
Rajpurohit, Y.S.; Bihani, S.C.; Waldor, M.K.; Misra, H.S. Phosphorylation of Deinococcus radiodurans RecA regulates its activity and may contribute to radioresistance. J. Biol. Chem., 2016, 291(32), 16672-16685.
[http://dx.doi.org/10.1074/jbc.M116.736389] [PMID: 27255712]
[35]
Gupta, M.; Sajid, A.; Sharma, K.; Ghosh, S.; Arora, G.; Singh, R.; Nagaraja, V.; Tandon, V.; Singh, Y. HupB, a nucleoid-associated protein of Mycobacterium tuberculosis, is modified by serine/threonine protein kinases in vivo. J. Bacteriol., 2014, 196(14), 2646-2657.
[http://dx.doi.org/10.1128/JB.01625-14] [PMID: 24816602]
[36]
Dai, J.; Gao, K.; Yao, T.; Lu, H.; Zhou, C.; Guo, M.; Dai, S.; Wang, L.; Xu, H.; Tian, B.; Hua, Y.; Zhao, Y. Late embryogenesis abundant group3 protein (DrLEA3) is involved in antioxidation in the extremophilic bacterium Deinococcus radiodurans. Microbiol. Res., 2020, 240, 126559.
[http://dx.doi.org/10.1016/j.micres.2020.126559] [PMID: 32721821]
[37]
Zhao, Y.; Lu, M.; Zhang, H.; Hu, J.; Zhou, C.; Xu, Q.; Ul Hussain Shah, A.M.; Xu, H.; Wang, L.; Hua, Y. Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J. Nucleic Acids Res., 2015, 43(11), 5550-5559.
[http://dx.doi.org/10.1093/nar/gkv444] [PMID: 25940620]
[38]
Wang, G.; Maier, R.J. Bacterial histone-like proteins: Roles in stress resistance. Curr. Genet., 2015, 61(4), 489-492.
[http://dx.doi.org/10.1007/s00294-015-0478-x] [PMID: 25677732]
[39]
Sakatos, A.; Babunovic, G.H.; Chase, M.R.; Dills, A.; Leszyk, J.; Rosebrock, T.; Bryson, B.; Fortune, S.M. Posttranslational modification of a histone-like protein regulates phenotypic resistance to isoniazid in mycobacteria. Sci. Adv., 2018, 4(5), eaao1478.
[http://dx.doi.org/10.1126/sciadv.aao1478] [PMID: 29732401]
[40]
Floc’h, K.; Lacroix, F.; Servant, P.; Wong, Y.S.; Kleman, J.P.; Bourgeois, D.; Timmins, J. Cell morphology and nucleoid dynamics in dividing Deinococcus radiodurans. Nat. Commun., 2019, 10(1), 3815.
[http://dx.doi.org/10.1038/s41467-019-11725-5] [PMID: 31444361]
[41]
Lo, W.S.; Trievel, R.C.; Rojas, J.R.; Duggan, L.; Hsu, J.Y.; Allis, C.D.; Marmorstein, R.; Berger, S.L. Phosphorylation of serine 10 in histone H3 is functionally linked in vitro and in vivo to Gcn5-mediated acetylation at lysine 14. Mol. Cell, 2000, 5(6), 917-926.
[http://dx.doi.org/10.1016/S1097-2765(00)80257-9] [PMID: 10911986]
[42]
Manning, L.R.; Manning, J.M. Contributions to nucleosome dynamics in chromatin from interactive propagation of phosphorylation/acetylation and inducible histone lysine basicities. Protein Sci., 2018, 27(3), 662-671.
[http://dx.doi.org/10.1002/pro.3359] [PMID: 29226473]
[43]
Chen, C.; Ghosh, S.; Grove, A. Substrate specificity of helicobacter pylori histone-like Hu protein is determined by insufficient stabilization of DNA flexure points. Biochem J 383, 2004, 2(2004), 343-351.
[http://dx.doi.org/10.1042/BJ20040938]
[44]
Kamau, E.; Tsihlis, N.D.; Simmons, L.A.; Grove, A. Surface salt bridges modulate the DNA site size of bacterial histone-like hu proteins. Biochem. J., 2005, 390(1), 49-55.
[http://dx.doi.org/10.1042/BJ20050274]
[45]
Ryan, V.T.; Grimwade, J.E.; Nievera, C.J.; Leonard, A.C. IHF and HU stimulate assembly of pre-replication complexes at Escherichia coli oriC by two different mechanisms. Mol. Microbiol., 2002, 46(1), 113-124.
[http://dx.doi.org/10.1046/j.1365-2958.2002.03129.x] [PMID: 12366835]

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