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Thermotoga maritima oriC involves a DNA unwinding element with distinct modules and a DnaA-oligomerizing region with a novel directional binding mode

Lu, Chuyuan Yoshida, Ryusei 吉田, 竜星 ヨシダ, リュウセイ Katayama, Tsutomu 片山, 勉 カタヤマ, ツトム Ozaki, Shogo 尾﨑, 省吾 オザキ, ショウゴ 九州大学

2023.07

概要

Initiation of chromosomal replication requires dynamic nucleoprotein complexes. In most eubacteria, the origin oriC contains multiple DnaA box sequences to which the ubiquitous DnaA initiators bind. I

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参考文献

1. Katayama, T., Kasho, K., and Kawakami, H. (2017) The DnaA Cycle in

Escherichia coli: activation, function and inactivation of the initiator

protein. Front. Microbiol. 8, 2496

2. Grimwade, J. E., and Leonard, A. C. (2021) Blocking, bending, and

binding: regulation of initiation of chromosome replication during the

Escherichia coli cell cycle by transcriptional modulators that interact with

origin DNA. Front. Microbiol. 12, 732270

3. Wola

nski, M., Donczew, R., Zawilak-Pawlik, A., and Zakrzewska-Czerwi

nska, J. (2015) oriC-encoded instructions for the initiation of bacterial

chromosome replication. Front. Microbiol. 5, 735

4. Costa, A., Hood, I. V., and Berger, J. M. (2013) Mechanisms for initiating

cellular DNA replication. Annu. Rev. Biochem. 82, 25–54

5. Kaguni, J. M. (2011) Replication initiation at the Escherichia coli chromosomal origin. Curr. Opin. Chem. Biol. 15, 606–613

Unwinding and DnaA oligomerization in T. maritima oriC

6. Ozaki, S. (2019) Regulation of replication initiation: lessons from Caulobacter crescentus. Genes Genet. Syst. 94, 183–196

7. Sakiyama, Y., Nagata, M., Yoshida, R., Kasho, K., Ozaki, S., and Katayama,

T. (2022) Concerted actions of DnaA complexes with DNA-unwinding

sequences within and flanking replication origin oriC promote DnaB

helicase loading. J. Biol. Chem. 298, 102051

8. Shimizu, M., Noguchi, Y., Sakiyama, Y., Kawakami, H., Katayama, T., and

Takada, S. (2016) Near-atomic structural model for bacterial DNA

replication initiation complex and its functional insights. Proc. Natl. Acad.

Sci. U.S.A. 113, E8021–E8030

9. Ozaki, S., and Katayama, T. (2012) Highly organized DnaA-oriC complexes recruit the single-stranded DNA for replication initiation. Nucl.

Acids Res. 40, 1648–1665

10. Felczak, M. M., and Kaguni, J. M. (2004) The box VII motif of Escherichia

coli DnaA protein is required for DnaA oligomerization at the E. coli

replication origin. J. Biol. Chem. 279, 51156–51162

11. Hayashi, C., Miyazaki, E., Ozaki, S., Abe, Y., and Katayama, T. (2020)

DnaB helicase is recruited to the replication initiation complex via

binding of DnaA domain I to the lateral surface of the DnaB N-terminal

domain. J. Biol. Chem. 295, 1131–1143

12. Ozaki, S., and Katayama, T. (2009) DnaA structure, function, and dynamics in the initiation at the chromosomal origin. Plasmid 62, 71–82

13. Erzberger, J. P., Mott, M. L., and Berger, J. M. (2006) Structural basis for

ATP-dependent DnaA assembly and replication-origin remodeling. Nat.

Struct. Mol. Biol. 13, 676–683

14. Kawakami, H., Keyamura, K., and Katayama, T. (2005) Formation of an

ATP-DnaA-specific initiation complex requires DnaA arginine 285, a

conserved motif in the AAA+ protein family. J. Biol. Chem. 280,

27420–27430

15. Noguchi, Y., Sakiyama, Y., Kawakami, H., and Katayama, T. (2015) The

Arg fingers of key DnaA protomers are oriented inward within the

replication origin oriC and stimulate DnaA subcomplexes in the initiation

complex. J. Biol. Chem. 290, 20295–20312

16. Ozaki, S., Noguchi, Y., Hayashi, Y., Miyazaki, E., and Katayama, T.

(2012) Differentiation of the DnaA-oriC Subcomplex for DNA unwinding in a replication initiation complex. J. Biol. Chem. 287,

37458–37471

17. Ozaki, S., Kawakami, H., Nakamura, K., Fujikawa, N., Kagawa, W., Park,

S. Y., et al. (2008) A common mechanism for the ATP-DnaA-dependent

formation of open complexes at the replication origin. J. Biol. Chem. 283,

8351–8362

18. Fujikawa, N., Kurumizaka, H., Nureki, O., Terada, T., Shirouzu, M.,

Katayama, T., et al. (2003) Structural basis of replication origin recognition by the DnaA protein. Nucl. Acids Res. 31, 2077–2086

19. Sutton, M. D., Carr, K. M., Vicente, M., and Kaguni, J. M. (1998) Escherichia

coli DnaA protein. The N-terminal domain and loading of DnaB helicase at

the E. coli chromosomal origin. J. Biol. Chem. 273, 34255–34262

20. Simmons, L. A., Felczak, M., and Kaguni, J. M. (2003) DnaA Protein of

Escherichia coli: oligomerization at the E. coli chromosomal origin is

required for initiation and involves specific N-terminal amino acids. Mol.

Microbiol. 49, 849–858

21. Abe, Y., Jo, T., Matsuda, Y., Matsunaga, C., Katayama, T., and Ueda, T.

(2007) Structure and function of DnaA N-terminal domains: specific sites

and mechanisms in inter-DnaA interaction and in DnaB helicase loading

on oriC. J. Biol. Chem. 282, 17816–17827

22. Keyamura, K., Abe, Y., Higashi, M., Ueda, T., and Katayama, T. (2009)

DiaA dynamics are coupled with changes in initial origin complexes

leading to helicase loading. J. Biol. Chem. 284, 25038–25050

23. Felczak, M. M., Simmons, L. A., and Kaguni, J. M. (2005) An

essential tryptophan of Escherichia coli DnaA protein functions in

oligomerization at the E. coli replication origin. J. Biol. Chem. 280,

24627–24633

24. Nozaki, S., and Ogawa, T. (2008) Determination of the minimum domain

II size of Escherichia coli DnaA protein essential for cell viability.

Microbiology 154, 3379–3384

25. Schaper, S., and Messer, W. (1995) Interaction of the initiator protein

DnaA of Escherichia coli with its DNA target. J. Biol. Chem. 270,

17622–17626

26. Sakiyama, Y., Kasho, K., Noguchi, Y., Kawakami, H., and Katayama, T.

(2017) Regulatory dynamics in the ternary DnaA complex for initiation of

chromosomal replication in Escherichia coli. Nucleic Acids Res. 45,

12354–12373

27. Rozgaja, T. A., Grimwade, J. E., Iqbal, M., Czerwonka, C., Vora, M., and

Leonard, A. C. (2011) Two oppositely oriented arrays of low-affinity

recognition sites in oriC guide progressive binding of DnaA during

Escherichia coli pre-RC assembly. Mol. Microbiol. 82, 475–488

28. McGarry, K. C., Ryan, V. T., Grimwade, J. E., and Leonard, A. C. (2004)

Two discriminatory binding sites in the Escherichia coli replication origin

are required for DNA strand opening by initiator DnaA-ATP. Proc. Natl.

Acad. Sci. U. S. A. 101, 2811–2816

29. Kumar, S., Farhana, A., and Hasnain, S. E. (2009) In-vitro helix opening of

M. tuberculosis oriC by DnaA occurs at precise location and is inhibited

by IciA like protein. PLoS One 4, e4139

30. Pei, H., Liu, J., Li, J., Guo, A., Zhou, J., and Xiang, H. (2007) Mechanism

for the TtDnaA-Tt-oriC cooperative interaction at high temperature and

duplex opening at an unusual AT-rich region in Thermoanaerobacter

tengcongensis. Nucl. Acids Res. 35, 3087–3099

31. Jaworski, P., Donczew, R., Mielke, T., Weigel, C., Stingl, K., and ZawilakPawlik, A. (2018) Structure and function of the Campylobacter jejuni

chromosome replication origin. Front. Microbiol. 9, 1–18

32. Dong, M. J., Luo, H., and Gao, F. (2023) DoriC 12.0: an updated database

of replication origins in both complete and draft prokaryotic genomes.

Nucl. Acids Res. 51, D117–D120

33. Hwang, D. S., and Kornberg, A. (1992) Opposed actions of regulatory

proteins, DnaA and IciA, in opening the replication origin of Escherichia

coli. J. Biol. Chem. 267, 23087–23091

34. Richardson, T. T., Harran, O., and Murray, H. (2016) The bacterial

DnaA-Trio replication origin element specifies single-stranded DNA

initiator binding. Nature 534, 412–416

35. Jaworski, P., Zyla-uklejewicz, D., Nowaczyk-cieszewska, M., Donczew, R.,

Mielke, T., Weigel, C., et al. (2021) Putative cooperative ATP–DnaA

binding to double-stranded DnaA Box and single-stranded DnaA-Trio

motif upon Helicobacter pylori replication initiation complex assembly.

Int. J. Mol. Sci. 22, 6643

36. Richardson, T. T., Stevens, D., Pelliciari, S., Harran, O., Sperlea, T., and

Murray, H. (2019) Identification of a basal system for unwinding a bacterial chromosome origin. EMBO J. 38, e101649

37. Chatterjee, S., Jha, J. K., Ciaccia, P., Venkova, T., and Chattoraj, D. K.

(2020) Interactions of replication initiator RctB with single-and doublestranded DNA in origin opening of Vibrio cholerae chromosome 2. Nucl.

Acids Res. 48, 11016–11029

38. Zhaxybayeva, O., Swithers, K. S., Lapierre, P., Fournier, G. P., Bickhart, D.

M., DeBoy, R. T., et al. (2009) On the chimeric nature, thermophilic

origin, and phylogenetic placement of the Thermotogales. Proc. Natl.

Acad. Sci. U. S. A. 106, 5865–5870

39. Kuwabara, T., and Igarashi, K. (2020) Thermotogales origin scenario of

eukaryogenesis. J. Theor. Biol. 492, 110192

40. Ozaki, S., Fujimitsu, K., Kurumizaka, H., and Katayama, T. (2006) The

DnaA homolog of the hyperthermophilic eubacterium Thermotoga

maritima forms an open complex with a minimal 149-bp origin region in

an ATP-dependent manner. Genes Cells 11, 425–438

41. Lopez, P., Forterre, P., le Guyader, H., and Philippe, H. (2000) Origin of

replication of Thermotoga maritima. Trends Genet. 16, 59–60

42. Swinger, K. K., and Rice, P. A. (2004) IHF and HU: flexible architects of

bent DNA. Curr. Opin. Struct. Biol. 14, 28–35

43. Ryan, V. T., Grimwade, J. E., Nievera, C. J., and Leonard, A. C.

(2002) IHF and HU stimulate assembly of pre-replication complexes

at Escherichia coli oriC by two different mechanisms. Mol. Microbiol.

46, 113–124

44. Kamashev, D., Agapova, Y., Rastorguev, S., Talyzina, A. A., Boyko, K. M.,

Korzhenevskiy, D. A., et al. (2017) Comparison of histone-like HU protein DNA-binding properties and HU/IHF protein sequence alignment.

PLoS One 12, e0188037

45. Chodavarapu, S., Felczak, M. M., Yaniv, J. R., and Kaguni, J. M. (2008)

Escherichia coli DnaA interacts with HU in initiation at the E. coli

replication origin. Mol. Microbiol. 67, 781–792

J. Biol. Chem. (2023) 299(7) 104888

17

Unwinding and DnaA oligomerization in T. maritima oriC

46. Hwang, D. S., and Kornberg, A. (1992) Opening of the replication origin

of Escherichia coli by DnaA protein with protein HU or IHF. J. Biol.

Chem. 267, 23083–23086

47. Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O.,

et al. (2021) Highly accurate protein structure prediction with AlphaFold.

Nature 596, 583

48. Sugiyama, R., Kasho, K., Miyoshi, K., Ozaki, S., Kagawa, W., Kurumizaka,

H., et al. (2019) A novel mode of DnaA-DnaA interaction promotes ADP

dissociation for reactivation of replication initiation activity. Nucl. Acids

Res. 47, 11209–11224

49. Majka, J., Zakrzewska-Czerwiñska, J., and Messer, W. (2001) sequence

recognition, cooperative interaction, and dimerization of the initiator

protein DnaA of Streptomyces. J. Biol. Chem. 276, 6243–6252

50. Hizver, J., Rozenberg, H., Frolow, F., Rabinovich, D., and Shakked, Z.

(2001) DNA bending by an adenine - Thymine tract and its role in gene

regulation. Proc. Natl. Acad. Sci. U. S. A. 98, 8490–8495

51. Yoshida, R., Ozaki, S., Kawakami, H., and Katayama, T. (2023) Singlestranded DNA recruitment mechanism in replication origin unwinding

by DnaA initiator protein and HU, an evolutionary ubiquitous nucleoid

protein. Nucl. Acids Res. https://doi.org/10.1093/nar/gkad389

52. Young, R. T., Czapla, L., Wefers, Z. O., Cohen, B. M., and Olson, W. K.

(2022) Revisiting DNA sequence-dependent deformability in high-

18 J. Biol. Chem. (2023) 299(7) 104888

53.

54.

55.

56.

57.

resolution structures: effects of flanking base pairs on dinucleotide

morphology and global chain configuration. Life 12, 759

Mack, D. R., Chiu, T. K., and Dickerson, R. E. (2001) Intrinsic bending

and deformability at the T-A step of CCTTTAAAGG: a comparative

analysis of T-A and A-T steps within A-tracts. J. Mol. Biol. 312,

1037–1049

Balaceanu, A., Buitrago, D., Walther, J., Hospital, A., Dans, P. D.,

and Orozco, M. (2019) Modulation of the helical properties of DNA:

next-to-nearest neighbour effects and beyond. Nucl. Acids Res. 47,

4418–4430

Soman, A., Liew, C. W., Teo, H. L., Berezhnoy, N. v, Olieric, V.,

Korolev, N., et al. (2021) The human telomeric nucleosome displays

distinct structural and dynamic properties. Nucl. Acids Res. 48,

5383–5396

Miyoshi, K., Tatsumoto, Y., Ozaki, S., and Katayama, T. (2021) Negative

feedback for DARS2 –Fis complex by ATP–DnaA supports the cell cyclecoordinated regulation for chromosome replication. Nucleic Acids Res.

49, 12820–12835

Wegrzyn, K., Fuentes-Perez, M. E., Bury, K., Rajewska, M., MorenoHerrero, F., and Konieczny, I. (2014) Sequence-specific interactions of

Rep proteins with ssDNA in the AT-rich region of the plasmid replication

origin. Nucl. Acids Res. 42, 7807–7818

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