Abe Y, Jo T, Matsuda Y, Matsunaga C, Katayama T & Ueda T (2007) Structure and
Function of DnaA N-terminal Domains. J. Biol. Chem. 282: 17816–17827
Balaceanu A, Buitrago D, Walther J, Hospital A, Dans PD & Orozco M (2019)
Modulation of the helical properties of DNA: next-to-nearest neighbour effects and
beyond. Nucleic Acids Res. 47: 4418–4430
Chatterjee S, Jha JK, Ciaccia P, Venkova T & Chattoraj DK (2020) Interactions of
replication initiator RctB with single- and double-stranded DNA in origin opening
of Vibrio cholerae chromosome 2. Nucleic Acids Res. 48: 11016–11029
Chodavarapu S, Felczak MM, Yaniv JR & Kaguni JM (2007) Escherichia coli DnaA
interacts with HU in initiation at the E. coli replication origin. Mol. Microbiol. 67:
781–792
Costa A, Hood I V. & Berger JM (2013) Mechanisms for Initiating Cellular DNA
Replication. Annu. Rev. Biochem. 82: 25–54
Dong M. J., Luo H & Gao F (2023) DoriC 12.0: an updated database of replication
origins in both complete and draft prokaryotic genomes. Nucleic Acids Res. 51:
D117–D120
Erzberger JP, Mott ML & Berger JM (2006) Structural basis for ATP-dependent DnaA
assembly and replication-origin remodeling. Nat. Struct. Mol. Biol. 13: 676–683
Felczak MM & Kaguni JM (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
Felczak MM, Simmons LA & Kaguni JM (2005) An Essential Tryptophan of
Escherichia coli DnaA Protein Functions in Oligomerization at the E. coli
Replication Origin. J. Biol. Chem. 280: 24627–24633
Fujikawa N (2003) Structural basis of replication origin recognition by the DnaA
protein. Nucleic Acids Res. 31: 2077–2086
Grimwade JE & Leonard AC (2021) Blocking, Bending, and Binding: Regulation of
Initiation of Chromosome Replication During the Escherichia coli Cell Cycle by
59
Transcriptional Modulators That Interact With Origin DNA. Front. Microbiol. 12:
732270
Hayashi C, Miyazaki E, Ozaki S, Abe Y & 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: 11131–11143
Hizver J, Rozenberg H, Frolow F, Rabinovich D & 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
Hwang DS & Kornberg A (1992a) Opposed actions of regulatory proteins, DnaA and
IciA, in opening the replication origin of Escherichia coli. J. Biol. Chem. 267:
23087–91
Hwang DS & Kornberg A (1992b) Opening of the replication origin of Escherichia coli
by DnaA protein with protein HU or IHF. J. Biol. Chem. 267: 23083–6
Jaworski P, Donczew R, Mielke T, Weigel C, Stingl K & Zawilak-Pawlik A (2018)
Structure and Function of the Campylobacter jejuni Chromosome Replication
Origin. Front. Microbiol. 9: 1–18
Jaworski P, Zyla-Uklejewicz D, Nowaczyk-Cieszewska M, Donczew R, Mielke T,
Weigel C & Zawilak-Pawlik A (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
Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool
K, Bates R, Žídek A, Potapenko A, et al (2021) Highly accurate protein structure
prediction with AlphaFold. Nature 596: 583–589
Kaguni JM (2011) Replication initiation at the Escherichia coli chromosomal origin.
Curr. Opin. Chem. Biol. 15: 606–613
Kamashev D, Agapova Y, Rastorguev S, Talyzina AA, Boyko KM, Korzhenevskiy DA,
Vlaskina A, Vasilov R, Timofeev VI & Rakitina T V. (2017) Comparison of
histone-like HU protein DNA-binding properties and HU/IHF protein sequence
alignment. PLoS One 12: e0188037
60
Katayama T, Kasho K & Kawakami H (2017) The DnaA Cycle in Escherichia coli:
Activation, Function and Inactivation of the Initiator Protein. Front. Microbiol. 8:
2496
Kawakami H, Keyamura K & 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
Keyamura K, Abe Y, Higashi M, Ueda T & Katayama T (2009) DiaA Dynamics Are
Coupled with Changes in Initial Origin Complexes Leading to Helicase Loading. J.
Biol. Chem. 284: 25038–25050
Kumar S, Farhana A & Hasnain SE (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
Kuwabara T & Igarashi K (2020) Thermotogales origin scenario of eukaryogenesis. J.
Theor. Biol. 492: 110192
Lopez P, Forterre P, le Guyader H & Philippe H (2000) Origin of replication of
Thermotoga maritima. Trends Genetics 16: 59–60
Mack DR, Chiu TK & Dickerson RE (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. Biol. Chem. 312: 1037–49
Majka J, Zakrzewska-Czerwiñska J & Messer W (2001) Sequence Recognition,
Cooperative Interaction, and Dimerization of the Initiator Protein DnaA of
Streptomyces. J. Biol. Chem. 276: 6243–6252
McGarry KC, Ryan VT, Grimwade JE & Leonard AC (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
Miyoshi K, Tatsumoto Y, Ozaki S & Katayama T (2021) Negative feedback for DARS2
–Fis complex by ATP–DnaA supports the cell cycle-coordinated regulation for
chromosome replication. Nucleic Acids Res. 49: 12820–12835
Noguchi Y, Sakiyama Y, Kawakami H & Katayama T (2015) The Arg Fingers of Key
DnaA Protomers Are Oriented Inward within the Replication Origin oriC and
61
Stimulate DnaA Subcomplexes in the Initiation Complex. J. Biol. Chem.290:
20295–20312
Nozaki S & Ogawa T (2008) Determination of the minimum domain II size of
Escherichia coli DnaA protein essential for cell viability. Microbiology 154: 3379–
3384
Ozaki S (2019) Regulation of replication initiation: lessons from Caulobacter
crescentus Genes Genet. Syst. 94: 183–196
Ozaki S, Fujimitsu K, Kurumizaka H & 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
Ozaki S & Katayama T (2009) DnaA structure, function, and dynamics in the initiation
at the chromosomal origin. Plasmid 62: 71–82
Ozaki S & Katayama T (2012) Highly organized DnaA– oriC complexes recruit the
single-stranded DNA for replication initiation. Nucleic Acids Res. 40: 1648–1665
Ozaki S, Kawakami H, Nakamura K, Fujikawa N, Kagawa W, Park S-Y, Yokoyama S,
Kurumizaka H & Katayama T (2008) A Common Mechanism for the ATP-DnaAdependent Formation of Open Complexes at the Replication Origin. J. Biol. Chem.
283: 8351–8362
Ozaki S, Noguchi Y, Hayashi Y, Miyazaki E & Katayama T (2012) Differentiation of
the DnaA-oriC Subcomplex for DNA Unwinding in a Replication Initiation
Complex. J. Biol. Chem. 287: 37458–37471
Pei H, Liu J, Li J, Guo A, Zhou J & Xiang H (2007) Mechanism for the TtDnaA-TtoriC cooperative interaction at high temperature and duplex opening at an unusual
AT-rich region in Thermoanaerobacter tengcongensis. Nucleic Acids Res. 35:
3087–3099
Richardson TT, Harran O & Murray H (2016) The bacterial DnaA-trio replication
origin element specifies single-stranded DNA initiator binding. Nature 534: 412–
416
62
Richardson TT, Stevens D, Pelliciari S, Harran O, Sperlea T & Murray H (2019)
Identification of a basal system for unwinding a bacterial chromosome origin.
EMBO J. 38: e101649
Rozgaja TA, Grimwade JE, Iqbal M, Czerwonka C, Vora M & Leonard AC (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
Ryan VT, Grimwade JE, Nievera CJ & Leonard AC (2002) IHF and HU stimulate
assembly of pre-replication complexes at Escherichia coli oriC by two different
mechanisms. Mol. Microbiol. 46: 113–124
Sakiyama Y, Kasho K, Noguchi Y, Kawakami H & Katayama T (2017) Regulatory
dynamics in the ternary DnaA complex for initiation of chromosomal replication in
Escherichia coli. Nucleic Acids Res. 45: 12354–12373
Sakiyama Y, Nagata M, Yoshida R, Kasho K, Ozaki S & 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
Schaper S & Messer W (1995)
Interaction of the Initiator Protein DnaA of Escherichia coli with Its DNA Target.
J. Biol. Chem.29:17622-17626
Shimizu M, Noguchi Y, Sakiyama Y, Kawakami H, Katayama T & 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
Simmons LA, Felczak M & Kaguni JM (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: 849–58
Soman A, Liew CW, Teo HL, Berezhnoy N V, Olieric V, Korolev N, Rhodes D &
Nordenskiöld L (2021) The human telomeric nucleosome displays distinct
structural and dynamic properties. Nucleic Acids Res. 48: 5383–5396
63
Sugiyama R, Kasho K, Miyoshi K, Ozaki S, Kagawa W, Kurumizaka H & Katayama T
(2019) A novel mode of DnaA-DnaA interaction promotes ADP dissociation for
reactivation of replication initiation activity. Nucleic Acids Res. 47: 11209–11224
Sutton MD, Carr KM, Vicente M & Kaguni JM (1998) Escherichia coli DnaA protein.
The N-terminal domain and loading of DnaB helicase at the E. coli chromosomal
origin. J. Biol. Chem. 273: 34255–62
Swinger KK & Rice PA (2004) IHF and HU: flexible architects of bent DNA. Curr.
Opin. Struct. Biol. 14: 28–35
Wegrzyn K, Fuentes-Perez ME, Bury K, Rajewska M, Moreno-Herrero F & Konieczny
I (2014) Sequence-specific interactions of Rep proteins with ssDNA in the AT-rich
region of the plasmid replication origin. Nucleic Acids Res. 42: 7807–7818
Wolański M, Donczew R, Zawilak-Pawlik A & Zakrzewska-Czerwińska J (2015) oriCencoded instructions for the initiation of bacterial chromosome replication. Front.
Microbiol. 5: 735
Yoshida R, Ozaki S, Kawakami H & Katayama T (2023) Single-stranded DNA
recruitment mechanism in replication origin unwinding by DnaA initiator protein
and HU, an evolutionary ubiquitous nucleoid protein. Nucleic Acids Res.
Young RT, Czapla L, Wefers ZO, Cohen BM & Olson WK (2022) Revisiting DNA
Sequence-Dependent Deformability in High-Resolution Structures: Effects of
Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration.
Life 12: 759
Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT,
Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, 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
64
Publication list
Lu, C., Yoshida, R., Katayama, T., & Ozaki, S. (2023). Thermotoga maritima oriC
involves a DNA unwinding element with distinct modules and a DnaA-oligomerizing
region with a novel directional binding mode. J. Biol. Chem., 104888. In Press.
65
Acknowledgement
This study was performed in the laboratory of Molecular Biology under supervision
of Assoc. Prof. Shogo Ozaki and Prof. Tsutomu Katayama. I thank Kenya, M., Ryusei,
Y. and Yasutaka, W. for their valid suggestions in this study.
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