Characterization of newly identified DnaA and DnaB proteins from Acetobacter

Research in Microbiology - Tập 167 - Trang 655-668 - 2016
Juraj Bugala1, Viera Cimová1, Peter Grones2, Jozef Grones1
1Department of Molecular Biology, Comenius University, Mlynská Dolina B2-122, 842 15 Bratislava, Slovak Republic
2Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden

Tài liệu tham khảo

Leonard, 2011, Regulation of DnaA assembly and activity: taking directions from the genome, Annu Rev Microbiol, 65, 19, 10.1146/annurev-micro-090110-102934 Kawakami, 2010, DnaA, ORC and Cdc6: similarity beyond the domains of life and diversity, Biochem Cell Biol, 88, 49, 10.1139/O09-154 Costa, 2013, Mechanisms for initiating cellular DNA replication, Annu Rev Biochem, 82, 25, 10.1146/annurev-biochem-052610-094414 Polaczek, 1990, Bending of the origin of replication of E. coli by binding of IHF at a specific site, New Biol, 2, 265 Grimwade, 2000, IHF redistributes bound initiator protein, DnaA, on supercoiled oriC of Escherichia coli, Mol Microbiol, 35, 835, 10.1046/j.1365-2958.2000.01755.x Ryan, 2004, Escherichia coli prereplication complex assembly is regulated by dynamic interplay among Fis, IHF DnaA, Mol Microbiol, 51, 1347, 10.1046/j.1365-2958.2003.03906.x LeBowitz, 1986, The Escherichia coli dnaB replication protein is a DNA helicase, J Biol Chem, 261, 4738, 10.1016/S0021-9258(17)38564-2 Jezewska, 1996, Binding of Escherichia coli primary replicative helicase DnaB protein to single-stranded DNA. Long-range allosteric conformational changes within the protein hexamer, Biochemistry, 35, 2129, 10.1021/bi952345d Weigel, 2002, Strand-specific loading of DnaB helicase by DnaA to a substrate mimicking unwound oriC, Mol Microbiol, 46, 1149, 10.1046/j.1365-2958.2002.03232.x Wickner, 1977, DNA or RNA priming of bacteriophage G4 DNA synthesis by Escherichia coli dnaG protein, Proc Natl Acad Sci U S A, 74, 2815, 10.1073/pnas.74.7.2815 Brendler, 1995, A protein that binds to the P1 origin core and the oriC 13mer region in a methylation-specific fashion is the product of the host seqA gene, EMBO J, 14, 4083, 10.1002/j.1460-2075.1995.tb00080.x Ozaki, 2009, DnaA structure, function and dynamics in the initiation at the chromosomal origin, Plasmid, 62, 71, 10.1016/j.plasmid.2009.06.003 Wolański, 2015, oriC-encoded instructions for the initiation of bacterial chromosome replication, Front Microbiol, 5, 735 Keyamura, 2007, The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP–DnaA-specific initiation complexes, Genes Dev, 21, 2083, 10.1101/gad.1561207 Keyamura, 2009, DiaA dynamics are coupled with changes in initial origin complexes leading to helicase loading, J Biol Chem, 284, 25038, 10.1074/jbc.M109.002717 Erzberger, 2002, The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation, EMBO J, 21, 4763, 10.1093/emboj/cdf496 Kawakami, 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, 10.1074/jbc.M502764200 Felczak, 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, 10.1074/jbc.M409695200 Ozaki, 2012, Highly organized DnaA–oriC complexes recruit the single-stranded DNA for replication initiation, Nucleic Acids Res, 40, 1648, 10.1093/nar/gkr832 Swinger, 2004, IHF and HU: flexible architects of bent DNA, Curr Opin Struct Biol, 14, 28, 10.1016/j.sbi.2003.12.003 Cassler, 1995, Cell cycle-specific changes in nucleoprotein complexes at a chromosomal replication origin, EMBO J, 14, 5833, 10.1002/j.1460-2075.1995.tb00271.x Marszalek, 1994, DnaA protein directs the binding of DnaB protein in initiation of DNA replication in Escherichia coli, J Biol Chem, 269, 4883, 10.1016/S0021-9258(17)37627-5 Wahle, 1989, The dnaB–dnaC replication protein complex of Escherichia coli. I. Formation and properties, J Biol Chem, 264, 2463, 10.1016/S0021-9258(19)81636-8 Tougu, 1996, The extreme C terminus of primase is required for interaction with DnaB at the replication fork, J Biol Chem, 271, 21391, 10.1074/jbc.271.35.21391 Bird, 2000, Mapping protein–protein interactions within a stable complex of DNA primase and DnaB helicase from Bacillus stearothermophilus, Biochemistry, 39, 171, 10.1021/bi9918801 Soultanas, 2002, Site-directed mutagenesis reveals roles for conserved amino acid residues in the hexameric DNA helicase DnaB from Bacillus stearothermophilus, Nucleic Acids Res, 30, 4051, 10.1093/nar/gkf527 Crameri, 1996, Improved green fluorescent protein by molecular evolution using DNA shuffling, Nat Biotechnol, 14, 315, 10.1038/nbt0396-315 Bilská, 2003, Optimization of transformation and electroporation of plasmid DNA with AC1 replicon into Acetobacter pasteurianus, Biológia, 58, 1029 Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method, Methods, 25, 402, 10.1006/meth.2001.1262 Pullman, 1960, Partial resolution of the enzymes catalyzing oxidative phosphorylation. I. Purification and properties of soluble, dinitrophenol-stimulated adenosine triphosphatase, J Biol Chem, 235, 3322, 10.1016/S0021-9258(20)81361-1 Matsutani, 2012, Genome-wide phylogenetic analysis of differences in thermotolerance among closely related Acetobacter pasteurianus strains, Microbiology, 158, 229, 10.1099/mic.0.052134-0 Beattie, 2015, A replisome's journey through the bacterial chromosome, Front Microbiol, 6, 562, 10.3389/fmicb.2015.00562 Källberg, 2012, Template-based protein structure modeling using the RaptorX web server, Nat Protoc, 7, 1511, 10.1038/nprot.2012.085 Grones, 2011, Nucleotide sequence analysis of small cryptic plasmid pGP2 from Acetobacter estunensis, Biologia, 66, 221, 10.2478/s11756-011-0017-2 Grones, 2012, Characterization of the theta replication plasmid pGR7 from Acetobacter aceti CCM 3610, Res Microbiol, 163, 419, 10.1016/j.resmic.2012.07.002 Babič, 2014, The Rep20 replication initiator from the pAG20 plasmid of Acetobacter aceti, Mol Biotechnol, 56, 1, 10.1007/s12033-013-9680-6 Abe, 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, 10.1074/jbc.M701841200 Hansen, 1991, Initiator (DnaA) protein concentration as a function of growth rate in Escherichia coli and Salmonella typhimurium, J Bacteriol, 173, 5194, 10.1128/jb.173.16.5194-5199.1991 Fuller, 1984, The dnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites, Cell, 38, 889, 10.1016/0092-8674(84)90284-8 Messer, 2002, The bacterial replication in initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication, FEMS Microbiol Rev, 26, 355 Giongo, 2010, Two genome sequences of the same bacterial strain, Gluconacetobacter diazotrophicus PAl 5, suggest a new standard in genome sequence submission, Stand Genomic Sci, 2, 309, 10.4056/sigs.972221 Ogino, 2011, Complete genome sequence of NBRC 3288, a unique cellulose-nonproducing strain of Gluconacetobacter xylinus isolated from vinegar, J Bacteriol, 193, 6997, 10.1128/JB.06158-11 Huang, 2003, WEB-THERMODYN: sequence analysis software for profiling DNA helical stability, Nucleic Acids Res, 31, 3819, 10.1093/nar/gkg562 Weigel, 1997, DnaA protein binding to individual DnaA boxes in the Escherichia coli replication origin, oriC., EMBO J, 16, 6574, 10.1093/emboj/16.21.6574 Schaeffer, 2005, Protein–protein interactions in the eubacterial replisome, IUBMB Life, 57, 5, 10.1080/15216540500058956 Simmons, 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, 10.1046/j.1365-2958.2003.03603.x Duderstadt, 2011, DNA stretching by bacterial initiators promotes replication origin opening, Nature, 478, 209, 10.1038/nature10455 Du, 2005, Crystal structure of the first KH domain of human poly(C) binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.7 Å, J Biol Chem, 280, 38823, 10.1074/jbc.M508183200 Grones, 2010, Cloning, expression, purification and characterization of replication protein from plasmid pGP2 from Acetobacter estunensis, Adv Biosci Biotechnol, 1, 417, 10.4236/abb.2010.15055 Azuma, 2009, Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus, Nucleic Acids Res, 37, 5768, 10.1093/nar/gkp612 Mott, 2008, Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators, Cell, 134, 623, 10.1016/j.cell.2008.09.058 Chiaramello, 1989, Expression of Escherichia coli dnaA and mioC genes as a function of growth rate, J Bacteriol, 171, 4272, 10.1128/jb.171.8.4272-4280.1989 Sutton, 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, 10.1074/jbc.273.51.34255