BSGatlas

dnaE

BSGatlas-gene-3425

BSGatlas

Description	Information
Coordinates	2991269..2994616
Genomic Size	3348 bp
Name	dnaE
Outside Links	SubtiWiki
	BsubCyc
Strand	-
Type	CDS

SubtiWiki

Description	Information
Alternative Name	dnaE
Category	SW 3 Information processing
	SW 3.1 Genetics
	SW 3.1.1 DNA replication
	SW 6 Groups of genes
	SW 6.1 Essential genes
Description	lagging strand DNA polymerase III (alpha subunit), part of the [SW\|replisome]
Enzyme Classifications	EC 2.7.7.7: DNA-directed DNA polymerase
Function	[[category\|SW 3.1.1]](lagging strand)
Is essential?	yes
Isoelectric point	6.02
Locus Tag	BSU_29230
Molecular weight	125.137
Name	dnaE
Product	lagging strand DNA polymerase III (alpha subunit)

RefSeq

Description	Information
Alternative Locus Tag	BSU29230
Description	Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 9799485, 9822387,10354411, 14593098, 20122408, 22333191, 24106089,29078353; Product type e: enzyme
Functions	16.9: Replicate
Locus Tag	BSU_29230
Name	dnaEC
Title	DNA polymerase III (alpha subunit), DnaE3
Type	CDS

BsubCyc

Description	Information
Citation	Barnes MH;Butler MM;Wright GE;Brown NC Antimicrobials targeted to the replication-specific DNA polymerases of gram-positive bacteria: target potential of dnaE. Infect Disord Drug Targets 12(5);327-31 (2012) PUBMED: 23017159
	Costes A;Lecointe F;McGovern S;Quevillon-Cheruel S;Polard P The C-Terminal Domain of the Bacterial SSB Protein Acts as a DNA Maintenance Hub at Active Chromosome Replication Forks. PLoS Genet 6(12);e1001238 (2010) PUBMED: 21170359
	Klocko AD;Schroeder JW;Walsh BW;Lenhart JS;Evans ML;Simmons LA Mismatch repair causes the dynamic release of an essential DNA polymerase from the replication fork. Mol Microbiol 82(3);648-63 (2011) PUBMED: 21958350
	Mangiameli SM;Merrikh CN;Wiggins PA;Merrikh H Transcription leads to pervasive replisome instability in bacteria. Elife 6 (2017) PUBMED: 28092263
	Rannou O;Le Chatelier E;Larson MA;Nouri H;Dalmais B;Laughton C;Janniere L;Soultanas P Functional interplay of DnaE polymerase, DnaG primase and DnaC helicase within a ternary complex, and primase to polymerase hand-off during lagging strand DNA replication in Bacillus subtilis. Nucleic Acids Res 41(10);5303-20 (2013) PUBMED: 23563155
	Sanders GM;Dallmann HG;McHenry CS Reconstitution of the B. subtilis replisome with 13 proteins including two distinct replicases. Mol Cell 37(2);273-81 (2010) PUBMED: 20122408
	Schroeder JW;Hirst WG;Szewczyk GA;Simmons LA The Effect of Local Sequence Context on Mutational Bias of Genes Encoded on the Leading and Lagging Strands. Curr Biol 26(5);692-7 (2016) PUBMED: 26923786
	Timinskas K;Balvociutė M;Timinskas A;Venclovas Č Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes. Nucleic Acids Res 42(3);1393-413 (2014) PUBMED: 24106089
Comment	16.9: Replicate
Description	DNA polymerase III (alpha subunit)
Enzyme Classifications	EC 2.7.7.7: DNA-directed DNA polymerase
Gene Ontology	GO:0003676 nucleic acid binding
	GO:0003677 DNA binding
	GO:0003824 catalytic activity
	GO:0003887 DNA-directed DNA polymerase activity
	GO:0005737 cytoplasm
	GO:0006260 DNA replication
	GO:0006261 DNA-dependent DNA replication
	GO:0008408 3'-5' exonuclease activity
	GO:0016740 transferase activity
	GO:0016779 nucleotidyltransferase activity
	GO:0090305 nucleic acid phosphodiester bond hydrolysis
Locus Tag	BSU29230
Molecular weight	125.349
Name	dnaE

Nicolas et al. predictions

Description	Information
Expression neg. correlated with	BSU27840, new_2845839_2845914_c, BSU27850, BSU11210, new_2844574_2844638_c, BSU11200, BSU11220, BSU11240, BSU11230, BSU11190
Expression pos. correlated with	BSU35280, BSU34770, BSU34750, BSU34760, BSU09910, BSU05950, BSU09810, BSU34740, BSU32890, BSU30350
Highly expressed condition	(Diami) Cells were grown in LB medium at 37°C. At OD540 of 0.3, the culture were divided into four subcultures and diamide 0.6 mM [Diami], paraquat 0.4 mM [Paraq], H2O2 0.1mM [H2O2] or no oxidative drug [Oxctl] were added to the medium. Samples were taken 10 minutes after addition
	(G135) Purified spores were obtained by growing cells in DSM medium (P. Schaeffer, J. Millet, J. P. Aubert, Proc Natl Acad Sci U S A 54, 704, Sep, 1965) at 37°C for 48 hours after which they were washed ten times in ice cold distilled waterover a period of 5 days. Purified spores were heat activated at 70°C in Tris 10 mM pH8.4 and germination was initiated by the addition of L-alanine 10 mM (A. Moir, J Bacteriol 146, 1106, Jun, 1981). After incubation for one hour at 37°C, the culture was diluted with an equal volume of 2X LBmedium and germinating cells were harvested at 135, 150 or 180 minutes after addition of L-alanine [G135, G150 and G180].
	(G150) Purified spores were obtained by growing cells in DSM medium (P. Schaeffer, J. Millet, J. P. Aubert, Proc Natl Acad Sci U S A 54, 704, Sep, 1965) at 37°C for 48 hours after which they were washed ten times in ice cold distilled waterover a period of 5 days. Purified spores were heat activated at 70°C in Tris 10 mM pH8.4 and germination was initiated by the addition of L-alanine 10 mM (A. Moir, J Bacteriol 146, 1106, Jun, 1981). After incubation for one hour at 37°C, the culture was diluted with an equal volume of 2X LBmedium and germinating cells were harvested at 135, 150 or 180 minutes after addition of L-alanine [G135, G150 and G180].
	(H2O2) Cells were grown in LB medium at 37°C. At OD540 of 0.3, the culture were divided into four subcultures and diamide 0.6 mM [Diami], paraquat 0.4 mM [Paraq], H2O2 0.1mM [H2O2] or no oxidative drug [Oxctl] were added to the medium. Samples were taken 10 minutes after addition
	(LBGstat) Cells were grown in Luria-Bertani medium (Sigma) supplemented with glucose 0.3 % [LBG] at 37°C with vigorous shaking in flasks. Overnight cultures were diluted 2000-fold in fresh pre-warmed medium and samples were collected during the exponential [exp], transition [tran] and stationary [stat] phases of the growth cycle .
	(LBGtran) Cells were grown in Luria-Bertani medium (Sigma) supplemented with glucose 0.3 % [LBG] at 37°C with vigorous shaking in flasks. Overnight cultures were diluted 2000-fold in fresh pre-warmed medium and samples were collected during the exponential [exp], transition [tran] and stationary [stat] phases of the growth cycle .
	(LBtran) Cells were grown in Luria-Bertani medium (Sigma) [LB] at 37°C with vigorous shaking in flasks. Overnight cultures were diluted 2000-fold in fresh pre-warmed medium and samples were collected during the exponential [exp], transition [tran] and stationary [stat] phases of the growth cycle .
	(M40t45) Cells were grown in LB medium at 37°C with vigorous shaking. An exponentially growing culture (O.D.600 approx. 0.25) was divided: one culture acted as the control [no mitomycin C , M0] while mitomycin was added to the second culture to a final concentration of 40 ng/ml [mitomycin, M40]. Samples were harvested at 0, 45 and 90 minutes after mitomycin addition [t0, t45 and t90].
	(M40t90) Cells were grown in LB medium at 37°C with vigorous shaking. An exponentially growing culture (O.D.600 approx. 0.25) was divided: one culture acted as the control [no mitomycin C , M0] while mitomycin was added to the second culture to a final concentration of 40 ng/ml [mitomycin, M40]. Samples were harvested at 0, 45 and 90 minutes after mitomycin addition [t0, t45 and t90].
	(Sw) Exponentially growing cells were spotted on 1 % agar LB plates and incubated at 37°C. Swarming cells were collected after 16 hours.
Lowely expressed condition	(BT) A fresh colony grown on an LB plate was used to inoculate 10 ml of LB and grown for 10 hoursat 30°C. This culture wasused to inoculate 10 ml of MSgg medium (S.S. Branda et al., J Bacteriol 186, 3970, Jun, 2004) and incubated with vigorous shaking. The cultures in MSgg were diluted to the same extent in 96 wells microtiterplates (5 μl for 1.5 ml of medium) and incubated without shaking at 30°C. Cells from the control cultures were harvested after 24 hours of incubation [BT]. Biofilms were harvested from 96 well plates after incubation for 36 hours [B36] and 60 hours [B60].
	(LoTm) Cells were grown in Spizizen’s minimal medium (SMM) (C. Anagnostopoulos, J. Spizizen, J Bacteriol 81, 741, May, 1961) with vigorous agitation. The control culture was grown at 37 °C [SMMPr]. For growth at high or low temperatures, pre-cultures were grown at 37 °C, diluted to an OD578nm of 0.1 and subsequently transferred to 51 °C [HiTm] and 16 °C [LoTm], respectively. For the growth at high salinity, the salinity of the medium was adjusted by adding NaCl (5 M stock solution) to produce a final concentration of 1.2 M [HiOs].
	(Pyr) A 5 ml aliquot of LB medium was inoculated using frozen culture stocks. After a few hours growth at 37°C, precultures were prepared by inoculating 5 ml of M9 with this LB culture at several different dilutions usually ranging from 500- to 2000-fold. The dilution range was chosen so that one of these precultures had grown to and OD600 of 0.5 - 1.0 after overnight inculation. The chosen M9 medium precultures [at OD600 of 0.5 - 1.0] were used to inoculate 100 mL of M9 medium in 500 mL non-baffled shake flasks to an OD600 of 0.02. Filter-sterilized carbon sources were added separately to the medium M9 at following concentration: D-Glucose 3g/L[Glu], L-Malic acid 4.5g/L[Mal], L-Malic acid + D-Glucose 3 and 2g/L[M+G], D-Fructose 3g/L[Fru], D-Gluconate 4g/L[Glucon], Pyruvate 6g/L[Pyr], Glycerol 6g/L[Gly], Glutamic acid + Succinic acid 2 and 2g/L[G+S]. Where necessary, carbon source solutions were pH neutralized with 4 M NaOH prior to addition to the medium. Cells were harvested during the exponential growth phase.
	(S5) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments.
	(S6) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments.
	(S7) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments.
	(S8) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments.
	(SMMPr) Cells were grown in Spizizen’s minimal medium (SMM) (C. Anagnostopoulos, J. Spizizen, J Bacteriol 81, 741, May, 1961) with vigorous agitation. The control culture was grown at 37 °C [SMMPr]. For growth at high or low temperatures, pre-cultures were grown at 37 °C, diluted to an OD578nm of 0.1 and subsequently transferred to 51 °C [HiTm] and 16 °C [LoTm], respectively. For the growth at high salinity, the salinity of the medium was adjusted by adding NaCl (5 M stock solution) to produce a final concentration of 1.2 M [HiOs].
	(T5.0H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H].
Name	dnaE

KEGG Pathways

Description	Information
Pathway	DNA replication (ko03030)
	Mismatch repair (ko03430)
	Homologous recombination (ko03440)

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