Construction of a mariner-based transposon vector for use in insertion sequence mutagenesis in selected members of the Rhizobiaceae

Perry, Benjamin J; Yost, Christopher K

doi:10.1186/s12866-014-0298-z

Table 3 Selected genes in RLV3841 cultured on TY agar with Tn insertions substantially below expected levels

From: Construction of a mariner-based transposon vector for use in insertion sequence mutagenesis in selected members of the Rhizobiaceae

Locus	Gene	Gene annotation	Potential insertions^A	Insertion density^B	Mean read count^C	Phenotypic class^D
Selected chromosomal house keeping genes
RL0924	atpI	Putative ATP synthase I	4	0.000	0.000	ES
RL0925	atpB	F0F1 ATP synthase subunit A	12	0.083	1.000	ES
RL0926	atpC	F0F1 ATP synthase subunit C	7	0.000	0.000	ES
RL0927	atpG	F0F1 ATP synthase subunit B'	7	0.000	0.000	ES
RL0928	atpF	F0F1 ATP synthase subunit B	4	0.000	0.000	ES
RL4405	atpC	F0F1 ATP synthase subunit Epsilon	3	0.333	1.000	ES
RL4407	atpD	F0F1 ATP synthase subunit Beta	23	0.043	1.000	ES
RL4408	atpG	F0F1 ATP synthase subunit Gamma	12	0.083	1.000	ES
RL4409	atpA	F0F1 ATP synthase subunit Alpha	22	0.000	0.000	ES
RL4410	atpH	F0F1 ATP synthase subunit Delta	8	0.125	1.000	ES
RL4412	priA	Primosome assembly protein PriA	23	0.261	4.000	GD
RL3408	dnaG	DNA primase	23	0.000	0.000	ES
RL3298	ftsZ	Cell division protein FtsZ	9	0.000	0.000	ES
RL3299	ftsA	Putative cell division protein FtsA	12	0.083	1.000	ES
RL3300	ftsQ	Putative cell division protein FtsQ	14	0.000	0.000	ES
RL3308	ftsW	Putative cell division protein FtsW	13	0.000	1.000	ES
RL3965	ftsH	Putative cell division protein FtsH	19	0.105	1.500	ES
RL2515	gyrB	DNA topoisomerase IV subunit B	26	0.115	9.333	ES
RL2401	gyrA	DNA gyrase subunit A	34	0.059	1.000	ES
RL1723	dnaE	DNA polymerase III subunit Alpha	51	0.078	1.000	ES
RL4697	dnaE	Putative DNA polymerase III subunit Alpha	76	0.961	23.562	NE
RL0334	dnaN	DNA polymerase III subunit Beta	14	0.071	1.000	ES
RL2099	recJ	Putative single-stranded-DNA-specific exonuclease	17	0.294	3.800	GD
RL1766	rpoB	DNA-directed RNA polymerase subunit Beta	64	0.016	1.000	ES
RL1767	rpoC	Putative DNA-directed RNA polymerase subunit Beta'	61	0.066	1.750	ES
RL1798	rpoA	Putative DNA-directed RNA polymerase subunit Alpha	12	0.000	0.000	ES
RL0059	-	Putative ATP-dependant helicase	18	0.778	21.714	NE
RL0582	-	Putative ATP-dependant helicase	39	0.949	18.730	NE
RL1551	dnaC	Putative replicative DNA helicase	24	0.042	24.000	ES
Selected plasmid borne genes
pRL120001	repA	Putative replication protein A	21	0.000	0.000	ES
pRL120002	repB	Putative replication protein B	9	0.000	0.000	ES
pRL120003	repC	Putative replication protein C	13	0.000	0.000	ES
pRL110001	repA	Putative replication protein A	25	0.040	1.000	ES
pRL110002	repB	Putative replication protein B	16	0.063	1.000	ES
pRL110003	repC	Putative replication protein C	15	0.067	1.000	ES
pRL100001	repA	Putative RepA replication protein	19	0.000	0.000	ES
pRL100002	repB	Putative RepB replication protein	6	0.000	0.000	ES
pRL100003	repC	Putative RepC replication protein	22	0.045	1.000	ES
pRL90001	repA	Putative replication partitioning protein	30	0.000	0.000	ES
pRL90002	repB	Putative replication partitioning protein	19	0.053	1.000	ES
pRL90003	repC	Putative replication initiation protein RepC	15	0.000	0.000	ES
pRL80001	repA	Putative replication protein RepA	38	0.000	0.000	ES
pRL80002	repB	Putative replication protein RepB	23	0.043	1.000	ES
pRL80003	repC	Putative replication initiation protein RepC	28	0.036	1.000	ES
pRL70092	repA	Putative replication protein	34	0.529	1.722	GD
pRL70093	repB	Putative replication protein B	22	0.455	1.100	GD
pRL70094	repC	Putative replication initiation protein RepC	33	0.455	1.200	GD
Previously experimentally confirmed genes with a TY- defective phenotype
RL4692	ctpA	Putative carboxy-terminal processing protease precursor	14	0.429	5.500	GD
RL3501	-	Conserved hypothetical membrane protein	42	0.667	3.107	GD
RL2815	fabF2	3-Oxoacyl acyl carrier protein synthase	11	0.364	1.000	GD
RL1375	phaD2	Putative Na+/H+ antiporter subunit D	26	0.192	1.400	GD
Examples of genes with higher than expected Tn insertions ^E
RL0868	-	Putative lipid A oxidase	16	1.000	113.688	GA
RL2661	-	Putative transmembrane component of ABC transporter	13	1.000	62.846	GA
RL0684	-	Putative transmembrane protein	27	0.963	64.346	GA

ES = Essential, GD = Growth Defect, NE = Neutral, GA = Growth Advantage.
^APotential insertions is the number of 'TA' nucleotide motifs within the gene.
^BInsertion density is the fraction of all 'TA' insertions sites with a Tn insertion.
^CMean read count is the mean number of Tn insertions at 'TA' sites with a Tn insertion.
^DGenes were designated to a phenotypic class based on the state most frequently observed in the TA sites within the boundaries of an annotated gene, except in the case of essential genes which could also have been assigned to the ES state if they contained a stretch of ES TA sites that was statistically significant based on the extreme value distribution. Please refer to the Materials and Methods section for more detail.
^EThree genes with the phenotypic classification of Growth-advantage were included to provide context to the insertional densities and mean read count of the Growth-advantage state compared to the essential state classification.

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ISSN: 1471-2180

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