Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis

Lau, Susanna KP; Fan, Rachel YY; Ho, Tom CC; Wong, Gilman KM; Tsang, Alan KL; Teng, Jade LL; Chen, Wenyang; Watt, Rory M; Curreem, Shirly OT; Tse, Herman; Yuen, Kwok-Yung; Woo, Patrick CY

doi:10.1186/2045-3701-1-22

Cell & Bioscience

Table 1 Single-strand breaks repair proteins in L. hongkongensis and their closest homologues

From: Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis

Repair pathways/Types of enzymes	Gene	Protein	Function of protein encoded	CDS	Closest match organism	Amino acid Identity (%)	Best E-value
Direct repair
	phrB	PhrB protein	Repairs UV radiation-induced DNA damage by catalyzing light-dependent monomerization of cyclobutyl pyrimidine dimers between adjacent bases	LHK_02646	L. nitroferrum	58.73	3.00E-131
	ogt	Ogt	Repairs alkylated guanine by transferring alkyl group at O-6 position to a cysteine residue in the enzyme	LHK_00364	Dechloromonas aromatica	46.67	4.00E-30
	ada	Regulatory protein Ada	Repairs alkylated guanine in DNA by transferring alkyl group at the O-6 position to a cysteine residue in the enzyme	LHK_00147	Colwellia psychrerythraea	44.29	1.00E-60
Base excision repair
DNA glycosylases	alkA	AlkA	Excises damaged DNA polymer formed due to alkylation lesions by hydrolyzing deoxyribose N-glycosidic bond	LHK_01743	Thiobacillus denitrificans	61.95	2.00E-62
	mutY	MutY	Adenine glycosylase active on G-A mispairs. Also corrects error-prone DNA synthesis due to oxidized guanine	LHK_02781	L. nitroferrum	63.29	1.00E-92
	ung	UNG	Excises uracil residues arised from misincorporation of dUMP residues by DNA polymerase or cytosine deamination	LHK_00013	L. nitroferrum	56.14	3.00E-58
				LHK_00723	Ralstonia pickettii	59.26	2.00E-33
Bifunctional glycosylases	mutM (fpg)	Formamido-pyrimidine-DNA glycosylase	Recognizes and removes damaged bases. Cleaves DNA backbone to generate single-strand break at site of base removal	LHK_00316	Neisseria flavescens	57.25	9.00E-90
	nth	Endonuclease III	Apurinic and/or apyrimidinic endonuclease activity and DNA N-glycosylase activity	LHK_01218	Methylococcus capsulatus	72.04	1.00E-81
AP endonucleases	xthA	Exodeoxyribo-nuclease III	Removes damaged DNA at cytosines and guanines	LHK_02447	C. violaceum	67.06	5.00E-94
	exoA (xthA2)	Exodeoxyribo-nuclease	Posseses 3' to 5' exonuclease, 3' phosphatase activities and makes DNA single-strand breaks at apurinic sites	LHK_03213	L. nitroferrum	73.73	1.00E-108
Nucleotide excision repair
Global genome repair factors	uvrA	Protein UvrA	DNA-binding ATPase, forms recognition complex composed of 2 UvrA and 2 UvrB subunits and scans DNA for abnormalities	LHK_01605	L. nitroferrum	82.89	0
	uvrB	Protein UvrB	Causes local melting of the DNA helix, probes one DNA strand for the presence of a lesion	LHK_00960	L. nitroferrum	82.18	0
	uvrC	Protein UvrC	Incises 5' and 3' sides of lesion	LHK_02627	L. nitroferrum	71	0
Transcription coupled repair factors
DNA-directed RNA polymerase (RNAP) complex	rpoB	RNAP subunit beta	Subunit of DNA-dependent RNA polymerase	LHK_00246	L. nitroferrum	85.26	0
	rpoC	RNAP subunit beta	Subunit of DNA-dependent RNA polymerase	LHK_00247	C. violaceum	87.09	0
	rpoA	RNAP subunit alpha	Subunit of DNA-dependent RNA polymerase	LHK_00279	L. nitroferrum	90.83	1.00E-171
	rpoE	RNAP delta factor	Participates in initiation and recycling phases of transcription	LHK_01458	L. nitroferrum	63.82	7.00E-54
	rpoZ	RNAP omega subunit	Promotes RNA polymerase assembly	LHK_00457	Methylobacillus flagellatus	73.91	1.00E-21
Transcription-repair coupling factor (TRCF)	mfd	TRCF	Recognizes RNAP-DNA-RNA complex blocked at template strand lesion, replaces RNAP, releases truncated transcript and recruits UvrABC repair system	LHK_00629	L. nitroferrum	73.95	0
Mismatch excision repair
Mismatch and loop recognition factors	mutS	DNA mismatch repair protein MutS	Mismatch recognition	LHK_00373	C. violaceum	67.73	0
Molecular matchmarker	mutL	DNA mismatch repair protein MutL	Promotes formation of a stable complex between two or more DNA-binding proteins	LHK_01012	C. violaceum	55.51	0
DNA exonucleases	xseA	Exodeoxyribo-nuclease 7 large subunit	Bidirectionally degrades single-stranded DNA	LHK_01101	C. violaceum	59.51	4.00E-125
	xseB	Exodeoxyribo-nuclease 7 small subunit	Bidirectionally degrades single-stranded DNA	LHK_02322	C. violaceum	65.28	6.00E-20
DNA polymerase III holoenzyme	dnaE	DNA polymerase III subunit alpha	Subunit of DNA polymerase	LHK_01389	L. nitroferrum	74.13	0
	dnaN	DNA polymerase III subunit beta	Subunit of DNA polymerase, initiates replication	LHK_03241	L. nitroferrum	72.5	3.00E-131
	holC	DNA polymerase III subunit chi	Subunit of DNA polymerase	LHK_01415	C. violaceum	50	2.00E-27
	holA	DNA polymerase III subunit delta	Subunit of DNA polymerase, interacts with gamma subunit to transfer beta subunit on DNA	LHK_00117	C. violaceum	67.28	7.00E-79
	holB	DNA polymerase III subunit delta	Subunit of DNA polymerase	LHK_02696	L. nitroferrum	57.36	3.00E-75
	dnaQ	DNA polymerase III subunit epsilon	Subunit of DNA polymerase, a 3'-5' exonuclease posseses proofreading function	LHK_00881	C. violaceum	71.74	6.00E-85
				LHK_01009	C. violaceum	62.7	4.00E-60
				LHK_02526	C. violaceum	51.52	3.00E-105
	dnaX	DNA polymerase III subunits gamma and tau	Subunits of DNA polymerase, tau subunit serves as scaffold in dimerization of the core complex while gamma subunit interacts with delta subunit to transfer beta subunit on DNA	LHK_00963	C. violaceum	82.17	2.00E-154
Other MMR factors	dam	DNA adenine methylase	Methylates DNA sequence GATC and protects DNA from cleavage by restriction endonuclease	LHK_01749	C. violaceum	83.92	8.00E-131
				LHK_02602	C. violaceum	75	9.00E-113
				LHK_00398	C. violaceum	75	9.00E-113
	vsr	Very short patch repair protein	Endonuclease, nicks double-stranded DNA	LHK_03243	Limnobacter sp. MED105	61.38	5.00E-48

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ISSN: 2045-3701

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