Whole Genome Sequencing and Analysis of an Anti Gram-positive Bacterium Gordonia WA4-43

doi:10.13560/j.cnki.biotech.bull.1985.2022-0612

Abstract

Abstract:

WA4-43 from the intestinal tract of cockroaches was the first Gordonia that was resistant to gram-positive bacteria. Whole-genome sequencing and comparative genome analysis of WA4-43 revealed the commonness and difference between WA4-43 and other Gordonia, providing a basis for subsequent research. Strain WA4-43 had inhibitory activity only against gram-positive bacteria. The strain WA4-43 was identified as G. terrae by morphological characteristics and molecular biological identification. Genome-wide bioinformatics analysis showed that the strain had a genome size of 5.44 Mb, GC content of 67.76%, and 4 963 protein coding genes, including 3 563, 4 178 and 1 870 genes annotated in GO, COG and KEGG databases, respectively. AntiSMASH predicted 13 secondary metabolite gene clusters in 8 types with an average homology of（22.67±24.72）%. PRISM 4 was used to predict compounds in gene clusters. Comparative genome analysis showed that the G. terrae gene cluster was conserved, but its homology was significantly lower than that of the known gene cluster, and it had the potential to synthesize new compounds.

Key words: Gordonia, whole genome sequencing, secondary metabolites, resistant to gram-positive bacteria, comparative genome

HE Meng-ying, LIU Wen-bin, LIN Zhen-ming, LI Er-tong, WANG Jie, JIN Xiao-bao. Whole Genome Sequencing and Analysis of an Anti Gram-positive Bacterium Gordonia WA4-43[J]. Biotechnology Bulletin, 2023, 39(2): 232-242.

Figures/Tables 14

References 38

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检测项目 Test item	结果 Result	检测项目 Test item	结果 Result
明胶水解	-	氧化酶	-
鼠李糖	+	过氧化氢酶	+
葡萄糖	+	尿素酶	+
木糖	+	生长耐受NaCl范围	1%-5%
甘露醇	+	H₂S产生	-

检测项目 Test item	结果 Result	检测项目 Test item	结果 Result
明胶水解	-	氧化酶	-
鼠李糖	+	过氧化氢酶	+
葡萄糖	+	尿素酶	+
木糖	+	生长耐受NaCl范围	1%-5%
甘露醇	+	H₂S产生	-

数据库 Database	数量 Amount	100≤长度<300 100≤Length <300	长度≥300 Length≥300
eggnog Annotation	4 178	1 847	2 181
GO Annotation	3 563	1 539	1 892
Kegg Annotation	1 870	686	1 117
Nr Annotation	4 835	2 230	2 311
Pfam Annotation	3 239	1 398	1 735
Swissprot Annotation	2 591	954	1 570
TrEMBL Annotation	2 591	954	1 570
All Annotated	4 837	2 230	2 311

数据库 Database	数量 Amount	100≤长度<300 100≤Length <300	长度≥300 Length≥300
eggnog Annotation	4 178	1 847	2 181
GO Annotation	3 563	1 539	1 892
Kegg Annotation	1 870	686	1 117
Nr Annotation	4 835	2 230	2 311
Pfam Annotation	3 239	1 398	1 735
Swissprot Annotation	2 591	954	1 570
TrEMBL Annotation	2 591	954	1 570
All Annotated	4 837	2 230	2 311

基因簇 Region	类型 Type	预测产生的化合物 Predicited production	同源性 Similarity/%
BGC1	Ectoine	Ectoine	75
BGC2	Terpene	SF2575	6
BGC3	Arylpolyene
BGC4	NRPS, betalactone
BGC5	NRPS	Ishigamide	11
BGC6	redox-cofactor
BGC7	NRPS
BGC8	NAPAA
BGC9	Terpene	Oxalomycin B	6
BGC10	RiPP-like	Kanglemycin A/Kanglemycin V1/Kanglemycin V2	5
BGC11	T1PKS, NRPS-like
BGC12	NRPS, siderophore	Desferrioxamine	33
BGC13	NRPS