Biotechnology Bulletin ›› 2023, Vol. 39 ›› Issue (2): 232-242.doi: 10.13560/j.cnki.biotech.bull.1985.2022-0612
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HE Meng-ying(), LIU Wen-bin, LIN Zhen-ming, LI Er-tong, WANG Jie, JIN Xiao-bao()
Received:
2022-05-19
Online:
2023-02-26
Published:
2023-03-07
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.
Fig. 1 Characteristics of strain WA4-43 A: Growth state of strain Gao’s No.1 medium. B: Strain gram staining light microscope(1 000×). C to D: Observed results of 10 000× and 20 000× by scanning electron microscope
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 | - |
Table 1 Physiological and biochemical characteristics of strain WA4-43
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 | - |
Fig. 3 Determination of antibacterial activity of strain WA4-43 by tube and plate method A: Methicillin-resistant Staphylococcus aureus. B: Staphylococcus aureus. C: Bacillus subtilis. D: Staphylococcu epidermidis. n=3
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 |
Table 2 Number and size of functionally annotated genes in strain WA4-43
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 |
Fig. 4 Genome circle map of strain WA4-43 Outer circle: Genome size. The second circle: Size of all plus-strand genes in the genome.The third circle: The size of all negative-strand genes in the genome.The fourth circle: Genome sequence repeats.The fifth circle: 49 blue TrNAand purple RRNA.The sixth circle: GC content. Innermost circle: GC-SKEw
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 |
Table 3 Prediction of secondary metabolic gene clusters in the genome of strain WA4-43
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 |
Fig. 8 Prediction of biosynthetic gene cluster compounds of strain WA4-43 A to C: Predict gene cluster 4 compound. D to E: Predict gene cluster 5 compound. F: Predict gene cluster 6 compound. G: Predict gene cluster 7 compound. H-J: Predict gene cluster 11 compound. K: Predict gene cluster 12 compound
基因编号 Gene ID | 基因功能 Gene function | 长度 Length/bp | Nr数据库 Nr database | GO数据库 GO database | TrEMBL数据库 TrEMBL database |
---|---|---|---|---|---|
GE002623 | Additional biosynthetic genes | 1 479 | Gordonia sp. IITR100 | Transferase activity;carbon-nitrogen ligase activity, with glutamine as amido-N-donor | Amidase |
GE002624 | Other genes | 1 674 | Gordonia sp. UCD-TK1 | oxidoreductase activity, acting on the CH-CH group of donors; oxidation-reduction process | FAD-binding dehydrogenase |
GE002625 | Other genes | 1 164 | Gordonia sp. v-85 | peroxidase activity; heme binding; oxidation-reduction process; cellular oxidant detoxification | Putative Iron-dependent peroxidase |
GE002626 | Core biosynthetic genes | 810 | Nocardia farcinica | proteolysis; peptidase activity; defense response to bacterium | Bacteriocin |
GE002627 | Transport-related genes | 1 734 | Nocardia farcinica | ATP binding; integral component of membrane; ATPase activity, coupled to transmembrane movement of substances; transmembrane transport | Multidrug ABC transporter ATP-binding protein |
GE002628 | Transport-related genes | 1 920 | Gordonia sp. IITR100 | ATP binding; integral component of membrane; ATPase activity, coupled to transmembrane movement of substances;transmembrane transport | ATP-binding cassette, subfamily B |
GE002629 | Other genes | 573 | Gordonia sp. UCD-TK1 | Uncharacterized protein |
Table 4 BGC10 gene prediction and database analysis
基因编号 Gene ID | 基因功能 Gene function | 长度 Length/bp | Nr数据库 Nr database | GO数据库 GO database | TrEMBL数据库 TrEMBL database |
---|---|---|---|---|---|
GE002623 | Additional biosynthetic genes | 1 479 | Gordonia sp. IITR100 | Transferase activity;carbon-nitrogen ligase activity, with glutamine as amido-N-donor | Amidase |
GE002624 | Other genes | 1 674 | Gordonia sp. UCD-TK1 | oxidoreductase activity, acting on the CH-CH group of donors; oxidation-reduction process | FAD-binding dehydrogenase |
GE002625 | Other genes | 1 164 | Gordonia sp. v-85 | peroxidase activity; heme binding; oxidation-reduction process; cellular oxidant detoxification | Putative Iron-dependent peroxidase |
GE002626 | Core biosynthetic genes | 810 | Nocardia farcinica | proteolysis; peptidase activity; defense response to bacterium | Bacteriocin |
GE002627 | Transport-related genes | 1 734 | Nocardia farcinica | ATP binding; integral component of membrane; ATPase activity, coupled to transmembrane movement of substances; transmembrane transport | Multidrug ABC transporter ATP-binding protein |
GE002628 | Transport-related genes | 1 920 | Gordonia sp. IITR100 | ATP binding; integral component of membrane; ATPase activity, coupled to transmembrane movement of substances;transmembrane transport | ATP-binding cassette, subfamily B |
GE002629 | Other genes | 573 | Gordonia sp. UCD-TK1 | Uncharacterized protein |
菌株 Strain | 序号 No. | 基因组大小 Size/Mb | GC含量 GC/% | 染色体 Contigs | rRNA数量 rRNA genes | tRNA数量 tRNA genes | 编码蛋白区数量 Number of coding sequence |
---|---|---|---|---|---|---|---|
WA4-43 | GCA 020520305.1 | 5.44 | 67.76 | 1 | 9 | 49 | 4 963 |
NCTC10669 | GCA 901542405.1 | 5.71 | 67.8 | 2 | 12 | 46 | 4 974 |
NRRL B-16283 | GCA 003183825.1 | 5.71 | 67.8 | 1 | 9 | 46 | 4 979 |
3612 | GCA 001698225.1 | 5.70 | 67.8 | 1 | 9 | 46 | 4 977 |
RL-JC02 | GCA 011290605.1 | 5.31 | 67.87 | 2 | 9 | 47 | 4 627 |
NRRL B-16283 | GCA 000716975.1 | 5.67 | 67.8 | 108 | 7 | 46 | 4 938 |
UMB0777 | GCA 002847865.1 | 5.70 | 67.7 | 180 | 3 | 46 | 5 007 |
K | GCA 005502725.1 | 5.19 | 68 | 155 | 9 | 45 | 4 480 |
C-6 | GCA 000390025.1 | 5.17 | 67.9 | 130 | 5 | 45 | 4 572 |
NBRC 100016 | GCA 000248035.2 | 5.67 | 67.8 | 130 | 6 | 46 | 4 956 |
Table 5 Comparison of genomic characteristics of 10 Gordonia terrae species
菌株 Strain | 序号 No. | 基因组大小 Size/Mb | GC含量 GC/% | 染色体 Contigs | rRNA数量 rRNA genes | tRNA数量 tRNA genes | 编码蛋白区数量 Number of coding sequence |
---|---|---|---|---|---|---|---|
WA4-43 | GCA 020520305.1 | 5.44 | 67.76 | 1 | 9 | 49 | 4 963 |
NCTC10669 | GCA 901542405.1 | 5.71 | 67.8 | 2 | 12 | 46 | 4 974 |
NRRL B-16283 | GCA 003183825.1 | 5.71 | 67.8 | 1 | 9 | 46 | 4 979 |
3612 | GCA 001698225.1 | 5.70 | 67.8 | 1 | 9 | 46 | 4 977 |
RL-JC02 | GCA 011290605.1 | 5.31 | 67.87 | 2 | 9 | 47 | 4 627 |
NRRL B-16283 | GCA 000716975.1 | 5.67 | 67.8 | 108 | 7 | 46 | 4 938 |
UMB0777 | GCA 002847865.1 | 5.70 | 67.7 | 180 | 3 | 46 | 5 007 |
K | GCA 005502725.1 | 5.19 | 68 | 155 | 9 | 45 | 4 480 |
C-6 | GCA 000390025.1 | 5.17 | 67.9 | 130 | 5 | 45 | 4 572 |
NBRC 100016 | GCA 000248035.2 | 5.67 | 67.8 | 130 | 6 | 46 | 4 956 |
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