Biotechnology Bulletin ›› 2022, Vol. 38 ›› Issue (9): 136-146.doi: 10.13560/j.cnki.biotech.bull.1985.2022-0112
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LI Ji-hong1,2(
), JING Yu-ling2, MA Gui-zhen1(), GUO Rong-jun2(), LI Shi-dong2
Received:2022-01-25
Online:2022-09-26
Published:2022-10-11
Contact:
MA Gui-zhen,GUO Rong-jun
E-mail:804797175@qq.com;guizhenma@sohu.com;guorj20150620@126.com
LI Ji-hong, JING Yu-ling, MA Gui-zhen, GUO Rong-jun, LI Shi-dong. Genome Construction of Achromobacter 77 and Its Characteristics on Chemotaxis and Antibiotic Resistance[J]. Biotechnology Bulletin, 2022, 38(9): 136-146.
Fig. 1 Demonstration of chemotactic response of strain 77 to fungal and root exudates The plate was divided into two parts for two parallel tests of the same treatment. A and B shows the inoculation site of the candidate chemotactic compounds and sterilized water,respectively,and C shows the inoculation site of the bacterial suspension of strain 77
| 名称Name | 数据Data |
|---|---|
| 基因组大小Genome size | 5 868 070 bp |
| Scaffold条数Number of Scaffolds | 1 |
| 染色体数Number of chromosomes | 1 |
| 质粒数Number of plasmids | 0 |
| GC含量GC content | 65.89% |
| CRISPR-Cas系统数量Number of CRISPR-Cas system | 7 |
| tRNA数目Number of tRNA | 55 |
| rRNA数量Number of rRNA | 13 |
| 基因组岛数量Number of genome island | 12 |
| 基因数目Number of CDS | 5 475 |
Table 1 Genome assembly of strain 77
| 名称Name | 数据Data |
|---|---|
| 基因组大小Genome size | 5 868 070 bp |
| Scaffold条数Number of Scaffolds | 1 |
| 染色体数Number of chromosomes | 1 |
| 质粒数Number of plasmids | 0 |
| GC含量GC content | 65.89% |
| CRISPR-Cas系统数量Number of CRISPR-Cas system | 7 |
| tRNA数目Number of tRNA | 55 |
| rRNA数量Number of rRNA | 13 |
| 基因组岛数量Number of genome island | 12 |
| 基因数目Number of CDS | 5 475 |
Fig. 2 Circle map of the genome of strain 77 The outside circle of the map shows the genome size. The second and third circles are CDS on the positive and negative chains. Different colors indicate the functional classification of different COG of CDS. The fourth circle is rRNA and tRNA. The fifth circle is GC content. The outward red part indicates that GC content in this region is higher than the average GC content in the whole genome. The higher the peak value,the greater the difference between GC content in this region and the average GC content. The interior blue part indicates that GC content in this region is lower than the average GC content in the whole genome. The higher the peak value,the greater the difference between GC content in this region and the average GC content. The interior circle is GC-SKEW
Fig. 3 KEGG annotated pathways of strain 77's genome The vertical coordinate represent the level2 classification of KEGG pathway,and the horizontal coordinate represents the number of genes under this classification. Different colors represent the level1 classification of KEGG pathway. The right column represents the number of genes under different level1 classifications. Since the same gene may be annotated into more than one level2 categories,de-redundancy is performed when counting the number of genes in level1 categories
Fig. 4 Annotated classification of COG functions of strain 77's genome
Fig. 5 Classification of GO functions annotation of strain 77's genome Each category shows TOP 10 GO annotations
| GO注释GO annotation | 基因数Number of genes |
|---|---|
| 代谢过程Metabolic process | 158 |
| 三羧酸循环Tricarboxylic acid cycle | 18 |
| 苹果酸代谢Malate metabolic process | 4 |
| 细胞氨基酸分解代谢 Cellular amino acid catabolic process | 5 |
| 胁迫应答Stress response | 22 |
| 抗生素分解Antibiotic decomposition | 2 |
| 药物跨膜运输Transmembrane transport of drugs | 2 |
| 细胞氧化解毒Cellular oxidant detoxification | 33 |
| 趋化性Chemotaxis | 33 |
| 细菌型鞭毛依赖运动 Bacterial-type flagellum-dependent cell motility | 18 |
Table 2 Statistics of catabolism and chemotaxis related genes in GO annotation of strain 77's genome
| GO注释GO annotation | 基因数Number of genes |
|---|---|
| 代谢过程Metabolic process | 158 |
| 三羧酸循环Tricarboxylic acid cycle | 18 |
| 苹果酸代谢Malate metabolic process | 4 |
| 细胞氨基酸分解代谢 Cellular amino acid catabolic process | 5 |
| 胁迫应答Stress response | 22 |
| 抗生素分解Antibiotic decomposition | 2 |
| 药物跨膜运输Transmembrane transport of drugs | 2 |
| 细胞氧化解毒Cellular oxidant detoxification | 33 |
| 趋化性Chemotaxis | 33 |
| 细菌型鞭毛依赖运动 Bacterial-type flagellum-dependent cell motility | 18 |
Fig. 6 Statistics of CAZyme annotation of strain 77's genome
| 基因类别 Gene classification | 基因名称 Gene name | 基因数量 Number of genes | 基因编号 Gene ID | KEGG数据库基因注释 Gene annotation in KEGG database |
|---|---|---|---|---|
| mcp | mcp | 9 | gene0255、gene0975、gene1020、gene2196、gene3307、gene3446、gene4030、gene4485、gene4827 | 甲基趋化受体蛋白Mcp |
| che | cheA | 1 | gene2189 | 感受器激酶CheA |
| cheW | 1 | gene2190 | 嘌呤结合趋化蛋白CheW | |
| cheR | 2 | gene2192、gene4468 | 甲基转移酶CheR | |
| cheB | 2 | gene2193、gene3711 | 趋化响应调节蛋白CheB | |
| cheBR | 1 | gene4467 | CheB/CheR融合蛋白 | |
| cheD | 1 | gene5023 | 趋化蛋白CheD | |
| wsp | wspF | 1 | gene3040 | 趋化响应调节蛋白WspF |
| wspD、wspB | 2 | gene3042、gene3044 | 趋化相关蛋白WspD、WspB | |
| wspC | 1 | gene3043 | 甲基转移酶WspC | |
| wspA | 1 | gene3045 | 甲基趋化受体蛋白WspA | |
| mot | motA | 1 | gene2381 | 鞭毛马达蛋白MotA |
| aer | aer | 2 | gene2219、gene2311 | 趋氧性受体蛋白Aer |
| tar | tar | 1 | gene4676 | 甲基趋化受体蛋白Ⅱ（天冬氨酸感受器受体） |
| - | - | 5 | gene0304、gene2191、gene2214、gene2215、gene2217 | 未知功能趋化蛋白 |
| - | - | 1 | gene3125 | 未知功能趋化蛋白 |
| - | - | 1 | gene3000 | 未知功能趋化蛋白 |
Table 3 Predictive classification of chemotactic genes of strain 77
| 基因类别 Gene classification | 基因名称 Gene name | 基因数量 Number of genes | 基因编号 Gene ID | KEGG数据库基因注释 Gene annotation in KEGG database |
|---|---|---|---|---|
| mcp | mcp | 9 | gene0255、gene0975、gene1020、gene2196、gene3307、gene3446、gene4030、gene4485、gene4827 | 甲基趋化受体蛋白Mcp |
| che | cheA | 1 | gene2189 | 感受器激酶CheA |
| cheW | 1 | gene2190 | 嘌呤结合趋化蛋白CheW | |
| cheR | 2 | gene2192、gene4468 | 甲基转移酶CheR | |
| cheB | 2 | gene2193、gene3711 | 趋化响应调节蛋白CheB | |
| cheBR | 1 | gene4467 | CheB/CheR融合蛋白 | |
| cheD | 1 | gene5023 | 趋化蛋白CheD | |
| wsp | wspF | 1 | gene3040 | 趋化响应调节蛋白WspF |
| wspD、wspB | 2 | gene3042、gene3044 | 趋化相关蛋白WspD、WspB | |
| wspC | 1 | gene3043 | 甲基转移酶WspC | |
| wspA | 1 | gene3045 | 甲基趋化受体蛋白WspA | |
| mot | motA | 1 | gene2381 | 鞭毛马达蛋白MotA |
| aer | aer | 2 | gene2219、gene2311 | 趋氧性受体蛋白Aer |
| tar | tar | 1 | gene4676 | 甲基趋化受体蛋白Ⅱ（天冬氨酸感受器受体） |
| - | - | 5 | gene0304、gene2191、gene2214、gene2215、gene2217 | 未知功能趋化蛋白 |
| - | - | 1 | gene3125 | 未知功能趋化蛋白 |
| - | - | 1 | gene3000 | 未知功能趋化蛋白 |
| 分泌系统Secretion system | 数量Amount |
|---|---|
| Ⅰ型 Type Ⅰ | 1 |
| Ⅱ型 Type Ⅱ | 11 |
| Ⅲ型 Type Ⅲ | 0 |
| Ⅳ型 Type Ⅳ | 2 |
| Ⅴ型 Type Ⅴ | 0 |
| Ⅵ型 Type Ⅵ | 17 |
Table 4 Classification in secretion system of strain 77
| 分泌系统Secretion system | 数量Amount |
|---|---|
| Ⅰ型 Type Ⅰ | 1 |
| Ⅱ型 Type Ⅱ | 11 |
| Ⅲ型 Type Ⅲ | 0 |
| Ⅳ型 Type Ⅳ | 2 |
| Ⅴ型 Type Ⅴ | 0 |
| Ⅵ型 Type Ⅵ | 17 |
Fig. 7 Predictive classification of drug resistance genes
Fig.8 Chemotactic responses of stain 77 to fungal and root exudates The red dots indicate the inoculation site of the candidate chemotactic compounds or sterile water,and the red arrows point to the arc-shaped chemotactic circle formed by the chemotactic response of strain 77
| 化合物浓度 Concentration/ （mmol.L-1） | 真菌或根分泌物 Fungal or root exudates | 根分泌物 Root exudate | 尖孢镰刀菌分泌物 Exudate of Fusarium oxysporum | ||||||
|---|---|---|---|---|---|---|---|---|---|
| 延胡索酸 Fumaric acid | α-酮戊二酸 α -ketoglutaric acid | 苹果酸 Malic acid | 琥珀酸 Succinic acid | 水杨酸 Salicylic acid | 对羟基苯乙酸4-Hyd-roxyphenylacetic acid | 镰刀菌酸 Fusaric acid | |||
| 0 | 0.278±0.002 d | 0.334±0.002 bc | 0.274±0.004 b | 0.285±0.012 c | 0.295±0.003 d | 0.642±0.008 b | 0.293±0.004 c | ||
| 0.5 | 0.323±0.003 b | 0.344±0.002 ab | 0.319±0.005 a | 0.315±0.004 a | 0.334±0.002 b | 0.775±0.003 a | 0.340±0.002 a | ||
| 1 | 0.351±0.001 a | 0.351±0.002 a | 0.312±0.002 a | 0.313±0.006 ab | 0.366±0.002 a | 0.760±0.019 a | 0.322±0.005 b | ||
| 2 | 0.304±0.009 c | 0.331±0.001 bc | 0.285±0.004 b | 0.298±0.011 bc | 0.317±0.006 bc | 0.049±0.002 c | 0.272±0.018 d | ||
| 4 | 0.299±0.012 c | 0.326±0.004 c | 0.272±0.006 bc | 0.291±0.002 c | 0.307±0.003 cd | 0.049±0.003 c | 0.111±0.007 e | ||
| 6 | 0.288±0.002 d | 0.308±0.002 d | 0.088±0.011 d | 0.243±0.012 d | 0.223±0.026 e | 0.053±0.002 c | 0.055±0.004 f | ||
| 8 | 0.063±0.002 e | 0.095±0.018 e | 0.052±0.002 e | 0.094±0.005 e | 0.054±0.003 f | 0.052±0.003 c | 0.054±0.005 f | ||
| 10 | 0.054±0.004 e | 0.056±0.007 f | 0.054±0.003 e | 0.058±0.002 f | 0.051±0.001 f | 0.053±0.001 c | 0.053±0.003 f | ||
Table 5 Effects of fungal and root exudate components on OD600 value of strain 77
| 化合物浓度 Concentration/ （mmol.L-1） | 真菌或根分泌物 Fungal or root exudates | 根分泌物 Root exudate | 尖孢镰刀菌分泌物 Exudate of Fusarium oxysporum | ||||||
|---|---|---|---|---|---|---|---|---|---|
| 延胡索酸 Fumaric acid | α-酮戊二酸 α -ketoglutaric acid | 苹果酸 Malic acid | 琥珀酸 Succinic acid | 水杨酸 Salicylic acid | 对羟基苯乙酸4-Hyd-roxyphenylacetic acid | 镰刀菌酸 Fusaric acid | |||
| 0 | 0.278±0.002 d | 0.334±0.002 bc | 0.274±0.004 b | 0.285±0.012 c | 0.295±0.003 d | 0.642±0.008 b | 0.293±0.004 c | ||
| 0.5 | 0.323±0.003 b | 0.344±0.002 ab | 0.319±0.005 a | 0.315±0.004 a | 0.334±0.002 b | 0.775±0.003 a | 0.340±0.002 a | ||
| 1 | 0.351±0.001 a | 0.351±0.002 a | 0.312±0.002 a | 0.313±0.006 ab | 0.366±0.002 a | 0.760±0.019 a | 0.322±0.005 b | ||
| 2 | 0.304±0.009 c | 0.331±0.001 bc | 0.285±0.004 b | 0.298±0.011 bc | 0.317±0.006 bc | 0.049±0.002 c | 0.272±0.018 d | ||
| 4 | 0.299±0.012 c | 0.326±0.004 c | 0.272±0.006 bc | 0.291±0.002 c | 0.307±0.003 cd | 0.049±0.003 c | 0.111±0.007 e | ||
| 6 | 0.288±0.002 d | 0.308±0.002 d | 0.088±0.011 d | 0.243±0.012 d | 0.223±0.026 e | 0.053±0.002 c | 0.055±0.004 f | ||
| 8 | 0.063±0.002 e | 0.095±0.018 e | 0.052±0.002 e | 0.094±0.005 e | 0.054±0.003 f | 0.052±0.003 c | 0.054±0.005 f | ||
| 10 | 0.054±0.004 e | 0.056±0.007 f | 0.054±0.003 e | 0.058±0.002 f | 0.051±0.001 f | 0.053±0.001 c | 0.053±0.003 f | ||
Fig. 9 Resistances of strain 77 to common antibiotics
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