基于苯酚降解的粪产碱杆菌Alcaligenes faecalis JF101的全基因组分析

doi:10.13560/j.cnki.biotech.bull.1985.2023-0281

摘要/Abstract

摘要：

粪产碱杆菌属对芳香族类物质表现出广泛的降解能力，本研究对1株粪产碱杆菌（Alcaligenes faecalis）JF101开展苯酚降解基因解析，并进一步挖掘其潜在功能。通过对菌株JF101全基因组测序、组装和功能注释，分析其降解苯酚的功能基因，并与5株近缘菌株开展比较基因组学研究。结果表明，JF101基因组大小为4 143 816 bp，GC含量为 57.44%，含有3 804个编码蛋白基因和55个tRNA、9个rRNA、5个sRNA，在COG、GO、KEGG数据库中分别注释到3 040、2 529、2 415个基因。鉴定了11个苯酚降解基因。比较基因组学表明，菌株JF101没有质粒，与同属的5株菌株有2 008个共有同源基因家族和5个特异基因家族。此外发现菌株JF101含有与相容性溶质转运相关的Trk、Kdp等基因，实验测定了其耐盐能力。通过对菌株JF101全基因组的解析，为进一步阐释其苯酚降解机制及发展实际工程应用奠定了基础。

关键词: 粪产碱杆菌, 苯酚降解, 全基因组测序

Abstract:

The genus Alcaligenes shows extensive degradation capacity for aromatic compounds. In the present study, the phenol-degrading genes in Alcaligenes faecalis JF101 were analyzed and the potential functions were explored. The whole genome of strain JF101 was sequenced, assembled and annotated for analyzing the genes involved in phenol degradation. Moreover, the comparative genomics with five related strains was carried out. Results showed that the whole genome size of strain JF101 was 4 143 816 bp, and the GC content was 57.44%, with 3 804 protein-coding genes, 55 tRNAs genes, 9 rRNAs genes and 5 sRNA. There were 3 040, 2 529 and 2 415 annotated genes in COG, GO and KEGG databases, respectively. Eleven genes involving in phenol degradation were identified. Comparative genomics revealed that strain JF101 had no plasmid, and shared 2 008 common homologous gene families and 5 specific gene families with the five related strains. In addition, the putative gene Trk and Kdp involved in compatible solute transport, were found in strain JF101, and the salt-tolerant ability was confirmed by experiments. The whole-genome analysis of strain JF101 will benefit the further elucidating mechanism of phenol degradation and developing engineering applications.

Key words: Alcaligenes faecalis, phenol degradation, whole genome sequencing

张傲洁, 李青云, 宋文红, 颜少慧, 唐爱星, 刘幽燕. 基于苯酚降解的粪产碱杆菌Alcaligenes faecalis JF101的全基因组分析[J]. 生物技术通报, 2023, 39(10): 292-303.

ZHANG Ao-jie, LI Qing-yun, SONG Wen-hong, YAN Shao-hui, TANG Ai-xing, LIU You-yan. Whole Genome Sequencing Analysis of a Phenol-degrading Strain Alcaligenes faecalis JF101[J]. Biotechnology Bulletin, 2023, 39(10): 292-303.

图/表 10

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Protein	Amino acid	Proposed function	Sequence similarrty	Identity similarity/%	Accession No
GL-1751	396	Muconate cycloisomerase	catB, Alcaligenes faecalis strain ZD02	97.0	ALO39907.1
GL-1752	311	Catechol 1,2-dioxygenase	catA, Alcaligenes faecalis strain ZD02	99.7	ALO39908.1
GL-1755	267	3-oxoadipate enol-lactonase	pcaD, Alcaligenes aquatilis strain QD168	98.5	AYN20737.1
GL-1756	91	Muconolactone D-isomerase	catC, Alcaligenes faecalis strain ZD02	100	ALO39912.1
GL-1849	334	Nif-specific regulatory protein	MOPR, Sediminispirochaeta smaragdinae DSM 11293	47.9	ADK82111.1
GL-1850	82	Phenol hydroxylase P0 protein	dmpK, Alcaligenes faecalis strain JQ135	97.6	ASR89481.1
GL-1851	332	Phenol hydroxylase P1 protein	dmpL, Alcaligenes faecalis strain ZD02	99.1	ALO39961.1
GL-1852	90	Phenol hydroxylase P2 protein	dmpM, Alcaligenes faecalis strain ZD02	100	ALO39962.1
GL-1853	498	Phenol hydroxylase P3 protein	dmpN, Psychrobacter sp. P2G3	86.7	AMN49709.1
GL-1854	120	Phenol hydroxylase P4 protein	dmpO, Alcaligenes faecalis strain ZD02	98.3	ALO39964.1
GL-1855	353	Phenol hydroxylase P5 protein	dmpP, Alcaligenes faecalis strain ZD02	98.9	ALO39965.1

Protein	Amino acid	Proposed function	Sequence similarrty	Identity similarity/%	Accession No
GL-1751	396	Muconate cycloisomerase	catB, Alcaligenes faecalis strain ZD02	97.0	ALO39907.1
GL-1752	311	Catechol 1,2-dioxygenase	catA, Alcaligenes faecalis strain ZD02	99.7	ALO39908.1
GL-1755	267	3-oxoadipate enol-lactonase	pcaD, Alcaligenes aquatilis strain QD168	98.5	AYN20737.1
GL-1756	91	Muconolactone D-isomerase	catC, Alcaligenes faecalis strain ZD02	100	ALO39912.1
GL-1849	334	Nif-specific regulatory protein	MOPR, Sediminispirochaeta smaragdinae DSM 11293	47.9	ADK82111.1
GL-1850	82	Phenol hydroxylase P0 protein	dmpK, Alcaligenes faecalis strain JQ135	97.6	ASR89481.1
GL-1851	332	Phenol hydroxylase P1 protein	dmpL, Alcaligenes faecalis strain ZD02	99.1	ALO39961.1
GL-1852	90	Phenol hydroxylase P2 protein	dmpM, Alcaligenes faecalis strain ZD02	100	ALO39962.1
GL-1853	498	Phenol hydroxylase P3 protein	dmpN, Psychrobacter sp. P2G3	86.7	AMN49709.1
GL-1854	120	Phenol hydroxylase P4 protein	dmpO, Alcaligenes faecalis strain ZD02	98.3	ALO39964.1
GL-1855	353	Phenol hydroxylase P5 protein	dmpP, Alcaligenes faecalis strain ZD02	98.9	ALO39965.1

菌株 Strain	基因组大小 Genome size/Mb	编码蛋白 Protein coding	rRNA数量 rRNA genes	tRNA数量 tRNA genes	GC含量 GC/%	质粒数 Number of plasmids
MUB14	4.35	3973	9	58	56.74	2（0.04 Mb, 0.06 Mb）
P156	4.04	3616	9	57	56.7	0
ZD02	4.23	3752	9	57	56.81	1（0.01 Mb）
c16	4.30	3847	9	57	56.3	0
ASM96730v2	4.23	3770	9	57	56.8	1（0.01 Mb）
JF101	4.14	3804	9	55	57.44	0

菌株 Strain	基因组大小 Genome size/Mb	编码蛋白 Protein coding	rRNA数量 rRNA genes	tRNA数量 tRNA genes	GC含量 GC/%	质粒数 Number of plasmids
MUB14	4.35	3973	9	58	56.74	2（0.04 Mb, 0.06 Mb）
P156	4.04	3616	9	57	56.7	0
ZD02	4.23	3752	9	57	56.81	1（0.01 Mb）
c16	4.30	3847	9	57	56.3	0
ASM96730v2	4.23	3770	9	57	56.8	1（0.01 Mb）
JF101	4.14	3804	9	55	57.44	0

相容性溶质转运相关基因 Compatible solutes transport genes	基因名称 Name	基因位置 Locus tag	基因长度 Length/bp	基因描述 Description
K⁺ transport system	Trk system Kdp system	GL-1953、GL-1954 GL-1574、GL-1575、GL-1576	455、217 568、237、687	Trk系统钾摄取蛋白 K+转运ATP酶A、B、C链
Proline and betaine transport	ProP system	GL-0834、GL-1501、GL-2239、GL-2295、GL-3438、GL-3579	452、436、565、423、425、510	MFS转运体，MHS家族，脯氨酸/甜菜碱转运体
Choline/glycine/proline betaine transport genes	betT、betS	GL-2836	706	胆碱/甘氨酸/脯氨酸甜菜碱转运蛋白