微生物学报  2016, Vol. 56 Issue (4): 570-577
http://dx.doi.org/10.13343/j.cnki.wsxb.20150277
中国科学院微生物研究所,中国微生物学会,中国菌物学会
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文章信息

张新建, 张广志, 杨合同
Xinjian Zhang, Guangzhi Zhang, Hetong Yang
节杆菌环境适应性的基因组学研究进展
Genomics basis of Arthrobacter spp. environmental adaptability-A review
微生物学报, 2016, 56(4): 570-577
Acta Microbiologica Sinica, 2016, 56(4): 570-577

文章历史

收稿日期:2015-06-23
修回日期:2015-08-11
网络出版日期:2015-09-22
节杆菌环境适应性的基因组学研究进展
张新建, 张广志, 杨合同     
山东省科学院生态研究所, 山东省应用微生物重点实验室, 山东济南 250014
摘要: 节杆菌分布广泛,能适应多种环境条件,而且多数节杆菌具有营养多功能性,能降解多种环境污染物,因而受到人们的广泛关注。近年来,随着多株节杆菌基因组的测序完成,人们对节杆菌环境适应性的分子机制有了全面的认识。基因组学研究结果表明,节杆菌在σ因子、氧化应激、渗透应激、饥饿应激、温度应激等胁迫应激反应相关基因方面的特点使其能够在多种环境条件下生存。本文挑选部分具有代表性的节杆菌基因组学研究,对其环境适应性的基因组学基础进行综述,以期为利用节杆菌进行环境污染修复提供理论基础,并为其它细菌的环境适应性机制研究提供参考。
关键词: 节杆菌    环境适应性    基因组学    
Genomics basis of Arthrobacter spp. environmental adaptability-A review
Xinjian Zhang, Guangzhi Zhang, Hetong Yang     
Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, China
Abstract:Arthrobacter species are found ecologically diverse and can survive in various environments. Many strains of these species have metabolic versatility and can degrade many environmental pollutants. Arthrobacter species are thought to play important roles in catabolism of environmental pollutants in nature. In recent years, the genomes of many Arthrobacter strains have been sequenced, which provides comprehensive information to clarify the molecular mechanisms related to environmental adaptability of Arthrobacter species. These genomics findings revealed several features that are commonly observed in Arthrobacter strains allowing for survival under stressful conditions. These include an array of genes associated with sigma factors and responses to oxidative, osmotic, starvation and temperature stresses. The genomics basis of their environmental adaptability are reviewed, which is expected to provide useful information for applying Arthrobacter strains in pollution remediation and shed some light on other bacterial environmental adaptability researches.
Key words: Arthrobacter spp.    environmental adaptability    genomics    

节杆菌(Arthrobacter spp.)是最常分离到的土壤细菌种类之一,在地球上分布广泛,几乎无处不在。从土壤到植物,从高山到海水,从考古壁画到临床样本,都可以分离到节杆菌[1, 2, 3, 4, 5]。节杆菌广泛分布的部分原因是它们具有能在饥饿、温度变化、电离辐射、氧自由基和有毒化合物等所致的胁迫环境下长期存活的能力[3]。例如,在新疆沙漠地区的土壤中能分离到节杆菌[6];在南极和北极地区、冰川淤积物、高山冰川的冰尘和冰穴中均能发现节杆菌[7];从华盛顿美国能源部放射性核素储罐的渗漏物中分离的细菌中,节杆菌是最普遍的种类之一[8]

节杆菌具有营养多功能性,能降解多种环境污染物,被认为是主要的有机物分解者。节杆菌被报道可以降解硝化甘油、多种苯衍生物、多环芳香族化合物、卤代醇、卤代烃、N-杂环化合物、杀虫剂和除草剂等多种化合物[9, 10, 11, 12, 13, 14]。此外,节杆菌对许多有毒的重金属和铬酸盐类物质具有很强的耐受性[15, 16, 17]。营养上的多功能性以及对多种胁迫的抗性,使节杆菌种群在多种生态位均处于优势地位。

近年来,随着基因组测序所需时间缩短和成本大大降低,已有多株节杆菌(Arthrobacter spp.) 完成了基因组测序[3, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34],截至2015年5月,GenBank 的Genome数据库已收录了47株节杆菌的基因组序列。这些序列的获得,为从基因组水平上全面了解节杆菌环境适应性的分子基础提供了重要信息。

1 节杆菌基因组基本特征

在GenBank中收录的47株节杆菌基因组中,有8株是完成图,表 1列出了这8株节杆菌基因组的一般特征。从表 1中可见,节杆菌的基因组大小为3.60–5.23 Mb,GC含量为59%–66%。Dsouza 等[7]对14株节杆菌进行了泛基因组分析 (pan-genome),其中包括7株南极节杆菌与7株温和地区的节杆菌(A. aurescens TC1、A. castelli DSM16402、A. chlorophenolicus A6、A. globiformis NBRC12137、Arthrobacter sp. Rue61a、A. phenanthrenivorans Sphe3和Arthrobacter sp. FB24)。结果发现这14株节杆菌的泛基因组包含14902个基因,显示了辅助基因的多样性。核心基因组(core-genome)含有1153个基因家族,代表节杆菌基因组中全部基因的27%。核心基因组中多数基因的COG (Clusters of Orthologous Groups)分类为氨基酸转运与代谢(E)、糖类转运与代谢(G)和翻译、核糖体结构和生物合成(J)[7]

表 1 节杆菌基因组的一般特征 Table 1 General features from completed Arthrobacter genomes
Strains Size/Mb (G+C)% Genes Proteins tRNA rRNA Accession No. References
Arthrobacter sp. IHBB 11108 3.60 59.0 3385 3318 46 6 NZ_CP011005 Unpublished
Arthrobacter sp. PAMC25486 4.59 62.8 4125 3976 53 18 NZ_CP007595 Unpublished
Arthrobacter sp. Rue61a 5.08 62.2 4667 4557 53 18 NC_018531 [29]
Arthrobacter sp. FB24 5.07 65.4 4601 4484 51 15 NC_008541 Unpublished
A. phenanthrenivorans Sphe3 4.54 65.4 4231 4098 50 12 NC_015145 [21]
A. arilaitensis Re117 3.92 59.3 3660 3492 64 19 NC_014550 [27]
A. chlorophenolicus A6 4.98 66.0 4661 4521 86 15 NC_011886 Unpublished
A. aurescens TC1 5.23 62.4 4755 4648 54 18 NC_008711 [3]
2 节杆菌抗环境胁迫的共性机制 2.1 σ因子

诱导选择性σ因子是细菌应对环境胁迫的重要策略,而选择性σ因子的数量与环境复杂性具有显著的相关性。金黄节杆菌(A. aurescens)TC1基因组中编码17个σ70家族的σ因子和1个RNA聚合酶σ70因子,而TC1的染色体和质粒上共编码34个转录因子[3]。与节杆菌(Arthrobacter sp.)Rue61a和另一株金黄节杆菌M2012083的数目相当,它们基因组中转录因子都为35个,σ70家族σ因子的数目分别为18和17个[9]。阿氏节杆菌(A. arilaitensis)Re117是奶酪表面栖居菌,与环境节杆菌相比,Re117菌株中σ70家族的σ因子数量(6个)减少,说明其适应了奶酪表面这一更加稳定的生态位[9, 27]

2.2 氧化应激

活性氧是有氧呼吸的副产物,金黄节杆菌TC1基因组中含有40多种氧化酶基因,氧化酶能产生H2O2,并产生其它的活性氧种类,可以破坏和导致细胞死亡。为应对这些活性氧自由基,在菌株TC1基因组中含有1个超氧化物歧化酶基因、4个过氧化氢酶基因和1个过氧化物酶相关基因。节杆菌Rue61a中含有3个过氧化氢酶的编码基因、1个谷胱甘肽过氧化物酶、1个过氧化物酶类似蛋白和几个过氧化物还原酶的编码基因。节杆菌Rue61a对超氧化物的脱毒作用,是通过Fe/Mn超氧化物歧化酶进行的,而且在线状质粒上还存在另外一个Fe/Mn超氧化物歧化酶基因,该酶还可能参与了喹哪啶的分解代谢[29]

2.3 渗透应激

细菌对高渗胁迫的反应往往包含多个方面,如钾离子的瞬间积累、通过吸收与合成使胞内有机渗透物质浓度增加等。在节杆菌Rue61a中含有负责调高渗透压的Trk/Ktr系统和摄取有机渗透物质的系统,包括几个脯氨酸/甜菜碱转运系统主要易化子超家族的蛋白基因、1个甜菜碱/肉毒碱/胆碱转运蛋白家族的蛋白和3个ABC类型的甜菜碱/ 肉毒碱/胆碱或脯氨酸/甜菜碱转运蛋白[29]。在金黄节杆菌M2012083基因组中,也存在多个利用外源胆碱作为底物合成甜菜碱以维持渗透平衡的相关基因,还可通过调节胞内水运动、甘油摄取和周质葡聚糖合成等过程降低渗透胁迫,上述过程由水通道蛋白Z、甘油摄取促进因子蛋白和渗透调节周质葡聚糖合成酶C等控制[9]

2.4 饥饿应激

在营养和其它胁迫下,土壤细菌往往需要rpoS和σB等RNA聚合酶选择性σ因子参与基因调节[35, 36],在碳饥饿反应中,rpoS的基因表达被碳饥饿感知蛋白RpsA抑制[37],在节杆菌Rue61a和金黄节杆菌TC1、M2012083基因组中均含有rpsA的同源基因[9]。该基因参与饥饿或平台期的应激反应,能通过苏氨酸合成途径,利用高丝氨酸合成高丝氨酸内酯。群体感应也能调节过氧化氢酶和超氧化物歧化酶的表达,进一步表明高丝氨酸内酯合成与氧化和饥饿胁迫相关。在金黄节杆菌TC1中还存在其它与饥饿应激有关的基因,如碳-饥饿蛋白基因能调节cAMP-CRP碳饥饿反应[3]

2.5 重金属抗性

能量依赖性外排泵是细菌对金属离子脱毒的主要机制,在节杆菌Rue61a基因组中存在阳离子扩散促进蛋白家族的逆向转运蛋白基因,可能与Zn2+和Co2+的耐受性有关。在线状质粒上存在镍、铜逆向转运蛋白类似基因。许多重要的重金属阳离子的外排泵系统是P型ATP酶,在染色体上存在介导Cu+/Ag+外排的P型ATP酶,在环状质粒上存在2个Cd2+/Zn2+/Pb2+运输的P型ATP酶,可能与Rue61a菌株对Pb2+的耐受性有关[29]。在金黄节杆菌TC1中,其质粒pTC2上含有3个铜、4个砷和1个钴-锌-镉抗性相关基因[3]

2.6 其它应激反应基因

节杆菌中往往含有编码广泛应激蛋白、热激蛋白、冷休克蛋白、一般应激蛋白、饥饿诱导蛋白和渗透调节蛋白的基因[3, 9]。广泛应激蛋白在细胞受到热、氧化、紫外线、饥饿等胁迫或进入平台生长期往往会诱导表达,生活在胁迫条件下的细菌含有的广泛应激蛋白数目往往比胞内寄生细菌多,如RicketsiaMycoplasmaChlamydia菌仅含有1个广泛应激蛋白基因,而盐杆菌Halobacterium sp. NRC-1含有8个[3]。在金黄节杆菌TC1和M2012083中都含有8个广泛应激蛋白,在节杆菌Rue61a 、FB24基因组中分别含有13个和15个[9]

3 不同节杆菌适应环境的特异机制 3.1 s-三嗪类化合物降解菌——金黄节杆菌TC1

金黄节杆菌(Arthrobacteraurescens) TC1是目前研究最透彻的节杆菌,该菌株最初从被阿特拉津污染的土壤中分离出来[38],研究表明它能代谢23种以上的s-三嗪类物质[39]。通过对其基因组及代谢能力分析,推测菌株TC1可以分解代谢500种以上结构不同的s-三嗪类化合物[40]

金黄节杆菌TC1的基因组含有1个环状染色体和2个环状质粒pTC1和pTC2。节杆菌TC1染色体和质粒上有约10%的基因在其基因组中存在旁系同源基因,而这些功能冗余性可能赋予了该菌株快速适应环境变化的能力。质粒pTC1上包含将阿特拉津降解到氰尿酸的基因,在pTC1上含有6个串联的16 kb重复序列,在这一重复区域含有三嗪水解酶基因(trzN)。trzN基因编码s-三嗪类物质生物降解途径的第一个酶,基因的多拷贝可通过剂量效应提高代谢能力,为与其它细菌竞争提供了优势,如Pseudomonas sp. ADP菌株仅含有1个三嗪水解酶基因[41]

3.2 喹哪啶降解菌——节杆菌Rue61a

由于甲基喹啉、喹啉和其它N-芳香杂环化合物等具有毒性和诱变活性,而且喹啉比其同素环萘类似物具有更高的极性,更容易进入深层土壤和地下水,因此引起人们的广泛关注。节杆菌(Arthrobacter sp.) Rue61a是从煤焦油精炼污水处理厂的污泥中分离获得,该菌株可以利用喹哪啶(2-甲基喹啉)作为唯一碳源和能量来源[42]

Rue61a菌株基因组含有1个环状染色体、1个环状质粒和1个线状质粒。Rue61a喹哪啶代谢途径上游相关基因成簇分布在线状质粒上,其编码的酶类可将喹哪啶转换成邻氨基苯甲酸盐,而邻氨基苯甲酸盐可通过CoA-硫酯代谢途径进一步降解[43]。除了喹哪啶,Rue61a还具有少数其它的芳环降解途径,能利用4-羟基替代的芳香羧酸,而木质素经原儿茶酸邻位分裂后的解聚产物就是这类物质,推测Rue61a可以利用木质素裂解微生物产生的低分子量芳香族化合物[29]

3.3 尼古丁降解菌——金黄节杆菌M2012083

金黄节杆菌(A. aurescens) M2012083是从烟草废弃物中分离的,其基因组大小约为4.63 Mb[34]。菌株M2012083中,所有与尼古丁降解有关的基因、如尼古丁脱氢酶、6-羟基-L-尼古丁氧化酶、酮脱氢酶等位于一个大小为68.6 kb的DNA片段上,该片段与另一株节杆菌(A. nicotinovorans) 质粒pAO1上的nic片段(大小为69.3 kb) 有98.1%核苷酸序列相似性[44]。但序列分析表明,在M2012083 中尼古丁降解相关基因位于染色体或另外一个非pAO1的质粒上[9]

3.4 奶酪表面栖居菌——阿氏节杆菌Re117

擦拭熟成的奶酪(Smear-ripened cheese)是利用细菌进行熟成的,在奶酪表面栖居的细菌在每cm2的面积上数量超过1010,这些细菌对于奶酪的颜色、味道、香气和质构特性有重要影响[45]。阿氏节杆菌(A. arilaitensis)是奶酪表面栖居主要的细菌种类之一,能产生黄色素,可能与奶酪的颜色形成有关[46]

由于奶酪跟土壤在营养成分等方面存在很大的不同,节杆菌Re117在基因组水平上,表现出与适应奶酪表面这一特殊生境相关的特点。与环境节杆菌相比,菌株Re117的基因组比较小(3.86 Mb),在缺失的基因中,有约20%的基因与糖类运输及代谢有关,可能与奶酪表面的糖类物质有限有关。但是Re117具有分解外源D-半乳糖酸的能力,D-半乳糖酸在牛奶和奶酪中存在,但在自然界中分布较少。Re117分解D-半乳糖酸的能力是通过近期基因水平转移实现的,获得了4个来源于革兰氏阴性菌的成簇基因。而且,Re117基因组中含有较多的铁摄取相关基因,这可能由于奶酪是一个高度贫铁的培养基。此外,奶酪在加工过程中往往会加盐以延长货架期,在Re117基因组中含有数量较多的甜菜碱及相关渗透物转运蛋白基因,这可能与耐盐性的提高有关[27]

4 结语

节杆菌分布广泛,能够在多种环境条件下生存,而且节杆菌具有营养多功能性,能降解多种环境污染物,上述特点使节杆菌成为经常分离到的污染物降解菌株。我们实验室在研究阿特拉津降解菌时,筛选到1株降解活性很高的节杆菌SD41,该菌株对土壤中的阿特拉津有很好的降解效果,能快速去除阿特拉津残留对作物造成的毒害,而且该菌株在土壤中的定殖能力强,是修复阿特拉津农残污染土壤的优良菌株[10]。此外,我们在从多处污染场地分离到的阿特拉津降解菌中,节杆菌是最常见的种类(未发表)。

近年来,多株节杆菌基因组序列的获得,使人们对其广泛环境适应能力的基因组学基础有了深入的了解。节杆菌基因组中存在的σ因子、氧化应激、渗透应激、饥饿应激、温度应激等胁迫应激反应相关基因,使其具备了突出的抗环境胁迫能力。而节杆菌中存在的质粒,往往赋予菌株对更多化合物的分解能力和对重金属的抗性,使其具有更强的环境竞争力。上述能力使节杆菌在降解环境污染物的过程中发挥着重要作用,而基因组学分析使人们对这些能力有了更加全面的认识。

在基因组水平对节杆菌环境适应能力的解析,对其它菌株也有重要的借鉴作用。随着基因组测序技术的快速发展,测序时间和成本大大减少,可以通过对目标菌株进行基因组学分析,了解其适应能力及降解能力,从而有助于判断其在环境污染修复方面的潜力。然而,基因组学的数据也不能作为唯一标准,在基因组中存在的基因是否真正表达以及表达水平如何等问题都需要通过实验来验证。而通过把转录组学、蛋白质组学等研究手段与基因组学分析相结合,将加深人们对微生物环境适应性的认识。

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