Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site.
Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site.
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DOI：
10.1186/1471-2164-8-180
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发表时间：
2007-06-19
期刊：
影响因子：
4.4
通讯作者：
Lovley DR
中科院分区：
文献类型：
--
作者：
Butler JE;He Q;Nevin KP;He Z;Zhou J;Lovley DR
被芳香族化合物污染的地下水和地下环境可以通过地杆菌物种就地修复，这些化合物的氧化与Fe(III)-氧化物的还原相结合。金属还原杆菌代谢许多芳香族化合物，但所涉及的酶尚不清楚。完整的G. metallireducens基因组包含一个300 kb的岛，可以编码降解苯酚、对甲酚、4-羟基苯甲醛、4-羟基苯甲酸酯、苯甲醇、苯甲醛和苯甲酸酯的酶。甲苯降解基因编码在一个单独的区域。在近亲物种中没有发现这些基因不能降解芳香族化合物。岛上丰富的转座子和噬菌体样基因表明了移动性，但核苷酸组成和与其他物种缺乏同源性并不表明最近的转移。推断的降解途径类似于以硝酸盐作为电子受体厌氧氧化芳香族化合物的物种。在这些途径中，芳香族化合物转化为苯甲酰辅酶a，然后转化为3-羟基酰辅酶a。然而，在G. metallireducens中没有能量昂贵的脱芳酶基因。在氧化苯甲酸酯的细胞中发现了转录物水平的全基因组变化。这些结果支持了预测的途径，确定了诱导的脂肪酸氧化基因，并确定了TCA循环向假定的atp生成琥珀酰辅酶a合成酶的明显转变。与该途径中几个基因的类似物也被诱导，一些假定的钼蛋白也是如此。通过与污染地分离物的基因组比较，发现芳香降解途径基因的含量非常相似，表明该菌株降解了许多相同的化合物。该菌株也缺乏经典的去芳香化酶，但含有两个拷贝的8个基因簇编码氧化还原蛋白，在苯甲酸盐氧化过程中被诱导了30倍。G. metallireducens似乎将芳香化合物转化为苯甲酰辅酶a，然后通过脂肪酸氧化转化为乙酰辅酶a，然后通过TCA循环转化为二氧化碳。负责芳香环去芳香化的酶可能是新的，这一步的能量投资可能被琥珀酸代谢的变化所抵消。对野外分离物的分析表明，推断的G. metallireducens的途径可能适用于模拟原位生物修复。
Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III)-oxides. Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known. The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, benzyl alcohol, benzaldehyde, and benzoate. Toluene degradation genes were encoded in a separate region. None of these genes was found in closely related species that cannot degrade aromatic compounds. Abundant transposons and phage-like genes in the island suggest mobility, but nucleotide composition and lack of synteny with other species do not suggest a recent transfer. The inferred degradation pathways are similar to those in species that anaerobically oxidize aromatic compounds with nitrate as an electron acceptor. In these pathways the aromatic compounds are converted to benzoyl-CoA and then to 3-hydroxypimelyl-CoA. However, in G. metallireducens there were no genes for the energetically-expensive dearomatizing enzyme. Whole-genome changes in transcript levels were identified in cells oxidizing benzoate. These supported the predicted pathway, identified induced fatty-acid oxidation genes, and identified an apparent shift in the TCA cycle to a putative ATP-yielding succinyl-CoA synthase. Paralogs to several genes in the pathway were also induced, as were several putative molybdo-proteins. Comparison of the aromatics degradation pathway genes to the genome of an isolate from a contaminated field site showed very similar content, and suggested this strain degrades many of the same compounds. This strain also lacked a classical dearomatizing enzyme, but contained two copies of an eight-gene cluster encoding redox proteins that was 30-fold induced during benzoate oxidation. G. metallireducens appears to convert aromatic compounds to benzoyl-CoA, then to acetyl-CoA via fatty acid oxidation, and then to carbon dioxide via the TCA cycle. The enzyme responsible for dearomatizing the aromatic ring may be novel, and energetic investments at this step may be offset by a change in succinate metabolism. Analysis of a field isolate suggests that the pathways inferred for G. metallireducens may be applicable to modeling in situ bioremediation.
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DOI：
10.1046/j.1432-1327.1998.2510946.x
发表时间：
1998-02-01
期刊：
EUROPEAN JOURNAL OF BIOCHEMISTRY
影响因子：
--
作者：
Boll, M;Fuchs, G
通讯作者：
Fuchs, G
DOI：
10.3109/10425179909033930
发表时间：
1999-01-01
期刊：
DNA SEQUENCE
影响因子：
--
作者：
Cronin, CN;Kim, J;McIntire, WS
通讯作者：
McIntire, WS
影响因子：
5.8
作者：
Gardy, JL;Laird, MR;Brinkman, FSL
通讯作者：
Brinkman, FSL
影响因子：
11.4
作者：
CORTAY, JC;NEGRE, D;COZZONE, AJ
通讯作者：
COZZONE, AJ
DOI：
10.1046/j.1432-1327.1998.2510916.x
发表时间：
1998-02-01
期刊：
EUROPEAN JOURNAL OF BIOCHEMISTRY
影响因子：
--
作者：
Breese, K;Fuchs, G
通讯作者：
Fuchs, G