Wöhlbrand Lars, Kallerhoff Birte, Lange Daniela, Hufnagel Peter, Thiermann Jürgen, Reinhardt Richard, Rabus Ralf
Max-Planck-Institute for Marine Microbiology, Bremen, Germany.
Proteomics. 2007 Jun;7(13):2222-39. doi: 10.1002/pmic.200600987.
The denitrifying "Aromatoleum aromaticum" strain EbN1 utilizes a wide range of aromatic and nonaromatic compounds under anoxic and oxic conditions. The recently determined genome revealed corresponding degradation pathways and predicted a fine-tuned regulatory network. In this study, differential proteomics (2-D DIGE and MS) was used to define degradation pathway-specific subproteomes and to determine their growth condition dependent regulation. Differential protein profiles were determined for cultures adapted to growth under 22 different substrate and redox conditions. In total, 354 different proteins were identified, 199 of which displayed significantly changed abundances. These regulated proteins mainly represented enzymes of the different degradation pathways, and revealed different degrees of growth condition specific regulation. In case of three substrate conditions (e.g. phenylalanine, anoxic), proteins previously predicted to be involved in their degradation were apparently not involved (e.g. Pdh, phenylacetaldehyde dehydrogenase). Instead, previously not considered proteins were specifically increased in abundance (e.g. EbA5005, predicted aldehyde:ferredoxin oxidoreductase), shedding new light on the respective pathways. Moreover, strong evidence was obtained for thus far unpredicted degradation pathways of three hitherto unknown substrates (e.g. o-aminobenzoate, anoxic). Comparing all identified regulated and nonregulated proteins provided first insights into regulatory hierarchies of special degradation pathways versus general metabolism in strain EbN1.
反硝化“芳香油嗜芳烃菌”菌株EbN1在缺氧和有氧条件下能利用多种芳香族和非芳香族化合物。最近测定的基因组揭示了相应的降解途径，并预测了一个精细调节的调控网络。在本研究中，采用差异蛋白质组学（二维差异凝胶电泳和质谱分析）来定义特定降解途径的亚蛋白质组，并确定其生长条件依赖性调控。针对适应在22种不同底物和氧化还原条件下生长的培养物，测定了差异蛋白质谱。总共鉴定出354种不同的蛋白质，其中199种蛋白质的丰度有显著变化。这些受调控的蛋白质主要代表不同降解途径的酶，并显示出不同程度的生长条件特异性调控。在三种底物条件下（例如苯丙氨酸，缺氧），先前预测参与其降解的蛋白质显然未参与（例如丙酮酸脱氢酶、苯乙醛脱氢酶）。相反，先前未被考虑的蛋白质丰度却特异性增加（例如EbA5005，预测的醛：铁氧化还原蛋白氧化还原酶），这为各自的途径提供了新的线索。此外，还获得了有力证据，证明三种迄今未知的底物（例如邻氨基苯甲酸，缺氧）存在迄今未预测到的降解途径。比较所有鉴定出的受调控和未受调控的蛋白质，首次深入了解了菌株EbN1中特殊降解途径与一般代谢的调控层次。
