Molecular diversity of nitrite reductase genes (nirK) in nitrifying bacteria
Molecular diversity of nitrite reductase genes (nirK) in nitrifying bacteria
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DOI：
10.1111/j.1462-2920.2006.01198.x
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发表时间：
2007-03-01
影响因子：
5.1
通讯作者：
Stein, Lisa Y.
中科院分区：
文献类型：
--
作者：
Cantera, J. Jason L.;Stein, Lisa Y.
根据硝化菌全基因组序列设计引物，从1株亚硝化单胞菌和4株亚硝化螺旋菌中扩增出含铜亚硝酸还原酶（nirK）基因的部分序列。推导出的NirK蛋白序列与其他含铜亚硝酸盐还原酶高度相似，包括保守的基序。NirK蛋白序列的系统发育比较将来自亚硝化单胞菌属、亚硝化螺旋菌属和硝化杆菌属物种的直系同源物放入多个不同的进化枝中。与nirK基因相关的产品没有扩增从7个额外的亚硝化单胞菌和亚硝化螺菌菌株通过PCR与nirK特异性引物，但是，从这些菌株中的4个提取的DNA产生可检测的信号，在低严格的Southern杂交探测与nirK基因片段氨氧化与已知的nirK基因序列。硝化细菌nirK基因的启动子区域的分析显示，保守的NsrR转录因子在只有一个分支的结合基序;其他可用的硝化细菌nirK基因启动子缺乏特征性的转录因子结合基序。综上所述，这些结果表明，nirK基因的序列和调控是不同的硝化细菌。这项研究提供了洞察使用nirK基因的分子多样性研究，建立了一个框架，以解决亚硝酸盐还原的起源和多样化的硝化细菌，并扩大了nirK直系同源物的数据库。
Sequences of copper-containing nitrite reductase (nirK) genes obtained from completed nitrifier genome sequences were used to design polymerase chain reaction (PCR) primers to amplify partial nirK sequences from one Nitrosomonas and four Nitrosospira isolates. Deduced NirK protein sequences were highly similar to other copper-containing nitrite reductases including conserved motifs. Phylogenetic comparisons of NirK protein sequences placed orthologues from Nitrosomonas, Nitrosospira and Nitrobacter species into multiple distinct clades. Products related to nirK genes were not amplified from seven additional Nitrosomonas and Nitrosospira isolates by PCR with nirK-specific primers; however, DNA extracted from four of these isolates produced detectable signals in low-stringency Southern hybridizations probed with nirK gene fragments from ammonia-oxidizers with known nirK gene sequences. Analysis of promoter regions of nitrifier nirK genes revealed conserved binding motifs for the NsrR transcription factor in only one clade; other available nitrifier nirK gene promoters lacked characterized transcription factor binding motifs. Taken together, these results indicate that the sequences and regulation of nirK genes are diverse among nitrifiers. This study provides insight to the use of nirK genes for molecular diversity studies, establishes a framework to resolve the origins and diversification of nitrite reduction among the nitrifiers, and expands the database of nirK orthologues.