Nucleotide sequence of regions homologous to nifH (nitrogenase Fe protein) from the nitrogen-fixing archaebacteria Methanococcus thermolithotrophicus and Methanobacterium ivanovii: evolutionary implications.

DNA fragments bearing sequence similarity to eubacterial nif H probes were cloned from two nitrogen-fixing archaebacteria, a thermophilic methanogen, Methanococcus (Mc.) thermolithotrophicus, and a mesophilic methanogen, Methanobacterium (Mb.) ivanovii. Regions carrying similarities with the probes were sequenced. They contained several open reading frames (ORF), separated by A + T-rich regions. The largest ORFs in both regions, an 876-bp sequence in Mc. thermolithotrophicus and a 789-bp sequence in Mb. ivanovii, were assumed to be ORFsnif H. They code for polypeptides of mol. wt. 32,025 and 28,347, respectively. Both ORFsnifH were preceded by potential ribosome binding sites and followed by potential hairpin structures and by oligo-T sequences, which may act as transcription termination signals. The codon usage was similar in both ORFsnifH and was analogous to that used in the Clostridium pasteurianum nifH gene, with a preference for codons ending with A or U. The ORFnifH deduced polypeptides contained 30% sequence matches with all eubacterial nifH products already sequenced. Four cysteine residues were found at the same position in all sequences, and regions surrounding the cysteine residues are highly conserved. Comparison of all pairs of methanogenic and eubacterial nifH sequences is in agreement with a distant phylogenetic position of archaebacteria and with a very ancient origin of nif genes. However, sequence similarity between Methanobacteriales and Methanococcales is low (around 50%) as compared to that found among eubacteria, suggesting a profound divergence between the two orders of methanogens. From comparison of amino acid sequences, C. pasteurianum groups with the other eubacteria, whereas comparison of nucleotide sequences seems to bring C. pasteurianum closer to methanogens. The latter result may be due to the high A + T content of both C. pasteurianum and methanogens ORFsnif H or may come from an ancient lateral transfer between Clostridium and methanogens.