The Complete Genome Sequence of Natrinema sp. J7-2, a Haloarchaeon Capable of Growth on Synthetic Media without Amino Acid Supplements

Natrinema sp. J7-2 is an extreme haloarchaeon capable of growing on synthetic media without amino acid supplements. Here we report the complete genome sequence of Natrinema sp. J7-2 which is composed of a 3,697,626-bp chromosome and a 95,989-bp plasmid pJ7-I. This is the first complete genome sequence of a member of the genus Natrinema. We demonstrate that Natrinema sp. J7-2 can use gluconate, glycerol, or acetate as the sole carbon source and that its genome encodes complete metabolic pathways for assimilating these substrates. The biosynthetic pathways for all 20 amino acids have been reconstructed, and we discuss a possible evolutionary relationship between the haloarchaeal arginine synthetic pathway and the bacterial lysine synthetic pathway. The genome harbors the genes for assimilation of ammonium and nitrite, but not nitrate, and has a denitrification pathway to reduce nitrite to N2O. Comparative genomic analysis suggests that most sequenced haloarchaea employ the TrkAH system, rather than the Kdp system, to actively uptake potassium. The genomic analysis also reveals that one of the three CRISPR loci in the Natrinema sp. J7-2 chromosome is located in an integrative genetic element and is probably propagated via horizontal gene transfer (HGT). Finally, our phylogenetic analysis of haloarchaeal genomes provides clues about evolutionary relationships of haloarchaea.Natrinema sp. J7-2 是一种极端嗜盐古菌（extreme haloarchaeon），可在无需添加氨基酸的合成培养基上生长。本研究报道了Natrinema sp. J7-2的完整基因组序列，其由一条3,697,626 bp的染色体与一条95,989 bp的质粒pJ7-I构成。这是首个属于Natrinema属（genus Natrinema）的菌株的完整基因组序列。研究证实，Natrinema sp. J7-2能够以葡萄糖酸盐、甘油或乙酸盐作为唯一碳源，其基因组编码了同化这些底物所需的完整代谢通路。本研究重构了该菌所有20种氨基酸的生物合成通路，并探讨了嗜盐古菌精氨酸合成通路与细菌赖氨酸合成通路之间可能存在的进化关联。该基因组携带铵与亚硝酸盐的同化基因，但不含硝酸盐同化基因，同时具备将亚硝酸盐还原为一氧化二氮（N₂O）的反硝化通路。比较基因组分析显示，绝大多数已测序的嗜盐古菌均采用TrkAH系统而非Kdp系统主动摄取钾离子。基因组分析还发现，Natrinema sp. J7-2染色体上的3个CRISPR位点（CRISPR loci）中有一个位于整合遗传元件中，推测其可通过水平基因转移（horizontal gene transfer, HGT）进行传播。最后，本研究通过对嗜盐古菌基因组的系统发育分析，为阐明嗜盐古菌的进化关系提供了新的线索。