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

Jie Feng,Fei Gan,Yang Li,Ziqian Zhang,Yuping Huang,Lei Wang,Bin Liu,Ping Shen,Yan Ren,Xiangdong Chen,Xiao-Feng Tang,Bing Tang,Valerie De Crécy-Lagard

doi:10.1371/journal.pone.0041621

Jie Feng, Fei Gan + Show 11 more

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https://doi.org/10.1371/journal.pone.0041621

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Abstract

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.

Highlights

Haloarchaea thrive in extremely saline environments such as solar salterns, salt lakes, and deposits
Analyses of the Nmn. pharaonis and Hbt. salinarum NRC-1 secretome showed the extensive use of the twin-arginine-translocation (Tat) pathway in haloarchaea [6,7,8], and the importance of Tat pathway has been experimentally confirmed in Haloferax volcanii [9,10]
J7-2 genome The genome of strain J7-2 is composed of a 3,697,626-bp chromosome and a 95,989-bp plasmid designated pJ7-I

Summary

Introduction

Haloarchaea thrive in extremely saline environments such as solar salterns, salt lakes, and deposits. These extremophiles have been widely studied because they are readily cultured and have unique features in terms of genetics, phylogeny, physiology, and ecology. Earlier studies on haloarchaea revealed some mechanisms of adaptation to extremely saline environments, i.e. a high intracellular salt concentrations and acidic proteome [1,2,3]. The genomic analysis of Halobacterium salinarum NRC-1, the first haloarchaeon sequenced, provided new information on the mechanisms by which haloarchaea adapt to saline environments, including high GC content, a large number of ion transporters and signal transduction pathways [4]. Only four (Haloarcula hispanica [23], Hfx. volcanii [24], Nmn. pharaonis [25] and Halorhabdus utahensis [26]) have been experimentally confirmed to be capable of growing in synthetic medium without amino acid supplements, and some metabolic pathways remain to be elucidated [27]

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