Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1

Abstract

Halobacteriumsp. NRC-1 is an extremely halophilic archaeon that is easily cultured and genetically tractable. Since its genome sequence was completed in 2000, a combination of genetic, transcriptomic, proteomic, and bioinformatic approaches have provided insights into both its extremophilic lifestyle as well as fundamental cellular processes common to all life forms. Here, we review post-genomic research on this archaeon, including investigations of DNA replication and repair systems, phototrophic, anaerobic, and other physiological capabilities, acidity of the proteome for function at high salinity, and role of lateral gene transfer in its evolution.

Figure 1

Physiology and transcriptomics of Halobacterium sp. NRC-1. An overview of relative transcript levels of selected genes is indicated, along with metabolic characteristics of the cell, indicated by rectangular box. The double line depicts the cell membrane. Square boxes, left to right: transcription levels in cells grown by aerobic respiration, anaerobic respiration using TMAO, and fermentation. Green, yellow, and red boxes indicate reduced, unchanged, and increased transcript levels, respectively. Abbreviations: Nuo: NADH oxidoreductase; MK/MKH₂: oxidized/reduced menaquinone; Cyb: cytochrome b₆ oxidoreductase; Cox: aa₃-type cytochrome oxidase; Cyd: quinol bd oxidase; Cba: ba₃-type oxidase; Dms: DMSO/TMAO reductase; TCA: tricarboxylic acid cycle; Bop: bacterio-opsin; Atp: ATP synthase

Figure 2

Gene knockout strategies in Halobacterium sp. NRC-1. A. Nonessential genes. After a suicide vector containing a deletion of a gene of interest (geneX) is integrated into the Halobacterium Δura3 host strain by selection of uracil prototrophy (Ura⁺), plasmid excision is selected with 5-fluoroorotic acid resistance (Foa^r), resulting in either replacement with the deleted allele (ΔgeneX) (left) or restoration of the wild-type allele (right). For genes that are essential for cell viability, only wild-type gene alleles are recovered. B. Essential genes. A pseudo-complementation strategy is used where an autonomously replicating plasmid vector which contains the functional gene of interest, geneX, is introduced into the host strain, e.g. by selection for mevinolin resistance (Mev^r). Knockout of the chromosomal copy may then be selected using selections described in part A.

Figure 3

Surface charge comparisons of the TBP-TFB-DNA complexes in Halobacterium and Homo sapiens. Acidic character of proteins is indicated by red and basic by blue. DNA strands are green (coding) and pink or orange (non-coding). Panels A and B show the modeled complex in Halobacterium using a dielectric constant of 48.4 (NaCl concentration of 5 M) while panels C and D show the Homo sapiens complexes using a dielectric constant of 80.0 (NaCl concentration of 0 M). Panels A and C show transcription going into the plane while B and D show transcription coming out of the plane.

Figure 4

"Bacterial" gene content in the Halobacterium sp. NRC-1 replicon pNRC200. A. Average bacterial character is plotted in a 40 ORF window (innermost plot in blue). Individual genes closely related to bacteria in Blast analysis are shown with blue dots while those identified through COG analysis are shown as red dots. IS elements are indicated by lines on the outermost circle. B. Quartet puzzling maximum-likelihood phylogenetic tree of ArgS sequences from archaea and three classes of bacteria. A probable LGT of an argS gene from a bacterium to Halobacterium (Hbt. NRC-1) is apparent. Two other haloarchaea (Haloferax volcanii: H. vo; Haloarcula marismortui: H. ma) contain archaeal-type ArgS-coding genes.