Genome sequence of Halobacterium species NRC-1

Abstract

We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1, harboring a dynamic 2,571,010-bp genome containing 91 insertion sequences representing 12 families and organized into a large chromosome and 2 related minichromosomes. The Halobacterium NRC-1 genome codes for 2,630 predicted proteins, 36% of which are unrelated to any previously reported. Analysis of the genome sequence shows the presence of pathways for uptake and utilization of amino acids, active sodium-proton antiporter and potassium uptake systems, sophisticated photosensory and signal transduction pathways, and DNA replication, transcription, and translation systems resembling more complex eukaryotic organisms. Whole proteome comparisons show the definite archaeal nature of this halophile with additional similarities to the Gram-positive Bacillus subtilis and other bacteria. The ease of culturing Halobacterium and the availability of methods for its genetic manipulation in the laboratory, including construction of gene knockouts and replacements, indicate this halophile can serve as an excellent model system among the archaea.

Figure 1

An integrated view of the biology of Halobacterium NRC-1. Aspects of energy production, nutrient uptake, membrane assembly, cation and anion transport, and signal transduction are depicted. ATP synthesis by chemiosmotic coupling of proton transport by the respiratory chain and by light-driven proton pumping by bacteriorhodopsin (BR) (purple oval) or chloride transport by halorhodopsin (HR) (blue oval) is shown. Below, the semiphosphorylated Entner–Doudoroff pathway is shown, and the presence of fatty acid oxidation and the citric acid cycle is indicated. Enzymes not yet identified are marked with asterisks. A variety of nutrient uptake systems (represented by yellow or brown structures) coded by the genome including glycerol 3-phosphate (UgpABCE) and ribose (RbsAC) ABC transporters, a lactate (LctP) transporter, formate-oxalate antiporter (OxiT), spermidine and putrescine uptake ABC transporter (PotABCD), and amino acid (PutP, Cat) and dipeptide (DppABCDF) transporters are shown. Other amino acid uptake systems, represented by a generic ABC transporter, are also likely to exist. Components of the protein translocation machinery (SecDEFY, SRP19, 54, SRα) (in black) are shown. Cation transporters (in green) shown are for K⁺ (TrkAH, and KdpABC), Na⁺ (NhaC), Cd²⁺ (ZntX and Cd efflux ATPase), Co²⁺ (CbiNOQ), Cu²⁺ (NosFY), Fe³⁺ (iron permease and HemUV), and Zn²⁺ (ZurMA). Anion transporters shown (in red) are for SO₄²⁻ (CysAT), PO₄³⁻ (PstABC and phosphate permease), Cl⁻ (chloride channel), and arsenate (ArsABC). A complex system of photoreceptors and signal transduction components are shown, including two sensory receptors (SRI shown in blue and SRII shown in orange), 17 transducers (Htr I, II, III, IV, V, VI, VII, VIII, IX, X, XII, XIII, XIV, XV, XVI, XVII, and XVIII) responding to light (hυ), O₂, or amino acids, as indicated. Transmission of the motility signal to the flagellar motor via CheAW and CheY is shown by arrows. Single examples of sensor kinases, membrane bound (white rhombus) or cytoplasmic, and response regulators are identified.