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Open Access Research article

A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T

Shivakumara Siddaramappa1, Jean F Challacombe1, Rosana E DeCastro2, Friedhelm Pfeiffer3, Diego E Sastre2, María I Giménez2, Roberto A Paggi2, John C Detter1, Karen W Davenport1, Lynne A Goodwin1, Nikos Kyrpides4, Roxanne Tapia1, Samuel Pitluck4, Susan Lucas4, Tanja Woyke4 and Julie A Maupin-Furlow5*

Author Affiliations

1 DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA

2 Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3250 4to Nivel, Mar del Plata, 7600, Argentina

3 Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany

4 DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA

5 Department of Microbiology and Cell Science, University of Florida, Bldg. 981, Museum Rd., P.O. Box 110700, Gainesville, FL, 32611-0700, USA

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BMC Genomics 2012, 13:165  doi:10.1186/1471-2164-13-165

Published: 4 May 2012

Abstract

Background

Natrialba magadii is an aerobic chemoorganotrophic member of the Euryarchaeota and is a dual extremophile requiring alkaline conditions and hypersalinity for optimal growth. The genome sequence of Nab. magadii type strain ATCC 43099 was deciphered to obtain a comprehensive insight into the genetic content of this haloarchaeon and to understand the basis of some of the cellular functions necessary for its survival.

Results

The genome of Nab. magadii consists of four replicons with a total sequence of 4,443,643 bp and encodes 4,212 putative proteins, some of which contain peptide repeats of various lengths. Comparative genome analyses facilitated the identification of genes encoding putative proteins involved in adaptation to hypersalinity, stress response, glycosylation, and polysaccharide biosynthesis. A proton-driven ATP synthase and a variety of putative cytochromes and other proteins supporting aerobic respiration and electron transfer were encoded by one or more of Nab. magadii replicons. The genome encodes a number of putative proteases/peptidases as well as protein secretion functions. Genes encoding putative transcriptional regulators, basal transcription factors, signal perception/transduction proteins, and chemotaxis/phototaxis proteins were abundant in the genome. Pathways for the biosynthesis of thiamine, riboflavin, heme, cobalamin, coenzyme F420 and other essential co-factors were deduced by in depth sequence analyses. However, approximately 36% of Nab. magadii protein coding genes could not be assigned a function based on Blast analysis and have been annotated as encoding hypothetical or conserved hypothetical proteins. Furthermore, despite extensive comparative genomic analyses, genes necessary for survival in alkaline conditions could not be identified in Nab. magadii.

Conclusions

Based on genomic analyses, Nab. magadii is predicted to be metabolically versatile and it could use different carbon and energy sources to sustain growth. Nab. magadii has the genetic potential to adapt to its milieu by intracellular accumulation of inorganic cations and/or neutral organic compounds. The identification of Nab. magadii genes involved in coenzyme biosynthesis is a necessary step toward further reconstruction of the metabolic pathways in halophilic archaea and other extremophiles. The knowledge gained from the genome sequence of this haloalkaliphilic archaeon is highly valuable in advancing the applications of extremophiles and their enzymes.