Abstract
Halophilic archaeon Halolamina pelagica CDK2, showcasing plant growth-promoting properties and endurance towards harsh environmental conditions (high salinity, heavy metals, high temperature and UV radiation) was sequenced earlier. Pan-genome of Halolamina genus was created and investigated for strain-specific genes of CDK2, which might confer it with features helping it to withstand high abiotic stress. Pathways and subsystems in CDK2 were compared with other Halolamina strain CGHMS and analysed using KEGG and RAST. A genome-scale metabolic model was reconstructed from the genome of H. pelagica CDK2. Results implicated strain-specific genes like thermostable carboxypeptidase and DNA repair protein MutS which might protect the proteins and DNA from high temperature and UV denaturation respectively. A bifunctional trehalose synthase gene responsible for trehalose biosynthesis was also annotated specifying the need for low salt compatible solute strategy, the probable reason behind the ability of this haloarchaea to survive in a wide range of salt concentrations. A modified shikimate and mevalonate pathways were also identified in CDK2, along with many ABC transporters for metal uptakes like zinc and cobalt through pathway analysis. Probable employment of one multifunctional ABC transporter in place of two for similar metals (Nickel/cobalt and molybdenum/tungsten) might be employed as a strategy for energy conservation. The findings of the present study could be utilized for future research relating metabolic model for flux balance analysis and the genetic repertoire imparting resistance to harsh conditions can be transferred to crops for improving their tolerance to abiotic stresses.
Highlights
Until 1970, archaebacteria were placed in the domain "Bacteria"
Comprehensive genome analysis of halophilic archaea, H. pelagica CDK2 revealed genes such as alkaline phosphatase and pyrophosphokinase involved in P solubilisation coinciding with our previous research.[45]
Strainspecific attributes of H. pelagica CDK2 like thermostable carboxypeptidase and DNA repair protein MutS required for the integrity of protein and DNA respectively from high-temperature denaturation is reported
Summary
Until 1970, archaebacteria were placed in the domain "Bacteria". It was only after 1970, that these microorganisms were grouped into the third domain of life called the "Archaea".1 Amongst archaea, halophilic archaea have acquired considerable attention because of their ability to withstand high salinity. Extreme salinity but these halophilic archaea are known to escape high metal toxicity, low levels of oxygen and high UV rays.[2] Their existence has been reported in the extra-terrestrial environment.[3] The Rann of Kutch, Gujarat, India experiences extremely hot climate (50-55°C), severe UV radiation, and metal toxicity. This makes Rann of Kutch a suitable niche for analysing genes and pathways present in native extremophilic microorganisms which assist them in their adaptation and survival. There have been many studies on pathway analysis of bacteria through GEMs.[8,9] no significant findings have been reported so far on archaea especially halophilic archaea except for the Halobacterium salinarum model.[10,11] Since, H. pelagica CDK2 is well adapted to their niches and physical surroundings altering their nutritional capabilities and pathways the GEM of H. pelagica CDK2 will have its own significance
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