Elucidating metabolic pathways through genomic analysis in highly heavy metal-resistant Halobacterium salinarum strains

Abstract

The annotated and predicted genomes of five archaeal strains (AS1, AS2, AS8, AS11 and AS19), isolated from Sfax solar saltern sediments (Tunisia) and affiliated with Halobacterium salinarum, were performed by RAST webserver (Rapid Annotation using Subsystem Technology) and NCBI prokaryotic genome annotation pipeline (PGAP). The results showed the ability of strains to use a reduced semi-phosphorylative Entner-Doudoroff pathway for glucose degradation and an Embden-Meyerhof one for gluconeogenesis. They could use glucose, fructose, glycerol, and acetate as sole source of carbon and energy. ATP synthase, various cytochromes and aerobic respiration proteins were encoded. All strains showed fermentation capability through the arginine deiminase pathway and facultative anaerobic respiration using electron acceptors (Dimethyl sulfoxide and trimethylamine N-oxide). Several biosynthesis pathways for many amino acids were identified. Comparative and pangenome analyses between the strains and the well-studied halophilic archaea Halobacterium NRC-1 highlighted a notable dissimilarity. Besides, the strains shared a core genome of 1973 genes and an accessory genome of 767 genes. 129, 94, 67, 15 and 29 unique genes were detected in the AS1, AS2, AS8, AS11 and AS19 genomes, respectively. Most of these unique genes code for hypothetical proteins. The strains displayed plant-growth promoting characteristics under heavy metal stress (Ammonium assimilation, phosphate solubilization, chemotaxis, cell motility and production of indole acetic acid, siderophore and phenazine). Therefore, they could be used as a biofertilizer to promote plant growth. The genomes encoded numerous biotechnologically relevant genes responsible for vitamin biosynthesis, including cobalamin, folate, biotin, pantothenate, riboflavin, thiamine, menaquinone, nicotinate, and nicotinamide. The carotenogenetic pathway of the studied strains was also predicted. Consequently, the findings of this study contribute to a better understanding of the halophilic archaea metabolism providing valuable insights into their ecophysiology as well as relevant biotechnological applications.

Keywords: Biotechnological applications; Comparative genomics; Halobacterium salinarum; Halophilic archaea; Metabolism.

Graphical abstract

Fig. 1

Location map of the solar saltern of Sfax (Tunisia) and sampling sites.

Fig. 2

Comparative genome analysis of the five archaeal strains (AS1, AS2, AS8, AS11 and AS19) using the RAST SEED viewer with Halobacterium NRC-1 as reference. A threshold of 80 % sequence identity was used. The blue lines represent the highest genes sequence similarity and the red lines indicate the absence of homologs.

Fig. 3

Growth kinetics (a, b, c, d and e) and growth rate (f) of the five archaeal strains (AS1, AS2, AS8, AS11 and AS19) with different carbon source (glucose, fructose, glycerol and acetate). Values are means of three replications ± SD.

Fig. 4

Proposed main steps in the mevalonate, isoprene and carotenoid biosynthesis pathways of the five archaeal strains. Acetyl-CoA: Acetyl-Coenzyme A; Mevalonate 5-P: Mevalonate 5-Phosphate; Isopentenyl-P: Isopentenyl-Phosphate; DH-IDR: Dihydroisopentenyldehydrorhodopsin; IDR: Isopentenyldehydrorhodopsin; DH-BABR: Dihydrobisanhyrobacterioruberin; BABR: Bisanhydrobacterioruberin; TH-BABR: Tetrahydrobisanhyro-bacterioruberin; MABR: Monoanhydrobacterioruberin; EC 2.3.1.9: Acetyl-CoA acetyltransferase; EC 2.3.3.10: Hydroxymethylglutaryl-CoA synthase; EC 1.1.1.34: Hydroxymethylglutaryl-CoA reductase; EC 2.7.1.36: Mevalonate kinase; EC 4.1.1.99: Phosphomevalonate decarboxylase; EC 2.7.4.26: Isopentenyl phosphate kinase; EC 5.3.3.2: Isopentenyl-diphosphate delta-isomerase; EC 25.1.29 (Crt E): Geranylgeranyl diphosphate synthaseEC 2.5.1.31: Undecaprenyl diphosphate synthase; EC2.5.1.32 (CrtB): Phytoene synthase; EC 1.14.99 (CrtI): Phytoene desaturase; EC 2.5.1 (LyeJ): Lycopene elongase and CrtY: Lycopene cyclase. EC 2.5.1.1∗: dimethylallyltransferase; EC 2.5.1.10∗: geranyltranstransferase and 4.2.1.161 (CruF)∗: Carotenoid hydratase are absent (Red color).