Genome analysis of the salt-resistant Paludifilum halophilum DSM 102817T reveals genes involved in flux-tuning of ectoines and unexplored bioactive secondary metabolites

Abstract

Paludi lum halophilum is the rst member of the genus Paludi lum in the Thermoactinomycetaceae family. The thermohalophilic bacterium was isoated from the solar saltern of Sfax, in Tunisia and was shown to be able to produce ectoines in relatively high-yield and cope with salt stress conditions. In this study, the whole genome of P. halophilum was sequenced and analysed. Analysis revealed 3,789,765 base pairs with average GC % content of 51.5%. A total of 3,775 genes were predicted of which 3616 were protein-coding genes and 73 were RNA genes. The genes encoding key enzymes for ectoines synthesis were identi ed from the bacterial genome next to a gene cluster (ehuABCD) encoding a bindingprotein-dependent ABC transport system responsible for ectoines mobility through the cell membrane.With the aid of KEGG analysis, we found that the central catabolic network of P. halophilum comprises the pathways of glycolysis, tricarboxylic acid (TCA) cycle, and pentose phosphate pathway (PPP). In addition, anaplerotic pathways replenishing oxaloacetate and glutamate synthesis from central metabolism, both needed for high ectoines biosynthetic uxes were identi ed through several key enzymes. Furthermore, a total of 18 antiSMASH-predicted putative biosynthetic gene clusters (BGCs) for secondary metabolites with high novelty and diversity were identi ed in P. halophilum genome, including biosynthesis of Colabomycine-A, Fusaricidin-E, Zwittermycin A, Streptomycin, Mycosubtilin and Meilingmycin. Based on these data, P. halophilum emerged as a promising source for ectoines and antimicrobials with the potential to be scaled up for industrial production, which could bene t the pharmaceutical and cosmetic industries.

Guilty by association: Importers, exporters and MscS‐type mechanosensitive channels encoded in biosynthetic gene clusters for the stress‐protectant ectoine

“…EhuB is the substrate‐binding protein of the EhuABCD ABC system from Sinorhizobium meliloti , a transporter for ectoines when they are used as nutrients (Hanekop et al, 2007; Jebbar et al, 2005). However, Ehu‐type transporters have also been previously found juxtapositioned to ectoine/hydroxyectoine biosynthetic gene clusters (Frikha‐Dammak et al, 2021; Richter et al, 2019), implying a role for these transporters for the acquisition of ectoines as osmostress protectants. Compared with the S. meliloti EhuB protein, the 134 EhuB substrate‐binding proteins in our dataset (Table 1) had a degree of amino acid sequence identity ranging between 74% and 33%.…”

“…Transporter as nutrients (Hanekop et al, 2007;Jebbar et al, 2005). However, Ehu-type transporters have also been previously found juxtapositioned to ectoine/hydroxyectoine biosynthetic gene clusters (Frikha-Dammak et al, 2021;Richter et al, 2019), implying a role for these transporters for the acquisition of ectoines as osmostress protectants.…”

“…To date, ectoine importers belonging to four major transporter families have been identified: (i) binding protein‐dependent ATP‐binding cassette (ABC) systems, (ii) tripartite ATP‐independent periplasmic transporters (TRAP‐T), (iii) betaine‐choline‐carnitine‐transporters (BCCT), and (iv) systems of the major facilitator superfamily (MFS). In a limited number of instances, genes for ectoine importers were found to be associated with ectoine/hydroxyectoine biosynthetic operons (Frikha‐Dammak et al, 2021; Gregory & Boyd, 2021; Leon et al, 2018; Richter et al, 2019). A few of these osmotically inducible gene clusters even comprise a gene for an MscS‐type mechanosensitive channel, whose function is important for managing the cell's transition from high to low osmolarity surroundings (Booth, 2014; Czech et al, 2016; Widderich et al, 2016).…”

The Methods of Digging for “Gold” within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools

“…Ectoine is commonly used in the cosmetics industry, but clinical trials are also conducted to indicate its importance in the treatment of eye and respiratory diseases [142][143][144][145]. In silico studies for new microorganisms producing ectoine and hydroxyectoine can be improved by using BGC identification methods like antiSMASH [146][147][148]. Microorganisms identified in this way can be an alternative to those currently used.…”

Alleviation of Salt Stress via Habitat-Adapted Symbiosis

“…M30-35, isolated from the rhizosphere of Haloxylon ammodendron, a perennial C4 succulent xero-halophyte with exceptional drought and salt-tolerance abilities, was found to contain 34 genes possessing homology with genes associated with PGP traits and abiotic stress tolerance [29]. Recently, the genomes of many ST-PGPRs have also been sequenced, providing information on their salt tolerance and plant-growth-promoting attributes [30]. However, only a few reports have investigated the promoting effect of PGPRs isolated from halophytes on glycophyte growth under salt stress.…”