Analysis of the Complete Genome of the Alkaliphilic and Phototrophic Firmicute Heliorestis convoluta Strain HHT

Abstract

Despite significant interest and past work to elucidate the phylogeny and photochemistry of species of the Heliobacteriaceae, genomic analyses of heliobacteria to date have been limited to just one published genome, that of the thermophilic species Heliobacterium (Hbt.) modesticaldum str. Ice1T. Here we present an analysis of the complete genome of a second heliobacterium, Heliorestis (Hrs.) convoluta str. HHT, an alkaliphilic, mesophilic, and morphologically distinct heliobacterium isolated from an Egyptian soda lake. The genome of Hrs. convoluta is a single circular chromosome of 3.22 Mb with a GC content of 43.1% and 3263 protein-encoding genes. In addition to culture-based observations and insights gleaned from the Hbt. modesticaldum genome, an analysis of enzyme-encoding genes from key metabolic pathways supports an obligately photoheterotrophic lifestyle for Hrs. convoluta. A complete set of genes encoding enzymes for propionate and butyrate catabolism and the absence of a gene encoding lactate dehydrogenase distinguishes the carbon metabolism of Hrs. convoluta from its close relatives. Comparative analyses of key proteins in Hrs. convoluta, including cytochrome c553 and the Fo alpha subunit of ATP synthase, with those of related species reveal variations in specific amino acid residues that likely contribute to the success of Hrs. convoluta in its highly alkaline environment.

Editorial for the Special Issue: Advances in the Biology of Phototrophic Bacteria

“…This Special Issue highlights recent advances in these aspects. It includes results specifically on green sulfur bacteria (Chlorobi [3]), heliobacteria (Firmicutes [4]), Chloroflexi [5], Cyanobacteria [6,7] and phototrophic purple bacteria (Proteobacteria [8][9][10][11][12][13]). In addition, phylogenetic studies regarding photosynthesis and osmotic adaptation consider representatives of all of these phyla [14,15].…”

“…In addition, phylogenetic studies regarding photosynthesis and osmotic adaptation consider representatives of all of these phyla [14,15]. This Special Issue includes results on identification and genomic characterization of new isolates [9], the adaptation to specific ecological niches in regard to temperature [6], salinity [14] and pH [4]. It also considers aerobic phototrophic purple bacteria and the relations to oxygen and oxidative stress [8][9][10][11]13] as well as environmental interactions [5,7,12] and syntrophic relations [3].…”

“…Over evolutionary times, phototrophic bacteria that have conquered different ecological niches have given rise to the evolution of phylogenetic groups of species that are living today in these niches. This is depicted in specific ecological niches of phylogenetic distinct groups of phototrophic bacteria with examples of some heliobacteria in alkaline waters [4], of different groups of phototrophic purple bacteria adapted to marine and hypersaline habitats [14] and of certain genera of cyanobacteria with different temperature responses [6]. The last aspect was studied by comparison of temperature responses of 30 isolates of these genera and by a meta-analysis of 84 locations around the world [6] and revealed advantages of Tolypothrix strains at lower temperatures, Scytonema strains at higher temperatures and Nostoc strains at moderate temperatures [6].…”

“…Alkaliphilic heliobacteria of the genus Heliorestis live in soda lakes, grow optimally between pH 8.0 and 9.5 and form a phylogenetic distinct group among heliobacteria [4]. One of these, Hrs.…”

“…The analysis of the complete genome sequence of Hrs. convoluta provided insight into the molecular adaptation to alkaline conditions, the photoheterotrophic metabolism, nitrogen utilization, sulfur assimilation, and pigment biosynthesis pathways of heliobacteria [4]. Recent genome analyses of a larger number of heliobacteria have led to reconsidering their phylogeny and systematic treatment and confirmed the distinct phylogenetic position of the alkaliphilic Heliorestis species [21].…”