Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway

Abstract

Genes and genomes can evolve through interchanging genetic material, this leading to reticular evolutionary patterns. However, the importance of reticulate evolution in eukaryotes, and in particular of horizontal gene transfer (HGT), remains controversial. Given that metabolic pathways with taxonomically-patchy distributions can be indicative of HGT events, the eukaryotic nitrate assimilation pathway is an ideal object of investigation, as previous results revealed a patchy distribution and suggested that the nitrate assimilation cluster of dikaryotic fungi (Opisthokonta) could have been originated and transferred from a lineage leading to Oomycota (Stramenopiles). We studied the origin and evolution of this pathway through both multi-scale bioinformatic and experimental approaches. Our taxon-rich genomic screening shows that nitrate assimilation is present in more lineages than previously reported, although being restricted to autotrophs and osmotrophs. The phylogenies indicate a pervasive role of HGT, with three bacterial transfers contributing to the pathway origin, and at least seven well-supported transfers between eukaryotes. In particular, we propose a distinct and more complex HGT path between Opisthokonta and Stramenopiles than the one previously suggested, involving at least two transfers of a nitrate assimilation gene cluster. We also found that gene fusion played an essential role in this evolutionary history, underlying the origin of the canonical eukaryotic nitrate reductase, and of a chimeric nitrate reductase in Ichthyosporea (Opisthokonta). We show that the ichthyosporean pathway, including this novel nitrate reductase, is physiologically active and transcriptionally co-regulated, responding to different nitrogen sources; similarly to distant eukaryotes with independent HGT-acquisitions of the pathway. This indicates that this pattern of transcriptional control evolved convergently in eukaryotes, favoring the proper integration of the pathway in the metabolic landscape. Our results highlight the importance of reticulate evolution in eukaryotes, by showing the crucial contribution of HGT and gene fusion in the evolutionary history of the nitrate assimilation pathway.

Heat stress destabilizes symbiotic nutrient cycling in corals

“…S4 F ). In contrast to the coral host, algal symbionts possess the cellular machinery for assimilatory nitrate (NO 3 − ) reduction ( 49 ). Yet, during heat stress, expression of genes encoding for high-affinity nitrate transporters (NRT), nitrate reductases (NR), and nitrite reductases (NIR) showed consistent down-regulation ( Fig.…”

Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments

“…N. stella expresses the ammonium assimilation proteins glutamine synthetase (GS) and glutamate 2-oxo-glutarate aminotransferase (GOGAT), also known as glutamate synthase, a known route to assimilate ammonium in photosynthetic eukaryotes and fungi ( Fig. 2A ) ( 22 , 23 ). We identified several forms of eukaryotic GS genes in both species, with the most abundant GS clusters having their best match (66 to 75% amino acid identity) to Oomycetes.…”

“…S3). The first is a homolog to the eukaryotic nitrate transporter NRT2 ( 22 ). Phylogenetic analysis of our foraminiferal species and Globobulimina spp.…”

“…Transmission electron microscopy–nanoscale secondary ion mass spectrometry (TEM-nanoSIMS) isotopic studies of other foraminiferal species demonstrated that the assimilation of both nitrate and ammonium localize to “electron-opaque bodies” rather than kleptoplasts ( 13 , 16 ). In N. stella, ammonium assimilation is likely via the GS-GOGAT pathway, a route for assimilating ammonium produced from nitrate reduction in photosynthetic eukaryotes and fungi ( 22 , 23 ). Our phylogenetic analyses illustrate that N. stella GOGAT belongs to NADH-GOGAT ( 22 , 41 ) (fig.…”

Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites

“…In addition, gene fusion has been shown to have played an essential role in the evolution of the cellular life cycle, with composite gene formation seen in genes related to chromatin structure and nucleotide metabolism [12]. Also, Ocaña-Pallarès et al [13] concluded that there was a significant role for gene fusion in the origin of eukaryotes, as evidenced by SSN built from eukaryotic EUKaryotic restricted Nitrate Reductase (EUKNR) and similar eukaryotic and prokaryotic sequences. The result indicated that EUKNR was formed by a fusion of eukaryotic sulfite oxidases (SUOX, N-terminal) and NADH (C-terminal) reductases.…”