Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification

Abstract

Oxygenic photosynthesis evolved from anoxygenic ancestors before the rise of oxygen ~2.32 billion years ago; however, little is known about this transition. A high redox potential reaction center is a prerequisite for the evolution of the water-oxidizing complex of photosystem II. Therefore, it is likely that high-potential phototrophy originally evolved to oxidize alternative electron donors that utilized simpler redox chemistry, such as nitrite or Mn. To determine whether nitrite could have had a role in the transition to high-potential phototrophy, we sequenced and analyzed the genome of Thiocapsa KS1, a Gammaproteobacteria capable of anoxygenic phototrophic nitrite oxidation. The genome revealed a high metabolic flexibility, which likely allows Thiocapsa KS1 to colonize a great variety of habitats and to persist under fluctuating environmental conditions. We demonstrate that Thiocapsa KS1 does not utilize a high-potential reaction center for phototrophic nitrite oxidation, which suggests that this type of phototrophic nitrite oxidation did not drive the evolution of high-potential phototrophy. In addition, phylogenetic and biochemical analyses of the nitrite oxidoreductase (NXR) from Thiocapsa KS1 illuminate a complex evolutionary history of nitrite oxidation. Our results indicate that the NXR in Thiocapsa originates from a different nitrate reductase clade than the NXRs in chemolithotrophic nitrite oxidizers, suggesting that multiple evolutionary trajectories led to modern nitrite-oxidizing bacteria.

Figure 1

Metabolic diversity of Thiocapsa KS1. For details see main and supplemental text. APR, adenylylsulphate reductase complex; bd, cytochrome bd quinol oxidase; BFR, bacterioferritin; CA, carbonic anhydrase; CYN, cyanate hydratase; Cys, assimilatory sulfate reduction complexes; DSR, reverse dissimilatory sulfite reductase; FCC, sulfide dehydrogenase; FDH, formate dehydrogenase; HOX, HUP, HYD, HYN, hydrogenases (with enzyme classification indicated in brackets); NAP, periplasmic nitrate reductase; NIF, nitrogenase; NOR, nitric oxide reductase; NOS, nitrous oxide reductase; NXR, nitrite oxidoreductase; OTR, octaheme tetrathionate reductase; PHA, polyhydroxyalkanoate; PS, photosystem (type II reaction center); PTS, phosphotransferase system; RNF, H⁺/Na⁺-translocating NAD-ferredoxin reductase; SAT, sulfate adenylyltransferase; SIR, sulfite reductase; SOD, superoxide dismutase; SOE, sulfite-oxidizing enzyme; SOX, sulfur/thiosulfate oxidation protein complex; SQR, sulfide-quinone reductase; TCA cycle, tricarboxylic acid cycle; URE, urease. Enzyme complexes of the electron transport chain are labeled by Roman numerals: I, NADH dehydrogenase; II, succinate dehydrogenase/fumarate reductase; III, cytochrome bc₁ complex; IV, cbb₃-type cytochrome c oxidase; Orange, red, green and blue diamonds represent quinones, cytochrome c proteins, HiPIPs and ferredoxins, respectively.

Figure 2

High-potential RCIIs? Shown are known mutations that produce high-potential RCIIs. Sequence analysis detected no natural variants capable of forming hydrogen bonds at these positions (Supplementary Table S4). PufL is blue, PufM is red and PufC is gray.

Figure 3

Phylogenetic analyses of Thiocapsa KS1 NXR and related enzymes of the dimethyl sulfoxide reductase type II family. Bayesian inference tree of the large (NxrA) subunit. Names of validated enzymes are indicated (Clr, chlorate reductase; Ddh, dimethylsulfide dehydrogenase; Ebd, ethylbenzene dehydrogenase; NAR, nitrate reductase; Pcr, perchlorate reductase; Ser, selenatereductase). The arrow indicates the outgroup; the scale bar represents 10% estimated sequence divergence. Enzyme complexes with the active center located on the cytoplasmic side of the membrane are indicated in blue, complexes oriented toward the periplasm in red. Names of organisms containing a NXR are shown in green. Note the three independent origins of NXR.