A Hypothesis on How the Azolla Symbiosis Mitigates Nitrous Oxide Based on In Silico Analyses

Dilantha Gunawardana,Venura Herath

doi:10.3390/j5010013

Abstract

Nitrous oxide is a long-lived greenhouse gas that exists for 114 years in the atmosphere and is 298-fold more potent than carbon dioxide in its global warming potential. Two recent studies showcased the utility of Azolla plants for a lesser footprint in nitrous oxide production from urea and other supplements to the irrigated ecosystem, which mandates exploration since there is still no clear solution to nitrous oxide in paddy fields or in other ecosystems. Here, we propose a solution based on the evolution of a single cytochrome oxidase subunit II protein (WP_013192178.1) from the cyanobiont Trichormus azollae that we hypothesize to be able to quench nitrous oxide. First, we draw attention to a domain in the candidate protein that is emerging as a sensory periplasmic Y_Y_Y domain that is inferred to bind nitrous oxide. Secondly, we draw the phylogeny of the candidate protein showcasing the poor bootstrap support of its position in the wider clade showcasing its deviation from the core function. Thirdly, we show that the NtcA protein, the apical N-effecting transcription factor, can putatively bind to a promoter sequence of the gene coding for the candidate protein (WP_013192178.1), suggesting a function associated with heterocysts and N-metabolism. Our fourth point involves a string of histidines at the C-terminal extremity of the WP_013192178.1 protein that is missing on all other T. azollae cytochrome oxidase subunit II counterparts, suggesting that such histidines are perhaps involved in forming a Cu center. As the fifth point, we showcase a unique glycine-183 in a lengthy linker region containing multiple glycines that is absent in all proximal Nostocales cyanobacteria, which we predict to be a DNA binding residue. We propose a mechanism of action for the WP_013192178.1 protein based on our in silico analyses. In total, we hypothesize the incomplete and rapid conversion of a likely heterocystous cytochrome oxidase subunit II protein to an emerging nitrous oxide sensing/quenching subunit based on bioinformatics analyses and past literature, which can have repercussions to climate change and consequently, future human life.

Highlights

IntroductionBefore the oxygenation of the ancient world billions of years ago, prokaryotic lifeforms had to contend with nitrous oxide that saw its birth from corona discharge and not as lightning strikes— there is literature attributing nitrous oxide emanation to streaks of lightning—which anucleated microorganisms reduced using an enzyme designated as nitrous oxide reductase [1]
According to the structural classification of proteins (SCOP) classification, a protein that has >30% sequence identity belongs to the same protein/enzyme family, with most arbitrational cutoffs determined for coverage taken as >50% [14]
Nitric oxide is a potent toxic molecule and a reactive nitrogen species, as well as being a signaling molecule that needs to be handled carefully when it can putatively harm organisms such as cyanobacteria when produced by nitric oxide synthases [36]

Summary

Introduction

Before the oxygenation of the ancient world billions of years ago, prokaryotic lifeforms had to contend with nitrous oxide that saw its birth from corona discharge and not as lightning strikes— there is literature attributing nitrous oxide emanation to streaks of lightning—which anucleated microorganisms reduced using an enzyme designated as nitrous oxide reductase [1]. Nitrous oxide is a greenhouse gas that subsists in the atmosphere for 114 years and is 298-fold more potent than the benchmark gas of carbon dioxide in global warming potential [2,3]. Nitrous oxide reductases are known to be of the same protein fold as cytochrome oxidases (subunit II), the former being the more pre-historical one and the latter evolving from the ancient fossil of a fold, this is disputed [4]. There are two biochemical pathways for the formation of nitrous oxide: the conversion of nitric oxide to nitrous oxide by nitric oxide reductases or by ammonia

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