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ABSTRACT The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation in environmental acclimation are underexplored for organisms of the domain Archaea . Here, we have investigated the scale of post-transcriptional regulation in the extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating the transcriptome-wide locations of transcript processing sites (TPSs) and SmAP1 binding, the genome-wide locations of antisense RNAs (asRNAs), and the consequences of RNase_2099C knockout on the differential expression of all genes. This integrated analysis has discovered that 54% of all protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for putative post-transcriptional processing and regulation, with about 20% of genes likely being regulated by combinatorial schemes involving SmAP1, asRNAs, and RNase_2099C. Comparative analysis of mRNA levels (transcriptome sequencing [RNA-Seq]) and protein levels (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry [SWATH-MS]) for 2,579 genes over four phases of batch culture growth in complex medium generated additional evidence for the conditional post-transcriptional regulation of 7% of all protein-coding genes. We demonstrate that post-transcriptional regulation may act to fine-tune specialized and rapid acclimation to stressful environments, e.g., as a switch to turn on gas vesicle biogenesis to promote vertical relocation under anoxic conditions and modulate the frequency of transposition by insertion sequence (IS) elements of the IS 200 /IS 605 , IS 4 , and IS H3 families. Findings from this study are provided as an atlas in a public Web resource ( https://halodata.systemsbiology.net ). IMPORTANCE While the transcriptional regulation landscape of archaea has been extensively investigated, we currently have limited knowledge about post-transcriptional regulation and its driving mechanisms in this domain of life. In this study, we collected and integrated omics data from multiple sources and technologies to infer post-transcriptionally regulated genes and the putative mechanisms modulating their expression at the protein level in Halobacterium salinarum NRC-1. The results suggest that post-transcriptional regulation may drive environmental acclimation by regulating hallmark biological processes. To foster discoveries by other research groups interested in the topic, we extended our integrated data to the public in the form of an interactive atlas ( https://halodata.systemsbiology.net ). 

Iodic acid (HIO 3 ) is known to form aerosol particles in coastal marine regions, but predicted nucleation and growth rates are lacking. Using the CERN CLOUD (Cosmics Leaving Outdoor Droplets) chamber, we find that the nucleation rates of HIO 3 particles are rapid, even exceeding sulfuric acid–ammonia rates under similar conditions. We also find that ion-induced nucleation involves IO 3 − and the sequential addition of HIO 3 and that it proceeds at the kinetic limit below +10°C. In contrast, neutral nucleation involves the repeated sequential addition of iodous acid (HIO 2 ) followed by HIO 3 , showing that HIO 2 plays a key stabilizing role. Freshly formed particles are composed almost entirely of HIO 3 , which drives rapid particle growth at the kinetic limit. Our measurements indicate that iodine oxoacid particle formation can compete with sulfuric acid in pristine regions of the atmosphere. 

Abstract. Highly oxygenated organic molecules (HOMs) contributesubstantially to the formation and growth of atmospheric aerosol particles,which affect air quality, human health and Earth's climate. HOMs are formedby rapid, gas-phase autoxidation of volatile organic compounds (VOCs) suchas α-pinene, the most abundant monoterpene in the atmosphere. Due totheir abundance and low volatility, HOMs can play an important role innew-particle formation (NPF) and the early growth of atmospheric aerosols,even without any further assistance of other low-volatility compounds suchas sulfuric acid. Both the autoxidation reaction forming HOMs and theirNPF rates are expected to be strongly dependent ontemperature. However, experimental data on both effects are limited.Dedicated experiments were performed at the CLOUD (Cosmics Leaving OUtdoorDroplets) chamber at CERN to address this question. In this study, we showthat a decrease in temperature (from +25 to −50 ∘C) results ina reduced HOM yield and reduced oxidation state of the products, whereas theNPF rates (J1.7 nm) increase substantially.Measurements with two different chemical ionization mass spectrometers(using nitrate and protonated water as reagent ion, respectively) providethe molecular composition of the gaseous oxidation products, and atwo-dimensional volatility basis set (2D VBS) model provides their volatilitydistribution. The HOM yield decreases with temperature from 6.2 % at 25 ∘C to 0.7 % at −50 ∘C. However, there is a strongreduction of the saturation vapor pressure of each oxidation state as thetemperature is reduced. Overall, the reduction in volatility withtemperature leads to an increase in the nucleation rates by up to 3orders of magnitude at −50 ∘C compared with 25 ∘C. Inaddition, the enhancement of the nucleation rates by ions decreases withdecreasing temperature, since the neutral molecular clusters have increasedstability against evaporation. The resulting data quantify how the interplaybetween the temperature-dependent oxidation pathways and the associatedvapor pressures affect biogenic NPF at the molecularlevel. Our measurements, therefore, improve our understanding of purebiogenic NPF for a wide range of tropospherictemperatures and precursor concentrations.