ABSTRACT
Halobacterium salinarum NRC-1 is an extremophile that grows optimally at 4.3 M NaCl concentration. In spite of being an established model microorganism for the archaea domain, direct comparisons between its proteome and transcriptome during osmotic stress are still not available. Through RNA-seq-based transcriptomics, we compared a low salt (2.6 M NaCl) stress condition with 4.3 M of NaCl and found 283 differentially expressed loci. The more commonly found classes of genes were: ABC-type transporters and transcription factors. Similarities, and most importantly, differences between our findings and previously published datasets in similar experimental conditions are discussed. We validated three important biological processes differentially expressed: gas vesicles production (due to down-regulation of gvpA1b, gvpC1b, gvpN1b, and gvpO1b); archaellum formation (due to down-regulation of arlI, arlB1, arlB2, and arlB3); and glycerol metabolism (due to up-regulation of glpA1, glpB, and glpC). Direct comparison between transcriptomics and proteomics showed 58% agreement between mRNA and protein level changes, pointing to post-transcriptional regulation candidates. From those genes, we highlight rpl15e, encoding for the 50S ribosomal protein L15e, for which we hypothesize an ionic strength-dependent conformational change that guides post-transcriptional processing of its mRNA and, thus, possible salt-dependent regulation of the translation machinery.
ABSTRACT
Post-transcriptional processing of messenger RNA is an important regulatory strategy that allows relatively fast responses to changes in environmental conditions. In halophile systems biology, the protein perspective of this problem (i.e., ribonucleases which implement the cleavages) is generally more studied than the RNA perspective (i.e., processing sites). In the present in silico work, we mapped genome-wide transcriptional processing sites (TPS) in two halophilic model organisms, Halobacterium salinarum NRC-1 and Haloferax volcanii DS2. TPS were established by reanalysis of publicly available differential RNA-seq (dRNA-seq) data, searching for non-primary (monophosphorylated RNAs) enrichment. We found 2093 TPS in 43% of H. salinarum genes and 3515 TPS in 49% of H. volcanii chromosomal genes. Of the 244 conserved TPS sites found, the majority were located around start and stop codons of orthologous genes. Specific genes are highlighted when discussing antisense, ribosome and insertion sequence associated TPS. Examples include the cell division gene ftsZ2, whose differential processing signal along growth was detected and correlated with post-transcriptional regulation, and biogenesis of sense overlapping transcripts associated with IS200/IS605. We hereby present the comparative, transcriptomics-based processing site maps with a companion browsing interface.
Subject(s)
Archaeal Proteins/genetics , Gene Expression Regulation, Archaeal , Genome, Archaeal , Halobacterium salinarum/genetics , Haloferax volcanii/genetics , Transcription Initiation Site , Transcriptome , Archaeal Proteins/metabolism , Halobacterium salinarum/metabolism , Haloferax volcanii/metabolism , RNA-Seq , RibosomesABSTRACT
El objetivo del presente estudio fue evaluar el modelo NRC (1996) nivel I para la predicción de la ganancia diaria de peso en novillas suplementadas bajo condiciones tropicales. Para tal fin, se realizaron dos experimentos. En el experimento 1 se evaluaron 30 novillas divididas en dos grupos de 15 animales cada uno, el grupo suplementado (GS) presentó un peso inicial de 365,27 ± 24,40 kg, recibió concentrado a razón de 1% del peso vivo (5,5% PC, 2,85 Mcal ED) y el no suplementado (GNS) con un peso inicial de 367,47 ± 31,65 kg. En el experimento 2 se utilizaron 45 novillas divididas en dos grupos, el GSb con 22 animales, teniendo un peso inicial de 342,23 ± 36,04 kg se les proporcionó alimento a razón del 1% del peso vivo (13% PC; 3,15 Mcal ED) y el GNSb se constituyó por 23 animales teniendo un peso inicial promedio de 326,30 ± 31,53 kg. En ambos experimentos los animales fueron suplementados a lo largo de 45 días, y estuvieron pastoreando praderas de Estrella Africana (Cynodon nlemfuensis), Candelario (Pennisteum purpureum) y Ratana (Ischaemum indicum). En ambos experimentos no se observaron diferencias (P > 0,05) para los cambios de peso. El GS obtuvo ganancias diarias de peso (GDP) de 0,27 kg/d, mientras que el GNS mostró pérdidas de -0,05 kg/d; en el experimento 2 el GSb presentó GDP de 0,90 kg/d y el GNSb de 0,60 kg/d. La GDP predicha en el experimento 1 fue similar a la ganancia observada para el grupo suplementado (P > 0,05) en contraste con la presentada en el grupo no suplementado en el que la ganancia de peso fue sobrestimada (P < 0,05). En el segundo experimento, la predicción de la GDP tanto para el grupo suplementado como el no suplementado fue subestimada (P < 0,05). El nivel 1 del modelo de simulación NRC no fue apropiado para la predicción de los cambios de peso en novillas bajo condiciones tropicales.
The aim of this study was to evaluate the model NRC level 1 to predict the daily weight gain in heifers supplemented under tropical conditions. For this purpose, two experiments were done, in the first experiment 30 heifers were divided into two groups of fifteen animals each, the supplemented group (GS) showed an initial weight of 365.27 ± 24.40 kg, received commercial concentrate to the ratio of 1% of live weight (5.5% PC 2.85 Mcal ED) and the control group which was not supplemented (GNS) with an initial weight of 367.47 ± 31.65 kg. In the second study 45 heifers were divided in two groups, the GSb with 22 animals having an initial weight of 342.23 ± 36.4 kg and given concentrate to the rate of 1% of live weight (13% PC 3.5 Mcal ED) and the GNSb were made up of 23 animals having an initial average weight of 326.0 ± 31.3 kg. In both trials the animals were supplemented throughout for forty-five days and let them grazed on African Star grass (Cynodon nlemfuensis), Candelario grass (Pennisteum purpureum) and Ratana grass (Ischaemum indicum). In both experiments no differences were observed (P > 0.05) in weight change .The GS had daily weight gains (GDP) of 0.27 kg/d while the GNS showed losses of -0.05 kg/d. In the second trial the GSb showed a GDP of 0.90 kg/d and the GNSb of 0.60 kg/d. The predicted GDP of the first experiment was similar in comparison with the observed value for the supplemented group (P > 0.05), in contrast with that presented in the GNS group in which the daily weight gain was over estimated (P < 0.05). In the second trial the GDP predicted for both groups was under estimated (P < 0.05). The level 1 of the NRC simulation model does not seem to be appropriate for predicting changes in weight in heifers under tropical conditions.