Background: Phosphodiesterase 3A ( PDE3A ) gain-of-function mutations cause hypertension with brachydactyly (HTNB) and lead to stroke. Increased peripheral vascular resistance, rather than salt retention, is responsible. It is surprising that the few patients with HTNB examined so far did not develop cardiac hypertrophy or heart failure. We hypothesized that, in the heart, PDE3A mutations could be protective. Methods: We studied new patients. CRISPR-Cas9–engineered rat HTNB models were phenotyped by telemetric blood pressure measurements, echocardiography, microcomputed tomography, RNA-sequencing, and single nuclei RNA-sequencing. Human induced pluripotent stem cells carrying PDE3A mutations were established, differentiated to cardiomyocytes, and analyzed by Ca 2+ imaging. We used Förster resonance energy transfer and biochemical assays. Results: We identified a new PDE3A mutation in a family with HTNB. It maps to exon 13 encoding the enzyme’s catalytic domain. All hitherto identified HTNB PDE3A mutations cluster in exon 4 encoding a region N-terminally from the catalytic domain of the enzyme. The mutations were recapitulated in rat models. Both exon 4 and 13 mutations led to aberrant phosphorylation, hyperactivity, and increased PDE3A enzyme self-assembly. The left ventricles of our patients with HTNB and the rat models were normal despite preexisting hypertension. A catecholamine challenge elicited cardiac hypertrophy in HTNB rats only to the level of wild-type rats and improved the contractility of the mutant hearts, compared with wild-type rats. The β-adrenergic system, phosphodiesterase activity, and cAMP levels in the mutant hearts resembled wild-type hearts, whereas phospholamban phosphorylation was decreased in the mutants. In our induced pluripotent stem cell cardiomyocyte models, the PDE3A mutations caused adaptive changes of Ca 2+ cycling. RNA-sequencing and single nuclei RNA-sequencing identified differences in mRNA expression between wild-type and mutants, affecting, among others, metabolism and protein folding. Conclusions: Although in vascular smooth muscle, PDE3A mutations cause hypertension, they confer protection against hypertension-induced cardiac damage in hearts. Nonselective PDE3A inhibition is a final, short-term option in heart failure treatment to increase cardiac cAMP and improve contractility. Our data argue that mimicking the effect of PDE3A mutations in the heart rather than nonselective PDE3 inhibition is cardioprotective in the long term. Our findings could facilitate the search for new treatments to prevent hypertension-induced cardiac damage.
Gene expression in bacteria is a remarkably controlled and intricate process impacted by many factors. One such factor is the genomic position of a gene within a bacterial genome. Genes located near the origin of replication generally have a higher expression level, increased dosage, and are often more conserved than genes located farther from the origin of replication. The majority of the studies involved with these findings have only noted this phenomenon in a single gene or cluster of genes that was relocated to predetermined positions within a bacterial genome. In this work, we look at the overall expression levels from eleven bacterial data sets from Escherichia coli, Bacillus subtilis, Streptomyces, and Sinorhizobium meliloti. We have confirmed that gene expression tends to decrease when moving away from the origin of replication in majority of the replicons analysed in this study. This study sheds light on the impact of genomic location on molecular trends such as gene expression and highlights the importance of accounting for spatial trends in bacterial molecular analysis.
Genomic reorganization, like rearrangements and inversions, influence how genetic information is organized within bacterial genomes. Inversions in particular, facilitate genome evolution through gene gain and loss, and can alter gene expression. Previous studies investigating the impact inversions have on gene expression induced inversions targeting specific genes or examine inversions between distantly related species. This fails to encompass a genome wide perspective on naturally occurring inversions and their post adaptation impact on gene expression. Here we use bioinformatic techniques and multiple RNA-seq datasets to investigate the short- and long-range impact inversions have on genomic gene expression within <i>Escherichia coli</i>. We observed differences in gene expression between homologous inverted and non-inverted genes, even after long term exposure to adaptive selection. In 4% of inversions representing 33 genes, differential gene expression between inverted and non-inverted homologs was detected, with nearly two thirds (71%) of differentially expressed inverted genes having 9.4-85.6 fold higher gene expression. The identified inversions had more overlap than expected with nucleoid associated protein binding sites, which assist in genomic gene expression regulation. Some inversions can drastically impact gene expression even between different strains of <i>E.coli</i>, and could provide a mechanism for the diversification of genetic content through controlled expression changes.
Increasing evidence supports the notion that different regions of a genome have unique rates of molecular change. This variation is particularly evident in bacterial genomes where previous studies have reported gene expression and essentiality tend to decrease, whereas substitution rates usually increase with increasing distance from the origin of replication. Genomic reorganization such as rearrangements occur frequently in bacteria and allow for the introduction and restructuring of genetic content, creating gradients of molecular traits along genomes. Here, we explore the interplay of these phenomena by mapping substitutions to the genomes of Escherichia coli, Bacillus subtilis, Streptomyces, and Sinorhizobium meliloti, quantifying how many substitutions have occurred at each position in the genome. Preceding work indicates that substitution rate significantly increases with distance from the origin. Using a larger sample size and accounting for genome rearrangements through ancestral reconstruction, our analysis demonstrates that the correlation between the number of substitutions and the distance from the origin of replication is significant but small and inconsistent in direction. Some replicons had a significantly decreasing trend (E. coli and the chromosome of S. meliloti), whereas others showed the opposite significant trend (B. subtilis, Streptomyces, pSymA and pSymB in S. meliloti). dN, dS, and ω were examined across all genes and there was no significant correlation between those values and distance from the origin. This study highlights the impact that genomic rearrangements and location have on molecular trends in some bacteria, illustrating the importance of considering spatial trends in molecular evolutionary analysis. Assuming that molecular trends are exclusively in one direction can be problematic.
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