Biology subjects

Hu, E.-Z.

Publications and source records attributed to Hu, E.-Z..

3 recordsLinked to original sources

bioRxiv2023

Relationship between prokaryotic GC contents and environmental salinity

BackgroundThe correlation between GC content and halophilicity has received limited attention, despite the numerous environmental factors associated with GC content evolution. While higher GC content has been linked to halophiles in some archaeal cases, it is widely believed that selective pressure from high-intensity ultraviolet radiation in halophilic archaea drives GC content increase, as it prevents DNA photoproduct formation. However, this assumption has not been statistically analyzed in a phylogenetically independent manner prior to our study. ResultsUsing phylogenetic generalized least squares, we investigated the relationship between GC content and halophilicity in 1226 bacteria and 181 archaea. Our analysis found significant positive correlations in bacteria but not in archaea. Resampling analysis indicates that the absence of significant correlation in archaea may be due to the relatively small sample size. We also observed that the strength of the correlation is negatively influenced by the functional constraint of genomic components. Additionally, we found that halophilic bacteria and archaea do not have lower photoreactivity (a measure of DNA vulnerability to ultraviolet radiation) than the photoreactivity expected from their GC contents. ConclusionsIn contrast to previous assumptions, we did not find evidence to support the widespread photoprotection hypothesis or another hypothesis that high GC content in halophiles stabilizes nucleic acid structures. Instead, our findings align with a nonadaptive hypothesis. Halophilic prokaryotes likely evolved high GC content due to frequent GC-biased gene conversion in response to DNA double-strand breaks induced directly or indirectly by high salt concentrations.

evolutionary biology↗

bioRxiv2022

A Positive Correlation between CRISPR-Cas Spacer Abundance and Cell Cycle Duration Across the Bacteria Domain

CRISPR-Cas systems provide adaptive immunity for prokaryotic cells by recognizing and eliminating the recurrent genetic invaders whose sequences had been captured in a prior infection and stored in the CRISPR arrays as spacers. However, the biological/environmental factors determining the efficiency of this immune system have yet to be fully characterized. Recent studies in cultured bacteria showed that slowing the growth rate of bacterial cells could promote their acquisition of novel spacers. This study examined the relationship between the CRISPR-Cas content and the minimal doubling time across the bacteria and the archaea domains. Every completely sequenced genome could be used to predict a minimal doubling time. With a large dataset of 4142 bacterial samples, we found that the predicted minimal doubling times are positively correlated with spacer number and other parameters of the CRISPR-Cas systems, like array number, Cas gene cluster number, and Cas gene number. Different datasets gave different results. Weak results were obtained in analyzing bacterial empirical minimal doubling times and the archaea domain. Still, the conclusion of more spacers in slowly-grown prokaryotes was supported. In addition, we found that the minimal doubling times are negatively correlated with the occurrence of prophages, and the spacer numbers per array are negatively associated with the number of prophages. These observations support the existence of an evolutionary trade-off between bacterial growth and adaptive defense against virulent phages.

evolutionary biology↗

bioRxiv2021

Significant Correlation between Growth Temperature and Guanine-Cytosine Content in Bacteria

BackgroundGC pairs are generally more stable than AT pairs; GC-rich genomes were proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies consistently showed positive correlations between growth temperature and the GC contents of structural RNA genes. However, for the whole genome sequences and the silent sites of the codons in protein-coding genes, the relationship between GC content and growth temperature is in a long-lasting debate. ResultsWith a dataset much larger than previous studies (681 bacteria and 155 archaea with completely assembled genomes), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature (Topt) and GC content both in bacterial and archaeal structural RNA genes and in bacterial whole genome sequences, chromosomal sequences, plasmid sequences, core genes, and accessory genes. However, in the 155 archaea, we did not observe a significant positive correlation of Topt with whole-genome GC content (GCw) or GC content at four-fold degenerate sites. We randomly drew 155 samples from the 681 bacteria for 1000 rounds. In most cases (> 95%), the positive correlations between Topt and genomic GC contents became statistically nonsignificant (P > 0.05). This result suggested that the small sample sizes might account for the lack of positive correlations between growth temperature and genomic GC content in the 155 archaea and the bacterial samples of previous studies. Comparing the GC content among four categories (psychrophiles/psychrotrophiles, mesophiles, thermophiles, and hyperthermophiles) also revealed a positive correlation between GCw and growth temperature in bacteria. By including the GCw of incompletely assembled genomes, we expanded the sample size of archaea to 303. Positive correlations between GCw and Topt appear especially after excluding the halophilic archaea whose GC contents might be are strongly shaped by intense UV radiation. ConclusionsThis study explains the previous contradictory observations and ends a long debate. Prokaryotes growing in high temperatures have higher GC contents. Thermal adaptation is one possible explanation for the positive association. Meanwhile, we propose that the elevated efficiency of DNA repair in response to heat mutagenesis might have the by-product of increasing GC content like that happens in intracellular symbionts and marine bacterioplankton.

evolutionary biology↗