Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have

Aslam, Sidra; Lan, Xin-Ran; Zhang, Bowen; Chen, Zhenglin; Wang, Li; Niu, Deng-Ke

doi:10.1186/s12862-019-1365-8

Cited by 23 publications

(33 citation statements)

References 59 publications

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“…Similarly, in terms of oxygen dependence, affected taxa in a majority of analyzed jumps (80%) did not show a change compared to related unaffected taxa; but in about 10% jumps, affected taxa were more dependent on oxygen (aerobic instead of facultatively aerobic) and had experienced increased GC content. This is consistent with some previous studies that found increased GC content to be associated with increased oxygen-dependence (Aslam et al, 2019;Naya et al, 2002). However, previous studies do not identify specific instances of such associations.…”

Section: Habitats and Lifestyles Of Clades Experiencing Gc Jumpssupporting

confidence: 91%

“…Additionally, a number of ecological factors have been proposed to be correlated with GC content (Agashe and Shankar, 2014), e.g. host-association (Moran, 2002), aerobiosis (Aslam et al, 2019;Naya et al, 2002), nitrogen fixation (McEwan et al, 1998), and temperature (Musto et al, 2004). However, many factors do not show strong correlations with GC content after accounting for the phylogeny or other confounding factors (Aslam et al, 2019;Marashi and Ghalanbor, 2004;Vieira-Silva and Rocha, 2008;Wang et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

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Evolutionary jumps in bacterial GC content

Mahajan

Agashe

2021

Preprint

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The diversity of bacterial GC content (ranging from 13 75%) has been studied for many decades, yet its evolution remains incompletely understood. Since it is difficult to observe GC content evolve on realistic time scales in the laboratory, comparative approaches are instrumental for its study. Additionally, investigating phylogenetic patterns in a traits diversity can provide greater insight into its evolution; but this dimension is rarely studied systematically in the case of bacterial GC content. Therefore, we applied phylogenetic models – typically used for studying morphological or behavioral traits of animals and plants – to the study of this fundamental molecular trait. We find that GC content diversifies via a combination of gradual evolution and evolutionary jumps in multiple bacterial groups across two major bacterial phyla. In a systematic survey of these GC content jumps, we retrieved many well-studied cases of severe evolutionary reduction in GC content of endosymbiotic bacteria, but also identified GC content jumps in bacterial lineages beyond such peculiar contexts. Surprisingly, unlike prior reports that solely focused on reductions in GC, we found a comparable number of jumps with both increased and decreased GC content. Our preliminary analysis of potential ecological explanations of GC jumps suggests that most of these GC jumps are not concomitant with changes in previously implicated factors such as host association or oxygen dependence. Thus, the ecological and evolutionary drivers of rapid and large shifts in GC content remain open questions. Our systematic identification of bacterial lineages experiencing GC jumps provides new datasets and novel contexts to address these questions.

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Section: Habitats and Lifestyles Of Clades Experiencing Gc Jumpssupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Evolutionary jumps in bacterial GC content

Mahajan

Agashe

2021

Preprint

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“…Fifth, an excess of A:T>G:C has been observed in aerobically versus anaerobically grown Escherichia coli and the signal was driven by the lagging strand, spending more time in single-stranded condition (Shewaramani et al 2017). Interestingly, A>G substitutions, associated with oxidative damage, can be a key process, explaining a long-standing evolutionary puzzle of increased GC content of aerobic versus anaerobic bacteria (Naya et al 2002;Romero et al 2009;Aslam et al 2019).…”

Section: Discussionmentioning

confidence: 99%

Mammalian mitochondrial mutational spectrum as a hallmark of cellular and organismal aging

Mikhailova

Ushakova

Tretyakov

et al. 2019

Preprint

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It has been shown recently that mitochondrial (mtDNA) somatic variants are numerous enough to trace cellular lineages in our body. Here we extend this statement and demonstrate that mtDNA variants can be interpreted not only as neutral markers of cell divisions but the relative frequency of different mtDNA substitutions (i.e. mtDNA mutational spectrum) can inform us about important biological properties such as cell longevity. Analysing 7611 somatic mtDNA mutations from 37 types of human cancers and more than 2000 somatic mtDNA mutations from 25 healthy human tissues we observed that mtDNA mutational spectrum is associated with cell turnover rate: the ratio of T>C to G>A is increasing with cell longevity. To extend this logic we considered that, if universal, the discovered mutation bias may drive the differences in mtDNA mutational spectrum between mammalian species with short-(‘mice’) and long-(‘elephants’) lived oocytes. Based on presumably neutral polymorphisms in MT-CYB we reconstructed mutational spectra for 424 mammalian species and obtained that the fraction of T>C positively correlated with the species-specific generation length, which is a good proxy for oocyte longevity. Next, comparing complete mitochondrial genomes of 650 mammalian species we confirmed that exactly the same process shapes the nucleotide content of the most neutral sites in the whole mitochondrial genomes of short-(high T, low C) versus long-(low T, high C) lived mammals. Altogether analysing mtDNA mutations in time interval from dozens of years (somatic mutations) through the hundreds of thousands of years (within species polymorphisms) to millions of years (between species substitutions) we demonstrated that T>C/G>A positively correlates with cellular and organismal longevity. We hypothesize that the discovered mtDNA signature presents a chemical damage which is associated with the level of oxidative metabolism which, in turn, correlates with cellular and organismal longevity. The described properties of mtDNA mutational spectrum shed light on mtDNA replication, mtDNA evolution of mammals and can be used as a marker of cell longevity in single-cell analyses of heterogeneous samples.

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“…We also examined whether the contrast in the temperature category is correlated with the contrast in the GC content between terminal tips of the phylogenetic tree by referring (Aslam et al 2019). In total, 273 pairs of bacteria and 41 pairs of archaea were obtained from the phylogenetic tree (Parks et al 2020).…”

Section: Qualitative Data On Growth Temperature Lead To the Same Conclusionmentioning

confidence: 99%

A positive correlation between GC content and growth temperature in prokaryotes

Lan

Liu

et al. 2021

Preprint

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Because GC pairs are more stable than AT pairs, GC-rich sequences were proposed to be more adapted to high temperatures than AT-rich sequences. Previous studies consistently showed positive correlations between the 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. With a dataset much larger than previous studies (681 bacteria and 155 archaea), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature and GC content exists, both in the structural RNA genes of bacteria and archaea 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 optimal growth temperature with whole-genome GC content 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 optimal growth temperature and genomic GC content 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.

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Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have

Cited by 23 publications

References 59 publications

Evolutionary jumps in bacterial GC content

Evolutionary jumps in bacterial GC content

Mammalian mitochondrial mutational spectrum as a hallmark of cellular and organismal aging

A positive correlation between GC content and growth temperature in prokaryotes

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