Carbon limitation drives GC content evolution of a marine bacterium in an individual-based genome-scale model

Hellweger, Ferdi L.; Huang, Yongjie; Luo, Haiwei

doi:10.1038/s41396-017-0023-7

Cited by 49 publications

(57 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We measured C : N ratios in the narrow range of 4.5–4.6 : 1, close to published values for marine bacteria (5 : 1; Table ). Signatures of evolution to economize N content have been reported from marine bacterial proteomes (Grzymski and Dussaq ), including SAR11, while other studies have indicated that the low G + C content of genomic DNA in some plankton, including SAR11, is more likely to be a consequence of C limitation (Hellweger et al ). Regardless, our findings indicate a relatively small fraction of C and N biomass in these cells.…”

Section: Resultsmentioning

confidence: 98%

Elemental content and stoichiometry of SAR11 chemoheterotrophic marine bacteria

White

Giovannoni

Zhao

et al. 2019

Limnol Oceanogr Letters

View full text Add to dashboard Cite

We measured the carbon, nitrogen, and phosphorus content and production of cultured SAR11 cells in the genus Pelagibacter, from members of the 1a.1 and 1a.3 lineages, which are adapted to productive coastal waters and oligotrophic tropical/subtropical environments, respectively. The average growing SAR11 cell contained ~ 6.5 fg C, from which we calculated a global standing stock of 1.4 × 1013 g C. Calculations that consider uncertainties in cell turnover rates and growth efficiencies indicate this stock could oxidize 6% to 37% of gross ocean primary production. We also found that SAR11 do not incorporate 3H‐thymidine but do incorporate 3H‐leucine. We estimate conversion factors of 0.74–1.51 kg C mol−1 leu, which are comparable to the low end of published leucine conversion factors for marine chemoheterotrophic bacterioplankton production. The molar ratio of elements C : N : P in growing cells was on average 25 : 6 : 1, significantly less than the mean (~ 50 : 10 : 1) for heterotrophic bacteria, indicating these strains are C and N poor relative to P.

show abstract

Section: Resultsmentioning

confidence: 98%

Elemental content and stoichiometry of SAR11 chemoheterotrophic marine bacteria

White

Giovannoni

Zhao

et al. 2019

Limnol Oceanogr Letters

View full text Add to dashboard Cite

show abstract

“…Because A and T each contain one nitrogen atom less than G and C, respectively, the reduced usage of the G and C allows an organism to minimize the demand for the limiting nitrogen during replication and transcription. By contrast, carbon limitation could drive long-term elevation of the genomic GC-content (16,17), likely, because small (carbonpoor) amino acids are preferentially encoded by GC-rich codons (18).…”

Section: Introductionmentioning

confidence: 99%

Selection for reducing energy cost of protein production drives the GC content and amino acid composition bias in gene transfer agents

Kogay

Wolf

Koonin

et al. 2020

Preprint

View full text Add to dashboard Cite

Gene transfer agents (GTAs) are virus-like elements integrated into bacterial genomes, particularly, those of Alphaproteobacteria. The GTAs can be induced under nutritional stress, incorporate random fragments of bacterial DNA into mini-phage particles, lyse the host cells and infect neighboring bacteria, thus enhancing horizontal gene transfer. We show that the GTA genes evolve under pronounced positive selection for the reduction of the energy cost of protein production as shown by comparison of the amino acid compositions with both homologous viral genes and host genes. The energy saving in GTA genes is comparable to or even more pronounced than that in the genes encoding the most abundant, essential bacterial proteins. In cases when viruses acquire genes from GTAs, the bias in amino acid composition disappears in the course of evolution, showing that reduction of the energy cost of protein is an important factor of evolution of GTAs but not bacterial viruses. These findings strongly suggest that GTAs are bacterial adaptations rather than selfish, virus-like elements. Because GTA production kills the host cell and does not propagate the GTA genome, it appears likely that the GTAs are retained in the course of evolution via kin or group selection. Therefore, we hypothesize that GTA facilitate the survival of bacterial populations under energy-limiting conditions through the spread of metabolic and transport capabilities via horizontal gene transfer and increase of nutrient availability resulting from the altruistic suicide of GTA-producing cells. ImportanceKin and group selection remain controversial topics in evolutionary biology. We argue that these types of selection are likely to operate in bacterial populations by showing that bacterial Gene Transfer Agents (GTAs), but not related viruses, evolve under positive selection for the reduction of the energy cost of a GTA particle production. We hypothesize that GTAs are dedicated devices for the survival of bacteria under the conditions of nutrient limitation. The benefits conferred by GTAs under nutritional stress appear to include horizontal dissemination of genes that could provide bacteria with enhanced capabilities for nutrient utilization and the increase of nutrient availability through the lysis of GTA-producing bacteria.

show abstract

“…Achromatium was also not indicative of nitrogen or carbon limitation when compared to the model 251 suggested by Hellweger et al (2018). 252…”

mentioning

confidence: 78%

Heterozygous, polyploid, giant bacterium,Achromatium, possesses an identical functional inventory worldwide across drastically different ecosystems

Ionescu

Zoccarato

Zaduryan

et al. 2020

Preprint

View full text Add to dashboard Cite

Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain ca. 300 different chromosomes with allelic diversity typical of entire bacterial communities. Surveying all publicly available sediment sequence archives, we show Achromatia are common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Nevertheless, Achromatia display no ecotypic phylogenetic signal and contain a, globally identical, complete functional inventory. Achromatia cells from differing ecosystems (e.g. freshwater vs. saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest environmental adaptation occurs by increasing the copy number of relevant genes across the cell’s hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium, and its genomic features, reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.

show abstract

Carbon limitation drives GC content evolution of a marine bacterium in an individual-based genome-scale model

Cited by 49 publications

References 52 publications

Elemental content and stoichiometry of SAR11 chemoheterotrophic marine bacteria

Elemental content and stoichiometry of SAR11 chemoheterotrophic marine bacteria

Selection for reducing energy cost of protein production drives the GC content and amino acid composition bias in gene transfer agents

Heterozygous, polyploid, giant bacterium,Achromatium, possesses an identical functional inventory worldwide across drastically different ecosystems

Contact Info

Product

Resources

About