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We found that microcompartment shells could be purified in high yield when all seven H. ochraceum BMC shell genes were expressed from a synthetic operon in Escherichia coli.
A notable exception is the cso operon of Thiobacillus denitrificans, which consists of a complete set of carboxysome shell genes but lacks those for the RubisCO subunits [15].
Compared to the cyanobacterial "core" and "shell" genes, defined by comparing 13 cyanobacterial genomes [26], additional loss of function are apparent in the genome of NoAz (Table S2).
One emphasizing the shared shell genes and the other the less conserved cloud genes.
Most of gene evolution (that of shell genes) appeared therefore better interpreted in light of an ecological vision.
The shell genes are the gene families often observed among the genomes, while the cloud genes are rarely observed [ 52].
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In order to understand the consequences of the eroding forces acting on the NoAz genome, comparative analyses were performed to the comprehensive minimal bacterial gene set [25], and the "core" and "shell" gene sets identified in cyanobacteria [26], encompassing 200 and 682 genes respectively.
These HT-genes were found in lineage-specific core and shell gene classes.
Figure 3 also showed that the core and shell gene sets are equally subject to recombination.
These were used to refine the definition and identification of archaeal core, lineage-specific core, and shell gene classes.
We show by systematic and curated molecular phylogenetic analyses that a substantial fraction of genes in the lineage-specific core and shell gene sets was acquired from bacteria, implying directional and ongoing bacteria-to-archaea HGT.
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