An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences

Carels, Nicolas; León, Miguel Ponce de

doi:10.4137/bbi.s24021

Cited by 3 publications

(3 citation statements)

References 73 publications

(128 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Predominant bacterial species are GC-rich, 8 which raises the question of whether a cause and effect relationship exists between a bacterial species being GC-rich and its growth success 28 , 29 in the DTT environment. In fact, the positive correlation between GC3 and genome size suggests that, in the DTT, bacterial species with GC-rich genomes have a potentially more complex metabolism than those with GC-poor genomes, which would be an advantage for the bacteria in this niche.…”

Section: Discussionmentioning

confidence: 99%

A Metagenomic Analysis of Bacterial Microbiota in the Digestive Tract of Triatomines

Carels

Gumiel

Mota

et al. 2017

Bioinform Biol Insights

Self Cite

View full text Add to dashboard Cite

The digestive tract of triatomines (DTT) is an ecological niche favored by microbiota whose enzymatic profile is adapted to the specific substrate availability in this medium. This report describes the molecular enzymatic properties that promote bacterial prominence in the DTT. The microbiota composition was assessed previously based on 16S ribosomal DNA, and whole sequenced genomes of bacteria from the same genera were used to calculate the GC level of rare and prominent bacterial species in the DTT. The enzymatic reactions encoded by coding sequences of both rare and common bacterial species were then compared and revealed key functions explaining why some genera outcompete others in the DTT. Representativeness of DTT microbiota was investigated by shotgun sequencing of DNA extracted from bacteria grown in liquid Luria-Bertani broth (LB) medium. Results showed that GC-rich bacteria outcompete GC-poor bacteria and are the dominant components of the DTT microbiota. In addition, oxidoreductases are the main enzymatic components of these bacteria. In particular, nitrate reductases (anaerobic respiration), oxygenases (catabolism of complex substrates), acetate-CoA ligase (tricarboxylic acid cycle and energy metabolism), and kinase (signaling pathway) were the major enzymatic determinants present together with a large group of minor enzymes including hydrogenases involved in energy and amino acid metabolism. In conclusion, despite their slower growth in liquid LB medium, bacteria from GC-rich genera outcompete the GC-poor bacteria because their specific enzymatic abilities impart a selective advantage in the DTT.

show abstract

Section: Discussionmentioning

confidence: 99%

A Metagenomic Analysis of Bacterial Microbiota in the Digestive Tract of Triatomines

Carels

Gumiel

Mota

et al. 2017

Bioinform Biol Insights

Self Cite

View full text Add to dashboard Cite

show abstract

“…The interphase chromosome distribution in Arabidopsis follows the fractal globule distribution as in vertebrates [108], but the 3D distribution of Rabbi chromosomes is quite different since they have a parallel spatial arrangement [109]. These different chromosome distributions in interphase cells of vertebrates and plants are another layer of genome phenotype corresponding to a genome strategy coding for a molecular strategy pervading the whole cell machinery [89,91,110]. Such a biological framework cannot be modified within a short time, which means that it can be, eventually, negatively selected and lead to extinction in case of low fitness for drastic environmental changes since it implies a long evolutionary history correlated to evolutionary inertia to produce them.…”

Section: Genome Phenotype and Genome Strategymentioning

confidence: 99%

Plant Tolerance to Drought Stress with Emphasis on Wheat

Adel

Carels

2023

Plants

Self Cite

View full text Add to dashboard Cite

Environmental stresses, such as drought, have negative effects on crop yield. Drought is a stress whose impact tends to increase in some critical regions. However, the worldwide population is continuously increasing and climate change may affect its food supply in the upcoming years. Therefore, there is an ongoing effort to understand the molecular processes that may contribute to improving drought tolerance of strategic crops. These investigations should contribute to delivering drought-tolerant cultivars by selective breeding. For this reason, it is worthwhile to review regularly the literature concerning the molecular mechanisms and technologies that could facilitate gene pyramiding for drought tolerance. This review summarizes achievements obtained using QTL mapping, genomics, synteny, epigenetics, and transgenics for the selective breeding of drought-tolerant wheat cultivars. Synthetic apomixis combined with the msh1 mutation opens the way to induce and stabilize epigenomes in crops, which offers the potential of accelerating selective breeding for drought tolerance in arid and semi-arid regions.

show abstract

“…A curious observation made during the application of SELEX is that aptamers selected to bind arginine (Arg) in different laboratories using different protocols are predominantly composed of Arg codons (Knight and Landweber 1998 ). This fi nding, together with the fi nding that experiments simulating the early Earth's atmosphere (Miller 1987 ) yielded as many as ten different natural amino acids, lays the foundation for a theory that the genetic code evolved under primordial conditions (Wächtershäuser 1988 ;Orgel 2000 ) still dominant in modern proteins (Carels and Ponce de Leon 2015 ).…”

Section: Origin Of Codonsmentioning

confidence: 99%