Genetic Code and Its Variations

Suzuki, Tsutomu; Nagao, Asuteka

doi:10.1002/9780470015902.a0029263

Cited by 3 publications

(2 citation statements)

References 70 publications

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“…As we have shown, the genome of PSAC, the obligate nutritional symbiont of the blood-feeding leech H. acueceyetzin, does not only show the "typical" genomic characteristics of a long-term vertically transmitted endosymbiont, but has also evolved an alternative genetic code, reflected in at least 20.49% of its encoded proteins. This alternative genetic code matches the so-called genetic code 4, which features a UGA codon reassignment from STOP to tryptophan (Suzuki and Nagao, 2021). There are two main players involved in this reassignment: the peptide release factor 2 (encoded by prfB) and the anticodon of the transfer RNA tryptophan (trnW).…”

Section: Discussionmentioning

confidence: 85%

Evolution of an alternative genetic code in theProvidenciasymbiont of the haematophagous leechHaementeria acuecueyetzin

Manzano-Marı́n

Kvist

Oceguera‐Figueroa

2023

Preprint

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Strict blood-feeding animals are confronted with a strong B vitamin deficiency. Leeches from the Glossiphoniidae family, notably species ofPlacobdella,Placobdelloides, andHaementeriaare regarded as strict blood-feeders, and similarly to blood-feeding insects, have evolved specialised organs called bacteriomes to harbour symbiotic bacteria. Leeches of theHaementeriagenus are found exclusively in the Americas, with most species being South-American and only three found in North America. In these leeches, two pairs of globular bacteriomes attached to the oesophagus harbour intracellularly 'CandidatusProvidencia siddallii' bacteria. Previous work analysing a draft genome of theProvidenciasymbiont of the Mexican leechHaementeria officinalisshowed that, in this species, the bacteria hold a reduced genome with complete biosynthetic pathways for B vitamins. In this work, we aimed to expand our knowledge on the diversity and evolution ofProvidenciasymbionts ofHaementeriaspecies. For this purpose, we sequenced the genomes of theProvidenciasymbionts of the Mexican leechesHaementeria acuecueyetzinandHaementeria lopezi, as well as re-sequenced and closed the symbiont genome ofH. officinalis. We found that all genomes are highly syntenic, mirroring ancient insect endosymbionts and suggesting a conserved gene order at the start of theProvidencia-Haementeriaassociation. Additionally, we found B vitamin pathways to be conserved among these symbionts, pointing to a common biosynthetic machinery and low variation in this trait. Lastly and most notably, we found that the symbiont ofH. acuecueyetzinhas evolved an alternative genetic code, affecting a portion of its proteome and showing evidence of a rather recent and likely intermediate stage of genetic code reassignment.

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Section: Discussionmentioning

confidence: 85%

Evolution of an alternative genetic code in theProvidenciasymbiont of the haematophagous leechHaementeria acuecueyetzin

Manzano-Marı́n

Kvist

Oceguera‐Figueroa

2023

Preprint

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show abstract

“…As we have shown, the genome of PSAC, the obligate nutritional symbiont of the blood-feeding leech H. acueceyetzin , does not only show the “typical” genomic characteristics of a long-term vertically transmitted endosymbiont, but has also evolved a lineage-specific alternative genetic code, reflected in at least 20.49% of its encoded proteins. The alternative genetic code matches the so-called genetic code 4, which features a UG A codon reassignment from STOP to tryptophan ( Suzuki and Nagao 2021 ). Alternatively, it can be proposed that the ancestor of P. siddallii used genetic code 4, and this was subsequently reverted to 11.…”

Section: Discussionmentioning

confidence: 99%

Evolution of an Alternative Genetic Code in the Providencia Symbiont of the Hematophagous Leech Haementeria acuecueyetzin

Manzano-Marín,

Kvist,

Oceguera-Figueroa

2023

Genome Biology and Evolution

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Strict blood-feeding animals are confronted with a strong B-vitamin deficiency. Blood-feeding leeches from the Glossiphoniidae family, similarly to hematophagous insects, have evolved specialized organs called bacteriomes to harbor symbiotic bacteria. Leeches of the Haementeria genus have two pairs of globular bacteriomes attached to the esophagus which house intracellular “Candidatus Providencia siddallii” bacteria. Previous work analyzing a draft genome of the Providencia symbiont of the Mexican leech Haementeria officinalis showed that, in this species, the bacteria hold a reduced genome capable of synthesizing B vitamins. In this work, we aimed to expand our knowledge on the diversity and evolution of Providencia symbionts of Haementeria. For this purpose, we sequenced the symbiont genomes of three selected leech species. We found that all genomes are highly syntenic and have kept a stable genetic repertoire, mirroring ancient insect endosymbionts. Additionally, we found B-vitamin pathways to be conserved among these symbionts, pointing to a conserved symbiotic role. Lastly and most notably, we found that the symbiont of H. acuecueyetzin has evolved an alternative genetic code, affecting a portion of its proteome and showing evidence of a lineage-specific and likely intermediate stage of genetic code reassignment.

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The Evolution of Life Is a Road Paved with the DNA Quadruplet Symmetry and the Supersymmetry Genetic Code

Rosandić

Paar

2023

IJMS

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Symmetries have not been completely determined and explained from the discovery of the DNA structure in 1953 and the genetic code in 1961. We show, during 10 years of investigation and research, our discovery of the Supersymmetry Genetic Code table in the form of 2 × 8 codon boxes, quadruplet DNA symmetries, and the classification of trinucleotides/codons, all built with the same physiochemical double mirror symmetry and Watson–Crick pairing. We also show that single-stranded RNA had the complete code of life in the form of the Supersymmetry Genetic Code table simultaneously with instructions of codons’ relationship as to how to develop the DNA molecule on the principle of Watson–Crick pairing. We show that the same symmetries between the genetic code and DNA quadruplet are highly conserved during the whole evolution even between phylogenetically distant organisms. In this way, decreasing disorder and entropy enabled the evolution of living beings up to sophisticated species with cognitive features. Our hypothesis that all twenty amino acids are necessary for the origin of life on the Earth, which entirely changes our view on evolution, confirms the evidence of organic natural amino acids from the extra-terrestrial asteroid Ryugu, which is nearly as old as our solar system.

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Genetic Code and Its Variations

Cited by 3 publications

References 70 publications

Evolution of an alternative genetic code in theProvidenciasymbiont of the haematophagous leechHaementeria acuecueyetzin

Evolution of an alternative genetic code in theProvidenciasymbiont of the haematophagous leechHaementeria acuecueyetzin

Evolution of an Alternative Genetic Code in the Providencia Symbiont of the Hematophagous Leech Haementeria acuecueyetzin

The Evolution of Life Is a Road Paved with the DNA Quadruplet Symmetry and the Supersymmetry Genetic Code

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