ArticleBMC genomics2011
Amino acids biosynthesis and nitrogen assimilation pathways: a great genomic deletion during eukaryotes evolution.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 74 citations in OpenAlex.
- Highly multiplexed mammalian metabolic engineering with a shotgun approach.Nature biotechnology · 2026Article
- The effect of rumen-protected methionine and guanidinoacetic acid on growth performance, hematological indices, and immune-related gene expression in suckling Holstein Calves.Veterinary and animal science · 2026Article
- Outsourcing of energetically costly amino acids at the origin of animals.Nature communications · 2026Article
- Five hundred million years of hunger: how animals evolved to survive essential amino acid scarcity.Emerging topics in life sciences · 2025Article
- Article
- Genomic and Transcriptomic Profiling of Amino Acid Compositions in Common Carp Fillets.Animals : an open access journal from MDPI · 2025Article
- Bacterial Amino Acid Auxotrophies Enable Energetically Costlier Proteomes.International journal of molecular sciences · 2025Article
- Quantitative Proteomic Analysis of Brassica Napus Reveals Intersections Between Nutrient Deficiency Responses.Plant, cell & environment · 2025Article
- The genome of the polyextremophilic yeast, Naganishia friedmannii, reveals adaptations involved in stress response pathways, carbohydrate metabolism expansion, and a limited DNA repair repertoire.FEMS yeast research · 2025Article
- Exploring Metabolic Approaches for Epithelial Ovarian Cancer Therapy.Journal of cellular physiology · 2025Review
- Phenotypic and genomic characterization ofApplied and environmental microbiology · 2024Article
- Transcriptomics reveal a unique phago-mixotrophic response to low nutrient concentrations in the prasinophyteISME communications · 2024Article
- Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta.The ISME journal · 2023Article
- Article
- Transcriptome Profiling Reveals Molecular Changes during Flower Development between Male Sterile and Fertile Chinese Cabbage (Life (Basel, Switzerland) · 2021Article
- Article
- The origin of phagocytosis in Earth history.Interface focus · 2020Review
- Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Review
- Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway.PLoS genetics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBesides being building blocks for proteins, amino acids are also key metabolic intermediates in living cells. Surprisingly a variety of organisms are incapable of synthesizing some of them, thus named Essential Amino Acids (EAAs). How certain ancestral organisms successfully competed for survival after losing key genes involved in amino acids anabolism remains an open question. Comparative genomics searches on current protein databases including sequences from both complete and incomplete genomes among diverse taxonomic groups help us to understand amino acids auxotrophy distribution.
resultsHere, we applied a methodology based on clustering of homologous genes to seed sequences from autotrophic organisms Saccharomyces cerevisiae (yeast) and Arabidopsis thaliana (plant). Thus we depict evidences of presence/absence of EAA biosynthetic and nitrogen assimilation enzymes at phyla level. Results show broad loss of the phenotype of EAAs biosynthesis in several groups of eukaryotes, followed by multiple secondary gene losses. A subsequent inability for nitrogen assimilation is observed in derived metazoans.
conclusionsA Great Deletion model is proposed here as a broad phenomenon generating the phenotype of amino acids essentiality followed, in metazoans, by organic nitrogen dependency. This phenomenon is probably associated to a relaxed selective pressure conferred by heterotrophy and, taking advantage of available homologous clustering tools, a complete and updated picture of it is provided.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.