Branched-chain amino acid specialization drove diversification within Calditenuaceae (Caldarchaeia) and enables their cultivation.
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| Format: | Artículo científico |
| Language: | en |
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Nature communications
2026
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| author | Lai, Dengxun Mosier, Damon Palmer, Marike Mayali, Xavier Johnston, Juliet Saldivar, Walter Covington, Jonathan K Jiao, Jian-Yu Murali, Ranjani Seymour, Cale O Liu, Lan Hua, Zheng-Shuang Li, Wen-Jun Weber, Peter K Pett-Ridge, Jennifer Colman, Daniel R Boyd, Eric S Nunoura, Takuro Dodsworth, Jeremy A Hedlund, Brian P |
| author_facet | Lai, Dengxun Mosier, Damon Palmer, Marike Mayali, Xavier Johnston, Juliet Saldivar, Walter Covington, Jonathan K Jiao, Jian-Yu Murali, Ranjani Seymour, Cale O Liu, Lan Hua, Zheng-Shuang Li, Wen-Jun Weber, Peter K Pett-Ridge, Jennifer Colman, Daniel R Boyd, Eric S Nunoura, Takuro Dodsworth, Jeremy A Hedlund, Brian P Lai, Dengxun Mosier, Damon Palmer, Marike Mayali, Xavier Johnston, Juliet Saldivar, Walter Covington, Jonathan K Jiao, Jian-Yu Murali, Ranjani Seymour, Cale O Liu, Lan Hua, Zheng-Shuang Li, Wen-Jun Weber, Peter K Pett-Ridge, Jennifer Colman, Daniel R Boyd, Eric S Nunoura, Takuro Dodsworth, Jeremy A Hedlund, Brian P |
| collection | PubMed - marine biology |
| contents | Branched-chain amino acid specialization drove diversification within Calditenuaceae (Caldarchaeia) and enables their cultivation. Lai, Dengxun Mosier, Damon Palmer, Marike Mayali, Xavier Johnston, Juliet Saldivar, Walter Covington, Jonathan K Jiao, Jian-Yu Murali, Ranjani Seymour, Cale O Liu, Lan Hua, Zheng-Shuang Li, Wen-Jun Weber, Peter K Pett-Ridge, Jennifer Colman, Daniel R Boyd, Eric S Nunoura, Takuro Dodsworth, Jeremy A Hedlund, Brian P Amino Acids, Branched-Chain Phylogeny Metagenome In Situ Hybridization, Fluorescence Archaea Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching members of the archaeal phylum Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Metagenome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×10 cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through the TCA cycle coupled with aerobic respiration and through production of branched-chain organic acids by overflow metabolism. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities. |
| format | Artículo científico |
| id | pubmed_41639055 |
| institution | PubMed |
| language | en |
| publishDate | 2026 |
| publisher | Nature communications |
| record_format | pubmed |
| spellingShingle | Branched-chain amino acid specialization drove diversification within Calditenuaceae (Caldarchaeia) and enables their cultivation. Lai, Dengxun Mosier, Damon Palmer, Marike Mayali, Xavier Johnston, Juliet Saldivar, Walter Covington, Jonathan K Jiao, Jian-Yu Murali, Ranjani Seymour, Cale O Liu, Lan Hua, Zheng-Shuang Li, Wen-Jun Weber, Peter K Pett-Ridge, Jennifer Colman, Daniel R Boyd, Eric S Nunoura, Takuro Dodsworth, Jeremy A Hedlund, Brian P Amino Acids, Branched-Chain Phylogeny Metagenome In Situ Hybridization, Fluorescence Archaea Branched-chain amino acid specialization drove diversification within Calditenuaceae (Caldarchaeia) and enables their cultivation. Lai, Dengxun Mosier, Damon Palmer, Marike Mayali, Xavier Johnston, Juliet Saldivar, Walter Covington, Jonathan K Jiao, Jian-Yu Murali, Ranjani Seymour, Cale O Liu, Lan Hua, Zheng-Shuang Li, Wen-Jun Weber, Peter K Pett-Ridge, Jennifer Colman, Daniel R Boyd, Eric S Nunoura, Takuro Dodsworth, Jeremy A Hedlund, Brian P Amino Acids, Branched-Chain Phylogeny Metagenome In Situ Hybridization, Fluorescence Archaea Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching members of the archaeal phylum Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Metagenome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×10 cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through the TCA cycle coupled with aerobic respiration and through production of branched-chain organic acids by overflow metabolism. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities. |
| title | Branched-chain amino acid specialization drove diversification within Calditenuaceae (Caldarchaeia) and enables their cultivation. |
| topic | Amino Acids, Branched-Chain Phylogeny Metagenome In Situ Hybridization, Fluorescence Archaea |
| url | https://pubmed.ncbi.nlm.nih.gov/41639055/ |