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| Main Authors: | , , |
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| Format: | Artículo científico |
| Language: | en |
| Published: |
iScience
2026
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| Online Access: | https://pubmed.ncbi.nlm.nih.gov/41623458/ |
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| _version_ | 1868266092657377280 |
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| author | Li, Qing-Mei He, Li-Sheng Wang, Yong |
| author_facet | Li, Qing-Mei He, Li-Sheng Wang, Yong Li, Qing-Mei He, Li-Sheng Wang, Yong |
| collection | PubMed - marine biology |
| contents | Small proteins from prokaryotes in the marine water column at full ocean depth. Li, Qing-Mei He, Li-Sheng Wang, Yong Small proteins (SPs, ≤50 aa) are often overlooked in genomics. We conducted the first systematic analysis of prokaryotic SPs across the full ocean-depth gradient. From 433,311 short open reading frames (sORFs) predicted from 71 western Pacific metagenomes, we identified 193,281 SP clusters. Filtration yielded 75,581 prevalent SPs, including 4,307 high-confidence clusters (RfSPs). Notably, 87.09% of RfSPs lacked non-marine homologs, and ∼70% contained unknown domains. While most (65.57%) were phylum-specific, twelve were distributed across ≥5 phyla, and some were prophage-associated. Geographically, twenty-three core RfSPs were universally present. Co-occurrence analysis revealed that interacting RfSPs typically originated from the same or adjacent zones. Finally, we confirmed the transcription of 8.20% RfSP clusters in deep-sea metatranscriptomes. The zone-specific transcription of certain RfSPs suggests adaptive functions, such as stress response and molecular chaperoning, in distinct marine environments. Our study reveals SPs as a critical strategy for prokaryotic adaptation to deep-sea stressors. |
| format | Artículo científico |
| id | pubmed_41623458 |
| institution | PubMed |
| language | en |
| publishDate | 2026 |
| publisher | iScience |
| record_format | pubmed |
| spellingShingle | Small proteins from prokaryotes in the marine water column at full ocean depth. Li, Qing-Mei He, Li-Sheng Wang, Yong Small proteins from prokaryotes in the marine water column at full ocean depth. Li, Qing-Mei He, Li-Sheng Wang, Yong Small proteins (SPs, ≤50 aa) are often overlooked in genomics. We conducted the first systematic analysis of prokaryotic SPs across the full ocean-depth gradient. From 433,311 short open reading frames (sORFs) predicted from 71 western Pacific metagenomes, we identified 193,281 SP clusters. Filtration yielded 75,581 prevalent SPs, including 4,307 high-confidence clusters (RfSPs). Notably, 87.09% of RfSPs lacked non-marine homologs, and ∼70% contained unknown domains. While most (65.57%) were phylum-specific, twelve were distributed across ≥5 phyla, and some were prophage-associated. Geographically, twenty-three core RfSPs were universally present. Co-occurrence analysis revealed that interacting RfSPs typically originated from the same or adjacent zones. Finally, we confirmed the transcription of 8.20% RfSP clusters in deep-sea metatranscriptomes. The zone-specific transcription of certain RfSPs suggests adaptive functions, such as stress response and molecular chaperoning, in distinct marine environments. Our study reveals SPs as a critical strategy for prokaryotic adaptation to deep-sea stressors. |
| title | Small proteins from prokaryotes in the marine water column at full ocean depth. |
| url | https://pubmed.ncbi.nlm.nih.gov/41623458/ |