He, L.-S. | bioRxiv Science

bioRxiv2024

Small proteins from prokaryotes in marine water column at full ocean depth

Small proteins (SPs,[≤] 50 amino acids) are usually ignored by automated bioinformatic algorithms and difficult to be detected by traditional protein purification. In this study, 193,281 prokaryotic SP clusters were generated using 433,311 small open reading frames (sORFs) predicted in assemblies of 71 full-ocean-depth marine water metagenomes from the western pacific. Further filtration with at least 5 copies per million reads resulted in 75,581 prevalent SP clusters, among which 4,307 clusters have coding capacity as predicted by RNAcode. For these RNAcode-filtered SP (RfSP) clusters hosted largely by Proteobacteria, Thaumarchaeota and Marinimicrobia, 29.16% of them show homology () in all prokaryotic genomes. About 2% of the RfSP clusters were estimated as potential antimicrobial peptides and were distributed across all depth zones. Transcription of 7.96% of the RfSP clusters was verified in 12 deep-sea metatranscriptomes, and translation of 34 prevalent SP clusters was detected in 14 metaproteomes. The transcribed RfSP clusters are involved in processes such as DNA stability under stress condition, betaine transport and cell division regulation for a rapid response to varying deep-sea environments. This study uncovers a vast reservoir of SPs with pivotal functions in potential antibiotic activities, hyperoxide detoxification and pressure resistance for fitness of marine prokaryotes in deep ocean.

bioinformatics↗

bioRxiv2020

Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli

The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes. Several novel environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment. This study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales. IMPORTANCEEnvironmental Tenericutes bacteria were recently discovered in numerous environments. However, our current collection of Tenericutes genomes was overrepresented by those for pathogens. Our phylogenomics study displays the relationships between all the available Tenericutes, as well as those between Tenericutes and the clades in Bacilli, which casts lights into the uncertain boundary between the environmental lineages of Tenericutes and Bacilli. By comparing the genomes of the environmental and pathogenic Tenericutes, we revealed the metabolic pathways and adaptive strategies of the Tenericutes in the different environments and hosts. We also predicted the metabolism of the two major gut lineages RF39 and RFN20 of Tenericutes, indicating their potential importance in stabilization of the gut microbiome and contribution to human health.

microbiology↗