Ribosomes: The New Role of Ribosomal Proteins as Natural Antimicrobials

Hurtado-Rios, Jessica J.; Carrasco-Navarro, Ulises; Almanza-Perez, Julio César; Ponce‐Alquicira, Edith

doi:10.3390/ijms23169123

Cited by 30 publications

(17 citation statements)

References 89 publications

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“…Most of the c_AMPs (2,201 out of the 2,642) in conserved ribosomal genomic contexts are homologous to ribosomal proteins ( Fig. 3D ), congruent with the observation that, in some species, ribosomal proteins have antimicrobial properties 50 . Seventy-seven of the c_AMPs that were homologous to ribosomal proteins were homologous to a gene in their immediate vicinity (up to 1 gene up/downstream).…”

Section: Resultssupporting

confidence: 82%

Computational exploration of the global microbiome for antibiotic discovery

Santos-Júnior,

Torres,

Duan

et al. 2023

Preprint

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Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine learning-based approach to predict prokaryotic antimicrobial peptides (AMPs) by leveraging a vast dataset of 63,410 metagenomes and 87,920 microbial genomes. This led to the creation of AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, the majority of which were previously unknown. We observed that AMP production varies by habitat, with animal-associated samples displaying the highest proportion of AMPs compared to other habitats. Furthermore, within different human-associated microbiota, strain-level differences were evident. To validate our predictions, we synthesized and experimentally tested 50 AMPs, demonstrating their efficacy against clinically relevant drug-resistant pathogens both in vitro and in vivo. These AMPs exhibited antibacterial activity by targeting the bacterial membrane. Additionally, AMPSphere provides valuable insights into the evolutionary origins of peptides. In conclusion, our approach identified AMP sequences within prokaryotic microbiomes, opening up new avenues for the discovery of antibiotics.

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Section: Resultssupporting

confidence: 82%

Computational exploration of the global microbiome for antibiotic discovery

Santos-Júnior,

Torres,

Duan

et al. 2023

Preprint

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“…The translated protein sequences of all short-read DNA sequences predicted their basic nature. The ribosomal proteins are basic and have potential antimicrobial activity ( Hurtado-Rios et al., 2022 ). Similarly, NAC transcription factors are basic proteins that have a role in defense and contribute to plant immunity ( Kikuchi et al., 2000 ; Yuan et al., 2019 ).…”

Section: Resultsmentioning

confidence: 99%

In silico characterization of differentially expressed short-read nucleotide sequences identified in dieback stress-induced transcriptomic analysis reveals their role as antimicrobial peptides

Ijaz

Haq²,

Malik³

et al. 2023

Front. Plant Sci.

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We investigated the in silico characterization of short-length nucleotide sequences that were differentially expressed in dieback stress-induced transcriptomic analysis. They displayed homology with C-terminal flanking peptides and defensins-like proteins, revealing their antimicrobial activity. Their predicted fingerprints displayed protein signatures related to antimicrobial peptides. These short-length RGAs have been shown to possess structural motifs such as APLT P-type ATPase, casein kinase II (CK2), protein kinase 3, protein kinase C (PKC), and N-glycosylation site that are the attributes of disease resistance genes. The prediction of arginine and lysine residues in active binding sites in ligand docking analysis prophesied them as antimicrobial peptides due to their strong relation with antimicrobial activity. The in silico structural–functional characterization has predicted their role in resistance against microbial pathogens. Moreover, the predicted antimicrobial peptide regions showed their homology with the signature domain of PR-5-like protein and AMP family Thaumatin

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“…Ribosomal protein L13 was the one with the highest number of fragments. Hurtado-Rios and collaborators [ 37 ] have recently discussed the role of ribosomal proteins as moonlighting proteins, which are those capable of performing more than one biochemical or biophysical function within the same polypeptide chain, highlighting them as natural antimicrobials [ 37 , 38 , 39 ]. Recently, a C-terminal fragment of the 60S ribosomal protein L27 was isolated from the skin of S. asotus and identified as AMP [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

Revealing Natural Intracellular Peptides in Gills of Seahorse Hippocampus reidi

et al. 2023

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The seahorse is a marine teleost fish member of the Syngnathidae family that displays a complex variety of morphological and reproductive behavior innovations and has been recognized for its medicinal importance. In the Brazilian ichthyofauna, the seahorse Hippocampus reidi is among the three fish species most used by the population in traditional medicine. In this study, a protocol was performed based on fast heat inactivation of proteases plus liquid chromatography coupled to mass spectrometry to identify native peptides in gills of seahorse H. reidi. The MS/MS spectra obtained from gills allowed the identification of 1080 peptides, of which 1013 peptides were present in all samples and 67 peptide sequences were identified in an additional LC-MS/MS run from an alkylated and reduced pool of samples. The majority of peptides were fragments of the internal region of the amino acid sequence of the precursor proteins (67%), and N- and C-terminal represented 18% and 15%, respectively. Many peptide sequences presented ribosomal proteins, histones and hemoglobin as precursor proteins. In addition, peptide fragments from moronecidin-like protein, described with antimicrobial activity, were found in all gill samples of H. reidi. The identified sequences may reveal new bioactive peptides.

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Ribosomes: The New Role of Ribosomal Proteins as Natural Antimicrobials

Cited by 30 publications

References 89 publications

Computational exploration of the global microbiome for antibiotic discovery

Computational exploration of the global microbiome for antibiotic discovery

In silico characterization of differentially expressed short-read nucleotide sequences identified in dieback stress-induced transcriptomic analysis reveals their role as antimicrobial peptides

Revealing Natural Intracellular Peptides in Gills of Seahorse Hippocampus reidi

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