Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni DOI Creative Commons
Kathrin Froschauer, Sarah L. Svensson, Rick Gelhausen

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 30, 2025

Abstract In contrast to transcriptome maps, bacterial small protein (≤50-100 aa) coding landscapes, including overlapping genes, are poorly characterized. However, an emerging number of proteins have crucial roles in physiology and virulence. Here, we present a Ribo-seq-based high-resolution translatome map for the major foodborne pathogen Campylobacter jejuni . Besides conventional Ribo-seq, employed translation initiation site (TIS) profiling start codons also developed termination (TTS) approach, which revealed stop not apparent from reference genome virulence loci. Our integrated approach combined with independent validation expanded proteome by two-fold, CioY, new 34 aa component CioAB oxidase. Overall, our study generates annotation C. landscape, provided interactive browser, showcases strategy applying Ribo-seq other species enrich understanding proteomes.

Language: Английский

Discovery of antimicrobial peptides in the global microbiome with machine learning DOI Creative Commons
Célio Dias Santos Júnior, Marcelo D. T. Torres, Yiqian Duan

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(14), P. 3761 - 3778.e16

Published: June 5, 2024

Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine-learning-based approach predict antimicrobial peptides (AMPs) within global microbiome and leverage vast dataset of 63,410 metagenomes 87,920 prokaryotic genomes from environmental host-associated habitats create AMPSphere, comprehensive catalog comprising 863,498 non-redundant peptides, few which match existing databases. AMPSphere provides insights into evolutionary origins including by duplication or gene truncation longer sequences, we observed that AMP production varies habitat. To validate our predictions, synthesized tested 100 AMPs against clinically relevant drug-resistant pathogens human gut commensals both in vitro vivo. A total 79 were active, with 63 targeting pathogens. These active exhibited antibacterial activity disrupting bacterial membranes. In conclusion, identified nearly one million an open-access resource for antibiotic discovery.

Language: Английский

Citations

94
Small Proteins; Big Questions DOI
Todd A. Gray, Gisela Storz, Kai Papenfort

et al.

Journal of Bacteriology, Journal Year: 2021, Volume and Issue: 204(1)

Published: July 26, 2021

In recent years, there has been increased appreciation that a whole category of proteins, small proteins around 50 amino acids or fewer in length, missed by annotation as well genetic and biochemical assays. With the recognition are stable within cells have regulatory functions, intensified study these proteins.

Language: Английский

Citations

58
Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures DOI Creative Commons
Alyssa Zi-Xin Leong, Pey Yee Lee, M. Aiman Mohtar

et al.

Journal of Biomedical Science, Journal Year: 2022, Volume and Issue: 29(1)

Published: March 17, 2022

A short open reading frame (sORFs) constitutes ≤ 300 bases, encoding a microprotein or sORF-encoded protein (SEP) which comprises 100 amino acids. Traditionally dismissed by genome annotation pipelines as meaningless noise, sORFs were found to possess coding potential with ribosome profiling (RIBO-Seq), unveiled sORF-based transcripts at various locations. Nonetheless, the existence of corresponding microproteins that are stable and functional was little substantiated experimental evidence initially. With recent advancements in multi-omics, identification, validation, characterisation have become feasible. In this review, we discuss history development an emerging research field microproteins. particular, focus on array bioinformatics OMICS approaches used for predicting, sequencing, validating, characterizing these recently discovered entities. These strategies include RIBO-Seq detects sORF via footprints, mass spectrometry (MS)-based proteomics sequencing resultant Subsequently, our discussion extends incorporating CRISPR/Cas9 screen protein-protein interaction (PPI) studies. Our review discusses not only detection methodologies, but also highlight challenges solutions identifying validating their The novelty lies within its validation role microproteins, could contribute towards future landscape microproteomics.

Language: Английский

Citations

50
Shining in the dark: the big world of small peptides in plants DOI Creative Commons
Yan‐Zhao Feng, Qingfeng Zhu, Jiao Xue

et al.

aBIOTECH, Journal Year: 2023, Volume and Issue: 4(3), P. 238 - 256

Published: April 8, 2023

Abstract Small peptides represent a subset of dark matter in plant proteomes. Through differential expression patterns and modes action, small act as important regulators growth development. Over the past 20 years, many have been identified due to technical advances genome sequencing, bioinformatics, chemical biology. In this article, we summarize classification experimental strategies used identify them well their potential use agronomic breeding. We review biological functions molecular mechanisms plants, discuss current problems peptide research highlight future directions field. Our provides crucial insight into plants will contribute better understanding roles biotechnology agriculture.

Language: Английский

Citations

26
No country for old methods: New tools for studying microproteins DOI Creative Commons
Fabiola Valdivia-Francia, Ataman Sendoel

iScience, Journal Year: 2024, Volume and Issue: 27(2), P. 108972 - 108972

Published: Jan. 20, 2024

Microproteins encoded by small open reading frames (sORFs) have emerged as a fascinating frontier in genomics. Traditionally overlooked due to their size, recent technological advancements such ribosome profiling, mass spectrometry-based strategies and advanced computational approaches led the annotation of more than 7000 sORFs human genome. Despite vast progress, only tiny portion these microproteins been characterized an important challenge field lies identifying functionally relevant understanding role different cellular contexts. In this review, we explore sORF research, focusing on new methodologies that facilitated identification functional characterization. Leveraging tools hold great promise for dissecting diverse roles will ultimately pave way pathogenesis diseases therapeutic targets.

Language: Английский

Citations

12
The power of small signaling peptides in crop and horticultural plants DOI Creative Commons

Chao Ji,

Hui Li,

Zilin Zhang

et al.

The Crop Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

1
Innovations in heart failure management: The role of cutting-edge biomarkers and multi-omics integration DOI Creative Commons
José Mesquita Bastos,

Brendon Colaco,

Rui Baptista

et al.

Journal of Molecular and Cellular Cardiology Plus, Journal Year: 2025, Volume and Issue: 11, P. 100290 - 100290

Published: March 1, 2025

Heart failure (HF) remains a major cause of morbidity and mortality worldwide represents challenge for diagnosis, prognosis treatment due to its heterogeneity. Traditional biomarkers such as BNP NT-proBNP are valuable but insufficient capture the complexity HF, especially phenotypes HF with preserved ejection fraction (HFpEF). Recent advances in multi-omics technology novel cell-free DNA (cfDNA), microRNAs (miRNAs), ST2 galectin-3 offer transformative potential management. This review explores integration these innovative into clinical practice highlights their benefits, improved diagnostic accuracy, enhanced risk stratification non-invasive monitoring capabilities. By leveraging approaches, including lipidomics metabolomics, clinicians can uncover new pathways, refine classification phenotypes, develop personalized therapeutic strategies tailored individual patient profiles. Remarkable proteomics metabolomics have identified associated key mechanisms mitochondrial dysfunction, inflammation fibrosis, paving way targeted therapies early interventions. Despite promising results, significant challenges remain translating findings routine care, high costs, technical limitations need large-scale validation studies. report argues an integrative, multi-omics-based model overcome obstacles emphasizes importance collaboration between researchers, policy makers. linking science practical applications, approaches redefine management lead better outcomes more sustainable healthcare systems.

Language: Английский

Citations

1
Interfacial properties of cellulose derivatives from guinea grass (Megathyrsus maximus) DOI Creative Commons

Iris Silva,

Barí Agüero, Nelson Barrios

et al.

Journal of Surfactants and Detergents, Journal Year: 2025, Volume and Issue: unknown

Published: March 10, 2025

Abstract The utilization of sustainable feedstocks in surfactant production is crucial for reducing environmental impact, enhancing resource efficiency, and aligning with global efforts toward a circular economy green chemistry. In this research, cellulose derivatives were synthesized by methylating fibers extracted from Guinea grass ( Megathyrsus maximus ) their interfacial properties as surfactants evaluated. characterized using Fourier‐transform infrared spectroscopy (FTIR), which revealed distinct stretching vibration absorption bands indicative methyl groups. Thermogravimetric analysis (TGA) identified dual‐stage decomposition process, consistent reported behavior methylcellulose. Time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS) further confirmed the presence ether groups, H 5 CO + detected characteristic fragment methylated samples. Functional evaluations demonstrated that double‐methylated exhibited hydrophilic–lipophilic balance (HLB) 12.7 surface tension 55 dyne/cm when compared to mono or unmethylated fibers. Additionally, displayed enhanced foaming activity, emulsion stability, water solubility. These cellulose‐based comparable synthetic counterparts, emphasizing potential industrial applications role advancing material development.

Language: Английский

Citations

1
Small Open Reading Frame-Encoded Micro-Peptides: An Emerging Protein World DOI Open Access
Xiao‐Ping Dong, Kun Zhang,

Chengfeng Xun

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(13), P. 10562 - 10562

Published: June 23, 2023

Small open reading frames (sORFs) are often overlooked features in genomes. In the past, they were labeled as noncoding or “transcriptional noise”. However, accumulating evidence from recent years suggests that sORFs may be transcribed and translated to produce sORF-encoded polypeptides (SEPs) with less than 100 amino acids. The vigorous development of computational algorithms, ribosome profiling, peptidome has facilitated prediction identification many new SEPs. These SEPs revealed involved a wide range basic biological processes, such gene expression regulation, embryonic development, cellular metabolism, inflammation, even carcinogenesis. To effectively understand potential functions SEPs, we discuss history newly emerging research on particular, review recently discovered bioinformatics tools for identifying, predicting, validating well variety biochemical experiments characterizing SEP functions. Lastly, this underlines challenges future directions identifying their encoded micropeptides, providing significant reference upcoming peptides.

Language: Английский

Citations

19
Biological factors and statistical limitations prevent detection of most noncanonical proteins by mass spectrometry DOI Creative Commons
Aaron Wacholder, Anne‐Ruxandra Carvunis

PLoS Biology, Journal Year: 2023, Volume and Issue: 21(12), P. e3002409 - e3002409

Published: Dec. 4, 2023

Ribosome profiling experiments indicate pervasive translation of short open reading frames (ORFs) outside annotated protein-coding genes. However, shotgun mass spectrometry (MS) typically detect only a small fraction the predicted protein products this noncanonical translation. The rarity detection could that most proteins are rapidly degraded and not present in cell; alternatively, it reflect technical limitations. Here, we leveraged recent advances ribosome MS to investigate factors limiting yeast. We show low rate ORF can largely be explained by size levels does they unstable or biologically insignificant. In particular, encoded evolutionarily young genes, including those with well-characterized biological roles, too lowly expressed detected at current sensitivities. Additionally, find decoy biases give misleading estimates false discovery rates, potentially leading detections. After accounting for these issues, found strong evidence 4 data, which were also supported evolution data. These results illustrate power validate unannotated genes profiling, but its substantial limitations finding many relevant proteins.

Language: Английский

Citations

18