An ancient and still ongoing genetic conflict between transposable elements and their repressors DOI Creative Commons
Rachele Cagliani, Diego Forni, Alessandra Mozzi

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 23, 2024

Abstract Background. Transposable element (TE) mobilization poses a significant fitness challenge to host genomes. Consequently, variety of systems have emerged silence TE activity. Just like TEs, such are widespread across the tree life and their evolution is expected be shaped by intra-genomic conflicts. To test this hypothesis, we performed an evolutionary analysis control different timescales. Results. We show that substantial fraction genes were targets positive selection during primate evolution, as well more recent history human populations, with abundant signatures in proteins piRNA pathway. In these proteins, was strongest intrinsically disordered regions (IDRs), particularly those low conformational entropy, contributed modulate ensemble features sequence patterning. primates, larger number TEs also resulted reduced accumulation new mobile elements, assessed genomic or occurrences. Across longer time frames, uncover wide variability content PIWI-containing unprecedented diversity domain architectures for eukaryotes. Finally, identify bacterial Argonaute closest prokaryotic relative unusual conservation IDR huge distances. Conclusions. Our data provide insight into eukaryotes and, through analyses over deep distances, contribute information rapidly growing evo-immuno discipline.

Language: Английский

Headmen, shamans, and mothers: Natural and sexual selection for computational services DOI
Edward H. Hagen, Zachary H. Garfield, Aaron D. Lightner

et al.

Evolution and Human Behavior, Journal Year: 2025, Volume and Issue: 46(1), P. 106651 - 106651

Published: Jan. 1, 2025

Language: Английский

Citations

1
Signalling by co-operative higher-order assembly formation: linking evidence at molecular and cellular levels DOI Creative Commons
Boštjan Kobe, Jeffrey D. Nanson, Mikayla Hoad

et al.

Biochemical Journal, Journal Year: 2025, Volume and Issue: 482(05), P. 275 - 294

Published: March 1, 2025

The concept of higher-order assembly signalling or by co-operative formation (SCAF) was proposed based on the structures assemblies formed proteins featuring domains from death-fold family and Toll/interleukin-1 receptor domain family. Because these form filamentous upon stimulation activate downstream pathways through induced proximity, they were envisioned to sharpen response thresholds extreme co-operativity assembly. Recent findings demonstrate that a central feature SCAF mechanism is nucleation barrier allows switch-like, digital 'all-or-none' minute stimuli. In agreement, this features in cell-death innate immunity activation where binary decision required. Here, we broaden encapsulate essential kinetic properties open-ended signalling, compare other such as biomolecular condensates, review how operates cells.

Language: Английский

Citations

1
Conservation of antiviral systems across domains of life reveals immune genes in humans DOI

Jean Cury,

Matthieu Haudiquet,

Veronica Hernandez Trejo

et al.

Cell Host & Microbe, Journal Year: 2024, Volume and Issue: 32(9), P. 1594 - 1607.e5

Published: Aug. 28, 2024

Language: Английский

Citations

7
Temporal expression classes and functions of vaccinia virus and mpox (monkeypox) virus genes DOI Creative Commons
Yining Deng,

Santiago Navarro-Forero,

Zhilong Yang

et al.

mBio, Journal Year: 2025, Volume and Issue: unknown

Published: March 20, 2025

ABSTRACT Poxviruses comprise pathogens that are highly pathogenic to humans and animals, causing diseases such as smallpox mpox (formerly monkeypox). The family also contains members developed vaccine vectors oncolytic agents fight other diseases. Vaccinia virus is the prototype poxvirus used eradicate smallpox. Poxvirus genes follow a cascade temporal expression pattern, categorized into early, intermediate, late stages using distinct transcription factors. This review comprehensively summarized classification of over 200 vaccinia genes. relationships between classes functions, well different branches immune responses, were discussed. Based on orthologs, we classified all genes, including few not previously annotated with orthologs in viruses. Additionally, reviewed functions based up-to-date published papers. provides readily usable resource for researchers working biology, medical countermeasures, utility development.

Language: Английский

Citations

0
Innate immune mechanisms of infection: what we know and potential conserved mechanisms affecting sleep during infection DOI Creative Commons

Mark R. Zielinski,

Sean D. Carey,

John A. Craig

et al.

Neurobiology of Sleep and Circadian Rhythms, Journal Year: 2025, Volume and Issue: unknown, P. 100121 - 100121

Published: April 1, 2025

Language: Английский

Citations

0
Advancing RNA phage biology through meta-omics DOI Creative Commons
Jens Hör

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(8)

Published: April 22, 2025

Abstract Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in 1960s, they have been used as important models to understand principal processes of life, including translation and genetic code. While phages were generally thought rare oddities nature, meta-omics methods rapidly changing this simplistic view by studying diverse biomes unprecedented resolution. Metatranscriptomics dramatically expanded number known from tens thousands, revealed widespread abundance, discovered several new families potential largely unknown hosts, biology, environmental impact. At same time, (meta)genomic analyses bacterial hosts discovering an arsenal defense systems bacteria employ protect themselves predation, whose functions immunity against we only beginning understand. Here, I review how approaches advancing field phage biology a focus might fight them.

Language: Английский

Citations

0
The role of noncoding RNAs in bacterial immunity DOI Creative Commons
David Mayo-Muñoz, Huijuan Li, Mario Rodríguez Mestre

et al.

Trends in Microbiology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 1, 2024

HighlightsNoncoding RNAs (ncRNAs) have emerged as pivotal players in bacteria–phage conflicts.Many bacterial immune systems depend on ncRNAs for both structure and function.ncRNAs are key regulators of responses.Phages use to counteract defenses.AbstractThe evolutionary arms race between bacteria phages has driven the development diverse anti-phage defense mechanisms. Recent studies identified noncoding conflicts, including CRISPR-Cas, toxin–antitoxin (TA), reverse transcriptase (RT)-based defenses; however, our understanding their roles immunity is still emerging. In this review, we explore multifaceted immunity, offering insights into contributions anti-defense mechanisms, influence regulatory networks, potential biotechnological applications. Finally, highlight outstanding questions field spark future research directions.

Language: Английский

Citations

1
There and back again: Discovering antiviral and antiphage defenses using deep homology DOI
Edward M. Culbertson, Tera C. Levin

Cell Host & Microbe, Journal Year: 2024, Volume and Issue: 32(9), P. 1466 - 1468

Published: Sept. 1, 2024

Language: Английский

Citations

0
An ancient and still ongoing genetic conflict between transposable elements and their repressors DOI Creative Commons
Rachele Cagliani, Diego Forni, Alessandra Mozzi

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 23, 2024

Abstract Background. Transposable element (TE) mobilization poses a significant fitness challenge to host genomes. Consequently, variety of systems have emerged silence TE activity. Just like TEs, such are widespread across the tree life and their evolution is expected be shaped by intra-genomic conflicts. To test this hypothesis, we performed an evolutionary analysis control different timescales. Results. We show that substantial fraction genes were targets positive selection during primate evolution, as well more recent history human populations, with abundant signatures in proteins piRNA pathway. In these proteins, was strongest intrinsically disordered regions (IDRs), particularly those low conformational entropy, contributed modulate ensemble features sequence patterning. primates, larger number TEs also resulted reduced accumulation new mobile elements, assessed genomic or occurrences. Across longer time frames, uncover wide variability content PIWI-containing unprecedented diversity domain architectures for eukaryotes. Finally, identify bacterial Argonaute closest prokaryotic relative unusual conservation IDR huge distances. Conclusions. Our data provide insight into eukaryotes and, through analyses over deep distances, contribute information rapidly growing evo-immuno discipline.

Language: Английский

Citations

0