The Evasion of Antiviral Innate Immunity by Chicken DNA Viruses

Gao, Li; Zheng, Shijun; Wang, Yongqiang

doi:10.3389/fmicb.2021.771292

Cited by 7 publications

(7 citation statements)

References 101 publications

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“…Altogether, this highlights the importance of utilizing enrichment techniques that are tailored to the environment of interest and the research questions being asked. Whether the purpose is to assign taxonomy [74], reveal mechanisms to avoid host defenses [75], identify auxiliary metabolic genes [76], or investigate mobile reservoirs for antimicrobial resistance genes [77,78], obtaining functional gene predictions is a critical step in analyses of viral communities. However, it can be quite challenging to assign functional predictions to viral genes annotated from metagenomic environmental data due to their large sequence diversity and the undercharacterization of viruses.…”

Section: Discussionmentioning

confidence: 99%

Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

Kosmopoulos,

Klier,

Langwig

et al. 2023

Preprint

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Viruses, the majority of which are uncultivated, are among the most abundant biological entities in microbiomes and ecosystems on Earth. From selfishly altering community-wide microbial physiology to driving microbiome dynamics, viruses (particularly bacteriophage) are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can leverage computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remains understudied. Here, we compare viral communities from paired viromes and metagenomes obtained from 51 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes were more abundant and species rich than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment. Overall, our results here show that choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits.

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Section: Discussionmentioning

confidence: 99%

Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

Kosmopoulos,

Klier,

Langwig

et al. 2023

Preprint

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“…ChTLR21was the most upregulated of all selected chTLRs in our study, and suggested it involved in the host recognition of early E. tenella infection. chTLR21 mainly recognises CpG oligodeoxynucleotides (CPG‐ODN) of pathogens and dimerises and recruits the adaptor factor MyD88, resulting in inflammatory cytokine secretion 32 . Zhang et al reported that chTLR21 was downregulated in the bursa while it upregulated in the Harderian gland when the chicken was infected with fowl adenovirus (FAdVs) 33 .…”

Section: Discussionmentioning

confidence: 99%

“…chTLR21 mainly recognises CpG oligodeoxynucleotides (CPG-ODN) of pathogens and dimerises and recruits the adaptor factor MyD88, resulting in inflammatory cytokine secretion. 32 Zhang et al reported that chTLR21 was downregulated in the bursa while it upregulated in the Harderian gland when the chicken was infected with fowl adenovirus (FAdVs). 33 Zhang et al reported…”

Section: Changes In Hdp Gene Expression In the Caecum Of E Tenella-in...mentioning

confidence: 99%

Expression of Toll‐like receptors and host defence peptides in the cecum of chicken challenged with Eimeria tenella

Wang,

Bai

et al. 2024

Parasite Immunology

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Chicken coccidiosis, caused by Eimeria protozoa, affects poultry farming. Toll‐like receptors (TLRs) and host defence peptides (HDPs) help host innate immune responses to eliminate invading pathogens, but their roles in Eimeria tenella infection remain poorly understood. Herein, 14‐day‐old chickens were treated orally with 50,000 E. tenella oocysts and the cecum was dissected at different timepoints. mRNA expression of 10 chicken TLRs (chTLRs) and five HDPs was measured by quantitative real‐time PCR. chTLR7 and chTLR15 were upregulated significantly at 3 h post‐infection while other chTLRs were downregulated (p < .05). chTLR1a, chTLR1b, chTLR2b and chTLR4 peaked at 36 h post‐infection, chTLR3, chTLR5 and chTLR15 peaked at 72 h post‐infection and chTLR21 expression was highest among chTLRs, peaking at 48 h post‐infection (p < 0.05). For HDPs, cathelicidin (CATH) 1 to 3 and B1 peaked at 48 h post‐infection, liver‐expressed antimicrobial peptide 2 peaked at 96 h post‐infection, and CATH 2 expression was highest among HDPs. CATH2 and CATH3 were markedly upregulated at 3 h post‐infection (p < .05). The results provide insight into innate immune molecules during E. tenella infection in chicken, and indicate that innate immune responses may mediate resistance to chicken coccidiosis.

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“…Phages are known to encode multiple proteins to counter bacterial defenses 20,25,26 . In most cases, each anti-defense phage protein inhibits only a narrow range of defense systems.…”

Section: Discussionmentioning

confidence: 99%

Phages reconstitute NAD⁺to counter bacterial immunity

Osterman,

Samra,

Rousset

et al. 2024

Preprint

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Bacteria defend against phage infection via a variety of antiphage defense systems. Many defense systems were recently shown to deplete cellular nicotinamide adenine dinucleotide (NAD+) in response to infection, by breaking NAD+to ADP-ribose (ADPR) and nicotinamide. It was demonstrated that NAD+depletion during infection deprives the phage from this essential molecule and impedes phage replication. Here we show that a substantial fraction of phages possess enzymatic pathways allowing reconstitution of NAD+from its degradation products in infected cells. We describe NAD+reconstitution pathway 1 (NARP1), a two-step pathway in which one enzyme phosphorylates ADPR to generate ADPR-pyrophosphate (ADPR-PP), and the second enzyme conjugates ADPR-PP and nicotinamide to generate NAD+. Phages encoding the NARP1 pathway can overcome a diverse set of defense systems, including Thoeris, DSR1, DSR2, SIR2-HerA, and SEFIR, all of which deplete NAD+as part of their defensive mechanism. Phylogenetic analyses show that NARP1 is primarily encoded on phage genomes, suggesting a phage-specific function in countering bacterial defenses. A second pathway, NARP2, allows phages to overcome bacterial defenses by building NAD+via metabolites different than ADPR-PP. Our findings report a unique immune evasion strategy where viruses rebuild molecules depleted by defense systems, thus overcoming host immunity.

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The Evasion of Antiviral Innate Immunity by Chicken DNA Viruses

Cited by 7 publications

References 101 publications

Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

Expression of Toll‐like receptors and host defence peptides in the cecum of chicken challenged with Eimeria tenella

Phages reconstitute NAD⁺to counter bacterial immunity

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The Evasion of Antiviral Innate Immunity by Chicken DNA Viruses

Cited by 7 publications

References 101 publications

Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

Expression of Toll‐like receptors and host defence peptides in the cecum of chicken challenged with Eimeria tenella

Phages reconstitute NAD+to counter bacterial immunity

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Product

Resources

About

Phages reconstitute NAD⁺to counter bacterial immunity