Glycosylation of ALV-J envelope protein at sites 17 and 193 is pivotal in the virus replication

Glycans on envelope glycoprotein (Env) of the subgroup J avian leukosis virus (ALV-J) play an essential role in virion integrity and infection process. In this study, we found that among the 13 predicted N-linked glycosylation sites (NGSs) in gp85 of Tibetan chicken strain TBC-J6, N17 and N193/N191 are pivotal in the virus replication. Further research illustrated that mutation at N193 weakened Env-receptor binding in blocking assay of viral entrance, co-immunoprecipitation and ELISA. Our studies also showed that N17 was involved in Env protein processing and later virion incorporation, based on the detection of p27 and Env protein in the supernatant and gp37 in the cell culture. This report is a systematic research on clarifying the biological function of NGSs on ALV-J gp85 , which would provide valuable insights in the role of gp85 in ALV life cycle as well as anti-ALV-J strategies. Importance ALV-J is a retrovirus that can cause multiple types of tumors in chickens. Among all the viral proteins, the heavily glycosylated envelope protein is especially crucial. Glycosylation plays a major role in Env protein function, including protein processing, receptor attachment and immune evasion. Notably, viruses isolated recently seem to lose the 6 th and 11 st NGSs, which are proved to be important in receptor binding. In our study, the 1 st (N17) and 8 th (N193) NGS of gp85 of strain TBC-J6 can largely influence the titer of this virus. Deglycosylation at N193 weakened Env-receptor binding, while mutation at N17 influenced Env protein processing. This study systemically analyzed the function of NGSs in ALV-J in different aspects, which may help us to understand the lifecycle of ALV-J and provide antiviral targets for the control of ALV-J.

Genome-Wide Run of Homozygosity Analysis Reveals Candidate Genomic Regions Associated with Environmental Adaptations of Tibetan Native Chickens

Background In Tibet, two most important breeds are Tibetan chicken and Lhasa white chicken, and the duo exhibit specific adaptations to high altitude and produce indispensable protein for humans living in the plateau. These breeds were partly included in conservation plans as their biodiversity is important as a genetic resource. However, population genetic analysis of the chickens is rarely investigated. Based on whole-genome sequencing data of 113 chickens from 4 Tibetan chicken population including Shigatse (SH), Nyemo (NM), Dagze (DZ) and Nyingchi (LZ), as well as Lhasa white (LW) chicken population, we performed genetic diversity and differentiation, run of homozygosity (ROH), genomic inbreeding and selection signature analyses. Results Our results showed high genetic diversity across the five chicken populations. The linkage disequilibrium decay was highest in LZ, and moderate level of genetic differentiation was found between LZ and other populations (Fst ranging from 0.05 to 0.10). Furthermore, the highest ROH-based inbreeding estimate (FROH) was 0.11 in LZ, whereas it ranges from 0.04 to 0.06 in the other four chicken populations. In total, 74, 111, 62, 42 and 54 ROHs containing SNPs with concurrency ranked top 1% were identified for SH, NM, DZ, LZ and LW, respectively. BDNF, CCDC34, LGR4, LIN7C, GLS, LOC101747789, MYO1B, STAT1 and STAT4 were shared genes harbored by these ROHs in the five populations, suggesting their important roles in adaptation of the chickens. Combined with selection signature analysis, we also identified a common candidate genomic region harboring AMY2A, NTNG1 and VAV3 genes. These genes have been reported to contribute to digestion, neurite growth and high-altitude adaptation, which could be involved in selection during evolution process. Conclusions High genetic diversity was observed in Tibetan native chickens. Nyingchi population, possessing highest FROH, is genetically distant from other chicken population. Candidate genes in ROH islands could aid the genetic characterization of the five Tibetan native chicken populations. Our findings contribute to the understanding of genetic diversity and offer valuable insights for the genetic mechanism of adaptation, as well as provide veritable tools that can help in the design and implementation of breeding and conservation strategies for Tibetan native chickens.

HIF-1 regulates energy metabolism of Tibetan chicken brain during embryo development under hypoxia

The Tibetan chickens (Gallus gallus; TBC) are an indigenous breed distributed in Qinghai-Tibet Plateau that are well adapted to a hypoxic environment. The energy metabolism of embryo brains in TBCs under hypoxia has been little reported. This study investigated changes in energy metabolism of TBCs brain during embryo development under hypoxia. We found TBCs exhibited a change of glycolysis and TCA cycle during embryo development under hypoxia. HIF-1 potentially involved this by directly inducing the overexpression of PDK1 and glycolytic genes, hexokinase(HK1) and lactate dehydrogenase A (LDHA) to increase glycolysis of TBCs to adapt hypoxia. Although these may not be unique to TBCs, as we had also found similar results in Dwarf Laying Chickens (DLCs), a lowland chicken breed, TBCs had stronger regulating ability. In summary, our study revealed HIF-1 induced energy metabolism change in TBCs brain via upregulating expressions of PDK1 and other HIF-1 target genes like HK1, LDHA to increase glycolysis for TBCs hypoxia adaptation during embryo development. It indicates the potential application of TBCs energy metabolism research for other animals living on the Qinghai-Tibet Plateau.

Comprehensive Analysis of Coding and Non-coding RNA Transcriptomes Related to Hypoxic Adaptation in Tibetan Chickens

Background: Tibetan chickens, a unique native breed in the Qinghai-Tibet Plateau of China, have a suite of adaptive features to tolerate the high-altitude hypoxic environment. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have roles in the hypoxic adaptation of high-altitude animals, although their exact involvement remains unclear.Results: This study aimed to elucidate the global landscape of mRNAs, lncRNAs, and miRNAs using transcriptome sequencing in order to construct a regulatory network of competing endogenous RNAs (ceRNAs) and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos. In total, 354 differentially expressed genes (DEGs), 389 differentially expressed lncRNAs (DELs), and 73 differentially expressed miRNAs (DEMs) were identified between Tibetan (TC) and Chahua chickens (CH). Functional analysis revealed that several important DEMs and their target DELs and DEGs are involved in angiogenesis (including blood vessel development and blood circulation) and energy metabolism (including glucose, carbohydrate, and lipid metabolism). The ceRNA network was then constructed with the predicted DEGs-DEMs-DELs interactions, which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens.Conclusions: These transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism. These results provide insight into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.

Pectoral muscle transcriptome analyses reveal high-altitude adaptations in Tibetan chickens

The largest muscles in fowl are the pectorals, which provide the power required for birds to fly. Tibetan chickens show specific adaptations to high-altitude conditions, but changes in the muscle transcriptome associated with these adaptations have not been characterized yet. Therefore, in this study, we used next-generation sequencing technologies to generate eight libraries of mRNA sequences for four Tibetan chickens and four Beijing fatty chickens. A comprehensive transcriptome analysis was performed. In the eight samples, 12 333 annotated protein-coding genes were expressed. Among these, 48 differentially expressed genes were found; all of which were upregulated in Tibetan chickens. These differentially expressed genes were mainly involved in kidney morphogenesis, which indicates that hypoxia has an important effect on renal tubule development. Only nine genes were involved in Kyoto Encyclopedia of Genes and Genomes pathways, such as the endocytosis pathway, the MAPK signaling pathway, the calcium signaling pathway and the TGF-beta signaling pathway. The differentially expressed genes identified in this study will be used to facilitate future research into the Tibetan chicken.