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Khan MZ, Wang J, Ma Y, Chen T, Ma M, Ullah Q, Khan IM, Khan A, Cao Z, Liu S. Genetic polymorphisms in immune- and inflammation-associated genes and their association with bovine mastitis resistance/susceptibility. Front Immunol 2023; 14:1082144. [PMID: 36911690 PMCID: PMC9997099 DOI: 10.3389/fimmu.2023.1082144] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/06/2023] [Indexed: 02/25/2023] Open
Abstract
Bovine mastitis, the inflammation of the mammary gland, is a contagious disease characterized by chemical and physical changes in milk and pathological changes in udder tissues. Depressed immunity and higher expression of inflammatory cytokines with an elevated milk somatic cell count can be observed during mastitis in dairy cattle. The use of somatic cell count (SCC) and somatic cell score (SCS) as correlated traits in the indirect selection of animals against mastitis resistance is in progress globally. Traditional breeding for mastitis resistance seems difficult because of the low heritability (0.10-0.16) of SCC/SCS and clinical mastitis. Thus, genetic-marker-selective breeding to improve host genetics has attracted considerable attention worldwide. Moreover, genomic selection has been found to be an effective and fast method of screening for dairy cattle that are genetically resistant and susceptible to mastitis at a very early age. The current review discusses and summarizes the candidate gene approach using polymorphisms in immune- and inflammation-linked genes (CD4, CD14, CD46, TRAPPC9, JAK2, Tf, Lf, TLRs, CXCL8, CXCR1, CXCR2, C4A, C5, MASP2, MBL1, MBL2, LBP, NCF1, NCF4, MASP2, A2M, and CLU, etc.) and their related signaling pathways (Staphylococcus aureus infection signaling, Toll-like receptor signaling, NF-kappa B signaling pathway, Cytokine-cytokine receptor, and Complement and coagulation cascades, etc.) associated with mastitis resistance and susceptibility phenotypic traits (IL-6, interferon-gamma (IFN-γ), IL17, IL8, SCS, and SCC) in dairy cattle.
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Affiliation(s)
- Muhammad Zahoor Khan
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Faculty of Veterinary and Animal Sciences, The University of Agriculture, Dera Ismail Khan, Pakistan
| | - Jingjun Wang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yulin Ma
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Tianyu Chen
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Mei Ma
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qudrat Ullah
- Faculty of Veterinary and Animal Sciences, The University of Agriculture, Dera Ismail Khan, Pakistan
| | - Ibrar Muhammad Khan
- Anhui Province Key Laboratory of Embryo Development and Reproduction Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Adnan Khan
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuai Liu
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Yang J, Tang Y, Liu X, Zhang J, Zahoor Khan M, Mi S, Wang C, Yu Y. Characterization of peripheral white blood cells transcriptome to unravel the regulatory signatures of bovine subclinical mastitis resistance. Front Genet 2022; 13:949850. [PMID: 36204322 PMCID: PMC9530456 DOI: 10.3389/fgene.2022.949850] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Abstract
Subclinical bovine mastitis is a pathogenic infection of the breast characterized by a marked decrease in milk production and quality. As it has no obvious clinical symptoms, diagnosis and treatment are challenging. Therefore, searching for biomarkers in cows’ peripheral white blood cells is valuable for preventing and treating subclinical mastitis. Thus, in this study, the transcriptome of peripheral blood from healthy and subclinical mastitis cows was characterized to find the regulatory signatures of bovine subclinical mastitis using RNA-seq. A total of 287 differentially expressed genes (DEGs) and 70 differentially expressed lncRNAs (DELs) were detected, and 37 DELs were documented near known Quantitative Trait Loci (QTL) associated with the mastitis of cows. Bioinformatic analysis indicated that lncRNAs MSTRG25101.2, MSTRG.56327.1, and MSTRG.18968.1, which are adjacent to the SCS QTL and SCC QTL, may be candidate lncRNAs that influence the pathogenesis of mastitis in cows by up-regulating the expression of genes TLR4, NOD2, CXCL8, and OAS2. Moreover, the alternative splicing (AS) pattern of transcriptional sequence differences between healthy cows and subclinical mastitis cows suggested a molecular mechanism of mastitis resistance and susceptibility. A total of 2,212 differential alternative splicing (DAS) events, corresponding to 1,621 unique DAS genes, were identified in both groups and significantly enriched in immune and inflammatory pathways. Of these, 29 DAS genes were subject to regulation by 32 alternative splicing SNPs, showing diverse and specific splicing patterns and events. It is hypothesized that the PIK3C2B and PPRPF8 splice variants associated with AS SNPs (rs42705933 and rs133847062) may be risk factors for susceptibility to bovine subclinical mastitis. Altogether, these key blood markers associated with resistance to subclinical mastitis and SNPs associated with alternative splicing of genes provide the basis for genetic breeding for resistance to subclinical mastitis in cows.
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Affiliation(s)
- Jinyan Yang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yongjie Tang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xueqin Liu
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jinning Zhang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Muhammad Zahoor Khan
- Department of Animal Sciences, Faculty of Veterinary and Animal Sciences, University of Agriculture, Dera Ismail Khan, Pakistan
| | - Siyuan Mi
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chuduan Wang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Yu
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Ying Yu,
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Ju Z, Jiang Q, Wang J, Wang X, Yang C, Sun Y, Zhang Y, Wang C, Gao Y, Wei X, Hou M, Huang J. Genome-wide methylation and transcriptome of blood neutrophils reveal the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-infected mastitis cows. BMC Genomics 2020; 21:102. [PMID: 32000686 PMCID: PMC6993440 DOI: 10.1186/s12864-020-6526-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/22/2020] [Indexed: 12/15/2022] Open
Abstract
Background Neutrophils are the first effectors of inflammatory response triggered by mastitis infection, and are important defense cells against pathogenic Escherichia coli (E. coli). DNA methylation, as a critical epigenetic mechanism for regulating gene function, is involved in bovine mastitis. Results In this study, we sequenced the blood neutrophils of healthy and E. coli-infected mastitic half-sib cows for the overall DNA methylation levels using transcriptome sequencing and reduced representation bisulfite sequencing. The methylation levels in the mastitis cows (MCs) were decreased compared with healthy cows (HCs). A total of 494 differentially methylated regions were identified, among which 61 were up-methylated and 433 were down-methylated (MCs vs. HCs). The expression levels of 1094 differentially expressed genes were up-regulated, and 245 genes were down-regulated. Twenty-nine genes were found in methylation and transcription data, among which seven genes’ promoter methylation levels were negatively correlated with expression levels, and 11 genes were differentially methylated in the exon regions. The bisulfite sequencing PCR and quantitative real-time PCR validation results demonstrated that the promoter methylation of CITED2 and SLC40A1 genes affected differential expression. The methylation of LGR4 exon 5 regulated its own alternative splicing. The promoter methylation of bta-miR-15a has an indirect effect on the expression of its target gene CD163. The CITED2, SLC40A1, and LGR4 genes can be used as candidates for E. coli-induced mastitis resistance. Conclusions This study explored the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-induced mastitis, thereby helping explain the function of DNA methylation in the pathogenesis of mastitis and provided new target genes and epigenetic markers for mastitis resistance breeding in dairy cattle.
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Affiliation(s)
- Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Jinpeng Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Yan Sun
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Yaran Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Yaping Gao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Xiaochao Wei
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Minghai Hou
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China.,Engineering Center of Animal Breeding and Reproduction, Jinan, Shandong, 250100, People's Republic of China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China. .,Engineering Center of Animal Breeding and Reproduction, Jinan, Shandong, 250100, People's Republic of China.
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SNP Diversity in CD14 Gene Promoter Suggests Adaptation Footprints in Trypanosome Tolerant N'Dama ( Bos taurus) but not in Susceptible White Fulani ( Bos indicus) Cattle. Genes (Basel) 2020; 11:genes11010112. [PMID: 31963925 PMCID: PMC7017169 DOI: 10.3390/genes11010112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/23/2019] [Accepted: 01/13/2020] [Indexed: 12/12/2022] Open
Abstract
Immune response to infections has been shown to be mediated by genetic diversity in pattern recognition receptors, leading to disease tolerance or susceptibility. We elucidated naturally occurring variations within the bovine CD14 gene promoter in trypanosome-tolerant (N'Dama) and susceptible (White Fulani) cattle, with genomic and computational approaches. Blood samples were collected from White Fulani and N'Dama cattle, genomic DNA extracted and the entire promoter region of the CD14 gene amplified by PCR. We sequenced this region and performed in silico computation to identify SNP variants, transcription factor binding sites, as well as micro RNAs in the region. CD14 promoter sequences were compared with the reference bovine genome from the Ensembl database to identify various SNPs. Furthermore, we validated three selected N'Dama specific SNPs using custom Taqman SNP genotyping assay for genetic diversity. In all, we identified a total of 54 and 41 SNPs at the CD14 promoter for N'Dama and White Fulani respectively, including 13 unique SNPs present in N'Dama only. The significantly higher SNP density at the CD14 gene promoter region in N'Dama may be responsible for disease tolerance, possibly an evolutionary adaptation. Our genotype analysis of the three loci selected for validation show that mutant alleles (A/A, C/C, and A/A) were adaptation profiles within disease tolerant N'Dama. A similar observation was made for our haplotype analysis revealing that haplotypes H1 (ACA) and H2 (ACG) were significant combinations within the population. The SNP effect prediction revealed 101 and 89 new transcription factor binding sites in N'Dama and White Fulani, respectively. We conclude that disease tolerant N'Dama possessing higher SNP density at the CD14 gene promoter and the preponderance of mutant alleles potentially confirms the significance of this promoter in immune response, which is lacking in susceptible White Fulani. We, therefore, recommend further in vitro and in vivo study of this observation in infected animals, as the next step for understanding genetic diversity relating to varying disease phenotypes in both breeds.
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Chen DF, Cui XZ, Cao WM, Meng W. Neutrophil Cytosolic Factor 1 Contributes to the Development of Sepsis. Inflammation 2019; 42:811-817. [PMID: 30465301 DOI: 10.1007/s10753-018-0935-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To identify differentially expressed genes in sepsis and potential key role of reactive oxygen species (ROS) genes associated with sepsis. Gene expression dataset was available from GSE46599. Firstly, we screened the differentially expressed genes between sepsis and healthy samples. Then, the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tools were utilized to perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses at the functional level. Differentially expressed genes mediating ROS levels were validated in the next investigation and analysis. We identified 1094 genes expressed differentially between normal and sepsis samples, including 655 upregulated genes and 439 downregulated genes. At the functional level, GO and KEGG pathway enrichment analysis showed that those differentially expressed genes were majorly associated with the immune response and metabolic process in sepsis. Further analysis revealed that neutrophil cytosolic factor 1(NCF1), a critical gene in the ROS system, upregulated in THP-1 cell and monocytes under lipopolysaccharides stimulation. Moreover, we identified the upregulation of NCF1 in a sepsis model. We screened the differentially expressed genes from the global level and identified NCF1 might be a critical target gene in sepsis.
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Affiliation(s)
- Dei-Fang Chen
- The Outpatient Department of Jinan Central Hospital, Jinan Central Hospital, Jinan, 250014, Shandong, China
| | - Xiu-Zhen Cui
- The Surgical Department of Jinan First People Hospital, Jinan First People Hospital, Jinan, 250014, Shandong, China
| | - Wen-Ming Cao
- The Gynecology Department of Changle County People's Hospital, Changle County People's Hospital, Jinan, 250014, Shandong, China
| | - Wen Meng
- The Intravenous Drug Centralization Division of Jinan Central Hospital, Jinan Central Hospital, Jinan, 250014, Shandong, China.
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Mitra SD, Ganaie F, Bankar K, Velu D, Mani B, Vasudevan M, Shome R, Rahman H, Kumar Ghosh S, Shome BR. Genome-wide analysis of mammary gland shows modulation of transcriptome landscape with alternative splice variants in Staphylococcus aureus mastitis in mice. Gene 2019; 735:144278. [PMID: 31821873 DOI: 10.1016/j.gene.2019.144278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 11/22/2019] [Accepted: 11/24/2019] [Indexed: 01/25/2023]
Abstract
Epidemiological mapping shows Staphylococcus aureus to be the leading mastitis causing pathogen in India with diverse genetic lineages circulating in the dairy cattle population. We previously reported that endemic clonal strains of S. aureus isolated from subclinical mastitis lead to specific alteration of epigenetic modulators resulting in deviating immune response in intramammary infection mouse model. However, the extent of transcriptome modulation and associated alternative splicing in S. aureus mastitis is poorly understood. Hence, to gain a deeper insight of the extent of modulation of transcriptome landscape, we expanded the study here using high throughput, paired-end RNA sequencing analysis of the mouse mammary gland inoculated with three strains of S. aureus (SA1, SA2, and SA3) possessing specific genotype, virulence and enterotoxin traits. Overall, we detected 35,878 transcripts in S. aureus inoculated mammary gland, 23% more than those annotated in the reference genome. Expression of 20,756 transcripts was > 1 fragment per kilobase of transcript per million mapped fragments and 25.95% of multi-exonic genes were alternatively spliced. We noted Alternative Splicing (AS) events for > 100 immune-related genes. S. aureus infection quantitatively altered AS events in mice mammary gland. Collectively, the majority of differentially expressed significant genes clustered into immune-associated, cell adhesion and metabolic process categories. We observed AS events for 379 transcripts of genes putatively encoding several splicing associated proteins and transcription factors besides inflammatory mediators. The present analysis provides new insights into global transcriptome landscape and AS events in host-defense related genes in response to S. aureus intramammary infection, suggesting the need for studies focusing on multi-target and/or network therapeutics approach to combat mastitis.
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Affiliation(s)
- Susweta Das Mitra
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India; Department of Biotechnology, Assam University, Silchar, AS, India; School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, KA, India
| | - Feroze Ganaie
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India; Department of Medicine, Division of Pulmonary/Allergy/Critical care, University of Alabama at Birmingham, AL, USA
| | - Kiran Bankar
- Bionivid Technology Pvt. Ltd., Bangalore, KA, India
| | - Dhanikachalam Velu
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India
| | - Bhuvana Mani
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India
| | | | - Rajeswari Shome
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India
| | - Habibur Rahman
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India; International Livestock Research Institute, Pusa, DL, India
| | | | - Bibek Ranjan Shome
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India.
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Yang L, Guo R, Ju Z, Wang X, Jiang Q, Liu Y, Zhao H, He K, Li J, Huang J. Production of an aberrant splice variant of CCL5 is not caused by genetic mutation in the mammary glands of mastitis‑infected Holstein cows. Mol Med Rep 2019; 19:4159-4166. [PMID: 30942444 PMCID: PMC6472127 DOI: 10.3892/mmr.2019.10103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/21/2019] [Indexed: 01/09/2023] Open
Abstract
Genetic mutations, including single nucleotide polymorphisms (SNPs), result in aberrant alternatively splicing of gene and involves in susceptibility of inflammatory diseases, including bovine mastitis. C‑C motif chemokine ligand 5 (CCL5) is an immune‑associated gene, but its alternative splicing (AS) mechanism of gene expression has not yet been understood. The present study identified the splice variant of CCL5 and the compared differential expression of various transcripts between healthy and mastitic mammary gland tissue from cows. A novel transcript lacking exon 2 with a deletion of 112 bp (referred to as CCL5‑AS) was identified in the mammary gland. The expression of CCL5‑AS was lower compared with CCL5‑reference in the healthy and mastitic mammary tissues. A total of two novel SNPs (g.1647 C>T and g.1804 G>A) were identified in exon 2 of CCL5. Using the splicing mini‑gene reporter assay in bovine mammary epithelial cells (MAC‑T) and 293T cells, it was confirmed that the production of CCL5‑AS was not caused by the two SNPs. The present findings suggested that alternative splicing is one of the mechanisms of CCL5 expression regulation and is involved in mastitis infection, but that genetic mutation was not responsible for the generation of the abnormal transcript of CCL5 in cows.
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Affiliation(s)
- Ling Yang
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, Hebei 056021, P.R. China
| | - Ruiqing Guo
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, Hebei 056021, P.R. China
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, P.R. China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, P.R. China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, P.R. China
| | - Yong Liu
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, Hebei 056021, P.R. China
| | - Han Zhao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, P.R. China
| | - Kaili He
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, Hebei 056021, P.R. China
| | - Jianbin Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, P.R. China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, P.R. China
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Palyzová A, Svobodová K, Sokolová L, Novák J, Novotný Č. Metabolic profiling of Fusarium oxysporum f. sp. conglutinans race 2 in dual cultures with biocontrol agents Bacillus amyloliquefaciens, Pseudomonas aeruginosa, and Trichoderma harzianum. Folia Microbiol (Praha) 2019; 64:779-787. [PMID: 30746611 DOI: 10.1007/s12223-019-00690-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/05/2019] [Indexed: 11/26/2022]
Abstract
There are increasing efforts to identify biocontrol-active microbial metabolites in order to improve strategies for biocontrol of phytopathogens. In this work, Fusarium oxysporum f. sp. conglutinans was confronted with three different biocontrol agents: Trichoderma harzianum, Bacillus amyloliquefaciens, and Pseudomonas aeruginosa in dual culture bioassays. Metabolites produced during the microbial interactions were screened by a matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). T. harzianum exhibited the strongest inhibition of growth of F. oxysporum resulting in overlay of the pathogen colony with its mycelium. Recorded metabolite profiles suggested a direct attack of F. oxysporum mycelium by T. harzianum and B. amyloliquefaciens by means of membrane-attacking peptaibols and a set of antimicrobial lipopeptides and siderophores, respectively. The direct mode of the biocontrol activity of T. harzianum and B. amyloliquefaciens corresponded to their ability to suppress F. oxysporum production of mycotoxin beauvericin suggesting that this ability is not specific only for Trichoderma species. In the case of P. aeruginosa, siderophores pyoverdine E/D and two rhamnolipids were produced as major bacterial metabolites; the rhamnolipid production was blocked by F. oxysporum. The results showed that this type of biocontrol activity was the least effective against F. oxysporum. The effective application of MALDI-MS profiling to the screening of nonvolatile microbial metabolites produced during the interaction of the phytopathogen and the biocontrol microorganisms was demonstrated.
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Affiliation(s)
- Andrea Palyzová
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Kateřina Svobodová
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Lucie Sokolová
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Jiří Novák
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Čeněk Novotný
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic.
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Zhang Y, Wang X, Jiang Q, Hao H, Ju Z, Yang C, Sun Y, Wang C, Zhong J, Huang J, Zhu H. DNA methylation rather than single nucleotide polymorphisms regulates the production of an aberrant splice variant of IL6R in mastitic cows. Cell Stress Chaperones 2018; 23:617-628. [PMID: 29353404 PMCID: PMC6045551 DOI: 10.1007/s12192-017-0871-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/22/2017] [Accepted: 12/21/2017] [Indexed: 12/28/2022] Open
Abstract
Interleukin-6 receptor-alpha (IL6R) interacts with IL6 and forms a ligand-receptor complex, which can stimulate various cellular responses, such as cell proliferation, cell differentiation, and activation of inflammatory processes. Both genetic mutation and epigenetic modification regulate gene transcription. We identified a novel splice variant of bovine IL6R, designated as IL6R-TV, which is characterized by the skipping of exon 2 of the NCBI-referenced IL6R gene (IL6R-reference). The expression levels of IL6R-TV and IL6R-reference transcripts were lower in normal mammary gland tissues. These transcripts play a potential role during inflammatory infection. We also detected two putative functional SNPs (g.19711 T > C and g.19731 G > C) located within the upstream 100 bp of exon 2. These SNPs formed two haplotypes (T-G and C-C). Two mutant pSPL3 exon-trapping plasmids (pSPL3-T-G and pSPL3-C-C) were transferred into the bovine mammary epithelial cells (MAC-T) and human embryonic kidney 293 T cells (HEK293T) to investigate the relationship between the two SNPs and the aberrant splicing of IL6R. DNA methylation levels of the alternatively spliced exon in normal and mastitis-infected mammary gland tissues were quantified through nested bisulfate sequencing PCR (BSP) and cloning sequencing. We found that DNA methylation regulated IL6R transcription. The DNA methylation level was high in mastitis-infected mammary gland tissues and stimulated IL6R expression, thereby promoting the inclusion of the alternatively spliced exon. The upregulated expression of the two transcripts was due to DNA methylation modification rather than genetic mutations.
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Affiliation(s)
- Yan Zhang
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, People's Republic of China
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Haisheng Hao
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, People's Republic of China
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Yan Sun
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Jinming Huang
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, People's Republic of China.
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China.
- College of Life Sciences, Shandong Normal University, Jinan, Shandong, People's Republic of China.
| | - Huabin Zhu
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, People's Republic of China.
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Ju Z, Huang J, Jiang Q, Wang C, Wang X, Zhao S. Identification of bta-miR-15a∼16a cluster expression, localization and regulated target in Holsteins. Mol Cell Probes 2018; 40:8-12. [PMID: 29859243 DOI: 10.1016/j.mcp.2018.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/25/2018] [Accepted: 05/29/2018] [Indexed: 01/07/2023]
Abstract
Bovine mastitis is an inflammation response of the mammary gland tissues caused mainly by pathogenic bacteria in cows. Previous studies showed that bta-miR-15a and bta-miR-16a modulate immunity and inflammation responses. In this study, we investigated the expression pattern and tissue localization of bta-miR-15a and bta-miR-16a. The expression levels of bta-miR-15a and bta-miR-16a were significantly upregulated in mammary tissues and blood neutrophils of mastitis-infected cows, compared with those of healthy cows (P < 0.05). Through in situ hybridization, we examined the tissue localization of bta-miR-15a and bta-miR-16a and found that they were expressed in the ductal and acinar cells of mammary gland tissues, where they had a stronger expression signal in the mammary tissues of cows with mastitis than that in healthy cows' tissues. Moreover, we identified CD163 as the target gene of bta-miR-15a and bta-miR-16a. Luciferase assay indicated that bta-miR-15a, bta-miR-16a, and bta-miR-15a∼16a cluster led to the significant reduction in the luciferase activity of CD163 3'UTR vector (P < 0.05). Meanwhile, the luciferase activity had a significantly low value compared with that of single bta-miR-15a or bta-miR-16a plasmid (P < 0.05) in the presence of bta-miR-15a∼16a cluster. The bta-miR-15a∼16a cluster may function more effectively in inhibiting luciferase reporter gene activity of target gene CD163 than single miRNA. Our study provides an insight into the relationship between bovine mastitis and gene expression of bta-miR-15a/16a, which suggested that bta-miR-15a∼16a cluster may play a role against mastitis by binding to target CD163 gene in Holstein dairy cattle.
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Affiliation(s)
- Zhihua Ju
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education in China, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No.159 North of Industry Road, Jinan, 250131, Shandong, China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No.159 North of Industry Road, Jinan, 250131, Shandong, China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No.159 North of Industry Road, Jinan, 250131, Shandong, China
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No.159 North of Industry Road, Jinan, 250131, Shandong, China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No.159 North of Industry Road, Jinan, 250131, Shandong, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education in China, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Wang XG, Ju ZH, Hou MH, Jiang Q, Yang CH, Zhang Y, Sun Y, Li RL, Wang CF, Zhong JF, Huang JM. Deciphering Transcriptome and Complex Alternative Splicing Transcripts in Mammary Gland Tissues from Cows Naturally Infected with Staphylococcus aureus Mastitis. PLoS One 2016; 11:e0159719. [PMID: 27459697 PMCID: PMC4961362 DOI: 10.1371/journal.pone.0159719] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/06/2016] [Indexed: 11/20/2022] Open
Abstract
Alternative splicing (AS) contributes to the complexity of the mammalian proteome and plays an important role in diseases, including infectious diseases. The differential AS patterns of these transcript sequences between the healthy (HS3A) and mastitic (HS8A) cows naturally infected by Staphylococcus aureus were compared to understand the molecular mechanisms underlying mastitis resistance and susceptibility. In this study, using the Illumina paired-end RNA sequencing method, 1352 differentially expressed genes (DEGs) with higher than twofold changes were found in the HS3A and HS8A mammary gland tissues. Gene ontology and KEGG pathway analyses revealed that the cytokine–cytokine receptor interaction pathway is the most significantly enriched pathway. Approximately 16k annotated unigenes were respectively identified in two libraries, based on the bovine Bos taurus UMD3.1 sequence assembly and search. A total of 52.62% and 51.24% annotated unigenes were alternatively spliced in term of exon skipping, intron retention, alternative 5′ splicing and alternative 3ʹ splicing. Additionally, 1,317 AS unigenes were HS3A-specific, whereas 1,093 AS unigenes were HS8A-specific. Some immune-related genes, such as ITGB6, MYD88, ADA, ACKR1, and TNFRSF1B, and their potential relationships with mastitis were highlighted. From Chromosome 2, 4, 6, 7, 10, 13, 14, 17, and 20, 3.66% (HS3A) and 5.4% (HS8A) novel transcripts, which harbor known quantitative trait locus associated with clinical mastitis, were identified. Many DEGs in the healthy and mastitic mammary glands are involved in immune, defense, and inflammation responses. These DEGs, which exhibit diverse and specific splicing patterns and events, can endow dairy cattle with the potential complex genetic resistance against mastitis.
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Affiliation(s)
- Xiu Ge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, P.R. China
| | - Zhi Hua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, P.R. China
| | - Ming Hai Hou
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, P.R. China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, P.R. China
| | - Chun Hong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, P.R. China
| | - Yan Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, P.R. China
| | - Yan Sun
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, P.R. China
| | - Rong Ling Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, P.R. China
| | - Chang Fa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, P.R. China
| | - Ji Feng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, P.R. China
| | - Jin Ming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, P.R. China
- * E-mail:
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12
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Ju Z, Wang C, Wang X, Yang C, Sun Y, Jiang Q, Wang F, Li M, Zhong J, Huang J. Role of an SNP in Alternative Splicing of Bovine NCF4 and Mastitis Susceptibility. PLoS One 2015; 10:e0143705. [PMID: 26600390 PMCID: PMC4658021 DOI: 10.1371/journal.pone.0143705] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/09/2015] [Indexed: 01/21/2023] Open
Abstract
Neutrophil cytosolic factor 4 (NCF4) is component of the nicotinamide dinucleotide phosphate oxidase complex, a key factor in biochemical pathways and innate immune responses. In this study, splice variants and functional single-nucleotide polymorphism (SNP) of NCF4 were identified to determine the variability and association of the gene with susceptibility to bovine mastitis characterized by inflammation. A novel splice variant, designated as NCF4-TV and characterized by the retention of a 48 bp sequence in intron 9, was detected in the mammary gland tissues of infected cows. The expression of the NCF4-reference main transcript in the mastitic mammary tissues was higher than that in normal tissues. A novel SNP, g.18174 A>G, was also found in the retained 48 bp region of intron 9. To determine whether NCF4-TV could be due to the g.18174 A>G mutation, we constructed two mini-gene expression vectors with the wild-type or mutant NCF4 g.18174 A>G fragment. The vectors were then transiently transfected into 293T cells, and alternative splicing of NCF4 was analyzed by reverse transcription-PCR and sequencing. Mini-gene splicing assay demonstrated that the aberrantly spliced NCF4-TV with 48 bp retained fragment in intron 9 could be due to g.18174 A>G, which was associated with milk somatic count score and increased risk of mastitis infection in cows. NCF4 expression was also regulated by alternative splicing. This study proposes that NCF4 splice variants generated by functional SNP are important risk factors for mastitis susceptibility in dairy cows.
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Affiliation(s)
- Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
- * E-mail: (ZJ); (JH)
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Yan Sun
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Fei Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Mengjiao Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
- * E-mail: (ZJ); (JH)
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