1
|
Raza SHA, Khan R, Pant SD, Shah MA, Quan G, Feng L, Cheng G, Gui LS, Zan L. Genetic variation in the OPN gene affects milk composition in Chinese Holstein cows. Anim Biotechnol 2023; 34:893-899. [PMID: 34779705 DOI: 10.1080/10495398.2021.2001343] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The aim of this study was to investigate the association between genotypes and haplotypes of OPN, and milk composition in dairy cows. A total of 317 Chinese Holstein cows were genotyped via DNA sequencing in this study. Three single nucleotide polymorphisms (SNPs), g.2916G > A, g.58675C > T and g.58899C > A, and eight haplotypes were identified. Of the eight possible haplotypes, four haplotypes i.e., Hap2 (ACC; 55.30%), Hap6 (GCC, 15.6%), Hap1 (ACA, 13.6%) and Hap4 (ATC, 5.70%), were considered to be major with a cumulative estimated frequency of >90%. Single markers (g.2916G > A and g.58899C > A) and Haplotype Hap6/4 were found to be associated with an increase in butter-fat percentage (p < 0.05). Taken together, our results provided evidence that polymorphisms in OPN are associated with milk composition, and could potentially be used for marker-assisted selection in Chinese Holstein cows.
Collapse
Affiliation(s)
| | - Rajwali Khan
- Department of Livestock Management, Breeding and Genetic, The University of Agriculture Peshawar, Pakistan
| | - Sameer D Pant
- Graham Centre for Agricultural Innovation, Charles Sturt University, Australia
| | - Mujahid Ali Shah
- Faculty of Fisheries and Protection of Water, University of South Bohemia in Ceske Budejovice, Czech Republic
| | - Guobo Quan
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Long Feng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Lin-Sheng Gui
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- National Beef Cattle Improvement Center, Northwest A&F University, Yangling, China
| |
Collapse
|
2
|
Rosinski-Chupin I, Sauvage E, Fouet A, Poyart C, Glaser P. Conserved and specific features of Streptococcus pyogenes and Streptococcus agalactiae transcriptional landscapes. BMC Genomics 2019; 20:236. [PMID: 30902048 PMCID: PMC6431027 DOI: 10.1186/s12864-019-5613-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/14/2019] [Indexed: 12/11/2022] Open
Abstract
Background The human pathogen Streptococcus pyogenes, or group A Streptococcus, is responsible for mild infections to life-threatening diseases. To facilitate the characterization of regulatory networks involved in the adaptation of this pathogen to its different environments and their evolution, we have determined the primary transcriptome of a serotype M1 S. pyogenes strain at single-nucleotide resolution and compared it with that of Streptococcus agalactiae, also from the pyogenic group of streptococci. Results By using a combination of differential RNA-sequencing and oriented RNA-sequencing we have identified 892 transcription start sites (TSS) and 885 promoters in the S. pyogenes M1 strain S119. 8.6% of S. pyogenes mRNAs were leaderless, among which 81% were also classified as leaderless in S. agalactiae. 26% of S. pyogenes transcript 5′ untranslated regions (UTRs) were longer than 60 nt. Conservation of long 5′ UTRs with S. agalactiae allowed us to predict new potential regulatory sequences. In addition, based on the mapping of 643 transcript ends in the S. pyogenes strain S119, we constructed an operon map of 401 monocistrons and 349 operons covering 81.5% of the genome. One hundred fifty-six operons and 254 monocistrons retained the same organization, despite multiple genomic reorganizations between S. pyogenes and S. agalactiae. Genomic reorganization was found to more often go along with variable promoter sequences and 5′ UTR lengths. Finally, we identified 117 putative regulatory RNAs, among which nine were regulated in response to magnesium concentration. Conclusions Our data provide insights into transcriptome evolution in pyogenic streptococci and will facilitate the analysis of genetic polymorphisms identified by comparative genomics in S. pyogenes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5613-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Isabelle Rosinski-Chupin
- Ecology and Evolution of Resistance to Antibiotics, Institut Pasteur-APHP-Université Paris Saclay, UMR3525 CNRS, Paris, France.
| | - Elisabeth Sauvage
- Ecology and Evolution of Resistance to Antibiotics, Institut Pasteur-APHP-Université Paris Saclay, UMR3525 CNRS, Paris, France
| | - Agnès Fouet
- INSERM U1016, Institut Cochin, CNRS UMR 8104, Université Paris Descartes (UMR-S1016), Paris, France.,Centre Nationale de Référence des Streptocoques, Hôpitaux Universitaires Paris Centre, Cochin, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Claire Poyart
- INSERM U1016, Institut Cochin, CNRS UMR 8104, Université Paris Descartes (UMR-S1016), Paris, France.,Centre Nationale de Référence des Streptocoques, Hôpitaux Universitaires Paris Centre, Cochin, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Resistance to Antibiotics, Institut Pasteur-APHP-Université Paris Saclay, UMR3525 CNRS, Paris, France
| |
Collapse
|
3
|
Broglia L, Materne S, Lécrivain AL, Hahnke K, Le Rhun A, Charpentier E. RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B. RNA Biol 2018; 15:1336-1347. [PMID: 30290721 PMCID: PMC6284565 DOI: 10.1080/15476286.2018.1532253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Endoribonuclease Y (RNase Y) is a crucial regulator of virulence in Gram-positive bacteria. In the human pathogen Streptococcus pyogenes, RNase Y is required for the expression of the major secreted virulence factor streptococcal pyrogenic exotoxin B (SpeB), but the mechanism involved in this regulation remains elusive. Here, we demonstrate that the 5′ untranslated region of speB mRNA is processed by several RNases including RNase Y. In particular, we identify two RNase Y cleavage sites located downstream of a guanosine (G) residue. To assess whether this nucleotide is required for RNase Y activity in vivo, we mutated it and demonstrate that the presence of this G residue is essential for the processing of the speB mRNA 5′ UTR by RNase Y. Although RNase Y directly targets and processes speB, we show that RNase Y-mediated regulation of speB expression occurs primarily at the transcriptional level and independently of the processing in the speB mRNA 5′ UTR. To conclude, we demonstrate for the first time that RNase Y processing of an mRNA target requires the presence of a G. We also provide new insights on the speB 5′ UTR and on the role of RNase Y in speB regulation.
Collapse
Affiliation(s)
- Laura Broglia
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany.,c Institute for Biology , Humboldt University , Berlin , Germany.,d Department of Regulation in Infection Biology , Helmholtz Centre for Infection Research , Braunschweig , Germany
| | - Solange Materne
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany
| | - Anne-Laure Lécrivain
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany.,e The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology , Umeå University , Umeå , Sweden
| | - Karin Hahnke
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany
| | - Anaïs Le Rhun
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany.,d Department of Regulation in Infection Biology , Helmholtz Centre for Infection Research , Braunschweig , Germany.,e The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology , Umeå University , Umeå , Sweden
| | - Emmanuelle Charpentier
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany.,c Institute for Biology , Humboldt University , Berlin , Germany.,d Department of Regulation in Infection Biology , Helmholtz Centre for Infection Research , Braunschweig , Germany.,e The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology , Umeå University , Umeå , Sweden
| |
Collapse
|