The haemoglobin subunits alpha and beta: Old and new genetic variants in the Italian Mediterranean buffalo
Haemoglobin (HB), the most widely distributed respiratory pigment in the animal kingdom, is among the best characterized oxygen-binding proteins, both at functional and molecular level. However, very little information is available about the genomic features of HB in river buffalo (Bubalus bubalis), even though there are reports in literature confirming the presence of interesting polymorphisms at the protein level in Mediterranean buffalo. We hence address the characterization of exonic as well as intronic nucleotide polymorphism in the haemoglobin subunit alpha and beta in a set of nine Italian Mediterranean buffaloes exhibiting different HB phenotypes. The nine buffaloes were selected from a random set of 398 samples, previously analysed for their HB protein polymorphism, in order to account for both globin variants and the evolution of intron variability within the most common domesticated species of the family Bovidae. All four sequenced clones of the subunit alpha were 1311 bp, whereas the length of the five different sequenced clones of the subunit beta ranged from 1841 to 1960 bp, due to an insertion of 119 nucleotides. Six polymorphic sites were detected in the four amplicons of alpha subunit. Among them, two variations concern exclusively haplotype A, while four sequence variations were found to be specific to haplotype B. Several variations, both in exonic and intronic regions, were detected in the B. bubalis subunit beta. In conclusion, the nucleotide sequence variants observed in this work substantiate the known haemoglobin protein polymorphisms, and an updated protein nomenclature is provided here. In addition, we observed a high sequence similarity in the overall pattern of variation in the haemoglobin subunits, possibly the results of a concerted evolution, with relatively more extensive gene homogenization in river buffalo than in other ruminant species.
Bannister J. V., Bannister W. H., Wilson J. B., Lam H., Miller A., Huisman T. H. J. (2009): The Structure of Goat Hemoglobins V. A Fourth β Chain Variant (β-D-Malta; 69 Asp ↠ Gly) with Decreased Oxygen Affinity and Occurring at a High Frequency in Malta. Hemoglobin, 3, 57-75 https://doi.org/10.3109/03630267909069155
Bigi D., Zanon A. (2008): Atlas of Native Italian Breeds: Bovines, Equines, Sheep, Goats and Pigs Reared in Italy. Edagricole, Milan, Italy. (in Italian)
Carson Andrew R, Scherer Stephen W (2009): Identifying concerted evolution and gene conversion in mammalian gene pairs lasting over 100 million years. BMC Evolutionary Biology, 9, 156- https://doi.org/10.1186/1471-2148-9-156
Di Luccia Aldo, Iannibelli Luigi, Addato Erminia, Masala Bruno, Manca Laura, Ferrara Lino (1991): Evidence for the presence of two different β-globin chains in the hemoglobin of the river buffalo (Bubalus bubalis L.). Comparative Biochemistry and Physiology Part B: Comparative Biochemistry, 99, 887-892 https://doi.org/10.1016/0305-0491(91)90159-B
Di Luccia Aldo, Iannibelli Luigi, Ferranti Pasquale, Manca Laura, Masala Bruno, Ferrara Lino (1991): Electrophoretic and chromatographic evidence for allelic polymorphisms in the river buffalo α-globin gene complex. Biochemical Genetics, 29, 421-430 https://doi.org/10.1007/BF02399685
Elder, John F., Turner Bruce J. (1995): Concerted Evolution of Repetitive DNA Sequences in Eukaryotes. The Quarterly Review of Biology, 70, 297-320 https://doi.org/10.1086/419073
Ferranti P., Facchiano A., Zappacosta F., Vincenti D., Rullo R., Masala B., Di Luccia A. (2001): Primary structure of α-globin chains from river buffalo (Bubalus bubalis L.) hemoglobins. Journal of Protein Chemistry, 20, 171–179.https://doi.org/10.1023/A:1011027924391
Finnegan David J. (1989): Eukaryotic transposable elements and genome evolution. Trends in Genetics, 5, 103-107 https://doi.org/10.1016/0168-9525(89)90039-5
Ganley A.R.D. (2013): Concerted evolution. In: Maloy S., Hughes K. (eds): Brenner’s Encyclopedia of Genetics, Vol 2. Academic Press, San Diego, USA, 126–130.. , ,
Goossens M., Kan Y.Y. (1981): DNA analysis in the diagnosis of hemoglobin disorders. Methods in Enzymology, 76, 805–817.
Iorio Mario, Vincenti Donatella, Annunziata Mario, Rullo Rosario, Bonamassa Raffaele, Di Luccia Aldo, Pieragostini Elisa (2004): Biochemical and molecular investigations on qualitative and quantitative Hb polymorphism in the river buffalo (Bubalus bubalis L.) population reared in Southern Italy. Genetics and Molecular Biology, 27, 167-173 https://doi.org/10.1590/S1415-47572004000200007
Jiang Y., Wang X., Kijas J. W., Dalrymple B. P. (2015): Beta-globin gene evolution in the ruminants: evidence for an ancient origin of sheep haplotype B
. Animal Genetics, 46, 506-514 https://doi.org/10.1111/age.12318
Kleinschmidt T., Sgouros J.G. (1987): Hemoglobin sequences. Biological Chemistry Hoppe-Seyler, 368, 579–615.
Kumar Sudhir, Stecher Glen, Li Michael, Knyaz Christina, Tamura Koichiro, Battistuzzi Fabia Ursula (2018): MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35, 1547-1549 https://doi.org/10.1093/molbev/msy096
Liao Daiqing (1999): Concerted Evolution: Molecular Mechanism and Biological Implications. The American Journal of Human Genetics, 64, 24-30 https://doi.org/10.1086/302221
Murphy M., Brown G., Wallin C., Tatusova T., Pruitt K., Murphy T., Maglott D. (2006): Gene Help: Integrated Access to Genes of Genomes in the Reference Sequence. Collection. Available from https://www.ncbi.nlm.nih.gov/books/NBK3841/ (accessed Jan 10, 2018).
Perutz M.F. (1990): Frequency of abnormal human haemoglobins caused by C → T transitions in CpG dinucleotides. Journal of Molecular Biology, 213, 203-206 https://doi.org/10.1016/S0022-2836(05)80178-0
Philipsen Sjaak, Hardison Ross C. (2018): Evolution of hemoglobin loci and their regulatory elements. Blood Cells, Molecules, and Diseases, 70, 2-12 https://doi.org/10.1016/j.bcmd.2017.08.001
Pieragostini Elisa, Alloggio Ingrid, Petazzi Ferruccio (2010): Insights into Hemoglobin Polymorphism and Related Functional Effects on Hematological Pattern in Mediterranean Cattle, Goat and Sheep. Diversity, 2, 679-700 https://doi.org/10.3390/d2040679