The complete sequence of the gene encoding bovine alpha s2-casein

Evidence of additive genetic variation for major milk proteins in dairy cows: A meta-analysis

In the past, there have been reports of genetic parameters for milk proteins in various dairy cattle populations. The high variability among genetic parameter estimates has been caused by this. This study aimed to use a random-effects meta-analysis model to compile published estimates of genetic parameter for major milk proteins of α-lactalbumin, β-lactoglobulin, sum of whey proteins, casein, αs1-casein, αs2-casein, β-casein, and κ-casein in dairy cows. The study used a total of 140 heritability and 256 genetic correlation estimates from 23 papers published between 2004 and 2022. The estimated range of milk protein heritability is from 0.284 (for α-lactalbumin in milk) to 0.596 (for sum of whey proteins). The genetic correlation estimates between casein and milk yield, milk fat and protein percentages were -0.461, 0.693, and 0.976, respectively (p < 0.05). The genetic correlation estimates between milk proteins expressed as a percentage of milk were significant and varied from 0.177 (between β-lactoglobulin and κ-casein) to 0.892 (between αs1-casein and αs2-casein). Moderate-to-high heritability estimates for milk proteins and their low genetic associations with milk yield and composition indicated the possibility for improving milk proteins in a genetic selection plan with negligible correlated effects on production traits in dairy cows.

Sequencing and Characterization of αs2-Casein Gene (CSN1S2) in the Old-World Camels Have Proven Genetic Variations Useful for the Understanding of Species Diversification

The CSN1S2 gene encodes αs2-casein, the third most abundant protein in camel milk. Despite its importance in foals, human nutrition, and dairy processing, the CSN1S2 gene in camels has received little attention. This study presents the first complete characterization of the CSN1S2 gene sequence in Old-World camels (Camelus bactrianus and Camelus dromedarius). Additionally, the gene promoter, consisting of 752 bp upstream of exon 1, was analyzed. The entire gene comprises 17 exons, ranging in length from 24 bp (exons 4, 8, 11, and 13) to 280 bp (exon 17). Interesting was the identification of the exon 12 in both species. The promoter analysis revealed 24 putative binding sites in the Bactrian camel and 22 in dromedary camel. Most of these sites were typical elements associated with milk protein, such as C/EBP-α, C/EBP-β, Oct-1, and AP1. The SNP discovery showed relatively high genetic diversity compared to other camel casein genes (CSN1S1, CSN2, and CSN3), with a total of 34 polymorphic sites across the two species. Particularly noteworthy is the transition g.311G>A in the CSN1S2 promoter, creating a new putative consensus binding site for a C/EBP-β in the Bactrian camel. At the exon level, two novel variants were found. One was detected in exon 6 of the Bactrian camel (g.3639C>G), resulting in an amino acid replacement, p.36Ile>Met. The second variant was found in noncoding exon 17 of dromedary CSN1S2 (g.1511G>T). Although this mutation occurs in the 3'-UnTranslated Region, it represents the first example of exonic polymorphism in the CSN1S2 for this species. This SNP also affects the binding sites of different microRNAs, including the seed sequence of the miRNA 4662a-3p, highlighting its role as a regulatory factor for CSN1S2 gene. A PCR-RFLP was set up for genotyping a dromedary Tunisian population (n = 157), and the minor allele frequency was found to be 0.27 for the G allele, indicating a potential yield improvement margin. The interspersed elements (INEs) analysis revealed 10 INEs covering 7.34% and 8.14% of the CSN1S2 sequence in the Bactrian and dromedary camels, respectively. Furthermore, six elements (A, B, F, H, I, and L) are shared among cattle and camels and are partially found in other ruminants, suggesting a common ancestral origin of these retrotransposons. Conversely, elements C, D, E, and G are specific to camels.

TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors

BACKGROUND

Eukaryotic gene expression is controlled by cis-regulatory elements (CREs), including promoters and enhancers, which are bound by transcription factors (TFs). Differential expression of TFs and their binding affinity at putative CREs determine tissue- and developmental-specific transcriptional activity. Consolidating genomic datasets can offer further insights into the accessibility of CREs, TF activity, and, thus, gene regulation. However, the integration and analysis of multimodal datasets are hampered by considerable technical challenges. While methods for highlighting differential TF activity from combined chromatin state data (e.g., chromatin immunoprecipitation [ChIP], ATAC, or DNase sequencing) and RNA sequencing data exist, they do not offer convenient usability, have limited support for large-scale data processing, and provide only minimal functionality for visually interpreting results.

RESULTS

We developed TF-Prioritizer, an automated pipeline that prioritizes condition-specific TFs from multimodal data and generates an interactive web report. We demonstrated its potential by identifying known TFs along with their target genes, as well as previously unreported TFs active in lactating mouse mammary glands. Additionally, we studied a variety of ENCODE datasets for cell lines K562 and MCF-7, including 12 histone modification ChIP sequencing as well as ATAC and DNase sequencing datasets, where we observe and discuss assay-specific differences.

CONCLUSION

TF-Prioritizer accepts ATAC, DNase, or ChIP sequencing and RNA sequencing data as input and identifies TFs with differential activity, thus offering an understanding of genome-wide gene regulation, potential pathogenesis, and therapeutic targets in biomedical research.

Redundant and non-redundant cytokine-activated enhancers control Csn1s2b expression in the lactating mouse mammary gland

Enhancers are transcription factor platforms that synergize with promoters to control gene expression. Here, we investigate enhancers that activate gene expression several hundred-fold exclusively in the lactating mouse mammary gland. Using ChIP-seq for activating histone marks and transcription factors, we identify two candidate enhancers and one super-enhancer in the Csn1s2b locus. Through experimental mouse genetics, we dissect the lactation-specific distal enhancer bound by the mammary-enriched transcription factors STAT5 and NFIB and the glucocorticoid receptor. While deletions of canonical binding motifs for NFIB and STAT5, individually or combined, have a limited biological impact, a non-canonical STAT5 site is essential for enhancer activity during lactation. In contrast, the intronic enhancer contributes to gene expression only in late pregnancy and early lactation, possibly by interacting with the distal enhancer. A downstream super-enhancer, which physically interacts with the distal enhancer, is required for the functional establishment of the Csn1s2b promoter and gene activation. Lastly, NFIB binding in the promoter region fine-tunes Csn1s2b expression. Our study provides comprehensive insight into the anatomy and biology of regulatory elements that employ the JAK/STAT signaling pathway and preferentially activate gene expression during lactation.

Enhancers and promoters work together to actively regulate gene expression affecting several biological processes. Here, the authors provide molecular insights into the regulation of enhancers and super-enhancers in the Csn1s2b locus during lactation.

Complete CSN1S2 Characterization, Novel Allele Identification and Association With Milk Fatty Acid Composition in River Buffalo

The αs2-casein is one of the phosphoproteins secreted in all ruminants' milk, and it is the most hydrophilic of all caseins. However, this important gene (CSN1S2) has not been characterized in detail in buffaloes with only two alleles detected (reported as alleles A and B), and no association studies with milk traits have been carried out unlike what has been achieved for other species of ruminants. In this study, we sequenced the whole gene of two Mediterranean river buffalo homozygotes for the presence/absence of the nucleotide C (g.7539G>C) realized at the donor splice site of exon 7 and, therefore, responsible for the skipping of the same exon at mRNA level (allele B). A high genetic variability was found all over the two sequenced CSN1S2 alleles. In particular, 74 polymorphic sites were found in introns, six in the promoter, and three SNPs in the coding region (g.11072C>T, g.12803A>T, and g.14067A>G) with two of them responsible for amino acid replacements. Considering this genetic diversity, those found in the database and the SNP at the donor splice site of exon 7, it is possible to deduce at least eight different alleles (CSN1S2 A, B, B1, B2, C, D, E, and F) responsible for seven different possible translations of the buffalo αs2-casein. Haplotype data analysis suggests an evolutionary pathway of buffalo CSN1S2 gene consistent with our proposal that the published allele CSN1S2 A is the ancestral αs2-CN form, and the B2 probably arises from interallelic recombination (single crossing) between the alleles D and B (or B1). The allele CSN1S2 C is of new identification, while CSN1S2 B, B1, and B2 are deleted alleles because all are characterized by the mutation g.7539G>C. Two SNPs (g.7539G>C and g.14067A>G) were genotyped in 747 Italian buffaloes, and major alleles had a relative frequency of 0.83 and 0.51, respectively. An association study between these SNPs and milk traits including fatty acid composition was carried out. The SNP g.14067A>G showed a significant association (P < 0.05) on the content of palmitic acid in buffalo milk, thus suggesting its use in marker-assisted selection programs aiming for the improvement of buffalo milk fatty acid composition.

Non-parametric association analysis of additive and dominance effects of casein complex SNPs on milk content and quality in Murciano-Granadina goats

Goat milk casein proteins (αS1, αS2, β and κ) are encoded by four loci (CSN1S1, CSN1S2, CSN2 and CSN3, respectively) clustered within 250 kb in chromosome 6. In this study, 159 Murciano-Granadina goats were genotyped for 48 SNPs within the entire casein region. Phenotypes on milk yield and components were obtained from 2,594 dairy registries. Additive and dominance effects on milk composition and quality were studied using non-parametric tests and principal component analysis to prevent SNPs multicollinearity. Two deletions in exon 4 (CSN1S1 and CSN3), one in exon 7 (CSN2) and one in exon 15 (CSN1S2) have been found at frequencies ranging from 0.12 to 0.50. Bonferroni-corrected significant SNP additive and dominance effects were found for milk yield, fat, protein, dry matter and lactose, and somatic cells. Exons 15 and 7 were significantly associated with milk yield and components except for lactose and somatic cells, while exon 4 was significantly associated with milk yield and components except for protein and dry matter. SNPs' associations with somatic cells were less frequent and weaker than those with milk yield and components. As caseins increase, somatic cells decrease, reducing milk enzymatic activity and consumption suitability. Hence, including molecular information in breeding schemes may promote production efficiency, as selecting against undesirable alleles could prevent the compromises derived from their dominance effects.

Alternative splicing events expand molecular diversity of camel CSN1S2 increasing its ability to generate potentially bioactive peptides

In a previous study on camel milk from Kazakhstan, we reported the occurrence of two unknown proteins (UP1 and UP2) with different levels of phosphorylation. Here we show that UP1 and UP2 are isoforms of camel αs2-CN (αs2-CNsv1 and αs2-CNsv2, respectively) arising from alternative splicing events. First described as a 178 amino-acids long protein carrying eight phosphate groups, the major camel αs2-CN isoform (called here αs2-CN) has a molecular mass of 21,906 Da. αs2-CNsv1, a rather frequent (35%) isoform displaying a higher molecular mass (+1,033 Da), is present at four phosphorylation levels (8P to 11P). Using cDNA-sequencing, αs2-CNsv1 was shown to be a variant arising from the splicing-in of an in-frame 27-nucleotide sequence encoding the nonapeptide ENSKKTVDM, for which the presence at the genome level was confirmed. αs2-CNsv2, which appeared to be present at 8P to 12P, was shown to include an additional decapeptide (VKAYQIIPNL) revealed by LC-MS/MS, encoded by a 3'-extension of exon 16. Since milk proteins represent a reservoir of biologically active peptides, the molecular diversity generated by differential splicing might increase its content. To evaluate this possibility, we searched for bioactive peptides encrypted in the different camel αs2-CN isoforms, using an in silico approach. Several peptides, putatively released from the C-terminal part of camel αs2-CN isoforms after in silico digestion by proteases from the digestive tract, were predicted to display anti-bacterial and antihypertensive activities.

Effects of CSN1S2 Genotypes on Economic Traits in Chinese Dairy Goats

The aim of this study was to investigate allele frequencies at the CSN1S2 locus in two Chinese dairy goat breeds and the effects of its variation on dairy goat economic traits. Seven hundred and eight goats from Xinong Saanen (XS, n = 268) and Guanzhong (GZ, N = 440) breeds were selected. The milk samples of 268 XS goats were collected during the middle of lactation, body size parameters (708 goats) and daily milk yield (202 goats) were registered. The RFLP (restriction fragment length polymorphism) and SSCP (single strand conformation polymorphism) were used to detect the polymorphisms in CSN1S2. The Hardy-Weinberg (HW) equilibrium and the associations between body size, milk yield and composition and the genotypes were calculated. The results revealed that only A and F CSN1S2 alleles were found in the two Chinese dairy goat breeds. Allelic frequencies of A and F were 0.795, 0.205 and 0.739, 0.261 in Xinong Saanen and Guanzhong population respectively. Xinong Saanen breed was in Hardy-Weinberg equilibrium, while Guanzhong breed deviated from Hardy-Weinberg equilibrium (p<0.05). The association of polymorphism with economic traits indicated that the goats with FF genotype have higher milk fat and total solid concentration than those with AA and AF genotypes (p<0.05).

Short communication: molecular genetic characterization of ovine alpha(S1)-casein allele H caused by alternative splicing

Sequencing of ovine CSN1S1*H cDNA showed an absence of exon 8 in comparison with GenBank sequences; the absence was confirmed by protein sequencing. We demonstrated that this allelic aberration is the result of a deletion of 4 nucleotides, the last 3 of exon 8 and the first 1 of intron 8, which are replaced by an insertion of 13 nucleotides in the DNA sequence. The insertion is a precise duplication of a part of the adjacent intronic sequence of CSN1S1*C''. These sequence differences result in an inactivation of the splice donor sequence distal to exon 8, leading to upstream exon skipping during the serial splice reactions of the ovine CSN1S1*H pre-mRNA, and may affect the specific casein expression as well as protein characteristics.

Identification and quantification of alphaS1, alphaS2, beta, and kappa-caseins in water buffalo milk by reverse phase-high performance liquid chromatography and mass spectrometry

A method for the simultaneous quantitation of alpha(S1), alpha(S2), beta, and kappa-caseins in water buffalo (Bubalus bubalis) milk using reverse phase high-performance liquid chromatography was developed. The molecular masses of the peaks separated by the described chromatographic protocol were determined by ESI-MS. alpha(S1)- and kappa-caseins were found to be heteromorphic in several individual milk samples. In particular, alpha(S1)-casein showed two peaks with a molecular mass of 23,490 Da and 23,516 Da, and kappa-casein showed three peaks with molecular masses of 19,165 Da, 19,177 Da, and 19,247 Da. Only one form for beta-casein (24,033 Da) and alpha(S2)-casein (22,741 Da) were detected. The mean values of casein fraction concentration observed throughout the individual samples were 8.89 gL(-1) with a relative standard deviation (RSD) of 20% for alpha(S1)-casein, 5.08 gL(-1) with a RSD of 25% for alpha(S2)-casein, 20.91 gL(-1) with a RSD of 16% for beta-casein, and 4.13 gL(-1) with a RSD of 24% for kappa-casein. Linear and second-order polynomial correlations with total nitrogen were calculated for all casein fractions.

Casein haplotypes and their association with milk production traits in Norwegian Red cattle

A high resolution SNP map was constructed for the bovine casein region to identify haplotype structures and study associations with milk traits in Norwegian Red cattle. Our analyses suggest separation of the casein cluster into two haplotype blocks, one consisting of the CSN1S1, CSN2 and CSN1S2 genes and another one consisting of the CSN3 gene. Highly significant associations with both protein and milk yield were found for both single SNPs and haplotypes within the CSN1S1-CSN2-CSN1S2 haplotype block. In contrast, no significant association was found for single SNPs or haplotypes within the CSN3 block. Our results point towards CSN2 and CSN1S2 as the most likely loci harbouring the underlying causative DNA variation. In our study, the most significant results were found for the SNP CSN2_67 with the C allele consistently associated with both higher protein and milk yields. CSN2_67 calls a C to an A substitution at codon 67 in β-casein gene resulting in histidine replacing proline in the amino acid sequence. This polymorphism determines the protein variants A1/B (CSN2_67 A allele) versus A2/A3 (CSN2_67 C allele). Other studies have suggested that a high consumption of A1/B milk may affect human health by increasing the risk of diabetes and heart diseases. Altogether these results argue for an increase in the frequency of the CSN2_67 C allele or haplotypes containing this allele in the Norwegian Red cattle population by selective breeding.

Molecular characterization of bovine CSN1S2*B and extensive distribution of zebu-specific milk protein alleles in European cattle

The B allele of the bovine alpha (S2)-casein gene (CSN1S2) was characterized at the molecular level and the distribution of zebu-specific milk protein alleles was determined in 26 cattle breeds originating from 3 continents. The CSN1S2*B allele is characterized by a C --> T transition affecting nucleotide 17 of exon 3, which leads to a change in the eighth amino acid of the mature protein, from Ser to Phe (i.e., TCC --> TTC). DNA-based methods were developed to identify carriers of CSN1S2*B and the other alleles (CSN1S2*A, C, and D) at the same locus. CSN1S2*B and other zebu-specific milk protein alleles and casein haplotypes are widely distributed in European cattle breeds, particularly those of southeastern origin. Alleles CSN1S2*B and CSN3*H are important in searching for zebu imprints in European cattle breeds. Diversity estimates at the milk protein loci were highest in the zebus followed by southeastern European taurines. Anatolian Black had the highest number of zebu alleles among European taurines. Common, group, and intergroup haplotypes occurred in the breeds and demonstrated relationships that concurred with developmental histories, genetic makeup, and, in particular, exposed the extent of zebu influence on southeastern European cattle.

Cloning and characterization of alpha(s2)-casein gene of Riverine buffalo

The present study was carried out to characterize the alpha(s2)-casein gene in Riverine buffalo. Total RNA was extracted from the mammary tissue of buffalo and alpha(s2)-casein cDNA were synthesized by RT-PCR, then cloned using pDRIVE-cloning vector and sequenced. The sequencing revealed that the size of alpha(s2)-casein was 669 bp with GC content of 41.11%. The gene encoded for 222 amino acid precursors and that it possessed 15 amino acids signal peptide. The similarity of buffalo alpha(s2)-casein mRNA sequence with that of cattle, sheep, goat, pig and camel were estimated as 97.9, 93.6, 93.4, 73.5 and 73.0%, respectively. In the phylogenetic trees, constructed from the data of the alpha(s2)-casein mRNA sequences as well as protein sequences, it has been observed that the cattle and buffalo were in the same group whereas sheep and goat formed another group. The camel and swine were placed in two separate groups.

A review of protein structure and gene organisation for proteins associated with mineralised tissue and calcium phosphate stabilisation encoded on human chromosome 4

Several proteins associated with mineralised tissue (teeth and bone) or involved in calcium phosphate stabilisation in the body fluids, milk and saliva have been mapped to the q arm of human chromosome 4. These include the dentine/bone proteins dentine sialophosphoprotein (DSPP), dentine matrix protein 1 (DMP1), bone sialoprotein (BSP), matrix extracellular phosphoglycoprotein, osteopontin (OPN), enamelin, ameloblastin, milk caseins, salivary statherin, and proline-rich proteins. The proposed function of those that are multiphosphorylated is: (i) the stabilisation of calcium phosphate in solution (e.g. casein, statherin) preventing spontaneous precipitation and seeded-crystal growth or (ii) promoting biomineralisation (e.g. the phosphophoryn domain of DSPP), where the protein described as a template macromolecule, is proposed to act as a nucleator/promoter of crystal growth. The genes of these proteins have been subjected to conserved chromosomal synteny during mammalian evolution. The multiphosphorylated proteins statherin, caseins, phosphophoryn, BSP and OPN have been characterised as intrinsically disordered. The codon usage patterns for the amino acid serine reveal a bias for AGC and AGT codons within the human genes dspp, dmp1 and bsp, mouse dspp and dmp1 but not significantly for statherin or caseins. This pattern was also observed in the gene encoding hen phosvitin that also contains stretches of multiphosphorylated serines and in the dmp1 gene sequences of mammalian, reptilian and avian classes. In conclusion, these intrinsically disordered multiphosphorylated proteins are the translation products of genes displaying examples of codon usage bias, internal repeats and conserved chromosomal synteny within the mammalian class.

Nomenclature of the Proteins of Cows’ Milk—Sixth Revision

This report of the American Dairy Science Association Committee on the Nomenclature, Classification, and Methodology of Milk Proteins reviews changes in the nomenclature of milk proteins necessitated by recent advances of our knowledge of milk proteins. Identification of major caseins and whey proteins continues to be based upon their primary structures. Nomenclature of the immunoglobulins consistent with new international standards has been developed, and all bovine immunoglobulins have been characterized at the molecular level. Other significant findings related to nomenclature and protein methodology are elucidation of several new genetic variants of the major milk proteins, establishment by sequencing techniques and sequence alignment of the bovine caseins and whey proteins as the reference point for the nomenclature of all homologous milk proteins, completion of crystallographic studies for major whey proteins, and advances in the study of lactoferrin, allowing it to be added to the list of fully characterized milk proteins.

Mineralized tissue and vertebrate evolution: the secretory calcium-binding phosphoprotein gene cluster

Gene duplication creates evolutionary novelties by using older tools in new ways. We have identified evidence that the genes for enamel matrix proteins (EMPs), milk caseins, and salivary proteins comprise a family descended from a common ancestor by tandem gene duplication. These genes remain linked, except for one EMP gene, amelogenin. These genes show common structural features and are expressed in ontogenetically similar tissues. Many of these genes encode secretory Ca-binding phosphoproteins, which regulate the Ca-phosphate concentration of the extracellular environment. By exploiting this fundamental property, these genes have subsequently diversified to serve specialized adaptive functions. Casein makes milk supersaturated with Ca-phosphate, which was critical to the successive mammalian divergence. The innovation of enamel led to mineralized feeding apparatus, which enabled active predation of early vertebrates. The EMP genes comprise a subfamily not identified previously. A set of genes for dentine and bone extracellular matrix proteins constitutes an additional cluster distal to the EMP gene cluster, with similar structural features to EMP genes. The duplication and diversification of the primordial genes for enameldentinebone extracellular matrix may have been important in core vertebrate feeding adaptations, the mineralized skeleton, the evolution of saliva, and, eventually, lactation. The order of duplication events may help delineate early events in mineralized skeletal formation, which is a major characteristic of vertebrates.

Structure and regulation of the murine gamma-casein gene

The murine casein locus consists of five genes, which are coordinately regulated during mammary development. The levels of casein-specific mRNAs in mammary epithelial cells increase during the second half of pregnancy and remain high during lactation. The murine gamma-casein gene, which corresponds to the alphaS2-casein gene in ruminants, was isolated from a mouse bacterial artificial chromosome (BAC) library (strain 129SV). The gene contains 14 exons, which are distributed over 14 kb of DNA sequence. The expression pattern of the murine gamma-casein gene mimics that of the neighbouring beta-casein gene in terms of developmental induction in vivo. In cell culture, both the beta- and gamma-casein promoter are synergistically induced by prolactin and glucocorticoids. Glucocorticoid induction is critically dependent on prolactin-mediated activation of STAT5 in both promoters. Several consensus STAT5 binding sites were identified in the gamma-casein promoter, some of which may have an additive effect on prolactin induction. mRNA levels of gamma- and beta-casein are similar in lactating mammary tissue. However, promoter segments derived from the gamma-casein gene are significantly less active in cell culture than comparable fragments of the beta-casein promoter. Promoter hybrids between the gamma- and beta-casein promoters revealed that the critical sequences which are responsible for the different in vitro activity are located in a short promoter proximal region.

Multispecies comparison of the casein gene loci and evolution of casein gene family

Caseins, the major milk proteins, are present in a genomic cluster spanning 250-350 kb. The divergence at the coding level between human, rodent, and cattle sequences is rather extensive for most of the genes in this region. Nevertheless, comparative analysis of genomic sequences harboring the casein gene cluster region of these species (with equal evolutionary distances 79-88 Myr) shows that the organization and orientation of the genes is highly conserved. The conserved gene structure indicates that the molecular diversity of the casein genes is achieved through variable use of exons in different species and high evolutionary divergence. Comparative analysis also revealed the presence within two species of uncharacterized casein family members and ruled out the previously held notion that another gene family, located in this region, is primate-specific. Several other new genes as well as conserved noncoding sequences with potential regulatory functions were identified. All genes identified in this region are, or are predicted to be, secreted proteins involved in mineral homeostasis, nutrition, and/or host defense, and are mostly expressed in the mammary and/or salivary glands. These observations suggest a possible common ancestry for the genes in this region.

An allele associated with a non-detectable amount of alpha s2 casein in goat milk

The goat CSN1S2 locus is characterized by the presence of three alleles, A, B and C, all associated with about 2.5 g/l of protein per allele. The SDS-PAGE analysis of 441 individual milk samples obtained from goats belonging to a population reared in Southern Italy showed that the milk produced by three goats did not apparently contain alpha s2-casein, whereas milk produced by 37 goats showed a less intense electrophoretic band of this casein fraction (about 50%). These results can be explained by hypothesizing the presence of another allele at this locus, CSN1S2o, associated with a 'null' content of alpha s2-casein. Southern blot, PCR and PCR-RFLP analyses of the DNA region containing the CSN1S2 gene of individuals producing milk with and without alpha s2-casein did not show differences between the two groups. As a consequence, goats producing milk without alpha s2-casein carry an apparently intact gene. The first results obtained by sequencing part of the CSN1S2o allele revealed a G-->A transition at nucleotide 80 of the 11th exon which creates a stop codon and could be responsible for the absence of the alpha s2-casein in goat milk. This mutation eliminates a NcoI restriction site. A test based on this polymorphism has been established in order to identify carriers of the CSN1S2o allele.

Comparative aspects of milk caseins

The caseins comprise the major protein component of milk of most mammals and are secreted as micelles that also carry high concentrations of calcium. They are phosphoproteins that represent the products of four genes, equivalent to those that encode the bovine alpha s1, alpha s2, beta, and kappa-caseins. There is considerable variation in the relative proportions of the particular caseins across species. The primary sequences of the alpha s1, alpha s2, and beta-caseins also show considerable species variation consistent with rapidly evolving genes that are proposed to have a common precursor. In contrast, the kappa-caseins exhibit features that demonstrate a separate origin and function where they are proposed to stabilise the micelle structure. This review focuses on comparative aspects of the caseins across a number of species for which information is now available.

Regulation of milk protein gene expression

Studies using both transgenic mice and transfected mammary epithelial cells have established that composite response elements containing multiple binding sites for several transcription factors mediate the hormonal and developmental regulation of milk protein gene expression. Activation of signal transduction pathways by lactogenic hormones and cell-substratum interactions activate transcription factors and change chromatin structure and milk protein gene expression. The casein promoters have binding sites for signal transducers and activators of transcription 5, Yin Yang 1, CCAAT/enhancer binding protein, and the glucocorticoid receptor. The whey protein gene promoters have binding sites for nuclear factor I, as well as the glucocorticoid receptor and the signal transducers and activators of transcription 5. The functional importance of some of these factors in mammary gland development and milk protein gene expression has been elucidated by studying mice in which some of these factors have been deleted.

SINEs and LINEs share common 3' sequences: a review

There are now five reported examples in which the 3' ends of tRNA-derived SINEs are derived from the 3' ends of LINEs. These examples include representative sequences from turtles, fish, mammals and plants (Ohshima et al., 1996, Mol. Cell. Biol., 16, 3756 3764; Okada and Hamada, 1997, J. Mol. Evol. 44, Suppl 1:S52-S56). In this review, we discuss the generality of this architecture of SINEs, adding new examples of pairs of SINEs and LINEs, which include one complete and two probable examples from this laboratory and one complete example from the laboratory of Arian Smit. This organization of SINEs and LINEs provides the basis for a simple general scheme by which SINEs might acquire retropositional activity.

Physical mapping of the murine casein locus reveals the gene order as alpha-beta-gamma-epsilon-kappa

The murine casein locus has been characterized by long-range restriction mapping and the analysis of large fragment genomic clones. Cloned sequences from five mouse casein genes (alpha, beta, gamma, epsilon, kappa) were used to screen a murine (strain 129) genomic library in a bacterial artificial chromosome vector (BAC). Of the nine clones isolated, two contained three casein genes alpha, beta, gamma and gamma, epsilon, kappa, respectively. The following combinations were found in other clones: alpha + beta, beta + gamma; and gamma + epsilon. Thus, the gene order in the locus can be deduced to be alpha-beta-gamma-epsilon-kappa. This order was confirmed by restriction analysis of the clones. A contig map of the clones and flanking sequences has been established by characterizing seven BAC clones, which together span approximately 470 kb. Long-range restriction analysis of genomic DNA indicates that the murine casein locus is confined to a 250-kb partial Xho I fragment. The alpha and beta casein genes were shown to be arranged in a tail-to-tail orientation.

Structure and expression of the mouse casein gene locus

The analysis of yeast artificial chromosomes (YACs) containing the complete mouse casein gene locus revealed the presence of five casein genes, alpha-, beta-, gamma-, delta-, and kappa-casein, in this order, in the locus. The alpha- and beta-casein genes are only 10 kb apart and have convergent transcriptional orientations. The distance between the beta-casein gene and the alpha s2-like gamma-casein gene is about 70 kb, and these genes have divergent transcriptional orientations. The gamma- and delta-casein genes, both encoding a alpha s2-like casein, are linked within 60 kb and convergently transcribed. The kappa-casein gene is located about 100 kb from the delta-gene. Except for the presence of the delta-casein gene, the organization of the mouse casein locus resembles that of the bovine locus, including the transcriptional orientation of the genes. In contrast to the other casein genes, which are strongly induced at mid-lactation, expression of the delta-casein gene is abruptly induced upon parturition. Comparative analysis of alpha s2-like sequences from various species suggests that the ancestral alpha s2-like gene duplicated around the time of radiation of the rodent and artiodactylid ancestors.

The 3' ends of tRNA-derived SINEs originated from the 3' ends of LINEs: a new example from the bovine genome

Our group demonstrated recently that the 3' ends of several families of tRNA-derived SINEs (short interspersed repetitive elements) originated from the 3' ends of LINEs (long interspersed repetitive elements) [Ohshima et al. (1996) Mol. Cell. Biol. 16:3756-3764]. Two fully characterized examples of such organization were provided by the tortoise Pol III/SINE and the salmonid HpaI family of SINEs, and two probable examples were provided by the tobacco TS family of SINEs and the salmon SmaI family of SINEs. This organization of SINEs can explain their potential to retropose in the genome since it appears reasonable that the sites for recognition of LINEs by reverse transcriptase should be located within the 3'-end sequences of LINEs. We now add another example to this category of SINEs. In the bovine genome, there are Bov-tA SINEs, which belong to the superfamily of tRNA-derived families of SINEs, and Bov-B LINEs, which were recently demonstrated to belong to a LINE family. Moreover, Bov-tA and Bov-B share the same 3'-end tail. We propose a possible scenario whereby the composite structure of the bovine Bov-tA family of SINEs might have been generated from the Bov-B family of LINEs during evolution.

Structures and functionalities of milk proteins

During the last decade, marked progress has been made in the study of the fine details of the structures of milk proteins such as caseins, beta-lactoglobulin, alpha-lactalbumin, and lactotransferrin. Many of the functional properties of the individual milk proteins, as well as the milk protein products, may be described at the molecular level. This article is an attempt to thoroughly review the three-dimensional structures of major milk proteins, and to correlate them with the functional aspects of these proteins as food ingredients.

FISH mapping of the alpha-S2 casein gene on river buffalo and cattle chromosomes identifies a nomenclature discrepancy in the bovine karyotype

A mixture of five genomic clones spanning the alpha-S2 casein gene (CSN1S2) were mapped to river buffalo (Bubalus bubalis L.) and cattle (Bos taurus L.) chromosomes by fluorescence in situ hybridization (FISH) and R-banding. Clear probe hybridization signals were detected on river buffalo chromosome 7q, band 32, and the homologous cattle chromosome. These mapping data allow the indirect assignment of the entire cattle U15 syntenic group to river buffalo chromosome 7. The assignment of U15 to river buffalo chromosome 7 is discussed in the light of chromosomal nomenclature discrepancies involving the homologous cattle chromosome.

Mammary gland expression of transgenes and the potential for altering the properties of milk

Transgenic animals are a useful in vivo experimental model for assessing the ability and impact of foreign gene expression in a biological system. Transgenic mice are most commonly used, while transgenic sheep, goats, pigs and cows have also been developed for specific, "applied" purposes. Most of the work directed at targeting expression of transgenes to the mammary gland of an animal, by using a milk gene promoter, has been with the intent of either studying promoter function or recovering the desired protein from the milk. Transgenic technology can also be used to alter the functional and physical properties of milk resulting in novel manufacturing properties. The properties of milk have been altered by adding a new protein with the aim of improving the milk, not of recovering the protein for other uses.

Expression analysis of the individual bovine beta-, alpha s2- and kappa-casein genes in transgenic mice

To identify cis-acting regulatory elements involved in the regulation of expression of the casein genes, the bovine beta-, alpha s2- and kappa-casein genes were isolated from cosmid libraries and introduced into the murine germline. Bovine casein expression was analysed at the RNA and protein level. The bovine beta-casein gene, including 16 kb of 5'- and 8 kb of 3'-flanking region, appeared to be expressed in all 12 transgenic mouse lines analysed. In 50% of these lines expression levels in milk exceeded 1 mg/ml. Three lines displayed expression levels comparable with or well above (20 mg/ml) the beta-casein levels in bovine milk. Transgene expression was restricted to the mammary gland. Strong induction of expression occurred at parturition and thus resembled the bovine rather than the murine pattern. In spite of this high-level tissue-specific and developmentally regulated expression, beta-casein expression levels were integration-site-dependent, suggesting that not all elements involved in regulation of expression were included in this beta-casein clone. Neither the bovine alpha s2- nor the kappa-casein gene, including 8 kb and 5 kb of 5'- and 1.5 kb and 19 kb of 3'-flanking sequences respectively, were properly expressed in transgenic mice. However, they were transcribed in stably transfected mouse mammary epithelial cells. This indicates that regulatory elements required for high-level, mammary gland-specific expression are not present in the alpha s2- and kappa-casein clones used in this study and are probably located elsewhere in the casein gene locus.

Porcine SINE-associated microsatellite markers: evidence for new artiodactyl SINEs

Approximately 24% (170/710) of porcine (dG-dT)n.(dC-dA)n microsatellites isolated in our laboratory are associated with a previously described porcine Short Interdispersed Element (SINE) termed PRE-1 SINE. Another 5.6% (40/710) of the microsatellites were adjacent to two previously unidentified SINE sequences, which we have designated ARE-1P (Artiodactyl Repetitive Element-1 Porcine) and ARE-2P. The ARE repeats were also found in bovine microsatellite and genomic sequences in the GenBank database. Genotypic information was obtained from 68.9% of primers where at least one primer sequence was obtained from the PRE-1 SINE and 66.6% of primer pairs designed from the ARE SINEs. The use of primers derived from SINEs significantly increases the number of primer pairs available for genetic linkage studies in swine.

Bovine Alu-like sequences mediate transposition of a new site-specific retroelement

We describe a new family of 3.1-kb repetitive sequences which is present in the bovine genome. The 5' and 3' ends of the unit are flanked with sequences homologous to the 5' and 3' halves of the bovine Alu-like monomer (BM), respectively. Distribution of the 5' ends of the family members in the genome is not random. They are close to the truncated bovine Alu-like dimer (BD) which, in some cases, is followed by 40-bp repeated sequences containing block A of the RNA polymerase III promoter. The ORFs found within the unit code for peptides homologous to amino-acid sequences characteristic for reverse transcriptases (RT). The family members may be considered as mutant mobile elements whose propagation in the genomes was accomplished by means of a process including site-specific recognition with BD. Because of this, we call this family the bovine dimer-driven family (BDDF).

The identification of nuclear and mitochondrial genes by sequencing randomly chosen clones from a marsupial mammary gland cDNA library

To increase the number of genes that can be mapped to the genome of the tammar wallaby (Macropus eugenii), we sequenced 100 randomly chosen clones from a mammary gland cDNA library. Provisional identifications were made of seven nuclear genes and one mitochondrial gene encoding two caseins, beta-galactosidase, acetyl-coenzyme A synthetase, lipoprotein lipase, inorganic pyrophosphatase, an ATP-dependent RNA helicase, and cytochrome c oxidase I. Highly conserved genes, such as that encoding acetyl-coenzyme A synthetase, were easily identified even from cross-kingdom matches. Genes which are highly divergent, however, such as those encoding the mature casein peptides, could not be aligned with homologues in the databases. Even in an organ where there is high mRNA species redundancy, the sequence characterization of expressed sequence tags provides a rapid means of gene identification for mapping purposes.

Structure and function of milk protein genes

Interspecies comparisons of cDNA and mosaic milk protein genes have confirmed their high rate of evolution, but the overall gene organization has been conserved. The three Ca-sensitive casein genes, which share common motifs in the promoter region and contain similar sequences that encode signal peptide and multiple phosphorylation sites, probably derived from a common ancestor. alpha s1- and alpha s2-casein genes, divided into many small exons, undergo complex splicing, and the deleted caseins arise from exon skipping. The four bovine casein genes are clustered on 200 kb of chromosome 6. alpha-Lactalbumin and beta-lactoglobulin pseudogenes occur in ruminants. Study of the expression of native and modified milk protein genes in mammary cell lines and transgenic animals and DNA footprinting have shown the occurrence of important regulatory motifs in the proximal 5' flanking region, including one recognized by a specific mammary nuclear factor. Good stage- and tissue-specific expression has been obtained in transgenic animals with milk protein genes having less than a 3-kb 5' flanking region. Better knowledge of both the structure and function of milk protein genes, which has already allowed the use of powerful techniques for the rapid identification of alleles, offers the potential for the genetic modification of milk composition.

Bovine alpha s2-casein D is generated by exon VIII skipping

Bovine alpha s2-casein D (CasD) differs from the common type A by the deletion of a stretch of 9 amino acids (aa) starting at a position not precisely known, either at aa 50, 51, or 52. The sequence of cloned PCR-amplified genomic DNA from three homozygous cows, two unrelated females carrying the CasD allele and one carrying the CasA allele, did not reveal any deletion and showed two identical nucleotide (nt) substitutions in the 1.7-kb region of both CasD alleles encompassing codons 43-75 in the cDNA encoding alpha s2-CasA. This strongly suggests that the deleted bovine alpha s2-CasD arises from skipping the 27-nt exon, now identified as exon VIII, which encodes aa 51-59 of alpha s2-CasA. The G-->T transversion (allele A-->D) affecting the last nt of exon VIII, i.e., the 5' consensus splicing site, might be responsible for the altered splicing of the primary transcript of alpha s2-CasD.