Structure and expression of the guinea-pig alpha-lactalbumin gene

A Comparative Review of the Extrinsic and Intrinsic Factors Regulating Lactose Synthesis

Milk is critical for the survival of all mammalian offspring, where its production by a mammary gland is also positively associated with its lactose concentration. A clearer understanding of the factors that regulate lactose synthesis stands to direct strategies for improving neonatal health while also highlighting opportunities to manipulate and improve milk production and composition. In this review we draw a cross-species comparison of the extra- and intramammary factors that regulate lactose synthesis, with a special focus on humans, dairy animals, and rodents. We outline the various factors known to influence lactose synthesis including diet, hormones, and substrate supply, as well as the intracellular molecular and genetic mechanisms. We also discuss the strengths and limitations of various in vivo and in vitro systems for the study of lactose synthesis, which remains an important research gap.

Cloning and comparative analysis of gene structure in promoter site of alpha-s1 casein gene in Naeinian goat and sheep

The 5' end or alpha-S1 casein promoter has a significant role in milk protein gene expression. The understanding of the translation process of alpha-S1 casein mutants will provide us an opportunity to make the best selection in livestock providing more proteins in milk. Blood samples were taken from three hundred of Naeinian goats and sheep, and DNA extraction was done using modified salting out method. Polymerase chain reactions (PCR) were carried out using a specific primer pairs for amplification a fragment of 1133 bp from part of 5'-UTR and exon 1 of alpha s1 casein gene. The AluI and HinfI restriction enzyme treatment of all samples provided the same homozygous AA genotype in both species. Subsequently, one sample of each species was selected and cloned, and the final sequences were analyzed by BioEdit, CLC genomic, Mega4 and DNASIS MAX software. Several polymorphisms are recognized between Naeinian goat and sheep that are presented on motif sites. In this research, the interested location, including exon I and a part of 5', was analyzed, and genetic element comparisons were done between Naeinian goat and sheep. The number and location of probable binding sites can have a crucial role as a result of antagonistic and synergistic effects on gene regulation activities.

Investigating the genetic polymorphism of sheep milk proteins: a useful tool for dairy production

Sheep is the second most important dairy species after cow worldwide, and especially in the Mediterranean and Middle East regions. In some countries, the difficult environmental conditions require a peculiar adaptation and, in these contexts, sheep are able to provide higher quality protein than cattle. In the least-developed countries, the amount of dairy sheep and ovine milk production is progressively increasing. In order to improve dairy productions, in particular those with local connotations, it is necessary to obtain in-depth information regarding milk quality and rheological properties. The genetic polymorphisms of milk proteins are often associated with quantitative and qualitative parameters in milk and are potential candidate markers that should be included in breeding strategies similar to those already available for cattle. Due to the current and growing interest in this topic and considering the large amount of new information, the aim of this study was to review the literature on sheep milk protein polymorphisms with a particular emphasis on recent findings in order to give scientists useful support. Moreover, the effects of different protein variants on milk yield and composition are discussed.

Lack of functional alpha-lactalbumin prevents involution in Cape fur seals and identifies the protein as an apoptotic milk factor in mammary gland involution

BACKGROUND

The mammary gland undergoes a sophisticated programme of developmental changes during pregnancy/lactation. However, little is known about processes involving initiation of apoptosis at involution following weaning. We used fur seals as models to study the molecular process of involution as these animals display a unique mammary gland phenotype. Fur seals have long lactation periods whereby mothers cycle between secreting copious quantities of milk for 2 to 3 days suckling pups on land, with trips to sea alone to forage for up to 23 days during which time mammary glands remain active without initiating apoptosis/involution.

RESULTS

We show the molecular basis by which alpha-lactalbumin (LALBA), a secreted milk protein, is absent in Cape fur seals and demonstrate an apoptotic function for LALBA when exposed to mammary cells.

CONCLUSION

We propose that apoptosis does not occur in fur seal mammary glands due to lack of LALBA in fur seal milk, allowing evasion of involution during a foraging trip. Our work identifies LALBA as a milk factor that feeds back on the mammary gland to regulate involution.

Cloning and characterization of ovine alphaS1-casein gene promoter: a transfection study in rat mammary gland cell line

Promoter regions of milk protein genes are frequently used to produce pharmaceutically and medically important proteins in the mammary gland of transgenic animals and also can be used for the construction of an inducible eukaryotic expression vector. The aim of the present study was to clone, sequence and characterize the regulatory elements in ovine alphaS1-CSNGP. For the first time we have cloned and sequenced region extending from - 2136 to +49 bp containing 5'-flanking region and exon I. Computational analysis of the sequence showed presence of core promoter elements viz., TATA box, CAAT box and initiator sequence. Mammary gland specific sequences included MGF/STAT 5, MPBF, Yu Lee 2, 4 and 5, Oka box C and hormone responsive elements (HRE) viz., GRE, PRE, PRL, IRE and also Polyoma enhancer 3 sequences. Computational analysis data is validated by following the reporter gene expression studies in rat breast cell line. Six reporter gene constructs under the control of full length, proximal, distal, minimal and proximal-distal fused promoter segments were constructed to assess the effect of presence or absence of few selected regulatory elements on expression ability of the promoter. Based on qualitative evaluation of fluorescence, the pGFP-F/VspI showed highest fluorescence followed by pGFP-P, pGFP-F/SpeI, pGFPminimal and pGFP-D.

Computer analysis of distribution of putative cis- and trans-regulatory elements in milk protein gene promoters

Multiple alignment of 28 milk protein gene promoters belonging to seven protein superfamilies is described. In these gene promoters three groups of common motifs were found: group I--specific for all milk protein gene promoters; group II--specific only for one gene superfamily; and group III--motifs shared by several gene superfamilies. Motifs of group I and III do not have any preferential location in the promoters, while group II motifs are located in the proximal part, from -36 to -224. Milk protein gene promoters were analysed for presence of putative binding sites for nine transcription factors important for the expression of this group of genes. The transcription factor binding sites for C/EBP, CTF/NF1, MAF and MGF were found in all promoters investigated. The set of putative transcription factor binding sites or response elements for GRE, IRE, PMF, STR and YY1 is unique for every gene superfamily.

Structure and sequence of the bovine butyrophilin gene

The complete sequence of the bovine butyrophilin gene (BTN) is described and compared with the mouse gene (Btn). Both genes contain seven exons separated by six introns, and the organisation of exons is closely associated with structural domains of the protein. Individual exons of BTN and Btn are 68-87% similar in sequence. There are no canonical TATA or CCAAT boxes associated with the transcription initiation sites in the genes of either species. However, a number of potential binding sites for transcription factors were identified in the 5'-flanking DNA, some of which may function in regulating expression of the gene in mammary tissue. Conservation of a 110-bp region in the promoters of BTN and Btn may have some functional significance. Cloning and sequencing of BTN provides an additional mammary-specific gene promoter that may be used for driving the expression of transgenes in the lactating mammary gland, and for determining the basis for tissue-specific gene expression. In addition, the sequence of BTN may be used to map intragenic polymorphisms and identify quantitative trait loci in commercial livestock.

Molecular divergence of lysozymes and alpha-lactalbumin

The vast number of proteins that sustain the currently living organisms have been generated from a relatively small number of ancestral genes that has involved a variety of processes. Lysozyme is an ancient protein whose origin goes back an estimated 400 to 600 million years. This protein was originally a bacteriolytic defensive agent and has been adapted to serve a digestive function on at least two occasions, separated by nearly 40 million years. The origins of the related goose type and T4 phage lysozyme that are distinct from the more common C type are obscure. They share no discernable amino acid sequence identity and yet they possess common secondary and tertiary structures. Lysozyme C gene also gave rise, after gene duplication 300 to 400 million years ago, to a gene that currently codes for alpha-lactalbumin, a protein expressed only in the lactating mammary gland of all but a few species of mammals. It is required for the synthesis of lactose, the sugar secreted in milk. alpha-Lactalbumin shares only 40% identity in amino acid sequence with lysozyme C, but it has a closer spatial structure and gene organization. Although structurally similar, functionally they are quite distinct. Specific amino acid substitutions in alpha-lactalbumin account for the loss of the enzyme activity of lysozyme and the acquisition of the features necessary for its role in lactose synthesis. Evolutionary implications are as yet unclear but are being unraveled in many laboratories.

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.

Variants within the 5'-flanking regions of bovine milk-protein-encoding genes. III. Genes encoding the Ca-sensitive caseins αs1, α s2 and β

The 5'-flanking regions of the Ca-sensitive casein-encoding gene family were analysed for DNA variants by automated DNA sequencing of 13 cows belonging to seven breeds. About 1 kbp of each 5'-flanking region, including non-coding exon I, was amplified by PCR and sequenced bidirectionally. A total number of 34 variable sites (17 for the α s1, 10 for the α s2, and 7 for the β casein encoding gene) was identified. Variants were computer-analysed for location in putative regulatory sites in order to predict potential influences on gene expression.

Isolation and characterization of vertebrate lysozyme genes

Lysozyme genes have been model genes in molecular genetics. The chicken lysozyme c gene was among the first genes to be isolated and characterized, but since then, many other members of the lysozyme gene family have been isolated and characterized. Of all the members of the gene family, the conventional lysozyme c gene has been the most extensively studied at the molecular level. General properties of members of the lysozyme gene family are that they are relatively small genes of less than 10 kilobases in length, and are made up of four exons and three introns. There has been a long history of gene duplication events within the lysozyme gene family, and in several cases, eg., stomach lysozymes, this has led to the evolution of novel biological functions. Initially the structure of the lysozyme c gene appeared to support the exon theory of genes, but the recent characterization of additional lysozymes shows that the predictions of this theory are not supported. Lysozyme genes continue to yield new insights into the molecular processes moulding the vertebrate genome.

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.

Exon organization and sequence of the genes encoding alpha-lactalbumin and beta-lactoglobulin from the tammar wallaby (Macropodidae, Marsupialia)

Clones encompassing the genes encoding alpha-lactalbumin and beta-lactoglobulin were isolated from a tammar wallaby genomic library, the exons localized using end-labeled oligonucleotides and the DNA sequences determined. The tammar beta-lactoglobulin gene has the same 7 exon-6 intron structure as the sheep homologue. Potential binding sites for mammary gland-specific transcription factors were identified, on the basis of similarity to sites in the sheep gene, in the promoter region of the tammar beta-lactoglobulin gene. The tammar gene encoding alpha-lactalbumin appears to contain four introns rather than three as are present in the eutherian homologues, or the evolutionarily related lysozyme gene. The additional intron appears to occur within the 5' noncoding region of the tammar gene.

Computer-aided analysis of potential transcription-factor binding sites in the rabbit beta-casein gene promoter

Computer analysis of putative cis- and trans-regulatory sequences in the promoter region of the rabbit beta-casein gene is described. Nucleotide sequences up to 2096 bp upstream of the initiation site were compared to known consensus sequences of both ubiquitous and specific transcription factor motifs as well as to those described as characteristic for milk protein genes. Our analysis demonstrated that 5 independent motifs described for milk protein gene promoters exist. Four of them--'Groenen structure', 'Yu-Lee' 1 and 6 sequence and 'Oka box A'--were found in the beta-casein gene promoter; surprisingly, no typical milk box was found. More than one hundred and fifty putative binding motifs were found, representing 56 various consensus sequences. These sequences are located both inside and outside structures typical of milk protein gene promoters and include sequences homologous to mammary gland specific, hormone specific and ubiquitous transcription factors. Our analysis suggests that milk protein gene promoters can bind many transcription factors and assure complex regulation by hormonal and tissue specific factors.

YY1 represses beta-casein gene expression by preventing the formation of a lactation-associated complex

Site-specific mutagenesis of the highly conserved milk box (-140 to -110) region suggested that beta-casein expression is regulated by a hormone-mediated relief of repression (M. Schmitt-Ney, W. Doppler, R. K. Ball, and B. Groner, Mol. Cell. Biol. 11:3745-3755, 1991). However, when this sequence was placed upstream of a heterologous thymidine kinase promoter, it activated reporter gene expression. This apparent paradox was resolved when the trans-acting factor YY1, capable of acting as both a positive and negative regulator, was shown to interact with the milk box region, using bacterially expressed YY1 and specific oligonucleotide and antibody competition experiments. Second, it was demonstrated that extracts prepared from several cell types contained a protein(s) interacting with the mammary gland-specific factor (MGF) binding site, previously shown to be required for beta-casein promoter activity (Schmitt-Ney et al., Mol. Cell. Biol. 11:3745-3755, 1991). Sequence analysis of this site revealed similarity to the gamma interferon-activated sequence, suggesting that MGF may be related to the stat91 signaling protein. Finally, using an oligonucleotide encompassing both the YY1 and MGF sites, we detected a slow-mobility complex only in extracts from mammary glands at late pregnancy and lactation (lactation-associated complex [LAC]). Site-specific mutation of the YY1 binding site led to an enhancement in LAC DNA binding activity, while mutation of the MGF site decreased detectable LAC. These results support a model in which lactogenic stimuli lead to a decrease in YY1 binding, and subsequent increased formation of LAC at a nearby binding site, to stimulate beta-casein transcription.

YY1 represses beta-casein gene expression by preventing the formation of a lactation-associated complex

Site-specific mutagenesis of the highly conserved milk box (-140 to -110) region suggested that beta-casein expression is regulated by a hormone-mediated relief of repression (M. Schmitt-Ney, W. Doppler, R. K. Ball, and B. Groner, Mol. Cell. Biol. 11:3745-3755, 1991). However, when this sequence was placed upstream of a heterologous thymidine kinase promoter, it activated reporter gene expression. This apparent paradox was resolved when the trans-acting factor YY1, capable of acting as both a positive and negative regulator, was shown to interact with the milk box region, using bacterially expressed YY1 and specific oligonucleotide and antibody competition experiments. Second, it was demonstrated that extracts prepared from several cell types contained a protein(s) interacting with the mammary gland-specific factor (MGF) binding site, previously shown to be required for beta-casein promoter activity (Schmitt-Ney et al., Mol. Cell. Biol. 11:3745-3755, 1991). Sequence analysis of this site revealed similarity to the gamma interferon-activated sequence, suggesting that MGF may be related to the stat91 signaling protein. Finally, using an oligonucleotide encompassing both the YY1 and MGF sites, we detected a slow-mobility complex only in extracts from mammary glands at late pregnancy and lactation (lactation-associated complex [LAC]). Site-specific mutation of the YY1 binding site led to an enhancement in LAC DNA binding activity, while mutation of the MGF site decreased detectable LAC. These results support a model in which lactogenic stimuli lead to a decrease in YY1 binding, and subsequent increased formation of LAC at a nearby binding site, to stimulate beta-casein transcription.

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.

Expression of major histocompatibility complex class I antigens at low levels in the thymus induces T cell tolerance via a non-deletional mechanism

Transgenic CBA (H-2k haplotype) mice expressing the H-2 Kb major histocompatibility complex (MHC) class I gene under control of transcriptional promoter elements from a milk protein gene display high-level H-2 Kb transcription in lactating mammary glands and low-level transcription in skin and thymus of male and virgin female transgenic mice. However, H-2 Kb antigen could be detected only in lactating mammary gland epithelial cells by immunohistological methods. All transgenic mice are tolerant of H-2 Kb since they fail to reject skin grafts from mice expressing H-2 Kb molecules. Furthermore, anti-H-2 Kb cytotoxic responses could not be generated using responder T cells from transgenic mice but T cells from the same mice proliferated, in the presence of interleukin-2, in response to stimulator cells expressing H-2 Kb. Tolerance to H-2 Kb is induced in the thymus since CBA mice grafted with thymus tissue from transgenic mice fail to reject H-2 Kb disparate skin grafts. However, experiments with double-transgenic mice also expressing a T cell receptor with anti-H-2 Kb specificity reveal that tolerance induction is not brought about by elimination of thymocytes bearing H-2 Kb-reactive receptors. Instead, a non-deletional mechanism which results in down-modulation of both CD8 and T cell receptor expression in peripheral T cells correlates with the induction of tolerance in these mice. These data reveal that extremely low levels of self-antigen expression in the thymus are sufficient to induce tolerance via non-deletional mechanisms.

Isolation and characterization of the mouse alpha-lactalbumin-encoding gene: interspecies comparison, tissue- and stage-specific expression

The murine alpha-lactalbumin-encoding gene (m alpha La) was isolated and completely sequenced. The 2.3-kb transcription unit shared a similar organization with that of its counterparts from other species. Sequence comparison for the proximal 5'-flanking region indicated the presence of a consensus motif that occurs in all milk-protein-encoding genes, except the kappa-casein-encoding gene. This may correspond to the binding site for the recently identified mammary-gland-specific factor. The m alpha La gene occurs in a single copy per haploid genome and is specifically expressed in the mammary gland where it is induced during late pregnancy.

The prospects for domesticating milk protein genes

It is possible to convert milk glands of transgenic animals into bioreactors producing heterologous proteins such as scarce human pharmaceuticals. To predictably and successfully engineer the milk gland, we will need a thorough understanding of its physiology. Expression studies in transgenic animals have located mammary specific and hormone inducible transcription elements in the promoter/upstream regions of milk protein genes, and transfection studies in cell lines or primary cells have identified constitutive and hormone inducible elements. Most importantly, it appears that in addition to individual promoter based transcription elements structural features of milk protein chromosomal loci may contribute to the tight developmental and hormonal regulation. I will discuss milk protein gene regulation with emphasis on regulatory differences between genes and species, and the possibility that transcription elements function only properly within genetically defined chromatin domains. Novel strategies to build mammary expression vectors and to test their functionality without pursuing the standard transgenic route will be presented. Finally, I will discuss homologous recombination with the goal to target milk protein genes. Only through the domestication of milk protein genes will we be able to use their full potential in the mammary bioreactor.

Functional conversion of the homologous proteins alpha-lactalbumin and lysozyme by exon exchange

Exons of eukaryotic genes that encode proteins frequently appear to encode structural and/or functional protein units [Gilbert, W. (1978) Nature (London) 271, 501; Blake, C.C.F. (1979) Nature (London) 277, 598]. alpha-Lactalbumin and c-type lysozyme are functionally quite different but structurally highly homologous proteins. Their gene organizations have been shown to be virtually the same and their exon structures are identical. The exon 2 region of hen lysozyme contains most of the amino acid residues that make up its catalytic cleft. In this study, we engineered a hybrid protein in which the exon 2 region of goat alpha-lactalbumin was replaced with that of hen lysozyme. This conferred catalytic activity on the alpha-lactalbumin, which is a nonenzymatic protein in its native structural form.

Sequence of the murine alpha-lactalbumin-encoding cDNA: interspecies comparison of the coding frame and deduced pre-protein

The structure of the mouse alpha-lactalbumin-encoding mRNA was deduced from sequence analysis of eight cDNA clones. The almost full-length mRNA of 732 nucleotides [poly(A) tail excluded] and the deduced pre-protein share 85% and 86% homology with their rat counterpart, respectively. Interspecies comparison of the pre-protein showed the occurrence of an extra amino acid (aa) in the signal peptide and of two mutations affecting two reported invariant aa residues at positions 44 and 107, which weakens the assumption that both aa residues might play a significant structural and/or functional role.

Transgenic mice carrying the guinea-pig alpha-lactalbumin gene transcribe milk protein genes in their sebaceous glands during lactation

We have generated transgenic mice carrying the entire guinea-pig alpha-lactalbumin gene. Lactating transgenic mice expressed high levels of correctly initiated and processed guinea-pig alpha-lactalbumin mRNA in the secretory epithelium of their mammary glands, and secreted guinea-pig alpha-lactalbumin in their milk. Transcripts were detectable after 7 days of pregnancy, indicating that the transgene was under correct hormonal control. Whereas no or negligible transcription was detectable in all other tissues tested, high levels of transcripts were found in the skin of lactating transgenic mice. Guinea-pig alpha-lactalbumin protein was undetectable in the skin, however. In situ hybridization analysis showed that expression was localized to the undifferentiated cells in the basal layer of the sebaceous glands. Further studies revealed high levels of endogenous beta-casein mRNA in normal lactating mouse skin, demonstrating that the transcription of milk protein genes in lactating mouse skin is a normal event, and is not peculiar to the transgene. This surprising finding highlights the developmental relationship of the mammary gland to other specialized structures of the skin, supports a role for epithelial-extracellular matrix interactions in the regulation of milk protein gene expression in vivo, and identifies the skin as a particularly accessible model system in which to study the regulation of milk protein gene expression. In addition, the guinea-pig alpha-lactalbumin gene will be a source of regulatory sequences with which to direct heterologous gene expression to the sebaceous glands of transgenic mice.

Sequence of the goat alpha-lactalbumin-encoding gene: comparison with the bovine gene and evidence of related sequences in the goat genome

The isolation and characterization of a genomic clone encoding goat alpha-lactalbumin (alpha LA) are described, and its sequence was aligned with that of its bovine counterpart. The 5'-flanking regions are highly homologous, but two small insertions were found in the goat sequence. One of these insertions fills the gap found in the so-called 'milk-box' consensus sequence of the bovine gene. Southern analysis indicates the presence of several alpha LA-related sequences in the goat genome, as previously observed in cow and sheep, which suggests that the relevant duplication event(s) occurred before divergence of these ruminant species.

Molecular cloning and characterization of human pyruvate dehydrogenase beta subunit gene

A genomic clone encompassing the entire gene for the human pyruvate dehydrogenase beta subunit (PDH beta) has been isolated by screening a leukocyte genomic library with a nick-translated human foreskin fibroblast PDH beta cDNA probe. The 18-kilobase clone was characterized by restriction enzyme analysis, extensive DNA sequencing, and primer-extension analysis. The PDH beta structural gene is composed of 10 exons and 9 introns. All intron-exon splice junctions follow the GT/AG rule. The Alu family was found in introns 2 and 8. The 5' flanking region of the PDH beta gene contains a "CAAT" consensus promoter sequence but no "TATA" sequence. Primer-extension analysis indicated that the PDH beta gene transcription start site is an adenine residue located 132 bases upstream from the initiation codon in exon 1.

Efficient tissue-specific expression of bovine alpha-lactalbumin in transgenic mice

Transgenic mice carrying a 3.2-kb genomic fragment comprising the bovine alpha-lactalbumin gene transcription unit with 750 bp and 336 bp of 5' and 3' flanking regions, respectively, were generated. Tissue-specific expression of the transgene was observed in five out of the six lines analyzed at levels close to the endogenous gene in two of them.

The bovine and ovine genomes contain multiple sequences homologous to the alpha-lactalbumin-encoding gene

Bovine and ovine (pseudo)genes homologous to the alpha-lactalbumin-encoding gene are described. In both cases, sequence analysis reveals homology extending downstream from exon 2. Southern analysis indicates the presence of a family of alpha-lactalbumin-related sequences in the bovine genome.

The 5' splice site: phylogenetic evolution and variable geometry of association with U1RNA

The 5' splice site sequences of 3294 introns from various organisms (1-672) were analyzed in order to determine the rules governing evolution of this sequence, which may shed light on the mechanism of cleavage at the exon-intron junction. The data indicate that, currently, in all organisms, a common sequence 1GUAAG6U and its derivatives are used as well as an additional sequence and its derivatives, which differ in metazoa (G/1GUgAG6U), lower eucaryotes (1GUAxG6U) and higher plants (AG/1GU3A). They all partly resemble the prototype sequence AG/1GUAAG6U whose 8 contigous nucleotides are complementary to the nucleotides 4-11 of U1RNA, which are perfectly conserved in the course of phylogenetic evolution. Detailed examination of the data shows that U1RNA can recognize different parts of 5' splice sites. As a rule, either prototype nucleotides at position -2 and -1 or at positions 4, 5 or 6 or at positions 3-4 are dispensable provided that the stability of the U1RNA-5' splice site hybrid is conserved. On the basis of frequency of sequences, the optimal size of the hybridizable region is 5-7 nucleotides. Thus, the cleavage at the exon-intron junction seems to imply, first, that the 5' splice site is recognized by U1RNA according to a "variable geometry" program; second, that the precise cleavage site is determined by the conserved sequence of U1RNA since it occurs exactly opposite to the junction between nucleotides C9 and C10 of U1RNA. The variable geometry of the U1RNA-5' splice site association provides flexibility to the system and allows diversification in the course of phylogenetic evolution.

The scanning model for translation: an update

The small (40S) subunit of eukaryotic ribosomes is believed to bind initially at the capped 5'-end of messenger RNA and then migrate, stopping at the first AUG codon in a favorable context for initiating translation. The first-AUG rule is not absolute, but there are rules for breaking the rule. Some anomalous observations that seemed to contradict the scanning mechanism now appear to be artifacts. A few genuine anomalies remain unexplained.