Dietary fatty acids that constitute a large proportion of bad cholesterol in humans are mainly derived from fatty components of milk and beef with genetic selection providing a pathway for reduction. This study investigated imputed genomic sequence to identify a candidate causal mutation influencing Pentadecanoic acid (C15:0). C15:0 represents less than 1% of fatty acids found in beef and is investigated as a model region due to a strong GWAS signal not previously reported. The animal population was a designed backcross experiment with 406 heifers and steers born in 1996–1997 with phenotypes, sired by three Jersey (J) × Limousin (L) bulls out of J and L dams. Animals were raised on pasture and slaughtered at 22–28 mo with subcutaneous fat from over the longissimus dorsi muscle used to extract nine fatty acids which were presented as a percentage of total fatty acids including C15:0. A GWAS with the Illumina BovineHD SNP array identified SNP 2:5601419 as the most significant. A surrounding ∼200kb region (2:5500178–5698040) was investigated containing 61 SNP from the BovineHD panel. Sequence data were imputed for 350 animals (Fimpute software) in this region using reference sequence from 103 bulls acquired from the 1000 bull genomes project including 66 J, 35 L and 2 of the JxL sires from this population. Genotype concordance rate was 96% for this ∼200kb region for the 2 sires with sequence data. GWAS was performed using 242 progeny of the two sequenced sires with 664 remaining SNPs after removing 2612 loci that were homozygous. The five most significant SNPs were 2:5601419 (FDR = 9.20E-08), 2:5604335 (FDR = 1.31E-07), 2:5596919 (FDR = 1.38E-07), 2:5575950 (FDR = 1.53E-07) and 2:5565799 (FDR = 1.84E-07) with the first, second and third SNPs overlapping with the BovineHD panel. Although a large proportion of the 664 SNPs were significant (P < 0.001) in the GWAS, when the GWAS was run with a fixed adjustment for 2:5601419 genotype, there were no remaining significant (P < 0.001) SNPs, indicating that this SNP is accounting for the genetic control of C15:0 in this region. The SNP 2:5601419 is within the coding sequence of gene A7MB61_BOVIN. With the top 3 SNPs all overlapping with the BovineHD panel, the imputation to sequence did not reveal any additional variants of interest. The ability of imputed sequence to identify new mutations causing variation in meat quality traits in this population requires further study, including more regions with better sequence coverage of all 3 sire families.

Summary A quantitative trait locus (QTL) study was carried out in two countries, recording live animal and carcass composition traits. Back‐cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin breed backgrounds. The New Zealand cattle were reared on pasture to carcass weights averaging 229 kg, whilst the Australian cattle were reared on grass and finished on grain (for at least 180 days) to carcass weights averaging 335 kg. From 11 live animal traits and 31 carcass composition traits respectively, 5 and 22 QTL were detected in combined‐sire analyses, which were significant ( P < 0.05) on a genome‐wise basis. Fourteen significant traits for carcass composition QTL were on chromosome 2 and these were traits associated with muscling and fatness. This chromosome carried a variant myostatin allele (F94L), segregating from the Limousin ancestry. Despite very different cattle management systems between the two countries, the two populations had a large number of QTL in common. Of the 18 traits which were common to both countries, and which had significant QTL at the genome‐wise level, eight were significant in both countries.

The aldo-keto reductases (AKRs) are one of the three enzyme superfamilies that perform oxidoreduction on a wide variety of natural and foreign substrates. A systematic nomenclature for the AKR superfamily was adopted in 1996 and was updated in September 2000 (visit www.med.upenn.edu/akr). Investigators have been diligent in submitting sequences of functional proteins to the Web site. With the new additions, the superfamily contains 114 proteins expressed in prokaryotes and eukaryotes that are distributed over 14 families (AKR1–AKR14). The AKR1 family contains the aldose reductases, the aldehyde reductases, the hydroxysteroid dehydrogenases and steroid 5β-reductases, and is the largest. Other families of interest include AKR6, which includes potassium channel β-subunits, and AKR7 the aflatoxin aldehyde reductases. Two new families include AKR13 (yeast aldose reductase) and AKR14 (Escherichia coli aldehyde reductase). Crystal structures of many AKRs and their complexes with ligands are available in the PDB and accessible through the Web site. Each structure has the characteristic (α/β)8-barrel motif of the superfamily, a conserved cofactor binding site and a catalytic tetrad, and variable loop structures that define substrate specificity. Although the majority of AKRs are monomeric proteins of about 320 amino acids in length, the AKR2, AKR6 and AKR7 family may form multimers. To expand the nomenclature to accommodate multimers, we recommend that the composition and stoichiometry be listed. For example, AKR7A1:AKR7A4 (1:3) would designate a tetramer of the composition indicated. The current nomenclature is recognized by the Human Genome Project (HUGO) and the Web site provides a link to genomic information including chromosomal localization, gene boundaries, human ESTs and SNPs and much more.

In order to understand more fully the structural features of aldo-keto reductases (AKRs) that determine their substrate specificities it would be desirable to obtain crystal structures of an AKR with a substrate at the active site. Unfortunately the reaction mechanism does not allow a binary complex between enzyme and substrate and to date ternary complexes of enzyme, NADP(H) and substrate or product have not been achieved. Previous crystal structures, in conjunction with numerous kinetic and theoretical analyses, have led to the general acceptance of the active site tyrosine as the general acid-base catalytic residue in the enzyme. This view is supported by the generation of an enzymatically inactive site-directed mutant (tyrosine-48 to phenylalanine) in human aldose reductase [AKR1B1]. However, crystallization of this mutant was unsuccessful. We have attempted to generate a trapped cofactor/substrate complex in pig aldehyde reductase [AKR1A2] using a tyrosine 50 to phenylalanine site-directed mutant. We have been successful in the generation of the first high resolution binary AKR-Y50F:NADP(H) crystal structure, but we were unable to generate any ternary complexes. The binary complex was refined to 2.2A and shows a clear lack of density due to the missing hydroxyl group. Other residues in the active site are not significantly perturbed when compared to other available reductase structures. The mutant binds cofactor (both oxidized and reduced) more tightly but shows a complete lack of binding of the aldehyde reductase inhibitor barbitone as determined by fluorescence titrations. Attempts at substrate addition to the active site, either by cocrystallization or by soaking, were all unsuccessful using pyridine-3-aldehyde, 4-carboxybenzaldehyde, succinic semialdehyde, methylglyoxal, and other substrates. The lack of ternary complex formation, combined with the significant differences in the binding of barbitone provides some experimental proof of the proposal that the hydroxyl group on the active site tyrosine is essential for substrate binding in addition to its major role in catalysis. We propose that the initial event in catalysis is the binding of the oxygen moiety of the carbonyl-group of the substrate through hydrogen bonding to the tyrosine hydroxyl group.

Chinese hamster ovary (CHO) reductase is an enzyme belonging to the aldo-keto reductase (AKR) superfamily that is induced by the aldehyde-containing protease inhibitor ALLN (Inoue, Sharma, Schimke, et al., J Biol Chem 1993;268: 5894). It shows 70% sequence identity to human aldose reductase (Hyndman, Takenoshita, Vera, et al., J Biol Chem 1997;272:13286), which is a target for drug design because of its implication in diabetic complications. We have determined the crystal structure of CHO reductase complexed with nicotinamide adenine dinucleotide phosphate (NADP)+ to 2.4 A resolution. Similar to aldose reductase and other AKRs, CHO reductase is an alpha/beta TIM barrel enzyme with cofactor bound in an extended conformation. All key residues involved in cofactor binding are conserved with respect to other AKR members. CHO reductase shows a high degree of sequence identity (91%) with another AKR member, FR-1 (mouse fibroblast growth factor-regulated protein), especially around the variable C-terminal end of the protein and has a similar substrate binding pocket that is larger than that of aldose reductase. However, there are distinct differences that can account for differences in substrate specificity. Trp111, which lies horizontal to the substrate pocket in all other AKR members is perpendicular in CHO reductase and is accompanied by movement of Leu300. This coupled with movement of loops A, B, and C away from the active site region accounts for the ability of CHO reductase to bind larger substrates. The position of Trp219 is significantly altered with respect to aldose reductase and appears to release Cys298 from steric constraints. These studies show that AKRs such as CHO reductase are excellent models for examining the effects of subtle changes in amino acid sequence and alignment on binding and catalysis.

The chemical adsorption of organic phosphate compounds to alumina has been used to create surface linkers for protein immobilization. A number of particulate alumina supports were screened for their physical properties and ability to bind organic phosphate compounds. Two aluminas, termed C1 and CPC, were selected based on their suitability for subsequent testing as protein immobilization supports. Papain was successfully immobilized to these supports when derivatized with phosphate compounds containing free terminal carboxyl groups. Protein binding was enhanced when support carboxyl groups were activated with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide. The level of papain immobilization was dependent upon the length of the linker used and the mass of protein exposed to the support.

Particulate aluminum oxides (alumina) were examined as supports for the immobilization of the proteolytic enzyme papain. Two alumina supports termed C1 and CPC were derivatized using organic phosphate linkers to create free carboxyl groups using a two-step process. Papain binding to these derivatized aluminas was performed using the water soluble carbodiimide 1-ethyl-3-(dimethylaminopropyl) carbodiimide. Reactions were optimal at 10 mM carbodiimide. The immobilized protein showed similar kinetic constants when compared to the solution protein. The pH dependence and thermal stability were essentially identical. The immobilized papain showed a blue shift in the intrinsic fluorescence emission maxima. Papain modified with the active site-specific fluorescent probe acrylodan showed overlapping emission maxima. These results are interpreted as retention of the hydrophobic environment of the active site with a perturbation in the structure of the rest of the protein caused by its association with the negatively charged surface.