Isolation, properties and primary structure of coypu and chinchilla pancreatic ribonuclease

Molecular paleoscience: systems biology from the past

Experimental paleomolecular biology, paleobiochemistry, and paleogenetics are closely related emerging fields that infer the sequences of ancient genes and proteins from now-extinct organisms, and then resurrect them for study in the laboratory. The goal of paleogenetics is to use information from natural history to solve the conundrum of modern genomics: How can we understand deeply the function of biomolecular structures uncovered and described by modern chemical biology? Reviewed here are the first 20 cases where biomolecular resurrections have been achieved. These show how paleogenetics can lead to an understanding of the function of biomolecules, analyze changing function, and put meaning to genomic sequences, all in ways that are not possible with traditional molecular biological studies.

Cloning and expression in insect cells of two pancreatic lipases and a procolipase from Myocastor coypus

The physiological role of pancreatic lipases has traditionally been assigned solely to triacylglyceride metabolism, while the digestion of phospholipids requires the presence of the pancreatic phospholipase A2, a 14-kDa enzyme unrelated to pancreatic lipases. However, in the guinea pig, it was observed that the pancreatic phospholipase A2 was absent and that a guinea pig pancreatic-lipase-related protein 2 (GPL-RP2) was responsible for phospholipase activity, in contrast to the situation observed in other mammalian species. As the guinea pig is a member of the hystricomorph rodents, it was of interest to investigate if other species within this evolutionary suborder display similar characteristics. The coypu (Myocastor coypus) also a member of the hystricomorph rodents, was chosen for further investigations. The cDNAs encoding two pancreatic lipases and a procolipase from the coypu were cloned, expressed and characterized. One lipase, CoPL-RP2, was identified as belonging to the RP2 subfamily, while the second, CoPL, was found to belong to the classical pancreatic lipase subfamily. Enzymic characterization and sequence data suggest a role for coypu colipase as a specific cofactor for CoPL, while this coypu colipase cannot be an important cofactor for CoPL-RP2 in vivo. Also, the new lipase cDNA sequences were used in a phylogentic analysis to reinvestigate the taxonomical position of the hystricomorph rodents (e.g. coypu and guinea pig) with respect to the myomorph rodents (e.g. rat and mouse).

Comparative biochemistry of the guinea-pig: a partial checklist

A great deal is known about guinea-pig biochemistry, but the information is scattered and difficult to assemble. The guinea-pig also possesses a number of unusual biochemical features which add to its interest. For these reasons we have compiled a list of biochemical characteristics of the guinea-pig, organized in a series of tables, with brief discussions of some of the entries.

Origin of the duplicated ribonuclease gene in guinea-pig: comparison of the amino acid sequences with those of two close relatives: capybara and cuis ribonuclease

The amino acid sequences of the pancreatic ribonuclease from capybara (Hydrochoerus hydrochaeris) and cuis (Galea musteloides) were determined. Both species belong to the same superfamily of the hystricomorph rodents as the guinea-pig. In guinea-pig pancreas two ribonucleases are present as a result of a recent gene duplication, but in capybara and cuis pancreas only one single ribonuclease has been found. A most parsimonious tree of ribonucleases indicates that the gene duplication leading to both guinea-pig ribonucleases occurred before the divergence of guinea-pig from capybara and cuis. This would mean that changes in expression of the ribonuclease genes have occurred in these taxa. Cuis and capybara ribonuclease have no Asn-X-Ser/Thr sequences and are carbohydrate-free proteins. Capybara ribonuclease has leucine at position 114, a position occupied by proline in the cis-configuration in bovine pancreatic ribonuclease.

The primary structures of pancreatic ribonucleases from African porcupine and casiragua, two hystricomorph rodent species

The amino acid sequences of the pancreatic ribonucleases from African porcupine (Hystrix cristata) and casiragua (Proechimys guairae, a caviomorph rodent species related to the coypu) were determined. The ribonucleases were isolated form minces of pancreatic tissue which had been used for the extraction of the insulins. The results of the sequence determinations of residues 67-78 in both enzymes were ambiguous. Therefore, homology with other ribonucleases has been used in deriving these sequences. At position 94 aspartic acid was found, while all other ribonuclease sequenced to date have asparagine at this position. This may indicate a specific deamidation as a result of the acidic conditions during the extraction of insulin. The amino acid sequence of African porcupine ribonuclease shows a close relationship with those of the South-American caviomorph rodents, which implies that the hystricomorph suborder of the rodents, to which both the African porcupine and the caviomorphs belong, is a natural (evolutionary) taxon. Both porcupine and casiragua ribonuclease are glycoproteins with complex-type carbohydrate chains attached to asparagine-34.

Evolutionary changes in protein composition -- evidence for an optimal strategy

The information contained in the composition of different proteins of the same family is analyzed. It is found that within each family the gain in information per amino acid replacement is constant. This finding is interpreted to imply that evolutionary changes in proteins follow an "optimal" path in the sense that they maximize the number of potentially functional sequences that can be generated by T accepted point mutations from a given protein, subject to restrictions due to biological function.

The amino-acid sequence of kangaroo pancreatic ribonuclease

Red kangaroo (Macropus rufus) ribonuclease was isolated from pancreatic tissue by affinity chromatography. The amino acid sequence was determined by automatic sequencing of overlapping large fragments and by analysis of shorter peptides obtained by digestion with a number of proteolytic enzymes. The polypeptide chain consists of 122 amino acid residues. Compared to other ribonucleases, the N-terminal residue and residue 114 are deleted. In other pancreatic ribonucleases position 114 is occupied by a cis proline residue in an external loop at the surface of the molecule. Other remarkable substitutions are the presence of a tyrosine residue at position 123 instead of a serine which forms a hydrogen bond with the pyrimidine ring of a nucleotide substrate, and a number of hydrophobichydrophilic interchanges in the sequence 51-55, which forms part of an alpha-helix in bovine ribonuclease and exhibits few substitutions in the placental mammals. Kangaroo ribonuclease contains no carbohydrate, although the enzyme possesses a recognition site for carbohydrate attachment in the sequence Asn-Val-Thr (62-64). The enzyme differs at about 35-40% of the positions from all other mammalian pancreatic ribonucleases sequenced to date, which is in agreement with the early divergence between the marsupials and the placental mammals. From fragmentary data a tentative sequence of red-necked wallaby (Macropus rufogriseus) pancreatic ribonuclease has been derived. Eight differences with the kangaroo sequence were found.

Comparison of various immunological methods for distinguishing among mammalian pancreatic ribonucleases of known amino acid sequence

Fourteen mammalian pancreatic ribonucleases of known amino acid sequence were compared by 1 or more of 3 different immunological methods: standard quantitative micro-complement fixation, spot-plate micro-complement fixation, and inhibition of phage inactivation. It was found that, while the results obtained by the 3 techniques were correlated with one another, the standard micro-complement fixation procedure was most versatile, economical of materials, and easiest to execute. The standard MC'F technique was more sensitive than the spot-plate technique to differences in amino acid sequence. The inhibition of phage inactivation method was more sensitive than the standard method for measuring differences among closely related RNases but proved impractical for amino acid differences over 15%; the MC'F method could be extended to at least 30% sequence differences. The standard method, moreover, readily detected the single amino acid difference between dromedary and camel RNases. A linear relationship was found between immunological distance (y) in the MC'F test and percent sequence difference (x) which fit the equation y = 7x. The strength of the correlation between immunological distance and percent sequence difference is consistent with the proposal that a large fraction of the evolutionary substitutions of amino acids in ribonuclease are immunologically detectable. This could be explained either by a multideterminant hypothesis or by a pauci-determinant hypothesis which says that substitutions occurring outside determinants produce small conformational changes influencing determinant reactivity.

Guinea-pig pancreatic ribonucleases. Isolation, properties, primary structure and glycosidation

Two ribonucleases were isolated from guinea-pig pancreas by extraction with 0.125 M sulfuric acid, precipitation with acetone and chromatography on carboxymethyl-cellulose. The amino acid sequences were determined from tryptic digests of the aminoethylated proteins. The tryptic peptides were positioned in the sequence by homology with other pancreatic ribonucleases. Both ribonucleases not only differ in the presence (ribonuclease B) or absence of carbohydrate (ribonuclease A), but also at 31 positions of the amino acid sequence. In guinea-pig ribonuclease B a leucine/proline heterogeneity was found at position 64. The carbohydrate in guinea-pig ribonuclease B is attached to asparagine residues at positions 21 and 34. The carbohydrate-free guinea-pig ribonuclease A possesses a recognition site for sugar attachment in the sequence Asn-Val-Ser (62-64).