Amino acid sequences of stomach and nonstomach lysozymes of ruminants

Summary Complete amino acid sequences are presented for lysozymesc from camel and goat stomachs and compared to sequences of other lysozymesc. Tree analysis suggests that the rate of amino acid replacement went up as soon as lysozyme was recruited for the stomach function in early ruminants. The two lysozymes from goat stomach are the products of a gene duplication that probably took place before the divergence of cow, goat, and deer about 25 million years ago. Partial sequences of three lysozymes from goat tears indicated that (a) the goat tear family of lysozymes may have diverged from the stomach lysozyme family by an ancient duplication and (b) later duplications are probably responsible for the multiple forms of tear and milk lysozymes in ruminants.     

cDNA and amino acid sequences of rainbow trout (Oncorhynchus mykiss) lysozymes and their implications for the evolution of lysozyme and lactalbumin

Summary The complete 129-amino-acid sequences of two rainbow trout lysozymes (I and II) isolated from kidney were established using protein chemistry microtechniques. The two sequences differ only at position 86, I having aspartic acid and II having alanine. A cDNA clone coding for rainbow trout lysozyme was isolated from a cDNA library made from liver mRNA. Sequencing of the cloned cDNA insert, which was 1 kb in length, revealed a 432-bp open reading frame encoding an amino-terminal peptide of 15 amino acids and a mature enzyme of 129 amino acids identical in sequence to II. Forms I and II from kidney and liver were also analyzed using enzymatic amplification via PCR and direct sequencing; both organs contain mRNA encoding the two lysozymes. Evolutionary trees relating DNA sequences coding for lysozymesc and α-lactalbumins provide evidence that the gene duplication giving rise to conventional vertebrate lysozymesc and to lactalbumin preceded the divergence of fishes and tetrapods about 400 Myr ago. Evolutionary analysis also suggests that amino acid replacements may have accumulated more slowly on the lineage leading to fish lysozyme than on those leading to mammal and bird lysozymes.     

Ancient origin of lactalbumin from lysozyme: Analysis of DNA and amino acid sequences

Summary Parsimony trees relating DNA sequences coding for lysozymesc and -lactalbumins suggest that the gene duplication that allowed lactalbumin to evolve from lysozyme preceded the divergence of mammals and birds. Comparisons of the amino acid sequences of additional lysozymes and lactalbumins are consistent with this view. When all base positions are considered, the probability that the duplication leading to the lactalbumin gene occurred after the start to mammalian evolution is estimated to be 0.05–0.10. Elimination of the phylogenetic noise generated by fast evolution and compositional bias at third positions of codons reduced this probability to 0.002–0.03. Thus the gene duplication may have long preceded the acquisition of lactalbumin function.     

Recruitment of lysozyme as a major enzyme in the mouse gut: Duplication,divergence, and regulatory evolution

Summary Two major types of lysozymec (M and P) occur in the mouse genus,Mus, and have been purified from an inbred laboratory strain (C58/J) ofM. domesticus. They differ in physical, catalytic, and antigenic properties as well as by amino acid replacements at 6 of 49 positions in the amino-terminal sequence. Comparisons with four other mammalian lysozymesc of known sequence suggest that M and P are related by a gene duplication that took place before the divergence of the rat and mouse lineages. M lysozyme is present in most tissues; achieves its highest concentration in the kidney, lung, and spleen; and corresponds to the lysozyme partially sequenced before from another strain ofM. domesticus. InM. domesticus and several related species, P lysozyme was detected chiefly in the small intestine, where it is probably produced mainly by Paneth cells. A survey of M and P levels in 22 species of muroid rodents (fromMus and six other genera) of known phylogenetic relationships suggests that a mutation that derepressed the P enzyme arose about 4 million years ago in the ancestor of the housemouse group of species. Additional regulatory shifts affecting M and P levels have taken place along lineages leading to other muroid species. Our survey of 187 individuals of wild house mice and their closest allies reveals a correlation between latitude of origin and level of intestinal lysozyme.     

Congruency of phylogenies derived from different proteins

Summary This communication examines the question of phylogenetic congruency- i.e., whether or not the branching order of evolutionary trees is independent of the protein studied. It was found that trees constructed for birds on the basis of immunological comparison of their transferrins, albumins, and ovalbumins agree approximately with a published tree based on the amino acid sequences of their lysozymesc. This congruency is especially noteworthy with respect to the phylogenetic position of the chachalaca, a Mexican bird classified on morphological grounds in the family Cracidae of the order Galliformes. At the protein level, this species differs as much from non-cracid galliform birds as does the duck, which belongs to another order. Despite the organismal similarity between cracid and non-cracid galliform birds, the molecular relationship is remote. If this contrast between organismal and molecular results had been based on comparative studies with only lysozyme, one could have ascribed the contrast to the possibility that chachalaca lysozyme was paralogous, rather than orthologous, to the other bird lysozymesc. Examination of several proteins is thus desirable in cases of possible paralogy.This work was supported in part by grants GB-42028X from NSF and GM-21509 from NIH     

General Properties of Endo-N-acetylmuramidase of Bacillus subtilis YT-25

The enzymatic behaviour, amino acid composition and some physical properties of a new endo-N-acetylmuramidase (B-enzyme) of Bacillus subtilis YT–25 were determined and compared with hen’s egg white lysozyme. The molecular weight was estimated to be about 13000 by the sedimentation equilibrium method. The isoelectric point was pH 9.8. The amino acid composition indicates that the enzyme is rich in basic amino acids, especially lysin. Maximal activity on the lysis of cell walls of M. lysodeikticus occurred at pH 6.2. The enzyme was stable at pH 3.5 ~ 6.0. The specific activity for the lysis of cell walls of M. lysodeikticus was less than fourth part of that of hen’s egg white lysozyme. Digest of cell walls of M. lysodeikticus with B-enzyme consisted greater numbers of high molecular products than digest with egg white lysozyme. Substrate specificity of B-enzyme seemed to be different from that of egg white lysozyme.     

Evolution of the bovine lysozyme gene family: Changes in gene expression and reversion of function

Recruitment of lysozyme to a digestive function in ruminant artiodactyls is associated with amplification of the gene. At least four of the approximately ten genes are expressed in the stomach, and several are expressed in nonstomach tissues. Characterization of additional lysozymelike sequences in the bovine genome has identified most, if not all, of the members of this gene family. There are at least six stomachlike lysozyme genes, two of which are pseudogenes. The stomach lysozyme pseudogenes show a pattern of concerted evolution similar to that of the functional stomach genes. At least four nonstomach lysozyme genes exist. The nonstomach lysozyme genes are not monophyletic. A gene encoding a tracheal lysozyme was isolated, and the stomach lysozyme of advanced ruminants was found to be more closely related to the tracheal lysozyme than to the stomach lysozyme of the camel or other nonstomach lysozyme genes of ruminants. The tracheal lysozyme shares with stomach lysozymes of advanced ruminants the deletion of amino acid 103, and several other adaptive sequence characteristics of stomach lysozymes. I suggest here that tracheal lysozyme has reverted from a functional stomach lysozyme. Tracheal lysozyme then represents a second instance of a change in lysozyme gene expression and function within ruminants. Correspondence to: D.M. Irwin     

Inhibition of two mitochondrial enzymes by gold(III) halo complexes. Evidence for a binding mechanism

Fumarase (EC 4.2.1.2) and mitochondrial L-malate dehydrogenase (EC 1.1.1.37) were both inhibited by NaAuCl₄ and KAuBr₄. The inhibition for both was measured as a function of gold complex concentration and aquation time, and the NaAuCl₄ inhibition was also measured in the presence of 0.15 M NaCl. Regeneration of the enzyme activity after NaAuCl₄ inhibition using L-cysteine, L-methionine and NaCN was also investigated. Sodium dodecyl sulfate (SDS) acrylamide gel electrophoresis and amino acid analysis was performed on the NaAuCl₄ inhibited enzymes as well as on ribonuclease A (EC 3.1.26.2), lysozyme (EC 3.2.1.17) and liver alcohol dehydrogenase (EC 1.1.1.1). It was observed that the inhibition was proportional to the gold complex concentration but decreased markedly after aquation of the complex. In the presence of NaCl the initial rate of inactivation is essentially unaffected unless the complex has been aquated and then the initial rate is increased. Gel electrophoresis on gold complex-enzyme mixtures show polymerization for ribonuclease and lysozyme and amino acid analysis indicates that no oxidation has taken place. From these results, a binding mechanism is postulated for the inhibition of the dehydrogenases by direct displacement of a halide ligand, probably by two groups on the enzyme, at least one of which may be a sulfur containing acid.     

Evolutionary aspects of cytochromec oxidase

The presence of additional subunits in cytochrome oxidase distinguish the multicellular eukaryotic enzyme from that of a simple unicellular bacterial enzyme. The number of these additional subunits increases with increasing evolutionary stage of the organism. Subunits I–III of the eukaryotic enzyme are related to the three bacterial subunits, and they are encoded on mito-chondrial DNA. The additional subunits are nuclear encoded. Experimental evidences are presented here to indicate that the lower enzymatic activity of the mammalian enzyme is due to the presence of nuclear-coded subunits. Dissociation of some of the nuclear-coded subunits (e.g., VIa) by laurylmaltoside and anions increased the activity of the rat liver enzyme to a value similar to that of the bacterial enzyme. Further, it is shown that the intraliposomal nucleotides influence the kinetics of ferrocytochromec oxidation by the reconstituted enzyme from bovine heart but not fromP. denitrificans. The regulatory function attributed to the nuclear-coded subunits of mammalian cytochromec oxidase is also demonstrated by the tissue-specific response of the reconstituted enzyme from bovine heart but not from bovine liver to intraliposomal ADP. These enzymes from bovine heart and liver differ in the amino acid sequences of subunits VIa, VIIa, and VIII. The results presented here are taken to indicate a regulation of cytochromec oxidase activity by nuclear-coded subunits which act like receptors for allosteric effectors and influence the catalytic activity of the core enzyme via conformational changes.     

Papaya (Carica papaya) Lysozyme Is a Member of the Family 19 (Basic, Class II) Chitinases

The most comprehensive studies on a plant lysozyme (EC 3.2.1.17) are those on the enzyme from papaya (Carica papaya) latex, published in 1967 and 1969. However, the N-terminal amino acid sequence of five amino acid sequence of this enzyme, determined by manual Edman degradation, did not allow assignment to any of the much later-classified families of glycosyl hydrolases. N-Terminal sequence analysis of 22 residues of papaya lysozyme now shows unambiguously that the enzyme belongs to the family 19 chitinases. It has properties similar to those of basic class I chitinases with lysozyme activity, such as cleavage specificity at the C-1 of N-acetylmuramic acid with inversion of configuration, but as it lacks an N-terminal hevein domain, it should be classified as a class II chitinase. Received: 3 February 1999 / Accepted 25 July 1999     

Rapid Nonsynonymous Evolution of the Iron-Sulfur Protein in Anthropoid Primates

Cytochrome c (CYC) and 9 of the 13 subunits of cytochrome c oxidase (complex IV; COX) were previously shown to have accelerated rates of nonsynonymous substitution in anthropoid primates. Cytochrome b, the mtDNA encoded subunit of ubiquinol-cytochrome c reductase (complex III), also showed an accelerated nonsynonymous substitution rate in anthropoid primates but rate information about the nuclear encoded subunits of complex III has been lacking.We now report that phylogenetic and relative rates analysis of a nuclear encoded catalytically active subunit of complex III, the ironsulfur protein (ISP), shows an accelerated rate of amino acid replacement similar to cytochrome b. Because both ISP and subunit 9, whose function is not directly related to electron transport, are produced by cleavage into two subunits of the initial translation product of a single gene, it is probable that these two subunits of complex III have essentially identical underlying rates of mutation. Nevertheless, we find that the catalytically active ISP has an accelerated rate of amino acid replacement in anthropoid primates whereas the catalytically inactive subunit 9 does not.     

Protein purification and nucleotide sequence of a lysozyme from the bacteria-induced larvae of the fall webworm,Hyphantria cunea

A protein with lytic activity against Micrococcus luteus was purified from the hemolymph of the fall webworm, Hyphantria cunea, larvae challenged with live E. coli. A bacteriolytic protein of about 14,000 daltons in mass was purified by cation exchange chromatography and reverse-phased HPLC. The optimum pH and optimum temperature range for activity were around pH 6.2 and 50°C, respectively, in a 100 mM phosphate buffer. The aminoterminal amino acid sequence of this protein was determined and the corresponding cDNA was isolated and analyzed. The deduced protein of 142 amino acid residues was composed of a putative leader sequence of 20 residues and the mature enzyme of 122 residues. The cloned lysozyme gene was strongly induced in response to bacterial injection, implying that the enzyme is a part of the immune response of H. cunea. Comparison with other known lysozyme sequences shows that our lysozyme belongs to the chicken lysozyme. Arch. Insect Biochem. Physiol. 35:335–345, 1997.© 1997 Wiley-Liss, Inc.     

Gene Transfer of a Part of a β-Lactamase Gene?

β-Lactamase is an enzyme which catalyzes the hydrolysis of the β-lactam ring of penicillins and cephalosporins. By similarity analysis of amino acid sequences in a database, the amino acid sequence deduced from the nucleotide sequence of the upstream region of cytochrome c oxidase subunit II from Paracoccus denitrificans was found to have an unusually high score of homology to that of a portion of β-lactamases from Gram-negative bacteria. Furthermore, the nucleotide sequences corresponding only to this region had a very high score of similarity among them. The phylogenetic tree constructed on the basis of the amino acid sequences was in accord with that constituted on the 5S rRNA's. Moreover, the molar G + C contents and the codon usage were similar to those in their respective bacteria. It is suggested, therefore, that the nucleotide sequence in P. denitrificans was positioned by a transfer of a part of a β-lactamase gene formed as a result of gene duplication or it was formed by a deletion of the essential region of the β-lactamase gene, although no β-lactamase gene has been yet detected in P. denitrificans.     

Expanding knowledge of the Rubisco kinetics variability in plant species: environmental and evolutionary trends

The present study characterizes the kinetic properties of ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) from 28 terrestrial plant species, representing different phylogenetic lineages, environmental adaptations and photosynthetic mechanisms. Our findings confirm that past atmospheric CO₂/O₂ ratio changes and present environmental pressures have influenced Rubisco kinetics. One evolutionary adaptation to a decreasing atmospheric CO₂/O₂ ratio has been an increase in the affinity of Rubisco for CO₂ (K_c falling), and a consequent decrease in the velocity of carboxylation (k_cat^c), which in turn has been ameliorated by an increase in the proportion of leaf protein accounted by Rubisco. The trade‐off between K_c and k_cat^c was not universal among the species studied and deviations from this relationship occur in extant forms of Rubisco. In species adapted to particular environments, including carnivorous plants, crassulacean acid metabolism species and C₃ plants from aquatic and arid habitats, Rubisco has evolved towards increased efficiency, as demonstrated by a higher k_cat^c/K_c ratio. This variability in kinetics was related to the amino acid sequence of the Rubisco large subunit. Phylogenetic analysis identified 13 residues under positive selection during evolution towards specific Rubisco kinetic parameters. This crucial information provides candidate amino acid replacements, which could be implemented to optimize crop photosynthesis under a range of environmental conditions.     

Molecular Divergence of Lysozymes and α-Lactalbumin

Abstract

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 α-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. α-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 α-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.     

Yak (Bos Grunniens) Stomach Lysozyme: Molecular Cloning,Expression and its Antibacterial Activities

The cDNA coding for stomach lysozyme in yak was cloned. The cloned cDNA contains a 432 bp open reading frame and encodes 143 amino acids (16.24 KDa) with a signal peptide of 18 amino acids. Further analysis revealed that its amino acid sequence shares many common properties with cow milk lysozyme. Expression of this gene was also detected in mammary gland tissue by RT-PCR. Phylogenetic relationships among yak stomach lysozyme and 8 cow lysozymes indicated that the yak enzyme is more closely related to both cow milk lysozyme and the pseudogene ΨNS4 than cow stomach lysozyme. Recombinant yak lysozyme purified by Ni²⁺-column showed a molecular weight of 33.78 kDa and exhibited lytic activity against Staphylococcus aureus, providing evidence of its antibacterial activities.     

Intracellular Peptidase of Bac. subtilis

A peptidase was isolated from the cells of amylase-producing Bac. subtilis by means of cell lysis with egg white lysozyme, followed by freezing and thawing, salting out, dialysis and ion-exchanger column chromatography. The enzyme required manganese ion to show the enzyme activity. Also the enzyme was stable in the presence of magnesium ion. The enzyme hydrolyzed various synthetic peptides by stepwise removal of the amino terminal amino acid of peptides and thus the peptidase was found to be aminopeptidase.     

Evolution of the primate cytochrome c oxidase subunit II gene

We examined the nucleotide and amino acid sequence variation of the cytochrome c oxidase subunit II (COII) gene from 25 primates (4 hominoids, 8 Old World monkeys, 2 New World monkeys, 2 tarsiers, 7 lemuriforms, 2 lorisiforms). Marginal support was found for three phylogenetic conclusions: (1) sister-group relationship between tarsiers and a monkey/ape clade, (2) placement of the aye-aye (Daubentonia) sister to all other strepsirhine primates, and (3) rejection of a sister-group relationship of dwarf lemurs (i.e., Cheirogaleus) with lorisiform primates. Stronger support was found for a sister-group relationship between the ring-tail lemur (Lemur catta) and the gentle lemurs (Hapalemur). In congruence with previous studies on COII, we found that the monkeys and apes have undergone a nearly two-fold increase in the rate of amino acid replacement relative to other primates. Although functionally important amino acids are generally conserved among all primates, the acceleration in amino acid replacements in higher primates is associated with increased variation in the amino terminal end of the protein. Additionally, the replacement of two carboxyl-bearing residues (glutamate and aspartate) at positions 114 and 115 may provide a partial explanation for the poor enzyme kinetics in cross-reactions between the cytochromes c and cytochrome c oxidases of higher primates and other mammals. Correspondence to: R.L. Honeycutt     

The Amino Acid Sequence of Wood Duck Lysozyme

The amino acid sequence of wood duck (Aix sponsa) lysozyme was analyzed. Carboxymethylated lysozyme was digested with trypsin and the resulting peptides were sequenced. The established amino acid sequence had the highest similarity to duck III lysozyme with four amino acid substitutions, and had eighteen amino acid substitutions from chicken lysozyme. The valine at position 75 was newly detected in chicken-type lysozymes. In the active site, Tyr34 and Glu57 were found at subsites F and D, respectively, when compared with chicken lysozyme.     

Requirements for perpendicular helix pairing

Cassette mutagenesis was used to produce a library of mutations at the interface of the N- and C-terminal helices of Saccharomyces cerevisiae iso-1-cytochrome c. The library is random and comprises >98% mutations. Over 11,000 candidates were assayed for function by selecting for the ability of yeast, with the mutated gene as their sole cytochrome c source, to grow on nonfermentable carbon sources. We estimate that ≈0.5% of the 160,000 total amino acid combinations at these four residues result in a functional cytochrome c. Significant correlations are found between the phenotype of yeast harboring the alleles and both the Dayhoff mutation matrix and transfer free energies (cyclohexane-to-water and n-octanol-to-water). Similar correlations are observed with respect to growth rate. Finally, sequences that are consistent with function follow a binary amino acid pattern. © 1996 Wiley-Liss, Inc.