Multiple L1 progenitors in prosimian primates: Phylogenetic evidence from ORF1 sequences

One of the uncertainties regarding the evolution of L1 elements is whether there are numerous progenitor genes. We present phylogenetic evidence from ORF1 sequences of slow loris (Nycticebus coucang) and galago (Galago crassicaudatus) that there were at least two distinct progenitors, active at the same time, in the ancestor of this family of prosimian primates. A maximum parsimony analysis that included representative L1s from human, rabbit, and rodents, along with the prosimian sequences, revealed that one of the galago L1s (Gc11) grouped very strongly with the slow loris sequences. The remaining galago elements formed their own unique and strongly supported clade. An analysis of replacement and silent site changes for each link of the most parsimonious tree indicated that during the descent of the Gc11 sequence approximately two times more synonymous than nonsynonymous substitutions had occurred, implying that the Gc11 founder was functional for some time after the split of galago and slow loris. Strong purifying selection was also evident on the galago branch of the tree. These data indicate that there were two distinct and contemporaneous L1 progenitors in the lorisoid ancestor, evolving under purifying selection, that were retained as functional L1s in the galago lineage (and presumably also in the slow loris). The prosimian ORF1 sequences could be further subdivided into subfamilies. ORF1 sequences from both the galago and slow loris have a premature termination codon near the 3′ end, not shared by the other mammalian sequences, that shortens the open reading frame by 288 bp. An analysis of synonymous and nonsynonymous substitutions for the 5′ and 3′ portions, that included intra- and inter-subfamily comparisons, as well as comparisons among the other mammalian sequences, suggested that this premature stop codon is a prosimian acquisition that has rendered the 3′ portion of ORF1 in these primates noncoding. Presented at the NATO Advanced Research Workshop onGenome Organization and Evolution, Spetsai, Greece, 16–22 September 1992     

The antecubital organ of the primate slow loris (Nycticebus coucang coucang)

A study of the ‘antecubital organ’ of the slow loris (Nycticebus coucang coucang), was undertaken in light and electron microscopes. As distinct from other prosimian primates there is a complete absence of interstitial cells in the gland suggesting its different functional role. The acinar cells in the ‘antecubital organ’ of slow loris contain large number of smooth ER and electron-dense secretory granules. The granules are seen both in the apical region of the cells as well as in their basal cytoplasmic processes. Some of these processes appear to terminate close to a blood capillary. The structural features of the ‘antecubital organ’ of slow loris suggest that it is a mixed gland of both exocrine and endocrine nature.     

Mother-infant interactions in slow lorises (Nycticebus bengalensis) and pygmy lorises (Nycticebus pygmaeus)

The study had three purposes: (1) to obtain information about mother-infant interactions in a rarely studied nocturnal prosimian, the pygmy loris (Nycticebus pygmaeus); (2) to compare pygmy lorises with a closely related and better-studied nocturnal prosimian, the Bengal slow loris (Nycticebus bengalensis); and (3) to determine how the presence of a second offspring affected mother-infant interactions in pygmy lorises. Three Bengal slow loris mothers and 3 pygmy loris mothers served as subjects, along with their 10 offspring (4 Bengal slow loris singletons, 2 pygmy loris singletons and 2 sets of pygmy loris twins). Observations were carried out in a zoo research facility for the first 24 weeks of the infants' lives. Although the two species differ in size and reproductive patterns, mother-infant interactions were similar. The primary modes of infant and adult contact were ventral and passive contact, respectively. Mothers parked their infants from the first week, and infants followed from the second week. Mothers displayed little protection or rejection, and there was little aggression. Infants solicited play and social grooming from their mothers. Pygmy loris mothers engaged in social grooming and play with their infants more frequently and for longer periods if the infant was a singleton rather than a twin.     

Excretion of radiolabeled estradiol metabolites in the slow loris (Nycticebus coucang)

The excretion pattern of estradiol was studied in the slow loris Nycticebus coucang) and the ring-tailed lemur (Lemur catta) in order to compare steroid excretion in two representative prosimian species. Daily urinary estrone conjugate measurements in the female loris provided little information when applied over prolonged periods. As a result of these negative data, a metabolic study was performed to determine if estrogen excretion patterns in the slow loris differed from those in the lemur, where urinary assays proved a useful tool in characterizing reproductive cycles. Radio-labeled estradiol was injected intravenously, and serial urine and fecal collections were analyzed for radiolabeled metabolites. The results of these studies demonstrate that more than 92% of the radiolabel was excreted in the feces of the loris, in contrast to only 16% excreted in the feces of the lemur.     

Distinct subfamilies of primate L1Gg retroposons, with some elements carrying tandem repeats in the 5'' region.

Two subfamilies of L1 elements, differing dramatically in the first 1.2 kb of sequence at their 5' ends, were identified in the prosimian primate, Galago garnetti. Interesting patterns of sequence similarity were observed between the galago subfamilies, and with the L1s from human and from another prosimian, the slow loris. Furthermore, members of one of the subfamilies have six to eight tandemly repeated units of 73 bp, starting about 730 bp from their 5' ends. Such tandem repeats have not been reported in other primate L1s, but a striking sequence similarity was found between the galago tandem repeats and those previously described at the 5' termini of some mouse L1s [Loeb, D. D. et al. Mol. Cell. Biol. 6, 168-182, 1986]. Although the similar sequence indicates a shared, conserved function, the galago repeats are sub-terminal and therefore cannot serve as portable RNA polymerase II promoters, as has been suggested for the mouse tandem repeats.     

Reproduction in the slender loris (Loris tardigradus malabaricus)

A breeding colony of slender lorises (Loris tardigradus malabaricus) was studied to obtain data for comparison with other prosimian species, to contribute reproductive information for improving management of captive lorises, and to resolve some uncertainties in the literature regarding reproduction in the slender loris. At the Duke University Primate Center, a female slender loris reached sexual maturity at approximately ten months of age and conceived at one year of age. The length of the estrous cycle was 29–40 days, with copulation occurring over two consecutive days during estrus. Gestation length was 166–169 days. Litter size for each six births was one. Conception did not occur during an immediate post-partum estrus, but four months after birth, resulting in a 9 1/2-month interbirth interval. There was no evidence of reproductive seasonality. Lactation lasted between five and seven months. Reproductive rates of slender lorises are among the lowest of primates less than 500 g. Differences in reproductive parameters may exist between different subspecies of slender lorises.     

Sperm-sperm associations in the loris epididymis

In a few mammals, the passage of maturing spermatozoa through the epididymis is characterized by development of persistent associations between one or more neighboring cells over the acrosomal region. The converse situation is described here in the loris, Nycticebus coucang, a prosimian primate. Loris spermatozoa released at spermiation enter the caput epididymidis as single cells and then become stacked in rouleaux of 2–8 spermatozoa there, the peri-acrosomal plasmalemma of one being linked by a unique junctional complex to that of its neighbor. However, by the time the cauda is reached, all the spermatozoa have separated again to lie as single cells, which now display major aggregations of ordered material over the concave surface of the acrosome. The functional significance of these unusual sperm surface-related phenomena in the loris epididymis is not clear.     

Amino acid sequence of myoglobin from the molluscBursatella leachii

The complete amino acid sequence of myoglobin from the triturative stomach of gastropodic molluscBursatella leachii has been determined. It is composed of 146 amino acid residues, is acetylated at the N-terminus, and contains a single histidine residue at position 95 which corresponds to the heme-binding proximal histidine. The E7 distal histidine, which is conserved widely in myoglobins and hemoglobins, is replaced by valine inBursatella myoglobin. The amino acid sequence ofBursatella myoglobin shows strong homology (73–84%) with those ofAplysia andDolabella myoglobins.     

Reproduction in the slow loris (Nycticebus coucang)

The reproductive biology of the slow loris (Nycticebus coucang) is poorly documented because of infrequent captive breeding success and the absence of field studies of this species. Reproductive data were collected from a breeding colony of slow lorises held at the Duke University Primate Center for the past 10 years. Nineteen infants were born, with a sex ratio of 1:1 and a neonatal mortality rate of 15.8%. In all cases, litter size was one. Females born in the colony copulated for the first time between 18 and 24 months of age. A male that reached sexual maturity in the colony sired his first offspring at the age of 17 months. Estrous cycles ranged in duration from 29–45 days, with copulations usually occurring for 1 day of estrus. Gestation length averaged 192.2 days. Although a postpartum estrus was observed in three cases of infant death, no conceptions resulted. Lactation lasted approximately 6 months. A clear birth peak was observed, with 12 out of 19 births occurring in March, April, and May. The comparatively low basal metabolic rate of this species may account for the unusually low reproductive rate of the slow loris in comparison with other prosimian primates.     

Binding mode of azide to ferric Aplysia limacina myoglobin. Crystallographic analysis at 1.9 A resolution

The binding mode of azide to the ferric form of Aplysia limacina myoglobin has been studied by X-ray crystallography. The three-dimensional structure of the complex has been refined at 1.9 A resolution to a crystallographic R-factor of 13.9%, including 126 ordered solvent molecules. Azide binds to the heme iron, at the sixth co-ordination position, and is oriented towards the outer part of the distal site crevice. This orientation is stabilized by an ionic interaction with the side-chain of Arg66 (E10) which, from an outer orientation in the 'aquo-met' ligand-free myoglobin, folds back towards the distal site in the presence of the anionic ligand. In the absence of a hydrogen bond donor residue at the distal E7 position in Aplysia limacina myoglobin, a different polar residue, Arg66 at the E10 topological position, has been selected by molecular evolution in order to grant ligand stabilization.     

Interactions between a wild Bornean orang-utan and a Philippine slow loris in a peat-swamp forest

All documented orang-utan–loris interactions have been from Sumatra, where lorises were opportunistically preyed upon by orang-utans. In this paper, we describe two accounts of the Bornean orang-utan (Pongo pygmaeus wurmbii) interacting with the Philippine slow loris (Nycticebus menagensis). The interactions were by two adolescent female orang-utans. No attempts to catch the loris were observed on either occasion. Neither interaction was hostile. During the second observation, which was more detailed, we considered the behaviour to be play rather than aggression or attempted predation. Based upon the lack of interest from the adult females during these rare encounters, we propose that the behaviour represents play or non-aggressive exploration rather than predation.     

Perturbation of Critical Prolines in Gloeobacter violaceus Ligand-gated Ion Channel (GLIC) Supports Conserved Gating Motions among Cys-loop Receptors

Gloeobacter violaceus ligand-gated ion channel (GLIC) has served as a valuable structural and functional model for the eukaryotic Cys-loop receptor superfamily. In Cys-loop and other receptors, we have previously demonstrated the crucial roles played by several conserved prolines. Here we explore the role of prolines in the gating transitions of GLIC. As conventional substitutions at some positions resulted in nonfunctional proteins, we used in vivo non-canonical amino acid mutagenesis to determine the specific structural requirements at these sites. Receptors were expressed heterologously in Xenopus laevis oocytes, and whole-cell electrophysiology was used to monitor channel activity. Pro-119 in the Cys-loop, Pro-198 and Pro-203 in the M1 helix, and Pro-299 in the M4 helix were sensitive to substitution, and distinct roles in receptor activity were revealed for each. In the context of the available structural data for GLIC, the behaviors of Pro-119, Pro-203, and Pro-299 mutants are consistent with earlier proline mutagenesis work. However, the Pro-198 site displays a unique phenotype that gives evidence of the importance of the region surrounding this residue for the correct functioning of GLIC.     

X-ray crystal structure of a recombinant human myoglobin mutant at 2.8 A resolution

We have grown crystals in trigonal space group P3(2)21 of a mutant human myoglobin, aquomet form, in which lysine at position 45 has been replaced by arginine and cysteine at position 110 has been replaced by alanine. Suitable crystals of native recombinant human myoglobin have not been obtained. We have used the molecular replacement method to determine the X-ray crystal structure of the mutant at 2.8 A resolution. At the present stage of refinement, the crystallographic R-value for the model, with tightly restrained stereochemistry, is 0.158 for 5.0 to 2.8 A data. As expected, the overall structure is quite similar to the sperm whale myoglobin structure. Arginine 45 adopts a well-ordered conformation similar to that found in aquomet sperm whale myoglobin.     

Amino acid substitutions in the ε-subunit of the F1F0-ATPase of Escherichia coli

A mutant strain of Escherichia coli was isolated in which Gly-48 of the mature ε-subunit of the energy-transducing adenosine triphosphatase was replaced by Asp. This amino acid substitution caused inhibition of ATPase activity (about 70%), loss of ATP-dependent proton translocation and lowered oxidative phosphorylation, but did not affect proton translocation through the F₀. Purified F₁-ATPase from the mutant strain bound to stripped membranes with the same affinity as the normal F₁-ATPase. Partial revertant strains were isolated in which Pro-47 of the ε-subunit was replaced by Ser or Thr. Pro-47 and Gly-48 are predicted to be residues 2 and 3 in a Type II β-turn and the Gly-48 to Asp substitution is predicted to cause a change from a Type II to a Type I or III β-turn. Space-filling models of the β-turn (residues 46–49) in the normal, mutant and partial revertant ε-subunits indicate that the peptide oxygen between Pro-47 and Gly-48 is in a different position to the peptide oxygen between Pro-47 and Asp-48 and that the substitution of Pro-47 by either Ser or Thr restores an oxygen close to the original position. It is suggested that the peptide oxygen between Pro-47 and Gly-48 of the ε-subunit is involved either structurally in inter-subunit H-bonding or directly in proton movements through the F₁-ATPase.     

Different requirements for productive interaction between the active site of HIV-1 proteinase and substrates containing -hydrophobic*hydrophobic- or -aromatic*pro- cleavage sites.

The sequence requirements for HIV-1 proteinase catalyzed cleavage of oligopeptides containing two distinct types of junctions (-hydrophobic*hydrophobic- or -aromatic*Pro-) has been investigated. For the first type of junction (-hydrophobic*hydrophobic-) the optimal residues in the P2 and P2' positions were found to be Val and Glu, respectively, in accord with recent statistical analysis of natural cleavage sites [Poorman, R. A., Tomasselli, A. G., Heinrikson, R. L., & Kézdy, F. J. (1991) J. Biol. Chem. 266, 14554-14561]. For the -aromatic*Pro- type of junction, in the specific sequence context studied here, the value of Glu in the P2' position was again observed. An explanation for the inefficient cleavage observed for peptides with the sequence -Val-Tyr*Pro- has been provided from molecular modeling of the putative enzyme-substrate complex. A significant effect upon cleavage rates due to the amino acid in the P5 position has also been documented. While lysine in the P5 position in one sequence of the -hydrophobic*hydrophobic- type produces a peptide cleaved very efficiently (kcat greater than 15 s-1 for Lys-Ala-Arg-Val-Nle*p-nitrophenylalanine-P2'-Ala-Nle-NH2, for P2' = Glu, Gln, Ile, Val, or Ala), for substrates of the -aromatic*Pro- type, the P5 residue can exert either a positive or negative effect on cleavage rates. These results have again been interpreted in light of molecular modeling. We suggest that interaction of the substrate sequence on the periphery of the active site cleft may influence the match of the enzyme-substrate pair and, hence, control the efficiency of catalysis.(ABSTRACT TRUNCATED AT 250 WORDS)     

X-ray crystal structure of the fluoride derivative of Aplysia limacina ferric myoglobin at 2.0 A resolution. Stabilization of the fluoride ion by hydrogen bonding to Arg66 (E10)

The X-ray crystal structure of the fluoride derivative of Aplysia limacina ferric myoglobin has been solved and refined at 2.0 A resolution; the crystallographic R-factor is 13.6%. The fluoride ion binds to the sixth co-ordination position of the heme iron, 2.2 A from the metal. Binding of the negatively charged ligand on the distal side of the heme pocket of this myoglobin, which lacks the distal His, is associated with a network of hydrogen bonds that includes the fluoride ion, the residue Arg66 (E10), the heme propionate III, three ordered water molecules and backbone or side-chain atoms from the CD region. A comparison of fluoride and oxygen dissociation rate constants of A. limacina myoglobin, sperm whale (Physeter catodon) myoglobin and Glycera dibranchiata monomeric hemoglobin, suggests that the conformational readjustment of Arg66 (E10) in A. limacina myoglobin may represent the molecular basis for ligand stabilization, in the absence of a hydrogen-bond donor residue at the distal E7 position.     

Crystal structure of myoglobin form a synthetic gene

Crystal have been grown of myoglobin produced in Escherichia coli from a synthetic gene, and the structure has been solved to 1.9 Å resolution. The space group of the crystals is P6, which is different from previously solved myoglobin crystal forms. The synthetic myoglobin is essentially identical to myoglobin isolated from sperm whale tissue, except for the retention of the initiator methionine at the N-terminus and the substitution of asparagine for aspartic acid at position 122. Superposition of the coordinates of native and synthetic sperm whale myoglobins reveals only minor changes in the positions of main chain atoms and roeientation of some surface side chains. Crystals of variant of the “synthetic” myoglobin have also been grown for structural analysis of the role of key amino acid residues in ligand and specificity.     

Molecular Evolution of Prolactin in Primates

Pituitary prolactin, like growth hormone (GH) and several other protein hormones, shows an episodic pattern of molecular evolution in which sustained bursts of rapid change contrast with long periods of slow evolution. A period of rapid change occurred in the evolution of prolactin in primates, leading to marked sequence differences between human prolactin and that of nonprimate mammals. We have defined this burst more precisely by sequencing the coding regions of prolactin genes for a prosimian, the slow loris (Nycticebus pygmaeus), and a New World monkey, the marmoset (Callithrix jacchus). Slow loris prolactin is very similar in sequence to pig prolactin, so the episode of rapid change occurred during primate evolution, after the separation of lines leading to prosimians and higher primates. Marmoset prolactin is similar in sequence to human prolactin, so the accelerated evolution occurred before divergence of New World monkeys and Old World monkeys/apes. The burst of change was confined largely to coding sequence (nonsynonymous sites) for mature prolactin and is not marked in other components of the gene sequence. This and the observations that (1) there was no apparent loss of function during the episode of rapid evolution, (2) the rate of evolution slowed toward the basal rate after this burst, and (3) the distribution of substitutions in the prolactin molecule is very uneven support the idea that this episode of rapid change was due to positive adaptive selection. In the slow loris and marmoset there is no evidence for duplication of the prolactin gene, and evidence from another New World monkey (Cebus albifrons) and from the chimpanzee and human genome sequences, suggests that this is the general position in primates, contrasting with the situation for GH genes. The chimpanzee prolactin sequence differs from that of human at two residues and comparison of human and chimpanzee prolactin gene sequences suggests that noncoding regions associated with regulating expression may be evolving differently from other noncoding regions.     

Reproductive biology of the slender loris (Loris lydekkerianus lydekkerianus)

The slender loris (Loris lydekkerianus lydekkerianus), a nocturnal prosimian, was studied for 21 months in its natural habitat of scrub jungle in Dindigul, south India. Here we report on its reproductive biology. Identified and unidentified lorises were observed for a total of 2,656 h. Reproductive seasonality was seen, with births and oestrus observed to be highest in April-June and October-December. The mating system was promiscuous with 1 female mating successively with 3-4 males. A gestation period of 5.5 months and an inter-birth interval of 7 months were recorded. Adult females had a reproductive potential of 4 infants per year. The findings presented in this paper constitute the first information on the life history parameters of wild slender lorises.