Evolution of bindin in the pantropical sea urchin Tripneustes: comparisons to bindin of other genera

Bindin, a sea urchin sperm protein, mediates sperm-egg attachment and membrane fusion and is thus important in species recognition and speciation. Patterns of bindin variation differed among three genera that had been studied previously. In two genera of the superorder Camarodonta, Echinometra and Strongylocentrotus, both of which contain sympatric species, bindin is highly variable within and between species; a region of the molecule evolves at high rates under strong positive selection. In Arbacia, which belongs to the superorder Stirodonta and whose extant species are all allopatric, bindin variation is low, and there is no evidence of positive selection. We cloned and sequenced bindin from Tripneustes, a sea urchin that belongs to the Camarodonta but whose three species are found in different oceans. Worldwide sampling of bindin alleles shows that the bindin of Tripneustes (1) contains the highly conserved core characteristic of all other bindins characterized to date, (2) has an intron in the same position, and (3) has approximately the same length. Its structure is more like that of bindin from other camarodont sea urchins than to bindin from the stirodont ARBACIA: The resemblances to other camarodonts include a glycine-rich repeat structure upstream of the core and lack of a hydrophobic domain 3' of the core, a characteristic of Arbacia bindin. Yet the mode of evolution of Tripneustes bindin is more like that of Arbacia. Differences between bindins of the Caribbean Tripneustes ventricosus and the eastern Pacific T. depressus, separated for 3 my by the Isthmus of Panama, are limited to four amino acid changes and a single indel. There are no fixed amino acid differences or indels between T. depressus from the eastern Pacific and T. gratilla from the Indo-Pacific. Bindin of Tripneustes, like that of Arbacia, also shows no evidence of diversifying selection that would manifest itself in a higher proportion of amino acid replacements than of silent nucleotide substitutions. When the rate of intrageneric bindin divergence is standardized by dividing it by cytochrome oxidase I (COI) divergence, Tripneustes and Arbacia show a lower ratio of bindin to COI substitutions between the species of each genus than exists between the species of either Echinometra or Strongylocentrotus. Thus, mode of bindin evolution is not correlated with phylogenetic affinities or molecular structure, but rather with whether the species in a genus are allopatric or sympatric. For a molecule involved in gametic recognition, this would suggest a pattern of evolution via reinforcement. However, in bindin the process that gave rise to this pattern is not likely to have been selection to avoid hybridization, because there is no excess of amino acid replacements between species versus within species in the bindins of Echinometra and Strongylocentrotus, as would have been expected if specific recognition were the driving force in their evolution. We suggest instead that the pattern of reinforcement is a secondary effect of the ability of species with rapidly evolving bindins to coexist in sympatry.     

The sequence of the Arbacia punctulata bindin cDNA and implications for the structural basis of species-specific sperm adhesion and fertilization

Bindin is the major protein component of the acrosome granule of sea urchin sperm which mediates the species-specific adhesion of sperm to the egg surface during fertilization. Bindin isolated from both Arbacia punctulata and Strongylocentrotus purpuratus sperm demonstrate a distinct adhesive preference for eggs of the same species although a significant amount of cross-species reactivity is observed. Here we describe the isolation and sequence of A. punctulata bindin cDNA clones and a comparison of the predicted protein sequence with the sequence previously reported for S. purpuratus bindin (Gao et al., 1986, Proc. Natl. Acad. Sci., USA 83, 8634-8638). Bindins from these genera show substantial sequence similarity in both the mature bindin domain and the probindin precursor region. The most striking identity is a region of 42 conserved amino acids in the central part of the mature bindins. This conserved domain may be responsible for conserved functions of bindin. Regions flanking this conserved element on both the amino and carboxyl side are more highly divergent, suggesting that they are responsible for the species-specific properties of bindin. The mature A. punctulata sequence contains a putative transmembrane segment between residues 431 and 451 that is absent from S. purpuratus bindin. This structural element may account for the previous observation that isolated A. punctulata bindin uniquely forms multilamellar structures reminiscent of lipid bilayers and binds significant amounts of phospholipid and detergent. The structure of this hydrophobic segment also displays a number of similarities to viral fusion peptides.     

Structural requirements for species-specific induction of the sperm acrosome reaction by sea urchin egg sulfated fucan

The sulfated fucan (SF) of egg jelly induces the acrosome reaction (AR) of sea urchin sperm. Strongylocentrotus franciscanus (Sf) SF is sulfated only at the 2-position. Strongylocentrotus purpuratus (Sp) has two SF isotypes, each one being female specific. One is rich in sulfate at both the 2- and 4-positionS (SF-1), and the other is rich in sulfate at the 4-position, but not the 2-position (SF-2). Sf SF is poor at inducing the AR of Sp sperm, presumably due to lack of 4-sulfation. Sp SF-1 is better at inducing the AR of Sf sperm than Sp SF-2, hypothetically due to increased 2-sulfation. Chemical oversulfation of Sf SF increases the percentage of AR of Sp sperm, showing that 4-sulfation is important for recognition of SF by Sp sperm. Chemically oversulfated Sp SF-2 is better at inducing the Sf sperm AR, presumably because of increased 2-sulfation. The species, Strongylocentrotus drobachiensis (Sd), has an SF-2 that is exclusively 2-sulfated (like Sf), except the glycosidic linkage in Sd is alpha(1-->4), whereas in Sf it is alpha(1-->3). Sd SF-2 does not induce the AR of Sf sperm, showing the strict requirement for the alpha(1-->3) linkage in recognition between Sf sperm and SF. Egg jelly from Echinometra lucunter (El) contains sulfated galactan (SG) which differs from Sf SF only in that the monosaccharide is L-galactose, not L-fucose. This SG and Sf SF are equally potent in inducing the AR of Sf sperm, showing that modification at C6 of L-fucose is not important for proper recognition between SF and Sf sperm receptors. This system permits study of the structural basis for recognition between sulfated polysaccharide and receptors controlling signal transduction pathways in animal cells.     

Comparison of the bindin proteins of Strongylocentrotus franciscanus, S. purpuratus, and Lytechinus variegatus: sequences involved in the species specificity of fertilization.

Bindin is the sea urchin sperm acrosomal protein that is responsible for the species-specific adhesion of the sperm to the egg. Two new bindin cDNA sequences that contain the entire open reading frame for the binding precursor are reported: one for Strongylocentrotus franciscanus and one for Lytechinus variegatus. Both contain inverted repetitive sequences in their 3' untranslated regions, and the S. franciscanus cDNA contains an inverted repetitive sequence match between the 5' untranslated region and the coding region. The middle third of the mature bindin sequence is highly conserved in all three species, and the flanking sequences share short repeated sequences that vary in number between the species. Cross-fertilization data are reported for the species S. purpuratus, S. franciscanus, L. variegatus, and L. pictus. A barrier to cross-fertilization exists between the sympatric Strongylocentrotus species, but there is no barrier between the allopatric Lytechinus species.     

Adaptive evolution of sperm bindin tracks egg incompatibility in neotropical sea urchins of the genus Echinometra

Bindin is a gamete recognition protein known to control species-specificsperm-egg adhesion and membrane fusion in sea urchins. Previousanalyses have shown that diversifying selection on bindin aminoacid sequence is found when gametically incompatible speciesare compared, but not when species are compatible. The presentstudy analyzes bindin polymorphism and divergence in the threeclosely related species of Echinometra in Central America: E.lucunter and E. viridis from the Caribbean, and E. vanbruntifrom the eastern Pacific. The eggs of E. lucunter have evolveda strong block to fertilization by sperm of its neotropicalcongeners, whereas those of the other two species have not.As in the Indo-West Pacific (IWP) Echinometra, the neotropicalspecies show high intraspecific bindin polymorphism in the samegene regions as in the IWP species. Maximum likelihood analysisshows that many of the polymorphic codon sites are under mildpositive selection. Of the fixed amino acid replacements, mosthave accumulated along the bindin lineage of E. lucunter. Weanalyzed the data with maximum likelihood models of variationin positive selection across lineages and codon sites, and withmodels that consider sites and lineages simultaneously. Ourresults show that positive selection is concentrated along theE. lucunter bindin lineage, and that codon sites with aminoacid replacements fixed in this species show by far the highestsignal of positive selection. Lineage-specific positive selectionparalleling egg incompatibility provides support that adaptiveevolution of sperm proteins acts to maintain recognition ofbindin by changing egg receptors. Because both egg incompatibilityand bindin divergence are greater between allopatric speciesthan between sympatric species, the hypothesis of selectionagainst hybridization (reinforcement) cannot explain why adaptiveevolution has been confined to a single lineage in the AmericanEchinometra. Instead, processes acting to varying degrees withinspecies (e.g., sperm competition, sexual selection, and sexualconflict) are more promising explanations for lineage-specificpositive selection on bindin.     

Crassostrea angulata Bindin Gene and the Divergence of Fucose-Binding Lectin Repeats Among Three Species of Crassostrea

Bindin is a major protein for species-specific recognition between sperm and congenetic egg in many free-spawning marine invertebrates. We cloned a novel bindin gene from the oyster Crassostrea angulata by 3′ and 5′ rapid amplification of cDNA ends. The full-length bindin cDNA was 1,049 bp with a 771-bp open reading frame encoding 257 amino acids. The deduced amino acid sequence contained a putative signal peptide of 24 amino acids. The length of the bindin genomic DNA was 8,508 bp containing four exons and three introns. Three haplotypes of F-lectin repeat were detected from seven sequences of F-lectin repeat of six male oysters. Both neighbor-joining and minimum-evolution phylogenetic trees show that haplotype an1 was close to Crassostrea gigas while an2 and an3 were close to Crassostrea sikamea. Intron-4 in the middle of F-lectin repeat is highly variable in both size and sequence. We classified intron-4 into three types according to their size and the F-lectin repeat they were located in. Intron-4 may play an important role in recombination. We compared the number of nonsynonymous substitutions (Dn) and synonymous substitutions (Ds) per nucleotide site among 19 F-lectin haplotypes of the three species. Dn/Ds ratios suggested that positive selection occurred between C. gigas and C. sikamea and between C. gigas and C. angulata. Nine positive selected positions (p > 90%) are identified among 19 haplotypes of three species. They are located on the F-lectin binding face around the three recognition motif residues. We assume that these nine clustered amino acids are related with species-specific recognition.     

Characterization of the Sperm Molecule Bindin in the Sea Urchin Genus <Emphasis Type="Italic">Paracentrotus</Emphasis>

Bindin is a sea urchin gamete-recognition protein that plays an essential role in the specificity of egg–sperm interactions and thus may be evolving under sexual selection and be related to speciation. Bindin has been found to evolve under strong selection in some sea urchin genera and neutrally in others. In this study, we characterized bindin in the two extant species of the genus Paracentrotus: P. lividus from the Atlanto-Mediterranean region and P. gaimardi from Brazil. The structure of the bindin molecule in Paracentrotus is similar to that of other genera studied thus far, consisting of a conserved core flanked by two variable regions and an intron of variable length located at the same conserved position as in other genera. Polymorphism in P. lividus is caused mainly by point substitutions and insertions/deletions, and length variations are caused mainly by the number of repeated motifs in the flanking regions. There is no evidence of recombination. Positive selection is acting on amino acid sites located in two regions flanking the conserved core.     

Bimodal effects of cellular amino acids on Na+-dependent amino acid transport in ehrlich cells

Cells depleted of amino acids show lower rates of glycine or aminoisobutyric acid uptake than do freshly isolated cells. In the amino acid-depleted cells, addition of valinomycin stimulates amino acid influx at least to the level observed in freshly isolated cells. In cells containing high levels of cellular amino acids, valinomycin has little effect on influx of amino acids. It is concluded that the transport of amino acids in freshly isolated cells is elevated compared to depleted cells because the cells are hyperpolarized by the continuous loss of cellular amino acids during the transport assay. During this hyperpolarization by amino acid loss, transport of amino acids is not further stimulated by valinomycin at low external [K⁺] ($\text{10 mM ± 5 mM}$).With the exception of preloading with glycine, cells preloaded with a single amino acid to a concentration greater than 20 mM show reduced rates of glycine and aminoisobutyric acid influx at early times (less than 15 min) compared to amino acid-depleted cells. The reduction of infiux is transient and by 30 min, influx is greater in preloaded than in amino acid-depleted cells.Knowing that increases and decreases in the membrane potential are achieved by using varying external [K⁺] in the presence of valinomycin and propranolol, and using amino acid-depleted cells, it can be shown that an increased membrane potential increases the $\text{V}$ for glycine and aminoisobutyric acid influx. A decrease in the potential difference results in a decreased $\text{V}$. Changes in $\text{K}{}_{\mathrm{<mtext>m</mtext>}}$ also occur when the membrane potential is varied.     

Locale and level of bindin mRNA in maturing testis of the sea urchin, Strongylocentrotus purpuratus

This first study of the onset of spermatogenesis in the sea urchin, Strongylocentrotus purpuratus, was undertaken using individuals reared in the laboratory. Spermatogenesis commences about 11-12 months after metamorphosis in these animals. Bindin message accumulates in late spermatocytes and early spermatids which lie in the luminal germinal layer. Bindin message accumulates later than does the testis-specific histone, H2b-1, suggesting that different classes of genes are sequentially activated during the differentiation of sperm. We correlate the number of bindin mRNA molecules with morphological structure and with quantitative aspects of gonad maturation including the number of nuclei and of sperm. The results suggest that the bindin mRNA concentration in total RNA from testis at different stages of maturation reflects the change in the proportion of expressing cells in the total cell population of the testis.     

Cytochrome P-450 and drug metabolism in intestinal villous and crypt cells of rats: effect of dietary iron.

The amino acid sequence of the $\text{Spirulina maxima}$ ferredoxin has been determined. $\text{Spirulina maxima}$ is a blue green algae and is a procaryote. The ferredoxins of the plant-algal type sequenced to date have all been isolated from eucaryotes. The $\text{S. maxima}$ ferredoxin was composed of 98 amino acids arranged in a single polypeptide chain.The sequences of the various procaryote-eucaryote ferredoxins are compared and the differences discussed.     

Identification and characterization of a new methylated amino acid in ribosomal protein L33 of Escherichiacoli

Methylated amino acids from ribosomal protein L33 of various $\text{Escherichia}\text{coli}$ strains (Q13, B and MRE600) were analyzed. It was found that while protein L33 from $\text{E.}\text{coli}$ Q13 contains two methylated neutral amino acids (peaks I and II), only one methylated neutral amino acid (peak I) was found in protein L33 derived from both $\text{E.}\text{coli}$ strains B and MRE600. The methylated amino acid present in peak I was identified as N-monomethylalanine by ion-exchange column chromatography, high-voltage paper electrophoresis and descending paper chromatography using different solvent systems. This marks the first time that N-monomethylalanine was found in any ribosomal protein.     

Positive selection and sequence rearrangements generate extensive polymorphism in the gamete recognition protein bindin

Bindin is a gamete recognition protein of sea urchins that mediates species-specific attachment of sperm to an egg-surface receptor during fertilization. Sequences of bindin from closely related urchins show fixed species-specific differences. Within species, highly polymorphic bindin alleles result from point substitution, insertion/deletion, and recombination. Since speciation, positive selection favoring allelic variants has generated diversity in bindin polypeptides. Intraspecific bindin variation can be tolerated by the egg receptor, which suggests functional parallels between this system and other flexible recognition systems, including immune recognition. These results show that polymorphism in mate recognition loci required for rapid evolution of sexual isolation can arise within natural populations.      

Evaluation of Sequence Variation and Selection in the Bindin Locus of the Red Sea Urchin, Strongylocentrotus franciscanus

Recent evidence suggests that gamete recognition proteins may be subjected to directed evolutionary pressure that enhances sequence variability. We evaluated whether diversity enhancing selection is operating on a marine invertebrate fertilization protein by examining the intraspecific DNA sequence variation of a 273-base pair region located at the 5′ end of the sperm bindin locus in 134 adult red sea urchins (Strongylocentrotus franciscanus). Bindin is a sperm recognition protein that mediates species-specific gamete interactions in sea urchins. The region of the bindin locus examined was found to be polymorphic with 14 alleles. Mean pairwise comparison of the 14 alleles indicates moderate sequence diversity (p-distance = 1.06). No evidence of diversity enhancing selection was found. It was not possible to reject the null hypothesis that the sequence variation observed in S. franciscanus bindin is a result of neutral evolution. Statistical evaluation of expected proportions of replacement and silent nucleotide substitutions, observed versus expected proportions of radical replacement substitutions, and conformance to the McDonald and Kreitman test of neutral evolution all indicate that random mutation followed by genetic drift created the polymorphisms observed in bindin. Observed frequencies were also highly similar to results expected for a neutrally evolving locus, suggesting that the polymorphism observed in the 5′ region of S. franciscanus bindin is a result of neutral evolution. Received: 19 June 1998 / Accepted: 2 August 2000     

Effects of glucagon and insulin on liver lysosomes

Recent experimental evidence has been obtained, principally in the laboratory of Glenn Mortimore, that hepatic lysosomes can act as a pool of amino acids during fasting. This pool is generated through $\text{autophagy}$, whereby intracellular proteins are somehow captured by the lysosomes and then rapidly hydrolyzed to free amino acids by the lysosomal proteinases. Two important metabolic fates of these lysosomal digestive products can be: 1) conversion of the glucogenic amino acids into glucose, and 2) conversion of trimethyl-lysine into carnitine. The latter metabolite is required to transfer fatty acids to the mitochondrial site of β-oxidation. Most interesting is the observation that glucagon appears to induce lysosomal autophagy and the resulting degradation of intracellular proteins by decreasing the size of amino acid pools in the perfused liver. This effect of the hormone may be directed at the single amino acid glutamine, since adding it alone to the perfusate can prevent the increase in autophagy caused by glucagon. Insulin also rapidly inactivates hepatic autophagy and its ensuing proteolysis. The $\text{t}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}$ for the rate of los of autophagic vocuoles from the insulin-treated liver (or animal) is approximately 8 min. Thus, glucagon and insulin actively control intracellular protein catabolism that takes place within hepatic lysosomes, and this regulation by the two hormones may be one of their major molecular effects on gluconegenesis in the liver.     

Vanadium ion inhibition of alkaline phosphatase-catalyzed phosphate ester hydrolysis.

The intracellular location of guanylate cyclase was examined in sperm from two species of sea urchin, Strongylocentrotus purpuratus and Lytechinus pictus, and from the tube worm Chaetopterus variopedatus. Cells suspended in a medium isotonic with sea water were passed repeatedly through a 23-gauge hypodermic needle to break flagella from heads. This preparation was then fractionated by two methods, one based on centrifugation over a 25% sucrose medium and the other involving repeated differential centrifugation, to resolve flagella from heads. Guanylate cyclase specific activity was increased 3.5–4.5-fold in the flagellar fraction relative to the starting sperm homogenate. Relatively little activity was present in the head fraction where specific activity was $\text{1}\text{10}\text{–}\text{1}\text{100}$ that of the flagella. Plasma membranes were separated from axonemal microtubules by dialyzing flagella against low ionic strength buffer, followed by centrifugation over a 40% sucrose medium. Although the overall recovery of guanylate cyclase was low, the specific activity in the plasma membrane fraction was increased two- to threefold over the dialyzed flagella, and over 90% of the recovered activity resided in this fraction. Thus the flagellar plasma membrane is a site rich in guanylate cyclase. It could not be determined, however, whether this is the only intracellular locale of the enzyme.     

250 million years of bindin evolution

Bindin plays a central role in sperm-egg attachment and fusion in sea urchins (echinoids). Previous studies determined the DNA sequence of bindin in two orders of the class Echinoidea, representing 10% of all echinoid species. We report sequences of mature bindin from five additional genera, representing four new orders, including the distantly related sand dollars, heart urchins, and pencil urchins. The six orders in which bindin is now known include 70% of all echinoids, and indicate that bindin was present in the common ancestor of all extant sea urchins more than 250 million years ago. Over this span of evolutionary time there has been (1). remarkable conservation in the core region of bindin, particularly in a stretch of 29 amino acids that has not changed at all; (2). conservation of a motif of basic amino acids at the cleavage site between preprobindin and mature bindin; (3). more than a twofold change in length of mature bindin; and (4). emergence of high variation in the sequences outside the core, including the insertion of glycine-rich repeats in the bindins of some orders, but not others.     

Dihydroxyacid dehydratase: the site of hyperbaric oxygen poisoning in branch-chain amino acid biosynthesis.

Exposure of $\text{Escherichia}$$\text{coli}$ to hyperbaric oxygen results in rapid inactivation of dihydroxyacid dehydratase but not of other enzymes required for branched-chain amino acid biosynthesis. Unless branched-chain amino acids are supplied, protein synthesis and growth stops abruptly. The sensitivity of dihydroxyacid dehydratase thus accounts for the observed protective role of branched-chain amino acids which cannot be adequately synthesized during exposure to hyperoxia.     

The amino acid sequence of the Azotobacter vinelandii flavodoxin.

The amino acid sequence of a group II flavodoxin, the $\text{Azotobacter vinelandii}$ flavodoxin has been determined. The FMN-redox protein was shown to exist as a single polypeptide chain and to contain 179 amino acids. Despite the rather low amino acid sequence homology with the other flavodoxins sequenced, it is concluded that sequences of the group I and group II flavodoxins are homologous. The major differences between the group I and group II flavodoxins appears to be a lengthening in the C-terminal region in the group II flavodoxins.     

Structure of tetanus toxin. N-Terminal amino acid analysis of the two molecular forms of tetanus toxin and its composite chains.

N-Terminal amino acid analysis of the intracellular form of tetanus toxin revealed proline as the single terminal residue present in significant quantities. In agreement with new concepts on the structure of tetanus toxin, a second N-terminal amino acid (leucine) was exposed upon conversion to the extracellular form of the toxin molecule. These results were corroborated by analysis of the separate polypeptide chains of the extracellular toxin, and it is concluded that the light chain polypeptide constitutes the N-terminal region of the single chain toxin molecule originally synthesized by the bacterial cell. Treatment of the intracellular tetanus toxin with trypsin $\text{in vitro}$ resulted in the exposure of amino acids in addition to those found after conversion to the extracellular form effected by the bacterial protease during fermentation.     

Separation of aminoacyl-transfer RNAs by polyacrylamide gel electrophoresis

A polyacrylamide gel electrophoresis system for separating $\text{E.}$$\text{coli}$ tRNAs and aminoacyl-tRNAs is described. The tRNA was separated into 6 discrete bands which contained varyin aamounts of tRNA and therefore varying numbers of tRNA species. In order to locate specific tRNAs, tRNA was charged with a ¹⁴C amino acid and the aminoacyl-tRNA was located by autoradiography. With several amino acids, 2 isoaccepting species were found. In total, 30 aminoacyl-tRNAs were located.