Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least seven and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways.

An integrative re-evaluation of Typhlatya shrimp within the karst aquifer of the Yucatán Peninsula, Mexico

The Yucatán Peninsula, Mexico is a carbonate platform well-known for extensive karst networks of densely stratified aquifer ecosystems. This aquifer supports diverse anchialine fauna, including species of the globally distributed anchialine shrimp genus Typhlatya (Atyidae). Four species (T. campecheae, T. pearsei, T. dzilamensis and T. mitchelli) are endemic to the Peninsula, of which three are federally listed in Mexico. This first integrative evaluation (i.e., molecular, morphological, broad geographic and type locality sampling, and environmental data) of Yucatán Typhlatya reveals considerable species identity conflict in prior phylogenetic assessments, broad species ranges, syntopy within cave systems and five genetic lineages (of which two are new to science). Despite sampling from the type locality of endangered T. campecheae, specimens (and molecular data) were indistinguishable from vulnerable T. pearsei. Ancestral/divergence reconstructions support convergent evolution of a low-salinity ancestor for a post-Paleogene arc Yucatán + Cuba Typhlatya clade within the anchialine Atyidae clade. A secondary adaptation for the coastal-restricted euryhaline (2–37 psu), Typhlatya dzilamensis (unknown conservation status) was identified, while remaining species lineages were low-salinity (< 5 psu) adapted and found within the meteoric lens of inland and coastal caves. This study demonstrates the need for integrative/interdisciplinary approaches when conducting biodiversity assessments in complex and poorly studied aquifers.

Nitric oxide synthase/COX cross-talk: nitric oxide activates COX-1 but inhibits COX-2-derived prostaglandin production

It is recognized that there is molecular cross-talk between the inflammatory mediators NO and PGs that may regulate tissue homeostasis and contribute to pathophysiological processes. However, the literature is divided with respect to whether NO activates or inhibits PG production. In this study, we sought to determine whether conflicting observations could be accounted for by divergent effects of NO on the two cyclooxygenase (COX) isoforms. Exposure of resting macrophages to NO (30 microM) enhanced PGE2 release by 4. 5-fold. This enhancement was inhibited by indomethacin but not by the COX-2 selective inhibitor NS398. To separate the activation of phospholipase A2 and COX, we performed experiments using fibroblasts derived from COX-1-deficient or COX-2-deficient mice. These cells exhibit increased basal PG production, which is due to a constitutively stimulated cytosolic phospholipase A2 and enhanced basal expression of the remaining COX isozyme. The exposure of COX- 2-deficient cells to exogenous NO (10 microM) resulted in a 2.4-fold increase of PGE2 release above controls. Further studies indicated that NO stimulated PGE2 release in COX-2-deficient cells, without altering COX-1 mRNA or protein expression. In contrast, NO inhibited COX-2-derived PGE2 production in both LPS-stimulated macrophages and COX-1 knockout cells. This inhibition was associated with both decreased expression and nitration of COX-2. Thus, these studies demonstrate divergent effects of NO on the COX isoforms. The regulation of PGE production by NO is therefore complex and will depend on the local environment in which these pleiotropic mediators are produced.

Dynamics of cell cycle regulators: artifact-free analysis by recultivation of cells synchronized by centrifugal elutriation

Studies on the molecular properties of cell cycle regulators in animal cells require cell preparations highly enriched in particular cell cycle phases. Centrifugal elutriation is frequently used to synchronize cells because this technique was thought to cause only minimal distortions in protein expression or metabolic functions. However, in primary chicken erythroblasts, we consistently observed artefacts in mitotic cyclin mRNA expression and p70 S6 kinase activity, which were clearly caused by the elutriation procedure. Therefore, we modified the standard protocol by reseeding various elutriated fractions into preconditioned medium, a process termed recultivation, and harvesting after an appropriate amount of time. This avoided the pleiotropic effects caused by stress and lack of growth factor supply during elutriation. Using this recultivation procedure, highly synchronous progression starting from any given cell cycle phase could be achieved for a variety of cell types, including primary, factor-dependent cells of hematopoietic origin. Mitotic cyclin expression and S6 kinase activity was found to be normal again in recultivated cultures, as opposed to elutriated ones. Finally, monitoring of mitosis-specific cyclin A degradation in recultivated G2 phase cells showed that recultivation provided an excellent tool to follow cells through M phase into G1 without the requirement for a chemical cell cycle block.

Schizosaccharomyces pombe mutants that are defective in glycoprotein galactosylation

Several mutants of Schizosaccharomyces pombe were obtained that are defective in protein glycosylation. One of the mutants, strain Sp550, makes galactomannoproteins with about half of the wild-type amount of galactose, whereas another strain, Sp137, makes glycoproteins that are almost devoid of galactose. Nondenaturing gel electrophoresis of cell extracts of both mutants revealed that they make invertases with a greatly increased mobility relative to the wild type. Additional study showed that Sp137 invertase has a subunit molecular mass that is about half that reported for the wild-type enzyme, owing to a reduction in carbohydrate content, whereas the native multimeric state appears unaltered. Structural studies on bulk cell-wall glycoprotein from Sp137 showed that the N-linked carbohydrate chains consist of a typical branched core oligosaccharide to which is attached an unsubstituted alpha 1-->6-polymannose outer chain. Consequently, the cells are agglutinated by antibodies against alpha 1-->6-linked mannose and have N-linked carbohydrate chains that are structurally analogous to the mnn2 mutant of Saccharomyces cerevisiae.

Osteogenic protein-1, a bone morphogenic protein member of the TGF-beta superfamily, shares chemotactic but not fibrogenic properties with TGF-beta

We have previously shown that recombinant human osteogenic protein-1 (rhOP-1), a bone morphogenetic protein member of the TGF-beta superfamily, can induce new bone formation when implanted with an appropriate carrier at subcutaneous sites in rats and can restore completely large diaphyseal segmental defects in laboratory animals. The role of OP-1 in the early events of bone induction viz, chemotaxis of phagocytic leukocytes, and fibroblastic mesenchymal cells is currently unknown. In the present study, we examined the effect of rhOP-1 on chemotaxis of phagocytic leukocytes (human neutrophils and monocytes) and fibroblastic mesenchymal cells (infant foreskin fibroblasts). Since OP-1 is structurally related to TGF-beta 1, we assessed the effects of OP-1 on several other fibroblast functions (in addition to chemotaxis) known to be modulated by TGF-beta 1. Our results demonstrated that rhOP-1, like TGF-beta 1, is a potent chemoattractant for human neutrophils, monocytes, and fibroblasts. However, in contrast to TGF-beta 1, OP-1 does not to stimulate fibroblast mitogenesis, matrix synthesis [collagen and hyaluronic acid (hyaluronan)], or production of tissue inhibitor of metalloproteinase (TIMP), i.e., fibroblast functions associated with fibrogenesis. These results clearly demonstrate a dichotomy between these two members of the TGF-beta superfamily with a regard to fibrogenic effects on fibroblasts but a similarity in their chemotactic properties.

Schizosaccharomyces pombe glycosylation mutant with altered cell surface properties

Mutagenesis of Schizosaccharomyces pombe cells yielded a strain that made reduced amounts of invertase. A comparison of the O- and N-linked carbohydrate chains of the wild-type and mutant glycoproteins revealed that a single type of alpha 1-->2-linked mannose was missing in the mutant. Analysis of the wild-type galactomannoprotein showed that it contained a heterogeneous small "core" oligosaccharide fraction linked to asparagine with sugar compositions that ranged from Man9(GlcNAc)2- to Gal4Man10(GlcNAc)2-. The galactose units are in terminal positions of a Man10(GlcNAc)2- unit that is similar to the mannoprotein core of Saccharomyces cerevisiae. Attached to this core in a larger oligosaccharide fraction is an alpha 1-->6-linked polymannose chain that is substituted at position 2 with alpha-linked mannose and galactose. The O-linked sugars consist of mannose, alpha 1-->2-linked mannosylmannose and alpha 1-->2-linked galactosylmannose, along with small amounts of tri- and tetrasaccharides. The glycosylation mutant lacks alpha 1-->2-linked mannose on both the O-linked chains and the outer chain of the large N-linked chains, suggesting that it may be defective in regulation of an alpha 1,2-mannosyltransferase that adds mannose to glycoproteins in the Golgi.

Yeast glycoprotein biosynthesis: MNT1 encodes an alpha-1,2-mannosyltransferase involved in O-glycosylation

The Saccharomyces cerevisiae MNT1 gene encodes a Golgi mannosyltransferase. Gene disruption of the MNT1 locus leads to a greater than 90% reduction of specific alpha-1,2-mannosyltransferase activity with alpha-methylmannoside as acceptor. Null mutants of MNT1 are viable, have no apparent growth defect, and are blocked in the elongation of protein O-linked mannobiose. Structural analysis of the N-linked outer chain isolated from an mnn1 mnn10 mnt1 strain revealed no alteration in carbohydrate structure compared to the parental mnn1 mnn10 strain. The MNT1 gene is identical to KRE2, and mutations in the gene render cells resistant to the killer toxin K1 of S. cerevisiae, which suggests a role for O-mannosylated proteins in the resistance mechanism. In addition, MNT1 is part of a multigene family whose members are presumed to be yeast Golgi mannosyltransferases.

Vanadate-resistant yeast mutants are defective in protein glycosylation

Spontaneous recessive orthovanadate-resistant mutants of Saccharomyces cerevisiae were obtained in five complementation groups, and all show defects in protein glycosylation that mimic the previously isolated mnn mutants. Three of the groups are allelic to the known mnn8, mnn9, and mnn10 mutants, whereas the other two groups show other glycosylation defects. The vanadate-resistant phenotype was associated with enhanced hygromycin B sensitivity. The glycosylation phenotypes of the mutants are all reflections of defects in glycoprotein trafficking, and the easy isolation of vanadate-resistant or hygromycin B-sensitive mutants should facilitate the study of this process.

Separation of yeast asparagine-linked oligosaccharides by high-performance anion-exchange chromatography

Oligosaccharides obtained from Saccharomyces cerevisiae mannoproteins by digestion with endo-N-acetyl-beta-D-glucosaminidase H were fractionated by anion-exchange chromatography, by elution with 50-100mM NaOH without or with a sodium-acetate gradient, and detected with a pulsed amperometric detector (PAD). The elution times of homologous oligosaccharides fell on a straight line having a slope characteristic of the structural type. The response of the PAD detector per mole of oligosaccharide increased about 2-fold going from Man3GlcNAc to Man13GlcNAc, and appeared to depend primarily on the oxidation of the reducing-end N-acetylglucosamine unit common to all the oligosaccharides. The digestion of a Man10GlcNAc with jack-bean alpha-mannosidase was monitored by injecting portions of the crude reaction mixture, and the intermediates were characterized by their elution positions and n.m.r. spectra in the anomeric proton region. One commercial jack-bean alpha-mannosidase preparation contained a novel endolytic activity that released N-acetylglucosamine from the reducing ends of the oligosaccharides and was shown to convert P----6 alpha Man----6 alpha Man----6 beta Man----4 alpha beta GlcNAc to P----6 alpha Man----6 alpha Man----6 alpha beta Man plus free N-acetylglucosamine. Another commercial jack-bean alpha-mannosidase converted the Man10GlcNAc to a Man3GlcNAc having the structure alpha Man----6 beta Man----4 alpha beta GlcNAc, [formula: see text] whereas the Oerskovia sp. alpha-mannosidase converted the same oligosaccharide to a Man4GlcNAc having the structure alpha Man----6 alpha Man----6 beta Man----4 alpha beta GlcNAc. [formula: see text]

Revision of the oligosaccharide structures of yeast carboxypeptidase Y

The N-linked oligosaccharides from baker's yeast carboxypeptidase Y were analyzed by 1H NMR and specific mannosidase digestion and found to be identical to those from the Saccharomyces cerevisiae mnn9 mutant bulk mannoprotein. The results support the view that the mnn mutants make oligosaccharides that are a true reflection of the normal biosynthetic pathway and confirm that a recently revised yeast oligosaccharide structure is applicable to wild-type mannoproteins.

Localization of alpha 1----3-linked mannoses in the N-linked oligosaccharides of Saccharomyces cerevisiae mnn mutants

Neutral and phosphorylated N-linked oligosaccharides were isolated from Saccharomyces cerevisiae mnn9 and mnn9 gls1 mutant mannoproteins and separated into homologues that differed in the number of terminal alpha 1----3-linked mannoses. In each type of oligosaccharide, the addition of such mannose was shown to occur in an ordered rather than a random fashion. The results confirm and extend an earlier report that dealt with the N-linked oligosaccharides from yeast invertase [Trimble, R.B., & Atkinson, P.H. (1986) J. Biol. Chem. 261, 9815-9824], and they suggest that the postulated processing pathway can be generalized to include phosphorylated and glucose-containing N-linked oligomannosides. We conclude that this processing pathway is identical for the analogous oligosaccharides from the mnn9 and wild-type strains of S. cerevisiae. Analysis of the mnn2 mnn10 mannoprotein revealed that a similar modification occurred at the branched terminus of the outer chain as well as in the core in this mutant.

Structure of the phosphorylated N-linked oligosaccharides from the mnn9 and mnn10 mutants of Saccharomyces cerevisiae

The N-linked oligosaccharides, from Saccharomyces cerevisiae mnn1 mnn9 mutant mannoprotein extracted from the cells in hot citrate buffer, were separated by ion exchange into a monophosphate diester, a monophosphate monoester, a diphosphate diester, and a diphosphate monoester diester. The structures of the major components with diesterified phosphate were assigned as follows (where M = mannose), according to a recently revised oligosaccharide structure for the mnn mutants (Hernandez, L. M., Ballou, L., Alvarado, E., Gillece-Castro, B. L., Burlingame, A. L., and Ballou, C. E. (1989) J. Biol. Chem. 264, 11849-11856). formula; see text The monoester derivatives were mixtures of the possible isomers produced by removal of one or the other phosphoglycosyl-linked mannose units, and they were shown to arise by chemical degradation during isolation. The mnn1 mnn2 mnn10 acidic oligosaccharide fraction contained a mono- and a diphosphate ester. The monophosphate consisted predominantly of a single isomer with a mannosyl phosphate unit located at the end of the outer chain in an oligosaccharide with the following structure, where x may range from 2 to 12. The diphosphate had a mannosyl phosphate in this formula; see text position as well as one on the terminal alpha 1----6-linked mannose in the core. The presence in the mnn1 mnn9 or mnn1 mnn2 mnn10 background of the mnn4 or mnn6 mutations, which are known to regulate phosphorylation in yeast, reduced phosphorylation by 90% but did not eliminate it. AI-12522

Protein glycosylation defects in the Saccharomyces cerevisiae mnn7 mutant class. Support for the stop signal proposed for regulation of outer chain elongation

Total cell mannoprotein was isolated from Saccharomyces cerevisiae X2180 mutants that have defects in elongation of the outer chain attached to the N-linked core oligosaccharides (mnn7, mnn8, mnn9, and mnn10) (Ballou, L., Cohen, R. E., and Ballou, C. E. (1980) J. Biol. Chem. 255, 5986-5991). Comparison of the oligosaccharides released by endoglucosaminidase H digestion confirmed that the mnn9 mutation eliminates all but two mannoses of the outer chain, whereas the mnn8 and mnn10 strains produce outer chains of variable but similar lengths. The isolate designated mnn7 was found to be allelic with mnn8. Haploid mutants of the type mnn8 mnn9 or mnn9 mnn10 had the mnn9 phenotype, which established that the mnn9 defect is dominant and presumably acts at a processing step prior to the steps affected by mnn8 and mnn10. Analysis of the mnn1 mnn2 mnn10 oligosaccharides revealed that the heterogeneous outer chain contained 6-16 alpha 1----6-linked mannose units and each was terminated by a single alpha 1----2-linked mannose unit, whereas the core lacked one such unit that was present in the mnn9 oligosaccharide. The results are consistent with and support the hypothesis (Gopal, P. K., and Ballou, C. E. (1988) Proc. Natl. Acad. Sci. U.S.A. 84, 8824-8828) that addition of such a side-chain mannose unit is associated with termination of outer chain elongation in these mutants and may serve as a stop signal that regulates outer chain synthesis in the parent wild-type strain.

A new Saccharomyces cerevisiae mnn mutant N-linked oligosaccharide structure

We find that the N-linked Man8GlcNAc2- core oligosaccharide of Saccharomyces cerevisiae mnn mutant mannoproteins is enlarged by the addition of the outer chain to the alpha 1----3-linked mannose in the side chain that is attached to the beta 1----4-linked mannose rather than by addition to the terminal alpha 1----6-linked mannose. This conclusion is derived from structural studies on a phosphorylated oligosaccharide fraction and from mass spectral fragment analysis of neutral core oligosaccharides.

Effect of glycosylation on yeast invertase oligomer stability

Yeast external invertase is a glycoprotein that exists as a dimer that can associate to form tetramers, hexamers, and octamers (Chu, F., Watorek, W., and Maley, F. (1983) Arch. Biochem. Biophys. 223, 543-555; Esmon, P. C., Esmon, B. E., Schauer, I. E., Taylor, A., and Schekman, R. (1987) J. Biol. Chem., 262, 4395-4401), a process that is facilitated by the attached oligosaccharide chains. We have studied this association by high performance liquid chromatography on a gel filtration matrix, by which procedure wild-type bakers' yeast invertase gives two peaks, and invertase from a core mutant (mnn1 mnn9) of Saccharomyces cerevisiae X2180 gives three peaks. Concentration of an invertase solution by freezing drives the dimers into higher aggregates that, at 30 degrees C, re-equilibrate to a mixture of smaller forms, the composition of which depends on pH, concentration, and time. The invertase from a mutant, mnn1 mnn9 dpg1, which underglycosylates its glycoproteins and produces invertase with 4-7 oligosaccharide chains, forms oligomers of much lower stability than the mnn1 mnn9 invertase, which has 8-11 carbohydrate chains. Both of these mutants release external invertase from the periplasm into the medium during growth, but we conclude that defects in the cell wall structure may be more important in this release than an altered tendency of the invertases to aggregate. Investigation of aggregate formation by electron microscopy revealed that all invertases, including the internal nonglycosylated enzyme, form octamers under appropriate conditions.

A mutation that prevents glucosylation of the lipid-linked oligosaccharide precursor leads to underglycosylation of secreted yeast invertase

A mutant of Saccharomyces cerevisiae with the genotype mnn1 mnn2 mnn9 gls1 synthesizes mannoproteins with oligosaccharides having the composition Glc3Man10Glc-NAc2- owing to the mnn9 defect, which prevents synthesis of the outer chain, the mnn1 defect, which prevents branching of the core, and the gls1 mutation, which prevents deglucosylation of the resultant glycoprotein as a consequence of a defective glucosidase-I [Tsai, P.-K., Ballou, L., Esmon, B., Schekman, R. & Ballou, C. E. (1984) Proc. Natl. Acad. Sci. USA 81, 6340-6343]. (The mnn2 defect is not expressed in presence of the mnn9 mutation.) This strain spontaneously forms new colonies in which gls1 is suppressed owing to a defect in synthesis of dolichol phosphoglucose, the glucosylation substrate. The new mutant, designated mnn1 mnn2 mnn9 gls1 dpg1, synthesizes and secretes invertase (EC 3.2.1.26) that has a higher mobility on native gel electrophoresis than that made by the parent strain, the consequence of a reduction in both the size and the number of carbohydrate chains. The mannoprotein chains have the mnn1 mnn9 structure (Man10Glc-NAc2-), and the invertase is resolved by gel electrophoresis in sodium dodecyl sulfate into two major and two minor bands that represent homologs with about 4-7 carbohydrate units, in contrast to about 8-11 chains in the parent strain. Thus, the inability to glucosylate the lipid-linked precursor reduces the efficiency of glycosylation of the protein chains. The genetic defect is in synthesis of the glucose donor dolichol phosphoglucose, but the mutation is nonallelic with the reported alg5-1 mutation, which has a similar phenotype [Runge, K. W., Huffaker, T. C. & Robbins, P. W. (1984) J. Biol. Chem. 259, 412-417].

Isolation of glucose-containing high-mannose glycoprotein core oligosaccharides

The total cell wall mannoprotein has been isolated from a mutant of Saccharomyces cerevisiae that fails to remove the glucose units of the dolichol-linked precursor after transfer of the oligosaccharide to asparagine units in the protein. The oligosaccharides released from this mannoprotein by endoglucosaminidase H digestion show 1H NMR signals assignable to three alpha-linked glucose units as delta 5.52, 5.27, and 5.17, and a comparison with the chemical shifts of reference compounds shows that these signals are consistent with the structure alpha Glc----2 alpha Glc----3 alpha Man----2. This provides a direct confirmation for the structure previously assigned to the lipid-linked precursor. Analysis of the larger oligosaccharides confirms that the presence of the glucose units does not prevent elongation of the alpha 1----6-linked polymannose backbone or addition of alpha 1----3-linked mannose to the core.

Saccharomyces kluyveri mannoprotein mutants

Saccharomyces kluyveri cells were mutagenized with ethylmethane sulfonate and, after the cells had grown a few divisions to express any altered cell-surface antigenic structure, the culture was treated with rabbit antiserum directed against the wild type cells in order to enrich for mutants that failed to precipitate with the serum. Several mutant clones were obtained that proved to be altered in the carbohydrate component of the cell-wall mannoprotein. Whereas the wild type strain produces mannoprotein with carbohydrate side chains up to 8 mannose units in length (Zhang, W.-J., and Ballou, C. E. (1981) J. Biol. Chem. 256, 10073-10079), one of the mutants (designated mnn1) has side chains no longer than 3 mannoses. From a comparison of the carbohydrate structures of the mutant and wild type mannoproteins by beta-elimination, acetolysis, and methylation, it appears that this mutant is unable to add mannose in alpha 1 leads to 3 linkage to the alpha 1 leads to 2-linked di- and trisaccharide side chains, thus preventing elongation and branching of the chains that occur in the wild type. Another mutant, designated mnn2, was unable to make the octasaccharide chain, whereas a third class made oligosaccharides of all sizes but did so in ratios that differed from the wild type. These three classes of mutants involve different loci because they complemented each other in the heterozygous diploids.

Temperature-sensitive glucosamine auxotroph of Saccharomyces cerevisiae

Temperature-sensitive revertants were isolated from Saccharomyces cerevisiae D-glucosamine auxotrophs previously obtained in this laboratory (W. L. Whelan and C. E. Ballou, J. Bacteriol. 124:1545-1557, 1975). The auxotrophs lack the enzyme 2-amino-2-deoxy-D-glucose-6-phosphate ketol-isomerase (EC 5.3.1.19), and the revertants appear to be temperature sensitive in the formation of enzyme activity. The enzyme they produce under permissive conditions decays in activity at a rate comparable to that of the wild-type enzyme, and it has similar kinetic properties. The homozygous diploid mutant fails to sporulate at the nonpermissive temperature. Temperature shift experiments were carried out in an effort to determine what effect glucosamine deficiency had on mannoprotein secretion as reflected in the formation of external asparaginase. Although the results were complicated by the slow decay of the residual ketol-isomerase activity, they did show that mannoprotein synthesis or secretion was altered when the internal pool of D-glucosamine was depleted.