The relationship between N-terminal sequences and immunological characterization of crustacean hemocyanins

1. N-terminal amino acid sequences of seven crustacean hemocyanin subunits were determined and compared together with a number of known N-terminal sequences. 2. Within crustacean infraorders, relationships of subunits were established. Relationships based on N-terminal sequences were compared with a classification based on immunological characterization.     

Cytochrome c oxidase: structure, function, and membrane topology of the polypeptide subunits.

Mitochondrial cytochrome c oxidase and its bacterial homologs catalyze electron transfer and proton translocation reactions across membranes. The eukaryotic enzyme complex consists of a large number of polypeptide subunits. Three of the subunits (I, II, and III) are mitochondrially encoded while the remaining 6 (yeast) to 10 (bovine) are nuclear encoded. Antibody and chemical-labelling experiments suggest that subunits I-III and most (but not all) of the nuclear-encoded subunits span the inner mitochondrial membrane. Subunits I and II are the catalytic core of the enzyme. Subunit I contains haem a, haem a3 and CuB, while subunit II contains CuA and the cytochrome c binding site. Subunit III and most of the nuclear subunits are essential for the assembly of a functional catalytic enzyme. Some nuclear subunits are present as isozymes, although little functional difference has yet been detected between enzyme complexes composed of different isozymes. Therefore, any additional role attributed to the nuclear-encoded subunits beyond that of enzyme assembly must be tentative. We suggest that enough evidence exists to support the idea that modification of the larger nuclear subunits (IV, V, and possibly VI) can effect enzyme turnover in vitro. Whether this is a physiological control mechanism remains to be seen.     

Reconstitution of CF IA from overexpressed subunits reveals stoichiometry and provides insights into molecular topology

Yeast cleavage factor I (CF I) is an essential complex of five proteins that binds signal sequences at the 3' end of yeast mRNA. CF I is required for correct positioning of a larger protein complex, CPF, which contains the catalytic subunits executing mRNA cleavage and polyadenylation. CF I is composed of two parts, CF IA and Hrp1. The CF IA has only four subunits, Rna14, Rna15, Pcf11, and Clp1, but the structural organization has not been fully established. Using biochemical and biophysical methods, we demonstrate that CF IA can be reconstituted from bacterially expressed proteins and that it has 2:2:1:1 stoichiometry of its four proteins, respectively. We also describe mutations that disrupt the dimer interface of Rna14 while preserving the other subunit interactions. On the basis of our results and existing interaction data, we present a topological model for heterohexameric CF IA and its association with RNA and Hrp1.     

Structure and properties of hemocyanins. XII. Electron microscopy of dissociation products of Helix pomatia alpha-hemocyanin: quaternary structure

Electron microscopy of the dissociation products of α-hemocyanin of the snail Helix pomatia reveals two distinctly different conformations of $\text{1}\text{10}$-size molecules: a C(compact)-form at high ionic strength and pH near 8, and an L(loose)-form at low ionic strength and/or higher pH.The size and shape of the C-$\text{1}\text{10}$-size molecules indicate a dissociation of the $\text{1}\text{2}$-size molecules along the (10,9) helical grooves, which have been shown to be boundaries between the morphological units of the cylinder wall (Mellema &; Klug, 1972). The 5-fold collar is distributed evenly among the C-$\text{1}\text{10}$-size molecules.The C → L conformational change is characterized by a drastic loosening of the $\text{1}\text{10}$-size molecules to a flexible cluster of globules, with a concomitant decrease of sedimentation coefficient and increase of intrinsic viscosity and frictional ratio.The $\text{1}\text{20}$-size molecule appears as a flexible, linear chain of seven or eight globules with a diameter of 55 to 60 Å. These globules are inferred to be the minimal oxygen binding units with a molecular weight of about 50,000, linked together by short stretches of the polypeptide chain.Stable intermediate dissociation products, $\text{2}\text{10}$, $\text{3}\text{10}$ and $\text{4}\text{10}$-size molecules, were obtained by intramolecular crosslinking of $\text{1}\text{2}$-size molecules with dimethyl-suberimidate prior to dissociation.     

Membrane topology and quaternary structure of cardiac gap junction ion channels.

The membrane topology and quaternary structure of rat cardiac gap junction ion channels containing alpha 1 connexin (i.e. Cx43) have been examined using anti-peptide antibodies directed to seven different sites in the protein sequence, cleavage by an endogenous protease in heart tissue and electron microscopic image analysis of native and protease-cleaved two-dimensional membrane crystals of isolated cardiac gap junctions. Specificity of the peptide antibodies was established using dot immunoblotting, Western immunoblotting, immunofluorescence and immunoelectron microscopy. Based on the folding predicted by hydropathy analysis, five antibodies were directed to sites in cytoplasmic domains and two antibodies were directed to the two extracellular loop domains. Isolated gap junctions could not be labeled by the two extracellular loop antibodies using thin-section immunogold electron microscopy. This is consistent with the known narrowness of the extracellular gap region that presumably precludes penetration of antibody probes. However, cryo-sectioning rendered the extracellular domains accessible for immunolabeling. A cytoplasmic "loop" domain of at least Mr = 5100 (residues (101 to 142) is readily accessible to peptide antibody labeling. The native Mr = 43,000 protein can be protease-cleaved on the cytoplasmic side of the membrane, resulting in an Mr approximately 30,000 membrane-bound fragment. Western immunoblots showed that protease cleavage occurs at the carboxy tail of the protein, and the cleavage site resides between amino acid residues 252-271. Immunoelectron microscopy demonstrated that the Mr approximately 13,000 carboxy-terminal peptide(s) is released after protease cleavage and does not remain attached to the Mr approximately 30,000 membrane-bound fragment via non-covalent interactions. Electron microscopic image analysis of two-dimensional membrane crystals of cardiac gap junctions revealed that the ion channels are formed by a hexagonal arrangement of protein subunits. This quaternary arrangement is not detectably altered by protease cleavage of the alpha 1 polypeptide. Therefore, the Mr approximately 13,000 carboxyterminal domain is not involved in forming the transmembrane ion channel. The similar hexameric architecture of cardiac and liver gap junction connexins indicates conservation in the molecular design of the gap junction channels formed by alpha or beta connexins.     

Identification, structure, and properties of hemocyanins from Diplopod myriapoda.

Hemocyanins are copper-containing, respiratory proteins that occur in the hemolymph of many arthropod species. Here we report for the first time the presence of hemocyanins in the diplopod Myriapoda, demonstrating that these proteins are more widespread among the Arthropoda than previously thought. The hemocyanin of Spirostreptus sp. (Diplopoda: Spirostreptidae) is composed of two immunologically distinct subunits in the 75-kDa range that are most likely arranged in a 36-mer (6 x 6) native molecule. It has a high oxygen affinity (P(50) = 4.7 torr) but low cooperativity (h = 1.3 +/- 0.2). Spirostreptus hemocyanin is structurally similar to the single known hemocyanin from the myriapod taxon, Scutigera coleoptrata (Chilopoda), indicating a rather conservative architecture of the myriapod hemocyanins. Western blotting demonstrates shared epitopes of Spirostreptus hemocyanin with both chelicerate and crustacean hemocyanins, confirming its identity as an arthropod hemocyanin.     

The visual pigments of four deep-sea crustacean species

Summary The visual pigments of four mesopelagic crustacean species were studied at sea by means of microspectrophotometry. The absorbance maxima obtained for the visual pigments and their metarhodopsins, respectively, were: 493 nm and 481 nm (Systellaspis debilis), 485 nm and 480 nm (Acanthephyra curtirostris), 491 nm and 482 nm (A. smithi), and 495 nm and 487 nm (Sergestes tenuiremis). The spectral characteristics of the rhodopsins and metarhodopsins permit high photosensitivity and facilitate photoregeneration in a nearly monochromatic environment. Photic regeneration of rhodopsins from the deep-sea environment was demonstrated, and data were obtained which are consistent with the occurrence of dark regeneration. Specific optical density of the observed visual pigments was calculated for two species.     

Hemoglobins and hemocyanins: comparative aspects of structure and function.

Comparative studies of protein structure and function can be quite interesting by themselves, and even more interesting when interpreted with respect to an animal's physiology. In the case of fish hemoglobins, some success in the latter has been achieved but there are still many unsolved problems. It appears that comparative physiology and biochemistry have entered an era where results from comparative studies can shed a great deal of light on biochemical mechanisms in general. The trout hemoglobin system is an example. Distinctive hemoglobins in this system are presently being used as high resolution probes of the ligand-binding mechanism. Characterization of the multiple, structurally distinct subunits of the 60S Limulus hemocyanin molecule may similarly aid in understanding its function. Our studies suggest the possibility of using Limulus hemocyanin and other hemocyanins as structural homologs and analogs of more complex macromolecular arrays. The rapid development of molecular structural data from X-ray crystallographers combined with the vast data of comparative physiology and biochemistry makes this one of the most exciting areas in present day science.     

The effects of CO2 on sestonic stoichiometry and community structure of crustacean zooplankton in a eutrophic lake: Increased competitive ability of Bosmina

To explore the effects of CO₂ concentration on the sestonic stoichiometric values and the community structure of crustacean zooplankton in a eutrophic lake, in situ microcosm experiments were conducted at the Lake Taihu Ecosystem Station in spring and summer of 2012. The experimental treatments were three concentrations of CO₂, 270, 380 and 750 ppm, which represented preindustrial and present levels and the level predicted for the end of this century, respectively. The elevated atmospheric CO₂ concentration increased the sestonic C:P ratio, particularly in the spring when the C:P ratio was two-fold greater at the high level of CO₂ than at the low level of CO₂. As a result, the contribution of Bosmina to total crustacean zooplankton abundance increased, most likely because of the low phosphorus content and high adaptability to foods with large elemental ratio variation. The other dominant crustacean zooplankton genera, including Daphnia, Ceriodaphnia, Diaphanosoma and Sinocalanus, had no response to the change in pCO₂ during the microcosm experiments. The shift in crustacean zooplankton community structure between two seasons was primarily due to the transition of the phytoplankton community.     

Quadruplex DNA: sequence, topology and structure

G-quadruplexes are higher-order DNA and RNA structures formed from G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential quadruplex sequences have been identified in G-rich eukaryotic telomeres, and more recently in non-telomeric genomic DNA, e.g. in nuclease-hypersensitive promoter regions. The natural role and biological validation of these structures is starting to be explored, and there is particular interest in them as targets for therapeutic intervention. This survey focuses on the folding and structural features on quadruplexes formed from telomeric and non-telomeric DNA sequences, and examines fundamental aspects of topology and the emerging relationships with sequence. Emphasis is placed on information from the high-resolution methods of X-ray crystallography and NMR, and their scope and current limitations are discussed. Such information, together with biological insights, will be important for the discovery of drugs targeting quadruplexes from particular genes.     

The leukocidin pore: evidence for an octamer with four LukF subunits and four LukS subunits alternating around a central axis

The staphylococcal alpha-hemolysin (alphaHL) and leukocidin (Luk) polypeptides are members of a family of related beta-barrel pore-forming toxins. Upon binding to susceptible cells, alphaHL forms water-filled homoheptameric transmembrane pores. By contrast, Luk pores are formed by two classes of subunit, F and S, rendering a heptameric structure displeasing on symmetry grounds at least. Both the subunit stoichiometry and arrangement within the Luk pore have been contentious issues. Here we use chemical and genetic approaches to show that (1) the predominant, or perhaps the only, form of the Luk pore is an octamer; (2) the subunit stoichiometry is 1:1; and (3) the subunits are arranged in an alternating fashion about a central axis of symmetry, at least when a fused LukS-LukF construct is used. The experimental approaches we have used also open up new avenues for engineering the arrangement of the subunits of beta-barrel pore-forming toxins.     

A dynamic quaternary structure of bovine alpha-crystallin as indicated from intermolecular exchange of subunits

The structural bovine eye lens protein alpha-crystallin was dissociated in 7 M urea and its four subunits, A1, A2, B1, and B2, were separated by means of ion-exchange chromatography. Homopolymeric reaggregates of these subunits were prepared by removal of the denaturant via dialysis. It was found that subunits were exchanged upon incubation of mixtures of two homopolymers under native conditions. New hybrid species were formed within 24 h as demonstrated by isoelectric focusing. Moreover, native alpha-crystallin molecules also exchanged subunits when incubated with homopolymeric aggregates of B2 subunits. Subunit exchange between native alpha-crystallin molecules is postulated, and a "dynamic quaternary structure" is presented that allows the polydisperse protein to adapt to changes in cytoplasmic conditions upon aging of the lens tissue.     

Carbon, nitrogen and phosphorus stoichiometry of crustacean zooplankton in the Baltic Sea: implications for nutrient recycling

The carbon (C), nitrogen (N) and phosphorus (P) contents (%of dry weight) of some crustacean zooplankton were studied inthe Baltic Sea. The copepod Acartia sp. had a stable C and Ncontent (48.3 ± 0.8% C, 12.4 ± 0.2% N, C:N ratio4.5 ± 0.1). The P content was variable (1–2%),probably depending on developmental stage and season. Copepodsaccumulating fat, like Pseudocalanus minutus elongatus, hadhigher and more variable C content (50–60%), and lowerN and P content (7–12% N, 0.6–1.5% P). The highestC and lowest N and P contents were found in adult Limnocalanusmacrurus. However, the N:P ratio was apparently independentof fat content and between 14 and 27 for all copepods. The cladoceransBosmina longispina maritima and Evadne nordmanni had lower Ncontent (9.3–10.8%) and higher C:N ratio (5.1–5.7)than Acartia sp. The P content (1.2–1.4%) was similarto Acartia sp. and the N:P ratios (16–19) were in thelower range of that found for the copepods. The N:P ratio wasgenerally somewhat higher in the copepods than in seston, whichmost of the year had nearly Redfield C:N:P ratios. Potentially,nutrient recycling from crustacean zooplankton could enhanceN limitation of phytoplankton, but small stoichiometric differencessuggest that this effect is probably weak. The extent is dependenton the structure of the zooplankton community and the grossgrowth efficiencies. Acartia copepodites, which had nearly RedfieldN:P ratios, would have the opposite effect and enhance P limitationin late summer when seston N:P ratios increased.     

Immunological correlates between multiple isolated subunits of Androctonus australis and Limulus polyphemus hemocyanins: an evolutionary approach

Immunological cross-reactivities between isolated subunits of the scorpion Androctonus australis (Aa) and of the horseshoe crab Limulus polyphemus (Lp) hemocyanins were studied using subunit-specific antibodies prepared through immunoadsorption to pure immobilized subunits. Rocket immunoelectrophoreses of the various subunits of both hemocyanins were carried out at constant antigen concentration against the various subunit-specific antibody preparations. Then the data were analyzed through factorial correspondence analysis and compared to the respective intramolecular locations of the subunits in both hemocyanins. The results show that the dimeric subunits located in the central part of each (4 X 6)meric structure (Aa whole molecule and Lp half molecule) were strongly preserved. In addition, the (8 X 6)mer-forming subunit of Lp hemocyanin (LpIV) and the subunit occupying the same intramolecular position in Aa hemocyanin (Aa5A) were also strongly preserved. Besides the strong antigenic relatedness, less pronounced crossed immunoprecipitations or no precipitation at all were observed between subunits with homologous positions suggesting a minor structural and/or functional roles for these subunits. All the antigen-antibody combinations leading to an absence of immunoprecipitation were screened for the presence of soluble immunocomplexes by radioimmunological tests. In all cases, soluble immunocomplexes were observed. These results suggest the following evolution scenario. First, the central dimeric subunits, responsible of the dodecamer aggregation (Aa3C and 5B and LpV and VI) were already differentiated when Merostomata diverged from Arachnida. Second, the differentiation of the (8 X 6)mer-forming subunit occurred in the Merostomata ramification in a preserved subunit already possessing a functional advantage. Third, the differentiation of subunits Aa3A and Aa3B recently occurred in the scorpion ramification.     

In vitro reassembly of the membranous vesicle from Escherichia coli outer membrane components: Role of individual compnents and magnesium ions in reassembly

A method was developed for the reassembly of membranous vesicle from the sodium dcoxycholate-dissociated outer membrane components of Escherichia coli. The removal of the detergent by dialysis and the presence of Mg²⁺ were essential for the reassembly.Membrane protein alone did not form any membranous structure. Closed membranous vesicles similar to the native outer membrane were reassembled only when protein was mixed with both lipopolysaccharide and phospholipid in deoxycholate solution and subsequently dialyzed. The membrane showed a distinct trilaminar structure with a center-to-center distance between two dark lines of 53 Å, which is a characteristic of the native outer membrane. This characteristic trilaminar structure was shown to be due to the presence of lipopolysaccharide. Phospholipd was required for the vesicularization of membrane. Lipopolysaccharide and/or phospholipid formed a membranous structure in the absence of protein, while the morphology of their negatively stained sample was quite different from that of the native outer membrane unless the outer membrane protein was added to the reassembly mixture.The protein from the cytoplasmic membrane was unable to reform membranous vesicle with lipopolysaccharide and phospholipid, indicating that the reassembly system discriminated outer membrane proteins from cytoplasmic membrane proteins.     

The fine structure of fast and slow crustacean muscles

Known phasic and tonic muscle fibers of the crab Cancer magister were studied by electron microscopy. Phasic fibers have sarcomeres about 4.5 µ long, small polygonal myofibrils, and a well-developed sarcoplasmic reticulum. The thick myofilaments, disposed in hexagonal array, are each surrounded by six thin filaments. The tonic fibers have a sarcomere length of about 12 µ, larger myofibrils, a poorly developed sarcoplasmic reticulum, and a disorderly array of myofilaments. Each thick myofilament is surrounded by 10–12 thin filaments. The same morphological type of slow muscle has been found in the crustaceans, Macrocyclops albidus, Cypridopsis vidua, and Balanus cariosus, in each case in an anatomical location consistent with tonic action. A search of the literature indicates that this type of muscle is found in all classes of arthropods and is confined to visceral and postural muscles or specializations of these.     

Molecular mass of macromolecules and subunits and the quaternary structure of hemoglobin from the microcrustacean Daphnia magna

The molecular masses of macromolecules and subunits of the extracellular hemoglobin from the fresh-water crustacean Daphnia magna were determined by analytical ultracentrifugation, multiangle laser light scattering and electrospray ionization mass spectrometry. The hemoglobins from hypoxia-incubated, hemoglobin-rich and normoxia-incubated, hemoglobin-poor Daphnia magna were analyzed separately. The sedimentation coefficient of the macromolecule was 17.4 +/- 0.1 S, and its molecular mass was 583 kDa (hemoglobin-rich animals) determined by AUC and 590.4 +/- 11.1 kDa (hemoglobin-rich animals) and 597.5 +/- 49 kDa (hemoglobin-poor animals), respectively, determined by multiangle laser light scattering. Measurements of the hemoglobin subunit mass of hemoglobin-rich animals by electrospray ionization mass spectrometry revealed a significant peak at 36.482 +/- 0.0015 kDa, i.e. 37.715 kDa including two heme groups. The hemoglobin subunits are modified by O-linked glycosylation in the pre-A segments of domains 1. No evidence for phosphorylation of hemoglobin subunits was found. The subunit migration behavior during SDS/PAGE was shown to be influenced by the buffer system used (Tris versus phosphate). The subunit mass heterogeneity found using Tris buffering can be explained by glycosylation of hemoglobin subunits. Based on molecular mass information, Daphnia magna hemoglobin is demonstrated to consist of 16 subunits. The quaternary structure of the Daphnia magna hemoglobin macromolecule was assessed by three-dimensional reconstructions via single-particle analysis based on negatively stained electron microscopic specimens. It turned out to be much more complex than hitherto proposed: it displays D4 symmetry with a diameter of approximately 12 nm and a height of about 8 nm.     

H(+)-translocating NADH-quinone oxidoreductase (NDH-1) of Paracoccus denitrificans. Studies on topology and stoichiometry of the peripheral subunits.

The proton-translocating NADH-quinone oxidoreductase (NDH-1) of Paracoccus denitrificans is composed of at least 14 subunits (NQO1-14) and is located in the cytoplasmic membrane. In the present study, topological properties and stoichiometry of the 7 subunits (NQO1-6 and NQO9) of the P. denitrificans NDH-1 in the membranes were investigated using immunological techniques. Treatments with chaotropic reagents (urea, NaI, or NaBr) or with alkaline buffer (pH 10-12) resulted in partial or complete extraction of all the subunits from the membranes. Of interest is that when NaBr or urea were used, the NQO6 and NQO9 subunits remained in the membranes, whereas the other subunits were completely extracted, suggesting their direct association with the membrane part of the enzyme complex. Both deletion study and homologous expression study of the NQO9 subunit provided a clue that its hydrophobic N-terminal stretch plays an important role in such an association. In light of this observation and others, topological properties of the subunits in the NDH-1 enzyme complex are discussed. In addition, determination of stoichiometry of the peripheral subunits of the P. denitrificans NDH-1 was completed by radioimmunological methods. All the peripheral subunits are present as one molecule each in the enzyme complex. These results estimated the total number of cofactors in the P. denitrificans NDH-1; the enzyme complex contains one molecule of FMN and up to eight iron-sulfur clusters, 2x[2Fe-2S] and 6x[4Fe-4S], provided that the NQO6 subunit bears one [4Fe-4S] cluster.