Diversity and evolution of the thyroglobulin type-1 domain superfamily

Multidomain proteins are gaining increasing consideration for their puzzling, flexible utilization in nature. The presence of the characteristic thyroglobulin type-1 (Tg1) domain as a protein module in a variety of multicellular organisms suggests pivotal roles for this building block. To gain insight into the evolution of Tg1 domains, we performed searches of protein, expressed sequence tag, and genome databases. Tg1 domains were found to be Metazoa specific, and we retrieved a total of 170 Tg1 domain-containing protein sequences. Their architectures revealed a wide taxonomic distribution of proteins containing Tg1 domains followed or preceded by secreted protein, acidic, rich in cysteines (SPARC)-type extracellular calcium-binding domains. Other proteins contained lineage-specific domain combinations of peptidase inhibitory modules or domains with different biological functions. Phylogenetic analysis showed that Tg1 domains are highly conserved within protein structures, whereas insertion into novel proteins is followed by rapid diversification. Seven different basic types of protein architecture containing the Tg1 domain were identified in vertebrates. We examined the evolution of these protein groups by combining Tg1 domain phylogeny with additional analyses based on other characteristic domains. Testicans and secreted modular calcium binding protein (SMOCs) evolved from invertebrate homologs by introduction of vertebrate-specific domains, nidogen evolved by insertion of a Tg1 domain into a preexisting architecture, and the remaining four have unique architectures. Thyroglobulin, Trops, and the major histocompatibility complex class II-associated invariant chain are vertebrate specific, while an insulin-like growth factor-binding protein and nidogen were also identified in urochordates. Among vertebrates, we observed differences in protein repertoires, which result from gene duplication and domain duplication. Members of five groups have been characterized at the molecular level. All exhibit subtle differences in their specificities and function either as peptidase inhibitors (thyropins), substrates, or both. As far as the sequence is concerned, only a few conserved residues were identified. In combination with structural data, our analysis shows that the Tg1 domain fold is highly adaptive and comprises a relatively well-conserved core surrounded by highly variable loops that account for its multipurpose function in the animal kingdom.     

Dual concentration-dependent activity of thyroglobulin type-1 domain of testican: specific inhibitor and substrate of cathepsin L

The thyroglobulin type-1 (Tg-1) domain is a protein module that occurs in a variety of secreted and membrane proteins and is recognised as a potent inhibitor of cysteine peptidases. We present here some properties of the Tg-1 domain of human testican, a modularly organised proteoglycan secreted mainly by brain cells, the exact in vivo function of which is not yet clear. The domain was prepared as a recombinant protein in a Pichia pastoris expression system and its activity was demonstrated by specific and selective inhibition of cathepsin L (K(i) =0.14 nM). Interaction at high enzyme and inhibitor concentrations resulted in degradation of the domain by cathepsin L, which was not observed under conditions used for the determination of kinetic parameters. No inhibitory activity could be detected for cathepsin K, but it exhibited a very similar degradation pattern. Homology modelling provided a good explanation for the different behaviour observed with the two enzymes. Firstly, the steric fit between the interfaces of testican domain and cathepsin L is stabilised by numerous favourable forces, while no such interactions are evident in the complex with cathepsin K, and repulsive interactions even prevent access of the domain to the active site of papain. Secondly, the prolonged first loop of the domain occupies a position near the catalytic cysteine residue in a more substrate-like manner, enabling cleavage of the Gly22-Ala23 bond.     

Individual recombinant thyroglobulin type-1 domains are substrates for lysosomal cysteine proteinases

Thyroglobulin contains 11 repeats of a motif called thyroglobulin type-1 domain that show sequence similarity to some proteins exhibiting inhibitory activity against cysteine proteinases. Here we report that thyroglobulin decreases the activity of cathepsins B, H, L, and papain. To examine the possible involvement of particular type-1 domains in that decrease of activity, some individual thyroglobulin type-1 domains were expressed in E. coli. These recombinant domains proved to be substrates for cathepsins B, H, L, and papain instead of inhibitors. The cleavage points with cathepsins B and L on the second and the fourth domains were determined. The possible reasons for degradation are discussed.     

Plants and environment: Two decades of research at the Canberra phytotron

The research carried out at the Canberra phytotron, CERES, during the first twenty years of its operation is reviewed as a case study of the opportunities, problems and value of phytotron research. The climatic responses of a large number of species, both wild and domesticated, are examined as well as those of fungal and viral pathogens and rhizobial symbionts. Some aspects of the design of CERES are briefly considered, and a few aspects of the variation between plants in climatic response, with the C₄ photosynthetic syndrome taken as a case history of the linkages between biochemistry, anatomy and response to climate. Research in ecology, forestry, horticulture, plant pathology, rhizobial microbiology, anatomy and ultrastructure—and specific aspects of biochemistry, plant nutrition and genetics—are reviewed to indicate the range of botanical disciplines which can profit from access to a phytotron. The ecological research at CERES, much of it with trees and perennial grasses, particularly highlights the value of combining field and phytotron studies. Work on seed proteins, hybrid vigor and plant growth regulators is also reviewed. The next part of the paper considers the effects of the major environmental factors, temperature, daylength, irradiance, atmospheric CO₂ level and water stress, together with their interactions and the problems of correlating phytotron and field responses. The effect of these factors on the various processes of growth and development are considered, and the stages of development most sensitive to them. An evolutionary perspective on yield potential is then discussed, leading to a consideration of photosynthesis, translocation, partitioning and storage organ growth as yield-determining processes. The final part considers the uses of phytotrons in agricultural, horticultural and forestry research, in terms of examples from work at CERES on the manipulation of breeding systems, the clarification of plant breeding objectives, the use of phytotron conditions for selection, the prediction of adaptation and spread, and models for yield prediction and pest management. Several areas requiring more attention are identified, and some conclusions are drawn on the value of access to a phytotron such as CERES for botanical research of many kinds.     

Identification and domain mapping of Dictyostelium discoideum type-1 protein phosphatase inhibitor-2

The protein phosphatase type-1 catalytic subunit (PP1c) does not exist freely in the cell and its activity must be very strictly controlled. Several protein inhibitors of PP1c have been described including the classical mammalian inhibitor-1 (I-1) and inhibitor-2 (I-2). Association of these inhibitors with PP1c appears to involve multiple contacts and in the case of I-2 no less than five I-2 interaction subdomains have been proposed. In this report, we provide both in vitro and in vivo evidence that the Dictyostelium discoideum genome encodes a protein (DdI-2) that is an ortholog of mammalian I-2, being the first PP1c interacting protein characterized in this social amoeba. Despite the low overall sequence similarity of DdI-2 with other I-2 sequences and its long N-terminal extension, the five PP1c interaction motifs proposed for mammalian I-2 are reasonably conserved in the Dictyostelium ortholog. We demonstrate that DdI-2 interacts with and inhibits D. discoideum PP1c (DdPP1c), which we have previously characterized. Moreover, using yeast two-hybrid assays we show that a stable interaction of DdI-2 with DdPP1c requires multiple contacts.     

The rat asialoglycoprotein receptor binds the amino-terminal domain of thyroglobulin

We have previously reported that the rat hepatic lectin-1 (RHL-1) subunit of rat asialoglycoprotein receptor (ASGPr), the endocytic receptor found on the basolateral surface of hepatocytes, was expressed in rat thyroid tissue and localized on the apical surface of polarized rat thyroid FRT cells. Here we show that PC Cl3 cells, a differentiated rat thyroid cell line, bound thyroglobulin (Tg) via ASGPr. In fact, both the bacterial recombinant carbohydrate recognition domain of RHL-1 (rCRD(RHL-1)) and the anti-rCRD(RHL-1) antibody markedly inhibited (125)I-Tg binding to the cell surface of PC Cl3 cells. Ligand blot assays with deglycosylated Tg show that the rCRD(RHL-1) was able to interact with Tg even after remotion of sugars. The region of Tg involved in the binding to RHL-1 was investigated by ligand blot assays with biotinylated rCRD(RHL-1) on thermolysin-digested native and desialated rat thyroglobulin. It is shown that the rCRD(RHL-1) specifically recognized a thyroglobulin fragment with an apparent M(r) of 68,000, corresponding to the amino-terminal part of the molecule. To our knowledge, this is the first report that attributes to the amino-terminal portion of Tg molecule, containing its earliest and major hormonogenic site, the function of binding to a cell surface receptor of the thyroid. Moreover, we show that oligosaccharides are not the only molecular signals for binding to RHL-1, but amino acidic determinants could also play a role.     

Single channel function of recombinant type-1 inositol 1,4,5-trisphosphate receptor ligand binding domain splice variants.

In this study we describe the expression and function of the two rat type-1 inositol 1,4,5-trisphosphate receptor (InsP3R) ligand binding domain splice variants (SI+/-/SII+). Receptor protein from COS-1 cells transfected with the type-1 InsP3R expression plasmids (pInsP3R-T1, pInsP3R-T1ALT) or control DNA were incorporated into planar lipid bilayers and the single channel properties of the recombinant receptors were defined. The unitary conductance of the two splice variants were approximately 290 pS with Cs+ as charge carrier and approximately 65 pS with Ca2+ as charge carrier. Both InsP3R expression products consistently behaved like those of the native type-1 receptor isoform isolated from cerebellum in terms of their InsP3, Ca2+, and heparin sensitivity. An InsP3 receptor ligand binding domain truncation lacking the 310 amino-terminal amino acids (pInsP3R-DeltaT1ALT) formed tetrameric complexes but failed to bind InsP3 with high affinity, and did not form functional Ca2+ channels when reconstituted in lipid bilayers. These data suggest that 1) the ligand binding alternative splice site is functionally inert in terms of InsP3 binding and single channel function, and 2) the single channel properties of the expressed recombinant type-1 channel are essentially identical to those of the native channel. This work establishes a foundation from which molecular/biophysical approaches can be used to define the structure-function properties of the InsP3 receptor channel family.     

Subcellular localization and regulation of type-1C and type-5 phosphodiesterases

We investigated the subcellular localization of PDE5 in in vitro human myometrial cells. We demonstrated for the first time that PDE5 is localized in discrete cytoplasmic foci and vesicular compartments corresponding to centrosomes. We also found that PDE5 intracellular localization is not cell- or species-specific, as it is conserved in different animal and human cells. PDE5 protein levels are strongly regulated by the mitotic activity of the smooth muscle cells (SMCs), as they were increased in quiescent, contractile myometrial cultures, and conditions in which proliferation was inhibited. In contrast, PDE1C levels decreased in all conditions that inhibited proliferation. This mirrored the enzymatic activity of both PDE5 and PDE1C. Increasing cGMP intracellular levels by dbcGMP or sildenafil treatments did not block proliferation, while dbcAMP inhibited myometrial cell proliferation. Together, these results suggest that PDE5 regulation of cGMP intracellular levels is not involved in the control of SMC cycle progression, but may represent one of the markers of the contractile phenotype.     

Evolution of research on cellular motility over five decades

This short review traces how our knowledge of the molecular mechanisms of cellular movements originated and developed over the past 50 years. Work on actin-based and microtubule-based movements developed in different ways, but in both fields, the discovery of the key proteins drove progress. Starting from an inventory of zero molecules in 1960, both fields matured spectacularly, so we now know the atomic structures of the important proteins, understand the kinetics and thermodynamics of their interactions, have documented how the molecules behave in cells, and can test theories with molecularly explicit computer simulations of cellular processes.     

Two rings of negative charges in the cytosolic vestibule of type-1 ryanodine receptor modulate ion fluxes

The tetrameric ryanodine receptor calcium release channels (RyRs) are cation-selective channels that have pore architecture similar to that of K+ channels. We recently identified, in close proximity to the selectivity filter motif GGGIG, a conserved lumenal DE motif that has a critical role in RyR ion permeation and selectivity. Here, we substituted three aspartate residues (D4938, D4945, D4953) with asparagine and four glutamate residues (E4942, E4948, E4952, E4955) with glutamine hypothesized to line the cytosolic vestibule of the skeletal muscle RyR (RyR1). Mutant single channel properties were determined using the planar lipid bilayer method. Two mutants (D4938N, D4945N) showed a reduced K+ ion conductance, with D4938N also exhibiting a reduced selectivity for Ca2+ compared to K+. The cytosolic location of D4938 and D4945 was confirmed using the polycation neomycin. Both D4938N and D4945N exhibited an attenuated block by neomycin to a greater extent from the cytosolic than lumenal side. By comparison, charge neutralization of lumenal loop residues (D4899Q, E4900N) eliminated the block from the lumenal but not the cytosolic side. The results suggest that, in addition to negatively charged residues on the lumenal side, rings of four negative charges formed by D4938 and D4945 in the cytosolic vestibule determine RyR ion fluxes.     

Two decades of advancement in the assessment of fetal health.

Over the past twenty years there has been a substantial refining and extension of the tests available for the assessment of fetal health. This has particularly been related to the developed of reasonably-priced real-time ultrasound and an improved understanding of the relationship between aspects of fetal behaviour and state and fetal health. The impact of these developments is briefly reviewed.     

Two decades of describing the unseen majority of aquatic microbial diversity

Aquatic environments harbour large and diverse microbial populations that ensure their functioning and sustainability. In the current context of global change, characterizing microbial diversity has become crucial, and new tools have been developed to overcome the methodological challenges posed by working with microbes in nature. The advent of Sanger sequencing and now next-generation sequencing technologies has enabled the resolution of microbial communities to an unprecedented degree of precision. However, to correctly interpret microbial diversity and its patterns this revolution must also consider conceptual and methodological matters. This review presents advances, gaps and caveats of these recent approaches when considering microorganisms in aquatic ecosystems. We also discuss potentials and limitations of the available methodologies, from water sampling to sequence analysis, and suggest alternative ways to incorporate results in a conceptual and methodological framework. Together, these methods will allow us to gain an unprecedented understanding of microbial diversity in aquatic ecosystems.     

Two decades with dimorphic Chloride Intracellular Channels (CLICs)

Plasma membrane channels have been extensively studied, and their physiological roles are well established. In contrast, relatively little information is available about intracellular ion channels. Chloride Intracellular Channel (CLICs) proteins are a novel class of putative intracellular ion channels. They are widely expressed in different intracellular compartments, and possess distinct properties such as the presence of a single transmembrane domain, and a dimorphic existence as either a soluble or membranous form. How these soluble proteins unfold, target to, and auto-insert into the intracellular membranes to form functional integral ion channels is a complex biological question. Recent information from studies of their crystal structures, biophysical characterization and functional roles has provoked interest in these unusual channels.     

Characterization of the two oligosaccharides present in the preferential hormonogenic domain of human thyroglobulin

The N-terminal fragment of human thyroglobulin (residues 1 to 171) contains the preferential hormonogenic site of the molecule and 2 potential sites of N-glycosylation (Asn57 and Asn91). This fragment was isolated from a human thyroglobulin purified from a single goiter. The tryptic peptides bearing the glycosylation sites were separated by Bio-Gel P-30 and HPLC columns. The oligosaccharides borne at each site were analyzed, after tritium labeling, by concanavalin A-Sepharose and HPLC. At both sites the structures observed are heterogenous, with a majority of biantennary complex type structures.