Functional recycling of C2 domains throughout evolution: A comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches

The C2 domain is one of the most frequent and widely distributed calcium-binding motifs. Its structure comprises an eight-stranded beta-sandwich with two structural types as if the result of a circular permutation. Combining sequence, structural and modelling information, we have explored, at different levels of granularity, the functional characteristics of several families of C2 domains. At the coarsest level,the similarity correlates with key structural determinants of the C2 domain fold and, at the finest level, with the domain architecture of the proteins containing them, highlighting the functional diversity between the various subfamilies. The functional diversity appears as different conserved surface patches throughout this common fold. In some cases, these patches are related to substrate-binding sites whereas in others they correspond to interfaces of presumably permanent interaction between other domains within the same polypeptide chain. For those related to substrate-binding sites, the predictions overlap with biochemical data in addition to providing some novel observations. For those acting as protein-protein interfaces' our modelling analysis suggests that slight variations between families are a result of not only complementary adaptations in the interfaces involved but also different domain architecture. In the light of the sequence and structural genomic projects, the work presented here shows that modelling approaches along with careful sub-typing of protein families will be a powerful combination for a broader coverage in proteomics. (C) 2003 Elsevier Ltd. All rights reserved.

Changes in organic matter production and accumulation as a mechanism for isotopic evolution in the Mesoproterozoic ocean

Mesoproterozoic marine successions worldwide record a shift in average delta(13)C values from 0 to +3.5parts per thousand, with the latter value evident in successions younger than 1250 Ma. New carbon isotope data from the similar to 1300 to 1270 Ma Dismal Lakes Group, Arctic Canada, provide further insight into this fundamental transition. Data reveal that the shift to higher VC values was gradual and marked by occasional excursions to values less than 0 parts per thousand. When compared to records from older and younger marine successions, it is evident that the difference between isotopic minima and maxima increased with time, indicating that the marine system evolved to become isotopically more variable. We interpret these patterns to record an increase in the crustal inventory of organic carbon, reflecting eukaryotic diversification and a change in the locus of organic carbon burial to include anoxic deep marine sites where preservation potential was high. We speculate that the release of O-2 to Earth's surface environments associated with increased organic carbon storage induced irreversible changes in the Mesoproterozoic biosphere, presaging the more extreme environmental and evolutionary developments of the Neoproterozoic.

Orientation of the genetic variance-covariance matrix and the fitness surface for multiple male sexually selected traits

Stabilizing selection has been predicted to change genetic variances and covariances so that the orientation of the genetic variance-covariance matrix (G) becomes aligned with the orientation of the fitness surface, but it is less clear how directional selection may change G. Here we develop statistical approaches to the comparison of G with vectors of linear and nonlinear selection. We apply these approaches to a set of male sexually selected cuticular hydrocarbons (CHCs) of Drosophila serrata. Even though male CHCs displayed substantial additive genetic variance, more than 99% of the genetic variance was orientated 74.9degrees away from the vector of linear sexual selection, suggesting that open-ended female preferences may greatly reduce genetic variation in male display traits. Although the orientation of G and the fitness surface were found to differ significantly, the similarity present in eigenstructure was a consequence of traits under weak linear selection and strong nonlinear ( convex) selection. Associating the eigenstructure of G with vectors of linear and nonlinear selection may provide a way of determining what long-term changes in G may be generated by the processes of natural and sexual selection.

The origin and evolution of the surfactant system in fish: Insights into the evolution of lungs and swim bladders

Several times throughout their radiation fish have evolved either lungs or swim bladders as gas-holding structures. Lungs and swim bladders have different ontogenetic origins and can be used either for buoyancy or as an accessory respiratory organ. Therefore, the presence of air-filled bladders or lungs in different groups of fishes is an example of convergent evolution. We propose that air breathing could not occur without the presence of a surfactant system and suggest that this system may have originated in epithelial cells lining the pharynx. Here we present new data on the surfactant system in swim bladders of three teleost fish ( the air-breathing pirarucu Arapaima gigas and tarpon Megalops cyprinoides and the non-air-breathing New Zealand snapper Pagrus auratus). We determined the presence of surfactant using biochemical, biophysical, and morphological analyses and determined homology using immunohistochemical analysis of the surfactant proteins (SPs). We relate the presence and structure of the surfactant system to those previously described in the swim bladders of another teleost, the goldfish, and those of the air-breathing organs of the other members of the Osteichthyes, the more primitive air-breathing Actinopterygii and the Sarcopterygii. Snapper and tarpon swim bladders are lined with squamous and cuboidal epithelial cells, respectively, containing membrane-bound lamellar bodies. Phosphatidylcholine dominates the phospholipid (PL) profile of lavage material from all fish analyzed to date. The presence of the characteristic surfactant lipids in pirarucu and tarpon, lamellar bodies in tarpon and snapper, SP-B in tarpon and pirarucu lavage, and SPs ( A, B, and D) in swim bladder tissue of the tarpon provide strong evidence that the surfactant system of teleosts is homologous with that of other fish and of tetrapods. This study is the first demonstration of the presence of SP-D in the air-breathing organs of nonmammalian species and SP-B in actinopterygian fishes. The extremely high cholesterol/disaturated PL and cholesterol/PL ratios of surfactant extracted from tarpon and pirarucu bladders and the poor surface activity of tarpon surfactant are characteristics of the surfactant system in other fishes. Despite the paraphyletic phylogeny of the Osteichthyes, their surfactant is uniform in composition and may represent the vertebrate protosurfactant.

The crystal structure of a bacterial Class II ketol-acid reductolsomerase: Domain conservation and evolution

Ketol-acid reductoisomerase (KARI; EC 1.1.1.86) catalyzes two steps in the biosynthesis of branched-chain amino acids. Amino acid sequence comparisons across species reveal that there are two types of this enzyme: a short form (Class 1) found in fungi and most bacteria, and a long form (Class 11) typical of plants. Crystal structures of each have been reported previously. However, some bacteria such as Escherichia coli possess a long form, where the amino acid sequence differs appreciably from that found in plants. Here, we report the crystal structure of the E. coli enzyme at 2.6 A resolution, the first three-dimensional structure of any bacterial Class 11 KARI. The enzyme consists of two domains, one with mixed alpha/beta structure, which is similar to that found in other pyridine nucleotide-dependent dehydrogenases. The second domain is mainly alpha-helical and shows strong evidence of internal duplication. Comparison of the active sites between KARI of E. coli, Pseudomonas aeruginosa, and spinach shows that most residues occupy conserved positions in the active site. E. coli KARI was crystallized as a tetramer, the likely biologically active unit. This contrasts with P. aeruginosa KARI, which forms a dodecamer, and spinach KARI, a dimer. In the E. coli KARI tetramer, a novel subunit-to-subunit interacting surface is formed by a symmetrical pair of bulbous protrusions.

The effect of local galaxy surface density on star formation for HI selected galaxies

We present the result of investigations into two theories to explain the star formation rate (SFR)-density relationship. For regions of high galaxy density, either there are fewer star-forming galaxies or galaxies capable of forming stars are present but some physical process is suppressing their star formation. We use H I Parkes All-Sky Survey's (HIPASS) HI detected galaxies and infrared and radio fluxes to investigate SFRs and efficiencies with respect to local surface density. For nearby (vel < 10 000 km s(-1)) H I galaxies, we find a strong correlation between H I mass and SFR. The number of H I galaxies decreases with increasing local surface density. For H I galaxies (1000 < vel < 6000 km s(-1)), there is no significant change in the SFR or the efficiency of star formation with respect to local surface density. We conclude that the SFR-density relation is due to a decrease in the number of H I star-forming galaxies in regions of high galaxy density and not to the suppression of star formation.

40Ar/39Ar geochronological constraints on the evolution of lateritic iron deposits in the Quadrilatero Ferrifero, Minas Gerais, Brazil

Weathering profiles overlying the Sapecado, Pico and Andaime iron ore deposits, Quadrilátero Ferrífero (QF), Minas Gerais, Brazil, reach depths of 150–400 m and host world-class supergene iron orebodies. In addition to hosting supergene ore bodies of global economic significance, weathered banded iron-formations at the Quadrilátero Ferrífero and elsewhere (e.g., Carajás, Hamersley) are postulated to underlie some of the most ancient continuously exposed weathering profiles on earth. Laser incremental-heating 40Ar/39Ar results for 69 grains of hollandite-group manganese oxides extracted from 23 samples collected at depths ranging from 5 to 150 m at the Sapecado, Pico and Andaime deposits reveal ages ranging from ca. 62 to 14 Ma. Older Mn-oxides occur near the surface, while younger Mn-oxides occur at depth. However, many samples collected at the weathering–bedrock interface yield ages in the 51–41 Ma range, suggesting that the weathering profiles in the Quadrilátero Ferrífero had already reached their present depth in the Paleogene. The antiquity of the weathering profiles in the Quadrilátero Ferrífero is comparable to the antiquity of dated weathering profiles on banded iron-formations in the Carajás Region (Brazil) and the Hamersley Province, Western Australia. The age versus depth distributions obtained in this study, but not available for other regions containing similar supergene iron deposits, suggest that little further advance of the weathering front has occurred in the Quadrilátero Ferrífero lateritic profiles during the Neogene. The results suggest that weathering in some of these ancient landscapes is not controlled by the steady-state advance of weathering fronts through time, but may reflect climatic and geomorphological conditions prevailing in a remote past. The geochronological results also confirm that the ancient landsurfaces in the Quadrilátero Ferrífero probably remained immune to erosion for tens of millions of years. Deep weathering, mostly in the Paleogene, combined with low erosion rates, account for the abundance and widespread distribution of supergene iron, manganese, and aluminum orebodies in this region.

Clay mineralogical and isotopic (K-Ar, delta O-18, delta D) constraints on the evolution of the North Anatolian Fault Zone, Turkey

This study presents the first attempt to constrain the evolution of the North Anatolian Fault Zone (NAFZ) by age dating and isotope tracing of clay minerals formed during near-surface faulting. Extensive illitic clay mineralisation occurred along the NAFZ related to hydrothermal alteration of the fault gouges and pseudotachylytes. Samples representing the pre-fault protoliths outside the fault zone do not contain authigenic illitic clay minerals indicating that hydrothermal processes were confined to the areas within the fault zone. K-Ar age data indicate that the hydrothermal system and the associated illite authigenesis initiated at similar to 57 Ma. This process is interpreted to reflect the onset of significant strike-slip or transtensional faulting immediately after the continental collision related to the closure of the Neotethys Ocean. Following the initiation of the fault movements in the latest Paleocene-Early Eocene, displacements along the NAFZ have continued, with probably intensified fault activities at similar to 26 Ma and later than similar to 8 Ma. Oxygen isotope compositions of the illitic clays from different locations along the NAFZ are similar, with narrow ranges in delta O-18 values indicating clay precipitation from fluids with similar oxygen isotope compositions and crystallisation temperatures. The delta O-18 and delta D values of the calculated fluid isotopic composition (delta O-18=5.9 parts per thousand to 11.2 parts per thousand, delta D=-59 parts per thousand to -73 parts per thousand) are consistent with metamorphic and magmatic origin of fluids mobilised during active tectonism. The interpretation of the fluid flow history of the NAFZ is in agreement with that reported previously for some well-known large-scale high-angle fault zones, which similarly developed along collisional-type orogenic belts and are commonly associated with significant mesothermal ore mineralisation. (c) 2005 Elsevier B.V. All rights reserved.

(U-Th)/He and 40Ar/39Ar Geochronology of Weathering, Hamersley Province, Australia: Implications for weathering history and landscape Evolution

(U–Th)/He dating of goethite, when combined with quantification of diffusive 4He loss by the 4He/3He methodology, provides reliable corrected ages for minerals precipitated in weathering profiles. We have combined (U–Th)/He dating of supergene goethite with 40Ar/39Ar dating of supergene manganese oxides to study the weathering history and landscape evolution in the Hamersley Province, northwestern Australia. Incremental heating 40Ar/39Ar analysis of 187 grains of Mn oxides from 65 samples (44 hand specimens) collected from weathering profiles at seven field sites across the Hamersley Province yield precipitation ages ranging from 63.4 ± 0.9 to 1.5 ± 0.2 Ma. These results, combined with previous results of 40Ar/39Ar dating of Mn oxides (Vasconcelos, 1998 Vasconcelos, P.V., 1998. Unpub. report, pp. 1–278.Vasconcelos, 1998 and Cochrane, 2003), reveal a protracted and episodic history of weathering and landscape evolution, which was already ongoing in Late Cretaceous and spans the Palaeogene and Neogene. Seventy-three grains of goethite from 39 samples extracted from 21 hand specimens, collected from the same field sites where the Mn oxides originated, were dated by the (U–Th)/He method. Internally consistent (U–Th)/He ages, which range from 84.3 ± 12.2 to 3.3 ± 0.5 Ma, have been obtained for most samples when corrections are applied for 10% helium diffusive loss. The geochronological results obtained show remarkable similarity in the distribution of ages associated with supergene mineral precipitation. The widespread occurrence of iron oxides such as goethite in soils and weathering profiles and the successful application of (U–Th)/He dating of goethite offers great opportunities for extracting the wealth of palaeoclimatic and palaeoenvironmental information recorded by these profiles on the surface of terrestrial planets such as Earth and Mars.