Bystrow’s Paradox – gills,fossils, and the fish‐to‐tetrapod transition

Schoch, R.R. and Witzmann, F. 2011. Bystrow’s Paradox – gills, fossils, and the fish‐to‐tetrapod transition. —Acta Zoologica (Stockholm) 92 : 251–265. The issue of which breathing mechanism was used by the earliest tetrapods is still unsolved. Recent discoveries of stem tetrapods suggest the presence of internal gills and fish‐like underwater breathing. The same osteological features were used by Bystrow to infer a salamander‐like breathing through external gills in temnospondyl amphibians. This apparent contradiction – here called Bystrow’s Paradox – is resolved by reviewing the primary fossil evidence and the anatomy of the two gill types in extant taxa. Rather unexpectedly, we find that internal gills were present in a range of early crown tetrapods (temnospondyls), based on the anatomy of gill lamellae and location of branchial arteries on the ventral side of gill arch elements (ceratobranchials). Although it remains to be clarified which components are homologous in external and internal gills, both gill types are likely to have been present in Palaeozoic tetrapods – internal gills in aquatic adults of some taxa, and external gills in the larvae of these taxa and in larvae of numerous forms with terrestrial adults, which resorbed the external gills after the larval phase. Future developmental studies will hopefully clarify which mechanistic pathways are involved in gill formation and how these might have evolved.     

Key substrate recognition residues in the active site of a plant cytochrome P450, CYP73A1. Homology guided site-directed mutagenesis.

CYP73 enzymes are highly conserved cytochromes P450 in plant species that catalyse the regiospecific 4-hydroxylation of cinnamic acid to form precursors of lignin and many other phenolic compounds. A CYP73A1 homology model based on P450 experimentally solved structures was used to identify active site residues likely to govern substrate binding and regio-specific catalysis. The functional significance of these residues was assessed using site-directed mutagenesis. Active site modelling predicted that N302 and I371 form a hydrogen bond and hydrophobic contacts with the anionic site or aromatic ring of the substrate. Modification of these residues led to a drastic decrease in substrate binding and metabolism without major perturbation of protein structure. Changes to residue K484, which is located too far in the active site model to form a direct contact with cinnamic acid in the oxidized enzyme, did not influence initial substrate binding. However, the K484M substitution led to a 50% loss in catalytic activity. K484 may affect positioning of the substrate in the reduced enzyme during the catalytic cycle, or product release. Catalytic analysis of the mutants with structural analogues of cinnamic acid, in particular indole-2-carboxylic acid that can be hydroxylated with different regioselectivities, supports the involvement of N302, I371 and K484 in substrate docking and orientation.     

Adaptations for the oxidation of polycyclic aromatic hydrocarbons exhibited by the structure of human P450 1A2

Microsomal cytochrome P450 family 1 enzymes play prominent roles in xenobiotic detoxication and procarcinogen activation. P450 1A2 is the principal cytochrome P450 family 1 enzyme expressed in human liver and participates extensively in drug oxidations. This enzyme is also of great importance in the bioactivation of mutagens, including the N-hydroxylation of arylamines. P450-catalyzed reactions involve a wide range of substrates, and this versatility is reflected in a structural diversity evident in the active sites of available P450 structures. Here, we present the structure of human P450 1A2 in complex with the inhibitor alpha-naphthoflavone, determined to a resolution of 1.95 A. alpha-Naphthoflavone is bound in the active site above the distal surface of the heme prosthetic group. The structure reveals a compact, closed active site cavity that is highly adapted for the positioning and oxidation of relatively large, planar substrates. This unique topology is clearly distinct from known active site architectures of P450 family 2 and 3 enzymes and demonstrates how P450 family 1 enzymes have evolved to catalyze efficiently polycyclic aromatic hydrocarbon oxidation. This report provides the first structure of a microsomal P450 from family 1 and offers a template to study further structure-function relationships of alternative substrates and other cytochrome P450 family 1 members.     

Karyopherin-Centric Control of Nuclear Pores Based on Molecular Occupancy and Kinetic Analysis of Multivalent Binding with FG Nucleoporins

Intrinsically disordered Phe-Gly nucleoporins (FG Nups) within nuclear pore complexes exert multivalent interactions with transport receptors (Karyopherins (Kaps)) that orchestrate nucleocytoplasmic transport. Current FG-centric views reason that selective Kap translocation is promoted by alterations in the barrier-like FG Nup conformations. However, the strong binding of Kaps with the FG Nups due to avidity contradicts rapid Kap translocation in vivo. Here, using surface plasmon resonance, we innovate a means to correlate in situ mechanistic (molecular occupancy and conformational changes) with equilibrium (binding affinity) and kinetic (multivalent binding kinetics) aspects of Karyopherinβ1 (Kapβ1) binding to four different FG Nups. A general feature of the FxFG domains of Nup214, Nup62, and Nup153 is their capacity to extend and accommodate large numbers of Kapβ1 molecules at physiological Kapβ1 concentrations. A notable exception is the GLFG domain of Nup98, which forms a partially penetrable cohesive layer. Interestingly, we find that a slowly exchanging Kapβ1 phase forms an integral constituent within the FG Nups that coexists with a fast phase, which dominates transport kinetics due to limited binding with the pre-occupied FG Nups at physiological Kapβ1 concentrations. Altogether, our data reveal an emergent Kap-centric barrier mechanism that may underlie mechanistic and kinetic control in the nuclear pore complex.     

Life cycles,plasticity and palaeoecology in temnospondyl amphibians

In the largest early tetrapod clade, the temnospondyls, ontogenies were diverse and quite distinct from the life cycles of extant amphibians. Three well‐studied clades exemplify the diversity of these long‐extinct ontogenies, here analysed with respect to their bearing on developmental plasticity, reaction norms and evolution. Sclerocephalus readily adjusted by means of developmental evolution to different lake environments. In addition, plasticity (reaction norm) played a significant role, apparent both morphologically and by altered developmental traits. Size increase and extension of the ontogenetic trajectory gave larger predators, a phenomenon also found in the dissorophoid Micromelerpeton. Whereas Sclerocephalus was throughout preying on the same fishes, Micromelerpeton was able to fit into different trophic levels. In the branchiosaurid Apateon, a biphasic life cycle was established, with metamorphosis producing a terrestrial morph in some species; truncation of the ontogenetic trajectory gave a sexually mature larva as an alternative morph (neoteny). Plasticity was high in the larval morphs, permitting neotenes to live as filter feeders or small carnivores. Fine‐tuning of development permitted Apateon populations to adjust to specific lake properties and readily change from a filter‐feeding to carnivorous mode of life. In the nonmetamorphosing Triassic Gerrothorax, morphology was extremely conserved, but histology reveals much plasticity at the microscopical level, correlating with fluctuating salinity and water energy. In responding to environmental fluctuations by enhanced plasticity, the studied temnospondyls managed to populate lakes inhabitable to other tetrapods and fishes.     

Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae

The class Eurotiomycetes (Ascomycota, Pezizomycotina) is a monophyletic group comprising two major clades of very different ascomycetous fungi: (i) the subclass Eurotiomycetidae, a clade that contains most of the fungi previously recognized as Plectomycetes because of their mostly enclosed ascomata and prototunicate asci; and (ii) the subclass Chaetothyriomycetidae, a group of fungi that produce ascomata with an opening reminiscent of those produced by Dothideomycetes or Sordariomycetes. In this paper we use phylogenetic analyses based on data available from the Assembling the Fungal Tree of Life project (AFTOL), in addition to sequences in GenBank, to outline this important group of fungi. The Eurotiomycetidae include producers of toxic and useful secondary metabolites, fermentation agents used to make food products and enzymes, xerophiles and psychrophiles, and the important genetics model Aspergillus nidulans. The Chaetothyriomycetidae include the common black yeast fungi, some of which are pathogens of humans and animals, as well as some primarily lichenized groups newly found to be phylogenetically associated with this group. The recently proposed order Mycocaliciales shows a sister relationship with Eurotiomycetes. The great majority of human pathogenic Pezizomycotina are Eurotiomycetes, particularly in Eurotiales, Onygenales and Chaetothyriales. Due to their broad importance in basic research, industry and public health, several genome projects have focused on species in Onygenales and Eurotiales.     

An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny

The Sordariomycetes is one of the largest classes in the Ascomycota, and the majority of its species are characterized by perithecial ascomata and inoperculate unitunicate asci. It includes more than 600 genera with over 3000 species and represents a wide range of ecologies including pathogens and endophytes of plants, animal pathogens and mycoparasites. To test and refine the classification of the Sordariomycetes sensu Eriksson (2006), the phylogenetic relationship among 106 taxa from 12 orders out of 16 in the Sordariomycetes was investigated based on four nuclear loci (nSSU and nLSU rDNA, TEF and RPB2), using three species of the Leotiomycetes as outgroups. Three subclasses (i.e. Hypocreomycetidae, Sordariomycetidae and Xylariomycetidae) currently recognized in the classification are well supported with the placement of the Lulworthiales in either a basal group of the Sordariomycetes or a sister group of the Hypocreomycetidae. Except for the Microascales, our results recognize most of the orders as monophyletic groups. Melanospora species form a clade outside of the Hypocreales and are recognized as a distinct order in the Hypocreomycetidae. Glomerellaceae is excluded from the Phyllachorales and placed in Hypocreomycetidae incertae sedis. In the Sordariomycetidae, the Sordariales is a strongly supported clade and occurs within a well supported clade containing the Boliniales and Chaetosphaeriales. Aspects of morphology, ecology and evolution are discussed.     

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.     

The evolution of metamorphosis in temnospondyls

Temnospondyls, possible relatives of extant amphibians and crudely similar to recent salamanders, are known from larval, neotenic and metamorphosed stages. Here, ontogenetic data of various temnospondyl taxa are analysed in order to recognize metamorphosis. Here, metamorphosis is strictly defined as a shift from an aquatic to a terrestrial existence. Following a check-list of criteria, the most likely metamorphosis-induced changes are proved in three temnospondyl lineages: eryopids, zatrachydids and dissorophoids. In a few other, unrelated taxa, terrestrial adults are known but no larval or metamorphosing forms. The distribution of metamorphosis among the Temnospondyli does not strictly correlate with phylogeny, which highlights the widespread occurrence of neoteny. In each group, characteristic patterns of metamorphosis are described and compared. Among temnospondyls, dissorophoids had the most intensive type of metamorphosis, characterized by a condensed ontogeny and a relatively small body size. The result was a distinct transformed morphotype with far-reaching terrestrial adaptations.