The functional repertoire of prokaryote cellulosomes includes the serpin superfamily of serine proteinase inhibitors

Many of the Firmicutes bacteria responsible for plant polysaccharide degradation in Nature produce a multiprotein complex called a cellulosome, which co-ordinates glycoside hydrolase assembly, bacterial adhesion to substrate and polysaccharide hydrolysis. Cellulosomal proteins possess a dockerin module, which mediates their attachment to the scaffoldin protein via its interaction with cohesin modules, and only glycoside hydrolases and other carbohydrate active enzymes were known to reside within the cellulosome. We show here with Clostridium thermocellum ATCC 27405 that members of the serpin superfamily of serine proteinase inhibitors, which are best recognized for their conformational flexibility and co-ordination of key regulatory functions in multicellular eukaryotes, also reside within the cellulosome. These studies are the first to expand the cellulosome paradigm of protein complex assembly beyond glycoside hydrolase and carbohydrate active enzymes, and to include a newly identified functionality in the Firmicutes.     

An elastase inhibitor from equine leukocyte cytosol belongs to the serpin superfamily. Further characterization and amino acid sequence of the reactive center

Horse leukocyte elastase inhibitor rapidly forms stable, equimolar complexes with both human leukocyte elastase and cathepsin G, porcine pancreatic elastase, and bovine alpha-chymotrypsin. Formation of the inhibitor-pancreatic elastase complex results in peptide bond cleavage at the reactive site of the inhibitor so that a small peptide fragment representing the carboxyl-terminal sequence of the inhibitor is released. Sequence analysis of both this peptide, as well as that of an overlapping peptide obtained by enzymatic inactivation of native inhibitor with either Staphylococcus aureus metalloproteinase, Pseudomonas aeruginosa elastase, or cathepsin B, yields data which indicate that the reactive site encompasses a P1-P1' Ala-Met sequence. However, unlike the human endothelial plasminogen activator inhibitor, which also has a Met residue in the P1' position, oxidation of the horse inhibitor only slightly reduces its association rate constant with either of the elastolytic enzymes tested or with chymotrypsin. Comparison of the amino acid sequence at or near the reactive site of the horse inhibitor (P2-P18') with members of the serpin superfamily of proteinase inhibitors indicates that it not only belongs in this class but also represents the first example of a functionally active intracellular serpin.     

cDNA sequence coding for a rat glia-derived nexin and its homology to members of the serpin superfamily

Rat glial cells release a neurite-promoting factor with serine protease inhibitory activity. By using a rat glioma cDNA clone as a probe, it was possible to isolate rat cDNAs containing the entire sequence coding for this neurite-promoting factor. The largest rat cDNA (approximately 2100 bp) was characterized by DNA sequencing. It contained the entire coding region, 135 bp of the 5' nontranslated region, and about 750 bp of the 3' nontranslated region. The open reading frame coded for 397 amino acids including a putative signal peptide of 19 amino acids. The correct identity of the coding sequence was substantiated by the fact that the sequence of tryptic peptides, derived from the purified rat factor, matched exactly with the deduced amino acid sequence. The rat protein sequence had 84% homology with the corresponding protein from human glioma cells. Both amino acid sequences indicated that the proteins belong to the protease nexins [Baker, B.J., Low, D. A., Simmer, R. L., & Cunningham, D.D. (1980) Cell (Cambridge, Mass.) 21, 37-45] and therefore can be defined as glia-derived nexins (GDNs). Further analysis showed that both rat and human GDN belong to the serpin superfamily and share 41%, 32%, and 25% homology with human endothelial-cell-type plasminogen activator inhibitor, antithrombin III, and alpha-1 proteinase inhibitor, respectively.     

Primary structure of a member of the serpin superfamily of proteinase inhibitors from an insect, Manduca sexta

A cDNA clone isolated from a fat body cDNA library from an insect, Manduca sexta, has been sequenced and shown to code for a member of the serpin family of proteinase inhibitors. The cDNA has an open reading frame which codes for a 392-residue polypeptide of Mr = 43,500 with a hydrophobic NH2-terminal sequence which appears to be a signal peptide. An alignment of this amino acid sequence with 11 members of the serpin superfamily reveals that the insect protein is 25-30% identical with most members of the superfamily. The alignment was used to construct an evolutionary tree of the serpin sequences analyzed, which indicates that the progenitor of the M. sexta serpin and the human serpins most closely related to it diverged from other serpin genes prior to the divergence of the vertebrates and invertebrates. The M. sexta serpin is predicted to inhibit elastase due to the presence of alanine at the P1 position of its reactive center and is classified as an alaserpin. A glycoprotein of Mr = 47,000 isolated from hemolymph of M. sexta larvae has an NH2-terminal sequence identical to that deduced from the alaserpin cDNA clone and inhibits porcine pancreatic elastase and bovine chymotrypsin.     

The major progesterone-modulated proteins secreted into the sheep uterus are members of the serpin superfamily of serine protease inhibitors

The uterine milk proteins (UTMP) are a pair of structurally related basic glycoproteins that when newly synthesized carry phosphorylated mannosyl residues on their carbohydrate chains. They are the major proteins secreted by ovine endometrium under the influence of progesterone. RNA from a late pregnant ewe endometrium was isolated for use in in vitro translation assays and for constructing cDNA libraries. Translation experiments, initially with total cellular RNA and subsequently with RNA selected by hybridization with a specific cDNA, demonstrated the production of two polypeptides (Mr = 47,000 and 55,000) that were precipitated with antiserum to the UTMP. With microsomal membranes in the translation assay, there was increased production of an Mr = 57,000 form that was protected from protease digestion. Antibody screening of a cDNA library in lambda gt11 identified a short clone representing the 3' terminus of the mRNA that was shown by epitope selection experiments to be UTMP specific. This clone was then used to screen a lambda gt10 library. A longer clone (1.3 kilobases) was isolated and sequenced but lacked the 5' terminus to the mRNA. The latter sequence was obtained directly from the mRNA. Interesting features of the UTMP mRNA sequence, which was 1,352 bases long and contained a 1,287-base open reading frame, were two strong start codons, two potential sites for N-glycosylation and a repeat of 21 bases, six bases apart, that resulted in a repeat of seven amino acids. The inferred amino acid sequence agreed closely with the NH2-terminal amino acid sequence obtained directly from the UTMP and clearly placed the UTMP in the serpin superfamily of protease inhibitors. However, we have been unable to demonstrate inhibitory activity toward any serine protease so far tested.     

An evolutionary history of the FGF superfamily

Fibroblast growth factors (FGF) are associated with multiple developmental and metabolic processes in triploblasts, and perhaps also in diploblasts. The evolution of the FGF superfamily has accompanied the major morphological and functional innovations of metazoan species. The study of FGFs throughout species shows that the FGF superfamily can be subdivided in eight families in present-day organisms and has evolved through phases of gene duplications and gene losses. At least two major expansions of the superfamily can be recognized: a first expansion increased the number of FGFs from one or few archeo-FGFs to eight proto-FGFs, prototypic of the eight families. A second expansion, which took place during euchordate evolution, is associated with genome duplications. It increased the number of members in the families. Subsequent losses reduced that number to the present-day figures.     

A novel member of the serpin superfamily is encoded on a circular plasmid-like DNA species isolated from rabbit cells

A novel member of the serpin family of serine protease inhibitors is presented. A plasmid-like DNA was isolated from rabbit cells by its homology to the genome of Shope fibroma virus (SFV), a tumorigenic poxvirus of rabbits, and was shown elsewhere to encode a serpin-like protein [(1986) Mol. Cell. Biol. 6, 265-276]. Although significant DNA homology exists between the rabbit plasmid serpin open reading frame and the SFV terminal inverted repeat DNA there is no intact serpin counterpart encoded by this region of the SFV genome. The alignment of the novel plasmid-borne polypeptide with the serpin family of proteins confirms its status within this group.     

An overview of the Cape geophytes

The Cape Region (here treated as the winter rainfall region of southern Africa, thus including fynbos, renosterveld and succulent karoo vegetation) is the world's foremost centre of geophyte diversity. Some 2100 species in 20 families have been recorded from this area, 84% of them endemic. The most important families, with more than a hundred geophyte species each, are Iridaceae, Oxalidaceae, Hyacinthaceae, Orchidaceae, Amaryllidaceae and Asphodelaceae. Although southern Africa does not appear to have been the main diversification centre for the plant orders with highest geophyte representation (Asparagales and Liliales), it represents an active centre of transition to geophytism, such transitions having occurred independently in numerous plant groups, often followed by rapid speciation. Several Cape geophyte groups have consequently expanded across Africa to the Mediterranean Basin, and possibly to other winter rainfall regions. Remarkably high local species diversity in renosterveld vegetation, even in relatively homogeneous environments, suggests that pollinator specificity and phenology play an important role in niche partitioning. However, character diversity is also high in storage organs and leaves, and this could account for the high species diversity values recorded at larger spatial scales, especially across environmental gradients. Long-term climatic stability, combined with topoclimatic and edaphic diversity and regular fire occurrence, is likely to be responsible for the remarkable geophyte diversity of the Cape, as compared to other mediterranean-climate regions.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 27–43.     

An overview of radioimmunotherapy

Summary In reviewing the current state of affairs in radioimmunotherapy the paper focuses on the main difficulties thus far encountered and the procedures designed to avoid or circumvent these problems. The long range -emitters⁹⁰Y and¹⁸⁸Re have replaced¹³¹I as the isotopes currently receiving most attention for use in radioimmunotherapy, and a range of new chelators are under investigation for in vivo stability and immunogenicity. Approaches aimed at improving tumour targetting and antigen expression such as two-step pretargetting techniques, tumour necrosis treatment and cytokine pretreatment are summarised. Methods designed to improve host-Mab interactions are outlined and the need to incorporate successful ideas from current cancer therapies is emphasised.     

An overview of toxicogenomics

Toxicogenomics is a rapidly developing discipline that promises to aid scientists in understanding the molecular and cellular effects of chemicals in biological systems. This field encompasses global assessment of biological effects using technologies such as DNA microarrays or high throughput NMR and protein expression analysis. This review provides an overview of advancing multiple approaches (genomic, proteomic, metabonomic) that may extend our understanding of toxicology and highlights the importance of coupling such approaches with classical toxicity studies.     

An overview of Acipenseriformes

Acipenseriformes occupy a special place in the history of ideas concerning fish evolution, but in many respects, phylogenetic studies of the group remain in their infancy. Even such basic questions as the monophyly of Acipenser (the largest genus) are unanswered. We define relationships based on comparative osteology, which allows us to incorporate well-preserved fossils into analyses. Acipenseriformes has existed at least since the Lower Jurassic (approximately 200 MYBP), and all fossil and recent taxa are from the Holarctic. Phylogenetic relationships among Paleozoic and Early Mesozoic actinopterygians are problematic, but most workers agree that Acipenseriformes is monophyletic and derived from some component of paleonisciform fishes. (Paleonisciformes is a grade of primitive non-neopterygian actinopterygians, sensu Gardiner 1993.) Taxa discussed in comparison here are: Cheirolepis, Polypterus, Mimia, Moythomasia, Birgeria, Saurichthys, Lepisosteus and Amia. We review generic diversity within the four nominal families of fossil and recent Acipenseriformes (Chondrosteidae, Peipiaosteidae, Polyodontidae, and Acipenseridae), and provide a cladogram summarizing osteological characters for those four groups. Monophyly of the two extant families is well-supported, but there are no comprehensive studies of all of the known species and specimens of Chondrosteidae and Peipiaosteidae. As a result, sister-group relationships among Chondrosteidae, Peipiaosteidae, and Acipenseroidei (= Polyodontidae + Acipenseridae) are unresolved. We discuss five features fundamental to the biology of acipenseriforms that benefit from the availability of our new phylogenetic hypothesis: (1) specializations of jaws and operculum relevant to jaw protrusion, feeding, and ram ventilation; (2) anadromy or potamodromy and demersal spawning; (3) paedomorphosis and evolution of the group; (4) the bioégeography of Asian and North American polyodontids and scaphirhynchines; and (5) the great abundance of electroreceptive organs in the rostral and opercular regions. Finally, we summarize our nomenclatural recommendations.     

Necrosis and the serpin under't

Caspase proteases play essential roles in apoptotic cell death, while other proteases are active in necrotic cell death. In a recent paper in Cell, Luke et al. (2007) present findings demonstrating that a gene believed to be a natural protease inhibitor may have a role in preventing necrosis.     

An intracellular serpin regulates necrosis by inhibiting the induction and sequelae of lysosomal injury

Extracellular serpins such as antithrombin and alpha1-antitrypsin are the quintessential regulators of proteolytic pathways. In contrast, the biological functions of the intracellular serpins remain obscure. We now report that the C. elegans intracellular serpin, SRP-6, exhibits a prosurvival function by blocking necrosis. Minutes after hypotonic shock, srp-6 null animals underwent a catastrophic series of events culminating in lysosomal disruption, cytoplasmic proteolysis, and death. This newly defined hypo-osmotic stress lethal (Osl) phenotype was dependent upon calpains and lysosomal cysteine peptidases, two in vitro targets of SRP-6. By protecting against both the induction of and the lethal effects from lysosomal injury, SRP-6 also blocked death induced by heat shock, oxidative stress, hypoxia, and cation channel hyperactivity. These findings suggest that multiple noxious stimuli converge upon a peptidase-driven, core stress response pathway that, in the absence of serpin regulation, triggers a lysosomal-dependent necrotic cell death routine.     

An overview of the Notch signalling pathway

The Notch receptor plays a key role in modulating cell fate decisions throughout the development of invertebrate and vertebrate species. Four Notch homologues have been identified in the human genome and aberrant Notch function has been associated with a number of human diseases. An intriguing pathway of Notch signalling has been elucidated involving multiple proteolytic steps and this pathway offers several targets for potential therapeutic intervention. While a consensus model has emerged, in the details there is much that is contentious. This review will primarily focus on our current understanding of the proteolytic events involved in generating and regulating Notch signalling.     

An overview of the potassium channel family

Potassium channels, tetrameric integral membrane proteins that form aqueous pores through which K⁺ can flow, are found in virtually all organisms; the genomes of humans, Drosophila, and Caenorhabditis elegans contain 30-100 K⁺ channel genes each. The structure of a bacterial K⁺ channel, sequence comparisons with other channels and electrophysiological measurements have enabled conclusions about the mechanism of gating and ion flow to be drawn for many other channels.     

An evolutionary analysis of the helix-hairpin-helix superfamily of DNA repair glycosylases

The helix-hairpin-helix (HhH) superfamily of base excision repair DNA glycosylases is composed of multiple phylogenetically diverse enzymes that are capable of excising varying spectra of oxidatively and methyl-damaged bases. Although these DNA repair glycosylases have been widely studied through genetic, biochemical, and biophysical approaches, the evolutionary relationships of different HhH homologs and the extent to which they are conserved across phylogeny remain enigmatic. We provide an evolutionary framework for this pervasive and versatile superfamily of DNA glycosylases. Six HhH gene families (named AlkA: alkyladenine glycosylase; MpgII: N-methylpurine glycosylase II; MutY/Mig: A/G-specific adenine glycosylase/mismatch glycosylase; Nth: endonuclease III; OggI: 8-oxoguanine glycosylase I; and OggII: 8-oxoguanine glycosylase II) are identified through phylogenetic analysis of 234 homologs found in 94 genomes (16 archaea, 64 bacteria, and 14 eukaryotes). The number of homologs in each gene family varies from 117 in the Nth family (nearly every genome surveyed harbors at least one Nth homolog) to only five in the divergent OggII family (all from archaeal genomes). Sequences from all three domains of life are included in four of the six gene families, suggesting that the HhH superfamily diversified very early in evolution. The phylogeny provides evidence for multiple lineage-specific gene duplication events, most of which involve eukaryotic homologs in the Nth and AlkA gene families. We observe extensive variation in the number of HhH superfamily glycosylase genes present in different genomes, possibly reflecting major differences among species in the mechanisms and pathways by which damaged bases are repaired and/or disparities in the basic rates and spectra of mutation experienced by different genomes.