The astacin protein family in Caenorhabditis elegans.

In the nematode Caenorhabditis elegans, 40 genes code for astacin-like proteins (nematode astacins, NAS). The astacins are metalloproteases present in bacteria, invertebrates and vertebrates and serve a variety of physiological functions like digestion, hatching, peptide processing, morphogenesis and pattern formation. With the exception of one distorted pseudogene, all the other C. elegans astacins are expressed and are evidently functional. For 13 genes we found splicing patterns differing from the Genefinder predictions in WormBase, sometimes markedly. The GFP expression pattern for NAS-4 shows a specific localization in anterior pharynx cells and in the whole digestive tract (as the secreted form). In contrast, NAS-7 is found in the head of adult hermaphrodites, but not in pharynx cells or in the lumen of the digestive tract. In embryos, NAS-7 fluorescence becomes detectable just before hatching. In C. elegans astacins, three basic structural and functional moieties can be discerned: a prepro portion, the central catalytic chain and long C-terminal extensions with presumably regulatory functions. Within the regulatory moiety, EFG-like, CUB, SXC, and TSP-1 domains can be distinguished. Based on structural differences of the regulatory unit we established six NAS subgroups, which seemingly represented different functional and evolutionary clusters. This pattern deduced exclusively from the domain arrangement in the regulatory moiety is perfectly reflected in an evolutionary tree constructed solely from amino acid sequence information of the catalytic chain. Related catalytic chains tend to have related regulatory extensions. The notable gene, NAS-39 shows a striking resemblance to human BMP-1 and the tolloids.

[1]  W. Bode,et al.  Implications of the three-dimensional structure of astacin for the structure and function of the astacin family of zinc-endopeptidases. , 1993, European journal of biochemistry.

[2]  I. Yiallouros,et al.  The roles of Glu93 and Tyr149 in astacin‐like zinc peptidases , 2000, FEBS letters.

[3]  J. Thompson,et al.  Using CLUSTAL for multiple sequence alignments. , 1996, Methods in enzymology.

[4]  Andrew Smith Genome sequence of the nematode C-elegans: A platform for investigating biology , 1998 .

[5]  P. Bork,et al.  The CUB domain. A widespread module in developmentally regulated proteins. , 1993, Journal of molecular biology.

[6]  T. Moore,et al.  Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans , 2001, Nature Genetics.

[7]  L. Stateva,et al.  The Astacins: structure and function of a new protein family , 1997 .

[8]  Jonathan P. Bollback,et al.  Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology , 2001, Science.

[9]  J. Huelsenbeck,et al.  Potential applications and pitfalls of Bayesian inference of phylogeny. , 2002, Systematic biology.

[10]  R. Wolz,et al.  Meprins A and B. , 1995, Methods in enzymology.

[11]  L. Bini,et al.  Aspartyl proteases in Caenorhabditis elegans. Isolation, identification and characterization by a combined use of affinity chromatography, two-dimensional gel electrophoresis, microsequencing and databank analysis. , 1999, European journal of biochemistry.

[12]  John P. Huelsenbeck,et al.  MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..

[13]  A. Sieron,et al.  Structure and function of procollagen C-proteinase (mTolloid) domains determined by protease digestion, circular dichroism, binding to procollagen type I, and computer modeling. , 2000, Biochemistry.

[14]  H. Ponstingl,et al.  A protease from Astacus fluviatilis as an aid in protein sequencing. , 1982, Analytical biochemistry.

[15]  E. Brown,et al.  Genomic analysis of gene expression in C. elegans. , 2000, Science.

[16]  H. Rackwitz,et al.  Activation of pro-astacin. Immunological and model peptide studies on the processing of immature astacin, a zinc-endopeptidase from the crayfish Astacus astacus. , 2001, European journal of biochemistry.

[17]  G. Pfleiderer,et al.  Zur Evolution der Endopeptidasen, X. Die Spaltungsspezifität der niedermolekularen Protease ausAstacus leptodactylusESCH. , 1969 .

[18]  Y. Dong,et al.  Systematic functional analysis of the Caenorhabditis elegans genome using RNAi , 2003, Nature.

[19]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[20]  Gary Ruvkun,et al.  Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes , 2003, Nature.

[21]  W. Wood The Nematode Caenorhabditis elegans , 1988 .

[22]  J. Peter-Katalinic,et al.  Activation mechanism of pro-astacin: role of the pro-peptide, tryptic and autoproteolytic cleavage and importance of precise amino-terminal processing. , 2002, Journal of molecular biology.

[23]  H. Dörsam,et al.  Low molecular mass protease: evidence for a new family of proteolytic enzymes , 1981, FEBS letters.

[24]  P. Zipperlen,et al.  Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans , 2000, Genome Biology.

[25]  G. Vogt,et al.  Biosynthesis of Astacus protease, a digestive enzyme from crayfish , 2004, Histochemistry.

[26]  Andrew G Fraser,et al.  Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAi. , 2003, Genes & development.

[27]  Sebastian A. Leidel,et al.  Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III , 2000, Nature.

[28]  M. Blaxter,et al.  Caenorhabditis elegans is a nematode. , 1998, Science.

[29]  Yuji Kohara,et al.  Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi , 2001, Current Biology.

[30]  V. Reinke,et al.  Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Joshua M. Stuart,et al.  A Gene Expression Map for Caenorhabditis elegans , 2001, Science.

[32]  G. Sarkis,et al.  Proteases of the nematode Caenorhabditis elegans. , 1988, Archives of biochemistry and biophysics.

[33]  S F Altschul,et al.  Local alignment statistics. , 1996, Methods in enzymology.

[34]  R. Huber,et al.  Refined 1.8 A X-ray crystal structure of astacin, a zinc-endopeptidase from the crayfish Astacus astacus L. Structure determination, refinement, molecular structure and comparison with thermolysin. , 1994, Journal of molecular biology.

[35]  R. Huber,et al.  Structure of astacin and implications for activation of astacins and zinc-ligation of collagenases , 1992, Nature.

[36]  V. Rosen,et al.  Purification and characterization of other distinct bone-inducing factors. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[37]  M. Blaxter,et al.  An Abundant, trans-spliced mRNA from Toxocara canis Infective Larvae Encodes a 26-kDa Protein with Homology to Phosphatidylethanolamine-binding Proteins (*) , 1995, The Journal of Biological Chemistry.

[38]  Gary Ruvkun,et al.  A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity , 2003, Nature Genetics.

[39]  P. Chomczyński,et al.  Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. , 1987, Analytical biochemistry.

[40]  T. Ishihara,et al.  hch‐1, a gene required for normal hatching and normal migration of a neuroblast in C. elegans, encodes a protein related to TOLLOID and BMP‐1. , 1996, The EMBO journal.

[41]  Neil D. Rawlings,et al.  Handbook of proteolytic enzymes , 1998 .

[42]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[43]  P. Zipperlen,et al.  Functional genomic analysis of C. elegans chromosome I by systematic RNA interference , 2000, Nature.

[44]  Marc Vidal,et al.  WorfDB: the Caenorhabditis elegans ORFeome Database , 2003, Nucleic Acids Res..

[45]  W. James Kent,et al.  The Intronerator: exploring introns and alternative splicing in Caenorhabditis elegans , 2000, Nucleic Acids Res..

[46]  R. Zwilling,et al.  Cloning and characterization of a cDNA coding for Astacus embryonic astacin, a member of the astacin family of metalloproteases from the crayfish Astacus astacus. , 1998, European journal of biochemistry.

[47]  C. Hauer,et al.  Molecular cloning and sequence analysis of flavastacin: an O-glycosylated prokaryotic zinc metalloendopeptidase. , 1995, Archives of biochemistry and biophysics.

[48]  S. Whelan,et al.  A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. , 2001, Molecular biology and evolution.

[49]  G. Pfleiderer,et al.  Zur Evolution der Endopeptidasen, III. Eine Protease vom Molekulargewicht 11000 und eine trypsinähnliche Fraktion aus Astacus fluviatilis Fabr. , 1967 .

[50]  D. Slonim,et al.  Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome , 2003, Development.

[51]  V. Rosen,et al.  Novel regulators of bone formation: molecular clones and activities. , 1988 .

[52]  K. Titani,et al.  Amino acid sequence of a unique protease from the crayfish Astacus fluviatilis. , 1987, Biochemistry.

[53]  H. Hutter,et al.  Conservation and novelty in the evolution of cell adhesion and extracellular matrix genes. , 2000, Science.