Defining a similarity threshold for a functional protein sequence pattern: The signal peptide cleavage site

Nielsen, Henrik; Engelbrecht, Jacob; Heijne, Gunnar von; Brunak, Søren

doi:10.1002/(sici)1097-0134(199602)24:2<165::aid-prot4>3.0.co;2-i

Cited by 87 publications

(53 citation statements)

References 33 publications

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“…A potential leader peptide with a cleavage site at positions 18 and 19 (ACL-GL) was detected by using the SignalP algorithm (37). Use of the TopPred II algorithm (9) suggested with 95% reliability that the GaiA protein is an integral membrane protein with nine membranespanning domains (Fig.…”

Section: Resultsmentioning

confidence: 99%

Characterization of a Novel Intracellularly Activated Gene from Salmonella enterica Serovar Typhi

et al. 2002

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A Salmonella enterica serovar Typhi gene that is selectively up-regulated upon bacterial invasion of eukaryotic cells was characterized. The open reading frame encodes a 298-amino-acid hydrophobic polypeptide (30.8 kDa), which is predicted to be an integral membrane protein with nine membrane-spanning domains. The protein is closely related (87 to 94% reliability) to different transport and permease systems. Gene expression under laboratory conditions was relatively weak; however, sevenfold induction was observed in a high-osmolarity medium (300 mM NaCl). The growth pattern in a laboratory medium of a serovar Typhi strain Ty2 derivative containing a 735-bp in-frame deletion in this gene, named gaiA (for gene activated intracellularly), was not affected. In contrast, the mutant was partially impaired in intracellular survival in murine peritoneal macrophages, as well as in human monocyte-derived macrophages. However, in the case of human macrophages, this survival defect was modest and evident only at late infection times (24 h). Despite the distinct intracellular survival kinetics displayed in macrophages of different species, the gaiA null mutant was significantly affected in its potential to trigger apoptosis in both murine and human macrophages. Provision of the gaiA gene in trans resulted in complementation of these phenotypes. Interestingly, the absence of a functional gaiA gene caused a marked attenuation in the mouse mucin model, as shown by the increase (3 orders of magnitude) in the 50% lethal dose of the mutant strain over that of the parental strain Ty2 (P < 0.05). Altogether, these data indicate that the product encoded by the gaiA gene is required for triggering apoptosis and bacterial survival within murine macrophages, which is consistent with the in vivo results obtained in the mouse mucin model. However, gaiA was not required for initial intracellular survival in human cells, indicating that its role in the natural host might be more complex than is suggested by the studies performed in the murine system.

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Section: Resultsmentioning

confidence: 99%

Characterization of a Novel Intracellularly Activated Gene from Salmonella enterica Serovar Typhi

et al. 2002

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“…The a-Gals from Carica papaya (AAP04002), rice (Oryza sativa; BAB12750), Phaseolus vulgaris (AAA73964), and Coffea arabica (AAA33022), were selected with respect to their catalytic characterization and homology to GGT. Like the hydrolases, GGT has a melibiase domain, including an a-Gal motif, and contains also a putative signal peptide, which indicates entering into the secretory pathway (Dey and Pridham, 1972;Zhu and Goldstein, 1994;Nielsen et al, 1996).…”

Section: Ggt Is Highly Homologous To Acid A-gals Of Family 27 Of Glycmentioning

confidence: 99%

Cloning, Functional Expression, and Characterization of the Raffinose Oligosaccharide Chain Elongation Enzyme, Galactan:Galactan Galactosyltransferase, from Common Bugle Leaves

2004

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Galactan:galactan galactosyltransferase (GGT) is a unique enzyme of the raffinose family oligosaccharide (RFO) biosynthetic pathway. It catalyzes the chain elongation of RFOs without using galactinol (a-galactosyl-myoinositol) by simply transferring a terminal a-galactosyl residue from one RFO molecule to another one. Here, we report the cloning and functional expression of a cDNA encoding GGT from leaves of the common bugle (Ajuga reptans), a winter-hardy long-chain RFO-storing Lamiaceae. The cDNA comprises an open reading frame of 1215 bp. Expression in tobacco (Nicotiana plumbaginifolia) protoplasts resulted in a functional recombinant protein, which showed GGT activity like the previously described purified, native GGT enzyme. At the amino acid level, GGT shows high homologies ([60%) to acid plant a-galactosidases of the family 27 of glycosylhydrolases. It is clearly distinct from the family 36 of glycosylhydrolases, which harbor galactinol-dependent raffinose and stachyose synthases as well as alkaline a-galactosidases. Physiological studies on the role of GGT confirmed that GGT plays a key role in RFO chain elongation and carbon storage. When excised leaves were exposed to chilling temperatures, levels of GGT transcripts, enzyme activities, and long-chain RFO concentrations increased concomitantly. On a whole-plant level, chilling temperatures induced GGT expression mainly in the roots and fully developed leaves, both known RFO storage organs of the common bugle, indicating an adaptation of the metabolism from active growth to transient storage in the cold.

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“…Position -8 is located in the signal peptide. Interestingly, however, the motif of type I signal peptidase (Nielsen et al, 1996(Nielsen et al, , 1997, by which the signal peptide of class I HLA is cleaved, is also located at positions -12 and -10, such that cleavage can occur between positions -10 and -9. If this is the case, it is possible that position -8 is also located in the α1 domain and participate in the binding to a peptide or TCR.…”

Section: Discussionmentioning

confidence: 99%

Inferring natural selection operating on conservative and radical substitution at single amino acid sites

Suzuki

2007

Genes Genet. Syst.

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Natural selection operating on amino acid substitution at single amino acid sites can be detected by comparing the rates of synonymous (r S ) and nonsynonymous (r N ) nucleotide substitution at single codon sites. Amino acid substitutions can be classified as conservative or radical according to whether they retain the properties of the substituted amino acid. Here methods for comparing the rates of conservative (r C ) and radical (r R ) nonsynonymous substitution with r S at single codon sites were developed to detect natural selection operating on these substitutions at single amino acid sites. A method for comparing r C and r R at single codon sites was also developed to detect biases toward these substitutions at single amino acid sites. Charge was used as the property of the amino acids. In a computer simulation, false-positive rates of these methods were always < 5%, unless termination sites were included in the computation of the numbers of sites and estimates of transition/transversion rate ratio were highly biased. The frequency of detection of natural selection operating on conservative substitution was almost independent of the presence of natural selection operating on radical substitution, and vice versa. Natural selection operating specifically on conservative and radical substitution was detected more efficiently by comparing r S with r C and r S with r R than by comparing r S with r N . These methods also appeared to be robust against the occurrence of recombination during evolution. In an analysis of class I human leukocyte antigen, negative selection operating on conservative substitution, but not positive selection operating on radical substitution, was observed at some of the codon sites with r R > r C , suggesting that r R > r C may not necessarily be an indicator of positive selection operating on radical substitution.

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Defining a similarity threshold for a functional protein sequence pattern: The signal peptide cleavage site

Cited by 87 publications

References 33 publications

Characterization of a Novel Intracellularly Activated Gene from Salmonella enterica Serovar Typhi

Characterization of a Novel Intracellularly Activated Gene from Salmonella enterica Serovar Typhi

Cloning, Functional Expression, and Characterization of the Raffinose Oligosaccharide Chain Elongation Enzyme, Galactan:Galactan Galactosyltransferase, from Common Bugle Leaves

Inferring natural selection operating on conservative and radical substitution at single amino acid sites

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