Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase

Eisenhaber, Birgit; Bork, Peer; Eisenhaber, Frank

doi:10.1093/protein/11.12.1155

Cited by 226 publications

(198 citation statements)

References 1 publication

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“…In general, we find that the big-PI predictor (18,19) produces scores that are reasonably well correlated with processing efficiency, although there are exceptions in both directions: some of our poorly processed mutants obtained a score superior to 4, e.g. rm24 and rm41 (HCGG), rm16 (ESEGR), and rm27 (EGGSR), while some mutants that obtained less than 1.5 were in fact comparable with the wild type, e.g.…”

Section: Fig 6 Analysis Of Mutants Containing Chimeric Gpi Additionmentioning

confidence: 74%

“…In addition, Caras and colleagues found that, for optimal processing, the site should be located between 10 and 12 residues upstream of the C-terminal hydrophobic sequence (10). A systematic analysis of all reported GPI-anchored proteins and of the effects of mutations in their C-terminal region has led Eisenhaber et al (18,19) to formulate a prediction algorithm, which confirmed that the volumes of the side chains located near the cleavage site exert a major influence, probably because they must be accommodated within the catalytic pocket of a transamidase (15). Several components of the transamidase complex have recently been cloned (20,21).…”

mentioning

confidence: 99%

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Addition of a Glycophosphatidylinositol to Acetylcholinesterase

Coussen

Ayon

Goff

et al. 2001

Journal of Biological Chemistry

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We introduced various mutations and modifications in the GPI anchoring signal of rat acetylcholinesterase (AChE). 1) The resulting mutants, expressed in transiently transfected COS cells, were initially produced at the same rate, in an active form, but the fraction of GPI-anchored AChE and the steady state level of AChE activity varied over a wide range. 2) Productive interaction with the GPI addition machinery led to GPI anchoring, secretion of uncleaved protein, and secretion of a cleaved protein, in variable proportions. Unproductive interaction led to degradation; poorly processed molecules were degraded rather than retained intracellularly or secreted. 3) An efficient glypiation appeared necessary but not sufficient for a high level of secretion; the cleaved, secreted protein was possibly generated as a by-product of transamidation. 4) Glypiation was influenced by a wider context than the triplet / ؉ 1/ ؉ 2, particularly ؊ 1. 5) Glypiation was not affected by the closeness of the site to the ␣ 10 helix of the catalytic domain. 6) A cysteine could simultaneously form a disulfide bond and serve as an site; however, there was a mutual interference between glypiation and the formation of an intercatenary disulfide bond, at a short distance upstream of . 7) Glypiation was not affected by the presence of an N-glycosylation site at or in its vicinity or by the addition of a short hydrophilic, highly charged peptide (FLAG; DYKDDDDK) at the C terminus of the hydrophobic region.

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Section: Fig 6 Analysis Of Mutants Containing Chimeric Gpi Additionmentioning

confidence: 74%

mentioning

confidence: 99%

Addition of a Glycophosphatidylinositol to Acetylcholinesterase

Coussen

Ayon

Goff

et al. 2001

Journal of Biological Chemistry

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“…The signal peptide was predicted with SignalP Version 3.0 (http:// www.cbs.dtu.dk/services/SignalP/) (Bendtsen et al 2004), and the hydrophobic profile was made using the Kyte-Doolittle method (Kyte and Doolittle 1982). GPI modification was predicted using Big-PI (http://mendel.imp.ac.at/gpi/gpi_ server.html) (Eisenhaber et al 1998). The phylogenetic tree was constructed with MEGA3.1 (Kumar et al 2004 (Hubbell et al 2002).…”

Section: Sequence and Phylogenetic Analysesmentioning

confidence: 99%

Molecular characterization, expression pattern, and function analysis of the OsBC1L family in rice

et al. 2009

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COBRA-like proteins play important roles in cell expansion and cell wall biosynthesis in Arabidopsis. In rice, a COBRA-like gene, BRITTLE CULM1 (BC1), has been identified as a regulator controlling the culm mechanical strength. Analysis of the rice genome indicated that BC1 belongs to an 11-member multigene family, termed the OsBC1L family in this study. Based on sequence comparisons and phylogenetic analysis, the OsBC1L family comprises two main subgroups. Expression patterns examined by microarray and reverse transcription polymerase chain reaction revealed that OsBC1L genes exhibit universal or specific expression patterns. Through T-DNA or Tos17 insertion mutant lines, the functions of six OsBC1L family members have been examined by investigating the phenotype variations of knockout mutants under normal growth conditions. Results suggest that the OsBC1L genes perform a range of functions and participate in various developmental processes in rice.

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“…We performed in silico analysis for the predicted NTNG1 proteins concerning the possibility of a potential cleavage site for glycosylphosphatidylinositol (GPI) anchoring following the o þ 2 rule, 8 by using the DGPI website available at ExPASy Proteomics tools (www.expasy.org/tools/).…”

Section: In Silico Analysis Of Ntng1mentioning

confidence: 99%

Disruption of Netrin G1 by a balanced chromosome translocation in a girl with Rett syndrome

et al. 2005

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We have identified a girl with characteristic features of Rett syndrome (RTT) who carries a de novo balanced translocation involving chromosomes 1 and 7. Both breakpoints were mapped by fluorescence in situ hybridization with selected genomic clones from the regions of interest. Southern blot hybridisations, utilizing probes derived from breakpoint spanning BACs, detected several aberrant fragments specific for the patient. Sequence analysis of the cloned junction fragment indicated that on chromosome 1 the predominantly brain-expressed Netrin G1 (NTNG1) gene is disrupted, whereas on chromosome 7 there was no indication for a truncated gene. The chromosome 1 breakpoint lies within the 3 0 part of NTNG1 and affects alternatively spliced transcripts, suggesting that the phenotype in this patient is the result of disturbed NTNG1 expression. In silico translation of the NTNG1 splice variants predicted protein isoforms with different C-termini: one membrane bound through a glycosylphosphatidylinositol anchor and the other soluble. The membrane-bound protein isoform would be affected by the breakpoint, whereas the soluble form would remain intact. Our results suggest that the central nervous system is sensitive to NTNG1 expression levels and that NTNG1 is a novel candidate disease gene for RTT.

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Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase

Cited by 226 publications

References 1 publication

Addition of a Glycophosphatidylinositol to Acetylcholinesterase

Addition of a Glycophosphatidylinositol to Acetylcholinesterase

Molecular characterization, expression pattern, and function analysis of the OsBC1L family in rice

Disruption of Netrin G1 by a balanced chromosome translocation in a girl with Rett syndrome

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