메뉴 건너뛰기




Volumn 1828, Issue 12, 2013, Pages 2937-2943

Bioinformatics perspective on rhomboid intramembrane protease evolution and function

Author keywords

Bioinformatics; Classification; Evolution; Intramembrane proteolysis; Rhomboid protease; Structure

Indexed keywords

BACTERIAL ENZYME; CHYMOTRYPSIN; MEMBRANE PROTEIN; PROTEINASE; RHOMBOID INTRAMEMBRANE PROTEASE; SERINE PROTEINASE; SUBTILISIN; UNCLASSIFIED DRUG;

EID: 84885175357     PISSN: 00052736     EISSN: 18792642     Source Type: Journal    
DOI: 10.1016/j.bbamem.2013.06.031     Document Type: Review
Times cited : (20)

References (47)
  • 3
    • 84859426282 scopus 로고    scopus 로고
    • MEROPS: The database of proteolytic enzymes, their substrates and inhibitors
    • N.D. Rawlings, A.J. Barrett, and A. Bateman MEROPS: the database of proteolytic enzymes, their substrates and inhibitors Nucleic Acids Res. 40 2012 D343 D350
    • (2012) Nucleic Acids Res. , vol.40
    • Rawlings, N.D.1    Barrett, A.J.2    Bateman, A.3
  • 4
  • 5
    • 0037150672 scopus 로고    scopus 로고
    • Identification of signal peptide peptidase, a presenilin-type aspartic protease
    • DOI 10.1126/science.1070925
    • A. Weihofen, K. Binns, M.K. Lemberg, K. Ashman, and B. Martoglio Identification of signal peptide peptidase, a presenilin-type aspartic protease Science 296 2002 2215 2218 (Pubitemid 34680305)
    • (2002) Science , vol.296 , Issue.5576 , pp. 2215-2218
    • Weihofen, A.1    Binns, K.2    Lemberg, M.K.3    Ashman, K.4    Martoglio, B.5
  • 6
    • 0033535553 scopus 로고    scopus 로고
    • Two transmembrane aspartates in presenilin-1 required for presenilin endoproteolysis and gamma-secretase activity
    • M.S. Wolfe, W. Xia, B.L. Ostaszewski, T.S. Diehl, W.T. Kimberly, and D.J. Selkoe Two transmembrane aspartates in presenilin-1 required for presenilin endoproteolysis and gamma-secretase activity Nature 398 1999 513 517
    • (1999) Nature , vol.398 , pp. 513-517
    • Wolfe, M.S.1    Xia, W.2    Ostaszewski, B.L.3    Diehl, T.S.4    Kimberly, W.T.5    Selkoe, D.J.6
  • 7
    • 0035913908 scopus 로고    scopus 로고
    • Drosophila Rhomboid-1 defines a family of putative intramembrane serine proteases
    • DOI 10.1016/S0092-8674(01)00525-6
    • S. Urban, J.R. Lee, and M. Freeman Drosophila rhomboid-1 defines a family of putative intramembrane serine proteases Cell 107 2001 173 182 (Pubitemid 33035944)
    • (2001) Cell , vol.107 , Issue.2 , pp. 173-182
    • Urban, S.1    Lee, J.R.2    Freeman, M.3
  • 8
    • 29344444795 scopus 로고    scopus 로고
    • Site-2 protease regulated intramembrane proteolysis: Sequence homologs suggest an ancient signaling cascade
    • DOI 10.1110/ps.051766506
    • L.N. Kinch, K. Ginalski, and N.V. Grishin Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade Protein Sci. 15 2006 84 93 (Pubitemid 43004236)
    • (2006) Protein Science , vol.15 , Issue.1 , pp. 84-93
    • Kinch, L.N.1    Ginalski, K.2    Grishin, N.V.3
  • 9
    • 63949088399 scopus 로고    scopus 로고
    • Signal peptide peptidases: A family of intramembrane-cleaving proteases that cleave type 2 transmembrane proteins
    • T.E. Golde, M.S. Wolfe, and D.C. Greenbaum Signal peptide peptidases: a family of intramembrane-cleaving proteases that cleave type 2 transmembrane proteins Semin. Cell Dev. Biol. 20 2009 225 230
    • (2009) Semin. Cell Dev. Biol. , vol.20 , pp. 225-230
    • Golde, T.E.1    Wolfe, M.S.2    Greenbaum, D.C.3
  • 10
    • 80054893675 scopus 로고    scopus 로고
    • The rhomboid protease family: A decade of progress on function and mechanism
    • S. Urban, and S.W. Dickey The rhomboid protease family: a decade of progress on function and mechanism Genome Biol. 12 2011 231
    • (2011) Genome Biol. , vol.12 , pp. 231
    • Urban, S.1    Dickey, S.W.2
  • 11
    • 0037264371 scopus 로고    scopus 로고
    • The rhomboids: A nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers
    • E.V. Koonin, K.S. Makarova, I.B. Rogozin, L. Davidovic, M.C. Letellier, and L. Pellegrini The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers Genome Biol. 4 2003 R19
    • (2003) Genome Biol. , vol.4 , pp. 19
    • Koonin, E.V.1    Makarova, K.S.2    Rogozin, I.B.3    Davidovic, L.4    Letellier, M.C.5    Pellegrini, L.6
  • 14
    • 35948982252 scopus 로고    scopus 로고
    • Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases
    • DOI 10.1101/gr.6425307
    • M.K. Lemberg, and M. Freeman Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases Genome Res. 17 2007 1634 1646 (Pubitemid 350074859)
    • (2007) Genome Research , vol.17 , Issue.11 , pp. 1634-1646
    • Lemberg, M.K.1    Freeman, M.2
  • 15
    • 48149115851 scopus 로고    scopus 로고
    • Plant mitochondrial rhomboid, AtRBL12, has different substrate specificity from its yeast counterpart
    • B. Kmiec-Wisniewska, K. Krumpe, A. Urantowka, W. Sakamoto, E. Pratje, and H. Janska Plant mitochondrial rhomboid, AtRBL12, has different substrate specificity from its yeast counterpart Plant Mol. Biol. 68 2008 159 171
    • (2008) Plant Mol. Biol. , vol.68 , pp. 159-171
    • Kmiec-Wisniewska, B.1    Krumpe, K.2    Urantowka, A.3    Sakamoto, W.4    Pratje, E.5    Janska, H.6
  • 17
    • 77954078996 scopus 로고    scopus 로고
    • Rhomboid 4 (ROM4) affects the processing of surface adhesins and facilitates host cell invasion by Toxoplasma gondii
    • J.S. Buguliskis, F. Brossier, J. Shuman, and L.D. Sibley Rhomboid 4 (ROM4) affects the processing of surface adhesins and facilitates host cell invasion by Toxoplasma gondii PLoS Pathog. 6 2010 e1000858
    • (2010) PLoS Pathog. , vol.6 , pp. 1000858
    • Buguliskis, J.S.1    Brossier, F.2    Shuman, J.3    Sibley, L.D.4
  • 18
    • 26844540848 scopus 로고    scopus 로고
    • An Arabidopsis Rhomboid homolog is an intramembrane protease in plants
    • DOI 10.1016/j.febslet.2005.09.049, PII S0014579305011579
    • M.M. Kanaoka, S. Urban, M. Freeman, and K. Okada An Arabidopsis Rhomboid homolog is an intramembrane protease in plants FEBS Lett. 579 2005 5723 5728 (Pubitemid 41455654)
    • (2005) FEBS Letters , vol.579 , Issue.25 , pp. 5723-5728
    • Kanaoka, M.M.1    Urban, S.2    Freeman, M.3    Okada, K.4
  • 19
    • 84863685539 scopus 로고    scopus 로고
    • An Arabidopsis rhomboid protease has roles in the chloroplast and in flower development
    • E.P. Thompson, S.G. Smith, and B.J. Glover An Arabidopsis rhomboid protease has roles in the chloroplast and in flower development J. Exp. Bot. 63 2012 3559 3570
    • (2012) J. Exp. Bot. , vol.63 , pp. 3559-3570
    • Thompson, E.P.1    Smith, S.G.2    Glover, B.J.3
  • 25
    • 33750886311 scopus 로고    scopus 로고
    • Crystal structure of a rhomboid family intramembrane protease
    • Y. Wang, Y. Zhang, and Y. Ha Crystal structure of a rhomboid family intramembrane protease Nature 444 2006 179 180
    • (2006) Nature , vol.444 , pp. 179-180
    • Wang, Y.1    Zhang, Y.2    Ha, Y.3
  • 27
    • 84860711067 scopus 로고    scopus 로고
    • Conformational change in rhomboid protease GlpG induced by inhibitor binding to its S′ subsites
    • Y. Xue, S. Chowdhury, X. Liu, Y. Akiyama, J. Ellman, and Y. Ha Conformational change in rhomboid protease GlpG induced by inhibitor binding to its S′ subsites Biochemistry 51 2012 3723 3731
    • (2012) Biochemistry , vol.51 , pp. 3723-3731
    • Xue, Y.1    Chowdhury, S.2    Liu, X.3    Akiyama, Y.4    Ellman, J.5    Ha, Y.6
  • 28
    • 72149124813 scopus 로고    scopus 로고
    • Sequence-specific intramembrane proteolysis: Identification of a recognition motif in rhomboid substrates
    • K. Strisovsky, H.J. Sharpe, and M. Freeman Sequence-specific intramembrane proteolysis: identification of a recognition motif in rhomboid substrates Mol. Cell 36 2009 1048 1059
    • (2009) Mol. Cell , vol.36 , pp. 1048-1059
    • Strisovsky, K.1    Sharpe, H.J.2    Freeman, M.3
  • 29
    • 84878843045 scopus 로고    scopus 로고
    • Membrane immersion allows rhomboid proteases to achieve specificity by reading transmembrane segment dynamics
    • S.M. Moin, and S. Urban Membrane immersion allows rhomboid proteases to achieve specificity by reading transmembrane segment dynamics Elife 1 2012 e00173
    • (2012) Elife , vol.1 , pp. 00173
    • Moin, S.M.1    Urban, S.2
  • 30
    • 0042526632 scopus 로고    scopus 로고
    • Processing of Mgm1 by the rhomboid-type protease Pcp1 is required for maintenance of mitochondrial morphology and of mitochondrial DNA
    • DOI 10.1074/jbc.M211311200
    • M. Herlan, F. Vogel, C. Bornhovd, W. Neupert, and A.S. Reichert Processing of Mgm1 by the rhomboid-type protease Pcp1 is required for maintenance of mitochondrial morphology and of mitochondrial DNA J. Biol. Chem. 278 2003 27781 27788 (Pubitemid 36899969)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.30 , pp. 27781-27788
    • Herlan, M.1    Vogel, F.2    Bornhovd, C.3    Neupert, W.4    Reichert, A.S.5
  • 31
    • 80054841370 scopus 로고    scopus 로고
    • Rhomboid-7 over-expression results in Opa1-like processing and malfunctioning mitochondria
    • M. Rahman, and P. Kylsten Rhomboid-7 over-expression results in Opa1-like processing and malfunctioning mitochondria Biochem. Biophys. Res. Commun. 414 2011 315 320
    • (2011) Biochem. Biophys. Res. Commun. , vol.414 , pp. 315-320
    • Rahman, M.1    Kylsten, P.2
  • 32
    • 58149397651 scopus 로고    scopus 로고
    • Rhomboid-7 and HtrA2/Omi act in a common pathway with the Parkinson's disease factors Pink1 and Parkin
    • (discussion 173)
    • A.J. Whitworth, J.R. Lee, V.M. Ho, R. Flick, R. Chowdhury, and G.A. McQuibban Rhomboid-7 and HtrA2/Omi act in a common pathway with the Parkinson's disease factors Pink1 and Parkin Dis. Model. Mech. 1 2008 168 174 (discussion 173)
    • (2008) Dis. Model. Mech. , vol.1 , pp. 168-174
    • Whitworth, A.J.1    Lee, J.R.2    Ho, V.M.3    Flick, R.4    Chowdhury, R.5    McQuibban, G.A.6
  • 34
    • 79955667485 scopus 로고    scopus 로고
    • The mitochondrial intramembrane protease PARL cleaves human Pink1 to regulate Pink1 trafficking
    • C. Meissner, H. Lorenz, A. Weihofen, D.J. Selkoe, and M.K. Lemberg The mitochondrial intramembrane protease PARL cleaves human Pink1 to regulate Pink1 trafficking J. Neurochem. 117 2011 856 867
    • (2011) J. Neurochem. , vol.117 , pp. 856-867
    • Meissner, C.1    Lorenz, H.2    Weihofen, A.3    Selkoe, D.J.4    Lemberg, M.K.5
  • 35
    • 84869434856 scopus 로고    scopus 로고
    • Structure and function of bacterial dynamin-like proteins
    • M. Bramkamp Structure and function of bacterial dynamin-like proteins Biol. Chem. 393 2012 1203 1214
    • (2012) Biol. Chem. , vol.393 , pp. 1203-1214
    • Bramkamp, M.1
  • 36
    • 14044266249 scopus 로고    scopus 로고
    • EGF signal propagation during C. Elegans vulval development mediated by ROM-1 rhomboid
    • A. Dutt, S. Canevascini, E. Froehli-Hoier, and A. Hajnal EGF signal propagation during C. elegans vulval development mediated by ROM-1 rhomboid PLoS Biol. 2 2004 e334
    • (2004) PLoS Biol. , vol.2 , pp. 334
    • Dutt, A.1    Canevascini, S.2    Froehli-Hoier, E.3    Hajnal, A.4
  • 38
    • 1642422313 scopus 로고    scopus 로고
    • Intramembrane cleavage of ephrinB3 by the human rhomboid family protease, RHBDL2
    • DOI 10.1016/j.bbrc.2004.03.039, PII S0006291X04005339
    • J.C. Pascall, and K.D. Brown Intramembrane cleavage of ephrinB3 by the human rhomboid family protease, RHBDL2 Biochem. Biophys. Res. Commun. 317 2004 244 252 (Pubitemid 38401991)
    • (2004) Biochemical and Biophysical Research Communications , vol.317 , Issue.1 , pp. 244-252
    • Pascall, J.C.1    Brown, K.D.2
  • 40
    • 84855822415 scopus 로고    scopus 로고
    • Tumor necrosis factor signaling requires iRhom2 to promote trafficking and activation of TACE
    • C. Adrain, M. Zettl, Y. Christova, N. Taylor, and M. Freeman Tumor necrosis factor signaling requires iRhom2 to promote trafficking and activation of TACE Science 335 2012 225 228
    • (2012) Science , vol.335 , pp. 225-228
    • Adrain, C.1    Zettl, M.2    Christova, Y.3    Taylor, N.4    Freeman, M.5
  • 42
    • 79953269767 scopus 로고    scopus 로고
    • Rhomboid family pseudoproteases use the ER quality control machinery to regulate intercellular signaling
    • M. Zettl, C. Adrain, K. Strisovsky, V. Lastun, and M. Freeman Rhomboid family pseudoproteases use the ER quality control machinery to regulate intercellular signaling Cell 145 2011 79 91
    • (2011) Cell , vol.145 , pp. 79-91
    • Zettl, M.1    Adrain, C.2    Strisovsky, K.3    Lastun, V.4    Freeman, M.5
  • 43
    • 80655139177 scopus 로고    scopus 로고
    • ProPhylo: Partial phylogenetic profiling to guide protein family construction and assignment of biological process
    • M.K. Basu, J.D. Selengut, and D.H. Haft ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process BMC Bioinforma. 12 2011 434
    • (2011) BMC Bioinforma. , vol.12 , pp. 434
    • Basu, M.K.1    Selengut, J.D.2    Haft, D.H.3
  • 45
    • 83355168671 scopus 로고    scopus 로고
    • GlyGly-CTERM and rhombosortase: A C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease
    • D.H. Haft, and N. Varghese GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease PLoS One 6 2011 e28886
    • (2011) PLoS One , vol.6 , pp. 28886
    • Haft, D.H.1    Varghese, N.2
  • 47
    • 10044222704 scopus 로고    scopus 로고
    • CLANS: A Java application for visualizing protein families based on pairwise similarity
    • DOI 10.1093/bioinformatics/bth444
    • T. Frickey, and A. Lupas CLANS: a Java application for visualizing protein families based on pairwise similarity Bioinformatics 20 2004 3702 3704 (Pubitemid 40136822)
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3702-3704
    • Frickey, T.1    Lupas, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.