Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)

Nai Jyuan Wang; Chi Ching Lee; Chao Sheng Cheng; Wei Cheng Lo; Ya Fen Yang; Ming Nan Chen; Ping Chiang Lyu

doi:10.1186/1471-2164-13-S1-S9

Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)

Nai Jyuan Wang, Chi Ching Lee, Chao Sheng Cheng, Wei Cheng Lo, Ya Fen Yang, Ming Nan Chen, Ping Chiang Lyu^*

^*Corresponding author for this work

Research output: Contribution to journal › Conference article › peer-review

46 Scopus citations

Abstract

Background: Plant non-specific lipid transfer proteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, participating in plant defence activity against bacterial and fungal pathogens, and enhancing cell wall extension in tobacco. However, the lipid transfer mechanism of nsLTPs is still unclear, and comprehensive information of nsLTPs is difficult to obtain.

Methods: In this study, we identified 595 nsLTPs from 121 different species and constructed an nsLTPs database-nsLTPDB-which comprises the sequence information, structures, relevant literatures, and biological data of all plant nsLTPs http://nsltpdb.life.nthu.edu.tw/.

Results: Meanwhile, bioinformatics and statistics methods were implemented to develop a classification method for nsLTPs based on the patterns of the eight highly-conserved cysteine residues, and to suggest strict Prositestyled patterns for Type I and Type II nsLTPs. The pattern of Type I is C X₂ V X_5-7 C [V, L, I] × Y [L, A, V] X_8-13 CC ×G X₁₂ D × [Q, K, R] X₂ CXC X_16-21 P X₂ C X_13-15C, and that of Type II is C X₄ L X₂ C X_9-11 P [S, T] X2 CC X5 Q X2-4 C[L,F]C X₂ [A, L, I] × [D, N] P X_10-12 [K, R] X_4-5 C X_3-4 P X0-2 C. Moreover, we referred the Prosite-styled patterns to the experimental mutagenesis data that previously established by our group, and found that the residues with higher conservation played an important role in the structural stability or lipid binding ability of nsLTPs.

Conclusions: Taken together, this research has suggested potential residues that might be essential to modulate the structural and functional properties of plant nsLTPs. Finally, we proposed some biologically important sites of the nsLTPs, which are described by using a new Prosite-styled pattern that we defined.

Original language	English
Article number	S9
Journal	Series on Advances in Bioinformatics and Computational Biology
Volume	13
DOIs	https://doi.org/10.1186/1471-2164-13-S1-S9
State	Published - 2012
Externally published	Yes
Event	10th Asia Pacific Bioinformatics Conference, APBC 2012 - Melbourne, Australia Duration: 17 01 2012 → 19 01 2012

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Publisher Copyright:
© 2012 Wang et al.; licensee BioMed Central Ltd.

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10.1186/1471-2164-13-S1-S9

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@article{ae853705ec0e4bdd9554dc6dacf1b3c6,

title = "Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)",

abstract = "Background: Plant non-specific lipid transfer proteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, participating in plant defence activity against bacterial and fungal pathogens, and enhancing cell wall extension in tobacco. However, the lipid transfer mechanism of nsLTPs is still unclear, and comprehensive information of nsLTPs is difficult to obtain.Methods: In this study, we identified 595 nsLTPs from 121 different species and constructed an nsLTPs database-nsLTPDB-which comprises the sequence information, structures, relevant literatures, and biological data of all plant nsLTPs http://nsltpdb.life.nthu.edu.tw/.Results: Meanwhile, bioinformatics and statistics methods were implemented to develop a classification method for nsLTPs based on the patterns of the eight highly-conserved cysteine residues, and to suggest strict Prositestyled patterns for Type I and Type II nsLTPs. The pattern of Type I is C X2 V X5-7 C [V, L, I] × Y [L, A, V] X8-13 CC ×G X12 D × [Q, K, R] X2 CXC X16-21 P X2 C X13-15C, and that of Type II is C X4 L X2 C X9-11 P [S, T] X2 CC X5 Q X2-4 C[L,F]C X2 [A, L, I] × [D, N] P X10-12 [K, R] X4-5 C X3-4 P X0-2 C. Moreover, we referred the Prosite-styled patterns to the experimental mutagenesis data that previously established by our group, and found that the residues with higher conservation played an important role in the structural stability or lipid binding ability of nsLTPs.Conclusions: Taken together, this research has suggested potential residues that might be essential to modulate the structural and functional properties of plant nsLTPs. Finally, we proposed some biologically important sites of the nsLTPs, which are described by using a new Prosite-styled pattern that we defined.",

author = "Wang, {Nai Jyuan} and Lee, {Chi Ching} and Cheng, {Chao Sheng} and Lo, {Wei Cheng} and Yang, {Ya Fen} and Chen, {Ming Nan} and Lyu, {Ping Chiang}",

note = "Publisher Copyright: {\textcopyright} 2012 Wang et al.; licensee BioMed Central Ltd.; 10th Asia Pacific Bioinformatics Conference, APBC 2012 ; Conference date: 17-01-2012 Through 19-01-2012",

year = "2012",

doi = "10.1186/1471-2164-13-S1-S9",

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T1 - Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)

AU - Wang, Nai Jyuan

AU - Lee, Chi Ching

AU - Cheng, Chao Sheng

AU - Lo, Wei Cheng

AU - Yang, Ya Fen

AU - Chen, Ming Nan

AU - Lyu, Ping Chiang

PY - 2012

Y1 - 2012

N2 - Background: Plant non-specific lipid transfer proteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, participating in plant defence activity against bacterial and fungal pathogens, and enhancing cell wall extension in tobacco. However, the lipid transfer mechanism of nsLTPs is still unclear, and comprehensive information of nsLTPs is difficult to obtain.Methods: In this study, we identified 595 nsLTPs from 121 different species and constructed an nsLTPs database-nsLTPDB-which comprises the sequence information, structures, relevant literatures, and biological data of all plant nsLTPs http://nsltpdb.life.nthu.edu.tw/.Results: Meanwhile, bioinformatics and statistics methods were implemented to develop a classification method for nsLTPs based on the patterns of the eight highly-conserved cysteine residues, and to suggest strict Prositestyled patterns for Type I and Type II nsLTPs. The pattern of Type I is C X2 V X5-7 C [V, L, I] × Y [L, A, V] X8-13 CC ×G X12 D × [Q, K, R] X2 CXC X16-21 P X2 C X13-15C, and that of Type II is C X4 L X2 C X9-11 P [S, T] X2 CC X5 Q X2-4 C[L,F]C X2 [A, L, I] × [D, N] P X10-12 [K, R] X4-5 C X3-4 P X0-2 C. Moreover, we referred the Prosite-styled patterns to the experimental mutagenesis data that previously established by our group, and found that the residues with higher conservation played an important role in the structural stability or lipid binding ability of nsLTPs.Conclusions: Taken together, this research has suggested potential residues that might be essential to modulate the structural and functional properties of plant nsLTPs. Finally, we proposed some biologically important sites of the nsLTPs, which are described by using a new Prosite-styled pattern that we defined.

AB - Background: Plant non-specific lipid transfer proteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, participating in plant defence activity against bacterial and fungal pathogens, and enhancing cell wall extension in tobacco. However, the lipid transfer mechanism of nsLTPs is still unclear, and comprehensive information of nsLTPs is difficult to obtain.Methods: In this study, we identified 595 nsLTPs from 121 different species and constructed an nsLTPs database-nsLTPDB-which comprises the sequence information, structures, relevant literatures, and biological data of all plant nsLTPs http://nsltpdb.life.nthu.edu.tw/.Results: Meanwhile, bioinformatics and statistics methods were implemented to develop a classification method for nsLTPs based on the patterns of the eight highly-conserved cysteine residues, and to suggest strict Prositestyled patterns for Type I and Type II nsLTPs. The pattern of Type I is C X2 V X5-7 C [V, L, I] × Y [L, A, V] X8-13 CC ×G X12 D × [Q, K, R] X2 CXC X16-21 P X2 C X13-15C, and that of Type II is C X4 L X2 C X9-11 P [S, T] X2 CC X5 Q X2-4 C[L,F]C X2 [A, L, I] × [D, N] P X10-12 [K, R] X4-5 C X3-4 P X0-2 C. Moreover, we referred the Prosite-styled patterns to the experimental mutagenesis data that previously established by our group, and found that the residues with higher conservation played an important role in the structural stability or lipid binding ability of nsLTPs.Conclusions: Taken together, this research has suggested potential residues that might be essential to modulate the structural and functional properties of plant nsLTPs. Finally, we proposed some biologically important sites of the nsLTPs, which are described by using a new Prosite-styled pattern that we defined.

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U2 - 10.1186/1471-2164-13-S1-S9

DO - 10.1186/1471-2164-13-S1-S9

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T2 - 10th Asia Pacific Bioinformatics Conference, APBC 2012

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ER -

Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)

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