蛋白质乙酰化数据库 —— CPLA 1.0

短命女 2022-05-14 23:18 248阅读 0赞

For publication of results, please cite the following article:

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 <td> CPLA 1.0: an integrated database of protein lysine acetylation <a href="mailto:lzx@mail.ustc.edu.cn" rel="nofollow"> Zexian Liu </a> , Xinjiao Gao, Jun Cao, Haiyan Liu, Yanhong Zhou, Longping Wen, Xiangjiao Yang, Xuebiao Yao, <a href="mailto:renjian.sysu@gmail.com" rel="nofollow">Jian Ren </a> , <a href="mailto:xueyu@mail.hust.edu.cn" rel="nofollow">Yu Xue </a> . Nucleic Acids Research.2010.(Accepted ) </td> 
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There are two types of acetylation processes widely occurred in proteins. The first Nα-terminal acetylation is catalyzed a variety of N-terminal acetyltransferases (NATs), which cotranslationally transfer acetyl moieties from acetyl-coenzyme A (Acetyl-CoA) to the α-amino (Nα) group of protein amino-terminal residues. Although Nα-terminal acetylation is rare in prokaryotes, it was estimated that about 85% of eukaryotic proteins are Nα-terminally modified ([Polevoda *et al* ., 2000 ][Polevoda _et al_ ._ 2000] ; [Polevoda *et al* ., 2002 ][Polevoda _et al_ ._ 2002] ). The second type is Nε-lysine acetylation, which specifically modifies ε-amino group of protein lysine residues ([Yang *et al* ., 2007 ][Yang _et al_ ._ 2007] ; [Shahbazian *et al* ., 2007 ][Shahbazian _et al_ ._ 2007] ; [Smith *et al* ., 2009 ][Smith _et al_ ._ 2009] ). Although Nε-lysine acetylation is less common, it's one of the most important and ubiquitous post-translational modifications conserved in prokaryotes and eukaryotes. Moreover, the acetylation and deacetylation are dynamically and temporally regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), respectively ([Yang *et al* ., 2004 ][Yang _et al_ ._ 2004] ; [Lee *et al* ., 2007 ][Lee _et al_ ._ 2007] ).

In 1964, Allfrey et al. firstly observed that lysine acetylation of histones plays an essential role in regulation of gene expression ([Allfrey *et al* ., 1964 ][Allfrey _et al_ ._ 1964] ). Later and recent studies in epigenetics solidified this seminal discovery, and proposed acetylation as a key component of the "histone code" ([Jenuwein *et al* ., 2001 ][Jenuwein _et al_ ._ 2001] ). Beyond histones, a wide range of non-histone proteins can also be lysine acetylated, and involved in a variety of biological processes, such as transcription regulation ([Yuan *et al* ., 2005 ][Yuan _et al_ ._ 2005] ), DNA replication ([Terret *et al* ., 2009 ][Terret _et al_ ._ 2009] ; [Choudhary *et al* ., 2009 ][Choudhary _et al_ ._ 2009] ), cellular signaling ([Walkinshaw *et al* ., 2008 ][Walkinshaw _et al_ ._ 2008] ; [Spange *et al* ., 2009 ][Spange _et al_ ._ 2009] ), stress response ([Brunet *et al* ., 2004 ][Brunet _et al_ ._ 2004] ) and so on. Aberrance of lysine acetylation and deacetylation is associated with various diseases and cancers ([Kim *et al* ., 2006 ][Kim _et al_ ._ 2006] ). In particular, acetylation was demonstrated to be implicated in cellular metabolism and aging ([Wang *et al* ., 2010 ][Wang _et al_ ._ 2010] ; [Zhao *et al* ., 2010 ][Zhao _et al_ ._ 2010] ), while one class of NAD+ dependent HDACs of sirtuins might be potent drug target for promoting longevity ([Cohen *et al* ., 2004 ][Cohen _et al_ ._ 2004] ; [Wang *et al* ., 2010 ][Wang _et al_ ._ 2010 1] ).

Since the number of known acetylation sites is rapidly increased, it is an urgent topic to collect the experimental data and provide an integrated resource for the community. Recently, several public databases, such as [PhosphoSitePlus][] , [HPRD][] , [SysPTM][] , and [dbPTM][] , have already contained protein acetylation information. In these databases, both of Nα-terminal and Nε-lysine acetylation data were curated, while lysine acetylation sites are usually only a limited part of total sites. So, thousands of lysine acetylation sites in other species still remain to be collected.

Currently, the **[CPLA 1.0 ][CPLA 1.0]** database was updated on March 1st, 2010, containing ***3,311*** unique protein entries with ***7,151*** lysine acetylation sites. The online service of CPLA 1.0 was implemented in PHP + MySQL + JavaScript. And the local packages of CPLA 1.0 were developed in JAVA 1.5 (J2SE). The database will be updated routinely as new acetylated lysines are reported.

The **[CPLA 1.0 ][CPLA 1.0]** supports Windows, Unix/Linux and Mac and is freely available for academic researches at: [**http://cpla.biocuckoo.org/** ][http_cpla.biocuckoo.org_] .

[bg06.gif]: http://cpla.biocuckoo.org/images/bg06.gif
[Polevoda _et al_ ._ 2000]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11013267
[Polevoda _et al_ ._ 2002]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12049668
[Yang _et al_ ._ 2007]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17694074
[Shahbazian _et al_ ._ 2007]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17362198
[Smith _et al_ ._ 2009]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19816449
[Yang _et al_ ._ 2004]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14960713
[Lee _et al_ ._ 2007]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17380162
[Allfrey _et al_ ._ 1964]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14172992
[Jenuwein _et al_ ._ 2001]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11498575
[Yuan _et al_ ._ 2005]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15653507
[Terret _et al_ ._ 2009]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19907496
[Choudhary _et al_ ._ 2009]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19608861
[Walkinshaw _et al_ ._ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18425769
[Spange _et al_ ._ 2009]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18804549
[Brunet _et al_ ._ 2004]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14976264
[Kim _et al_ ._ 2006]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16916647
[Wang _et al_ ._ 2010]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20167787
[Zhao _et al_ ._ 2010]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20167786
[Cohen _et al_ ._ 2004]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15205477
[Wang _et al_ ._ 2010 1]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19945548
[PhosphoSitePlus]: http://www.phosphosite.org/
[HPRD]: http://www.hprd.org/
[SysPTM]: http://www.biosino.org.cn/SysPTM
[dbPTM]: http://dbptm.mbc.nctu.edu.tw/
[CPLA 1.0]: http://cpla.biocuckoo.org/index.php
[http_cpla.biocuckoo.org_]: http://cpla.biocuckoo.org/