BRCA1 Functions as a 5'- Nuclease Via PIN Domain Identified by Multiple Protein Sequence Alignments.
Sergei Tatishchev, Elizabeth Spiteri, Jean Lopategui. Cedars-Sinai Medical Center, Los Angeles, CA
Background: BRCA1 has been implicated in a multitude of biological processes. It co-localizes via conserved RING & BRCT domains with a number of proteins involved in DNA damage repair and cell cycle control. Despite extensive research, BRCA1 function has remained elusive. Thus, identification of new conserved domains is paramount to uncovering BRCA1 biological function. Recently, crystallographic studies and bioinformatics analyses of orthologous proteins have revealed a number of highly conserved amino acids up to hundreds of residues apart that form functional domains only when put in close proximity to each other within a tertiary protein structure. Using sequence alignment software and domain database search we tested our hypothesis that multiple alignments between BRCA1 proteins would reveal a set of phylogenetically conserved amino acids capable of forming a functional domain at the level of BRCA1 tertiary structure.
Design: BRCA1 protein sequences from divergent mammalian taxa were identified in the NCBI database. The sequences were aligned using the free online software ClustalW2. ExPASy Proteomics Server and Pfam protein database were used to identify a functional domain.
Results: An analysis of BRCA1 sequence alignments identified 5 highly conserved amino acids across all mammalian orders (Fig 1).
Four acidic residues (D853, E1066, D1123, D1151) and threonine (T1149) within exon 11 were identified as the PIN domain sequence (N-term-D-…-D/E-…-D-…-T/SxD-C-term). In PIN domains the acidic residues are spatially clustered to support coordination of Mg2+ ions forming the active site of 5'-nucleases. In eukaryotes, PIN-domain containing proteins are an integral part of the nonsense-mediated decay (NMD) process that functions to eliminate transcripts with premature termination codons.
Conclusions: Discovery of the PIN domain within BRCA1 sequence, for the first time, provides an insight into its potential biological function as a 5'-nuclease involved in tumor suppression & possibly NMD. In addition, the presented strategy to functionally characterize proteins involved in oncogenesis, such as BRCA1, is straightforward, requiring only publicly available protein sequences spanning divergent taxonomic groups and a handful of user-friendly bioinformatics tools.
Category: Special Category - Pan-genomic/Pan-proteomic approaches to Cancer
Monday, February 28, 2011 9:30 AM
Poster Session I Stowell-Orbison/Surgical Pathology/Autopsy Awards Poster Session # 245, Monday Morning