XMAn-A Homo sapiens Mutated Cancer Peptides Database

<p>To enable the identification of mutated peptide sequences in complex biological samples, in this work, a cancer protein database with mutation information collected from several public resources such as COSMIC, IARC P53, OMIM and UniProtKB, was developed. In-house developed Perl-scripts were used to search and process the data, and to translate each gene-level mutation into a mutated peptide sequence. The cancer mutation database comprises a total of 872,125 peptide entries from 25,642 protein IDs. A description line for each entry provides the parent protein ID and name, the cDNA- and protein-level mutation site and type, the originating database, and the cancer tissue type and corresponding hits. The database is FASTA formatted to enable data retrieval by commonly used tandem MS search engines. <br></p

XMAn: A <i>Homo sapiens</i> Mutated-Peptide Database for the MS Analysis of Cancerous Cell States

To enable the identification of mutated peptide sequences in complex biological samples, in this work, two novel cancer- and disease-related protein databases with mutation information collected from several public resources such as COSMIC, IARC P53, OMIM, and UniProtKB were developed. In-house developed Perl scripts were used to search and process the data and to translate each gene-level mutation into a mutated peptide sequence. The cancer and disease mutation databases comprise a total of 872 125 and 27 148 peptide entries from 25 642 and 2913 proteins, respectively. A description line for each entry provides the parent protein ID and name, the cDNA- and protein-level mutation site and type, the originating database, and the disease or cancer tissue type and corresponding hits. The two databases are FASTA-formatted to enable data retrieval by commonly used tandem MS search engines. While the largest number of mutations were encountered for the amino acids A/D/E/G/L/P/R/S, the global mutation profiles replicate closely the outcome of the 1000 Genomes Project aimed at cataloguing natural mutations in the human population. The affected proteins were primarily involved in transcription regulation, splicing, protein synthesis/folding/binding, redox/energy production, adhesion/motility, and to some extent in DNA damage repair and signaling. The applicability of the database to identifying the presence of mutated peptides was investigated with MCF-7 breast cancer cell extracts

Yeast Mitochondrial Transcription Factor Mtf1 Determines the Precision of Promoter-Directed Initiation of RNA Polymerase Rpo41

<div><p>Despite their clear T7-bacteriophage origin, mitochondrial RNA polymerases have evolved to require transcription factors. All mitochondrial polymerases contain an extra N-terminal domain that has no counterpart in the self-proficient phage enzyme, which is therefore hypothesized to interact with transcription factors. We studied a series of N-terminal deletion mutants of yeast mitochondrial RNA polymerase, Rpo41, and have found that the N-terminal region does not abolish the effects of Mtf1; rather it contributes directly to enzyme catalysis. Mtf1 can rescue the defective Rpo41 enzymes resulted from N-terminal domain deletions. Although Rpo41 appears to have retained all promoter recognition elements found in T7 RNAP, the elements are not independently functional, and Mtf1 is necessary and sufficient for holoenzyme promoter-directed transcription activity.</p></div

Interactions of Rpo41 with Mtf1 and promoter DNA.

<p>(A). Analytical gel filtration chromatograph of wild-type Rpo41 (2.8 μM) with Mtf1 (5.6 μM) (red) superimposed with that of Rpo41 (1 μM), Mtf1 (2 μM) and a 20bp promoter-containing DNA duplex (3 μM) (blue). The elution volume of Rpo41 alone is indicated (black arrow). The protein contents of the peak fractions of Rpo41 + Mtf1 and Rpo41 + Mtf1 + DNA were visualized after SDS-PAGE. (B). Analyses described in (A) performed with Rpo41 ΔN393.</p

Densitometry scanning of SDS with Mtf1 and Rpo41.

<p>^a Intensities were measured using fraction 10 of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136879#pone.0136879.g004" target="_blank">Fig 4A</a> for wild-type Rpo41 and fraction</p><p>^b<i>Free_Rpo</i>41 = <i>I</i>_<i>upper</i><i>—</i>[<i>I</i>_<i>lower</i> (<i>MW</i>_Rpo41 /<i>MW</i>_{Mtf 1})]</p><p>^c<i>Bound_Rpo</i>41 = <i>I</i>_<i>upper</i><i>—Free_Rpo</i>41</p><p>Densitometry scanning of SDS with Mtf1 and Rpo41.</p

Comparisons of promoter strength and structure.

<p>(A). Sequences and structures of the 65-bp constructs contain a linear promoter and a pre-melted region with or without 14S rRNA promoter. (B-D). transcripts yielded from the ab0ove constructs using Rpo41 wild-type or ΔN160 (0.5 μM) in the absence or presence of Mtf1 (2.5 μM), labeled with [γ-³²P]GTP, [γ-³²P]ATP, and [α-³²P]ATP, respectively.</p

Selective inhibitory effect of Mtf1 on holoenzyme activity.

<p>Selective inhibitory effect of Mtf1 on holoenzyme activity.</p

Activities of Rpo41 variants on a linear template.

<p>Transcription of 1 μM 70-bp linear DNA containing 14S rRNA (A) using 0.5 μM Rpo41 (wild-type or a variant) without or with 2.5 μM Mtf1 were performed in the presence of NTPs and [γ-³²P]ATP (B). (C). The intensities of 34- mer transcripts in (B) were calculated by Quantity One software (BioRad).</p

Serum ceruloplasmin concentrations in patients stratified by age.

<p>Serum ceruloplasmin concentrations in patients stratified by age.</p

Diagnostic accuracy of ceruloplasmin at the conventional cutoff value in whole group.

<p>Diagnostic accuracy of ceruloplasmin at the conventional cutoff value in whole group.</p