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proteogenomics

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https://www.readbyqxmd.com/read/28100699/proteogenomics-produces-comprehensive-and-highly-accurate-protein-coding-gene-annotation-in-a-complete-genome-assembly-of-malassezia-sympodialis
#1
Yafeng Zhu, Pär G Engström, Christian Tellgren-Roth, Charles D Baudo, John C Kennell, Sheng Sun, R Blake Billmyre, Markus S Schröder, Anna Andersson, Tina Holm, Benjamin Sigurgeirsson, Guangxi Wu, Sundar Ram Sankaranarayanan, Rahul Siddharthan, Kaustuv Sanyal, Joakim Lundeberg, Björn Nystedt, Teun Boekhout, Thomas L Dawson, Joseph Heitman, Annika Scheynius, Janne Lehtiö
Complete and accurate genome assembly and annotation is a crucial foundation for comparative and functional genomics. Despite this, few complete eukaryotic genomes are available, and genome annotation remains a major challenge. Here, we present a complete genome assembly of the skin commensal yeast Malassezia sympodialis and demonstrate how proteogenomics can substantially improve gene annotation. Through long-read DNA sequencing, we obtained a gap-free genome assembly for M. sympodialis (ATCC 42132), comprising eight nuclear and one mitochondrial chromosome...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28091603/repo-man-pp1-regulates-heterochromatin-formation-in-interphase
#2
Inês J de Castro, James Budzak, Maria L Di Giacinto, Lorena Ligammari, Ezgi Gokhan, Christos Spanos, Daniela Moralli, Christine Richardson, Jose I de Las Heras, Silvia Salatino, Eric C Schirmer, Katharine S Ullman, Wendy A Bickmore, Catherine Green, Juri Rappsilber, Sarah Lamble, Martin W Goldberg, Veronica Vinciotti, Paola Vagnarelli
Repo-Man is a protein phosphatase 1 (PP1) targeting subunit that regulates mitotic progression and chromatin remodelling. After mitosis, Repo-Man/PP1 remains associated with chromatin but its function in interphase is not known. Here we show that Repo-Man, via Nup153, is enriched on condensed chromatin at the nuclear periphery and at the edge of the nucleopore basket. Repo-Man/PP1 regulates the formation of heterochromatin, dephosphorylates H3S28 and it is necessary and sufficient for heterochromatin protein 1 binding and H3K27me3 recruitment...
January 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28031186/actg-novel-peptide-mapping-onto-gene-models
#3
Seunghyuk Choi, Hyunwoo Kim, Eunok Paek
: In many proteogenomic applications, mapping peptide sequences onto genome sequences can be very useful, because it allows us to understand origins of the gene products. Existing software tools either take the genomic position of a peptide start site as an input or assume that the peptide sequence exactly matches the coding sequence of a given gene model. In case of novel peptides resulting from genomic variations, especially structural variations such as alternative splicing, these existing tools cannot be directly applied unless users supply information about the variant, either its genomic position or its transcription model...
December 28, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28011598/reconstructing-metabolic-pathways-of-a-member-of-the-genus-pelotomaculum-suggesting-its-potential-to-oxidize-benzene-to-carbon-dioxide-with-direct-reduction-of-sulfate
#4
Xiyang Dong, Johannes Dröge, Christine von Toerne, Sviatlana Marozava, Alice C McHardy, Rainer U Meckenstock
The enrichment culture BPL is able to degrade benzene with sulfate as electron acceptor and is dominated by an organism of the genus Pelotomaculum Members of Pelotomaculum are usually known to be fermenters, undergoing syntrophy with anaerobic respiring microorganisms or methanogens. By using a metagenomic approach, we reconstructed a high-quality genome (∼2.97 Mbp, 99% completeness) for Pelotomaculum candidate BPL. The proteogenomic data suggested: (1) anaerobic benzene degradation was activated by a yet unknown mechanism for conversion of benzene to benzoyl-CoA; (2) the central benzoyl-CoA degradation pathway involved reductive dearomatization by a class II benzoyl-CoA reductase followed by hydrolytic ring cleavage and modified β-oxidation; (3) the oxidative acetyl-CoA pathway was utilized for complete oxidation to CO2 Interestingly, the genome of Pelotomaculum candidate BPL has all the genes for a complete sulfate reduction pathway including a similar electron transfer mechanism for dissimilatory sulfate reduction as in other Gram-positive sulfate-reducing bacteria...
December 22, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28003436/integrating-transcriptomic-and-proteomic-data-for-accurate-assembly-and-annotation-of-genomes
#5
T S Keshava Prasad, Ajeet Kumar Mohanty, Manish Kumar, Sreelakshmi K Sreenivasamurthy, Gourav Dey, Raja Sekhar Nirujogi, Sneha M Pinto, Anil K Madugundu, Arun H Patil, Jayshree Advani, Srikanth S Manda, Manoj Kumar Gupta, Sutopa B Dwivedi, Dhanashree S Kelkar, Brantley Hall, Xiaofang Jiang, Ashley Peery, Pavithra Rajagopalan, Soujanya D Yelamanchi, Hitendra S Solanki, Remya Raja, Gajanan J Sathe, Sandip Chavan, Renu Verma, Krishna M Patel, Ankit P Jain, Nazia Syed, Keshava K Datta, Aafaque Ahmed Khan, Manjunath Dammalli, Savita Jayaram, Aneesha Radhakrishnan, Christopher J Mitchell, Chan-Hyun Na, Nirbhay Kumar, Photini Sinnis, Igor V Sharakhov, Charles Wang, Harsha Gowda, Zhijian Tu, Ashwani Kumar, Akhilesh Pandey
Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models...
January 2017: Genome Research
https://www.readbyqxmd.com/read/27988178/a-novel-protein-coding-potential-of-long-intergenic-non-coding-rnas-lincrnas-in-the-kinetoplastid-protozoan-parasite-leishmania-major
#6
Harsh Pawar, Kalpana Pai, Milind S Patole
Cutaneous leishmaniasis (CL) is caused by a kinetoplastid protozoan parasite Leishmania major, as a skin ulcer at the site of the sandfly bite. CL is curable and in most cases ulcers heal spontaneously within three to six months leaving a scar and disfiguration. Complete genome of L. major was reported in 2005 at the very initial phase of kinetoplastid parasite genome sequencing project. Presently, L. major genome is most studied and comprehensively annotated genome and therefore, it is being used as a reference genome for annotating recently sequenced Leishmanial genomes...
December 14, 2016: Acta Tropica
https://www.readbyqxmd.com/read/27959540/unbiased-false-discovery-rate-estimation-for-shotgun-proteomics-based-on-the-target-decoy-approach
#7
Lev I Levitsky, Mark V Ivanov, Anna A Lobas, Mikhail V Gorshkov
Target-decoy approach (TDA) is the dominant strategy for false discovery rate (FDR) estimation in mass-spectrometry-based proteomics. One of its main applications is direct FDR estimation based on counting of decoy matches above a certain score threshold. The corresponding equations are widely employed for filtering of peptide or protein identifications. In this work we consider a probability model describing the filtering process and find that, when decoy counting is used for q value estimation and subsequent filtering, a correction has to be introduced into these common equations for TDA-based FDR estimation...
December 13, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27847095/proteomic-analysis-and-translational-perspective-of-hepatocellular-carcinoma-identification-of-diagnostic-protein-biomarkers-by-an-onco-proteogenomics-approach
#8
REVIEW
Shyh-Horng Chiou, King-Teh Lee
Hepatocellular carcinoma (HCC) has been ranked as the third leading cause of cancer-related mortality worldwide. Typically, patients are already in advanced stages of liver cirrhosis at the time of HCC diagnosis. Because HCC is often detected at a late stage and is highly aggressive, noninvasive biomarkers are urgently needed for early diagnosis. Recent advances in gene-expression profiling technologies have enabled molecular classification of HCC into defined subclasses that provide a firm basis for further study of potential mechanisms and biomarkers underlying the development of HCC...
November 2016: Kaohsiung Journal of Medical Sciences
https://www.readbyqxmd.com/read/27846794/genome-and-catabolic-subproteomes-of-the-marine-nutritionally-versatile-sulfate-reducing-bacterium-desulfococcus-multivorans-dsm-2059
#9
Marvin Dörries, Lars Wöhlbrand, Michael Kube, Richard Reinhardt, Ralf Rabus
BACKGROUND: Sulfate-reducing bacteria (SRB) are key players of the carbon- and sulfur-cycles in the sediments of the world's oceans. Habitat relevant SRBs are often members of the Desulfosarcina-Desulfococcus clade belonging to the deltaproteobacterial family of Desulfobacteraceae. Despite this environmental recognition, their molecular (genome-based) physiology and their potential to contribute to organic carbon mineralization as well as to adapt to changing environmental conditions have been scarcely investigated...
November 15, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27843720/proteogenomic-analyses-indicate-bacterial-methylotrophy-and-archaeal-heterotrophy-are-prevalent-below-the-grass-root-zone
#10
Cristina N Butterfield, Zhou Li, Peter F Andeer, Susan Spaulding, Brian C Thomas, Andrea Singh, Robert L Hettich, Kenwyn B Suttle, Alexander J Probst, Susannah G Tringe, Trent Northen, Chongle Pan, Jillian F Banfield
Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10-20 cm and 30-40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate...
2016: PeerJ
https://www.readbyqxmd.com/read/27815279/an-inducible-operon-is-involved-in-inulin-utilization-in-lactobacillus-plantarum-strains-as-revealed-by-comparative-proteogenomics-and-metabolic-profiling
#11
Nirunya Buntin, Tipparat Hongpattarakere, Jarmo Ritari, François P Douillard, Lars Paulin, Sjef Boeren, Sudarshan A Shetty, Willem M de Vos
: The draft genomes of Lactobacillus plantarum strains isolated from Asian fermented foods, infant feces, and shrimp intestines were sequenced and compared to those of well-studied strains. Among 28 strains of L. plantarum, variations in the genomic features involved in ecological adaptation were elucidated. The genome sizes ranged from approximately 3.1 to 3.5 Mb, of which about 2,932 to 3,345 protein-coding sequences (CDS) were predicted. The food-derived isolates contained a higher number of carbohydrate metabolism-associated genes than those from infant feces...
January 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27807831/quantitative-clinical-imaging-methods-for-monitoring-intratumoral-evolution
#12
Joo Yeun Kim, Robert A Gatenby
Solid tumors are multiscale, open, complex, dynamic systems: complex because they have many interacting components, dynamic because both the components and their interactions can change with time, and open because the tumor freely communicates with surrounding and even distant host tissue. Thus, it is not surprising that striking intratumoral variations are commonly observed in clinical imaging such as MRI and CT and that several recent studies found striking regional variations in the molecular properties of cancer cells from the same tumor...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27807744/computational-methods-in-mass-spectrometry-based-proteomics
#13
Sujun Li, Haixu Tang
This chapter introduces computational methods used in mass spectrometry-based proteomics, including those for addressing the critical problems such as peptide identification and protein inference, peptide and protein quantification, characterization of posttranslational modifications (PTMs), and data-independent acquisitions (DIA). The chapter concludes with emerging applications of proteomic techniques, such as metaproteomics, glycoproteomics, and proteogenomics.
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27797325/-adar-mediated-messenger-rna-editing-analysis-at-the-proteome-level
#14
REVIEW
A A Kliuchnikova, K G Kuznetsova, S A Moshkovskii
Post-transcriptional RNA editing by RNA specific adenosine deaminases (ADAR) was discovered more than two decades ago. It provides additional regulation of animal and human transcriptome. In most cases, it occurs in nervous tissue, where, as a result of the reaction, adenosine is converted to inosine in particular sites of RNA. In case of messenger RNA, during translation, inosine is recognized as guanine leading to amino acid substitutions. Those substitutions are shown to affect substantially the function of proteins, e...
July 2016: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/27786492/flexible-data-analysis-pipeline-for-high-confidence-proteogenomics
#15
Hendrik Weisser, James C Wright, Jonathan M Mudge, Petra Gutenbrunner, Jyoti S Choudhary
Proteogenomics leverages information derived from proteomic data to improve genome annotations. Of particular interest are "novel" peptides that provide direct evidence of protein expression for genomic regions not previously annotated as protein-coding. We present a modular, automated data analysis pipeline aimed at detecting such "novel" peptides in proteomic data sets. This pipeline implements criteria developed by proteomics and genome annotation experts for high-stringency peptide identification and filtering...
December 2, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27785359/pygeno-a-python-package-for-precision-medicine-and-proteogenomics
#16
Tariq Daouda, Claude Perreault, Sébastien Lemieux
pyGeno is a python package mainly intended for precision medicine applications that revolve around genomics and proteomics. It integrates reference sequences and annotations from Ensembl, genomic polymorphisms from the dbSNP database and data from next-gen sequencing into an easy to use, memory-efficient and fast framework, therefore allowing the user to easily explore subject-specific genomes and proteomes. Compared to a standalone program, pyGeno gives the user access to the complete expressivity of python, a general programming language...
2016: F1000Research
https://www.readbyqxmd.com/read/27775698/nitrogen-fixation-in-a-chemoautotrophic-lucinid-symbiosis
#17
Sten König, Olivier Gros, Stefan E Heiden, Tjorven Hinzke, Andrea Thürmer, Anja Poehlein, Susann Meyer, Magalie Vatin, Didier Mbéguié-A-Mbéguié, Jennifer Tocny, Ruby Ponnudurai, Rolf Daniel, Dörte Becher, Thomas Schweder, Stephanie Markert
The shallow water bivalve Codakia orbicularis lives in symbiotic association with a sulfur-oxidizing bacterium in its gills. The endosymbiont fixes CO2 and thus generates organic carbon compounds, which support the host's growth. To investigate the uncultured symbiont's metabolism and symbiont-host interactions in detail we conducted a proteogenomic analysis of purified bacteria. Unexpectedly, our results reveal a hitherto completely unrecognized feature of the C. orbicularis symbiont's physiology: the symbiont's genome encodes all proteins necessary for biological nitrogen fixation (diazotrophy)...
October 24, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27775567/a-proteogenomic-approach-to-understanding-myc-function-in-metastatic-medulloblastoma-tumors
#18
REVIEW
Jerome A Staal, Yanxin Pei, Brian R Rood
Brain tumors are the leading cause of cancer-related deaths in children, and medulloblastoma is the most prevalent malignant childhood/pediatric brain tumor. Providing effective treatment for these cancers, with minimal damage to the still-developing brain, remains one of the greatest challenges faced by clinicians. Understanding the diverse events driving tumor formation, maintenance, progression, and recurrence is necessary for identifying novel targeted therapeutics and improving survival of patients with this disease...
October 19, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27775198/mapping-the-triticum-aestivum-proteome
#19
Owen Duncan, Josua Trösch, Ricarda Fenske, Nicolas L Taylor, A Harvey Millar
Yield and quality improvement of bread wheat (Triticum aestivum) is a focus in efforts to meet new demands from population growth and changing human diets. As the complexity of the wheat genome is unravelled, determining how it is used to build the protein machinery of wheat plants is a key next step in explaining detailed aspects of wheat growth and development. The specific functions of wheat organs during vegetative development and the role of metabolism, protein degradation and remobilisation in driving grain production are the foundations of crop performance and have recently become accessible through studies of the wheat proteome...
October 24, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27734975/a-proteogenomic-approach-for-protein-level-evidence-of-genomic-variants-in-cancer-cells
#20
Jeonghun Yeom, Mohammad Humayun Kabir, Byungho Lim, Hee-Sung Ahn, Seon-Young Kim, Cheolju Lee
Variations in protein coding sequence may sometimes play important roles in cancer development. However, since variants may not express into proteins due to various cellular quality control systems, it is important to get protein-level evidence of the genomic variations. We present a proteogenomic strategy getting protein-level evidence of genomic variants, which we call sequential targeted LC-MS/MS based on prediction of peptide pI and Retention time (STaLPIR). Our approach shows improved peptide identification, and has the potential for the unbiased analysis of variant sequence as well as corresponding reference sequence...
October 13, 2016: Scientific Reports
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