Review
Biochemistry & Molecular Biology
Sofia Esteban-Serna, Hugh McCaughan, Sander Granneman
Summary: RNA-binding proteins (RBPs) regulate the lifespan of transcripts and are important in adaptive responses in microbes. UV cross-linking techniques, combined with RNA or protein purification, allow for the examination of protein-RNA interactions and the construction of RBP censuses and transcriptomic maps. Novel methods have expanded our understanding of RBPs in microorganisms. This technical evaluation assesses the advantages and limitations of UV cross-linking techniques, guiding researchers in selecting appropriate methods and experimental design for investigating RNA-binding activity.
MOLECULAR MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Seun O. Oladipupo, Jazmine D. Carroll, John F. Beckmann
Summary: Wolbachia-mediated cytoplasmic incompatibility (CI) is a condition where embryonic lethality occurs when eggs are fertilized by modified sperm, controlled by the Wolbachia proteins CidA and CidB. The mechanisms of how CidB induces CI and how CidA prevents sterilization by CidB are not yet understood. Pull-down assays were conducted to identify CidB substrates in mosquitos, revealing convergent interactions across taxa and potential candidate substrates such as P32, karyopherin alpha, ubiquitin-conjugating enzyme, and bicoid stabilizing factor. Further analysis on these candidates will elucidate the mechanisms of CI.
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
John P. McGee, Pei Su, Kenneth R. Durbin, Michael A. R. Hollas, Nicholas W. Bateman, G. Larry Maxwell, Thomas P. Conrads, Ryan T. Fellers, Rafael D. Melani, Jeannie M. Camarillo, Jared O. Kafader, Neil L. Kelleher
Summary: This study introduces a semi-automated single-ion mass spectrometry workflow for top-down tandem mass spectrometry analysis directly from tissue microenvironments. The results demonstrate that this method can identify multiple proteoforms in tumor samples within a short period of time, and effectively identify proteoform signatures in tumor and stromal regions.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Isabella T. Whitworth, Katherine B. Henke, Bing Yang, Mark Scalf, Brian L. Frey, David F. Jarrard, Lloyd M. Smith
Summary: RNA-protein interactions are vital for cellular homeostasis, and their identification is crucial for understanding cellular function. This study introduces a new method called hybridization purification of RNA-protein complexes followed by mass spectrometry (HyPR-MS), which enables the characterization of specific RNA-protein complexes in tissue samples. The researchers successfully isolated polyadenylated RNA and the long noncoding RNA MALAT1, and characterized their protein interactomes using this technique, demonstrating its feasibility.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Yu-Han Hsu, Greta Pintacuda, Ruize Liu, Eugeniu Nacu, Apri Kim, Kalliopi Tsafou, Natalie Petrossian, William Crotty, Jung Min Suh, Jackson Riseman, Jacqueline M. Martin, Julia C. Biagini, Daya Mena, Joshua K. T. Ching, Edyta Malolepsza, Taibo Li, Tarjinder Singh, Tian Ge, Shawn B. Egri, Benjamin Tanenbaum, Caroline R. Stanclift, Annie M. Apffel, Steven A. Carr, Monica Schenone, Jake Jaffe, Nadine Fornelos, Hailiang Huang, Kevin C. Eggan, Kasper Lage
Summary: Genetics have identified many schizophrenia risk genes and found common signals between schizophrenia and neurodevelopmental disorders. However, there is often a lack of functional interpretation of these genes in relevant brain cell types. In this study, the researchers investigated the protein network of six schizophrenia risk genes in induced cortical neurons, finding that it is enriched for common variant risk of schizophrenia and down-regulated in affected individuals. They also identified a sub-network centered on HCN1 that is enriched for common variant risk and contains proteins associated with rare protein-truncating mutations in schizophrenia and bipolar disorder. This study highlights the importance of brain cell-type-specific interactomes in interpreting genetic and transcriptomic data in schizophrenia and related disorders.
Article
Biochemical Research Methods
Aleksandra A. Petelski, Edward Emmott, Andrew Leduc, R. Gray Huffman, Harrison Specht, David H. Perlman, Nikolai Slavov
Summary: The study introduces the SCoPE2 protocol for single-cell protein analysis, which utilizes isobaric mass tags for labeling and achieves cost-effective quantitative protein analysis.
Article
Biology
Enisa Aruci, Jean-Michel Saliou, Jean-Francois Ferveur, Loic Briand
Summary: Insects use chemical signals for various purposes, such as finding food and communicating socially. The proboscis of Drosophila melanogaster plays a significant role in the detection of molecules related to feeding and sexual behavior. Through proteomic analysis, several soluble proteins, including odorant-binding proteins, were identified in the proboscis. These findings contribute to a better understanding of the complex function of the proboscis in chemical detection.
Article
Multidisciplinary Sciences
Louise Canon, Carlos Kikuti, Vicente J. Planelles-Herrero, Tianming Lin, Franck Mayeux, Helena Sirkia, Young il Lee, Leila Heidsieck, Leonid Velikovsky, Amandine David, Xiaoyan Liu, Dihia Moussaoui, Emma Forest, Peter Hook, Karl J. Petersen, Tomos E. Morgan, Aurelie Di Cicco, Julia Sires-Campos, Emmanuel Derivery, Daniel Levy, Cedric Delevoye, H. Lee Sweeney, Anne Houdusse
Summary: Canon et al. provide insights into the auto-inhibition and activation of the minus-end directed motor myosin VI. The study highlights how differential relief of auto-inhibition allows for fine control of myosin VI activity in vivo.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Mengting Pan, Yunming Liu, Xiaofang Zheng, Meijuan Zhou, Changjun You, Xiaoxia Dai
Summary: The study utilized a chemical proteomic method to identify and quantify CTP-binding proteins in human cells, revealing their roles in various biological processes. This approach could be widely applicable for profiling CTP-binding proteins in other biological samples.
CHINESE CHEMICAL LETTERS
(2021)
Article
Biochemical Research Methods
Paola A. Nocua, Jose M. Requena, Concepcion J. Puerta
Summary: Leishmania parasites exhibit precise gene regulation, mainly at the post-transcriptional level, to adapt to environmental changes. RNA binding proteins SCD6 and RBP42 in L. braziliensis play roles in mRNA-protein complex assembly and gene regulation. The interaction of these proteins with other cellular components could provide new insights for therapeutic targets against Leishmania infections.
JOURNAL OF PROTEOMICS
(2021)
Review
Biochemistry & Molecular Biology
Michele Spiniello, Mark Scalf, Amelia Casamassimi, Ciro Abbondanza, Lloyd M. Smith
Summary: RNA-binding proteins play a crucial role in the function of both coding and non-coding RNAs, and disruptions in RNA-protein interactions are associated with various pathological conditions. Different computational and experimental strategies have been developed to identify protein binders for specific RNA molecules. Among these, 'in cell' hybridization methods are considered the most reliable because they allow for the detection of proteins bound to specific RNAs in a cellular context.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Marcin Kolinski, Ewelina Kaluzna, Monika Piwecka
Summary: Understanding the molecular mechanisms of SARS-CoV-2 infection is crucial for developing effective therapeutic strategies against COVID-19. Studies have identified host factors, cellular pathways, and cellular responses involved in the viral replication cycle. The investigation of the RNA-protein interactome has helped in identifying potential host factors for antiviral therapy.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2022)
Article
Biochemical Research Methods
Van Kelly, Aymen al-Rawi, David Lewis, Georg Kustatscher, Tony Ly
Summary: This paper presents a method for low cell number proteomics analysis using protease digestion of mildly formaldehyde-fixed cells. The method allows for the quantitative characterization of proteomes from rare cell states, including immune cell subsets and cell cycle subphases. The authors demonstrate the usefulness of the method by characterizing the proteome changes across different cell cycle states and identifying periodic proteins that vary throughout the cell cycle. The dataset generated from this method can be used to classify proteomes into cell cycle states and shows potential for use in single-cell proteomics.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Wendell Albuquerque, Parviz Ghezellou, Leif Seidel, Johannes Burkert, Frank Will, Ralf Schweiggert, Bernhard Spengler, Holger Zorn, Martin Gand
Summary: This study presents the first comprehensive identification of proteome content from a white wine (cv. Silvaner). By using mass spectrometry-based proteomics, the wine protein composition was identified through in-solution and in-gel digestion methods after size exclusion chromatographic fractionation. A total of 154 characterized or uncharacterized proteins mainly from Vitis vinifera L. and Saccharomyces cerevisiae were identified, providing valuable information for wine authentication and understanding of organoleptic properties and stability.
Review
Biochemical Research Methods
Bal Govind Yadav, Aakanksha, Rahul Kumar, Satish Kumar Yadava, Ajay Kumar, Nirala Ramchiary
Summary: Proteomics has become a preferred choice in Brassica crop research, along with genomics and other molecular approaches. This comprehensive review summarizes different proteomic studies undertaken in Brassica crops, providing important insights into the role of proteins in controlling plant phenotypes and initiating future improvement programs.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Michele Spiniello, Maisie Steinbrink, Anthony J. Cesnik, Rachel M. Miller, Mark Scalf, Michael R. Shortreed, Lloyd M. Smith
Article
Biochemical Research Methods
Yunxiang Dai, Katherine E. Buxton, Leah Schaffer, Rachel M. Miller, Robert J. Millikin, Mark Scalf, Brian L. Frey, Michael R. Shortreed, Lloyd M. Smith
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Biochemical Research Methods
Wei Ouyang, Casper F. Winsnes, Martin Hjelmare, Anthony J. Cesnik, Lovisa Akesson, Hao Xu, Devin P. Sullivan, Shubin Dai, Jun Lan, Park Jinmo, Shaikat M. Galib, Christof Henkel, Kevin Hwang, Dmytro Poplavskiy, Bojan Tunguz, Russel D. Wolfinger, Yinzheng Gu, Chuanpeng Li, Jinbin Xie, Dmitry Buslov, Sergei Fironov, Alexander Kiselev, Dmytro Panchenko, Xuan Cao, Runmin Wei, Yuanhao Wu, Xun Zhu, Kuan-Lun Tseng, Zhifeng Gao, Cheng Ju, Xiaohan Yi, Hongdong Zheng, Constantin Kappel, Emma Lundberg
Article
Biochemical Research Methods
Zhijing Tan, Jianhui Zhu, Paul M. Stemmer, Liangliang Sun, Zhichang Yang, Kendall Schultz, Matthew J. Gaffrey, Anthony J. Cesnik, Xinpei Yi, Xiaohu Hao, Michael R. Shortreed, Tujin Shi, David M. Lubman
JOURNAL OF PROTEOME RESEARCH
(2020)
Correction
Biochemical Research Methods
Wei Ouyang, Casper F. Winsnes, Martin Hjelmare, Anthony J. Cesnik, Lovisa Akesson, Hao Xu, Devin P. Sullivan, Shubin Dai, Jun Lan, Park Jinmo, Shaikat M. Galib, Christof Henkel, Kevin Hwang, Dmytro Poplavskiy, Bojan Tunguz, Russel D. Wolfinger, Yinzheng Gu, Chuanpeng Li, Jinbin Xie, Dmitry Buslov, Sergei Fironov, Alexander Kiselev, Dmytro Panchenko, Xuan Cao, Runmin Wei, Yuanhao Wu, Xun Zhu, Kuan-Lun Tseng, Zhifeng Gao, Cheng Ju, Xiaohan Yi, Hongdong Zheng, Constantin Kappel, Emma Lundberg
Correction
Biochemical Research Methods
Wei Ouyang, Casper F. Winsnes, Martin Hjelmare, Anthony J. Cesnik, Lovisa Akesson, Hao Xu, Devin P. Sullivan, Shubin Dai, Jun Lan, Park Jinmo, Shaikat M. Galib, Christof Henkel, Kevin Hwang, Dmytro Poplavskiy, Bojan Tunguz, Russel D. Wolfinger, Yinzheng Gu, Chuanpeng Li, Jinbin Xie, Dmitry Buslov, Sergei Fironov, Alexander Kiselev, Dmytro Panchenko, Xuan Cao, Runmin Wei, Yuanhao Wu, Xun Zhu, Kuan-Lun Tseng, Zhifeng Gao, Cheng Ju, Xiaohan Yi, Hongdong Zheng, Constantin Kappel, Emma Lundberg
Article
Biochemistry & Molecular Biology
Lovisa Stenstrom, Diana Mahdessian, Christian Gnann, Anthony J. Cesnik, Wei Ouyang, Manuel D. Leonetti, Mathias Uhlen, Sara Cuylen-Haering, Peter J. Thul, Emma Lundberg
MOLECULAR SYSTEMS BIOLOGY
(2020)
Correction
Biochemical Research Methods
Wei Ouyang, Casper F. Winsnes, Martin Hjelmare, Anthony J. Cesnik, Lovisa Akesson, Hao Xu, Devin P. Sullivan, Shubin Dai, Jun Lan, Park Jinmo, Shaikat M. Galib, Christof Henkel, Kevin Hwang, Dmytro Poplavskiy, Bojan Tunguz, Russel D. Wolfinger, Yinzheng Gu, Chuanpeng Li, Jinbin Xie, Dmitry Buslov, Sergei Fironov, Alexander Kiselev, Dmytro Panchenko, Xuan Cao, Runmin Wei, Yuanhao Wu, Xun Zhu, Kuan-Lun Tseng, Zhifeng Gao, Cheng Ju, Xiaohan Yi, Hongdong Zheng, Constantin Kappel, Emma Lundberg
Article
Biochemical Research Methods
Anthony J. Cesnik, Rachel M. Miller, Khairina Ibrahim, Lei Lu, Robert J. Millikin, Michael R. Shortreed, Brian L. Frey, Lloyd M. Smith
Summary: Spritz is an open-source software tool developed for generating protein databases with sequence variations and PTMs annotations, enabling the identification and quantification of proteoforms by mass spectrometry. These sample-specific databases allow the identification of variant peptides, modified variant peptides, and variant proteoforms.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Multidisciplinary Sciences
Diana Mahdessian, Anthony J. Cesnik, Christian Gnann, Frida Danielsson, Lovisa Stenstrom, Muhammad Arif, Cheng Zhang, Trang Le, Fredric Johansson, Rutger Shutten, Anna Backstrom, Ulrika Axelsson, Peter Thul, Nathan H. Cho, Oana Carja, Mathias Uhlen, Adil Mardinoglu, Charlotte Stadler, Cecilia Lindskog, Burcu Ayoglu, Manuel D. Leonetti, Fredrik Ponten, Devin P. Sullivan, Emma Lundberg
Summary: The study comprehensively mapped spatial and temporal variations among individual human cell proteomes across the cell cycle, revealing that approximately one-fifth of the human proteome displays cell-to-cell variability. The researchers identified hundreds of proteins with previously unknown associations with mitosis and the cell cycle, and found evidence suggesting that some of these proteins have oncogenic functions.
Article
Biology
Rachel Knoener, Edward Evans, Jordan T. Becker, Mark Scalf, Bayleigh Benner, Nathan M. Sherer, Lloyd M. Smith
Summary: HIV-1 generates different classes of RNA that play distinct roles in viral replication, and understanding their interactions with host proteins is crucial. The HyPR-MSSV technique can isolate different types of HIV-1 RNA and identify their protein interactomes, revealing factors that impact HIV-1 gene expression.
Article
Biochemical Research Methods
Austin Carr, Brian L. Frey, Mark Scalf, Anthony J. Cesnik, Zach Rolfs, Kyndal A. Pike, Bing Yang, Mark P. Keller, David F. Jarrard, Michael R. Shortreed, Lloyd M. Smith
Summary: Interpreting proteomics data is challenging due to the large number of proteins quantified by mass spectrometry methods. Weighted gene correlation network analysis (WGCNA) can identify biologically related proteins by constructing protein correlation networks. To facilitate the adoption of WGCNA in proteomics, we developed MetaNetwork, an open-source application that allows users to perform sophisticated WGCNA workflows without coding skills. Using MetaNetwork, we successfully identified groups of proteins associated with prostate cancer and found dysregulation in protein expression and pathways.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Multidisciplinary Sciences
Rafael D. Melani, Vincent R. Gerbasi, Lissa C. Anderson, Jacek W. Sikora, Timothy K. Toby, Josiah E. Hutton, David S. Butcher, Fernanda Negrao, Henrique S. Seckler, Kristina Srzentic, Luca Fornelli, Jeannie M. Camarillo, Richard D. LeDuc, Anthony J. Cesnik, Emma Lundberg, Joseph B. Greer, Ryan T. Fellers, Matthew T. Robey, Caroline J. DeHart, Eleonora Forte, Christopher L. Hendrickson, Susan E. Abbatiello, Paul M. Thomas, Andy Kokaji, Josh Levitsky, Neil L. Kelleher
Summary: By studying the proteoforms expressed from human genes in different cell types and bodily fluids, we found that proteoforms provide a better description of protein-level biology and serve as more specific indicators of cell differentiation compared to proteins. In the context of liver transplantation, we utilized the Blood Proteoform Atlas to identify cell and proteoform signatures that distinguish normal graft function from graft dysfunction.
Article
Biochemical Research Methods
Richard D. LeDuc, Eric W. Deutsch, Pierre-Alain Binz, Ryan T. Fellers, Anthony J. Cesnik, Joshua A. Klein, Tim Van den Bossche, Ralf Gabriels, Arshika Yalavarthi, Yasset Perez-Riverol, Jeremy Carver, Wout Bittremieux, Shin Kawano, Benjamin Pullman, Nuno Bandeira, Neil L. Kelleher, Paul M. Thomas, Juan Antonio Vizcaino
Summary: It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide primary sequence. The ProForma 2.0 notation aims to unify the representation of proteoforms and peptidoforms, supporting different proteomics approaches and allowing the encoding of highly modified proteins and peptides using a human- and machine-readable string.
JOURNAL OF PROTEOME RESEARCH
(2022)
Correction
Multidisciplinary Sciences
Diana Mahdessian, Anthony J. Cesnik, Christian Gnann, Frida Danielsson, Lovisa Stenstrom, Muhammad Arif, Cheng Zhang, Trang Le, Fredric Johansson, Rutger Schutten, Anna Backstrom, Ulrika Axelsson, Peter Thul, Nathan H. Cho, Oana Carja, Mathias Uhlen, Adil Mardinoglu, Charlotte Stadler, Cecilia Lindskog, Burcu Ayoglu, Manuel D. Leonetti, Fredrik Ponten, Devin P. Sullivan, Emma Lundberg