Article
Biochemical Research Methods
Eunji Sung, Hyunchae Sim, Young-Chang Cho, Wonhwa Lee, Jong-Sup Bae, Minjia Tan, Sangkyu Lee
Summary: In this study, the authors identified acetylation and lactylation sites in Kupffer cells using global acylome technology. They found differences in the subcellular distributions and sequence motifs of modified proteins. Functional enrichment analyses provided insights into the roles of these modifications.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Food Science & Technology
Liuke Liang, Aowen Xie, Haojie Yang, Na Li, Ping'an Ma, Shan Wei, Shuaibing Zhang, Yangyong Lv, Yuansen Hu
Summary: Lysine acetylation (Kac) undergoes changes during artificial ageing of wheat seeds, affecting protein metabolism, response to intracellular stress, and protein storage and processing. Additionally, acetylation affects the activity of ROS-scavenging enzymes, leading to a gradual decrease in the defense ability of wheat seeds.
Article
Biochemical Research Methods
Diogo B. Lima, Mathieu Dupre, Magalie Duchateau, Quentin Giai Gianetto, Martial Rey, Mariette Matondo, Julia Chamot-Rooke
Summary: The software can integrate data from multiple experiments and search engines, enabling rapid and easy visualization, validation, and comparison of proteoform sequences with high performance. The effectiveness of the method was demonstrated on a large-scale Escherichia coli dataset, where ProteoCombiner accurately shortlisted proteoforms identified by multiple search engines.
Article
Biochemistry & Molecular Biology
Liang Yin, Gang Feng, Chun Huang, Weijuan Cai
Summary: This study investigated lysine acetylation in T2DM patients using quantitative proteomics, identifying differentially expressed acetylation sites and performing bioinformatics analysis. The results provide potential markers for prediabetes prediction and contribute to the understanding of T2DM pathogenesis.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Oncology
Xiaoqiang Chai, Jianfei Guo, Ruizhao Dong, Xuan Yang, Chao Deng, Chuanyuan Wei, JiaJie Xu, Weiyu Han, Jiacheng Lu, Chao Gao, Dongmei Gao, Cheng Huang, Aiwu Ke, Shuangqi Li, Huanping Li, Yingming Tian, Zhongkai Gu, Shuxian Liu, Hang Liu, Qilong Chen, Feng Liu, Jian Zhou, Jia Fan, Guoming Shi, Feizhen Wu, Jiabin Cai
Summary: This study characterized the role of lysine acetylation in hepatocellular carcinoma, revealing multiple acetylation sites and their changes in different tissues. The study also found a correlation between acetylation levels and prognosis in HCC patients.
CLINICAL AND TRANSLATIONAL MEDICINE
(2021)
Article
Biochemical Research Methods
Konrad Winkels, Tomas Koudelka, Philipp T. Kaulich, Matthias Leippe, Andreas Tholey
Summary: Top-down proteomics (TDP) can provide additional information about post-translational modifications and C-termini. In this study, TDP workflows were used to analyze the proteome of Caenorhabditis elegans, and the identified proteoforms were validated using a bottom-up proteomics (BUP) approach. The results showed low overlap between the two methods, with caveats in both workflows contributing to this. The study also demonstrated the applicability of reductive dimethylation in TDP to confirm biological N-termini.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Virology
Yogy Simanjuntak, Kira Schamoni-Kast, Alice Grun, Charlotte Uetrecht, Pietro Scaturro
Summary: This article discusses the harm caused by RNA viruses in human diseases and the latest research progress in revealing RNA virus replication and pathogenesis through mass spectrometry technology. Viruses often impact host functions and induce pathological functional abnormalities, and mass spectrometry techniques help uncover these processes and find new antiviral targets.
Article
Chemistry, Analytical
Francis Berthias, Hayden A. Thurman, Gayani Wijegunawardena, Haifan Wu, Alexandre A. Shvartsburg, Ole N. Jensen
Summary: Advances in proteomics have shown the ubiquity and biological importance of diverse proteoforms. The ability to separate and analyze intact isomeric proteoforms is crucial for understanding their functions. A novel technique using trapped IMS was demonstrated to achieve baseline resolution of isomeric proteoforms, opening new avenues in proteomics and epigenetics.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Jean Finlayson, Neusha Barakati, Paul R. Langlais, Janet Funk, Rocio Zapata Bustos, Dawn K. Coletta, Moulun Luo, Wayne T. Willis, Lawrence J. Mandarino
Summary: This study characterized ANT1 abundance and acetylation in human skeletal muscle using a novel method with small amounts of tissue samples. The findings indicate that acetylation of Lys23 reduces ADP binding to ANT1, providing insights into the potential effects of acetylation on ANT1 function in human muscle.
ANALYTICAL BIOCHEMISTRY
(2021)
Article
Cell Biology
Huriye Ercan, Ulrike Resch, Felicia Hsu, Goran Mitulovic, Andrea Bileck, Christopher Gerner, Jae-Won Yang, Margarethe Geiger, Ingrid Miller, Maria Zellner
Summary: Proteomics is an essential analytical technique for studying biological systems using different proteins. The study compared the qualitative and quantitative performance of two commonly used proteomics techniques, label-free shotgun and 2D-DIGE, using six technical and three biological replicates of the human prostate carcinoma cell line DU145. The results showed that label-free shotgun quickly provides an annotated proteome but with reduced robustness compared to 2D-DIGE, which offers qualitative and quantitative information on proteoforms and post-translational modifications. However, the 2D-DIGE technique requires more time and manual work. Ultimately, this work highlights the different outputs and applications of these two techniques for biological research.
Article
Biochemical Research Methods
Biying Hu, Dandan Li, Donge Tang, Yu Shangguan, Yuzhi Cao, Ruonan Guo, Shaodong Luan, Chen Yun, Stanislao Morgera, Berthold Hocher, Bernhard K. Kraemer, Yinglan Wang, Lianghong Yin, Yong Dai
Summary: The study identified significantly regulated acetylated proteins in GDM and PE patients, mainly enriched in endoplasmic reticulum stress and ferroptosis pathways. These findings help explore the underlying pathology, new biomarkers, and therapeutic targets of GDM and PE.
Review
Biochemistry & Molecular Biology
Keith E. Keenan, Derek K. Zachman, Matthew D. Hirschey
Summary: Protein modifications play a significant role in cell biology across various organisms. Discoveries in the early 20th century challenged traditional definitions of amino acids, and the advent of mass-spectrometry-based proteomics in the latter part led to a rapid increase in known protein modifications, with over 500 identified today. New computational tools in data science, machine learning, and artificial intelligence are expected to further advance the discovery and understanding of protein modifications in the future.
Article
Cell Biology
Martin Marek, Elizabeth Ramos-Morales, Gisele F. A. Picchi-Constante, Theresa Bayer, Carina Norstrom, Daniel Herp, Policarpo A. Sales-Junior, Eloise P. Guerra-Slompo, Kristin Hausmann, Alokta Chakrabarti, Tajith B. Shaik, Annika Merz, Edouard Troesch, Karin Schmidtkunz, Samuel Goldenberg, Raymond J. Pierce, Marina M. Mourao, Manfred Jung, Johan Schultz, Wolfgang Sippl, Nilson I. T. Zanchin, Christophe Romier
Summary: The zinc-dependent histone deacetylases in the protozoan parasite Trypanosoma cruzi have significantly diverged from their human counterparts, with tcDAC2 displaying essential deacetylase activity and major structural differences. Targeting these atypical HDACs can lead to selective chemical impairment of parasites.
Review
Biochemical Research Methods
Orlando Morales-Tarre, Ramiro Alonso-Bastida, Bolivar Arcos-Encarnacion, Leonor Perez-Martinez, Sergio Encarnacion-Guevara
Summary: Lysine acetylation is a crucial reversible post-translational modification regulated by enzymes and bromodomain-containing proteins, with implications in the progression of various diseases. The use of mass spectrometry-based proteomics and immunoprecipitation has expanded our knowledge on this modification, now reported in over 5000 human proteins.
EXPERT REVIEW OF PROTEOMICS
(2021)
Article
Biochemistry & Molecular Biology
Julia Sindlinger, Stefan Schoen, Juergen Eirich, Soren Kirchgaessner, Iris Finkemeier, Dirk Schwarzer
Summary: The researchers developed a series of peptide probes conjugated with different amino acid-CoA for studying NAT complex interactome. The results showed that these peptide probes could separate different subunits and provide insights into substrate specificity, demonstrating their usefulness in studying NAT complex interactome in physiological and pathological backgrounds.
Article
Microbiology
Eugene Koonin, Mart Krupovic, Valerian V. Dolja
Summary: Viruses are the most abundant biological entities on earth and show great genetic diversity. The number of virus species is estimated to be astronomically large, ranging from 10^7 to 10^9. Virus origins involve non-viral replicators capturing cellular proteins to become virus capsid subunits. The number of realms in the global virome is expected to significantly increase with the discovery of new distinct groups.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Yifan Zhou, Liang Zhou, Shuling Yan, Lanming Chen, Mart Krupovic, Yongjie Wang
Summary: This study assessed the utility of CRISPR spacer targeting, tRNA gene matching, and homology searches for the assignment of archaeal hosts of viruses and validated these approaches on metaviromes from Yangshan Harbor. The results showed a high diversity of archaeal viruses in the YSH virome and proposed three new viral families for the classification of marine archaeal viruses. The study highlights the importance of viral metagenomics in exploring the archaeal virome and provides new insights into the diversity, distribution, and evolution of marine archaeal viruses.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yunfeng Yang, Junfeng Liu, Xiaofei Fu, Fan Zhou, Shuo Zhang, Xuemei Zhang, Qihong Huang, Mart Krupovic, Qunxin She, Jinfeng Ni, Yulong Shen
Summary: Cell cycle regulation is crucial for all forms of life. A transcription factor called aCcr1 and its viral homologs control cell division in Sulfolobales. Over-expression of aCcr1 and its viral homologs leads to growth retardation and cell division failure, while its over-expression downregulates 17 genes, including cdvA. This study provides insights into the conserved mechanism of cell division regulation in archaeal cells and the manipulation of host cell cycle by viruses.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Rafael Laso-Perez, Fabai Wu, Antoine Cremiere, Daan R. Speth, John S. Magyar, Kehan Zhao, Mart Krupovic, Victoria J. Orphan
Summary: This study characterizes a family of ANME-1 archaea and its virome using metagenomics on hydrothermal samples from the Gulf of California. It reveals the diversity, ecology, and evolution of ANME-1 and uncovers the effect of virus-host dynamics. The study also discovers 16 undescribed virus families exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures.
NATURE MICROBIOLOGY
(2023)
Article
Ecology
Purificacion Lopez-Garcia, Ana Gutierrez-Preciado, Mart Krupovic, Maria Ciobanu, Philippe Deschamps, Ludwig Jardillier, Mario Lopez-Perez, Francisco Rodriguez-Valera, David Moreira
Summary: A metagenome-based method was used to estimate the virus-to-microbe ratio, and it was found that viruses may be much less abundant than previously thought, especially in non-aquatic environments.
Review
Biotechnology & Applied Microbiology
Stuart G. Siddell, Donald B. Smith, Evelien Adriaenssens, Poliane Alfenas-Zerbini, Bas E. Dutilh, Maria Laura Garcia, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Elliot J. Lefkowitz, Malgorzata Lobocka, Arcady R. Mushegian, Hanna M. Oksanen, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Nobuhiro Suzuki, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani, F. Murilo Zerbini
Summary: The International Committee on Taxonomy of Viruses (ICTV) is responsible for the development and oversight of virus taxonomy. It approves and ratifies taxonomic proposals and maintains a list of approved virus names. The ICTV has a democratic decision-making process with approximately 180 members who vote on proposals. Taxon-specific Study Groups, comprised of over 600 scientists, provide expertise and contribute to taxonomic proposals.
JOURNAL OF GENERAL VIROLOGY
(2023)
Article
Immunology
Soraya Matczak, Valerie Bouchez, Pauline Leroux, Thibaut Douche, Nils Collinet, Annie Landier, Quentin Giai Gianetto, Sophie Guillot, Julia Chamot-Rooke, Milena Hasan, Mariette Matondo, Sylvain Brisse, Julie Toubiana
Summary: By comparing the microbiological characteristics and expressed protein profiles between FIM2 and FIM3 fimbrial serotypes and genomic clades, differences were found that may have implications on pathogenesis and epidemiological emergence.
MICROBES AND INFECTION
(2023)
Article
Multidisciplinary Sciences
Morgan Gaia, Lingjie Meng, Eric Pelletier, Patrick Forterre, Chiara Vanni, Antonio Fernandez-Guerra, Olivier Jaillon, Patrick Wincker, Hiroyuki Ogata, Mart Krupovic, Tom O. Delmont
Summary: DNA viruses have a significant impact on the ecology and evolution of cellular organisms, but their overall diversity and evolutionary paths are still unclear. This study discovered plankton-infecting relatives of herpesviruses in the sunlit oceans, which belong to a new phylum named Mirusviricota. These mirusviruses exhibit chimaeric attributes connecting them to both herpesviruses and giant eukaryotic viruses, and they play a lasting role in the ecology of marine ecosystems and the evolution of eukaryotic DNA viruses.
Article
Biochemistry & Molecular Biology
Zhao Chen, Ying Liu, Yixuan Wang, Xincheng Du, Xiaoyuan Deng, Jialin Xiang, Yangyang Wang, Jiao Wang, Mart Krupovic, Shishen Du, Xiangdong Chen
Summary: A three-gene module was discovered in a haloarchaeal virus SNJ2, which regulates the switch between lysogeny and replicative cycle. Orf4 represses the expression of the viral integrase gene int(SNJ2) to maintain lysogeny, while Orf7 and Orf8 are required for the switch to the induced state. Comparative genomics analysis revealed that the three-gene module is common in haloarchaeal genomes, always present in the context of integrated proviruses.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Anamarija Butkovic, Valerian V. Dolja, Eugene Koonin, Mart Krupovic
Summary: Many plant viruses encode movement proteins (MPs) that help them move through plant channels called plasmodesmata. The 30K superfamily of MPs is the largest and most diverse variety, represented in 16 virus families, but its origin was unclear. This study found that the core structural domain of the 30K MPs is similar to the capsid proteins (CPs) of small RNA and DNA viruses infecting plants, specifically in the families Bromoviridae and Geminiviridae. The researchers hypothesize that the MPs evolved through the duplication or horizontal acquisition of the CP gene in a virus that infected an ancestor of vascular plants.
Article
Microbiology
Mart Krupovic, Valerian V. Dolja, Eugene V. Koonin
Summary: All extant eukaryotes descend from LECA, the last eukaryotic common ancestor, which had complex cellular organization. To gain insight into LECA biology and the origin of eukaryotic cells, we reconstructed the LECA virome by compiling an inventory of eukaryotic hosts of major virus taxa and inferring the origins of these viruses. The LECA virome can be traced back to a small set of bacterial viruses, possibly due to the bacterial origin of eukaryotic membranes in a syntrophic model of eukaryogenesis involving two endosymbiosis events.
NATURE MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Mark A. B. Kreutzberger, Virginija Cvirkaite-Krupovic, Ying Liu, Diana P. Baquero, Junfeng Liu, Ravi R. Sonani, Chris R. Calladine, Fengbin Wang, Mart Krupovic, Edward H. Egelman
Summary: Flagellar motility has independently evolved three times in bacteria, archaea, and eukaryotes. The supercoiled flagellar filaments in bacteria and archaea are composed of single proteins, while in eukaryotes, the flagellum contains hundreds of proteins. We used cryo-electron microscopy to determine the atomic structure of two additional archaeal type IV pili and reanalyzed previous structures to uncover the evolutionary link between the flagellar system and type IV pili in archaea. This study provides important insights into the evolution and function of flagellar systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Ecology
Dean Vik, Benjamin Bolduc, Simon Roux, Christine L. Sun, Akbar Adjie Pratama, Mart Krupovic, Matthew B. Sullivan
Summary: With the advancement of sequencing technologies and large-scale sampling and analytical efforts, our understanding of viral sequence space has greatly expanded. However, our knowledge of archaeal viruses outside extreme environments is limited due to the lack of a reliable and systematic approach to distinguish between bacterial and archaeal viruses in curated datasets. In this study, we upgraded our previous text-based tool (MArVD) by training and testing a random forest machine learning algorithm using a newly curated dataset of archaeal viruses. The optimized MArVD2 showed significant improvements in scalability, usability, and flexibility, and can accommodate user-defined training datasets as new archaeal viruses are discovered.
ISME COMMUNICATIONS
(2023)
Article
Virology
Anamarija Butkovic, Simona Kraberger, Zoe Smeele, Darren P. Martin, Kara Schmidlin, Rafaela S. Fontenele, Michelle R. Shero, Roxanne S. Beltran, Amy L. Kirkham, Maketalena Aleamotu'a, Jennifer M. Burns, Eugene Koonin, Arvind Varsani, Mart Krupovic
Summary: Anelloviruses, which are highly prevalent in mammals, including humans, have small circular single-stranded DNA genomes and encode unique proteins. The ORF1 protein of anelloviruses shows variation in size and has a projection domain predicted to have a role in virus-host interactions. The findings suggest classifying Anelloviridae as a new phylum, 'Commensaviricota', within the kingdom Shotokuvirae (realm Monodnaviria).
Meeting Abstract
Biophysics
Fengbin Wang, Virginija Cvirkaite-Krupovic, Matthijn Vos, Leticia Beltran, Jun Liu, Mart Krupovic, Edward H. Egelman
BIOPHYSICAL JOURNAL
(2022)