Article
Microbiology
Noah P. Bradley, Katherine L. Wahl, Jacob L. Steenwyk, Antonis Rokas, Brandt F. Eichman
Summary: Bacteria are rich sources of secondary metabolites with DNA-damaging properties, including genotoxins with antitumor/antibiotic properties. However, targeted discovery of biosynthetic gene clusters (BGCs) producing DNA-damaging agents from Streptomyces is lacking. This study identified two families of DNA repair enzymes, one specific for complex alkyl-DNA lesions and involved in self-resistance to antimicrobials, and the other likely involved in protection against an array of genotoxins. This work provides a framework for targeted discovery of new genotoxic compounds with therapeutic potential.
Article
Plant Sciences
Jose S. Rufian, Javier Rueda-Blanco, Diego Lopez-Marquez, Alberto P. Macho, Carmen R. Beuzon, Javier Ruiz-Albert
Summary: The effector protein HopZ1a from Pseudomonas syringae suppresses plant basal immunity by targeting the Arabidopsis thaliana mitogen-activated protein kinase kinase AtMKK7 through acetylation, leading to inhibition of immune signaling pathways. In vitro and in planta assays demonstrate the interaction between HopZ1a and AtMKK7, with acetylation of a lysine residue crucial for AtMKK7 kinase activity.
Article
Biochemistry & Molecular Biology
Shuntaro Nakamura, Takanori Nihira, Rikuya Kurata, Hiroyuki Nakai, Kazumi Funane, Enoch Y. Park, Takatsugu Miyazaki
Summary: Glycoside hydrolase family 65 (GH65) consists of glycoside hydrolases (GHs) and glycoside phosphorylases (GPs) acting on alpha-glucosidic linkages. Study on Flavobacterium johnsoniae GH65 enzyme (FjGH65A) revealed it as the first bacterial GH in GH65 family, showing hydrolytic activity via an anomer-inverting mechanism. The enzyme lacks phosphorolytic activity and differs in key amino acid residues from other known GH65 enzymes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Cell Biology
Shan Wu, Boon Heng Dennis Teo, Seng Yin Kelly Wee, Junjie Chen, Jinhua Lu
Summary: Nucleolar alarmins like nucleolin (NCL) can activate immune cells, suggesting a family of nucleolar alarmins that contribute to inducing self-limiting tissue inflammation and maintaining tissue homeostasis, with autoimmune diseases only occurring when surveillance breaks down.
CELL DEATH & DISEASE
(2021)
Article
Multidisciplinary Sciences
Atsushi Taguchi, Julia E. Page, Ho-Ching Tiffany Tsui, Malcolm E. Winkler, Suzanne Walker
Summary: The peptidoglycan cell wall is essential for the survival of bacteria. Membranebound proteins MpgA and MpgB in Streptococcus pneumoniae are important in maintaining cell wall integrity. Both MpgA and MpgB are muramidases, cutting nascent peptidoglycan at different positions along the sugar backbone.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Immunology
Devon Jeltema, Jihong Wang, Juan Cai, Nathan Kelley, Zhe Yang, Yuan He
Summary: The interaction between NEK7 and NLRP3 is crucial for the activation of the NLRP3 inflammasome. The catalytic domain of NEK7 plays a vital role in mediating its interaction with NLRP3 and inflammasome activation in mouse macrophages.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Astronomy & Astrophysics
Merced Montesinos, Diego Gonzalez
Summary: The article introduces new topological invariants in four dimensions, which are generalizations of the Nieh-Yan topological invariant, obtained through a systematic method. The explicit expressions of the new 4-forms for particular choices of 1-forms are provided, showing that the Nieh-Yan form arises as a particular case.
Article
Cell Biology
Branka Popovic, Benoit P. Nicolet, Aurelie Guislain, Sander Engels, Anouk P. Jurgens, Natali Paravinja, Julian J. Freen-van Heeren, Floris P. J. van Alphen, Maartje van den Biggelaar, Fiamma Salerno, Monika C. Wolkers
Summary: Potent T cell responses against infections and malignancies require precise regulation of toxic effector molecule production, which is defined by post-transcriptional events at 3' untranslated regions (3' UTRs). RNA binding proteins (RBPs) play a key role in this process. Through an RNA aptamer-based capture assay, >130 RBPs interacting with IFNG, TNF, and IL2 3' UTRs in human T cells were identified. RBP-RNA interactions show plasticity upon T cell activation. Furthermore, the regulation of cytokine production by RBPs is intricate and time-dependent, with different RBPs modulating cytokine production at different time points.
Article
Cell Biology
Jing Cai, Kyungsuk Choi, Hongde Li, Katiuska Daniela Pulgar Prieto, Yonggang Zheng, Duojia Pan
Summary: This study reveals that the essential role of YAP in liver and lung development can be bypassed by inactivation of the TEAD corepressor VGLL4, indicating that YAP's major physiological function is to antagonize VGLL4. The findings highlight the central importance of VGLL4-mediated transcriptional repression in regulating the Hippo pathway and provide insights into potential strategies for modulating Hippo signaling in cancer and regenerative medicine.
GENES & DEVELOPMENT
(2022)
Article
Biochemistry & Molecular Biology
Yaru Wang, Achen Zhao, Rafael J. L. Morcillo, Gang Yu, Hao Xue, Jose S. Rufian, Yuying Sang, Alberto P. Macho
Summary: This study reveals that the plant metabolic pathway mediated by pyruvate decarboxylases (PDCs) contributes to plant tolerance to bacterial wilt disease caused by Ralstonia solanacearum. Plants respond to infection by increasing PDC activity, and deficient PDC activity makes plants more susceptible to bacterial wilt. Treatment with pyruvic acid or acetic acid enhances plant tolerance to the disease, while an effector protein secreted by the pathogen inhibits PDCs' oligomerization and enzymatic activity, promoting disease and completion of the pathogenic life cycle.
Article
Multidisciplinary Sciences
Shukun Luo, Bruna G. Coutinho, Prikshat Dadhwal, Yasuhiro Oda, Jiahong Ren, Amy L. Schaefer, E. Peter Greenberg, Caroline S. Harwood, Liang Tong
Summary: Some plant-associated proteobacteria have LuxR family transcription factors known as PipR subfamily members that play important roles in interactions with plant hosts and bacterial virulence of plants. The ethanolamine derivative, HEHEAA, was identified as an effective effector of PipR-mediated gene regulation in the plant endophyte Pseudomonas GM79. Crystallization of a HEHEAA-responsive SBP revealed the molecular basis of PipR system responses to plant factors, showing that different PipR-associated SBPs bind different effectors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Food Science & Technology
Shalaka Bhawal, Ankita Kumari, Shikha Rana, Suman Kapila, Rajeev Kapila
Summary: This article discusses the potential health benefits of probiotics and their role in prevention and treatment. The focus is on the structural and functional aspects of surface effector molecules (surface proteins, cell-bound exopolysaccharide, lipoteichoic acid, pilli and peptidoglycan complex) of probiotic lactic acid bacteria, and their role in intestinal adhesion, immunomodulation, restoration of gut barrier integrity, anti-pathogenic and anti-biofilm, antioxidative, anti-tumor, anti-obesity, and anti-diabetic potentials.
Article
Multidisciplinary Sciences
Pauline Juyoux, Ioannis Galdadas, Dorothea Gobbo, Jill von Velsen, Martin Pelosse, Mark Tully, Oscar Vadas, Francesco Luigi Gervasio, Erika Pellegrini, Matthew W. Bowler
Summary: This study reveals the molecular mechanism of double phosphorylation activation of MAPK p38 alpha by MAP2Ks and identifies catalytically relevant interactions and the influence of MAP2K-disordered amino termini on pathway specificity.
Review
Cell Biology
Patrick J. Woida, Karla J. F. Satchell
Summary: The host immune response plays a crucial role in detecting and eliminating bacterial pathogens. Bacteria often coordinate virulence factors to manipulate the host response during infection. This review discusses the surveillance and signaling systems in the intestine that detect bacteria, as well as the toxins and effectors that bypass these signaling pathways. These factors not only promote infection and disease progression, but can also be repurposed as tools or therapeutics.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biology
Sepideh Fallah, Jean-Francois Beaulieu
Summary: This study reveals the regulatory mechanism of YAP1 in intestinal cell differentiation and demonstrates the impact of SFKs on YAP1 expression and intestinal cell specific gene expression. The results suggest that YAP1 and TAZ are not always interchangeable in regulating cell functions.
Article
Multidisciplinary Sciences
Khaled A. Aly, Mohamed Taha Moutaoufik, Sadhna Phanse, Qingzhou Zhang, Mohan Babu
Summary: This article highlights the association between mitochondrial protein networks and rare diseases, emphasizing the need for advanced proteomic and interactomic platforms to study this interaction. It also discusses innovative proteomic techniques for identifying disease-specific mitochondrial protein assemblies and mapping protein networks in different cellular tissues.
Article
Biochemistry & Molecular Biology
Jitender Mehla, George Liechti, Randy M. Morgenstein, J. Harry Caufield, Ali Hosseinnia, Alla Gagarinova, Sadhna Phanse, Norman Goodacre, Mary Brockett, Neha Sakhawalkar, Mohan Babu, Rong Xiao, Gaetano T. Montelione, Sergey Vorobiev, Tanneke den Blaauwen, John F. Hunt, Peter Uetz
Summary: YhcB, a conserved protein across gamma-proteobacteria with unknown function, plays a crucial role in cell division and affects envelope biogenesis. Based on its interactions with key proteins in divisome and elongasome, it is proposed to be renamed as ZapG for its association with the Z-ring. This study provides insights for future research on the protein family and cell transition from exponential to stationary survival.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Correction
Multidisciplinary Sciences
Kamran Rizzolo, Angela Yeou Hsiung Yu, Adedeji Ologbenla, Sa Rang Kim, Haojie Zhu, Koichiro Ishimori, Guillaume Thibault, Elisa Leung, Yi Wen Zhang, Mona Teng, Marta Haniszewski, Noha Miah, Sadhna Phanse, Zoran Minic, Sukyeong Lee, Julio Diaz Caballero, Mohan Babu, Francis T. F. Tsai, Tomohide Saio, Walid A. Houry
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Thiago Seraphim, Nardin Nano, Yiu Wing Sunny Cheung, Siripat Aluksanasuwan, Carolina Colleti, Yu-Qian Mao, Vaibhav Bhandari, Gavin Young, Larissa Holl, Sadhna Phanse, Yuliya Gordiyenko, Daniel R. Southworth, Carol Robinson, Visith Thongboonkerd, Lisandra M. Gava, Julio C. Borges, Mohan Babu, Leandro R. S. Barbosa, Carlos H. Ramos, Philipp Kukura, Walid A. Houry
Summary: The R2TP complex, formed by RUVBL1 and RUVBL2 ATPases, associates with PIH1D1 and RPAP3 proteins and plays a role in promoting the formation of macromolecular complexes. RPAP3 is identified as the central subunit of R2TP, linking PIH1D1 and RUVBL1/2. The study provides insights into the structure and function of the R2TP complex.
Review
Genetics & Heredity
Matineh Rahmatbakhsh, Alla Gagarinova, Mohan Babu
Summary: Microbial pathogens have evolved diverse strategies to manipulate host systems, causing diseases through changes in the host-pathogen proteome. Mass spectrometry-based proteomics approaches are utilized to study disease progression but present challenges in data analysis. The study reviews steps in temporal and spatial analysis, offering best practices for data preprocessing, statistical analysis, and biological information extraction. Guidance is provided for novices and established users, with future directions and data analysis codes available for testing.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Mara Zilocchi, Cheng Wang, Mohan Babu, Jingjing Li
Summary: The article discusses the qualitative and quantitative definitions of health, as well as understanding the molecular etiologies of diseases through a proteomic perspective. It highlights key proteomic approaches to identify pathogenic mutations and integrating omics data to define the borderline between health and disease.
Article
Biochemical Research Methods
Kevin Dick, Arezo Pattang, Julia Hooker, Nour Nissan, Michael Sadowski, Bradley Barnes, Le Hoa Tan, Daniel Burnside, Sadhna Phanse, Hiroyuki Aoki, Mohan Babu, Frank Dehne, Ashkan Golshani, Elroy R. Cober, James R. Green, Bahram Samanfar
Summary: By analyzing the protein-protein interaction network between humans and soybeans, potential important proteins related to human health and putative allergens can be identified. The study leverages advanced PPI predictors to predict interactions between humans and soybeans, exploring proteins related to immune and neurological pathways.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Sang Hyun Lim, Jamie Snider, Liron Birimberg-Schwartz, Wan Ip, Joana C. Serralha, Hugo M. Botelho, Miqueias Lopes-Pacheco, Madalena C. Pinto, Mohamed Taha Moutaoufik, Mara Zilocchi, Onofrio Laselva, Mohsen Esmaeili, Max Kotlyar, Anna Lyakisheva, Priscilla Tang, Lucia Lopez Vazquez, Indira Akula, Farzaneh Aboualizadeh, Victoria Wong, Ingrid Grozavu, Teuta Opacak-Bernardi, Zhong Yao, Meg Mendoza, Mohan Babu, Igor Jurisica, Tanja Gonska, Christine E. Bear, Margarida D. Amaral, Igor Stagljar
Summary: Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a chloride and bicarbonate channel that plays a critical role in maintaining fluid homeostasis. Mutations in CFTR are associated with Cystic Fibrosis (CF), the most common lethal autosomal recessive disorder in Caucasians. This study used a high-throughput screening technique to map the protein-protein interactions of CFTR and identify potential drug targets for CF treatment. They discovered candidate proteins, such as FGL2, that may have significant effects on CFTR function in CF pathophysiology.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Virology
Subha Dahal, Ran Cheng, Peter K. Cheung, Terek Been, Ramy Malty, Melissa Geng, Sarah Manianis, Lulzim Shkreta, Shahrazad Jahanshahi, Johanne Toutant, Rose Chan, Sean Park, Mark A. Brockman, Mohan Babu, Samira Mubareka, Karen Mossman, Arinjay Banerjee, Scott Gray-Owen, Martha Brown, Walid A. Houry, Benoit Chabot, David Grierson, Alan Cochrane
Summary: In this study, the medicinal chemistry optimization of a known HIV-1 inhibitor led to the discovery of a new derivative, GPS491, which showed potent anti-HIV-1 activity with reduced toxicity. The study demonstrated that GPS491 not only blocked HIV-1 replication, but also inhibited the replication of adenovirus and multiple coronaviruses. Furthermore, GPS491 induced changes in viral RNA processing and altered the accumulation/phosphorylation/function of splicing regulatory SR proteins. This study highlights the potential of targeting cellular factors involved in RNA processing for the development of broad-spectrum antiviral agents.
Article
Neurosciences
Elisabet Jakova, Mohamed Taha Moutaoufik, Jeremy S. Lee, Mohan Babu, Francisco S. Cayabyab
Summary: This study found that adenosine and A1R receptor ligands interact with alpha-syn to modulate its aggregation and neurodegeneration. A1R agonists and drugs promoting a knot conformation of alpha-syn can cause alpha-synucleinopathy and increase neuronal degeneration, whereas A1R antagonists and drugs promoting a loop conformation of alpha-syn can be harnessed for possible neuroprotective therapies.
TRANSLATIONAL NEURODEGENERATION
(2022)
Article
Multidisciplinary Sciences
Alla Gagarinova, Ali Hosseinnia, Matineh Rahmatbakhsh, Zoe Istace, Sadhna Phanse, Mohamed Taha Moutaoufik, Mara Zilocchi, Qingzhou Zhang, Hiroyuki Aoki, Matthew Jessulat, Sunyoung Kim, Khaled A. Aly, Mohan Babu
Summary: By studying genetic interactions among all transcription factor genes in E. coli, this research reveals condition-dependent interactions and uncovers the roles of uncharacterized transcription factors.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Khaled A. Aly, Mohamed Taha Moutaoufik, Mara Zilocchi, Sadhna Phanse, Mohan Babu
Summary: Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a rare early-onset neurodegenerative disease caused by mutations in the SACS gene. Understanding the function of Sacsin and using ARSACS disease models can improve our knowledge of this disease. Gene correction strategies and delivery methods provide hope for the development of therapeutics for ARSACS.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Mara Zilocchi, Matineh Rahmatbakhsh, Mohamed Taha Moutaoufik, Kirsten Broderick, Alla Gagarinova, Matthew Jessulat, Sadhna Phanse, Hiroyuki Aoki, Khaled A. Aly, Mohan Babu
Summary: Mitochondrial protein assemblies are crucial for neuronal and brain function. This study presents a co-fractionation-mass spectrometry platform to study native mitochondrial assemblies in brain and cultured nerve cells. The results show that co-fractionation-mass spectrometry can identify complexes and predict protein-protein interactions.
Article
Chemistry, Analytical
Premkumari Kumarathasan, Nazila Nazemof, Dalibor Breznan, Erica Blais, Hiroyuki Aoki, James Gomes, Renaud Vincent, Sadhna Phanse, Mohan Babu
Summary: This study evaluated the internalization and mitochondrial effects of silica nanoparticles (SiNPs) with different sizes and surface modifications. The findings suggest that physicochemical properties are determinants of SiNP exposure-related mitochondrial effects. Mitochondrial exposures combined with proteomic analysis can serve as a new approach in risk assessment, providing insights into related toxicity mechanisms.