Article
Biochemistry & Molecular Biology
Weber Beringui Feitosa, Patricia L. Morris
Summary: Mammalian oocytes undergo morphological, structural, and molecular changes during a process called oocyte aging. The SUMO pathway, specifically SUMO-2/3 and the SUMO-specific protease SENP-2, are involved in spindle morphology changes and chromosome movements during oocyte aging. Decreased UBC9 and differential ubiquitination patterns also correlate with in vitro oocyte aging. These findings suggest that age-related changes in SUMOylation and the deSUMOylation of key target proteins may contribute to spindle and chromosome alignment defects during mammalian oocyte postovulatory aging, with implications for ART-related human oocyte aging and fertilization success.
Review
Biochemistry & Molecular Biology
Jin-Taek Hwang, Ahyoung Lee, Changwon Kho
Summary: Post-translational modification (PTM) is an essential mechanism for enhancing the functional diversity of proteins and adjusting their signaling networks. The reversible conjugation of ubiquitin (Ub) and ubiquitin-like proteins (Ubls) to cellular proteins is among the most prevalent PTM, which modulates various cellular and physiological processes by altering the activity, stability, localization, trafficking, or interaction networks of its target molecules. The dysregulation of Ub/Ubl modifications is associated with various diseases, providing new targets for drug development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Avinash K. Singh, Sumit Murmu, Artur Krezel
Summary: Post-translational modifications (PTMs) of proteins, such as ubiquitination, play important regulatory roles in cellular processes. Defects in the ubiquitination process are associated with diseases, making it crucial to develop efficient methods for studying and targeting this process. This report describes the development of a simple and efficient chemoenzymatic strategy for synthesizing homogeneous ubiquitin conjugates, providing a valuable tool for understanding the complexity of ubiquitination and designing therapeutics.
Article
Biochemistry & Molecular Biology
Andrea G. Shergalis, Violeta L. Marin, David Y. Rhee, Sameera Senaweera, Rebecca L. McCloud, Judith A. Ronau, Charles W. Hutchins, Shaun McLoughlin, Kevin R. Woller, Scott E. Warder, Anil Vasudevan, Justin M. Reitsma
Summary: Molecular glues (MGs) are monovalent small molecules that enhance protein-protein interactions. Immunomodulatory drugs and indisulam have been found to exhibit a molecular glue effect. However, the discovery of new MGs remains challenging.
ACS CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sergey N. Zolov, Hisanori Imai, Mandy K. Losiewicz, Ravi S. J. Singh, Patrice E. Fort, Thomas W. Gardner
Summary: The study reveals that IGF-2 is the primary ligand defining basal retinal IR activity, with higher expression in adult rat retina and reduced levels in diabetes. Understanding the regulation of metabolic and prosurvival signaling in the retina could be influenced by these findings.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Plant Sciences
Byoung-Doo Lee, Yehyun Yim, Esther Canibano, Suk-Hwan Kim, Marta Garcia-Leon, Vicente Rubio, Sandra Fonseca, Nam-Chon Paek
Summary: The study reveals that COP1 plays a positive role in seed germination by directly ubiquitinating and promoting the degradation of the key repressor RGL2. This COP1-RGL2 regulatory module controls the expression of germination-promoting genes in Arabidopsis seeds.
Article
Surgery
Yuxiang Lin, Qingshui Wang, Yingying Lin, Meichen Jiang, Han Xiao, Jie Zhang, Rongrong Guo, Shaohong Kang, Yao Lin, Chuangui Song
Summary: Elevated levels of SUMO1/2/3 were associated with poorer survival outcomes for TNBC patients. A classifier was developed based on this association to predict chemotherapy response, and a nomogram was created to identify patients who may benefit from chemotherapy. The study also suggested that the activation of the SUMOylation pathway in TNBC might be induced by MYC signaling.
Article
Plant Sciences
Ross D. Etherington, Mark Bailey, Jean-Baptiste Boyer, Laura Armbruster, Xulyu Cao, Juliet C. Coates, Thierry Meinnel, Markus Wirtz, Carmela Giglione, Daniel J. Gibbs
Summary: This study reveals that Arabidopsis DOA10A-like E3 ligases regulate the turnover of SQUALENE EPOXIDASE 1 independently of the Ac/N-degron pathway. It also shows that DOA10 E3 ligases in Arabidopsis are not major players in the degradation of N-acetylated proteins.
Article
Medicine, General & Internal
Wanzhen Chen, Tingting Xu, Zhanpeng Yan, Xiao Zhang, Fangshi Zhu
Summary: The study revealed that UBA2 was highly expressed in gastric cancer tissues, which was associated with poor prognosis in patients and could be a key factor in the progression of gastric cancer.
ACTA MEDICA MEDITERRANEA
(2021)
Review
Multidisciplinary Sciences
Chongyang Li, Trent G. Nelson, Alfred C. O. Vertegaal, Pierre Thibault
Summary: The modification of proteins through UBLs, including ubiquitin, SUMO, NEDD8, ISG15, and FAT10, is involved in various cellular processes. Each UBL is associated with specific enzymes that alter the structure and fate of target proteins, resulting in a complex distribution of monomeric and polymeric modifications. Different techniques can be used to identify UBL modification sites and types, providing insights into UBL functions and their role in cellular homeostasis and human diseases.
NATURE REVIEWS METHODS PRIMERS
(2021)
Article
Biochemistry & Molecular Biology
Praveen Thangaraj, Akshaya Subbaih Balamurali, Krishnamoorthy Akkanna Subbiah, Nakkeeran Sevugapperumal, Thiribhuvanamala Gurudevan, Sivakumar Uthandi, Haripriya Shanmugam
Summary: In this study, the volatilomes of Mentha spicata immobilized in vermiculite balls were found to effectively inhibit the mycelial growth of Fusarium oxysporum f. sp. lycopersici. The volatilomes of M. spicata traveling a certain distance from the center of the PVC chamber demonstrated the maximum reduction in colony growth. Tomato plants inoculated with Fusarium wilt pathogens showed increased expressions of defense genes and transcription factors after exposure to the volatilomes.
Article
Plant Sciences
Sugitha Thankappan, Shobana Narayanasamy, A. P. Sridharan, A. K. Binodh, A. Nirmala Kumari, P. Parasuraman, Sivakumar Uthandi
Summary: The rhizospheric microbiome and their metabolites interact with plants, contributing to plant health through hormonal regulation, nutrient supply, and pathogen suppression. Chemical dialogues mediated by microbial volatile organic compounds (MVOCs) act as a mediator of communication and defense between plants and the rhizobiome, interfering with signaling processes. Volatile compounds in the rhizosphere, such as dimethyl di-sulfide, linalool, and hydrogen cyanide, have potent pathogen-suppressing abilities and can serve as eco-friendly alternatives to chemical pesticides. Volatile-based electronic noses enable rapid and noninvasive plant disease diagnosis.
PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY
(2022)
Article
Environmental Sciences
Manikandan Ariyan, Sugitha Thankappan, Priyadharshini Ramachandran, Sivakumar Uthandi
Summary: This study successfully produced xylitol from corncob hydrolysates using engineered E. coli, which is of great significance for the development of eco-friendly high-value green chemicals.
WASTE AND BIOMASS VALORIZATION
(2023)
Article
Energy & Fuels
Iniya Kumar Muniraj, P. Anbu, K. T. Parthiban, Sivakumar Uthandi
Summary: The aim of this study was to develop a new green process for the simultaneous depolymerization and valorization of lignin into high-value chemicals to meet the requirements of lignocellulosic biorefinery. A new Enzolv process using thermosolvent stable laccase (LccH) was developed for the delignification of Melia dubia woody biomass, resulting in the generation of high-value chemicals.
BIOMASS CONVERSION AND BIOREFINERY
(2022)
Article
Environmental Sciences
Vetrimurugan Elumalai, N. Rajmohan, Bongani Sithole, Peiyue Li, Sivakumar Uthandi, Johan van Tol
Summary: The sources of chemical constituents and hydrogeochemical processes of groundwater in the Mhlathuze catchment were identified. The groundwater in the area ranges from soft to very hard, with acidity ranging from acidic to alkaline. The dominant water type is NaCl, with CaMgCl facies. Various plots and analysis techniques confirmed the impact of silicate and carbonate mineral weathering, ion exchange reactions, and anthropogenic sources on the groundwater. Some wells were also influenced by evaporation. Groundwater is undersaturated with sulphate and chloride minerals and saturated with carbonate minerals. The study found evidence of mineral weathering and nitrification processes. Hierarchical cluster analysis indicated that evaporation, anthropogenic input, silicate and carbonate weathering, and nitrification are the sources of chemical constituents in the groundwater.
Article
Biotechnology & Applied Microbiology
Shobana Narayanasamy, Sugitha Thankappan, Sowmya Kumaravel, Sridar Ragupathi, Sivakumar Uthandi
Summary: This study compared the whole genome sequence of B. altitudinis FD48 to uncover the genetic determinants of its osmotic stress tolerance and plant growth-promoting traits. The analysis revealed a variety of genes associated with chemotaxis, plant nutrient acquisition, phytohormone synthesis, and tolerance to adverse environmental conditions. It sheds light on the genetic mechanisms and potential activity of B. altitudinis FD48 in resisting drought stress and promoting plant growth.
Article
Energy & Fuels
Daphy Meurial Chandra, Sugitha Thankappan, Sivakumar Uthandi
Summary: Microbes associated with earthworm casts in biomass conversion have implications for biorefineries. This study identified two cellulose and hemicellulose deconstructing microbes from earthworm casts. The isolates Bacillus subtilis DLC4, Bacillus subtilis SDX3, and Bacillus flexus PSX1 showed high cellulase and xylanase activities, making vermicasts a potential source for carbohydrate-modifying enzymes in biofuel and green chemical production.
BIOMASS CONVERSION AND BIOREFINERY
(2023)
Article
Biochemistry & Molecular Biology
Vinusri Sekar, Gnanam Ramasamy, Caroline Ravikumar, Raveendran Muthurajan, Sivakumar Uthandi, Rajamani Kandasamy, Patil Santosh Ganapati
Summary: This study investigated the anti-cancer potential of compounds from P. betle petiole, focusing on 4-Allylbenzene-1,2-diol. In silico studies and cytotoxicity assessments on bone cancer metastasis were performed, demonstrating the compound's multi-targeting ability and potential as a matrix metalloproteinase inhibitor. Further experimental validations are needed for targeted therapy in bone cancer metastasis.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Ricardo L. Couto-Rodriguez, Jin Koh, Sixue Chen, Julie A. Maupin-Furlow
Summary: Oxidative stress adaptation strategies are important for cell function and are associated with cardiac, neurodegenerative disease, and cancer. The halophilic archaeon Haloferax volcanii is used as a model organism due to its extreme tolerance to oxidants and close evolutionary relationship with eukaryotes. A study on H. volcanii reveals the association of lysine acetylation with oxidative stress responses, and the dynamic changes in the lysine acetylome in response to hypochlorite. These findings provide insights into the role of lysine acetylation in key biological processes and PTM crosstalk in Archaea.
Article
Agricultural Engineering
Santhoshkumar Subramaniam, Kumutha Karunanandham, A. S. M. Raja, Sivakumar Uthandi
Summary: The present study aimed to add value to cotton waste biomass using a more eco-friendly process called EnZolv, which effectively removes lignin from cotton stalk and cotton ginning mill waste. The optimized EnZolv process achieved a delignification rate of 78.68% in cotton stalk and 70.53% in ginning mill waste using specific parameters determined through Response Surface Methodology. These findings have significant implications for the utilization and sustainable management of cotton waste biomass.
BIORESOURCE TECHNOLOGY
(2023)
Article
Microbiology
Tamilarasi Mani, J. Beslin Joshi, R. Priyadharshini, Jeya Sundara Sharmila, Sivakumar Uthandi
Summary: The study demonstrated that flagellin or Flg22 peptide from Xad1 can trigger plant defense responses by activating ROS scavenging enzymes, increasing PR gene expression, and down-regulating PR2 gene, therefore enhancing plant immune system.
Article
Biochemistry & Molecular Biology
Ulrike Johnsen, Marius Ortjohann, Andreas Reinhardt, Jonathan M. Turner, Caleb Stratton, Katherine R. Weber, Karol M. Sanchez, Julie Maupin-Furlow, Christopher Davies, Peter Schoenheit
Summary: In this study, a novel transcriptional regulator called GfcR was identified, which acts as an activator in the degradation of both D-glucose and D-fructose. GfcR activates multiple enzymes involved in the catabolism of these sugars and directly binds to the promoters of regulated genes. Furthermore, specific intermediates of the degradation pathways were found to induce the activity of GfcR.
MOLECULAR MICROBIOLOGY
(2023)
Article
Microbiology
Huiyong Jia, Swathi Dantuluri, Shae Margulies, Victoria Smith, Rebecca Lever, Thorsten Allers, Jin Koh, Sixue Chen, Julie A. Maupin-Furlow
Summary: A newly identified dynamic type of nuclease complex has been found in the archaeon Haloferax volcanii, which lacks the canonical RNA exosome. The complex, composed of RecJ3, RecJ4, and aRNase J, primarily functions as a 3'-5' exonuclease and was discovered through its ATP-dependent association with SAMP1 and Cdc48a. RecJ3/4 appears to modulate the nuclease activities of aRNase J. While aRNase J is essential for growth, RecJ3/4, Cdc48a, and SAMPs are important for DNA damage recovery.
Article
Biochemistry & Molecular Biology
Mar Martinez Pastor, Saaz Sakrikar, Sungmin Hwang, Rylee K. Hackley, Andrew L. Soborowski, Julie A. Maupin-Furlow, Amy K. Schmid
Summary: Maintaining intracellular iron homeostasis is crucial for cellular metabolic needs and reducing oxidative stress. The transcriptional regulatory networks (TRNs) involved in iron response were studied in two haloarchaea, showing variations in regulatory complexity and metal specificity among different strains, likely influenced by environmental conditions and iron availability.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Oviya Govindaraj, Nellaiappan Olaganathan Gopal, Raja Asm, Sivakumar Uthandi
Summary: Lignocellulosic biomass from agriculture residues has gained attention for its conversion to useful by-products. This study optimized the EnZolv pretreatment process parameters for enhanced release of reducing sugar from banana fiber. The results showed that the pretreatment significantly increased sugar release and affected the composition of the biomass.
INDIAN JOURNAL OF MICROBIOLOGY
(2023)
