Chris West, Wanda Waterworth
Successful germination and seedling establishment are important determinants of crop yields and plant survival in natural environments. Germination potential is compromised by suboptimal environmental conditions that result in seed ageing and high levels of genome damage. However, the mutagenic and growth inhibitory potential of DNA damage accumulated in seeds on subsequent seedling growth remains largely unknown. Arabidopsis seeds deficient in the chromosomal break repair factors DNA LIGASE 4 and DNA LIGASE 6 exhibited hypersensitivity to the effects of natural ageing, with reduced germination vigour and seedling biomass relative to wild type seed...
March 22, 2023: Biochemical Journal
Lokesh Kumar Saini, Manisha Sharma, Barkha Ravi, Soma Ghosh, Sonam Pahuja, Nidhi Singh, Girdhar K Pandey
Plant growth and development are governed by selective protein synthesis and degradation. Ubiquitination mediated protein degradation is governed by activating enzyme E1 followed by conjugating enzyme E2 and E3 ligase. Plant Armadillo (ARM) repeat/U-box (PUB) protein family is one of the important classes of E3 ligase. We studied the function of AtPUB2 by loss-of-function (knockout and knock down mutants) and gain-of-function (CaMV 35S promoter driven overexpression lines) approach in Arabidopsis...
March 14, 2023: Biochemical Journal
Linna Han, Jessica B Lee, Elaine W Indermaur, Albert J Keung
Chemical tools to control the activities and interactions of chromatin components have broad impact on our understanding of cellular and disease processes. It is important to accurately identify their molecular effects to inform clinical efforts and interpretations of scientific studies. Chaetocin is a widely used chemical that decreases H3K9 methylation in cells. It is frequently attributed as a specific inhibitor of the histone methyltransferase activities of SUV39H1/SU(VAR)3-9, although prior observations showed chaetocin likely inhibits methyltransferase activity through covalent mechanisms involving its epipolythiodixopiperazine disulfide 'warhead' functionality...
March 10, 2023: Biochemical Journal
Hayley Whitfield, Sining He, Yinghong Gu, Colleen Sprigg, Hui-Fen Kuo, Tzyy-Jen Chiou, Andrew M Riley, Barry V L Potter, Andrew M Hemmings, Charles A Brearley
Myo-inositol tris/tetrakisphosphate kinases (ITPKs) catalyze diverse phosphotransfer reactions with myo-inositol phosphate and myo-inositol pyrophosphate substrates. However, the lack of structures of nucleotide-coordinated plant ITPKs thwarts a rational understanding of phosphotransfer reactions of the family. Arabidopsis possesses a family of four ITPKs of which two isoforms, ITPK1 and ITPK4, control inositol hexakisphosphate and inositol pyrophosphate levels directly or by provision of precursors. Here, we describe the specificity of Arabidopsis ITPK4 to pairs of enantiomers of diverse inositol polyphosphates and show how substrate specificity differs from Arabidopsis ITPK1...
March 10, 2023: Biochemical Journal
Wen-Tao Wu, Lian-Ying Xu, Zhi-Jun Yan, Ning Bi, Cai-Yuan Cheng, Fan Yang, Wei-Jun Yang, Jin-Shu Yang
Doublesex (DSX) proteins are members of the Doublesex/mab-3-related (DMRT) protein family and play crucial roles in sex determination and differentiation among the animal kingdom. In the present study, we identified two Doublesex (Dsx)-like mRNA isoforms in the brine shrimp Artemia franciscana (Kellogg 1906), which are generated by the combination of alternative promoters, alternative splicing and alternative polyadenylation. The two transcripts exhibited sex-biased enrichment, which we termed AfrDsxM and AfrDsxF...
February 28, 2023: Biochemical Journal
Josef Houser, Kristina Jendruchova, Andrea Knight, Martin Piskacek
The nine-amino-acid TransActivation Domains (9aaTAD) was identified in numerous transcription factors including Gal4, p53, E2A, MLL, c-Myc, N-Myc, and also in SP, KLF and SOX families. Most of the 9aaTAD domains interact with the KIX domain of transcription mediators MED15 and CBP to activate transcription. The NFkB activation domain occupied the same position on the KIX domain as the 9aaTADs of MLL, E2A and p53. Binding of the KIX domain is established by the two-point interaction involving 9aaTAD positions p3-4 and p6-7...
February 24, 2023: Biochemical Journal
Machi Toriu, Momoka Horie, Yuka Kumaki, Taku Yoneyama, Shin Kore-Eda, Susumu Mitsuyama, Keisuke Yoshida, Toru Hisabori, Yoshitaka Nishiyama
Translational elongation factor EF-Tu, which delivers aminoacyl-tRNA to the ribosome, is susceptible to inactivation by reactive oxygen species (ROS) in the cyanobacterium Synechocystis sp. PCC 6803. However, the sensitivity to ROS of chloroplast-localized EF-Tu (cpEF-Tu) of plants remains to be elucidated. In the present study, we generated a recombinant cpEF-Tu protein of Arabidopsis thaliana and examined its sensitivity to ROS in vitro. In cpEF-Tu that lacked a bound nucleotide, one of the two cysteine residues, Cys149 and Cys451, in the mature protein was sensitive to oxidation by H2O2, with the resultant formation of sulfenic acid...
February 24, 2023: Biochemical Journal
Renzo E Vera, Maria J Lamberti, Luciana Almada, Ezequiel Tolosa, Anne Vrabel, Ashley Sigafoos, Merih Deniz Toruner, Luis Flores, Viviana A Rivarola, Natalia B Rumie Vittar, Martin E Fernandez-Zapico
Carcinoma-associated fibroblasts (CAFs) play an important role in the progression of multiple malignancies. Secretion of cytokines and growth factors underlies the pro-tumoral effect of CAFs. Although this paracrine function has been extensively documented, the molecular mechanisms controlling the expression of these factors remain elusive. In this study, we provide evidence of a novel CAF transcriptional axis regulating the expression of SDF1, a major driver of cancer cell migration, involving the transcription factor GLI1 and histone acetyltransferase p300...
February 3, 2023: Biochemical Journal
Lucy Troman, Sara Alvira, Bertram Daum, Vicki Gold, Ian Collinson
Gram-negative bacteria are surrounded by two protein-rich membranes with a peptidoglycan layer sandwiched between them. Together they form the envelope (or cell wall), crucial for energy production, lipid biosynthesis, structural integrity, and for protection against physical and chemical environmental challenges. To achieve envelope biogenesis, periplasmic and outer-membrane proteins (OMPs) must be transported from the cytosol and through the inner-membrane, via the ubiquitous SecYEG protein-channel. Emergent proteins either fold in the periplasm or cross the peptidoglycan (PG) layer towards the outer-membrane for insertion through the b-barrel assembly machinery (BAM)...
January 26, 2023: Biochemical Journal
Gaurav Kumar, Sharmistha Sinha
The self-assembly of bacterial microcompartments is the result of several genetic, biochemical, and physical stimuli orchestrating inside the bacterial cell. In this work, we use 1,2-propanediol utilization microcompartments as a paradigm to identify the factors that physically drive the self-assembly of MCP proteins in vitro using its major shell protein and major encapsulated enzyme. We find that a major shell protein PduBB' tend to self-assemble under macromolecular crowded environment and suitable ionic strength...
January 23, 2023: Biochemical Journal
Juliette Bayot, Caroline Martin, Guillaume Chevreux, Jean-Michel Camadro, Francoise Auchere
Candida albicans is an opportunist pathogen responsible for a large spectrum of infections, from superficial mycosis to systemic diseases known as candidiasis. During infection in vivo, Candida albicans must adapt to host microenvironments and this adaptive response is crucial for the survival of this organism, as it facilitates the effective assimilation of alternative carbon sources others than glucose. We performed a global proteomic analysis on the global changes in protein abundance in response to changes in micronutrient levels, and, in parallel, explored changes in the intracellular redox and metabolic status of the cells...
January 10, 2023: Biochemical Journal
Manisha Banerjee, Namrata Waghamare, Prakash Kalwani, Deepak T Hurali, Rachna Agarwal, Anand Ballal
Thioredoxins (Trxs) are ubiquitous proteins that play vital roles in several physiological processes. Alr2205, a thioredoxin-like protein from Anabaena PCC 7120, was evolutionarily closer to the Trx-domain of the NADPH-Thioredoxin Reductase C than the other thioredoxins. The Alr2205 protein showed disulphide reductase activity despite the presence a non-canonical active site motif 'CPSC'. Alr2205 not only physically interacted with, but also acted as a physiological reductant of Alr4641 (2-Cys-Peroxiredoxin), supporting its peroxidase function...
January 3, 2023: Biochemical Journal
Luke Higgins, Henry Gerdes, Pedro R Cutillas
Phosphorylation constitutes the most common and best-studied regulatory post-translational modification in biological systems and archetypal signalling pathways driven by protein and lipid kinases are disrupted in essentially all cancer types. Thus, the study of the phosphoproteome stands to provide unique biological information on signalling pathway activity and on kinase network circuitry that is not captured by genetic or transcriptomic technologies. Here, we discuss the methods and tools used in phosphoproteomics and highlight how this technique has been used, and can be used in the future, for cancer research...
March 31, 2023: Biochemical Journal
Andrew Hitchcock, David J K Swainsbury, C Neil Hunter
The reaction centre (RC) in purple phototrophic bacteria is encircled by the primary light-harvesting complex 1 (LH1) antenna, forming the RC-LH1 'core' complex. The Qy absorption maximum of LH1 complexes ranges from ∼875-960 nm in bacteriochlorophyll (BChl) a-utilising organisms, to 1018 nm in the BChl b-containing complex from Blastochloris (Blc.) viridis. The red-shifted absorption of the Blc. viridis LH1 was predicted to be due in part to the presence of the γ subunit unique to Blastochloris spp...
March 29, 2023: Biochemical Journal
Gilbert Salloum, Anne R Bresnick, Jonathan M Backer
Macropinocytosis is defined as an actin-dependent but coat- and dynamin-independent endocytic uptake process, which generates large intracellular vesicles (macropinosomes) containing a non-selective sampling of extracellular fluid. Macropinocytosis provides an important mechanism of immune surveillance by dendritic cells and macrophages, but also serves as an essential nutrient uptake pathway for unicellular organisms and tumor cells. This review examines the cell biological mechanisms that drive macropinocytosis, as well as the complex signaling pathways - GTPases, lipid and protein kinases and phosphatases, and actin regulatory proteins - that regulate macropinosome formation, internalization, and disposition...
March 15, 2023: Biochemical Journal
Leonid A Sazanov
My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant 'black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma...
March 15, 2023: Biochemical Journal
Donald E Ingber
The field of mechanobiology, which focuses on the key role that physical forces play in control of biological systems, has grown enormously over the past few decades. Here, I provide a brief personal perspective on the development of the tensegrity theory that contributed to the emergence of the mechanobiology field, the key role that crossing disciplines has played in its development, and how it has matured over time. I also describe how pursuing questions relating to mechanochemical transduction and mechanoregulation can lead to the creation of novel technologies and open paths for development of new therapeutic strategies for a broad range of diseases and disorders...
February 27, 2023: Biochemical Journal
Arline Fernández-Silva, Ana L Juárez-Vázquez, Lilian González-Segura, Javier Andrés Juárez-Díaz, Rosario A Muñoz-Clares
Neither the Pseudomonas aeruginosa aldehyde dehydrogenase encoded by the PA4189 gene nor its ortholog proteins have been biochemically or structurally characterized and their physiological function is unknown. We cloned the PA4189 gene, obtained the PA4189 recombinant protein, and studied its structure-function relationships. PA4189 is an NAD+-dependent aminoaldehyde dehydrogenase highly efficient with protonated aminoacetaldehyde and 3-aminopropionaldehyde, which are much more preferred to the non-protonated species as indicated by pH studies...
February 27, 2023: Biochemical Journal
Hannah Tovell, Alexandra C Newton
Allosteric regulation of multi-domain protein kinases provides a common mechanism to acutely control kinase activity. Protein kinase C serves as a paradigm for multi-domain proteins whose activity is exquisitely tuned by interdomain conformational changes that keep the enzyme off in the absence of appropriate stimuli, but unleash activity in response to second messenger binding. Allosteric regulation of protein kinase C signaling has been optimized not just for itself: Alessi and colleagues discover that protein kinase C phosphorylates LRRK1, a kinase with even more domains, at sites on its CORB GTPase domain to allosterically activate LRRK1...
February 14, 2023: Biochemical Journal
Christophe Bailly, Maria Victoria Gomez Roldan
In agriculture, seeds are the most basic and vital input on which croplands productivity depends. These implies a good starting material, good production lines and good storage options. High-quality seed lots must be free of pests and pathogens and contain a required degree of genetic purity. Seeds need also to be stored in good condition between harvest and later sowing, to insure later on the field a good plant density and higher crop yield. In general, these parameters are already widely accepted and considered in many countries where advanced technologies evaluate them...
February 14, 2023: Biochemical Journal
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