Article
Biotechnology & Applied Microbiology
Chao Fan, Wei Zhang, Xiaoyun Su, Wangli Ji, Huiying Luo, Yuhong Zhang, Bo Liu, Bin Yao, Huoqing Huang, Xinxin Xu
Summary: In this study, a CRISPR/Cas9 genome-editing system was successfully established in H. insolens. By disrupting the pks and xyr1 genes, the important role of Xyr1 in cellulase expression regulation was demonstrated. This system allows efficient single gene destruction and accelerates research on the cellulase production regulation mechanism in H. insolens.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Review
Microbiology
George H. Jones
Summary: Streptomyces are bacteria found in soil that are known for their ability to sporulate and produce antibiotics and other secondary metabolites. Antibiotic production in Streptomyces is regulated by complex networks involving activators, repressors, signaling molecules, and other regulatory elements. This review discusses the impact of five ribonucleases (RNase E, RNase J, polynucleotide phosphorylase, RNase III, and oligoribonuclease) on antibiotic synthesis and proposes mechanisms for their effects.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Victor G. Stepanov, George E. Fox
Summary: A comprehensive search identified 89 expanded 5S rRNAs of 15 structural types in 15 archaeal and 36 bacterial genomes, with expansion segments ranging from 13 to 109 residues distributed among 17 insertion sites. These expanded versions are mainly found in specific bacterial strains and can coexist with normal 5S rRNA genes in multiple copies.
Article
Plant Sciences
Guimin Chen, Anton Stepanenko, Nikolai Borisjuk
Summary: Duckweeds are a group of fast-growing aquatic plants with various applications worldwide. The study on 5S rDNA genes in Landoltia punctata identified diverse NTS variants, which may contribute to understanding the evolution of plant rDNA. The findings could stimulate further research on molecular forces driving rDNA evolution.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Asya G. Davidian, Alexander G. Dyomin, Svetlana A. Galkina, Nadezhda E. Makarova, Sergey E. Dmitriev, Elena R. Gaginskaya
Summary: The analysis of turtle rDNA sequences revealed a specific insertion of NOR-5S rRNA gene with antisense orientation. This insertion exhibited specific expression in oocytes, playing a potential role in oocyte-specific translation. The NOR-5S rRNA predominance in ribosomes during vitellogenic oocytes suggests a distinct regulation of ribosomal RNA expression in this process.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Xin-Yi Chen, Shan-Shan Hu, Xiao-Can Xu, Ji-Liang Tang, Dong-Jie Tang
Summary: This study investigates the physiological function of exoribonuclease RNase D in the plant pathogen Xcc. The results show that RNase D is involved in the degradation of 5S rRNA and the production of exopolysaccharides (EPS) in Xcc. While the deletion of RNase D does not affect the growth and virulence of Xcc, its overexpression severely attenuates these traits. Additionally, RNase D in Xcc exhibits a different function in tRNA metabolism compared to its counterpart in E. coli. This finding expands our knowledge about the function of RNase D in bacteria.
Article
Agronomy
Yong-Bao Pan, James R. Todd, Lionel Lomax, Paul M. White Jr, Sheron A. Simpson, Brian E. Scheffler
Summary: Due to the complexity of polyploidy, whole genome sequencing and characterization of sugarcane have lagged behind. In this study, PCR amplification was used to analyze 171 accessions of Saccharum spp. and Tripidium spp., and specific amplicons were identified that could help breeders confirm and differentiate germplasm collections.
Article
Biochemistry & Molecular Biology
Alexander Dyomin, Svetlana Galkina, Arina Ilina, Elena Gaginskaya
Summary: In the majority of Animalia genomes, the 5S rRNA gene repeats are located outside of the nucleolar organiser (NOR). However, in the family Nototheniidae, a 5S rDNA sequence is inserted into the intergenic spacer between the 45S rDNA repeats. This sequence, termed NOR-5S rRNA gene, is colocalized with the 45S rDNA and is considered a maternal-type 5S rRNA template.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Mitsuru Okuwaki, Shoko Saito, Hiroko Hirawake-Mogi, Kyosuke Nagata
Summary: This study revealed that the nucleolar localization of NPM1 and the large ribosomal subunit precursors are mutually dependent. NPM1 plays a crucial role in maintaining the structure of large ribosomal subunits and the accumulation of late processing machinery in the nucleolus.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Lisa Lirussi, Ozlem Demir, Panpan You, Antonio Sarno, Rommie E. Amaro, Hilde Nilsen
Summary: RNA modifications play vital roles in proper RNA processing and maturation, with enzymes like SMUG1 able to recognize and process modified RNA substrates. SMUG1 interacts with dyskerin to regulate rRNA metabolism, impacting post-transcriptional regulation and quality control of rRNAs. Cells lacking SMUG1 show elevated levels of immature rRNA molecules and accumulation of 5hmU in mature rRNA, suggesting a crucial role for SMUG1 in RNA surveillance.
Review
Biochemistry & Molecular Biology
Lu Wang, Shuibin Lin
Summary: tRNAs are crucial regulators in mRNA translation by recognizing mRNA codons and bridging amino acids. These modified tRNAs form complex secondary structures that facilitate codon recognition and mRNA translation. Recent studies have highlighted the regulatory roles of tRNA modifications in mRNA translation networks, which are closely associated with developmental diseases and cancer progression.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Review
Biochemistry & Molecular Biology
Monica C. Pillon, Jacob Gordon, Meredith N. Frazier, Robin E. Stanley
Summary: HEPN RNases are a diverse class of RNA processing and degradation enzymes that require dimerization for activation. Despite conservation in their core fold, HEPN RNases exhibit structural deviations that contribute to their specialized functions. These enzymes are conserved throughout evolution and exist in both prokaryotes and eukaryotes with unique features and mechanisms of activation and inhibition.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Anna Ender, Maja Etzel, Stefan Hammer, Sven Findeiss, Peter Stadler, Mario Moerl
Summary: The study describes a synthetic riboswitch element that regulates tRNA maturation by either sequestering or exposing the 5'-leader region of tRNA precursor in response to a ligand. It provides evidence for the importance of the leader region structure in tRNA maturation and demonstrates the potential of ligand-dependent structural rearrangements in addressing individual maturation steps of stable non-coding RNAs as promising targets for regulatory devices in synthetic biology.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Jie Tang, Mahfuzur R. Shah, Dan Yao, Ying Jiang, Lianming Du, Kelei Zhao, Liheng Li, Meijin Li, Michal M. Waleron, Malgorzata Waleron, Krzysztof Waleron, Maurycy Daroch
Summary: In this study, a thermophilic strain, PKUAC-SCTAE412, recovered from Lotus Lake hot spring in China, was characterized using polyphasic approaches. The results supported the existence of a novel genus within Leptolyngbyaceae, which was further confirmed by genomic analyses. The complete genome of this strain provided insights into its adaptation to the hot spring environment and revealed a large number of genes possibly acquired through horizontal gene transfer. The study lays the foundation for future global ecogenomic and geogenomic studies.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hovik Panosyan, Franziska R. Traube, Caterina Brandmayr, Mirko Wagner, Thomas Carell
Summary: The study analyzed the tRNA modification profiles of thermophilic aerobic bacilli strains to identify variations in phylogeny. The modified tRNA bases were found to be genus-specific and could be used to distinguish between obligate and moderate thermophilic bacilli. The presence of certain modifications, such as Gm and ms(2)i(6)A, was more pronounced in obligate thermophilic species.
Article
Biotechnology & Applied Microbiology
Itxaso Montanchez, Anna Chao Kaberdina, Elena Sevillano, Lucia Gallego, Susana Rodriguez-Couto, Vladimir R. Kaberdin
FOLIA MICROBIOLOGICA
(2017)
Article
Biotechnology & Applied Microbiology
Ander Hernandez Plagaro, Peter B. Pearman, Vladimir R. Kaberdin
Review
Biology
Eliane Hajnsdorf, Vladimir R. Kaberdin
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2018)
Article
Multidisciplinary Sciences
Itxaso Montanchez, Elixabet Ogayar, Ander Hernandez Plagaro, Anna Esteve-Codina, Jessica Gomez-Garrido, Maite Orruno, Ines Arana, Vladimir R. Kaberdin
SCIENTIFIC REPORTS
(2019)
Article
Public, Environmental & Occupational Health
Z. Bravo, M. Orruno, T. Navascues, E. Ogayar, J. Ramos-Vivas, V. R. Kaberdin, I Arana
JOURNAL OF HOSPITAL INFECTION
(2019)
Article
Ecology
Maite Orruno, Claudia Parada, Elixabet Ogayar, Vladimir R. Kaberdin, Ines Arana
AQUATIC MICROBIAL ECOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Anna Chao Kaberdina, Olatz Ruiz-Larrabeiti, Sue Lin-Chao, Vladimir R. Kaberdin
MOLECULAR GENETICS AND GENOMICS
(2019)
Correction
Biochemistry & Molecular Biology
Anna Chao Kaberdina, Olatz Ruiz-Larrabeiti, Sue Lin-Chao, Vladimir R. Kaberdin
MOLECULAR GENETICS AND GENOMICS
(2019)
Article
Environmental Sciences
Itxaso Montanchez, Vladimir R. Kaberdin
MARINE ENVIRONMENTAL RESEARCH
(2020)
Article
Microbiology
Maite Orruno, Claudia Parada, Vladimir R. Kaberdin, Ines Arana
Summary: The study revealed that exposure to visible light reduces the culturability of Vibrio harveyi, likely leading to entry into the Viable but Non Culturable state (VBNC), while populations kept in darkness remained culturable for at least 21 days. Despite differences, both starved cell populations showed morphological changes by reducing their size. Furthermore, proteomic analysis indicated changes in cell envelope composition that may account for the different adaptation patterns observed in the absence and presence of visible light.
Article
Environmental Sciences
Elixabet Ogayar, Irene Larranaga, Ana Lomba, Vladimir R. Kaberdin, Ines Arana, Maite Orruno
Summary: Vibrio is a widely distributed bacterial genus, with climate change potentially increasing the incidence of Vibrio-associated diseases worldwide. Conventional culture-based methods may underestimate cell numbers, while using CARD-FISH can overcome this issue and improve the detection sensitivity and selectivity of marine vibrios.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Gunn-Guang Liou, Anna Chao Kaberdina, Wei-Syuan Wang, Vladimir R. Kaberdin, Sue Lin-Chao
Summary: By analyzing the physiology and gene expression of E. coli in low-oxygen environments, we identified genes involved in acid-stress adaptation, cell adhesion/biofilm formation, electron transport, oligopeptide transport, and anaerobic respiration/fermentation that are upregulated under microaerobic conditions. In contrast, genes involved in iron transport, aerobic respiration, and de novo nucleotide synthesis were downregulated. We also discovered and discussed the regulatory functions of differentially expressed noncoding small RNAs during microaerobic growth.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Daniel Fernandez-Remacha, Candela Gonzalez-Riancho, Miranda Lastra Osua, Aranzazu Gonzalez Arce, Itxaso Montanchez, Juan Maria Garcia-Lobo, Roger Estrada-Tejedor, Vladimir R. Kaberdin
Summary: Researchers isolated fungal strains producing laccases from a cave in northern Spain, identifying them as Gliomastix murorum and Conidiobolus thromboides. Further analysis showed that the laccases secreted by these fungi could degrade various industrial dyes. The study suggests promising applications of these enzymes in biotechnology.
Article
Microbiology
Asier Ramos-Pardo, Rocio Castro-Alvarez, Guillermo Quindos, Elena Eraso, Elena Sevillano, Vladimir R. Kaberdin
Summary: This study aimed to investigate the impact of external pH, substrate nature, and strain origin on the production of protease, lipase, and hemolysin in Candida albicans. The pH value had a significant effect on the detection of protease and lipase, while the activity of hemolysin was not affected by pH. Additionally, the anatomical origin of the isolates was found to be associated with the detected activities.
Article
Microbiology
Oleg N. Murashko, Kun-Hai Yeh, Chen-Hsin Albert Yu, Vladimir R. Kaberdin, Sue Lin-Chao
Summary: This study demonstrates that fluoride can impact gene expression posttranscriptionally by slowing down RNA degradation, thereby enhancing RNA stability and steady-state mRNA levels in E. coli.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Soojung Hahn, Gyuri Kim, Sang-Man Jin, Jae Hyeon Kim
Summary: This study utilized three-dimensional intestinal organoids to investigate the effects of metformin on inflammatory bowel disease (IBD) and found that metformin can enhance intestinal barrier function and reduce levels of inflammatory cytokines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
V. V. Sudarev, M. S. Gette, S. V. Bazhenov, O. M. Tilinova, E. V. Zinovev, I. V. Manukhov, A. I. Kuklin, Yu. L. Ryzhykau, A. V. Vlasov
Summary: This study investigated the self-assembly processes of ferritin-based protein complexes and obtained structurally characterized oligomeric states. These results provide new potential and opportunities for the application of ferritin in various fields.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Yalda Sabaghi, Farnaz Pourfarzad, Leila Zolghadr, Azita Bahrami, Tahereh Shojazadeh, Alireza Farasat, Nematollah Gheibi
Summary: p-Coumaric acid (p-CA) is a plant compound with anti-cancer activities. This study designed a nano-liposomal carrier containing p-CA to enhance its effectiveness against melanoma cells. The findings showed that the liposomal form of p-CA had a greater impact on the cells. Kinetic modeling indicated that the best fitting model was zero-order.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
M. D. Nazmul Hasan, Md Mahfuzur Rahman, Al Asmaul Husna, Nobuhiro Nozaki, Osamu Yamato, Naoki Miura
Summary: This study investigated the expression of ncRNAs other than miRNAs in different histologic subtypes of canine mammary gland tumors (MGT). Three aberrantly expressed ncRNAs were identified as potential biomarkers for differentiating MGT subtypes. YRNA and tRFs expression levels were found to be decreased in metastatic compared to primary MGT cell lines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Seine A. Shintani
Summary: In this study, the researchers used signal analysis to study the instantaneous amplitude and phase of sarcomeric oscillations in skeletal muscle. They identified two types of oscillations, sarcomeric oscillations and sarcosynced oscillations, and visualized their behavior during propagating waves. The researchers discovered the presence of sarcomeric defect holes and sarcomeric collision holes, which are important indicators for understanding the oscillation properties of sarcomeres. This finding has important implications for improving our understanding of muscle function and its regulatory mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Shuanglin Zhang, Yuzhong Jia, Guolan Ma, Yanyan Yang, Zhenzhen Cao, Antao Luo, Zefu Zhang, Shihan Li, Jie Wen, Hanfeng Liu, Jihua Ma
Summary: Bupleurum is an antiarrhythmic agent that may exert its effects by inhibiting L-type calcium channels.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Tomotaka Ohkubo, Yasuhiko Matsumoto, Hiroaki Sasaki, Kaoru Kinoshita, Yuki Ogasawara, Takashi Sugita
Summary: This study found that Citrobacter koseri inhibits the growth of Staphylococcus epidermidis, disrupting the balance between S. epidermidis and Staphylococcus aureus, and exacerbating inflammation in atopic dermatitis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Toshifumi Asano, Philipp Sasse, Takao Nakata
Summary: A Cre recombination-based fluorescent reporter system was developed to monitor cell-cell fusion. The system successfully detected the formation of multinuclear myotubes and placental syncytiotrophoblast. This tool could facilitate the study of cell-to-cell fusion.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Ke Shi, Yunlong Shan, Xiao Sun, Kuida Chen, Qiong Luo, Qiang Xu
Summary: This study found that low expression of TP53INP2 is associated with poor survival in colorectal cancer (CRC) patients. As the malignancy of CRC progresses, TP53INP2 expression gradually decreases. Knockdown of TP53INP2 promotes CRC cell proliferation and tumor growth. Mechanistically, TP53INP2 deficiency decreases phosphorylation of beta-catenin, leading to increased accumulation and enhanced nuclear translocation and transcriptional activity. Additionally, TP53INP2 sequesters TIM50, inhibiting its activation of beta-catenin. In conclusion, downregulation of TP53INP2 promotes CRC progression by activating beta-catenin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Martina Rossi, Fabio Tomaselli, Alejandro Hochkoeppler
Summary: Oligomeric enzymes are known for their higher catalytic rates compared to monomeric enzymes, but the extent of additivity in their activity is still not well understood. This study used tetrameric rabbit lactate dehydrogenase as a model to examine the kinetics of its catalytic action. Surprisingly, when the concentration of the limiting reactant exceeded that of a single subunit, there was a significant slowdown in the enzyme's conformational rearrangements.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Amin Sahraei, Mohammad Javad Shamsoddini, Fakhrossadat Mohammadi, Leila Hassani
Summary: This study explored the inhibitory effects of gallium curcumin, indium curcumin, and vanadyl curcumin on the amyloid fibrillation of hen egg white lysozyme, as well as the binding interactions of these metal complexes with the enzyme. The results showed that indium curcumin and vanadyl curcumin exhibited higher binding affinities and stronger inhibitory effects on amyloid fibrillation compared to gallium curcumin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Takahiro Sasaki, Yoshiki Kuse, Shinsuke Nakamura, Masamitsu Shimazawa
Summary: PGRN deficiency plays a significant role in cardiac remodeling and arrhythmias post-myocardial infarction (MI), potentially by promoting metabolic abnormalities in macrophages.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Hongwei Zhao, Yiqiang Li, Yibo Zhang, Chi Zhang
Summary: Electrical brain stimulation technology is commonly used to treat brain neurological disorders, but it can cause side effects. This study investigated the impact of electric fields on nerve fibers and revealed the possible origin of side effects. The findings provide guidance for selecting electrical parameters in clinical stimulation therapy.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Julia S. Scott, Lake-Ee Quek, Andrew J. Hoy, Johannes V. Swinnen, Zeyad D. Nassar, Lisa M. Butler
Summary: The fatty acid elongation enzyme ELOVL5 plays a critical role in promoting metastasis in prostate cancer. Knocking down ELOVL5 leads to the accumulation of malonyl-CoA, which inhibits fatty acid oxidation in mitochondria. This study highlights the importance of fatty acid elongation in regulating cell viability and provides a potential target for prostate cancer treatment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Zan Zhou, Wen-jun Jiang, Li Li, Jun-qiang Si
Summary: This study investigates the effect of noise exposure on cognitive function in mice and explores the underlying molecular mechanisms. The findings suggest that noise exposure leads to increased inflammation, increased phosphorylation of Tau protein, and decreased levels of postsynaptic density protein, resulting in cognitive impairment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)