Article
Biotechnology & Applied Microbiology
Ziyue Qin, Wencan Wang, Malik Ahsan Ali, Yihan Wang, Yan Zhang, Ming Zhang, Guangbin Zhou, Jian-Dong Yang, Changjun Zeng
Summary: This study revealed the dynamic m(6)A modification of mRNAs in boar sperm during cryopreservation, which may affect mRNA expression and are closely related to sperm motility, apoptosis, and metabolism.
Article
Multidisciplinary Sciences
Lara Bideyan, Wenxin Fan, Karolina Elibieta Kaczor-Urbanowicz, Christina Priest, David Casero, Peter Tontonoz
Summary: Liver X receptors play crucial roles in hepatic metabolism, affecting genes involved in fatty acid metabolism and broad sets of hepatic transcription factors. Loss of LXR binding in liver can lead to increased expression of certain genes and decreased expression of others.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Denise Brigitte Herbert, Thomas Gross, Oliver Rupp, Annette Becker
Summary: The global transcriptional response to mowing of red clover was characterized by comparing plants grown under greenhouse conditions with those growing on agriculturally used fields. Unexpectedly, it was found that biotic and abiotic stress related changes overlay the regrowth related transcriptional changes in field grown plants, and gibberellins were shown to play a role in the developmental program related to regrowth after mowing. This study provides insights into the physiological and developmental processes of mowing on red clover, potentially leading to yield improvement.
Article
Immunology
Xingzhu Geng, Xiaolin Wu, Qianting Yang, Henan Xin, Bin Zhang, Dakuan Wang, Liguo Liu, Song Liu, Qi Chen, Zisen Liu, Mingxia Zhang, Shouguo Pan, Xiaobing Zhang, Lei Gao, Qi Jin
Summary: Neutrophils have been recognized to play an important role in the pathogenesis of tuberculosis. In this study, global RNA-seq analysis of neutrophils from active tuberculosis patients, latent tuberculosis infections, and healthy controls revealed greater perturbations of gene expression patterns in neutrophils from active tuberculosis individuals. Functional enrichment analysis showed the activation of multiple pattern recognition receptor pathways in active tuberculosis. Additionally, genes related to endocytosis, secretory granules, and neutrophils degranulation were downregulated. The study also highlighted the potential inhibition of the NF-kappa B signaling pathway in active tuberculosis patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Wei Guo, Bolun Zhou, Fenglong Bie, Qilin Huai, Xuemin Xue, Lei Guo, Fengwei Tan, Qi Xue, Liang Zhao, Shugeng Gao
Summary: This study aims to comprehensively reveal the cellular characteristics and inter-cellular connections of MPLC. scRNA-seq was performed from 23 samples of six MPLC patients, combined with bulk whole-exome sequencing. Trajectory analysis was performed to investigate the transition of different cell types during the development of MPLC.
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
Article
Agriculture, Multidisciplinary
Yuanyuan Xu, Guochun Zhao, Xiangqin Ji, Jiming Liu, Tianyun Zhao, Yuan Gao, Shilun Gao, Yingying Hao, Yuhan Gao, Lixian Wang, Xuehuang Weng, Zhong Chen, Liming Jia
Summary: This study reveals the dynamic saponin accumulation and gene regulatory network of saponin biosynthesis in soapberry pericarps through combined metabolite profiling and transcriptome analysis. Key candidate genes and transcription factors (TFs) are identified, and their involvement in saponin biosynthesis is investigated. The results suggest that genes such as SmbHLH2, SmTCP4, and SmWRKY27 may play important roles in triterpenoid saponin biosynthesis by directly regulating the transcription of SmCYP71D-3 in soapberry pericarps.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Plant Sciences
Ruolin Hu, Jiali Wang, Huiqing Yang, Dayong Wei, Qinglin Tang, Yang Yang, Shibing Tian, Zhimin Wang
Summary: Male sterility is an attractive trait in plants as it prevents self-fertilization and aids in the production of high-quality hybrid seeds. This study focused on understanding the mechanism of anther development in eggplant. The researchers identified a transcription factor gene called SmMYB108 that plays a role in anther dehiscence. Overexpression of SmMYB108 in tobacco resulted in anther dehiscence. They also discovered that SmMYB108 functions as a transcriptional activator through its C-terminal activation region. Additionally, they found that genes related to anther development target the promoter of SmMYB108. These findings provide insights into the molecular mechanisms involved in regulating anther development.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Cell Biology
Matthew A. Reyer, Shriram Chennakesavalu, Emily M. Heideman, Xiangqian Ma, Magda Bujnowska, Lu Hong, Aaron R. Dinner, Carin K. Vanderpool, Jingyi Fei
Summary: Small RNAs (sRNAs) are important gene regulators in bacteria, acting post-transcriptionally by affecting translation and degradation of target mRNAs. Some sRNAs can regulate targets co-transcriptionally early in an mRNA's lifetime, potentially mediated by Rho-dependent termination. Data also reveals that certain kinetic steps and sRNA binding to target mRNA may dictate the regulation hierarchy within sRNA regulons.
Article
Biology
Tianliu Zhang, Tianzhen Wang, Qunhao Niu, Lei Xu, Yan Chen, Xue Gao, Huijiang Gao, Lupei Zhang, George E. Liu, Junya Li, Lingyang Xu
Summary: In this study, a high-resolution transcriptome atlas of beef cattle was generated through a large-scale gene expression analysis. Housekeeping genes, tissue-specific genes, and hub genes were identified, revealing their roles in cellular biology, tissue differentiation, and physiological processes. The conservation of these genes' expression patterns in bovine tissues was also observed. Furthermore, differentially expressed genes between beef and dairy cattle were identified, providing insights into the regulatory differences underlying economically important traits in bovine tissues.
Article
Multidisciplinary Sciences
Lirong Wang, Meng Du, Bo Wang, Huirong Duan, Benyin Zhang, Dong Wang, Yi Li, Jiuli Wang
Summary: Nitraria tangutorum exhibits excellent salt tolerance through complex regulatory mechanisms modulated by multiple genes, including catabolism of organic compounds, antioxidant defense, signaling pathways regulation, ion homeostasis maintenance, and cell expansion.
SCIENTIFIC REPORTS
(2022)
Article
Fisheries
Qian Liu, Fangshu Li, Wenjuan Liu, Baoyu Huang, Lingling Li, Xiaona Wang, Xiuxiu Sang, Juan Dong, Jilv Ma, Jiwen Chen, Lei Wei, Yaqiong Liu, Meiwei Zhang, Yijing Han, Xiaotong Wang
Summary: The study focused on the impact of NP on the immune system of marine mollusks, exploring its immunomodulatory capacity by analyzing the changes in immune-related genes and antioxidant enzyme activities. Results showed significant alterations in gene expression and antioxidant enzyme activities, indicating the influence of NP on the immune system of scallops.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Environmental Sciences
Umar Farouk Mustapha, You-Xing Peng, Yuan-Qing Huang, Daniel Assan, Fei Zhi, Gang Shi, Yang Huang, Guang-Li Li, Dong-Neng Jiang
Summary: This study presents the first report on the transcriptome analysis of gonads in differentiating spotted scat, revealing potential genes related to reproduction and gonadal development. The study provides insights into the expression patterns of sex and gonadal-related genes in differentiating gonads of this species.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Madhu Sudhana Saddala, Xu Yang, Shibo Tang, Hu Huang
Summary: This study identified the core set of sensome and pro-inflammatory genes and their regulators in retinal microglial cells using transcriptome and data mining approaches. The transcriptional regulators identified may play crucial roles in regulating the sensome and inflammatory genes of RMCs and contribute to the pathogenesis of retinal neurodegenerative diseases.
Article
Horticulture
Qun Liu, Zhiqing Wu, Bing Han, Can Wang, Xin Cui, Biao Wang, Chengyuan Liang
Summary: This study provides new insights into the regulatory mechanisms by which exogenous ABA hormones increase the biosynthesis of chicoric acid via TmbZIP1-Tm4CL1 modular regulation in Taraxacum mongolicum.
SCIENTIA HORTICULTURAE
(2023)
Article
Plant Sciences
Alejandro Aragon-Raygoza, Luis Herrera-Estrella, Alfredo Cruz-Ramirez
Summary: Gene expression analysis in Ceratopteris richardii revealed enriched functional categories related to histogenesis and cell division in the root tip transcriptional program, and conserved expression in the root meristem. However, divergence was observed in genes involved in root cap development.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Parasitology
Esteban Erben, Kevin Leiss, Bin Liu, Diana Inchaustegui Gil, Claudia Helbig, Christine Clayton
Summary: Trypanosoma brucei relies heavily on mRNA-binding proteins to control mRNA fate due to the lack of individual promoters for its protein-coding genes. Specific RNA-binding proteins like ZC3H22, RBP9, and DRBD7 play crucial roles in regulating gene expression and cell growth in different life stages of the parasite. Proteins that prefer long mRNAs may have short or degenerate binding sites, and binding preferences for certain nucleotides can affect untranslated regions.
Article
Biology
Larissa Melo do Nascimento, Franziska Egler, Katharina Arnold, Nina Papavasiliou, Christine Clayton, Esteban Erben
Summary: The study identified CFB2 as a crucial protein for stabilizing VSG mRNA, described cis acting elements within the VSG 3'-untranslated region that regulate the interaction, identified trans-acting factors present in the VSG messenger ribonucleoprotein particle, and mechanistically explained how CFB2 stabilizes the mRNA of this key pathogenicity factor. The approach used in this study has the potential to provide detailed biological insight into the metabolism of relatively abundant mRNAs in any eukaryote.
Article
Infectious Diseases
Julius Mulindwa, Geofrey Ssentamu, Enock Matovu, Kevin Kamanyi Marucha, Francisco Aresta-Branco, Claudia Helbig, Christine Clayton
Summary: Most researchers studying protist parasites use a limited number of laboratory-adapted isolates obtained decades ago, with little study on the effects of laboratory passages and in vitro culture adaptation. This study introduces two new strains of Trypanosoma brucei brucei, MAK65 and MAK98, showing changes in gene copy numbers during adaptation to culture. Trisomy and increased chromosome segments were observed in established cultured lines, providing useful strains for research on trypanosome differentiation and pathogenicity.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Parasitology
Tania Bishola, Christine Clayton
Summary: In Trypanosoma brucei, ZC3H28 protein plays a vital role in stabilizing specific mRNAs and increasing protein levels. Mass spectrometry revealed that ZC3H28 is associated with ribosomal proteins, various RNA-binding proteins, and is involved in regulating long and poorly translated mRNAs.
Article
Multidisciplinary Sciences
Franziska Falk, Kevin Kamanyi Marucha, Christine Clayton
Summary: Transcription in Trypanosoma brucei is mainly constitutive and polycistronic, relying on post-transcriptional mechanisms for gene expression control. EIF4E1 and 4EIP play crucial roles in regulating gene expression and parasite morphology transitions, while the relationship between TUT3 and 4EIP function remains unclear.
Article
Infectious Diseases
Tania Bishola Tshitenge, Lena Reichert, Bin Liu, Christine Clayton
Summary: This study demonstrates the developmental regulation of RBP10 and PGKC proteins in Trypanosoma brucei, which is essential for the parasite's growth and survival. The researchers identified six regulatory regions in the 3'-untranslated region of RBP10 mRNA and two independent regions in the 3'-untranslated region of PGKC mRNA that are responsible for developmental regulation. Despite the absence of obvious sequence similarities in these regulatory regions, trypanosome mRNAs have multiple regulatory sequences, potentially acting as a fail-safe mechanism to ensure correct regulation.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Biochemistry & Molecular Biology
Corinna Benz, Nora Muller, Sabine Kaltenbrunner, Hana Vachova, Marie Vancova, Julius Lukes, Vladimir Varga, Hassan Hashimi
Summary: In this study, a characterization of an orphaned X2 kinesin in Trypanosoma brucei was conducted. It was found that this kinesin interacts tightly with a likely inactive motor-like protein, TbPH1, and localizes to a poorly understood cytoskeletal structure called the microtubule quartet (MtQ). Another X2 kinesin, TbKifX2C, was also found to associate with the MtQ. Simultaneous ablation of TbKifX2A and TbPH1 resulted in morphological defects and an expansion of the flagellar pocket. This study provides insights into the co-evolution of the X2 kinesin family and the MtQ in trypanosomatids.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tania Bishola Tshitenge, Christine Clayton
Summary: The RNA-binding protein DRBD18 in Trypanosoma brucei is involved in the export and processing of mRNA through binding to polypyrimidine tract motifs in the 3'-untranslated regions of mRNA precursors.
Article
Biology
Bin Liu, Christine Clayton
Summary: The study found that T. brucei RBP10 targets specific mRNAs for destruction and may be related to the UA(U)(6) motif. In vitro binding experiments showed that RBP10 does not distinguish between UA(U)(6) and UACUCUCU motifs.
BMC RESEARCH NOTES
(2022)
Article
Biochemistry & Molecular Biology
Franziska Falk, Rafael Melo Palhares, Albina Waithaka, Christine Clayton
Summary: In this study, the functions of different versions of the cap-binding translation initiation factor EIF4E in Trypanosoma brucei were investigated. It was found that EIF4E2 is associated with the RNA-binding protein SLBP2 in bloodstream forms, while EIF4E5 has no impact on growth and differentiation. Additionally, EIF4E2 is strongly associated with a subset of mRNAs that are maximally abundant in the S-phase, with their abundances decreased in EIF4E2 knock-out cells.
MOLECULAR MICROBIOLOGY
(2022)
Article
Infectious Diseases
Albina Waithaka, Olena Maiakovska, Dirk Grimm, Larissa Melo do Nascimento, Christine Clayton
Summary: This study describes a trans splicing reporter system that can be used for studying and screening the roles of sequences and proteins in mRNA processing. The results suggest that splice factor and SR-domain proteins may play key roles in splice site definition.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Biology
Matus Valach, Sandrine Moreira, Celine Petitjean, Corinna Benz, Anzhelika Butenko, Olga Flegontova, Anna Nenarokova, Galina Prokopchuk, Tom Batstone, Pascal Lapebie, Lionnel Lemogo, Matt Sarrasin, Paul Stretenowich, Pragya Tripathi, Euki Yazaki, Takeshi Nara, Bernard Henrissat, B. Franz Lang, Michael W. Gray, Tom A. Williams, Julius Lukes, Gertraud Burger
Summary: This study presents the first nuclear genome sequence from a diplonemid, revealing its genome size and structure. The analysis shows that the metabolic capacity of diplonemids underwent significant expansion, potentially through horizontal gene transfer. Furthermore, the study finds that diplonemids have predatory capabilities, playing an important role in degrading cell walls of various organisms as an energy source.
Article
Biochemistry & Molecular Biology
Matus Valach, Corinna Benz, Lisbeth C. Aguilar, Ondrej Gahura, Drahomira Faktorova, Alena Zikova, Marlene Oeffinger, Gertraud Burger, Michael W. Gray, Julius Lukes
Summary: The mitoribosome in diplonemids, the sister-group of kinetoplastids, is even more complex than previously thought. It has a mass of >5 MDa, contains as many as 130 integral proteins, and exhibits a high protein-to-RNA ratio of 11:1. This unusual composition reflects significant structural reduction of ribosomal RNAs, increased size of canonical mitoribosomal proteins, and presence of lineage-specific components, shedding light on the early assembly stages of mitoribosomes and the impact of evolutionary divergence.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Drahomira Faktorova, Kristina Zahonova, Corinna Benz, Joel B. Dacks, Mark C. Field, Julius Lukes
Summary: Sec13 plays multiple roles in different cellular processes as a component of COPII endoplasmic reticulum export vesicle coat, nuclear pore complex (NPC), and Seh1-associated (SEA)/GATOR nutrient-sensing complex. Euglenozoa possesses two Sec13 paralogues, with Sec13a interacting with COPII and NPC, and Sec13b interacting with Sec16 and SEA/GATOR complex. This suggests a distinct organization of coatomer complexes in euglenozoan flagellates.
Article
Biochemistry & Molecular Biology
Marion Wargnies, Nicolas Plazolles, Robin Schenk, Oriana Villafraz, Jean-William Dupuy, Marc Biran, Sabine Bachmaier, Helene Baudouin, Christine Clayton, Michael Boshart, Frederic Bringaud
Summary: Trypanosomatids rearrange their genome using repeated sequences, impacting gene dosage and selecting adaptive traits to environmental pressure. In a specific example with PEPCK gene knockout, a rearrangement between two FRD genes produced a nonfunctional chimeric gene. This rearrangement led to growth impairment, suggesting a role for FRD in production of ROS.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)