Article
Biochemistry & Molecular Biology
Max A. B. Haase, Guojon Olafsson, Rachel L. Flores, Emmanuel Boakye-Ansah, Alex Zelter, Miles Sasha Dickinson, Luciana Lazar-Stefanita, David M. Truong, Charles L. Asbury, Trisha N. Davis, Jef D. Boeke
Summary: Forcing budding yeast to use human histones to chromatinize their DNA comes with a sudden fitness cost. Previous research suggested chromosomal aneuploidy and missense mutations as two potential adaptation modes to histone humanization. However, we found that aneuploidy in histone-humanized yeasts is specific to certain chromosomes with defined centromeric evolutionary origins, but these aneuploidies are not adaptive. Instead, a set of missense mutations in outer kinetochore proteins are driving the adaptation to human histones.
Article
Biochemistry & Molecular Biology
Rohan Dandage, Caroline M. Berger, Isabelle Gagnon-Arsenault, Kyung-Mee Moon, Richard Greg Stacey, Leonard J. Foster, Christian R. Landry
Summary: The study investigated protein-protein interactions in hybrids between yeast species, finding that most interactions are similar to those of the parents but with some altered instances. It suggests that the occurrence of chimeric protein complexes is frequent, potentially due to incompatibilities or imbalances between parental proteomes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Gisela Cairo, Anne MacKenzie, Dai Tsuchiya, Soni Lacefield
Summary: Time-lapse fluorescence microscopy has provided valuable insights into meiotic cell-cycle events. This protocol describes a method to conditionally deplete proteins from the nucleus during specific stages of meiosis, allowing for the monitoring of meiotic events using time-lapse microscopy. The technique was demonstrated by depleting the kinetochore protein Ctf19 and analyzing chromatin masses at the end of meiosis II.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Biotechnology & Applied Microbiology
Hong-Qi Chen, Ming-Ming Zhang, Qi Xing, Pei-Liang Ye, Tomohisa Hasunuma, Akihiko Kondo, Xin-Qing Zhao
Summary: In this study, engineered yeast strains with improved ethanol fermentation in the presence of inhibitors were developed by replacing native promoters with the constitutive PGK1 promoter for genes responsive to zinc sulfate. The engineered yeast strains showed enhanced ethanol production from corncob hydrolysate, with up to 19.5% more ethanol produced using a specific gene promoter replacement. These results provide a basis for further engineering yeast strains to enhance efficiency of lignocellulosic biorefinery.
BIOCHEMICAL ENGINEERING JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Yi-Hua Chen, Neng-Yuan Hu, Ding-Yu Wu, Lin-Lin Bi, Zheng-Yi Luo, Lang Huang, Jian-Lin Wu, Meng-Ling Wang, Jing-Ting Li, Yun-Long Song, Sheng-Rong Zhang, Wei Jie, Xiao-Wen Li, Shi-Zhong Zhang, Jian-Ming Yang, Tian-Ming Gao
Summary: Neuroplasticity in the medial prefrontal cortex is essential for fear extinction, particularly in the sustained plasticity of the parvalbumin neuronal network. The involvement of neuregulin 1-ErbB4 signaling in fear extinction and the dependence of fear extinction regulation by basal medial amygdala-projecting IL neurons on PV network configuration are also identified in this study. These findings reveal local molecular circuit mechanisms underlying mPFC-mediated control of fear extinction and suggest alternative therapeutic approaches for fear disorders.
MOLECULAR PSYCHIATRY
(2022)
Article
Microbiology
D. M. Hollenstein, J. Veis, N. Romanov, G. Gerecova, E. Ogris, M. Hartl, G. Ammerer, W. Reiter
Summary: A protein phosphatase PP2A(Rts1) plays a crucial role in the stress response of Saccharomyces cerevisiae, affecting the phosphorylation status of putative substrate proteins and antagonizing Rck2 signaling, which is regulated by the MAPKAP kinase.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Mark Boltengagen, Anke Samel-Pommerencke, David Fechtig, Ann E. Ehrenhofer-Murray
Summary: The acetylation of H4 lysine 16 in yeast regulates gene silencing by inhibiting the binding of heterochromatin complex SIR to chromatin. The SAS-I complex is a major provider of H4 K16Ac in yeast, and its absence leads to improper gene silencing. Replication disrupts histone marks, with H4 K16Ac appearing immediately and being influenced by transcription levels. Additionally, the acetyltransferases Esa1 and Sas2 redundantly regulate H4 K16Ac levels in yeast cells.
Article
Cell Biology
Stefan Bresson, Vadim Shchepachev, David Tollervey
Summary: The fungal cell wall is a crucial target for antifungal compounds, and the cell wall integrity (CWI) pathway regulates transcriptional responses to cell wall damage. In addition, RNA-binding proteins Mrn1 and Nab6 play a complementary role by stabilizing cell wall-related mRNAs. Lack of Nab6 leads to downregulation of these mRNAs, while CWI signaling and Nab6 work together to maintain appropriate cell wall gene expression during stress. Deletion of MRN1 partially alleviates the growth defects associated with Delta nab6, indicating an opposing function in mRNA destabilization. Our findings highlight the importance of a posttranscriptional pathway in cellular resistance to antifungal compounds.
Article
Biochemistry & Molecular Biology
Zhen Lin, Ping Luo, Dongmin Huang, Yulian Wu, Fangping Li, Huazhong Liu
Summary: The study reveals that exposure to ACR leads to impairment of oxidative-reductive balance, energy metabolism, lipid metabolism, nucleotide metabolism, and ribosome function in yeast cells. In response to acute ACR damage, yeast cells exhibit upregulation of glutathione synthesis, acceleration of protein degradation, and initiation of autophagy flux.
CHEMICO-BIOLOGICAL INTERACTIONS
(2021)
Article
Multidisciplinary Sciences
Yoon-Mo Yang, Katrin Karbstein
Summary: This study reveals that under high Na+, sorbitol, or pH stress, a physiologically relevant ribosome population arises through the dissociation of Rps26 from fully assembled ribosomes, enabling a translational response to these stresses. The chaperone Tsr2 is involved in the release and reincorporation of Rps26, repairing the subunit after the stress subsides.
Article
Biochemistry & Molecular Biology
Fabio Hedayioglu, Emma J. Mead, Patrick B. F. O'Connor, Matas Skiotys, Owen J. Sansom, Giovanna R. Mallucci, Anne E. Willis, Pavel Baranov, C. Mark Smales, Tobias von der Haar
Summary: The study validates two experimental tools for assessing ribosome binding to mRNAs, highlighting the usefulness of polysome profile reconstructions in evaluating dataset quality.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Dang Thi Tuong Vi, Shiori Fujii, Arvin Lapiz Valderrama, Ayaka Ito, Eri Matsuura, Ayaka Nishihata, Kaoru Irie, Yasuyuki Suda, Tomoaki Mizuno, Kenji Irie
Summary: Pbp1, the yeast ortholog of human Ataxin-2, plays a role in yeast cell growth on non-fermentable carbon sources. It regulates the expressions of genes involved in gluconeogenesis and mitochondrial function through multiple mechanisms.
Article
Biotechnology & Applied Microbiology
Qian Zhang, Ning Li, Yunbin Lyv, Shiqin Yu, Jingwen Zhou
Summary: This study demonstrates the use of caveolin to absorb exogenous oils and increase the production of naringenin. The caveolin-mediated oil transport system shows promising potential for low-cost industrial production.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sabrine Hedouin, Glennis A. Logsdon, Jason G. Underwood, Sue Biggins
Summary: This study used a targeted RNA isoform sequencing approach to identify the transcriptional landscape at and surrounding all centromeres in budding yeast. They found that most pericentromeres are transcribed throughout the cell cycle, but centromere accessibility to the transcription machinery is restricted to S-phase, which is controlled by the centromere-binding transcription factor Cbf1. Deletion of Cbf1 leads to an accumulation of cenRNAs at all phases of the cell cycle and increased chromosome mis-segregation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Kum-Kang So, Ngoc My Tieu Le, Ngoc-Luong Nguyen, Dae-Hyuk Kim
Summary: Lowering the expression temperature from 30 degrees C to 20 degrees C can improve the expression and functional assembly of fusion proteins in Saccharomyces cerevisiae, especially for complexly structured and difficult-to-express proteins.
MICROBIAL CELL FACTORIES
(2023)
Article
Multidisciplinary Sciences
Shin Yen Chong, Sam Cutler, Jing-Jer Lin, Cheng-Hung Tsai, Huai-Kuang Tsai, Sue Biggins, Toshio Tsukiyama, Yi-Chen Lo, Cheng-Fu Kao
NATURE COMMUNICATIONS
(2020)
Article
Cell Biology
Midori Ishii, Bungo Akiyoshi
JOURNAL OF CELL SCIENCE
(2020)
Article
Biophysics
Patryk Ludzia, Bungo Akiyoshi, Christina Redfield
BIOMOLECULAR NMR ASSIGNMENTS
(2020)
Article
Biology
Jacob A. Herman, Matthew P. Miller, Sue Biggins
Article
Biochemistry & Molecular Biology
Patryk Ludzia, Edward D. Lowe, Gabriele Marciano, Shabaz Mohammed, Christina Redfield, Bungo Akiyoshi
Summary: The structure and dynamics of the unconventional kinetoplastid kinetochore protein KKT4 were characterized using X-ray crystallography, NMR spectroscopy, and crosslinking mass spectrometry. KKT4 was found to have a microtubule-binding domain and a BRCT domain, which likely interacts with other proteins through phosphorylation.
Article
Biochemistry & Molecular Biology
Eelco C. Tromer, Thomas A. Wemyss, Patryk Ludzia, Ross F. Waller, Bungo Akiyoshi
Summary: This study demonstrates homology between axial element components of the synaptonemal complex and kinetoplastid kinetochore proteins, suggesting that the kinetoplastid kinetochore system evolved by repurposing meiotic components of chromosome synapsis. The identification of divergent orthologues in various eukaryotic supergroups provides insights into the evolutionary origin and history of these kinetochores, shedding light on the potential for new functional complexes to arise within this ancient eukaryotic gene family.
Article
Cell Biology
Gabriele Marciano, Midori Ishii, Olga O. Nerusheva, Bungo Akiyoshi
Summary: The study characterizes the KKT2 and KKT3 proteins in the kinetoplastid parasite Trypanosoma brucei, showing that they are important for the localization of various kinetochore proteins, with their central domains playing a critical role. Crystal structures of the KKT2 central domain reveal a unique zinc-binding domain that promotes its kinetochore localization, while mutations in the equivalent domain in KKT3 abolish its function. This work demonstrates the importance of the unique central domains in mediating the centromere localization of KKT2 and KKT3.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Cell Biology
Midori Ishii, Bungo Akiyoshi
Summary: This article discusses recent progress in understanding centromeres and kinetochores in non-traditional model eukaryotes. It specifically focuses on select lineages that lack CENP-A and highlights some organisms that might have hitherto unknown types of kinetochore proteins.
CURRENT OPINION IN CELL BIOLOGY
(2022)
Article
Cell Biology
Krishna K. Sarangapani, Lori B. Koch, Christian R. Nelson, Charles L. Asbury, Sue Biggins
Summary: Sarangapani, Koch, Nelson et al. demonstrate that phosphorylation by the evolutionarily conserved Mps1 kinase weakens kinetochore-microtubule attachments, aiding in mitotic error correction and ensuring accurate chromosome segregation.
JOURNAL OF CELL BIOLOGY
(2021)
Editorial Material
Microbiology
Patryk Ludzia, Bungo Akiyoshi
Summary: Recent advances in understanding the spatial integration of transcription and splicing sites have shed light on the mechanism that ensures monogenic antigen expression in trypanosomes.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sabrine Hedouin, Glennis A. Logsdon, Jason G. Underwood, Sue Biggins
Summary: This study used a targeted RNA isoform sequencing approach to identify the transcriptional landscape at and surrounding all centromeres in budding yeast. They found that most pericentromeres are transcribed throughout the cell cycle, but centromere accessibility to the transcription machinery is restricted to S-phase, which is controlled by the centromere-binding transcription factor Cbf1. Deletion of Cbf1 leads to an accumulation of cenRNAs at all phases of the cell cycle and increased chromosome mis-segregation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Anna K. de Regt, Cordell J. Clark, Charles L. Asbury, Sue Biggins
Summary: Tension plays a crucial role in stabilizing kinetochore-microtubule attachments and suppressing the destabilization activity of Aurora B kinase, ensuring accurate chromosome segregation.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Lara Lopez-Escobar, Benjamin Hanisch, Clare Halliday, Midori Ishii, Bungo Akiyoshi, Samuel Dean, Jack Daniel Sunter, Richard John Wheeler, Keith Gull
Summary: ESB1, a specific protein found in the expression site body (ESB) of Trypanosoma brucei, is crucial for the activation of monoallelic VSG gene transcription and antigenic variation. It associates with DNA near the active VSG promoter and recruits RNA polymerase I, indicating its role as a transcription regulator.
NATURE MICROBIOLOGY
(2022)
Article
Cell Biology
Midori Ishii, Patryk Ludzia, Gabriele Marciano, William Allen, Olga O. Nerusheva, Bungo Akiyoshi
Summary: The kinetoplastid parasite Trypanosoma brucei has unique kinetochore proteins, KKT2 and KKT3, which play important roles in chromosome segregation. KKT2's kinase activity is essential for accurate chromosome segregation, while KKT3's kinase activity is dispensable for cell growth. The divergent polo boxes of KKT2 and KKT3 initiate kinetochore assembly and interact with other kinetochore proteins.
MOLECULAR BIOLOGY OF THE CELL
(2022)
Article
Biochemistry & Molecular Biology
Andrew R. Popchock, Joshua D. Larson, Julien Dubrulle, Charles L. Asbury, Sue Biggins
Summary: Eukaryotic chromosome segregation requires a large machine called the kinetochore, which contains CENP-A and is responsible for nucleosome formation. This study investigates the functions of the chaperone protein HJURP in CENP-A deposition and the conservation of high AT DNA content at centromeres. Through a microscopy assay, it is found that CENP-A can arrive at centromeres without HJURP but stable incorporation requires HJURP and other DNA-binding proteins. Homopolymer AT runs in yeast centromeres are also essential for efficient CENP-A deposition. These findings provide insights into nucleosome formation and lay the foundation for future studies on kinetochore complexes.
