Article
Biochemistry & Molecular Biology
Andrey A. Shtyrov, Dmitrii M. Nikolaev, Vladimir N. Mironov, Andrey V. Vasin, Maxim S. Panov, Yuri S. Tveryanovich, Mikhail N. Ryazantsev
Summary: This study introduces simple models to estimate the direct effect of charged or polar residue substitutions in proteins from the rhodopsin family, without the need for extensive calculations. The models are based on absorption maximum values calculated at a theoretical level for the retinal chromophore in an external electrostatic field. The proposed approach was evaluated against various mutants and can be useful for interpreting experimental data and designing proteins with desired spectral properties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Ecology
Alexander L. Jaffe, Masae Konno, Yuma Kawasaki, Chihiro Kataoka, Oded Beja, Hideki Kandori, Keiichi Inoue, Jillian F. Banfield
Summary: This study found that Saccharibacteria Type-1 rhodopsins function as outward proton pumps and can rapidly uptake the chromophore retinal. The co-occurring microorganisms with Saccharibacteria showed evidence of the ability to produce retinal from beta-carotene, suggesting a potential association between them.
Correction
Chemistry, Multidisciplinary
Keiichi Kojima, Yuki Sudo
Summary: In this correction, the authors provide detailed information on the correction for the paper 'Convergent evolution of animal and microbial rhodopsins' published in RSC Adv. by Kojima et al., 2023, 13, 5367-5381,https://doi.org/10.1039/D2RA07073A.
Article
Chemistry, Physical
Tomotsumi Fujisawa, Kouhei Nishikawa, Jun Tamogami, Masashi Unno
Summary: ROA spectroscopy was used to study the conformation of the retinal Schiff base chromophore in green-light-absorbing proteorhodopsin, revealing that the chromophore structure potentially couples with proton pumping through the motion of the sixth helix. This unique spectral feature was not explained by the twisted structure of the retinal Schiff base but was reproduced by a structural model with a bent polyene chain on the beta-ionone ring side.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Editorial Material
Biochemistry & Molecular Biology
Jeffrey M. Friedman
Summary: This year's Lasker Award is awarded to Dieter Oesterhelt, Peter Hegemann, and Karl Deisseroth for their discovery of microbial opsins as light-activated ion conductors and the development of optogenetics using these proteins to regulate neural activity in awake, behaving animals. Optogenetics has revolutionized neuroscience and transformed our understanding of brain function.
Review
Biochemistry & Molecular Biology
Matthias Broser
Summary: The recently discovered Rhodopsin-cyclases from Chytridiomycota fungi exhibit unexpected properties, functioning exclusively as heterodimers with distinct retinal chromophores. The bimodal photoswitchable Neorhodopsin is particularly noteworthy for its near-infrared absorption and high fluorescence, which have not been observed in other retinal photoreceptors. This article discusses these properties in the context of retinal chromophore color-tuning approaches and provides a brief review of heterodimerization, shedding light on the development of optogenetic tools.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Microbiology
Andrey Rozenberg, Keiichi Inoue, Hideki Kandori, Oded Beja
Summary: Microbial rhodopsins are a diverse group of photoreceptive proteins that are present in all domains of cellular life and even encoded in viral genomes. They are classified into two families: type 1 rhodopsins and heliorhodopsins, both having seven transmembrane helices with similar structures but opposite membrane orientation. These rhodopsins are involved in a variety of light-driven energy and sensory transduction processes.
ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021
(2021)
Article
Biochemistry & Molecular Biology
Naoya Morimoto, Takashi Nagata, Keiichi Inoue
Summary: This study revealed that human and chicken RGRs form blue-absorbing pigments similar to bovine RGR, and they are bistable rhodopsins displaying a reversible photoreaction. These findings provide insight into the behavior of RGR as a retinal photoisomerase and aid in understanding its role in the visual system.
Article
Multidisciplinary Sciences
Marvin Seifert, Paul A. Roberts, George Kafetzis, Daniel Osorio, Tom Baden
Summary: Birds have a different retinal functional organization compared to mammals, where they are able to multiplex spectral and temporal information.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Masahiro Sugiura, Kazuki Ishikawa, Kota Katayama, Yuji Sumii, Rei Abe-Yoshizumi, Satoshi P. Tsunoda, Yuji Furutani, Norio Shibata, Leonid S. Brown, Hideki Kandori
Summary: This study reports on a novel photochemistry mediated by a microbial rhodopsin, which selectively transforms the all-trans form to the 7-cis form. The reaction occurs in the dark with the all-trans form, but isomerizes into the 7-cis form upon illumination, accompanied by changes in protein structure and protonation.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Microbiology
Gareth S. Kindler, Hon Lun Wong, Anthony W. D. Larkum, Michael Johnson, Fraser MacLeod, Brendan P. Burns
Summary: This study provides the first description of the community composition and functional potential of microbial mats found in the gypsum-rich and hypersaline region of Blue Holes, Shark Bay. The dominant groups were found to be Proteobacteria, Bacteroidetes/Chlorobi, and Planctomycetes, with a diverse community of potentially novel microorganisms also present. The study identified important microbial interactions and functional pathways in these mats.
FEMS MICROBIOLOGY ECOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Xiao Min Zhang, Tatsushi Yokoyama, Masayuki Sakamoto
Summary: Membrane potential, a critical parameter reflecting neuron excitability, is traditionally measured invasively by electrodes, but new fluorescent probe technologies offer high spatiotemporal resolution for individual cell activity. Genetically encoded voltage indicators show superior performance in accurately targeting genetic populations and revealing neuronal dynamics. Microbial rhodopsins, commonly used in optogenetics to manipulate neuronal activities, can also serve as fluorescent voltage indicators, with recent advances in their design and application summarized in this review.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Chemistry, Multidisciplinary
Saumik Sen, Rajiv K. Kar, Veniamin A. Borin, Igor Schapiro
Summary: The photoisomerization of retinal is a crucial primary event in the rhodopsin protein family, highly optimized in the protein for ultrafast, selective, and efficient reactions. Space saving mechanisms based on the rotation of multiple double bonds have been proposed to elucidate the highly complex process inside the protein.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Biology
Shoun Taguchi, Satomi Niwa, Hoang-Anh Dao, Yoshihiro Tanaka, Ryota Takeda, Shuya Fukai, Kazuya Hasegawa, Kazuki Takeda
Summary: Crystal structures and quantum mechanical calculations are used to investigate the interaction and conformation of the retinal chromophore in the K intermediate of bacteriorhodopsin. The results provide insights into light-driven proton pumping in bacteriorhodopsin. The accurate X-ray crystallographic analysis reveals an S-shaped conformation of the polyene chain of 13-cis retinal in the K structure.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Andras J. Toth, Anna Dunay, Marton Battay, Csaba Balint Illes, Andras Bittsanszky, Miklos Suth
Summary: The popularity of plant-based meat analogues is on the rise, but attention needs to be paid to their food safety risk compared to traditional meat products.
APPLIED SCIENCES-BASEL
(2021)
Article
Genetics & Heredity
Aida Bertoli-Avella, Ronja Hotakainen, Maryam Al Shehhi, Alice Urzi, Catarina Pareira, Anett Marais, Khoula Al Shidhani, Sumaya Aloraimi, Galina Morales-Torres, Steffen Fisher, Laura Demuth, Laila Abdel Moteleb Selim, Nihal Al Menabawy, Maryam Busehail, Mohammed AlShaikh, Naser Gilani, Dler Nooruldeen Chalabi, Nasser S. Alharbi, Majid Alfadhel, Mohammed Abdelrahman, Hanka Venselaar, Nadeem Anjum, Anjum Saeed, Malak Ali Alghamdi, Hamad Aljaedi, Hisham Arabi, Vasiliki Karageorgou, Suliman Khan, Zahra Hajjari, Mandy Radefeldt, Ruslan Al-Ali, Kornelia Tripolszki, Amer Jamhawi, Omid Paknia, Claudia Cozma, Huma Cheema, Najim Ameziane, Saleh Al-Muhsen, Peter Bauer
Summary: A previously unrecognized autosomal recessive disorder caused by AGR2 variants was identified, with implications for the molecular diagnosis and management of these patients. Loss of function in AGR2 likely leads to impairment of the mucociliary defense machinery, with potential drug targets needing to be identified through further studies.
JOURNAL OF MEDICAL GENETICS
(2022)
Article
Genetics & Heredity
Jet van der Spek, Joery den Hoed, Lot Snijders Blok, Alexander J. M. Dingemans, Dick Schijven, Christoffer Nellaker, Hanka Venselaar, Galuh D. N. Astuti, Tahsin Stefan Barakat, E. Martina Bebin, Stefanie Beck-Wodl, Gea Beunders, Natasha J. Brown, Theresa Brunet, Han G. Brunner, Philippe M. Campeau, Goran Cuturilo, Christian Gilissen, Tobias B. Haack, Irina Huning, Ralf A. Husain, Benjamin Kamien, Sze Chern Lim, Luca Lovrecic, Janine Magg, Ales Maver, Valancy Miranda, Danielle C. Monteil, Charlotte W. Ockeloen, Lynn S. Pais, Vasilica Plaiasu, Laura Raiti, Christopher Richmond, Angelika Riess, Eva M. C. Schwaibold, Marleen E. H. Simon, Stephanie Spranger, Tiong Yang Tan, Michelle L. Thompson, Bert B. A. de Vries, Ella J. Wilkins, Marjolein H. Willemsen, Clyde Francks, Lisenka E. L. M. Vissers, Simon E. Fisher, Tjitske Kleefstra
Summary: Common diagnostic next-generation sequencing strategies are not optimized to identify inherited variants in genes associated with dominant neurodevelopmental disorders. This study characterized 21 families with inherited CHD3 variants and found overlap in phenotype with de novo CHD3 variants. The study suggests a significant role of inherited variation in Snijders Blok-Campeau syndrome and highlights the need for further investigation.
GENETICS IN MEDICINE
(2022)
Article
Genetics & Heredity
Janine Reurink, Erik de Vrieze, Catherina H. Z. Li, Emma van Berkel, Sanne Broekman, Marco Aben, Theo Peters, Jaap Oostrik, Kornelia Neveling, Hanka Venselaar, Mariana Guimaraes Ramos, Christian Gilissen, Galuh D. N. Astuti, Jordi Corominas Galbany, Janneke J. C. van Lith-Verhoeven, Charlotte W. Ockeloen, Lonneke Haer-Wigman, Carel B. Hoyng, Frans P. M. Cremers, Hannie Kremer, Susanne Roosing, Erwin van Wijk
Summary: The pathogenicity of the USH2A c.2276 G > T variant as a common cause of autosomal recessive retinitis pigmentosa was confirmed through genetic and functional analyses. A zebrafish model was generated to validate the findings. This study has significant implications for genetic diagnosis and future treatment options for this disease.
NPJ GENOMIC MEDICINE
(2022)
Article
Genetics & Heredity
Laurens Wiel, Juliet E. Hampstead, Hanka Venselaar, Lisenka E. L. M. Vissers, Han G. Brunner, Rolph Pfundt, Gerrit Vriend, Joris A. Veltman, Christian Gilissen
Summary: We developed Meta-Domain HotSpot (MDHS) to identify mutation hotspots in protein domains and found three significantly enriched missense DNM hotspots in the ion transport protein domain family. These hotspots are associated with neurodevelopmental disorders and affect multiple genes.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Review
Biochemistry & Molecular Biology
Maarten van der Sande, Siebren Frolich, Simon J. van Heeringen
Summary: Gene regulatory networks (GRNs) are useful abstractions for understanding transcriptional dynamics in developmental systems. Computational prediction of GRNs has been applied to gene expression measurements, but these inferred networks are inaccurate and based on correlative interactions. This review highlights three approaches that significantly impact GRN inference: multi-omics, single cell sequencing, and neural networks. These developments have the potential to improve the quality of inferred GRNs.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Article
Genetics & Heredity
Linda A. J. Hendricks, Nicoline Hoogerbrugge, Hanka Venselaar, Stefan Aretz, Isabel Spier, Eric Legius, Hilde Brems, Robin de Putter, Kathleen B. M. Claes, Gareth Evans, Emma R. Woodward, Maurizio Genuardi, Fulvia Brugnoletti, Yvette van Ierland, Kim Dijke, Emma Tham, Bianca Tesi, Janneke H. M. Schuurs-Hoeijmakers, Maud Branchaud, Hector Salvador, Arne Jahn, Simon Schnaiter, Violetta Christophidou Anastasiadou, Joan Brunet, Carla Oliveira, Laura Roht, Ana Blatnik, Arvids Irmejs, Arjen R. Mensenkamp, Janet R. Vos
Summary: This study investigates the genotype and phenotype spectrum of PHTS in a large cohort, revealing a correlation between pathogenic PTEN variants and the phenotypic diversity of PHTS. Early-onset patients are often associated with missense variants, while late-onset patients are often associated with truncating variants. Additionally, different phenotypic characteristics are related to the type and domain of PTEN variants.
EUROPEAN JOURNAL OF MEDICAL GENETICS
(2022)
Article
Chemistry, Physical
Vesna Eric, Xinmeng Li, Lolita Dsouza, Sean K. Frehan, Annemarie Huijser, Alfred R. . Holzwarth, Francesco Buda, G. J. Agur Sevink, Huub J. M. de Groot, Thomas L. C. Jansen
Summary: In this study, the microscopic sources of disorder causing spectral width in chlorosomes are identified. It is found that hydrogen bonding motifs are essential for an accurate description of the spectral line shape and that exciton delocalization is consistent with the two-dimensional electronic spectra.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Multidisciplinary Sciences
Muhamed N. Hashem Eeza, Rico Singer, Yi Ding, Junling He, Zain Zuberi, Hans J. Baelde, Huub J. M. de Groot, Joerg Matysik, Herman P. Spaink, A. Alia
Summary: This study used non-invasive magnetic resonance imaging techniques to reveal significant fat infiltration and microstructural changes in the muscles of leptin-deficient zebrafish, leading to muscle wasting.
Article
Biochemistry & Molecular Biology
Glenn F. van Wigcheren, Jorge Cuenca-Escalona, Suzan Stelloo, Julia Brake, Eline Peeters, Sophie. K. Horrevorts, Siebren Frolich, Ivan Ramos-Tomillero, Yvonne Wesseling-Rozendaal, Carla M. L. van Herpen, Anja van de Stolpe, Michiel Vermeulen, I. Jolanda M. de Vries, Carl G. Figdor, Georgina Florez-Grau
Summary: Imbalanced immune responses characterized by suppressive myeloid cells are significant in cancer and autoimmunity. Understanding the induction mechanisms of myeloid-derived suppressor cells (MDSCs) and tolerogenic dendritic cells (TolDCs) can aid in developing immune-restoring therapies.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Sean K. Frehan, Lolita Dsouza, Xinmeng Li, Vesna Eric, Thomas L. C. Jansen, Guido Mul, Alfred R. Holzwarth, Francesco Buda, G. J. Agur Sevink, Huub J. M. de Groot, Annemarie Huijser
Summary: The antenna complex of green sulfur bacteria has been found to support highly efficient long-range exciton transfer through vibrationally induced quantum overlap between exciton states. Excitation energy is delocalized over the chlorosome in less than 1 ps at room temperature, followed by exciton transfer to the baseplate in 3 to 5 ps. The efficiency of this process is affected by the excitation photon energy and the structural disorder of the chlorosome.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Vesna Eric, Jorge Luis Castro, Xinmeng Li, Lolita Dsouza, Sean K. Frehan, Annemarie Huijser, Alfred R. Holzwarth, Francesco Buda, G. J. Agur Sevink, Huub J. M. de Groot, Thomas L. C. Jansen
Summary: Chlorosomes from green bacteria have efficient light capture and energy transfer abilities, inspiring developments in artificial light-harvesting and molecular optoelectronics. We examine two different organizations of the molecular building blocks and show how they affect light capture and energy transfer, potentially allowing the bacteria to adapt to changes in light conditions. Spectral simulations reveal how changes in the helicity of chlorosomal aggregates alter energy transfer, with contrasting energy pathways in different chlorosomes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemical Research Methods
Siebren Frolich, Maarten van der Sande, Tilman Schafers, Simon J. van Heeringen
Summary: Genomepy is a tool that can search, download, and preprocess genomic data for functional genomics experiments. It allows users to retrieve genomic resources from different organizations and versions, and automatically generate or download additional supporting data. Genomepy is freely available and can be installed through pip or Bioconda.
Article
Genetics & Heredity
Lot Snijders Blok, Jolijn Verseput, Dmitrijs Rots, Hanka Venselaar, A. Micheil Innes, Connie Stumpel, Katrin Ounap, Karit Reinson, Eleanor G. Seaby, Shane McKee, Barbara Burton, Katherine Kim, Johanna M. van Hagen, Quinten Waisfisz, Pascal Joset, Katharina Steindl, Anita Rauch, Dong Li, Elaine H. Zackai, Sarah E. Sheppard, Beth Keena, Hakon Hakonarson, Andreas Roos, Nicolai Kohlschmidt, Anna Cereda, Maria Iascone, Erika Rebessi, Kristin D. Kernohan, Philippe M. Campeau, Francisca Millan, Jesse A. Taylor, Hanns Lochmuller, Martin R. Higgs, Amalia Goula, Birgitta Bernhard, Danita J. Velasco, Andrew A. Schmanski, Zornitza Stark, Lyndon Gallacher, Lynn Pais, Paul C. Marcogliese, Shinya Yamamoto, Nicholas Raun, Taryn E. Jakub, Jamie M. Kramer, Joery den Hoed, Simon E. Fisher, Han G. Brunner, Tjitske Kleefstra
Summary: We studied WDR5, a broadly studied key protein involved in various biological functions. We found rare de novo germline missense variants in WDR5 that are associated with neurodevelopmental disorders. These variants may disrupt interactions of WDR5 with crucial proteins such as RbBP5 and/or KMT2A/C.
HUMAN GENETICS AND GENOMICS ADVANCES
(2023)
Meeting Abstract
Ophthalmology
Janine Reurink, Erik De Vrieze, Catherina H. Z. Li, Sanne Broekman, Theo Peters, Kornelia Neveling, Hanka Venselaar, Christian Gilissen, Janneke J. C. Van Lith-Verhoeven, Lonneke Haer-Wigman, Carel C. B. Hoyng, Frans P. Cremers, Hannie Kremer, Susanne Roosing, Erwin Van Wyk
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Lot Snijders Blok, Jolijn Verseput, Dmitrijs Rots, Hanka Venselaar, A. M. Innes, Connie Stumpel, Katrin Ounap, Karit Reinson, Eleanor G. Seaby, Shane Mckee, Barbara Burton, Johanna M. van Hagen, Quinten Waisfisz, Pascal Joset, Katharina Steindl, Anita Rauch, Dong Li, Elaine Zackai, Sarah Sheppard, Beth Keena, Hakon Hakonarson, Andreas Roos, Nicolai Kohlschmidt, Anna Cereda, Maria Iascone, Erika Rebessi, Kristin D. Kernohan, Philippe M. Campeau, Francisca Millan, Jesse A. Taylor, Birgitta Bernhard, Simon E. Fisher, Han G. Brunner, Tjitske Kleefstra
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)