Article
Biochemical Research Methods
Taiyu Chen, Yi Fang, Qiuyao Jiang, Gregory F. Dykes, Yongjun Lin, G. Dean Price, Benedict M. Long, Lu-Ning Liu
Summary: The carboxysome is an important prokaryotic organelle involved in carbon fixation. This study successfully engineered alpha-carboxysomes and found that incorporating certain components can enhance their CO2 fixation activities. Additionally, the structure of carboxysomes can be modified through different expression systems.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Microbiology
Matthew R. Melnicki, Markus Sutter, Cheryl A. Kerfeld
Summary: Bacterial microcompartments (BMCs) are self-assembling prokaryotic organelles that encapsulate enzymes within a polyhedral protein shell. The shells are composed of distinct domains forming pentagonal and hexagonal building blocks. Recent phylogenomic surveys have revealed specific structural features of BMCs' building blocks, suggesting distinct functional roles across diverse BMC families.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Andrew M. Stewart, Katie L. Stewart, Todd O. Yeates, Thomas A. Bobik
Summary: Bacterial microcompartments (MCPs) are large and diverse proteinaceous organelles that compartmentalize metabolic pathways and sequester toxic or volatile intermediates. Recent studies have expanded our understanding of MCP diversity, structure, function, and potential applications, revealing new types of MCPs and their associations with human disease. Structural studies have provided new insights into MCP assembly and mechanisms, while biotechnology applications are utilizing MCP principles for nanobioreactors, nanocontainers, and molecular scaffolds.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Review
Microbiology
Markus Sutter, Cheryl A. Kerfeld, Kathleen M. Scott
Summary: Carboxysomes are proteinaceous microcompartments responsible for a significant amount of CO2 fixation on Earth. They facilitate CO2 fixation by concentrating it in cells and converting HCO3- to CO2. The structural components and genetic context of atypical carboxysomes are described in this review.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Daniel S. Trettel, Chris Neale, Mingfei Zhao, S. Gnanakaran, C. Raul Gonzalez-Esquer
Summary: Bacterial microcompartments (BMCs) are protein organelles with an inner enzymatic core encased in a selectively permeable shell. It has been found that the properties of the shell affect ion permeability, which in turn influences the permeation rate of substrates.
SCIENTIFIC REPORTS
(2023)
Review
Environmental Sciences
Daniel A. Raba, Cheryl A. Kerfeld
Summary: The application of nanotechnology to plants, known as phytonanotechnology, has the potential to revolutionize plant research and agricultural production, improving crop yield and disease resistance.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2022)
Article
Biology
Markus Sutter, Cheryl A. Kerfeld
Summary: Bacterial microcompartments (BMCs) are protein-based organelles with unique shell proteins and selective permeability. We have developed a webserver tool using HMM profiles to analyze and categorize BMCs, providing users with information and a reference database.
Review
Microbiology
Jessica M. Ochoa, Todd O. Yeates
Summary: Bacterial microcompartments are organelle-like structures composed entirely of proteins that enhance metabolic functions. Recent studies have highlighted nuanced variations in microcompartment shell proteins, showing how variation and specialization enable complex molecular machine construction. Engineering synthetic miniaturized microcompartment shells provides additional frameworks for dissecting principles of microcompartment structure and assembly.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Review
Plant Sciences
Warren Shou Leong Ang, Jian Ann How, Jian Boon How, Oliver Mueller-Cajar
Summary: Carbon dioxide is often concentrated near the Rubisco active sites through liquid-liquid phase separation. Recent studies have shown that highly concentrated Rubisco condensates are formed by this mechanism. Rubisco condensates are essential for photosynthesis and growth, making them a powerful model for investigating the relationship between phase separation and biological structure-function.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Multidisciplinary Sciences
Cecilia Blikstad, Eli J. Dugan, Thomas G. Laughlin, Julia B. Turnsek, Mira D. Liu, Sophie R. Shoemaker, Nikoleta Vogiatzi, Jonathan P. Remis, David F. Savage
Summary: Carboxysomes are proteinaceous organelles that encapsulate key enzymes of CO2 fixation and play a central role in the bacterial CO2 concentrating mechanism. This study reveals the structural basis of carbonic anhydrase encapsulation into alpha-carboxysomes and highlights the importance of Rubisco as a central hub for mediating assembly through protein interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Lu-Ning Liu
Summary: Carboxysomes are bacterial microcompartments that encapsulate the primary CO2-fixing enzyme Rubisco within a virus-like protein shell. They play a central role in CO2 fixation in bacteria by providing elevated levels of CO2 to maximize carboxylation. Recent research has provided new insights into the assembly and functional maintenance of carboxysomes in bacteria and has explored their potential applications in synthetic biology.
TRENDS IN MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Zhaodong Li, Chao Wu, Xiang Gao, Bennett Addison, Shrameeta Shinde, Xin Wang, Xihan Chen, Jianping Yu, Drazenka Svedruzic, Jeffrey L. Blackburn, Wei Xiong
Summary: A new integrated photo-electrochemical system has been developed, allowing direct electron transfer to the photosynthetic system in living cyanobacteria. This system enables the conversion of CO2 into acetate by fueling cyanobacteria with both illumination and exogenous electrons. The energy conversion efficiency for acetate production under intermittent LED illumination and exogenous electron supply reached around 9%, suggesting potential for sustainable biofuel production.
ENERGY & ENVIRONMENTAL SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Daniel S. Trettel, William Resager, Beatrix M. Ueberheide, Conor C. Jenkins, Wade C. Winkler
Summary: Bacterial microcompartments (BMCs) are structures found in bacteria that are used for various metabolic purposes. By using chemical probes, the structure of a native BMC was observed, revealing that the shell layer is more dynamic than previously thought. Analysis of cross-linking chemical probes showed a complex multivalent network among cargo proteins, supporting the idea that biomolecular condensation drives interactions between cargo and shell proteins before encapsulation.
Article
Chemistry, Analytical
Cristina Chiva, Zahra Elhamraoui, Amanda Sole, Marc Serret, Mathias Wilhelm, Eduard Sabido
Summary: Mass spectrometry coupled to liquid chromatography is a powerful technology for proteome quantification in biomedical samples. However, the identification of all potential peptides for a given protein is challenging, and proteomics experiments often focus on a subset of peptides for protein quantitation. This study evaluated the stability of human proteotypic peptides and developed a deep learning model to predict peptide stability from tryptic sequences, providing a valuable resource for peptide selection in proteome quantification experiments.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Douglas F. Porter, Weili Miao, Xue Yang, Grant A. Goda, Andrew L. Ji, Laura K. H. Donohue, Maria M. Aleman, Daniel Dominguez, Paul A. Khavari
Summary: The study introduces a quantitative method called easyCLIP to identify proteins as RNA-binding proteins (RBPs) and define RBP target RNAs. By measuring RNA cross-link rates, the research found that specific cancer mutations can increase the binding of proteins to RNA. This approach helps to understand how disease-associated proteins impact RNA association.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Iris Wagner, Linda Grigoraki, Peter Enevoldson, Michael Clarkson, Sam Jones, Jane L. L. Hurst, Robert J. J. Beynon, Hilary Ranson
Summary: The rapid evaporative ionisation mass spectrometry (REIMS) method can accurately identify the species and age of mosquitoes, with high accuracy in both laboratory-reared and wild populations.
Article
Biochemical Research Methods
Martin Rusilowicz, David W. Newman, Declan R. Creamer, James Johnson, Kareena Adair, Victoria M. Harman, Chris M. Grant, Robert J. Beynon, Simon J. Hubbard
Summary: Protein quantitation via mass spectrometry requires the use of peptide proxies, and accurate quantitation often relies on the addition of an external standard. AlacatDesigner is a tool that assists in selecting suitable peptide candidates for recombinant protein standards. It considers factors such as target protein, existing databases, literature occurrence, potential post-translational modifications, and ionization potential within the mass spectrometer.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Taiyu Chen, Saba Riaz, Philip Davey, Ziyu Zhao, Yaqi Sun, Gregory F. Dykes, Fei Zhou, James Hartwell, Tracy Lawson, Peter J. Nixon, Yongjun Lin, Lu-Ning Liu
Summary: Researchers have successfully replaced plant Rubisco with a faster Rubisco in tobacco chloroplasts, resulting in a higher carboxylation rate and similar growth rate of transgenic plants compared to the wild-type under 1% CO2 concentration. This study represents a step towards engineering a fast and highly active Rubisco in chloroplasts to improve crop photosynthesis and growth.
Article
Multidisciplinary Sciences
Qi Sheng, Meng-Yao Zhang, Si -Min Liu, Zhuo-Wei Chen, Pei-Ling Yang, Hong-Su Zhang, Meng-Yun Liu, Kang Li, Long-Sheng Zhao, Ning-Hua Liu, Lu-Ning Liu, Xiu-Lan Chen, Jamie K. Hobbs, Simon J. Foster, Yu-Zhong Zhang, Hai-Nan Su
Summary: Braun's lipoprotein (Lpp) is important in stabilizing the cell envelope in Escherichia coli by linking the outer membrane to the peptidoglycan layer. Using atomic force microscopy, Lpp was found to be evenly distributed over the outer surface of the peptidoglycan sacculi at a high density. However, it is absent at the constriction site during cell division, indicating its involvement in the cell division process along with Pal and other envelope-associated proteins.
Article
Chemistry, Medicinal
Ines Ventura, Victoria Harman, Robert J. Beynon, Romana Santos
Summary: Biomedical adhesives still struggle with strong adhesion in wet environments. Marine invertebrates' biological adhesives show promising characteristics for underwater biomimetic adhesives. Through analysis of sea urchin Paracentrotus lividus adhesive proteins, researchers identified glycosylated protein candidates. The deeper characterization of these adhesive glycoproteins advances the development of sea urchin-inspired bioadhesives.
Article
Multidisciplinary Sciences
Guadalupe Gomez-Baena, Kieran C. Pounder, Josiah O. Halstead, Sarah A. Roberts, Amanda J. Davidson, Mark Prescott, Robert J. Beynon, Jane L. Hurst
Summary: Chemical communication by females in social species, such as laboratory rats, is important for competition and cooperation between females in determining reproductive success. Female rats target their deployment of scent information differently based on their sexual receptivity and the genetic identity of the individuals in the environment. The scent marks of female rats contain a complex mix of proteins, with clitoral gland secretion being dominant, and play a key role in female communication.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Leandro Xavier Neves, R. Alan Wilson, Philip Brownridge, Stephen W. W. Holman, Victoria M. M. Harman, Claire E. E. Eyers, Robert J. J. Beynon, William Castro-Borges
Summary: In this study, a detailed method for preserving the proteome of adult Schistosoma mansoni worms was described in order to enrich the tissues associated with the parasite's alimentary tract. The methodology employed label-free and QconCAT-based absolute quantification to detect S. mansoni oesophageal gland products. By stabilizing the proteome and minimizing sample degradation during dissection, the hidden proteome of target tissues, which are not readily available from total lysates due to their small volumes, could be accessed. This protocol can be used for the discovery of proteins with potential diagnostic and therapeutic utility in other Schistosoma species lacking quantitative proteomics characterization of specialized tissues.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Multidisciplinary Sciences
Taiyu Chen, Marta Hojka, Philip Davey, Yaqi Sun, Gregory F. Dykes, Fei Zhou, Tracy Lawson, Peter J. Nixon, Yongjun Lin, Lu-Ning Liu
Summary: Engineering carboxysomes into crop chloroplasts can enhance photosynthesis and crop yield. The authors successfully engineered functional CO2-fixing modules into tobacco chloroplasts, improving photosynthesis and productivity.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Owen Thwaites, Bern M. M. Christianson, Alexander J. J. Cowan, Frank Jackel, Lu-Ning Liu, Adrian M. M. Gardner
Summary: Elucidating the photosynthetic processes within RC-LH1 supercomplexes is crucial for understanding natural photosynthetic systems and developing artificial photosynthesis. This study examined the energy transfer in RC-LH1 supercomplexes of Rhodobacter sphaeroides and investigated the roles of transmembrane polypeptides PufX and PufY. The results showed that the absence of PufX increased the excitation energy transfer lifetime and distribution, while the absence of PufY led to conformational changes in LH1 subunits but did not affect the energy transfer lifetime significantly.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Multidisciplinary Sciences
Tao Ni, Qiuyao Jiang, Pei Cing Ng, Juan Shen, Hao Dou, Yanan Zhu, Julika Radecke, Gregory F. Dykes, Fang Huang, Lu-Ning Liu, Peijun Zhang
Summary: Carboxysomes are self-assembling proteinaceous organelles found in nature that enhance carbon fixation. This study synthetically engineers and determines cryoEM structure of minimal α-carboxysome shells to uncover the mechanism of shell assembly and encapsulation by CsoS2.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Matthew Faulkner, Robin Hoeven, Paul P. Kelly, Yaqi Sun, Helen Park, Lu-Ning Liu, Helen S. Toogood, Nigel S. Scrutton
Summary: This study demonstrates the potential of using environmental isolates as industrial hosts for chemicals biomanufacturing, showing the value of replacing or augmenting the use of biogenic feedstocks with CO2 utilization in non-sterile, industrialized bioreactors.
BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS
(2023)
Article
Materials Science, Biomaterials
Qiuyao Jiang, Tianpei Li, Jing Yang, Catherine M. Aitchison, Jiafeng Huang, Yu Chen, Fang Huang, Qiang Wang, Andrew I. Cooper, Lu-Ning Liu
Summary: Researchers engineered the protein organelle in bacteria cells to encapsulate hydrogenases, resulting in improved hydrogen production and catalytic efficiency. This study provides a framework for developing new bio-inspired electrocatalysts for sustainable fuel and chemical production.
JOURNAL OF MATERIALS CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Ruichao Mao, Han Zhang, Lihua Bie, Lu-Ning Liu, Jun Gao
Summary: Protein-protein interface interactions are crucial for efficient excitation energy transfer in photosystem II (PSII). This study constructs a large-scale model of the PSII-LHCII supercomplex and performs molecular dynamics simulations to investigate its interactions and assembly mechanisms. The results uncover the role of hydrophobic interactions in antenna-core association and highlight the importance of hydrogen bonds and salt bridges in interface binding. The findings provide insights into the self-organization and regulation of PSII-LHCII and lay the foundation for understanding assembly principles of photosynthetic supercomplexes and other macromolecular structures.
