Editorial Material
Biochemistry & Molecular Biology
Kelley A. Gallagher, Yves V. Brun
Summary: Bdellovibrio bacteriovorus divides in a non-binary manner, with chromosome segregation depending on the conserved ParA-ParB-parS system.
Article
Energy & Fuels
Yupeng Wang, Yucui Hou, He Li, Weize Wu, Shuhang Ren, Jianwei Li
Summary: Coal is believed to be derived from biomass, with lignin and lignite sharing a close structural relationship. Both lignin and lignite contain polycyclic aromatic clusters, but with differences in structural units.
Review
Immunology
Xinyu Gu, Qingfei Chu, Xiao Ma, Jing Wang, Chao Chen, Jun Guan, Yanli Ren, Shanshan Wu, Haihong Zhu
Summary: NKT cells play a crucial role in the immune system, particularly in liver diseases. Hepatic iNKT cells interact with other immune cells through direct cell-to-cell contact and cytokine secretion, bridging the innate and adaptive immune systems.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Agricultural Engineering
Cong-Cong Tang, Tian-Yang Wang, Rong Wang, Cristiano Varrone, Zixuan Gan, Zhang-Wei He, Zhi-Hua Li, Xiaochang C. Wang
Summary: This study investigated the role of Triclosan (TCS) in a microalgal-bacterial symbiosis (MABS) system treating wastewater. The findings showed that increased TCS stress led to a decrease in the removal efficiencies of NH4+-N, total nitrogen, and total phosphorus. The activities of microalgae were more affected than that of bacteria, and the accumulation of malondialdehyde increased, leading to increased permeability of cytomembrane and bioaccumulation of TCS. Additionally, the aggregation properties of microalgae and bacteria were enhanced with TCS loading increasing, affecting the migration of TCS.
BIORESOURCE TECHNOLOGY
(2023)
Article
Engineering, Environmental
Dexin Fang, Liping Huang, Jianping Fan, Hong Xiao, Ganxue Wu, Yingjun Wang, Zhenxing Zeng, Fei Shen, Shihuai Deng, Fangying Ji
Summary: This study investigates the relationship between the stacking pattern of layered double hydroxides (LDH) nanosheets and their ion-exchange behavior. The results show that LDH with a disordered stacking morphology exhibits larger pore space and faster exchange rate, which expands the potential application of LDH in phosphate sequestration.
CHEMICAL ENGINEERING JOURNAL
(2022)
Review
Chemistry, Multidisciplinary
Ke-Wei Chen, Tian-Yu Sun, Yun-Dong Wu
Summary: According to a survey of protein databases, it has been found that the majority of enzymes exist in oligomeric forms, with half of those in the UniProt database being homodimers. Recent advancements in experimental and computational techniques have allowed for a better understanding of the cooperative interactions between the subunits of dimeric enzymes. This review provides an overview of these advancements, including experimental and theoretical methods, as well as insights into substrate binding cooperativity and the molecular mechanisms of cooperative catalysis within homodimeric enzymes.
Review
Multidisciplinary Sciences
Gustavo Santoyo
Summary: This review examines the mechanisms used by plants to selectively recruit beneficial microbiomes and exclude potential pathogens. It discusses the role of root exudates, molecular recognition, and signaling in attracting beneficial microbiota and maintaining plant-microbiome homeostasis. The review also explores the environmental and biotic factors that influence microbial community dynamics and the interactions between different microbial species.
JOURNAL OF ADVANCED RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Claudia S. Nobrega, Ana Luisa Carvalho, Maria Joao Romao, Sofia R. Pauleta
Summary: In this study, the crystal structure of the bacterial peroxidase from Neisseria gonorrhoeae was obtained, revealing that cyanide and azide can inhibit the catalytic activity of the enzyme. This finding provides a new strategy for the search and development of inhibitors targeting this enzyme.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Guangping Huang, Wenyu Shi, Le Wang, Qingyue Qu, Zhenqiang Zuo, Jinfeng Wang, Fangqing Zhao, Fuwen Wei
Summary: This study established a high-quality gut microbiome catalog of giant pandas, uncovering microbial diversity, functions, and resistome landscapes. Wild pandas exhibit host genetic-specific microbial structures and functions, while captive pandas encode more multi-drug resistance genes.
Review
Biochemistry & Molecular Biology
Noriyoshi Manabe, Yoshiki Yamaguchi
Summary: Beta-glucans are components of fungal and plant cell walls, and are recognized as non-self-components in the host defense system. Their long chains can form a triple helix structure, potentially affecting interactions with beta-glucan-binding proteins. While details of beta-glucan binding and receptor signaling remain unclear, X-ray crystallography and NMR analyses have provided insights into their structure and interactions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ida Freda, Cecile Exertier, Anna Barile, Antonio Chaves-Sanjuan, Mirella Vivoli Vega, Michail N. Isupov, Nicholas J. Harmer, Elena Gugole, Paolo Swuec, Martino Bolognesi, Anita Scipioni, Carmelinda Savino, Martino Luigi Di Salvo, Roberto Contestabile, Beatrice Vallone, Angela Tramonti, Linda Celeste Montemiglio
Summary: Specificity in protein-DNA recognition is determined by the structural and chemical features of the targeted DNA molecule. Using cryo-EM and crystallography, we elucidated the interactions driving the DNA recognition and binding by PdxR, a bacterial transcription factor. Our findings revealed the importance of electrostatic interactions and DNA bending in the allosteric regulation of DNA binding by PdxR. This study provides detailed insights into the structure and dynamics of the PdxR-DNA complex and the regulatory mechanisms of the MocR family of transcription factors.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Agriculture, Multidisciplinary
Jin Li, Zhixiao He, Yumei Liang, Tao Peng, Zhong Hu
Summary: In recent years, marine macroalgae have gained attention from researchers worldwide due to their extensive biomass. The polysaccharides found in these algae have been widely studied in the fields of food, pharmaceuticals, and cosmetics due to their various bioactivities. However, there are many barriers to their application, such as their large molecular size, poor solubility, and low physiological activities. This review focuses on the structure, hydrolase families, metabolic pathways, and potential applications of seven macroalgae polysaccharides, aiming to enhance our understanding of their structure and metabolic pathways and facilitate the utilization of bioactive oligosaccharides.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biology
Xinxu Zhang, Zongbao Liu, Wei Xu, Jie Pan, Yuhan Huang, Mingwei Cai, Zhuhua Luo, Meng Li
Summary: Metagenomic exploration of the ocean's Yap Trench led to the discovery of three new monophyletic bacterial lineages named Candidatus Qinglongiota, Candidatus Heilongiota, and Candidatus Canglongiota. The genomes of these new lineages suggest a versatile lifestyle and a preference for oxygen-limited or particle-attached environments. Evolutionary analysis indicated the importance of gene gain and loss events, as well as horizontal gene transfer, in shaping the genomic and metabolic features of these new phyla.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Microbiology
Carolina dos Anjos, Leon G. Leanse, Martha S. Ribeiro, Fabio P. Sellera, Milena Dropa, Victor E. Arana-Chavez, Nilton Lincopan, Mauricio S. Baptista, Fabio C. Pogliani, Tianhong Dai, Caetano P. Sabino
Summary: Antimicrobial drug development is under scrutiny due to the worldwide antibiotic crisis. Antimicrobial blue light (aBL) has been recognized as a potential therapy for infections, but the specific targets for bacterial killing by aBL are still poorly understood and may vary depending on the bacterial species.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Adeline Y. Robin, Celine Brochier-Armanet, Quentin Bertrand, Caroline Barette, Eric Girard, Dominique Madern
Summary: This study provides a comprehensive understanding of the evolution and structure-function relationships of lactate dehydrogenase (LDH), identifying the link between eukaryotic and cyanobacterial LDHs and characterizing the role of specific amino acid positions in the regulation of LDH activity.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Mengru Yang, Nicolas Wenner, Gregory Dykes, Yan Li, Xiaojun Zhu, Yaqi Sun, Fang Huang, Jay C. D. Hinton, Lu-Ning Liu
Summary: This study investigates the de novo biogenesis of Pdu metabolosomes in bacteria and characterizes the roles of key constituents in the formation and positioning of functional metabolosomes. The results show that Pdu metabolosomes undertake both Shell first and Cargo first assembly pathways, and the internal cargo core is formed through ordered assembly of multiple enzyme complexes, exhibiting liquid-like properties.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Tao Ni, Yaqi Sun, Will Burn, Monsour M. J. Al-Hazeem, Yanan Zhu, Xiulian Yu, Lu-Ning Liu, Peijun Zhang
Summary: This study reveals the distinct 3D organization of Rubisco inside Carboxysomes in cyanobacteria and chemoautotrophs, using cryo-electron tomography. The study also discovers that the interaction between CsoS2 and Rubiscos differs in different types of Carboxysomes. These findings provide critical knowledge of the assembly principles of Carboxysomes and may contribute to the design and repurposing of carboxysome structures for new functions.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jiafeng Huang, Qiuyao Jiang, Mengru Yang, Gregory F. Dykes, Samantha L. Weetman, Wei Xin, Hai-Lun He, Lu-Ning Liu
Summary: The study develops an approach to determine the interior pH conditions and inorganic carbon accumulation within carboxysome shells. The results demonstrate that the interior pH of the shells is lower than the cytoplasmic pH and can be modulated. This study is crucial for understanding the mechanisms underlying the permeability of carboxysomal shells and the enhancement of CO2 carboxylation.
Article
Plant Sciences
Long-Sheng Zhao, Chun-Yang Li, Xiu-Lan Chen, Qiang Wang, Yu-Zhong Zhang, Lu-Ning Liu
Summary: Visualization of the photosynthetic complexes in the thylakoid membranes of a cyanobacterium reveals their native architecture and interactions, providing insights into the organization and adaptation of the photosynthetic apparatus under environmental stress. This study sheds light on the molecular mechanisms of efficient light harvesting and energy conversion.
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
Biochemistry & Molecular Biology
Laura Bracun, Atsushi Yamagata, Bern M. Christianson, Mikako Shirouzu, Lu-Ning Liu
Summary: In this study, the structure of RC-LH1 supercomplex from purple photosynthetic bacteria Rhodobacter capsulatus is reported using cryo-EM. The RC-LH1 complexes in Rba. capsulatus are exclusively monomers surrounded by a LH1 ring. Insertion of transmembrane polypeptide PufX leads to a large opening within the LH1 ring. Comparison of PufX from different Rhodobacter species reveals the important residues involved in RC-LH1 dimerization.
Editorial Material
Microbiology
Weimin Ma, Lu-Ning Liu, Qiang Wang, Deqiang Duanmu, Bao-Sheng Qiu
FRONTIERS IN MICROBIOLOGY
(2023)
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
Biochemistry & Molecular Biology
Long-Sheng Zhao, Peng Wang, Kang Li, Quan-Bao Zhang, Fei-Yu He, Chun-Yang Li, Hai-Nan Su, Xiu-Lan Chen, Lu-Ning Liu, Yu-Zhong Zhang
Summary: This study reports the structure of the photosynthetic PSI-ACPI supercomplex in cryptophyte algae, which represents a unique structure in the evolution of photosynthesis. The supercomplex consists of a PSI core and ACPI subunits, with ACPI-S mediating the association and energy transfer between them. This research provides important insights into the energy transfer mechanisms of cryptophyte PSI-LHCI and the evolution of photosynthesis in the red lineage.
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.
