scholarly journals Positioning the Model Bacterial Organelle, the Carboxysome

mBio ◽  
2021 ◽  
Vol 12 (3) ◽  
Author(s):  
Joshua S. MacCready ◽  
Anthony G. Vecchiarelli
Keyword(s):  
Self Assembly ◽  
Distribution System ◽  
Carbon Fixation ◽  
Bacterial Metabolism ◽  
Positioning System ◽  
Carbon Source Utilization ◽  
Metabolic Reactions ◽  
Future Work ◽  
Protein Shell ◽  
Liquid Liquid Phase Separation

ABSTRACT Bacterial microcompartments (BMCs) confine a diverse array of metabolic reactions within a selectively permeable protein shell, allowing for specialized biochemistry that would be less efficient or altogether impossible without compartmentalization. BMCs play critical roles in carbon fixation, carbon source utilization, and pathogenesis. Despite their prevalence and importance in bacterial metabolism, little is known about BMC “homeostasis,” a term we use here to encompass BMC assembly, composition, size, copy-number, maintenance, turnover, positioning, and ultimately, function in the cell. The carbon-fixing carboxysome is one of the most well-studied BMCs with regard to mechanisms of self-assembly and subcellular organization. In this minireview, we focus on the only known BMC positioning system to date—the maintenance of carboxysome distribution (Mcd) system, which spatially organizes carboxysomes. We describe the two-component McdAB system and its proposed diffusion-ratchet mechanism for carboxysome positioning. We then discuss the prevalence of McdAB systems among carboxysome-containing bacteria and highlight recent evidence suggesting how liquid-liquid phase separation (LLPS) may play critical roles in carboxysome homeostasis. We end with an outline of future work on the carboxysome distribution system and a perspective on how other BMCs may be spatially regulated. We anticipate that a deeper understanding of BMC organization, including nontraditional homeostasis mechanisms involving LLPS and ATP-driven organization, is on the horizon.

scholarly journals Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Tianpei Li ◽  
Qiuyao Jiang ◽  
Jiafeng Huang ◽  
Catherine M. Aitchison ◽  
Fang Huang ◽  
...  
Keyword(s):  
Hydrogen Production ◽  
Self Assembly ◽  
Rational Design ◽  
Carbon Fixation ◽  
Catalytic Performance ◽  
Enzyme Activation ◽  
Production Of Hydrogen ◽  
Catalytically Active ◽  
Oxygen Sensitive ◽  
Protein Shell

Abstract Compartmentalization is a ubiquitous building principle in cells, which permits segregation of biological elements and reactions. The carboxysome is a specialized bacterial organelle that encapsulates enzymes into a virus-like protein shell and plays essential roles in photosynthetic carbon fixation. The naturally designed architecture, semi-permeability, and catalytic improvement of carboxysomes have inspired rational design and engineering of new nanomaterials to incorporate desired enzymes into the protein shell for enhanced catalytic performance. Here, we build large, intact carboxysome shells (over 90 nm in diameter) in the industrial microorganism Escherichia coli by expressing a set of carboxysome protein-encoding genes. We develop strategies for enzyme activation, shell self-assembly, and cargo encapsulation to construct a robust nanoreactor that incorporates catalytically active [FeFe]-hydrogenases and functional partners within the empty shell for the production of hydrogen. We show that shell encapsulation and the internal microenvironment of the new catalyst facilitate hydrogen production of the encapsulated oxygen-sensitive hydrogenases. The study provides insights into the assembly and formation of carboxysomes and paves the way for engineering carboxysome shell-based nanoreactors to recruit specific enzymes for diverse catalytic reactions.

scholarly journals Structure of a headful DNA-packaging bacterial virus at 2.9 Å resolution by electron cryo-microscopy

2017 ◽  
Vol 114 (14) ◽  
pp. 3601-3606 ◽  
Author(s):  
Haiyan Zhao ◽  
Kunpeng Li ◽  
Anna Y. Lynn ◽  
Keith E. Aron ◽  
Guimei Yu ◽  
...  
Keyword(s):  
Self Assembly ◽  
Noncovalent Interactions ◽  
Dna Packaging ◽  
Protein Subunits ◽  
Significant Strength ◽  
Phage Dna ◽  
Mortise And Tenon ◽  
Α Helix ◽  
Β Sheet ◽  
Protein Shell

The enormous prevalence of tailed DNA bacteriophages on this planet is enabled by highly efficient self-assembly of hundreds of protein subunits into highly stable capsids. These capsids can stand with an internal pressure as high as ∼50 atmospheres as a result of the phage DNA-packaging process. Here we report the complete atomic model of the headful DNA-packaging bacteriophage Sf6 at 2.9 Å resolution determined by electron cryo-microscopy. The structure reveals the DNA-inflated, tensed state of a robust protein shell assembled via noncovalent interactions. Remarkable global conformational polymorphism of capsid proteins, a network formed by extended N arms, mortise-and-tenon–like intercapsomer joints, and abundant β-sheet–like mainchain:mainchain intermolecular interactions, confers significant strength yet also flexibility required for capsid assembly and DNA packaging. Differential formations of the hexon and penton are mediated by a drastic α–helix-to-β–strand structural transition. The assembly scheme revealed here may be common among tailed DNA phages and herpesviruses.

Self-assembly of aniline oligomers and their induced polyaniline supra-molecular structures

2013 ◽  
Vol 67 (8) ◽  
Author(s):  
Jing Feng ◽  
Xinli Jing ◽  
Yu Li
Keyword(s):  
Recent Work ◽  
Self Assembly ◽  
Chemical Oxidation ◽  
Molecular Structures ◽  
Oxidation Products ◽  
Assembly Process ◽  
Controllable Synthesis ◽  
Aniline Oligomers ◽  
Future Work

AbstractAniline chemical oxidative polymerisation (COP), which produces various polyaniline (PANI) and oligoaniline supra-molecular structures, can be regarded as an in situ self-assembly process. This review provides a brief introduction to recent work on the structural characters and self-assembly behaviours of oligomeric aniline chemical oxidation products; it is focused on the relationships between the oligomeric species and morphology of the final products such as PANI nanoparticles, nanofibres/rods, nanotubes or oligoaniline nanosheets, micro/nanospheres in aniline COP systems. Several mechanisms proposed as explanations for the formation of typical supra-molecular structures are discussed in order to illustrate the roles of aniline oligomers. This article concludes with our perspectives on future work remaining to be done to uncover the formation mechanism of supra-molecular structures constructed by aniline chemical oxidation products and their controllable synthesis.

scholarly journals A new class of disordered elements controls DNA replication through initiator self-assembly

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Matthew W Parker ◽  
Maren Bell ◽  
Mustafa Mir ◽  
Jonchee A Kao ◽  
Xavier Darzacq ◽  
...  
Keyword(s):  
Dna Replication ◽  
Self Assembly ◽  
Origin Recognition Complex ◽  
Replication Initiation ◽  
Linear Arrangement ◽  
New Class ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Liquid Liquid Phase Separation

The initiation of DNA replication in metazoans occurs at thousands of chromosomal sites known as origins. At each origin, the Origin Recognition Complex (ORC), Cdc6, and Cdt1 co-assemble to load the Mcm2-7 replicative helicase onto chromatin. Current replication models envisage a linear arrangement of isolated origins functioning autonomously; the extent of inter-origin organization and communication is unknown. Here, we report that the replication initiation machinery of D. melanogaster unexpectedly undergoes liquid-liquid phase separation (LLPS) upon binding DNA in vitro. We find that ORC, Cdc6, and Cdt1 contain intrinsically disordered regions (IDRs) that drive LLPS and constitute a new class of phase separating elements. Initiator IDRs are shown to regulate multiple functions, including chromosome recruitment, initiator-specific co-assembly, and Mcm2-7 loading. These data help explain how CDK activity controls replication initiation and suggest that replication programs are subject to higher-order levels of inter-origin organization.

scholarly journals TDP-43 oligomers detected as initial intermediate species during aggregate formation

2018 ◽  
Author(s):  
Rachel L. French ◽  
Ashley N. Reeb ◽  
Himani Aligireddy ◽  
Niraja Kedia ◽  
Dhruva D. Dhavale ◽  
...  
Keyword(s):  
Self Assembly ◽  
Rna Binding ◽  
Initial Time ◽  
Intermediate Step ◽  
Liquid Droplets ◽  
Clinical Genetic ◽  
Lateral Sclerosis ◽  
Cytoplasmic Aggregate ◽  
Liquid Liquid Phase Separation

ABSTRACTAggregates of the RNA binding protein TDP-43 are a hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), which are neurodegenerative disorders with overlapping clinical, genetic and pathological features. Mutations in the TDP-43 gene are causative of ALS, supporting its central role in pathogenesis. The process of TDP-43 aggregation remains poorly understood and whether this includes formation of intermediate complexes is unknown. We characterized aggregates derived from purified TDP-43 as a function of time and analyzed them under semi-denaturing conditions. Our assays identified oligomeric complexes at the initial time points prior to the formation of large aggregates, suggesting that ordered oligomerization is an intermediate step of TDP-43 aggregation. In addition, we analyzed liquid-liquid phase separation of TDP-43 and detected similar oligomeric assembly upon the maturation of liquid droplets into solid-like fibrils. These results strongly suggest that the oligomers form during the early steps of TDP-43 misfolding. Importantly, ALS-linked mutations A315T and M337V significantly accelerate aggregation, rapidly decreasing the monomeric population and shortening the oligomeric phase. We also show that the aggregates generated from purified protein seed intracellular aggregation, which is detected by established markers of TDP-43 pathology. Remarkably, cytoplasmic aggregate propagation is detected earlier with A315T and M337V and is 50% more widespread than with wild-type aggregates. Our findings provide evidence for a controlled process of TDP-43 self-assembly into intermediate structures that provide a scaffold for aggregation. This process is altered by ALS-linked mutations, underscoring the role of perturbations in TDP-43 homeostasis in protein aggregation and ALS-FTD pathogenesis.

Adiabatic Absorption by Absorbent Atomization for Improving Absorption Heat Transformer Performance

2020 ◽  
Vol 142 (5) ◽  
Author(s):  
Yigal Evron ◽  
Khaled Gommed ◽  
Gershon Grossman
Keyword(s):  
Distribution System ◽  
Distribution Systems ◽  
Waste Heat ◽  
Heat Pumps ◽  
Low Grade ◽  
Liquid Distribution ◽  
Experimental Step ◽  
Higher Temperature ◽  
Future Work ◽  
Heat Transformer

Abstract Absorption heat transformers (AHTs) are a type of absorption heat pumps that are primarily driven by low-grade (typically waste) heat and produce higher temperature (high-grade) heat. Under the Indus3Es project, a 10 kW LiBr-H2O “Lab Scale” absorption heat transformer was built as a first experimental step toward larger scales. The focus was on the high-pressure vessel (HPV) (absorber and evaporator) design. To enhance performance, the aim was to obtain complete adiabatic absorption prior to the main absorption process accompanied by heat transfer. This maximizes the temperature within the absorber. This is particularly beneficial for absorption heat transformers, compared to chillers, because obtaining an elevated temperature is the objective. To obtain adiabatic absorption, atomizing spray nozzles were used as the liquid absorbent distribution system. This method proved successful; complete adiabatic absorption was obtained before the droplets contacted the absorber heat exchange surfaces. However, the spray nozzles must be supplied with pressurized liquid and are potentially more delicate than alternative liquid distribution systems. Therefore, future work may focus on determining the required atomization level to avoid excessive pressures and nozzle requirements.

Proliferating droplets formed via prebiotic polymerisation: the missing link between chemistry and biology on the origin of life

2020 ◽  
Author(s):  
Muneyuki Matsuo ◽  
Kensuke Kurihara
Keyword(s):  
Phase Separation ◽  
Origin Of Life ◽  
Self Assembly ◽  
Primitive Cell ◽  
Material Development ◽  
Steady Growth ◽  
Prebiotic Molecules ◽  
The Origin Of Life ◽  
Acid Thioesters ◽  
Liquid Liquid Phase Separation

Abstract The hypothesis that prebiotic molecules were transformed into polymers that evolved into proliferating molecular assemblages and eventually a primitive cell was first proposed about a hundred years ago. However, no proliferating model prebiotic system has yet been realised because different conditions are required for polymer generation and self-assembly of polymers. In this study, we identified conditions suitable for concurrent peptide generation and self-assembly, and we showed how a proliferating peptide-based droplet could be created by using synthesised amino acid thioesters as prebiotic monomers. Oligopeptides generated from the monomers spontaneously formed droplets through liquid–liquid phase separation in water. The droplets underwent a steady growth–division cycle by periodic addition of monomers through autocatalytic self-reproduction. Heterogeneous enrichment of RNA and lipids within droplets enabled RNA to protect the droplet from dissolution by lipids. These results provide experimental platforms for origin-of-life research and open up novel directions in peptide-based material development.

scholarly journals Self-assembly of amphiphilic truncated cones to form hollow nanovesicles

RSC Advances ◽  
2018 ◽  
Vol 8 (24) ◽  
pp. 13526-13536
Author(s):  
Yali Wang ◽  
Xuehao He
Keyword(s):  
Capsid Protein ◽  
Self Assembly ◽  
Brownian Dynamics ◽  
The Self ◽  
Truncated Cone ◽  
Anisotropic Interactions ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations ◽  
Protein Shell

To mimic the unique properties of capsid (protein shell of a virus), we performed Brownian dynamics simulations of the self-assembly of amphiphilic truncated cone particles with anisotropic interactions.

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