Deciphering the molecular principles of bacterial metabolosome biogenesis

Lead Research Organisation: University of Liverpool
Department Name: Institute of Integrative Biology

Abstract

Pathogenic bacteria, such as Salmonella, thrive in mammalian intestines and can cause severe health issues in human, including food poisoning, massive gut inflammation and cardiovascular disease. There were estimated 535,000 cases of Salmonella gastrointestinal infections worldwide in 2017, and 91,857 cases in the EU in 2018. Salmonella cells produce a specialised nano-scale organelle, known as the bacterial microcompartment. These organelles provide a suite of unique metabolic advantages that allow Salmonella to become the predominant species in the hostile environment of the host gut. The organelle uses a shell that is made of thousands of proteins to sequester multiple enzymes used for 1,2-propanediol utilisation (Pdu). This unique structure allows the Pdu organelles to protect bacterial cells from toxic metabolites and to enhance the cell's metabolism. Although the importance of Pdu organelles for the metabolism of bacterial pathogens is appreciated, little is known about how bacterial cells generate and then modulate these organelles to confer adaptive cellular metabolism to survive in the sophisticated gut environment.

We have recently reported the exact protein stoichiometry of Pdu organelles and have established a new structural model of the organelle. We have also developed systems for tagging Pdu proteins with fluorescent markers and depleting target proteins, so that we can track specific building proteins using microscopes and study their functions in bacterial cells. Using the developed systems, we have discovered that the cargo enzymes and shell proteins self-assemble independently in Salmonella. We have also shown that the locations and movement of Pdu organelles are confined within the bacterial cell. Standing on these exciting scientific and technical breakthroughs and an established research team with complementary expertise, we now aim to do an in-depth exploration of how Pdu organelles are synthesized and how the organisation of Pdu organelles is coordinated within the Salmonella cell.

We will first determine the multi-step assembly that individual building proteins undergo to form higher-ordered assemblies, identify the proteins that make up the enzyme and shell assemblies, and elucidate how enzyme and shell assemblies associate together to form an intact organelle. In the second section of our programme, we will characterise the structures and functions of small linker proteins that drive the assembly of cargos to have a "liquid-like" dynamic phase and ascertain that the phase separation mechanism is vital for mediating the protein interactions and formation of a functional protein organelle. Finally, we will use state-of-the-art fluorescence microscopy to probe how the Pdu organelles are generated, located, and modulated to perform such important functions in bacterial cells.

This ambitious and multidisciplinary research project has both fundamental and applied significance. Pdu MCPs represents an ideal model system for uncovering the principles of protein self-assembly and the generation of multi-protein complexes in biology. We will learn the basic physics and chemistry of how thousands of proteins assemble together to build a functional entity within a bacterial cell, and determine how the cell precisely and efficiently controls the formation and function of metabolic organelles. We anticipate that our findings will provide a deeper understanding of the biosynthesis and maintenance of natural bacterial organelles and protein assemblies. The research may inform strategies for the engineering of biological "factories" for the enhancement of cell metabolism and energy production in diverse biotechnological applications. Moreover, the essential protein-protein interactions that we find are required to mediate the assembly of Pdu organelles could represent novel therapeutic targets to disrupt the production of Pdu organelles and thus ablate the ability of Salmonella to thrive in the human gut.

Technical Summary

Bacterial microcompartments (BMCs) are intracellular proteinaceous organelles that spatially organise and confine metabolic reactions. The 1,2-propanediol utilisation microcompartments (Pdu MCPs) in pathogenic Salmonella sequester enzymatic pathways that produce toxic metabolites using a virus-like shell. This confers growth advantages to Salmonella within the human microbiome. The pathway that thousands of protein subunits self-assemble in order and time to form functional Pdu MCPs in cells remains elusive. We have recently developed approaches for the isolation, proteomics, genetic modification and cell imaging to explore the Pdu MCP biogenesis in Salmonella. Our preliminary results indicated that Pdu MCP shell and core enzymes undergo the separated assembly and that formation of enzyme assemblies is mediated by specific intrinsically disordered short peptides.

We hypothesise that Pdu MCPs possess a "concomitant" biogenesis pathway and cargo enzymes form liquid-like protein assemblies driven by liquid-liquid phase separation. Using proteomics and confocal microscopy, we will first explore how individual building components assemble to form the shell and enzyme assemblage and then the entire Pdu MCPs. Next, we will determine the structures of key disordered peptides and their interactions with cargos using NMR and isothermal titration calorimetry. We will also corroborate the liquid-like properties of enzyme assemblies using fluorescence recovery after photobleaching. Finally, we will use live-cell fluorescence imaging to explore the biogenic sites, subcellular partitioning and movement of Pdu MCPs, to elucidate how Salmonella integrates Pdu MCPs with the bacterial cytoskeleton. Advanced knowledge of Pdu MCP biogenesis, protein interactions and encapsulation will inform the engineering of bio-factories for optimising metabolic performance, producing toxic proteins, and may lead to therapeutics for preventing colonisation of the human GI tract by Salmonella.
 
Title AFM 
Description atomic force microscopy imaging on biological samples 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact We have applied high-resolution AFM imaging on many biological samples. Recently we have established a hybrid AFM/confocal/TIRF microscopy for studying cell dynamics. Structural variability, coordination, and adaptation of a native photosynthetic machinery. Zhao LS, Huokko T, Wilson S, Simpson DM, Wang Q, Ruban AV, Mullineaux CW, Zhang YZ*, Lu-Ning Liu*. Nature Plants, 2020, 6(7): 869-882. DOI: 10.1038/s41477-020-0694-3. AFM imaging on amyloid morphology provides further motivation to investigate the role of oxidative stress in AMA pathogenicity. The study has led to a paper published: Davies HA, Phelan MM, Wilkinson MC, Migrino RQ, Truran S, Franco DA, Liu LN, Longmore CJ, Madine J. Oxidative stress alters morphology and toxicity of aortic medial amyloid. Biophys J, 2015, 109(11): 2363-2370. Unfolding pathway and intermolecular interactions of the cytochrome subunit in the bacterial photosynthetic reaction center. Leanne C. Miller, Longsheng Zhao, Daniel P. Canniffe, David Martin, Lu-Ning Liu*. Biochim Biophys Acta - Bioenergetics, 2020, 1861(8): 148204, DOI: 10.1016/j.bbabio.2020.148204. AFM imaging on exosome structure has revealed that CLL cells secrete exosomes that alter the transcriptome and behaviour of recipient cells. Such communication with microenvironment is likely to have an important role in CLL disease biology. The study has led to a paper published: Farahani M, Rubbi C, Liu LN, Slupsky JR, Kalakonda N. CLL exosomes modulate the transcriptome and behaviour of recipient stromal cells and are selectively enriched in miR-202-3p. PLoS ONE, 2015, 10(10): e0141429. 
 
Title AFM force measurement to study protein interaction 
Description apply atomic force microscopy force measurement to study the protein unfolding and interaction of membrane protein complexes 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? Yes  
Impact Using state-of-the-art Atomic Force Microscopy (AFM), we have deciphered the nanoscale structure of the photosynthetic membranes that are extracted from a purple photosynthetic bacterium (Blastochloris viridis). Additionally, we applied single-molecule force spectroscopy (SMFS) to "pull" out protein peptides from the photosynthetic complexes in their working conditions. This allowed us to monitor the stepwise unfolding process of the structural components of photosynthetic complexes and detect the mechanical forces required in the unfolding process. Unfolding pathway and intermolecular interactions of the cytochrome subunit in the bacterial photosynthetic reaction center. Leanne C. Miller, Longsheng Zhao, Daniel P. Canniffe, David Martin, Lu-Ning Liu*. Biochim Biophys Acta - Bioenergetics, 2020, 1861(8): 148204, 
URL https://www.sciencedirect.com/science/article/pii/S0005272820300542?via%3Dihub
 
Title Absolute proteomic quantification of protein assemblies 
Description use Qconcat method based on quantitative mass spectrometry to determine the stoichiometry of protein components in macromolecular complexes. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? No  
Impact Decoding the stoichiometric composition and organisation of bacterial metabolosomes. Yang M, Simpson DM, Wenner N, Brownridge P, Harman VM, Hinton JCD, Beynon RJ, Lu-Ning Liu* Nature Communications, 2020, 11(1): 1976. DOI: 10.1038/s41467-020-15888-4. 
URL https://www.nature.com/articles/s41467-020-15888-4
 
Title alpha-carboxysome QconCAT quantification 
Description The entire Skyline project and raw data for a-carboxysome QconCAT quantification have been deposited at Panorama Public with the access URL (https://panoramaweb.org/Wb6olk.url) and the ProteomeXchange ID PXD031494. Raw LC-MSMS data for label-free quantification have been deposited to the ProteomeXchange Consortium via the PRIDE (73) partner repository with the access URL (https://www.ebi.ac.uk/pride/archive/projects/PXD031420). 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact Carboxysomes are anabolic bacterial microcompartments that play an essential role in carbon fixation in cyanobacteria and some chemoautotrophs. This self-assembling organelle encapsulates the key CO2-fixing enzymes, Rubisco, and carbonic anhydrase using a polyhedral protein shell that is constructed by hundreds of shell protein paralogs. The a-carboxysome from the chemoautotroph Halothiobacillus neapolitanus serves as a model system in fundamental studies and synthetic engineering of carboxysomes. Here we adopt a QconCAT-based quantitative mass spectrometry approach to determine the stoichiometric composition of native a-carboxysomes from H. neapolitanus. We further performed an in-depth comparison of the protein stoichiometry of native and recombinant a-carboxysomes heterologously generated in Escherichia coli to evaluate the structural variability and remodeling of a-carboxysomes. Our results provide insight into the molecular principles that mediate carboxysome assembly, which may aid in rational design and reprogramming of carboxysomes in new contexts for biotechnological applications. 
URL https://www.ebi.ac.uk/pride/archive/projects/PXD031420
 
Description Pdu bioengineering - Warren 
Organisation University of Kent
Country United Kingdom 
Sector Academic/University 
PI Contribution provide analytical tools and constructs
Collaborator Contribution provide plasmids and protocols
Impact Not yet
Start Year 2021