ORCID Profile
0000-0002-8195-5348
Current Organisation
Monash University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Enzymes | Microbial Genetics | Biochemistry and cell biology | Structural biology (incl. macromolecular modelling) | Microbiology | Microbial genetics | Bacteriology | Enzymes | Microbiology | Bacteriology
ANZSRC Socio-Economic Objective (SEO)
Hydrogen-based Energy Systems (incl. Internal Hydrogen Combustion Engines) | Atmospheric Processes and Dynamics |
Related Links
Publications
Structural basis of substrate recognition and catalysis by fucosyltransferase 8
Publisher: Elsevier BV
Date: 05-2020
The structure of the bacterial iron–catecholate transporter Fiu suggests that it imports substrates via a two-step mechanism
Publisher: Elsevier BV
Date: 12-2019
Engineering bacteriocin‐mediated resistance against the plant pathogen Pseudomonas syringae
Publisher: Wiley
Date: 03-12-2019
DOI: 10.1111/PBI.13294
Microbial oxidation of atmospheric trace gases
Publisher: Springer Science and Business Media LLC
Date: 12-04-2022
DOI: 10.1038/S41579-022-00724-X
Abstract: The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H
Beware of proteins bearing gifts: protein antibiotics that use iron as a Trojan horse
Publisher: Oxford University Press (OUP)
Date: 19-10-2012
Abstract: Multicellular organisms limit the availability of free iron to prevent the utilization of this essential nutrient by microbial pathogens. As such, bacterial pathogens possess a variety of mechanisms for obtaining iron from their hosts, including a number of ex les of vertebrate pathogens that obtain iron directly from host proteins. Recently, two novel members of the colicin M bacteriocin family were discovered in Pectobacterium that suggest that this phytopathogen possesses such a system. These bacteriocins (pectocin M1 and M2) consist of a cytotoxic domain homologous to that of colicin M fused to a horizontally acquired plant-like ferredoxin. This ferredoxin domain substitutes the portion of colicin M required for receptor binding and translocation, presumably fulfilling this role by parasitizing an existing ferredoxin-based iron acquisition pathway. The ability of susceptible strains of Pectobacterium to utilize plant ferredoxin as an iron source was also demonstrated, providing additional evidence for the existence of such a system. If this hypothesis is correct, it represents the first ex le of iron piracy directly from a host protein by a phytopathogen and serves as a testament of the flexibility of evolution in creating new bacteriocin specificities.
Structural basis for bacterial energy extraction from atmospheric hydrogen
Publisher: Springer Science and Business Media LLC
Date: 08-03-2023
DOI: 10.1038/S41586-023-05781-7
Abstract: Diverse aerobic bacteria use atmospheric H 2 as an energy source for growth and survival 1 . This globally significant process regulates the composition of the atmosphere, enhances soil bio ersity and drives primary production in extreme environments 2,3 . Atmospheric H 2 oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfamily 4,5 . However, it remains unresolved how these enzymes overcome the extraordinary catalytic challenge of oxidizing picomolar levels of H 2 amid ambient levels of the catalytic poison O 2 and how the derived electrons are transferred to the respiratory chain 1 . Here we determined the cryo-electron microscopy structure of the Mycobacterium smegmatis hydrogenase Huc and investigated its mechanism. Huc is a highly efficient oxygen-insensitive enzyme that couples oxidation of atmospheric H 2 to the hydrogenation of the respiratory electron carrier menaquinone. Huc uses narrow hydrophobic gas channels to selectively bind atmospheric H 2 at the expense of O 2 , and 3 [3Fe–4S] clusters modulate the properties of the enzyme so that atmospheric H 2 oxidation is energetically feasible. The Huc catalytic subunits form an octameric 833 kDa complex around a membrane-associated stalk, which transports and reduces menaquinone 94 Å from the membrane. These findings provide a mechanistic basis for the biogeochemically and ecologically important process of atmospheric H 2 oxidation, uncover a mode of energy coupling dependent on long-range quinone transport, and pave the way for the development of catalysts that oxidize H 2 in ambient air.
Mycobacteria tolerate carbon monoxide by remodelling their respiratory chain
Publisher: Cold Spring Harbor Laboratory
Date: 09-04-2020
DOI: 10.1101/2020.04.08.032912
Abstract: Carbon monoxide (CO) is a gas infamous for its acute toxicity. The toxicity of CO predominantly stems from its tendency to form carbonyl complexes with transition metals, thus inhibiting the heme-prosthetic groups of proteins, including the terminal oxidases of the respiratory chain. While CO has been proposed as an antibacterial agent, the evidence supporting its toxicity towards bacteria is equivocal, and its cellular targets remain poorly defined. In this work, we investigate the physiological response of mycobacteria to CO. We show that Mycobacterium smegmatis is highly resistant to the toxic effects of CO, exhibiting normal growth parameters when cultured in its presence. We profiled the proteome of M. smegmatis during growth in CO, identifying strong induction of cytochrome bd oxidase and members of the dos regulon, but relatively few other changes. We show that the activity of cytochrome bd oxidase is resistant to CO, whereas cytochrome bcc-aa 3 oxidase is strongly inhibited by this gas. Consistent with these findings, growth analysis shows that M. smegmatis lacking cytochrome bd oxidase displays a significant growth defect in the presence of CO, while induction of the dos regulon appears to be unimportant for adaption to CO. Altogether, our findings suggest that M. smegmatis has considerable resistance to CO and benefits from respiratory flexibility to withstand its inhibitory effects. Carbon monoxide has an infamous reputation as a toxic gas and it has been suggested that it has potential as an antibacterial agent. Despite this, the means by which bacteria resist its toxic effects are not well understood. In this study we determine the physiological response of Mycobacterium smegmatis to growth in CO. We show for the first time that the cytochrome bd oxidase is inherently resistant to CO and is deployed by M. smegmatis to tolerate the presence of this gas. Further, we show that aside from this remodelling of its respiratory chain, M. smegmatis makes few other functional changes to its proteome, suggesting it has a high level of inherent resistance to CO.
Cellular and Structural Basis of Synthesis of the Unique Intermediate Dehydro-F420-0 in Mycobacteria
Publisher: American Society for Microbiology
Date: 30-06-2020
DOI: 10.1128/MSYSTEMS.00389-20
Abstract: Mycobacteria are major environmental microorganisms and cause many significant diseases, including tuberculosis. Mycobacteria make an unusual vitamin-like compound, F 420 , and use it to both persist during stress and resist antibiotic treatment. Understanding how mycobacteria make F 420 is important, as this process can be targeted to create new drugs to combat infections like tuberculosis. In this study, we show that mycobacteria make F 420 in a way that is different from other bacteria. We studied the molecular machinery that mycobacteria use to make F 420 , determining the chemical mechanism for this process and identifying a novel chemical intermediate. These findings also have clinical relevance, given that two new prodrugs for tuberculosis treatment are activated by F 420 .
The crystal structure of the TonB-dependent transporter YncD reveals a positively charged substrate-binding site
Publisher: International Union of Crystallography (IUCr)
Date: 27-04-2020
DOI: 10.1107/S2059798320004398
Abstract: The outer membrane of Gram-negative bacteria is highly impermeable to hydrophilic molecules of larger than 600 Da, protecting these bacteria from toxins present in the environment. In order to transport nutrients across this impermeable membrane, Gram-negative bacteria utilize a erse family of outer-membrane proteins called TonB-dependent transporters. The majority of the members of this family transport iron-containing substrates. However, it is becoming increasingly clear that TonB-dependent transporters target chemically erse substrates. In this work, the structure and phylogenetic distribution of the TonB-dependent transporter YncD are investigated. It is shown that while YncD is present in some enteropathogens, including Escherichia coli and Salmonella spp., it is also widespread in Gammaproteobacteria and Betaproteobacteria of environmental origin. The structure of YncD was determined, showing that despite a distant evolutionary relationship, it shares structural features with the ferric citrate transporter FecA, including a compact positively charged substrate-binding site. Despite these shared features, it is shown that YncD does not contribute to the growth of E. coli in pure culture under iron-limiting conditions or with ferric citrate as an iron source. Previous studies of transcriptional regulation in E. coli show that YncD is not induced under iron-limiting conditions and is unresponsive to the ferric uptake regulator (Fur). These observations, combined with the data presented here, suggest that YncD is not responsible for the transport of an iron-containing substrate.
Protein target highlights in CASP15 : Analysis of models by structure providers
Publisher: Wiley
Date: 26-07-2023
DOI: 10.1002/PROT.26545
Abstract: We present an in‐depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three‐dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.
Trace gas oxidizers are widespread and active members of soil microbial communities
Publisher: Springer Science and Business Media LLC
Date: 04-01-2021
DOI: 10.1038/S41564-020-00811-W
Abstract: Soil microorganisms globally are thought to be sustained primarily by organic carbon sources. Certain bacteria also consume inorganic energy sources such as trace gases, but they are presumed to be rare community members, except within some oligotrophic soils. Here we combined metagenomic, biogeochemical and modelling approaches to determine how soil microbial communities meet energy and carbon needs. Analysis of 40 metagenomes and 757 derived genomes indicated that over 70% of soil bacterial taxa encode enzymes to consume inorganic energy sources. Bacteria from 19 phyla encoded enzymes to use the trace gases hydrogen and carbon monoxide as supplemental electron donors for aerobic respiration. In addition, we identified a fourth phylum (Gemmatimonadota) potentially capable of aerobic methanotrophy. Consistent with the metagenomic profiling, communities within soil profiles from erse habitats rapidly oxidized hydrogen, carbon monoxide and to a lesser extent methane below atmospheric concentrations. Thermodynamic modelling indicated that the power generated by oxidation of these three gases is sufficient to meet the maintenance needs of the bacterial cells capable of consuming them. Diverse bacteria also encode enzymes to use trace gases as electron donors to support carbon fixation. Altogether, these findings indicate that trace gas oxidation confers a major selective advantage in soil ecosystems, where availability of preferred organic substrates limits microbial growth. The observation that inorganic energy sources may sustain most soil bacteria also has broad implications for understanding atmospheric chemistry and microbial bio ersity in a changing world.
Atmospheric hydrogen oxidation extends to the domain archaea
Publisher: Cold Spring Harbor Laboratory
Date: 13-12-2022
DOI: 10.1101/2022.12.13.520232
Abstract: Diverse aerobic bacteria use atmospheric hydrogen (H 2 ) and carbon monoxide (CO) as energy sources to support growth and survival. Though recently discovered, trace gas oxidation is now recognised as a globally significant process that serves as the main sink in the biogeochemical H 2 cycle and sustains microbial bio ersity in oligotrophic ecosystems. While trace gas oxidation has been reported in nine phyla of bacteria, it was not known whether archaea also use atmospheric H 2 . Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H 2 and CO to sub-atmospheric levels. Oxidation occurred during both growth and survival across a wide range of temperatures (10 to 70°C). Genomic analysis demonstrated that A. brierleyi encodes a canonical carbon monoxide dehydrogenase and, unexpectedly, four distinct [NiFe]-hydrogenases from subgroups not known to mediate aerobic H 2 uptake. Quantitative proteomic analyses showed that A. brierleyi differentially produced these enzymes in response to electron donor and acceptor availability. A previously unidentified group 1 [NiFe]-hydrogenase, with a unique genetic arrangement, is constitutively expressed and upregulated during stationary phase and aerobic hydrogenotrophic growth. Another archaeon, Metallosphaera sedula , was also found to oxidize atmospheric H 2 . These results suggest that trace gas oxidation is a common trait of aerobic archaea, which likely plays a role in their survival and niche expansion, including during dispersal through temperate environments. These findings also demonstrate that atmospheric H 2 consumption is a cross-domain phenomenon, suggesting an ancient origin of this trait, and identify previously unknown microbial and enzymatic sinks of atmospheric H 2 and CO.
The modular nature of the β-barrel assembly machinery, illustrated in Borrelia burgdorferi
Publisher: Wiley
Date: 30-09-2016
DOI: 10.1111/MMI.13527
Abstract: Diderm bacteria have an outer membrane that provides defense against environmental factors including antibiotics. Understanding the process of outer membrane biogenesis is, therefore, of critical importance in order to envisage new treatments of these bacterial pathogens. Borrelia burgdorferi is the pathogen responsible for Lyme disease. Its outer membrane contains integral, β-barrel proteins as well as swathes of externally exposed lipoproteins. Previous work has demonstrated that the β-barrel assembly machine (BAM complex) in B. burgdorferi and other Spirochetes shares several similarities with the BAM complex in other bacterial lineages, such as the Proteobacteria that includes Escherichia coli. However, Iqbal et al. () have identified the inner membrane protein TamB as a subunit of the BAM complex in Spirochetes. This latest study highlights the modular nature of the BAM complex, and suggests that in some bacterial lineages the BAM complex and translocation and assembly module (the TAM) function as a single unit.
Discovery, characterization and in vivo activity of pyocin SD2, a protein antibiotic from Pseudomonas aeruginosa
Publisher: Portland Press Ltd.
Date: 28-07-2016
DOI: 10.1042/BCJ20160470
Abstract: Increasing rates of antibiotic resistance among Gram-negative pathogens such as Pseudomonas aeruginosa means alternative approaches to antibiotic development are urgently required. Pyocins, produced by P. aeruginosa for intraspecies competition, are highly potent protein antibiotics known to actively translocate across the outer membrane of P. aeruginosa. Understanding and exploiting the mechanisms by which pyocins target, penetrate and kill P. aeruginosa is a promising approach to antibiotic development. In this work we show the therapeutic potential of a newly identified tRNase pyocin, pyocin SD2, by demonstrating its activity in vivo in a murine model of P. aeruginosa lung infection. In addition, we propose a mechanism of cell targeting and translocation for pyocin SD2 across the P. aeruginosa outer membrane. Pyocin SD2 is concentrated at the cell surface, via binding to the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide (LPS), from where it can efficiently locate its outer membrane receptor FpvAI. This strategy of utilizing both the CPA and a protein receptor for cell targeting is common among pyocins as we show that pyocins S2, S5 and SD3 also bind to the CPA. Additional data indicate a key role for an unstructured N-terminal region of pyocin SD2 in the subsequent translocation of the pyocin into the cell. These results greatly improve our understanding of how pyocins target and translocate across the outer membrane of P. aeruginosa. This knowledge could be useful for the development of novel anti-pseudomonal therapeutics and will also support the development of pyocin SD2 as a therapeutic in its own right.
The crystal structure of the TonB-dependent transporter YncD reveals a positively charged substrate binding site
Publisher: Cold Spring Harbor Laboratory
Date: 31-01-2020
DOI: 10.1101/2020.01.29.925891
Abstract: The outer membrane of Gram-negative bacteria is highly impermeable to hydrophilic molecules larger than 600 Da, protecting these bacteria from toxins present in the environment. In order to transport nutrients across this impermeable membrane, Gram-negative bacteria utilise a erse family of outer-membrane proteins called TonB-dependent transporters. The majority of this family transport iron-containing substrates. However, it is becoming increasingly clear that TonB-dependent transporters target chemically erse substrates. In this work, we investigate the structure and phylogenetic distribution of the TonB-dependent transporter YncD. We show that while YncD is present in some enteropathogens including E. coli and Salmonella spp., it is also widespread in Gamma and Betaproteobacteria of environmental origin. We determine the structure of YncD, showing that despite a distant evolutionary relationship, it shares structural features with the ferriccitrate transporter FecA, including a compact positively-charged substrate-binding site. Despite these shared features, we show that YncD does not contribute to the growth of E. coli in pure culture under-iron limiting conditions or with ferric-citrate as an iron source. Previous studies on transcriptional regulation in E. coli show that YncD is not induced under iron-limiting conditions and is unresponsive to the Ferric uptake regulator (Fur). These observations combined with the data we present, suggest that YncD is not responsible for the transport of an iron-containing substrate.
Cellular and structural basis of synthesis of the unique intermediate dehydro-F420-0 in mycobacteria
Publisher: Cold Spring Harbor Laboratory
Date: 28-02-2020
DOI: 10.1101/2020.02.27.968891
Abstract: F 420 is a low-potential redox cofactor used by erse bacteria and archaea. In mycobacteria, this cofactor has multiple roles, including adaptation to redox stress, cell wall biosynthesis, and activation of the clinical antitubercular prodrugs pretomanid and delamanid. A recent biochemical study proposed a revised biosynthesis pathway for F 420 in mycobacteria it was suggested that phosphoenolpyruvate served as a metabolic precursor for this pathway, rather than 2-phospholactate as long proposed, but these findings were subsequently challenged. In this work, we combined metabolomic, genetic, and structural analyses to resolve these discrepancies and determine the basis of F 420 biosynthesis in mycobacterial cells. We show that, in whole cells of Mycobacterium smegmatis , phosphoenolpyruvate rather than 2-phospholactate stimulates F 420 biosynthesis. Analysis of F 420 biosynthesis intermediates present in M. smegmatis cells harboring genetic deletions at each step of the biosynthetic pathway confirmed that phosphoenolpyruvate is then used to produce the novel precursor compound dehydro-F 420 -0. To determine the structural basis of dehydro-F 420 -0 production, we solved high-resolution crystal structures of the enzyme responsible (FbiA) in apo, substrate, and product bound forms. These data show the essential role of a single alent cation in coordinating the catalytic pre-complex of this enzyme and demonstrate that dehydro-F 420 -0 synthesis occurs through a direct substrate transfer mechanism. Together, these findings resolve the biosynthetic pathway of F 420 in mycobacteria and have significant implications for understanding the emergence of antitubercular prodrug resistance.
Structures of the Ultra-High-Affinity Protein–Protein Complexes of Pyocins S2 and AP41 and Their Cognate Immunity Proteins from Pseudomonas aeruginosa
Publisher: Elsevier BV
Date: 08-2015
Plumage redness signals mitochondrial function in the House Finch
Publisher: Cold Spring Harbor Laboratory
Date: 08-08-2019
DOI: 10.1101/728873
Abstract: Carotenoid coloration is widely recognized as a signal of in idual condition in various animals, but despite decades of study, the mechanisms that link carotenoid coloration to condition remain unresolved. Most birds with red feathers convert yellow dietary carotenoids to red carotenoids in an oxidation process requiring the gene encoding the putative cytochrome P450 enzyme CYP2J19. Here, we tested the hypothesis that the process of carotenoid oxidation and feather pigmentation is functionally linked to mitochondrial performance. Consistent with this hypothesis, we observed high levels of red ketolated carotenoids associated with the hepatic mitochondria of molting wild house finches ( Haemorhous mexicanus ), and upon fractionation, we found the highest concentration of ketolated carotenoids in the inner mitochondrial membrane. We further found that the redness of growing feathers was positively related to the performance of liver mitochondria. Structural modeling of CYP2J19 supports a direct role of this protein in carotenoid ketolation that may be functionally linked to cellular respiration. These observations suggest that feather coloration serves as a signal of core functionality through inexorable links to cellular respiration in the mitochondria.
A Highly Conserved Bacterial D-Serine Uptake System Links Host Metabolism and Virulence
Publisher: Public Library of Science (PLoS)
Date: 04-01-2016
The Structure of a Conserved Domain of TamB Reveals a Hydrophobic β Taco Fold.
Publisher: Elsevier BV
Date: 12-2017
A widely distributed hydrogenase oxidises atmospheric H(2)during bacterial growth
Publisher: Springer Science and Business Media LLC
Date: 09-07-2020
DOI: 10.1038/S41396-020-0713-4
Abstract: Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H 2 ) using group 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to recycle H 2 produced by nitrogenase. However, given this hydrogenase is also present in various heterotrophs and lithoautotrophs lacking nitrogenases, it may play a wider role in bacterial metabolism. Here we investigated the role of this enzyme in three species from different phylogenetic lineages and ecological niches: Acidithiobacillus ferrooxidans (phylum Proteobacteria), Chloroflexus aggregans (phylum Chloroflexota), and Gemmatimonas aurantiaca (phylum Gemmatimonadota). qRT-PCR analysis revealed that the group 2a [NiFe]-hydrogenase of all three species is significantly upregulated during exponential growth compared to stationary phase, in contrast to the profile of the persistence-linked group 1h [NiFe]-hydrogenase. Whole-cell biochemical assays confirmed that all three strains aerobically respire H 2 to sub-atmospheric levels, and oxidation rates were much higher during growth. Moreover, the oxidation of H 2 supported mixotrophic growth of the carbon-fixing strains C. aggregans and A. ferrooxidans . Finally, we used phylogenomic analyses to show that this hydrogenase is widely distributed and is encoded by 13 bacterial phyla. These findings challenge the current persistence-centric model of the physiological role of atmospheric H 2 oxidation and extend this process to two more phyla, Proteobacteria and Gemmatimonadota. In turn, these findings have broader relevance for understanding how bacteria conserve energy in different environments and control the biogeochemical cycling of atmospheric trace gases.
Developing high-affinity, oxygen-insensitive [NiFe]-hydrogenases as biocatalysts for energy conversion
Publisher: Portland Press Ltd.
Date: 25-09-2023
DOI: 10.1042/BST20230120
Lectin-Like Bacteriocins from Pseudomonas spp. Utilise D-Rhamnose Containing Lipopolysaccharide as a Cellular Receptor
Publisher: Public Library of Science (PLoS)
Date: 06-02-2014
Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family
Publisher: Oxford University Press (OUP)
Date: 10-05-2016
DOI: 10.1093/GBE/EVW112
Recombinant expression, purification, crystallization and preliminary X-ray diffraction analysis of the C-terminal DUF490963–1138domain of TamB fromEscherichia coli
Publisher: International Union of Crystallography (IUCr)
Date: 27-08-2014
DOI: 10.1107/S2053230X14017403
Abstract: TamB is a recently described inner membrane protein that, together with its partner protein TamA, is required for the efficient secretion of a subset of autotransporter proteins in Gram-negative bacteria. In this study, the C-terminal DUF490 963–1138 domain of TamB was overexpressed in Escherichia coli K-12, purified and crystallized using the sitting-drop vapour-diffusion method. The crystals belonged to the primitive trigonal space group P 3 1 21, with unit-cell parameters a = b = 57.34, c = 220.74 Å, and diffracted to 2.1 Å resolution. Preliminary secondary-structure and X-ray diffraction analyses are reported. Two molecules are predicted to be present in the asymmetric unit. Experimental phasing using selenomethionine-labelled protein will be undertaken in the future.
Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea
Publisher: Oxford University Press (OUP)
Date: 14-04-2021
Abstract: Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
Uncovering the Metabolic Strategies of the Dormant Microbial Majority: towards Integrative Approaches.
Publisher: American Society for Microbiology
Date: 25-06-2019
DOI: 10.1128/MSYSTEMS.00107-19
Abstract: A grand challenge in microbiology is to understand how the dormant majority lives. In natural environments, most microorganisms are not growing and instead exist in a spectrum of dormant states.
Structure of the bacterial plant-ferredoxin receptor FusA
Publisher: Springer Science and Business Media LLC
Date: 31-10-2016
DOI: 10.1038/NCOMMS13308
Abstract: Iron is a limiting nutrient in bacterial infection putting it at the centre of an evolutionary arms race between host and pathogen. Gram-negative bacteria utilize TonB-dependent outer membrane receptors to obtain iron during infection. These receptors acquire iron either in concert with soluble iron-scavenging siderophores or through direct interaction and extraction from host proteins. Characterization of these receptors provides invaluable insight into pathogenesis. However, only a subset of virulence-related TonB-dependent receptors have been currently described. Here we report the discovery of FusA, a new class of TonB-dependent receptor, which is utilized by phytopathogenic Pectobacterium spp. to obtain iron from plant ferredoxin. Through the crystal structure of FusA we show that binding of ferredoxin occurs through specialized extracellular loops that form extensive interactions with ferredoxin. The function of FusA and the presence of homologues in clinically important pathogens suggests that small iron-containing proteins represent an iron source for bacterial pathogens.
Structure of protease-cleavedEscherichia coliα-2-macroglobulin reveals a putative mechanism of conformational activation for protease entrapment
Publisher: International Union of Crystallography (IUCr)
Date: 30-06-2015
DOI: 10.1107/S1399004715008548
Abstract: Bacterial α-2-macroglobulins have been suggested to function in defence as broad-spectrum inhibitors of host proteases that breach the outer membrane. Here, the X-ray structure of protease-cleaved Escherichia coli α-2-macroglobulin is described, which reveals a putative mechanism of activation and conformational change essential for protease inhibition. In this competitive mechanism, protease cleavage of the bait-region domain results in the untethering of an intrinsically disordered region of this domain which disrupts native interdomain interactions that maintain E. coli α-2-macroglobulin in the inactivated form. The resulting global conformational change results in entrapment of the protease and activation of the thioester bond that covalently links to the attacking protease. Owing to the similarity in structure and domain architecture of Escherichia coli α-2-macroglobulin and human α-2-macroglobulin, this protease-activation mechanism is likely to operate across the erse members of this group.
An obligate aerobe adapts to hypoxia by hybridising fermentation with carbon storage
Publisher: Cold Spring Harbor Laboratory
Date: 12-09-2023
Mycobacteria Tolerate Carbon Monoxide by Remodeling Their Respiratory Chain
Publisher: American Society for Microbiology
Date: 29-06-2021
DOI: 10.1128/MSYSTEMS.01292-20
Abstract: Carbon monoxide has an infamous reputation as a toxic gas, and it has been suggested that it has potential as an antibacterial agent. Despite this, how bacteria resist its toxic effects is not well understood.
Energy extraction from air: structural basis of atmospheric hydrogen oxidation
Publisher: Cold Spring Harbor Laboratory
Date: 10-10-2022
DOI: 10.1101/2022.10.09.511488
Abstract: Diverse aerobic bacteria use atmospheric H 2 as an energy source for growth and survival. This recently discovered yet globally significant process regulates the composition of the atmosphere, enhances soil bio ersity, and drives primary production in certain extreme environments. Atmospheric H 2 oxidation has been attributed to still uncharacterised members of the [NiFe]-hydrogenase superfamily. However, it is unresolved how these enzymes overcome the extraordinary catalytic challenge of selectively oxidizing picomolar levels of H 2 amid ambient levels of the catalytic poison O 2 , and how the derived electrons are transferred to the respiratory chain. Here we determined the 1.52 Å resolution CryoEM structure of the mycobacterial hydrogenase Huc and investigated its mechanism by integrating kinetics, electrochemistry, spectroscopy, mass spectrometry, and molecular dynamics simulations. Purified Huc is an oxygen-insensitive enzyme that couples the oxidation of atmospheric H 2 at its large subunit to the hydrogenation of the respiratory electron carrier menaquinone at its small subunit. The enzyme uses a narrow hydrophobic gas channel to selectively bind atmospheric H 2 at the expense of O 2 , while three [3Fe-4S] clusters and their unusual ligation by a D-histidine modulate the electrochemical properties of the enzyme such that atmospheric H 2 oxidation is energetically feasible. Huc forms an 833 kDa complex composed of an octamer of catalytic subunits around a membrane-associated central stalk, which extracts and transports menaquinone a remarkable 94 Å from the membrane, enabling its reduction. These findings provide a mechanistic basis for the biogeochemically and ecologically critical process of atmospheric H 2 oxidation. Through the first characterisation of a group 2 [NiFe]-hydrogenase, we also uncover a novel mode of energy coupling dependent on long-range quinone transport and pave way for the development of biocatalysts that oxidize H 2 in ambient air.
The Crystal Structure of the Lipid II-degrading Bacteriocin Syringacin M Suggests Unexpected Evolutionary Relationships between Colicin M-like Bacteriocins
Publisher: Elsevier BV
Date: 11-2012
Target highlights in CASP14 : Analysis of models by structure providers
Publisher: Wiley
Date: 10-10-2021
DOI: 10.1002/PROT.26247
Abstract: The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three‐dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically‐relevant properties of proteins.
Two uptake hydrogenases differentially interact with the aerobic respiratory chain during mycobacterial growth and persistence
Publisher: Elsevier BV
Date: 12-2019
The architecture and stabilisation of flagellotropic tailed bacteriophages
Publisher: Springer Science and Business Media LLC
Date: 27-07-2020
DOI: 10.1038/S41467-020-17505-W
Abstract: Flagellotropic bacteriophages engage flagella to reach the bacterial surface as an effective means to increase the capture radius for predation. Structural details of these viruses are of great interest given the substantial drag forces and torques they face when moving down the spinning flagellum. We show that the main capsid and auxiliary proteins form two nested chainmails that ensure the integrity of the bacteriophage head. Core stabilising structures are conserved in herpesviruses suggesting their ancestral origin. The structure of the tail also reveals a robust yet pliable assembly. Hexameric rings of the tail-tube protein are braced by the N-terminus and a β-hairpin loop, and interconnected along the tail by the splayed β-hairpins. By contrast, we show that the β-hairpin has an inhibitory role in the tail-tube precursor, preventing uncontrolled self-assembly. Dyads of acidic residues inside the tail-tube present regularly-spaced motifs well suited to DNA translocation into bacteria through the tail.
Plumage redness signals mitochondrial function in the house finch
Publisher: The Royal Society
Date: 25-09-2019
Abstract: Carotenoid coloration is widely recognized as a signal of in idual condition in various animals, but despite decades of study, the mechanisms that link carotenoid coloration to condition remain unresolved. Most birds with red feathers convert yellow dietary carotenoids to red carotenoids in an oxidation process requiring the gene encoding the putative cytochrome P450 enzyme CYP2J19. Here, we tested the hypothesis that the process of carotenoid oxidation and feather pigmentation is functionally linked to mitochondrial performance. Consistent with this hypothesis, we observed high levels of red ketolated carotenoids associated with the hepatic mitochondria of moulting wild house finches ( Haemorhous mexicanus ), and upon fractionation, we found the highest concentration of ketolated carotenoids in the inner mitochondrial membrane. We further found that the redness of growing feathers was positively related to the performance of liver mitochondria. Structural modelling of CYP2J19 supports a direct role of this protein in carotenoid ketolation that may be functionally linked to cellular respiration. These observations suggest that feather coloration serves as a signal of core functionality through inexorable links to cellular respiration in the mitochondria.
Structure of the atypical bacteriocin pectocin M 2 implies a novel mechanism of protein uptake
Publisher: Wiley
Date: 18-06-2014
DOI: 10.1111/MMI.12655
Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils
Publisher: Proceedings of the National Academy of Sciences
Date: 03-11-2021
Abstract: Diverse microbial life has been detected in the cold desert soils of Antarctica once thought to be barren. Here, we provide metagenomic, biogeochemical, and culture-based evidence that Antarctic soil microorganisms are phylogenetically and functionally distinct from those in other soils and adopt various metabolic and ecological strategies. The most abundant community members are metabolically versatile aerobes that use ubiquitous atmospheric trace gases to potentially meet energy, carbon, and, through metabolic water production, hydration needs. Lineages capable of harvesting solar energy, oxidizing edaphic inorganic substrates, or adopting symbiotic lifestyles were also identified. Altogether, these findings provide insights into microbial adaptation to extreme water and energy limitation and will inform ongoing efforts to conserve the unique bio ersity on this continent.
Bacteriocins active against plant pathogenic bacteria
Publisher: Portland Press Ltd.
Date: 21-11-2012
DOI: 10.1042/BST20120206
Abstract: Gram-negative phytopathogens cause significant losses in a erse range of economically important crop plants. The effectiveness of traditional countermeasures, such as the breeding and introduction of resistant cultivars, is often limited by the dearth of available sources of genetic resistance. An alternative strategy to reduce loss to specific bacterial phytopathogens is to use narrow-spectrum protein antibiotics such as colicin-like bacteriocins as biocontrol agents. A number of colicin-like bacteriocins active against phytopathogenic bacteria have been described previously as have strategies for their application to biocontrol. In the present paper, we discuss these strategies and our own recent work on the identification and characterization of candidate bacteriocins and how these potent and selective antimicrobial agents can be effectively applied to the control of economically important plant disease.
Ferredoxin Containing Bacteriocins Suggest a Novel Mechanism of Iron Uptake in Pectobacterium spp
Publisher: Public Library of Science (PLoS)
Date: 09-03-2012
BonA from Acinetobacter baumannii Forms a Divisome-Localized Decamer That Supports Outer Envelope Function
Publisher: American Society for Microbiology
Date: 31-08-2021
Abstract: The pathogen Acinetobacter baumannii is considered an urgent threat to human health. A. baumannii is highly resistant to treatment with antibiotics, in part due to its protective cell envelope. This bacterium is only distantly related to other bacterial pathogens, so its cell envelope has distinct properties and contains components distinct from those of other bacteria that support its function.
FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants.
Publisher: Public Library of Science (PLoS)
Date: 02-08-2018
Protease-associated import systems are widespread in Gram-negative bacteria
Publisher: Public Library of Science (PLoS)
Date: 15-10-2019
Lipid II-Degrading M-Class Bacteriocins
Publisher: Wiley
Date: 16-06-2014
DOI: 10.1002/9781119951438.EIBC2272
Abstract: Lipid II ‐degrading M‐class bacteriocins are protein antibiotics that kill a narrow spectrum of bacterial strains through cleavage of lipid II , thereby leading to an arrest of cell wall synthesis and cell lysis. A number of M‐class bacteriocins have been structurally and functionally characterized, which include colicin M from Escherichia coli , syringacin M from Pseudomonas syringae , and pyocin M (PaeM) from P. aeruginosa . In each case, these bacteriocins have been shown to kill bacteria closely related to the producing strain, with selectivity mediated through the presence of a specific outer membrane receptor. Cell killing requires uptake of the bacteriocin into the periplasm where it is able to cleave lipid II in a metal‐dependent manner. Calcium and magnesium have been shown to support enzymatic activity, and X‐ray crystal structures of syringacin M and PaeM, respectively, show these ions bound at the putative active site. Extensive structural and mutagenesis studies have enabled delineation of the functional domains of the M‐class bacteriocins that mediate receptor binding, translocation across the outer membrane, and cytotoxic activity.
Determination of the molecular basis for coprogen import by Gram-negative bacteria
Publisher: International Union of Crystallography (IUCr)
Date: 05-04-2019
DOI: 10.1107/S2052252519002926
Abstract: In order to survive in mixed microbial communities, some species of fungi secrete coprogens, siderophores that facilitate capture of the scarce nutrient iron. The TonB-dependent transporter FhuE is integrated in the outer membrane of Gram-negative bacteria and has been reported to scavenge these fungally produced coprogens. In this work, an Escherichia coli strain was engineered that is dependent solely on FhuE for its access to siderophore-sequestered iron. Using this tool, it is shown that while FhuE is highly active in the import of coprogens, it has some level of promiscuity, acting as a low-affinity transporter for related siderophores. The crystal structure of FhuE in complex with coprogen was determined, providing a structural basis to explain this selective promiscuity. The structural data, in combination with functional analysis, presented in this work show that FhuE has evolved to specifically engage with planar siderophores. A potential evolutionary driver, and a critical consequence of this selectivity, is that it allows FhuE to exclude antibiotics that mimic nonplanar hydroxamate siderophores: these toxic molecules could otherwise cross the outer membrane barrier through a Trojan horse mechanism.
The structure of the iron-catecholate transporter Fiu suggests substrate import occurs via a 2-step mechanism
Publisher: Cold Spring Harbor Laboratory
Date: 09-09-2019
DOI: 10.1101/763268
Abstract: The Ferric Iron Uptake (Fiu) transporter from Escherichia coli functions in the transport of iron-catecholate complexes across the bacterial outer membrane, providing the bacterium with iron which is an essential element for growth. Recently, it became clear that Fiu also represents a liability: its activity allows the import of antimicrobial compounds that have evolved to mimic catecholate. In this work we have determined the structure of Fiu and analyzed its function to address how Fiu and related transporters from other bacterial species can bind catecholate in a surface-exposed cavity. In addition, the crystal structure of Fiu reveals the presence of a large, selectively gated cavity in the interior of this transporter. This chamber is large enough to accommodate the Fiu substrate and may act to regulate substrate import. These data provide insight into the mechanism of substrate uptake by Fiu and related transporters identified in Pseudomonas aeruginosa and Acinetobacter baumannii . As Fiu and its homologues are the targets of substrate mimicking antibiotics, these data will assist in the development of antibiotics that target these receptors for cell entry.
A genome compendium reveals diverse metabolic adaptations of Antarctic soil microorganisms
Publisher: Cold Spring Harbor Laboratory
Date: 06-08-2020
DOI: 10.1101/2020.08.06.239558
Abstract: A surprising ersity and abundance of microorganisms resides in the cold desert soils of Antarctica. The metabolic processes that sustain them, however, are poorly understood. In this study, we used metagenomic and biogeochemical approaches to study the microbial communities in 16 physicochemically erse mountainous and glacial soils from remote sites in South Victoria Land, north of the Mackay Glacier. We assembled 451 metagenome-assembled genomes from 18 bacterial and archaeal phyla, constituting the largest resource of Antarctic soil microbial genomes to date. The most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen and carbon monoxide to meet energy, carbon, and, through metabolic water production, hydration needs. Phylogenetic analysis and structural modelling infer that bacteria from nine phyla can scavenge atmospheric hydrogen using a previously unreported enzyme family, the group 1l [NiFe]-hydrogenases. Consistently, gas chromatography measurements confirmed most soils rapidly consume atmospheric hydrogen and carbon monoxide, and provide the first experimental evidence of methane oxidation in non-maritime Antarctica. We also recovered genomes of microorganisms capable of oxidizing other inorganic compounds, including nitrogen, sulfur, and iron compounds, as well as harvesting solar energy via photosystems and novel microbial rhodopsins. Bacterial lineages defined by symbiotic lifestyles, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also surprisingly abundant. We conclude that the dominant microorganisms in Antarctic soils adopt mixotrophic strategies for energy and sometimes carbon acquisition, though they co-exist with erse bacteria and archaea that adopt more specialist lifestyles. These unprecedented insights and associated genome compendium will inform efforts to protect bio ersity in this continent.
BonA from Acinetobacter baumannii forms a divisome-localized decamer that supports outer envelope function
Publisher: Cold Spring Harbor Laboratory
Date: 02-09-2020
DOI: 10.1101/2020.09.01.278697
Abstract: Acinetobacter baumannii is a high-risk pathogen due to the rapid global spread of multi-drug resistant lineages. Its phylogenetic ergence from other ESKAPE pathogens means that determinants of its antimicrobial resistance can be difficult to extrapolate from other widely studied bacteria. A recent study showed that A. baumannii upregulates production of an outer-membrane lipoprotein, which we designate BonA, in response to challenge with polymyxins. Here we show that BonA has limited sequence similarity and distinct structural features compared to lipoproteins from other bacterial species. Analyses through X-ray crystallography, small-angle X-ray scattering, electron microscopy, and multiangle light scattering demonstrate that BonA has a dual BON-domain architecture and forms a decamer via an unusual oligomerization mechanism. This analysis also indicates this decamer is transient, suggesting dynamic oligomerization plays a role in BonA function. Antisera recognizing BonA shows it is an outer membrane protein localized to the isome. Loss of BonA modulates the density of the outer membrane, consistent with a change in its structure or link to the peptidoglycan, and prevents motility in a clinical strain (ATCC 17978). Consistent with these findings, the dimensions of the BonA decamer are sufficient to permeate the peptidoglycan layer, with the potential to form a membrane-spanning complex during cell ision.
Structural basis of substrate recognition and catalysis by fucosyltransferase 8
Publisher: Cold Spring Harbor Laboratory
Date: 15-02-2020
DOI: 10.1101/2020.02.14.949818
Abstract: Fucosylation of the inner-most N-acetyl-glucosamine (GlcNAc) of N-glycans by fucosyltransferase 8 (FUT8) is an important step in the maturation of complex and hybrid N-glycans. This simple modification can have a dramatic impact on the activity and half-life of glycoproteins. These effects are relevant to understanding the invasiveness of some cancers, the development of monoclonal antibody therapeutics, and to a congenital disorder of glycosylation. The acceptor substrate preferences of FUT8 are well characterised and provide a framework for understanding N-glycan maturation in the Golgi, however the structural basis for these substrate preferences and the mechanism through which catalysis is achieved remains unknown. Here, we describe several structures of mouse and human FUT8 in the apo state and in complex with guanosine diphosphate (GDP), a mimic of the donor substrate, and a glycopeptide acceptor substrate. These structures provide insights into: a unique conformational change associated with donor substrate binding common strategies employed by fucosyltransferases to coordinate GDP features that define acceptor substrate preferences and a likely mechanism for enzyme catalysis. Together with molecular dynamics simulations, the structures also reveal how FUT8 dimerisation plays an important role in defining the acceptor substrate binding site. Collectively, this information significantly builds on our understanding of the core-fucosylation process.
The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre
Publisher: Wiley
Date: 09-10-2019
DOI: 10.1111/MMI.14396
Abstract: The discovery of a Salmonella-targeting phage from the waterways of the United Kingdom provided an opportunity to address the mechanism by which Chi-like bacteriophage (phage) engages with bacterial flagellae. The long tail fibre seen on Chi-like phages has been proposed to assist the phage particle in docking to a host cell flagellum, but the identity of the protein that generates this fibre was unknown. We present the results from genome sequencing of this phage, YSD1, confirming its close relationship to the original Chi phage and suggesting candidate proteins to form the tail structure. Immunogold labelling in electron micrographs revealed that YSD1_22 forms the main shaft of the tail tube, while YSD1_25 forms the distal part contributing to the tail spike complex. The long curling tail fibre is formed by the protein YSD1_29, and treatment of phage with the antibodies that bind YSD1_29 inhibits phage infection of Salmonella. The host range for YSD1 across Salmonella serovars is broad, but not comprehensive, being limited by antigenic features of the flagellin subunits that make up the Salmonella flagellum, with which YSD1_29 engages to initiate infection.
Reductive evolution in outer membrane protein biogenesis has not compromised cell surface complexity in Helicobacter pylori
Publisher: Wiley
Date: 21-10-2017
DOI: 10.1002/MBO3.513
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University Of Glasgow
Location: United Kingdom of Great Britain and Northern Ireland
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