1
|
Lidbury IDEA, Hitchcock A, Groenhof SRM, Connolly AN, Moushtaq L. New insights in bacterial organophosphorus cycling: From human pathogens to environmental bacteria. Adv Microb Physiol 2024; 84:1-49. [PMID: 38821631 DOI: 10.1016/bs.ampbs.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
In terrestrial and aquatic ecosystems, phosphorus (P) availability controls primary production, with consequences for climate regulation and global food security. Understanding the microbial controls on the global P cycle is a prerequisite for minimising our reliance on non-renewable phosphate rock reserves and reducing pollution associated with excessive P fertiliser use. This recognised importance has reinvigorated research into microbial P cycling, which was pioneered over 75 years ago through the study of human pathogenic bacteria-host interactions. Immobilised organic P represents a significant fraction of the total P pool. Hence, microbes have evolved a plethora of mechanisms to transform this fraction into labile inorganic phosphate, the building block for numerous biological molecules. The 'genomics era' has revealed an extraordinary diversity of organic P cycling genes exist in the environment and studies going 'back to the lab' are determining how this diversity relates to function. Through this integrated approach, many hitherto unknown genes and proteins that are involved in microbial P cycling have been discovered. Not only do these fundamental discoveries push the frontier of our knowledge, but several examples also provide exciting opportunities for biotechnology and present possible solutions for improving the sustainability of how we grow our food, both locally and globally. In this review, we provide a comprehensive overview of bacterial organic P cycling, covering studies on human pathogens and how this knowledge is informing new discoveries in environmental microbiology.
Collapse
Affiliation(s)
- Ian D E A Lidbury
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom.
| | - Andrew Hitchcock
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom; Plants, Photosynthesis, and Soil, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Sophie R M Groenhof
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Alex N Connolly
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Laila Moushtaq
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| |
Collapse
|
2
|
Alrafaie AM, Stafford GP. Enterococcal bacteriophage: A survey of the tail associated lysin landscape. Virus Res 2023; 327:199073. [PMID: 36787848 DOI: 10.1016/j.virusres.2023.199073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Bacteriophages are viruses that exclusively infect bacteria which require local degradation of cell barriers. This degradation is accomplished by various lysins located mainly within the phage tail structure. In this paper we surveyed and analysed the genomes of 506 isolated bacteriophage and prophage infecting or harboured within the genomes of the medically important Enterococcus faecalis and faecium. We highlight and characterise the major features of the genomes of phage in the morphological groups podovirus, siphovirus and myovirus, and explore their categorisation according to the new ICTV classifications, with a focus on putative extracellular lysins chiefly within tail modules. Our analysis reveals a range of potential cell-wall targeting enzyme domains that are part of tail, tape measure or other predicted base structures of these phages or prophages. These largely fall into protein domains targeting pentapeptide or glycosidic linkages within peptidoglycan but also potentially the enterococcal polysaccharide antigen (EPA) and wall teichoic acids of these species (i.e., Pectinesterases and Phosphodiesterases). Notably, there is a great variety of domain architectures that reveal the diversity of evolutionary solutions to attack the Enterococcus cell wall. Despite this variety, most phage and prophage possess a putative endopeptidase (70%), reflecting the ubiquity of this cell surface barrier. We also identified a predicted lytic transglycosylase domain belonging to the glycosyl hydrolase (GH) family 23 and present exclusively within tape measure proteins. Our data also reveal distinct features of the genomes of podo-, sipho- and myo-type viruses that most likely relate to their size and complexity. Overall, we lay a foundation for expression of recombinant TAL proteins and engineering of enterococcal and other phage that will be invaluable for researchers in this field.
Collapse
Affiliation(s)
- Alhassan M Alrafaie
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, United Kingdom; Department of Medical Laboratory Sciences, College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia.
| | - Graham P Stafford
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, United Kingdom.
| |
Collapse
|
3
|
Shropshire H, Jones RA, Aguilo-Ferretjans MM, Scanlan DJ, Chen Y. Proteomics insights into the Burkholderia cenocepacia phosphorus stress response. Environ Microbiol 2021; 23:5069-5086. [PMID: 33684254 DOI: 10.1111/1462-2920.15451] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/02/2021] [Indexed: 11/26/2022]
Abstract
The Burkholderia cepacia complex is a group of Burkholderia species that are opportunistic pathogens causing high mortality rates in patients with cystic fibrosis. An environmental stress often encountered by these soil-dwelling and pathogenic bacteria is phosphorus limitation, an essential element for cellular processes. Here, we describe cellular and extracellular proteins differentially regulated between phosphate-deplete (0 mM, no added phosphate) and phosphate-replete (1 mM) growth conditions using a comparative proteomics (LC-MS/MS) approach. We observed a total of 128 and 65 unique proteins were downregulated and upregulated respectively, in the B. cenocepacia proteome. Of those downregulated proteins, many have functions in amino acid transport/metabolism. We have identified 24 upregulated proteins that are directly/indirectly involved in inorganic phosphate or organic phosphorus acquisition. Also, proteins involved in virulence and antimicrobial resistance were differentially regulated, suggesting B. cenocepacia experiences a dramatic shift in metabolism under these stress conditions. Overall, this study provides a baseline for further research into the biology of Burkholderia in response to phosphorus stress.
Collapse
Affiliation(s)
- Holly Shropshire
- BBSRC Midlands Integrative Biosciences Training Partnership, University of Warwick, Coventry, CV4 7AL, UK.,School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Rebekah A Jones
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| |
Collapse
|
4
|
Lidbury IDEA, Murphy ARJ, Fraser TD, Bending GD, Jones AME, Moore JD, Goodall A, Tibbett M, Hammond JP, Scanlan DJ, Wellington EMH. Identification of extracellular glycerophosphodiesterases in Pseudomonas and their role in soil organic phosphorus remineralisation. Sci Rep 2017; 7:2179. [PMID: 28526844 PMCID: PMC5438359 DOI: 10.1038/s41598-017-02327-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/10/2017] [Indexed: 11/11/2022] Open
Abstract
In soils, phosphorus (P) exists in numerous organic and inorganic forms. However, plants can only acquire inorganic orthophosphate (Pi), meaning global crop production is frequently limited by P availability. To overcome this problem, rock phosphate fertilisers are heavily applied, often with negative environmental and socio-economic consequences. The organic P fraction of soil contains phospholipids that are rapidly degraded resulting in the release of bioavailable Pi. However, the mechanisms behind this process remain unknown. We identified and experimentally confirmed the function of two secreted glycerolphosphodiesterases, GlpQI and GlpQII, found in Pseudomonas stutzeri DSM4166 and Pseudomonas fluorescens SBW25, respectively. A series of co-cultivation experiments revealed that in these Pseudomonas strains, cleavage of glycerolphosphorylcholine and its breakdown product G3P occurs extracellularly allowing other bacteria to benefit from this metabolism. Analyses of metagenomic and metatranscriptomic datasets revealed that this trait is widespread among soil bacteria with Actinobacteria and Proteobacteria, specifically Betaproteobacteria and Gammaproteobacteria, the likely major players.
Collapse
Affiliation(s)
- Ian D E A Lidbury
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, West Midlands, CV4 7AL, United Kingdom.
| | - Andrew R J Murphy
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Tandra D Fraser
- School of Agriculture, Policy, and Development, University of Reading, Earley Gate, Whiteknights, Reading, RG6 6AR, United Kingdom
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Alexandra M E Jones
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Jonathan D Moore
- The Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Andrew Goodall
- School of Agriculture, Policy, and Development, University of Reading, Earley Gate, Whiteknights, Reading, RG6 6AR, United Kingdom
| | - Mark Tibbett
- School of Agriculture, Policy, and Development, University of Reading, Earley Gate, Whiteknights, Reading, RG6 6AR, United Kingdom
| | - John P Hammond
- School of Agriculture, Policy, and Development, University of Reading, Earley Gate, Whiteknights, Reading, RG6 6AR, United Kingdom
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Elizabeth M H Wellington
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, West Midlands, CV4 7AL, United Kingdom
| |
Collapse
|