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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.
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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
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Wei Y, Feng LJ, Yuan XZ, Wang SG, Xia PF. Developing a Base Editing System for Marine Roseobacter Clade Bacteria. ACS Synth Biol 2023. [PMID: 37436915 DOI: 10.1021/acssynbio.3c00259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
The Roseobacter clade bacteria are of great significance in marine ecology and biogeochemical cycles, and they are potential microbial chassis for marine synthetic biology due to their versatile metabolic capabilities. Here, we adapted a CRISPR-Cas-based system, base editing, with the combination of nuclease-deactivated Cas9 and deaminase for Roseobacter clade bacteria. Taking the model roseobacter Roseovarius nubinhibens as an example, we achieved precise and efficient genome editing at single-nucleotide resolution without generating double-strand breaks or requesting donor DNAs. Since R. nubinhibens can metabolize aromatic compounds, we interrogated the key genes in the β-ketoadipate pathway with our base editing system via the introduction of premature STOP codons. The essentiality of these genes was demonstrated, and for the first time, we determined PcaQ as a transcription activator experimentally. This is the first report of CRISPR-Cas-based genome editing in the entire clade of Roseobacter bacteria. We believe that our work provides a paradigm for interrogating marine ecology and biogeochemistry with direct genotype-and-phenotype linkages and potentially opens a new avenue for the synthetic biology of marine Roseobacter bacteria.
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Affiliation(s)
- Ying Wei
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Li-Juan Feng
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Xian-Zheng Yuan
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
- Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao 266237, China
| | - Shu-Guang Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
- Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao 266237, China
| | - Peng-Fei Xia
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
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López-Lara IM, Geiger O. Membrane lipid composition defines membrane protein spectrum. Trends Microbiol 2023; 31:323-325. [PMID: 36813608 DOI: 10.1016/j.tim.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023]
Abstract
In addition to glycerophospholipids, bacterial membranes often include amino acid-containing acyloxyacyl lipids. The functional implications of these aminolipids are largely unknown. However, a recent study by Stirrup et al. expands our understanding and shows that they are major determinants for membrane properties and the relative abundance of distinct membrane proteins in bacterial membranes.
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Affiliation(s)
- Isabel M López-Lara
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Colonia Chamilpa, Cuernavaca, Morelos, Mexico
| | - Otto Geiger
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Colonia Chamilpa, Cuernavaca, Morelos, Mexico.
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Li CY, Mausz MA, Murphy A, Zhang N, Chen XL, Wang SY, Gao C, Aguilo-Ferretjans MM, Silvano E, Lidbury IDEA, Fu HH, Todd JD, Chen Y, Zhang YZ. Ubiquitous occurrence of a dimethylsulfoniopropionate ABC transporter in abundant marine bacteria. THE ISME JOURNAL 2023; 17:579-587. [PMID: 36707613 PMCID: PMC10030565 DOI: 10.1038/s41396-023-01375-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/28/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur compound in marine environments with important functions in both microorganisms and global biogeochemical carbon and sulfur cycling. The SAR11 clade and marine Roseobacter group (MRG) represent two major groups of heterotrophic bacteria in Earth's surface oceans, which can accumulate DMSP to high millimolar intracellular concentrations. However, few studies have investigated how SAR11 and MRG bacteria import DMSP. Here, through comparative genomics analyses, genetic manipulations, and biochemical analyses, we identified an ABC (ATP-binding cassette)-type DMSP-specific transporter, DmpXWV, in Ruegeria pomeroyi DSS-3, a model strain of the MRG. Mutagenesis suggested that DmpXWV is a key transporter responsible for DMSP uptake in strain DSS-3. DmpX, the substrate binding protein of DmpXWV, had high specificity and binding affinity towards DMSP. Furthermore, the DmpX DMSP-binding mechanism was elucidated from structural analysis. DmpX proteins are prevalent in the numerous cosmopolitan marine bacteria outside the SAR11 clade and the MRG, and dmpX transcription was consistently high across Earth's entire global ocean. Therefore, DmpXWV likely enables pelagic marine bacteria to efficiently import DMSP from seawater. This study offers a new understanding of DMSP transport into marine bacteria and provides novel insights into the environmental adaption of marine bacteria.
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Affiliation(s)
- Chun-Yang Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Michaela A Mausz
- School of Life Sciences, University of Warwick, CV4 7AL, Coventry, UK
| | - Andrew Murphy
- School of Life Sciences, University of Warwick, CV4 7AL, Coventry, UK
| | - Nan Zhang
- School of Bioengineering, Qilu University of Technology, Jinan, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shu-Yan Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | | | - Eleonora Silvano
- School of Life Sciences, University of Warwick, CV4 7AL, Coventry, UK
| | - Ian D E A Lidbury
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Hui-Hui Fu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, NR4 7TJ, Norwich, UK
| | - Yin Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- School of Life Sciences, University of Warwick, CV4 7AL, Coventry, UK.
| | - Yu-Zhong Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
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