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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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2
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Zhai L, Bonds AC, Smith CA, Oo H, Chou JCC, Welander PV, Dassama LMK. Novel sterol binding domains in bacteria. eLife 2024; 12:RP90696. [PMID: 38329015 PMCID: PMC10942540 DOI: 10.7554/elife.90696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
Abstract
Sterol lipids are widely present in eukaryotes and play essential roles in signaling and modulating membrane fluidity. Although rare, some bacteria also produce sterols, but their function in bacteria is not known. Moreover, many more species, including pathogens and commensal microbes, acquire or modify sterols from eukaryotic hosts through poorly understood molecular mechanisms. The aerobic methanotroph Methylococcus capsulatus was the first bacterium shown to synthesize sterols, producing a mixture of C-4 methylated sterols that are distinct from those observed in eukaryotes. C-4 methylated sterols are synthesized in the cytosol and localized to the outer membrane, suggesting that a bacterial sterol transport machinery exists. Until now, the identity of such machinery remained a mystery. In this study, we identified three novel proteins that may be the first examples of transporters for bacterial sterol lipids. The proteins, which all belong to well-studied families of bacterial metabolite transporters, are predicted to reside in the inner membrane, periplasm, and outer membrane of M. capsulatus, and may work as a conduit to move modified sterols to the outer membrane. Quantitative analysis of ligand binding revealed their remarkable specificity for 4-methylsterols, and crystallographic structures coupled with docking and molecular dynamics simulations revealed the structural bases for substrate binding by two of the putative transporters. Their striking structural divergence from eukaryotic sterol transporters signals that they form a distinct sterol transport system within the bacterial domain. Finally, bioinformatics revealed the widespread presence of similar transporters in bacterial genomes, including in some pathogens that use host sterol lipids to construct their cell envelopes. The unique folds of these bacterial sterol binding proteins should now guide the discovery of other proteins that handle this essential metabolite.
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Affiliation(s)
- Liting Zhai
- Department of Chemistry and Sarafan ChEM-H, Stanford UniversityStanfordUnited States
| | - Amber C Bonds
- Department of Earth System Science, Stanford UniversityStanfordUnited States
| | - Clyde A Smith
- Department of Chemistry and Stanford Synchrotron Radiation Lightsource, Stanford UniversityStanfordUnited States
| | - Hannah Oo
- Department of Chemistry and Sarafan ChEM-H, Stanford UniversityStanfordUnited States
| | | | - Paula V Welander
- Department of Earth System Science, Stanford UniversityStanfordUnited States
| | - Laura MK Dassama
- Department of Chemistry and Sarafan ChEM-H, Stanford UniversityStanfordUnited States
- Department of Microbiology and Immunology, Stanford University School of MedicineStanfordUnited States
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3
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Gwak JH, Awala SI, Kim SJ, Lee SH, Yang EJ, Park J, Jung J, Rhee SK. Transcriptomic Insights into Archaeal Nitrification in the Amundsen Sea Polynya, Antarctica. J Microbiol 2023; 61:967-980. [PMID: 38062325 DOI: 10.1007/s12275-023-00090-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/27/2023] [Accepted: 10/23/2023] [Indexed: 12/19/2023]
Abstract
Antarctic polynyas have the highest Southern Ocean summer primary productivity, and due to anthropogenic climate change, these areas have formed faster recently. Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant microorganisms in the ocean and play a primary role in the global nitrogen cycle. We utilized metagenomics and metatranscriptomics to gain insights into the physiology and metabolism of AOA in polar oceans, which are associated with ecosystem functioning. A polar-specific ecotype of AOA, from the "Candidatus Nitrosomarinus"-like group, was observed to be dominant in the Amundsen Sea Polynya (ASP), West Antarctica, during a succession of summer phytoplankton blooms. AOA had the highest transcriptional activity among prokaryotes during the bloom decline phase (DC). Metatranscriptomic analysis of key genes involved in ammonia oxidation, carbon fixation, transport, and cell division indicated that this polar AOA ecotype was actively involved in nitrification in the bloom DC in the ASP. This study revealed the physiological and metabolic traits of this key polar-type AOA in response to phytoplankton blooms in the ASP and provided insights into AOA functions in polar oceans.
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Affiliation(s)
- Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - So-Jeong Kim
- Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Republic of Korea
| | - Sang-Hoon Lee
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Eun-Jin Yang
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jisoo Park
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jinyoung Jung
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Ruffolo F, Dinhof T, Murray L, Zangelmi E, Chin JP, Pallitsch K, Peracchi A. The Microbial Degradation of Natural and Anthropogenic Phosphonates. Molecules 2023; 28:6863. [PMID: 37836707 PMCID: PMC10574752 DOI: 10.3390/molecules28196863] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Phosphonates are compounds containing a direct carbon-phosphorus (C-P) bond, which is particularly resistant to chemical and enzymatic degradation. They are environmentally ubiquitous: some of them are produced by microorganisms and invertebrates, whereas others derive from anthropogenic activities. Because of their chemical stability and potential toxicity, man-made phosphonates pose pollution problems, and many studies have tried to identify biocompatible systems for their elimination. On the other hand, phosphonates are a resource for microorganisms living in environments where the availability of phosphate is limited; thus, bacteria in particular have evolved systems to uptake and catabolize phosphonates. Such systems can be either selective for a narrow subset of compounds or show a broader specificity. The role, distribution, and evolution of microbial genes and enzymes dedicated to phosphonate degradation, as well as their regulation, have been the subjects of substantial studies. At least three enzyme systems have been identified so far, schematically distinguished based on the mechanism by which the C-P bond is ultimately cleaved-i.e., through either a hydrolytic, radical, or oxidative reaction. This review summarizes our current understanding of the molecular systems and pathways that serve to catabolize phosphonates, as well as the regulatory mechanisms that govern their activity.
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Affiliation(s)
- Francesca Ruffolo
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, I-43124 Parma, Italy (E.Z.)
| | - Tamara Dinhof
- Institute of Organic Chemistry, Faculty of Chemistry, University of Vienna, A-1090 Vienna, Austria;
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, A-1090 Vienna, Austria
| | - Leanne Murray
- School of Biological Sciences and Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, I-43124 Parma, Italy (E.Z.)
| | - Jason P. Chin
- School of Biological Sciences and Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Katharina Pallitsch
- Institute of Organic Chemistry, Faculty of Chemistry, University of Vienna, A-1090 Vienna, Austria;
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, I-43124 Parma, Italy (E.Z.)
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Shah BS, Ford BA, Varkey D, Mikolajek H, Orr C, Mykhaylyk V, Owens RJ, Paulsen IT. Marine picocyanobacterial PhnD1 shows specificity for various phosphorus sources but likely represents a constitutive inorganic phosphate transporter. THE ISME JOURNAL 2023:10.1038/s41396-023-01417-w. [PMID: 37087502 DOI: 10.1038/s41396-023-01417-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023]
Abstract
Despite being fundamental to multiple biological processes, phosphorus (P) availability in marine environments is often growth-limiting, with generally low surface concentrations. Picocyanobacteria strains encode a putative ABC-type phosphite/phosphate/phosphonate transporter, phnDCE, thought to provide access to an alternative phosphorus pool. This, however, is paradoxical given most picocyanobacterial strains lack known phosphite degradation or carbon-phosphate lyase pathway to utilise alternate phosphorus pools. To understand the function of the PhnDCE transport system and its ecological consequences, we characterised the PhnD1 binding proteins from four distinct marine Synechococcus isolates (CC9311, CC9605, MITS9220, and WH8102). We show the Synechococcus PhnD1 proteins selectively bind phosphorus compounds with a stronger affinity for phosphite than for phosphate or methyl phosphonate. However, based on our comprehensive ligand screening and growth experiments showing Synechococcus strains WH8102 and MITS9220 cannot utilise phosphite or methylphosphonate as a sole phosphorus source, we hypothesise that the picocyanobacterial PhnDCE transporter is a constitutively expressed, medium-affinity phosphate transporter, and the measured affinity of PhnD1 to phosphite or methyl phosphonate is fortuitous. Our MITS9220_PhnD1 structure explains the comparatively lower affinity of picocyanobacterial PhnD1 for phosphate, resulting from a more limited H-bond network. We propose two possible physiological roles for PhnD1. First, it could function in phospholipid recycling, working together with the predicted phospholipase, TesA, and alkaline phosphatase. Second, by having multiple transporters for P (PhnDCE and Pst), picocyanobacteria could balance the need for rapid transport during transient episodes of higher P availability in the environment, with the need for efficient P utilisation in typical phosphate-deplete conditions.
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Affiliation(s)
- Bhumika S Shah
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia.
| | - Benjamin A Ford
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Deepa Varkey
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Halina Mikolajek
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Christian Orr
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Vitaliy Mykhaylyk
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Raymond J Owens
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Structural Biology, Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
| | - Ian T Paulsen
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia.
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Yu Z, Li W, Ge C, Sun X, Wang J, Shen X, Yuan Q. Functional expansion of the natural inorganic phosphorus starvation response system in Escherichia coli. Biotechnol Adv 2023; 66:108154. [PMID: 37062526 DOI: 10.1016/j.biotechadv.2023.108154] [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] [Received: 12/07/2022] [Revised: 04/08/2023] [Accepted: 04/09/2023] [Indexed: 04/18/2023]
Abstract
Phosphorus, an indispensable nutrient, plays an essential role in cell composition, metabolism, and signal transduction. When inorganic phosphorus (Pi) is scarce, the Pi starvation response in E. coli is activated to increase phosphorus acquisition and drive the cells into a non-growing state to reduce phosphorus consumption. In the six decades of research history, the initiation, output, and shutdown processes of the Pi starvation response have been extensively studied. Simultaneously, Pi starvation has been used in biosensor development, recombinant protein production, and natural product biosynthesis. In this review, we focus on the output process and the applications of the Pi starvation response that have not been summarized before. Meanwhile, based on the current status of mechanistic studies and applications, we propose practical strategies to develop the natural Pi starvation response into a multifunctional and standardized regulatory system in four aspects, including response threshold, temporal expression, intensity range, and bifunctional regulation, which will contribute to its broader application in more fields such as industrial production, medical analysis, and environmental protection.
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Affiliation(s)
- Zheng Yu
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wenna Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chang Ge
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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Transcriptomic-Guided Phosphonate Utilization Analysis Unveils Evidence of Clathrin-Mediated Endocytosis and Phospholipid Synthesis in the Model Diatom, Phaeodactylum tricornutum. mSystems 2022; 7:e0056322. [PMID: 36317887 PMCID: PMC9765203 DOI: 10.1128/msystems.00563-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Phosphonates are important components of marine organic phosphorus, but their bioavailability and catabolism by eukaryotic phytoplankton remain enigmatic. Here, diatom Phaeodactylum tricornutum was used to investigate the bioavailability of phosphonates and describe the underlying molecular mechanism. The results showed that 2-aminoethylphosphonic acid (2-AEP) can be utilized as an alternative phosphorus source. Comparative transcriptomics revealed that the utilization of 2-AEP comprised 2 steps, including molecular uptake through clathrin-mediated endocytosis and incorporation into the membrane phospholipids in the form of diacylglyceryl-2-AEP (DAG-2-AEP). In the global ocean, we found the prevalence and dynamic expression pattern of key genes that are responsible for vesicle formation (CLTC, AP-2) and DAG-AEP synthesis (PCYT2, EPT1) in diatom assemblages. This study elucidates a distinctive mechanism of phosphonate utilization by diatoms, and discusses the ecological implications. IMPORTANCE Phosphonates contribute ~25% of total dissolved organic phosphorus in the ocean, and are found to be important for marine phosphorus biogeochemical cycle. As a type of biogenic phosphonate produced by microorganisms, 2-aminoethylphosphonic acid (2-AEP) widely exists in the ocean. It is well known that 2-AEP can be cleaved and utilized by prokaryotes, but its ability to support the growth of eukaryotic phytoplankton remains unclear. Our research identified the bioavailability of 2-AEP for the diatom Phaeodactylum tricornutum, and proposed a distinctive metabolic pathway of 2-AEP utilization. Different from the enzymatic hydrolysis of phosphonates, the results suggested that P. tricornutum utilizes 2-AEP by incorporating it into phospholipid instead of cleaving the C-P bond. Moreover, the ubiquitous distribution of associated representative gene transcripts in the environmental assemblages and the higher gene transcript abundance in the cold regions were observed, which suggests the possible environmental adaption of 2-AEP utilization by diatoms.
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Ford BA, Ranjit P, Mabbutt BC, Paulsen IT, Shah BS. ProX from marine Synechococcus spp. show a sole preference for glycine-betaine with differential affinity between ecotypes. Environ Microbiol 2022; 24:6071-6085. [PMID: 36054310 PMCID: PMC10087775 DOI: 10.1111/1462-2920.16168] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/09/2022] [Indexed: 01/12/2023]
Abstract
Osmotic stress, caused by high or fluctuating salt concentrations, is a crucial abiotic factor affecting microbial growth in aquatic habitats. Many organisms utilize common responses to osmotic stress, generally requiring active extrusion of toxic inorganic ions and accumulation of compatible solutes to protect cellular machinery. We heterologously expressed and purified predicted osmoprotectant, proline/glycine betaine-binding proteins (ProX) from two phylogenetically distinct Synechococcus spp. MITS9220 and WH8102. Homologues of this protein are conserved only among Prochlorococcus LLIV and Synechococcus clade I, III and CRD1 strains. Our biophysical characterization show Synechococcus ProX exists as a dimer, with specificity solely for glycine betaine but not to other osmoprotectants tested. We discovered that MITS9220_ProX has a 10-fold higher affinity to glycine betaine than WH8102_ProX, which is further elevated (24-fold) in high salt conditions. The stronger affinity and effect of ionic strength on MITS9220_ProX glycine betaine binding but not on WH8102_ProX alludes to a novel regulatory mechanism, providing critical functional insights into the phylogenetic divergence of picocyanobacterial ProX proteins that may be necessary for their ecological success.
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Affiliation(s)
- Benjamin A Ford
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Pramita Ranjit
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | | | - Ian T Paulsen
- School of Natural Sciences, Macquarie University, Sydney, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Bhumika S Shah
- School of Natural Sciences, Macquarie University, Sydney, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
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Li Y, Dong R, Guo J, Wang L, Zhao J. Effects of Mn 2+ and humic acid on microbial community structures, functional genes for nitrogen and phosphorus removal, and heavy metal resistance genes in wastewater treatment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 313:115028. [PMID: 35398637 DOI: 10.1016/j.jenvman.2022.115028] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/26/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
Considering the wide occurrence of Mn2+ and humic acid (HA) in environmental media, the effects of Mn2+ (5-16 mg/L) and HA (10 mg/L) on microbial community structures, functional genes for nitrogen and phosphorus removal, and heavy metal resistance genes (HMRGs) were investigated in wastewater treatment using sequencing batch bioreactors (SBRs). The treatment efficiencies of influent chemical oxygen demands (COD), NH4+-N, and PO43--P were unaffected during the entire operational processes irrespective of whether Mn2+ and HA were supplied. Although the functional prediction of genetic information via sequencing analysis showed that the microbial activity was not influenced by Mn2+ and HA from different SBRs, the abundance of dominant phyla (Proteobacteria, Actinobacteriota, Firmicutes, and Bacteroidota), classes (Saccharimonadia, Gammaproteobacteria, and Bacilli), and genera (unidentified_Chloroplast, TM7a, Micropruina, Candidatus_Competibacter, Lactobacillus, OLB12, and Pediococcus) was different. Compared to the SBR without Mn2+ and HA supplementation, the abundance of functional genes for nitrogen and phosphorus removal (narG, nirS, nosZ, ppk, and phoD) and HMRGs (corA and mntA) significantly increased under Mn2+ stress, but significantly decreased with the addition of HA except for genes nirS and ppk. The abundance of genes corA and mntA was related to the partially dominant microbes and functional genes, and might be reduced by supplying HA. This study provides insight into the effects of Mn2+ and HA on functional genes for nitrogen and phosphorus removal and HMRGs in wastewater treatment.
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Affiliation(s)
- Yonghui Li
- School of Life Sciences, Luoyang Normal University, Luoyang, 471934, China
| | - Rong Dong
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, China
| | - Jiaxin Guo
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, China
| | - Lan Wang
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, China
| | - Jianguo Zhao
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, China.
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Sørensen PE, Baig S, Stegger M, Ingmer H, Garmyn A, Butaye P. Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli. Front Microbiol 2021; 12:782757. [PMID: 34966369 PMCID: PMC8711792 DOI: 10.3389/fmicb.2021.782757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/23/2021] [Indexed: 01/19/2023] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is one of the most important bacterial pathogens affecting poultry worldwide. The emergence of multidrug-resistant pathogens has renewed the interest in the therapeutic use of bacteriophages (phages). However, a major concern for the successful implementation of phage therapy is the emergence of phage-resistant mutants. The understanding of the phage-host interactions, as well as underlying mechanisms of resistance, have shown to be essential for the development of a successful phage therapy. Here, we demonstrate that the strictly lytic Escherichia phage vB_EcoM-P10 rapidly selected for resistance in the APEC ST95 O1 strain AM621. Whole-genome sequence analysis of 109 spontaneous phage-resistant mutant strains revealed 41 mutants with single-nucleotide polymorphisms (SNPs) in their core genome. In 32 of these, a single SNP was detected while two SNPs were identified in a total of nine strains. In total, 34 unique SNPs were detected. In 42 strains, including 18 strains with SNP(s), gene losses spanning 17 different genes were detected. Affected by genetic changes were genes known to be involved in phage resistance (outer membrane protein A, lipopolysaccharide-, O- antigen-, or cell wall-related genes) as well as genes not previously linked to phage resistance, including two hypothetical genes. In several strains, we did not detect any genetic changes. Infecting phages were not able to overcome the phage resistance in host strains. However, interestingly the initial infection was shown to have a great fitness cost for several mutant strains, with up to ∼65% decrease in overall growth. In conclusion, this study provides valuable insights into the phage-host interaction and phage resistance in APEC. Although acquired resistance to phages is frequently observed in pathogenic E. coli, it may be associated with loss of fitness, which could be exploited in phage therapy.
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Affiliation(s)
- Patricia E. Sørensen
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Sharmin Baig
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - An Garmyn
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
| | - Patrick Butaye
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
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11
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Structural dynamics in the evolution of a bilobed protein scaffold. Proc Natl Acad Sci U S A 2021; 118:2026165118. [PMID: 34845009 PMCID: PMC8694067 DOI: 10.1073/pnas.2026165118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2021] [Indexed: 11/18/2022] Open
Abstract
Proteins conduct numerous complex biological functions by use of tailored structural dynamics. The molecular details of how these emerged from ancestral peptides remains mysterious. How does nature utilize the same repertoire of folds to diversify function? To shed light on this, we analyzed bilobed proteins with a common structural core, which is spread throughout the tree of life and is involved in diverse biological functions such as transcription, enzymatic catalysis, membrane transport, and signaling. We show here that the structural dynamics of the structural core differentiate predominantly via terminal additions during a long-period evolution. This diversifies substrate specificity and, ultimately, biological function. Novel biophysical tools allow the structural dynamics of proteins and the regulation of such dynamics by binding partners to be explored in unprecedented detail. Although this has provided critical insights into protein function, the means by which structural dynamics direct protein evolution remain poorly understood. Here, we investigated how proteins with a bilobed structure, composed of two related domains from the periplasmic-binding protein–like II domain family, have undergone divergent evolution, leading to adaptation of their structural dynamics. We performed a structural analysis on ∼600 bilobed proteins with a common primordial structural core, which we complemented with biophysical studies to explore the structural dynamics of selected examples by single-molecule Förster resonance energy transfer and Hydrogen–Deuterium exchange mass spectrometry. We show that evolutionary modifications of the structural core, largely at its termini, enable distinct structural dynamics, allowing the diversification of these proteins into transcription factors, enzymes, and extracytoplasmic transport-related proteins. Structural embellishments of the core created interdomain interactions that stabilized structural states, reshaping the active site geometry, and ultimately altered substrate specificity. Our findings reveal an as-yet-unrecognized mechanism for the emergence of functional promiscuity during long periods of evolution and are applicable to a large number of domain architectures.
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12
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Fang L, Xu L, Zhang N, Shi Q, Shi T, Ma X, Wu X, Li QX, Hua R. Enantioselective degradation of the organophosphorus insecticide isocarbophos in Cupriavidus nantongensis X1 T: Characteristics, enantioselective regulation, degradation pathways, and toxicity assessment. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126024. [PMID: 33992014 DOI: 10.1016/j.jhazmat.2021.126024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
The chiral pesticide enantiomers often show selective efficacy and non-target toxicity. In this study, the enantioselective degradation characteristics of the chiral organophosphorus insecticide isocarbophos (ICP) by Cupriavidus nantongensis X1T were investigated systematically. Strain X1T preferentially degraded the ICP R isomer (R-ICP) over the S isomer (S-ICP). The degradation rate constant of R-ICP was 42-fold greater than S-ICP, while the former is less bioactive against pest insects but more toxic to humans than the latter. The concentration ratio of S-ICP to R-ICP determines whether S-ICP can be degraded by strain X1T. S-ICP started to degrade only when the ratio (CS-ICP/CR-ICP) was greater than 62. Divalent metal cations could improve the degradation ability of strain X1T. The detected metabolites that were identified suggested a novel hydrolysis pathway, while the hydrolytic metabolites were less toxic to fish and green algae than those from P-O bond breakage. The crude enzyme degraded both R-ICP and S-ICP in a similar rate, indicating that enantioselective degradation was due to the transportation of strain X1T. The strain X1T also enantioselectively degraded the chiral organophosphorus insecticides isofenphos-methyl and profenofos. The enantioselective degradation characteristics of strain X1T make it suitable for remediation of chiral organophosphorus insecticide contaminated soil and water.
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Affiliation(s)
- Liancheng Fang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Luyuan Xu
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Nan Zhang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Qiongying Shi
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Taozhong Shi
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xin Ma
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xiangwei Wu
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, HI 96822, United States
| | - Rimao Hua
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China.
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13
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Chandravanshi M, Kant Tripathi S, Prasad Kanaujia S. An updated classification and mechanistic insights into ligand binding of the substrate-binding proteins. FEBS Lett 2021; 595:2395-2409. [PMID: 34379808 DOI: 10.1002/1873-3468.14174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 11/11/2022]
Abstract
Substrate-binding proteins (SBPs) mediate ligand translocation and have been classified into seven clusters (A-G). Although the substrate specificities of these clusters are known to some extent, their ligand-binding mechanism(s) remain(s) incompletely understood. In this study, the list of SBPs belonging to different clusters was updated (764 SBPs) compared to the previously reported study (504 SBPs). Furthermore, a new cluster referred to as cluster H was identified. Results reveal that SBPs follow different ligand-binding mechanisms. Intriguingly, the majority of the SBPs follow the "one domain movement" rather than the well-known "Venus Fly-trap" mechanism. Moreover, SBPs of a few clusters display subdomain conformational movement rather than the complete movement of the N- and C-terminal domains.
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Affiliation(s)
- Monika Chandravanshi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India
| | - Sisir Kant Tripathi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India
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14
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Periplasmic-binding protein-based biosensors and bioanalytical assay platforms: Advances, considerations, and strategies for optimal utility. TALANTA OPEN 2021. [DOI: 10.1016/j.talo.2021.100038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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15
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Murphy ARJ, Scanlan DJ, Chen Y, Adams NBP, Cadman WA, Bottrill A, Bending G, Hammond JP, Hitchcock A, Wellington EMH, Lidbury IDEA. Transporter characterisation reveals aminoethylphosphonate mineralisation as a key step in the marine phosphorus redox cycle. Nat Commun 2021; 12:4554. [PMID: 34315891 PMCID: PMC8316502 DOI: 10.1038/s41467-021-24646-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
The planktonic synthesis of reduced organophosphorus molecules, such as alkylphosphonates and aminophosphonates, represents one half of a vast global oceanic phosphorus redox cycle. Whilst alkylphosphonates tend to accumulate in recalcitrant dissolved organic matter, aminophosphonates do not. Here, we identify three bacterial 2-aminoethylphosphonate (2AEP) transporters, named AepXVW, AepP and AepSTU, whose synthesis is independent of phosphate concentrations (phosphate-insensitive). AepXVW is found in diverse marine heterotrophs and is ubiquitously distributed in mesopelagic and epipelagic waters. Unlike the archetypal phosphonate binding protein, PhnD, AepX has high affinity and high specificity for 2AEP (Stappia stellulata AepX Kd 23 ± 4 nM; methylphosphonate Kd 3.4 ± 0.3 mM). In the global ocean, aepX is heavily transcribed (~100-fold>phnD) independently of phosphate and nitrogen concentrations. Collectively, our data identifies a mechanism responsible for a major oxidation process in the marine phosphorus redox cycle and suggests 2AEP may be an important source of regenerated phosphate and ammonium, which are required for oceanic primary production.
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Affiliation(s)
- Andrew R J Murphy
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Nathan B P Adams
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
- Nanotemper Technologies GmbH, Flößergasse 4, Munich, Germany
| | - William A Cadman
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Andrew Bottrill
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Gary Bending
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - John P Hammond
- School of Agriculture, Policy, and Development, University of Reading, Earley Gate, Whiteknights, Reading, UK
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | | | - Ian D E A Lidbury
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
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16
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Keller JP, Marvin JS, Lacin H, Lemon WC, Shea J, Kim S, Lee RT, Koyama M, Keller PJ, Looger LL. In vivo glucose imaging in multiple model organisms with an engineered single-wavelength sensor. Cell Rep 2021; 35:109284. [PMID: 34161775 DOI: 10.1016/j.celrep.2021.109284] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 03/06/2020] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
Glucose is arguably the most important molecule in metabolism, and its dysregulation underlies diabetes. We describe a family of single-wavelength genetically encoded glucose sensors with a high signal-to-noise ratio, fast kinetics, and affinities varying over four orders of magnitude (1 μM to 10 mM). The sensors allow mechanistic characterization of glucose transporters expressed in cultured cells with high spatial and temporal resolution. Imaging of neuron/glia co-cultures revealed ∼3-fold faster glucose changes in astrocytes. In larval Drosophila central nervous system explants, intracellular neuronal glucose fluxes suggested a rostro-caudal transport pathway in the ventral nerve cord neuropil. In zebrafish, expected glucose-related physiological sequelae of insulin and epinephrine treatments were directly visualized. Additionally, spontaneous muscle twitches induced glucose uptake in muscle, and sensory and pharmacological perturbations produced large changes in the brain. These sensors will enable rapid, high-resolution imaging of glucose influx, efflux, and metabolism in behaving animals.
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Affiliation(s)
- Jacob P Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Jonathan S Marvin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Haluk Lacin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - William C Lemon
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jamien Shea
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Soomin Kim
- Harvard Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard Medical School, Brigham and Women's Hospital, Cambridge, MA, USA
| | - Richard T Lee
- Harvard Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard Medical School, Brigham and Women's Hospital, Cambridge, MA, USA; The Cardiovascular Division, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Cambridge, MA, USA
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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17
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Selective uptake determines the variation in degradation of organophosphorus pesticides by Lactobacillus plantarum. Food Chem 2021; 360:130106. [PMID: 34034058 DOI: 10.1016/j.foodchem.2021.130106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/08/2021] [Accepted: 05/13/2021] [Indexed: 01/10/2023]
Abstract
Organophosphorus pesticides (OPPs) are widely used worldwide, leading to varying degrees of residues in food. Lactic acid bacteria (LAB) can degrade OPPs by producing phosphatase. This study explored the reasons for the variation in the degradation of different OPPs by Lactobacillus plantarum. The results showed that the degradation effects of OPPs by L. plantarum (intact cells) varied greatly, the degradation rate constant of phoxim was 1.65-fold higher than that of dichlorvos. However, the phosphatase extracted from L. plantarum had no degradation selectivity for OPPs in vitro. It was speculated that the selective uptake of cells determines this degradation selectivity. The results of molecular docking supported this hypothesis because there was no difference in the binding energies between phosphatase and OPPs, while the binding energies between phosphate-binding protein and pesticides were different, and they were negatively correlated with the degradation rate constants of the eight OPPs by L. plantarum.
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18
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Structure- and mechanism-guided design of single fluorescent protein-based biosensors. Nat Chem Biol 2021; 17:509-518. [PMID: 33558715 DOI: 10.1038/s41589-020-00718-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/02/2020] [Indexed: 12/22/2022]
Abstract
Intensiometric genetically encoded biosensors, based on allosteric modulation of the fluorescence of a single fluorescent protein, are powerful tools for enabling imaging of neural activities and other cellular biochemical events. The archetypical example of such biosensors is the GCaMP series of Ca2+ biosensors, which have been steadily improved over the past two decades and are now indispensable tools for neuroscience. However, no other biosensors have reached levels of performance, or had revolutionary impacts within specific disciplines, comparable to that of the Ca2+ biosensors. Of the many reasons why this has been the case, a critical one has been a general black-box view of biosensor structure and mechanism. With this Perspective, we aim to summarize what is known about biosensor structure and mechanisms and, based on this foundation, provide guidelines to accelerate the development of a broader range of biosensors with performance comparable to that of the GCaMP series.
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19
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Poddar N, Badilla C, Maghool S, Osborne TH, Santini JM, Maher MJ. Structural and Functional Investigation of the Periplasmic Arsenate-Binding Protein ArrX from Chrysiogenes arsenatis. Biochemistry 2021; 60:465-476. [PMID: 33538578 DOI: 10.1021/acs.biochem.0c00555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The anaerobic bacterium Chrysiogenes arsenatis respires using the oxyanion arsenate (AsO43-) as the terminal electron acceptor, where it is reduced to arsenite (AsO33-) while concomitantly oxidizing various organic (e.g., acetate) electron donors. This respiratory activity is catalyzed in the periplasm of the bacterium by the enzyme arsenate reductase (Arr), with expression of the enzyme controlled by a sensor histidine kinase (ArrS) and a periplasmic-binding protein (PBP), ArrX. Here, we report for the first time, the molecular structure of ArrX in the absence and presence of bound ligand arsenate. Comparison of the ligand-bound structure of ArrX with other PBPs shows a high level of conservation of critical residues for ligand binding by these proteins; however, this suite of PBPs shows different structural alterations upon ligand binding. For ArrX and its homologue AioX (from Rhizobium sp. str. NT-26), which specifically binds arsenite, the structures of the substrate-binding sites in the vicinity of a conserved and critical cysteine residue contribute to the discrimination of binding for these chemically similar ligands.
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Affiliation(s)
- Nilakhi Poddar
- School of Chemistry and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville 3052, Australia
| | - Consuelo Badilla
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Shadi Maghool
- School of Chemistry and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville 3052, Australia
| | - Thomas H Osborne
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Megan J Maher
- School of Chemistry and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville 3052, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3083, Australia
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20
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Gräwe A, Stein V. Linker Engineering in the Context of Synthetic Protein Switches and Sensors. Trends Biotechnol 2020; 39:731-744. [PMID: 33293101 DOI: 10.1016/j.tibtech.2020.11.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/17/2022]
Abstract
Linkers play critical roles in the construction of synthetic protein switches and sensors as they functionally couple a receptor with an actuator. With an increasing number of molecular toolboxes and experimental strategies becoming available that can be applied to engineer protein switches and sensors with tailored response functions, optimising the connecting linkers remains an idiosyncratic and empiric process. This review aims to provide an in-depth analysis of linker motifs, the biophysical properties they confer, and how they impact the performance of synthetic protein switches and sensors while identifying trends, mechanisms, and strategies that underlie the most potent switches and sensors.
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Affiliation(s)
- Alexander Gräwe
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany; Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Viktor Stein
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany; Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany.
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21
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Sabatini BL, Tian L. Imaging Neurotransmitter and Neuromodulator Dynamics In Vivo with Genetically Encoded Indicators. Neuron 2020; 108:17-32. [PMID: 33058762 DOI: 10.1016/j.neuron.2020.09.036] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/10/2020] [Accepted: 09/25/2020] [Indexed: 12/16/2022]
Abstract
The actions of neuromodulation are thought to mediate the ability of the mammalian brain to dynamically adjust its functional state in response to changes in the environment. Altered neurotransmitter (NT) and neuromodulator (NM) signaling is central to the pathogenesis or treatment of many human neurological and psychiatric disorders, including Parkinson's disease, schizophrenia, depression, and addiction. To reveal the precise mechanisms by which these neurochemicals regulate healthy and diseased neural circuitry, one needs to measure their spatiotemporal dynamics in the living brain with great precision. Here, we discuss recent development, optimization, and applications of optical approaches to measure the spatial and temporal profiles of NT and NM release in the brain using genetically encoded sensors for in vivo studies.
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Affiliation(s)
- Bernardo L Sabatini
- Howard Hughes Medical Institute, Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
| | - Lin Tian
- Departments of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA.
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22
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Zemerov SD, Roose BW, Farenhem KL, Zhao Z, Stringer MA, Goldman AR, Speicher DW, Dmochowski IJ. 129Xe NMR-Protein Sensor Reveals Cellular Ribose Concentration. Anal Chem 2020; 92:12817-12824. [PMID: 32897053 PMCID: PMC7649717 DOI: 10.1021/acs.analchem.0c00967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Dysregulation of cellular ribose uptake can be indicative of metabolic abnormalities or tumorigenesis. However, analytical methods are currently limited for quantifying ribose concentration in complex biological samples. Here, we utilize the highly specific recognition of ribose by ribose-binding protein (RBP) to develop a single-protein ribose sensor detectable via a sensitive NMR technique known as hyperpolarized 129Xe chemical exchange saturation transfer (hyper-CEST). We demonstrate that RBP, with a tunable ribose-binding site and further engineered to bind xenon, enables the quantitation of ribose over a wide concentration range (nM to mM). Ribose binding induces the RBP "closed" conformation, which slows Xe exchange to a rate detectable by hyper-CEST. Such detection is remarkably specific for ribose, with the minimal background signal from endogenous sugars of similar size and structure, for example, glucose or ribose-6-phosphate. Ribose concentration was measured for mammalian cell lysate and serum, which led to estimates of low-mM ribose in a HeLa cell line. This highlights the potential for using genetically encoded periplasmic binding proteins such as RBP to measure metabolites in different biological fluids, tissues, and physiologic states.
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Affiliation(s)
- Serge D. Zemerov
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Benjamin W. Roose
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Kelsey L. Farenhem
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Zhuangyu Zhao
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Madison A. Stringer
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Aaron R. Goldman
- Proteomics and Metabolomics Facility, The Wistar Institute,
Philadelphia, PA 19104, USA
| | - David W. Speicher
- Proteomics and Metabolomics Facility, The Wistar Institute,
Philadelphia, PA 19104, USA
- Molecular and Cellular Oncogenesis Program, The Wistar
Institute, Philadelphia, PA 19104, USA
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
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23
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N'Guetta PEY, Fink MM, Rizk SS. Engineering a fluorescence biosensor for the herbicide glyphosate. Protein Eng Des Sel 2020; 33:gzaa021. [PMID: 32930799 DOI: 10.1093/protein/gzaa021] [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] [Received: 12/30/2019] [Revised: 03/25/2020] [Accepted: 07/24/2020] [Indexed: 11/13/2022] Open
Abstract
Glyphosate, the active ingredient in RoundUp, is the most widely used herbicide on the globe, and has recently been linked to an increased risk in non-Hodgkin's lymphoma in exposed individuals. Therefore, detection and monitoring of glyphosate levels in water and soil is important for public safety. Here, we describe a biosensor for glyphosate based on an engineered Escherichia coli phosphonate-binding protein (PhnD). Mutations in the binding pocket were introduced to convert PhnD into a glyphosate-binding protein. A fluorescence group attached near the hinge of the protein was added to monitor binding of glyphosate and to determine its concentration in unknown samples. The resulting engineered biosensor can detect glyphosate in tap water and in soil samples treated with the herbicide at submicromolar concentrations, well below the limit for drinking water in the USA. Incorporating this biosensor in a device would allow rapid and continuous monitoring of glyphosate in water and soil samples.
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Affiliation(s)
| | - Maggie M Fink
- Department of Chemistry and Biochemistry, Indiana University, South Bend, IN 46615, USA
| | - Shahir S Rizk
- Department of Chemistry and Biochemistry, Indiana University, South Bend, IN 46615, USA
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24
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Pal A, Tian L. Imaging voltage and brain chemistry with genetically encoded sensors and modulators. Curr Opin Chem Biol 2020; 57:166-176. [PMID: 32823064 DOI: 10.1016/j.cbpa.2020.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 01/21/2023]
Abstract
Neurons and glia are functionally organized into circuits and higher-order structures that allow the precise information processing required for complex behaviors. To better understand the structure and function of the brain, we must understand synaptic connectivity, action potential generation and propagation, as well as well-orchestrated molecular signaling. Recently, dramatically improved sensors for voltage, intracellular calcium, and neurotransmitters/modulators, combined with advanced microscopy provide new opportunities for in vivo dissection of cellular and circuit activity in awake, behaving animals. This review focuses on the current trends in genetically encoded sensors for molecules and cellular events and their potential applicability to the study of nervous system in health and disease.
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Affiliation(s)
- Akash Pal
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Lin Tian
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA.
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25
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Fang L, Shi Q, Xu L, Shi T, Wu X, Li QX, Hua R. Enantioselective Uptake Determines Degradation Selectivity of Chiral Profenofos in Cupriavidus nantongensis X1 T. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6493-6501. [PMID: 32459959 DOI: 10.1021/acs.jafc.0c00132] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Organophosphorus insecticides account for approximately 28% of the global commercial insecticide market, while 40% of them are chiral enantiomers. Chiral enantiomers differ largely in their toxicities. Enantiomers that are less active or inactive do not offer the needed efficacy but pollute the environment and cause toxicities to non-target species. Cupriavidus nantongensis X1T, a recently isolated bacterial strain, could degrade S-profenofos 2.3-fold faster than R-profenofos, while the latter is the active enantiomer potently against pest insects and has greater mammalian safety. The degradation enzyme encoded by opdB was expressed via Escherichia coli and purified. The degradation kinetics of R- and S-profenofos showed that both the purified OpdB and crude enzyme extracts had no enantiomer degradation selectivity, which strongly indicated that the degradation selectivity occurred in the uptake process. Metabolite analyses suggested a novel dealkylation pathway. This is the first report of bacterial selective uptake of organophosphates. Selective degradation of S-profenofos over R-profenofos by the strain X1T suggests a concept of co-application of racemic pesticides and degradation-selective bacteria to minimize contamination and non-target toxicity problems.
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Affiliation(s)
- Liancheng Fang
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China
| | - Qiongying Shi
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China
| | - Luyuan Xu
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China
| | - Taozhong Shi
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China
| | - Xiangwei Wu
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, Hawaii 96822, United States
| | - Rimao Hua
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China
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26
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Stosiek N, Talma M, Klimek-Ochab M. Carbon-Phosphorus Lyase-the State of the Art. Appl Biochem Biotechnol 2020; 190:1525-1552. [PMID: 31792787 DOI: 10.1007/s12010-019-03161-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 10/23/2019] [Indexed: 11/27/2022]
Abstract
Organophosphonates are molecules that contain a very chemically stable carbon-phosphorus (C-P) bond. Microorganisms can utilize phosphonates as potential source of crucial elements for their growth, as developed several pathways to metabolize these compounds. One among these pathways is catalyzed by C-P lyase complex, which has a broad substrate specifity; therefore, it has a wide application in degradation of herbicides deposited in the environment, such as glyphosate. This multi-enzyme system accurately recognized in Escherichia coli and genetic studies have demonstrated that it is encoded by phn operon containing 14 genes (phnC-phnP). The phn operon is a member of the Pho regulon induced by phosphate starvation. Ability to degradation of phosphonates is also found in other microorganisms, especially soil and marine bacteria, that have homologous genes to those in E. coli. Despite the existence of differences in structure and composition of phn gene cluster, each of these strains contains phnGHIJKLM genes necessary in the C-P bond cleavage mechanism. The review provides a detailed description and summary of achievements on the C-P lyase enzymatic pathway over the last 50 years.
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Affiliation(s)
- Natalia Stosiek
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - Michał Talma
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Magdalena Klimek-Ochab
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
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Recent advances in the use of genetically encodable optical tools to elicit and monitor signaling events. Curr Opin Cell Biol 2020; 63:114-124. [PMID: 32058267 DOI: 10.1016/j.ceb.2020.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 02/06/2023]
Abstract
Cells rely on a complex network of spatiotemporally regulated signaling activities to effectively transduce information from extracellular cues to intracellular machinery. To probe this activity architecture, researchers have developed an extensive molecular tool kit of fluorescent biosensors and optogenetic actuators capable of monitoring and manipulating various signaling activities with high spatiotemporal precision. The goal of this review is to provide readers with an overview of basic concepts and recent advances in the development and application of genetically encodable biosensors and optogenetic tools for understanding signaling activity.
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Bernhard M, Diefenbach M, Biesalski M, Laube B. Electrical Sensing of Phosphonates by Functional Coupling of Phosphonate Binding Protein PhnD to Solid-State Nanopores. ACS Sens 2020; 5:234-241. [PMID: 31829017 DOI: 10.1021/acssensors.9b02097] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Combining the stability of solid-state nanopores with the unique sensing properties of biological components in a miniaturized electrical hybrid nanopore device is a challenging approach to advance the sensitivity and selectivity of small-molecule detection in healthcare and environment analytics. Here, we demonstrate a simple method to design an electrical hybrid nanosensor comprising a bacterial binding protein tethered to a solid-state nanopore allowing high-affinity detection of phosphonates. The diverse family of bacterial substrate-binding proteins (SBPs) binds specifically and efficiently to various substances and has been implicated as an ideal biorecognition element for analyte detection in the design of hybrid bionanosensors. Here, we demonstrate that the coupling of the purified phosphonate binding protein PhnD via primary amines to the reactive NHS groups of P(DMAA-co-NMAS) polymers inside a single track-etched nanopore in poly(ethylene terephthalate) (PET) foils results in ligand-specific and concentration-dependent changes in the nanopore current. Application of the phosphonate 2-aminoethylphosphonate (2AEP) or ethylphosphonate (EP) induces a large conformational rearrangement in PnhD around the hinge in a venus flytrap mechanism resulting in a concentration depended on increase of the single pore current with binding affinities of 27 and 373 nM, respectively. Thus, the specificity and stability of this simple hybrid sensor concept combine the advantages of both, the diversity of ligand-specific substrate-binding proteins and solid-state nanopores encouraging further options to produce robust devices amenable to medical or environmental high-throughput-based applications in nanotechnology.
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Affiliation(s)
- Max Bernhard
- Department of Biology, Neurophysiology and Neurosensory Systems, Technische Universität Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Mathias Diefenbach
- Department of Chemistry, Laboratory of Macromolecular Chemistry and Paper Chemistry, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Markus Biesalski
- Department of Chemistry, Laboratory of Macromolecular Chemistry and Paper Chemistry, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Bodo Laube
- Department of Biology, Neurophysiology and Neurosensory Systems, Technische Universität Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
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Andreoni A, Davis CM, Tian L. Measuring brain chemistry using genetically encoded fluorescent sensors. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019. [DOI: 10.1016/j.cobme.2019.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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30
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Kostyuk AI, Demidovich AD, Kotova DA, Belousov VV, Bilan DS. Circularly Permuted Fluorescent Protein-Based Indicators: History, Principles, and Classification. Int J Mol Sci 2019; 20:E4200. [PMID: 31461959 PMCID: PMC6747460 DOI: 10.3390/ijms20174200] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/22/2019] [Accepted: 08/24/2019] [Indexed: 12/28/2022] Open
Abstract
Genetically encoded biosensors based on fluorescent proteins (FPs) are a reliable tool for studying the various biological processes in living systems. The circular permutation of single FPs led to the development of an extensive class of biosensors that allow the monitoring of many intracellular events. In circularly permuted FPs (cpFPs), the original N- and C-termini are fused using a peptide linker, while new termini are formed near the chromophore. Such a structure imparts greater mobility to the FP than that of the native variant, allowing greater lability of the spectral characteristics. One of the common principles of creating genetically encoded biosensors is based on the integration of a cpFP into a flexible region of a sensory domain or between two interacting domains, which are selected according to certain characteristics. Conformational rearrangements of the sensory domain associated with ligand interaction or changes in the cellular parameter are transferred to the cpFP, changing the chromophore environment. In this review, we highlight the basic principles of such sensors, the history of their creation, and a complete classification of the available biosensors.
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Affiliation(s)
- Alexander I Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | | | - Daria A Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Vsevolod V Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
| | - Dmitry S Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.
- Pirogov Russian National Research Medical University, Moscow 117997, Russia.
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Converting a Periplasmic Binding Protein into a Synthetic Biosensing Switch through Domain Insertion. BIOMED RESEARCH INTERNATIONAL 2019; 2019:4798793. [PMID: 30719443 PMCID: PMC6335823 DOI: 10.1155/2019/4798793] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/17/2018] [Indexed: 12/22/2022]
Abstract
All biosensing platforms rest on two pillars: specific biochemical recognition of a particular analyte and transduction of that recognition into a readily detectable signal. Most existing biosensing technologies utilize proteins that passively bind to their analytes and therefore require wasteful washing steps, specialized reagents, and expensive instruments for detection. To overcome these limitations, protein engineering strategies have been applied to develop new classes of protein-based sensor/actuators, known as protein switches, responding to small molecules. Protein switches change their active state (output) in response to a binding event or physical signal (input) and therefore show a tremendous potential to work as a biosensor. Synthetic protein switches can be created by the fusion between two genes, one coding for a sensor protein (input domain) and the other coding for an actuator protein (output domain) by domain insertion. The binding of a signal molecule to the engineered protein will switch the protein function from an “off” to an “on” state (or vice versa) as desired. The molecular switch could, for example, sense the presence of a metabolite, pollutant, or a biomarker and trigger a cellular response. The potential sensing and response capabilities are enormous; however, the recognition repertoire of natural switches is limited. Thereby, bioengineers have been struggling to expand the toolkit of molecular switches recognition repertoire utilizing periplasmic binding proteins (PBPs) as protein-sensing components. PBPs are a superfamily of bacterial proteins that provide interesting features to engineer biosensors, for instance, immense ligand-binding diversity and high affinity, and undergo large conformational changes in response to ligand binding. The development of these protein switches has yielded insights into the design of protein-based biosensors, particularly in the area of allosteric domain fusions. Here, recent protein engineering approaches for expanding the versatility of protein switches are reviewed, with an emphasis on studies that used PBPs to generate novel switches through protein domain insertion.
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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33
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Manav MC, Sofos N, Hove-Jensen B, Brodersen DE. The Abc of Phosphonate Breakdown: A Mechanism for Bacterial Survival. Bioessays 2018; 40:e1800091. [DOI: 10.1002/bies.201800091] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/13/2018] [Indexed: 12/11/2022]
Affiliation(s)
- M. Cemre Manav
- Department of Molecular Biology and Genetics; Aarhus University; DK-8000 Aarhus Denmark
| | - Nicholas Sofos
- Department of Molecular Biology and Genetics; Aarhus University; DK-8000 Aarhus Denmark
| | - Bjarne Hove-Jensen
- Department of Molecular Biology and Genetics; Aarhus University; DK-8000 Aarhus Denmark
| | - Ditlev E. Brodersen
- Department of Molecular Biology and Genetics; Aarhus University; DK-8000 Aarhus Denmark
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34
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Chu WT, Wang J. Quantifying the Intrinsic Conformation Energy Landscape Topography of Proteins with Large-Scale Open-Closed Transition. ACS CENTRAL SCIENCE 2018; 4:1015-1022. [PMID: 30159398 PMCID: PMC6107866 DOI: 10.1021/acscentsci.8b00274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Indexed: 06/08/2023]
Abstract
Large-scale conformational changes of proteins, including the open-closed transitions, are crucial for a variety of protein functions. These open-closed transitions are often associated with ligand binding. However, the understandings of the underlying mechanisms of the conformational changes within proteins during the open-closed transitions are still challenging at present. In this study, we quantified the intrinsic underlying conformational energy landscapes of five different proteins with large-scale open-closed transitions. This is realized by exploring the underlying density of states and the intrinsic conformational energy landscape topography measure Λ. Λ is a dimensionless ratio of conformational energy gap δE versus conformational energy roughness δE and configurational entropy S or size of the intrinsic conformational energy landscape. By quantifying the Λ of intrinsic open-closed conformational (Λoc) and intrinsic global folding (Λglobal) energy landscapes, we show that both intrinsic open-closed conformation energy and entropy landscapes are funneled toward the closed state. Furthermore, our results indicate the strong correlations between Λ and thermodynamics (conformational state transition temperature against trapping temperature) as well as between Λ and kinetics (open-closed kinetic time) of these proteins. This shows that the intrinsic conformational landscape topography determines both the conformational thermodynamic stability and kinetic speed of the conformational dynamics. Our investigations provide important insights for understanding the fundamental mechanisms of the protein conformational dynamics in a physical and global way.
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Affiliation(s)
- Wen-Ting Chu
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jin Wang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- Department
of Chemistry & Physics, State University
of New York at Stony Brook, Stony
Brook, New York 11794, United States
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35
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Teixeira RD, Guzzo CR, Arévalo SJ, Andrade MO, Abrahão J, de Souza RF, Farah CS. A bipartite periplasmic receptor-diguanylate cyclase pair (XAC2383-XAC2382) in the bacterium Xanthomonas citri. J Biol Chem 2018; 293:10767-10781. [PMID: 29728456 DOI: 10.1074/jbc.ra118.003475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 04/27/2018] [Indexed: 11/06/2022] Open
Abstract
The second messenger cyclic diguanylate monophosphate (c-di-GMP) is a central regulator of bacterial lifestyle, controlling several behaviors, including the switch between sessile and motile states. The c-di-GMP levels are controlled by the interplay between diguanylate cyclases (DGCs) and phosphodiesterases, which synthesize and hydrolyze this second messenger, respectively. These enzymes often contain additional domains that regulate activity via binding of small molecules, covalent modification, or protein-protein interactions. A major challenge remains to understand how DGC activity is regulated by these additional domains or interaction partners in specific signaling pathways. Here, we identified a pair of co-transcribed genes (xac2382 and xac2383) in the phytopathogenic, Gram-negative bacterium Xanthomonas citri subsp. citri (Xac), whose mutations resulted in opposing motility phenotypes. We show that the periplasmic cache domain of XAC2382, a membrane-associated DGC, interacts with XAC2383, a periplasmic binding protein, and we provide evidence that this interaction regulates XAC2382 DGC activity. Moreover, we solved the crystal structure of XAC2383 with different ligands, indicating a preference for negatively charged phosphate-containing compounds. We propose that XAC2383 acts as a periplasmic sensor that, upon binding its ligand, inhibits the DGC activity of XAC2382. Of note, we also found that this previously uncharacterized signal transduction system is present in several other bacterial phyla, including Gram-positive bacteria. Phylogenetic analysis of homologs of the XAC2382-XAC2383 pair supports several independent origins that created new combinations of XAC2382 homologs with a conserved periplasmic cache domain with different cytoplasmic output module architectures.
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Affiliation(s)
- Raphael D Teixeira
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000
| | - Cristiane R Guzzo
- the Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-900, and
| | - Santiago Justo Arévalo
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000
| | - Maxuel O Andrade
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000
| | - Josielle Abrahão
- the Departamento de Química Orgânica, Instituto de Química, Universidade de Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Robson F de Souza
- the Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-900, and
| | - Chuck S Farah
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000,
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36
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Badilla C, Osborne TH, Cole A, Watson C, Djordjevic S, Santini JM. A new family of periplasmic-binding proteins that sense arsenic oxyanions. Sci Rep 2018; 8:6282. [PMID: 29674678 PMCID: PMC5908839 DOI: 10.1038/s41598-018-24591-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/06/2018] [Indexed: 01/21/2023] Open
Abstract
Arsenic contamination of drinking water affects more than 140 million people worldwide. While toxic to humans, inorganic forms of arsenic (arsenite and arsenate), can be used as energy sources for microbial respiration. AioX and its orthologues (ArxX and ArrX) represent the first members of a new sub-family of periplasmic-binding proteins that serve as the first component of a signal transduction system, that’s role is to positively regulate expression of arsenic metabolism enzymes. As determined by X-ray crystallography for AioX, arsenite binding only requires subtle conformational changes in protein structure, providing insights into protein-ligand interactions. The binding pocket of all orthologues is conserved but this alone is not sufficient for oxyanion selectivity, with proteins selectively binding either arsenite or arsenate. Phylogenetic evidence, clearly demonstrates that the regulatory proteins evolved together early in prokaryotic evolution and had a separate origin from the metabolic enzymes whose expression they regulate.
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Affiliation(s)
- Consuelo Badilla
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Thomas H Osborne
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Ambrose Cole
- Institute of Structural & Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, WC1E 7HX, London, UK
| | - Cameron Watson
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Snezana Djordjevic
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK.
| | - Joanne M Santini
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK.
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37
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Hook JL, Islam MN, Parker D, Prince AS, Bhattacharya S, Bhattacharya J. Disruption of staphylococcal aggregation protects against lethal lung injury. J Clin Invest 2018; 128:1074-1086. [PMID: 29431734 DOI: 10.1172/jci95823] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/04/2018] [Indexed: 01/23/2023] Open
Abstract
Infection by Staphylococcus aureus strain USA300 causes tissue injury, multiorgan failure, and high mortality. However, the mechanisms by which the bacteria adhere to, then stabilize on, mucosal surfaces before causing injury remain unclear. We addressed these issues through the first real-time determinations of USA300-alveolar interactions in live lungs. We found that within minutes, inhaled USA300 established stable, self-associated microaggregates in niches at curved, but not at flat, regions of the alveolar wall. The microaggregates released α-hemolysin toxin, causing localized alveolar injury, as indicated by epithelial dye loss, mitochondrial depolarization, and cytosolic Ca2+ increase. Spread of cytosolic Ca2+ through intercellular gap junctions to adjoining, uninfected alveoli caused pulmonary edema. Systemic pretreatment with vancomycin, a USA300-cidal antibiotic, failed to protect mice infected with inhaled WT USA300. However, vancomycin pretreatment markedly abrogated mortality in mice infected with mutant USA300 that lacked the aggregation-promoting factor PhnD. We interpret USA300-induced mortality as having resulted from rapid bacterial aggregation in alveolar niches. These findings indicate, for the first time to our knowledge, that alveolar microanatomy is critical in promoting the aggregation and, hence, in causing USA300-induced alveolar injury. We propose that in addition to antibiotics, strategies for bacterial disaggregation may constitute novel therapy against USA300-induced lung injury.
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Affiliation(s)
- Jaime L Hook
- Lung Biology Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine
| | - Mohammad N Islam
- Lung Biology Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine
| | | | | | - Sunita Bhattacharya
- Lung Biology Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine.,Department of Pediatrics, and
| | - Jahar Bhattacharya
- Lung Biology Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine.,Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA
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38
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The molecular basis of phosphite and hypophosphite recognition by ABC-transporters. Nat Commun 2017; 8:1746. [PMID: 29170493 PMCID: PMC5700983 DOI: 10.1038/s41467-017-01226-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 08/30/2017] [Indexed: 11/10/2022] Open
Abstract
Inorganic phosphate is the major bioavailable form of the essential nutrient phosphorus. However, the concentration of phosphate in most natural habitats is low enough to limit microbial growth. Under phosphate-depleted conditions some bacteria utilise phosphite and hypophosphite as alternative sources of phosphorus, but the molecular basis of reduced phosphorus acquisition from the environment is not fully understood. Here, we present crystal structures and ligand binding affinities of periplasmic binding proteins from bacterial phosphite and hypophosphite ATP-binding cassette transporters. We reveal that phosphite and hypophosphite specificity results from a combination of steric selection and the presence of a P-H…π interaction between the ligand and a conserved aromatic residue in the ligand-binding pocket. The characterisation of high affinity and specific transporters has implications for the marine phosphorus redox cycle, and might aid the use of phosphite as an alternative phosphorus source in biotechnological, industrial and agricultural applications. Some bacteria can use inorganic phosphite and hypophosphite as sources of inorganic phosphorus. Here, the authors report crystal structures of the periplasmic proteins that bind these reduced phosphorus species and show that a P-H…π interaction between the ligand and binding site determines their specificity.
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39
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Gavrilov S, Podosokorskaya O, Alexeev D, Merkel A, Khomyakova M, Muntyan M, Altukhov I, Butenko I, Bonch-Osmolovskaya E, Govorun V, Kublanov I. Respiratory Pathways Reconstructed by Multi-Omics Analysis in Melioribacter roseus, Residing in a Deep Thermal Aquifer of the West-Siberian Megabasin. Front Microbiol 2017; 8:1228. [PMID: 28713355 PMCID: PMC5492636 DOI: 10.3389/fmicb.2017.01228] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/16/2017] [Indexed: 01/19/2023] Open
Abstract
Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metabolically versatile thermophilic bacterium, inhabiting subsurface biosphere of the West-Siberian megabasin and capable of growing on various substrates and electron acceptors. Genomic analysis followed by inhibitor studies and membrane potential measurements of aerobically grown M. roseus cells revealed the activity of aerobic respiratory electron transfer chain comprised of respiratory complexes I and IV, and an alternative complex III. Phylogeny reconstruction revealed that oxygen reductases belonged to atypical cc(o/b)o3-type and canonical cbb3–type cytochrome oxidases. Also, two molybdoenzymes of M. roseus were affiliated either with Ttr or Psr/Phs clades, but not with typical respiratory arsenate reductases of the Arr clade. Expression profiling, both at transcripts and protein level, allowed us to assign the role of the terminal respiratory oxidase under atmospheric oxygen concentration for the cc(o/b)o3 cytochrome oxidase, previously proposed to serve for oxygen detoxification only. Transcriptomic analysis revealed the involvement of both molybdoenzymes of M. roseus in As(V) respiration, yet differences in the genomic context of their gene clusters allow to hypothesize about their distinct roles in arsenate metabolism with the ‘Psr/Phs’-type molybdoenzyme being the most probable candidate respiratory arsenate reductase. Basing on multi-omics data, the pathways for aerobic and arsenate respiration were proposed. Our results start to bridge the vigorously increasing gap between homology-based predictions and experimentally verified metabolic processes, what is especially important for understudied microorganisms of novel lineages from deep subsurface environments of Eurasia, which remained separated from the rest of the biosphere for several geological periods.
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Affiliation(s)
- Sergey Gavrilov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscow, Russia
| | - Olga Podosokorskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscow, Russia
| | - Dmitry Alexeev
- Saint Petersburg State University of Information Technologies, Mechanics and OpticsSt. Petersburg, Russia
| | - Alexander Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscow, Russia
| | - Maria Khomyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscow, Russia
| | - Maria Muntyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
| | - Ilya Altukhov
- Federal Research and Clinical Centre of Physico-Chemical MedicineMoscow, Russia.,Moscow Institute of Physics and TechnologyDolgoprudny, Russia
| | - Ivan Butenko
- Federal Research and Clinical Centre of Physico-Chemical MedicineMoscow, Russia
| | - Elizaveta Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscow, Russia
| | - Vadim Govorun
- Federal Research and Clinical Centre of Physico-Chemical MedicineMoscow, Russia.,Moscow Institute of Physics and TechnologyDolgoprudny, Russia
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscow, Russia.,Laboratory of Microbial Genomics, Immanuel Kant Baltic Federal UniversityKaliningrad, Russia
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40
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Ribeiro LF, Warren TD, Ostermeier M. Construction of Protein Switches by Domain Insertion and Directed Evolution. Methods Mol Biol 2017; 1596:43-55. [PMID: 28293879 DOI: 10.1007/978-1-4939-6940-1_3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A protein switch is a protein that changes between inactive ("off") and active ("on") states in response to a biomolecule or physical signal. These switches can be created by fusing two domains in such a way that the activity of the output domain is regulated by the input domain's recognition of an input signal (such as the binding of a molecule, recognition of light). Here, we describe several methods for randomly fusing two domains to create domain insertion libraries from which protein switches can be identified by selections and/or screens.
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Affiliation(s)
- Lucas F Ribeiro
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD, 21218, USA
| | - Tiana D Warren
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD, 21218, USA
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD, 21218, USA.
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Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
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Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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Tullman J, Nicholes N, Dumont MR, Ribeiro LF, Ostermeier M. Enzymatic protein switches built from paralogous input domains. Biotechnol Bioeng 2015; 113:852-8. [DOI: 10.1002/bit.25852] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/25/2015] [Accepted: 10/05/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Jennifer Tullman
- Department of Chemical and Biomolecular EngineeringJohns Hopkins University3400 N. Charles St. Maryland Hall 119BaltimoreMD21218
| | - Nathan Nicholes
- Department of Chemical and Biomolecular EngineeringJohns Hopkins University3400 N. Charles St. Maryland Hall 119BaltimoreMD21218
| | - Matt R. Dumont
- Department of Chemical and Biomolecular EngineeringJohns Hopkins University3400 N. Charles St. Maryland Hall 119BaltimoreMD21218
| | - Lucas F. Ribeiro
- Department of Chemical and Biomolecular EngineeringJohns Hopkins University3400 N. Charles St. Maryland Hall 119BaltimoreMD21218
| | - Marc Ostermeier
- Department of Chemical and Biomolecular EngineeringJohns Hopkins University3400 N. Charles St. Maryland Hall 119BaltimoreMD21218
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Li N, Chen H, Williams HN. Genome-wide comparative analysis of ABC systems in the Bdellovibrio-and-like organisms. Gene 2015; 562:132-7. [PMID: 25707746 DOI: 10.1016/j.gene.2015.02.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/14/2015] [Accepted: 02/19/2015] [Indexed: 11/28/2022]
Abstract
Bdellovibrio-and-like organisms (BALOs) are gram-negative, predatory bacteria with wide variations in genome sizes and GC content and ecological habitats. The ATP-binding cassette (ABC) systems have been identified in several prokaryotes, fungi and plants and have a role in transport of materials in and out of cells and in cellular processes. However, knowledge of the ABC systems of BALOs remains obscure. A total of 269 putative ABC proteins were identified in BALOs. The genes encoding these ABC systems occupy nearly 1.3% of the gene content in freshwater Bdellovibrio strains and about 0.7% in their saltwater counterparts. The proteins found belong to 25 ABC system families based on their structural characteristics and functions. Among these, 16 families function as importers, 6 as exporters and 3 are involved in various cellular processes. Eight of these 25 ABC system families were deduced to be the core set of ABC systems conserved in all BALOs. All Bacteriovorax strains have 28 or less ABC systems. On the contrary, the freshwater Bdellovibrio strains have more ABC systems, typically around 51. In the genome of Bdellovibrio exovorus JSS (CP003537.1), 53 putative ABC systems were detected, representing the highest number among all the BALO genomes examined in this study. Unexpected high numbers of ABC systems involved in cellular processes were found in all BALOs. Phylogenetic analysis suggests that the majority of ABC proteins can be assigned into many separate families with high bootstrap supports (>50%). In this study, a general framework of sequence-structure-function connections for the ABC systems in BALOs was revealed providing novel insights for future investigations.
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Affiliation(s)
- Nan Li
- School of the Environment, Florida A&M University, Tallahassee, FL, USA
| | - Huan Chen
- National High Magnetic Field Laboratory, Tallahassee, FL, USA
| | - Henry N Williams
- School of the Environment, Florida A&M University, Tallahassee, FL, USA.
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Abstract
Biofilm formation on central lines or peripheral catheters is a serious threat to patient well-being. Contaminated vascular devices can act as a nidus for bloodstream infection and systemic pathogen dissemination. Staphylococcal biofilms are the most common cause of central-line-associated bloodstream infections, and antibiotic resistance makes them difficult to treat. As an alternative to antibiotic intervention, we sought to identify anti-staphylococcal biofilm targets for the development of a vaccine or antibody prophylactic. A screening strategy was devised using a microfluidic system to test antibody-mediated biofilm inhibition under biologically relevant conditions of shear flow. Affinity-purified polyclonal antibodies to target antigen PhnD inhibited both Staphylococcus epidermidis and S. aureus biofilms. PhnD-specific antibodies blocked biofilm development at the initial attachment and aggregation stages, and deletion of phnD inhibited normal biofilm formation. We further adapted our microfluidic biofilm system to monitor the interaction of human neutrophils with staphylococcal biofilms and demonstrated that PhnD-specific antibodies also serve as opsonins to enhance neutrophil binding, motility, and biofilm engulfment. These data support the identification of PhnD as a lead target for biofilm intervention strategies performed either by vaccination or through passive administration of antibodies.
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Ruggiero A, Dattelbaum JD, Staiano M, Berisio R, D'Auria S, Vitagliano L. A loose domain swapping organization confers a remarkable stability to the dimeric structure of the arginine binding protein from Thermotoga maritima. PLoS One 2014; 9:e96560. [PMID: 24832102 PMCID: PMC4022495 DOI: 10.1371/journal.pone.0096560] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/09/2014] [Indexed: 01/08/2023] Open
Abstract
The arginine binding protein from Thermatoga maritima (TmArgBP), a substrate binding protein (SBP) involved in the ABC system of solute transport, presents a number of remarkable properties. These include an extraordinary stability to temperature and chemical denaturants and the tendency to form multimeric structures, an uncommon feature among SBPs involved in solute transport. Here we report a biophysical and structural characterization of the TmArgBP dimer. Our data indicate that the dimer of the protein is endowed with a remarkable stability since its full dissociation requires high temperature as well as SDS and urea at high concentrations. In order to elucidate the atomic level structural properties of this intriguing protein, we determined the crystallographic structures of the apo and the arginine-bound forms of TmArgBP using MAD and SAD methods, respectively. The comparison of the liganded and unliganded models demonstrates that TmArgBP tertiary structure undergoes a very large structural re-organization upon arginine binding. This transition follows the Venus Fly-trap mechanism, although the entity of the re-organization observed in TmArgBP is larger than that observed in homologous proteins. Intriguingly, TmArgBP dimerizes through the swapping of the C-terminal helix. This dimer is stabilized exclusively by the interactions established by the swapping helix. Therefore, the TmArgBP dimer combines a high level of stability and conformational freedom. The structure of the TmArgBP dimer represents an uncommon example of large tertiary structure variations amplified at quaternary structure level by domain swapping. Although the biological relevance of the dimer needs further assessments, molecular modelling suggests that the two TmArgBP subunits may simultaneously interact with two distinct ABC transporters. Moreover, the present protein structures provide some clues about the determinants of the extraordinary stability of the biomolecule. The availability of an accurate 3D model represents a powerful tool for the design of new TmArgBP suited for biotechnological applications.
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Affiliation(s)
| | - Jonathan D Dattelbaum
- Department of Chemistry, University of Richmond, Richmond, Virginia, United States of America
| | - Maria Staiano
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Napoli, Italy
| | - Sabato D'Auria
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy
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Munshi P, Stanley CB, Ghimire-Rijal S, Lu X, Myles DA, Cuneo MJ. Molecular details of ligand selectivity determinants in a promiscuous β-glucan periplasmic binding protein. BMC STRUCTURAL BIOLOGY 2013; 13:18. [PMID: 24090243 PMCID: PMC3850815 DOI: 10.1186/1472-6807-13-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/27/2013] [Indexed: 01/07/2023]
Abstract
BACKGROUND Members of the periplasmic binding protein (PBP) superfamily utilize a highly conserved inter-domain ligand binding site that adapts to specifically bind a chemically diverse range of ligands. This paradigm of PBP ligand binding specificity was recently altered when the structure of the Thermotoga maritima cellobiose-binding protein (tmCBP) was solved. The tmCBP binding site is bipartite, comprising a canonical solvent-excluded region (subsite one), adjacent to a solvent-filled cavity (subsite two) where specific and semi-specific ligand recognition occur, respectively. RESULTS A molecular level understanding of binding pocket adaptation mechanisms that simultaneously allow both ligand specificity at subsite one and promiscuity at subsite two has potentially important implications in ligand binding and drug design studies. We sought to investigate the determinants of ligand binding selectivity in tmCBP through biophysical characterization of tmCBP in the presence of varying β-glucan oligosaccharides. Crystal structures show that whilst the amino acids that comprise both the tmCBP subsite one and subsite two binding sites remain fixed in conformation regardless of which ligands are present, the rich hydrogen bonding potential of water molecules may facilitate the ordering and the plasticity of this unique PBP binding site. CONCLUSIONS The identification of the roles these water molecules play in ligand recognition suggests potential mechanisms that can be utilized to adapt a single ligand binding site to recognize multiple distinct ligands.
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Affiliation(s)
- Parthapratim Munshi
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA,Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN 37132, USA,Current address. Shiv Nadar University, Department of Chemistry, Oak Ridge National Laboratory, Uttar Pradesh, India
| | - Christopher B Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Sudipa Ghimire-Rijal
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xun Lu
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dean A Myles
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew J Cuneo
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Akerboom J, Carreras Calderón N, Tian L, Wabnig S, Prigge M, Tolö J, Gordus A, Orger MB, Severi KE, Macklin JJ, Patel R, Pulver SR, Wardill TJ, Fischer E, Schüler C, Chen TW, Sarkisyan KS, Marvin JS, Bargmann CI, Kim DS, Kügler S, Lagnado L, Hegemann P, Gottschalk A, Schreiter ER, Looger LL. Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics. Front Mol Neurosci 2013; 6:2. [PMID: 23459413 PMCID: PMC3586699 DOI: 10.3389/fnmol.2013.00002] [Citation(s) in RCA: 493] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 02/11/2013] [Indexed: 12/17/2022] Open
Abstract
Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, “RCaMPs,” engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca2+-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca2+]) and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2) or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca2+ affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan, and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics.
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Affiliation(s)
- Jasper Akerboom
- Janelia Farm Research Campus, Howard Hughes Medical Institute Ashburn, VA, USA
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48
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Abstract
Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Recent efforts in protein engineering have significantly increased the performance of GECIs. The state-of-the art single-wavelength GECI, GCaMP3, has been deployed in a number of model organisms and can reliably detect three or more action potentials in short bursts in several systems in vivo. Through protein structure determination, targeted mutagenesis, high-throughput screening, and a battery of in vitro assays, we have increased the dynamic range of GCaMP3 by severalfold, creating a family of "GCaMP5" sensors. We tested GCaMP5s in several systems: cultured neurons and astrocytes, mouse retina, and in vivo in Caenorhabditis chemosensory neurons, Drosophila larval neuromuscular junction and adult antennal lobe, zebrafish retina and tectum, and mouse visual cortex. Signal-to-noise ratio was improved by at least 2- to 3-fold. In the visual cortex, two GCaMP5 variants detected twice as many visual stimulus-responsive cells as GCaMP3. By combining in vivo imaging with electrophysiology we show that GCaMP5 fluorescence provides a more reliable measure of neuronal activity than its predecessor GCaMP3. GCaMP5 allows more sensitive detection of neural activity in vivo and may find widespread applications for cellular imaging in general.
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49
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Ha JH, Shinsky SA, Loh SN. Stepwise conversion of a binding protein to a fluorescent switch: application to Thermoanaerobacter tengcongensis ribose binding protein. Biochemistry 2013; 52:600-12. [PMID: 23302025 DOI: 10.1021/bi301105u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Alternate frame folding (AFF) is a protein engineering methodology the purpose of which is to convert an ordinary binding protein into a molecular switch. The AFF modification entails duplicating an amino- or carboxy-terminal segment of the protein and appending it to the opposite end of the molecule. This duplication allows the protein to interconvert, in a ligand-dependent fashion, between two mutually exclusive native folds: the wild-type structure and a circularly permuted form. The fold shift can be detected by placement of extrinsic fluorophores at sites sensitive to the engineered conformational change. Here, we apply the AFF mechanism to create several ribose-sensing proteins derived from Thermoanaerobacter tengcongensis ribose binding protein. Our purpose is to systematically explore the parameters of the AFF design. These considerations include the site of circular permutation, the length and location of the duplicated segment, thermodynamic and kinetic optimization of the switching mechanism, and placement of extrinsic fluorophores. Three of the four AFF variants created here undergo the expected conformational shift and exhibit a ribose-dependent fluorescence change. The fourth construct fails to switch folds upon addition of ribose, likely because the circularly permuted form folds much more slowly than the nonpermuted form. This disparity apparently introduces a kinetic barrier that partitions the refolding molecules to the nonpermuted structure. The results of this study serve as a guideline for applying the AFF modification to other proteins of biomedical, diagnostic, and industrial interest.
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Affiliation(s)
- Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
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50
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An optimized fluorescent probe for visualizing glutamate neurotransmission. Nat Methods 2013; 10:162-70. [PMID: 23314171 PMCID: PMC4469972 DOI: 10.1038/nmeth.2333] [Citation(s) in RCA: 632] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 12/11/2012] [Indexed: 11/08/2022]
Abstract
We describe an intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) with signal-to-noise ratio and kinetics appropriate for in vivo imaging. We engineered iGluSnFR in vitro to maximize its fluorescence change, and we validated its utility for visualizing glutamate release by neurons and astrocytes in increasingly intact neurological systems. In hippocampal culture, iGluSnFR detected single field stimulus-evoked glutamate release events. In pyramidal neurons in acute brain slices, glutamate uncaging at single spines showed that iGluSnFR responds robustly and specifically to glutamate in situ, and responses correlate with voltage changes. In mouse retina, iGluSnFR-expressing neurons showed intact light-evoked excitatory currents, and the sensor revealed tonic glutamate signaling in response to light stimuli. In worms, glutamate signals preceded and predicted postsynaptic calcium transients. In zebrafish, iGluSnFR revealed spatial organization of direction-selective synaptic activity in the optic tectum. Finally, in mouse forelimb motor cortex, iGluSnFR expression in layer V pyramidal neurons revealed task-dependent single-spine activity during running.
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