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  1. Article ; Online: A retrospective chart review assessing antibiotic treatment of hospitalized patients with discordant

    Stoddart, Clare / Kuo, Irene / Spence, Matthew A / Palmore, Tara N

    Antimicrobial stewardship & healthcare epidemiology : ASHE

    2024  Volume 4, Issue 1, Page(s) e57

    Abstract: Clostridioides ... ...

    Abstract Clostridioides difficile
    Language English
    Publishing date 2024-04-23
    Publishing country England
    Document type Journal Article
    ISSN 2732-494X
    ISSN (online) 2732-494X
    DOI 10.1017/ash.2024.60
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  2. Article ; Online: Evo-velocity: Protein language modeling accelerates the study of evolution.

    Sandhu, Mahakaran / Spence, Matthew A / Jackson, Colin J

    Cell systems

    2022  Volume 13, Issue 4, Page(s) 271–273

    Abstract: Understanding how protein sequences have evolved is one of the defining challenges in modern biology. In this issue of Cell Systems, Hie et al. describe a novel phylogenetic approach, dubbed "evo-velocity," that exploits protein language modeling to ... ...

    Abstract Understanding how protein sequences have evolved is one of the defining challenges in modern biology. In this issue of Cell Systems, Hie et al. describe a novel phylogenetic approach, dubbed "evo-velocity," that exploits protein language modeling to overcome many limitations of traditional phylogenetic analysis.
    MeSH term(s) Biological Evolution ; Language ; Phylogeny
    Language English
    Publishing date 2022-04-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 2854138-8
    ISSN 2405-4720 ; 2405-4712
    ISSN (online) 2405-4720
    ISSN 2405-4712
    DOI 10.1016/j.cels.2022.03.004
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  3. Article ; Online: Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors.

    Meger, Anthony T / Spence, Matthew A / Sandhu, Mahakaran / Matthews, Dana / Chen, Jackie / Jackson, Colin J / Raman, Srivatsan

    Cell systems

    2024  Volume 15, Issue 4, Page(s) 374–387.e6

    Abstract: How a protein's function influences the shape of its fitness landscape, smooth or rugged, is a fundamental question in evolutionary biochemistry. Smooth landscapes arise when incremental mutational steps lead to a progressive change in function, as ... ...

    Abstract How a protein's function influences the shape of its fitness landscape, smooth or rugged, is a fundamental question in evolutionary biochemistry. Smooth landscapes arise when incremental mutational steps lead to a progressive change in function, as commonly seen in enzymes and binding proteins. On the other hand, rugged landscapes are poorly understood because of the inherent unpredictability of how sequence changes affect function. Here, we experimentally characterize the entire sequence phylogeny, comprising 1,158 extant and ancestral sequences, of the DNA-binding domain (DBD) of the LacI/GalR transcriptional repressor family. Our analysis revealed an extremely rugged landscape with rapid switching of specificity, even between adjacent nodes. Further, the ruggedness arises due to the necessity of the repressor to simultaneously evolve specificity for asymmetric operators and disfavors potentially adverse regulatory crosstalk. Our study provides fundamental insight into evolutionary, molecular, and biophysical rules of genetic regulation through the lens of fitness landscapes.
    MeSH term(s) Phylogeny
    Language English
    Publishing date 2024-03-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2854138-8
    ISSN 2405-4720 ; 2405-4712
    ISSN (online) 2405-4720
    ISSN 2405-4712
    DOI 10.1016/j.cels.2024.03.002
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  4. Article ; Online: Ancestral sequence reconstruction for protein engineers.

    Spence, Matthew A / Kaczmarski, Joe A / Saunders, Jake W / Jackson, Colin J

    Current opinion in structural biology

    2021  Volume 69, Page(s) 131–141

    Abstract: In addition to its value in the study of molecular evolution, ancestral sequence reconstruction (ASR) has emerged as a useful methodology for engineering proteins with enhanced properties. Proteins generated by ASR often exhibit unique or improved ... ...

    Abstract In addition to its value in the study of molecular evolution, ancestral sequence reconstruction (ASR) has emerged as a useful methodology for engineering proteins with enhanced properties. Proteins generated by ASR often exhibit unique or improved activity, stability, and/or promiscuity, all of which are properties that are valued by protein engineers. Comparison between extant proteins and evolutionary intermediates generated by ASR also allows protein engineers to identify substitutions that have contributed to functional innovation or diversification within protein families. As ASR becomes more widely adopted as a protein engineering approach, it is important to understand the applications, limitations, and recent developments of this technique. This review highlights recent exemplifications of ASR, as well as technical aspects of the reconstruction process that are relevant to protein engineering.
    MeSH term(s) Biological Evolution ; Evolution, Molecular ; Humans ; Phylogeny ; Protein Engineering ; Proteins/genetics
    Chemical Substances Proteins
    Language English
    Publishing date 2021-05-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2021.04.001
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    Zs.A 3206: Show issues Location:
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  5. Article ; Online: Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade.

    Burnim, Audrey A / Spence, Matthew A / Xu, Da / Jackson, Colin J / Ando, Nozomi

    eLife

    2022  Volume 11

    Abstract: Ribonucleotide reductases (RNRs) are used by all free-living organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a ...

    Abstract Ribonucleotide reductases (RNRs) are used by all free-living organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a conserved fold and radical-based mechanism for nucleotide reduction. Here, we structurally aligned the diverse RNR family by the conserved catalytic barrel to reconstruct the first large-scale phylogeny consisting of 6779 sequences that unites all extant classes of the RNR family and performed evo-velocity analysis to independently validate our evolutionary model. With a robust phylogeny in-hand, we uncovered a novel, phylogenetically distinct clade that is placed as ancestral to the classes I and II RNRs, which we have termed clade Ø. We employed small-angle X-ray scattering (SAXS), cryogenic-electron microscopy (cryo-EM), and AlphaFold2 to investigate a member of this clade from
    MeSH term(s) DNA ; Nucleotides ; Phylogeny ; Ribonucleotide Reductases/genetics ; Scattering, Small Angle ; X-Ray Diffraction
    Chemical Substances Nucleotides ; DNA (9007-49-2) ; Ribonucleotide Reductases (EC 1.17.4.-)
    Language English
    Publishing date 2022-09-01
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.79790
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  6. Article ; Online: Analysis of insertions and extensions in the functional evolution of the ribonucleotide reductase family.

    Burnim, Audrey A / Xu, Da / Spence, Matthew A / Jackson, Colin J / Ando, Nozomi

    Protein science : a publication of the Protein Society

    2022  Volume 31, Issue 12, Page(s) e4483

    Abstract: Ribonucleotide reductases (RNRs) are used by all free-living organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a ...

    Abstract Ribonucleotide reductases (RNRs) are used by all free-living organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a conserved fold and radical-based mechanism for nucleotide reduction. In this work, we expand on our recent phylogenetic inference of the entire RNR family and describe the evolutionarily relatedness of insertions and extensions around the structurally homologous catalytic barrel. Using evo-velocity and sequence similarity network (SSN) analyses, we show that the N-terminal regulatory motif known as the ATP-cone domain was likely inherited from an ancestral RNR. By combining SSN analysis with AlphaFold2 predictions, we also show that the C-terminal extensions of class II RNRs can contain folded domains that share homology with an Fe-S cluster assembly protein. Finally, using sequence analysis and AlphaFold2, we show that the sequence motif of a catalytically essential insertion known as the finger loop is tightly coupled to the catalytic mechanism. Based on these results, we propose an evolutionary model for the diversification of the RNR family.
    MeSH term(s) Ribonucleotide Reductases/genetics ; Ribonucleotide Reductases/metabolism ; Phylogeny ; Catalysis ; Nucleotides
    Chemical Substances Ribonucleotide Reductases (EC 1.17.4.-) ; Nucleotides
    Language English
    Publishing date 2022-10-29
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.4483
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3407: Show issues Location:
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  7. Article ; Online: A Comprehensive Phylogenetic Analysis of the Serpin Superfamily.

    Spence, Matthew A / Mortimer, Matthew D / Buckle, Ashley M / Minh, Bui Quang / Jackson, Colin J

    Molecular biology and evolution

    2021  Volume 38, Issue 7, Page(s) 2915–2929

    Abstract: Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been ... ...

    Abstract Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer due to their unexpectedly high homology. Here, we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6,000-sequence phylogeny that encompasses serpins from all kingdoms of life. We show that in addition to a central "hub" of highly conserved serpins, there has been extensive diversification of the superfamily into many novel functional clades. Our analysis indicates that the hub proteins are ancient and are similar because of convergent evolution, rather than the alternative hypothesis of horizontal gene transfer. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.
    Language English
    Publishing date 2021-03-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msab081
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    Zs.A 2137: Show issues Location:
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  8. Article ; Online: Structural and evolutionary approaches to the design and optimization of fluorescence-based small molecule biosensors.

    Kaczmarski, Joe A / Mitchell, Joshua A / Spence, Matthew A / Vongsouthi, Vanessa / Jackson, Colin J

    Current opinion in structural biology

    2019  Volume 57, Page(s) 31–38

    Abstract: Biosensors that selectively report on the presence of specific small molecule analytes have applications in many fields of research, medicine and biotechnology. Here, we review recent advances and emerging approaches in the design and optimisation of ... ...

    Abstract Biosensors that selectively report on the presence of specific small molecule analytes have applications in many fields of research, medicine and biotechnology. Here, we review recent advances and emerging approaches in the design and optimisation of genetically encoded fluorescence-based small molecule biosensors. We discuss how natural sensory proteins can be exploited to produce novel biosensors and the strategies for optimizing ligand specificity and fluorescence readout. Finally, we provide insight into high-throughput sensor optimisation and discuss the challenges that are faced when designing novel biosensors.
    MeSH term(s) Biosensing Techniques/methods ; Directed Molecular Evolution/methods ; Fluorescence ; Protein Engineering ; Small Molecule Libraries/analysis
    Chemical Substances Small Molecule Libraries
    Language English
    Publishing date 2019-02-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2019.01.013
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  9. Article ; Online: Ancestral Sequence Reconstruction Identifies Structural Changes Underlying the Evolution of

    Joho, Yvonne / Vongsouthi, Vanessa / Spence, Matthew A / Ton, Jennifer / Gomez, Chloe / Tan, Li Lynn / Kaczmarski, Joe A / Caputo, Alessandro T / Royan, Santana / Jackson, Colin J / Ardevol, Albert

    Biochemistry

    2022  Volume 62, Issue 2, Page(s) 437–450

    Abstract: The improved production, recycling, and removal of plastic waste, such as polyethylene terephthalate (PET), are pressing environmental and economic issues for society. Biocatalytic (enzymatic) PET depolymerization is potentially a sustainable, low-energy ...

    Abstract The improved production, recycling, and removal of plastic waste, such as polyethylene terephthalate (PET), are pressing environmental and economic issues for society. Biocatalytic (enzymatic) PET depolymerization is potentially a sustainable, low-energy solution to PET recycling, especially when compared with current disposal methods such as landfills, incineration, or gasification. IsPETase has been extensively studied for its use in PET depolymerization; however, its evolution from cutinases is not fully understood, and most engineering studies have neglected the majority of the available sequence space remote from the active site. In this study, ancestral protein reconstruction (ASR) has been used to trace the evolutionary trajectory from ancient serine hydrolases to IsPETase, while ASR and the related design approach, protein repair one-stop shop, were used to identify enzyme variants with improved activity and stability. Kinetic and structural characterization of these variants reveals new insights into the evolution of PETase activity and the role of second-shell mutations around the active site. Among the designed and reconstructed variants, we identified several with melting points 20 °C higher than that of IsPETase and two variants with significantly higher catalytic activity.
    MeSH term(s) Hydrolases/chemistry ; Burkholderiales/genetics ; Burkholderiales/metabolism ; Catalytic Domain ; Mutation ; Polyethylene Terephthalates/metabolism
    Chemical Substances Hydrolases (EC 3.-) ; Polyethylene Terephthalates
    Language English
    Publishing date 2022-08-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.2c00323
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    Zs.A 217: Show issues Location:
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  10. Article ; Online: Dynamic charge acceptance and hydrogen evolution of a new MXene additive in advanced lead-acid batteries via a rapid screening three-electrode method.

    Kang, Shuai / Shang, Mingwei / Spence, Matthew A / Andrew, Michael / Liu, Shuangyi / Niu, Junjie

    Chemical communications (Cambridge, England)

    2018  Volume 54, Issue 28, Page(s) 3456–3459

    Abstract: A methodology to screen additives in lead-acid batteries is critical. We developed a three-electrode system that can rapidly check the dynamic charge acceptance (DCA) and hydrogen evolution of electrodes. The electrode with 2% MXene and 0.2% carbon black ...

    Abstract A methodology to screen additives in lead-acid batteries is critical. We developed a three-electrode system that can rapidly check the dynamic charge acceptance (DCA) and hydrogen evolution of electrodes. The electrode with 2% MXene and 0.2% carbon black shows a better DCA, which indicates its great potential in the start-stop technology.
    Language English
    Publishing date 2018-04-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/C8CC00086G
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