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Liu Y, Tian X, Zhang F, Zhang WB. Probing the Topological Effects on Stability Enhancement and Therapeutic Performance of Protein Bioconjugates: Tadpole, Macrocycle versus Figure-of-Eight. Adv Healthc Mater 2024:e2400466. [PMID: 39091049 DOI: 10.1002/adhm.202400466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 07/22/2024] [Indexed: 08/04/2024]
Abstract
Chemical topology provides a unique dimension for making therapeutic protein bioconjugates with native structure and intact function, yet the effects of topology remain elusive. Herein, the design, synthesis, and characterization of therapeutic protein bioconjugates in three topologies (i.e., tadpole, macrocycle, and figure-of-eight), are reported. The interferon α2b (IFN) and albumin binding domain (ABD) are selected as the model proteins for bioconjugation and proof-of-concept. The biosynthesis of these topological isoforms is accomplished via direct expression in cells using SpyTag-SpyCatcher chemistry and/or split-intein-mediated ligation for topology diversification. The corresponding topologies are proven with combined techniques of LC-MS, SDS-PAGE, and controlled proteolytic digestion. While the properties of these topological isoforms are similar in most cases, the figure-of-eight-shaped bioconjugate, f8-IFN-ABD, exhibits the best thermal stability and anti-aggregation properties along with prolonged half-life and enhanced tumor retention relative to the tadpole-shaped control, tadp-IFN-ABD, and the macrocyclic control, c-IFN-ABD, showcasing considerable topological effects. The work expands the topological diversity of proteins and demonstrates the potential advantages of leveraging chemical topology for functional benefits beyond multi-function integration in protein therapeutics.
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Affiliation(s)
- Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Xibao Tian
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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2
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Young PG, Paynter JM, Wardega JK, Middleditch MJ, Payne LS, Baker EN, Squire CJ. Domain structure and cross-linking in a giant adhesin from the Mobiluncus mulieris bacterium. Acta Crystallogr D Struct Biol 2023; 79:971-979. [PMID: 37860959 PMCID: PMC10619420 DOI: 10.1107/s2059798323007507] [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: 06/16/2023] [Accepted: 08/27/2023] [Indexed: 10/21/2023] Open
Abstract
Cell-surface proteins known as adhesins enable bacteria to colonize particular environments, and in Gram-positive bacteria often contain autocatalytically formed covalent intramolecular cross-links. While investigating the prevalence of such cross-links, a remarkable example was discovered in Mobiluncus mulieris, a pathogen associated with bacterial vaginosis. This organism encodes a putative adhesin of 7651 residues. Crystallography and mass spectrometry of two selected domains, and AlphaFold structure prediction of the remainder of the protein, were used to show that this adhesin belongs to the family of thioester, isopeptide and ester-bond-containing proteins (TIE proteins). It has an N-terminal domain homologous to thioester adhesion domains, followed by 51 immunoglobulin (Ig)-like domains containing ester- or isopeptide-bond cross-links. The energetic cost to the M. mulieris bacterium in retaining such a large adhesin as a single gene or protein construct suggests a critical role in pathogenicity and/or persistence.
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Affiliation(s)
- Paul G. Young
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Jacob M. Paynter
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Julia K. Wardega
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Martin J. Middleditch
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Leo S. Payne
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Edward N. Baker
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Christopher J. Squire
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
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3
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The long and the short of Periscope Proteins. Biochem Soc Trans 2022; 50:1293-1302. [PMID: 36196877 DOI: 10.1042/bst20220194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022]
Abstract
Bacteria sense, interact with, and modify their environmental niche by deploying a molecular ensemble at the cell surface. The changeability of this exposed interface, combined with extreme changes in the functional repertoire associated with lifestyle switches from planktonic to adherent and biofilm states necessitate dynamic variability. Dynamic surface changes include chemical modifications to the cell wall; export of diverse extracellular biofilm components; and modulation of expression of cell surface proteins for adhesion, co-aggregation and virulence. Local enrichment for highly repetitive proteins with high tandem repeat identity has been an enigmatic phenomenon observed in diverse bacterial species. Preliminary observations over decades of research suggested these repeat regions were hypervariable, as highly related strains appeared to express homologues with diverse molecular mass. Long-read sequencing data have been interrogated to reveal variation in repeat number; in combination with structural, biophysical and molecular dynamics approaches, the Periscope Protein class has been defined for cell surface attached proteins that dynamically expand and contract tandem repeat tracts at the population level. Here, I review the diverse high-stability protein folds and coherent interdomain linkages culminating in the formation of highly anisotropic linear repeat arrays, so-called rod-like protein 'stalks', supporting roles in bacterial adhesion, biofilm formation, cell surface spatial competition, and immune system modulation. An understanding of the functional impacts of dynamic changes in repeat arrays and broader characterisation of the unusual protein folds underpinning this variability will help with the design of immunisation strategies, and contribute to synthetic biology approaches including protein engineering and microbial consortia construction.
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Ma Q, Lei H, Cao Y. Intramolecular covalent bonds in Gram-positive bacterial surface proteins. Chembiochem 2022; 23:e202200316. [PMID: 35801833 DOI: 10.1002/cbic.202200316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/07/2022] [Indexed: 11/09/2022]
Abstract
Gram-positive bacteria experience considerable mechanical perturbation when adhering to host surfaces during colonization and infection. They have evolved various adhesion proteins that are mechanically robust to ensure strong surface adhesion. Recently, it was discovered that these adhesion proteins contain rare, extra intramolecular covalent bonds that stabilize protein structures and participate in surface bonding. These intramolecular covalent bonds include isopeptides, thioesters, and ester bonds, which often form spontaneously without the need for additional enzymes. With the development of single-molecule force spectroscopy techniques, the detailed mechanical roles of these intramolecular covalent bonds have been revealed. In this review, we summarize the recent advances in this area of research, focusing on the link between the mechanical stability and function of these covalent bonds in Gram-positive bacterial surface proteins. We also highlight the potential impact of these discoveries on the development of novel antibiotics and chemical biology tools.
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Affiliation(s)
- Quan Ma
- Nanjing University, Department of Physics, CHINA
| | - Hai Lei
- Nanjing University, Department of Physics, CHINA
| | - Yi Cao
- Nanjing University, Department of Physics, 22 Hankou Road, 210093, Nanjing, CHINA
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Large-Scale Discovery of Microbial Fibrillar Adhesins and Identification of Novel Members of Adhesive Domain Families. J Bacteriol 2022; 204:e0010722. [PMID: 35608365 PMCID: PMC9210967 DOI: 10.1128/jb.00107-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Fibrillar adhesins are bacterial cell surface proteins that mediate interactions with the environment, including host cells during colonization or other bacteria during biofilm formation. These proteins are characterized by a stalk that projects the adhesive domain closer to the binding target. Fibrillar adhesins evolve quickly and thus can be difficult to computationally identify, yet they represent an important component for understanding bacterium-host interactions. To detect novel fibrillar adhesins, we developed a random forest prediction approach based on common characteristics we identified for this protein class. We applied this approach to Firmicutes and Actinobacteria proteomes, yielding over 6,500 confidently predicted fibrillar adhesins. To verify the approach, we investigated predicted fibrillar adhesins that lacked a known adhesive domain. Based on these proteins, we identified 24 sequence clusters representing potential novel members of adhesive domain families. We used AlphaFold to verify that 15 clusters showed structural similarity to known adhesive domains, such as the TED domain. Overall, our study has made a significant contribution to the number of known fibrillar adhesins and has enabled us to identify novel members of adhesive domain families involved in bacterial pathogenesis. IMPORTANCE Fibrillar adhesins are a class of bacterial cell surface proteins that enable bacteria to interact with their environment. We developed a machine learning approach to identify fibrillar adhesins and applied this classification approach to the Firmicutes and Actinobacteria Reference Proteomes database. This method allowed us to detect a high number of novel fibrillar adhesins and also novel members of adhesive domain families. To confirm our predictions of these potential adhesin protein domains, we predicted their structure using the AlphaFold tool.
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van Leeuwen HC, Roelofs D, Corver J, Hensbergen P. Phylogenetic analysis of the bacterial Pro-Pro-endopeptidase domain reveals a diverse family including secreted and membrane anchored proteins. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100024. [PMID: 34841315 PMCID: PMC8610288 DOI: 10.1016/j.crmicr.2021.100024] [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] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 11/21/2022] Open
Abstract
Bacterial Pro-Pro-endopeptidase (PPEP) is the latest member of the metalloendopeptidase class (E.C. 3.4.24.89). PPEP homologs are found in two firmicutes orders, clostridiales and bacillales spread over 9 genera and more than 130 species. Some PPEP homologs have acquired additional anchor domains that bind noncovalently to various elements of the bacterial peptidoglycan cell wall. Prototype family members, PPEP-1 and PPEP-2, target bacterial surface adhesion proteins, but homologs could target other extracellular proteins.
Pro-Pro-endopeptidases (PPEP, EC 3.4.24.89) are secreted, zinc metalloproteases that have the unusual capacity to cleave a peptide bond between two prolines, a bond that is generally less sensitive to proteolytic cleavage. Two well studied members of the family are PPEP-1 and PPEP-2, produced by Clostridioides difficile, a human pathogen, and Paenibacillus alvei, a bee secondary invader, respectively. Both proteases seem to be involved in mediating bacterial adhesion by cleaving cell surface anchor proteins on the bacterium itself. By using basic alignment and phylogenetic profiling analysis, this work shows that the complete family of proteins that contain a PPEP domain includes proteins from more than 130 species spread over 9 genera. These analyses also suggest that the PPEP domain spread through horizontal gene transfer events between species within the Firmicutes’ classes Bacilli and Clostridia. Bacterial species containing PPEP homologs are found in diverse habitats, varying from human pathogens and gut microbiota to free-living bacteria, which were isolated from various environments, including extreme conditions such as hot springs, desert soil and salt lakes. The phylogenetic tree reveals the relationships between family members and suggests that smaller subgroups could share cleavage specificity, substrates and functional similarity. Except for PPEP-1 and PPEP-2, no cleavage specificity, specific physiological target, or function has been assigned for any of the other PPEP-family members. Some PPEP proteins have acquired additional domains that recognize and bind noncovalently to various elements of the bacterial peptidoglycan cell-wall, anchoring these PPEPs. Secreted or anchored to the cell-wall surface PPEP proteins seem to perform various functions.
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Affiliation(s)
- Hans C van Leeuwen
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, Lange Kleiweg 137, 2288 GJ Rijswijk, the Netherlands
| | - Dick Roelofs
- KeyGene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands
| | - Jeroen Corver
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC Leiden, the Netherlands
| | - Paul Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC Leiden, the Netherlands
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Amaya C, Cameron CJF, Devarkar SC, Seager SJH, Gerstein MB, Xiong Y, Schlieker C. Nodal modulator (NOMO) is required to sustain endoplasmic reticulum morphology. J Biol Chem 2021; 297:100937. [PMID: 34224731 PMCID: PMC8327139 DOI: 10.1016/j.jbc.2021.100937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 06/24/2021] [Accepted: 07/01/2021] [Indexed: 12/03/2022] Open
Abstract
The endoplasmic reticulum (ER) is a membrane-bound organelle responsible for protein folding, lipid synthesis, and calcium homeostasis. Maintenance of ER structural integrity is crucial for proper function, but much remains to be learned about the molecular players involved. To identify proteins that support the structure of the ER, we performed a proteomic screen and identified nodal modulator (NOMO), a widely conserved type I transmembrane protein of unknown function, with three nearly identical orthologs specified in the human genome. We found that overexpression of NOMO1 imposes a sheet morphology on the ER, whereas depletion of NOMO1 and its orthologs causes a collapse of ER morphology concomitant with the formation of membrane-delineated holes in the ER network positive for the lysosomal marker lysosomal-associated protein 1. In addition, the levels of key players of autophagy including microtubule-associated protein light chain 3 and autophagy cargo receptor p62/sequestosome 1 strongly increase upon NOMO depletion. In vitro reconstitution of NOMO1 revealed a "beads on a string" structure likely representing consecutive immunoglobulin-like domains. Extending NOMO1 by insertion of additional immunoglobulin folds results in a correlative increase in the ER intermembrane distance. Based on these observations and a genetic epistasis analysis including the known ER-shaping proteins Atlastin2 and Climp63, we propose a role for NOMO1 in the functional network of ER-shaping proteins.
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Affiliation(s)
- Catherine Amaya
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Christopher J F Cameron
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Swapnil C Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Sebastian J H Seager
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Mark B Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA; Department of Computer Science, Yale University, New Haven, Connecticut, USA; Department of Statistics and Data Science, Yale University, New Haven, Connecticut, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Christian Schlieker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut, USA.
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8
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Betts NS, Collins HM, Shirley NJ, Cuesta-Seijo JA, Schwerdt JG, Phillips RJ, Finnie C, Fincher GB, Dockter C, Skadhauge B, Bulone V. Identification and spatio-temporal expression analysis of barley genes that encode putative modular xylanolytic enzymes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 308:110792. [PMID: 34034860 DOI: 10.1016/j.plantsci.2020.110792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/30/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Arabinoxylans are cell wall polysaccharides whose re-modelling and degradation during plant development are mediated by several classes of xylanolytic enzymes. Here, we present the identification and new annotation of twelve putative (1,4)-β-xylanase and six β-xylosidase genes, and their spatio-temporal expression patterns during vegetative and reproductive growth of barley (Hordeum vulgare cv. Navigator). The encoded xylanase proteins are all predicted to contain a conserved carbohydrate-binding module (CBM) and a catalytic glycoside hydrolase (GH) 10 domain. Additional domains in some xylanases define three discrete phylogenetic clades: one clade contains proteins with an additional N-terminal signal sequence, while another clade contains proteins with multiple CBMs. Homology modelling revealed that all fifteen xylanases likely contain a third domain, a β-sandwich folded from two non-contiguous sequence segments that bracket the catalytic GH domain, which may explain why the full length protein is required for correct folding of the active enzyme. Similarly, predicted xylosidase proteins share a highly conserved domain structure, each with an N-terminal signal peptide, a split GH 3 domain, and a C-terminal fibronectin-like domain. Several genes appear to be ubiquitously expressed during barley growth and development, while four newly annotated xylanase and xylosidase genes are expressed at extremely high levels, which may be of broader interest for industrial applications where cell wall degradation is necessary.
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Affiliation(s)
- Natalie S Betts
- School of Agriculture, Food and Wine, Waite Campus, Glen Osmond SA 5064 Australia.
| | - Helen M Collins
- School of Agriculture, Food and Wine, Waite Campus, Glen Osmond SA 5064 Australia.
| | - Neil J Shirley
- School of Agriculture, Food and Wine, Waite Campus, Glen Osmond SA 5064 Australia
| | - Jose A Cuesta-Seijo
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark.
| | - Julian G Schwerdt
- School of Agriculture, Food and Wine, Waite Campus, Glen Osmond SA 5064 Australia.
| | - Renee J Phillips
- School of Agriculture, Food and Wine, Waite Campus, Glen Osmond SA 5064 Australia.
| | - Christine Finnie
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Geoffrey B Fincher
- School of Agriculture, Food and Wine, Waite Campus, Glen Osmond SA 5064 Australia.
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark.
| | - Birgitte Skadhauge
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark.
| | - Vincent Bulone
- School of Agriculture, Food and Wine, Waite Campus, Glen Osmond SA 5064 Australia; Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden.
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Gago-Córdoba C, Val-Calvo J, Abia D, Díaz-Talavera A, Miguel-Arribas A, Aguilar Suárez R, van Dijl JM, Wu LJ, Meijer WJJ. A Conserved Class II Type Thioester Domain-Containing Adhesin Is Required for Efficient Conjugation in Bacillus subtilis. mBio 2021; 12:e00104-21. [PMID: 33727345 PMCID: PMC8092201 DOI: 10.1128/mbio.00104-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
Conjugation, the process by which a DNA element is transferred from a donor to a recipient cell, is the main horizontal gene transfer route responsible for the spread of antibiotic resistance and virulence genes. Contact between a donor and a recipient cell is a prerequisite for conjugation, because conjugative DNA is transferred into the recipient via a channel connecting the two cells. Conjugative elements encode proteins dedicated to facilitating the recognition and attachment to recipient cells, also known as mating pair formation. A subgroup of the conjugative elements is able to mediate efficient conjugation during planktonic growth, and mechanisms facilitating mating pair formation will be particularly important in these cases. Conjugative elements of Gram-negative bacteria encode conjugative pili, also known as sex pili, some of which are retractile. Far less is known about mechanisms that promote mating pair formation in Gram-positive bacteria. The conjugative plasmid pLS20 of the Gram-positive bacterium Bacillus subtilis allows efficient conjugation in liquid medium. Here, we report the identification of an adhesin gene in the pLS20 conjugation operon. The N-terminal region of the adhesin contains a class II type thioester domain (TED) that is essential for efficient conjugation, particularly in liquid medium. We show that TED-containing adhesins are widely conserved in Gram-positive bacteria, including pathogens where they often play crucial roles in pathogenesis. Our study is the first to demonstrate the involvement of a class II type TED-containing adhesin in conjugation.IMPORTANCE Bacterial resistance to antibiotics has become a serious health care problem. The spread of antibiotic resistance genes between bacteria of the same or different species is often mediated by a process named conjugation, where a donor cell transfers DNA to a recipient cell through a connecting channel. The first step in conjugation is recognition and attachment of the donor to a recipient cell. Little is known about this first step, particularly in Gram-positive bacteria. Here, we show that the conjugative plasmid pLS20 of Bacillus subtilis encodes an adhesin protein that is essential for effective conjugation. This adhesin protein has a structural organization similar to adhesins produced by other Gram-positive bacteria, including major pathogens, where the adhesins serve in attachment to host tissues during colonization and infection. Our findings may thus also open novel avenues to design drugs that inhibit the spread of antibiotic resistance by blocking the first recipient-attachment step in conjugation.
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Affiliation(s)
- César Gago-Córdoba
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - David Abia
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - Alberto Díaz-Talavera
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - Rocío Aguilar Suárez
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan Maarten van Dijl
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Wilfried J J Meijer
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
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Sharma S, Subramani S, Popa I. Does protein unfolding play a functional role in vivo? FEBS J 2020; 288:1742-1758. [PMID: 32761965 DOI: 10.1111/febs.15508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022]
Abstract
Unfolding and refolding of multidomain proteins under force have yet to be recognized as a major mechanism of function for proteins in vivo. In this review, we discuss the inherent properties of multidomain proteins under a force vector from a structural and functional perspective. We then characterize three main systems where multidomain proteins could play major roles through mechanical unfolding: muscular contraction, cellular mechanotransduction, and bacterial adhesion. We analyze how key multidomain proteins for each system can produce a gain-of-function from the perspective of a fine-tuned quantized response, a molecular battery, delivery of mechanical work through refolding, elasticity tuning, protection and exposure of cryptic sites, and binding-induced mechanical changes. Understanding how mechanical unfolding and refolding affect function will have important implications in designing mechano-active drugs against conditions such as muscular dystrophy, cancer, or novel antibiotics.
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Affiliation(s)
- Sabita Sharma
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Smrithika Subramani
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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Tol-Pal System and Rgs Proteins Interact to Promote Unipolar Growth and Cell Division in Sinorhizobium meliloti. mBio 2020; 11:mBio.00306-20. [PMID: 32605980 PMCID: PMC7327166 DOI: 10.1128/mbio.00306-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Bacterial cell proliferation involves cell growth and septum formation followed by cell division. For cell growth, bacteria have evolved different complex mechanisms. The most prevalent growth mode of rod-shaped bacteria is cell elongation by incorporating new peptidoglycans in a dispersed manner along the sidewall. A small share of rod-shaped bacteria, including the alphaproteobacterial Rhizobiales, grow unipolarly. Here, we identified and initially characterized a set of Rgs (rhizobial growth and septation) proteins, which are involved in cell division and unipolar growth of Sinorhizobium meliloti and highly conserved in Rhizobiales. Our data expand the knowledge of components of the polarly localized machinery driving cell wall growth and suggest a complex of Rgs proteins with components of the divisome, differing in composition between the polar cell elongation zone and the septum. Sinorhizobium meliloti is an alphaproteobacterium belonging to the Rhizobiales. Bacteria from this order elongate their cell wall at the new cell pole, generated by cell division. Screening for protein interaction partners of the previously characterized polar growth factors RgsP and RgsM, we identified the inner membrane components of the Tol-Pal system (TolQ and TolR) and novel Rgs (rhizobial growth and septation) proteins with unknown functions. TolQ, Pal, and all Rgs proteins, except for RgsE, were indispensable for S. meliloti cell growth. Six of the Rgs proteins, TolQ, and Pal localized to the growing cell pole in the cell elongation phase and to the septum in predivisional cells, and three Rgs proteins localized to the growing cell pole only. The putative FtsN-like protein RgsS contains a conserved SPOR domain and is indispensable at the early stages of cell division. The components of the Tol-Pal system were required at the late stages of cell division. RgsE, a homolog of the Agrobacterium tumefaciens growth pole ring protein GPR, has an important role in maintaining the normal growth rate and rod cell shape. RgsD is a periplasmic protein with the ability to bind peptidoglycan. Analysis of the phylogenetic distribution of the Rgs proteins showed that they are conserved in Rhizobiales and mostly absent from other alphaproteobacterial orders, suggesting a conserved role of these proteins in polar growth.
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