1
|
Lee AR, Carter RS, Imani AS, Dommaraju SR, Hudson GA, Mitchell DA, Freeman MF. Discovery of Borosin Catalytic Strategies and Function through Bioinformatic Profiling. ACS Chem Biol 2024; 19:1116-1124. [PMID: 38695893 PMCID: PMC11221551 DOI: 10.1021/acschembio.4c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Borosins are ribosomally synthesized and post-translationally modified peptides (RiPPs) containing backbone α-N-methylations. These modifications confer favorable pharmacokinetic properties including increased membrane permeability and resistance to proteolytic degradation. Previous studies have biochemically and bioinformatically explored several borosins, revealing (1) numerous domain architectures and (2) diverse core regions lacking conserved sequence elements. Due to these characteristics, large-scale computational identification of borosin biosynthetic genes remains challenging and often requires additional, time-intensive manual inspection. This work builds upon previous findings and updates the genome-mining tool RODEO to automatically evaluate borosin biosynthetic gene clusters (BGCs) and identify putative precursor peptides. Using the new RODEO module, we provide an updated analysis of borosin BGCs identified in the NCBI database. From our data set, we bioinformatically predict and experimentally characterize a new fused borosin domain architecture, in which the modified natural product core is encoded N-terminal to the methyltransferase domain. Additionally, we demonstrate that a borosin precursor peptide is a native substrate of shewasin A, a reported aspartyl peptidase with no previously identified substrates. Shewasin A requires post-translational modification of the leader peptide for proteolytic maturation, a feature not previously observed in RiPPs. Overall, this work provides a user-friendly and open-access tool for the analysis of borosin BGCs and we demonstrate its utility to uncover additional biosynthetic strategies within the borosin class of RiPPs.
Collapse
Affiliation(s)
- Aileen R. Lee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, St. Paul, Minnesota, 55108, USA
| | - Riley S. Carter
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Aman S. Imani
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, St. Paul, Minnesota, 55108, USA
| | - Shravan R. Dommaraju
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Graham A. Hudson
- California Institute of Quantitative Biosciences (QB3); University of California, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Michael F. Freeman
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, St. Paul, Minnesota, 55108, USA
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, 55108, USA
| |
Collapse
|
2
|
Lee AR, Carter RS, Imani AS, Dommaraju SR, Hudson GA, Mitchell DA, Freeman MF. Computationally guided exploration of borosin biosynthetic strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574750. [PMID: 38260703 PMCID: PMC10802470 DOI: 10.1101/2024.01.09.574750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Borosins are ribosomally synthesized and post-translationally modified peptides containing backbone α- N -methylations. Identification of borosin precursor peptides is difficult because (1) there are no conserved sequence elements among borosin precursor peptides and (2) the biosynthetic gene clusters contain numerous domain architectures and peptide fusions. To tackle this problem, we updated the genome mining tool RODEO to automatically evaluate putative borosin BGCs and identify precursor peptides. Enabled by the new borosin module, we analyzed all borosin BGCs found in available sequence data and assigned precursor peptides to previously orphan borosin methyltransferases. Additionally, we bioinformatically predict and experimentally characterize a new fused borosin domain architecture, in which the modified core is N-terminal to the methyltransferase domain. Finally, we demonstrate that a borosin precursor peptide is the native substrate of shewasin A, a previously characterized pepsin-like aspartic peptidase whose native biological function was unknown.
Collapse
|
3
|
The Retropepsin-Type Protease APRc as a Novel Ig-Binding Protein and Moonlighting Immune Evasion Factor of Rickettsia. mBio 2021; 12:e0305921. [PMID: 34872352 PMCID: PMC8649778 DOI: 10.1128/mbio.03059-21] [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] [Indexed: 12/03/2022] Open
Abstract
Rickettsiae are obligate intracellular Gram-negative bacteria transmitted by arthropod vectors. Despite their reduced genomes, the function(s) of the majority of rickettsial proteins remains to be uncovered. APRc is a highly conserved retropepsin-type protease, suggested to act as a modulator of other rickettsial surface proteins with a role in adhesion/invasion. However, APRc’s function(s) in bacterial pathogenesis and virulence remains unknown. This study demonstrates that APRc targets host serum components, combining nonimmune immunoglobulin (Ig)-binding activity with resistance to complement-mediated killing. We confirmed nonimmune human IgG binding in extracts of different rickettsial species and intact bacteria. Our results revealed that the soluble domain of APRc is capable of binding to human (h), mouse, and rabbit IgG and different classes of human Ig (IgG, IgM, and IgA) in a concentration-dependent manner. APRc-hIgG interaction was confirmed with total hIgG and normal human serum. APRc-hIgG displayed a binding affinity in the micromolar range. We provided evidence of interaction preferentially through the Fab region and confirmed that binding is independent of catalytic activity. Mapping the APRc region responsible for binding revealed the segment between amino acids 157 and 166 as one of the interacting regions. Furthermore, we demonstrated that expression of the full-length protease in Escherichia coli is sufficient to promote resistance to complement-mediated killing and that interaction with IgG contributes to serum resistance. Our findings position APRc as a novel Ig-binding protein and a novel moonlighting immune evasion factor of Rickettsia, contributing to the arsenal of virulence factors utilized by these intracellular pathogens to aid in host colonization.
Collapse
|
4
|
Soares A, Niedermaier S, Faro R, Loos A, Manadas B, Faro C, Huesgen PF, Cheung AY, Simões I. An atypical aspartic protease modulates lateral root development in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2157-2171. [PMID: 30778561 DOI: 10.1093/jxb/erz059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/05/2019] [Indexed: 05/25/2023]
Abstract
Few atypical aspartic proteases (APs) present in plants have been functionally studied to date despite having been implicated in developmental processes and stress responses. Here we characterize a novel atypical AP that we name Atypical Aspartic Protease in Roots 1 (ASPR1), denoting its expression in Arabidopsis roots. Recombinant ASPR1 produced by transient expression in Nicotiana benthamiana was active and displayed atypical properties, combining optimum acidic pH, partial sensitivity to pepstatin, pronounced sensitivity to redox agents, and unique specificity preferences resembling those of fungal APs. ASPR1 overexpression suppressed primary root growth and lateral root development, implying a previously unknown biological role for an AP. Quantitative comparison of wild-type and aspr1 root proteomes revealed deregulation of proteins associated with both reactive oxygen species and auxin homeostasis in the mutant. Together, our findings on ASPR1 reinforce the diverse pattern of enzymatic properties and biological roles of atypical APs and raise exciting questions on how these distinctive features impact functional specialization among these proteases.
Collapse
Affiliation(s)
- André Soares
- PhD Programme in Experimental Biology and Biomedicine, Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, Portugal
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Stefan Niedermaier
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Rosário Faro
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Andreas Loos
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Carlos Faro
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Alice Y Cheung
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Isaura Simões
- Institute for Interdisciplinary Research, University of Coimbra, Portugal
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| |
Collapse
|
5
|
Soares A, Ribeiro Carlton SM, Simões I. Atypical and nucellin-like aspartic proteases: emerging players in plant developmental processes and stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2059-2076. [PMID: 30715463 DOI: 10.1093/jxb/erz034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Members of the pepsin-like family (A1) of aspartic proteases (APs) are widely distributed in plants. A large number of genes encoding putative A1 APs are found in different plant genomes, the vast majority of which exhibit distinct features when compared with the so-called typical APs (and, therefore, grouped as atypical and nucellin-like APs). These features include the absence of the plant-specific insert; an unusually high number of cysteine residues; the nature of the amino acids preceding the first catalytic aspartate; and unexpected localizations. The over-representation of atypical and nucellin-like APs in plants is suggestive of greater diversification of protein functions and a more regulatory role for these APs, as compared with the housekeeping function generally attributed to typical APs. New functions have been uncovered for non-typical APs, with proposed roles in biotic and abiotic stress responses, chloroplast metabolism, and reproductive development, clearly suggesting functional specialization and tight regulation of activity. Furthermore, unusual enzymatic properties have also been documented for some of these proteases. Here, we give an overview of the current knowledge on the distinctive features and functions of both atypical and nucellin-like APs, and discuss this emerging pattern of functional complexity and specialization among plant pepsin-like proteases.
Collapse
Affiliation(s)
- André Soares
- PhD Programme in Experimental Biology and Biomedicine, Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | | | - Isaura Simões
- Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| |
Collapse
|
6
|
Kinross J, Mirnezami R, Alexander J, Brown R, Scott A, Galea D, Veselkov K, Goldin R, Darzi A, Nicholson J, Marchesi JR. A prospective analysis of mucosal microbiome-metabonome interactions in colorectal cancer using a combined MAS 1HNMR and metataxonomic strategy. Sci Rep 2017; 7:8979. [PMID: 28827587 PMCID: PMC5566496 DOI: 10.1038/s41598-017-08150-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/07/2017] [Indexed: 02/07/2023] Open
Abstract
Colon cancer induces a state of mucosal dysbiosis with associated niche specific changes in the gut microbiota. However, the key metabolic functions of these bacteria remain unclear. We performed a prospective observational study in patients undergoing elective surgery for colon cancer without mechanical bowel preparation (n = 18). Using 16 S rRNA gene sequencing we demonstrated that microbiota ecology appears to be cancer stage-specific and strongly associated with histological features of poor prognosis. Fusobacteria (p < 0.007) and ε- Proteobacteria (p < 0.01) were enriched on tumour when compared to adjacent normal mucosal tissue, and fusobacteria and β-Proteobacteria levels increased with advancing cancer stage (p = 0.014 and 0.002 respecitvely). Metabonomic analysis using 1H Magic Angle Spinning Nuclear Magnetic Resonsance (MAS-NMR) spectroscopy, demonstrated increased abundance of taurine, isoglutamine, choline, lactate, phenylalanine and tyrosine and decreased levels of lipids and triglycerides in tumour relative to adjacent healthy tissue. Network analysis revealed that bacteria associated with poor prognostic features were not responsible for the modification of the cancer mucosal metabonome. Thus the colon cancer mucosal microbiome evolves with cancer stage to meet the demands of cancer metabolism. Passenger microbiota may play a role in the maintenance of cancer mucosal metabolic homeostasis but these metabolic functions may not be stage specific.
Collapse
Affiliation(s)
- James Kinross
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Reza Mirnezami
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - James Alexander
- Division of Digestive Diseases, Faculty of Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Richard Brown
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Alasdair Scott
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Dieter Galea
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Kirill Veselkov
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Rob Goldin
- Centre for Pathology, Faculty of Medicine, Imperial College London, London, UK
| | - Ara Darzi
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Jeremy Nicholson
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Julian R Marchesi
- Division of Digestive Diseases, Faculty of Medicine, Department of Surgery and Cancer, Imperial College London, London, UK.
- School of Biosciences, Cardiff University, Cardiff, UK.
| |
Collapse
|
7
|
Almeida CM, Manso JA, Figueiredo AC, Antunes L, Cruz R, Manadas B, Bur D, Pereira PJB, Faro C, Simões I. Functional and structural characterization of synthetic cardosin B-derived rennet. Appl Microbiol Biotechnol 2017; 101:6951-6968. [DOI: 10.1007/s00253-017-8445-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 11/29/2022]
|