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Favretto F, Jiménez-Faraco E, Conter C, Dominici P, Hermoso JA, Astegno A. Structural Basis for Cyclosporin Isoform-Specific Inhibition of Cyclophilins from Toxoplasma gondii. ACS Infect Dis 2023; 9:365-377. [PMID: 36653744 PMCID: PMC9926490 DOI: 10.1021/acsinfecdis.2c00566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cyclosporin (CsA) has antiparasite activity against the human pathogen Toxoplasma gondii. A possible mechanism of action involves CsA binding to T. gondii cyclophilins, although much remains to be understood. Herein, we characterize the functional and structural properties of a conserved (TgCyp23) and a more divergent (TgCyp18.4) cyclophilin isoform from T. gondii. While TgCyp23 is a highly active cis-trans-prolyl isomerase (PPIase) and binds CsA with nanomolar affinity, TgCyp18.4 shows low PPIase activity and is significantly less sensitive to CsA inhibition. The crystal structure of the TgCyp23:CsA complex was solved at the atomic resolution showing the molecular details of CsA recognition by the protein. Computational and structural studies revealed relevant differences at the CsA-binding site between TgCyp18.4 and TgCyp23, suggesting that the two cyclophilins might have distinct functions in the parasite. These studies highlight the extensive diversification of TgCyps and pave the way for antiparasite interventions based on selective targeting of cyclophilins.
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Affiliation(s)
- Filippo Favretto
- Department
of Biotechnology, University of Verona, Strada Le Grazie 15, 37134Verona, Italy
| | - Eva Jiménez-Faraco
- Department
of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano (IQFR), CSIC, Serrano 119, 28006Madrid, Spain
| | - Carolina Conter
- Department
of Biotechnology, University of Verona, Strada Le Grazie 15, 37134Verona, Italy
| | - Paola Dominici
- Department
of Biotechnology, University of Verona, Strada Le Grazie 15, 37134Verona, Italy
| | - Juan A. Hermoso
- Department
of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano (IQFR), CSIC, Serrano 119, 28006Madrid, Spain,
| | - Alessandra Astegno
- Department
of Biotechnology, University of Verona, Strada Le Grazie 15, 37134Verona, Italy,
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Muruaga EJ, Briones G, Roset MS. Biochemical and functional characterization of Brucella abortus cyclophilins: So similar, yet so different. Front Microbiol 2022; 13:1046640. [DOI: 10.3389/fmicb.2022.1046640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
Brucella spp. are the etiological agent of animal and human brucellosis. We have reported previously that cyclophilins of Brucella (CypA and CypB) are upregulated within the intraphagosomal replicative niche and required for stress adaptation and host intracellular survival and virulence. Here, we characterize B. abortus cyclophilins, CypA, and CypB from a biochemical standpoint by studying their PPIase activity, chaperone activity, and oligomer formation. Even though CypA and CypB are very similar in sequence and share identical chaperone and PPIase activities, we were able to identify outstanding differential features between them. A series of differential peptide loops were predicted when comparing CypA and CypB, differences that might explain why specific antibodies (anti-CypA or anti-CypB) were able to discriminate between both cyclophilins without cross-reactivity. In addition, we identified the presence of critical amino acids in CypB, such as the Trp134 which is responsible for the cyclosporin A inhibition, and the Cys128 that leads to CypB homodimer formation by establishing a disulfide bond. Here, we demonstrated that CypB dimer formation was fully required for stress adaptation, survival within HeLa cells, and mouse infection in B. abortus. The presence of Trp134 and the Cys128 in CypB, which are not present in CypA, suggested that two different kinds of cyclophilins have evolved in Brucella, one with eukaryotic features (CypB), another (CypA) with similar features to Gram-negative cyclophilins.
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Trincone A. Application-Oriented Marine Isomerases in Biocatalysis. Mar Drugs 2020; 18:md18110580. [PMID: 33233366 PMCID: PMC7700177 DOI: 10.3390/md18110580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/23/2022] Open
Abstract
The class EC 5.xx, a group of enzymes that interconvert optical, geometric, or positional isomers are interesting biocatalysts for the synthesis of pharmaceuticals and pharmaceutical intermediates. This class, named “isomerases,” can transform cheap biomolecules into expensive isomers with suitable stereochemistry useful in synthetic medicinal chemistry, and interesting cases of production of l-ribose, d-psicose, lactulose, and d-phenylalanine are known. However, in two published reports about potential biocatalysts of marine origin, isomerases are hardly mentioned. Therefore, it is of interest to deepen the knowledge of these biocatalysts from the marine environment with this specialized in-depth analysis conducted using a literature search without time limit constraints. In this review, the focus is dedicated mainly to example applications in biocatalysis that are not numerous confirming the general view previously reported. However, from this overall literature analysis, curiosity-driven scientific interest for marine isomerases seems to have been long-standing. However, the major fields in which application examples are framed are placed at the cutting edge of current biotechnological development. Since these enzymes can offer properties of industrial interest, this will act as a promoter for future studies of marine-originating isomerases in applied biocatalysis.
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Affiliation(s)
- Antonio Trincone
- Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei, 34, 80078 Pozzuoli, Italy
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Kaushik V, Prasad S, Goel M. Biophysical and biochemical characterization of a thermostable archaeal cyclophilin from Methanobrevibacter ruminantium. Int J Biol Macromol 2019; 139:139-152. [DOI: 10.1016/j.ijbiomac.2019.07.149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 01/03/2023]
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Zhang Z, Yu Z, Wang Z, Ma K, Xu X, Alvarezc PJJ, Zhu L. Understanding of aerobic sludge granulation enhanced by sludge retention time in the aspect of quorum sensing. BIORESOURCE TECHNOLOGY 2019; 272:226-234. [PMID: 30342427 DOI: 10.1016/j.biortech.2018.10.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 06/08/2023]
Abstract
Aerobic granular sludge (AGS) reactors with different sludge retention times (SRTs) were established for enhanced functional microorganism enrichment and granular formation. Results showed that higher total nitrogen (TN) removal efficiency and compact granules were achieved in the 6-day-SRT reactor. Also, Xanthomonadaceae, Rhodobacteraceae and Hyphomonadaceae with AHL-producing and EPS-secreting functions also enriched under 6-day SRT. For investigating the enhanced mechanism of sludge granulation, typical quorum sensing signals of acylated-homoserine-lactones (AHLs) and extracellular polymeric substances (EPS) were analyzed. Tryptophan-and-protein-like substances were major EPS components in granules formed at 6-day SRT. Meanwhile, most detected AHLs, i.e. C8-HSL and 3OHC8-HSL, were correlated positively with contents of tryptophan-and-protein-like substances. According to AHLs add-back test, AHLs especially those with 8-carbon sidechains, played important roles in aerobic sludge granulation via secreting special extracellular proteins by functional microbes enrichment.
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Affiliation(s)
- Zhiming Zhang
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China
| | - Zhuodong Yu
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China
| | - Zihao Wang
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China
| | - Ke Ma
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China
| | - Xiangyang Xu
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China; Zhejiang Provincial Engineering Laboratory of Water Pollution Control, 388 Yuhangtang Road, Hangzhou 310058, China
| | - Pedro J J Alvarezc
- Department of Civil and Environmental Engineering, Rice University, 6100 Main St., Houston, TX 77005, USA
| | - Liang Zhu
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China; Zhejiang Provincial Engineering Laboratory of Water Pollution Control, 388 Yuhangtang Road, Hangzhou 310058, China.
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Structural basis of interaction between dimeric cyclophilin 1 and Myb1 transcription factor in Trichomonas vaginalis. Sci Rep 2018; 8:5410. [PMID: 29615721 PMCID: PMC5882848 DOI: 10.1038/s41598-018-23821-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/21/2018] [Indexed: 11/08/2022] Open
Abstract
Cyclophilin 1 (TvCyP1), a cyclophilin type peptidyl-prolyl isomerase present in the human parasite Trichomonas vaginalis, interacts with Myb1 and assists in its nuclear translocation. Myb1 regulates the expression of ap65-1 gene that encodes for a disease causing cytoadherence enzyme. Here, we determined the crystal structures of TvCyP1 and its complex with the minimum TvCyP1-binding sequence of Myb1 (Myb1104-111), where TvCyP1 formed a homodimer, unlike other single domain cyclophilins. In the complex structure, one Myb1104-111 peptide was bound to each TvCyP1 protomer, with G106-P107 and Y105 fitting well into the active site and auxiliary S2 pocket, respectively. NMR data further showed that TvCyP1 can catalyze the cis/trans isomerization of P107 in Myb1104-111. Interestingly, in the well-folded Myb1 protein (Myb135-141), the minimum binding sequence adopted a different conformation from that of unstructured Myb1104-111 peptide, that could make P107 binding to the active site of TvCyP1 difficult. However, NMR studies showed that similar to Myb1104-111 peptide, Myb135-141 also interacted with the active site of TvCyP1 and the dynamics of the Myb135-141 residues near P107 was reduced upon interaction. Together, the structure of TvCyP1 and detailed structural insights on TvCyP1-Myb1 interaction provided here could pave the way for newer drugs to treat drug-resistant strains.
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Microbial cyclophilins: specialized functions in virulence and beyond. World J Microbiol Biotechnol 2017; 33:164. [PMID: 28791545 DOI: 10.1007/s11274-017-2330-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/05/2017] [Indexed: 01/18/2023]
Abstract
Cyclophilins belong to the superfamily of peptidyl-prolyl cis/trans isomerases (PPIases, EC: 5.2.1.8), the enzymes that catalyze the cis/trans isomerization of peptidyl-prolyl peptide bonds in unfolded and partially folded polypeptide chains and native state proteins. Cyclophilins have been extensively studied, since they are involved in multiple cellular processes related to human pathologies, such as neurodegenerative disorders, infectious diseases, and cancer. However, the presence of cyclophilins in all domains of life indicates a broader biological importance. In this mini-review, we summarize current advances in the study of microbial cyclophilins. Apart from their anticipated role in protein folding and chaperoning, cyclophilins are involved in several other biological processes, such as cellular signal transduction, adaptation to stress, control of pathogens virulence, and modulation of host immune response. Since many existing family members do not have well-defined functions and novel ones are being characterized, the requirement for further studies on their biological role and molecular mechanism of action is apparent.
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