1
|
Kaewkla O, Perkins M, Thamchaipenet A, Saijuntha W, Sukpanoa S, Suriyachadkun C, Chamroensaksri N, Chumroenphat T, Franco CMM. Description of Streptomyces naphthomycinicus sp. nov., an endophytic actinobacterium producing naphthomycin A and its genome insight for discovering bioactive compounds. Front Microbiol 2024; 15:1353511. [PMID: 38694805 PMCID: PMC11061393 DOI: 10.3389/fmicb.2024.1353511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/01/2024] [Indexed: 05/04/2024] Open
Abstract
Endophytic actinobacteria are a group of bacteria living inside plant tissue without harmful effects, and benefit the host plant. Many can inhibit plant pathogens and promote plant growth. This study aimed to identify a strain of Streptomyces as a novel species and study its antibiotics production. An endophytic actinobacterium, strain TML10T was isolated from a surface-sterilized leaf of a Thai medicinal plant (Terminalia mucronata Craib and Hutch). As a result of a polyphasic taxonomy study, strain TML10T was identified as a member of the genus Streptomyces. Strain TML10T was an aerobic actinobacterium with well-developed substrate mycelia with loop spore chains and spiny surface. Chemotaxonomic data, including cell wall components, major menaquinones, and major fatty acids, confirmed the affiliation of strain TML10T to the genus Streptomyces. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with a genome comparison study, allowed the genotypic and phenotypic differentiation of strain TML10T and the closest related type strains. The digital DNA-DNA hybridization (dDDH), Average nucleotide identity Blast (ANIb), and ANIMummer (ANIm) values between strain TML10T and the closest type strain, Streptomyces musisoli CH5-8T were 38.8%, 88.5%, and 90.8%, respectively. The name proposed for the new species is Streptomyces naphthomycinicus sp. nov. (TML10T = TBRC 15050T = NRRL B-65638T). Strain TML10T was further studied for liquid and solid-state fermentation of antibiotic production. Solid-state fermentation with cooked rice provided the best conditions for antibiotic production against methicillin-resistant Staphylococcus aureus. The elucidation of the chemical structures from this strain revealed a known antimicrobial agent, naphthomycin A. Mining the genome data of strain TML10T suggested its potential as a producer of antbiotics and other valuable compounds such as ε-Poly-L-lysine (ε-PL) and arginine deiminase. Strain TML10T contains the arcA gene encoding arginine deiminase and could degrade arginine in vitro.
Collapse
Affiliation(s)
- Onuma Kaewkla
- Center of Excellence in Biodiversity Research, Mahasarakham University, Maha Sarakham, Thailand
- Department of Medical Biotechnology, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Mike Perkins
- Deparment of Chemistry, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | | | - Weerachai Saijuntha
- Center of Excellence in Biodiversity Research, Mahasarakham University, Maha Sarakham, Thailand
- Faculty of Medicine, Mahasarakham University, Maha Sarakham, Thailand
| | - Sudarat Sukpanoa
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Nitcha Chamroensaksri
- National Biobank of Thailand (NBT), National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Theeraphan Chumroenphat
- Aesthetic Sciences and Health Program, Faculty of Thai Traditional and Alternative Medicine, Ubon Ratchathani Rajabhat University, Ubon Ratchathani, Thailand
| | | |
Collapse
|
2
|
Jastrząb R, Tomecki R, Jurkiewicz A, Graczyk D, Szczepankowska AK, Mytych J, Wolman D, Siedlecki P. The strain-dependent cytostatic activity of Lactococcus lactis on CRC cell lines is mediated through the release of arginine deiminase. Microb Cell Fact 2024; 23:82. [PMID: 38481270 PMCID: PMC10938756 DOI: 10.1186/s12934-024-02345-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/20/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most commonly diagnosed cancers, posing a serious public health challenge that necessitates the development of new therapeutics, therapies, and prevention methods. Among the various therapeutic approaches, interventions involving lactic acid bacteria (LAB) as probiotics and postbiotics have emerged as promising candidates for treating and preventing CRC. While human-isolated LAB strains are considered highly favorable, those sourced from environmental reservoirs such as dairy and fermented foods are also being recognized as potential sources for future therapeutics. RESULTS In this study, we present a novel and therapeutically promising strain, Lactococcus lactis ssp. lactis Lc4, isolated from dairy sources. Lc4 demonstrated the ability to release the cytostatic agent - arginine deiminase (ADI) - into the post-cultivation supernatant when cultured under conditions mimicking the human gut environment. Released arginine deiminase was able to significantly reduce the growth of HT-29 and HCT116 cells due to the depletion of arginine, which led to decreased levels of c-Myc, reduced phosphorylation of p70-S6 kinase, and cell cycle arrest. The ADI release and cytostatic properties were strain-dependent, as was evident from comparison to other L. lactis ssp. lactis strains. CONCLUSION For the first time, we unveil the anti-proliferative properties of the L. lactis cell-free supernatant (CFS), which are independent of bacteriocins or other small molecules. We demonstrate that ADI, derived from a dairy-Generally Recognized As Safe (GRAS) strain of L. lactis, exhibits anti-proliferative activity on cell lines with different levels of argininosuccinate synthetase 1 (ASS1) expression. A unique feature of the Lc4 strain is also its capability to release ADI into the extracellular space. Taken together, we showcase L. lactis ADI and the Lc4 strain as promising, potential therapeutic agents with broad applicability.
Collapse
Affiliation(s)
- Rafał Jastrząb
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Adolfa Pawińskiego 5A, Warsaw, 02-106, Poland
- Olimp Laboratories, Pustynia 84F, Debica, 39-200, Poland
| | - Rafał Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Adolfa Pawińskiego 5A, Warsaw, 02-106, Poland
- Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw, 02-089, Poland
| | - Aneta Jurkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Adolfa Pawińskiego 5A, Warsaw, 02-106, Poland
| | - Damian Graczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Adolfa Pawińskiego 5A, Warsaw, 02-106, Poland
| | - Agnieszka K Szczepankowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Adolfa Pawińskiego 5A, Warsaw, 02-106, Poland
| | | | - Damian Wolman
- Olimp Laboratories, Pustynia 84F, Debica, 39-200, Poland
| | - Pawel Siedlecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Adolfa Pawińskiego 5A, Warsaw, 02-106, Poland.
| |
Collapse
|
3
|
Gan Q, Fan C. Orthogonal Translation for Site-Specific Installation of Post-translational Modifications. Chem Rev 2024; 124:2805-2838. [PMID: 38373737 PMCID: PMC11230630 DOI: 10.1021/acs.chemrev.3c00850] [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: 02/21/2024]
Abstract
Post-translational modifications (PTMs) endow proteins with new properties to respond to environmental changes or growth needs. With the development of advanced proteomics techniques, hundreds of distinct types of PTMs have been observed in a wide range of proteins from bacteria, archaea, and eukarya. To identify the roles of these PTMs, scientists have applied various approaches. However, high dynamics, low stoichiometry, and crosstalk between PTMs make it almost impossible to obtain homogeneously modified proteins for characterization of the site-specific effect of individual PTM on target proteins. To solve this problem, the genetic code expansion (GCE) strategy has been introduced into the field of PTM studies. Instead of modifying proteins after translation, GCE incorporates modified amino acids into proteins during translation, thus generating site-specifically modified proteins at target positions. In this review, we summarize the development of GCE systems for orthogonal translation for site-specific installation of PTMs.
Collapse
Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas 72701, United States
| |
Collapse
|
4
|
Roy A, Niharika, Chakraborty S, Mishra J, Singh SP, Patra SK. Mechanistic aspects of reversible methylation modifications of arginine and lysine of nuclear histones and their roles in human colon cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:261-302. [PMID: 37019596 DOI: 10.1016/bs.pmbts.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Developmental proceedings and maintenance of cellular homeostasis are regulated by the precise orchestration of a series of epigenetic events that eventually control gene expression. DNA methylation and post-translational modifications (PTMs) of histones are well-characterized epigenetic events responsible for fine-tuning gene expression. PTMs of histones bear molecular logic of gene expression at chromosomal territory and have become a fascinating field of epigenetics. Nowadays, reversible methylation on histone arginine and lysine is gaining increasing attention as a significant PTM related to reorganizing local nucleosomal structure, chromatin dynamics, and transcriptional regulation. It is now well-accepted and reported that histone marks play crucial roles in colon cancer initiation and progression by encouraging abnormal epigenomic reprogramming. It is becoming increasingly clear that multiple PTM marks at the N-terminal tails of the core histones cross-talk with one another to intricately regulate DNA-templated biological processes such as replication, transcription, recombination, and damage repair in several malignancies, including colon cancer. These functional cross-talks provide an additional layer of message, which spatiotemporally fine-tunes the overall gene expression regulation. Nowadays, it is evident that several PTMs instigate colon cancer development. How colon cancer-specific PTM patterns or codes are generated and how they affect downstream molecular events are uncovered to some extent. Future studies would address more about epigenetic communication, and the relationship between histone modification marks to define cellular functions in depth. This chapter will comprehensively highlight the importance of histone arginine and lysine-based methylation modifications and their functional cross-talk with other histone marks from the perspective of colon cancer development.
Collapse
|
5
|
Wu JF, Wei XP, Li JY, Sun WX. Recombinant Expression and Characterization of an Arginine Deiminase from Pseudomonas sp. LJY. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822060163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
|
6
|
Safrhansova L, Hlozkova K, Starkova J. Targeting amino acid metabolism in cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2022; 373:37-79. [PMID: 36283767 DOI: 10.1016/bs.ircmb.2022.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Metabolic rewiring is a characteristic hallmark of cancer cells. This phenomenon sustains uncontrolled proliferation and resistance to apoptosis by increasing nutrients and energy supply. However, reprogramming comes together with vulnerabilities that can be used against tumor and can be applied in targeted therapy. In the last years, the genetic background of tumors has been identified thoroughly and new therapies targeting those mutations tested. Nevertheless, we propose that targeting the phenotype of cancer cells could be another way of treatment aiming to avoid drug resistance and non-responsiveness of cancer patients. Amino acid metabolism is part of the altered processes in cancer cells. Amino acids are building blocks and also sensors of signaling pathways regulating main biological processes. In this comprehensive review, we described four amino acids (asparagine, arginine, methionine, and cysteine) which have been actively investigated as potential targets for anti-tumor therapy. Asparagine depletion is successfully used for decades in the treatment of acute lymphoblastic leukemia and there is a strong implication to apply it to other types of tumors. Arginine auxotrophic tumors are great candidates for arginine-starvation therapy. Higher requirement for essential amino acids such as methionine and cysteine point out promising targetable weaknesses of cancer cells.
Collapse
Affiliation(s)
- Lucie Safrhansova
- CLIP - Childhood Leukaemia Investigation Prague, Prague, Czech Republic; Dept. of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Katerina Hlozkova
- CLIP - Childhood Leukaemia Investigation Prague, Prague, Czech Republic; Dept. of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Julia Starkova
- CLIP - Childhood Leukaemia Investigation Prague, Prague, Czech Republic; Dept. of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic; University Hospital Motol, Prague, Czech Republic.
| |
Collapse
|
7
|
Wang W, Li M, Miao M, Zhang T. Characterization of a recombinant arginine deiminase from
Halothermothrix orenii
and its application in citrulline production. Biotechnol Appl Biochem 2022; 70:526-536. [PMID: 35761421 DOI: 10.1002/bab.2375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/08/2022] [Indexed: 11/07/2022]
Abstract
In recent years, arginine deiminase (ADI, EC 3.5.3.6) has attracted much attention as a biocatalyst that produces the functional amino acid l-citrulline from l-arginine and also as an anticancer enzyme. Here, we identified and characterized a putative ADI from the thermophilic bacterium Halothermothrix orenii. The H. orenii ADI (H-ADI) protein was expressed in Escherichia coli BL21(DE3) with a specific activity of 91.8 U/mg protein at 55°C and pH 6.5. The enzyme remained at 74% relative activity after incubation at 45°C for 180 min, only 25% at 50°C. The melting temperature was 56°C. H-ADI is not a metal-requiring enzyme; Ni2+ slightly improved the catalytic activity. The Km and Vmax for l-arginine were 55.5 mM and 156.8 μmol/min/mg protein, respectively. Moreover, three residues (Arg183, Arg237, and His273) were key to the formation of l-citrulline, as analyzed by alanine-scanning mutagenesis. Finally, the enzymatic synthesis of l-citrulline was carried out at 50°C with a conversion ratio reaching 99.03%. Together, these findings show that H-ADI is a promising biocatalyst for the production of l-citrulline.
Collapse
Affiliation(s)
- Wenyu Wang
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi China
| | - Mengli Li
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi China
| | - Ming Miao
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi China
- International Joint Laboratory on Food Safety Jiangnan University Wuxi China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi China
| |
Collapse
|
8
|
Rechiche O, Lee TV, Lott JS. Structural characterization of human peptidyl-arginine deiminase type III by X-ray crystallography. Acta Crystallogr F Struct Biol Commun 2021; 77:334-340. [PMID: 34605437 PMCID: PMC8488854 DOI: 10.1107/s2053230x21009195] [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: 03/04/2021] [Accepted: 09/04/2021] [Indexed: 11/10/2022] Open
Abstract
The Ca2+-dependent enzyme peptidyl-arginine deiminase type III (PAD3) catalyses the deimination of arginine residues to form citrulline residues in proteins such as keratin, filaggrin and trichohyalin. This is an important post-translation modification that is required for normal hair and skin formation in follicles and keratocytes. The structure of apo human PAD3 was determined by X-ray crystallography to a resolution of 2.8 Å. The structure of PAD3 revealed a similar overall architecture to other PAD isoforms: the N-terminal and middle domains of PAD3 show sequence and structural variety, whereas the sequence and structure of the C-terminal catalytic domain is highly conserved. Structural analysis indicates that PAD3 is a dimer in solution, as is also the case for the PAD2 and PAD4 isoforms but not the PAD1 isoform.
Collapse
Affiliation(s)
- Othman Rechiche
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Althouse Laboratory, Science Drive, State College, PA 16801, USA
| | - T. Verne Lee
- School of Biological Sciences, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
| | - J. Shaun Lott
- School of Biological Sciences, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
| |
Collapse
|
9
|
Tam SY, Chung SF, Chen YW, So YH, So PK, Cheong WL, Wong KY, Leung YC. Design of a structure-based fluorescent biosensor from bioengineered arginine deiminase for rapid determination of L-arginine. Int J Biol Macromol 2020; 165:472-482. [PMID: 32971169 DOI: 10.1016/j.ijbiomac.2020.09.134] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/07/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022]
Abstract
Rationally designed mutations on recombinant arginine deiminase (ADI) could act as a 'turn-off' L-arginine (L-Arg) fluorescent biosensor and provide an alternative method for rapid determination of L-Arg. Double mutations were introduced on the Cys251➔Ser251 and Thr265➔Cys265 of recombinant ADI, rendering a single cysteine present on the protein surface for the site-specific attachment of a fluorophore, fluorescein-5-maleimide. The double mutations on ADI (265C) and its fluorescein-labelled form (265Cf) conserved the catalytic efficiency of wild-type ADI. Upon binding to L-Arg, 265Cf induced structural conformational changes and rendered the fluorescein moiety to move closer to Trp264, resulting in fluorescence quenching. The duration of fluorescence quenching was dependant on the L-Arg concentration. A linear relationship between the time at the maximum rate of fluorescence change and L-Arg concentrations, which ranged from 2.5 to 100 μM, was found with R2 = 0.9988. The measurement time was within 0.15-4 min. Determination of L-Arg concentration in fetal bovine serum could be achieved by the standard addition method and without sample pre-treatment. The result showed a good agreement with the one determined by mass spectrometry, suggesting our biosensor as a promising tool for the detection of L-Arg in biological samples.
Collapse
Affiliation(s)
- Suet-Ying Tam
- Department of Applied Biology and Chemical Technology, Lo Ka Chung Research Centre for Natural Anti-Cancer Drug Development and State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Sai-Fung Chung
- Department of Applied Biology and Chemical Technology, Lo Ka Chung Research Centre for Natural Anti-Cancer Drug Development and State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yu Wai Chen
- Department of Applied Biology and Chemical Technology, Lo Ka Chung Research Centre for Natural Anti-Cancer Drug Development and State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yik-Hing So
- Department of Applied Biology and Chemical Technology, Lo Ka Chung Research Centre for Natural Anti-Cancer Drug Development and State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Pui-Kin So
- Department of Applied Biology and Chemical Technology, Lo Ka Chung Research Centre for Natural Anti-Cancer Drug Development and State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Wing-Lam Cheong
- Department of Science, School of Science and Technology, The Open University of Hong Kong, Hong Kong
| | - Kwok-Yin Wong
- Department of Applied Biology and Chemical Technology, Lo Ka Chung Research Centre for Natural Anti-Cancer Drug Development and State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | - Yun-Chung Leung
- Department of Applied Biology and Chemical Technology, Lo Ka Chung Research Centre for Natural Anti-Cancer Drug Development and State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| |
Collapse
|
10
|
Feng Q, Bian X, Liu X, Wang Y, Zhou H, Ma X, Quan C, Yao Y, Zheng Z. Intracellular expression of arginine deiminase activates the mitochondrial apoptosis pathway by inhibiting cytosolic ferritin and inducing chromatin autophagy. BMC Cancer 2020; 20:665. [PMID: 32677906 PMCID: PMC7367323 DOI: 10.1186/s12885-020-07133-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/02/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Based on its low toxicity, arginine starvation therapy has the potential to cure malignant tumors that cannot be treated surgically. The Arginine deiminase (ADI) gene has been identified to be an ideal cancer-suppressor gene. ADI expressed in the cytosol displays higher oncolytic efficiency than ADI-PEG20 (Pegylated Arginine Deiminase by PEG 20,000). However, it is still unknown whether cytosolic ADI has the same mechanism of action as ADI-PEG20 or other underlying cellular mechanisms. METHODS The interactions of ADI with other protein factors were screened by yeast hybrids, and verified by co-immunoprecipitation and immunofluorescent staining. The effect of ADI inhibiting the ferritin light-chain domain (FTL) in mitochondrial damage was evaluated by site-directed mutation and flow cytometry. Control of the mitochondrial apoptosis pathway was analyzed by Western Blotting and real-time PCR experiments. The effect of p53 expression on cancer cells death was assessed by siTP53 transfection. Chromatin autophagy was explored by immunofluorescent staining and Western Blotting. RESULTS ADI expressed in the cytosol inhibited the activity of cytosolic ferritin by interacting with FTL. The inactive mutant of ADI still induced apoptosis in certain cell lines of ASS- through mitochondrial damage. Arginine starvation also generated an increase in the expression of p53 and p53AIP1, which aggravated the cellular mitochondrial damage. Chromatin autophagy appeared at a later stage of arginine starvation. DNA damage occurred along with the entire arginine starvation process. Histone 3 (H3) was found in autophagosomes, which implies that cancer cells attempted to utilize the arginine present in histones to survive during arginine starvation. CONCLUSIONS Mitochondrial damage is the major mechanism of cell death induced by cytosolic ADI. The process of chromatophagy does not only stimulate cancer cells to utilize histone arginine but also speeds up cancer cell death at a later stage of arginine starvation.
Collapse
Affiliation(s)
- Qingyuan Feng
- Department of Otorhinolaryngology Head and Neck Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xuzhao Bian
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xuan Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ying Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Huiting Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaojing Ma
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Chunju Quan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yi Yao
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Zhongliang Zheng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| |
Collapse
|
11
|
Xu Z, Rivera-Hernandez T, Moyle PM. Development of an Enzyme-Mediated, Site-Specific Method to Conjugate Toll-Like Receptor 2 Agonists onto Protein Antigens: Toward a Broadly Protective, Four Component, Group A Streptococcal Self-Adjuvanting Lipoprotein-Fusion Combination Vaccine. ACS Infect Dis 2020; 6:1770-1782. [PMID: 32407620 DOI: 10.1021/acsinfecdis.0c00047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Subunit vaccines composed of protein antigens covalently attached to Toll-like receptor (TLR) agonists elicit superior immune responses compared to mixtures of antigens and TLR agonists. Among different conjugation approaches, enzyme-mediated ligation is one of the few that provides an opportunity for the generation of homogeneous, molecularly defined products in which protein antigens are maintained with native structures, which is most critical to elicit protective immune responses upon vaccination. Four highly conserved protein antigens from Group A Streptococcus (GAS) have the potential to be safe and efficacious vaccine candidates. After a TLR2 agonist fibroblast-stimulating lipopeptide-1 (FSL-1) was successfully attached onto each antigen using sortase A and techniques for their purification were developed, a combination vaccine containing interleukin 8 (IL-8) protease (Streptococcus pyogenes cell envelope proteinase [SpyCEP]), Group A Streptococcal C5a peptidase (SCPA), anchorless virulence factor arginine deiminase (ADI), and trigger factor (TF)-TLR2 conjugates was produced. This combination was assessed for immunity in mice and compared with mixtures of the four antigens with FSL-1 or alum. High titer antigen-specific IgG antibodies were detected from all vaccine groups, with antibodies elicited from FSL-1 conjugates around 10-fold higher compared to the FSL-1 mixture group. Furthermore, the FSL-1 conjugates afforded a more balanced TH1/TH2 immune response than the alum-adjuvanted group, suggesting that this combination vaccine represents a promising candidate for the prevention of GAS diseases. Thus, we established a conjugation platform that allows for the production of defined, site-specific antigen-adjuvant conjugates, which maintain the native three-dimensional structure of antigens and can be potentially applied to a variety of protein antigens.
Collapse
Affiliation(s)
- Zhenghui Xu
- School of Pharmacy, The University of Queensland, 20 Cornwall Street, Woolloongabba, Queensland 4102, Australia
| | - Tania Rivera-Hernandez
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
- Cátedras CONACYT - Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City 06720, México
| | - Peter Michael Moyle
- School of Pharmacy, The University of Queensland, 20 Cornwall Street, Woolloongabba, Queensland 4102, Australia
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| |
Collapse
|
12
|
Pols T, Singh S, Deelman-Driessen C, Gaastra BF, Poolman B. Enzymology of the pathway for ATP production by arginine breakdown. FEBS J 2020; 288:293-309. [PMID: 32306469 PMCID: PMC7818446 DOI: 10.1111/febs.15337] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 01/02/2023]
Abstract
In cells, the breakdown of arginine to ornithine and ammonium ion plus carbon dioxide is coupled to the generation of metabolic energy in the form of ATP. The arginine breakdown pathway is minimally composed of arginine deiminase, ornithine transcarbamoylase, carbamate kinase, and an arginine/ornithine antiporter; ammonia and carbon dioxide most likely diffuse passively across the membrane. The genes for the enzymes and transporter have been cloned and expressed, and the proteins have been purified from Lactococcus lactis IL1403 and incorporated into lipid vesicles for sustained production of ATP. Here, we study the kinetic parameters and biochemical properties of the individual enzymes and the antiporter, and we determine how the physicochemical conditions, effector composition, and effector concentration affect the enzymes. We report the KM and VMAX values for catalysis and the native oligomeric state of all proteins, and we measured the effect of pathway intermediates, pH, temperature, freeze-thaw cycles, and salts on the activity of the cytosolic enzymes. We also present data on the protein-to-lipid ratio and lipid composition dependence of the antiporter.
Collapse
Affiliation(s)
- Tjeerd Pols
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Shubham Singh
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Cecile Deelman-Driessen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Bauke F Gaastra
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| |
Collapse
|
13
|
Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a "bond rotation" catalytic mechanism. J Biol Chem 2020; 295:2113-2124. [PMID: 31914412 PMCID: PMC7029115 DOI: 10.1074/jbc.ra119.011752] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/24/2019] [Indexed: 01/07/2023] Open
Abstract
A recently discovered ornithine-ammonia cycle (OAC) serves as a conduit in the nitrogen storage and remobilization machinery in cyanobacteria. The OAC involves an arginine catabolic reaction catalyzed by the arginine dihydrolase ArgZ whose catalytic mechanism is unknown. Here we determined the crystal structures at 1.2-3.0 Å of unliganded ArgZ from the cyanobacterium Synechocystis sp. PCC6803 and of ArgZ complexed with its substrate arginine, a covalently linked reaction intermediate, or the reaction product ornithine. The structures reveal that a key residue, Asn71, in the ArgZ active center functions as the determinant distinguishing ArgZ from other members of the guanidino group-modifying enzyme superfamily. The structures, along with biochemical evidence from enzymatic assays coupled with electrospray ionization MS techniques, further suggest that ArgZ-catalyzed conversion of arginine to ornithine, ammonia, and carbon dioxide consists of two successive cycles of amine hydrolysis. Finally, we show that arginine dihydrolases are broadly distributed among bacteria and metazoans, suggesting that the OAC may be frequently used for redistribution of nitrogen from arginine catabolism or nitrogen fixation.
Collapse
|
14
|
Microbial enzymes for deprivation of amino acid metabolism in malignant cells: biological strategy for cancer treatment. Appl Microbiol Biotechnol 2020; 104:2857-2869. [PMID: 32037468 DOI: 10.1007/s00253-020-10432-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/23/2020] [Accepted: 02/03/2020] [Indexed: 12/17/2022]
Abstract
Amino acid deprivation therapy (AADT) is emerging as a promising strategy for the development of novel therapeutics against cancer. This biological therapy relies upon the differences in the metabolism of cancer and normal cells. The rapid growth of tumors results in decreased expression of certain enzymes leading to auxotrophy for some specific amino acids. These auxotrophic tumors are targeted by amino acid-depleting enzymes. The depletion of amino acid selectively inhibits tumor growth as the normal cells can synthesize amino acids by their usual machinery. The enzymes used in AADT are mostly obtained from microbes for their easy availability. Microbial L-asparaginase is already approved by FDA for the treatment of acute lymphoblastic leukemia. Arginine deiminase and methionase are under clinical trials and the therapeutic potential of lysine oxidase, glutaminase and phenylalanine ammonia lyase is also being explored. The present review provides an overview of microbial amino acid depriving enzymes. Various attributes of these enzymes like structure, mode of action, production, formulations, and targeted cancers are discussed. The challenges faced and the combat strategies to establish AADT in standard cancer armamentarium are also reviewed.Key Points • Amino acid deprivation therapy is a potential therapy for auxotrophic tumors. • Microbial enzymes are used due to their ease of manipulation and high productivity. • Enzyme properties are improved by PEGylation, encapsulation, and genetic engineering. • AADT can be employed as combinational therapy for better containment of cancer.
Collapse
|
15
|
Zarei M, Rahbar MR, Nezafat N, Negahdaripour M, Morowvat MH, Ghasemi Y. Computational Analysis of Arginine Deiminase Sequences to Provide a Guideline for Protein Engineering. CURR PROTEOMICS 2020. [DOI: 10.2174/1570164616666190619111852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background:Arginine deiminase of Mycoplasma hominis, an arginine catabolizing enzyme, is currently in clinical trial for the treatment of arginine auxotrophic cancers. However, some drawbacks such as instability and antigenicity have limited its application as a protein drug. Arginine Deiminase (ADI) belongs to the guanidino-group modifying enzyme superfamily. Despite differences in the primary amino acid sequences of various members of this superfamily, the folding and secondary structures are conserved in all members. Despite structural similarities, ADIs in various species have different levels of catalytic activity and physicochemical properties due to the differences in their primary amino acid sequences. Therefore, investigating and comparing sequences between different ADI producing bacterial strains could be helpful in the rational engineering of ADI.Objective:In the current research, we used an in-silico approach to characterize and classify the available reviewed protein sequences of ADI.Results:102 ADI sequences from SwissProt database were extracted. Subsequently, based on clustering analyses, the sequence sets were divided into five distinct groups. Different physicochemical properties, solubility, and antigenicity of the enzymes were determined. Some ADI sequences were introduced as well-suited candidates for protein engineering; Lactobacillus fermentum ADI for low pI value, Mycobacterium avium ADI for high aliphatic index, Bacillus licheniformis ADI for low GRAVY index, Bradyrhizobium diazoefficiens ADI for low antigenicity and high stability index, and among Mycoplasma ADIs, Mycoplasma arthritidis ADI for high stability and aliphatic index, and Mycoplasma capricolum for low antigenicity.
Collapse
Affiliation(s)
- Mahboubeh Zarei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
16
|
Zarei M, Rahbar MR, Morowvat MH, Nezafat N, Negahdaripour M, Berenjian A, Ghasemi Y. Arginine Deiminase: Current Understanding and Applications. Recent Pat Biotechnol 2019; 13:124-136. [PMID: 30569861 DOI: 10.2174/1872208313666181220121400] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/07/2018] [Accepted: 12/25/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Arginine deiminase (ADI), an arginine catabolizing enzyme, is considered as an anti-tumor agent for the treatment of arginine auxotrophic cancers. However, some obstacles limit its clinical applications. OBJECTIVE This review will summarize the clinical applications of ADI, from a brief history to its limitations, and will discuss the different ways to deal with the clinical limitations. METHOD The structure analysis, cloning, expression, protein engineering and applications of arginine deiminase enzyme have been explained in this review. CONCLUSION Recent patents on ADI are related to ADI engineering to increase its efficacy for clinical application. The intracellular delivery of ADI and combination therapy seem to be the future strategies in the treatment of arginine auxotrophic cancers. Applying ADIs with optimum features from different sources and or ADI engineering, are promising strategies to improve the clinical application of ADI.
Collapse
Affiliation(s)
- Mahboubeh Zarei
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Reza Rahbar
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hossein Morowvat
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aydin Berenjian
- School of Engineering, Faculty of Science & Engineering, The University of Waikato, Hamilton, New Zealand
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
17
|
X-Ray Crystallography in Structure-Function Characterization of Therapeutic Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1148:81-103. [DOI: 10.1007/978-981-13-7709-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
18
|
Maggi M, Scotti C. Enzymes in Metabolic Anticancer Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1148:173-199. [PMID: 31482500 DOI: 10.1007/978-981-13-7709-9_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cancer treatment has greatly improved over the last 50 years, but it remains challenging in several cases. Useful therapeutic targets are normally unique peculiarities of cancer cells that distinguish them from normal cells and that can be tackled with appropriate drugs. It is now known that cell metabolism is rewired during tumorigenesis and metastasis as a consequence of oncogene activation and oncosuppressors inactivation, leading to a new cellular homeostasis typically directed towards anabolism. Because of these modifications, cells can become strongly or absolutely dependent on specific substrates, like sugars, lipids or amino acids. Cancer addictions are a relevant target for therapy, as removal of an essential substrate can lead to their selective cell-cycle arrest or even to cell death, leaving normal cells untouched. Enzymes can act as powerful agents in this respect, as demonstrated by asparaginase, which has been included in the treatment of Acute Lymphoblastic Leukemia for half a century. In this review, a short outline of cancer addictions will be provided, focusing on the main cancer amino acid dependencies described so far. Therapeutic enzymes which have been already experimented at the clinical level will be discussed, along with novel potential candidates that we propose as new promising molecules. The intrinsic limitations of their present molecular forms, along with molecular engineering solutions to explore, will also be presented.
Collapse
Affiliation(s)
- Maristella Maggi
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy.
| | - Claudia Scotti
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy
| |
Collapse
|
19
|
Cai X, Jiang H, Zhang T, Jiang B, Mu W, Miao M. Thermostability and Specific-Activity Enhancement of an Arginine Deiminase from Enterococcus faecalis SK23.001 via Semirational Design for l-Citrulline Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:8841-8850. [PMID: 30047723 DOI: 10.1021/acs.jafc.8b02858] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
l-Citrulline is a nonessential amino acid with a variety of physiological functions and can be enzymatically produced by arginine deiminase (ADI, EC 3.5.3.6). The enzymatic-production approach is of immense interest because of its mild conditions, high yield, low cost, and environmental benignity. However, the major hindrances of l-citrulline industrialization are the poor thermostability and enzyme activity of ADI. Hence, in this work, directed evolution and site-directed mutagenesis aided with in silico screening, including the use of b-factor values and HoTMuSiC, were applied to a previously identified ADI from Enterococcus faecalis SK23.001 ( EfADI), and a triple-site variant R15K-F269Y-G292P was obtained. The triple-site variant displays a 2.5-fold higher specific enzyme activity (333 U mg-1), a lower Km value of 6.4 mM, and a 6.1-fold longer half-life ( t1/2,45°C = 86.7 min) than wild-type EfADI. This work provides a protein-engineering strategy to improve enzyme activity and thermostability, which might be transferrable to other ADIs and enzymes.
Collapse
Affiliation(s)
- Xue Cai
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , China
| | - Hangyu Jiang
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , China
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , China
- International Joint Laboratory on Food Safety , Jiangnan University , Wuxi , Jiangsu 214122 , China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , China
- International Joint Laboratory on Food Safety , Jiangnan University , Wuxi , Jiangsu 214122 , China
| | - Ming Miao
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , China
| |
Collapse
|
20
|
Jiang H, Huang K, Mu W, Jiang B, Zhang T. Characterization of a recombinant arginine deiminase from Enterococcus faecalis SK32.001 for L-citrulline production. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
21
|
Maneerat K, Yongkiettrakul S, Jiemsup S, Tongtawe P, Gottschalk M, Srimanote P. Expression and Characterization of Serotype 2 Streptococcus suis Arginine Deiminase. J Mol Microbiol Biotechnol 2017; 27:133-146. [PMID: 28456803 DOI: 10.1159/000452952] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 10/25/2016] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Arginine deiminase (ArcA) has been speculated to facilitate the intracellular survival of Streptococcus suis under acidic conditions. However, the physical and biological properties and function of SS2-ArcA have not yet been elucidated. METHODS Recombinant SS2-ArcA (rSS2-ArcA) was expressed and purified using Ni-NTA affinity chromatography. Under various pH and temperature conditions, the enzymatic properties of purified rSS2-ArcA and crude native SS2-ArcA were determined. RESULTS The SS2-arcA-deduced amino acid sequence contained a conserved catalytic triad (Cys399-His273-Glu218). The optimum temperature and pH of 47-kDa rSS2-ArcA and crude native SS2-ArcA were 42°C and pH 7.2. The rSS2-ArcA and crude native SS2-ArcA were stable for 3 h at 4 and 25°C, respectively. The pH stability and dependency tests suggested that rSS2-ArcA and crude native SS2-ArcA were functionally active in acidic conditions. The L-arginine substrate binding affinity (Km) values of rSS2-ArcA (specific activity 16.00 U/mg) and crude native SS2-ArcA (specific activity 0.23 U/mg) were 0.058 and 0.157 mM, respectively. rSS2-ArcA exhibited a weak binding affinity with the common ArcA inhibitors L-canavanine and L-NIO. Furthermore, the partial inactivation of SS2-ArcA significantly impaired the viability and growth of SS2 at pH 4.0, 6.0, and 7.5. CONCLUSIONS This study profoundly demonstrated the involvement of ArcA enzymatic activity in S. suis survival under acidic conditions.
Collapse
Affiliation(s)
- Krissana Maneerat
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | | | | | | | | | | |
Collapse
|
22
|
Koushik S, Joshi N, Nagaraju S, Mahmood S, Mudeenahally K, Padmavathy R, Jegatheesan SK, Mullangi R, Rajagopal S. PAD4: pathophysiology, current therapeutics and future perspective in rheumatoid arthritis. Expert Opin Ther Targets 2017; 21:433-447. [PMID: 28281906 DOI: 10.1080/14728222.2017.1294160] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Peptidyl arginine deiminase 4 (PAD4) is an enzyme that plays an important role in gene expression, turning out genetic code into functional products in the body. It is involved in a key post translational modification, which involves the conversion of arginine to citrulline. It regulates various processes such as apoptosis, innate immunity and pluripotency, while its dysregulation has a great impact on the genesis of various diseases. Over the last few years PAD4 has emerged as a potential therapeutic target for the treatment of rheumatoid arthritis (RA). Areas covered: In this review, we discuss the basic structure and function of PAD4, along with the role of altered PAD4 activity in the onset of RA and other maladies. We also elucidate the role of PAD4 variants in etiology of RA among several ethnic groups and the current pre-clinical inhibitors to regulate PAD4. Expert opinion: Citrullination has a crucial role in RA and several other disorders. Since PAD4 is an initiator of the citrullination, it is an important therapeutic target for inflammatory diseases. Therefore, an in depth knowledge of the roles and activity of PAD4 is required to explore more effective ways to conquer PAD4 related ailments, especially RA.
Collapse
Affiliation(s)
- Sindhu Koushik
- a Bioinformatics , Jubilant Biosys Ltd ., Bangalore , India
| | - Nivedita Joshi
- a Bioinformatics , Jubilant Biosys Ltd ., Bangalore , India
| | | | - Sameer Mahmood
- a Bioinformatics , Jubilant Biosys Ltd ., Bangalore , India
| | | | | | | | | | | |
Collapse
|
23
|
Han RZ, Xu GC, Dong JJ, Ni Y. Arginine deiminase: recent advances in discovery, crystal structure, and protein engineering for improved properties as an anti-tumor drug. Appl Microbiol Biotechnol 2016; 100:4747-60. [DOI: 10.1007/s00253-016-7490-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 02/06/2023]
|
24
|
Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase. Sci Rep 2015; 5:11969. [PMID: 26132828 PMCID: PMC4487231 DOI: 10.1038/srep11969] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/12/2015] [Indexed: 01/08/2023] Open
Abstract
Citrullination is a post-translational modification of higher organisms that deiminates arginines in proteins and peptides. It occurs in physiological processes but also pathologies such as multiple sclerosis, fibrosis, Alzheimer’s disease and rheumatoid arthritis (RA). The reaction is catalyzed by peptidylarginine deiminases (PADs), which are found in vertebrates but not in lower organisms. RA has been epidemiologically associated with periodontal disease, whose main infective agent is Porphyromonas gingivalis. Uniquely among microbes, P. gingivalis secretes a PAD, termed PPAD (Porphyromonas peptidylarginine deiminase), which is genetically unrelated to eukaryotic PADs. Here, we studied function of PPAD and its substrate-free, substrate-complex, and substrate-mimic-complex structures. It comprises a flat cylindrical catalytic domain with five-fold α/β-propeller architecture and a C-terminal immunoglobulin-like domain. The PPAD active site is a funnel located on one of the cylinder bases. It accommodates arginines from peptide substrates after major rearrangement of a “Michaelis loop” that closes the cleft. The guanidinium and carboxylate groups of substrates are tightly bound, which explains activity of PPAD against arginines at C-termini but not within peptides. Catalysis is based on a cysteine-histidine-asparagine triad, which is shared with human PAD1-PAD4 and other guanidino-group modifying enzymes. We provide a working mechanism hypothesis based on 18 structure-derived point mutants.
Collapse
|
25
|
Trejo-Soto PJ, Aguayo-Ortiz R, Yépez-Mulia L, Hernández-Campos A, Medina-Franco JL, Castillo R. Insights into the structure and inhibition of Giardia intestinalis arginine deiminase: homology modeling, docking, and molecular dynamics studies. J Biomol Struct Dyn 2015; 34:732-48. [PMID: 26017138 DOI: 10.1080/07391102.2015.1051115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Giardia intestinalis arginine deiminase (GiADI) is an important metabolic enzyme involved in the energy production and defense of this protozoan parasite. The lack of this enzyme in the human host makes GiADI an attractive target for drug design against G. intestinalis. One approach in the design of inhibitors of GiADI could be computer-assisted studies of its crystal structure, such as docking; however, the required crystallographic structure of the enzyme still remains unresolved. Because of its relevance, in this work, we present a three-dimensional structure of GiADI obtained from its amino acid sequence using the homology modeling approximation. Furthermore, we present an approximation of the most stable dimeric structure of GiADI identified through molecular dynamics simulation studies. An in silico analysis of druggability using the structure of GiADI was carried out in order to know if it is a good target for design and optimization of selective inhibitors. Potential GiADI inhibitors were identified by docking of a set of 3196 commercial and 19 in-house benzimidazole derivatives, and molecular dynamics simulation studies were used to evaluate the stability of the ligand-enzyme complexes.
Collapse
Affiliation(s)
- Pedro Josué Trejo-Soto
- a Facultad de Química, Departamento de Farmacia , Universidad Nacional Autónoma de México , México, DF 04510 , Mexico
| | - Rodrigo Aguayo-Ortiz
- a Facultad de Química, Departamento de Farmacia , Universidad Nacional Autónoma de México , México, DF 04510 , Mexico
| | - Lilián Yépez-Mulia
- b Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, IMSS , México, DF 06720 , Mexico
| | - Alicia Hernández-Campos
- a Facultad de Química, Departamento de Farmacia , Universidad Nacional Autónoma de México , México, DF 04510 , Mexico
| | - José Luis Medina-Franco
- a Facultad de Química, Departamento de Farmacia , Universidad Nacional Autónoma de México , México, DF 04510 , Mexico
| | - Rafael Castillo
- a Facultad de Química, Departamento de Farmacia , Universidad Nacional Autónoma de México , México, DF 04510 , Mexico
| |
Collapse
|
26
|
Fuhrmann J, Clancy K, Thompson PR. Chemical biology of protein arginine modifications in epigenetic regulation. Chem Rev 2015; 115:5413-61. [PMID: 25970731 PMCID: PMC4463550 DOI: 10.1021/acs.chemrev.5b00003] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Jakob Fuhrmann
- Department
of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Kathleen
W. Clancy
- Department of Biochemistry and Molecular Pharmacology and Program in Chemical
Biology, University of Massachusetts Medical
School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Paul R. Thompson
- Department of Biochemistry and Molecular Pharmacology and Program in Chemical
Biology, University of Massachusetts Medical
School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| |
Collapse
|
27
|
Cheng F, Zhu L, Lue H, Bernhagen J, Schwaneberg U. Directed arginine deiminase evolution for efficient inhibition of arginine-auxotrophic melanomas. Appl Microbiol Biotechnol 2014; 99:1237-47. [PMID: 25104032 DOI: 10.1007/s00253-014-5985-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 12/11/2022]
Abstract
Arginine deiminase (ADI) is a therapeutic protein for cancer therapy of arginine-auxotrophic tumors. However, ADI's application as anticancer drug is hampered by its low activity for arginine under physiological conditions mainly due to its high "K M" (S₀.₅) values which are often 1 magnitude higher than the arginine concentration in blood (0.10-0.12 mM arginine in human plasma). Previous evolution campaigns were directed by us with the aim of boosting activity of PpADI (ADI from Pseudomonas plecoglossicida, k cat = 0.18 s(-1); S₀.₅ = 1.30 mM), and yielded variant M6 with slightly reduced S₀.₅ values and enhanced k cat (S₀.₅ = 0.81 mM; k cat = 11.64 s(-1)). In order to further reduce the S₀.₅ value and to increase the activity of PpADI at physiological arginine concentration, a more sensitive screening system based on ammonia detection in 96-well microtiter plate to reliably detect ≥0.005 mM ammonia was developed. After screening ~5,500 clones with the ammonia detection system (ADS) in two rounds of random mutagenesis and site-directed mutagenesis, variant M19 with increased k cat value (21.1 s(-1); 105.5-fold higher compared to WT) and reduced S₀.₅ value (0.35 mM compared to 0.81 mM (M6) and 1.30 mM (WT)) was identified. Improved performance of M19 was validated by determining IC₅₀ values for two melanoma cell lines. The IC₅₀ value for SK-MEL-28 dropped from 8.67 (WT) to 0.10 (M6) to 0.04 μg/mL (M19); the IC₅₀ values for G361 dropped from 4.85 (WT) to 0.12 (M6) to 0.05 μg/mL (M19).
Collapse
Affiliation(s)
- Feng Cheng
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | | | | | | | | |
Collapse
|
28
|
Wang Y, Li YZ. Cultivation to improve in vivo solubility of overexpressed arginine deiminases in Escherichia coli and the enzyme characteristics. BMC Biotechnol 2014; 14:53. [PMID: 24908259 PMCID: PMC4072490 DOI: 10.1186/1472-6750-14-53] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 06/03/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Overexpression of foreign genes in Escherichia coli cells is an efficient means to obtain recombinant proteins. The technique is, however, often hampered by misfolding, degradation, aggregation and formation in inclusion bodies of products. RESULTS In this study, we reported that in vivo solubility of overexpressed arginine deiminases (ADI) improved by changing the cultivation conditions. ADI is enzymes that convert L-arginine to L-citrulline. After codon optimization, we synthesized the ADI gene of Pseudomonas putida and constructed it for overexpression in E. coli cells. The rADI products were mainly in inclusion body forms. We performed a series of optimization to enhance solubility of the protein. Co-expression with the GroES-GroEL chaperone team increased approximately 5-fold of the rADI activity. In addition the combination of L-arginine and D-glucose in the Luria-Bertani (LB) growth medium further increased the total activity to about 15 times. Separate L-arginine and D-glucose or the addition of other saccharides or amino acids had no such effects. The solubilization effects of the combination of L-arginine and D-glucose were further confirmed in the overexpression of another ADI from Listeria welshimeri. The enzymatic and conversion characteristics of the rADI products were further determined. CONCLUSIONS Combined addition of L-arginine and D-glucose in the LB medium significantly improved in vivo solubility of rADI proteins. The present study suggested a new strategy to increase the solubilization of overexpressed recombinant proteins in E. coli cells.
Collapse
Affiliation(s)
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, P, R, China.
| |
Collapse
|
29
|
Lewis CA, Wolfenden R. The nonenzymatic decomposition of guanidines and amidines. J Am Chem Soc 2013; 136:130-6. [PMID: 24359273 DOI: 10.1021/ja411927k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
To establish the rates and mechanisms of decomposition of guanidine and amidine derivatives in aqueous solution and the rate enhancements produced by the corresponding enzymes, we examined their rates of reaction at elevated temperatures and used the Arrhenius equation to extrapolate the results to room temperature. The similar reactivities of methylguanidine and 1,1,3,3-tetramethylguanidine and their negative entropies of activation imply that their decomposition proceeds by hydrolysis rather than elimination. The influence of changing pH on the rate of decomposition is consistent with attack by hydroxide ion on the methylguanidinium ion (k2 = 5 × 10(-6) M(-1) s(-1) at 25 °C) or with the kinetically equivalent attack by water on uncharged methylguanidine. At 25 °C and pH 7, N-methylguanidine is several orders of magnitude more stable than acetamidine, urea, or acetamide. Under the same conditions, the enzymes arginase and agmatinase accelerate substrate hydrolysis 4 × 10(14)-fold and 6 × 10(12)-fold, respectively, by mechanisms that appear to involve metal-mediated water attack. Arginine deiminase accelerates substrate hydrolysis 6 × 10(12)-fold by a mechanism that (in contrast to the mechanisms employed by arginase and agmatinase) is believed to involve attack by an active-site cysteine residue.
Collapse
Affiliation(s)
- Charles A Lewis
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | | |
Collapse
|
30
|
Structure-informed design of an enzymatically inactive vaccine component for group A Streptococcus. mBio 2013; 4:mBio.00509-13. [PMID: 23919999 PMCID: PMC3735194 DOI: 10.1128/mbio.00509-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Streptococcus pyogenes (group A Streptococcus [GAS]) causes ~700 million human infections/year, resulting in >500,000 deaths. There is no commercial GAS vaccine available. The GAS surface protein arginine deiminase (ADI) protects mice against a lethal challenge. ADI is an enzyme that converts arginine to citrulline and ammonia. Administration of a GAS vaccine preparation containing wild-type ADI, a protein with inherent enzymatic activity, may present a safety risk. In an approach intended to maximize the vaccine safety of GAS ADI, X-ray crystallography and structural immunogenic epitope mapping were used to inform vaccine design. This study aimed to knock out ADI enzyme activity without disrupting the three-dimensional structure or the recognition of immunogenic epitopes. We determined the crystal structure of ADI at 2.5 Å resolution and used it to select a number of amino acid residues for mutagenesis to alanine (D166, E220, H275, D277, and C401). Each mutant protein displayed abrogated activity, and three of the mutant proteins (those with the D166A, H275A, and D277A mutations) possessed a secondary structure and oligomerization state equivalent to those of the wild type, produced high-titer antisera, and avoided disruption of B-cell epitopes of ADI. In addition, antisera raised against the D166A and D277A mutant proteins bound to the GAS cell surface. The inactivated D166A and D277A mutant ADIs are ideal for inclusion in a GAS vaccine preparation. There is no human ortholog of ADI, and we confirm that despite limited structural similarity in the active-site region to human peptidyl ADI 4 (PAD4), ADI does not functionally mimic PAD4 and antiserum raised against GAS ADI does not recognize human PAD4. We present an example of structural biology informing human vaccine design. We previously showed that the administration of the enzyme arginine deiminase (ADI) to mice protected the mice against infection with multiple GAS serotypes. In this study, we determined the structure of GAS ADI and used this information to improve the vaccine safety of GAS ADI. Catalytically inactive mutant forms of ADI retained structure, recognition by antisera, and immunogenic epitopes, rendering them ideal for inclusion in GAS vaccine preparations. This example of structural biology informing vaccine design may underpin the formulation of a safe and efficacious GAS vaccine.
Collapse
|
31
|
Cheng C, Chen J, Fang C, Xia Y, Shan Y, Liu Y, Wen G, Song H, Fang W. Listeria monocytogenes aguA1, but not aguA2, encodes a functional agmatine deiminase: biochemical characterization of its catalytic properties and roles in acid tolerance. J Biol Chem 2013; 288:26606-15. [PMID: 23918931 DOI: 10.1074/jbc.m113.477380] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Listeria monocytogenes is adaptable to low pH environments and therefore crosses the intestinal barrier to establish systemic infections. L. monocytogenes aguA1 and aguA2 encode putative agmatine deiminases (AgDIs) AguA1 and AguA2. Transcription of aguA1 and aguA2 was significantly induced at pH 5.0. Deletion of aguA1 significantly impaired its survival both in gastric fluid at pH 2.5 and in mouse stomach, whereas aguA2 deletion did not show significant defect of survival in gastric fluid. With agmatine as the sole substrate, AguA1 expressed in Escherichia coli was optimal at 25 °C and over a wide range of pH from 3.5 to 10.5. Recombinant AguA2 showed no deiminase activity. Site-directed mutagenesis revealed that all nine AguA1 mutants completely lost enzymatic activity. AguA2 acquired AgDI activity only when Cys-157 was mutated to glycine. AguA1 mutation at the same site, G157C, also inactivated the enzyme. Thus, we have discovered Gly-157 as a novel residue other than the known catalytic triad (Cys-His-Glu/Asp) in L. monocytogenes that is critical for enzyme activity. Of the two putative AgDIs, we conclude that only AguA1 functionally participates in the AgDI pathway and mediates acid tolerance in L. monocytogenes.
Collapse
Affiliation(s)
- Changyong Cheng
- From the Zhejiang University Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, and Key Laboratory of Molecular Animal Nutrition of the Ministry of Education, Hangzhou, Zhejiang 310058, China
| | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Hering S, Sieg A, Kreikemeyer B, Fiedler T. Kinetic characterization of arginine deiminase and carbamate kinase from Streptococcus pyogenes M49. Protein Expr Purif 2013; 91:61-8. [PMID: 23867361 DOI: 10.1016/j.pep.2013.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/27/2013] [Accepted: 07/08/2013] [Indexed: 11/28/2022]
Abstract
Streptococcus pyogenes (group A Streptococcus, GAS) is an important human pathogen causing mild superficial infections of skin and mucous membranes, but also life-threatening systemic diseases. S. pyogenes and other prokaryotic organisms use the arginine deiminase system (ADS) for survival in acidic environments. In this study, the arginine deiminase (AD), and carbamate kinase (CK) from S. pyogenes M49 strain 591 were heterologously expressed in Escherichia coli DH5α, purified, and kinetically characterized. AD and CK from S. pyogenes M49 share high amino acid sequence similarity with the respective enzymes from Lactococcus lactis subsp. lactis IL1403 (45.6% and 53.5% identical amino acids) and Enterococcus faecalis V583 (66.8% and 66.8% identical amino acids). We found that the arginine deiminase of S. pyogenes is not allosterically regulated by the intermediates and products of the arginine degradation (e.g., ATP, citrulline, carbamoyl phosphate). The Km and Vmax values for arginine were 1.13±0.12mM (mean±SD) and 1.51±0.07μmol/min/mg protein. The carbamate kinase is inhibited by ATP but unaffected by arginine and citrulline. The Km and Vmax values for ADP were 0.72±0.08mM and 1.10±0.10μmol/min/mg protein and the Km for carbamoyl phosphate was 0.65±0.07mM. The optimum pH and temperature for both enzymes were 6.5 and 37°C, respectively.
Collapse
Affiliation(s)
- Silvio Hering
- Rostock University Medical Centre, Institute of Medical Microbiology, Virology, and Hygiene, Schillingallee 70, 18057 Rostock, Germany
| | | | | | | |
Collapse
|
33
|
Yoon JK, Frankel AE, Feun LG, Ekmekcioglu S, Kim KB. Arginine deprivation therapy for malignant melanoma. Clin Pharmacol 2012; 5:11-9. [PMID: 23293541 PMCID: PMC3534294 DOI: 10.2147/cpaa.s37350] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Despite recent development of promising immunotherapeutic and targeted drugs, prognosis in patients with advanced melanoma remains poor, and a cure for this disease remains elusive in most patients. The success of melanoma therapy depends on a better understanding of the biology of melanoma and development of drugs that effectively target the relevant genes or proteins essential for tumor cell survival. Melanoma cells frequently lack argininosuccinate synthetase, an essential enzyme for arginine synthesis, and as a result they become dependent on the availability of exogenous arginine. Accordingly, a therapeutic approach involving depletion of available arginine has been shown to be effective in preclinical studies. Early clinical studies have demonstrated sufficient antitumor activity to give rise to cautious optimism. In this article, the rationale for arginine deprivation therapy is discussed. Additionally, various strategies for depleting arginine are discussed and the preclinical and clinical investigations of arginine deprivation therapy in melanoma are reviewed.
Collapse
Affiliation(s)
- Jung-Ki Yoon
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA ; Hwasung Public Health Center, Hwasung, South Korea
| | | | | | | | | |
Collapse
|
34
|
Cugini C, Stephens DN, Nguyen D, Kantarci A, Davey ME. Arginine deiminase inhibits Porphyromonas gingivalis surface attachment. MICROBIOLOGY-SGM 2012; 159:275-285. [PMID: 23242802 DOI: 10.1099/mic.0.062695-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The oral cavity is host to a complex microbial community whose maintenance depends on an array of cell-to-cell interactions and communication networks, with little known regarding the nature of the signals or mechanisms by which they are sensed and transmitted. Determining the signals that control attachment, biofilm development and outgrowth of oral pathogens is fundamental to understanding pathogenic biofilm development. We have previously identified a secreted arginine deiminase (ADI) produced by Streptococcus intermedius that inhibited biofilm development of the commensal pathogen Porphyromonas gingivalis through downregulation of genes encoding the major (fimA) and minor (mfa1) fimbriae, both of which are required for proper biofilm development. Here we report that this inhibitory effect is dependent on enzymic activity. We have successfully cloned, expressed and defined the conditions to ensure that ADI from S. intermedius is enzymically active. Along with the cloning of the wild-type allele, we have created a catalytic mutant (ADIC399S), in which the resulting protein is not able to catalyse the hydrolysis of l-arginine to l-citrulline. P. gingivalis is insensitive to the ADIC399S catalytic mutant, demonstrating that enzymic activity is required for the effects of ADI on biofilm formation. Biofilm formation is absent under l-arginine-deplete conditions, and can be recovered by the addition of the amino acid. Taken together, the results indicate that arginine is an important signal that directs biofilm formation by this anaerobe. Based on our findings, we postulate that ADI functions to reduce arginine levels and, by a yet to be identified mechanism, signals P. gingivalis to alter biofilm development. ADI release from the streptococcal cell and its cross-genera effects are important findings in understanding the nature of inter-bacterial signalling and biofilm-mediated diseases of the oral cavity.
Collapse
Affiliation(s)
- Carla Cugini
- Department of Oral Medicine Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA.,Department of Molecular Genetics, The Forsyth Institute, Cambridge, MA, USA
| | | | - Daniel Nguyen
- Department of Periodontology, The Forsyth Institute, Cambridge, MA, USA
| | - Alpdogan Kantarci
- Department of Periodontology, The Forsyth Institute, Cambridge, MA, USA
| | - Mary E Davey
- Department of Oral Medicine Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA.,Department of Molecular Genetics, The Forsyth Institute, Cambridge, MA, USA
| |
Collapse
|
35
|
Teo CY, Shave S, Chor ALT, Salleh AB, Rahman MBBA, Walkinshaw MD, Tejo BA. Discovery of a new class of inhibitors for the protein arginine deiminase type 4 (PAD4) by structure-based virtual screening. BMC Bioinformatics 2012; 13 Suppl 17:S4. [PMID: 23282142 PMCID: PMC3521205 DOI: 10.1186/1471-2105-13-s17-s4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is an autoimmune disease with unknown etiology. Anticitrullinated protein autoantibody has been documented as a highly specific autoantibody associated with RA. Protein arginine deiminase type 4 (PAD4) is the enzyme responsible for catalyzing the conversion of peptidylarginine into peptidylcitrulline. PAD4 is a new therapeutic target for RA treatment. In order to search for inhibitors of PAD4, structure-based virtual screening was performed using LIDAEUS (Ligand discovery at Edinburgh university). Potential inhibitors were screened experimentally by inhibition assays. RESULTS Twenty two of the top-ranked water-soluble compounds were selected for inhibitory screening against PAD4. Three compounds showed significant inhibition of PAD4 and their IC50 values were investigated. The structures of the three compounds show no resemblance with previously discovered PAD4 inhibitors, nor with existing drugs for RA treatment. CONCLUSION Three compounds were discovered as potential inhibitors of PAD4 by virtual screening. The compounds are commercially available and can be used as scaffolds to design more potent inhibitors against PAD4.
Collapse
Affiliation(s)
- Chian Ying Teo
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Malaysia
| | | | | | | | | | | | | |
Collapse
|
36
|
Gallego P, Planell R, Benach J, Querol E, Perez-Pons JA, Reverter D. Structural characterization of the enzymes composing the arginine deiminase pathway in Mycoplasma penetrans. PLoS One 2012; 7:e47886. [PMID: 23082227 PMCID: PMC3474736 DOI: 10.1371/journal.pone.0047886] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 09/24/2012] [Indexed: 11/19/2022] Open
Abstract
The metabolism of arginine towards ATP synthesis has been considered a major source of energy for microorganisms such as Mycoplasma penetrans in anaerobic conditions. Additionally, this pathway has also been implicated in pathogenic and virulence mechanism of certain microorganisms, i.e. protection from acidic stress during infection. In this work we present the crystal structures of the three enzymes composing the gene cluster of the arginine deiminase pathway from M. penetrans: arginine deiminase (ADI), ornithine carbamoyltransferase (OTC) and carbamate kinase (CK). The arginine deiminase (ADI) structure has been refined to 2.3 Å resolution in its apo-form, displaying an "open" conformation of the active site of the enzyme in comparison to previous complex structures with substrate intermediates. The active site pocket of ADI is empty, with some of the catalytic and binding residues far from their active positions, suggesting major conformational changes upon substrate binding. Ornithine carbamoyltransferase (OTC) has been refined in two crystal forms at 2.5 Å and 2.6 Å resolution, respectively, both displaying an identical dodecameric structure with a 23-point symmetry. The dodecameric structure of OTC represents the highest level of organization in this protein family and in M.penetrans it is constituted by a novel interface between the four catalytic homotrimers. Carbamate kinase (CK) has been refined to 2.5 Å resolution and its structure is characterized by the presence of two ion sulfates in the active site, one in the carbamoyl phosphate binding site and the other in the β-phosphate ADP binding pocket of the enzyme. The CK structure also shows variations in some of the elements that regulate the catalytic activity of the enzyme. The relatively low number of metabolic pathways and the relevance in human pathogenesis of Mycoplasma penetrans places the arginine deiminase pathway enzymes as potential targets to design specific inhibitors against this human parasite.
Collapse
Affiliation(s)
- Pablo Gallego
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Raquel Planell
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jordi Benach
- Experiments Division, ALBA Synchrotron Light Source, Barcelona, Spain
| | - Enrique Querol
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep A. Perez-Pons
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| |
Collapse
|
37
|
Shi D, Yu X, Zhao G, Ho J, Lu S, Allewell NM, Tuchman M. Crystal structure and biochemical properties of putrescine carbamoyltransferase from Enterococcus faecalis: Assembly, active site, and allosteric regulation. Proteins 2012; 80:1436-47. [PMID: 22328207 DOI: 10.1002/prot.24042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 01/03/2012] [Accepted: 01/11/2012] [Indexed: 11/09/2022]
Abstract
Putrescine carbamoyltransferase (PTCase) catalyzes the conversion of carbamoylputrescine to putrescine and carbamoyl phosphate (CP), a substrate of carbamate kinase (CK). The crystal structure of PTCase has been determined and refined at 3.2 Å resolution. The trimeric molecular structure of PTCase is similar to other carbamoyltransferases, including the catalytic subunit of aspartate carbamoyltransferase (ATCase) and ornithine carbamoyltransferase (OTCase). However, in contrast to other trimeric carbamoyltransferases, PTCase binds both CP and putrescine with Hill coefficients at saturating concentrations of the other substrate of 1.53 ± 0.03 and 1.80 ± 0.06, respectively. PTCase also has a unique structural feature: a long C-terminal helix that interacts with the adjacent subunit to enhance intersubunit interactions in the molecular trimer. The C-terminal helix appears to be essential for both formation of the functional trimer and catalytic activity, since truncated PTCase without the C-terminal helix aggregates and has only 3% of native catalytic activity. The active sites of PTCase and OTCase are similar, with the exception of the 240's loop. PTCase lacks the proline-rich sequence found in knotted carbamoyltransferases and is unknotted. A Blast search of all available genomes indicates that 35 bacteria, most of which are Gram-positive, have an agcB gene encoding PTCase located near the genes that encode agmatine deiminase and CK, consistent with the catabolic role of PTCase in the agmatine degradation pathway. Sequence comparisons indicate that the C-terminal helix identified in this PTCase structure will be found in all other PTCases identified, suggesting that it is the signature feature of the PTCase family of enzymes.
Collapse
Affiliation(s)
- Dashuang Shi
- Center for Genetic Medicine Research and Department of Integrative Systems Biology, Children's National Medical Center, The George Washington University, Washington, District of Columbia 20010, USA.
| | | | | | | | | | | | | |
Collapse
|
38
|
Ke Z, Guo H. Ab initio QM/MM free-energy studies of arginine deiminase catalysis: the protonation state of the Cys nucleophile. J Phys Chem B 2011; 115:3725-33. [PMID: 21395290 PMCID: PMC3070061 DOI: 10.1021/jp200843s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first step of the hydrolytic deimination of L-arginine catalyzed by arginine deiminase is examined using ab initio quantum mechanical/molecular mechanical molecular dynamics simulations. Two possible protonation states of the nucleophilic Cys406 residue were investigated, and the corresponding activation free energies were obtained via umbrella sampling. Our calculations indicated a reaction free-energy barrier of 21.3 kcal/mol for the neutral cysteine, which is in reasonably good agreement with the experimental k(cat) value of 6.3 s(-1), i.e., a barrier of 16.7 kcal/mol. On the other hand, the deprotonated Cys nucleophile yields a free-energy barrier of 6.7 kcal/mol, much lower than the experimental result. The reaction free-energy barriers along with other data suggest that the Cys nucleophile is dominated by its protonated state in the Michaelis complex, and the reaction barrier corresponds largely to its deprotonation.
Collapse
Affiliation(s)
- Zhihong Ke
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, 87131
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, 87131
| |
Collapse
|
39
|
Morada M, Smid O, Hampl V, Sutak R, Lam B, Rappelli P, Dessì D, Fiori PL, Tachezy J, Yarlett N. Hydrogenosome-localization of arginine deiminase in Trichomonas vaginalis. Mol Biochem Parasitol 2010; 176:51-4. [PMID: 21074581 DOI: 10.1016/j.molbiopara.2010.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 10/12/2010] [Accepted: 10/13/2010] [Indexed: 11/26/2022]
Abstract
The arginine dihydrolase (ADH) pathway has an analogous function to the urea cycle in mitochondria-containing cells, by removing nitrogen from amino acids and generating ATP. Subcellular localization of the ADH pathway enzymes in Trichomonas vaginalis revealed that arginine deiminase (ADI) localizes to the hydrogenosome, a mitochondrion-like organelle of anaerobic protists. However the other enzymes of the ADH pathway, ornithine carbamyltransferase and carbamate kinase localize to the cytosol. Three gene sequences of T. vaginalis ADI (ADI 1-3) were identified in the T. vaginalis genome, all having putative mitochondrial targeting sequences. The ADI sequences were cloned and used to probe T. vaginalis using a carboxyterminal di-hemogglutinin epitope tag which demonstrated co-localization with malic enzyme confirming the hydrogenosome localization of this enzyme.
Collapse
Affiliation(s)
- Mary Morada
- Haskins Laboratories, Pace University, New York, NY 10038, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Rodríguez SB, Stitt BL, Ash DE. Cysteine 351 is an essential nucleophile in catalysis by Porphyromonas gingivalis peptidylarginine deiminase. Arch Biochem Biophys 2010; 504:190-6. [PMID: 20850413 DOI: 10.1016/j.abb.2010.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Revised: 09/08/2010] [Accepted: 09/08/2010] [Indexed: 10/19/2022]
Abstract
Peptidylarginine deiminase (PAD), which catalyzes the deimination of the guanidino group from peptidylarginine residues, belongs to a superfamily of guanidino group modifying enzymes that have been shown to produce an S-alkylthiouronium ion intermediate during catalysis. Thiol-directed reagents iodoacetamide and iodoacetate inactivate recombinant PAD, and substrate protects the enzyme from inactivation. Activity measurements together with peptide mapping by mass spectrometry of PAD modified in the absence and presence of substrate demonstrated that cysteine-351 is modified by iodoacetamide. The pK(a) value of the cysteine residue, 7.7±0.2 as determined by iodoacetamide modification, agrees well with a critical pK value identified in pH rate studies. The role of cysteine-351 in catalysis was tested by site-directed mutagenesis in which the cysteine was replaced with serine to eliminate the proposed nucleophilic interaction. Binding studies carried out using fluorescence spectrometry established the structural integrity of the C351S PAD. However, the C351S PAD variant was catalytically inactive, exhibiting <0.01% wild-type activity. These results indicate that Cys 351 is a nucleophile that initiates the enzymatic reaction.
Collapse
Affiliation(s)
- Sofía B Rodríguez
- Department of Biochemistry, Temple University School of Medicine, Philadelphia, PA 19140, United States
| | | | | |
Collapse
|
41
|
Morada M, Manzur M, Lam B, Tan C, Tachezy J, Rappelli P, Dessì D, Fiori PL, Yarlett N. Arginine metabolism in Trichomonas vaginalis infected with Mycoplasma hominis. MICROBIOLOGY-SGM 2010; 156:3734-3743. [PMID: 20656780 PMCID: PMC3068705 DOI: 10.1099/mic.0.042192-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Both Mycoplasma hominis and Trichomonas vaginalis utilize arginine as an energy source via the arginine dihydrolase (ADH) pathway. It has been previously demonstrated that M. hominis forms a stable intracellular relationship with T. vaginalis; hence, in this study we examined the interaction of two localized ADH pathways by comparing T. vaginalis strain SS22 with the laboratory-generated T. vaginalis strain SS22-MOZ2 infected with M. hominis MOZ2. The presence of M. hominis resulted in an approximately 16-fold increase in intracellular ornithine and a threefold increase in putrescine, compared with control T. vaginalis cultures. No change in the activity of enzymes of the ADH pathway could be demonstrated in SS22-MOZ2 compared with the parent SS22, and the increased production of ornithine could be attributed to the presence of M. hominis. Using metabolic flow analysis it was determined that the elasticity of enzymes of the ADH pathway in SS22-MOZ2 was unchanged compared with the parent SS22; however, the elasticity of ornithine decarboxylase (ODC) in SS22 was small, and it was doubled in SS22-MOZ2 cells. The potential benefit of this relationship to both T. vaginalis and M. hominis is discussed.
Collapse
Affiliation(s)
- Mary Morada
- Haskins Laboratories, Pace University, NY 10038, USA
| | | | - Brian Lam
- The Department of Chemistry and Physical Sciences, Pace University, NY 10038, USA.,Haskins Laboratories, Pace University, NY 10038, USA
| | - Cho Tan
- The Department of Chemistry and Physical Sciences, Pace University, NY 10038, USA.,Haskins Laboratories, Pace University, NY 10038, USA
| | - Jan Tachezy
- Department of Parasitology, Charles University, Prague, Czech Republic
| | - Paola Rappelli
- Department of Biomedical Sciences, Division of Experimental and Clinical Microbiology, University of Sassari, 07100 Sassari, Italy
| | - Daniele Dessì
- Department of Biomedical Sciences, Division of Experimental and Clinical Microbiology, University of Sassari, 07100 Sassari, Italy
| | - Pier L Fiori
- Department of Biomedical Sciences, Division of Experimental and Clinical Microbiology, University of Sassari, 07100 Sassari, Italy
| | - Nigel Yarlett
- The Department of Chemistry and Physical Sciences, Pace University, NY 10038, USA.,Haskins Laboratories, Pace University, NY 10038, USA
| |
Collapse
|
42
|
Linsky T, Fast W. Mechanistic similarity and diversity among the guanidine-modifying members of the pentein superfamily. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1943-53. [PMID: 20654741 DOI: 10.1016/j.bbapap.2010.07.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 07/13/2010] [Accepted: 07/14/2010] [Indexed: 11/24/2022]
Abstract
The pentein superfamily is a mechanistically diverse superfamily encompassing both noncatalytic proteins and enzymes that catalyze hydrolase, dihydrolase and amidinotransfer reactions on guanidine substrates. Despite generally low sequence identity, they possess a conserved structural fold and display common mechanistic themes in catalysis. The structurally characterized catalytic penteins possess a conserved core of residues that include a Cys, His and two polar, guanidine-binding residues. All known catalytic penteins use the core Cys to attack the substrate's guanidine moiety to form a covalent thiouronium adduct and all cleave one or more of the guanidine C--N bonds. The mechanistic information compiled to date supports the hypothesis that this superfamily may have evolved divergently from a catalytically promiscuous ancestor.
Collapse
Affiliation(s)
- Thomas Linsky
- Graduate Program in Biochemistry, The University of Texas at Austin, USA
| | | |
Collapse
|
43
|
Ke Z, Wang S, Xie D, Zhang Y. Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4. J Phys Chem B 2009; 113:16705-10. [PMID: 20028143 PMCID: PMC2801900 DOI: 10.1021/jp9080614] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein arginine deiminase 4 (PAD4) catalyzes the citrullination of the peptidylarginine via two successive stages: deimination and hydrolysis. Herein, by employing state-of-the-art Born-Oppenheimer ab initio QM/MM molecular dynamics simulations with the umbrella sampling method, we characterized the catalytic mechanism of the hydrolysis reaction: first, the nucleophilic attack of a water molecule to the C(zeta) of the thiouronium intermediate yields a stable tetrahedral intermediate, and then the S-C(zeta) bond breaks to generate the final product, citrulline. Throughout the hydrolysis reaction, His471 and Asp473 play pivotal catalytic roles by first enhancing the nucleophilic ability of the active water through forming shorter and low-barrier hydrogen bonds and then by serving as proton-accepting groups to deprotonate the water molecule, which is consistent with experimental findings. At the transition state, the spontaneous proton transfer among the reactive water, His471 and Asp473 have been observed. The determined overall free energy barrier for this hydrolysis stage is 16.5 kcal x mol(-1), which is lower than the barrier of 20.9 kcal x mol(-1) for the deimination stage determined previously with the same computational approach [J. Phys. Chem. B 2009, 113, 12750-12758]. Thus, the rate-determining step of the PAD4-catalyzed citrullination is the first step of the deimination. Our current work further demonstrates the strength and applicability of the ab initio QM/MM MD approach in simulating enzyme reactions.
Collapse
Affiliation(s)
- Zhihong Ke
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
- Department of Chemistry, New York University, New York, NY 10003
| | - Shenglong Wang
- Department of Chemistry, New York University, New York, NY 10003
| | - Daiqian Xie
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY 10003
| |
Collapse
|
44
|
Kozai M, Sasamori E, Fujihara M, Yamashita T, Taira H, Harasawa R. Growth inhibition of human melanoma cells by a recombinant arginine deiminase expressed in Escherichia coli. J Vet Med Sci 2009; 71:1343-7. [PMID: 19887741 DOI: 10.1292/jvms.001343] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have cloned the arginine deiminase (ADI) gene from Mycoplasma hominis PG21 genomic DNA by polymerase chain reaction, and changed four TGA tryptophan codons (stop codon in E. coli) to TGG codons in the coding region by site-directed mutagenesis in order to express in E. coli. The recombinant ADI (rADI) was purified to apparent homogeneity by Ni-affinity chromatography after extraction from inclusion bodies followed by refolding. The rADI expressed in E. coli was estimated to be 50 kDa. Dimeric forms of rADI exerted enzymatic activity. We found that high concentration of potassium dihydrogenphosphate (PDP) and L-arginine addition in refolding reaction increases the enzyme activity. The specific activity of rADl was calculated as 0.618 U/mg. In addition, the enzyme activity of purified rADI remained for at least one month in 100 mM PDP solution (pH 6.5), but diminished within one week in 100 mM PDP solution (pH 7.4). Anti-tumor activity of the purified rADI was estimated to be 0.036 U/ml as 50% growth inhibitory activity against human melanoma cell line G-361.
Collapse
Affiliation(s)
- Megumi Kozai
- Department of Veterinary Microbiology, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka 020-8550, Japan
| | | | | | | | | | | |
Collapse
|
45
|
Bernardes N, Seruca R, Chakrabarty AM, Fialho AM. Microbial-based therapy of cancer: current progress and future prospects. Bioeng Bugs 2009; 1:178-90. [PMID: 21326924 DOI: 10.4161/bbug.1.3.10903] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 12/02/2009] [Indexed: 12/12/2022] Open
Abstract
The use of bacteria in the regression of certain forms of cancer has been recognized for more than a century. Much effort, therefore, has been spent over the years in developing wild-type or modified bacterial strains to treat cancer. However, their use at the dose required for therapeutic efficacy has always been associated with toxicity problems and other deleterious effects. Recently, the old idea of using bacteria in the treatment of cancer has attracted considerable interest and new genetically engineered attenuated strains as well as microbial compounds that might have specific anticancer activity without side effects are being evaluated for their ability to act as new anticancer agents. This involves the use of attenuated bacterial strains and expressing foreign genes that encode the ability to convert non-toxic prodrugs to cytotoxic drugs. Novel strategies also include the use of bacterial products such as proteins, enzymes, immunotoxins and secondary metabolites, which specifically target cancer cells and cause tumor regression through growth inhibition, cell cycle arrest or apoptosis induction. In this review we describe the current knowledge and discuss the future directions regarding the use of bacteria or their products, in cancer therapy.
Collapse
Affiliation(s)
- Nuno Bernardes
- Institute for Biotechnology and Bioengineering (IBB), Center for Biological and Chemical Engineering, Instituto Superior Tecnico, Lisbon, Portugal
| | | | | | | |
Collapse
|
46
|
Ke Z, Zhou Y, Hu P, Wang S, Xie D, Zhang Y. Active site cysteine is protonated in the PAD4 Michaelis complex: evidence from Born-Oppenheimer ab initio QM/MM molecular dynamics simulations. J Phys Chem B 2009; 113:12750-8. [PMID: 19507815 DOI: 10.1021/jp903173c] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The protein arginine deiminase 4 (PAD4) catalyzes the citrullination of the peptidylarginine and plays a critical role in rheumatoid arthritis (RA) and gene regulation. Understanding its catalytic mechanism is not only of fundamental importance but also of significant medical interest for the rational design of new inhibitors. By employing on-the-fly Born-Oppenheimer ab initio QM/MM molecular dynamics simulations, we have demonstrated that it is unlikely for the active site cysteine and histidine to exist as a thiolate-imidazolium ion pair in the PAD4 Michaelis reactant complex. Instead, a substrate-assisted proton transfer mechanism for the deimination reaction step has been characterized: both Cys645 and His471 in the PAD4 active site are neutral prior to the reaction; the deprotonation of Cys645 by the substrate arginine occurs in concert with the nucleophilic addition of the Cys thiolate to Czeta of the substrate, and leads to a covalent tetrahedral intermediate; then, the Czeta-Neta1 bond cleaves and the resulted ammonia is displaced by a solvent water molecule. The initial deprotonation and nucleophilic attack step is found to be rate-determining. The computed free energy barrier with B3LYP(6-31G*) QM/MM MD simulations and umbrella sampling is 20.9 kcal.mol(-1), consistent with the experimental kinetic data. During the deimination, His471 plays an important role in stabilizing the transition state through the formation of the hydrogen bond with the guanidinium group. Our current studies further demonstrated the viability and strength of the ab initio QM/MM molecular dynamics approach in simulating enzyme reactions.
Collapse
Affiliation(s)
- Zhihong Ke
- Department of Chemistry, New York University, New York, New York 10003, USA
| | | | | | | | | | | |
Collapse
|
47
|
Wang Y, Monzingo AF, Hu S, Schaller TH, Robertus JD, Fast W. Developing dual and specific inhibitors of dimethylarginine dimethylaminohydrolase-1 and nitric oxide synthase: toward a targeted polypharmacology to control nitric oxide. Biochemistry 2009; 48:8624-35. [PMID: 19663506 DOI: 10.1021/bi9007098] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecules that block nitric oxide's (NO) biosynthesis are of significant interest. For example, nitric oxide synthase (NOS) inhibitors have been suggested as antitumor therapeutics, as have inhibitors of dimethylarginine dimethylaminohydrolase (DDAH), an enzyme that catabolizes endogenous NOS inhibitors. Dual-targeted inhibitors hold promise as more effective reagents to block NO biosynthesis than single-targeted compounds. In this study, a small set of known NOS inhibitors are surveyed as inhibitors of recombinant human DDAH-1. From these, an alkylamidine scaffold is selected for homologation. Stepwise lengthening of one substituent converts an NOS-selective inhibitor into a dual-targeted NOS/DDAH-1 inhibitor and then into a DDAH-1 selective inhibitor, as seen in the inhibition constants of N5-(1-iminoethyl)-, N5-(1-iminopropyl)-, N5-(1-iminopentyl)- and N(5)-(1-iminohexyl)-l-ornithine for neuronal NOS (1.7, 3, 20, >1,900 microM, respectively) and DDAH-1 (990, 52, 7.5, 110 microM, respectively). A 1.9 A X-ray crystal structure of the N5-(1-iminopropyl)-L-ornithine:DDAH-1 complex indicates covalent bond formation between the inhibitor's amidino carbon and the active-site Cys274, and solution studies show reversible competitive inhibition, consistent with a reversible covalent mode of DDAH inhibition by alkylamidine inhibitors. These represent a versatile scaffold for the development of a targeted polypharmacological approach to control NO biosynthesis.
Collapse
Affiliation(s)
- Yun Wang
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, Texas 78712, USA
| | | | | | | | | | | |
Collapse
|
48
|
Li Z, Kulakova L, Li L, Galkin A, Zhao Z, Nash TE, Mariano PS, Herzberg O, Dunaway-Mariano D. Mechanisms of catalysis and inhibition operative in the arginine deiminase from the human pathogen Giardia lamblia. Bioorg Chem 2009; 37:149-61. [PMID: 19640561 DOI: 10.1016/j.bioorg.2009.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 06/06/2009] [Accepted: 06/08/2009] [Indexed: 11/27/2022]
Abstract
Giardia lamblia arginine deiminase (GlAD), the topic of this paper, belongs to the hydrolase branch of the guanidine-modifying enzyme superfamily, whose members employ Cys-mediated nucleophilic catalysis to promote deimination of l-arginine and its naturally occurring derivatives. G. lamblia is the causative agent in the human disease giardiasis. The results of RNAi/antisense RNA gene-silencing studies reported herein indicate that GlAD is essential for G. lamblia trophozoite survival and thus, a potential target for the development of therapeutic agents for the treatment of giardiasis. The homodimeric recombinant protein was prepared in Escherichia coli for in-depth biochemical characterization. The 2-domain GlAD monomer consists of a N-terminal domain that shares an active site structure (depicted by an insilico model) and kinetic properties (determined by steady-state and transient state kinetic analysis) with its bacterial AD counterparts, and a C-terminal domain of unknown fold and function. GlAD was found to be active over a wide pH range and to accept l-arginine, l-arginine ethyl ester, N(alpha)-benzoyl-l-arginine, and N(omega)-amino-l-arginine as substrates but not agmatine, l-homoarginine, N(alpha)-benzoyl-l-arginine ethyl ester or a variety of arginine-containing peptides. The intermediacy of a Cys424-alkylthiouronium ion covalent enzyme adduct was demonstrated and the rate constants for formation (k(1)=80s(-1)) and hydrolysis (k(2)=35s(-1)) of the intermediate were determined. The comparatively lower value of the steady-state rate constant (k(cat)=2.6s(-1)), suggests that a step following citrulline formation is rate-limiting. Inhibition of GlAD using Cys directed agents was briefly explored. S-Nitroso-l-homocysteine was shown to be an active site directed, irreversible inhibitor whereas N(omega)-cyano-l-arginine did not inhibit GlAD but instead proved to be an active site directed, irreversible inhibitor of the Bacillus cereus AD.
Collapse
Affiliation(s)
- Zhimin Li
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Expression of Arginine Deiminase from Pseudomonas plecoglossicida CGMCC2039 in Escherichia coli and Its Anti-Tumor Activity. Curr Microbiol 2009; 58:593-8. [DOI: 10.1007/s00284-009-9376-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 01/21/2009] [Accepted: 01/23/2009] [Indexed: 10/21/2022]
|
50
|
Kwan JM, Fialho AM, Kundu M, Thomas J, Hong CS, Das Gupta TK, Chakrabarty AM. Bacterial proteins as potential drugs in the treatment of leukemia. Leuk Res 2009; 33:1392-9. [PMID: 19250673 DOI: 10.1016/j.leukres.2009.01.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2008] [Revised: 12/19/2008] [Accepted: 01/24/2009] [Indexed: 11/28/2022]
Abstract
Azurin and Laz are bacterial proteins that have been shown to exert anticancer effects against a variety of solid tumors. Their effects on liquid cancers have never been studied. We now show that they are also effective against liquid-borne cancers such as leukemia. Azurin and Laz can each enter in two leukemia cell lines but Laz exerts a greater cytotoxic effect on both K562 and HL60 cells, while having little effect on peripheral blood mononuclear cells, where they have very limited entry. In addition to Azurin and Laz, we have recently identified another protein, Pa-CARD, from Pseudomonas aeruginosa that carries a caspase recruitment domain (CARD)-like domain. This CARD domain polypeptide, called Pa-CARD, demonstrates cytotoxic activity against leukemia cells. In the leukemia cell lines, HL60 and K562, the anticancer activity of Laz and Pa-CARD is mediated through cell cycle arrest at the G2/M phase involving the Wee1 protein stabilization and the depletion of phosphorylated AKT-Ser-473, the active form of a serine/threonine kinase that is often dysregulated in many cancer types.
Collapse
Affiliation(s)
- Jennifer M Kwan
- Department of Microbiology and Immunology, University of Illinois College of Medicine at Chicago, 835 S. Wolcott, Chicago, IL 60612, USA
| | | | | | | | | | | | | |
Collapse
|