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Kasapoglu AG, Ilhan E, Aydin M, Yigider E, Inal B, Buyuk I, Taspinar MS, Ciltas A, Agar G. Characterization of Two-Component System gene ( TCS) in melatonin-treated common bean under salt and drought stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1733-1754. [PMID: 38162914 PMCID: PMC10754802 DOI: 10.1007/s12298-023-01406-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/21/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
The two-component system (TCS) generally consists of three elements, namely the histidine kinase (HK), response regulator (RR), and histidine phosphotransfer (HP) gene families. This study aimed to assess the expression of TCS genes in P. vulgaris leaf tissue under salt and drought stress and perform a genome-wide analysis of TCS gene family members using bioinformatics methods. This study identified 67 PvTCS genes, including 10 PvHP, 38 PvRR, and 19 PvHK, in the bean genome. PvHK2 had the maximum number of amino acids with 1261, whilst PvHP8 had the lowest number with 87. In addition, their theoretical isoelectric points were between 4.56 (PvHP8) and 9.15 (PvPRR10). The majority of PvTCS genes are unstable. Phylogenetic analysis of TCS genes in A. thaliana, G. max, and bean found that PvTCS genes had close phylogenetic relationships with the genes of other plants. Segmental and tandem duplicate gene pairs were detected among the TCS genes and TCS genes have been subjected to purifying selection pressure in the evolutionary process. Furthermore, the TCS gene family, which has an important role in abiotic stress and hormonal responses in plants, was characterized for the first time in beans, and its expression of TCS genes in bean leaves under salt and drought stress was established using RNAseq and qRT-PCR analyses. The findings of this study will aid future functional and genomic studies by providing essential information about the members of the TCS gene family in beans. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01406-5.
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Affiliation(s)
- Ayse Gul Kasapoglu
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, 25050 Erzurum, Turkey
| | - Emre Ilhan
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, 25050 Erzurum, Turkey
| | - Murat Aydin
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, 25050 Erzurum, Turkey
| | - Esma Yigider
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, 25050 Erzurum, Turkey
| | - Behcet Inal
- Department of Agricultural Biotechnology, Faculty of Agriculture, Siirt University, 56100 Siirt, Turkey
| | - Ilker Buyuk
- Department of Biology, Faculty of Science, Ankara University, 06100 Ankara, Turkey
| | - Mahmut Sinan Taspinar
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, 25050 Erzurum, Turkey
| | - Abdulkadir Ciltas
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, 25050 Erzurum, Turkey
| | - Guleray Agar
- Department of Biology, Faculty of Science, Ataturk University, 25050 Erzurum, Turkey
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Alkatheri AH, Yap PSX, Abushelaibi A, Lai KS, Cheng WH, Erin Lim SH. Microbial Genomics: Innovative Targets and Mechanisms. Antibiotics (Basel) 2023; 12:antibiotics12020190. [PMID: 36830101 PMCID: PMC9951906 DOI: 10.3390/antibiotics12020190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Multidrug resistance (MDR) has become an increasing threat to global health because bacteria can develop resistance to antibiotics over time. Scientists worldwide are searching for new approaches that go beyond traditional antibiotic discovery and development pipelines. Advances in genomics, however, opened up an unexplored therapeutic opportunity for the discovery of new antibacterial agents. Genomic approaches have been used to discover several novel antibiotics that target critical processes for bacterial growth and survival, including histidine kinases (HKs), LpxC, FabI, peptide deformylase (PDF), and aminoacyl-tRNA synthetases (AaRS). In this review, we will discuss the use of microbial genomics in the search for innovative and promising drug targets as well as the mechanisms of action for novel antimicrobial agents. We will also discuss future directions on how the utilization of the microbial genomics approach could improve the odds of antibiotic development having a more successful outcome.
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Affiliation(s)
- Asma Hussain Alkatheri
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Polly Soo-Xi Yap
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor 47500, Malaysia
| | - Aisha Abushelaibi
- Office of Campus Director, Abu Dhabi Colleges, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Kok-Song Lai
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Wan-Hee Cheng
- Faculty of Health and Life Sciences, INTI International University, Persiaran Perdana BBN, Nilai 71800, Malaysia
| | - Swee-Hua Erin Lim
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
- Correspondence:
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Jin S, Hui M, Lu Y, Zhao Y. An overview on the two-component systems of Streptomyces coelicolor. World J Microbiol Biotechnol 2023; 39:78. [PMID: 36645528 DOI: 10.1007/s11274-023-03522-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/10/2023] [Indexed: 01/17/2023]
Abstract
The two-component system (TCS) found in various organisms is a regulatory system, which is involved in the response by the organism to stimuli, thereby regulating the internal behavior of the cell. It is commonly found in prokaryotes and is an important signaling system in bacteria. TCSs are involved in the regulation of physiological and morphological differentiation of the industrially important microbes from the genus Streptomyces, which produce a vast array of bioactive secondary metabolites (SMs). Genetic engineering of TCSs can substantially increase the yield of target SMs, which is valuable for industrial-scale production. Research on TCS has mainly been completed in the model strain Streptomyces coelicolor. In this review, we summarize the recent advances in the functional identification and elucidation of the regulatory mechanisms of various TCSs in S. coelicolor, with a focus on their roles in the biosynthesis of important SMs.
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Affiliation(s)
- Shangping Jin
- College of Bioengineering, Henan University of Technology, 100 Lianhua Street, 450001, Zhengzhou, China
| | - Ming Hui
- College of Bioengineering, Henan University of Technology, 100 Lianhua Street, 450001, Zhengzhou, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, 100 Guilin Road, 200234, Shanghai, China.
| | - Yawei Zhao
- College of Bioengineering, Henan University of Technology, 100 Lianhua Street, 450001, Zhengzhou, China.
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Chen H, Yu C, Wu H, Li G, Li C, Hong W, Yang X, Wang H, You X. Recent Advances in Histidine Kinase-Targeted Antimicrobial Agents. Front Chem 2022; 10:866392. [PMID: 35860627 PMCID: PMC9289397 DOI: 10.3389/fchem.2022.866392] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/16/2022] [Indexed: 11/15/2022] Open
Abstract
The prevalence of antimicrobial-resistant pathogens significantly limited the number of effective antibiotics available clinically, which urgently requires new drug targets to screen, design, and develop novel antibacterial drugs. Two-component system (TCS), which is comprised of a histidine kinase (HK) and a response regulator (RR), is a common mechanism whereby bacteria can sense a range of stimuli and make an appropriate adaptive response. HKs as the sensor part of the bacterial TCS can regulate various processes such as growth, vitality, antibiotic resistance, and virulence, and have been considered as a promising target for antibacterial drugs. In the current review, we highlighted the structural basis and functional importance of bacterial TCS especially HKs as a target in the discovery of new antimicrobials, and summarize the latest research progress of small-molecule HK-inhibitors as potential novel antimicrobial drugs reported in the past decade.
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Affiliation(s)
- Hongtong Chen
- Laboratory of Pharmacology/Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chengqi Yu
- School of Basic Medical Science, Capital Medical University, Beijing, China
| | - Han Wu
- School of Pharmacy, Minzu University of China, Beijing, China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, China
| | - Guoqing Li
- Laboratory of Pharmacology/Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Congran Li
- Laboratory of Pharmacology/Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Hong
- Beijing Institute of Collaborative Innovation, Beijing, China
| | - Xinyi Yang
- Laboratory of Pharmacology/Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Xinyi Yang, ; Hao Wang, ; Xuefu You,
| | - Hao Wang
- School of Pharmacy, Minzu University of China, Beijing, China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, China
- Institute of National Security, Minzu University of China, Beijing, China
- *Correspondence: Xinyi Yang, ; Hao Wang, ; Xuefu You,
| | - Xuefu You
- Laboratory of Pharmacology/Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Xinyi Yang, ; Hao Wang, ; Xuefu You,
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Anti-Quorum Sensing Activities of Gliptins against Pseudomonas aeruginosa and Staphylococcus aureus. Biomedicines 2022; 10:biomedicines10051169. [PMID: 35625906 PMCID: PMC9138634 DOI: 10.3390/biomedicines10051169] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 12/24/2022] Open
Abstract
The development of bacterial resistance to traditional antibiotics constitutes an emerging public health issue. Promising approaches have been innovated to conquer bacterial resistance, and targeting bacterial virulence is one of these approaches. Bacterial virulence mitigation offers several merits, as antivirulence agents do not affect the growth of bacteria and hence do not induce bacteria to develop resistance. In this direction, numerous drugs have been repurposed as antivirulence agents prior to their clinical use alone or in combination with traditional antibiotics. Quorum sensing (QS) plays a key role in controlling bacterial virulence. In the current study, dipeptidase inhibitor-4 (DPI-4) antidiabetic gliptins were screened for their antivirulence and anti-quorum sensing (anti-QS) activities against Gram-negative Pseudomonas aeruginosa and Gram-positive Staphylococcus aureus. Upon assessing their antibiofilm activities, the ten tested gliptins significantly diminished biofilm formation. In particular, sitagliptin exhibited the most efficient antibiofilm activity, so it was chosen as a representative of all gliptins to further investigate its antivirulence activity. Sitagliptin significantly protected mice from P. aeruginosa and S. aureus pathogenesis. Furthermore, sitagliptin downregulated QS-encoding genes in P. aeruginosa and S. aureus. To test the anti-QS activities of gliptins, a detailed molecular docking study was conducted to evaluate the gliptins’ binding affinities to P. aeruginosa and S. aureus QS receptors, which helped explain the anti-QS activities of gliptins, particularly sitagliptin and omarigliptin. In conclusion, this study evaluates the possible antivirulence and anti-QS activities of gliptins that could be promising novel candidates for the treatment of aggressive Gram-negative or -positive bacterial infections either alone or as adjuvants to other antibiotics.
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Liao B, Ye X, Chen X, Zhou Y, Cheng L, Zhou X, Ren B. The two-component signal transduction system and its regulation in Candida albicans. Virulence 2021; 12:1884-1899. [PMID: 34233595 PMCID: PMC8274445 DOI: 10.1080/21505594.2021.1949883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/13/2021] [Accepted: 06/18/2021] [Indexed: 02/08/2023] Open
Abstract
Candida albicans, which can cause superficial and life-threatening systemic infections, is the most common opportunistic fungal pathogen in the human microbiome. The two-component system is one of the most important C. albicans signal transduction pathways, regulating the response to oxidative and osmotic stresses, adhesion, morphogenesis, cell wall synthesis, virulence, drug resistance, and the host-pathogen interactions. Notably, some components of this signaling pathway have not been found in the human genome, indicating that the two-component system of C. albicans can be a potential target for new antifungal agents. Here, we summarize the composition, signal transduction, and regulation of the two-component system of C. albicans to emphasize its essential roles in the pathogenesis of C. albicans and the new therapeutic target for antifungal drugs.
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Affiliation(s)
- Biaoyou Liao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases& West China School of Stomatology, Sichuan University, Chengdu, China
| | - Xingchen Ye
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases& West China School of Stomatology, Sichuan University, Chengdu, China
| | - Xi Chen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases& West China School of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yujie Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases& West China School of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lei Cheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases& West China School of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases& West China School of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Biao Ren
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases& West China School of Stomatology, Sichuan University, Chengdu, China
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Zhao J, Zou L, Li Y, Liu X, Zeng C, Xu C, Jiang B, Guo X, Song X. HisPhosSite: A comprehensive database of histidine phosphorylated proteins and sites. J Proteomics 2021; 243:104262. [PMID: 33984507 DOI: 10.1016/j.jprot.2021.104262] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/14/2021] [Accepted: 05/03/2021] [Indexed: 01/15/2023]
Abstract
Histidine phosphorylation is critically important in a variety of cellular processes including signal transduction, cell cycle, proliferation, differentiation, and apoptosis. It is estimated to account for 6% of all phosphorylated amino acids. However, due to the acid lability of the PN bond, the study of pHis lags far behind that of pSer, pThr, and pTyr. Recently, the development and use of pHis-specific antibodies and methodologies have led to a resurgence in the study of histidine phosphorylation. Although a considerable number of pHis proteins and sites have been discovered, most of them have not been manually curated and integrated to any databases. There is a lack of a data repository for pHis, and such work is expected to help further systemic studies of pHis. Thus, we present a comprehensive resource database of histidine phosphorylation (HisPhosSite) by curating experimentally validated pHis proteins and sites and compiling putative pHis sites with ortholog search. HisPhosSite contains 776 verified pHis sites and 2702 verified pHis proteins in 38 eukaryotic and prokaryotic species and 15,378 putative pHis sites and 10,816 putative pHis proteins in 1366 species. HisPhosSite provides rich annotations of pHis sites and proteins and multiple search engines (including motif search and BLAST search) for users to locate pHis sites of interest. HisPhosSite is available at http://reprod.njmu.edu.cn/hisphossite. SIGNIFICANCE: Histidine phosphorylation is involved in a variety of cellular processes as well as cancers, and it has been proved to be more common than previously thought. The HisPhosSite database was developed to collect pHis data from published literatures with experimental evidences. Unification of the identified pHis proteins and sites will give researchers an informative resource for histidine phosphorylation. HisPhosSite has a user-friendly interface with multiple search engines for users to locate pHis sites of interest. In addition, the database provides rich structural and functional annotations. HisPhosSite will help future studies and elucidation of the functions of histidine phosphorylation.
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Affiliation(s)
- Jian Zhao
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Lingxiao Zou
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Yan Li
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Center of Pathology and Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Xiaofei Liu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Cong Zeng
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Chen Xu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Bin Jiang
- College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu 211166, China.
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China.
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Awais M, Hussain W, Khan YD, Rasool N, Khan SA, Chou KC. iPhosH-PseAAC: Identify Phosphohistidine Sites in Proteins by Blending Statistical Moments and Position Relative Features According to the Chou's 5-Step Rule and General Pseudo Amino Acid Composition. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:596-610. [PMID: 31144645 DOI: 10.1109/tcbb.2019.2919025] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Protein phosphorylation is one of the key mechanism in prokaryotes and eukaryotes and is responsible for various biological functions such as protein degradation, intracellular localization, the multitude of cellular processes, molecular association, cytoskeletal dynamics, and enzymatic inhibition/activation. Phosphohistidine (PhosH) has a key role in a number of biological processes, including central metabolism to signalling in eukaryotes and bacteria. Thus, identification of phosphohistidine sites in a protein sequence is crucial, and experimental identification can be expensive, time-taking, and laborious. To address this problem, here, we propose a novel computational model namely iPhosH-PseAAC for prediction of phosphohistidine sites in a given protein sequence using pseudo amino acid composition (PseAAC), statistical moments, and position relative features. The results of the proposed predictor are validated through self-consistency testing, 10-fold cross-validation, and jackknife testing. The self-consistency validation gave the 100 percent accuracy, whereas, for cross-validation, the accuracy achieved is 94.26 percent. Moreover, jackknife testing gave 97.07 percent accuracy for the proposed model. Thus, the proposed model iPhosH-PseAAC for prediction of iPhosH site has the great ability to predict the PhosH sites in given proteins.
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Rozenberg A, Oppermann J, Wietek J, Fernandez Lahore RG, Sandaa RA, Bratbak G, Hegemann P, Béjà O. Lateral Gene Transfer of Anion-Conducting Channelrhodopsins between Green Algae and Giant Viruses. Curr Biol 2020; 30:4910-4920.e5. [DOI: 10.1016/j.cub.2020.09.056] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/31/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022]
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Chen SK, Guan HH, Wu PH, Lin LT, Wu MC, Chang HY, Chen NC, Lin CC, Chuankhayan P, Huang YC, Lin PJ, Chen CJ. Structural insights into the histidine-containing phospho-transfer protein and receiver domain of sensor histidine kinase suggest a complex model in the two-component regulatory system in Pseudomonas aeruginosa. IUCRJ 2020; 7:934-948. [PMID: 32939285 PMCID: PMC7467158 DOI: 10.1107/s2052252520009665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
In Pseudomonas aeruginosa, an important opportunistic pathogen that causes numerous acute and chronic infections, the hybrid two-component system (TCS) regulates the swarming ability and biofilm formation with a multistep phospho-relay, and consists of hybrid-sensor histidine kinase (HK), histidine-containing phospho-transfer protein (Hpt) and response regulator (RR). In this work, two crystal structures of HptB and the receiver domain of HK PA1611 (PA1611REC) of P. aeruginosa have been determined in order to elucidate their interactions for the transfer of the phospho-ryl group. The structure of HptB folds into an elongated four-helix bundle - helices α2, α3, α4 and α5, covered by the short N-terminal helix α1. The imidazole side chain of the conserved active-site histidine residue His57, located near the middle of helix α3, protrudes from the bundle and is exposed to solvent. The structure of PA1611REC possesses a conventional (β/α)5 topology with five-stranded parallel β-sheets folded in the central region, surrounded by five α-helices. The divalent Mg2+ ion is located in the negatively charged active-site cleft and interacts with Asp522, Asp565 and Arg567. The HptB-PA1611REC complex is further modeled to analyze the binding surface and interactions between the two proteins. The model shows a shape complementarity between the convex surface of PA1611REC and the kidney-shaped HptB with fewer residues and a different network involved in interactions compared with other TCS complexes, such as SLN1-R1/YPD1 from Saccharomyces cerevisiae and AHK5RD/AHP1 from Arabidopsis thaliana. These structural results provide a better understanding of the TCS in P. aeruginosa and could potentially lead to the discovery of a new treatment for infection.
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Affiliation(s)
- Shao-Kang Chen
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City 701, Taiwan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Hong-Hsiang Guan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Pei-Hsun Wu
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Li-Ting Lin
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Meng-Chun Wu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City 701, Taiwan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Hwan-You Chang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Nai-Chi Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Chien-Chih Lin
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Phimonphan Chuankhayan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Yen-Chieh Huang
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Pei-Ju Lin
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chun-Jung Chen
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City 701, Taiwan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
- Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan
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Liu P, Wang S, Wang X, Yang X, Li Q, Wang C, Chen C, Shi Q, Ren Z, Wang L. Genome-wide characterization of two-component system (TCS) genes in melon (Cucumis melo L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 151:197-213. [PMID: 32229405 DOI: 10.1016/j.plaphy.2020.03.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/12/2020] [Accepted: 03/14/2020] [Indexed: 06/10/2023]
Abstract
To better understand cytokinin signaling in melon (Cucumis melo L.), one of the most important fruit crops in the Cucurbitaceae family, we identified and characterized melon two-component system (TCS) genes in this study. The results showed that there were 51 genes encoding putative TCS proteins in melon, and these TCS genes were classified into 3 subgroups, with 17 HK(L)s (histidine kinase/histidine-kinase like; 9 HKs and 8 HKLs), 9 HPs (histidine phosphotransfer proteins; 6 authentic and 3 pseudo), and 25 RRs (response regulators; 8 Type-A, 11 Type-B and 6 pseudo). The identity values of these cytokinin signaling proteins were revealed by analyzing their conserved motifs, domains and amino acid sequences. By analyzing TCS genes in different plant species, we found that melon HK(L)s, HPs and RRs had closer phylogenetic relationships with cucumber genes than with the genes of other plants, and the expansion of melon cytokinin signaling genes might be attributed to segmental duplication events. Analysis of the putative promoter regions (2-kb upstream regions of the start codon) revealed the enrichment of stress- and hormone-response cis-elements. The involvement of these putative TCS genes in melon cytokinin signaling was further supported by qRT-PCR data.
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Affiliation(s)
- Panjing Liu
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Shuoshuo Wang
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xiangfei Wang
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xiaoyu Yang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Qiang Li
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Chao Wang
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Chunhua Chen
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Qinghua Shi
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Zhonghai Ren
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.
| | - Lina Wang
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.
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12
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Ahmad B, Azeem F, Ali MA, Nawaz MA, Nadeem H, Abbas A, Batool R, Atif RM, Ijaz U, Nieves-Cordones M, Chung G. Genome-wide identification and expression analysis of two component system genes in Cicer arietinum. Genomics 2020; 112:1371-1383. [DOI: 10.1016/j.ygeno.2019.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/19/2019] [Accepted: 08/11/2019] [Indexed: 10/26/2022]
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13
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Wang FF, Qian W. The roles of histidine kinases in sensing host plant and cell-cell communication signal in a phytopathogenic bacterium. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180311. [PMID: 30967026 DOI: 10.1098/rstb.2018.0311] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
It has long been known that phytopathogenic bacteria react to plant-specific stimuli or environmental factors. However, how bacterial cells sense these environmental cues remains incompletely studied. Recently, three kinds of histidine kinases (HKs) were identified as receptors to perceive plant-associated or quorum-sensing signals. Among these kinases, HK VgrS detects iron depletion by binding to ferric iron via an ExxE motif, RpfC binds diffusible signal factor (DSF) by its N-terminal peptide and activates its autokinase activity through relaxation of autoinhibition, and PcrK specifically senses plant hormone-cytokinin and elicits bacterial responses to oxidative stress. These HKs are critical sensors that regulate the virulence of a Gram-negative bacterium, Xanthomonas campestris pv. campestris. Research progress on the signal perception of phytopathogenic bacterial HKs suggests that inter-kingdom signalling between host plants and pathogens controls pathogenesis and can be used as a potential molecular target to protect plants from bacterial diseases. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.
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Affiliation(s)
- Fang-Fang Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , People's Republic of China
| | - Wei Qian
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , People's Republic of China
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14
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Balakrishnan S, Ibrahim KS, Duraisamy S, Sivaji I, Kandasamy S, Kumarasamy A, Kumar NS. Antiquorum sensing and antibiofilm potential of biosynthesized silver nanoparticles of Myristica fragrans seed extract against MDR Salmonella enterica serovar Typhi isolates from asymptomatic typhoid carriers and typhoid patients. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:2844-2856. [PMID: 31836973 DOI: 10.1007/s11356-019-07169-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
Globally, Salmonella infection poses a major public health problem. Here, we report antibiofilm activity and quorum sensing inhibition of aqueous seeds extract of Myristica fragrans (nutmeg) and biosynthesized silver nanoparticles (AgNPs) against multidrug resistant (MDR) Salmonella enterica serovar Typhi (S. Typhi) isolated from typhoid patients and asymptomatic carriers. S. Typhi isolates revealed higher percentage (46%) of biofilm production identified by tissue culture plate (TCP) than Congo red agar (CRA) and tube adherence (TA) methods. The inhibition of biofilm-producing MDR S. Typhi isolates and pigment production of Chromobacterium violaceum (indicator bacteria) demonstrated the quorum sensing potential of nutmeg. The aqueous seed extract of nutmeg exhibited 87% of antibiofilm activity, while the biosynthesized AgNPs showed 99.1% of antibiofilm activity. Molecular docking studies of bioactive compounds of nutmeg against transcriptional regulatory protein RcsB and sensor kinase protein RcsC revealed interaction with the target proteins. It is proposed that biosynthesized AgNPs could be used as one of the effective candidates in treating asymptomatic typhoid carriers or typhoid patients and to control the subsistence of biofilm-producing S. Typhi strains or other pathogenic bacteria in the environment or industrial settings.
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Affiliation(s)
- Senthilkumar Balakrishnan
- Department of Medical Microbiology, College of Health and Medical Sciences, Haramaya University, Harar Campus, P.O. Box 235, Harar, Ethiopia.
| | - Kalibulla Syed Ibrahim
- PG and Research Department of Botany, PSG College of Arts & Science, Coimbatore, Tamil Nadu, 641014, India
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Senbagam Duraisamy
- Department of Marine Biotechnology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | - Ilakkia Sivaji
- Department of Biotechnology, Muthayammal College of Arts & Science, Rasipuram, Tamil Nadu, 637408, India
| | - Selvam Kandasamy
- PG & Research Department of Biotechnology, Mahendra Arts and Science College (Autonomous), Kalippatti, Tamil Nadu, 637501, India
| | - Anbarasu Kumarasamy
- Department of Marine Biotechnology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
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15
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Zhou Y, Liu X, Li C, Liu M, Jiang L, Liu Y. Chemical shift assignments of the catalytic and ATP-binding domain of HK853 from Thermotoga maritime. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:173-176. [PMID: 30673936 DOI: 10.1007/s12104-019-09872-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
HK853 is a transmembrane protein from Thermotoga maritime, which belongs to HK853/RR468 two-component signal transduction system (TCS) and acts as a sensor histidine kinase. HK853 is mainly composed of a transmembrane domain, dimerization and histidine-containing phosphotransfer domain (HK853DHp), catalytic and ATP-binding domain (HK853CA) and several linkers. HK853 can be completely autophosphorylated, which is the first step for signal transduction of TCS. HK853CA is an essential domain for its kinase function, since HK853CA could bind with ATP and convert it to ADP. Here, we report the backbone and part of side chain assignments of HK853CA. By analyzing the chemical shifts of HN, N, CO, Cα and Cβ, the secondary structure was predicted and contrasted with the published crystal structure of HK853CA. The result showed that our predicted structure could basically fit into the crystal structure. Thus, the chemical shift assignments of HK853CA are the starting point for further structural and dynamics study.
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Affiliation(s)
- Yuan Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, 430071, China
- Graduate University of Chinese Academy of Science, Beijing, 100049, China
| | - Xinghong Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, 430071, China
- Graduate University of Chinese Academy of Science, Beijing, 100049, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, 430071, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yixiang Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, 430071, China.
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16
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Nichols JME, Paschke P, Peak-Chew S, Williams TD, Tweedy L, Skehel M, Stephens E, Chubb JR, Kay RR. The Atypical MAP Kinase ErkB Transmits Distinct Chemotactic Signals through a Core Signaling Module. Dev Cell 2019; 48:491-505.e9. [PMID: 30612939 PMCID: PMC6397043 DOI: 10.1016/j.devcel.2018.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/15/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022]
Abstract
Signaling from chemoattractant receptors activates the cytoskeleton of crawling cells for chemotaxis. We show using phosphoproteomics that different chemoattractants cause phosphorylation of the same core set of around 80 proteins in Dictyostelium cells. Strikingly, the majority of these are phosphorylated at an [S/T]PR motif by the atypical MAP kinase ErkB. Unlike most chemotactic responses, ErkB phosphorylations are persistent and do not adapt to sustained stimulation with chemoattractant. ErkB integrates dynamic autophosphorylation with chemotactic signaling through G-protein-coupled receptors. Downstream, our phosphoproteomics data define a broad panel of regulators of chemotaxis. Surprisingly, targets are almost exclusively other signaling proteins, rather than cytoskeletal components, revealing ErkB as a regulator of regulators rather than acting directly on the motility machinery. ErkB null cells migrate slowly and orientate poorly over broad dynamic ranges of chemoattractant. Our data indicate a central role for ErkB and its substrates in directing chemotaxis.
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Affiliation(s)
- John M E Nichols
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; MRC Laboratory for Molecular Cell Biology, University College London, Gower St., London WC1E 6BT, UK.
| | - Peggy Paschke
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Cancer Research UK (CRUK) Beatson Institute, University of Glasgow, Bearsden, Glasgow G61 1BD, UK.
| | - Sew Peak-Chew
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Thomas D Williams
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Luke Tweedy
- Cancer Research UK (CRUK) Beatson Institute, University of Glasgow, Bearsden, Glasgow G61 1BD, UK
| | - Mark Skehel
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Elaine Stephens
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Pfizer Inc, 1 Burtt Road, Andover, MA 01810, USA
| | - Jonathan R Chubb
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower St., London WC1E 6BT, UK
| | - Robert R Kay
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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Kinome Expansion in the Fusarium oxysporum Species Complex Driven by Accessory Chromosomes. mSphere 2018; 3:3/3/e00231-18. [PMID: 29898984 PMCID: PMC6001611 DOI: 10.1128/msphere.00231-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/23/2018] [Indexed: 12/23/2022] Open
Abstract
Isolates of Fusarium oxysporum are adapted to survive a wide range of host and nonhost conditions. In addition, F. oxysporum was recently recognized as the top emerging opportunistic fungal pathogen infecting immunocompromised humans. The sensory and response networks of these fungi undoubtedly play a fundamental role in establishing the adaptability of this group. We have examined the kinomes of 12 F. oxysporum isolates and highlighted kinase families that distinguish F. oxysporum from other fungi, as well as different isolates from one another. The amplification of kinases involved in environmental signal relay and regulating downstream cellular responses clearly sets Fusarium apart from other Ascomycetes. Although the functions of many of these kinases are still unclear, their specific proliferation highlights them as a result of the evolutionary forces that have shaped this species complex and clearly marks them as targets for exploitation in order to combat disease. The Fusarium oxysporum species complex (FOSC) is a group of soilborne pathogens causing severe disease in more than 100 plant hosts, while individual strains exhibit strong host specificity. Both chromosome transfer and comparative genomics experiments have demonstrated that lineage-specific (LS) chromosomes contribute to the host-specific pathogenicity. However, little is known about the functional importance of genes encoded in these LS chromosomes. Focusing on signaling transduction, this study compared the kinomes of 12 F. oxysporum isolates, including both plant and human pathogens and 1 nonpathogenic biocontrol strain, with 7 additional publicly available ascomycete genomes. Overall, F. oxysporum kinomes are the largest, facilitated in part by the acquisitions of the LS chromosomes. The comparative study identified 99 kinases that are present in almost all examined fungal genomes, forming the core signaling network of ascomycete fungi. Compared to the conserved ascomycete kinome, the expansion of the F. oxysporum kinome occurs in several kinase families such as histidine kinases that are involved in environmental signal sensing and target of rapamycin (TOR) kinase that mediates cellular responses. Comparative kinome analysis suggests a convergent evolution that shapes individual F. oxysporum isolates with an enhanced and unique capacity for environmental perception and associated downstream responses. IMPORTANCE Isolates of Fusarium oxysporum are adapted to survive a wide range of host and nonhost conditions. In addition, F. oxysporum was recently recognized as the top emerging opportunistic fungal pathogen infecting immunocompromised humans. The sensory and response networks of these fungi undoubtedly play a fundamental role in establishing the adaptability of this group. We have examined the kinomes of 12 F. oxysporum isolates and highlighted kinase families that distinguish F. oxysporum from other fungi, as well as different isolates from one another. The amplification of kinases involved in environmental signal relay and regulating downstream cellular responses clearly sets Fusarium apart from other Ascomycetes. Although the functions of many of these kinases are still unclear, their specific proliferation highlights them as a result of the evolutionary forces that have shaped this species complex and clearly marks them as targets for exploitation in order to combat disease.
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18
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Wilke KE, Fihn CA, Carlson EE. Screening serine/threonine and tyrosine kinase inhibitors for histidine kinase inhibition. Bioorg Med Chem 2018; 26:5322-5326. [PMID: 29706527 DOI: 10.1016/j.bmc.2018.04.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 10/17/2022]
Abstract
Histidine kinases of bacterial two-component systems are promising antibacterial targets. Despite their varied, numerous roles, enzymes in the histidine kinase superfamily share a catalytic core that may be exploited to inhibit multiple histidine kinases simultaneously. Characterized by the Bergerat fold, the features of the histidine kinase ATP-binding domain are not found in serine/threonine and tyrosine kinases. However, because each kinase family binds the same ATP substrate, we sought to determine if published serine/threonine and tyrosine kinase inhibitors contained scaffolds that would also inhibit histidine kinases. Using select assays, 222 inhibitors from the Roche Published Kinase Set were screened for binding, deactivation, and aggregation of histidine kinases. Not only do the results of our screen support the distinctions between ATP-binding domains of different kinase families, but the lead molecule identified also presents inspiration for further histidine kinase inhibitor development.
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Affiliation(s)
- Kaelyn E Wilke
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, United States
| | - Conrad A Fihn
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN 55455, United States
| | - Erin E Carlson
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, United States; Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN 55455, United States; Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55454, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, United States; Department of Molecular and Cellular Biochemistry, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, United States.
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19
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Salas-Delgado G, Ongay-Larios L, Kawasaki-Watanabe L, López-Villaseñor I, Coria R. The yeasts phosphorelay systems: a comparative view. World J Microbiol Biotechnol 2017; 33:111. [PMID: 28470426 DOI: 10.1007/s11274-017-2272-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/25/2017] [Indexed: 12/23/2022]
Abstract
Cells contain signal transduction pathways that mediate communication between the extracellular environment and the cell interior. These pathways control transcriptional programs and posttranscriptional processes that modify cell metabolism in order to maintain homeostasis. One type of these signal transduction systems are the so-called Two Component Systems (TCS), which conduct the transfer of phosphate groups between specific and conserved histidine and aspartate residues present in at least two proteins; the first protein is a sensor kinase which autophosphorylates a histidine residue in response to a stimulus, this phosphate is then transferred to an aspartic residue located in a response regulator protein. There are classical and hybrid TCS, whose difference consists in the number of proteins and functional domains involved in the phosphorelay. The TCS are widespread in bacteria where the sensor and its response regulator are mostly specific for a given stimulus. In eukaryotic organisms such as fungi, slime molds, and plants, TCS are present as hybrid multistep phosphorelays, with a variety of arrangements (Stock et al. in Annu Rev Biochem 69:183-215, 2000; Wuichet et al. in Curr Opin Microbiol 292:1039-1050, 2010). In these multistep phosphorelay systems, several phosphotransfer events take place between different histidine and aspartate residues localized in specific domains present in more than two proteins (Thomason and Kay, in J Cell Sci 113:3141-3150, 2000; Robinson et al. in Nat Struct Biol 7:626-633, 2000). This review presents a brief and succinct description of the Two-component systems of model yeasts, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, Cryptococcus neoformans and Kluyveromyces lactis. We have focused on the comparison of domain organization and functions of each component present in these phosphorelay systems.
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Affiliation(s)
- Griselda Salas-Delgado
- Departamento de Genética Molecular, Instituto de FisiologíaCelular, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Laura Kawasaki-Watanabe
- Departamento de Genética Molecular, Instituto de FisiologíaCelular, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Imelda López-Villaseñor
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Roberto Coria
- Departamento de Genética Molecular, Instituto de FisiologíaCelular, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México.
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20
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Wang N, She Z, Ingar Z, Martic S, Kraatz HB. A Bioorganometallic Approach to Study Histidine Kinase Autophosphorylations. Chemistry 2017; 23:3152-3158. [PMID: 28081291 DOI: 10.1002/chem.201605253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Indexed: 12/12/2022]
Abstract
Auto-phosphorylation of bacterial histidine kinases PhoR, PhoQ, and EnvZ has been investigated using adenosine-5'-[γ-ferrocene] triphosphate (Fc-ATP) as a cosubstrate for the first time. The study has been carried out in solution and on surface. Results from biochemical multiplex assay and surface electrochemical/optical methods are consistent, which successfully demonstrates that Fc-ATP is an efficient cosubstrate for histidine kinase auto-phosphorylations. The study also has discovered that the concentration of Fc-ATP influences the autophosphorylation efficiency. This developed methodology will provide a powerful tool in studying such biological processes towards further understanding of the involved mechanism.
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Affiliation(s)
- Nan Wang
- Beijing Key Laboratory of Photoelectronic/, Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Zhe She
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
| | - Zakiyya Ingar
- Department of Physical and Environmental Science, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
| | - Sanela Martic
- Department of Chemistry, Oakland University, 2200 North Squirrel Road, Rochester, Michigan, 48309, USA
| | - Heinz-Bernhard Kraatz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
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21
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Adams FG. A key regulatory mechanism of antimicrobial resistance in pathogenic Acinetobacter baumannii. MICROBIOLOGY AUSTRALIA 2017. [DOI: 10.1071/ma17046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Acinetobacter baumannii is a Gram-negative bacterial pathogen that has become a pressing global health issue in recent decades. Although virulence factors for this pathogen have been identified, details of how they are regulated are largely unknown. One widely employed regulatory mechanism that bacteria, such as A. baumannii, have adopted is through two component signal transduction systems (TCS). TCS consist of two proteins; a histidine kinase and response regulator. The histidine kinase allows the bacterium to sense alterations in the extracellular milieu, transmitting the information to the response regulator which prompts the cell to modify gene expression levels accordingly. Bacteria can encode multiple TCS, where each system can mediate specific responses to particular conditions or stressors. Identifying those conditions in which these TCS are expressed, and the genes they regulate known as their ‘regulon', is vital for understanding how A. baumannii survives and persists within the hospital environment or the human host during infection. As we enter the post-antibiotic era, knowledge of TCS could prove to be invaluable, as they offer an alternative target for the treatment of multidrug resistant bacterial infections.
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Boibessot T, Zschiedrich CP, Lebeau A, Bénimèlis D, Dunyach-Rémy C, Lavigne JP, Szurmant H, Benfodda Z, Meffre P. The Rational Design, Synthesis, and Antimicrobial Properties of Thiophene Derivatives That Inhibit Bacterial Histidine Kinases. J Med Chem 2016; 59:8830-8847. [PMID: 27575438 DOI: 10.1021/acs.jmedchem.6b00580] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The emergence of multidrug-resistant bacteria emphasizes the urgent need for novel antibacterial compounds targeting unique cellular processes. Two-component signal transduction systems (TCSs) are commonly used by bacteria to couple environmental stimuli to adaptive responses, are absent in mammals, and are embedded in various pathogenic pathways. To attenuate these signaling pathways, we aimed to target the TCS signal transducer histidine kinase (HK) by focusing on their highly conserved adenosine triphosphate-binding domain. We used a structure-based drug design strategy that begins from an inhibitor-bound crystal structure and includes a significant number of structurally simplifiying "intuitive" modifications to arrive at the simple achiral, biaryl target structures. Thus, ligands were designed, leading to a series of thiophene derivatives. These compounds were synthesized and evaluated in vitro against bacterial HKs. We identified eight compounds with significant inhibitory activities against these proteins, two of which exhibited broad-spectrum antimicrobial activity. The compounds were also evaluated as adjuvants for the treatment of resistant bacteria. One compound was found to restore the sensivity of these bacteria to the respective antibiotics.
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Affiliation(s)
- Thibaut Boibessot
- EA7352 CHROME, Rue du Dr G. Salan, University of Nîmes , 30021 Nîmes cedex 1, France
| | - Christopher P Zschiedrich
- Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences , Pomona, California 91766, United States.,Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Alexandre Lebeau
- EA7352 CHROME, Rue du Dr G. Salan, University of Nîmes , 30021 Nîmes cedex 1, France
| | - David Bénimèlis
- EA7352 CHROME, Rue du Dr G. Salan, University of Nîmes , 30021 Nîmes cedex 1, France
| | - Catherine Dunyach-Rémy
- Institut National de la Santé et de la Recherche Médicale, U1047, Montpellier University , CHU de Nîmes, Place du Pr R. Debré, 30029 Nîmes, France
| | - Jean-Philippe Lavigne
- Institut National de la Santé et de la Recherche Médicale, U1047, Montpellier University , CHU de Nîmes, Place du Pr R. Debré, 30029 Nîmes, France
| | - Hendrik Szurmant
- Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences , Pomona, California 91766, United States.,Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Zohra Benfodda
- EA7352 CHROME, Rue du Dr G. Salan, University of Nîmes , 30021 Nîmes cedex 1, France.,IBMM, UMR-CNRS5247, Université de Montpellier , Place Eugène Bataillon, 34095 Montpellier, France
| | - Patrick Meffre
- EA7352 CHROME, Rue du Dr G. Salan, University of Nîmes , 30021 Nîmes cedex 1, France.,IBMM, UMR-CNRS5247, Université de Montpellier , Place Eugène Bataillon, 34095 Montpellier, France
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Atanelishvili I, Shirai Y, Akter T, Noguchi A, Ash KT, Misra S, Ghatak S, Silver RM, Bogatkevich GS. D1398G Variant of MET Is Associated with Impaired Signaling of Hepatocyte Growth Factor in Alveolar Epithelial Cells and Lung Fibroblasts. PLoS One 2016; 11:e0162357. [PMID: 27584154 PMCID: PMC5008815 DOI: 10.1371/journal.pone.0162357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 08/22/2016] [Indexed: 02/07/2023] Open
Abstract
Pulmonary fibrosis represents the terminal stage of a diverse group of lung diseases including scleroderma associated interstitial lung disease. The molecular mechanisms underlying the pathogenesis of lung fibrosis are not well understood and there is a great need for more effective treatment for this lethal disease. We recently discovered a small fragment of hepatocyte growth factor (HGF) receptor MET as a peptide designated “M10,” with strong antifibrotic properties. Furthermore, we showed that aspartic acid at position 1398 of MET is essential for M10 generation. The current study was undertaken to investigate the D1398G variant of MET in which aspartic acid at position 1398 was mutated to glycine resulting in loss of M10. We demonstrate that lung fibroblasts, A549, and primary alveolar epithelial cells (AEC) expressing D1398G MET exhibit reduced auto-phosphorylation on tyrosine residues and reduced activation of Ras and MAPK. HGF treatment of scleroderma lung fibroblasts as well as HGF treatment of TGFβ-treated normal lung fibroblasts transfected with wild type MET is associated with decreased collagen, connective tissue growth factor (CTGF, CCN2) and smooth muscle α-actin (SMA). However, HGF has no such effects in cells transfected with MET D1398G. Cisplatin- and FasL-induced apoptosis is significantly reduced in AEC transfected with MET wild type, but not in AEC transfected with MET D1398G. We conclude that the D1398G variant of MET is associated with compromised phosphorylation and impaired HGF signaling in lung fibroblasts and AEC, two cell types implicated in the pathogenesis of pulmonary fibrosis associated with scleroderma. Ongoing studies will explore the frequency of this variant and its relationship to pulmonary outcomes in scleroderma patients.
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Affiliation(s)
- Ilia Atanelishvili
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Yuichiro Shirai
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Department of Allergy and Rheumatology, Nippon Medical School, Tokyo, Japan
| | - Tanjina Akter
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Atsushi Noguchi
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Kurt T. Ash
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Suniti Misra
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Sibnath Ghatak
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Richard M. Silver
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Galina S. Bogatkevich
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
- * E-mail:
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24
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Alvarez AF, Barba-Ostria C, Silva-Jiménez H, Georgellis D. Organization and mode of action of two component system signaling circuits from the various kingdoms of life. Environ Microbiol 2016; 18:3210-3226. [DOI: 10.1111/1462-2920.13397] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/17/2016] [Accepted: 05/23/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Adrian F. Alvarez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México; 04510 México City, México
| | - Carlos Barba-Ostria
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México; 04510 México City, México
| | - Hortencia Silva-Jiménez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México; 04510 México City, México
| | - Dimitris Georgellis
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México; 04510 México City, México
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25
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Xiao Q, Miao B, Bi J, Wang Z, Li Y. Prioritizing functional phosphorylation sites based on multiple feature integration. Sci Rep 2016; 6:24735. [PMID: 27090940 PMCID: PMC4835696 DOI: 10.1038/srep24735] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/04/2016] [Indexed: 12/15/2022] Open
Abstract
Protein phosphorylation is an important type of post-translational modification that is involved in a variety of biological activities. Most phosphorylation events occur on serine, threonine and tyrosine residues in eukaryotes. In recent years, many phosphorylation sites have been identified as a result of advances in mass-spectrometric techniques. However, a large percentage of phosphorylation sites may be non-functional. Systematically prioritizing functional sites from a large number of phosphorylation sites will be increasingly important for the study of their biological roles. This study focused on exploring the intrinsic features of functional phosphorylation sites to predict whether a phosphosite is likely to be functional. We found significant differences in the distribution of evolutionary conservation, kinase association, disorder score, and secondary structure between known functional and background phosphorylation datasets. We built four different types of classifiers based on the most representative features and found that their performances were similar. We also prioritized 213,837 human phosphorylation sites from a variety of phosphorylation databases, which will be helpful for subsequent functional studies. All predicted results are available for query and download on our website (Predict Functional Phosphosites, PFP, http://pfp.biosino.org/).
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Affiliation(s)
- Qingyu Xiao
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Benpeng Miao
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Jie Bi
- University of Chinese Academy of Sciences, Beijing, P. R. China.,Key Lab of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Zhen Wang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Yixue Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, P. R. China
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26
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Yu PL, Chen LH, Chung KR. How the Pathogenic Fungus Alternaria alternata Copes with Stress via the Response Regulators SSK1 and SHO1. PLoS One 2016; 11:e0149153. [PMID: 26863027 PMCID: PMC4749125 DOI: 10.1371/journal.pone.0149153] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/27/2016] [Indexed: 01/06/2023] Open
Abstract
The tangerine pathotype of Alternaria alternata is a necrotrophic fungal pathogen causing brown spot disease on a number of citrus cultivars. To better understand the dynamics of signal regulation leading to oxidative and osmotic stress response and fungal infection on citrus, phenotypic characterization of the yeast SSK1 response regulator homolog was performed. It was determined that SSK1 responds to diverse environmental stimuli and plays a critical role in fungal pathogenesis. Experiments to determine the phenotypes resulting from the loss of SSK1 reveal that the SSK1 gene product may be fulfilling similar regulatory roles in signaling pathways involving a HOG1 MAP kinase during ROS resistance, osmotic resistance, fungicide sensitivity and fungal virulence. The SSK1 mutants display elevated sensitivity to oxidants, fail to detoxify H2O2 effectively, induce minor necrosis on susceptible citrus leaves, and displays resistance to dicarboximide and phenylpyrrole fungicides. Unlike the SKN7 response regulator, SSK1 and HOG1 confer resistance to salt-induced osmotic stress via an unknown kinase sensor rather than the “two component” histidine kinase HSK1. SSK1 and HOG1 play a moderate role in sugar-induced osmotic stress. We also show that SSK1 mutants are impaired in their ability to produce germ tubes from conidia, indicating a role for the gene product in cell differentiation. SSK1 also is involved in multi-drug resistance. However, deletion of the yeast SHO1 (synthetic high osmolarity) homolog resulted in no noticeable phenotypes. Nonetheless, our results show that A. alternata can sense and react to different types of stress via SSK1, HOG1 and SKN7 in a cooperative manner leading to proper physiological and pathological functions.
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Affiliation(s)
- Pei-Ling Yu
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung-Hsing University, Taichung, Taiwan
| | - Li-Hung Chen
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung-Hsing University, Taichung, Taiwan
| | - Kuang-Ren Chung
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung-Hsing University, Taichung, Taiwan
- * E-mail:
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27
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Surujon D, Ratner DI. Use of a Probabilistic Motif Search to Identify Histidine Phosphotransfer Domain-Containing Proteins. PLoS One 2016; 11:e0146577. [PMID: 26751210 PMCID: PMC4709007 DOI: 10.1371/journal.pone.0146577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/18/2015] [Indexed: 11/18/2022] Open
Abstract
The wealth of newly obtained proteomic information affords researchers the possibility of searching for proteins of a given structure or function. Here we describe a general method for the detection of a protein domain of interest in any species for which a complete proteome exists. In particular, we apply this approach to identify histidine phosphotransfer (HPt) domain-containing proteins across a range of eukaryotic species. From the sequences of known HPt domains, we created an amino acid occurrence matrix which we then used to define a conserved, probabilistic motif. Examination of various organisms either known to contain (plant and fungal species) or believed to lack (mammals) HPt domains established criteria by which new HPt candidates were identified and ranked. Search results using a probabilistic motif matrix compare favorably with data to be found in several commonly used protein structure/function databases: our method identified all known HPt proteins in the Arabidopsis thaliana proteome, confirmed the absence of such motifs in mice and humans, and suggests new candidate HPts in several organisms. Moreover, probabilistic motif searching can be applied more generally, in a manner both readily customized and computationally compact, to other protein domains; this utility is demonstrated by our identification of histones in a range of eukaryotic organisms.
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Affiliation(s)
- Defne Surujon
- Program in Biochemistry and Biophysics, Amherst College, Amherst, Massachusetts, United States of America
| | - David I. Ratner
- Program in Biochemistry and Biophysics, Amherst College, Amherst, Massachusetts, United States of America
- Department of Biology, Amherst College, Amherst, Massachusetts, United States of America
- * E-mail:
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28
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Ansell BRE, McConville MJ, Baker L, Korhonen PK, Young ND, Hall RS, Rojas CAA, Svärd SG, Gasser RB, Jex AR. Time-Dependent Transcriptional Changes in Axenic Giardia duodenalis Trophozoites. PLoS Negl Trop Dis 2015; 9:e0004261. [PMID: 26636323 PMCID: PMC4670223 DOI: 10.1371/journal.pntd.0004261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/03/2015] [Indexed: 12/27/2022] Open
Abstract
Giardia duodenalis is the most common gastrointestinal protozoan parasite of humans and a significant contributor to the global burden of both diarrheal disease and post-infectious chronic disorders. Although G. duodenalis can be cultured axenically, significant gaps exist in our understanding of the molecular biology and metabolism of this pathogen. The present study employed RNA sequencing to characterize the mRNA transcriptome of G. duodenalis trophozoites in axenic culture, at log (48 h of growth), stationary (60 h), and declining (96 h) growth phases. Using ~400-times coverage of the transcriptome, we identified 754 differentially transcribed genes (DTGs), mainly representing two large DTG groups: 438 that were down-regulated in the declining phase relative to log and stationary phases, and 281 that were up-regulated. Differential transcription of prominent antioxidant and glycolytic enzymes implicated oxygen tension as a key factor influencing the transcriptional program of axenic trophozoites. Systematic bioinformatic characterization of numerous DTGs encoding hypothetical proteins of unknown function was achieved using structural homology searching. This powerful approach greatly informed the differential transcription analysis and revealed putative novel antioxidant-coding genes, and the presence of a near-complete two-component-like signaling system that may link cytosolic redox or metabolite sensing to the observed transcriptional changes. Motif searching applied to promoter regions of the two large DTG groups identified different putative transcription factor-binding motifs that may underpin global transcriptional regulation. This study provides new insights into the drivers and potential mediators of transcriptional variation in axenic G. duodenalis and provides context for static transcriptional studies. Giardia is the most common gastrointestinal protozoan parasite of humans. This parasite causes diarrheal disease and is correlated with post-infectious conditions such as irritable bowel syndrome. In the absence of a vaccine, treatment is limited to drugs such as metronidazole, against which clinical resistance is reported. Effective control of Giardia requires a detailed understanding of its biology, and in turn, complete characterization of the standard in vitro culture system. Using RNA sequencing assisted by informatics to functionally annotate hypothetical proteins, we investigated transcriptional changes in axenic Giardia trophozoites at three growth phases over 96 hours. We found two large groups of differentially transcribed genes that indicate changes in the antioxidant system and central carbon metabolism over time. A putative novel signaling pathway may act together with putative transcription factor-binding motifs to regulate these transcriptional changes. Our results suggest that dissolved oxygen in Giardia culture medium may cause oxidative stress early during in vitro growth and that oxygen depletion may limit the efficiency of glycolysis in the declining phase. This work enhances our understanding of the transcriptional flexibility and metabolism of Giardia in vitro.
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Affiliation(s)
- Brendan R. E. Ansell
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
| | - Malcolm J. McConville
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Louise Baker
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Ross S. Hall
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Cristian A. A. Rojas
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Staffan G. Svärd
- Department of Cell & Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Aaron R. Jex
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
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29
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Salvado B, Vilaprinyo E, Sorribas A, Alves R. A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes. PeerJ 2015; 3:e1183. [PMID: 26339559 PMCID: PMC4558063 DOI: 10.7717/peerj.1183] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/23/2015] [Indexed: 12/17/2022] Open
Abstract
Two Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS/PR proteins in order to identify the various topologies used by nature and enable a systematic study of the dynamics associated with those topologies. To create such a census, we analyzed the proteomes of 7,609 organisms from all domains of life with fully sequenced and annotated genomes. To begin, we survey each proteome searching for proteins containing domains that are associated with internal signal transmission within TCS/PR: Histidine Kinase (HK), Response Regulator (RR) and Histidine Phosphotranfer (HPt) domains, and analyze how these domains are arranged in the individual proteins. Then, we find all types of operon organization and calculate how much more likely are proteins that contain TCS/PR domains to be coded by neighboring genes than one would expect from the genome background of each organism. Finally, we analyze if the fusion of domains into single TCS/PR proteins is more frequently observed than one might expect from the background of each proteome. We find 50 alternative ways in which the HK, HPt, and RR domains are observed to organize into single proteins. In prokaryotes, TCS/PR coding genes tend to be clustered in operons. 90% of all proteins identified in this study contain just one of the three domains, while 8% of the remaining proteins combine one copy of an HK, a RR, and/or an HPt domain. In eukaryotes, 25% of all TCS/PR proteins have more than one domain. These results might have implications for how signals are internally transmitted within TCS/PR cascades. These implications could explain the selection of the various designs in alternative circumstances.
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Affiliation(s)
- Baldiri Salvado
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida , Lleida, Catalonya , Spain
| | - Ester Vilaprinyo
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida , Lleida, Catalonya , Spain ; IRBLleida , Lleida, Catalonya , Spain
| | - Albert Sorribas
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida , Lleida, Catalonya , Spain
| | - Rui Alves
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida , Lleida, Catalonya , Spain
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30
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Osmosensing and osmoregulation in unicellular eukaryotes. World J Microbiol Biotechnol 2015; 31:435-43. [DOI: 10.1007/s11274-015-1811-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/27/2015] [Indexed: 10/24/2022]
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31
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Wilke K, Francis S, Carlson EE. Inactivation of multiple bacterial histidine kinases by targeting the ATP-binding domain. ACS Chem Biol 2015; 10:328-35. [PMID: 25531939 PMCID: PMC4301073 DOI: 10.1021/cb5008019] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 12/19/2014] [Indexed: 01/14/2023]
Abstract
Antibacterial agents that exploit new targets will be required to combat the perpetual rise of bacterial resistance to current antibiotics. We are exploring the inhibition of histidine kinases, constituents of two-component systems. Two-component systems are the primary signaling pathways that bacteria utilize to respond to their environment. They are ubiquitous in bacteria and trigger various pathogenic mechanisms. To attenuate these signaling pathways, we sought to broadly target the histidine kinase family by focusing on their highly conserved ATP-binding domain. Development of a fluorescence polarization displacement assay facilitated high-throughput screening of ∼53 000 diverse small molecules for binding to the ATP-binding pocket. Of these compounds, nine inhibited the catalytic activity of two or more histidine kinases. These scaffolds could provide valuable starting points for the design of broadly effective HK inhibitors, global reduction of bacterial signaling, and ultimately, a class of antibiotics that function by a new mechanism of action.
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Affiliation(s)
- Kaelyn
E. Wilke
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Samson Francis
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Erin E. Carlson
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
- Department
of Molecular and Cellular Biochemistry, Indiana University, 212 South Hawthorne Drive, Bloomington, Indiana 47405, United States
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32
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Bem AE, Velikova N, Pellicer MT, Baarlen PV, Marina A, Wells JM. Bacterial histidine kinases as novel antibacterial drug targets. ACS Chem Biol 2015; 10:213-24. [PMID: 25436989 DOI: 10.1021/cb5007135] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bacterial histidine kinases (HKs) are promising targets for novel antibacterials. Bacterial HKs are part of bacterial two-component systems (TCSs), the main signal transduction pathways in bacteria, regulating various processes including virulence, secretion systems and antibiotic resistance. In this review, we discuss the biological importance of TCSs and bacterial HKs for the discovery of novel antibacterials, as well as published TCS and HK inhibitors that can be used as a starting point for structure-based approaches to develop novel antibacterials.
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Affiliation(s)
- Agnieszka E. Bem
- Host−Microbe
Interactomics, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
| | - Nadya Velikova
- Instituto
de Biomedicina
de Valencia-Consejo Superior de Investigaciones Cientificas (IBV-CSIC), Jaume Roig 11, 46010-Valencia, Spain
| | - M. Teresa Pellicer
- R&D Department Interquim, Ferrer HealthTech, Joan Buscalla 10, 08137-Sant Cugat del Valles Barcelona, Spain
| | - Peter van Baarlen
- Host−Microbe
Interactomics, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
| | - Alberto Marina
- Instituto
de Biomedicina
de Valencia-Consejo Superior de Investigaciones Cientificas (IBV-CSIC), Jaume Roig 11, 46010-Valencia, Spain
- Centro de Investigacion
Biomedica en Red de Enfermedades Raras (CIBER-ISCIII), Jaume Roig 11, 46010-Valencia, Spain
| | - Jerry M. Wells
- Host−Microbe
Interactomics, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
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33
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Komis G, Takáč T, Bekešová S, Vadovič P, Samaj J. Affinity-based SDS PAGE identification of phosphorylated Arabidopsis MAPKs and substrates by acrylamide pendant Phos-Tag™. Methods Mol Biol 2014; 1171:47-63. [PMID: 24908119 DOI: 10.1007/978-1-4939-0922-3_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Protein phosphorylation is the most abundant and best studied protein posttranslational modification, dedicated to the regulation of protein function and subcellular localization as well as to protein-protein interactions. Identification and quantitation of the dynamic, conditional protein phosphorylation can be achieved by either metabolic labeling of the protein of interest with (32)P-labeled ATP followed by autoradiographic analysis, the use of specific monoclonal or polyclonal antibodies against the phosphorylated protein species and finally by phosphoproteome delineation using mass spectrometry.Hereby we present a fourth alternative which relies on the enforced-affinity-based-electrophoretic separation of phosphorylated from non-phosphorylated protein species by standard SDS-PAGE systems co-polymerized with Phos-Tag™ and Mn(2+) or Zn(2+) cations. Phosphate groups of phosphorylated Ser, Thr, and Tyr residues form complexes with Mn(2+) and Zn(2+) cations with polyacrylamide immobilized Phos-Tag™. Following appropriate treatment of the gels, separated proteins can be quantitatively transferred to PVDF or nitrocellulose membranes and probed with common-not phosphorylation state specific-antibodies and delineate the occurrence of a certain phosphoprotein species against its non-phosphorylated counterpart.
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Affiliation(s)
- George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 11, 783 71, Olomouc, Czech Republic,
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34
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Chung KR. Stress Response and Pathogenicity of the Necrotrophic Fungal Pathogen Alternaria alternata. SCIENTIFICA 2012; 2012:635431. [PMID: 24278721 PMCID: PMC3820455 DOI: 10.6064/2012/635431] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 10/03/2012] [Indexed: 05/07/2023]
Abstract
The production of host-selective toxins by the necrotrophic fungus Alternaria alternata is essential for the pathogenesis. A. alternata infection in citrus leaves induces rapid lipid peroxidation, accumulation of hydrogen peroxide (H2O2), and cell death. The mechanisms by which A. alternata avoids killing by reactive oxygen species (ROS) after invasion have begun to be elucidated. The ability to coordinate of signaling pathways is essential for the detoxification of cellular stresses induced by ROS and for pathogenicity in A. alternata. A low level of H2O2, produced by the NADPH oxidase (NOX) complex, modulates ROS resistance and triggers conidiation partially via regulating the redox-responsive regulators (YAP1 and SKN7) and the mitogen-activated protein (MAP) kinase (HOG1) mediated pathways, which subsequently regulate the genes required for the biosynthesis of siderophore, an iron-chelating compound. Siderophore-mediated iron acquisition plays a key role in ROS detoxification because of the requirement of iron for the activities of antioxidants (e.g., catalase and SOD). Fungal strains impaired for the ROS-detoxifying system severely reduce the virulence on susceptible citrus cultivars. This paper summarizes the current state of knowledge of signaling pathways associated with cellular responses to multidrugs, oxidative and osmotic stress, and fungicides, as well as the pathogenicity/virulence in the tangerine pathotype of A. alternata.
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Affiliation(s)
- Kuang-Ren Chung
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL 32611, USA
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35
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Lavín JL, García-Yoldi A, Ramírez L, Pisabarro AG, Oguiza JA. Two-component signal transduction in Agaricus bisporus: a comparative genomic analysis with other basidiomycetes through the web-based tool BASID2CS. Fungal Genet Biol 2012; 55:77-84. [PMID: 23123423 DOI: 10.1016/j.fgb.2012.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 09/28/2012] [Accepted: 09/29/2012] [Indexed: 11/16/2022]
Abstract
Two-component systems (TCSs) are signal transduction mechanisms present in many eukaryotes, including fungi that play essential roles in the regulation of several cellular functions and responses. In this study, we carry out a genomic analysis of the TCS proteins in two varieties of the white button mushroom Agaricus bisporus. The genomes of both A. bisporus varieties contain eight genes coding for TCS proteins, which include four hybrid Histidine Kinases (HKs), a single histidine-containing phosphotransfer (HPt) protein and three Response Regulators (RRs). Comparison of the TCS proteins among A. bisporus and the sequenced basidiomycetes showed a conserved core complement of five TCS proteins including the Tco1/Nik1 hybrid HK, HPt protein and Ssk1, Skn7 and Rim15-like RRs. In addition, Dual-HKs, unusual hybrid HKs with 2 HK and 2 RR domains, are absent in A. bisporus and are limited to various species of basidiomycetes. Differential expression analysis showed no significant up- or down-regulation of the Agaricus TCS genes in the conditions/tissue analyzed with the exception of the Skn7-like RR gene (Agabi_varbisH97_2|198669) that is significantly up-regulated on compost compared to cultured mycelia. Furthermore, the pipeline web server BASID2CS (http://bioinformatics.unavarra.es:1000/B2CS/BASID2CS.htm) has been specifically designed for the identification, classification and functional annotation of putative TCS proteins from any predicted proteome of basidiomycetes using a combination of several bioinformatic approaches.
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Affiliation(s)
- José L Lavín
- Genetics and Microbiology Research Group, Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Spain
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Schippers JHM, Nguyen HM, Lu D, Schmidt R, Mueller-Roeber B. ROS homeostasis during development: an evolutionary conserved strategy. Cell Mol Life Sci 2012; 69:3245-57. [PMID: 22842779 PMCID: PMC11114851 DOI: 10.1007/s00018-012-1092-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 07/09/2012] [Accepted: 07/09/2012] [Indexed: 12/22/2022]
Abstract
The balance between cellular proliferation and differentiation is a key aspect of development in multicellular organisms. Recent studies on Arabidopsis roots revealed distinct roles for different reactive oxygen species (ROS) in these processes. Modulation of the balance between ROS in proliferating cells and elongating cells is controlled at least in part at the transcriptional level. The effect of ROS on proliferation and differentiation is not specific for plants but appears to be conserved between prokaryotic and eukaryotic life forms. The ways in which ROS is received and how it affects cellular functioning is discussed from an evolutionary point of view. The different redox-sensing mechanisms that evolved ultimately result in the activation of gene regulatory networks that control cellular fate and decision-making. This review highlights the potential common origin of ROS sensing, indicating that organisms evolved similar strategies for utilizing ROS during development, and discusses ROS as an ancient universal developmental regulator.
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Affiliation(s)
- Jos H. M. Schippers
- Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Hung M. Nguyen
- Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Dandan Lu
- Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Romy Schmidt
- Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Bernd Mueller-Roeber
- Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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López E, Wang X, Madero L, López-Pascual J, Latterich M. Functional phosphoproteomic mass spectrometry-based approaches. Clin Transl Med 2012; 1:20. [PMID: 23369623 PMCID: PMC3560980 DOI: 10.1186/2001-1326-1-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 08/20/2012] [Indexed: 01/25/2023] Open
Abstract
Mass Spectrometry (MS)-based phosphoproteomics tools are crucial for understanding the structure and dynamics of signaling networks. Approaches such as affinity purification followed by MS have also been used to elucidate relevant biological questions in health and disease. The study of proteomes and phosphoproteomes as linked systems, rather than research studies of individual proteins, are necessary to understand the functions of phosphorylated and un-phosphorylated proteins under spatial and temporal conditions. Phosphoproteome studies also facilitate drug target protein identification which may be clinically useful in the near future. Here, we provide an overview of general principles of signaling pathways versus phosphorylation. Likewise, we detail chemical phosphoproteomic tools, including pros and cons with examples where these methods have been applied. In addition, basic clues of electrospray ionization and collision induced dissociation fragmentation are detailed in a simple manner for successful phosphoproteomic clinical studies.
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Affiliation(s)
- Elena López
- Hospital Universitario Niño Jesús, Av, Menéndez Pelayo 65, 28009, Madrid, Spain.
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38
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Pyysalo S, Ohta T, Rak R, Sullivan D, Mao C, Wang C, Sobral B, Tsujii J, Ananiadou S. Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC Bioinformatics 2012; 13 Suppl 11:S2. [PMID: 22759456 PMCID: PMC3384257 DOI: 10.1186/1471-2105-13-s11-s2] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We present the preparation, resources, results and analysis of three tasks of the BioNLP Shared Task 2011: the main tasks on Infectious Diseases (ID) and Epigenetics and Post-translational Modifications (EPI), and the supporting task on Entity Relations (REL). The two main tasks represent extensions of the event extraction model introduced in the BioNLP Shared Task 2009 (ST'09) to two new areas of biomedical scientific literature, each motivated by the needs of specific biocuration tasks. The ID task concerns the molecular mechanisms of infection, virulence and resistance, focusing in particular on the functions of a class of signaling systems that are ubiquitous in bacteria. The EPI task is dedicated to the extraction of statements regarding chemical modifications of DNA and proteins, with particular emphasis on changes relating to the epigenetic control of gene expression. By contrast to these two application-oriented main tasks, the REL task seeks to support extraction in general by separating challenges relating to part-of relations into a subproblem that can be addressed by independent systems. Seven groups participated in each of the two main tasks and four groups in the supporting task. The participating systems indicated advances in the capability of event extraction methods and demonstrated generalization in many aspects: from abstracts to full texts, from previously considered subdomains to new ones, and from the ST'09 extraction targets to other entities and events. The highest performance achieved in the supporting task REL, 58% F-score, is broadly comparable with levels reported for other relation extraction tasks. For the ID task, the highest-performing system achieved 56% F-score, comparable to the state-of-the-art performance at the established ST'09 task. In the EPI task, the best result was 53% F-score for the full set of extraction targets and 69% F-score for a reduced set of core extraction targets, approaching a level of performance sufficient for user-facing applications. In this study, we extend on previously reported results and perform further analyses of the outputs of the participating systems. We place specific emphasis on aspects of system performance relating to real-world applicability, considering alternate evaluation metrics and performing additional manual analysis of system outputs. We further demonstrate that the strengths of extraction systems can be combined to improve on the performance achieved by any system in isolation. The manually annotated corpora, supporting resources, and evaluation tools for all tasks are available from http://www.bionlp-st.org and the tasks continue as open challenges for all interested parties.
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Affiliation(s)
- Sampo Pyysalo
- School of Computer Science, University of Manchester, Manchester, UK
- National Centre for Text Mining, University of Manchester, Manchester, UK
| | - Tomoko Ohta
- Department of Computer Science, University of Tokyo, Tokyo, Japan
| | - Rafal Rak
- School of Computer Science, University of Manchester, Manchester, UK
- National Centre for Text Mining, University of Manchester, Manchester, UK
| | - Dan Sullivan
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Chunhong Mao
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Chunxia Wang
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Bruno Sobral
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Sophia Ananiadou
- School of Computer Science, University of Manchester, Manchester, UK
- National Centre for Text Mining, University of Manchester, Manchester, UK
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Gao S, Xu S, Fang Y, Fang J. Using multitask classification methods to investigate the kinase-specific phosphorylation sites. Proteome Sci 2012; 10 Suppl 1:S7. [PMID: 22759584 PMCID: PMC3380725 DOI: 10.1186/1477-5956-10-s1-s7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Identification of phosphorylation sites by computational methods is becoming increasingly important because it reduces labor-intensive and costly experiments and can improve our understanding of the common properties and underlying mechanisms of protein phosphorylation. Methods A multitask learning framework for learning four kinase families simultaneously, instead of studying each kinase family of phosphorylation sites separately, is presented in the study. The framework includes two multitask classification methods: the Multi-Task Least Squares Support Vector Machines (MTLS-SVMs) and the Multi-Task Feature Selection (MT-Feat3). Results Using the multitask learning framework, we successfully identify 18 common features shared by four kinase families of phosphorylation sites. The reliability of selected features is demonstrated by the consistent performance in two multi-task learning methods. Conclusions The selected features can be used to build efficient multitask classifiers with good performance, suggesting they are important to protein phosphorylation across 4 kinase families.
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Affiliation(s)
- Shan Gao
- Applied Bioinformatics Laboratory, Kansas University, 2034 Becker Dr,, Lawrence, KS 66047, USA.
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Xu Y, Teng D, Lei Y. MinePhos: a literature mining system for protein phoshphorylation information extraction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012; 9:311-315. [PMID: 21576755 DOI: 10.1109/tcbb.2011.85] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The rapid growth of scientific literature calls for automatic and efficient ways to facilitate extracting experimental data on protein phosphorylation. Such information is of great value for biologists in studying cellular processes and diseases such as cancer and diabetes. Existing approaches like RLIMS-P are mainly rule based. The performance lays much reliance on the completeness of rules. We propose an SVM-based system known as MinePhos which outperforms RLIMS-P in both precision and recall of information extraction when tested on a set of articles randomly chosen from PubMed.
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Affiliation(s)
- Yun Xu
- University of Science and Technology of China, Hefei and Anhui Province Key Laboratory of High Performance Computing, Hefei
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41
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Zhou G, Wang J, Qiu L, Feng MG. A Group III histidine kinase (mhk1) upstream of high-osmolarity glycerol pathway regulates sporulation, multi-stress tolerance and virulence of Metarhizium robertsii, a fungal entomopathogen. Environ Microbiol 2011; 14:817-29. [PMID: 22118192 DOI: 10.1111/j.1462-2920.2011.02643.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role of Metarhizium robertsii Group III histidine kinase (mhk1) in regulating various phenotypes of the fungal entomopathogen and the transcripts of 25 downstream genes likely associated with the phenotypes were probed by constructing Δmhk1 and Δmhk1/mhk1 mutants. All examined Δmhk1 phenotypes except unchanged sensitivity to fungicide (dimethachlon) differed significantly from those of wild type and Δmhk1/mhk1, which were similar to each other. Significant phenotypic changes in Δmhk1 included increased conidial yields on two media, increased tolerance to H(2)O(2) , decreased tolerance to menadione, increased tolerance to hyperosmolarity, increased conidial thermotolerance, decreased conidial UV-B resistance and reduced virulence to Tenebrio molitor larvae. The mhk1 disruption elevated the transcripts of nine genes, including two associated with conidiation (flbC and hymA) and three encoding catalases but decreased seven other gene transcripts, including three for superoxide dismultases, under normal conditions. The high-osmolarity glycerol pathway MAPK phosphorylation level in Δmhk1 culture was increased 1.0- to 1.8-fold by KCl, sucrose and menadione stresses but reduced drastically by H(2)O(2) or heat (40°C) stress, accompanied with different transcript patterns of all examined genes under the stresses. Our results confirmed the crucial role of mhk1 in regulating the expression of the downstream genes and associated phenotypes important for the fungal biocontrol potential.
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Affiliation(s)
- Gang Zhou
- Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
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42
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Tang Y, Sheng X, Stumpf MPH. The roles of contact residue disorder and domain composition in characterizing protein-ligand binding specificity and promiscuity. MOLECULAR BIOSYSTEMS 2011; 7:3280-6. [PMID: 22002096 DOI: 10.1039/c1mb05325f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Most protein chains interact with only one ligand but a small number of protein chains can bind several ligands, and many examples are available in the protein-ligand complex database of PDB. Among these proteins, some show preferences for the ligands or types of ligands they bind; however, so far we have only poor understanding of what determines protein-ligand binding and its specificity. Here we investigate the structural and functional properties of proteins in protein-ligand complexes. Analysis of the protein-ligand complex dataset from the PDB structure database reveals that proteins with more interactions have more disordered contact residues. Those proteins containing few disordered contact residues that bind multiple ligands have a tendency to consist of several domains. Analysis of physicochemical properties of hub contact residues binding multiple ligands indicates that they are enriched for hydrophilic, charged, polar and His-Asp catalytic triad residues. Finally, in order to differentiate proteins binding different classes of ligands, we mapped the three most prominent classes of ligands onto different superfamily domains. Our results demonstrate that contact residue disorder and ordered multiple domains are complementary factors that play a crucial role in determining ligand binding specificity and promiscuity.
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Affiliation(s)
- Yurong Tang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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Buschart A, Gremmer K, El-Mowafy M, van den Heuvel J, Mueller PP, Bilitewski U. A novel functional assay for fungal histidine kinases group III reveals the role of HAMP domains for fungicide sensitivity. J Biotechnol 2011; 157:268-77. [PMID: 21963586 DOI: 10.1016/j.jbiotec.2011.09.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/24/2011] [Accepted: 09/16/2011] [Indexed: 11/25/2022]
Abstract
Signal transduction systems comprising histidine kinases are suggested as new molecular targets of antibiotics. The important human fungal pathogen Candida albicans possesses three histidine kinases, one of which is the type III histidine kinase CaNik1, which activates the MAP kinase Hog1. We established a screening system for inhibitors of this class of histidine kinases by functional expression of the CaNIK1 gene in S. cerevisiae. This transformant was susceptible to fungicides to which the wild type strain was resistant, such as fludioxonil and ambruticin. Growth inhibition correlated with phosphorylation of Hog1 and was dependent on an intact Hog1 pathway. At the N-terminus the histidine kinase CaNik1 has four amino acid repeats of 92 amino acids each and one truncated repeat of 72 amino acids. Within these repeats we identified 9 HAMP domains with a paired structure. We constructed mutants in which one or two pairs of these domains were deleted. S. cerevisiae transformants expressing the full-length CaNIK1 showed the highest sensitivity to the fungicides, any truncation reduced the susceptibility of the transformants to the fungicides. This indicates that the HAMP domains are decisive for the mode of action of the antifungal compounds.
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Affiliation(s)
- Anna Buschart
- Helmholtz Centre for Infection Research, Department of Biological Systems Analysis, Inhoffenstr.7, 38124 Braunschweig, Germany
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Weber B, Lindell K, El Qaidi S, Hjerde E, Willassen NP, Milton DL. The phosphotransferase VanU represses expression of four qrr genes antagonizing VanO-mediated quorum-sensing regulation in Vibrio anguillarum. MICROBIOLOGY-SGM 2011; 157:3324-3339. [PMID: 21948044 PMCID: PMC3352281 DOI: 10.1099/mic.0.051011-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Vibrio anguillarum utilizes quorum sensing to regulate stress responses required for survival in the aquatic environment. Like other Vibrio species, V. anguillarum contains the gene qrr1, which encodes the ancestral quorum regulatory RNA Qrr1, and phosphorelay quorum-sensing systems that modulate the expression of small regulatory RNAs (sRNAs) that destabilize mRNA encoding the transcriptional regulator VanT. In this study, three additional Qrr sRNAs were identified. All four sRNAs were positively regulated by σ54 and the σ54-dependent response regulator VanO, and showed a redundant activity. The Qrr sRNAs, together with the RNA chaperone Hfq, destabilized vanT mRNA and modulated expression of VanT-regulated genes. Unexpectedly, expression of all four qrr genes peaked at high cell density, and exogenously added N-acylhomoserine lactone molecules induced expression of the qrr genes at low cell density. The phosphotransferase VanU, which phosphorylates and activates VanO, repressed expression of the Qrr sRNAs and stabilized vanT mRNA. A model is presented proposing that VanU acts as a branch point, aiding cross-regulation between two independent phosphorelay systems that activate or repress expression of the Qrr sRNAs, giving flexibility and precision in modulating VanT expression and inducing a quorum-sensing response to stresses found in a constantly changing aquatic environment.
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Affiliation(s)
- Barbara Weber
- Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-901 87, Sweden
| | - Kristoffer Lindell
- Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-901 87, Sweden
| | - Samir El Qaidi
- Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-901 87, Sweden
| | - Erik Hjerde
- Department of Chemistry, Faculty of Science and Technology, University of Tromsø, Tromsø 9037, Norway
| | - Nils-Peder Willassen
- Department of Chemistry, Faculty of Science and Technology, University of Tromsø, Tromsø 9037, Norway
| | - Debra L Milton
- Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-901 87, Sweden
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Yago JI, Lin CH, Chung KR. The SLT2 mitogen-activated protein kinase-mediated signalling pathway governs conidiation, morphogenesis, fungal virulence and production of toxin and melanin in the tangerine pathotype of Alternaria alternata. MOLECULAR PLANT PATHOLOGY 2011; 12:653-65. [PMID: 21726368 PMCID: PMC6640243 DOI: 10.1111/j.1364-3703.2010.00701.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Fungi respond and adapt to different environmental stimuli via signal transduction systems. We determined the function of a yeast SLT2 mitogen-activated protein (MAP) kinase homologue (AaSLT2) in Alternaria alternata, the fungal pathogen of citrus. Analysis of the loss-of-function mutant indicated that AaSLT2 is required for the production of a host-selective toxin, and is crucial for fungal pathogenicity. Moreover, the A. alternata slt2 mutants displayed hypersensitivity to cell wall-degrading enzymes and chemicals such as Calcofluor white and Congo red. This implicates an important role of AaSLT2 in the maintenance of cell wall integrity in A. alternata. The A. alternata slt2 mutants were also hypersensitive to a heteroaromatic compound, 2-chloro-5-hydroxypyridine, and a plant growth regulator, 2,3,5-triiodobenzoic acid. Developmentally, the AaSLT2 gene product was shown to be critical for conidial formation and hyphal elongation. Compared with the wild-type, the mutants produced fewer but slightly larger conidia with less transverse septae. The mutants also accumulated lower levels of melanin and chitin. Unlike the wild-type progenitor, the A. alternata slt2 mutants produced globose, swollen hyphae that did not elongate in a straight radial direction. All defective phenotypes in the mutant were restored by transformation and expression of a wild-type copy of AaSLT2 under the control of its endogenous promoter. This study highlights an important role of the AaSLT2 MAP kinase-mediated signalling pathway, regulating diverse physiological, developmental and pathological functions, in the tangerine pathotype of A. alternata.
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Affiliation(s)
- Jonar Ingan Yago
- Citrus Research and Education Center and Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850, USA
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Abstract
Phosphorylation of proteins is an essential signalling mechanism in eukaryotic and prokaryotic cells. Although N-phosphorylation of basic amino acid is known for its importance in biological systems, it is still poorly explored in terms of products and mechanisms. In the present study, two MS fragmentation methods, ECD (electron-capture dissociation) and CID (collision-induced dissociation), were tested as tools for analysis of N-phosphorylation of three model peptides, RKRSRAE, RKRARKE and PLSRTLSVAAKK. The peptides were phosphorylated by reaction with monopotassium phosphoramidate. The results were confirmed by 1H NMR and 31P NMR studies. The ECD method was found useful for the localization of phosphorylation sites in unstable lysine-phosphorylated peptides. Its main advantage is a significant reduction of the neutral losses related to the phosphoramidate moiety. Moreover, the results indicate that the ECD–MS may be useful for analysis of regioselectivity of the N-phosphorylation reaction. Stabilities of the obtained lysine-phosphorylated peptides under various conditions were also tested.
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Casino P, Rubio V, Marina A. The mechanism of signal transduction by two-component systems. Curr Opin Struct Biol 2010; 20:763-71. [DOI: 10.1016/j.sbi.2010.09.010] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 08/31/2010] [Accepted: 09/17/2010] [Indexed: 11/29/2022]
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Csikász-Nagy A, Cardelli L, Soyer OS. Response dynamics of phosphorelays suggest their potential utility in cell signalling. J R Soc Interface 2010; 8:480-8. [PMID: 20702449 PMCID: PMC3061117 DOI: 10.1098/rsif.2010.0336] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Phosphorelays are extended two-component signalling systems found in diverse bacteria, lower eukaryotes and plants. Only few of these systems are characterized, and we still lack a full understanding of their signalling abilities. Here, we aim to achieve a global understanding of phosphorelay signalling and its dynamical properties. We develop a generic model, allowing us to systematically analyse response dynamics under different assumptions. Using this model, we find that the steady-state concentration of phosphorylated protein at the final layer of a phosphorelay is a linearly increasing, but eventually saturating function of the input. In contrast, the intermediate layers can display ultrasensitivity. We find that such ultrasensitivity is a direct result of the phosphorelay biochemistry; shuttling of a single phosphate group from the first to the last layer. The response dynamics of the phosphorelay results in tolerance of cross-talk, especially when it occurs as cross-deactivation. Further, it leads to a high signal-to-noise ratio for the final layer. We find that a relay length of four, which is most commonly observed, acts as a saturating point for these dynamic properties. These findings suggest that phosphorelays could act as a mechanism to reduce noise and effects of cross-talk on the final layer of the relay and enforce its input–response relation to be linear. In addition, our analysis suggests that middle layers of phosphorelays could embed thresholds. We discuss the consequence of these findings in relation to why cells might use phosphorelays along with enzymatic kinase cascades.
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Affiliation(s)
- Attila Csikász-Nagy
- Microsoft Research-University of Trento Centre for Computational and Systems Biology (CoSBi), Povo (Trento), Italy.
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Lin CH, Chung KR. Specialized and shared functions of the histidine kinase- and HOG1 MAP kinase-mediated signaling pathways in Alternaria alternata, a filamentous fungal pathogen of citrus. Fungal Genet Biol 2010; 47:818-27. [PMID: 20601043 DOI: 10.1016/j.fgb.2010.06.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 06/02/2010] [Accepted: 06/17/2010] [Indexed: 12/16/2022]
Abstract
Signal transduction pathways are critical for the coordination of complex cellular processes in cells. In Alternaria alternata, a necrotrophic fungal pathogen of citrus, cloning and characterization of a gene coding a Group III histidine kinase (AaHSK1) and the yeast HOG1 ortholog (AaHOG1) showed the two genes to operate, both uniquely and synergistically, in a number of physiological and pathological functions. Systemic loss-of-function genetics in A. alternata revealed that AaHSK1 is a primary regulator for cellular resistance to sugar osmotic stress and for sensitivity to dicarboximide or phenylpyrrole fungicides. These functions were likely modulated by unknown mechanisms rather than solely by the AaHOG1-mediated pathway. AaHOG1, which conferred cellular resistance to salts and oxidative stress, also bypassed AaHSK1, even though deletion of AaHSK1 affected AaHOG1 phosphorylation. Phosphorylation of AaHOG1 was increased when the fungus was treated with osmotic stress, fungicides or H(2)O(2). Fungal mutants impaired in AaHSK1, AaHOG1, AaAP1 (encoding a redox-responsive transcription factor) or AaFUS3 (encoding a MAP kinase) were all hypersensitive to 2-chloro-5-hydroxypyridine (CHP) or 2,3,5-triiodobenzoic acid (TIBA). An AaHOG1::sGFP (synthetic green fluorescent protein) fusion protein became localized in the nucleus in response to H(2)O(2), CHP, TIBA, fungicides, but not glucose. Glucose, however, enhanced AaHOG1 phosphorylation and nuclear localization in the AaHSK1 deficient background. Accumulation of the AaHSK1 gene transcript was negatively regulated by AaHOG1, AaAP1 or AaFUS3. AaHOG1 was necessary for fungal pathogenicity, yet AaHSK1 was completely dispensable for pathogenicity. Our results highlight a dramatic flexibility and uniqueness in the signaling pathways that are involved in responding to diverse environmental stimuli in A. alternata.
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Affiliation(s)
- Ching-Hsuan Lin
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
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50
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Giusti C, Luciani MF, Ravens S, Gillet A, Golstein P. Autophagic cell death in Dictyostelium requires the receptor histidine kinase DhkM. Mol Biol Cell 2010; 21:1825-35. [PMID: 20375146 PMCID: PMC2877641 DOI: 10.1091/mbc.e09-11-0976] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Through random mutagenesis, the receptor histidine kinase DhkM was found essential for autophagic cell death (ACD) in Dictyostelium. DhkM is the most downstream known molecule required for this model ACD. Different DhkM mutants showed distinct non-vacuolizing ACD phenotypes and genetically separated previously undissociated late cell death events. Dictyostelium constitutes a genetically tractable model for the analysis of autophagic cell death (ACD). During ACD, Dictyostelium cells first transform into paddle cells and then become round, synthesize cellulose, vacuolize, and die. Through random insertional mutagenesis, we identified the receptor histidine kinase DhkM as being essential for ACD. Surprisingly, different DhkM mutants showed distinct nonvacuolizing ACD phenotypes. One class of mutants arrested ACD at the paddle cell stage, perhaps through a dominant-negative effect. Other mutants, however, progressed further in the ACD program. They underwent rounding and cellulose synthesis but stopped before vacuolization. Moreover, they underwent clonogenic but not morphological cell death. Exogenous 8-bromo-cAMP restored vacuolization and death. A role for a membrane receptor at a late stage of the ACD pathway is puzzling, raising questions as to which ligand it is a receptor for and which moieties it phosphorylates. Together, DhkM is the most downstream-known molecule required for this model ACD, and its distinct mutants genetically separate previously undissociated late cell death events.
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Affiliation(s)
- Corinne Giusti
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Marseille F-13288, France
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