1
|
Wang J, Zou Z, Hu M, Shan X, Zhang Y, Miao Y, Zhang X, Islam N, Hu Q. Riemerella anatipestifer UvrC is required for iron utilization, biofilm formation and virulence. Avian Pathol 2024; 53:247-256. [PMID: 38420684 DOI: 10.1080/03079457.2024.2317431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024]
Abstract
UvrC is a subunit of excinuclease ABC, which mediates nucleotide excision repair (NER) in bacteria. Our previous studies showed that transposon Tn4531 insertion in the UvrC encoding gene Riean_1413 results in reduced biofilm formation by Riemerella anatipestifer strain CH3 and attenuates virulence of strain YZb1. In this study, whether R. anatipestifer UvrC has some biological functions other than NER was investigated. Firstly, the uvrC of R. anatipestifer strain Yb2 was in-frame deleted by homologous recombination, generating deletion mutant ΔuvrC, and its complemented strain cΔuvrC was constructed based on Escherichia coli - R. anatipestifer shuttle plasmid pRES. Compared to the wild-type (WT) R. anatipestifer strain Yb2, uvrC deleted mutant ΔuvrC significantly reduced biofilm formation, tolerance to H2O2- and HOCl-induced oxidative stress, iron utilization, and adhesion to and invasion of duck embryonic hepatocytes, but not its growth curve and proteolytic activity. In addition, animal experiments showed that the LD50 value of ΔuvrC in ducklings was about 13-fold higher than that of the WT, and the bacterial loads in ΔuvrC infected ducklings were significantly lower than those in Yb2-infected ducklings, indicating uvrC deletion in R. anatipestifer attenuated virulence. Taken together, the results of this study indicate that R. anatipestifer UvrC is required for iron utilization, biofilm formation, oxidative stress tolerance and virulence of strain Yb2, demonstrating multiple functions of UvrC.RESEARCH HIGHLIGHTSDeletion of uvrC in R. anatipestfer Yb2 significantly reduced its biofilm formation.uvrC deletion led to reduced tolerance to H2O2- and HOCl-induced oxidative stress.The iron utilization of uvrC deleted mutant was significantly reduced.The uvrC deletion in R. anatipestifer Yb2 attenuated its virulence.
Collapse
Affiliation(s)
- Jialing Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Zuocheng Zou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Mengmeng Hu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Xinggen Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Ying Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Yiqin Miao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - XiaoYing Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Nazrul Islam
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Qinghai Hu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| |
Collapse
|
2
|
Gomes LGR, Dutra JCF, Profeta R, Dias MV, García GJY, Rodrigues DLN, Goés Neto A, Aburjaile FF, Tiwari S, Soares SC, Azevedo V, Jaiswal AK. Systematic review of reverse vaccinology and immunoinformatics data for non-viral sexually transmitted infections. AN ACAD BRAS CIENC 2023; 95:e20230617. [PMID: 38055447 DOI: 10.1590/0001-3765202320230617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/27/2023] [Indexed: 12/08/2023] Open
Abstract
Sexually Transmitted Infections (STIs) are a public health burden rising in developed and developing nations. The World Health Organization estimates nearly 374 million new cases of curable STIs yearly. Global efforts to control their spread have been insufficient in fulfilling their objective. As there is no vaccine for many of these infections, these efforts are focused on education and condom distribution. The development of vaccines for STIs is vital for successfully halting their spread. The field of immunoinformatics is a powerful new tool for vaccine development, allowing for the identification of vaccine candidates within a bacterium's genome and allowing for the design of new genome-based vaccine peptides. The goal of this review was to evaluate the usage of immunoinformatics in research focused on non-viral STIs, identifying fields where research efforts are concentrated. Here we describe gaps in applying these techniques, as in the case of Treponema pallidum and Trichomonas vaginalis.
Collapse
Affiliation(s)
- Lucas Gabriel R Gomes
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Joyce C F Dutra
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Microbiologia, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Rodrigo Profeta
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Mariana V Dias
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Glen J Y García
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Bioinformática, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Diego Lucas N Rodrigues
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
- Universidade Federal de Minas Gerais (UFMG), Escola de Veterinária, Departamento de Medicina Veterinária, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Aristóteles Goés Neto
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Microbiologia, Laboratório de Biologia Molecular e Computacional de Fungos, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Flávia F Aburjaile
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
- Universidade Federal de Minas Gerais (UFMG), Escola de Veterinária, Departamento de Medicina Veterinária, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
- Universidade Federal da Bahia, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, Ondina, 40170-115 Salvador, BA, Brazil
- Universidade Federal da Bahia, Instituto de Ciências da Saúde, Av. Reitor Miguel Calmon, s/n, Vale do Canela, 40110-902 Salvador, BA, Brazil
| | - Siomar C Soares
- Universidade Federal do Triângulo Mineiro (UFTM), Instituto de Ciências Biológicas e Naturais, Departamento de Microbiologia, Imunologia, e Parasitologia, Rua Vigário Carlos, 100, Abadia, 38025-180 Uberaba, MG, Brazil
| | - Vasco Azevedo
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Arun K Jaiswal
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| |
Collapse
|
3
|
Krachler AM, Sirisaengtaksin N, Monteith P, Paine CET, Coates CJ, Lim J. Defective phagocyte association during infection of Galleria mellonella with Yersinia pseudotuberculosis is detrimental to both insect host and microbe. Virulence 2021; 12:638-653. [PMID: 33550901 PMCID: PMC7889024 DOI: 10.1080/21505594.2021.1878672] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 11/03/2022] Open
Abstract
Adhesins facilitate bacterial colonization and invasion of host tissues and are considered virulence factors, but their impact on immune-mediated damage as a driver of pathogenesis remains unclear. Yersinia pseudotuberculosis encodes for a multivalent adhesion molecule (MAM), a mammalian cell entry (MCE) family protein and adhesin. MAMs are widespread in Gram-negative bacteria and enable enteric bacteria to colonize epithelial tissues. Their role in bacterial interactions with the host innate immune system and contribution to pathogenicity remains unclear. Here, we investigated howY. pseudotuberculosis MAM contributes to pathogenesis during infection of the Galleria mellonella insect model. We show that Y. pseudotuberculosis MAM is required for efficient bacterial binding and uptake by hemocytes, the host phagocytes. Y. pseudotuberculosis interactions with insect and mammalian phagocytes are determined by bacterial and host factors. Loss of MAM, and deficient microbe-phagocyte interaction, increased pathogenesis in G. mellonella. Diminished phagocyte association also led to increased bacterial clearance. Furthermore, Y. pseudotuberculosis that failed to engage phagocytes hyperactivated humoral immune responses, most notably melanin production. Despite clearing the pathogen, excessive melanization also increased phagocyte death and host mortality. Our findings provide a basis for further studies investigating how microbe- and host-factors integrate to drive pathogenesis in a tractable experimental system.
Collapse
Affiliation(s)
- Anne Marie Krachler
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston, Houston, TX, USA
| | - Natalie Sirisaengtaksin
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston, Houston, TX, USA
| | - Pauline Monteith
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - C. E. Timothy Paine
- School of Environmental and Rural Sciences, University of New England, Armidale, Australia
| | - Christopher J. Coates
- Department of Biosciences, College of Science, Swansea University, Swansea, Wales UK
| | - Jenson Lim
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| |
Collapse
|
4
|
Ahlawat S, Singh AK, Shankar A, Yadav A, Sharma KK. Infected insect gut reveals differentially expressed proteins for cellular redox, metal resistance and secretion system in Yersinia enterocolitica-Helicoverpa armigera pathogenic model. Biotechnol Lett 2021; 43:1845-1867. [PMID: 34165641 DOI: 10.1007/s10529-021-03157-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Mouse infection models are frequently used to study the host-pathogen interaction studies. However, due to several constraints, there is an urgent need for a simple, rapid, easy to handle, inexpensive, and ethically acceptable in vivo model system for studying the virulence of enteropathogens. Thus, the present study was performed to develop the larvae of Helicoverpa armigera as a rapid-inexpensive in vivo model system to evaluate the effect of Yersinia enterocolitica strain 8081 on its midgut via a label-free proteomic approach. RESULTS Helicoverpa armigera larvae fed with Yersinia enterocolitica strain 8081 manifested significant reduction in body weight and damage in midgut. On performing label-free proteomic study, secretory systems, putative hemolysin, and two-component system emerged as the main pathogenic proteins. Further, proteome comparison between control and Yersinia added diet-fed (YADF) insects revealed altered cytoskeletal proteins in response to increased melanization (via a prophenoloxidase cascade) and free radical generation. In concurrence, FTIR-spectroscopy, and histopathological and biochemical analysis confirmed gut damage in YADF insects. Finally, the proteome data suggests that the mechanism of infection and the host response in Y. enterocolitica-H. armigera system mimics Yersinia-mammalian gut interactions. CONCLUSIONS All data from current study collectively suggest that H. armigera larva can be considered as a potential in vivo model system for studying the enteropathogenic infection by Y. enterocolitica strain 8081.
Collapse
Affiliation(s)
- Shruti Ahlawat
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Amarjeet Kumar Singh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Akshay Shankar
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Asha Yadav
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
| |
Collapse
|
5
|
de Laia ML, Moreira LM, Gonçalves JF, Ferro MIT, Rodrigues ACP, dos Santos JN, Felestrino ÉB, Ferro JA. Gene expression analysis identifies hypothetical genes that may be critical during the infection process of Xanthomonas citri subsp. citri. ELECTRON J BIOTECHN 2019. [DOI: 10.1016/j.ejbt.2019.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
6
|
Kimura S, Sakai Y, Ishiguro K, Suzuki T. Biogenesis and iron-dependency of ribosomal RNA hydroxylation. Nucleic Acids Res 2018; 45:12974-12986. [PMID: 29069499 PMCID: PMC5727448 DOI: 10.1093/nar/gkx969] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/09/2017] [Indexed: 12/15/2022] Open
Abstract
Post-transcriptional modifications of ribosomal RNAs (rRNAs) are involved in ribosome biogenesis and fine-tuning of translation. 5-Hydroxycytidine (ho5C), a modification of unknown biogenesis and function, is present at position 2501 of Escherichia coli 23S rRNA. We conducted a genome-wide screen in E. coli to identify genes required for ho5C2501 formation, and found a previously-uncharacterized gene, ydcP (renamed rlhA), iron-sulfur cluster (isc) genes, and a series of genes responsible for prephenate biosynthesis, indicating that iron-sulfur clusters and prephenate are required for ho5C2501 formation. RlhA interacted with precursors of the 50S ribosomal subunit, suggesting that this protein is directly involved in formation of ho5C2501. RlhA belongs to a family of enzymes with an uncharacterized peptidase U32 motif and conserved Cys residues in the C-terminal region. These elements were essential for ho5C2501 formation. We also found that the frequency of ho5C2501 is modulated by environmental iron concentration. Together, our results reveal a novel biosynthetic pathway for RNA hydroxylation and its response to iron.
Collapse
Affiliation(s)
- Satoshi Kimura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yusuke Sakai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
7
|
Chanclud E, Lacombe B. Plant Hormones: Key Players in Gut Microbiota and Human Diseases? TRENDS IN PLANT SCIENCE 2017; 22:754-758. [PMID: 28843313 DOI: 10.1016/j.tplants.2017.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 07/07/2017] [Accepted: 07/09/2017] [Indexed: 05/27/2023]
Abstract
It is well established that plant hormones such as auxins, cytokinins (CKs), and abscisic acid (ABA) not only govern important plant physiological traits but are key players in plant-microbe interactions. A poorly appreciated fact, however, is that both microbes and animals produce and perceive plant hormones and their mimics. Moreover, dietary plant hormones impact on human physiological process such as glucose assimilation, inflammation, and cell division. This leads us to wonder whether plant hormones could ensure functions in microbes per se as well as in animal-microbe interactions. We propose here and explore the hypothesis that plant hormones play roles in animal-microbiota relationships, with consequences for human health.
Collapse
Affiliation(s)
- Emilie Chanclud
- Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA)/SupAgro/Université de Montpellier, Institut de Biologie Intégrative des Plantes 'Claude Grignon', 34060 Montpellier, France; Present address: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Benoît Lacombe
- Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA)/SupAgro/Université de Montpellier, Institut de Biologie Intégrative des Plantes 'Claude Grignon', 34060 Montpellier, France.
| |
Collapse
|
8
|
A Noise Trimming and Positional Significance of Transposon Insertion System to Identify Essential Genes in Yersinia pestis. Sci Rep 2017; 7:41923. [PMID: 28165493 PMCID: PMC5292949 DOI: 10.1038/srep41923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 12/30/2016] [Indexed: 01/14/2023] Open
Abstract
Massively parallel sequencing technology coupled with saturation mutagenesis has provided new and global insights into gene functions and roles. At a simplistic level, the frequency of mutations within genes can indicate the degree of essentiality. However, this approach neglects to take account of the positional significance of mutations - the function of a gene is less likely to be disrupted by a mutation close to the distal ends. Therefore, a systematic bioinformatics approach to improve the reliability of essential gene identification is desirable. We report here a parametric model which introduces a novel mutation feature together with a noise trimming approach to predict the biological significance of Tn5 mutations. We show improved performance of essential gene prediction in the bacterium Yersinia pestis, the causative agent of plague. This method would have broad applicability to other organisms and to the identification of genes which are essential for competitiveness or survival under a broad range of stresses.
Collapse
|
9
|
Thakur M, Kumar MBJ, Muniyappa K. Mycobacterium tuberculosis UvrB Is a Robust DNA-Stimulated ATPase That Also Possesses Structure-Specific ATP-Dependent DNA Helicase Activity. Biochemistry 2016; 55:5865-5883. [PMID: 27618337 DOI: 10.1021/acs.biochem.6b00558] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Much is known about the Escherichia coli nucleotide excision repair (NER) pathway; however, very little is understood about the proteins involved and the molecular mechanism of NER in mycobacteria. In this study, we show that Mycobacterium tuberculosis UvrB (MtUvrB), which exists in solution as a monomer, binds to DNA in a structure-dependent manner. A systematic examination of MtUvrB substrate specificity reveals that it associates preferentially with single-stranded DNA, duplexes with 3' or 5' overhangs, and linear duplex DNA with splayed arms. Whereas E. coli UvrB (EcUvrB) binds weakly to undamaged DNA and has no ATPase activity, MtUvrB possesses intrinsic ATPase activity that is greatly stimulated by both single- and double-stranded DNA. Strikingly, we found that MtUvrB, but not EcUvrB, possesses the DNA unwinding activity characteristic of an ATP-dependent DNA helicase. The helicase activity of MtUvrB proceeds in the 3' to 5' direction and is strongly modulated by a nontranslocating 5' single-stranded tail, indicating that in addition to the translocating strand it also interacts with the 5' end of the substrate. The fraction of DNA unwound by MtUvrB decreases significantly as the length of the duplex increases: it fails to unwind duplexes longer than 70 bp. These results, on one hand, reveal significant mechanistic differences between MtUvrB and EcUvrB and, on the other, support an alternative role for UvrB in the processing of key DNA replication intermediates. Altogether, our findings provide insights into the catalytic functions of UvrB and lay the foundation for further understanding of the NER pathway in M. tuberculosis.
Collapse
Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science , Bangalore 560012, India
| | - Mohan B J Kumar
- Department of Biochemistry, Indian Institute of Science , Bangalore 560012, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science , Bangalore 560012, India
| |
Collapse
|
10
|
Dentovskaya SV, Ivanov SA, Kopylov PK, Shaikhutdinova RZ, Platonov ME, Kombarova TI, Gapel’chenkova TV, Balakhonov SV, Anisimov AP. Selective Protective Potency of Yersinia pestis ΔnlpD Mutants. Acta Naturae 2015; 7:102-8. [PMID: 25927007 PMCID: PMC4410401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It has recently been shown that the NlpD lipoprotein is essential to Yersinia pestis virulence and that subcutaneous administration of the nlpD mutant could protect mice against bubonic and pneumonic plague better than the EV vaccine strain [PLoS One 2009. V. 4. № 9. e7023]. In this study, similar ΔnlpD mutants were generated on the basis of other Y. pestis parent strains, including strains from the subspecies microtus, which is avirulent to guinea pigs and humans. Comparative testing confirmed that immunization of mice with ΔnlpD mutants induces immunity 105 times more potent than the one induced by the administration of the EV vaccine strain. At the same time, NlpD- bacteria failed to protect guinea pigs in the case of a subcutaneous challenge with Y. pestis, inducing a 106 times less potent protection compared with that conferred by immunization with the EV vaccine strain. The possible causes of the observed phenomena are discussed.
Collapse
Affiliation(s)
- S. V. Dentovskaya
- State Research Center for Applied Microbiology, Obolensk, Moscow Region, 142279, Russia
| | - S. A. Ivanov
- State Research Center for Applied Microbiology, Obolensk, Moscow Region, 142279, Russia
| | - P. Kh. Kopylov
- State Research Center for Applied Microbiology, Obolensk, Moscow Region, 142279, Russia
| | - R. Z. Shaikhutdinova
- State Research Center for Applied Microbiology, Obolensk, Moscow Region, 142279, Russia
| | - M. E. Platonov
- State Research Center for Applied Microbiology, Obolensk, Moscow Region, 142279, Russia
| | - T. I. Kombarova
- State Research Center for Applied Microbiology, Obolensk, Moscow Region, 142279, Russia
| | - T. V. Gapel’chenkova
- State Research Center for Applied Microbiology, Obolensk, Moscow Region, 142279, Russia
| | - S. V. Balakhonov
- Irkutsk Antiplague Research Institute of Siberia and Far East, Trilissera Str., 78, 664047, Irkutsk, Russia
| | - A. P. Anisimov
- State Research Center for Applied Microbiology, Obolensk, Moscow Region, 142279, Russia
| |
Collapse
|
11
|
Tavares DA, Simões AS, Bootsma HJ, Hermans PWM, de Lencastre H, Sá-Leão R. Non-typeable pneumococci circulating in Portugal are of cps type NCC2 and have genomic features typical of encapsulated isolates. BMC Genomics 2014; 15:863. [PMID: 25283442 PMCID: PMC4200197 DOI: 10.1186/1471-2164-15-863] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 09/29/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Pneumococcus is a major human pathogen and the polysaccharide capsule is considered its main virulence factor. Nevertheless, strains lacking a capsule, named non-typeable pneumococcus (NT), are maintained in nature and frequently colonise the human nasopharynx. Interest in these strains, not targeted by any of the currently available pneumococcal vaccines, has been rising as they seem to play an important role in the evolution of the species. Currently, there is a paucity of data regarding this group of pneumococci. Also, questions have been raised on whether they are true pneumococci. We aimed to obtain insights in the genetic content of NT and the mechanisms leading to non-typeability and to genetic diversity. RESULTS A collection of 52 NT isolates representative of the lineages circulating in Portugal between 1997 and 2007, as determined by pulsed-field gel electrophoresis and multilocus sequence typing, was analysed. The capsular region was sequenced and comparative genomic hybridisation (CGH) using a microarray covering the genome of 10 pneumococcal strains was carried out. The presence of mobile elements was investigated as source of intraclonal variation. NT circulating in Portugal were found to have similar capsular regions, of cps type NCC2, i.e., having aliB-like ORF1 and aliB-like ORF2 genes. The core genome of NT was essentially similar to that of encapsulated strains. Also, competence genes and most virulence genes were present. The few virulence genes absent in all NT were the capsular genes, type-I and type-II pili, choline-binding protein A (cbpA/pspC), and pneumococcal surface protein A (pspA). Intraclonal variation could not be entirely explained by the presence of prophages and other mobile elements. CONCLUSIONS NT circulating in Portugal are a homogeneous group belonging to cps type NCC2. Our observations support the theory that they are bona-fide pneumococcal isolates that do not express the capsule but are otherwise essentially similar to encapsulated pneumococci. Thus we propose that NT should be routinely identified and reported in surveillance studies.
Collapse
Affiliation(s)
- Débora A Tavares
- />Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica (ITQB) António Xavier, Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| | - Alexandra S Simões
- />Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica (ITQB) António Xavier, Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| | - Hester J Bootsma
- />Laboratory of Paediatric Infectious Diseases, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Peter WM Hermans
- />Laboratory of Paediatric Infectious Diseases, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
- />Crucell – Johnson and Johnson, Leiden, the Netherlands
| | - Hermínia de Lencastre
- />Laboratory of Molecular Genetics, ITQB, UNL, Oeiras, Portugal
- />Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY USA
| | - Raquel Sá-Leão
- />Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica (ITQB) António Xavier, Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| |
Collapse
|
12
|
Abstract
Plague has been a scourge of mankind for centuries, and outbreaks continue to the present day. The virulence mechanisms employed by the etiological agent Yersinia pestis are reviewed in the context of the available prophylactic and therapeutic strategies for plague. Although antibiotics are available, resistance is emerging in this dangerous pathogen. Therapeutics used in the clinic are discussed and innovative approaches to the design and development of new therapeutic compounds are reviewed. Currently there is no licensed vaccine available for prevention of plague in the USA or western Europe, although both live attenuated strains and killed whole-cell extracts have been used historically. Live strains are still approved for human use in some parts of the world, such as the former Soviet Union, but poor safety profiles render them unacceptable to many countries. The development of safe, effective next-generation vaccines, including the recombinant subunit vaccine currently used in clinical trials is discussed.
Collapse
Affiliation(s)
- Petra C F Oyston
- Biomedical Sciences, Dstl Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK
| | | |
Collapse
|
13
|
The nucleotide excision repair system of Borrelia burgdorferi is the sole pathway involved in repair of DNA damage by UV light. J Bacteriol 2013; 195:2220-31. [PMID: 23475971 DOI: 10.1128/jb.00043-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
To survive and avoid accumulation of mutations caused by DNA damage, the genomes of prokaryotes encode a variety of DNA repair pathways most well characterized in Escherichia coli. Some of these are required for the infectivity of various pathogens. In this study, the importance of 25 DNA repair/recombination genes for Borrelia burgdorferi survival to UV-induced DNA damage was assessed. In contrast to E. coli, where 15 of these genes have an effect on survival of UV irradiation, disruption of recombinational repair, transcription-coupled repair, methyl-directed mismatch correction, and repair of arrested replication fork pathways did not decrease survival of B. burgdorferi exposed to UV light. However, the disruption of the B. burgdorferi nucleotide excision repair (NER) pathway (uvrA, uvrB, uvrC, and uvrD) resulted in a 10- to 1,000-fold increase in sensitivity to UV light. A functional NER pathway was also shown to be required for B. burgdorferi resistance to nitrosative damage. Finally, disruption of uvrA, uvrC, and uvrD had only a minor effect upon murine infection by increasing the time required for dissemination.
Collapse
|
14
|
Bielecki P, Lukat P, Hüsecken K, Dötsch A, Steinmetz H, Hartmann RW, Müller R, Häussler S. Mutation in Elongation Factor G Confers Resistance to the Antibiotic Argyrin in the Opportunistic PathogenPseudomonas aeruginosa. Chembiochem 2012; 13:2339-45. [DOI: 10.1002/cbic.201200479] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Indexed: 11/12/2022]
|
15
|
Fröhlich A, Gaupels F, Sarioglu H, Holzmeister C, Spannagl M, Durner J, Lindermayr C. Looking deep inside: detection of low-abundance proteins in leaf extracts of Arabidopsis and phloem exudates of pumpkin. PLANT PHYSIOLOGY 2012; 159:902-14. [PMID: 22555880 PMCID: PMC3387715 DOI: 10.1104/pp.112.198077] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 04/24/2012] [Indexed: 05/20/2023]
Abstract
The field of proteomics suffers from the immense complexity of even small proteomes and the enormous dynamic range of protein concentrations within a given sample. Most protein samples contain a few major proteins, which hamper in-depth proteomic analysis. In the human field, combinatorial hexapeptide ligand libraries (CPLL; such as ProteoMiner) have been used for reduction of the dynamic range of protein concentrations; however, this technique is not established in plant research. In this work, we present the application of CPLL to Arabidopsis (Arabidopsis thaliana) leaf proteins. One- and two-dimensional gel electrophoresis showed a decrease in high-abundance proteins and an enrichment of less abundant proteins in CPLL-treated samples. After optimization of the CPLL protocol, mass spectrometric analyses of leaf extracts led to the identification of 1,192 proteins in control samples and an additional 512 proteins after the application of CPLL. Upon leaf infection with virulent Pseudomonas syringae DC3000, CPLL beads were also used for investigating the bacterial infectome. In total, 312 bacterial proteins could be identified in infected Arabidopsis leaves. Furthermore, phloem exudates of pumpkin (Cucurbita maxima) were analyzed. CPLL prefractionation caused depletion of the major phloem proteins 1 and 2 and improved phloem proteomics, because 67 of 320 identified proteins were detectable only after CPLL treatment. In sum, our results demonstrate that CPLL beads are a time- and cost-effective tool for reducing major proteins, which often interfere with downstream analyses. The concomitant enrichment of less abundant proteins may facilitate a deeper insight into the plant proteome.
Collapse
Affiliation(s)
| | | | - Hakan Sarioglu
- Institute of Biochemical Plant Pathology (A.F., F.G., C.H., J.D., C.L.), Department of Protein Science (H.S.), and Institute of Bioinformatics and Systems Biology (M.S.), Helmholtz Zentrum München, German Research Center for Environmental Health, D–85764 Neuherberg, Germany
| | - Christian Holzmeister
- Institute of Biochemical Plant Pathology (A.F., F.G., C.H., J.D., C.L.), Department of Protein Science (H.S.), and Institute of Bioinformatics and Systems Biology (M.S.), Helmholtz Zentrum München, German Research Center for Environmental Health, D–85764 Neuherberg, Germany
| | - Manuel Spannagl
- Institute of Biochemical Plant Pathology (A.F., F.G., C.H., J.D., C.L.), Department of Protein Science (H.S.), and Institute of Bioinformatics and Systems Biology (M.S.), Helmholtz Zentrum München, German Research Center for Environmental Health, D–85764 Neuherberg, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology (A.F., F.G., C.H., J.D., C.L.), Department of Protein Science (H.S.), and Institute of Bioinformatics and Systems Biology (M.S.), Helmholtz Zentrum München, German Research Center for Environmental Health, D–85764 Neuherberg, Germany
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology (A.F., F.G., C.H., J.D., C.L.), Department of Protein Science (H.S.), and Institute of Bioinformatics and Systems Biology (M.S.), Helmholtz Zentrum München, German Research Center for Environmental Health, D–85764 Neuherberg, Germany
| |
Collapse
|
16
|
Graille M, Figaro S, Kervestin S, Buckingham RH, Liger D, Heurgué-Hamard V. Methylation of class I translation termination factors: structural and functional aspects. Biochimie 2012; 94:1533-43. [PMID: 22266024 DOI: 10.1016/j.biochi.2012.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 01/07/2012] [Indexed: 12/23/2022]
Abstract
During protein synthesis, release of polypeptide from the ribosome occurs when an in frame termination codon is encountered. Contrary to sense codons, which are decoded by tRNAs, stop codons present in the A-site are recognized by proteins named class I release factors, leading to the release of newly synthesized proteins. Structures of these factors bound to termination ribosomal complexes have recently been obtained, and lead to a better understanding of stop codon recognition and its coordination with peptidyl-tRNA hydrolysis in bacteria. Release factors contain a universally conserved GGQ motif which interacts with the peptidyl-transferase centre to allow peptide release. The Gln side chain from this motif is methylated, a feature conserved from bacteria to man, suggesting an important biological role. However, methylation is catalysed by completely unrelated enzymes. The function of this motif and its post-translational modification will be discussed in the context of recent structural and functional studies.
Collapse
Affiliation(s)
- Marc Graille
- IBBMC, Université Paris-Sud 11, CNRS UMR8619, Orsay Cedex, F-91405, France.
| | | | | | | | | | | |
Collapse
|
17
|
Eshghi A, Pinne M, Haake DA, Zuerner RL, Frank A, Cameron CE. Methylation and in vivo expression of the surface-exposed Leptospira interrogans outer-membrane protein OmpL32. MICROBIOLOGY-SGM 2011; 158:622-635. [PMID: 22174381 DOI: 10.1099/mic.0.054767-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent studies have revealed that bacterial protein methylation is a widespread post-translational modification that is required for virulence in selected pathogenic bacteria. In particular, altered methylation of outer-membrane proteins has been shown to modulate the effectiveness of the host immune response. In this study, 2D gel electrophoresis combined with MALDI-TOF MS identified a Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130 protein, corresponding to ORF LIC11848, which undergoes extensive and differential methylation of glutamic acid residues. Immunofluorescence microscopy implicated LIC11848 as a surface-exposed outer-membrane protein, prompting the designation OmpL32. Indirect immunofluorescence microscopy of golden Syrian hamster liver and kidney sections revealed expression of OmpL32 during colonization of these organs. Identification of methylated surface-exposed outer-membrane proteins, such as OmpL32, provides a foundation for delineating the role of this post-translational modification in leptospiral virulence.
Collapse
Affiliation(s)
- Azad Eshghi
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Marija Pinne
- Department of Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA.,Research Service, 151, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - David A Haake
- Division of Infectious Diseases, 111F, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, USA.,Department of Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA
| | - Richard L Zuerner
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center (NADC), Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Ames, IA, USA
| | - Ami Frank
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center (NADC), Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Ames, IA, USA
| | - Caroline E Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| |
Collapse
|
18
|
Chen YC, Chung YT. A conserved GTPase YchF of Vibrio vulnificus is involved in macrophage cytotoxicity, iron acquisition, and mouse virulence. Int J Med Microbiol 2011; 301:469-74. [PMID: 21570909 DOI: 10.1016/j.ijmm.2011.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 12/21/2010] [Accepted: 02/11/2011] [Indexed: 11/16/2022] Open
Abstract
Vibrio vulnificus, a highly virulent marine bacterium, causes serious wound infections and fatal septicemia in many areas of the world. To identify V. vulnificus genes required for killing macrophages, we made an insertional mutant library of V. vulnificus and screened it for reduced macrophage cytotoxicity. One mutant defective in macrophage cytotoxicity had an insertion in ychF, a gene encoding a putative GTPase. In addition to reduced cytotoxicity, this mutant had attenuated growth in iron-limited medium and reduced virulence in iron-overloaded mice. The ychF mutation also down-regulated the transcription level of the rtxA1 gene. RtxA1 mutants significantly decreased cytotoxicity to macrophages compared to wild-type bacteria. Overall, these results show that YchF elicits macrophage cytotoxicity through an rtxA1 pathway and is important for mouse virulence.
Collapse
Affiliation(s)
- Yu-Chung Chen
- Department of Biotechnology, College of Pharmacy and Science, Chia Nan University of Pharmacy and Science, Tainan, Taiwan.
| | | |
Collapse
|
19
|
Sambir M, Ivanova LB, Bryksin AV, Godfrey HP, Cabello FC. Functional analysis of Borrelia burgdorferi uvrA in DNA damage protection. FEMS Microbiol Lett 2011; 317:172-80. [PMID: 21272060 DOI: 10.1111/j.1574-6968.2011.02226.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Bacterial pathogens face constant challenges from DNA-damaging agents generated by host phagocytes. Although Borrelia burgdorferi appears to have much fewer DNA repair enzymes than pathogens with larger genomes, it does contain homologues of uvrA and uvrB (subunits A and B of excinuclease ABC). As a first step to exploring the physiologic function of uvrA(Bbu) and its possible role in survival in the host in the face of DNA-damaging agents, a partially deleted uvrA mutant was isolated by targeted inactivation. While growth of this mutant was markedly inhibited by UV irradiation, mitomycin C (MMC) and hydrogen peroxide at doses that lacked effect on wild-type B. burgdorferi, its response to pH 6.0-6.8 and reactive nitrogen intermediates was similar to that of the wild-type parental strain. The sensitivity of the inactivation mutant to UV irradiation, MMC and peroxide was complemented by an extrachromosomal copy of uvrA(Bbu). We conclude that uvrA(Bbu) is functional in B. burgdorferi.
Collapse
Affiliation(s)
- Mariya Sambir
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | | | | | | | | |
Collapse
|
20
|
Zou YX, Mo ZL, Hao B, Ye XH, Guo DS, Zhang PJ. Screening of genes expressed in vivo after infection by Vibrio anguillarum M3. Lett Appl Microbiol 2010; 51:564-9. [PMID: 20849396 DOI: 10.1111/j.1472-765x.2010.02935.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Genes uniquely expressed in vivo may contribute to the overall pathogenicity of an organism and are likely to serve as potential targets for the development of new vaccine. This study aims to screen the genes expressed in vivo after Vibrio anguillarum infection by in vivo-induced antigen technology (IVIAT). METHODS AND RESULTS The convalescent-phase sera were obtained from turbot (Scophthalmus maximus) survived after infection by the virulent V. anguillarum M3. The pooled sera were thoroughly adsorbed with M3 cells and Escherichia coli BL21 (DE3) cells. A genomic expression library of M3 was constructed and screened for the identification of immunogenic proteins by colony immunoblot analysis with the adsorbed sera. After three rounds of screening, 19 putative in vivo-induced (ivi) genes were obtained. These ivi genes were catalogued into four functional groups: regulator/signalling, metabolism, biological process and hypothetical proteins. Three ivi genes were insertion-mutated, and the growth and 50% lethal dose (LD(50) ) of these mutants were evaluated. CONCLUSIONS The identification of ivi genes in V. anguillarum M3 sheds light on understanding the bacterial pathogenesis and provides novel targets for the development of new vaccines and diagnostic reagents. SIGNIFICANCE AND IMPACT OF THE STUDY To the best of our knowledge, this is the first report describing in vivo-expressed genes of V. anguillarum using IVIAT. The screened ivi genes in this study could be new virulent factors and targets for the development of vaccine, which may have implications for the development of diagnostic regents.
Collapse
Affiliation(s)
- Y-X Zou
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | | | | | | | | |
Collapse
|
21
|
Abstract
The rapid increasing number of completed bacterial genomes provides a good opportunity to compare their proteomes. This study was undertaken to specifically compare and contrast their secretomes-the fraction of the proteome with predicted N-terminal signal sequences, both type I and type II. A total of 176 theoretical bacterial proteomes were examined using the ExProt program. Compared with the Gram-positives, the Gram-negative bacteria were found, on average, to contain a larger number of potential Sec-dependent sequences. In the Gram-negative bacteria but not in the others, there was a positive correlation between proteome size and secretome size, while there was no correlation between secretome size and pathogenicity. Within the Gram-negative bacteria, intracellular pathogens were found to have the smallest secretomes. However, the secretomes of certain bacteria did not fit into the observed pattern. Specifically, the secretome of Borrelia burgdoferi has an unusually large number of putative lipoproteins, and the signal peptides of mycoplasmas show closer sequence similarity to those of the Gram-negative bacteria. Our analysis also suggests that even for a theoretical minimal genome of 300 open reading frames, a fraction of this gene pool (up to a maximum of 20%) may code for proteins with Sec-dependent signal sequences.
Collapse
|
22
|
Stubben CJ, Duffield ML, Cooper IA, Ford DC, Gans JD, Karlyshev AV, Lingard B, Oyston PCF, de Rochefort A, Song J, Wren BW, Titball RW, Wolinsky M. Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens. BMC Genomics 2009; 10:501. [PMID: 19874620 PMCID: PMC2774872 DOI: 10.1186/1471-2164-10-501] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2009] [Accepted: 10/29/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND New and improved antimicrobial countermeasures are urgently needed to counteract increased resistance to existing antimicrobial treatments and to combat currently untreatable or new emerging infectious diseases. We demonstrate that computational comparative genomics, together with experimental screening, can identify potential generic (i.e., conserved across multiple pathogen species) and novel virulence-associated genes that may serve as targets for broad-spectrum countermeasures. RESULTS Using phylogenetic profiles of protein clusters from completed microbial genome sequences, we identified seventeen protein candidates that are common to diverse human pathogens and absent or uncommon in non-pathogens. Mutants of 13 of these candidates were successfully generated in Yersinia pseudotuberculosis and the potential role of the proteins in virulence was assayed in an animal model. Six candidate proteins are suggested to be involved in the virulence of Y. pseudotuberculosis, none of which have previously been implicated in the virulence of Y. pseudotuberculosis and three have no record of involvement in the virulence of any bacteria. CONCLUSION This work demonstrates a strategy for the identification of potential virulence factors that are conserved across a number of human pathogenic bacterial species, confirming the usefulness of this tool.
Collapse
Affiliation(s)
- Chris J Stubben
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Cheung MY, Zeng NY, Tong SW, Li WYF, Xue Y, Zhao KJ, Wang C, Zhang Q, Fu Y, Sun Z, Sun SSM, Lam HM. Constitutive expression of a rice GTPase-activating protein induces defense responses. THE NEW PHYTOLOGIST 2008; 179:530-545. [PMID: 19086295 DOI: 10.1111/j.1469-8137.2008.02473.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
G-proteins (guanine nucleotide-binding proteins that usually exhibit GTPase activities) and related signal transduction processes play important roles in mediating plant defense responses; here, a rice (Oryza sativa) cDNA clone, OsGAP1, encoding a GTPase-activating protein (GAP) that also contains a protein kinase C conserved region 2 (C2) domain is reported. An interacting G-protein partner for the OsGAP1 protein was identified by yeast two-hybrid library screening and confirmed by co-immunoprecipitation; the GTPase-activation activity of OsGAP1 on this interacting G-protein was demonstrated using in vitro assays. OsGAP1 was induced by wounding in rice and the presence of the R locus Xa14 enhances such induction. Gain-of-function tests in transgenic rice and Arabidopsis thaliana showed that constitutive expression of OsGAP1 led to increased resistance to bacterial pathogens in both monocots and dicots.
Collapse
Affiliation(s)
- Ming-Yan Cheung
- Department of Biology and
- State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | | | - Suk-Wah Tong
- Department of Biology and
- State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Wing-Yen Francisca Li
- Department of Biology and
- State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Yan Xue
- State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Kai-Jun Zhao
- Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunlian Wang
- Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Zhang
- Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yaping Fu
- China National Rice Research Institute, Hangzhou, China
| | - Zongxiu Sun
- China National Rice Research Institute, Hangzhou, China
| | - Samuel Sai-Ming Sun
- Department of Biology and
- State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Hon-Ming Lam
- Department of Biology and
- State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| |
Collapse
|
24
|
Fernebro J, Blomberg C, Morfeldt E, Wolf-Watz H, Normark S, Normark BH. The influence of in vitro fitness defects on pneumococcal ability to colonize and to cause invasive disease. BMC Microbiol 2008; 8:65. [PMID: 18423011 PMCID: PMC2375889 DOI: 10.1186/1471-2180-8-65] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 04/18/2008] [Indexed: 11/16/2022] Open
Abstract
Background Streptococcus pneumoniae is a genetically diverse major human pathogen, yet a common colonizer of the nasopharynx. Here we analyzed the influence of defects affecting in vitro growth rate, on the ability of S. pneumoniae to colonize and to cause invasive disease in vivo. Results Of eleven different clinical isolates one serotype 14 carrier isolate showed a significantly longer generation time as compared to other isolates, and was severely attenuated in mice. To directly investigate the impact of growth rate on virulence, a panel of mutants in five non-essential housekeeping genes was constructed in the virulent TIGR4 background by insertion-deletion mutagenesis. Three of these mutants (ychF, hemK and yebC) were, to different degrees, growth defective, and showed a reduced invasiveness in an intranasal murine challenge model that correlated to their in vitro growth rate, but remained capable of colonizing the upper airways. The growth defect, as well as virulence defect of the hemK insertion-deletion mutant, was mediated by polarity effects on the downstream yrdC gene, encoding a probable chaperone in ribosome assembly. Conclusion We conclude that large fitness defects are needed to completely prevent pneumococci from causing invasive disease after intranasal challenge. However, even severe growth defects still allow pneumococci to persistently colonize the upper airways.
Collapse
Affiliation(s)
- Jenny Fernebro
- Swedish Institute for Infectious Disease Control, 171 82 Solna, Sweden.
| | | | | | | | | | | |
Collapse
|
25
|
Garbom S, Olofsson M, Björnfot AC, Srivastava MK, Robinson VL, Oyston PCF, Titball RW, Wolf-Watz H. Phenotypic characterization of a virulence-associated protein, VagH, of Yersinia pseudotuberculosis reveals a tight link between VagH and the type III secretion system. MICROBIOLOGY-SGM 2007; 153:1464-1473. [PMID: 17464060 DOI: 10.1099/mic.0.2006/000323-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Recently, a number of attenuated mutants of Yersinia pseudotuberculosis have been identified using a bioinformatics approach. One of the target genes identified in that study was vagH, which the authors now characterized further. VagH shows homology to HemK of Escherichia coli, possessing methyltransferase activity similar to that of HemK, and targeting release factors 1 and 2. Microarray studies comparing the wild-type and the vagH mutant revealed that the mRNA levels of only a few genes were altered in the mutant. By proteome analysis, expression of the virulence determinant YopD was found to be increased, indicating a possible connection between VagH and the virulence plasmid-encoded type III secretion system (T3SS). Further analysis showed that Yop expression and secretion were repressed in a vagH mutant. This phenotype could be suppressed by trans-complementation with the wild-type vagH gene or by deletion of the negative regulator yopD. Also, in a similar manner to a T3SS-negative mutant, the avirulent vagH mutant was rapidly cleared from Peyer's patches and could not reach the spleen after oral infection of mice. In a manner analogous to that of T3SS mutants, the vagH mutant could not block phagocytosis by macrophages. However, a vagH mutant showed no defects in the T3SS-independent ability to proliferate intracellularly and replicated to levels similar to those of the wild-type in macrophages. In conclusion, the vagH mutant exhibits a virulence phenotype similar to that of a T3SS-negative mutant, indicating a tight link between VagH and type III secretion in Y. pseudotuberculosis.
Collapse
Affiliation(s)
- Sara Garbom
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
| | - Martina Olofsson
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
| | | | - Manoj Kumar Srivastava
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, S-90183 Umeå, Sweden
| | | | - Petra C F Oyston
- Biomedical Sciences, Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - Richard W Titball
- Biomedical Sciences, Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - Hans Wolf-Watz
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
| |
Collapse
|
26
|
Wang Y, Ding L, Hu Y, Zhang Y, Yang B, Chen S. The flhDC gene affects motility and biofilm formation in Yersinia pseudotuberculosis. ACTA ACUST UNITED AC 2007; 50:814-21. [DOI: 10.1007/s11427-007-0101-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Accepted: 09/30/2007] [Indexed: 10/22/2022]
|
27
|
Affiliation(s)
- Michael F Loughlin
- The University of Nottingham, Division of Food Sciences, School of Biosciences, Sutton Bonnington Campus, Loughborough, Leicestershire, LE12 5RD, UK ;
| |
Collapse
|
28
|
Mans JJ, Baker HV, Oda D, Lamont RJ, Handfield M. Distinctive characteristics of transcriptional profiles from two epithelial cell lines upon interaction with Actinobacillus actinomycetemcomitans. ACTA ACUST UNITED AC 2006; 21:261-7. [PMID: 16842512 DOI: 10.1111/j.1399-302x.2006.00281.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Transcriptional profiling and gene ontology analyses were performed to investigate the unique responses of two different epithelial cell lines to an Actinobacillus actinomycetemcomitans challenge. A total of 2867 genes were differentially regulated among all experimental conditions. The analysis of these 2867 genes revealed that the predominant specific response to infection in HeLa cells was associated with the regulation of enzyme activity, RNA metabolism, nucleoside and nucleic acid transport and protein modification. The predominant specific response in immortalized human gingival keratinocytes (IHGK) was associated with the regulation of angiogenesis, chemotaxis, transmembrane receptor protein tyrosine kinase signaling, cell differentiation, apoptosis and response to stress. Of particular interest, stress response genes were significantly - yet differently - affected in both cell lines. In HeLa cells, only three regulated genes impacted the response to stress, and the response to unfolded protein was the only term that passed the ontology filters. This strikingly contrasted with the profiles obtained for IHGK, in which 61 regulated genes impacted the response to stress and constituted an extensive network of cell responses to A. actinomycetemcomitans interaction (response to pathogens, oxidative stress, unfolded proteins, DNA damage, starvation and wounding). Hence, while extensive similarities were found in the transcriptional profiles of these two epithelial cell lines, significant differences were highlighted. These differences were predominantly found in pathways that are associated with host-pathogen interactions.
Collapse
Affiliation(s)
- J J Mans
- Center for Molecular Microbiology, Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | | | | | | | | |
Collapse
|
29
|
Abstract
Yersinia pestis is the causative agent of plague, which diverged from Yersinia pseudotuberculosis within the past 20,000 years. Although these two species share a high degree of homology at the DNA level (>90%), they differ radically in their pathogenicity and transmission. In this review, we briefly outline the known virulence factors that differentiate these two species and emphasize genetic studies that have been conducted comparing Y. pestis and Y. pseudotuberculosis. These comparisons have led to a better understanding of the genetic contributions to the differences in the virulence and pathogenicity between these two organisms and have generated information that can be applied in future diagnostic and vaccine development. Comparison of the genetic differences between Y. pestis and Y. pseudotuberculosis has also lent insight into the emergence of acute pathogens from organisms causing milder diseases.
Collapse
Affiliation(s)
- Xiao-Zhe Huang
- Division of Communicable Immunology, Department of Bacterial Diseases, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.
| | | | | |
Collapse
|
30
|
Heurgué-Hamard V, Champ S, Mora L, Merkulova-Rainon T, Merkoulova-Rainon T, Kisselev LL, Buckingham RH. The glutamine residue of the conserved GGQ motif in Saccharomyces cerevisiae release factor eRF1 is methylated by the product of the YDR140w gene. J Biol Chem 2004; 280:2439-45. [PMID: 15509572 DOI: 10.1074/jbc.m407252200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Polypeptide release factors from eubacteria and eukaryotes, although similar in function, belong to different protein families. They share one sequence motif, a GGQ tripeptide that is vital to release factor (RF) activity in both kingdoms. In bacteria, the Gln residue of the motif in RF1 and RF2 is modified to N(5)-methyl-Gln by the S-adenosyl l-methionine-dependent methyltransferase PrmC and the absence of Gln methylation decreases the release activity of Escherichia coli RF2 in vitro severalfold. We show here that the same modification is made to the GGQ motif of Saccharomyces cerevisiae release factor eRF1, the first time that N(5)-methyl-Gln has been found outside the bacterial kingdom. The product of the YDR140w gene is required for the methylation of eRF1 in vivo and for optimal yeast cell growth. YDR140w protein has significant homology to PrmC but lacks the N-terminal domain thought to be involved in the recognition of the bacterial release factors. Overproduced in S. cerevisiae, YDR140w can methylate eRF1 from yeast or man in vitro using S-adenosyl l-methionine as methyl donor provided that eRF3 and GTP are also present, suggesting that the natural substrate of the methyltransferase YDR140w is the ternary complex eRF1.eRF3.GTP.
Collapse
Affiliation(s)
- Valérie Heurgué-Hamard
- UPR9073 du CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
| | | | | | | | | | | | | |
Collapse
|