1
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Sahranavardfard P, Madjd Z, Emami Razavi AN, Ghanadan AR, Firouzi J, Khosravani P, Ghavami S, Ebrahimie E, Ebrahimi M. An Integrative Analysis of The Micro-RNAs Contributing in Stemness, Metastasis and B-Raf Pathways in Malignant Melanoma and Melanoma Stem Cell. CELL JOURNAL 2021; 23:261-272. [PMID: 34308569 PMCID: PMC8286452 DOI: 10.22074/cellj.2021.7311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/14/2020] [Indexed: 11/11/2022]
Abstract
Objective Epithelial-mesenchymal transition (EMT) and the stemness potency in association with BRAF mutation are
in dispensable to the progression of melanoma. Recently, microRNAs (miRNAs) have been introduced as the regulator
of a multitude of oncogenic functions in most of tumors. Therefore identifying and interpreting the expression patterns of
these miRNAs is essential. The present study sought to find common miRNAs regulating all three important pathways
in melanoma development.
Materials and Methods In this experimental study, 18 miRNAs that importantly contribute to EMT and have a role
in regulating self-renewal and the BRAF pathway were selected based on current literature and cross-analysis with
available databases. Subsequently, their expression patterns were evaluated in 20 melanoma patients, normal tissues,
serum from patients and control subjects, and melanospheres. Pattern discovery and integrative regulatory network
analysis were used to find the most important miRNAs in melanoma progression.
Results Among 18 selected miRNAs, miR-205, -141, -203, -15b, and -9 were differentially expressed in tumor samples
than normal tissues. Among them, miR-205, -15b, and -9 significantly expressed in serum samples and healthy donors.
Attribute Weighting and decision trees (DT) analysis presented evidence that the combination of miR-205, -203, -9, and
-15b can regulate self-renewal and EMT process, by affecting CDH1, CCND1, and VEGF expression.
Conclusion We suggested here that miR-205, -15b, -203, -9 pattern as the key miRNAs linked to melanoma status,
the pluripotency, proliferation, and motility of malignant cells. However, further investigations are required to find the
mechanisms underlying the combinatory effects of the above mentioned miRNAs.
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Affiliation(s)
- Parisa Sahranavardfard
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Zahra Madjd
- Department of Pathology, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Nader Emami Razavi
- Iran National Tumor Bank, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Reza Ghanadan
- Iran National Tumor Bank, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran.,Department of Dermatopathology, Razi Skin Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Firouzi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Pardis Khosravani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Sciences, University of Manitoba, Manitoba, Canada. .,Biology of Breathing, Children Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada.,Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Research Institute in Oncology and Hematology, Cancer Care Manitoba, University of Manitoba, Winnipeg, Canada
| | - Esmaeil Ebrahimie
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia. .,Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne, Australia
| | - Marzieh Ebrahimi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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2
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Jamalkandi SA, Kouhsar M, Salimian J, Ahmadi A. The identification of co-expressed gene modules in Streptococcus pneumonia from colonization to infection to predict novel potential virulence genes. BMC Microbiol 2020; 20:376. [PMID: 33334315 PMCID: PMC7745498 DOI: 10.1186/s12866-020-02059-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 12/02/2020] [Indexed: 11/14/2022] Open
Abstract
Background Streptococcus pneumonia (pneumococcus) is a human bacterial pathogen causing a range of mild to severe infections. The complicated transcriptome patterns of pneumococci during the colonization to infection process in the human body are usually determined by measuring the expression of essential virulence genes and the comparison of pathogenic with non-pathogenic bacteria through microarray analyses. As systems biology studies have demonstrated, critical co-expressing modules and genes may serve as key players in biological processes. Generally, Sample Progression Discovery (SPD) is a computational approach traditionally used to decipher biological progression trends and their corresponding gene modules (clusters) in different clinical samples underlying a microarray dataset. The present study aimed to investigate the bacterial gene expression pattern from colonization to severe infection periods (specimens isolated from the nasopharynx, lung, blood, and brain) to find new genes/gene modules associated with the infection progression. This strategy may lead to finding novel gene candidates for vaccines or drug design. Results The results included essential genes whose expression patterns varied in different bacterial conditions and have not been investigated in similar studies. Conclusions In conclusion, the SPD algorithm, along with differentially expressed genes detection, can offer new ways of discovering new therapeutic or vaccine targeted gene products. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02059-0.
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Affiliation(s)
- Sadegh Azimzadeh Jamalkandi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Morteza Kouhsar
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Jafar Salimian
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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3
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Alanazi IO, Al Shehri ZS, Ebrahimie E, Giahi H, Mohammadi-Dehcheshmeh M. Non-coding and coding genomic variants distinguish prostate cancer, castration-resistant prostate cancer, familial prostate cancer, and metastatic castration-resistant prostate cancer from each other. Mol Carcinog 2019; 58:862-874. [PMID: 30644608 DOI: 10.1002/mc.22975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 12/11/2022]
Abstract
A considerable number of deposited variants has provided new possibilities for knowledge discovery in different types of prostate cancer. Here, we analyzed variants located on 3'UTR, 5'UTR, CDs, Intergenic, and Intronic regions in castration-resistant prostate cancer (8496 variants), familial prostate cancer (3241 variants), metastatic castration-resistant prostate cancer (3693 variants), and prostate cancer (16599 variants). Chromosome regions 10p15-p14 and 2p13 were highly enriched (P < 0.00001) for variants located in 3'UTR, 5'UTR, CDs, intergenic, and intronic regions in castration-resistant prostate cancer. In contrast, 10p15-p14, 10q23.3, 12q13.11, 13q12.3, 1q25, and 8p22 regions were enriched (P < 0.001) in familial prostate cancer. In metastatic castration-resistant prostate cancer, 10p15-p14, 10q23.3, 11q22-q23, 14q21.1, and 14q32.13 were highly variant regions (P < 0.001). Chromosome 2 and chromosome 1 hosted many enriched variant regions. AKR1C3, BRCA1, BRCA2, CHGA, CYP19A1, HOXB13, KLK3, and PTEN contained the highest number of 3'UTR, 5'UTR, CDs, Intergenic, and Intronic variants. Network analysis showed that these genes are upstream of important functions including prostate gland development, tumor recurrence, prostate cancer-specific survival, tumor progression, cancer mortality, long-term survival, cancer recurrence, angiogenesis, and AR. Interestingly, all of EGFR, JAK2, NR3C1, PDZD2, and SEMA3C genes had single nucleotide polymorphisms (SNP) in castration-resistant prostate cancer, consistent with high selection pressure on these genes during drug treatment and consequent resistance. High occurrence of variants in 3'UTRs suggests the importance of regulatory variants in different types of prostate cancer; an area that has been neglected compared with coding variants. This study provides a comprehensive overview of genomic regions contributing to different types of prostate cancer.
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Affiliation(s)
- Ibrahim O Alanazi
- National Center for Biotechnology, Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Zafer S Al Shehri
- Clinical Laboratory Department, College of Applied Medical Sciences, Shaqra University, KSA, Al dawadmi, Saudi Arabia
| | - Esmaeil Ebrahimie
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.,School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, The University of South Australia, Adelaide, SA, Australia.,Institute of Biotechnology, Shiraz University, Shiraz, Iran.,Faculty of Science and Engineering, School of Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Hassan Giahi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Manijeh Mohammadi-Dehcheshmeh
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, South Australia, Australia
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4
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Eutsey RA, Woolford CA, Aggarwal SD, Cuevas RA, Hiller NL. Gene Expression Analysis in the Pneumococcus. Methods Mol Biol 2019; 1968:79-88. [PMID: 30929207 DOI: 10.1007/978-1-4939-9199-0_7] [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] [Indexed: 06/09/2023]
Abstract
Bacterial cells modify their gene expression profiles throughout different stages of growth and in response to environmental cues. Analyses of gene expression across conditions reveal both conserved and condition-specific gene responses of bacteria to adapt to these dynamic conditions. In this chapter, we present a guide to pneumococcal RNA extraction for use in the NanoString nCounter platform. The nCounter is a highly effective method to measure gene expression of bacteria not only in a planktonic mode of growth but also in the presence of host cells where the RNA of interest represents only a small portion of the total material.
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Affiliation(s)
- Rory A Eutsey
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Carol A Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Surya D Aggarwal
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Rolando A Cuevas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
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5
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Mohammadi-Dehcheshmeh M, Niazi A, Ebrahimi M, Tahsili M, Nurollah Z, Ebrahimi Khaksefid R, Ebrahimi M, Ebrahimie E. Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots of Medicago truncatula by Integration of Machine Learning, Promoter Analysis, and Direct Merging Meta-Analysis. FRONTIERS IN PLANT SCIENCE 2018; 9:1550. [PMID: 30483277 PMCID: PMC6240842 DOI: 10.3389/fpls.2018.01550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/03/2018] [Indexed: 05/25/2023]
Abstract
Plant root symbiosis with Arbuscular mycorrhizal (AM) fungi improves uptake of water and mineral nutrients, improving plant development under stressful conditions. Unraveling the unified transcriptomic signature of a successful colonization provides a better understanding of symbiosis. We developed a framework for finding the transcriptomic signature of Arbuscular mycorrhiza colonization and its regulating transcription factors in roots of Medicago truncatula. Expression profiles of roots in response to AM species were collected from four separate studies and were combined by direct merging meta-analysis. Batch effect, the major concern in expression meta-analysis, was reduced by three normalization steps: Robust Multi-array Average algorithm, Z-standardization, and quartiling normalization. Then, expression profile of 33685 genes in 18 root samples of Medicago as numerical features, as well as study ID and Arbuscular mycorrhiza type as categorical features, were mined by seven models: RELIEF, UNCERTAINTY, GINI INDEX, Chi Squared, RULE, INFO GAIN, and INFO GAIN RATIO. In total, 73 genes selected by machine learning models were up-regulated in response to AM (Z-value difference > 0.5). Feature weighting models also documented that this signature is independent from study (batch) effect. The AM inoculation signature obtained was able to differentiate efficiently between AM inoculated and non-inoculated samples. The AP2 domain class transcription factor, GRAS family transcription factors, and cyclin-dependent kinase were among the highly expressed meta-genes identified in the signature. We found high correspondence between the AM colonization signature obtained in this study and independent RNA-seq experiments on AM colonization, validating the repeatability of the colonization signature. Promoter analysis of upregulated genes in the transcriptomic signature led to the key regulators of AM colonization, including the essential transcription factors for endosymbiosis establishment and development such as NF-YA factors. The approach developed in this study offers three distinct novel features: (I) it improves direct merging meta-analysis by integrating supervised machine learning models and normalization steps to reduce study-specific batch effects; (II) seven attribute weighting models assessed the suitability of each gene for the transcriptomic signature which contributes to robustness of the signature (III) the approach is justifiable, easy to apply, and useful in practice. Our integrative framework of meta-analysis, promoter analysis, and machine learning provides a foundation to reveal the transcriptomic signature and regulatory circuits governing Arbuscular mycorrhizal symbiosis and is transferable to the other biological settings.
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Affiliation(s)
- Manijeh Mohammadi-Dehcheshmeh
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA, Australia
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | | | | | - Zahra Nurollah
- Department of Biotechnology, Shahrekord University, Shahrekord, Iran
| | - Reyhaneh Ebrahimi Khaksefid
- Department of Biotechnology, Shahrekord University, Shahrekord, Iran
- School of Agriculture Food and Wine, Department of Plant Science, The University of Adelaide, Adelaide, SA, Australia
| | - Mahdi Ebrahimi
- Max-Planck-Institute for Informatics, Saarbrucken, Germany
| | - Esmaeil Ebrahimie
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA, Australia
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Division of Information Technology, Engineering and the Environment, School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, SA, Australia
- Faculty of Science and Engineering, School of Biological Sciences, Flinders University, Adelaide, SA, Australia
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6
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Molecular characterization of Brassica napus stress related transcription factors, BnMYB44 and BnVIP1, selected based on comparative analysis of Arabidopsis thaliana and Eutrema salsugineum transcriptomes. Mol Biol Rep 2018; 45:1111-1124. [DOI: 10.1007/s11033-018-4262-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
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7
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Nutritional Regulation of the Sae Two-Component System by CodY in Staphylococcus aureus. J Bacteriol 2018; 200:JB.00012-18. [PMID: 29378891 DOI: 10.1128/jb.00012-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 01/23/2018] [Indexed: 01/22/2023] Open
Abstract
Staphylococcus aureus subverts innate defenses during infection in part by killing host immune cells to exacerbate disease. This human pathogen intercepts host cues and activates a transcriptional response via the S. aureus exoprotein expression (SaeR/SaeS [SaeR/S]) two-component system to secrete virulence factors critical for pathogenesis. We recently showed that the transcriptional repressor CodY adjusts nuclease (nuc) gene expression via SaeR/S, but the mechanism remained unknown. Here, we identified two CodY binding motifs upstream of the sae P1 promoter, which suggested direct regulation by this global regulator. We show that CodY shares a binding site with the positive activator SaeR and that alleviating direct CodY repression at this site is sufficient to abrogate stochastic expression, suggesting that CodY represses sae expression by blocking SaeR binding. Epistasis experiments support a model that CodY also controls sae indirectly through Agr and Rot-mediated repression of the sae P1 promoter. We also demonstrate that CodY repression of sae restrains production of secreted cytotoxins that kill human neutrophils. We conclude that CodY plays a previously unrecognized role in controlling virulence gene expression via SaeR/S and suggest a mechanism by which CodY acts as a master regulator of pathogenesis by tying nutrient availability to virulence gene expression.IMPORTANCE Bacterial mechanisms that mediate the switch from a commensal to pathogenic lifestyle are among the biggest unanswered questions in infectious disease research. Since the expression of most virulence genes is often correlated with nutrient depletion, this implies that virulence is a response to the lack of nourishment in host tissues and that pathogens like S. aureus produce virulence factors in order to gain access to nutrients in the host. Here, we show that specific nutrient depletion signals appear to be funneled to the SaeR/S system through the global regulator CodY. Our findings reveal a strategy by which S. aureus delays the production of immune evasion and immune-cell-killing proteins until key nutrients are depleted.
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8
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Ebrahimie E, Fruzangohar M, Moussavi Nik SH, Newman M. Gene Ontology-Based Analysis of Zebrafish Omics Data Using the Web Tool Comparative Gene Ontology. Zebrafish 2017; 14:492-494. [DOI: 10.1089/zeb.2016.1290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Esmaeil Ebrahimie
- Alzheimer's Disease Genetics Laboratory, Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
- Division of Information Technology, Engineering and the Environment, School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, Australia
- Faculty of Science and Engineering, School of Biological Sciences, Flinders University, Adelaide, Australia
| | - Mario Fruzangohar
- Australian Centre for Plant Functional Genomics (ACPFG), School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Seyyed Hani Moussavi Nik
- Alzheimer's Disease Genetics Laboratory, Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Morgan Newman
- Alzheimer's Disease Genetics Laboratory, Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
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9
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Chai MH, Weiland F, Harvey RM, Hoffmann P, Ogunniyi AD, Paton JC. Proteomic comparisons of opaque and transparent variants of Streptococcus pneumoniae by two dimensional-differential gel electrophoresis. Sci Rep 2017; 7:2453. [PMID: 28550292 PMCID: PMC5446427 DOI: 10.1038/s41598-017-02465-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/11/2017] [Indexed: 11/09/2022] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) is a human pathogen, accounting for massive global morbidity and mortality. Although asymptomatic colonization of the nasopharynx almost invariably precedes disease, the critical determinants enabling pneumococcal progression from this niche to cause invasive disease are poorly understood. One mechanism proposed to be central to this transition involves opacity phase variation, whereby pneumococci harvested from the nasopharynx are typically transparent, while those simultaneously harvested from the blood are opaque. Here, we used two dimensional-differential gel electrophoresis (2D-DIGE) to compare protein expression profiles of transparent and opaque variants of 3 pneumococcal strains, D39 (serotype 2), WCH43 (serotype 4) and WCH16 (serotype 6A) in vitro. One spot comprising a mixture of capsular polysaccharide biosynthesis protein and other proteins was significantly up-regulated in the opaque phenotype in all 3 strains; other proteins were differentially regulated in a strain-specific manner. We conclude that pneumococcal phase variation is a complex and multifactorial process leading to strain-specific pathogenicity.
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Affiliation(s)
- Melissa H Chai
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Florian Weiland
- Adelaide Proteomics Centre, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.,Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia, 5005, Australia.,Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Richard M Harvey
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Peter Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.,Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Abiodun D Ogunniyi
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia. .,Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia.
| | - James C Paton
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
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10
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Watkins ER, Maiden MC, Gupta S. Metabolic competition as a driver of bacterial population structure. Future Microbiol 2016; 11:1339-1357. [PMID: 27660887 DOI: 10.2217/fmb-2016-0079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Understanding the processes whereby diversity arises and is maintained in pathogen populations is pivotal for designing disease control interventions. A particular problem is the maintenance of strain structure in bacterial pathogen populations despite frequent genetic exchange. Although several theoretical frameworks have been put forward to explain this widespread phenomenon, few have focused on the role of genes encoding metabolic functions, despite an increasing recognition of their importance in pathogenesis and transmission. In this article, we review the literature for evidence of metabolic niches within the host and discuss theoretical frameworks which examine ecological interactions between metabolic genes. We contend that metabolic competition is an important phenomenon which contributes to the maintenance of population structure and diversity of many bacterial pathogens.
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Affiliation(s)
- Eleanor R Watkins
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Martin Cj Maiden
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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11
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Fleming E, Camilli A. ManLMN is a glucose transporter and central metabolic regulator in Streptococcus pneumoniae. Mol Microbiol 2016; 102:467-487. [PMID: 27472033 PMCID: PMC5116393 DOI: 10.1111/mmi.13473] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2016] [Indexed: 01/24/2023]
Abstract
Streptococcus pneumoniae is a common colonizer of the human nasopharynx and a leading cause of bacterial pneumonia and otitis media, among other invasive diseases. During both colonization and invasive disease S. pneumoniae ferments host-derived carbohydrates as its primary means of generating energy. This pathogen is adept at transporting and metabolizing a wide variety of carbohydrates. We found the highly conserved PTS ManLMN contributes to growth on glucose and is also essential for growth on a variety of nonpreferred carbohydrates, suggesting it is a multisubstrate transporter. Exploration of this phenotype revealed ManLMN is required for inducing expression of downstream metabolic genes in response to carbohydrate stimuli. We further demonstrate that ManLMN's role as a constitutively expressed transporter is likely unique and integral to pneumococcus's strategy of carbon catabolite repression (CCR). Using a selection for suppressors, we explored how ManLMN is integrated into the CCR regulatory framework in S. pneumoniae. We identified two hypothetical small proteins and the virulence regulator SmrC as potential mediators of CCR in connection with ManLMN. Characterization of these two hypothetical proteins revealed they influence transcriptional regulation of carbohydrate transporters. We propose a model unifying these observations in which ManLMN is a versatile surveyor of available carbohydrates in S. pneumoniae.
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Affiliation(s)
- Eleanor Fleming
- Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Howard Hughes Medical Institute, and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA, 02111, USA
| | - Andrew Camilli
- Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Howard Hughes Medical Institute, and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA, 02111, USA.
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12
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In Vitro Analysis of Predicted DNA-Binding Sites for the Stl Repressor of the Staphylococcus aureus SaPIBov1 Pathogenicity Island. PLoS One 2016; 11:e0158793. [PMID: 27388898 PMCID: PMC4936726 DOI: 10.1371/journal.pone.0158793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/22/2016] [Indexed: 12/27/2022] Open
Abstract
The regulation model of the Staphylococcus aureus pathogenicity island SaPIbov1 transfer was recently reported. The repressor protein Stl obstructs the expression of SaPI proteins Str and Xis, latter which is responsible for mobilization initiation. Upon Φ11 phage infection of S. aureus. phage dUTPase activates the SaPI transfer via Stl-dUTPase complex formation. Our aim was to predict the binding sites for the Stl repressor within the S. aureus pathogenicity island DNA sequence. We found that Stl was capable to bind to three 23-mer oligonucleotides, two of those constituting sequence segments in the stl-str, while the other corresponding to sequence segment within the str-xis intergenic region. Within these oligonucleotides, mutational analysis revealed that the predicted binding site for the Stl protein exists as a palindromic segment in both intergenic locations. The palindromes are built as 6-mer repeat sequences involved in Stl binding. The 6-mer repeats are separated by a 5 oligonucleotides long, nonspecific sequence. Future examination of the interaction between Stl and its binding sites in vivo will provide a molecular explanation for the mechanisms of gene repression and gene activation exerted simultaneously by the Stl protein in regulating transfer of the SaPIbov1 pathogenicity island in S. aureus.
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13
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Alanazi IO, Ebrahimie E. Computational Systems Biology Approach Predicts Regulators and Targets of microRNAs and Their Genomic Hotspots in Apoptosis Process. Mol Biotechnol 2016; 58:460-79. [DOI: 10.1007/s12033-016-9938-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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14
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Dang XY, Chu WW, Shi HC, Yu SG, Han HY, Gu SH, Chen J. Genetic variants in ABCA1 promoter affect transcription activity and plasma HDL level in pigs. Gene 2014; 555:414-20. [PMID: 25445391 DOI: 10.1016/j.gene.2014.11.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/11/2014] [Accepted: 11/19/2014] [Indexed: 01/03/2023]
Abstract
Excess accumulation of cholesterol in plasma may result in coronary artery disease. Numerous studies have demonstrated that ATP-binding cassette protein A1 (ABCA1) mediates the efflux of cholesterol and phospholipids to apolipoproteins, a process necessary for plasma high density lipoprotein (HDL) formation. Higher plasma levels of HDL are associated with lower risk for cardiovascular disease. Studies of human disease and animal models had shown that an increased hepatic ABCA1 activity relates to an enhanced plasma HDL level. In this study, we hypothesized that functional mutations in the ABCA1 promoter in pigs may affect gene transcription activity, and consequently the HDL level in plasma. The promoter region of ABCA1 was comparatively scanned by direct sequencing with pool DNA of high- and low-HDL groups (n=30 for each group). Two polymorphisms, c. - 608A>G and c. - 418T>A, were revealed with reverse allele distribution in the two groups. The two polymorphisms were completely linked and formed only G-A or A-T haplotypes when genotyped in a larger population (n=526). Furthermore, we found that the G-A/G-A genotype was associated with higher HDL and ABCA1 mRNA level than A-T/A-T genotype. Luciferase assay also revealed that G-A haplotype promoter had higher activity than A-T haplotype. Single-nucleotide mutant assay showed that c.-418T>A was the causal mutation for ABCA1 transcription activity alteration. Conclusively, we identified two completely linked SNPs in porcine ABCA1 promoter region which have influence on the plasma HDL level by altering ABCA1 gene transcriptional activity.
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Affiliation(s)
- Xiao-yong Dang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wei-wei Chu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Heng-chuan Shi
- Laboratory Department, Jiangsu Province Official Hospital, Nanjing 210024, PR China
| | - Shi-gang Yu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hai-yin Han
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shu-Hua Gu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jie Chen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China.
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15
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A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: application to Arabidopsis. J Theor Biol 2014; 364:364-76. [PMID: 25303887 DOI: 10.1016/j.jtbi.2014.09.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 09/27/2014] [Accepted: 09/29/2014] [Indexed: 11/22/2022]
Abstract
Cis regulatory elements (CREs), located within promoter regions, play a significant role in the blueprint for transcriptional regulation of genes. There is a growing interest to study the combinatorial nature of CREs including presence or absence of CREs, the number of occurrences of each CRE, as well as of their order and location relative to their target genes. Comparative promoter analysis has been shown to be a reliable strategy to test the significance of each component of promoter architecture. However, it remains unclear what level of difference in the number of occurrences of each CRE is of statistical significance in order to explain different expression patterns of two genes. In this study, we present a novel statistical approach for pairwise comparison of promoters of Arabidopsis genes in the context of number of occurrences of each CRE within the promoters. First, using the sample of 1000 Arabidopsis promoters, the results of the goodness of fit test and non-parametric analysis revealed that the number of occurrences of CREs in a promoter sequence is Poisson distributed. As a promoter sequence contained functional and non-functional CREs, we addressed the issue of the statistical distribution of functional CREs by analyzing the ChIP-seq datasets. The results showed that the number of occurrences of functional CREs over the genomic regions was determined as being Poisson distributed. In accordance with the obtained distribution of CREs occurrences, we suggested the Audic and Claverie (AC) test to compare two promoters based on the number of occurrences for the CREs. Superiority of the AC test over Chi-square (2×2) and Fisher's exact tests was also shown, as the AC test was able to detect a higher number of significant CREs. The two case studies on the Arabidopsis genes were performed in order to biologically verify the pairwise test for promoter comparison. Consequently, a number of CREs with significantly different occurrences was identified between the promoters. The results of the pairwise comparative analysis together with the expression data for the studied genes revealed the biological significance of the identified CREs.
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