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Yang Y, Wang P, Qaidi SE, Hardwidge PR, Huang J, Zhu G. Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance. Appl Microbiol Biotechnol 2024; 108:328. [PMID: 38717672 PMCID: PMC11078800 DOI: 10.1007/s00253-023-12971-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 05/12/2024]
Abstract
Pseudogenes are defined as "non-functional" copies of corresponding parent genes. The cognition of pseudogenes continues to be refreshed through accumulating and updating research findings. Previous studies have predominantly focused on mammals, but pseudogenes have received relatively less attention in the field of microbiology. Given the increasing recognition on the importance of pseudogenes, in this review, we focus on several aspects of microorganism pseudogenes, including their classification and characteristics, their generation and fate, their identification, their abundance and distribution, their impact on virulence, their ability to recombine with functional genes, the extent to which some pseudogenes are transcribed and translated, and the relationship between pseudogenes and viruses. By summarizing and organizing the latest research progress, this review will provide a comprehensive perspective and improved understanding on pseudogenes in microorganisms. KEY POINTS: • Concept, classification and characteristics, identification and databases, content, and distribution of microbial pseudogenes are presented. • How pseudogenization contribute to pathogen virulence is highlighted. • Pseudogenes with potential functions in microorganisms are discussed.
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Affiliation(s)
- Yi Yang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China
| | - Pengzhi Wang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China
| | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Jinlin Huang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Jiangsu Key Lab of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- College of Bioscience and Biotechnology, Yangzhou University, 12 East Wenhui Road Yangzhou, Jiangsu, 225009, China.
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China.
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China.
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Sugawara-Mikami M, Tanigawa K, Kawashima A, Kiriya M, Nakamura Y, Fujiwara Y, Suzuki K. Pathogenicity and virulence of Mycobacterium leprae. Virulence 2022; 13:1985-2011. [PMID: 36326715 PMCID: PMC9635560 DOI: 10.1080/21505594.2022.2141987] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Leprosy is caused by Mycobacterium leprae (M. leprae) and M. lepromatosis, an obligate intracellular organism, and over 200,000 new cases occur every year. M. leprae parasitizes histiocytes (skin macrophages) and Schwann cells in the peripheral nerves. Although leprosy can be treated by multidrug therapy, some patients relapse or have a prolonged clinical course and/or experience leprosy reaction. These varying outcomes depend on host factors such as immune responses against bacterial components that determine a range of symptoms. To understand these host responses, knowledge of the mechanisms by which M. leprae parasitizes host cells is important. This article describes the characteristics of leprosy through bacteriology, genetics, epidemiology, immunology, animal models, routes of infection, and clinical findings. It also discusses recent diagnostic methods, treatment, and measures according to the World Health Organization (WHO), including prevention. Recently, the antibacterial activities of anti-hyperlipidaemia agents against other pathogens, such as M. tuberculosis and Staphylococcus aureus have been investigated. Our laboratory has been focused on the metabolism of lipids which constitute the cell wall of M. leprae. Our findings may be useful for the development of future treatments.
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Affiliation(s)
- Mariko Sugawara-Mikami
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan.,West Yokohama Sugawara Dermatology Clinic, Yokohama, Japan
| | - Kazunari Tanigawa
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Akira Kawashima
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Mitsuo Kiriya
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Yasuhiro Nakamura
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Yoko Fujiwara
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Koichi Suzuki
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
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Tanigawa K, Hayashi Y, Hama K, Yamashita A, Yokoyama K, Luo Y, Kawashima A, Maeda Y, Nakamura Y, Harada A, Kiriya M, Karasawa K, Suzuki K. Mycobacterium leprae promotes triacylglycerol de novo synthesis through induction of GPAT3 expression in human premonocytic THP-1 cells. PLoS One 2021; 16:e0249184. [PMID: 33770127 PMCID: PMC7997041 DOI: 10.1371/journal.pone.0249184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 03/12/2021] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium leprae (M. leprae) is the etiological agent of leprosy, and the skin lesions of lepromatous leprosy are filled with numerous foamy or xanthomatous histiocytes that are parasitized by M. leprae. Lipids are an important nutrient for the intracellular survival of M. leprae. In this study, we attempted to determine the intracellular lipid composition and underlying mechanisms for changes in host cell lipid metabolism induced by M. leprae infection. Using high-performance thin-layer chromatography (HPTLC), we demonstrated specific induction of triacylglycerol (TAG) production in human macrophage THP-1 cells following M. leprae infection. We then used [14C] stearic acid tracing to show incorporation of this newly synthesized host cell TAG into M. leprae. In parallel with TAG accumulation, expression of host glycerol-3-phosphate acyltransferase 3 (GPAT3), a key enzyme in de novo TAG synthesis, was significantly increased in M. leprae-infected cells. CRISPR/Cas9 genome editing of GPAT3 in THP-1 cells (GPAT3 KO) dramatically reduced accumulation of TAG following M. leprae infection, intracellular mycobacterial load, and bacteria viability. These results together suggest that M. leprae induces host GPAT3 expression to facilitate TAG accumulation within macrophages to maintain a suitable environment that is crucial for intracellular survival of these bacilli.
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Affiliation(s)
- Kazunari Tanigawa
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Itabashi-ku, Tokyo, Japan
| | - Yasuhiro Hayashi
- Department of Biological Chemistry, Faculty of Pharma-Science, Teikyo University, Itabashi-ku, Tokyo, Japan
| | - Kotaro Hama
- Department of Physical Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Itabashi-ku, Tokyo, Japan
| | - Atsushi Yamashita
- Department of Biological Chemistry, Faculty of Pharma-Science, Teikyo University, Itabashi-ku, Tokyo, Japan
| | - Kazuaki Yokoyama
- Department of Physical Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Itabashi-ku, Tokyo, Japan
| | - Yuqian Luo
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Itabashi-ku, Tokyo, Japan
| | - Akira Kawashima
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Itabashi-ku, Tokyo, Japan
| | - Yumi Maeda
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama-shi, Tokyo, Japan
| | - Yasuhiro Nakamura
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Itabashi-ku, Tokyo, Japan
| | - Ayako Harada
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Itabashi-ku, Tokyo, Japan
| | - Mitsuo Kiriya
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Itabashi-ku, Tokyo, Japan
| | - Ken Karasawa
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Itabashi-ku, Tokyo, Japan
| | - Koichi Suzuki
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Itabashi-ku, Tokyo, Japan
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama-shi, Tokyo, Japan
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Bao Y, Wang L, Sun J. Post-translational knockdown and post-secretional modification of EsxA determine contribution of EsxA membrane permeabilizing activity for mycobacterial intracellular survival. Virulence 2021; 12:312-328. [PMID: 33356823 PMCID: PMC7808419 DOI: 10.1080/21505594.2020.1867438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Current genetic studies (e.g. gene knockout) have suggested that EsxA and EsxB function as secreted virulence factors that are essential for Mycobaterium tuberculosis (Mtb) intracellular survival, specifically in mediating phagosome rupture and translocation of Mtb to the cytosol of host cells, which further facilitates Mtb intracellular replicating and cell-to-cell spreading. The EsxA-mediated intracellular survival is presumably achieved by its pH-dependent membrane-permeabilizing activity (MPA). However, the data from other studies have generated a discrepancy regarding the role of EsxA MPA in mycobacterial intracellular survival, which has raised a concern that genetic manipulations, such as deletion of esxB-esxA operon or RD-1 locus, may affect other codependently secreted factors that could be also directly involved cytosolic translocation, or stimulate extended disturbance on other genes’ expression. To avoid the drawbacks of gene knockout, we first engineered a Mycobacterium marinum (Mm) strain, in which a DAS4+ tag was fused to the C-terminus of EsxB to allow inducible knockdown of EsxB (also EsxA) at the post-translational level. We also engineered an Mm strain by fusing a SpyTag (ST) to the C-terminus of EsxA, which allowed inhibition of EsxA-ST MPA at the post-secretional level through a covalent linkage to SpyCatcher-GFP. Both post-translational knockdown and functional inhibition of EsxA resulted in attenuation of Mm intracellular survival in lung epithelial cells or macrophages, which unambiguously confirms the direct role of EsxA MPA in mycobacterial intracellular survival.
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Affiliation(s)
- Yanqing Bao
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso , El Paso, Texas, USA
| | - Lin Wang
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso , El Paso, Texas, USA
| | - Jianjun Sun
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso , El Paso, Texas, USA
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Bai Y, Qu Y, Wu Z, Ren Y, Cheng Z, Lu Y, Hu J, Lou J, Zhao J, Chen C, Mao H. Absolute quantification and analysis of extracellular vesicle lncRNAs from the peripheral blood of patients with lung cancer based on multi-colour fluorescence chip-based digital PCR. Biosens Bioelectron 2019; 142:111523. [DOI: 10.1016/j.bios.2019.111523] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/03/2019] [Accepted: 07/16/2019] [Indexed: 01/08/2023]
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Chavarro-Portillo B, Soto CY, Guerrero MI. Mycobacterium leprae's evolution and environmental adaptation. Acta Trop 2019; 197:105041. [PMID: 31152726 DOI: 10.1016/j.actatropica.2019.105041] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 11/24/2022]
Abstract
Leprosy is an ancient disease caused by the acid-fast bacillus Mycobacterium leprae, also known as Hansen's bacillus. M. leprae is an obligate intracellular microorganism with a marked Schwann cell tropism and is the only human pathogen capable of invading the superficial peripheral nerves. The transmission mechanism of M. leprae is not fully understood; however, the nasal mucosa is accepted as main route of M. leprae entry to the human host. The complete sequencing and the comparative genome analysis show that M. leprae underwent a genome reductive evolution process, as result of lifestyle change and adaptation to different environments; some of lost genes are homologous to those of host cells. Thus, M. leprae reduced its genome size to 3.3 Mbp, contributing to obtain the lowest GC content (approximately 58%) among mycobacteria. The M. leprae genome contains 1614 open reading frames coding for functional proteins, and 1310 pseudogenes corresponding to 41% of the genome, approximately. Comparative analyses to different microorganisms showed that M. leprae possesses the highest content of pseudogenes among pathogenic and non-pathogenic bacteria and archaea. The pathogen adaptation into host cells, as the Schwann cells, brought about the reduction of the genome and induced multiple gene inactivation. The present review highlights the characteristics of genome's reductive evolution that M. leprae experiences in the genetic aspects compared with other pathogens. The possible mechanisms of pseudogenes formation are discussed.
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Sharma M, Das M, Diana D, Wedderburn A, Anindya R. Identification of novel open reading frames in the intergenic regions of Mycobacterium leprae genome and detection of transcript by qRT-PCR. Microb Pathog 2018; 124:316-321. [DOI: 10.1016/j.micpath.2018.08.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 10/28/2022]
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Soares CT, Trombone APF, Fachin LRV, Rosa PS, Ghidella CC, Ramalho RF, Pinilla MG, Carvalho AF, Carrara DN, Soares FA, Belone AFF. Differential Expression of MicroRNAs in Leprosy Skin Lesions. Front Immunol 2017; 8:1035. [PMID: 28970833 PMCID: PMC5609578 DOI: 10.3389/fimmu.2017.01035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 08/10/2017] [Indexed: 12/19/2022] Open
Abstract
Leprosy, a chronic infectious disease caused by Mycobacterium leprae, is a major public health problem in poor and developing countries of the Americas, Africa, and Asia. MicroRNAs (miRNAs), which are small non-coding RNAs (18–24 nucleotides), play an important role in regulating cell and tissue homeostasis through translational downregulation of messenger RNAs (mRNAs). Deregulation of miRNA expression is important for the pathogenesis of various neoplastic and non-neoplastic diseases and has been the focus of many publications; however, studies on the expression of miRNAs in leprosy are rare. Herein, an extensive evaluation of differentially expressed miRNAs was performed on leprosy skin lesions using microarrays. Leprosy patients, classified according to Ridley and Jopling’s classification or reactional states (R1 and R2), and healthy controls (HCs) were included. Punch biopsies were collected from the borders of leprosy lesions (10 tuberculoid, 10 borderline tuberculoid, 10 borderline borderline, 10 borderline lepromatous, 4 lepromatous, 14 R1, and 9 R2) and from 9 HCs. miRNA expression profiles were obtained using the Agilent Microarray platform with miRBase, which consists of 1,368 Homo sapiens (hsa)-miRNA candidates. TaqMan quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) was used to validate differentially expressed miRNAs. Sixty-four differentially expressed miRNAs, including 50 upregulated and 14 downregulated (fold change ≥2.0, p-value ≤ 0.05) were identified after comparing samples from patients to those of controls. Twenty differentially expressed miRNAs were identified exclusively in the reactional samples (14 type 1 and 6 type 2). Eight miRNAs were validated by RT-PCR, including seven upregulated (hsa-miR-142-3p, hsa-miR-142-5p, hsa-miR-146b-5p, hsa-miR-342-3p, hsa-miR-361-3p, hsa-miR-3653, and hsa-miR-484) and one downregulated (hsa-miR-1290). These miRNAs were differentially expressed in leprosy and several other diseases, especially those related to the immune response. Moreover, the integration of analysis of validated mi/mRNAs obtained from the same samples allowed target pairs opposite expression pattern of hsa-miRNA-142-3p and AKR1B10, hsa-miRNA-342-3p and FAM180b, and hsa-miRNA-484 and FASN. This study identified several miRNAs that might play an important role in the molecular pathogenesis of the disease. Moreover, these deregulated miRNAs and their respective signaling pathways might be useful as therapeutic markers, therapeutic targets, which could help in the development of drugs to treat leprosy.
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Affiliation(s)
- Cleverson T Soares
- Department of Anatomic Pathology, Instituto Lauro de Souza Lima, São Paulo, Brazil
| | - Ana P F Trombone
- Department of Health Science, Universidade do Sagrado Coração, São Paulo, Brazil
| | - Luciana R V Fachin
- Department of Anatomic Pathology, Instituto Lauro de Souza Lima, São Paulo, Brazil
| | - Patricia S Rosa
- Division of Research and Education, Instituto Lauro de Souza Lima, São Paulo, Brazil
| | - Cássio C Ghidella
- Ambulatory of Leprosy, Jardim Guanabara Health Center, Rondonópolis, Brazil
| | - Rodrigo F Ramalho
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Mabel G Pinilla
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center, São Paulo, Brazil.,Department of Medical Technology, School of Medicine, University of Concepción, Concepción, Chile
| | - Alex F Carvalho
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center, São Paulo, Brazil.,Department of Preventive Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Dirce N Carrara
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Fernando A Soares
- Department of Anatomic Pathology, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Andrea F F Belone
- Department of Anatomic Pathology, Instituto Lauro de Souza Lima, São Paulo, Brazil
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El Karkouri K, Kowalczewska M, Armstrong N, Azza S, Fournier PE, Raoult D. Multi-omics Analysis Sheds Light on the Evolution and the Intracellular Lifestyle Strategies of Spotted Fever Group Rickettsia spp. Front Microbiol 2017; 8:1363. [PMID: 28775717 PMCID: PMC5517468 DOI: 10.3389/fmicb.2017.01363] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/05/2017] [Indexed: 11/13/2022] Open
Abstract
Arthropod-borne Rickettsia species are obligate intracellular bacteria which are pathogenic for humans. Within this genus, Rickettsia slovaca and Rickettsia conorii cause frequent and potentially severe infections, whereas Rickettsia raoultii and Rickettsia massiliae cause rare and milder infections. All four species belong to spotted fever group (SFG) rickettsiae. However, R. slovaca and R. raoultii cause scalp eschar and neck lymphadenopathy (SENLAT) and are mainly associated with Dermacentor ticks, whereas the other two species cause Mediterranean spotted fever (MSF) and are mainly transmitted by Rhipicephalus ticks. To identify the potential genes and protein profiles and to understand the evolutionary processes that could, comprehensively, relate to the differences in virulence and pathogenicity observed between these four species, we compared their genomes and proteomes. The virulent and milder agents displayed divergent phylogenomic evolution in two major clades, whereas either SENLAT or MSF disease suggests a discrete convergent evolution of one virulent and one milder agent, despite their distant genetic relatedness. Moreover, the two virulent species underwent strong reductive genomic evolution and protein structural variations, as well as a probable loss of plasmid(s), compared to the two milder species. However, an abundance of mobilome genes was observed only in the less pathogenic species. After infecting Xenopus laevis cells, the virulent agents displayed less up-regulated than down-regulated proteins, as well as less number of identified core proteins. Furthermore, their similar and distinct protein profiles did not contain some genes (e.g., ompA/B and rickA) known to be related to rickettsial adhesion, motility and/or virulence, but may include other putative virulence-, antivirulence-, and/or disease-related proteins. The identified evolutionary forces herein may have a strong impact on intracellular expressions and strategies in these rickettsiae, and that may contribute to the emergence of distinct virulence and diseases in humans. Thus, the current multi-omics data provide new insights into the evolution and fitness of SFG virulence and pathogenicity, and intracellular pathogenic bacteria.
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Affiliation(s)
- Khalid El Karkouri
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, Centre National De La Recherche Scientifique 7278, IRD 198, Institut National De La Santé Et De La Recherche Médicale U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille UniversitéMarseille, France
| | - Malgorzata Kowalczewska
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, Centre National De La Recherche Scientifique 7278, IRD 198, Institut National De La Santé Et De La Recherche Médicale U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille UniversitéMarseille, France
| | - Nicholas Armstrong
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, Centre National De La Recherche Scientifique 7278, IRD 198, Institut National De La Santé Et De La Recherche Médicale U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille UniversitéMarseille, France
| | - Said Azza
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, Centre National De La Recherche Scientifique 7278, IRD 198, Institut National De La Santé Et De La Recherche Médicale U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille UniversitéMarseille, France
| | - Pierre-Edouard Fournier
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, Centre National De La Recherche Scientifique 7278, IRD 198, Institut National De La Santé Et De La Recherche Médicale U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille UniversitéMarseille, France
| | - Didier Raoult
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, Centre National De La Recherche Scientifique 7278, IRD 198, Institut National De La Santé Et De La Recherche Médicale U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille UniversitéMarseille, France
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Zheng H, Liu E, Shi T, Ye L, Konno T, Oda M, Ji ZS. Strand-specific RNA-seq analysis of the Lactobacillus delbrueckii subsp. bulgaricus transcriptome. MOLECULAR BIOSYSTEMS 2016; 12:508-19. [PMID: 26675359 DOI: 10.1039/c5mb00547g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Lactobacillus delbrueckii subsp. bulgaricus 2038 (Lb. bulgaricus 2038) is an industrial bacterium that is used as a starter for dairy products. We proposed several hypotheses concerning its industrial features previously. Here, we utilized RNA-seq to explore the transcriptome of Lb. bulgaricus 2038 from four different growth phases under whey conditions. The most abundantly expressed genes in the four stages were mainly involved in translation (for the logarithmic stage), glycolysis (for control/lag stages), lactic acid production (all the four stages), and 10-formyl tetrahydrofolate production (for the stationary stage). The high expression of genes like d-lactate dehydrogenase was thought as a result of energy production, and consistent expression of EPS synthesis genes, the restriction-modification (RM) system and the CRISPR/Cas system were validated for explaining the advantage of this strain in yoghurt production. Several postulations, like NADPH production through GapN bypass, converting aspartate into carbon-skeleton intermediates, and formate production through degrading GTP, were proved not working under these culture conditions. The high expression of helicase genes and co-expressed amino acids/oligopeptides transporting proteins indicated that the helicase might mediate the strain obtaining nitrogen source from the environment. The transport system of Lb. bulgaricus 2038 was found to be regulated by antisense RNA, hinting the potential application of non-coding RNA in regulating lactic acid bacteria (LAB) gene expression. Our study has primarily uncovered Lb. bulgaricus 2038 transcriptome, which could gain a better understanding of the regulation system in Lb. bulgaricus and promote its industrial application.
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Affiliation(s)
- Huajun Zheng
- Laboratory of Medical Foods, Shanghai Institute of Planned Parenthood Research, 2140 Xie-Tu Road, Shanghai 200032, China.
| | - Enuo Liu
- Laboratory of Medical Foods, Shanghai Institute of Planned Parenthood Research, 2140 Xie-Tu Road, Shanghai 200032, China.
| | - Tao Shi
- Laboratory of Medical Foods, Shanghai Institute of Planned Parenthood Research, 2140 Xie-Tu Road, Shanghai 200032, China.
| | - Luyi Ye
- Laboratory of Medical Foods, Shanghai Institute of Planned Parenthood Research, 2140 Xie-Tu Road, Shanghai 200032, China.
| | - Tomonobu Konno
- Division of Research and Development, Meiji Co., Ltd, 540 Naruda, Odawara, Kanagawa 250-0862, Japan
| | - Munehiro Oda
- Graduate School of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa City, Kanagawa 252-0880, Japan
| | - Zai-Si Ji
- Laboratory of Medical Foods, Shanghai Institute of Planned Parenthood Research, 2140 Xie-Tu Road, Shanghai 200032, China. and Division of Research and Development, Meiji Co., Ltd, 540 Naruda, Odawara, Kanagawa 250-0862, Japan
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11
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Su Z, Zhu J, Xu Z, Xiao R, Zhou R, Li L, Chen H. A Transcriptome Map of Actinobacillus pleuropneumoniae at Single-Nucleotide Resolution Using Deep RNA-Seq. PLoS One 2016; 11:e0152363. [PMID: 27018591 PMCID: PMC4809551 DOI: 10.1371/journal.pone.0152363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/13/2016] [Indexed: 12/21/2022] Open
Abstract
Actinobacillus pleuropneumoniae is the pathogen of porcine contagious pleuropneumoniae, a highly contagious respiratory disease of swine. Although the genome of A. pleuropneumoniae was sequenced several years ago, limited information is available on the genome-wide transcriptional analysis to accurately annotate the gene structures and regulatory elements. High-throughput RNA sequencing (RNA-seq) has been applied to study the transcriptional landscape of bacteria, which can efficiently and accurately identify gene expression regions and unknown transcriptional units, especially small non-coding RNAs (sRNAs), UTRs and regulatory regions. The aim of this study is to comprehensively analyze the transcriptome of A. pleuropneumoniae by RNA-seq in order to improve the existing genome annotation and promote our understanding of A. pleuropneumoniae gene structures and RNA-based regulation. In this study, we utilized RNA-seq to construct a single nucleotide resolution transcriptome map of A. pleuropneumoniae. More than 3.8 million high-quality reads (average length ~90 bp) from a cDNA library were generated and aligned to the reference genome. We identified 32 open reading frames encoding novel proteins that were mis-annotated in the previous genome annotations. The start sites for 35 genes based on the current genome annotation were corrected. Furthermore, 51 sRNAs in the A. pleuropneumoniae genome were discovered, of which 40 sRNAs were never reported in previous studies. The transcriptome map also enabled visualization of 5'- and 3'-UTR regions, in which contained 11 sRNAs. In addition, 351 operons covering 1230 genes throughout the whole genome were identified. The RNA-Seq based transcriptome map validated annotated genes and corrected annotations of open reading frames in the genome, and led to the identification of many functional elements (e.g. regions encoding novel proteins, non-coding sRNAs and operon structures). The transcriptional units described in this study provide a foundation for future studies concerning the gene functions and the transcriptional regulatory architectures of this pathogen.
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Affiliation(s)
- Zhipeng Su
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiawen Zhu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhuofei Xu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Ran Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
- * E-mail: (HC); (LL)
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
- * E-mail: (HC); (LL)
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12
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Belone ADFF, Rosa PS, Trombone APF, Fachin LRV, Guidella CC, Ura S, Barreto JA, Pinilla MG, de Carvalho AF, Carraro DM, Soares FA, Soares CT. Genome-Wide Screening of mRNA Expression in Leprosy Patients. Front Genet 2015; 6:334. [PMID: 26635870 PMCID: PMC4653304 DOI: 10.3389/fgene.2015.00334] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/05/2015] [Indexed: 11/13/2022] Open
Abstract
Leprosy, an infectious disease caused by Mycobacterium leprae, affects millions of people worldwide. However, little is known regarding its molecular pathophysiological mechanisms. In this study, a comprehensive assessment of human mRNA was performed on leprosy skin lesions by using DNA chip microarrays, which included the entire spectrum of the disease along with its reactional states. Sixty-six samples from leprotic lesions (10TT, 10BT, 10BB, 10BL, 4LL, 14R1, and 10R2) and nine skin biopsies from healthy individuals were used as controls (CC) (ages ranged from 06 to 83 years, 48 were male and 29 female). The evaluation identified 1580 differentially expressed mRNAs [Fold Change (FC) ≥ 2.0, p ≤ 0.05] in diseased lesions vs. healthy controls. Some of these genes were observed in all forms of the disease (CD2, CD27, chit1, FA2H, FAM26F, GZMB, MMP9, SLAMF7, UBD) and others were exclusive to reactional forms (Type "1" reaction: GPNMB, IL1B, MICAL2, FOXQ1; Type "2" reaction: AKR1B10, FAM180B, FOXQ1, NNMT, NR1D1, PTX3, TNFRSF25). In literature, these mRNAs have been associated with numerous pathophysiological processes and signaling pathways and are present in a large number of diseases. The role of these mRNAs maybe studied in the context of developing new diagnostic markers and therapeutic targets for leprosy.
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Affiliation(s)
- Andrea de Faria F Belone
- Department of Anatomic Pathology, Instituto Lauro de Souza Lima São Paulo, Brazil ; Department of Anatomic Pathology, A.C. Camargo Cancer Center São Paulo, Brazil
| | - Patrícia S Rosa
- Division of Research and Education, Instituto Lauro de Souza Lima São Paulo, Brazil
| | - Ana P F Trombone
- Department of Health Science, Universidade do Sagrado Coração São Paulo, Brazil
| | - Luciana R V Fachin
- Department of Anatomic Pathology, Instituto Lauro de Souza Lima São Paulo, Brazil
| | - Cássio C Guidella
- Ambulatory of Leprosy, Jardim Guanabara Health Center Rondonópolis, Brazil
| | - Somei Ura
- Division of Research and Education, Instituto Lauro de Souza Lima São Paulo, Brazil
| | - Jaison A Barreto
- Division of Dermathology, Instituto Lauro de Souza Lima São Paulo, Brazil
| | - Mabel G Pinilla
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center Sao Paulo, Brazil
| | - Alex F de Carvalho
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center Sao Paulo, Brazil
| | - Dirce M Carraro
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center Sao Paulo, Brazil
| | - Fernando A Soares
- Department of Anatomic Pathology, A.C. Camargo Cancer Center São Paulo, Brazil
| | - Cleverson T Soares
- Department of Anatomic Pathology, Instituto Lauro de Souza Lima São Paulo, Brazil
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13
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Tsai CH, Liao R, Chou B, Palumbo M, Contreras LM. Genome-wide analyses in bacteria show small-RNA enrichment for long and conserved intergenic regions. J Bacteriol 2015; 197:40-50. [PMID: 25313390 PMCID: PMC4288687 DOI: 10.1128/jb.02359-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 10/02/2014] [Indexed: 12/21/2022] Open
Abstract
Interest in finding small RNAs (sRNAs) in bacteria has significantly increased in recent years due to their regulatory functions. Development of high-throughput methods and more sophisticated computational algorithms has allowed rapid identification of sRNA candidates in different species. However, given their various sizes (50 to 500 nucleotides [nt]) and their potential genomic locations in the 5' and 3' untranslated regions as well as in intergenic regions, identification and validation of true sRNAs have been challenging. In addition, the evolution of bacterial sRNAs across different species continues to be puzzling, given that they can exert similar functions with various sequences and structures. In this study, we analyzed the enrichment patterns of sRNAs in 13 well-annotated bacterial species using existing transcriptome and experimental data. All intergenic regions were analyzed by WU-BLAST to examine conservation levels relative to species within or outside their genus. In total, more than 900 validated bacterial sRNAs and 23,000 intergenic regions were analyzed. The results indicate that sRNAs are enriched in intergenic regions, which are longer and more conserved than the average intergenic regions in the corresponding bacterial genome. We also found that sRNA-coding regions have different conservation levels relative to their flanking regions. This work provides a way to analyze how noncoding RNAs are distributed in bacterial genomes and also shows conserved features of intergenic regions that encode sRNAs. These results also provide insight into the functions of regions surrounding sRNAs and into optimization of RNA search algorithms.
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Affiliation(s)
- Chen-Hsun Tsai
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Rick Liao
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Brendan Chou
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas, USA
| | - Michael Palumbo
- Computational Biology and Statistics, Wadsworth Center, Albany, New York, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
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14
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Haning K, Cho SH, Contreras LM. Small RNAs in mycobacteria: an unfolding story. Front Cell Infect Microbiol 2014; 4:96. [PMID: 25105095 PMCID: PMC4109619 DOI: 10.3389/fcimb.2014.00096] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/03/2014] [Indexed: 01/10/2023] Open
Abstract
Mycobacteria represent a class of powerful pathogens, including those causing tuberculosis and leprosy, which continue to be worldwide health challenges. In the last 20 years, an abundance of non-coding, small RNAs (sRNAs) have been discovered in model bacteria and gained significant attention as regulators of cellular responses, including pathogenesis. Naturally, a search in mycobacteria followed, revealing over 200 sRNAs thus far. Characterization of these sRNAs is only beginning, but differential expression under environmental stresses suggests relevance to mycobacterial pathogenesis. This review provides a comprehensive overview of the current knowledge of sRNAs in mycobacteria, including historical perspective and techniques used for identification and characterization.
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Affiliation(s)
- Katie Haning
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at AustinAustin, TX, USA
| | - Seung Hee Cho
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at AustinAustin, TX, USA
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at AustinAustin, TX, USA
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at AustinAustin, TX, USA
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15
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PCR-based techniques for leprosy diagnosis: from the laboratory to the clinic. PLoS Negl Trop Dis 2014; 8:e2655. [PMID: 24722358 PMCID: PMC3983108 DOI: 10.1371/journal.pntd.0002655] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/07/2013] [Indexed: 12/16/2022] Open
Abstract
In leprosy, classic diagnostic tools based on bacillary counts and histopathology have been facing hurdles, especially in distinguishing latent infection from active disease and diagnosing paucibacillary clinical forms. Serological tests and IFN-gamma releasing assays (IGRA) that employ humoral and cellular immune parameters, respectively, are also being used, but recent results indicate that quantitative PCR (qPCR) is a key technique due to its higher sensitivity and specificity. In fact, advances concerning the structure and function of the Mycobacterium leprae genome led to the development of specific PCR-based gene amplification assays for leprosy diagnosis and monitoring of household contacts. Also, based on the validation of point-of-care technologies for M. tuberculosis DNA detection, it is clear that the same advantages of rapid DNA detection could be observed in respect to leprosy. So far, PCR has proven useful in the determination of transmission routes, M. leprae viability, and drug resistance in leprosy. However, PCR has been ascertained to be especially valuable in diagnosing difficult cases like pure neural leprosy (PNL), paucibacillary (PB), and patients with atypical clinical presentation and histopathological features compatible with leprosy. Also, the detection of M. leprae DNA in different samples of the household contacts of leprosy patients is very promising. Although a positive PCR result is not sufficient to establish a causal relationship with disease outcome, quantitation provided by qPCR is clearly capable of indicating increased risk of developing the disease and could alert clinicians to follow these contacts more closely or even define rules for chemoprophylaxis.
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Abstract
Efforts to understand the molecular basis of mycobacterial gene regulation are dominated by a protein-centric view. However, there is a growing appreciation that noncoding RNA, i.e., RNA that is not translated, plays a role in a wide variety of molecular mechanisms. Noncoding RNA comprises rRNA, tRNA, 4.5S RNA, RnpB, and transfer-messenger RNA, as well as a vast population of regulatory RNA, often dubbed "the dark matter of gene regulation." The regulatory RNA species comprise 5' and 3' untranslated regions and a rapidly expanding category of transcripts with the ability to base-pair with mRNAs or to interact with proteins. Regulatory RNA plays a central role in the bacterium's response to changes in the environment, and in this article we review emerging information on the presence and abundance of different types of noncoding RNA in mycobacteria.
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17
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Akama T, Luo Y, Sellitti DF, Kawashima A, Tanigawa K, Yoshihara A, Ishido Y, Nakamura K, Tanoue A, Suzuki K. Thyroglobulin increases thyroid cell proliferation via the suppression of specific microRNAs. Mol Endocrinol 2014; 28:368-79. [PMID: 24479877 DOI: 10.1210/me.2013-1266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Thyroglobulin (Tg), stored in the follicular lumen, has also been shown recently to perform two unexpected roles: as an autocrine negative-feedback suppressor of thyroid function in the presence of TSH and as a potent inducer of thyroid cell growth in the absence of TSH. However, the underlying molecular mechanism(s) remain unclear. To elucidate a molecular pathway linking Tg to increased cell proliferation, we examined the regulation of microRNAs (miRNAs) by Tg using an miRNA microarray. We identified 21 miRNAs whose expression was significantly suppressed by Tg in rat thyroid FRTL-5 cells. Using specific miRNA analogs, we determined that miR-16, miR-24, and miR-195 mediate the induction of thyroid cell growth by Tg. The expression of miR-16 and miR-195 target genes, Mapk8, Ccne1, and Cdc6, which were previously shown to be essential for TSH-stimulated thyroid cell growth, were also induced by Tg. Moreover, the Tg-induced expression of these genes was reduced by overexpression of miR-16 and miR-195. Similarly, the induction of c-Myc by Tg was reduced by miR-24 overexpression. These results suggest that Tg could alter thyroid cell proliferation by increasing the expression of cell division-related genes such as Mapk8, Ccne1, Cdc6, and c-Myc through its suppression of specific microRNAs (miR-16, miR-24, and miR-195). In addition, we identified phosphatidylinositol 3-kinase as a key signaling pathway, linking Tg with cell proliferation. The present data support an important role for miRNAs as effectors for the effect of Tg on cell proliferation and perhaps other functions of Tg in the thyroid cell.
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Affiliation(s)
- Takeshi Akama
- Laboratory of Molecular Diagnostics (T.A., Y.L., A.K., K.T., A.Y, Y.I., K.N., K.S.), Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama-shi, Tokyo 189-0002, Japan; Department of Medicine, Uniformed Services University of the Health Sciences (D.F.S.), Bethesda, Maryland 20814-4799; and Department of Pharmacology, National Research Institute for Child Health and Development (K.N., A.T.), Setagaya-ku, Tokyo 157-8538, Japan
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18
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Comprehensive analysis of prokaryotes in environmental water using DNA microarray analysis and whole genome amplification. Pathogens 2013; 2:591-605. [PMID: 25437334 PMCID: PMC4235703 DOI: 10.3390/pathogens2040591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/16/2013] [Accepted: 10/24/2013] [Indexed: 11/28/2022] Open
Abstract
The microflora in environmental water consists of a high density and diversity of bacterial species that form the foundation of the water ecosystem. Because the majority of these species cannot be cultured in vitro, a different approach is needed to identify prokaryotes in environmental water. A novel DNA microarray was developed as a simplified detection protocol. Multiple DNA probes were designed against each of the 97,927 sequences in the DNA Data Bank of Japan and mounted on a glass chip in duplicate. Evaluation of the microarray was performed using the DNA extracted from one liter of environmental water samples collected from seven sites in Japan. The extracted DNA was uniformly amplified using whole genome amplification (WGA), labeled with Cy3-conjugated 16S rRNA specific primers and hybridized to the microarray. The microarray successfully identified soil bacteria and environment-specific bacteria clusters. The DNA microarray described herein can be a useful tool in evaluating the diversity of prokaryotes and assessing environmental changes such as global warming.
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19
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Akama T, Nakamura K, Tanoue A, Suzuki K. Design of tiling arrays and their application to bacterial transcriptome analysis. Methods Mol Biol 2013; 1067:23-34. [PMID: 23975783 DOI: 10.1007/978-1-62703-607-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Whole-genome sequencing and annotation have clarified total gene number and structure in a variety of organisms. Microarrays have facilitated transcriptome analysis through the use of probes that target a large number of genes based on genomic information. However, microarrays are limited in that they can only examine known or predicted genes; non-annotated genes and noncoding regions cannot be accounted for.Recent advances in technology have led to the design of tiling arrays, which contain a vastly increased number of spotted probes, and at higher density. Tiling arrays cover the entire genome of a prokaryotic species in an unbiased fashion by designing a large number of probes. Upon hybridization of total RNA, all the transcribed regions of the genome, irrespective of gene annotation, can be detected. As opposed to next-generation sequencing, tiling arrays are cost-effective, easy to analyze, and have been used for experiments as diverse as transcriptome analysis, ChIP-chip, and DNA sequence variation detection. In this chapter, the methods for bacterial tiling array slide design, RNA sample preparation, hybridization, and data analysis are described.
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Affiliation(s)
- Takeshi Akama
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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20
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Degang Y, Akama T, Hara T, Tanigawa K, Ishido Y, Gidoh M, Makino M, Ishii N, Suzuki K. Clofazimine modulates the expression of lipid metabolism proteins in Mycobacterium leprae-infected macrophages. PLoS Negl Trop Dis 2012; 6:e1936. [PMID: 23236531 PMCID: PMC3516583 DOI: 10.1371/journal.pntd.0001936] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 10/20/2012] [Indexed: 12/20/2022] Open
Abstract
Mycobacterium leprae (M. leprae) lives and replicates within macrophages in a foamy, lipid-laden phagosome. The lipids provide essential nutrition for the mycobacteria, and M. leprae infection modulates expression of important host proteins related to lipid metabolism. Thus, M. leprae infection increases the expression of adipophilin/adipose differentiation-related protein (ADRP) and decreases hormone-sensitive lipase (HSL), facilitating the accumulation and maintenance of lipid-rich environments suitable for the intracellular survival of M. leprae. HSL levels are not detectable in skin smear specimens taken from leprosy patients, but re-appear shortly after multidrug therapy (MDT). This study examined the effect of MDT components on host lipid metabolism in vitro, and the outcome of rifampicin, dapsone and clofazimine treatment on ADRP and HSL expression in THP-1 cells. Clofazimine attenuated the mRNA and protein levels of ADRP in M. leprae-infected cells, while those of HSL were increased. Rifampicin and dapsone did not show any significant effects on ADRP and HSL expression levels. A transient increase of interferon (IFN)-β and IFN-γ mRNA was also observed in cells infected with M. leprae and treated with clofazimine. Lipid droplets accumulated by M. leprae-infection were significantly decreased 48 h after clofazimine treatment. Such effects were not evident in cells without M. leprae infection. In clinical samples, ADRP expression was decreased and HSL expression was increased after treatment. These results suggest that clofazimine modulates lipid metabolism in M. leprae-infected macrophages by modulating the expression of ADRP and HSL. It also induces IFN production in M. leprae-infected cells. The resultant decrease in lipid accumulation, increase in lipolysis, and activation of innate immunity may be some of the key actions of clofazimine. Leprosy, caused by Mycobacterium leprae (M. leprae), is an ancient infectious disease that remains the leading infectious cause of disability. After infection, M. leprae lives inside host macrophages that contain a large amount of lipids, which is thought to be an essential microenvironment for M. leprae to survive in host cells. M. leprae infection increases lipid accumulation in macrophages and decreases the metabolic breakdown of lipids (catabolism). In addition, the treatment of leprosy with multidrug therapy (MDT) reverses the effect of infection on the modulation of lipid metabolism. We therefore aimed to use cultured human macrophage cells to determine which of the three MDT drugs (clofazimine, dapsone, or rifampicin) is responsible for this effect. We found that only clofazimine affects lipid accumulation and catabolism in M. leprae-infected cells in vitro. The amounts of lipids accumulated in the cells decreased when clofazimine was added to the cell culture medium. Clofazimine also activated immune responses in M. leprae-infected cells. These results suggest that the effectiveness of clofazimine against leprosy is due to the modulation of lipid metabolism and activation of immune reactions in M. leprae-infected host cells.
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Affiliation(s)
- Yang Degang
- Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
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21
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Tanigawa K, Degang Y, Kawashima A, Akama T, Yoshihara A, Ishido Y, Makino M, Ishii N, Suzuki K. Essential role of hormone-sensitive lipase (HSL) in the maintenance of lipid storage in Mycobacterium leprae-infected macrophages. Microb Pathog 2012; 52:285-91. [PMID: 22553833 DOI: 10.1016/j.micpath.2012.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mycobacterium leprae (M. leprae), the causative agent of leprosy, parasitizes within the foamy or enlarged phagosome of macrophages where rich lipids accumulate. Although the mechanisms for lipid accumulation in the phagosome have been clarified, it is still unclear how such large amounts of lipids escape degradation. To further explore underlying mechanisms involved in lipid catabolism in M. leprae-infected host cells, we examined the expression of hormone-sensitive lipase (HSL), a key enzyme in fatty acid mobilization and lipolysis, in human macrophage THP-1 cells. We found that infection by live M. leprae significantly suppressed HSL expression levels. This suppression was not observed with dead M. leprae or latex beads. Macrophage activation by peptidoglycan (PGN), the ligand for toll-like receptor 2 (TLR2), increased HSL expression; however, live M. leprae suppressed this increase. HSL expression was abolished in the slit-skin smear specimens from patients with lepromatous and borderline leprosy. In addition, the recovery of HSL expression was observed in patients who experienced a lepra reaction, which is a cell-mediated, delayed-type hypersensitivity immune response, or in patients who were successfully treated with multi-drug therapy. These results suggest that M. leprae suppresses lipid degradation through inhibition of HSL expression, and that the monitoring of HSL mRNA levels in slit-skin smear specimens may be a useful indicator of patient prognosis.
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Affiliation(s)
- Kazunari Tanigawa
- Leprosy Research Center, National Institute of Infectious Diseases, 4-2-1 Aoba-cho, Higashimurayama, Tokyo 189-0002, Japan
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22
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Pellin D, Miotto P, Ambrosi A, Cirillo DM, Di Serio C. A genome-wide identification analysis of small regulatory RNAs in Mycobacterium tuberculosis by RNA-Seq and conservation analysis. PLoS One 2012; 7:e32723. [PMID: 22470422 PMCID: PMC3314655 DOI: 10.1371/journal.pone.0032723] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 02/03/2012] [Indexed: 12/29/2022] Open
Abstract
We propose a new method for smallRNAs (sRNAs) identification. First we build an effective target genome (ETG) by means of a strand-specific procedure. Then we propose a new bioinformatic pipeline based mainly on the combination of two types of information: the first provides an expression map based on RNA-seq data (Reads Map) and the second applies principles of comparative genomics leading to a Conservation Map. By superimposing these two maps, a robust method for the search of sRNAs is obtained. We apply this methodology to investigate sRNAs in Mycobacterium tuberculosis H37Rv. This bioinformatic procedure leads to a total list of 1948 candidate sRNAs. The size of the candidate list is strictly related to the aim of the study and to the technology used during the verification process. We provide performance measures of the algorithm in identifying annotated sRNAs reported in three recent published studies.
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Affiliation(s)
- Danilo Pellin
- University Centre for Statistics in the Biomedical Sciences, Università Vita-Salute San Raffaele, Milan, Italy
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Ambrosi
- University Centre for Statistics in the Biomedical Sciences, Università Vita-Salute San Raffaele, Milan, Italy
| | | | - Clelia Di Serio
- University Centre for Statistics in the Biomedical Sciences, Università Vita-Salute San Raffaele, Milan, Italy
- * E-mail:
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23
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Akama T, Sue M, Kawashima A, Wu H, Tanigawa K, Suzuki S, Hayashi M, Yoshihara A, Ishido Y, Ishii N, Suzuki K. Identification of microRNAs that mediate thyroid cell growth induced by TSH. Mol Endocrinol 2012; 26:493-501. [PMID: 22301781 DOI: 10.1210/me.2011-1004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
TSH is a major regulator of thyroid cell growth and endocrine function. It is known that cAMP and phosphatidylinositol 3-kinase (PI3K) are responsible for mediating the action of TSH. Activation of these signals results in the induction of a series of transcription factors and cell cycle regulating proteins, which induce cell proliferation. In addition to such canonical transcriptional regulation, it was recently shown that microRNA (miRNA or miR) constitutes another key mechanism for the regulation of gene expression. However, whether TSH action is mediated by miRNA in the thyroid is unknown. In this study, we have performed miRNA microarray analysis and demonstrated that TSH significantly decreases expression of 47 miRNA in thyroid cells. Among these, we have shown, using their specific agonists, that overexpression of miR-16 and miR-195 suppressed cell cycle progression and DNA synthesis that was induced by TSH. In silico analysis predicted that Mapk8, Ccne1, and Cdc6, the expression of which was up-regulated by TSH, are potential target genes for these miRNA, and overexpression of miR-16 and miR-195 suppressed expression of these target genes. The decrease of miR-16 and miR-195 expression by TSH was reproduced by forskolin and N(6),2'-O-dibutyryladenosine cAMP and reversed by the protein kinase A inhibitor H89 and the PI3K inhibitor LY294002. These results suggest that TSH activates cAMP/protein kinase A and PI3K cascades to decrease miR-16 and miR-195, which induce Mapk8, Ccne1, and Cdc6 to activate cell proliferation.
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Affiliation(s)
- Takeshi Akama
- Laboratory of Molecular Diagnostics, Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, 4-2-1 Aoba-cho, Higashimurayama-shi, Tokyo, Japan
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24
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Kumar R, Lawrence ML, Watt J, Cooksey AM, Burgess SC, Nanduri B. RNA-seq based transcriptional map of bovine respiratory disease pathogen "Histophilus somni 2336". PLoS One 2012; 7:e29435. [PMID: 22276113 PMCID: PMC3262788 DOI: 10.1371/journal.pone.0029435] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 11/28/2011] [Indexed: 01/08/2023] Open
Abstract
Genome structural annotation, i.e., identification and demarcation of the boundaries for all the functional elements in a genome (e.g., genes, non-coding RNAs, proteins and regulatory elements), is a prerequisite for systems level analysis. Current genome annotation programs do not identify all of the functional elements of the genome, especially small non-coding RNAs (sRNAs). Whole genome transcriptome analysis is a complementary method to identify “novel” genes, small RNAs, regulatory regions, and operon structures, thus improving the structural annotation in bacteria. In particular, the identification of non-coding RNAs has revealed their widespread occurrence and functional importance in gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Histophilus somni, one of the causative agents of Bovine Respiratory Disease (BRD) as well as bovine infertility, abortion, septicemia, arthritis, myocarditis, and thrombotic meningoencephalitis. In this study, we report a single nucleotide resolution transcriptome map of H. somni strain 2336 using RNA-Seq method. The RNA-Seq based transcriptome map identified 94 sRNAs in the H. somni genome of which 82 sRNAs were never predicted or reported in earlier studies. We also identified 38 novel potential protein coding open reading frames that were absent in the current genome annotation. The transcriptome map allowed the identification of 278 operon (total 730 genes) structures in the genome. When compared with the genome sequence of a non-virulent strain 129Pt, a disproportionate number of sRNAs (∼30%) were located in genomic region unique to strain 2336 (∼18% of the total genome). This observation suggests that a number of the newly identified sRNAs in strain 2336 may be involved in strain-specific adaptations.
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Affiliation(s)
- Ranjit Kumar
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Mark L. Lawrence
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - James Watt
- Eagle Applied Sciences LLC, San Antonio, Texas, United States of America
| | - Amanda M. Cooksey
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Shane C. Burgess
- College of Agriculture and Life Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Bindu Nanduri
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
- * E-mail:
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Koo JT, Lathem WW. Global discovery of small noncoding RNAs in pathogenic Yersinia species. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 954:305-14. [PMID: 22782777 DOI: 10.1007/978-1-4614-3561-7_38] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jovanka T Koo
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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Suzuki K, Tanigawa K, Kawashima A, Miyamura T, Ishii N. Chimpanzees used for medical research shed light on the pathoetiology of leprosy. Future Microbiol 2011; 6:1151-7. [PMID: 22004034 DOI: 10.2217/fmb.11.97] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Leprosy is a chronic infectious disorder caused by Mycobacterium leprae, which mainly affects skin and peripheral nerves. It is classified as either paucibacillary or multibacillary based upon clinical manifestations and slit-skin smear results. It is speculated that leprosy develops after a long latency period following M. leprae infection. However, the actual time of infection and the duration of latency have never been proven in human patients. To date, four cases of spontaneous leprosy have been reported in chimpanzees who were caught in West Africa in infancy and used for medical research in the USA and Japan. One of these chimpanzees was extensively studied in Japan, and single-nucleotide polymorphism analysis for the M. leprae genome was conducted. This analysis revealed that the chimpanzee was infected with M. leprae during infancy in West Africa and the pathognomonic signs of leprosy appeared after at least 30 years of incubation. Analysis of leprosy in chimpanzees can contribute not only to medical research but also to the understanding of the pathoetiology of leprosy.
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Affiliation(s)
- Koichi Suzuki
- Laboratory of Molecular Diagnostics, Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, 4-2-1 Aoba-cho, Higashimurayama, Tokyo 189-0002, Japan.
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Suzuki K, Akama T, Kawashima A, Yoshihara A, Yotsu RR, Ishii N. Current status of leprosy: epidemiology, basic science and clinical perspectives. J Dermatol 2011; 39:121-9. [PMID: 21973237 DOI: 10.1111/j.1346-8138.2011.01370.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Leprosy has affected humans for millennia and remains an important health problem worldwide, as evidenced by nearly 250 000 new cases detected every year. It is a chronic infectious disorder, caused by Mycobacterium leprae, that primarily affects the skin and peripheral nerves. Recent advances in basic science have improved our knowledge of the disease. Variation in the cellular immune response is the basis of a range of clinical manifestations. The introduction of multidrug therapy has significantly contributed to a decrease in the prevalence of the disease. However, leprosy control activities, including monitoring and prevention programs, must be maintained.
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Affiliation(s)
- Koichi Suzuki
- Leprosy Research Center, National Institute of Infectious Diseases Department of Dermatology, National Center for Global Health and Medicine, Tokyo, Japan.
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Kumar R, Burgess SC, Lawrence ML, Nanduri B. TAAPP: Tiling Array Analysis Pipeline for Prokaryotes. GENOMICS PROTEOMICS & BIOINFORMATICS 2011; 9:56-62. [PMID: 21641563 PMCID: PMC5054164 DOI: 10.1016/s1672-0229(11)60008-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 01/11/2011] [Indexed: 12/01/2022]
Abstract
High-density tiling arrays provide closer view of transcription than regular microarrays and can also be used for annotating functional elements in genomes. The identified transcripts usually have a complex overlapping architecture when compared to the existing genome annotation. Therefore, there is a need for customized tiling array data analysis tools. Since most of the initial tiling arrays were conducted in eukaryotes, data analysis methods are well suited for eukaryotic genomes. For using whole-genome tiling arrays to identify previously unknown transcriptional elements like small RNA and antisense RNA in prokaryotes, existing data analysis tools need to be tailored for prokaryotic genome architecture. Furthermore, automation of such custom data analysis workflow is necessary for biologists to apply this powerful platform for knowledge discovery. Here we describe TAAPP, a web-based package that consists of two modules for prokaryotic tiling array data analysis. The transcript generation module works on normalized data to generate transcriptionally active regions (TARs). The feature extraction and annotation module then maps TARs to existing genome annotation. This module further categorizes the transcription profile into potential novel non-coding RNA, antisense RNA, gene expression and operon structures. The implemented workflow is microarray platform independent and is presented as a web-based service. The web interface is freely available for acedemic use at http://lims.lsbi.mafes.msstate.edu/TAAPP-HTML/.
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Affiliation(s)
- Ranjit Kumar
- College of Veterinary Medicine, Mississippi State University, MS 39762, USA.
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Singh P, Cole ST. Mycobacterium leprae: genes, pseudogenes and genetic diversity. Future Microbiol 2011; 6:57-71. [PMID: 21162636 DOI: 10.2217/fmb.10.153] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Leprosy, which has afflicted human populations for millenia, results from infection with Mycobacterium leprae, an unculturable pathogen with an exceptionally long generation time. Considerable insight into the biology and drug resistance of the leprosy bacillus has been obtained from genomics. M. leprae has undergone reductive evolution and pseudogenes now occupy half of its genome. Comparative genomics of four different strains revealed remarkable conservation of the genome (99.995% identity) yet uncovered 215 polymorphic sites, mainly single nucleotide polymorphisms, and a handful of new pseudogenes. Mapping these polymorphisms in a large panel of strains defined 16 single nucleotide polymorphism-subtypes that showed strong geographical associations and helped retrace the evolution of M. leprae.
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Affiliation(s)
- Pushpendra Singh
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, CH-1015 Lausanne, Switzerland
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Lai AG, Denton-Giles M, Mueller-Roeber B, Schippers JHM, Dijkwel PP. Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana. Genome Biol Evol 2011; 3:627-40. [PMID: 21622917 PMCID: PMC3157834 DOI: 10.1093/gbe/evr038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genome sequencing of closely related individuals has yielded valuable insights that link genome evolution to phenotypic variations. However, advancement in sequencing technology has also led to an escalation in the number of poor quality–drafted genomes assembled based on reference genomes that can have highly divergent or haplotypic regions. The self-fertilizing nature of Arabidopsis thaliana poses an advantage to sequencing projects because its genome is mostly homozygous. To determine the accuracy of an Arabidopsis drafted genome in less conserved regions, we performed a resequencing experiment on a ∼371-kb genomic interval in the Landsberg erecta (Ler-0) accession. We identified novel structural variations (SVs) between Ler-0 and the reference accession Col-0 using a long-range polymerase chain reaction approach to generate an Illumina data set that has positional information, that is, a data set with reads that map to a known location. Positional information is important for accurate genome assembly and the resolution of SVs particularly in highly duplicated or repetitive regions. Sixty-one regions with misassembly signatures were identified from the Ler-0 draft, suggesting the presence of novel SVs that are not represented in the draft sequence. Sixty of those were resolved by iterative mapping using our data set. Fifteen large indels (>100 bp) identified from this study were found to be located either within protein-coding regions or upstream regulatory regions, suggesting the formation of novel alleles or altered regulation of existing genes in Ler-0. We propose future genome-sequencing experiments to follow a clone-based approach that incorporates positional information to ultimately reveal haplotype-specific differences between accessions.
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Affiliation(s)
- Alvina G Lai
- Institute of Molecular BioSciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
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Peng J, Yang J, Jin Q. An integrated approach for finding overlooked genes in Shigella. PLoS One 2011; 6:e18509. [PMID: 21483688 PMCID: PMC3071730 DOI: 10.1371/journal.pone.0018509] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Accepted: 03/08/2011] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The completion of numerous genome sequences introduced an era of whole-genome study. However, many genes are missed during genome annotation, including small RNAs (sRNAs) and small open reading frames (sORFs). In order to improve genome annotation, we aimed to identify novel sRNAs and sORFs in Shigella, the principal etiologic agents of bacillary dysentery. METHODOLOGY/PRINCIPAL FINDINGS We identified 64 sRNAs in Shigella, which were experimentally validated in other bacteria based on sequence conservation. We employed computer-based and tiling array-based methods to search for sRNAs, followed by RT-PCR and northern blots, to identify nine sRNAs in Shigella flexneri strain 301 (Sf301) and 256 regions containing possible sRNA genes. We found 29 candidate sORFs using bioinformatic prediction, array hybridization and RT-PCR verification. We experimentally validated 557 (57.9%) DOOR operon predictions in the chromosomes of Sf301 and 46 (76.7%) in virulence plasmid.We found 40 additional co-expressed gene pairs that were not predicted by DOOR. CONCLUSIONS/SIGNIFICANCE We provide an updated and comprehensive annotation of the Shigella genome. Our study increased the expected numbers of sORFs and sRNAs, which will impact on future functional genomics and proteomics studies. Our method can be used for large scale reannotation of sRNAs and sORFs in any microbe with a known genome sequence.
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Affiliation(s)
- Junping Peng
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Jian Yang
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Qi Jin
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
- * E-mail:
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Exogenous control of the expression of Group I CD1 molecules competent for presentation of microbial nonpeptide antigens to human T lymphocytes. Clin Dev Immunol 2011; 2011:790460. [PMID: 21603161 PMCID: PMC3095450 DOI: 10.1155/2011/790460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/12/2011] [Accepted: 01/19/2011] [Indexed: 12/21/2022]
Abstract
Group I CD1 (CD1a, CD1b, and CD1c) glycoproteins expressed on immature and mature dendritic cells present nonpeptide antigens (i.e., lipid or glycolipid molecules mainly of microbial origin) to T cells. Cytotoxic CD1-restricted T lymphocytes recognizing mycobacterial lipid antigens were found in tuberculosis patients. However, thanks to a complex interplay between mycobacteria and CD1 system, M. tuberculosis possesses a successful tactic based, at least in part, on CD1 downregulation to evade CD1-dependent immunity. On the ground of these findings, it is reasonable to hypothesize that modulation of CD1 protein expression by chemical, biological, or infectious agents could influence host's immune reactivity against M. tuberculosis-associated lipids, possibly affecting antitubercular resistance. This scenario prompted us to perform a detailed analysis of the literature concerning the effect of external agents on Group I CD1 expression in order to obtain valuable information on the possible strategies to be adopted for driving properly CD1-dependent immune functions in human pathology and in particular, in human tuberculosis.
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Abstract
Regulatory small RNAs (sRNAs), also known as non-coding RNA, are not translated into proteins and widespread in prokaryotes and eukaryotes. sRNAs involve in multiple fundamental cellular events. They are emerging regulatory elements that are gaining momentum. Knowledge of sRNA largely originates from eukaryotes. Prokaryotic sRNAs, particularly those of pathogen are only recently explored. The main types, function, and methodology to predict pathogen sRNAs are summarized in this review. Special focus is sRNAs regulating pathogen gene expression, particularly that of Mycobacterium tuberculosis, which is hitherto the most successful pathogen afflicting mankind.
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Affiliation(s)
- Yexin Zhou
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, School of Life Sciences, Southwest University, Chongqing 400715, China
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Wiker HG, Tomazella GG, de Souza GA. A quantitative view on Mycobacterium leprae antigens by proteomics. J Proteomics 2011; 74:1711-9. [PMID: 21278007 DOI: 10.1016/j.jprot.2011.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 12/09/2010] [Accepted: 01/10/2011] [Indexed: 11/29/2022]
Abstract
Leprosy is an ancient disease and the focus of the researchers' scrutiny for more than a century. However, many of the molecular aspects related to transmission, virulence, antigens and immune responses are far from known. Initially, the implementation of recombinant DNA library screens raised interesting antigen candidates. Finally, the availability of Mycobacterium leprae genomic information showed an intriguing genome reduction which is now largely used in comparative genomics. While predictive in silico tools are commonly used to identify possible antigens, proteomic approaches have not yet been explored fully to study M. leprae biology. Quantitative information obtained at the protein level, and its analysis as part of a complex system, would be a key feature to be used to help researchers to validate and understand many of such in silico predictions. Through a re-analysis of data from a previous publication of our group, we could easily tackle many questions regarding antigen prediction and pseudogene expression. Several well known antigens are among the quantitatively dominant proteins, while several major proteins have not been explored as antigens. We argue that combining proteomic approaches together with bioinformatic workflows is a required step in the characterization of important pathogens.
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Affiliation(s)
- Harald G Wiker
- The Gade Institute, Section for Microbiology and Immunology, University of Bergen, Norway.
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Dittmar T, Zänker KS. Horizontal gene transfers with or without cell fusions in all categories of the living matter. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 714:5-89. [PMID: 21506007 PMCID: PMC7120942 DOI: 10.1007/978-94-007-0782-5_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This article reviews the history of widespread exchanges of genetic segments initiated over 3 billion years ago, to be part of their life style, by sphero-protoplastic cells, the ancestors of archaea, prokaryota, and eukaryota. These primordial cells shared a hostile anaerobic and overheated environment and competed for survival. "Coexist with, or subdue and conquer, expropriate its most useful possessions, or symbiose with it, your competitor" remain cellular life's basic rules. This author emphasizes the role of viruses, both in mediating cell fusions, such as the formation of the first eukaryotic cell(s) from a united crenarchaeon and prokaryota, and the transfer of host cell genes integrated into viral (phages) genomes. After rising above the Darwinian threshold, rigid rules of speciation and vertical inheritance in the three domains of life were established, but horizontal gene transfers with or without cell fusions were never abolished. The author proves with extensive, yet highly selective documentation, that not only unicellular microorganisms, but the most complex multicellular entities of the highest ranks resort to, and practice, cell fusions, and donate and accept horizontally (laterally) transferred genes. Cell fusions and horizontally exchanged genetic materials remain the fundamental attributes and inherent characteristics of the living matter, whether occurring accidentally or sought after intentionally. These events occur to cells stagnating for some 3 milliard years at a lower yet amazingly sophisticated level of evolution, and to cells achieving the highest degree of differentiation, and thus functioning in dependence on the support of a most advanced multicellular host, like those of the human brain. No living cell is completely exempt from gene drains or gene insertions.
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Affiliation(s)
- Thomas Dittmar
- Inst. Immunologie, Universität Witten/Herdecke, Stockumer Str. 10, Witten, 58448 Germany
| | - Kurt S. Zänker
- Institute of Immunologie, University of Witten/Herdecke, Stockumer Str. 10, Witten, 58448 Germany
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Abstract
PURPOSE OF REVIEW After tuberculosis, leprosy (Mycobacterium leprae) and Buruli ulcer (M. ulcerans infection) are the second and third most common mycobacterial infections in humankind, respectively. Recent advances in both diseases are summarized. RECENT FINDINGS Leprosy remains a public health problem in some countries, and new case detections indicate active transmission. Newly identified M. lepromatosis, closely related to M. leprae, may cause disseminated leprosy in some regions. In genome-wide screening in China, leprosy susceptibility associates with polymorphisms in seven genes, many involved with innate immunity. World Health Organization multiple drug therapy administered for 1 or 2 years effectively arrests disseminated leprosy but disability remains a public health concern. Relapse is infrequent, often associated with higher pretreatment M. leprae burdens. M. ulcerans, a re-emerging environmental organism, arose from M. marinum and acquired a virulence plasmid coding for mycolactone, a necrotizing, immunosuppressive toxin. Geographically, there are multiple strains of M. ulcerans, with variable pathogenicity and immunogenicity. Molecular epidemiology is describing M. ulcerans evolution and genotypic variants. First-line therapy for Buruli ulcer is rifampin + streptomycin, sometimes with surgery, but improved regimens are needed. SUMMARY Leprosy and Buruli ulcer are important infections with significant public health implications. Modern research is providing new insights into molecular epidemiology and pathogenesis, boding well for improved control strategies.
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Aikawa C, Maruyama F, Nakagawa I. The dawning era of comprehensive transcriptome analysis in cellular microbiology. Front Microbiol 2010; 1:118. [PMID: 21687718 PMCID: PMC3109594 DOI: 10.3389/fmicb.2010.00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 10/06/2010] [Indexed: 01/19/2023] Open
Abstract
Bacteria rapidly change their transcriptional patterns during infection in order to adapt to the host environment. To investigate host–bacteria interactions, various strategies including the use of animal infection models, in vitro assay systems and microscopic observations have been used. However, these studies primarily focused on a few specific genes and molecules in bacteria. High-density tiling arrays and massively parallel sequencing analyses are rapidly improving our understanding of the complex host–bacterial interactions through identification and characterization of bacterial transcriptomes. Information resulting from these high-throughput techniques will continue to provide novel information on the complexity, plasticity, and regulation of bacterial transcriptomes as well as their adaptive responses relative to pathogenecity. Here we summarize recent studies using these new technologies and discuss the utility of transcriptome analysis.
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Affiliation(s)
- Chihiro Aikawa
- Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University Tokyo, Japan
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Muro EM, Mah N, Moreno-Hagelsieb G, Andrade-Navarro MA. The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons. Nucleic Acids Res 2010; 39:1732-8. [PMID: 21051341 PMCID: PMC3061063 DOI: 10.1093/nar/gkq1067] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Almost 50 years following the discovery of the prokaryotic operon, the functional relevance of gene order within operons remains unclear. In this work, we take advantage of the eroded genome of Mycobacterium leprae to add evidence supporting the notion that functionally less important genes have a tendency to be located at the end of its operons. M. leprae’s genome includes 1133 pseudogenes and 1614 protein-coding genes and can be compared with the close genome of M. tuberculosis. Assuming M. leprae’s pseudogenes to represent dispensable genes, we have studied the position of these pseudogenes in the operons of M. leprae and of their orthologs in M. tuberculosis. We observed that both tend to be located in the 3′ (downstream) half of the operon (P-values of 0.03 and 0.18, respectively). Analysis of pseudogenes in all available prokaryotic genomes confirms this trend (P-value of 7.1 × 10−7). In a complementary analysis, we found a significant tendency for essential genes to be located at the 5′ (upstream) half of the operon (P-value of 0.006). Our work provides an indication that, in prokarya, functionally less important genes have a tendency to be located at the end of operons, while more relevant genes tend to be located toward operon starts.
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Affiliation(s)
- Enrique M Muro
- Computational Biology and Data Mining Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle Strasse 10, 13125, Berlin, Germany.
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Genomic and transcriptomic studies in Mycobacterium avium subspecies paratuberculosis. Vet Immunol Immunopathol 2010; 138:303-11. [PMID: 21047690 DOI: 10.1016/j.vetimm.2010.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Microarray technology is an important tool in functional genomic research. It has enabled a deeper analysis of genomic diversity among bacteria belonging to the Mycobacterium avium complex (MAC). In addition, the expression of thousands of genes can be studied simultaneously in a single experiment. With the complete genome sequence of a bovine isolate of M. avium subspecies paratuberculosis, and the independent construction of DNA microarrays in our laboratories, transcriptomic studies for this veterinary pathogen are now possible. Furthermore, the bovine genome sequence project is completed and bovine arrays have been developed to examine host responses to infection with M. avium subsp. paratuberculosis. Collectively, genomic and transcriptomic data has yielded novel insights surrounding the genetic regulation and biology of Johne's disease.
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Toledo-Arana A, Solano C. Deciphering the physiological blueprint of a bacterial cell: revelations of unanticipated complexity in transcriptome and proteome. Bioessays 2010; 32:461-7. [PMID: 20486131 DOI: 10.1002/bies.201000020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the last few months, several pioneer genome-wide transcriptomic, proteomic and metabolomic studies have revolutionised the understanding of bacterial biological processes, leading to a picture that resembles eukaryotic complexity. Technological advances such as next-generation high-throughput sequencing and high-density oligonucleotide microarrays have allowed the determination, in several bacteria, of the entire boundaries of all expressed transcripts. Consequently, novel RNA-mediated regulatory mechanisms have been discovered including multifunctional RNAs. Moreover, resolution of bacterial proteome organisation (interactome) and global protein localisation (localizome) have unveiled an unanticipated complexity that highlights the significance of protein multifunctionality and localisation in the cell. Also, analysis of a complete bacterial metabolic network has again revealed a high fraction of multifunctional enzymes and an unexpectedly high level of metabolic responses and adaptation. Altogether, these novel approaches have permitted the deciphering of the entire physiological landscape of one of the smallest bacteria, Mycoplasma pneumoniae. Here, we summarise and discuss recent findings aimed at defining the blueprint of any prokaryote.
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Affiliation(s)
- Alejandro Toledo-Arana
- Laboratory of Microbial Biofilms, Instituto de Agrobiotecnología, Universidad Pública de Navarra-CSIC-Gobierno de Navarra, Campus de Arrosadía, Pamplona, Spain.
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Suzuki K, Takigawa W, Tanigawa K, Nakamura K, Ishido Y, Kawashima A, Wu H, Akama T, Sue M, Yoshihara A, Mori S, Ishii N. Detection of Mycobacterium leprae DNA from archaeological skeletal remains in Japan using whole genome amplification and polymerase chain reaction. PLoS One 2010; 5:e12422. [PMID: 20865042 PMCID: PMC2928730 DOI: 10.1371/journal.pone.0012422] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Accepted: 08/04/2010] [Indexed: 11/19/2022] Open
Abstract
Background Identification of pathogen DNA from archaeological human remains is a powerful tool in demonstrating that the infectious disease existed in the past. However, it is very difficult to detect trace amounts of DNA remnants attached to the human skeleton, especially from those buried in a humid atmosphere with a relatively high environmental temperature such as in Asia. Methodology/Principal Findings Here we demonstrate Mycobacterium leprae DNA from archaeological skeletal remains in Japan by polymerase chain reaction, DNA sequencing and single nucleotide polymorphism (SNP) analysis. In addition, we have established a highly sensitive method of detecting DNA using a combination of whole genome amplification and polymerase chain reaction, or WGA-PCR, which provides superior sensitivity and specificity in detecting DNA from trace amounts of skeletal materials. Conclusion/Significance We have detected M. leprae DNA in archaeological skeletal remains for the first time in the Far East. Its SNP genotype corresponded to type 1; the first detected case worldwide of ancient M. leprae DNA. We also developed a highly sensitive method to detect ancient DNA by utilizing whole genome amplification.
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Affiliation(s)
- Koichi Suzuki
- Laboratory of Molecular Diagnostics, Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
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Kumar R, Shah P, Swiatlo E, Burgess SC, Lawrence ML, Nanduri B. Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays. BMC Genomics 2010; 11:350. [PMID: 20525227 PMCID: PMC2887815 DOI: 10.1186/1471-2164-11-350] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 06/03/2010] [Indexed: 11/10/2022] Open
Abstract
Background The identification of non-coding transcripts in human, mouse, and Escherichia coli has revealed their widespread occurrence and functional importance in both eukaryotic and prokaryotic life. In prokaryotes, studies have shown that non-coding transcripts participate in a broad range of cellular functions like gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Streptococcus pneumoniae (pneumococcus), an obligate human respiratory pathogen responsible for significant worldwide morbidity and mortality. Tiling microarrays enable genome wide mRNA profiling as well as identification of novel transcripts at a high-resolution. Results Here, we describe a high-resolution transcription map of the S. pneumoniae clinical isolate TIGR4 using genomic tiling arrays. Our results indicate that approximately 66% of the genome is expressed under our experimental conditions. We identified a total of 50 non-coding small RNAs (sRNAs) from the intergenic regions, of which 36 had no predicted function. Half of the identified sRNA sequences were found to be unique to S. pneumoniae genome. We identified eight overrepresented sequence motifs among sRNA sequences that correspond to sRNAs in different functional categories. Tiling arrays also identified approximately 202 operon structures in the genome. Conclusions In summary, the pneumococcal operon structures and novel sRNAs identified in this study enhance our understanding of the complexity and extent of the pneumococcal 'expressed' genome. Furthermore, the results of this study open up new avenues of research for understanding the complex RNA regulatory network governing S. pneumoniae physiology and virulence.
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Affiliation(s)
- Ranjit Kumar
- Department of Basic sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
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43
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Akama T, Tanigawa K, Kawashima A, Wu H, Ishii N, Suzuki K. Analysis of Mycobacterium leprae gene expression using DNA microarray. Microb Pathog 2010; 49:181-5. [PMID: 20553838 DOI: 10.1016/j.micpath.2010.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 05/19/2010] [Accepted: 05/20/2010] [Indexed: 10/19/2022]
Abstract
Mycobacterium leprae, the causative agent of leprosy, does not grow under in vitro condition, making molecular analysis of this bacterium difficult. For this reason, bacteriological information regarding M. leprae gene function is limited compared with other mycobacterium species. In this study, we performed DNA microarray analysis to clarify the RNA expression profile of the Thai53 strain of M. leprae grown in footpads of hypertensive nude rats (SHR/NCrj-rnu). Of 1605 M. leprae genes, 315 showed signal intensity twofold higher than the median. These genes include Acyl-CoA metabolic enzymes and drug metabolic enzymes, which might be related to the virulence of M. leprae. In addition, consecutive RNA expression profile and in silico analyses enabled identification of possible operons within the M. leprae genome. The present results will shed light on M. leprae gene function and further our understanding of the pathogenesis of leprosy.
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Affiliation(s)
- Takeshi Akama
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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44
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Yu WH, Høvik H, Chen T. A hidden Markov support vector machine framework incorporating profile geometry learning for identifying microbial RNA in tiling array data. Bioinformatics 2010; 26:1423-30. [PMID: 20395286 DOI: 10.1093/bioinformatics/btq162] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION RNA expression signals detected by high-density genomic tiling microarrays contain comprehensive transcriptomic information of the target organism. Current methods for determining the RNA transcription units are still computation intense and lack the discriminative power. This article describes an efficient and accurate methodology to reveal complicated transcriptional architecture, including small regulatory RNAs, in microbial transcriptome profiles. RESULTS Normalized microarray data were first subject to support vector regression to estimate the profile tendency by reducing noise interruption. A hybrid supervised machine learning algorithm, hidden Markov support vector machines, was then used to classify the underlying state of each probe to 'expression' or 'silence' with the assumption that the consecutive state sequence was a heterogeneous Markov chain. For model construction, we introduced a profile geometry learning method to construct the feature vectors, which considered both intensity profiles and changes of intensities over the probe spacing. Also, a robust strategy was used to dynamically evaluate and select the training set based only on prior computer gene annotation. The algorithm performed better than other methods in accuracy on simulated data, especially for small expressed regions with lower (<1) SNR (signal-to-noise ratio), hence more sensitive for detecting small RNAs. AVAILABILITY AND IMPLEMENTATION Detail implementation steps of the algorithm and the complete result of the transcriptome analysis for a microbial genome Porphyromonas gingivalis W83 can be viewed at http://bioinformatics.forsyth.org/mtd.
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Affiliation(s)
- Wen-Han Yu
- Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, USA
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45
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Leroy Q, Raoult D. Review of microarray studies for host-intracellular pathogen interactions. J Microbiol Methods 2010; 81:81-95. [PMID: 20188126 DOI: 10.1016/j.mimet.2010.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 02/12/2010] [Accepted: 02/16/2010] [Indexed: 12/17/2022]
Abstract
Obligate intracellular bacteria are privileged soldiers on the battlefield that represent host-pathogen interactions. Microarrays are a powerful technology that can increase our knowledge about how bacteria respond to and interact with their hosts. This review summarizes the limitations inherent to host-pathogen interaction studies and essential strategies to improve microarray investigations of intracellular bacteria. We have compiled the comparative genomic and gene expression analyses of obligate intracellular bacteria currently available from microarrays. In this review we explore ways in which microarrays can be used to identify polymorphisms in different obligate intracellular bacteria such as Coxiella burnetii, Chlamydia trachomatis, Ehrlichia chaffeensis, Rickettsia prowazekii and Tropheryma whipplei. These microarray studies reveal that, while genomic content is highly conserved in obligate intracellular bacteria, genetic polymorphisms can potentially occur to increase bacterial pathogenesis. Additionally, changes in the gene expression of C. trachomatis throughout its life cycle, as well as changes in the gene expression profile of the pathogens R. prowazekii, Rickettsia rickettsii, Rickettsia typhi, T. whipplei and C. trachomatis following environmental changes, are discussed. Finally, an in vivo model of Rickettsia conorii within the skin is discussed. The gene expression analyses highlight the capacity of obligate intracellular bacteria to adapt to environmental changes and potentially to thwart the host response.
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Affiliation(s)
- Quentin Leroy
- Université de la Méditerranée, URMITE IRD-CNRS 6236, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille cedex 05, France
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46
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Høvik H, Chen T. Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays. BMC Bioinformatics 2010; 11:82. [PMID: 20144223 PMCID: PMC2836303 DOI: 10.1186/1471-2105-11-82] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 02/09/2010] [Indexed: 12/27/2022] Open
Abstract
Background Current commercial high-density oligonucleotide microarrays can hold millions of probe spots on a single microscopic glass slide and are ideal for studying the transcriptome of microbial genomes using a tiling probe design. This paper describes a comprehensive computational pipeline implemented specifically for designing tiling probe sets to study microbial transcriptome profiles. Results The pipeline identifies every possible probe sequence from both forward and reverse-complement strands of all DNA sequences in the target genome including circular or linear chromosomes and plasmids. Final probe sequence lengths are adjusted based on the maximal oligonucleotide synthesis cycles and best isothermality allowed. Optimal probes are then selected in two stages - sequential and gap-filling. In the sequential stage, probes are selected from sequence windows tiled alongside the genome. In the gap-filling stage, additional probes are selected from the largest gaps between adjacent probes that have already been selected, until a predefined number of probes is reached. Selection of the highest quality probe within each window and gap is based on five criteria: sequence uniqueness, probe self-annealing, melting temperature, oligonucleotide length, and probe position. Conclusions The probe selection pipeline evaluates global and local probe sequence properties and selects a set of probes dynamically and evenly distributed along the target genome. Unique to other similar methods, an exact number of non-redundant probes can be designed to utilize all the available probe spots on any chosen microarray platform. The pipeline can be applied to microbial genomes when designing high-density tiling arrays for comparative genomics, ChIP chip, gene expression and comprehensive transcriptome studies.
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Affiliation(s)
- Hedda Høvik
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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47
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Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L. Transcriptome complexity in a genome-reduced bacterium. Science 2009; 326:1268-71. [PMID: 19965477 DOI: 10.1126/science.1176951] [Citation(s) in RCA: 349] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To study basic principles of transcriptome organization in bacteria, we analyzed one of the smallest self-replicating organisms, Mycoplasma pneumoniae. We combined strand-specific tiling arrays, complemented by transcriptome sequencing, with more than 252 spotted arrays. We detected 117 previously undescribed, mostly noncoding transcripts, 89 of them in antisense configuration to known genes. We identified 341 operons, of which 139 are polycistronic; almost half of the latter show decaying expression in a staircase-like manner. Under various conditions, operons could be divided into 447 smaller transcriptional units, resulting in many alternative transcripts. Frequent antisense transcripts, alternative transcripts, and multiple regulators per gene imply a highly dynamic transcriptome, more similar to that of eukaryotes than previously thought.
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Affiliation(s)
- Marc Güell
- Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain
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Sharma CM, Vogel J. Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol 2009; 12:536-46. [PMID: 19758836 DOI: 10.1016/j.mib.2009.07.006] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 07/23/2009] [Accepted: 07/28/2009] [Indexed: 01/27/2023]
Abstract
Following the pioneering screens for small regulatory RNAs (sRNAs) in Escherichia coli in 2001, sRNAs are now being identified in almost every branch of the eubacterial kingdom. Experimental strategies have become increasingly important for sRNA discovery, thanks to increased availability of tiling arrays and fast progress in the development of high-throughput cDNA sequencing (RNA-Seq). The new technologies also facilitate genome-wide discovery of potential target mRNAs by sRNA pulse-expression coupled to transcriptomics, and immunoprecipitation with RNA-binding proteins such as Hfq. Moreover, the staggering rate of new sRNAs demands mechanistic analysis of target regulation. We will also review the available toolbox for wet lab-based research, including in vivo and in vitro reporter systems, genetic methods and biochemical co-purification of sRNA interaction partners.
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Affiliation(s)
- Cynthia Mira Sharma
- RNA Biology Group, Max Planck Institute for Infection Biology, Charitéplatz 1, D-10117 Berlin, Germany
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Nakamura K, Akama T, Bang PD, Sekimura S, Tanigawa K, Wu H, Kawashima A, Hayashi M, Suzuki K, Ishii N. Detection of RNA expression from pseudogenes and non-coding genomic regions of Mycobacterium leprae. Microb Pathog 2009; 47:183-7. [PMID: 19555754 DOI: 10.1016/j.micpath.2009.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 05/20/2009] [Accepted: 06/12/2009] [Indexed: 10/20/2022]
Abstract
We have previously reported that some pseudogenes are expressed in Mycobacterium leprae (M. leprae), the causative agent of leprosy, and that their expression levels alter upon infection of macrophages. We attempted to further examine the expression of pseudogene and non-coding genomic region in M. leprae, in this study. 19 Pseudogenes, 17 non-coding genomic regions, and 21 coding genes expression in M. leprae maintained in the footpads of the hypertensive nude rat (SHR/NCrj-rnu) were examined by reverse transcriptase polymerase chain reaction (RT-PCR). The expression of some of these pseudogenes, non-coding genomic regions and coding genes were also examined in M. leprae from skin smear specimens obtained from patients with lepromatous leprosy by RT-PCR. Transcripts from pseudogenes, non-coding genomic regions and coding genes examined in this study were clearly observed in M. leprae. The expression patterns of some of these transcripts vary greatly among different leprosy patients. These results indicate that some of pseudogenes and non-coding genomic regions are transcribed in M. leprae and analysis of RNA expression patterns including pseudogene and non-coding genomic region in M. leprae may be useful in understanding the pathological states of infected patients.
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Affiliation(s)
- Kazuaki Nakamura
- Department of Bioregulation, Leprosy Research Center, National Institute of Infectious Diseases, Aoba-cho, Higashimurayama, Tokyo, Japan
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