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Traxler RM, Bell ME, Lasker B, Headd B, Shieh WJ, McQuiston JR. Updated Review on Nocardia Species: 2006-2021. Clin Microbiol Rev 2022; 35:e0002721. [PMID: 36314911 PMCID: PMC9769612 DOI: 10.1128/cmr.00027-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
This review serves as an update to the previous Nocardia review by Brown-Elliott et al. published in 2006 (B. A. Brown-Elliott, J. M. Brown, P. S. Conville, and R. J. Wallace. Jr., Clin Microbiol Rev 19:259-282, 2006, https://doi.org/10.1128/CMR.19.2.259-282.2006). Included is a discussion on the taxonomic expansion of the genus, current identification methods, and the impact of new technology (including matrix-assisted laser desorption ionization-time of flight [MALDI-TOF] and whole genome sequencing) on diagnosis and treatment. Clinical manifestations, the epidemiology, and geographic distribution are briefly discussed. An additional section on actinomycotic mycetoma is added to address this often-neglected disease.
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Affiliation(s)
- Rita M. Traxler
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Melissa E. Bell
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Brent Lasker
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Brendan Headd
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Wun-Ju Shieh
- Infectious Diseases Pathology Branch (IDPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - John R. McQuiston
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
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Li Y, Khandia R, Papadakis M, Alexiou A, Simonov AN, Khan AA. An investigation of codon usage pattern analysis in pancreatitis associated genes. BMC Genom Data 2022; 23:81. [PMID: 36434531 PMCID: PMC9700901 DOI: 10.1186/s12863-022-01089-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 10/10/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Pancreatitis is an inflammatory disorder resulting from the autoactivation of trypsinogen in the pancreas. The genetic basis of the disease is an old phenomenon, and evidence is accumulating for the involvement of synonymous/non-synonymous codon variants in disease initiation and progression. RESULTS The present study envisaged a panel of 26 genes involved in pancreatitis for their codon choices, compositional analysis, relative dinucleotide frequency, nucleotide disproportion, protein physical properties, gene expression, codon bias, and interrelated of all these factors. In this set of genes, gene length was positively correlated with nucleotide skews and codon usage bias. Codon usage of any gene is dependent upon its AT and GC component; however, AGG, CGT, and CGA encoding for Arg, TCG for Ser, GTC for Val, and CCA for Pro were independent of nucleotide compositions. In addition, Codon GTC showed a correlation with protein properties, isoelectric point, instability index, and frequency of basic amino acids. We also investigated the effect of various evolutionary forces in shaping the codon usage choices of genes. CONCLUSIONS This study will enable us to gain insight into the molecular signatures associated with the disease that might help identify more potential genes contributing to enhanced risk for pancreatitis. All the genes associated with pancreatitis are generally associated with physiological function, and mutations causing loss of function, over or under expression leads to an ailment. Therefore, the present study attempts to envisage the molecular signature in a group of genes that lead to pancreatitis in case of malfunction.
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Affiliation(s)
- Yuanyang Li
- Third-Grade Pharmacological Laboratory On Chinese Medicine Approved By State Administration of Traditional Chinese Medicine, Medical College of China Three Gorges, Yichang, China ,grid.254148.e0000 0001 0033 6389College of Medical Science, China Three Gorges University, Yichang, China
| | - Rekha Khandia
- grid.411530.20000 0001 0694 3745Department of Biochemistry and Genetics, Barkatullah University, Bhopal, MP 462026 India
| | - Marios Papadakis
- grid.412581.b0000 0000 9024 6397Department of Surgery II, University Hospital Witten-Herdecke, University of Witten-Herdecke, Heusnerstrasse 40, 42283 Wuppertal, Germany
| | - Athanasios Alexiou
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, Australia ,AFNP Med Austria, Vienna, Austria
| | | | - Azmat Ali Khan
- grid.56302.320000 0004 1773 5396Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451 Saudi Arabia
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The p38 MAPK/PMK-1 Pathway Is Required for Resistance to Nocardia farcinica Infection in Caenorhabditis elegance. Pathogens 2022; 11:pathogens11101071. [PMID: 36297128 PMCID: PMC9609018 DOI: 10.3390/pathogens11101071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 12/02/2022] Open
Abstract
Nocardia farcinica is an opportunistic pathogen that causes nocardiosis primarily in patients with compromised immune systems. In this study, we used the genetically tractable organism Caenorhabditis elegans as a model to study the innate immune responses to N. farcinica infection. We found that unlike other pathogenic bacteria such as Pseudomonas aeruginosa and Staphylococcus aureus, N. farcinica failed to kill adult worms. In another words, adult worms exposed to N. farcinica exhibited a normal lifespan, compared with those fed the standard laboratory food bacterium Escherichia coli OP50. Interestingly, deletion of three core genes (pmk-1, nsy-1 and sek-1) in the p38 MAPK/PMK-1 pathway reduced the survival of worm exposure to N. farcinica, highlighting a crucial role of this pathway for C. elegans in resistance to N. farcinica. Furthermore, our results revealed that N. farcinica exposure up-regulated the level of PMK-1 phosphorylation. The activation of PMK-1 promoted nuclear translocation of a transcription factor SKN-1/Nrf2, which in turn mediated N. farcinica infection resistance in C. elegans. Our results provide an excellent example that the integrity of immune system is key aspect for counteract with pathogenesis of N. farcinica.
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Soueges S, Bouiller K, Botelho-Nevers E, Gagneux-Brunon A, Chirouze C, Rodriguez-Nava V, Dumitrescu O, Triffault-Fillit C, Conrad A, Lebeaux D, Hodille E, Valour F, Ader F. Prognosis and factors associated with disseminated nocardiosis: a ten-year retrospective multicenter study. J Infect 2022; 85:130-136. [PMID: 35654278 DOI: 10.1016/j.jinf.2022.05.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 11/24/2022]
Abstract
OBJECTIVES Nocardiosis is a rare opportunistic infection that is frequently associated with dissemination (i.e. involvement of several body sites). Identifying the factors associated with Nocardia spp. dissemination may help improving the management of patients with nocardiosis. METHODS This 10-year (2010-2020) retrospective multicenter cohort study included adult patients with Nocardia-confirmed infections. The first objective was to determine the factors associated with disseminated nocardiosis. The secondary endpoints were to determine and compare the management and the 12-month overall mortality in patients with localized and disseminated nocardiosis. Univariate and multivariate logistic regression analyses were used. RESULTS Nocardia spp. infection was confirmed in 110 patients, of whom 38 (34.5%) had disseminated nocardiosis. In univariate analysis, the factors associated with dissemination were immunosuppressive conditions: having an auto-immune disease and receiving high-dose corticosteroid (31.5% vs 8.3%, P=0.003 and 52.6% vs 26.3%, P=0.007, respectively). Absolute lymphocyte count <1G/L at diagnosis was the only biomarker associated with dissemination (57.2% vs 26.3%, P=0.007). Nocardia farcinica was not only the most frequent species identified in patient specimens (n=22, 20%) but was also associated with a higher rate of dissemination (36.8% vs 11.1%, P=0.002). Multivariate analysis confirmed the association between auto-immune diseases, lymphopenia, N. farcinica species and the higher rate of dissemination. Even though patients with disseminated nocardiosis were treated longer and more often with an antibiotic combination therapy, their 12-month overall mortality was significantly higher than that of patients with localized nocardiosis (36.8% vs 18%). CONCLUSIONS Dissemination of Nocardia spp. is favoured by auto-immune diseases, lymphopenia, and infection with N. farcinica.
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Affiliation(s)
- Sarah Soueges
- Département des Maladies infectieuses et tropicales, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Kevin Bouiller
- Maladies Infectieuses et Tropicales-Centre Hospitalier Universitaire, F-25030 Besançon, France; UMR-CNRS 6249 Chrono-Environnement, Université Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Elisabeth Botelho-Nevers
- Service d'Infectiologie, CHU de Saint-Etienne, F-42270 Saint-Etienne, France; Centre d'investigation clinique-INSERM 1408, CHU de Saint-Etienne, F-42055 Saint-Etienne, France; CIRI - Centre International de Recherche en Infectiologie, Team GIMAP, Université de Lyon, Université Jean Monnet, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, F42023 Saint-Etienne, France
| | - Amandine Gagneux-Brunon
- Service d'Infectiologie, CHU de Saint-Etienne, F-42270 Saint-Etienne, France; Centre d'investigation clinique-INSERM 1408, CHU de Saint-Etienne, F-42055 Saint-Etienne, France; CIRI - Centre International de Recherche en Infectiologie, Team GIMAP, Université de Lyon, Université Jean Monnet, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, F42023 Saint-Etienne, France
| | - Catherine Chirouze
- Maladies Infectieuses et Tropicales-Centre Hospitalier Universitaire, F-25030 Besançon, France; UMR-CNRS 6249 Chrono-Environnement, Université Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Veronica Rodriguez-Nava
- Institut des Agents Infectieux, Laboratoire de Biologie Médicale de Référence de Nocardioses, Hospices Civils de Lyon, F-69004, Lyon, France; UMR Ecologie Microbienne, CNRS 5557, INRA 1418, VetAgro Sup et Université Lyon 1, F-69363 Lyon, France
| | - Oana Dumitrescu
- Institut des Agents Infectieux, Laboratoire de Biologie Médicale de Référence de Nocardioses, Hospices Civils de Lyon, F-69004, Lyon, France; Centre International de Recherche en Infectiologie (CIRI), Inserm 1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, F-69007, France
| | - Claire Triffault-Fillit
- Département des Maladies infectieuses et tropicales, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Anne Conrad
- Département des Maladies infectieuses et tropicales, Hospices Civils de Lyon, F-69004, Lyon, France; Centre International de Recherche en Infectiologie (CIRI), Inserm 1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, F-69007, France
| | - David Lebeaux
- Service de Microbiologie, Unité Mobile D'Infectiologie, AP-HP, Hôpital Européen Georges Pompidou, F-75015, Paris, France; Université de Paris, 75006, Paris, France
| | - Elisabeth Hodille
- Institut des Agents Infectieux, Laboratoire de Biologie Médicale de Référence de Nocardioses, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Florent Valour
- Département des Maladies infectieuses et tropicales, Hospices Civils de Lyon, F-69004, Lyon, France; Centre International de Recherche en Infectiologie (CIRI), Inserm 1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, F-69007, France
| | - Florence Ader
- Département des Maladies infectieuses et tropicales, Hospices Civils de Lyon, F-69004, Lyon, France; Centre International de Recherche en Infectiologie (CIRI), Inserm 1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, F-69007, France.
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Wei Y, Chen T, Yang W, Li H, Fang C, Liu Q, Chen Y, Mei Q. Detection of a novel antigen for Crohn's disease. Scand J Gastroenterol 2021; 56:1427-1433. [PMID: 34487462 DOI: 10.1080/00365521.2021.1973088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND AIMS Accurate serological assays are desirable for the diagnosis of inflammatory bowel disease (IBD). We identify an antigen-like substance called Crohn's disease (CD) antibody binding polypeptide (CABP). As a serological marker, anti-CABP may contribute to the diagnosis of IBD. The present study aims to evaluate the clinical role of anti-CABP as a serological antibody for IBD. METHODS Using enzyme-linked immunosorbent assay (ELISA), serum anti-CABP, anti-Saccharomyces cerevisiae antibody (ASCA) and perinuclear anti-neutrophil cytoplasmic antibody (pANCA), titers were tested in 168 CD patients, 123 ulcerative colitis (UC) patients and 170 controls. The correlation between serum antibody and clinical characteristics was investigated. The diagnostic potential of the anti-CABP was evaluated by receiver operating characteristic (ROC) analysis. RESULTS The titers of anti-CABP (IgA or IgG) and ASCA IgG of CD patients were significantly higher than non-CD group (all p < .01). In the differential diagnosis of CD and non-CD, anti-CABP IgA revealed an area under the curve (AUC) of 0.706 and anti-CABP IgG demonstrated an AUC of 0.788. As an individual antibody, anti-CABP could effectively distinguish CD from non-CD (AUC 0.816), and the diagnostic efficacy was better than that of ASCA (AUC 0.680). The combined use of anti-CABP, ASCA and pANCA significantly improved the diagnostic value (AUC 0.857). Anti-CABP positive rates were associated with perianal lesions and disease location in CD patients (both p < .05). CONCLUSIONS Our results suggested that anti-CABP could be used as a serological marker to assist the diagnosis of CD. CLINICAL TRIAL REGISTRATION This trial is registered with clinical trial registration unique identifier ChiCTR2000037094.
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Affiliation(s)
- Yarong Wei
- Department of Gastroenterology, the Key Laboratory of Digestive Diseases of Anhui Province, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | | | - Wu Yang
- Shanxi Ruihao Biotechnology Co. LTD, Taiyuan, China
| | - Huihui Li
- Department of Gastroenterology, the Key Laboratory of Digestive Diseases of Anhui Province, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chen Fang
- Department of Gastroenterology, the Key Laboratory of Digestive Diseases of Anhui Province, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiuyuan Liu
- Department of Gastroenterology, the Key Laboratory of Digestive Diseases of Anhui Province, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yonghao Chen
- Department of Gastroenterology, the Key Laboratory of Digestive Diseases of Anhui Province, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiao Mei
- Department of Gastroenterology, the Key Laboratory of Digestive Diseases of Anhui Province, the First Affiliated Hospital of Anhui Medical University, Hefei, China
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Wu X, Zhou H, Li L, Wang E, Zhou X, Gu Y, Wu X, Shen L, Zeng W. Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability. Microorganisms 2020; 8:microorganisms8050716. [PMID: 32408484 PMCID: PMC7284689 DOI: 10.3390/microorganisms8050716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 11/26/2022] Open
Abstract
Halotolerant microorganisms are promising in bio-treatment of hypersaline industrial wastewater. Four halotolerant bacteria strains were isolated from wastewater treatment plant, of which a strain LZH-9 could grow in the presence of up to 14% (w/v) NaCl, and it removed 81.9% chemical oxygen demand (COD) at 96 h after optimization. Whole genome sequencing of Lysinibacillus pakistanensis LZH-9 and comparative genomic analysis revealed metabolic versatility of different species of Lysinibacillus, and abundant genes involved in xenobiotics biodegradation, resistance to toxic compound, and salinity were found in all tested species of Lysinibacillus, in which Horizontal Gene Transfer (HGT) contributed to the acquisition of many important properties of Lysinibacillus spp. such as toxic compound resistance and osmotic stress resistance as revealed by phylogenetic analyses. Besides, genome wide positive selection analyses revealed seven genes that contained adaptive mutations in Lysinibacillus spp., most of which were multifunctional. Further expression assessment with Codon Adaption Index (CAI) also reflected the high metabolic rate of L. pakistanensis to digest potential carbon or nitrogen sources in organic contaminants, which was closely linked with efficient COD removal ability of strain LZH-9. The high COD removal efficiency and halotolerance as well as genomic evidences suggested that L. pakistanensis LZH-9 was promising in treating hypersaline industrial wastewater.
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Affiliation(s)
- Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Han Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Enhui Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Xiangyu Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Yichao Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Xiaoyan Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
- Correspondence: ; Tel.: +86-0731-88877472
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Lienkamp AC, Heine T, Tischler D. Glutathione: A powerful but rare cofactor among Actinobacteria. ADVANCES IN APPLIED MICROBIOLOGY 2020; 110:181-217. [PMID: 32386605 DOI: 10.1016/bs.aambs.2019.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Glutathione (γ-l-glutamyl-l-cysteinylglycine, GSH) is a powerful cellular redox agent. In nature only the l,l-form is common among the tree of life. It serves as antioxidant or redox buffer system, protein regeneration and activation by interaction with thiol groups, unspecific reagent for conjugation during detoxification, marker for amino acid or peptide transport even through membranes, activation or solubilization of compounds during degradative pathways or just as redox shuttle. However, the role of GSH production and utilization in bacteria is more complex and especially little is known for the Actinobacteria. Some recent reports on GSH use in degradative pathways came across and this is described herein. GSH is used by transferases to activate and solubilize epoxides. It allows funneling epoxides as isoprene oxide or styrene oxide into central metabolism. Thus, the distribution of GSH synthesis, recycling and application among bacteria and especially Actinobacteria are highlighted including the pathways and contributing enzymes.
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Affiliation(s)
- Anna C Lienkamp
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Thomas Heine
- Environmental Microbiology, Faculty of Chemistry and Physics, TU Bergakademie Freiberg, Freiberg, Germany
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany.
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Ding H, Wang JN, Zhang DS, Ma ZJ. Derivatives of Holomycin and Cyclopropaneacetic Acid fromStreptomycessp. DT-A37. Chem Biodivers 2017. [DOI: 10.1002/cbdv.201700140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hui Ding
- Institute of Marine Biology; Ocean College; Zhejiang University; Zhoushan Campus, No. 1 Zheda Road Zhoushan 316021 P. R. China
| | - Jia-Nan Wang
- Institute of Marine Biology; Ocean College; Zhejiang University; Zhoushan Campus, No. 1 Zheda Road Zhoushan 316021 P. R. China
| | - Da-Shan Zhang
- Institute of Marine Biology; Ocean College; Zhejiang University; Zhoushan Campus, No. 1 Zheda Road Zhoushan 316021 P. R. China
| | - Zhong-Jun Ma
- Institute of Marine Biology; Ocean College; Zhejiang University; Zhoushan Campus, No. 1 Zheda Road Zhoushan 316021 P. R. China
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Chen W, Liu Y, Zhang L, Gu X, Liu G, Shahid M, Gao J, Ali T, Han B. Nocardia cyriacigeogica from Bovine Mastitis Induced In vitro Apoptosis of Bovine Mammary Epithelial Cells via Activation of Mitochondrial-Caspase Pathway. Front Cell Infect Microbiol 2017; 7:194. [PMID: 28573110 PMCID: PMC5435817 DOI: 10.3389/fcimb.2017.00194] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/03/2017] [Indexed: 11/13/2022] Open
Abstract
Nocardia is one of the causing agents of bovine mastitis and increasing prevalence of nocardial mastitis in shape of serious outbreaks has been reported from many countries. However, the mechanisms by which this pathogen damages the bovine mammary epithelial cells (bMECs) is not yet studied. Therefore, this study was designed with the aim to evaluate the apoptotic effects elicited by Nocardia and to investigate the pathway by which the Nocardia induce apoptosis in bMECs. Clinical Nocardia cyriacigeorgica strain from bovine mastitis was used to infect the bMECs for different time intervals, viz. 1, 3, 6, 12, and 18 h, and then the induced effects on bMECs were studied using adhesion and invasion assays, release of lactate dehydrogenase (LDH), apoptosis analysis by annexin V and propidium iodide (PI) double staining, morphological, and ultrastructural observations under scanning electron microscope (SEM) and transmission electron microscope (TEM), mitochondrial transmembrane potential (ΔΨm) assay using flow cytometry, and the protein quantification of mitochondrial cytochrome c and caspase-9 and caspase-3 by western blotting. The results of this study showed that N. cyriacigeorgica possessed the abilities of adhesion and invasion to bMECs. N. cyriacigeorgica was found to collapse mitochondrial transmembrane potential, significantly (p < 0.05) release mitochondrial cytochrome c and ultimately induce cell apoptosis. Additionally, it promoted casepase-9 (p < 0.01) and casepase-3 (p < 0.05) levels, significantly (p < 0.01) increased the release of LDH and promoted DNA fragmentation which further confirmed the apoptosis. Furthermore, N. cyriacigeorgica induced apoptosis/necrosis manifested specific ultrastructure features under TEM, such as swollen endoplasmic reticulum, cristae degeneration, and swelling of mitochondria, vesicle formation on the cell surface, rupturing of cell membrane and nuclear membrane, clumping, fragmentation, and margination of chromatin. The present study is the first comprehensive insight into patho-morphological ultrastructural features of apoptosis/necrosis induced by N. cyriacigeorgica, which concluded that the clinical N. cyriacigeorgica induced apoptotic changes in the bMECs through mitochondrial-caspase dependent apoptotic pathway.
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Affiliation(s)
- Wei Chen
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Yongxia Liu
- Department of Veterinary Clinics, College of Veterinary Medicine, Shandong Agricultural UniversityTai'an, China
| | - Limei Zhang
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Xiaolong Gu
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Gang Liu
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Muhammad Shahid
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Jian Gao
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Tariq Ali
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Bo Han
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
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Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer. Int J Mol Sci 2016; 17:ijms17081304. [PMID: 27517915 PMCID: PMC5000701 DOI: 10.3390/ijms17081304] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 07/31/2016] [Accepted: 08/02/2016] [Indexed: 11/17/2022] Open
Abstract
Riemerella anatipestifer (RA) belongs to the Flavobacteriaceae family and can cause a septicemia disease in poultry. The synonymous codon usage patterns of bacteria reflect a series of evolutionary changes that enable bacteria to improve tolerance of the various environments. We detailed the codon usage patterns of RA isolates from the available 12 sequenced genomes by multiple codon and statistical analysis. Nucleotide compositions and relative synonymous codon usage (RSCU) analysis revealed that A or U ending codons are predominant in RA. Neutrality analysis found no significant correlation between GC12 and GC₃ (p > 0.05). Correspondence analysis and ENc-plot results showed that natural selection dominated over mutation in the codon usage bias. The tree of cluster analysis based on RSCU was concordant with dendrogram based on genomic BLAST by neighbor-joining method. By comparative analysis, about 50 highly expressed genes that were orthologs across all 12 strains were found in the top 5% of high CAI value. Based on these CAI values, we infer that RA contains a number of predicted highly expressed coding sequences, involved in transcriptional regulation and metabolism, reflecting their requirement for dealing with diverse environmental conditions. These results provide some useful information on the mechanisms that contribute to codon usage bias and evolution of RA.
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Chakraborti P, Banerjee R, Roy A, Mandal S, Mukhopadhyay S. Molecular characterization influencing metal resistance in the Cupriavidus/Ralstonia genomes. J Biomol Struct Dyn 2015; 33:2330-46. [PMID: 26156561 DOI: 10.1080/07391102.2015.1069214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Our environment is stressed with a load of heavy and toxic metals. Microbes, abundant in our environment, are found to adapt well to this metal-stressed condition. A comparative study among five Cupriavidus/Ralstonia genomes can offer a better perception of their evolutionary mechanisms to adapt to these conditions. We have studied codon usage among 1051 genes common to all these organisms and identified 15 optimal codons frequently used in highly expressed genes present within 1051 genes. We found the core genes of Cupriavidus metallidurans CH34 have a different optimal codon choice for arginine, glycine and alanine in comparison with the other four bacteria. We also found that the synonymous codon usage bias within these 1051 core genes is highly correlated with their gene expression. This supports that translational selection drives synonymous codon usage in the core genes of these genomes. Synonymous codon usage is highly conserved in the core genes of these five genomes. The only exception among them is C. metallidurans CH34. This genomewide shift in synonymous codon choice in C. metallidurans CH34 may have taken place due to the insertion of new genes in its genomes facilitating them to survive in heavy metal containing environment and the co-evolution of the other genes in its genome to achieve a balance in gene expression. Structural studies indicated the presence of a longer N-terminal region containing a copper-binding domain in the cupC proteins of C. metallidurans CH3 that helps it to attain higher binding efficacy with copper in comparison with its orthologs.
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Affiliation(s)
- Pratim Chakraborti
- a Apt Software Avenues Pvt. Ltd, Unit G 301, Block DC , City Centre , Sector I, Salt Lake, Kolkata 700064 , India
| | - Rachana Banerjee
- b Department of Biophysics, Molecular Biology and Bioinformatics , University of Calcutta , 92, A.P.C. Road, Kolkata 700009 , India
| | - Ayan Roy
- c NBU Bioinformatics Facility, Department of Botany , University of North Bengal , Raja Rammohanpur, Siliguri 734013 , India
| | - Sunanda Mandal
- b Department of Biophysics, Molecular Biology and Bioinformatics , University of Calcutta , 92, A.P.C. Road, Kolkata 700009 , India
| | - Subhasish Mukhopadhyay
- b Department of Biophysics, Molecular Biology and Bioinformatics , University of Calcutta , 92, A.P.C. Road, Kolkata 700009 , India
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A case of community-acquired pneumonia due to influenza A virus and Nocardia farcinica co-infection. J Infect Chemother 2014; 20:506-8. [PMID: 24855916 DOI: 10.1016/j.jiac.2014.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 04/20/2014] [Accepted: 04/21/2014] [Indexed: 12/20/2022]
Abstract
Nocardia spp. has not been reported previously as a cause of post-influenza pneumonia. Here we present a first case of post-influenza bacterial pneumonia due to Nocardia farcinica. Initial reason for hospitalization of the 90 year old female patient was a pneumonia with the symptoms of fever and productive cough. A rapid test for influenza antigen was positive for influenza A virus. Treatment with Zanamivir and piperacillin was initiated. However, after 1 week of treatment, the infiltration shadows on chest X-ray had worsened. Because the expectorated sputum collected on admission for culture was found to be positive for Nocardia spp., piperacillin was replaced with trimethoprim/sulfamethoxazole, and a chest X-ray showed some improvement. Although pulmonary nocardiosis with co-infection with influenza A is extremely rare, clinicians should be alert to the possibility.
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Vera-Cabrera L, Ortiz-Lopez R, Elizondo-Gonzalez R, Ocampo-Candiani J. Complete genome sequence analysis of Nocardia brasiliensis HUJEG-1 reveals a saprobic lifestyle and the genes needed for human pathogenesis. PLoS One 2013; 8:e65425. [PMID: 23755230 PMCID: PMC3670865 DOI: 10.1371/journal.pone.0065425] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 04/24/2013] [Indexed: 01/17/2023] Open
Abstract
Nocardia brasiliensis is an important etiologic agent of mycetoma. These bacteria live as a saprobe in soil or organic material and enter the tissue via minor trauma. Mycetoma is characterized by tumefaction and the production of fistula and abscesses, with no spontaneous cure. By using mass sequencing, we determined the complete genomic nucleotide sequence of the bacteria. According to our data, the genome is a circular chromosome 9,436,348-bp long with 68% G+C content that encodes 8,414 proteins. We observed orthologs for virulence factors, a higher number of genes involved in lipid biosynthesis and catabolism, and gene clusters for the synthesis of bioactive compounds, such as antibiotics, terpenes, and polyketides. An in silico analysis of the sequence supports the conclusion that the bacteria acquired diverse genes by horizontal transfer from other soil bacteria, even from eukaryotic organisms. The genome composition reflects the evolution of bacteria via the acquisition of a large amount of DNA, which allows it to survive in new ecological niches, including humans.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Chromosome Mapping
- Chromosomes, Bacterial/chemistry
- Chromosomes, Bacterial/metabolism
- DNA Transposable Elements
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Gene Expression Regulation, Bacterial
- Gene Transfer, Horizontal
- Genome, Bacterial
- Humans
- Metabolic Networks and Pathways/genetics
- Molecular Sequence Annotation
- Mycetoma/microbiology
- Mycetoma/pathology
- Nocardia/drug effects
- Nocardia/genetics
- Nocardia/metabolism
- Nocardia/pathogenicity
- Nocardia Infections/microbiology
- Nocardia Infections/pathology
- Sequence Analysis, DNA
- Soil Microbiology
- Virulence Factors/genetics
- Virulence Factors/metabolism
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Affiliation(s)
- Lucio Vera-Cabrera
- Laboratorio Interdisciplinario de Investigación Dermatológica, Servicio de Dermatología, Hospital Universitario, UANL, Monterrey, NL, México.
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Actinobacterial peroxidases: an unexplored resource for biocatalysis. Appl Biochem Biotechnol 2011; 164:681-713. [PMID: 21279698 DOI: 10.1007/s12010-011-9167-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 01/10/2011] [Indexed: 10/18/2022]
Abstract
Peroxidases are redox enzymes that can be found in all forms of life where they play diverse roles. It is therefore not surprising that they can also be applied in a wide range of industrial applications. Peroxidases have been extensively studied with particular emphasis on those isolated from fungi and plants. In general, peroxidases can be grouped into haem-containing and non-haem-containing peroxidases, each containing protein families that share sequence similarity. The order Actinomycetales comprises a large group of bacteria that are often exploited for their diverse metabolic capabilities, and with recent increases in the number of sequenced genomes, it has become clear that this metabolically diverse group of organisms also represents a large resource for redox enzymes. It is therefore surprising that, to date, no review article has been written on the wide range of peroxidases found within the actinobacteria. In this review article, we focus on the different types of peroxidases found in actinobacteria, their natural role in these organisms and how they compare with the more well-described peroxidases. Finally, we also focus on work remaining to be done in this research field in order for peroxidases from actinobacteria to be applied in industrial processes.
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Larkin MJ, Kulakov LA, Allen CCR. Genomes and Plasmids in Rhodococcus. BIOLOGY OF RHODOCOCCUS 2010. [DOI: 10.1007/978-3-642-12937-7_3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Gao J, Chen LL. Theoretical methods for identifying important functional genes in bacterial genomes. Res Microbiol 2009; 161:1-8. [PMID: 19900539 DOI: 10.1016/j.resmic.2009.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 10/05/2009] [Accepted: 10/21/2009] [Indexed: 12/30/2022]
Abstract
Some functional genes, such as essential genes, highly expressed genes and horizontally transferred genes, play important roles in the survival and pathogenicity of bacteria. This review attempts to summarize current computational methods in identifying the above functional genes from bacterial genomes, which is of significant importance in exploring the bacterial genomes.
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Affiliation(s)
- Junxiang Gao
- School of Information and Communication Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, PR China
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Thioredoxins in redox maintenance and survival during oxidative stress of Bacteroides fragilis. J Bacteriol 2009; 191:3384-91. [PMID: 19286811 DOI: 10.1128/jb.01665-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The anaerobe Bacteroides fragilis is a gram-negative, opportunistic pathogen that is highly aerotolerant and can persist in aerobic environments for extended periods. In this study, the six B. fragilis thioredoxins (Trxs) were investigated to determine their role during oxidative stress. Phylogenetic analyses of Trx protein sequences indicated that four of the six Trxs (TrxA, TrxC, TrxD, and TrxF) belong to the M-type Trx class but were associated with two different M-type lineages. TrxE and TrxG were most closely associated to Y-type Trxs found primarily in cyanobacteria. Single and multiple trx gene deletions were generated to determine functional differences between the Trxs. The trxA gene was essential, but no anaerobic growth defects were observed for any other single trx deletion or for the DeltatrxC DeltatrxD::cfxA DeltatrxE DeltatrxF DeltatrxG quintuple mutant. Regulation of the trx genes was linked to the oxidative stress response, and all were induced by aerobic conditions. The DeltatrxC DeltatrxE DeltatrxF DeltatrxG and the DeltatrxC DeltatrxD::cfxA DeltatrxE DeltatrxF DeltatrxG multiple deletion strains were impaired during growth in oxidized media, but single trx gene mutants did not have a phenotype in this assay. TrxD was protective during exposure to the thiol oxidant diamide, and expression of trxD was induced by diamide. Diamide-induced expression of trxC, trxE, and trxF increased significantly in a trxD mutant strain, suggesting that there is some capacity for compensation in this complex Trx system. These data provide insight into the role of individual Trxs in the B. fragilis oxidative stress response.
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A novel aryl acylamidase fromNocardia farcinicahydrolyses polyamide. Biotechnol Bioeng 2009; 102:1003-11. [DOI: 10.1002/bit.22139] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Puigbò P, Bravo IG, Garcia-Vallve S. CAIcal: a combined set of tools to assess codon usage adaptation. Biol Direct 2008; 3:38. [PMID: 18796141 PMCID: PMC2553769 DOI: 10.1186/1745-6150-3-38] [Citation(s) in RCA: 358] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 09/16/2008] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Codon Adaptation Index (CAI) was first developed to measure the synonymous codon usage bias for a DNA or RNA sequence. The CAI quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. RESULTS We describe here CAIcal, a web-server available at http://genomes.urv.es/CAIcal that includes a complete set of utilities related with the CAI. The server provides useful important features, such as the calculation and graphical representation of the CAI along either an individual sequence or a protein multiple sequence alignment translated to DNA. The automated calculation of CAI and its expected value is also included as one of the CAIcal tools. The software is also free to be downloaded as a stand alone application for local use. CONCLUSION The CAIcal server provides a complete set of tools to assess codon usage adaptation and to help in genome annotation.
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Affiliation(s)
- Pere Puigbò
- Department of Biochemistry and Biotechnology, Rovira i Virgili University (URV), Campus Sescelades, c/Marcelli Domingo s/n, 43007 Tarragona, Spain.
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Guzmán E, Romeu A, Garcia-Vallve S. Completely sequenced genomes of pathogenic bacteria: a review. Enferm Infecc Microbiol Clin 2008; 26:88-98. [PMID: 18341921 DOI: 10.1157/13115544] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Six out of ten completely sequenced bacterial genomes are pathogenic or opportunistic bacteria. The genome sequence of at least one strain of all the principal pathogenic bacteria will soon be available. This information should enable us to identify genes that encode virulence factors. As these genes are potential targets for drugs and vaccines, their identification should have considerable repercussions on prevention, diagnosis, and treatment of the main bacterial infectious diseases. Comparison of genome sequences of several strains of the same species should allow identification of the genetic clues responsible for the differing behavior of related bacterial pathogens. This article reviews the genomes from pathogenic bacteria that have been or are currently being sequenced, describes the main tasks to be accomplished after a genome sequence becomes available, and discusses the benefits of having the genome sequence of bacterial pathogens.
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Affiliation(s)
- Eduard Guzmán
- Institut Català de la Salut, Area Bàsica de Salut, Tarragona, Spain.
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The implication of life style on codon usage patterns and predicted highly expressed genes for three Frankia genomes. Antonie van Leeuwenhoek 2008; 93:335-46. [DOI: 10.1007/s10482-007-9211-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Accepted: 11/12/2007] [Indexed: 11/27/2022]
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Puigbò P, Bravo IG, Garcia-Vallvé S. E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). BMC Bioinformatics 2008; 9:65. [PMID: 18230160 PMCID: PMC2246156 DOI: 10.1186/1471-2105-9-65] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Accepted: 01/29/2008] [Indexed: 11/26/2022] Open
Abstract
Background The Codon Adaptation Index (CAI) is a measure of the synonymous codon usage bias for a DNA or RNA sequence. It quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. Extreme values in the nucleotide or in the amino acid composition have a large impact on differential preference for synonymous codons. It is thence essential to define the limits for the expected value of CAI on the basis of sequence composition in order to properly interpret the CAI and provide statistical support to CAI analyses. Though several freely available programs calculate the CAI for a given DNA sequence, none of them corrects for compositional biases or provides confidence intervals for CAI values. Results The E-CAI server, available at , is a web-application that calculates an expected value of CAI for a set of query sequences by generating random sequences with G+C and amino acid content similar to those of the input. An executable file, a tutorial, a Frequently Asked Questions (FAQ) section and several examples are also available. To exemplify the use of the E-CAI server, we have analysed the codon adaptation of human mitochondrial genes that codify a subunit of the mitochondrial respiratory chain (excluding those genes that lack a prokaryotic orthologue) and are encoded in the nuclear genome. It is assumed that these genes were transferred from the proto-mitochondrial to the nuclear genome and that its codon usage was then ameliorated. Conclusion The E-CAI server provides a direct threshold value for discerning whether the differences in CAI are statistically significant or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences.
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Affiliation(s)
- Pere Puigbò
- Evolutionary Genomics Group, Department of Biochemistry and Biotechnology, Rovira i Virgili University (URV), Campus Sescelades, c/Marcelli Domingo s/n, 43007 Tarragona, Spain.
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Puigbò P, Romeu A, Garcia-Vallvé S. HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. Nucleic Acids Res 2007; 36:D524-7. [PMID: 17933767 PMCID: PMC2238906 DOI: 10.1093/nar/gkm831] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The highly expressed genes database (HEG-DB) is a genomic database that includes the prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection. The current version of the database contains general features for almost 200 genomes under translational selection, including the correspondence analysis of the relative synonymous codon usage for all genes, and the analysis of their highly expressed genes. For each genome, the database contains functional and positional information about the predicted group of highly expressed genes. This information can also be accessed using a search engine. Among other statistical parameters, the database also provides the Codon Adaptation Index (CAI) for all of the genes using the codon usage of the highly expressed genes as a reference set. The 'Pathway Tools Omics Viewer' from the BioCyc database enables the metabolic capabilities of each genome to be explored, particularly those related to the group of highly expressed genes. The HEG-DB is freely available at http://genomes.urv.cat/HEG-DB.
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Affiliation(s)
- Pere Puigbò
- Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University (URV), c/Marcel-li Domingo, s/n. Campus Sescelades, 43007 Tarragona, Spain.
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Rocha ER, Tzianabos AO, Smith CJ. Thioredoxin reductase is essential for thiol/disulfide redox control and oxidative stress survival of the anaerobe Bacteroides fragilis. J Bacteriol 2007; 189:8015-23. [PMID: 17873045 PMCID: PMC2168685 DOI: 10.1128/jb.00714-07] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Results of this study showed that the anaerobic, opportunistic pathogen Bacteroides fragilis lacks the glutathione/glutaredoxin redox system and possesses an extensive number of putative thioredoxin (Trx) orthologs. Analysis of the genome sequence revealed six Trx orthologs and an absence of genes required for synthesis of glutathione and glutaredoxins. In addition, it was shown that the thioredoxin reductase (TrxB)/Trx system is the major or sole redox system for thiol/disulfide cellular homeostasis in this anaerobic bacterium. Expression of the B. fragilis trxB gene was induced following treatment with diamide or H(2)O(2) or exposure to oxygen. This inducible trxB expression was OxyR independent. Northern blot hybridization analysis showed that the trxB mRNA was cotranscribed with lolA as a bicistronic transcript or was present as a monocistronic transcript that was also highly induced under the same conditions. The role of LolA, a prokaryotic periplasmic lipoprotein-specific molecular chaperone in the thiol/disulfide redox system, is unknown. A trxB deletion mutant was more sensitive to the effects of diamide and oxygen than the parent strain. In addition, the trxB mutant was unable to grow in culture media without addition of a reductant. Furthermore, the trxB mutant was not able to induce intraabdominal abscess formation in a mouse model, whereas the parent strain was. Taken together, these data strongly suggest that TrxB/Trx is the major, if not the sole, thiol/disulfide redox system in this anaerobe required for survival and abscess formation in a peritoneal cavity infection model.
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Affiliation(s)
- Edson R Rocha
- Department of Microbiology & Immunology, East Carolina University Brody School of Medicine, 600 Moye Blvd., Greenville, NC 27834, USA
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Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, van Sinderen D. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev 2007; 71:495-548. [PMID: 17804669 PMCID: PMC2168647 DOI: 10.1128/mmbr.00005-07] [Citation(s) in RCA: 597] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Actinobacteria constitute one of the largest phyla among bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context.
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Affiliation(s)
- Marco Ventura
- Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, parco Area delle Scienze 11a, 43100 Parma, Italy.
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Wu G, Nie L, Freeland SJ. The effects of differential gene expression on coding sequence features: Analysis by one-way ANOVA. Biochem Biophys Res Commun 2007; 358:1108-13. [PMID: 17517370 DOI: 10.1016/j.bbrc.2007.05.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 05/08/2007] [Indexed: 10/23/2022]
Abstract
It is well-established that non-random patterns in coding DNA sequence (CDS) features can be partially explained by translational selection. Recent extensions of microarray and proteomic expression data have stimulated many genome-wide investigations of the relationships between gene expression and various CDS features. However, only modest correlations have been found. Here we introduced the one-way ANOVA, a more powerful extension of previous grouping methods, to re-examine these relationships at the whole genome scale for Saccharomyces cerevisiae, where genome-wide protein abundance has been recently quantified. Our results clarify that coding sequence features are inappropriate for use as genome-wide estimators for protein expression levels. This analysis also demonstrates that one-way ANOVA is a powerful and simple method to explore the influence of gene expression on CDS features.
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Affiliation(s)
- Gang Wu
- Department of Biological Sciences, University of Maryland at Baltimore County, Baltimore, MD 21250, USA.
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