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Lin Y, Han J, Barkema HW, Wang Y, Gao J, Kastelic JP, Han B, Qin S, Deng Z. Comparative Genomic Analyses of Lactococcus garvieae Isolated from Bovine Mastitis in China. Microbiol Spectr 2023; 11:e0299522. [PMID: 37154706 PMCID: PMC10269658 DOI: 10.1128/spectrum.02995-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 04/17/2023] [Indexed: 05/10/2023] Open
Abstract
Lactococcus garvieae is an emerging zoonotic pathogen, but there are few reports regarding bovine mastitis. The prevalence of L. garvieae represents an increasing disease threat and global public health risk. Thirty-nine L. garvieae isolates were obtained from 2,899 bovine clinical mastitis milk samples in 6 provinces of China from 2017 to 2021. Five clonal complexes were determined from 32 multilocus sequence types (MLSTs) of L. garvieae: sequence type 46 (ST46) was the predominant sequence type, and 13 novel MLSTs were identified. All isolates were resistant to chloramphenicol and clindamycin, but susceptible to penicillin, ampicillin, amoxicillin-clavulanic acid, imipenem, ceftiofur, enrofloxacin, and marbofloxacin. Based on genomic analyses, L. garvieae had 6,310 genes, including 1,015 core, 3,641 accessory, and 1,654 unique genes. All isolates had virulence genes coding for collagenase, fibronectin-binding protein, glyceraldehyde-3-phosphate dehydrogenase, superoxide dismutase, and NADH oxidase. Most isolates had lsaD and mdtA antimicrobial resistance (AMR) genes. Based on COG (Clusters of Orthologous Genes database) results, the functions of defense, transcription and replication, and recombination and repair were enhanced in unique genes, whereas functions of translation, ribosomal structure, and biogenesis were enhanced in core genes. The KEGG functional categories enriched in unique genes included human disease and membrane transport, whereas COG functional categories enriched in core genes included energy metabolism, nucleotide metabolism, and translation. No gene was significantly associated with host specificity. In addition, analysis of core genome single nucleotide polymorphisms (SNPs) implied potential host adaptation of some isolates in several sequence types. In conclusion, this study characterized L. garvieae isolated from mastitis and detected potential adaptations of L. garvieae to various hosts. IMPORTANCE This study provides important genomic insights into a bovine mastitis pathogen, Lactococcus garvieae. Comprehensive genomic analyses of L. garvieae from dairy farms have not been reported. This study is a detailed and comprehensive report of novel features of isolates of L. garvieae, an important but poorly characterized bacterium, recovered in the past 5 years in 6 Chinese provinces. We documented diverse genetic features, including predominant sequence type ST46 and 13 novel MLSTs. Lactococcus garvieae had 6,310 genes, including 1,015 core, 3,641 accessory, and 1,654 unique genes. All isolates had virulence genes coding for collagenase, fibronectin-binding protein, glyceraldehyde-3-phosphate dehydrogenase, superoxide dismutase, and NADH oxidase and resistance to chloramphenicol and clindamycin. Most isolates had lsaD and mdtA antimicrobial resistance genes. However, no gene was significantly associated with host specificity. This is the first report that characterized L. garvieae isolates from bovine mastitis and revealed potential host adaptations of L. garvieae to various hosts.
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Affiliation(s)
- Yushan Lin
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jinge Han
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, People’s Republic of China
| | - Herman W. Barkema
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Yue Wang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jian Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - John P. Kastelic
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Bo Han
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Shunyi Qin
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, People’s Republic of China
| | - Zhaoju Deng
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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2
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Desiderato CK, Hasenauer KM, Reich SJ, Goldbeck O, Holivololona L, Ovchinnikov KV, Reiter A, Oldiges M, Diep DB, Eikmanns BJ, Riedel CU. Garvicin Q: characterization of biosynthesis and mode of action. Microb Cell Fact 2022; 21:236. [PMID: 36368990 PMCID: PMC9652874 DOI: 10.1186/s12934-022-01952-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
Bacteriocins are ribosomally synthesized antimicrobial peptides, that either kill target bacteria or inhibit their growth. Bacteriocins are used in food preservation and are of increasing interest as potential alternatives to conventional antibiotics. In the present study, we show that Lactococcus petauri B1726, a strain isolated from fermented balsam pear, produces a heat-stable and protease-sensitive compound. Following genome sequencing, a gene cluster for production of a class IId bacteriocin was identified consisting of garQ (encoding for the bacteriocin garvicin Q), garI (for a putative immunity protein), garC, and garD (putative transporter proteins). Growth conditions were optimized for increased bacteriocin activity in supernatants of L. petauri B1726 and purification and mass spectrometry identified the compound as garvicin Q. Further experiments suggest that garvicin Q adsorbs to biomass of various susceptible and insusceptible bacteria and support the hypothesis that garvicin Q requires a mannose-family phosphotransferase system (PTSMan) as receptor to kill target bacteria by disruption of membrane integrity. Heterologous expression of a synthetic garQICD operon was established in Corynebacterium glutamicum demonstrating that genes garQICD are responsible for biosynthesis and secretion of garvicin Q. Moreover, production of garvicin Q by the recombinant C. glutamicum strain was improved by using a defined medium yet product levels were still considerably lower than with the natural L. petauri B1726 producer strain.Collectively, our data identifies the genetic basis for production of the bacteriocin garvicin Q by L. petauri B1726 and provides insights into the receptor and mode of action of garvicin Q. Moreover, we successfully performed first attempts towards biotechnological production of this interesting bacteriocin using natural and heterologous hosts.
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Affiliation(s)
- Christian K. Desiderato
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Katharina M. Hasenauer
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Sebastian J. Reich
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Oliver Goldbeck
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Lalaina Holivololona
- grid.19477.3c0000 0004 0607 975XFaculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Kirill V. Ovchinnikov
- grid.19477.3c0000 0004 0607 975XFaculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Alexander Reiter
- grid.8385.60000 0001 2297 375XInstitute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425 Jülich, Germany ,grid.1957.a0000 0001 0728 696XInstitute of Biotechnology, RWTH Aachen University, 52062 Aachen, Germany
| | - Marco Oldiges
- grid.8385.60000 0001 2297 375XInstitute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425 Jülich, Germany ,grid.1957.a0000 0001 0728 696XInstitute of Biotechnology, RWTH Aachen University, 52062 Aachen, Germany
| | - Dzung B. Diep
- grid.19477.3c0000 0004 0607 975XFaculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Bernhard J. Eikmanns
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Christian U. Riedel
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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Tavares GC, Carvalho AF, Pereira FL, Rezende CP, Azevedo VAC, Leal CAG, Figueiredo HCP. Transcriptome and Proteome of Fish-Pathogenic Streptococcus agalactiae Are Modulated by Temperature. Front Microbiol 2018; 9:2639. [PMID: 30450092 PMCID: PMC6224512 DOI: 10.3389/fmicb.2018.02639] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/16/2018] [Indexed: 12/23/2022] Open
Abstract
Streptococcus agalactiae is one of the most important pathogens associated with streptococcosis outbreaks in Nile tilapia farms worldwide. High water temperature (above 27°C) has been described as a predisposing factor for the disease in fish. At low temperatures (below 25°C), fish mortalities are not usually observed in farms. Temperature variation can modulate the expression of genes and proteins involved in metabolism, adaptation, and bacterial pathogenicity, thus increasing or decreasing the ability to infect the host. This study aimed to evaluate the transcriptome and proteome of a fish-pathogenic S. agalactiae strain SA53 subjected to in vitro growth at different temperatures using a microarray and label-free shotgun LC-HDMSE approach. Biological triplicates of isolates were cultured in BHIT broth at 22 or 32°C for RNA and protein isolation and submitted for transcriptomic and proteomic analyses. In total, 1,730 transcripts were identified in SA53, with 107 genes being differentially expressed between the temperatures evaluated. A higher number of genes related to metabolism, mainly from the phosphotransferase system (PTS) and ATP-binding cassette (ABC) transport system, were upregulated at 32°C. In the proteome analysis, 1,046 proteins were identified in SA53, of which 81 were differentially regulated between 22 and 32°C. Proteins involved in defense mechanisms, lipid transport and metabolism, and nucleotide transport and metabolism were upregulated at 32°C. A higher number of interactions were observed in proteins involved in nucleotide transport and metabolism. We observed a low correlation between the transcriptome and proteome datasets. Our study indicates that the transcriptome and proteome of a fish-adapted S. agalactiae strain are modulated by temperature, particularly showing differential expression of genes/proteins involved in metabolism, virulence factors, and adaptation.
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Affiliation(s)
- Guilherme C Tavares
- AQUACEN-National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Alex F Carvalho
- AQUACEN-National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Felipe L Pereira
- AQUACEN-National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Cristiana P Rezende
- AQUACEN-National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A C Azevedo
- LGCM-Laboratory of Cellular and Molecular Genetics, Biological Science Institute, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Carlos A G Leal
- AQUACEN-National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Henrique C P Figueiredo
- AQUACEN-National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
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Mendez J, Cascales D, Garcia-Torrico AI, Guijarro JA. Temperature-Dependent Gene Expression in Yersinia ruckeri: Tracking Specific Genes by Bioluminescence During in Vivo Colonization. Front Microbiol 2018; 9:1098. [PMID: 29887855 PMCID: PMC5981175 DOI: 10.3389/fmicb.2018.01098] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/08/2018] [Indexed: 11/26/2022] Open
Abstract
Yersinia ruckeri is a bacterium causing fish infection processes at temperatures below the optimum for growth. A derivative Tn5 transposon was used to construct a library of Y. ruckeri mutants with transcriptional fusions between the interrupted genes and the promoterless luxCDABE and lacZY operons. In vitro analysis of β-galactosidase activity allowed the identification of 168 clones having higher expression at 18°C than at 28°C. Among the interrupted genes a SAM-dependent methyltransferase, a diguanylated cyclase, three genes involved in legionaminic acid synthesis and three transcriptional regulators were defined. In order to determine, via bioluminescence emission, the in vivo expression of some of these genes, two of the selected mutants were studied. In one of them, the acrR gene coding a repressor involved in regulation of the AcrAB-TolC expulsion pump was interrupted. This mutant was found to be highly resistant to compounds such as chloramphenicol, tetracycline, and ciprofloxacin. Although acrR mutation was not related to virulence in Y. ruckeri, this mutant was useful to analyze acrR expression in fish tissues in vivo. The other gene studied was osmY which is activated under osmotic stress and is involved in virulence. In this case, complemented mutant was used for experiments with fish. In vivo analysis of bioluminescence emission by these two strains showed higher values for acrR in gut, liver and adipose tissue, whereas osmY showed higher luminescence in gut and, at the end of the infection process, in muscle tissue. Similar results were obtained in ex vivo assays using rainbow trout tissues. The results indicated that this kind of approach was useful for the identification of genes related to virulence in Y. ruckeri and also for the in vivo and in vitro studies of each of the selected genes.
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Affiliation(s)
- Jessica Mendez
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, Instituto de Biotecnología de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Desirée Cascales
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, Instituto de Biotecnología de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Ana I Garcia-Torrico
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, Instituto de Biotecnología de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Jose A Guijarro
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, Instituto de Biotecnología de Asturias, Universidad de Oviedo, Oviedo, Spain
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5
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Detection of virulence-related genes in Lactococcus garvieae and their expression in response to different conditions. Folia Microbiol (Praha) 2017; 63:291-298. [DOI: 10.1007/s12223-017-0566-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
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6
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Castro R, Reguera-Brito M, López-Campos GH, Blanco MM, Aguado-Urda M, Fernández-Garayzábal JF, Gibello A. How does temperature influences the development of lactococcosis? Transcriptomic and immunoproteomic in vitro approaches. JOURNAL OF FISH DISEASES 2017; 40:1285-1297. [PMID: 28093775 DOI: 10.1111/jfd.12601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 06/06/2023]
Abstract
Lactococcus garvieae is the aetiological agent of lactococcosis, a haemorrhagic septicaemia that affects marine and freshwater fish, with special incidence and economic relevance in farmed rainbow trout. Water temperature is one of the most important predisposing factors in the development of lactococcosis outbreaks. Lactococcosis in trout usually occur when water temperatures rise to about 18 °C, while fish carriers remain asymptomatic at temperatures below 13 °C. The aim of this work was to analyse the differences in the complete transcriptome response of L. garvieae grown at 18 °C and at 13 °C and to identify the immunogenic proteins expressed by this bacterium at 18 °C. Our results show that water temperature influences the expression of L. garvieae genes involved in the lysis of part of the bacterial cell population and in the cold response bacterial adaptation. Moreover, the surface immunogenic protein profile at 18 °C suggests an important role of the lysozyme-like enzyme, WxL surface proteins and some putative moonlighting proteins (proteins with more than one function, usually associated with different cellular locations) as virulence factors in L. garvieae. The results of this study could provide insights into the understanding of the virulence mechanisms of L. garvieae in fish.
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Affiliation(s)
- R Castro
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
| | - M Reguera-Brito
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
| | - G H López-Campos
- Health and Biomedical Informatics Research Unit, Medical School, University of Melbourne, Melbourne, VIC, Australia
| | - M M Blanco
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
| | - M Aguado-Urda
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
| | - J F Fernández-Garayzábal
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
- Animal Health Surveillance Center (VISAVET), Complutense University, Madrid, Spain
| | - A Gibello
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
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van der Meulen SB, de Jong A, Kok J. Early Transcriptome Response of Lactococcus lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and tRNAs. Front Microbiol 2017; 8:1704. [PMID: 28959239 PMCID: PMC5603721 DOI: 10.3389/fmicb.2017.01704] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/23/2017] [Indexed: 01/02/2023] Open
Abstract
Bacteria can deploy various mechanisms to combat environmental stresses. Many genes have previously been identified in Lactococcus lactis that are involved in sensing the stressors and those that are involved in regulating and mounting a defense against the stressful conditions. However, the expression of small regulatory RNAs (sRNAs) during industrially relevant stress conditions has not been assessed yet in L. lactis, while sRNAs have been shown to be involved in many stress responses in other bacteria. We have previously reported the presence of hundreds of putative regulatory RNAs in L. lactis, and have used high-throughput RNA sequencing (RNA-seq) in this study to assess their expression under six different stress conditions. The uniformly designed experimental set-up enabled a highly reliable comparison between the different stress responses and revealed that many sRNAs are differentially expressed under the conditions applied. The primary stress responses of L. lactis NCDO712 was benchmarked to earlier work and, for the first time, the differential expression was assessed of transfer RNAs (tRNAs) and the genes from the six recently sequenced plasmids of NCDO712. Although, we only applied stresses for 5 min, the majority of the well-known specific stress-induced genes are already differentially expressed. We find that most tRNAs decrease after all stresses applied, except for a small number, which are increased upon cold stress. Starvation was shown to induce the highest differential response, both in terms of number and expression level of genes. Our data pinpoints many novel stress-related uncharacterized genes and sRNAs, which calls for further assessment of their molecular and cellular function. These insights furthermore could impact the way parameters are designed for bacterial culture production and milk fermentation, as we find that very short stress conditions already greatly alter gene expression.
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Affiliation(s)
- Sjoerd B van der Meulen
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands.,Top Institute Food and NutritionWageningen, Netherlands
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands.,Top Institute Food and NutritionWageningen, Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands.,Top Institute Food and NutritionWageningen, Netherlands
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Yin YR, Meng ZH, Hu QW, Jiang Z, Xian WD, Li LH, Hu W, Zhang F, Zhou EM, Zhi XY, Li WJ. The Hybrid Strategy of Thermoactinospora rubra YIM 77501 T for Utilizing Cellulose as a Carbon Source at Different Temperatures. Front Microbiol 2017; 8:942. [PMID: 28611745 PMCID: PMC5447088 DOI: 10.3389/fmicb.2017.00942] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/10/2017] [Indexed: 01/02/2023] Open
Abstract
Thermoactinospora rubra YIM 77501T is an aerobic, Gram-positive, spore-forming and cellulose degrading thermophilic actinomycete isolated from a sandy soil sample of a volcano. Its growth temperature range is 28–60°C. The genomic sequence of this strain revealed that there are 27 cellulase genes belonging to six glycoside hydrolase families. To understand the strategy that this strain uses to utilize carbon sources such as cellulose at different temperatures, comparative transcriptomics analysis of T. rubra YIM 77501T was performed by growing it with cellulose (CMC) and without cellulose (replaced with glucose) at 30, 40, and 50°C, respectively. Transcriptomic analyses showed four cellulase genes (TrBG2, TrBG3, TrBG4, and ThrCel6B) were up-regulated at 30, 40, and 50°C. The rate of gene expression of TrBG2, TrBG3, TrBG4, and ThrCel6B were 50°C > 30°C > 40°C. One cellulase gene (TrBG1) and two cellulase genes (TrBG5 and ThrCel6A) were up-regulated only at 30 and 50°C, respectively. These up-regulated cellulase genes were cloned and expressed in Escherichia coli. The enzymatic properties of up-regulated cellulases showed a variety of responses to temperature. Special up-regulated cellulases TrBG1 and ThrCel6A displayed temperature acclimation for each growth condition. These expression patterns revealed that a hybrid strategy was used by T. rubra to utilize carbon sources at different temperatures. This study provides genomic, transcriptomics, and experimental data useful for understanding how microorganisms respond to environmental changes and their application in enhancing cellulose hydrolysis for animal feed and bioenergy production.
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Affiliation(s)
- Yi-Rui Yin
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
| | - Zhao-Hui Meng
- Department of Cardiology, The First Affiliated Hospital of Kunming Medical UniversityKunming, China
| | - Qing-Wen Hu
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
| | - Zhao Jiang
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
| | - Lin-Hua Li
- Department of Cardiology, The First Affiliated Hospital of Kunming Medical UniversityKunming, China
| | - Wei Hu
- Department of Cardiology, The First Affiliated Hospital of Kunming Medical UniversityKunming, China
| | - Feng Zhang
- Key Laboratory of Biopesticide and Chemical Biology, School of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - En-Min Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
| | - Xiao-Yang Zhi
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
| | - Wen-Jun Li
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of SciencesÜrümqi, China
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Transcriptomic Analysis of Laribacter hongkongensis Reveals Adaptive Response Coupled with Temperature. PLoS One 2017; 12:e0169998. [PMID: 28085929 PMCID: PMC5234827 DOI: 10.1371/journal.pone.0169998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/27/2016] [Indexed: 12/17/2022] Open
Abstract
Bacterial adaptation to different hosts requires transcriptomic alteration in response to the environmental conditions. Laribacter hongkongensis is a gram-negative, facultative anaerobic, urease-positive bacillus caused infections in liver cirrhosis patients and community-acquired gastroenteritis. It was also found in intestine from commonly consumed freshwater fishes and drinking water reservoirs. Since L. hongkongensis could survive as either fish or human pathogens, their survival mechanisms in two different habitats should be temperature-regulated and highly complex. Therefore, we performed transcriptomic analysis of L. hongkongensis at body temperatures of fish and human in order to elucidate the versatile adaptation mechanisms coupled with the temperatures. We identified numerous novel temperature-induced pathways involved in host pathogenesis, in addition to the shift of metabolic equilibriums and overexpression of stress-related proteins. Moreover, these pathways form a network that can be activated at a particular temperature, and change the physiology of the bacteria to adapt to the environments. In summary, the dynamic of transcriptomes in L. hongkongensis provides versatile strategies for the bacterial survival at different habitats and this alteration prepares the bacterium for the challenge of host immunity.
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Miura S, Himaki T, Takahashi J, Iwahashi H. THE ROLE OF TRANSCRIPTOMICS: PHYSIOLOGICAL EQUIVALENCE BASED ON GENE EXPRESSION PROFILES. ACTA ACUST UNITED AC 2017. [DOI: 10.7831/ras.5.21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shiori Miura
- The United Graduate School of Agricultural Science, Gifu University
| | - Takehiro Himaki
- The United Graduate School of Agricultural Science, Gifu University
| | - Junko Takahashi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hitoshi Iwahashi
- The United Graduate School of Agricultural Science, Gifu University
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11
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Strain-level visualized analysis of cold-stressed Vibrio parahaemolyticus based on MALDI-TOF mass fingerprinting. Microb Pathog 2015; 88:16-21. [PMID: 26255031 DOI: 10.1016/j.micpath.2015.08.002] [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] [Received: 03/28/2015] [Revised: 07/29/2015] [Accepted: 08/03/2015] [Indexed: 11/23/2022]
Abstract
In this study, strain-level visualized analysis of cold-stressed Vibrio parahaemolyticus based on matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass fingerprinting was investigated. All the peptide mass fingerprinting profiles obtained were analyzed by self-organized map (SOM) and cluster analysis. Our results showed that the peptide mass fingerprinting profiles of V. parahaemolyticus substantially changed under cold stress at strain level. The cold-stressed V. parahaemolyticus strains were distributed to 14 neurons by SOM classification, almost totally different from the controls. This is the first time that so many strains had been chosen to study bacterial cold stress responses, which can help promote an overall understanding to stress responses of cold-stressed strains.
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Guijarro JA, Cascales D, García-Torrico AI, García-Domínguez M, Méndez J. Temperature-dependent expression of virulence genes in fish-pathogenic bacteria. Front Microbiol 2015. [PMID: 26217329 PMCID: PMC4496569 DOI: 10.3389/fmicb.2015.00700] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Virulence gene expression in pathogenic bacteria is modulated by environmental parameters. A key factor in this expression is temperature. Its effect on virulence gene expression in bacteria infecting warm-blooded hosts is well documented. Transcription of virulence genes in these bacteria is induced upon a shift from low environmental to a higher host temperature (37°C). Interestingly, host temperatures usually correspond to the optimum for growth of these pathogenic bacteria. On the contrary, in ectothermic hosts such as fish, molluscs, and amphibians, infection processes generally occur at a temperature lower than that for the optimal growth of the bacteria. Therefore, regulation of virulence gene expression in response to temperature shift has to be modulated in a different way to that which is found in bacteria infecting warm-blooded hosts. The current understanding of virulence gene expression and its regulation in response to temperature in fish-pathogenic bacteria is limited, but constant extension of our knowledge base is essential to enable a rational approach to the problem of the bacterial fish diseases affecting the aquaculture industry. This is an interesting issue and progress needs to be made in order to diminish the economic losses caused by these diseases. The intention of this review is, for the first time, to compile the scattered results existing in the field in order to lay the groundwork for future research. This article is an overview of those relevant virulence genes that are expressed at temperatures lower than that for optimal bacterial growth in different fish-pathogenic bacteria as well as the principal mechanisms that could be involved in their regulation.
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Affiliation(s)
- José A. Guijarro
- *Correspondence: José A. Guijarro, Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, Instituto de Biotecnología de Asturias, Universidad de Oviedo, C/Julían Clavería 6, 33006 Oviedo, Spain,
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Kim M, Zorraquino V, Tagkopoulos I. Microbial forensics: predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles. PLoS Comput Biol 2015; 11:e1004127. [PMID: 25774498 PMCID: PMC4361189 DOI: 10.1371/journal.pcbi.1004127] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 01/14/2015] [Indexed: 01/13/2023] Open
Abstract
A tantalizing question in cellular physiology is whether the cellular state and environmental conditions can be inferred by the expression signature of an organism. To investigate this relationship, we created an extensive normalized gene expression compendium for the bacterium Escherichia coli that was further enriched with meta-information through an iterative learning procedure. We then constructed an ensemble method to predict environmental and cellular state, including strain, growth phase, medium, oxygen level, antibiotic and carbon source presence. Results show that gene expression is an excellent predictor of environmental structure, with multi-class ensemble models achieving balanced accuracy between 70.0% (±3.5%) to 98.3% (±2.3%) for the various characteristics. Interestingly, this performance can be significantly boosted when environmental and strain characteristics are simultaneously considered, as a composite classifier that captures the inter-dependencies of three characteristics (medium, phase and strain) achieved 10.6% (±1.0%) higher performance than any individual models. Contrary to expectations, only 59% of the top informative genes were also identified as differentially expressed under the respective conditions. Functional analysis of the respective genetic signatures implicates a wide spectrum of Gene Ontology terms and KEGG pathways with condition-specific information content, including iron transport, transferases, and enterobactin synthesis. Further experimental phenotypic-to-genotypic mapping that we conducted for knock-out mutants argues for the information content of top-ranked genes. This work demonstrates the degree at which genome-scale transcriptional information can be predictive of latent, heterogeneous and seemingly disparate phenotypic and environmental characteristics, with far-reaching applications. The transcriptional profile of an organism contains clues about the environmental context in which it has evolved and currently lives, its behavior and cellular state. It is yet unclear, however, how much information can be efficiently extracted and how it can be used to classify new samples with respect to their environmental and genetic characteristics. Here, we have constructed an extensive transcriptome compendium of Escherichia coli that we have further enriched via an iterative learning approach. We then apply an ensemble of various machine learning algorithms to infer environmental and cellular information such as strain, growth phase, medium, oxygen level, antibiotic and carbon source. Functional analysis of the most informative genes provides mechanistic insights and palpable hypotheses regarding their role in each environmental or genetic context. Our work argues that genome-scale gene expression can be a multi-purpose marker for identifying latent, heterogeneous cellular and environmental states and that optimal classification can be achieved with a feature set of a couple hundred genes that might not necessarily have the most pronounced differential expression in the respective conditions.
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Affiliation(s)
- Minseung Kim
- Department of Computer Science, University of California, Davis, Davis, California, United States of America
- UC Davis Genome Center, University of California, Davis, Davis, California, United States of America
| | - Violeta Zorraquino
- UC Davis Genome Center, University of California, Davis, Davis, California, United States of America
| | - Ilias Tagkopoulos
- Department of Computer Science, University of California, Davis, Davis, California, United States of America
- UC Davis Genome Center, University of California, Davis, Davis, California, United States of America
- * E-mail:
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López-Campos G, Aguado-Urda M, Blanco MM, Gibello A, Cutuli MT, López-Alonso V, Martín-Sánchez F, Fernández-Garayzábal JF. Lactococcus garvieae: a small bacteria and a big data world. Health Inf Sci Syst 2015; 3:S5. [PMID: 25960872 PMCID: PMC4416232 DOI: 10.1186/2047-2501-3-s1-s5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Objective To describe the importance of bioinformatics tools to analyze the big data yielded from new "omics" generation-methods, with the aim of unraveling the biology of the pathogen bacteria Lactococcus garvieae. Methods The paper provides the vision of the large volume of data generated from genome sequences, gene expression profiles by microarrays and other experimental methods that require biomedical informatics methods for management and analysis. Results The use of biomedical informatics methods improves the analysis of big data in order to obtain a comprehensive characterization and understanding of the biology of pathogenic organisms, such as L. garvieae. Conclusions The "Big Data" concepts of high volume, veracity and variety are nowadays part of the research in microbiology associated with the use of multiple methods in the "omic" era. The use of biomedical informatics methods is a requisite necessary to improve the analysis of these data.
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Affiliation(s)
- Guillermo López-Campos
- Health and Biomedical Informatics Centre (HABIC), The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Mónica Aguado-Urda
- Faculty of Veterinary Sciences, Department of Animal Health, Complutense University, Madrid, 28040, Spain
| | - María Mar Blanco
- Faculty of Veterinary Sciences, Department of Animal Health, Complutense University, Madrid, 28040, Spain
| | - Alicia Gibello
- Faculty of Veterinary Sciences, Department of Animal Health, Complutense University, Madrid, 28040, Spain
| | - María Teresa Cutuli
- Faculty of Veterinary Sciences, Department of Animal Health, Complutense University, Madrid, 28040, Spain
| | - Victoria López-Alonso
- Computational Biology Unit, National Institute of Health "Carlos III", Madrid, 28220, Spain
| | - Fernando Martín-Sánchez
- Health and Biomedical Informatics Centre (HABIC), The University of Melbourne, Melbourne, Victoria, 3010, Australia
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Abstract
Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.
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