Genetic characterisation of Farmer’s Lung causing strains of thermophilic actinobacteria

Alexandra Ntemiri

Research output: ThesisMaster's Thesis

Abstract

Farmers Lung Disease (FLD) is one of the most common hypersensitivity pneumonitis (HP). HP or extrinsic allergic alveolitis is a group of immunologically mediated pulmonary diseases caused by repeated inhalation of bioaerosolised antigens present in organic dust. Small diametre particles reach the distal gas exchange areas of the lung causing systemic IgG production, activation of the complement, attraction of macrophages and subsequently, inflammation to the interstitium, alveoli, middle and terminal airways. Chronic exposure could eventually lead to severe fibrosis and lung damage.
There are many potential causative agents for the various HPs and the thermophilic actinobacterium Saccharopolyspora rectivirgula has been reported as the major antigenic source for FLD. In a previous study on the serologic reaction of FLD patients, specific binding of patient IgG2 to S. rectivirgula antigens was demonstrated. The identical N-terminal sequence of the two antigenic proteins was also determined.
We performed whole genome sequencing (WGS) for S. rectivirgula type strain (DSM 43747) using Roche 454 GS sequencer and used the amino acid sequence to interrogate the annotated bacterial genome for the actual product. A putative secreted protein (SRE1) was retrieved carrying the sequence of interest at the N-terminal. Further bioinformatic analysis revealed that the protein had a transglycosylase and a LysM domain and belonged to the NOG06569 orthologous group which contains 130 proteins involved in cell wall macromolecule catabolic processes in 59 bacterial species, mostly actinobacteria.
This protein family is dominated by resuscitation promoting factors (Rpfs), proteins which stimulate culturability in latent bacterial spores. Rpfs are common in actinobacteria and in pathogenic species they play a role in establishing virulence. Mycobacterium tuberculosis can escape antibiotic treatment while being in latency and regain viability through Rpfs and eventually affect the host. Furthermore, Rpfs and proteins alike have been repeatedly reported to be immunogenic themselves.
We believe that SRE1 corresponds to the previously isolated FLD antigen and we suggest its classification among the Rpf proteins.
Future work will confirm the functional role of the protein and of similar products encoded in S. rectivirgula, and its implication in FLD. Importantly, apart from iv improving FLD serodiagnosis, the role of reactivity of Rpf proteins in FLD may provide further insight into the pathogenicity of tuberculosis.
LanguageEnglish
QualificationMPhil
Awarding Institution
  • University Of Strathclyde
Supervisors/Advisors
  • Herron, Paul, Supervisor
Award date23 May 2013
Place of PublicationGlasgow
Publisher
Publication statusPublished - 23 May 2013

Fingerprint

Farmer's Lung
Actinobacteria
Lung Diseases
Proteins
Extrinsic Allergic Alveolitis
Resuscitation
Antigens
Virulence
Saccharopolyspora
Immunoglobulin G
Bacterial Spores
Bacterial Genomes
Lung
Complement Activation
Serologic Tests
Computational Biology
Dust
Mycobacterium tuberculosis
Cell Wall
Inhalation

Keywords

  • Farmer's lung
  • thermophilic actinobacteria

Cite this

Ntemiri, Alexandra. / Genetic characterisation of Farmer’s Lung causing strains of thermophilic actinobacteria. Glasgow : University of Strathclyde, 2013.
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title = "Genetic characterisation of Farmer’s Lung causing strains of thermophilic actinobacteria",
abstract = "Farmers Lung Disease (FLD) is one of the most common hypersensitivity pneumonitis (HP). HP or extrinsic allergic alveolitis is a group of immunologically mediated pulmonary diseases caused by repeated inhalation of bioaerosolised antigens present in organic dust. Small diametre particles reach the distal gas exchange areas of the lung causing systemic IgG production, activation of the complement, attraction of macrophages and subsequently, inflammation to the interstitium, alveoli, middle and terminal airways. Chronic exposure could eventually lead to severe fibrosis and lung damage.There are many potential causative agents for the various HPs and the thermophilic actinobacterium Saccharopolyspora rectivirgula has been reported as the major antigenic source for FLD. In a previous study on the serologic reaction of FLD patients, specific binding of patient IgG2 to S. rectivirgula antigens was demonstrated. The identical N-terminal sequence of the two antigenic proteins was also determined.We performed whole genome sequencing (WGS) for S. rectivirgula type strain (DSM 43747) using Roche 454 GS sequencer and used the amino acid sequence to interrogate the annotated bacterial genome for the actual product. A putative secreted protein (SRE1) was retrieved carrying the sequence of interest at the N-terminal. Further bioinformatic analysis revealed that the protein had a transglycosylase and a LysM domain and belonged to the NOG06569 orthologous group which contains 130 proteins involved in cell wall macromolecule catabolic processes in 59 bacterial species, mostly actinobacteria.This protein family is dominated by resuscitation promoting factors (Rpfs), proteins which stimulate culturability in latent bacterial spores. Rpfs are common in actinobacteria and in pathogenic species they play a role in establishing virulence. Mycobacterium tuberculosis can escape antibiotic treatment while being in latency and regain viability through Rpfs and eventually affect the host. Furthermore, Rpfs and proteins alike have been repeatedly reported to be immunogenic themselves.We believe that SRE1 corresponds to the previously isolated FLD antigen and we suggest its classification among the Rpf proteins.Future work will confirm the functional role of the protein and of similar products encoded in S. rectivirgula, and its implication in FLD. Importantly, apart from iv improving FLD serodiagnosis, the role of reactivity of Rpf proteins in FLD may provide further insight into the pathogenicity of tuberculosis.",
keywords = "Farmer's lung, thermophilic actinobacteria",
author = "Alexandra Ntemiri",
year = "2013",
month = "5",
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Ntemiri, A 2013, 'Genetic characterisation of Farmer’s Lung causing strains of thermophilic actinobacteria', MPhil, University Of Strathclyde, Glasgow.

Genetic characterisation of Farmer’s Lung causing strains of thermophilic actinobacteria. / Ntemiri, Alexandra.

Glasgow : University of Strathclyde, 2013.

Research output: ThesisMaster's Thesis

TY - THES

T1 - Genetic characterisation of Farmer’s Lung causing strains of thermophilic actinobacteria

AU - Ntemiri, Alexandra

PY - 2013/5/23

Y1 - 2013/5/23

N2 - Farmers Lung Disease (FLD) is one of the most common hypersensitivity pneumonitis (HP). HP or extrinsic allergic alveolitis is a group of immunologically mediated pulmonary diseases caused by repeated inhalation of bioaerosolised antigens present in organic dust. Small diametre particles reach the distal gas exchange areas of the lung causing systemic IgG production, activation of the complement, attraction of macrophages and subsequently, inflammation to the interstitium, alveoli, middle and terminal airways. Chronic exposure could eventually lead to severe fibrosis and lung damage.There are many potential causative agents for the various HPs and the thermophilic actinobacterium Saccharopolyspora rectivirgula has been reported as the major antigenic source for FLD. In a previous study on the serologic reaction of FLD patients, specific binding of patient IgG2 to S. rectivirgula antigens was demonstrated. The identical N-terminal sequence of the two antigenic proteins was also determined.We performed whole genome sequencing (WGS) for S. rectivirgula type strain (DSM 43747) using Roche 454 GS sequencer and used the amino acid sequence to interrogate the annotated bacterial genome for the actual product. A putative secreted protein (SRE1) was retrieved carrying the sequence of interest at the N-terminal. Further bioinformatic analysis revealed that the protein had a transglycosylase and a LysM domain and belonged to the NOG06569 orthologous group which contains 130 proteins involved in cell wall macromolecule catabolic processes in 59 bacterial species, mostly actinobacteria.This protein family is dominated by resuscitation promoting factors (Rpfs), proteins which stimulate culturability in latent bacterial spores. Rpfs are common in actinobacteria and in pathogenic species they play a role in establishing virulence. Mycobacterium tuberculosis can escape antibiotic treatment while being in latency and regain viability through Rpfs and eventually affect the host. Furthermore, Rpfs and proteins alike have been repeatedly reported to be immunogenic themselves.We believe that SRE1 corresponds to the previously isolated FLD antigen and we suggest its classification among the Rpf proteins.Future work will confirm the functional role of the protein and of similar products encoded in S. rectivirgula, and its implication in FLD. Importantly, apart from iv improving FLD serodiagnosis, the role of reactivity of Rpf proteins in FLD may provide further insight into the pathogenicity of tuberculosis.

AB - Farmers Lung Disease (FLD) is one of the most common hypersensitivity pneumonitis (HP). HP or extrinsic allergic alveolitis is a group of immunologically mediated pulmonary diseases caused by repeated inhalation of bioaerosolised antigens present in organic dust. Small diametre particles reach the distal gas exchange areas of the lung causing systemic IgG production, activation of the complement, attraction of macrophages and subsequently, inflammation to the interstitium, alveoli, middle and terminal airways. Chronic exposure could eventually lead to severe fibrosis and lung damage.There are many potential causative agents for the various HPs and the thermophilic actinobacterium Saccharopolyspora rectivirgula has been reported as the major antigenic source for FLD. In a previous study on the serologic reaction of FLD patients, specific binding of patient IgG2 to S. rectivirgula antigens was demonstrated. The identical N-terminal sequence of the two antigenic proteins was also determined.We performed whole genome sequencing (WGS) for S. rectivirgula type strain (DSM 43747) using Roche 454 GS sequencer and used the amino acid sequence to interrogate the annotated bacterial genome for the actual product. A putative secreted protein (SRE1) was retrieved carrying the sequence of interest at the N-terminal. Further bioinformatic analysis revealed that the protein had a transglycosylase and a LysM domain and belonged to the NOG06569 orthologous group which contains 130 proteins involved in cell wall macromolecule catabolic processes in 59 bacterial species, mostly actinobacteria.This protein family is dominated by resuscitation promoting factors (Rpfs), proteins which stimulate culturability in latent bacterial spores. Rpfs are common in actinobacteria and in pathogenic species they play a role in establishing virulence. Mycobacterium tuberculosis can escape antibiotic treatment while being in latency and regain viability through Rpfs and eventually affect the host. Furthermore, Rpfs and proteins alike have been repeatedly reported to be immunogenic themselves.We believe that SRE1 corresponds to the previously isolated FLD antigen and we suggest its classification among the Rpf proteins.Future work will confirm the functional role of the protein and of similar products encoded in S. rectivirgula, and its implication in FLD. Importantly, apart from iv improving FLD serodiagnosis, the role of reactivity of Rpf proteins in FLD may provide further insight into the pathogenicity of tuberculosis.

KW - Farmer's lung

KW - thermophilic actinobacteria

M3 - Master's Thesis

PB - University of Strathclyde

CY - Glasgow

ER -