Final Report Summary - RICKOCHET (Origin and evolution of host-association and pathogenicity in the Rickettsiales)
Objectives
The main objective of project RICKOCHET was to gain insight in the emergence of host-interaction within a certain group of pathogenic bacteria known as Rickettsiales. Several bacteria that are part of this group are known to be the causative agent of diseases, such as typhus and ehrlichiosis. Gaining insight in how such pathogenic bacteria evolve would possibly help us combatting the diseases they transmit. In the current project, I have used novel emerging technologies such as next-generation sequencing and single cell genomics to gain insight in the origin and evolution of the Rickettsiales.
Results and conclusions
By initiating collaborations with Prof. Matthias Horn (University of Vienna, Austria) and Dr. Ramunas Stepanauskas (Bigelow Center for Ocean Sciences, Maine, USA), I received genomic material from several novel alphaproteobacterial lineages that were distantly related to the Rickettsiales. The material received from Prof. Horn included two endosymbiotic lineages, C36 and EI3, both isolated from Acanthamoebe spp. In collaboration with Dr. Stepanauskas, I received genetic material generated from 3 individual alphaproteobacterial cells. Two of these, O14 and N20, were isolated from oceanic waters off the coast of Maine, USA, and the remaining cell (L4) was isolated form lake water.
Upon receiving the genetic material from the collaborators (above), sequence libraries were prepared. These libraries were sequenced using an Illumina HiSeq sequencer. The obtained sequence data was assembled, resulting in near-complete genomes of the 2 endosymbiont lineages, and 3 partial genomes of the aquatic single cells (N20, O14 an L4). The following main findings were obtained:
Endosymbiont genomes
Phylogenomic analyses of the EI3 and C36 endosymbiont genomes revealed that these belong to new alphaproeobacterial lineages. Whereas C36 seems to group within the Rickettsiales, being distantly related to ‘Candidatus Midichloria mitochondrii’, EI3 seems to be part of a group that includes ‘Candidatus Odyssella thessalonicensis’, which may represent a sister clade to the Rickettsiales rather than be an intricate part of it. Analyses of the gene content of C36 and EI3 revealed that both contain many genes involved in host interaction processes that are also found in many of the human pathogens that are part of the Rickettsiales. This finding substantiates the idea that protists such as Acanthamoebe spp. (the host of C36 and EI3) represent training grounds for lineages representing human pathogens. The results of the genome analyses of C36 and EI3 will be published in 2 additional papers (currently in progress).
L4 genome
Comparative and phylogenomic analyses of the L4 single cell genome (which is approximately 50% complete) revealed that L4 represents a deeply branching lineage of the Rickettsiaceae. Uniquely, the genome of this lineage contains flagellar genes, as well as genes that are indicative of a parasitic lifestyle (such as ADP:ATP translocase genes). Given the anticipated ‘facultative intracellular nature’ of L4, this lineage represents a missing link in the emergence of the Rickettsiaceae, which includes many pathogens for humans (including several Rickettsia and Orientia spp.). Further analysis of the L4 genome is ongoing and will be published soon (manuscript in preparation).
The O14 and N20 genomes
The O14 and N20 single cell genomes are part of a deeply rooting alphaproteobacterial clade that is placed at the base of the Rickettsiales. Given that analyses of their genome content do not show any signs of intracellular lifestyle, these represent excellent outgroups for studying the emergence of intracellular lifestyle of the Rickettsiales. Currently, we are in the process of performing such an analyses, which will be published later this year (2014).
(Socio-economical) Impact to the fellow
The ERG funding has allowed the fellow to dedicate time and resources to deepen and expand his scientific knowledge in a specific area and to increase his network of collaborators. During the period that he fellow has enjoyed the ERG support, he has significantly matured scientifically, obtaining a high level of independence. Perhaps this is best illustrated by the fact that the fellow was quite successful in obtaining funding from national and international funding agencies. For example, in 2012, the fellow obtained a highly prestigious ERC starting grant (1,7 M€), and in 2013, he received a Future Research Leader award from the Swedish council for Strategic Research (1,2 M€). By securing this type of funding, the fellow has secured his scientific future. Moreover, the fellow was recently habilitated and is currently in the process of being promoted to a lecturer at the hosting institute (Uppsala University). Altogether, it is safe to say that the reintegration of the fellow has been very successful.
More information about the research activities of the fellow can be found at: www.ettemalab.org
The main objective of project RICKOCHET was to gain insight in the emergence of host-interaction within a certain group of pathogenic bacteria known as Rickettsiales. Several bacteria that are part of this group are known to be the causative agent of diseases, such as typhus and ehrlichiosis. Gaining insight in how such pathogenic bacteria evolve would possibly help us combatting the diseases they transmit. In the current project, I have used novel emerging technologies such as next-generation sequencing and single cell genomics to gain insight in the origin and evolution of the Rickettsiales.
Results and conclusions
By initiating collaborations with Prof. Matthias Horn (University of Vienna, Austria) and Dr. Ramunas Stepanauskas (Bigelow Center for Ocean Sciences, Maine, USA), I received genomic material from several novel alphaproteobacterial lineages that were distantly related to the Rickettsiales. The material received from Prof. Horn included two endosymbiotic lineages, C36 and EI3, both isolated from Acanthamoebe spp. In collaboration with Dr. Stepanauskas, I received genetic material generated from 3 individual alphaproteobacterial cells. Two of these, O14 and N20, were isolated from oceanic waters off the coast of Maine, USA, and the remaining cell (L4) was isolated form lake water.
Upon receiving the genetic material from the collaborators (above), sequence libraries were prepared. These libraries were sequenced using an Illumina HiSeq sequencer. The obtained sequence data was assembled, resulting in near-complete genomes of the 2 endosymbiont lineages, and 3 partial genomes of the aquatic single cells (N20, O14 an L4). The following main findings were obtained:
Endosymbiont genomes
Phylogenomic analyses of the EI3 and C36 endosymbiont genomes revealed that these belong to new alphaproeobacterial lineages. Whereas C36 seems to group within the Rickettsiales, being distantly related to ‘Candidatus Midichloria mitochondrii’, EI3 seems to be part of a group that includes ‘Candidatus Odyssella thessalonicensis’, which may represent a sister clade to the Rickettsiales rather than be an intricate part of it. Analyses of the gene content of C36 and EI3 revealed that both contain many genes involved in host interaction processes that are also found in many of the human pathogens that are part of the Rickettsiales. This finding substantiates the idea that protists such as Acanthamoebe spp. (the host of C36 and EI3) represent training grounds for lineages representing human pathogens. The results of the genome analyses of C36 and EI3 will be published in 2 additional papers (currently in progress).
L4 genome
Comparative and phylogenomic analyses of the L4 single cell genome (which is approximately 50% complete) revealed that L4 represents a deeply branching lineage of the Rickettsiaceae. Uniquely, the genome of this lineage contains flagellar genes, as well as genes that are indicative of a parasitic lifestyle (such as ADP:ATP translocase genes). Given the anticipated ‘facultative intracellular nature’ of L4, this lineage represents a missing link in the emergence of the Rickettsiaceae, which includes many pathogens for humans (including several Rickettsia and Orientia spp.). Further analysis of the L4 genome is ongoing and will be published soon (manuscript in preparation).
The O14 and N20 genomes
The O14 and N20 single cell genomes are part of a deeply rooting alphaproteobacterial clade that is placed at the base of the Rickettsiales. Given that analyses of their genome content do not show any signs of intracellular lifestyle, these represent excellent outgroups for studying the emergence of intracellular lifestyle of the Rickettsiales. Currently, we are in the process of performing such an analyses, which will be published later this year (2014).
(Socio-economical) Impact to the fellow
The ERG funding has allowed the fellow to dedicate time and resources to deepen and expand his scientific knowledge in a specific area and to increase his network of collaborators. During the period that he fellow has enjoyed the ERG support, he has significantly matured scientifically, obtaining a high level of independence. Perhaps this is best illustrated by the fact that the fellow was quite successful in obtaining funding from national and international funding agencies. For example, in 2012, the fellow obtained a highly prestigious ERC starting grant (1,7 M€), and in 2013, he received a Future Research Leader award from the Swedish council for Strategic Research (1,2 M€). By securing this type of funding, the fellow has secured his scientific future. Moreover, the fellow was recently habilitated and is currently in the process of being promoted to a lecturer at the hosting institute (Uppsala University). Altogether, it is safe to say that the reintegration of the fellow has been very successful.
More information about the research activities of the fellow can be found at: www.ettemalab.org