Dr. Susanne Pohl

Research Associate

I am a “wet-lab“ postdoctoral researcher, based in the Centre for Bacterial Cell Biology. I did my PhD at the Ernst Moritz Arndt University of Greifswald, Germany, in collaboration with the company BASF, with research focusing on the sulphur metabolism of Corynebacterim glutamicum.

In recent years, my research has focused mostly on oxidative stress and protein secretion, in the Gram-positive bacteria Bacillus subtilis and Bacillus anthracis.

I was involved in several industrial- and EU-funded projects, including the EU-funded BaSysBio programme.

In my current position I am using synthetic biology approaches to engineering Bacillus, and characterising the resulting strains using state-of-the-art proteomics and transcriptomics (RNA seq).

Research Interests

  • Synthetic biology
  • Bacillus molecular biology
  • RNA-seq
  • Proteomics
  • Protein secretion

Publications

  • [DOI] P. Nicolas, U. Mäder, E. Dervyn, T. Rochat, A. Leduc, N. Pigeonneau, E. Bidnenko, E. Marchadier, M. Hoebeke, S. Aymerich, D. Becher, P. Bisicchia, E. Botella, O. Delumeau, G. Doherty, E. L. Denham, M. J. Fogg, V. Fromion, A. Goelzer, A. Hansen, E. Härtig, C. R. Harwood, G. Homuth, H. Jarmer, M. Jules, E. Klipp, L. Le Chat, F. Lecointe, P. Lewis, W. Liebermeister, A. March, R. A. Mars, P. Nannapaneni, D. Noone, S. Pohl, B. Rinn, F. Rügheimer, P. K. Sappa, F. Samson, M. Schaffer, B. Schwikowski, L. Steil, J. Stülke, T. Wiegert, K. M. Devine, A. J. Wilkinson, J. M. van Dijl, M. Hecker, U. Völker, P. Bessières, and P. Noirot, “Condition-dependent transcriptome reveals high-level regulatory architecture in bacillus subtilis,” Science, vol. 335, iss. 6072, pp. 1103-1106, 2012.
    [Bibtex]
    @Article{Nicolas:2012:Science:22383849,
    author = "Nicolas, P and M{\"a}der, U and Dervyn, E and Rochat, T and Leduc, A and Pigeonneau, N and Bidnenko, E and Marchadier, E and Hoebeke, M and Aymerich, S and Becher, D and Bisicchia, P and Botella, E and Delumeau, O and Doherty, G and Denham, E L and Fogg, M J and Fromion, V and Goelzer, A and Hansen, A and H{\"a}rtig, E and Harwood, C R and Homuth, G and Jarmer, H and Jules, M and Klipp, E and Le Chat, L and Lecointe, F and Lewis, P and Liebermeister, W and March, A and Mars, R A and Nannapaneni, P and Noone, D and Pohl, S and Rinn, B and R{\"u}gheimer, F and Sappa, P K and Samson, F and Schaffer, M and Schwikowski, B and Steil, L and St{\"u}lke, J and Wiegert, T and Devine, K M and Wilkinson, A J and van Dijl, J M and Hecker, M and V{\"o}lker, U and Bessi{\`e}res, P and Noirot, P",
    title = {Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis},
    abstract = {Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature. We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for \~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.},
    journal = "Science",
    year = "2012",
    volume = "335",
    number = "6072",
    pages = "1103-1106",
    month = "Mar",
    pmid = "22383849",
    url = "http://www.hubmed.org/display.cgi?uids=22383849",
    doi = "10.1126/science.1206848"
    }
  • [DOI] J. M. Buescher, W. Liebermeister, M. Jules, M. Uhr, J. Muntel, E. Botella, B. Hessling, R. J. Kleijn, L. Le Chat, F. Lecointe, U. Mäder, P. Nicolas, S. Piersma, F. Rügheimer, D. Becher, P. Bessieres, E. Bidnenko, E. L. Denham, E. Dervyn, K. M. Devine, G. Doherty, S. Drulhe, L. Felicori, M. J. Fogg, A. Goelzer, A. Hansen, C. R. Harwood, M. Hecker, S. Hubner, C. Hultschig, H. Jarmer, E. Klipp, A. Leduc, P. Lewis, F. Molina, P. Noirot, S. Peres, N. Pigeonneau, S. Pohl, S. Rasmussen, B. Rinn, M. Schaffer, J. Schnidder, B. Schwikowski, J. M. Van Dijl, P. Veiga, S. Walsh, A. J. Wilkinson, J. Stelling, S. Aymerich, and U. Sauer, “Global network reorganization during dynamic adaptations of bacillus subtilis metabolism,” Science, vol. 335, iss. 6072, pp. 1099-1103, 2012.
    [Bibtex]
    @Article{Buescher:2012:Science:22383848,
    author = "Buescher, J M and Liebermeister, W and Jules, M and Uhr, M and Muntel, J and Botella, E and Hessling, B and Kleijn, R J and Le Chat, L and Lecointe, F and M{\"a}der, U and Nicolas, P and Piersma, S and R{\"u}gheimer, F and Becher, D and Bessieres, P and Bidnenko, E and Denham, E L and Dervyn, E and Devine, K M and Doherty, G and Drulhe, S and Felicori, L and Fogg, M J and Goelzer, A and Hansen, A and Harwood, C R and Hecker, M and Hubner, S and Hultschig, C and Jarmer, H and Klipp, E and Leduc, A and Lewis, P and Molina, F and Noirot, P and Peres, S and Pigeonneau, N and Pohl, S and Rasmussen, S and Rinn, B and Schaffer, M and Schnidder, J and Schwikowski, B and Van Dijl, J M and Veiga, P and Walsh, S and Wilkinson, A J and Stelling, J and Aymerich, S and Sauer, U",
    title = {Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism},
    abstract = {Adaptation of cells to environmental changes requires dynamic interactions between metabolic and regulatory networks, but studies typically address only one or a few layers of regulation. For nutritional shifts between two preferred carbon sources of Bacillus subtilis, we combined statistical and model-based data analyses of dynamic transcript, protein, and metabolite abundances and promoter activities. Adaptation to malate was rapid and primarily controlled posttranscriptionally compared with the slow, mainly transcriptionally controlled adaptation to glucose that entailed nearly half of the known transcription regulation network. Interactions across multiple levels of regulation were involved in adaptive changes that could also be achieved by controlling single genes. Our analysis suggests that global trade-offs and evolutionary constraints provide incentives to favor complex control programs.},
    journal = "Science",
    year = "2012",
    volume = "335",
    number = "6072",
    pages = "1099-1103",
    month = "Mar",
    pmid = "22383848",
    url = "http://www.hubmed.org/display.cgi?uids=22383848",
    doi = "10.1126/science.1206871"
    }
  • [DOI] W. Y. Tu, S. Pohl, J. Gray, N. J. Robinson, C. R. Harwood, and K. J. Waldron, “Cellular iron distribution in bacillus anthracis,” J bacteriol, vol. 194, iss. 5, pp. 932-940, 2012.
    [Bibtex]
    @Article{Tu:2012:J-Bacteriol:22178968,
    author = "Tu, W Y and Pohl, S and Gray, J and Robinson, N J and Harwood, C R and Waldron, K J",
    title = {Cellular iron distribution in Bacillus anthracis},
    abstract = {Although successful iron acquisition by pathogens within a host is a prerequisite for the establishment of infection, surprisingly little is known about the intracellular distribution of iron within bacterial pathogens. We have used a combination of anaerobic native liquid chromatography, inductively coupled plasma mass spectrometry, principal-component analysis, and peptide mass fingerprinting to investigate the cytosolic iron distribution in the pathogen Bacillus anthracis. Our studies identified three of the major iron pools as being associated with the electron transfer protein ferredoxin, the miniferritin Dps2, and the superoxide dismutase (SOD) enzymes SodA1 and SodA2. Although both SOD isozymes were predicted to utilize manganese cofactors, quantification of the metal ions associated with SodA1 and SodA2 in cell extracts established that SodA1 is associated with both manganese and iron, whereas SodA2 is bound exclusively to iron in vivo. These data were confirmed by in vitro assays using recombinant protein preparations, showing that SodA2 is active with an iron cofactor, while SodA1 is cambialistic, i.e., active with manganese or iron. Furthermore, we observe that B. anthracis cells exposed to superoxide stress increase their total iron content more than 2-fold over 60 min, while the manganese and zinc contents are unaffected. Notably, the acquired iron is not localized to the three identified cytosolic iron pools.},
    journal = "J Bacteriol",
    year = "2012",
    volume = "194",
    number = "5",
    pages = "932-940",
    month = "Mar",
    pmid = "22178968",
    url = "http://www.hubmed.org/display.cgi?uids=22178968",
    doi = "10.1128/JB.06195-11"
    }
  • [DOI] W. Y. Tu, S. Pohl, K. Gizynski, and C. R. Harwood, “The iron-binding protein dps2 confers peroxide stress resistance on bacillus anthracis,” J bacteriol, vol. 194, iss. 5, pp. 925-931, 2012.
    [Bibtex]
    @Article{Tu:2012:J-Bacteriol:22155779,
    author = "Tu, W Y and Pohl, S and Gizynski, K and Harwood, C R",
    title = {The iron-binding protein Dps2 confers peroxide stress resistance on Bacillus anthracis},
    abstract = {Iron is an essential nutrient that is implicated in most cellular oxidation reactions. However, iron is a highly reactive element that, if not appropriately chaperoned, can react with endogenously and exogenously generated oxidants such as hydrogen peroxide to generate highly toxic hydroxyl radicals. Dps proteins (DNA-binding proteins from starved cells) form a distinct class (the miniferritins) of iron-binding proteins within the ferritin superfamily. Bacillus anthracis encodes two Dps-like proteins, Dps1 and Dps2, the latter being one of the main iron-containing proteins in the cytoplasm. In this study, the function of Dps2 was characterized in vivo. A B. anthracis Δdps2 mutant was constructed by double-crossover mutagenesis. The growth of the Δdps2 mutant was unaffected by excess iron or iron-limiting conditions, indicating that the primary role of Dps2 is not that of iron sequestration and storage. However, the Δdps2 mutant was highly sensitive to H(2)O(2), and pretreatment of the cells with the iron chelator deferoxamine mesylate (DFM) significantly reduced its sensitivity to H(2)O(2) stress. In addition, the transcription of dps2 was upregulated by H(2)O(2) treatment and derepressed in a perR mutant, indicating that dps2 is a member of the regulon controlled by the PerR regulator. This indicates that the main role of Dps2 is to protect cells from peroxide stress by inhibiting the iron-catalyzed production of OH.},
    journal = "J Bacteriol",
    year = "2012",
    volume = "194",
    number = "5",
    pages = "925-931",
    month = "Mar",
    pmid = "22155779",
    url = "http://www.hubmed.org/display.cgi?uids=22155779",
    doi = "10.1128/JB.06005-11"
    }
  • [DOI] W. Y. Tu, S. Pohl, P. Summpunn, S. Hering, S. Kerstan, and C. R. Harwood, “Comparative analysis of the responses of related pathogenic and environmental bacteria to oxidative stress,” Microbiology, vol. 158, iss. Pt 3, pp. 636-647, 2012.
    [Bibtex]
    @Article{Tu:2012:Microbiology:22174384,
    author = "Tu, W Y and Pohl, S and Summpunn, P and Hering, S and Kerstan, S and Harwood, C R",
    title = {Comparative analysis of the responses of related pathogenic and environmental bacteria to oxidative stress},
    abstract = {Bacillus anthracis, the causative agent of anthrax, is exposed to host-mediated antibacterial activities, such as reactive oxygen species (ROS), during the early stages of its disease process. The ability to resist these host-mediated stresses is an essential characteristic of a successful pathogen while it is generally assumed that non-pathogenic environmental bacteria succumb to these antimicrobial activities. In order to gain insights into the underlying mechanisms that pathogens use to resist host-mediated oxidative stress, we have compared the oxidative stress responses of B. anthracis and Bacillus subtilis, a well-studied environmental bacterium. Among the four putative catalases encoded by B. anthracis we identified KatB as the main vegetative catalase. Comparative analysis of catalase production in B. anthracis and B. subtilis in response to superoxide and peroxide stress reveals different expression profiles, even though both are regulated by the PerR repressor, which senses and responds to peroxide stress. A B. anthracis perR deletion mutant exhibits enhanced KatB activity and is hyper-resistant to peroxide stress. Superoxide dismutase A1 (SodA1) is the main contributor to the intracellular superoxide dismutase activity in vegetative cells and the gene encoding this enzyme is constitutively expressed. Although aspects of the ROS detoxifying systems of B. anthracis and B. subtilis are similar, their responses to superoxide stress are different. The observed differences are likely to reflect adaptations to specific environmental niches.},
    journal = "Microbiology",
    year = "2012",
    volume = "158",
    number = "Pt 3",
    pages = "636-647",
    month = "Mar",
    pmid = "22174384",
    url = "http://www.hubmed.org/display.cgi?uids=22174384",
    doi = "10.1099/mic.0.057000-0"
    }
  • [DOI] S. Pohl, W. Y. Tu, P. D. Aldridge, C. Gillespie, H. Hahne, U. Mäder, T. D. Read, and C. R. Harwood, “Combined proteomic and transcriptomic analysis of the response of bacillus anthracis to oxidative stress,” Proteomics, vol. 11, iss. 15, pp. 3036-3055, 2011.
    [Bibtex]
    @Article{Pohl:2011:Proteomics:21726052,
    author = "Pohl, S and Tu, W Y and Aldridge, P D and Gillespie, C and Hahne, H and M{\"a}der, U and Read, T D and Harwood, C R",
    title = {Combined proteomic and transcriptomic analysis of the response of Bacillus anthracis to oxidative stress},
    abstract = {The endospore-forming Gram-positive pathogen Bacillus anthracis is responsible for the usually fatal disease, inhalational anthrax. The success of this pathogen is dependent on its ability to subvert elements of the innate immune system of its animal hosts. B. anthracis spores, which are the main infective agent, are engulfed and germinate in patrolling alveolar macrophages. In order for the infection to progress, the resulting vegetative cells must resist the antimicrobial oxidative burst mounted by the host NADPH oxidase complex. The response of B. anthracis to this and other macrophage-related stresses is therefore of major importance to the success of this pathogen, and consequently we have analysed the superoxide and peroxide stress stimulons of B. anthracis strain UM23C1-2 by means of a combined transcriptomics and proteomics approach. The results show distinct patterns of expression in response to paraquat (endogenous superoxide) and hydrogen peroxide stress. While the main response to paraquat is the induction of iron uptake pathways, the response to peroxide predominantly involves the induction of protection and repair mechanisms. Comparisons between the responses of B. anthracis and related soil bacterium, B. subtilis, reveal differences that are likely to be relevant to their respective habitats.},
    journal = "Proteomics",
    year = "2011",
    volume = "11",
    number = "15",
    pages = "3036-3055",
    month = "Aug",
    pmid = "21726052",
    url = "http://www.hubmed.org/display.cgi?uids=21726052",
    doi = "10.1002/pmic.201100085"
    }
  • [DOI] S. Pohl and C. R. Harwood, “Heterologous protein secretion by bacillus species from the cradle to the grave,” Adv appl microbiol, vol. 73, pp. 1-25, 2010.
    [Bibtex]
    @Article{Pohl:2010:Adv-Appl-Microbiol:20800757,
    author = "Pohl, S and Harwood, C R",
    title = {Heterologous protein secretion by bacillus species from the cradle to the grave},
    abstract = {The Gram-positive bacterium Bacillus subtilis and some of its close relatives are widely used for the industrial production of enzymes for the detergents, food, and beverage industries. The choice of these organisms is based almost exclusively on the high capacity of their secretion systems that are, under the right conditions, able to secrete proteins at grams per liter concentrations. In contrast, there are relatively few examples of Bacillus species being used for the cytoplasmic production of proteins. The range of proteins that are capable of high-level production and secretion is limited by a combination of characteristics of both the target protein and the host bacterium. The secretion pathway includes checkpoints that are designed to validate the authenticity of pathway substrates. Although many of these checkpoints are known, only some can be overcome by reengineering the host. As a result, the yield of heterologous protein production is extremely variable. In this review, we consider the Bacillus protein secretion pathway from the synthesis of the target protein (cradle) to its emergence at the outer surface of the complex cell wall (grave), and discuss the roles of the various checkpoints both with respect to the target protein and their role on cell homeostasis.},
    journal = "Adv Appl Microbiol",
    year = "2010",
    volume = "73",
    number = "",
    pages = "1-25",
    month = "",
    pmid = "20800757",
    url = "http://www.hubmed.org/display.cgi?uids=20800757",
    doi = "10.1016/S0065-2164(10)73001-X"
    }