Howard Shuman - Research Summary

Intracellular bacterial pathogens

Our group is interested in how intracellular bacterial pathogens interact with and commandeer host cell functions during infection.  We have studied the intracellular human pathogen, Legionella pneumophila for more than 30 years.  This gram-negative species causes an acute febrile pneumonia called Legionnaires’ disease.  People become infected with Legionella when they inhale contaminated aerosols.  This can happen when cooling and ventilation systems, fountains, or whirlpools become contaminated.  In these environments, Legionella replicates in single-celled amoebae.  In human lungs these bacteria can infect and replicate in alveolar macrophages.

In order to understand how Legionella is able to survive and grow inside amoebae and macrophages, we use genetic and genomic approaches to ask which functions in the bacteria and which ones in the host are important for infection.  We found that Legionella has a “Type IV Secretion System” called the Icm/Dot System that translocates protein “effectors” to the host cell and that these effectors dramatically alter organelle trafficking in host cells as is shown in the accompanying diagram.  The Legionella – containing vacuole, (LCV) is where the bacteria grow within cells in a nutrient-rich, protected niche.

We are currently pursuing the following projects:

(i) Discovery of host factors required for infection:  We used libraries of well-characterized small molecule inhibitors, including many FDA-approved drugs that target specific functions in host cells, to look for factors that are required for L. pneumophila to carry out a successful infection.  Several classes of molecules including: G-protein coupled receptor agonists, phospho-tyrosine signaling inhibitors, and calcium active compounds can completely block intracellular replication of Legionella and protect macrophages from lethal infection.

(ii) SNARE-like effectors: We discovered a family of Legionella effectors that strongly resemble Q-SNARE proteins that mediate membrane fusion events in eukaryotic cells.  We found that these proteins form a complex with a human host cell R-SNARE protein called VAMP4.

(iii) Evolution of Legionella virulence:  We would like to understand the selective processes that enable Legionella to adapt to a broad-host range intracellular environment.  Although L. pneumophila is a successful pathogen of most amoebae, we hypothesized that there must exist amoebae and other protist predators that are able to consume Legionella for food.  By creating experimental microcosms from environmental samples we discovered novel genera and species of protists that consume virulent Legionella.  We hypothesize that these protists provide a strong selective pressure for Legionella to acquire and maintain large numbers of effector-encoding genes.  In order to find out how many effector-encoding genes exist, we determined the genome sequences of 40 different Legionella species. We found that there are > 500 orthologous groups of effector-encoding genes in genomes of these species, confirming the extensive collection of effectors in Legionella.

(iv) Coxiella burnetii, Q fever and desiccation resistance:

Coxiella burnetii is the agent of Q fever, a flu-like disease that is common in agricultural areas.  Although Legionella and Coxiella are very closely related by 16S rRNA similarity and use almost identical Icm/Dot Type IV secretion systems, their collection of effectors is quite different and C. burnetii exhibits very different biological properties than Legionella.  For example, it is much more infectious than Legionella; a single C. burnetii cell is enough to cause severe disease in people and animals.  It is also very resistant to environmental stresses including heat and desiccation.  It grows inside cells within an acidic phagolysosome and is strongly anti-apoptotic.  We found that several drugs that inhibit the intracellular trafficking of cholesterol completely block intracellular growth of Coxiella in human macrophages.  We are currently trying to understand the molecular basis of desiccation resistance in Coxiella.  Resistance to dryness plays an important role in transmission because most people contract Q fever by inhaling dust that is contaminated with material containing Coxiella.

Opportunistic Multidrug Resistant Pathogens

Acinetobacter baumannii is an opportunistic bacterial pathogen that is becoming increasingly difficult to treat due to the lack of effective antibiotic therapies.  Little is known about the virulence determinants that contribute to its ability to cause life-threatening diseases such as pneumonia and skin and soft tissue infections.  We carried out a forward genetic screen to look for genes that are required for virulence in a model host.  Several of the genes that are required for virulence appear to be involved in resistance to environmental stresses.  We hypothesize that resistance to oxidative damage may be important for this organism’s ability to overcome host innate immune defenses.

Bibliography 2010-2015:

Amaro F, Wang W, Gilbert JA, Anderson, OR, Shuman HA. Diverse protist grazers select for virulence-related traits in Legionella. ISME J 2015 In the Press. doi:10.1038/ismej.2014.248

Jacobs AC, Thompson MG, Gebhardt M, Corey BW, Yildirim S, Shuman HA, Zurawski  DV. Genetic Manipulation of Acinetobacter baumannii. Curr Protoc Microbiol. 2014  Nov 3;35:6G.2.1-6G.2.11. doi: 10.1002/9780471729259.mc06g02s35. PubMed PMID: 25367274.

Czyż DM, Potluri LP, Jain-Gupta N, Riley SP, Martinez JJ, Steck TL, Crosson S, Shuman HA, Gabay JE. Host-directed antimicrobial drugs with broad-spectrum efficacy against intracellular bacterial pathogens. MBio. 2014 Jul 29;5(4):e01534-14. doi: 10.1128/mBio.01534-14. PubMed PMID: 25073644; PubMed Central PMCID: PMC4128363.  

Lifshitz Z, Burstein D, Peeri M, Zusman T, Schwartz K, Shuman HA, Pupko T, Segal G. Computational modeling and experimental validation of the Legionella and Coxiella virulence-related type-IVB secretion signal. Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):E707-15. doi: 10.1073/pnas.1215278110. Epub 2013 Feb 4. PubMed PMID: 23382224; PubMed Central PMCID: PMC3581968.  

Franco IS, Shohdy N, Shuman HA. The Legionella pneumophila effector VipA is an actin nucleator that alters host cell organelle trafficking. PLoS Pathog. 2012 Feb;8(2):e1002546. doi: 10.1371/journal.ppat.1002546. Epub 2012 Feb 23. PubMed PMID: 22383880; PubMed Central PMCID: PMC3285593.  

Amaro F, Gilbert JA, Owens S, Trimble W, Shuman HA. Whole-genome sequence of the human pathogen Legionella pneumophila serogroup 12 strain 570-CO-H. J Bacteriol. 2012 Mar;194(6):1613-4. doi: 10.1128/JB.06626-11. PubMed PMID: 22374950; PubMed Central PMCID: PMC3294838.  

Faucher SP, Mueller CA, Shuman HA. Legionella pneumophila Transcriptome during Intracellular Multiplication in Human Macrophages. Front Microbiol. 2011 Apr 4;2:60. doi: 10.3389/fmicb.2011.00060. eCollection 2011. PubMed PMID: 21747786; PubMed Central PMCID: PMC3128937.  

Levi A, Folcher M, Jenal U, Shuman HA. Cyclic diguanylate signaling proteins control intracellular growth of Legionella pneumophila. MBio. 2011 Jan 11;2(1):e00316-10. doi: 10.1128/mBio.00316-10. PubMed PMID: 21249170; PubMed Central PMCID: PMC3023162.  

Anderson OR, Wang W, Faucher SP, Bi K, Shuman HA. A new heterolobosean amoeba  Solumitrus palustris n. g., n. sp. isolated from freshwater marsh soil. J Eukaryot Microbiol. 2011 Jan-Feb;58(1):60-7. doi: 10.1111/j.1550-7408.2010.00520.x. PubMed PMID: 21182560.  

Hovel-Miner G, Faucher SP, Charpentier X, Shuman HA. ArgR-regulated genes are derepressed in the Legionella-containing vacuole. J Bacteriol. 2010 Sep;192(17):4504-16. doi: 10.1128/JB.00465-10. Epub 2010 Jul 9. PubMed PMID: 20622069; PubMed Central PMCID: PMC2937375.  

Faucher SP, Friedlander G, Livny J, Margalit H, Shuman HA. Legionella pneumophila 6S RNA optimizes intracellular multiplication. Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7533-8. doi: 10.1073/pnas.0911764107. Epub 2010 Apr 5. PubMed PMID: 20368425; PubMed Central PMCID: PMC2867745.