Alan J. Wolfe, PhD

Alan J. Wolfe, PhD



Major Research Interests: Bacterial protein acetylation and the urinary microbiome


My laboratory is composed of two groups. One group studies the female bladder microbiome and its impact on women’s health and disease. The other group investigates protein acetylation and its influence on bacterial physiology. Both groups interact often.

The female urinary microbiome and its role in health and disease A broad range of lower urinary tract (LUT) diagnoses affect women; these include urinary tract infections (UTI), bladder pain syndromes, urinary incontinence (UI) and overactive bladder (OAB). LUT problems are common and costly. At least 50% of women experience a UTI during their lifetime and a critical subgroup of UTI patients experiences recurrent UTIs. Bladder pain syndromes are poorly understood and thus poorly treated, despite significant research investment. UI and OAB are also highly prevalent with substantial economic costs, accounting for >$20 billion/year in the US, and affecting 30-60% of middle-aged and older women in the general population.

The Wolfe lab is an integral part of the Loyola Urinary Education and Research Collaborative [LUEREC], a multidisciplinary translational research team co-directed by Dr. Wolfe. In 2012, LUEREC reported the first definitive evidence that bacteria colonize the normal female urinary tract, an observation subsequently confirmed by others. These results overturn the longstanding dogma that urine is sterile. This recent documentation that the FUM exists provides an opportunity to advance our understanding of the etiology of diverse LUT disorders.

Indeed, we recently reported that the bacteria that comprise the FUM are distinct from those that cause overt clinical UTI, that the FUM of women with UI differs from that of women with no LUT symptoms, and that the FUM has clinical relevance, linking it to clinical symptoms and outcomes, including associations with urinary symptom levels, treatment response, and UTI risk.

Protein acetylation in bacteria
Nε-lysine (protein) acetylation in bacteria has recently emerged as an abundant and stoichiometrically relevant post-translational modification in diverse bacteria, including both Gram-negatives and Gram-positives. There are two known mechanisms by which protein acetylation occurs. The first is the canonical enzymatic reaction catalyzed by an acetyltransferase that uses acetyl-CoA as an acetyl donor. The second mechanism is non-enzymatic acetylation that uses the small, high-energy central metabolite acetyl phosphate (acP) as the acetyl donor. As such, bacterial protein acetylation resembles eukaryotic protein acetylation, including non-enzymatic acetylation, which occurs in mitochondria. We infer that acetylation in bacteria works much like it does in eukaryotes and that it exerts a similar impact on protein function and cellular physiology.

In this context, we submit that the most important outstanding questions in this new field are the following: (i) how do bacteria regulate acetylation, (ii) does acetylation affect bacterial protein function, (iii) how does altered function affect cellular physiology and (iv) can we develop approaches to facilitate future studies? To answer these questions, we have formed a multidisciplinary collaboration with chemists, structural biologists, and chemical engineers.

 Reviews, Book Chapters, Commentaries, Editorials

1. Brubaker, L., and Wolfe, A.J. 2017. Year in Review 2016: The Female Urinary Microbiota. Nature Reviews Urology. In Press.

2. Mueller, E., Wolfe, AJ and Brubaker, L. 2017. The Female Urinary Microbiota. Current Op in Urology review. In Press.

3. Brubaker, L. and Wolfe, A.J. 2017. The Female Urinary Microbiota, Urinary Health and Common Urinary Disorders. Annals of Translational Medicine.

4. Schwaderer, A.L. and Wolfe, A.J. 2017. The Association Between Bacteria and Urinary Stones. Annals of Translational Medicine. In Press.

5. Brubaker, L and Wolfe AJ. 2016. The Urinary Microbiota: A Paradigm Shift for Bladder Disorders? Current Opinions in Obstretrics and Gynecology. Oct;28(5):407-12.

6. Losada L, Amundsen CL, Ashton-Miller J, Chai T, Close C, Damaser M, DiSanto M, Dmochowski R, Fraser MO, Kielb SJ, Kuchel G, Mueller ER, Parker-Autry C, Wolfe AJ, Mallampalli MP. Expert Panel Recommendations on Lower Urinary Tract Health of Women Across Their Life Span. J Womens Health (Larchmt). 2016 Jun 10. [Epub ahead of print] PMID:27285829

7. Thomas-White K, Brady M, Wolfe AJ, Mueller ER. 2016. The Bladder is Not Sterile: History and Current Discoveries on the Urinary Microbiome. Curr Bladder Dysfunct Rep. Mar;11(1):18-24. Epub 2016 Jan 30. PMID:27182288

8. Wolfe, A. J. Bacterial protein acetylation: new discoveries unanswered questions. 2016. Curr Genet. May;62(2):335-41. PMID:26660885

9. Brubaker, L. and Wolfe, A. J. 2015 May 21. The New World of the Urinary Microbiome in Women. American Journal of Obstetrics & Gynecology. pii: S0002-9378(15)00508-6. doi:10.1016/j.ajog.2015.05.032. [Epub ahead of print] PMID: 26003055

10. Wolfe, A. J. and Brubaker, L. 2015. “Sterile urine” and the presence of bacteria. Eur Urol. Aug;68(2):173-4. PMID: 25774008 Highlighted by Eur Urol August 2015

11. Wolfe, A. J. 2015. Glycolysis for the Microbiome Generation. Microbiol Spectr. 2015 Jun;3(3). doi: 10.1128/microbiolspec.MBP-0014-2014. PMID:26185089

12. Wolfe, A. J. 2014. The female urinary microbiome: A comparison of women with and without urgency urinary incontinence. UroToday.

13. Josenhans, C., Jung, K., Rao, C. V., Wolfe, A. J. 2014. A Tale of Two Machines: A review of the BLAST meeting, Tucson, AZ, January 20-24, 2013. Molecular Microbiology. 91(1): 6-25. PMID: 24125587

Primary Peer Reviewed Research

1. Malki K, Shapiro JW, Price TK, Hilt EE, Thomas-White K, Sircar T, Rosenfeld AB, Kuffel G, Zilliox MJ, Wolfe AJ, Putonti C. Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome. 2016. PLoS One. 2016 Nov 18;11(11):e0166757. doi: 10.1371/journal.pone.0166757. PMID:27861551

2. Filippova EV, Wawrzak Z, Ruan J, Pshenychnyi S, Schultz RM, Wolfe AJ, Anderson WF. 2016. Crystal structure of nonphosphorylated receiver domain of the stress response regulator RcsB from Escherichia coli. Protein Sci. Sep 27. doi: 10.1002/pro.3050. [Epub ahead of print] PMID: 27670836

3. Meyer JG, D'Souza AK, Sorensen DJ, Rardin MJ, Wolfe AJ, Gibson BW, Schilling B. 2016. Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH). J Am Soc Mass Spectrom. Nov;27(11):1758-1771. PMID:27590315

4. Thomas-White, KJ, Kliethermes, S, Rickey, L., Lukacz, ES, Richter, HE, Moalli, P, Zimmern, P, Norton, P, Kusek, JW, Wolfe, AJ, Brubaker, L for the National Institute of Diabetes and Digestive and Kidney Diseases Urinary Incontinence Treatment Network. Evaluation of the urinary microbiota of women with uncomplicated stress urinary incontinence. American Journal of Obstretrics and Gynecology. 2016 Aug 4. pii: S0002-9378(16)30522-1. doi: 10.1016/j.ajog.2016.07.049. [Epub ahead of print]

5. Price, T. K., Dune, T., Hilt, E. E., Thomas-White, K. J., Kliethermes, S., Brincat, C., Brubaker, L., Wolfe, A. J., Mueller, E. R., Schreckenberger, P. 2016. The Clinical Urine Culture: Enhanced Techniques Improve Detection of Clinically Relevant Microorganisms. Journal of Clinical Microbiology. May;54(5):1216-22. PMID:26962083

6. Lima BP, Lennon CW, Ross W, Gourse RL, Wolfe AJ. 2016. In vitro evidence that RNAP acetylation and acetyl phosphate-dependent CpxR phosphorylation affect cpxP transcription regulation. FEMS Microbiol Lett. Mar;363(5):fnw011 PMID: 26790713

7. Schilling B, MacLean B, Held JM, Sahu AK, Rardin MJ, Sorensen DJ, Peters T, Wolfe AJ, Hunter CL, MacCoss MJ, Gibson BW. 2015. Multiplexed, scheduled high-resolution parallel reaction monitoring on a full scan QqTOF instrument with integrated data-dependent and targeted mass spectrometric workflows. Anal Chem. Oct 20;87(20):10222-9. PMID: 26398777

8. Barr-Baer, E., Saxena,V., Hilt, E.E., Thomas-White, K., Schober, M., Li, B., Becknell, B., Hains, D.S., Wolfe, A.J., and Schwarderer, A.L. 2015. The Interaction between Enterobacteriaceae and Calcium Oxalate Deposits, PLoS One. Oct 8;10(10):e0139575. PMID: 26448465

9. Thomas-White, K., Hilt, E.E., Fok, C., Pearce, M.M., Mueller, E.R., Kliethermes, S., Jacobs, K., Zilliox, M.J., Brincat, C., Price, T.K., Kuffel, G., Schreckenberger, P.C., Gai, X. Brubaker, L. and Wolfe, A. J. 2015. Incontinence Medication Response Relates to the Female Urinary Microbiota, Int Urogynecol J. May;27(5):723-33. PMID: 26423260

10. Schilling B, Christensen D, Davis R, Sahu AK, Hu LI, Walker-Peddakotla A, Sorensen DJ, Zemaitatis B, Gibson BW, Wolfe AJ. 2015. Protein acetylation dynamics in response to carbon overflow in Escherichia coli Mol Microbiol. Dec;98(5):847-63. PMID: 26264774

11. Pearce MM, Zilliox MJ, Thomas-White KJ, Richter HE, Nager CW, Visco AG, Nygaard IE, Barber MD, Schaffer J, Moalli P, Sung VW, Smith AL, Rogers R, Nolen TL, Wallace D, Meikle SF, Gai X, Wolfe AJ, Brubaker L; Pelvic Floor Disorders Network. 2015. The female urinary microbiota in urgency urinary incontinence. Am J Obstet Gynecol. Am J Obstet Gynecol. 2015 Sep;213(3):347 PMID:26210757

12. Wolfe A. J. Glycolysis for the Microbiome Generation. 2015. Microbiol Spectr. Jun;3(3). doi: 10.1128/microbiolspec.MBP-0014-2014. PMID:26185089

13. van Rensburg, J., Fortney, K., Chen, L., Krieger, A., Lima, B., Wolfe, A. J., Katz, B., Zhang, Z.Y., and Spinola, S. Development and Validation of a High-throughput Cell-based Screen to Identify Activators of a Bacterial Two-component Signal Transduction System. AAC. Jul;59(7):3789-99. PMID:25870061

14. Nienhouse, V., Gao, X., Dong, Q., Nelson, D.E., Toh, E., McKinley, K., Schreckenberger, P., Shibata, N., Fok, C.S., Kenton, K., Mueller, E.R., Brubaker, L., Wolfe, A.J., and Radek, K.A. Interplay between Bladder Microbiota and Urinary Antimicrobial Peptides: Mechanisms for Human Urinary Tract Infection Risk and Symptom Severity. PLoS ONE. Dec 8;9(12):e114185. PMID:25486068

15. AbouElfetouh, A., Kuhn, M. L., Hu, L. I., Scholle, M. D., Sorensen, D. J., Sahu, A. K., Becher, D., Antelmann, H., Mrksich, M., Anderson, W. F., Gibson, B. W., Schilling, B., and Wolfe, A. J. 2015. The E. coli sirtuin CobB reverses both acetyl-coenzyme A- and acetyl phosphate-dependent lysine acetylations. MicrobiologyOpen. Feb;4(1):66-83. PMID:25417765

16. Le, P., Pearce, M.M., Zhang, S., Campbell, E.M., Fok, C.S., Mueller, E.R., Brincat, C.A., Wolfe, A.J. and Brubaker, L. 2014. IL22 Regulates Human Urothelial Cell Sensory and Innate Functions through Modulation of the Acetylcholine Response, Immunoregulatory Cytokines and Antimicrobial Peptides: Assessment of an in vitro Model. PLoS One. Oct 29;9(10):e111375. PMID:25354343

17. Pearce, M.M., Hilt, E.E., Rosenfeld, A.B., Zilliox, M.J., Thomas-White, K., Fok, C., Kliethermes, S., Schreckenberger, P., Brubaker, L., Gai, X., Wolfe, A.J. 2014. The Female Urinary Microbiome: A Comparison of Women With and Without Urgency Urinary Incontinence. mBio. Jul 8;5(4). pii: e01283-14. doi: 10.1128/mBio.01283-14. PMID:25006228 a. Highlighted in Nature Reviews Urology advance online publication 29 July 2014; doi:10.1038/nrurol.2014.186.

18. Beckham, K.S., Connolly, J.P., Ritchie, J.M., Wang, D., Gawthorne, J.A., Tahoun, A., Gally, D.L., Burgess, K., Burchmore, R.J., Smith, B.O., Beatson, S.A., Byron, O., Wolfe, A.J., Douce, G.R., Roe, A.J. 2014. The Metabolic Enzyme AdhE Controls the Virulence of Escherichia coli O157:H7. Mol Microbiol. 93(1):199-211 PMID:24846743

19. Kuhn, M. L., Zemaitaitis, B., Hu, L. I., Sahu, A., Sorensen, D., Minasov, G., Lima, B. P., Scholle, M., Mrksich, M., Anderson, W. F., Gibson, B. W., Schilling, B., and Wolfe, A. J. 2014. Structural, kinetic and global mass spectrometric characterization of acetyl phosphate-dependent bacterial protein acetylation. PLoS One. Apr 22;9(4):e94816. doi: 10.1371/journal.pone.0094816. eCollection 2014. PMID:24756028 a. Highlighted by the Advanced Photon Source at Argonne National Laboratory

20. Brubaker, L., Nager, C. W., Richter, H. E., Visco, A., Nygaard, I., Barber, M. D., Schaffer, J., Meikle, S., Wallace, D., Shibata, N., and Wolfe, A. J. 2014. Urinary Bacteria in Adult Women with Urgency Urinary Incontinence. International Urogynecology Journal. Sep;25(9):1179-84. PMID: 24515544

21. Hilt, E., McKinley, K., Pearce, M. M., Rosenfeld, A. B., Zilliox, M. J., Mueller, E. R., Brubaker, L., Gai, X., Wolfe, A. J., and Schreckenberger, P. 2014. Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. J. Clin. Microbio. 52:871-6. PMID: 24371246

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