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Martin Pavelka, Ph.D.

Martin Pavelka, Ph.D.

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About Me

Faculty Appointments

Professor - Department of Microbiology and Immunology (SMD)

Credentials

Post-doctoral Training & Residency

Department of Microbiology and Immunology, Albert Einstein College of Medicine (Bronx, NY). 1994 - 1999

Education

PhD | Univ Rochester Sch Med/Dent. Microbiology. 1994

MS | Univ Rochester Sch Med/Dent. Microbiology. 1991

BS | Cleveland St University. Biology. 1988

Awards

Awardee, URMC Excellence in Research. 2006 - 2006

Recipient of a Burroughs Wellcome Fund Career Award in the Biomedical Sciences. 1997

Public Heath Service NIH Predoctoral Trainee. 1990 - 1993

Graduated magna cum laude - Cleveland State University. 1988

Doretta C. Thelker Award, Cleveland State University. 1988

Research

1. Research Projects in Progress

My research expertise is in the genetics, physiology, and biochemistry of the cell envelopes of bacterial respiratory pathogens, with a special focus on the cell wall peptidoglycan.

Tuberculosis Research
1. Biosynthesis of the mycobacterial cell w...
1. Research Projects in Progress

My research expertise is in the genetics, physiology, and biochemistry of the cell envelopes of bacterial respiratory pathogens, with a special focus on the cell wall peptidoglycan.

Tuberculosis Research
1. Biosynthesis of the mycobacterial cell wall. Our current research activities focus on understanding the genetics and biochemistry of cell envelope biosynthesis in Mycobacterium tuberculosis and related mycobacteria with the goal of identifying new targets that can be translated into the development of novel anti-tuberculosis drugs. Our studies focus on four aspects of the peptidoglycan of mycobacteria: 1) identifying the enzymes responsible for DAP-DAP cross links in the cell wall and their importance for cell survival under non-replicating conditions, 2) understanding the role of carbohydrate hydroxylation and amino acid amidation on peptidoglycan physiology, 3) understanding the function of unusual L,D-transpeptidase enzymes that may modify the cell wall, and 4) understanding the factors that contribute to antibiotic resistance in M. tuberculosis. These research activities include collaborations with Dr. Dean Crick and Dr. Sebabrata Mahapatra (Colorado State University, Fort Collins, CO).

2. We are also collaborating with Dr. Scott Butler in the Department of Microbiology and Immunology here at the UR to investigate the function of toxin-antitoxin genes in M. tuberculosis and their potential role in latency in tuberculosis.

Tularemia and Biodefense Research
1. Development of genetic tools for Francisella tularensis and investigations into tularemia pathogenesis. Our early work on Francisella was to develop genetic methods to manipulate Francisella tularensis, the causative agent of tularemia and a Category A Select Agent. This work focused on developing new plasmid vectors, selectable markers, a method of allelic exchange and transposon mutagenesis, single-copy chromosomal integration systems, and protein secretion reporter systems. Future plans include the development of projects to investigate Francisella cell wall physiology and the roles that cell envelope components have in the innate immune response and tularemia pathogenesis.

Publications

Journal Articles

Susceptibility of bacterial species commonly found in abdominal abscesses to low-dose photodynamic therapy: Effects of methylene blue concentration, fluence rate, and fluence.

Photochemistry and photobiology.. 2025 March 26 Epub 03/26/2025.

Exploring the Role of a Putative Secondary Metabolite Biosynthesis Pathway in Pathogenesis Using a Tadpole Model.

Miller NJ, Dimitrakopoulou D, Baglia LA, Pavelka MS, Robert J

Microorganisms.. 2024 May 3112 (6)Epub 05/31/2024.

Amphibians as a model to study the role of immune cell heterogeneity in host and mycobacterial interactions.

Paiola M, Dimitrakopoulou D, Pavelka MS, Robert J

Developmental and comparative immunology.. 2023 February 139 :104594. Epub 11/18/2022.

LdtC Is a Key l,d-Transpeptidase for Peptidoglycan Assembly in Mycobacterium smegmatis.

Francis ZK, Sanders AN, Crick DC, Mahapatra S, Islam MN, Pavelka MS

Journal of bacteriology.. 2023 January 26205 (1):e0042422. Epub 12/21/2022.

Methylene blue photodynamic therapy of bacterial species found in human abscesses: Planktonic, biofilm, and 3D silicone models.

Chan H, Pavelka MS, Baran TM

Proceedings of SPIE--the International Society for Optical Engineering.. 2023 12358 Epub 03/14/2023.

Developing Tadpole as a Comparative Animal Model to Study Pathogenicity.

Lopez A, Shoen C, Cynamon M, Dimitrakopoulou D, Paiola M, Pavelka MS, Robert J

International journal of molecular sciences.. 2021 January 1522 (2)Epub 01/15/2021.

Distinct Host-Mycobacterial Pathogen Interactions between Resistant Adult and Tolerant Tadpole Life Stages of .

Rhoo KH, Edholm ES, Forzán MJ, Khan A, Waddle AW, Pavelka MS, Robert J

The Journal of immunology : official journal of the American Association of Immunologists.. 2019 November 15203 (10):2679-2688. Epub 10/07/2019.

L,D-Transpeptidase Specific Probe Reveals Spatial Activity of Peptidoglycan Cross-Linking.

Pidgeon SE, Apostolos AJ, Nelson JM, Shaku M, Rimal B, Islam MN, Crick DC, Kim SJ, Pavelka MS, Kana BD, Pires MM

ACS chemical biology.. 2019 October 1814 (10):2185-2196. Epub 09/16/2019.

Snappy cell division in Actinobacteria.

Pavelka MS

Nature chemical biology.. 2019 March 15 (3):208-209. Epub 1900 01 01.

In Silico Screen and Structural Analysis Identifies Bacterial Kinase Inhibitors which Act with ?-Lactams To Inhibit Mycobacterial Growth.

Wlodarchak N, Teachout N, Beczkiewicz J, Procknow R, Schaenzer AJ, Satyshur K, Pavelka M, Zuercher W, Drewry D, Sauer JD, Striker R

Molecular pharmaceutics.. 2018 November 515 (11):5410-5426. Epub 10/18/2018.

Distinct MHC class I-like interacting invariant T cell lineage at the forefront of mycobacterial immunity uncovered in .

Edholm ES, Banach M, Hyoe Rhoo K, Pavelka MS, Robert J

Proceedings of the National Academy of Sciences of the United States of America.. 2018 April 24115 (17):E4023-E4031. Epub 04/02/2018.

-based suicide vector mediated allelic exchange in .

Gregoire SA, Byam J, Pavelka MS

Microbiology.. 2017 October 163 (10):1399-1408. Epub 1900 01 01.

The RipA and RipB Peptidoglycan Endopeptidases Are Individually Nonessential to Mycobacterium smegmatis.

Martinelli DJ, Pavelka MS

Journal of bacteriology.. 2016 May 198 (9):1464-75. Epub 04/14/2016.

One of these is not like the others.

Pavelka MS

Trends in microbiology.. 2015 November 23 (11):668-670. Epub 10/01/2015.

Activation of the aryl hydrocarbon receptor during development enhances the pulmonary CD4+ T-cell response to viral infection.

Boule LA, Winans B, Lambert K, Vorderstrasse BA, Topham DJ, Pavelka MS, Lawrence BP

American journal of physiology. Lung cellular and molecular physiology.. 2015 August 1309 (3):L305-13. Epub 06/12/2015.

Revisiting the Gram-negative lipoprotein paradigm.

LoVullo ED, Wright LF, Isabella V, Huntley JF, Pavelka MS

Journal of bacteriology.. 2015 May 197 (10):1705-15. Epub 03/09/2015.

Structure-function analysis of VapB4 antitoxin identifies critical features of a minimal VapC4 toxin-binding module.

Jin G, Pavelka MS, Butler JS

Journal of bacteriology.. 2015 April 197 (7):1197-207. Epub 01/26/2015.

Genetic characterization of mycobacterial L,D-transpeptidases.

Sanders AN, Wright LF, Pavelka MS

Microbiology.. 2014 August 160 (Pt 8):1795-1806. Epub 05/21/2014.

Genetics of Peptidoglycan Biosynthesis.

Pavelka MS, Mahapatra S, Crick DC

Microbiology spectrum.. 2014 August 2 (4):MGM2-0034-2013. Epub 1900 01 01.

Phenotypic analysis of Eschericia coli mutants lacking L,D-transpeptidases.

Sanders AN, Pavelka MS

Microbiology.. 2013 September 159 (Pt 9):1842-1852. Epub 07/07/2013.

Mycobacteriophage Ms6 LysA: a peptidoglycan amidase and a useful analytical tool.

Mahapatra S, Piechota C, Gil F, Ma Y, Huang H, Scherman MS, Jones V, Pavelka MS, Moniz-Pereira J, Pimentel M, McNeil MR, Crick DC

Applied and environmental microbiology.. 2013 February 79 (3):768-73. Epub 11/16/2012.

Updating and curating metabolic pathways of TB.

Slayden RA, Jackson M, Zucker J, Ramirez MV, Dawson CC, Crew R, Sampson NS, Thomas ST, Jamshidi N, Sisk P, Caspi R, Crick DC, McNeil MR, Pavelka MS, Niederweis M, Siroy A, Dona V, McFadden J, Boshoff H, Lew JM

Tuberculosis.. 2013 January 93 (1):47-59. Epub 02/01/2013.

Directed evolution of Mycobacterium tuberculosis ?-lactamase reveals gatekeeper residue that regulates antibiotic resistance and catalytic efficiency.

Feiler C, Fisher AC, Boock JT, Marrichi MJ, Wright L, Schmidpeter PA, Blankenfeldt W, Pavelka M, DeLisa MP

PloS one.. 2013 8 (9):e73123. Epub 09/04/2013.

TetR-based gene regulation systems for Francisella tularensis.

LoVullo ED, Miller CN, Pavelka MS, Kawula TH

Applied and environmental microbiology.. 2012 October 78 (19):6883-9. Epub 07/20/2012.

A role for the class A penicillin-binding protein PonA2 in the survival of Mycobacterium smegmatis under conditions of nonreplication.

Patru MM, Pavelka MS

Journal of bacteriology.. 2010 June 192 (12):3043-54. Epub 04/16/2010.

Single-copy chromosomal integration systems for Francisella tularensis.

Lovullo ED, Molins-Schneekloth CR, Schweizer HP, Pavelka MS

Microbiology.. 2009 April 155 (Pt 4):1152-1163. Epub 1900 01 01.

Improved shuttle vectors for Francisella tularensis genetics.

Lovullo ED, Sherrill LA, Pavelka MS

FEMS microbiology letters.. 2009 February 291 (1):95-102. Epub 12/04/2008.

Allelic exchange of unmarked mutations in Mycobacterium tuberculosis.

Pavelka MS

Methods in molecular biology.. 2008 435 :191-201. Epub 1900 01 01.

Beta-lactamase can function as a reporter of bacterial protein export during Mycobacterium tuberculosis infection of host cells.

McCann JR, McDonough JA, Pavelka MS, Braunstein M

Microbiology.. 2007 October 153 (Pt 10):3350-3359. Epub 1900 01 01.

Codominance of TLR2-dependent and TLR2-independent modulation of MHC class II in Mycobacterium tuberculosis infection in vivo.

Kincaid EZ, Wolf AJ, Desvignes L, Mahapatra S, Crick DC, Brennan PJ, Pavelka MS, Ernst JD

The Journal of immunology : official journal of the American Association of Immunologists.. 2007 September 1179 (5):3187-95. Epub 1900 01 01.

Biosafety and selectable markers.

Titball RW, Sjostedt A, Pavelka MS, Nano FE

Annals of the New York Academy of Sciences.. 2007 June 1105 :405-17. Epub 04/07/2007.

Another brick in the wall.

Pavelka MS

Trends in microbiology.. 2007 April 15 (4):147-9. Epub 02/28/2007.

Genetic tools for highly pathogenic Francisella tularensis subsp. tularensis.

LoVullo ED, Sherrill LA, Perez LL, Pavelka MS

Microbiology.. 2006 November 152 (Pt 11):3425-3435. Epub 1900 01 01.

The twin-arginine translocation pathway of Mycobacterium smegmatis is functional and required for the export of mycobacterial beta-lactamases.

McDonough JA, Hacker KE, Flores AR, Pavelka MS, Braunstein M

Journal of bacteriology.. 2005 November 187 (22):7667-79. Epub 1900 01 01.

An unusual mutation results in the replacement of diaminopimelate with lanthionine in the peptidoglycan of a mutant strain of Mycobacterium smegmatis.

Consaul SA, Wright LF, Mahapatra S, Crick DC, Pavelka MS

Journal of bacteriology.. 2005 March 187 (5):1612-20. Epub 1900 01 01.

Characterization of novel Mycobacterium tuberculosis and Mycobacterium smegmatis mutants hypersusceptible to beta-lactam antibiotics.

Flores AR, Parsons LM, Pavelka MS

Journal of bacteriology.. 2005 March 187 (6):1892-900. Epub 1900 01 01.

Genetic analysis of the beta-lactamases of Mycobacterium tuberculosis and Mycobacterium smegmatis and susceptibility to beta-lactam antibiotics.

Flores AR, Parsons LM, Pavelka MS

Microbiology.. 2005 February 151 (Pt 2):521-532. Epub 1900 01 01.

Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan.

Raymond JB, Mahapatra S, Crick DC, Pavelka MS

The Journal of biological chemistry.. 2005 January 7280 (1):326-33. Epub 11/02/2004.

Use of a novel allele of the Escherichia coli aacC4 aminoglycoside resistance gene as a genetic marker in mycobacteria.

Consaul SA, Pavelka MS

FEMS microbiology letters.. 2004 May 15234 (2):297-301. Epub 1900 01 01.

A method for the enzymatic synthesis and HPLC purification of the peptidoglycan precursor UDP-N-acetylmuramic acid.

Raymond JB, Price NP, Pavelka MS

FEMS microbiology letters.. 2003 December 5229 (1):83-9. Epub 1900 01 01.

Extragenic suppression of the requirement for diaminopimelate in diaminopimelate auxotrophs of Mycobacterium smegmatis.

Consaul SA, Jacobs WR, Pavelka MS

FEMS microbiology letters.. 2003 August 8225 (1):131-5. Epub 1900 01 01.

Vaccine efficacy of a lysine auxotroph of Mycobacterium tuberculosis.

Pavelka MS, Chen B, Kelley CL, Collins FM, Jacobs Jr WR

Infection and immunity.. 2003 July 71 (7):4190-2. Epub 1900 01 01.

Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis.

Gokulan K, Rupp B, Pavelka MS, Jacobs WR, Sacchettini JC

The Journal of biological chemistry.. 2003 May 16278 (20):18588-96. Epub 03/10/2003.

Specialized transduction: an efficient method for generating marked and unmarked targeted gene disruptions in Mycobacterium tuberculosis, M. bovis BCG and M. smegmatis.

Bardarov S, Bardarov S, Pavelka MS, Sambandamurthy V, Larsen M, Tufariello J, Chan J, Hatfull G, Jacobs WR

Microbiology.. 2002 October 148 (Pt 10):3007-3017. Epub 1900 01 01.

Comparison of the construction of unmarked deletion mutations in Mycobacterium smegmatis, Mycobacterium bovis bacillus Calmette-Guérin, and Mycobacterium tuberculosis H37Rv by allelic exchange.

Pavelka MS, Jacobs WR

Journal of bacteriology.. 1999 August 181 (16):4780-9. Epub 1900 01 01.

Cloning of the dapB gene, encoding dihydrodipicolinate reductase, from Mycobacterium tuberculosis.

Pavelka MS, Weisbrod TR, Jacobs WR

Journal of bacteriology.. 1997 April 179 (8):2777-82. Epub 1900 01 01.

Biosynthesis of diaminopimelate, the precursor of lysine and a component of peptidoglycan, is an essential function of Mycobacterium smegmatis.

Pavelka MS, Jacobs WR

Journal of bacteriology.. 1996 November 178 (22):6496-507. Epub 1900 01 01.

Allelic exchange in Mycobacterium tuberculosis with long linear recombination substrates.

Balasubramanian V, Pavelka MS, Bardarov SS, Martin J, Weisbrod TR, McAdam RA, Bloom BR, Jacobs WR

Journal of bacteriology.. 1996 January 178 (1):273-9. Epub 1900 01 01.

Characterization of KpsT, the ATP-binding component of the ABC-transporter involved with the export of capsular polysialic acid in Escherichia coli K1.

Pavelka MS, Hayes SF, Silver RP

The Journal of biological chemistry.. 1994 August 5269 (31):20149-58. Epub 1900 01 01.

Identification of two genes, kpsM and kpsT, in region 3 of the polysialic acid gene cluster of Escherichia coli K1.

Pavelka MS, Wright LF, Silver RP

Journal of bacteriology.. 1991 August 173 (15):4603-10. Epub 1900 01 01.

Books

Molecular Genetics of Mycobacteria (2014)

Chapter: Genetics of Peptidoglycan synthesis

Chromosomal Mutagenesis. Humana Press. (2008)

Chapter: Allelic exchange of unmarked mutations in Mycobacterium tuberculosis.

Molecular Genetics of the mycobacteria. (2000)

Chapter: Genetics of mycobacterial metabolism.

Thesis: The role of kpsT in the expression of capsular polysialic acid in Escher (1994)

Polysialic acid. (1993)

Chapter: Genetic and molecular analysis of the polysialic acid gene cluster of Escherichia coli K1.