Faculty

Patrick C. Cirino
Dr. Patrick C. Cirino

Associate Professor
Joint Appointments in Biomedical Engineering and Biology & Biochemistry

Office Location: S337, Engineering Building 1; Laboratory: S294, Engineering Building 1
Phone: 713-743-4399   |   Fax: 713-743-4323
Email: pccirino [at] uh.edu
Website: Cirino Lab
Research Themes in the Cirino Lab: Biocatalysis, Protein & Metabolic Engineering, Synthetic Biology, Directed Evolution

Education: 

Postdoctoral Associate, University of Florida
Ph.D., California Inst. of Technology, 2004
B.S., Chemical Engineering, Ohio University, 1997

Professional Experience: 

Assistant Professor, Chemical Engineering, Pennsylvania State University, 2004 – 2010
Associate Professor, Chemical Engineering, Pennsylvania State University, 2010
Associate Professor, Chemical & Biomolecular Engineering, University of Houston, 2011 – present

Courses: 

CHEE 2331, Chemical Processes

CHEE 2332, Chemical Engineering Thermo I

ENGI 2334, Introduction to Thermodynamics

CHEE 3462, Unit Operations

CHEE 4361, Practices Lab

Research Interests: 

Research in the Cirino lab generally aims to improve “biocatalysis” (broadly, enzyme- and/or microbial-based conversion of chemical feedstocks into higher value chemical products). This includes advancing production of renewable fuels and chemicals, and repurposing or otherwise harnessing often complex natural chemical transformations orchestrated by one or more enzymes. This is accomplished through protein and metabolic engineering, and synthetic biology applications. Most notably, we have pioneered the customization and use of bacterial transcription factors as genetically-encoded biosensors/molecular reporters for high-throughput biocatalyst screening. Current projects include:

  • design of biosensors for minimal polyketides / engineering type-III polyketide product specificity
  • engineering E. coli for anaerobic biological activation of short-chain alkanes via fumarate addition
  • directed evolution of alkylsuccinate synthase substrate specificity
  • engineering ligand specificity of the ItcR repressor for biosensor applications;

In collaboration with other labs, we more broadly develop and apply molecular and synthetic biology tools. For example, we are developing controllable / inducible gene expression systems in human T-cells using an engineered bacterial repressor protein (MarR) (collaborations Navin Varadarajan (UH) and Dmitry Nevozhay (MD Anderson Cancer Center). Working with Jacinta Conrad (UH), we are designing novel, tunable “appendage” mutants of E. coli and M. hydrocarbonoclasticus; these are useful for studying/engineering bacterial adhesion in bioremediation applications, and bacteria-driven emulsions.

 

We gratefully acknowledge the National Science Foundation for numerous grants to support these research projects.

Research Group: 

Graduate student projects and other research details can be found on the Cirino Lab Website.

 

Current Lab Members:

Graduate Students

  • Ehsan Bahrami (current Ph.D. student)
  • Nam Nguyen (current Ph.D. student)
  • Yixi Wang (current Ph.D. student)

Undergraduate Students

  • Tania Pena Reyes (University of Chicago - Rowley Scholarship)
  • Ana Alvarez (Volunteer)
  • Carson Bush  (2021 SURF recipient)
  • Joshua Nwose

 

Former Lab Members:

Postdocs

  • Dr. Joseph Gredell (now Senior Scientist at Novozymes)
  • Dr. Shuang-Yan Tang (now Professor at Chinese Academy of Sciences, Institute of Microbiology)
  • Dr. Hui Li

Graduate Students

  • Aarti Doshi (PhD 2020); Research Scientist at Tessera Therapeutics
  • Zhiqing Wang (PhD 2019); Research Scientist at Mascoma LLC
  • Shuai Qian (PhD 2018); Senior Scientist at Solugen
  • Ye Li (PhD 2017); Assistant Professor, Jiangnan University
  • Shaza Abnouf (PhD student of N Varadarajan (primary advisor))
  • Christopher Frei (PhD 2016); Senior Scientist, Manus Biosynthesis
  • Balakrishnan Ramesh (PhD student of N Varadarajan (primary advisor)); Scientist at Muufri, Inc
  • Dr. Olubolaji Akinterinwa (PhD 2010): Scientist at Procter & Gamble

  • Dr. Jonathan Chin (PhD 2010); Senior Scientist at Algenol Biofuels
  • Dr. Reza Khankal (PhD 2010); Glycos Biotechnology then Chevron
  • Dr. Hossein Fazelinia (PhD 2009 co-advised by C.Maranas); Children’s Hospital, Philadelphia
  • Lexan Lhu (M.S.; Joule Biotechnologies, MA)
  • Francesca Luziatelli (visiting PhD student from U of Tuscia, Italy)
  • Ryan McLay (co-advised) (graduated M.S. student)

  • Lois Eppihimer (lab manager)

Former Undergraduate Researchers

  • Tasnuva Haider (volunteer)
  • Ibrahim Hassan (volunteer)
  • Anthara Krishnan (volunteer)
  • Nam Nguyen - SURF
  • Priya Patel – SURF
  • Zheng You (volunteer)
  • Diep Nguyen – SURF
  • Jennie Nguyen - SURF
  • Aya Elsaadi - SURF
  • Rachel Dunn - PURS
  • Justin Hood (volunteer)
  • Danielle Valcourt (REU, Notre Dame)
  • Katy Norman (REU, Trinity)
  • Wayne Andrade (UH, volunteer)
  • Chelsea Kraynak (University of MD, REU summer 2012)
  • Oliver Chou (U Colorado Boulder) REU
  • Kyle Schutter (Brown University REU; now CEO of Takamoto Biogas Ltd.)
  • Nicholas Linn (NC State) - REU
  • Ajay Padaki
  • Berook T. Alemayehu (U Maryland: Baltimore County) REU
  • Audrey Leung (University of Iowa) REU
  • Alex Teng (UC Berkeley) - REU
  • Caroline Monroe (Penn State)
  • Anthony Tascone (Penn State)
  • Renae Patch (Penn State)
  • Garrett Tobin (Penn State)
  • Jeremy Sargent (Penn State)
  • J. Lane Weaver (Penn State)
  • Jon P. Badalamenti (Penn State)
  • Lucien E Weiss (Penn State)
  • Julie Sawlsville (Penn State)
  • Geoff Geise (Penn State) - REU
  • Doug Haag (Penn State)
  • Megan Rex (Penn State)
  • Chris Cottle (Penn State)
  • Panagiotis A Papadopoulos (Penn State)
  • Matthew Zapadka (Penn State)
  • Galen Lynch (PSU)
  • Noah Johnson (PSU)
  • Chris Frei (PSU)
  • Trevor Wiley
  • Erica Trump (West Virginia U) – REU
  • Nimrah Ahmed
  • Shariful Alam
  • Aubrey Dolly
  • Daniel Seong

Work-Study Students

  • Joshua Nwose
  • Hiba Ahmed
  • Chiemela Ubani
  • Marilu Serna
  • Arlene Sanchez
  • Ghazal Nemati
  • Christian Miles                   
  • Mulbah Kallen
  • Louis Avila
  • Zeal Patel
  • Areeba Ahmed
  • Sana Basheer
  • Ryan Noraas
  • Tiffany Veet
  • Khai Van
  • Jon Ajak

Awards & Honors: 

2006 N.S.F. CAREER Award Recipient

Professional Activities: 

Associate Editor: BMC Biotechnology

Editorial Board Member: PLOS One

Board of Advisors, Ohio University Dept. of Chemical & Biomolecular Engineering

Guest Editor, AIChE Journal (2020, honoring Frances Arnold)

Guest Editor, Current Opinion in Biotechnology (multiple issues)

Guest Editor, Journal of Biomedicine and Biotechnology (2010)

ACS BIOT 2012 Program Chair

ACS Symposium Chair 2008, 2009; 2014 (CATL); 2015, 2016

SIMB Biocatalysis program co-chair, 2010 - 2014

Proposal Reviewing: NSF, NIH, DOE (BER, BES), ARPA-E, USDA, others...

Selected Publications

  1. A Doshi, F Sadeghi, N Varadarajan, PC Cirino,

    Small-molecule inducible transcriptional control in mammalian cells. Critical Reviews in Biotechnology 40 (8), 1131-1150

    , 2020
  2. Z Wang, A Doshi, R Chowdhury, Y Wang, CD Maranas, PC Cirino,

    Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid. Protein Engineering, Design and Selection 33

    , 2020
  3. S Qian, Y Li, PC Cirino,

    Biosensor-guided improvements in salicylate production by recombinant Escherichia coli. Microbial Cell Factories 18.

    , 2019
  4. CS Frei, S Qian, PC Cirino,

    New engineered phenolic biosensors based on the AraC regulatory protein. Protein Engineering, Design and Selection 31 (6), 213-220

    , 2018
  5. RB McLay, HN Nguyen, YA Jaimes-Lizcano, NK Dewangan, Simone Alexandrova, Debora F Rodrigues, Patrick C Cirino, Jacinta C Conrad,

    Level of Fimbriation Alters the Adhesion of Escherichia coli Bacteria to Interfaces. Langmuir 34 (3), 1133-1142

    , 2018
  6. Y Li, S Qian, R Dunn, PC Cirino,

    Engineering Escherichia coli to increase triacetic acid lactone (TAL) production using an optimized TAL sensor-reporter system. Journal of Industrial Microbiology and Biotechnology 45 (9), 789-793

    , 2018
  7. Y Li, Z Wang, PC Cirino,

    Design and characterization of new β-glucuronidase active site variants with altered substrate specificity. Biotechnology letters 40 (1), 111-118

    , 2018
  8. Frei CS, Wang ZQ, Qian S, Deutsch S, Sutter M, & Cirino PC,

    Analysis of amino acid substitutions in AraC variants that respond to triacetic acid lactone. Protein Science, 25(4), 804-814. doi: 10.1002/pro.2873

    , 2016
  9. Qian S, & Cirino PC,

    Using metabolite-responsive gene regulators to improve microbial biosynthesis. Current Opinion in Chemical Engineering, 14, 93-102. doi: 10.1016/j.coche.2016.08.020

    , 2016
  10. Sharma S, Jaimes-Lizcano YA, McLay RB, Cirino PC, & Conrad, JC,

    Subnanometric Roughness Affects the Deposition and Mobile Adhesion of Escherichia coli on Silanized Glass Surfaces. Langmuir, 32(21), 5422-5433. doi: 10.1021/acs.langmuir.6b00883

    , 2016
  11. Wang ZQ, & Cirino PC,

    New and improved tools and methods for enhanced biosynthesis of natural products in microorganisms. Current Opinion in Biotechnology, 42, 159-168. doi: 10.1016/j.copbio.2016.05.003

    , 2016
  12. Li Y and PC Cirino,

    Recent advances in engineering proteins for biocatalysis. Biotechnology & Bioengineering, 111(7), 1273-1287.

    , 2014
  13. Grisewood MJ, Gifford NP, Pantazes RJ, Li Y, Cirino PC, Janik MJ, and CD Maranas,

    OptZyme: computational enzyme redesign using transition state analogues. PLoS One.8(10):e75358

    , 2013
  14. Qian S and PC Cirino,

    Protein engineering as an enabling tool for synthetic biology. In Synthetic Biology: Tools and Applications. 23-42. Edited by H. Zhao. Elsevier

    , 2013
  15. Tang SY, Qian S, Akinterinwa O, Frei CS, Gredell JA, and PC Cirino,

    Screening for enhancedtriacetic acid lactone production by recombinant Escherichia coli expressing a designedtriacetic acid lactone reporter. Journal of the American Chemical Society. 135:10099-10103

    , 2013
  16. Gredell JA, Frei CS and PC Cirino,

    Protein and RNA engineering to customize microbial molecular reporting. Biotechnology Journal. 7(4):477-99

    , 2012
  17. Ramesh B, Sendra VG, Cirino PC, and N Varadarajan,

    Single-cell characterization of autotransporter-mediated Escherichia coli surface display of disulfide bond-containing proteins. Journal of Biological Chemistry. 287(46):38580-9.

    , 2012
  18. Akinterinwa O and PC Cirino,

    Anaerobic obligatory xylitol production in Escherichia coli strains devoid of native fermentation pathways. Applied and Environmental Microbiology.77(2):706-9

    , 2011
  19. Chin JW and PC Cirino,

    Strain engineering strategies for improving whole-cell biocatalysis: engineering Escherichia coli to overproduce xylitol as an example. Nanoscale Biocatalysis: Methods in Molecular Biology, 743:185-203

    , 2011
  20. Chin JW and PC Cirino,

    Improved NADPH supply for xylitol production by engineered Escherichia coli with glycolytic mutations. Biotechnol. Progress, 27(2):333-41

    , 2011
  21. Chin, J. W.; Cirino, P. C.,

    Improved NADPH Supply for Xylitol Production by Engineered Escherichia Coli with Glycolytic Mutations. Biotechnology Progress 2011, 27 (2), 333-341.

    , 2011
  22. Fasan R, Crook NC, Landwehr M, Cirino PC, and FH Arnold,

    Improved product-per-glucose yields in P450 dependent propane biotransformations using engineered E. coli. Biotechnol Bioeng., 108(3):500-10

    , 2011
  23. Fasan, R.; Crook, N. C.; Peters, M. W.; Meinhold, P.; Buelter, T.; Landwehr, M.; Cirino, P. C.; Arnold, F. H.,

    Improved NADPH supply for xylitol production by engineered Escherichia coli with glycolytic mutations. Biotechnol. Progress, 27(2):333-41

    , 2011
  24. Tang SY and Cirino PC,

    Design and application of a novel mevalonate-responsive regulatory protein. Angewandte Chemie International Edition. 50(5):1084-6

    , 2011
  25. Cirino PC,

    Metabolic engineering strategies for production of commodity and fine chemicals: Escherichia coli as a platform organism. Manual of Industrial Microbiology and Biotechnology. ASM Press, ISBN: 9781555815127

    , 2010
  26. Tang SY and PC Cirino,

    Elucidating residue roles in engineered variants of AraC regulatory protein. Protein Sci. 19(2):291-8

    , 2010
  27. Akinterinwa O and PC Cirino,

    Heterologous expression of D-xylulokinase from Pichia stipitis enables high levels of xylitol production by engineered Escherichia coli growing on xylose. Metab Eng. 11(1):48. Cover article

    , 2009
  28. Akinterinwa, O and PC Cirino,

    Catabolism and Metabolic Fueling Processes. In: The Metabolic Pathway Engineering Handbook, ISBN: 9780849339233

    , 2009
  29. Chin JW, Khankal R, Monroe CA, Maranas CD, and PC Cirino,

    Analysis of NADPH supply during xylitol production by engineered Escherichia coli. Biotechnol. Bioeng. 102(1):209.Spotlight article

    , 2009
  30. Fazelinia H, Cirino PC, and CD Maranas,

    OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold. Protein Sci. 18(1):180

    , 2009
  31. Frei CS and PC Cirino,

    Combinatorial Enzyme Engineering. In: Protein Engineering and Design. J.R. Cochran and S. Park, Eds. Publisher: CRC; 1 edition, ISBN-10: 1420076582

    , 2009
  32. Khankal R, Chin JW, Ghosh D, and PC Cirino,

    Transcriptional effects of CRP* expression in Escherichia coli. J. Biol. Eng. 3:13

    , 2009
  33. Khoury GA, Fazelinia H, Cirino PC, and CD Maranas,

    Computationally driven redesign of Candida boidinii xylose reductase for altered cofactor specificity. Protein Sci.18(10):2125-38. Cover article

    , 2009
  34. Akinterinwa O, Khankal R, and PC Cirino,

    Metabolic Engineering for Bioproduction of Sugar Alcohols. Curr Opin Biotechnol. 19(5):461

    , 2008
  35. Cirino PC and Sun L,

    Advancing Biocatalysis through Enzyme, Cellular, and Platform Engineering. Biotechnol. Progr. 24(3):515

    , 2008
  36. Khankal R, Chin JW, PC Cirino,

    Role of xylose transporters in Escherichia coli engineered for xylitol production. J. Biotechnol. 134(3-4):246

    , 2008
  37. Khankal R, Luziatelli F, Chin JW, Frei CS and PC Cirino,

    Comparison between three common Escherichia coli lab strains as platforms for xylitol production. Biotechnol Lett.30(9):1645

    , 2008
  38. Tang SY, Fazelinia H, and PC Cirino,

    AraC regulatory protein mutants with altered effector specificity. J. Am. Chem. Soc. 130(15):5267

    , 2008
  39. Weiss LE, Badalamenti JP, Weaver JL, Tascone AR, Weiss PS, Richard TL, and PC Cirino,

    Engineering motility as a phenotypic response to LuxI/R-dependent quorum sensing in Escherichia coli. Biotechnol Bioeng. 100(6):1251. Spotlight article

    , 2008
  40. Badalamenti JP, Weiss LE, Buckno CJ, Richard TL, Weiss PS, and PC Cirino,

    Synthetic Sports: A Bacterial Relay Race. IET Synth. Biol. 1:61

    , 2007
  41. Fazelinia H, Cirino PC, and CD Maranas,

    Extending IPRO in protein library design for ligand specificity. Biophys. J. 92(6):2120

    , 2007
  42. Cirino PC, Chin JW and LO Ingram,

    Engineering Escherichia coli for Xylitol Production from Glucose-Xylose Mixtures. Biotechnol. Bioeng. 95: 1167

    , 2006
  43. Cirino PC and FH Arnold,

    A self-sufficient peroxide-driven hydroxylation biocatalyst. Angew. Chem.-Int. Edit. 42: 3299

    , 2003
  44. Cirino PC and R Georgescu,

    Screening for thermostability. Methods Mol Biol. 230: 117

    , 2003
  45. Cirino PC, Mayer KM, and D Umeno,

    Generating mutant libraries using error-prone PCR. Methods Mol Biol. 231: 3

    , 2003
  46. Cirino PC, Tang Y, Takahashi K, Tirrell DA and FH Arnold,

    Global Incorporation of Norleucine in Place of Methionine in Cytochrome P450 BM-3 Heme Domain Increases Peroxygenase Activity. Biotechnol. Bioeng. 83: 729

    , 2003
  47. Salazar O*, Cirino PC* (*equal contributions) and FH Arnold,

    Thermostabilization of a Cytochrome P450 Peroxygenase. ChemBioChem. 4: 891

    , 2003
  48. Cirino PC and FH Arnold,

    Regioselectivity and activity of cytochrome P450 BM-3 and mutant F87A in reactions driven by hydrogen peroxide. Adv. Synth. Catal. 344: 932

    , 2002
  49. Cirino PC and FH Arnold,

    Protein engineering of oxygenases for biocatalysis. Curr. Opin. Chem. Biol. 6: 130

    , 2002

Editorials / Edited Volumes

  1. Alper H, Cirino P, Nevoigt E, and Sriram G,

    Applications of Synthetic Biology in Microbial Biotechnology. J Biomedicine Biotechnology. Article ID 918391

    , 2010

 


Patents

  1. Cirino PC and Ingram LO, inventors, Materials and methods for the efficient production of xylitol in E. coli, U.S. Patent Application Serial No. 20070072280. Licensed to BioEnergy International
    Date: 09/01/2005
  2. Arnold FH and Cirino PC, inventors. Thermostable peroxide-driven cytochrome P450 oxygenase variants and methods of use. U.S. Patent No. 7,435,570. Licensed to Codexis
    Date: 08/11/2004
  3. Cirino PC and Arnold FH, inventors. Peroxide-driven cytochrome P450 oxygenase variants. U.S. Patent No. 7,704,715. Licensed to Codexis
    Date: 04/16/2002