Patrick C. Cirino

Faculty

Dr. Patrick C. Cirino

Professor
Undergraduate Program Director
Joint Appointments in Biomedical Engineering and Biology & Biochemistry

Office Location S337, Engineering Building 1; Laboratory: S294, Engineering Building 1

Phone 713-743-1496

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 – 2022

Professor, Chemical & Biomolecular Engineering, University of Houston, 2022 – 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.

NSF logo

Research Group

Cirino Lab members

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...

Google Scholar

Patents

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
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
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

Selected Publications

A Doshi, I Bandey, D Nevozhay, N Varadarajan, PC Cirino, Design and characterization of a salicylic acid-inducible gene expression system for Jurkat cells. Journal of Biotechnology 346, 11-14, 2022
Y Wang, N Nguyen, SH Lee, Q Wang, JA May, R Gonzalez, PC Cirino, Engineering Escherichia coli for anaerobic alkane activation: Biosynthesis of (1‐methylalkyl)succinates. Biotechnology and Bioengineering 119 (1), 315-320, 2022
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
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
S Qian, Y Li, PC Cirino, Biosensor-guided improvements in salicylate production by recombinant Escherichia coli. Microbial Cell Factories 18., 2019
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
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
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
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
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
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
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
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
Li Y and PC Cirino, Recent advances in engineering proteins for biocatalysis. Biotechnology & Bioengineering, 111(7), 1273-1287., 2014
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
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
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
Gredell JA, Frei CS and PC Cirino, Protein and RNA engineering to customize microbial molecular reporting. Biotechnology Journal. 7(4):477-99, 2012
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
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
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
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
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
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
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
Tang SY and Cirino PC, Design and application of a novel mevalonate-responsive regulatory protein. Angewandte Chemie International Edition. 50(5):1084-6, 2011
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
Tang SY and PC Cirino, Elucidating residue roles in engineered variants of AraC regulatory protein. Protein Sci. 19(2):291-8, 2010

Editorials / Edited Volumes

Alper H, Cirino P, Nevoigt E, and Sriram G, Applications of Synthetic Biology in Microbial Biotechnology. J Biomedicine Biotechnology. Article ID 918391, 2020

More Publications

SELECTED PUBLICATIONS

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
Akinterinwa, O and PC Cirino, Catabolism and Metabolic Fueling Processes. In: The Metabolic Pathway Engineering Handbook, ISBN: 9780849339233, 2009
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
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
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
Khankal R, Chin JW, Ghosh D, and PC Cirino, Transcriptional effects of CRP* expression in Escherichia coli. J. Biol. Eng. 3:13, 2009
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
Akinterinwa O, Khankal R, and PC Cirino, Metabolic Engineering for Bioproduction of Sugar Alcohols. Curr Opin Biotechnol. 19(5):461, 2008
Cirino PC and Sun L, Advancing Biocatalysis through Enzyme, Cellular, and Platform Engineering. Biotechnol. Progr. 24(3):515, 2008
Khankal R, Chin JW, PC Cirino, Role of xylose transporters in Escherichia coli engineered for xylitol production. J. Biotechnol. 134(3-4):246, 2008
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
Tang SY, Fazelinia H, and PC Cirino, AraC regulatory protein mutants with altered effector specificity. J. Am. Chem. Soc. 130(15):5267, 2008
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
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
Fazelinia H, Cirino PC, and CD Maranas, Extending IPRO in protein library design for ligand specificity. Biophys. J. 92(6):2120, 2007
Cirino PC, Chin JW and LO Ingram, Engineering Escherichia coli for Xylitol Production from Glucose-Xylose Mixtures. Biotechnol. Bioeng. 95: 1167, 2006
Cirino PC and FH Arnold, A self-sufficient peroxide-driven hydroxylation biocatalyst. Angew. Chem.-Int. Edit. 42: 3299, 2003
Cirino PC and R Georgescu, Screening for thermostability. Methods Mol Biol. 230: 117, 2003
Cirino PC, Mayer KM, and D Umeno, Generating mutant libraries using error-prone PCR. Methods Mol Biol. 231: 3, 2003
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
Salazar O*, Cirino PC* (*equal contributions) and FH Arnold, Thermostabilization of a Cytochrome P450 Peroxygenase. ChemBioChem. 4: 891, 2003
Cirino PC and FH Arnold, Protein engineering of oxygenases for biocatalysis. Curr. Opin. Chem. Biol. 6: 130, 2002
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