Chemical & Biomolecular Engineering

Top 20 Doctoral Program—National Research Council

Location

Dept. of Chemical & Biomolecular Engineering
University of Houston
S222 Engineering Bldg 1,
Houston, TX 77204-4004
Phone: 713-743-4300
Campus Map

Faculty

Dr. Patrick C. Cirino

Associate Professor of Chemical and Biomolecular Engineering

Associate Professor of Biology and Biochemistry

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

Tel: (713) 743-4399 | Fax: (713) 743-4323

Email: pccirino [at] uh [dot] edu

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 (Fall Semester)
  • ENGI 2334, Introduction to Thermodynamics

Research Interests

Click here to jump to information about our lab & group

Our research was recently highlighted! (click to link)   (This appeared in: International Innovation)

Nature provides a vast collection of biological systems which have evolved mechanisms to achieve catalysis, regulation, molecular recognition, and energy utilization with incredible efficiency. Our ability to successfully re-design and harness such systems is integral to realizing a future of cost-effective "green" chemistry, renewable fuels and chemicals, bioremediation, and "next-generation" therapeutics.

Research in the Cirino laboratory interfaces Chemical Engineering with the biological sciences, with emphases in biomolecular engineering, metabolic engineering, and biocatalysis.  Recent research efforts are summarized in the poster presentations below (right click to view larger images).  By applying biological design principles at the molecular level (e.g., engineer proteins) as well as the systems level (e.g., engineer metabolic pathways and gene regulation) we are creating novel microbial strains with improved biocatalytic efficiency (e.g. increased supply of NADPH to transformations of interest), and we are designing novel biosensors by customizing regulatory proteins, with broad applications in synthetic biology and biocatalyst development.

Protein Engineering/Molecular Recognition

We are using combinatorial (evolutionary) as well as rational (structure-based) protein design techniques to engineer transcriptional regulatory proteins to serve as customized biosensors. These proteins are being designed to recognize specific non-native molecules of interest ("effectors") and report their presence and concentration by regulating expression of a reporter gene.  Such endogenous biosensors serve as powerful tools in synthetic biology and facilitate subsequent protein engineering and metabolic engineering efforts in our lab and others.

New molecular reporters from AraC regulator protein with altered effector specificity
(Click to view a larger image)

Metabolic Engineering

Metabolic engineering is defined as the improvement of cellular activities by manipulation of enzymatic, transport, and regulatory functions of the cell with the use of recombinant DNA technology. Current research in our lab is aimed at modifying microbial metabolism to carry out new or improved bioconversions for the production of various secondary metabolites. This typically requires expression of foreign genes in an amenable microbial host (e.g. E. coli).  Several stages of genetic optimization are then required to improve efficiency and productivity.  As strategies to improve strain performance parameters are developed and tested, we gain new insights into microbial metabolism and physiology, further informing the design process.

In one example, we engineer the metabolism of E. coli to create biocatalytic strains which maximize yields on reducing equivalents in the form of NADPH, derived from renewable biomass sugars. This reducing power is subsequently channeled away from aerobic respiration and into driving reactions of interest, such as the reduction of xylose to xylitol (a sweetener and synthetic building block molecule).

In other examples, we are improving flux of precursors metabolites (e.g. acetyl-CoA and malonyl-CoA) toward the synthesis  of secondary metabolites (natural products such as polyketides and isoprenoids) by genetically modified bacteria.  This is largely accomplished via a "directed evolution" strategy in which large numbers of genetic variants are created and screened for improved properties.  This in turn requires high throughput screening of target compounds, which we achieve by creating customized molecular reporters derived from natural regulatory proteins.

Additional projects include engineering oxygenase enzymes to accommodate new or improved activities, and implementing our custom-designed regulatory proteins in high-throughput screening of novel enzyme and microbial biocatalysts (see above).  All research projects draw from a broad base of knowledge and experimental techniques spanning many disciplines, the common goal being that we use biology to solve problems pertinent to the expanding field of Chemical Engineering.

Computation and modeling contribute to many areas of our research by reducing experimental variables and guiding experimental efforts. Likewise, experimental results can provide information leading to improved biological models. This complementary exchange of information is realized through collaborations with Dr. Costas Maranas at Penn State University.

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


Research Group

Click here for a tour of the lab!​

 

Dr. Cirino's Resea​rch Group:​

cirino_group.jpg

 

Lab Members:

Graduate Students

  • Christopher Frei
  • Ye Li
  • Shuai Qian
  • Zhiqing wang
  • Bala Ramesh (primary advisor is Dr. Navin Varadarajan)
  • Shaza Abnouf (primary advisor is Dr. Navin Varadarajan)

Undergraduate Students

  • Justin Hood (UH)
  • Aya Elsaadi (UH)

 

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) LINK HERE
  • Dr. Hui Li

Graduate Students

  • Dr. Olubolaji Akinterinwa (PhD 2010): currently at Procter & Gamble
  • Dr. Jonathan Chin (PhD 2010): currently at Algenol Biofuels
  • Dr. Reza Khankal (PhD 2010): currently at Glycos Biotechnology
  • Dr. Hossein Fazelinia (Ph.D.  2009 co-advised by C.Maranas)
  • Lexan Lhu (M.S.; employed at Joule Biotechnologies, MA)
  • Christopher Frei (M.S. 2010): now a Ph.D. student in Cirino lab
  • Francesca Luziatelli (visiting student from U of Tuscia, Italy)
  • Lois Eppihimer (lab manager)

Undergraduate Researchers

  • Wayne Andrade (UH)
  • Chelsea Kraynak (University of MD, REU summer 2012)
  • Oliver Chou (U Colorado Boulder)
  • Kyle Schutter (Brown University; now CEO of Takamoto Biogas Ltd.)
  • Nicholas Linn (NC State)
  • Berook T. Alemayehu (U Maryland: Baltimore County)
  • Audrey Leung (University of Iowa)
  • 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)
  • Doug Haag (Penn State)
  • Megan Rex (Penn State)
  • Chris Cottle (Penn State)
  • Panagiotis A Papadopoulos (Penn State)
  • Matthew Zapadka (Penn State)
  • Samhita Banavar (PA Governor’s school for high school students)

Work-Study Students

  • Ryan Noraas
  • Tiffany Veet
  • Khai Van
  • John Ajak

Awards and Honors

  • 2006 N.S.F. CAREER Award Recipient
  • Associate Editor: BMC Biotechnology
  • Editorial Board Member: Biotechnology Letters, Biotechnology Journal, Journal of Biological Engineering
  • Guest Editor, “Applications of Synthetic Biology in Microbial Biotechnology”, Journal of Biomedicine and Biotechnology (2009)
  • ACS BIOT 2012 Program Chair
  • SIM Biocatalysis program co-chair, 2010 - 2014

Professional Activities

  • Councilor, Institute of Biological Engineering (IBE), 2006-2010
  • Faculty Advisor, Penn State iGEM Undergrad Research (Synthetic Biology) 2006 - 2009
  • Instructor, Fundamentals of Bioseparation Techniques, Penn State Biotechnology Training Program (2004 - 2010)

Selected Publications

  1. Li Y and PC Cirino,

    Recent advances in engineering proteins for biocatalysis. Biotechnology & Bioengineering

    , 2014
  2. 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
  3. 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
  4. Tang SY, Qian S, Akinterinwa O, Frei CS, Gredell JA, and PC Cirino,

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

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

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

    , 2012
  6. 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
  7. 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
  8. 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
  9. Fasan, R.; Crook, N. C.; Peters, M. W.; Meinhold, P.; Buelter, T.; Landwehr, M.; Cirino, P. C.; Arnold, F. H.,,

    Improved Product-Per-Glucose Yields in P450-Dependent Propane Biotransformations Using Engineered Escherichia coli. Biotechnology and Bioengineering 2011, 108 (3), 500-510.

    , 2011
  10. 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
  11. 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
  12. 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
  13. Tang SY and Cirino PC,

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

    , 2011
  14. 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
  15. Tang SY and PC Cirino,

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

    , 2010
  16. 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
  17. Akinterinwa, O and PC Cirino,

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

    , 2009
  18. 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
  19. 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
  20. 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
  21. Khankal R, Chin JW, Ghosh D, and PC Cirino,

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

    , 2009
  22. 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
  23. Akinterinwa O, Khankal R, and PC Cirino,

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

    , 2008
  24. Cirino PC and Sun L,

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

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

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

    , 2008
  26. 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
  27. Tang SY, Fazelinia H, and PC Cirino,

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

    , 2008
  28. 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
  29. 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
  30. Fazelinia H, Cirino PC, and CD Maranas,

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

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

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

    , 2006
  32. Cirino PC and FH Arnold,

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

    , 2003
  33. Cirino PC and R Georgescu,

    Screening for thermostability. Methods Mol Biol. 230: 117

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

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

    , 2003
  35. 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
  36. Salazar O*, Cirino PC* (*equal contributions) and FH Arnold,

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

    , 2003
  37. 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
  38. 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
    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
    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
    04/16/2002