Becker Lab

Research Interests

proline metabolism, redox enzymology, redox regulation of proteins and gene expression, substrate channeling in enzymes

Research Overview

The amino acid proline has multifaceted roles including carbon and nitrogen flux, protein synthesis, osmolyte balance, and stress protection. There is growing evidence that proline metabolism can influence cell survival outcomes in microorganisms, plants, and animals. Proline effects diverse signaling pathways by the generation of reactive oxygen species (ROS) due to proline oxidation being coupled to the respiratory electron transport chain and contributing to cellular bioenergetics. Overall proline has become a very important metabolite that is thought to be involved in many cellular processes that impact human health and disease.

The overall goal of our research is to understand the mechanisms of proline metabolic enzymes and how proline metabolism impacts stress response and the intracellular redox environment. All organisms convert proline to glutamate in two enzymatic steps. In the first step, proline is oxidized to ∆¹-pyrroline-5-carboxylate (P5C) by the flavin-dependent enzyme PRODH. P5C is then hydrolyzed nonenzymatically to glutamic semialdehyde (GSA), which is oxidized to glutamate by the NAD dependent enzyme, P5C dehydrogenase (P5CDH). In Gram-negative bacteria, the PRODH and P5CDH domains are fused onto the same polypeptide called the proline utilization A (PutA) protein. Proline biosynthesis from glutamate involves three enzymatic steps.  The initial two steps are catalyzed by g-glutamyl kinase (GK) and g-glutamyl phosphate reductase (GPR). GK generates g-glutamyl phosphate, which is then reduced by GPR to produce GSA.  In bacteria and lower eukaryotes such as yeast, GK and GPR are discrete monofunctional enzymes.  In animals and plants, the GK and GPR domains are fused together into the bifunctional enzyme P5C synthase (P5CS). After GSA cyclizes to P5C, P5C is reduced to proline by P5C reductase (P5CR).

PubMed Articles

Recent Publication List:

Zhang, L. and Becker, D.F. (2015) Connecting Proline Metabolism and Signaling Pathways in Plant Senescence Front Plant Sci 6:552

Sanyal, N.; Arentson, B.W.; Luo, M.; Tanner, J.J., Becker, D.F. (2015) First Evidence for Substrate Channeling Between Proline Catabolic Enzymes: A Validation of Domain Fusion Analysis for Predicting Protein-Protein Interactions J Biol Chem 290(4): 2225-34

Zhang, L.; Alfano, J.R.; Becker, D.F. (2015) Proline Metabolism Increases katG Expression and Oxidative Stress Resitance in Escherichia coli J Bacteriol 197(3): 431-40

Luo, M.; Christgen, S.; Sanyal, N.; Arentson, B.W.; Becker, D.F.; Tanner, J.J. (2014) Evidence that the C-Terminal Domain of a Type B PutA Protein Contributes to Aldehyde Dehydrogenase Activity and Substrate Channeling Biochemistry 53(35): 5661-73

Liang, X.; Dickman, M.B.; Becker, D.F. (2014) Proline Biosynthesis is Required for Endoplasmic Reticulum Stress Tolerance in Saccharomyces cerevisiae J Biol Chem 289(40): 27794-806

Arentson B.W.; Luo, M.; Pemberton T.A.; Tanner, J.J.; Becker, D.F. (2014) Kinetic and Structural Characterization of Tunnel-Perturbing Mutants in Bradyrhizobium japonicum Proline Utilization A Biochemistry 53(31): 5150-61

Singh, H.; Arentson, B.W.; Becker, D.F.; Tanner J.J. (2014) Structures of the PutA Peripheral Membrane Flavoenzyme Reveal a Dynamic Substrate-Channeling Tunnel and the Quinone-Binding Site PNAS 111(9): 3389-94

Pemberton T.A.; Srivastava, D.; Sanyal N.; Henzl, M.T.; Becker, D.F.; Tanner, J.J. (2014) Structural studies of yeast Δ(1)-pyrroline-5-carboxylate dehydrogenase (ALDH4A1): active site flexibility and oligomeric state. Biochemistry 53(8): 1350-9

Moxley, M.A.; Sanyal, N.; Krishnan, N.; Tanner, J.J.; Becker, D.F. (2014) Evidence for hysteretic substrate channeling in the proline dehydrogenase and Δ1-pyrroline-5-carboxylate dehydrogenase coupled reaction of proline utilization A (PutA) J Biol Chem 289(6) 3639-51

News and Alumni

Recent News

• Shelbi Christgen defended her PhD dissertation  (July 21, 2017)
• Joshua Floth Awarded MMoD Fellowship (June 2017)
• Navasonsa Krishnan accepted new position at AbbVie Pharmaceuticals
• Mike Moxely is a new Assistant Professor at U Nebraska-Kearney

Alumni

• Shelbi Christgen (PhD, 2017) Postdoctoral Associate, University of Nebraska-Lincoln (schristgen@huskers.unl.edu)
• Joshua Floth (BS, 2016) Gradaute Student, University of Nebraska-Lincoln (flothjl@gmail.com)
• Julia Zhang (PhD, 2015) Postdoctoral Associate, University of Nebraska-Lincoln (juliazhang87@gmail.com)
• Ben Arentson (PhD, 2013) Quality Manager Poet Biorefining (ben.arentson@gmail.com)
• Nikhilesh Sanyal (PhD, 2013) Scientific Associate at InVentiv Health (nikhilesh1@gmail.com)
  • Recent Article by Nik
• Michael Moxley (PhD, 2012) Assistant Professor, University of Nebraska-Kearney (mmox23@gmail.com)
  • Recent paper by Mike
• Sathish Natarajan (Postdoctoral Associate, 2009-2012) Assistant Professor, Department of Nutrition and Health Sciences, University of Nebraska-Lincoln
  • Recent paper by Sathish
• Ashley Haile (MS, 2008) Nurse, University of Maryland Medical Center (ahaile1@umaryland.edu)
• Navasona Krishnan (PhD, 2008)  Senior Scientist at AbbVie Biopharmaceutical Company (krishnn@cshl.edu)
• Yuzhen Zhou (PhD, 2008) Professor, Huaiyin Normal University (zyz@hytc.edu.cn)
• Weimin Zhang (Postdoctoral Associate, 2004-2007) Manager, Analytical R&D, Impax Laboratories
• Qi Cheng (Postdoctoral Associate, 2004-2006)
• Srimevan Wanduragala (Postdoctoral Associate, 2003-2006) Senior Scientist-Analytical Development, Therapure Biopharma
• Vinod Nair (Postdoctoral Associate, 2001-2004) Senior Electrochemist & Supercapacitor Expert, Calgon Carbon Corporation (madhavanorama@gmail.com)
• Weidong Zhu (PhD, 2005) CHI-Lakeside Hospital (wdzhuwd@hotmail.com)
• Berevan Baban (MS, 2003) Senior Research Tech, Washington University-St. Louis (bbaban@biochem.wustl.edu)
  • Recent paper from Berevan
• Padmanetra Bellur (MS, 2003) Biotechnology Professional

Past News

• Joshua Floth selected to the ASBMB Honor Society for Undergraduate Researchers (April, 2016)
• Shelbi Christgen awarded Milton E. Mohr Biotechnology Fellowship (May, 2015)
• Joshua Floth awarded  Dr. Benjamin M. Sahagian Scholarship (May, 2015)
• Shelbi Christgen awarded a MMoD Fellowship from the NIH T32 Program at UNL (2014-present)

2024 MMOD Symposium

Sagar Patel, Gunjan Purohit, Oseeyi Daudu, Tyrell Rossman, Dr. Becker, Norhan Fawaz