James Coker
James Coker is the Director of the Center for Biotechnology Education, which is a part of the Advanced Academic Programas in the Krieger School of Arts and Sciences at Johns Hopkins.
As a Professor and Scientist, James studies life in Earth’s extreme environments and harnesses the unique adaptations of the microorganisms living there for use in biotechnology applications. Using biochemical and genomics approaches, he has discovered several new enzymes and a novel genome-wide system of gene regulation. His research also has helped catalog the limits of life and thereby where it is possible for it to exist in the Universe.
As an Academic Administrator, James has worked to improve STEM education by working with the Center for the Integration of Research, Teaching, and Learning as well as UTeach to train the university faculty and secondary education teachers of tomorrow. He has also long been an advocate of increasing access to education for adult and military students as well as career changers and underserved populations. One example of this was the development of the first Micromasters in Bioinformatics, which was offered on the edX platform and acted as a cost cutting bridge to help bring more students into graduate education. In its three year history, the Micromasters had over 75,000 enrollments with students from 174 different countries. Another example is the introduction of adaptive learning to 100/200-level high enrollment classes, which has led to statistically significant increases in both student success and retention.
In addition to his roles as an Academic, Administrator, and Scientist, James has played an active role in shared governance at the University and State-level. He was elected by his peers to represent them on UMGC’s Academic Advisory Board (i.e. Faculty Senate) where he served in the Executive Committee as Secretary and Vice Chair. He was selected by the UMUC President to serve on the Faculty Advisory Council at the Maryland Higher Education Commission where he was elected (voted by other members of the Council) to serve as Secretary, Vice Chair, and Chair.
James earned two Bachelor of Science degrees in Zoology and Microbiology and Molecular Genetics, as well as a Minor in Philosophy, from Oklahoma State University and received his Ph.D. in Biochemistry, Molecular Biology, and Microbiology from The Pennsylvania State University.
As a Professor and Scientist, James studies life in Earth’s extreme environments and harnesses the unique adaptations of the microorganisms living there for use in biotechnology applications. Using biochemical and genomics approaches, he has discovered several new enzymes and a novel genome-wide system of gene regulation. His research also has helped catalog the limits of life and thereby where it is possible for it to exist in the Universe.
As an Academic Administrator, James has worked to improve STEM education by working with the Center for the Integration of Research, Teaching, and Learning as well as UTeach to train the university faculty and secondary education teachers of tomorrow. He has also long been an advocate of increasing access to education for adult and military students as well as career changers and underserved populations. One example of this was the development of the first Micromasters in Bioinformatics, which was offered on the edX platform and acted as a cost cutting bridge to help bring more students into graduate education. In its three year history, the Micromasters had over 75,000 enrollments with students from 174 different countries. Another example is the introduction of adaptive learning to 100/200-level high enrollment classes, which has led to statistically significant increases in both student success and retention.
In addition to his roles as an Academic, Administrator, and Scientist, James has played an active role in shared governance at the University and State-level. He was elected by his peers to represent them on UMGC’s Academic Advisory Board (i.e. Faculty Senate) where he served in the Executive Committee as Secretary and Vice Chair. He was selected by the UMUC President to serve on the Faculty Advisory Council at the Maryland Higher Education Commission where he was elected (voted by other members of the Council) to serve as Secretary, Vice Chair, and Chair.
James earned two Bachelor of Science degrees in Zoology and Microbiology and Molecular Genetics, as well as a Minor in Philosophy, from Oklahoma State University and received his Ph.D. in Biochemistry, Molecular Biology, and Microbiology from The Pennsylvania State University.
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Papers by James Coker
In this dissertation, I present an analysis of the cold-active beta-galactosidase (BgaS) from the Arthrobacter sp. SB. A study of the primary sequence and modeled structure of BgaS showed that many of the proposed adaptations for optimal activity in the cold did not hold true for this enzyme. Consequently, I decided to alter the BgaS enzyme to determine the contributions of specific amino acids to activity and stability at low temperatures.
I first examined the area of BgaS that aligned with the domain five mobile loop of the LacZ beta-galactosidase of Escherichia coli. In LacZ this area (residues 794-803) aids the binding of substrate and alterations at residue 794 increased the catalytic efficiency of the enzyme with lactose. However, when similar mutations were made in bgaS, they caused either a complete loss or a decrease of activity showing that although this area is also important for BgaS function the alterations affect the enzymes differently.
To further explore the low temperature activity of BgaS, I screened for second site revertants of a null mutant resulting from a G803D change. Restoration of activity was accomplished with the addition of only two mutations (E229D and V405A). Separation of these two mutations into a wild type background yielded an enzyme with a three fold increase in catalytic efficiency with little effect on the thermostability. This shows that small and subtle changes to the enzyme can further increase the activity at low temperatures.
I also explored the thermostability of BgaS through directed mutagenesis and directed evolution studies. The rational mutagenesis targeted the C-terminal portion of BgaS, an area in LacZ known to affect thermostability. From this study, I discovered that a single cysteine to glycine or cysteine to serine mutation resulted in an increase in thermal optimum for BgaS and in another closely related enzyme. The directed evolution study primarily targeted the active site in an attempt to create a more active version of BgaS. One mutant obtained from this screen, with a single alteration in amino acid sequence, created an enzyme with more activity and a 3.3 fold increase in the time it remained active at 30C, compared to BgaS.
Through the combination of mutational analysis and biochemical characterization, I have shown that the introduction of a limited number of amino acid changes are sufficient to alter the activity and/or thermal properties of an enzyme whereas previous studies have suggested that multiple alterations would be required. I have also increased the thermal optimum of three closely related enzymes by altering one amino acid. Considering the large size of the beta-galactosidase subunit, the finding that one change in the C-terminal 25 residues has any effect on the enzyme, not to mention an up to 20C increase in temperature optimum, is quite interesting. Taken as a whole, this work illustrates that small, unpredicted changes in the amino acid sequence of even large enzymes can have dramatic effects on their thermostability and/or activity.
halophilic Archaea. This paper presents initial results for two mesophiles, a methanogen, Methanosarcina acetivorans, and a halophile, Halobacterium sp. NRC-1, and for two Antarctic cold adapted Archaea, a methanogen, Methanococcoides burtonii, and a halophile, Halorubrum lacusprofundi. Neither mesophile is active at temperatures below 5C, but both cold-adapted microorganisms show significant growth at sub-zero temperatures (-2C and -1C, respectively), extending previous low temperature limits for both species by 4–5C. At low temperatures, both H. lacusprofundi and
M. burtonii form multicellular aggregates, which appear to be embedded in extracellular polymeric substances. This is the first detection of this phenomenon in Antarctic species of Archaea at cold temperatures. The low-temperature limits for both psychrophilic species fall within the temperature
range experienced on present-day Mars and could permit survival and growth, particularly in subsurface environments. We also discuss the results of our experiments in the context of known exoplanet systems, several of which include planets that intersect the Habitable Zone. In most cases, those planets
follow orbits with significant eccentricity, leading to substantial temperature excursions. However, a handful of the known gas giant exoplanets could potentially harbour habitable terrestrial moons.
In this dissertation, I present an analysis of the cold-active beta-galactosidase (BgaS) from the Arthrobacter sp. SB. A study of the primary sequence and modeled structure of BgaS showed that many of the proposed adaptations for optimal activity in the cold did not hold true for this enzyme. Consequently, I decided to alter the BgaS enzyme to determine the contributions of specific amino acids to activity and stability at low temperatures.
I first examined the area of BgaS that aligned with the domain five mobile loop of the LacZ beta-galactosidase of Escherichia coli. In LacZ this area (residues 794-803) aids the binding of substrate and alterations at residue 794 increased the catalytic efficiency of the enzyme with lactose. However, when similar mutations were made in bgaS, they caused either a complete loss or a decrease of activity showing that although this area is also important for BgaS function the alterations affect the enzymes differently.
To further explore the low temperature activity of BgaS, I screened for second site revertants of a null mutant resulting from a G803D change. Restoration of activity was accomplished with the addition of only two mutations (E229D and V405A). Separation of these two mutations into a wild type background yielded an enzyme with a three fold increase in catalytic efficiency with little effect on the thermostability. This shows that small and subtle changes to the enzyme can further increase the activity at low temperatures.
I also explored the thermostability of BgaS through directed mutagenesis and directed evolution studies. The rational mutagenesis targeted the C-terminal portion of BgaS, an area in LacZ known to affect thermostability. From this study, I discovered that a single cysteine to glycine or cysteine to serine mutation resulted in an increase in thermal optimum for BgaS and in another closely related enzyme. The directed evolution study primarily targeted the active site in an attempt to create a more active version of BgaS. One mutant obtained from this screen, with a single alteration in amino acid sequence, created an enzyme with more activity and a 3.3 fold increase in the time it remained active at 30C, compared to BgaS.
Through the combination of mutational analysis and biochemical characterization, I have shown that the introduction of a limited number of amino acid changes are sufficient to alter the activity and/or thermal properties of an enzyme whereas previous studies have suggested that multiple alterations would be required. I have also increased the thermal optimum of three closely related enzymes by altering one amino acid. Considering the large size of the beta-galactosidase subunit, the finding that one change in the C-terminal 25 residues has any effect on the enzyme, not to mention an up to 20C increase in temperature optimum, is quite interesting. Taken as a whole, this work illustrates that small, unpredicted changes in the amino acid sequence of even large enzymes can have dramatic effects on their thermostability and/or activity.
halophilic Archaea. This paper presents initial results for two mesophiles, a methanogen, Methanosarcina acetivorans, and a halophile, Halobacterium sp. NRC-1, and for two Antarctic cold adapted Archaea, a methanogen, Methanococcoides burtonii, and a halophile, Halorubrum lacusprofundi. Neither mesophile is active at temperatures below 5C, but both cold-adapted microorganisms show significant growth at sub-zero temperatures (-2C and -1C, respectively), extending previous low temperature limits for both species by 4–5C. At low temperatures, both H. lacusprofundi and
M. burtonii form multicellular aggregates, which appear to be embedded in extracellular polymeric substances. This is the first detection of this phenomenon in Antarctic species of Archaea at cold temperatures. The low-temperature limits for both psychrophilic species fall within the temperature
range experienced on present-day Mars and could permit survival and growth, particularly in subsurface environments. We also discuss the results of our experiments in the context of known exoplanet systems, several of which include planets that intersect the Habitable Zone. In most cases, those planets
follow orbits with significant eccentricity, leading to substantial temperature excursions. However, a handful of the known gas giant exoplanets could potentially harbour habitable terrestrial moons.