James K. McCarthy, PhD

Staff Scientist



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James K. “Flip” McCarthy, PhD, is a staff scientist in Andrew E. Allen’s lab at the J. Craig Venter Institute. Dr. McCarthy’s long-term research centers on how marine diatoms, specifically the model organism, Phaeodactylum tricornutum, assimilate nitrate under the nitrate replete and depleted conditions encountered in the marine environment. Focusing on the expression of the genes and cognate proteins, involved in the transport, reduction and storage of nitrate, as well as the ultimate integration of nitrate with assimilated carbon, his current research seeks to unravel the mechanisms involved in the regulation of nitrate assimilation. Dr. McCarthy’s recent work produced a nitrate reductase mutant strain of P. tricornutum, described how the loss of function affected the morphology and viability of the cell and pointed to physiological and molecular mechanisms that drive vacuolar storage of nitrate and the possibility of nitrate reductase–vacuolar transport protein complexes.

Prior to joining JCVI, Dr. McCarthy was a post-doctoral fellow at Scripps Institution of Oceanography (UC San Diego) where he made the gene knockout of the first manganese (Mn) oxidase identified in Pseudomonas putida, GB-1, initiated the sequencing of the P. putida, GB-1 genome and helped characterize Mn-oxidation in two Pseudomonads. Dr. McCarthy received his B.A in English from Union College, Schenectady, NY. He then pursued a career as a cameraman, producer and writer for documentary and educational films and videos. Eventually, his keen interest in municipal-scale composting and alternative fuels led him to a Ph.D. in Microbiology and Molecular Genetics from Rutgers University.

Research Priorities

Components of the nitrate interactome in Phaeodactylum tricornutum

  • Cohort of metabolites critical to the cellular response to nitrate flux
  • Localization and activity of dual nitrite reductases and putative vacuolar nitrate transporters
  • Protein-protein interactions/complexes that streamline nitrate assimilation

Distribution of lipids in P. tricornutum wild type vs. knockout cell lines

  • Variation in lipid fractions, between whole cells and organelles: chloroplasts and vacuoles, are mediated by nitrate availability

Laboratory model for “luxury uptake” of nitrate by marine diatoms

  • In the ocean environment, diatoms outcompete other planktonic species in response to nitrate-rich upwelling conditions by taking up and storing nitrate beyond their immediate needs – “luxury uptake”.

Select Publications

Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms.
Scientific reports. 2018-03-19; 8.1: 4834.
PMID: 29556065
Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom.
The Plant cell. 2017-08-01; 29.8: 2047-2070.
PMID: 28765511
An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum.
Genome biology. 2015-05-20; 16.102.
PMID: 25990474
Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis.
Plant biotechnology journal. 2015-05-01; 13.4: 460-70.
PMID: 25302562
Elimination of manganese(II,III) oxidation in Pseudomonas putida GB-1 by a double knockout of two putative multicopper oxidase genes.
Applied and environmental microbiology. 2013-01-01; 79.1: 357-66.
PMID: 23124227
Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1.
Applied and environmental microbiology. 2008-05-01; 74.9: 2646-58.
PMID: 18344346
Geomicrobiology of manganese(II) oxidation.
Trends in microbiology. 2005-09-01; 13.9: 421-8.
PMID: 16054815
Improved catalytic efficiency and active site modification of 1,4-beta-D-glucan glucohydrolase A from Thermotoga neapolitana by directed evolution.
The Journal of biological chemistry. 2004-03-19; 279.12: 11495-502.
PMID: 14660638
Thermostable continuous coupled assay for measuring glucose using glucokinase and glucose-6-phosphate dehydrogenase from the marine hyperthermophile Thermotoga maritima.
Analytical biochemistry. 2003-07-15; 318.2: 196-203.
PMID: 12814622