James K. McCarthy, PhD

Staff Scientist

James K. “Flip” McCarthy 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 postdoctoral 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 PhD 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”.

Publications

Nature communications. 2019-10-07; 10.1: 4552.
Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom
Smith SR, Dupont CL, McCarthy JK, Broddrick JT, Oborník M, Horák A, Füssy Z, Cihlář J, Kleessen S, Zheng H, McCrow JP, Hixson KK, Araújo WL, Nunes-Nesi A, Fernie A, Nikoloski Z, Palsson BO, Allen AE
PMID: 31591397
Scientific reports. 2018-03-19; 8.1: 4834.
Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms
Rastogi A, Maheswari U, Dorrell RG, Vieira FRJ, Maumus F, Kustka A, McCarthy J, Allen AE, Kersey P, Bowler C, Tirichine L
PMID: 29556065
The Plant cell. 2017-08-01; 29.8: 2047-2070.
Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom
McCarthy JK, McCarthy JK, Smith SR, McCrow JP, Tan M, Zheng H, Beeri K, Roth RA, Roth R, Lichtle C, Lichtle C, Goodenough U, Bowler C, Bowler CP, Dupont CL, Dupont CL, Allen AE
PMID: 28765511
Genome biology. 2015-05-20; 16.102.
An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
Veluchamy A, Rastogi A, Lin X, Lombard B, Murik O, Thomas Y, Dingli F, Rivarola M, Ott S, Liu X, Sun Y, Rabinowicz PD, McCarthy J, Allen AE, Loew D, Bowler C, Tirichine L
PMID: 25990474
Plant biotechnology journal. 2015-05-01; 13.4: 460-70.
Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis
Weyman PD, Beeri K, Lefebvre SC, Rivera J, McCarthy JK, Heuberger AL, Peers G, Allen AE, Dupont CL
PMID: 25302562
Applied and environmental microbiology. 2013-01-01; 79.1: 357-66.
Elimination of manganese(II,III) oxidation in Pseudomonas putida GB-1 by a double knockout of two putative multicopper oxidase genes
Geszvain K, McCarthy JK, Tebo BM
PMID: 23124227
Applied and environmental microbiology. 2008-05-01; 74.9: 2646-58.
Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1
Dick GJ, Podell S, Johnson HA, Rivera-Espinoza Y, Bernier-Latmani R, McCarthy JK, Torpey JW, Clement BG, Gaasterland T, Tebo BM
PMID: 18344346
Trends in microbiology. 2005-09-01; 13.9: 421-8.
Geomicrobiology of manganese(II) oxidation
Tebo BM, Johnson HA, McCarthy JK, Templeton AS
PMID: 16054815
The Journal of biological chemistry. 2004-03-19; 279.12: 11495-502.
Improved catalytic efficiency and active site modification of 1,4-beta-D-glucan glucohydrolase A from Thermotoga neapolitana by directed evolution
McCarthy JK, Uzelac A, Davis DF, Eveleigh DE
PMID: 14660638

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”.