Jim Pesavento


School of Science » Biology
SMC Email Address: 
Contact Information: 

Brousseau Hall - 104

Email: jjp6@stmarys-ca.edu

Courses Taught

Recently Taught:

  • Bio 137: Molecular Biology
  • Bio 135: Biochemistry
  • Biology 1: Cell and Molecular Biology and Genetics Laboratory
  • Biology 1: Cell and Molecular Biology and Genetics
  • Jan 140: The Art And Science of Beer


(bold denotes Saint Mary's College undergraduate co-authors)

Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B. How many human proteoforms are there? Nat Chem Biol. 2018;14:206. http://dx.doi.org/10.1038/nchembio.2576.

Khan A, Eikani CK, Khan H, Iavarone AT, Pesavento JJ. Characterization of Chlamydomonas reinhardtii Core Histones by Top-Down Mass Spectrometry Reveals Unique Algae-Specific Variants and Post-Translational Modifications. J Proteome Res. 2018;17(1):23-32. doi: 10.1021/acs.jproteome.7b00780.

Petojevic T*, Pesavento JJ*, Costa A, Liang J, Wang Z, Berger JM, Botchan MR. Cdc45 (cell division cycle protein 45) guards the gate of the Eukaryote Replisome helicase stabilizing leading strand engagement. PNAS. 2015 Jan 20;112(3):E249-58. doi: 10.1073/pnas.1422003112. (* co-first author) 

Costa A, Renault L, Swuec P, Petojevic T, Pesavento J, Ilves I, MacLellan-Gibson K, Fleck RA, Botchan MR, Berger JM. DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome. Elife. 2014 Aug 12:e03273. doi: 10.7554/eLife.03273.


Zheng, Y., John, S., Pesavento, JJ., Schultz-Norton, JR., Schiltz, RL., Baek, S., Nardulli, AM., Hager, GL., Kelleher, NL., Mizzen, CA. Histone H1 phosphorylation is associated with transcription by RNA polymerases I and II. J Cell Biol. 2010. 189:407-15.


Ilves, I., Petojevic, T., Pesavento, JJ., Botchan, MR. Activation of the MCM2-7 Helicase by Association with Cdc45 and GINS Proteins. Mol Cell. 2010. 37: 247-258.


Pesavento, JJ., Bullock, CR., Mizzen, CA., Kelleher, NL. Two Dimensional Liquid Chromatography-Top Down Fourier Transform Mass Spectrometry Enables Extensive Characterization and Quantitation of Human Histone H4 PTMs. J Biol Chem. 2008. 283: 14927-37.


Yang, H., Pesavento, JJ., Starnes T., Cryderman, DE., Wallrath, LL., Kelleher, NL., Mizzen, CA. Preferential Dimethylation of Histone H4-Lys20 by Suv4-20. J Biol Chem. 2008. 283: 12085-92.


Frank, AM., Pesavento, JJ., Mizzen, CA., Kelleher NL., Pevzner, PA. Interpreting Top-Down Mass Spectra Using Spectral Alignment. Anal Chem. 2008. 80: 2499-505.


Pesavento, JJ., Yang, H., Kelleher, NL., Mizzen, CA. Certain and Progressive Methylation of Histone H4 at Lysine 20 During the Cell Cycle.  Mol Cell Bio.  2008.  28: 468-86.


Pesavento, JJ., Streeky, JS., Kelleher, NL, Mizzen, CA. Mild Performic Acid Oxidation Enhances Chromatographic and Top Down Mass Spectrometric Analyses of Histones.  Mol Cell Proteomics. 2007. 6: 1510-26.


Garcia, BA., Pesavento, JJ., Mizzen, CA., Kelleher, NL.  Pervasive Combinatorial Modification of Histone H3 Human Cells. Nat. Methods. 2007.  4: 487-9.


Pesavento, JJ., Mizzen, CA., Kelleher, NL., Quantitative Analysis of Modified Proteins and Positional Isomers by Tandem Mass Spectrometry: Human Histone H4. Anal Chem. 2006. 78: 4271-4280.


Boyne, MT., Pesavento, JJ., Mizzen, CA., Kelleher, NL.,  Precise Characterization of Human Histones in the H2A Gene Family by Top Down Mass Spectometry. J Prot Res. 2006. 2: 248-53


Siuti, N., Roth, MJ., Mizzen, CA., Kelleher, NL., Pesavento, JJ. Gene-Specific Characterization of Human Histone H2B by Electron Capture Dissociation. J Prot Res. 2006. 2: 233-239.


Kumar, S., Choi, WT., Dong, CZ., Madani, N., Tian, S., Liu, D., Wang, Y., Pesavento, J., Wang, J., Fan, X., Yuan, J., Fritzsche, WR., An, J., Sodroski, JG., Richman, DD., Huang, Z. SMM-Chemokines: A Class of Unnatural Synthetic Molecules as Chemical Probes of Chemokine Receptor Biology and Leads for Therapeutic Development. Chem. Biol. 2006. 12: 69-79


Tian, S., Choi, W., Liu, D., Pesavento, J., Wang, Y., An, J., Sodroski, JG., Huang, Z. Distinct Functional Sites for Human Immunodeficiency Virus Type 1 and Stromal Cell-Derived Factor 1a on CXCR4 Transmembrane Helical Domains. J. Virol. 2005. 79: 12667-73.


Pesavento, JJ., Kim, Y., Taylor, GK., Kelleher, NL. Shotgun Annotation of Histone Modifications:  A New Approach for Streamlined Characterization of Proteins by Top Down Mass Spectrometry. J. Am. Chem. Soc. 2004. 11: 3386-7.


Near, TJ., Pesavento, JJ., Cheng, CC. Phylogenetic investigations of Antarctic notothenioid fishes (Perciformes: Notothenioidei) using complete gene sequences of the mitochondrial encoded 16S rRNA. Mol Phylogenet Evol. 2004. 3: 881-91. 


Near, TJ., Pesavento, JJ., Cheng, CC. Mitochondrial DNA, morphology, and the phylogenetic relationships of Antarctic icefishes (Notothenioidei: Channichthyidae). Mol Phylogenet Evol. 2003. 28: 87-98.


Zhou, N., Luo, Z., Luo, J., Fan, X., Cayabyab, M., Hiraoka, M., Liu, D., Han, X.,  Pesavento, JJ., Dong, CZ., Wang, Y., Kaji, H., Sodroski, JG., Huang, Z. Exploring the Stereochemistry of CXCR4-Peptide Recognition and Inhibiting HIV-1 Entry with D-Peptides Derived from Chemokines. J. Biol. Chem. 2002. 277: 17476-17485.



Godbout, JP., Pesavento, JJ., Hartman, ME., Manson, SR. and Freund, GG.  Methylglyoxal Enhances Cisplatin-Induced Cytotoxicity By Activating PKCd.  J. Biol. Chem. 2002. 277: 2554-2561.


Scholarly Interests: 


  • Chromatin; Histone Modifications; Top Down Mass Spectrometry; Biosequestration


The industrialized world currently satisfies its energy needs by relying heavily on combustion of hydrocarbons, resulting in elevated levels of the greenhouse gas carbon dioxide. Over the course of the last 70 years, the atmospheric levels of carbon dioxide have increased by nearly 100 parts-per-million and is widely suspected as the main culprit in the increase of ocean and air temperature. In order to avoid irreversible harm to the planet, scientists have investigated means to generate power from renewable, emissionless sources (e.g., solar, wind, etc.) and also ways to sequester carbon dioxide from sources that generate it (e.g., coal-burning power plants). One such efficient and cost-effective way to sequester carbon dioxide is through the utilization of microalgae. Microalgae are single celled organisms that have the ability to grow photoautotrophically, using carbon dioxide as the sole source of organic carbon. To date, much of the research on algae-based carbon dioxide sequestering has focused on emissions from post-combustion flue gas, which generates up to 15% CO2. Not surprisingly, studies that have investigated microalgal strains for their suitability in CO2 sequestering have mainly focused on CO2 concentrations up to ~20%.

The fermented beverage industry (makers of beer, wine, spirits, etc.) produces, as a byproduct of fermentation, billions of kilograms of carbon dioxide annually, at concentrations of nearly 100% volume-by-volume. This presents many challenges for its successful adoption to microalgae-based CO2 capturing. While there is literature on how microalgae respond to extremely high-CO2 environments, there has yet to be a comprehensive study on long-term growth of microalgae in environments that produce ~100% CO2. To this end, a primary research interest of mine is to investigate whether C. kessleri, a microalgae strain tolerant to high CO2 concentrations, can efficiently capture CO2 emission from yeast fermentation.

At the end of the day, the acclimation of the microalgae C. kessleri to 100% CO2 environments may require adaptation at the genetic and epigenetic level. Long-term "experimental evolution" methods exposing microalgae to new environments have shown that these organisms can readily alter their genomic sequence and regulation of gene expression. In one study, these alterations enabled the microalgae to thrive better in the new environment by reducing the number of photoreceptors, shrinking in size, and downregulating many DNA repair proteins (allowing for the accumulation of more mutations). Surprisingly, there has been little work done on epigenetic changes in microalgae, specifically looking at changes in chromatin organization and modification in response to a dramatic environmental change. Chromatin organization, which, among other things, affects gene expression and genome stability, arises from intimate interactions between DNA and a class of small proteins called histones. Histones may alter DNA structure directly through protein:DNA electrostatic interactions or indirectly by serving as a binding platform for other chromatin-modifying proteins. In either case, the histone proteins carry out their intended functions by presenting a specific set of chemical modifications (e.g., acetylation, methylation, phosphorylation, etc.) located at specific amino acids (e.g. Lysine 9 of histone H3) within the termini of the protein. By presenting a specific set of modifications, there may be a "histone code" governing many genetic functions including turning on/off gene expression, compacting DNA into higher order structures, or even flagging a damaged region of DNA for repair. While the histone code for several epigenetic responses has been investigated heavily in plants (especially Arabidopsis), the histone code, and histone modifications in general, remains to be elucidated in microalgae. My second research interest lies in profiling and characterizing the microalgal histone code using high-resolution intact protein mass spectrometry.