Joseph Chen
( He/Him/His )Field: Cell and Molecular Biology
At SF State Since: 2006
Specialties: Bacterial Genetics and Physiology, Molecular Microbiology: how are subcellular components synthesized and assembled at the appropriate time and place in response to internal cues and environmental conditions?
External Personal Website:
Despite their small size, bacterial cells have well-defined temporal and spatial architecture: various protein components localize to specific subcellular sites to execute precise functions during appropriate developmental stages of the bacterial life cycle. The key question is how information encoded in the genomic blueprint is articulated into a complex, three-dimensional structure that changes over time. Multiple regulatory mechanisms—including transcriptional control, signal transduction, proteolysis, and protein-protein interactions—cooperatively implement the genetic program. Caulobacter crescentus has emerged as a prominent model for elucidating the coordination of these regulatory mechanisms. Insights obtained through studies of C. crescentus are being exploited to gain a deeper understanding of how conserved components can behave differently across species. In particular, we are examining conserved proteins in Sinorhizobium meliloti, which is a symbiont that fixes nitrogen for specific legumes. Such investigation will help reveal how genetic divergence leads to distinct physiologies, adapted for different ecological niches.
There are currently two main research projects in the lab:
- Conserved, localized proteins. In C.crescentus, various regulatory proteins follow defined patterns of subcellular localization that contribute to asymmetric cell morphology: organelles specifically develop at one pole but not the other. These regulatory components are conserved in S. meliloti, a related bacterium that induces nodule formation in plant roots during symbiosis. However, S. meliloti cells are morphologically symmetric compared to C. crescentus. We are examining how these conserved components function in S. meliloti to regulate the assembly of surface organelles and how this regulation affects host-microbe interaction.
- Microbial engineering. We are developing genetic tools to facilitate the study and modification of different bacterial species. For example, we showed that a taurine-regulated promoter can be used to modulate gene expression in various alphaproteobacteria.
- Aranda ML, Diaz M, Mena LG, Ortiz JI, Rivera-Nolan C, Sanchez DC, Sanchez MJ, Upchurch AM, Williams CS, Boorstin SN, Cardoso LM, Dominguez M, Elias S, Lopez EE, Ramirez RE, Romero PJ, Tigress FN, Wilson JA, Winstead R, Cantley JT, Chen JC, Fuse M, Goldman MA, Govindan B, Ingmire P, Knight JD, Pasion SG, Pennings PS, Sehgal RNM, de Vera PT, Kelley L, Schinske JN, Riggs B, Burrus LW, Tanner KD. Student-Authored Scientist Spotlights: Investigating the Impacts of Engaging Undergraduates as Developers of Inclusive Curriculum through a Service-Learning Course. CBE Life Sci Educ. 2021 Dec;20(4):ar55. doi: 10.1187/cbe.21-03-0060. PubMed PMID: 34546103.
- Eng T, Herbert RA, Martinez U, Wang B, Chen JC, Brown JB, Deutschbauer AM, Bissell MJ, Mortimer JC, Mukhopadhyay A. Iron Supplementation Eliminates Antagonistic Interactions Between Root-Associated Bacteria. Front Microbiol. 2020;11:1742. doi: 10.3389/fmicb.2020.01742. eCollection 2020. PubMed PMID: 32793173; PubMed Central PMCID: PMC7387576.
- Herbert RA, Eng T, Martinez U, Wang B, Langley S, Wan K, Pidatala V, Hoffman E, Chen JC, Bissell MJ, Brown JB, Mukhopadhyay A, Mortimer JC. Rhizobacteria Mediate the Phytotoxicity of a Range of Biorefinery-Relevant Compounds. Environ Toxicol Chem. 2019 Sep;38(9):1911-1922. doi: 10.1002/etc.4501. Epub 2019 Jul 26. Review. PubMed PMID: 31107972; PubMed Central PMCID: PMC6711798.
- Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP. Jungle Express is a versatile repressor system for tight transcriptional control. Nat Commun. 2018 Sep 6;9(1):3617. doi: 10.1038/s41467-018-05857-3. PubMed PMID: 30190458; PubMed Central PMCID: PMC6127294.
- Owens MT, Trujillo G, Seidel SB, Harrison CD, Farrar KM, Benton HP, Blair JR, Boyer KE, Breckler JL, Burrus LW, Byrd DT, Caporale N, Carpenter EJ, Chan YM, Chen JC, Chen L, Chen LH, Chu DS, Cochlan WP, Crook RJ, Crow KD, de la Torre JR, Denetclaw WF, Dowdy LM, Franklin D, Fuse M, Goldman MA, Govindan B, Green M, Harris HE, He ZH, Ingalls SB, Ingmire P, Johnson ARB, Knight JD, LeBuhn G, Light TL, Low C, Lund L, Márquez-Magaña LM, Miller-Sims VC, Moffatt CA, Murdock H, Nusse GL, Parker VT, Pasion SG, Patterson R, Pennings PS, Ramirez JC, Ramirez RM, Riggs B, Rohlfs RV, Romeo JM, Rothman BS, Roy SW, Russo-Tait T, Sehgal RNM, Simonin KA, Spicer GS, Stillman JH, Swei A, Timpe LC, Vredenburg VT, Weinstein SL, Zink AG, Kelley LA, Domingo CR, Tanner KD. Collectively Improving Our Teaching: Attempting Biology Department-wide Professional Development in Scientific Teaching. CBE Life Sci Educ. 2018 Spring;17(1). doi: 10.1187/cbe.17-06-0106. PubMed PMID: 29326102; PubMed Central PMCID: PMC6007775.
- Bezryadina AS, Preece DC, Chen JC, Chen Z. Optical disassembly of cellular clusters by tunable 'tug-of-war' tweezers. Light Sci Appl. 2016;5. doi: 10.1038/lsa.2016.158. Epub 2016 Oct 21. PubMed PMID: 27818838; PubMed Central PMCID: PMC5091843.
- Samadi A, Zhang C, Chen J, Reihani SN, Chen Z. Evaluating the toxic effect of an antimicrobial agent on single bacterial cells with optical tweezers. Biomed Opt Express. 2015 Jan 1;6(1):112-7. doi: 10.1364/BOE.6.000112. eCollection 2015 Jan 1. PubMed PMID: 25657879; PubMed Central PMCID: PMC4317123.
- Mostafavi M, Lewis JC, Saini T, Bustamante JA, Gao IT, Tran TT, King SN, Huang Z, Chen JC. Analysis of a taurine-dependent promoter in Sinorhizobium meliloti that offers tight modulation of gene expression. BMC Microbiol. 2014 Nov 25;14:295. doi: 10.1186/s12866-014-0295-2. PubMed PMID: 25420869; PubMed Central PMCID: PMC4254191.
- Zhang P, Hernandez D, Cannan D, Hu Y, Fardad S, Huang S, Chen JC, Christodoulides DN, Chen Z. Trapping and rotating microparticles and bacteria with moiré-based optical propelling beams. Biomed Opt Express. 2012 Aug 1;3(8):1891-7. doi: 10.1364/BOE.3.001891. Epub 2012 Jul 18. PubMed PMID: 22876352; PubMed Central PMCID: PMC3409707.
- Fields AT, Navarrete CS, Zare AZ, Huang Z, Mostafavi M, Lewis JC, Rezaeihaghighi Y, Brezler BJ, Ray S, Rizzacasa AL, Barnett MJ, Long SR, Chen EJ, Chen JC. The conserved polarity factor podJ1 impacts multiple cell envelope-associated functions in Sinorhizobium meliloti. Mol Microbiol. 2012 Jun;84(5):892-920. doi: 10.1111/j.1365-2958.2012.08064.x. Epub 2012 May 4. PubMed PMID: 22553970; PubMed Central PMCID: PMC3359409.
- Curtis PD, Quardokus EM, Lawler ML, Guo X, Klein D, Chen JC, Arnold RJ, Brun YV. The scaffolding and signalling functions of a localization factor impact polar development. Mol Microbiol. 2012 May;84(4):712-35. doi: 10.1111/j.1365-2958.2012.08055.x. Epub 2012 Apr 19. PubMed PMID: 22512778; PubMed Central PMCID: PMC3345042.
- Arellano BH, Ortiz JD, Manzano J, Chen JC. Identification of a dehydrogenase required for lactose metabolism in Caulobacter crescentus. Appl Environ Microbiol. 2010 May;76(9):3004-14. doi: 10.1128/AEM.02085-09. Epub 2010 Feb 26. PubMed PMID: 20190087; PubMed Central PMCID: PMC2863468.
- Chen JC, Stephens C. Bacterial cell cycle: completing the circuit. Curr Biol. 2007 Mar 20;17(6):R203-6. doi: 10.1016/j.cub.2007.01.031. PubMed PMID: 17371757.
- Chen JC, Hottes AK, McAdams HH, McGrath PT, Viollier PH, Shapiro L. Cytokinesis signals truncation of the PodJ polarity factor by a cell cycle-regulated protease. EMBO J. 2006 Jan 25;25(2):377-86. doi: 10.1038/sj.emboj.7600935. Epub 2006 Jan 5. PubMed PMID: 16395329; PubMed Central PMCID: PMC1383518.
- Judd EM, Comolli LR, Chen JC, Downing KH, Moerner WE, McAdams HH. Distinct constrictive processes, separated in time and space, divide caulobacter inner and outer membranes. J Bacteriol. 2005 Oct;187(20):6874-82. doi: 10.1128/JB.187.20.6874-6882.2005. PubMed PMID: 16199556; PubMed Central PMCID: PMC1251605.
- Chen JC, Viollier PH, Shapiro L. A membrane metalloprotease participates in the sequential degradation of a Caulobacter polarity determinant. Mol Microbiol. 2005 Feb;55(4):1085-103. doi: 10.1111/j.1365-2958.2004.04443.x. PubMed PMID: 15686556.
- Chen JC, Minev M, Beckwith J. Analysis of ftsQ mutant alleles in Escherichia coli: complementation, septal localization, and recruitment of downstream cell division proteins. J Bacteriol. 2002 Feb;184(3):695-705. doi: 10.1128/JB.184.3.695-705.2002. PubMed PMID: 11790739; PubMed Central PMCID: PMC139535.
- Chen JC, Beckwith J. FtsQ, FtsL and FtsI require FtsK, but not FtsN, for co-localization with FtsZ during Escherichia coli cell division. Mol Microbiol. 2001 Oct;42(2):395-413. doi: 10.1046/j.1365-2958.2001.02640.x. PubMed PMID: 11703663.
- Boyd D, Weiss DS, Chen JC, Beckwith J. Towards single-copy gene expression systems making gene cloning physiologically relevant: lambda InCh, a simple Escherichia coli plasmid-chromosome shuttle system. J Bacteriol. 2000 Feb;182(3):842-7. doi: 10.1128/JB.182.3.842-847.2000. PubMed PMID: 10633125; PubMed Central PMCID: PMC94354.
- Weiss DS, Chen JC, Ghigo JM, Boyd D, Beckwith J. Localization of FtsI (PBP3) to the septal ring requires its membrane anchor, the Z ring, FtsA, FtsQ, and FtsL. J Bacteriol. 1999 Jan;181(2):508-20. doi: 10.1128/JB.181.2.508-520.1999. PubMed PMID: 9882665; PubMed Central PMCID: PMC93405.
- Ghigo JM, Weiss DS, Chen JC, Yarrow JC, Beckwith J. Localization of FtsL to the Escherichia coli septal ring. Mol Microbiol. 1999 Jan;31(2):725-37. doi: 10.1046/j.1365-2958.1999.01213.x. PubMed PMID: 10027987.
- Chen JC, Weiss DS, Ghigo JM, Beckwith J. Septal localization of FtsQ, an essential cell division protein in Escherichia coli. J Bacteriol. 1999 Jan;181(2):521-30. doi: 10.1128/JB.181.2.521-530.1999. PubMed PMID: 9882666; PubMed Central PMCID: PMC93406.
- Coulson RM, Connor V, Chen JC, Ajioka JW. Differential expression of Leishmania major beta-tubulin genes during the acquisition of promastigote infectivity. Mol Biochem Parasitol. 1996 Nov 25;82(2):227-36. doi: 10.1016/0166-6851(96)02739-9. PubMed PMID: 8946388.