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David Stern
 &emdash;  Professor, President

David Stern
Office/Lab: 301/213
Affiliations:
  • Section of Plant Biology
  • School of Integrative Plant Science
  • Cornell University
Graduate Fields: Plant Biology; Genetics & Development; Biochemistry, Cell & Molecular Biology
Research Areas:

Publications

  • Arabidopsis Chloroplast Mini-Ribonuclease III Participates in rRNA Maturation and Intron Recycling 2015

    Hotto, A.M., Castandet, B., Gilet, L., Higdon, A., Condon, C., and Stern, D.B.
    The Plant Cell tpc.114.134452
    Full text...
  • A protein with an inactive pterin-4a-carbinolamine dehydratase domain is required for Rubisco biogenesis in plants 2014

    Feiz, L., Williams-Carrier, R., Belcher, S., Montano, M., Barkan, A, and Stern, D.B.
    Plant Journal 80,  862-869
    Full text...
  • RNA processing and decay in plastids 2013

    Germain, A., Hotto, A.M., Barkan, A., and Stern, D.B.
    Wiley Interdisciplinary Reviews: RNA 4,  295-316
    Full text...
  • RNase J participates in a pentatricopeptide repeat protein-mediated 5′ end maturation of chloroplast mRNAs. 2013

    Luro, S., Germain, A., Sharwood, R.E., and Stern, D.B.
    Nucleic Acids Research 41,  9141-9151
    Full text...
  • A molecular contribution to the assessment of the Tricholoma equestre species complex 2013

    Moukha, S., Ferandon, C., Beroard, E., Guinberteau, J., Castandet, B., Callac, P., Creppy, E., and Barroso, G.
    Fungal Biology 117,  145-155
    Full text...
  • Arabidopsis chloroplast quantitative editotype 2013

    Ruwe, H., Castandet, B., Schmitz-Linneweber, C., and Stern, D.B.
    FEBS Lett. 587,  1429-1433
    Full text...
  • The Plant Science Decadal Vision: Response to the Martin Commentary 2013

    Stern, D., and MacKenzie, S.
    Plant Cell 25,  4775-4776
    Full text...
  • Ribulose-1,5-bis-phosphate carboxylase/oxygenase accumulation factor1 is required for holoenzyme assembly in maize 2012

    Feiz, L., Williams-Carrier, R., Wostrikoff, K., Belcher, S., Barkan, A., and Stern, D.B.
    Plant Cell 24,  3435-3446
    Full text...
  • Ribonuclease II preserves chloroplast RNA homeostasis by increasing mRNA decay rates, and cooperates with polynucleotide phosphorylase in 3′ end maturation 2012

    Germain, A., Kim, S.H., Gutierrez, R., and Stern, D.B.
    Plant J. 72,  960-971
    Full text...
  • Plastid non-coding RNAs: emerging candidates for gene regulation 2012

    Hotto , A.M., Germain, A., and Stern, D.B.
    Trends Plant Sci. 17,  737-744
    Full text...
  • Ectopic expression of Rubisco subunits in maize mesophyll cells does not overcome barriers to cell type-specific accumulation. 2012

    Wostrikoff, K., Clark, A., Sato, S., Clemente, T., and Stern, D.
    Plant Physiology 160,  419-432
    Full text...
  • Overaccumulation of the chloroplast antisense RNA AS5 is correlated with decreased abundance of 5S rRNA in vivo and inefficient 5S rRNA maturation in vitro. 2011

    Sharwood, R.E., Hotto, A.M., Bollenbach, T.J., and Stern, D.B.
    RNA 17,  230-243
    Full text...
  • Chloroplast RNase J compensates for inefficient transcription termination by removal of antisense RNA 2011

    Sharwood, R.E., Halpert, M., Luro, S., Schuster, G., and Stern, D.B.
    RNA 17,  2165-2176
    Full text...
  • Unexpected diversity of chloroplast noncoding RNAs as revealed by deep sequencing of the Arabidopsis transcriptome G3 2011

    Hotto, A.M., Schmitz, R.J., Fei, Z., Ecker, J.E., and Stern, D.B.
    G3 (Bethesda) 1(7),  559–570
    Full text...
  • Mutational analysis of Arabidopsis chloroplast polynucleotide phosphorylase reveals roles for both RNase PH core domains in polyadenylation, RNA 3′-end maturation and intron degradation 2011

    Germain, A., Herlich, S., Larom, S., Kim, S.H., Schuster, G., and Stern, D.B.
    Plant J. 67,  381-394
    Full text...
  • Differential replication of two chloroplast genome forms in heteroplasmic Chlamydomonas reinhardtii gametes contributes to alternative inheritance patterns. 2010

    Nishimura, Y., and Stern, D.B.
    Genetics 185,  1167-1181
    Full text...
  • MRL1, a Conserved Pentatricopeptide Repeat Protein, Is Required for Stabilization of rbcL mRNA in Chlamydomonas and Arabidopsis 2010

    Johnson, X., Wostrikoff, K., Finazzi, G., Kuras, R., Schwarz, C., Bujaldon, S., Nickelsen, J., Stern, D.B., Wollman, F.A., and Vallon, O.
    Plant Cell 22,  234-248
    Full text...
  • Overexpression of a natural chloroplast-encoded antisense RNA in tobacco destabilizes 5S rRNA and retards plant growth 2010

    Hotto, A.M., Huston, Z.E., and Stern, D.B.
    , 10, 213. 10,  213
    Full text...
  • Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae) 2010

    Alverson, A.J., Wei, X.X., Rice, D.W., Stern, D.B., Barry, K., and Palmer, J.D.
    Molecular Biology and Evolution 27,  1436-1448
    Full text...
  • Transgenic maize lines with cell-type specific expression of fluorescent proteins in plastids 2010

    Sattarzadeh, A., Fuller, J., Moguel, S., Wostrikoff, K., Sato, S., Covshoff, S., Clemente, T., Hanson, M., and Stern, D.B.
    Plant Biotechnology Journal 8,  112-125
    Full text...
  • Developmental and cell type characterization of bundle sheath and mesophyll chloroplast transcript abundance in maize 2010

    Sharpe, R.M., Mahajan, A., Takacs, E.M., Stern, D.B,. and Cahoon, A.B.
    Curr. Genet. 57(2),  89-102
    Full text...
  • Chloroplast RNA metabolism 2010

    Stern, D.B., Goldschmidt-Clermont, M., and Hanson, M.R.
    Annu. Rev. Plant Biol. 61,  125-155
    Full text...
  • Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize 2010

    Williams-Carrier, R., Stiffler, N., Belcher, S., Kroeger, T., Stern, D.B., Monde, R.A., Coalter, R., and Barkan, A.
    Plant J. 6,  167-177
    Full text...
  • The RNA-binding proteins CSP41a and CSP41b may regulate transcription and translation of chloroplast-encoded RNAs in Arabidopsis 2009

    Bollenbach, T.J., Sharwood, R.E., Gutierrez, R., Lerbs-Mache, S., and Stern, D.B.
    Plant Molecular Biology 69,  541-552
    Full text...
  • Mating and tetrad separation of Chlamydomonas reinhardtii for genetic analysis 2009

    Jiang, X., and Stern, D.
    J. Vis. Exp. 30,  1274
    Full text...
  • Mitochondria and Chloroplasts 2009

    Newton, K.J., Stern, D.B., and Gabay-Laughnan, S.
    In Handbook of Maize (Bennetzen, J.L. and Hake, S.C. eds),  0: Springer
    Full text...
  • Abnormal physiological and molecular mutant phenotypes link chloroplast polynucleotide phosphorylase to the phosphorus deprivation response in Arabidopsis 2009

    Marchive, C., Yehudai-Resheff, S., Germain, A., Fei, Z.J., Jiang, X.S., Judkins, J., Wu, H., Fernie, A.R., Fait, A., and Stern, D.B.
    Plant Physiology 151,  905-924
    Full text...
  • Insect-machine interface based neurocybernetics 2009

    Bozkurt, A., Gilmour, R.F., Sinha, A., Stern, D., and Lal, A.
    IEEE T. Bio-Med. Eng. 56,  1727-1733
    Full text...
  • RNA polyadenylation and decay in mitochondria and chloroplasts 2009

    Schuster, G., and Stern, D.
    Prog. Mol. Biol. Transl. 85,  393-422
    Full text...
  • Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase 2009

    Zimmer, S.L., Schein, A., Zipor, G., Stern, D.B., and Schuster, G.
    Plant J. 59,  88-99
    Full text...
  • Organellar and metabolic processes 2008

    Stern, D.B.
    In The Chlamydomonas Sourcebook (Stern, D.B. ed.),  Oxford 0: Elsevier
    Full text...
  • Nuclear, chloroplast, and mitochondrial transcript abundance along a maize leaf developmental gradient 2008

    Cahoon, A.B., Takacs, E.M., Sharpe, R.M., and Stern, D.B.
    Plant Mol. Biol. 66,  33-46
    Full text...
  • Genome-based analysis of Chlamydomonas reinhardtii exoribonucleases and poly(A) polymerases predicts unexpected organellar and exosomal features 2008

    Zimmer, S.L., Fei, Z.J., and Stern, D.B.
    Genetics 179,  125-136
    Full text...
  • Integration of chloroplast nucleic acid metabolism into the phosphate deprivation response in Chlamydomonas reinhardtii 2007

    Yehudai-Resheff, S., Zimmer, S.L., Komine, Y., Stern, D.B.
    Plant Cell 19,  1023-1038
    Full text...
  • Rubisco large subunit translation is autoregulated in response to its assembly state in tobacco chloroplasts 2007

    Wostrikoff, K., and Stern, D.B.
    P. Natl. Acad. Sci. U S A 104,  6466-6471
    Full text...
  • The evolution of key animal and plant functions is revealed by analysis of the Chlamydomonas genome. 2007

    Merchant, S. S., Prochnik, S. E., Vallon, O., Harris, E. H., Karpowicz, S. J., Witman, G. B., … Maréchal-Drouard, L.
    Science 318,  245-250
    Full text...
  • Nuclear Suppressors Define Three Factors that Participate in Both 5’ and 3’ End Processing of mRNAs in Chlamydomonas chloroplasts 2006

    Rymarquis, L.A., Higgs, D.C., and Stern, D.B.
    Plant J. 46,  448-461
    Full text...
  • Adaptive Evolution of Chloroplast Genome Structure Inferred Using a Parametric Bootstrap Approach 2006

    Cui, L., Leebens-Mack, J., Wang, L.S., Tang, J., Rymarquis, L., Stern, D.B., and dePamphilis, C.W.
    BMC Evol. Biol. 6,  13
    Full text...
  • Chlamydomonas reinhardtii Encodes a Single sigma70-like Factor Which Likely Functions in Chloroplast Transcription 2006

    Bohne, A.V., Ihrimovitch, V., Weihe, A., and Stern, D.B.
    Curr. Genet. 49,  333-340
    Full text...
  • The sulfur acclimation SAC3 kinase is required for chloroplast transcriptional repression under sulfur limitation inChlamydomonas reinhardtii 2006

    Irihimovitch, V., and Stern, D.B.
    P. Natl. Acad. Sci. U S A 103,  7911-7916
    Full text...
  • Beyond Complementation: Map-Based Cloning in Chlamydomonas reinhardtii 2005

    Rymarquis, L.A., Handley, J.M., Thomas, M., and Stern, D.B.
    Plant Physiology 137,  557-566
    Full text...
  • A Spontaneous tRNA Suppressor of a Mutation in the Chlamydomonas reinhardtii Nuclear MCD1 Gene Required for Stability of the Chloroplast petD mRNA 2005

    Murakami, S., Kuehnle, K., and Stern, D.B.
    Nucleic Acids Research 33,  3372-3380
    Full text...
  • Microarray Analysis Confirms the Specificity of a Chlamydomonas reinhardtii Chloroplast RNA Stability Mutant 2005

    Erickson, B., Stern, D.B., and Higgs, D.C
    Plant Physiology 137,  534-544
    Full text...
  • A Proposed Mechanism for the Inhibitory Effects of Oxidative Stress on Rubisco Assembly and Its Subunit Expression 2005

    Cohen, I., Knopf, J.A., Irihimovitch, V., and Shapira, M.
    Plant Physiology 137,  738-746
    Full text...
  • RNR1, a 3’-5’ Exoribonuclease Belonging to the RNR Superfamily, Catalyzes 3’ Maturation of Chloroplast Ribosomal RNAs in Arabidopsis thaliana 2005

    Bollenbach, T.J., Lange, H., Gutierrez, R., Stern, D.B., and Gagliardi, D.
    Nucleic Acids Research 33,  2751-2763
    Full text...
  • Genetics and Genomics of Chloroplast Biogenesis: Maize as a Model System 2004

    Stern, D.B., Hanson, M.R., and Barkan, A.
    Trends in Plant Science 9,  293-301
    Full text...
  • Antisense Transcript and RNA Processing Alterations Suppress Instability of Polyadenylated mRNA in Chlamydomonas chloroplasts 2004

    Nishimura, Y., Kikis, E.A., Zimmer, S.L., Komine, Y., and Stern, D.B.
    Plant Cell 16,  2849-2869
    Full text...

Intern Projects

The underlying research themes in the Stern laboratory are chloroplast biology, bioenergy and nuclear-cytoplasmic interactions. Within this framework, we study how chloroplast genes and metabolic activities are regulated by the products of nuclear genes, usually acting at the transcriptional or post-transcriptional level. Areas of emphasis include the roles of ribonucleases and RNA-binding proteins and assembly of the carbon-fixing enzyme Rubisco. We are also using molecular and genetic techniques to adjust chloroplast metabolism for the production of useful hydrocarbons.
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Interns

Research Utilization

Chloroplasts are the organelles in which photosynthesis occurs, incorporating atmospheric carbon dioxide into sugars and carbohydrates. Thus, chloroplast function plays a key role in determining crop yield. Chloroplasts also carry out other metabolic functions and mediate responses to environmental stress. It is now possible to alter the chloroplast genome, raising the possibility of modifying stress responses or introducing new metabolic pathways into plants and algae.

The Stern laboratory investigates and manipulates gene expression and protein assembly in the chloroplast. Plant systems in use include green algae, which offer promise for bioenergy production; maize and the related “monocot model organism Setaria viridis; and the widely adopted dicot model Arabidopsis, Over the years, the laboratory has defined many aspects of chloroplast gene regulation, leading to two current projects that may have practical applications.

1)    Biofuel production: In the context of a multidisciplinary consortium, genes from Botryococcus braunii, a slow-growing microalga that produces high levels of triterpene oils, have been re-coded to facilitate efficient gene expression and inserted into the chloroplast of Chlamydomonas reinhardtii, which is much more tractable than Botryococcus, but does not harbor this pathway. The objective is to use a high-throughput genetic screen to obtain a rapidly-growing, high production Chlamydomonas strain that has gained the capacity to produce these oils. An additional goal is to engineer the green alga Chlorella, which is better adapted to scaled-up production,in a similar manner.

2)    Engineering photosynthesis: The laboratory has discovered two previously unknown proteins that are required in maize for the assembly of Rubisco, the enzyme complex that is responsible for fixing carbon during photosynthesis. Rubisco is a key target for improvement via biotechnology, partly because a competing reaction uses oxygen instead of carbon dioxide, and limits the efficiency of carbon fixation. Biotechnology approaches to engineer improved Rubisco have been limited in part by the challenge of assembling altered protein into functional complexes. The newly-discovered proteins may underpin the ability to assemble Rubisco in bacterial or cell-free systems. Furthermore, the assembly proteins themselves offer targets for improvement of plant yield through manipulation of Rubisco abundance in plants.

Collaboration and Consulting Opportunities

  • Chloroplast engineering for biofuel production
  • Assembly of Rubisco to enable enzyme engineering, manipulation of Rubisco abundance in plants

Public NSF

The multi-disciplinary research team will develop microfluidic lab-on-chip devices with capabilities to precisely assay and manipulate parallel samples at single-cell resolution. The devices will enable the integration of multiple experimental parameters on a single user-friendly platform. These devices will then be used to analyze and optimize the growth and hydrocarbon production potential of an engineered recombinant photosynthetic microalgae. The specific test case will be a recombinant, fast growing Chlamydomonas reinhardtii algal strain that will be engineered to express a high-yielding hydrocarbon biosynthetic gene system derived from the slow-growing microalaga, Botryococcus braunii. These specific hydrocarbons produced by these organisms are of particular interest because they can be readily converted into petroleum-equivalent fuels.

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Collaborations and Consulting

In the News

Research Overview

The underlying research themes in the Stern laboratory are chloroplast biology, bioenergy and nuclear-cytoplasmic interactions. Within this framework, we study how chloroplast genes and metabolic activities are regulated by the products of nuclear genes, usually acting at the transcriptional or post-transcriptional level. Areas of emphasis include the roles of ribonucleases and RNA-binding proteins and assembly of the carbon-fixing enzyme Rubisco. We are also using molecular and genetic techniques to adjust chloroplast metabolism for the production of useful hydrocarbons.