Senior Scientist

Yubing Li

Education and work

• BS in Microbiology. Nankai University, Tianjin, China (1997)
• MS in Microbiology. Nankai university, Tianjin, China (2000)
• PhD in Plant Molecular and Cell Biology. The Chinese University of Hong Kong, Hong Kong, China (2004)
• Postgraduate researcher. University of California, Riverside, CA (2006)
• Postdoctoral research associate. The Salk institute, San Diego, CA (2012)
• Senior research biologist. University of Florida, Gainesville, FL (2017)
• Senior scientist. The Foundation for Applied Molecular Evolution, Alachua, FL (2018-current)

Research summary

My research covers three main areas: 1) developing synthetic cells that could operate Artificially Expanded Genetic Information System (AEGIS) in vivo through synthetic biology and cell engineering; 2) developing novel biopharmaceuticals using AEGIS nucleosides and nucleotides through in vitro evolution and enzymatic reactions; 3) study endosymbiosis and eukaryotic cell evolution through experimental paleogenetic strategy and chloroplast protein transport systems.

Current projects include:

• Engineer a biosynthetic pathway to synthesize AEGIS nucleoside triphosphates in E.coli or other cell systems supporting ATGCKX 6-letter DNA replication in vivo.
• Synthesize alpha-32P labeled AEGIS nucleoside triphosphates through coupled enzymatic reactions and apply them in various in vitro or in vivo assay.
• Study and engineer DNA polymerases and kinases to support and detect ATGCKX 6-letter DNA replication in vivo and in vitro.
• Develop molecular tools for biomedical applications through in-vitro evolution and characterization of aptamers from nucleic acid libraries containing modified AEGIS nucleotides.
• Resurrect chloroplast ancestral proteins through phylogenetic studies and test their ability for translocation into chloroplasts under fold and unfold status to understand the early steps of endosymbiosis and the transition from prokaryotic cells to eukaryotes.

Recent Publications

Metabolic reconstructions identify plant 3-methylglutaconyl-CoA hydratase that is crucial for branched-chain amino acid catabolism in mitochondria
Latimer S., Li Y., Nguyen T.TH., Soubeyrand E., Fatihi A., Elowsky C.G., Block A., Pichersky E., Basset G.J.
Plant J. (2018) 95 (2), 358-370. doi: 10.1111/tpj.13955
<Abstract>

The proteinogenic branched-chain amino acids (BCAAs) leucine, isoleucine and valine are essential nutrients for mammals. In plants, BCAAs double as alternative energy sources when carbohydrates become limiting, the catabolism of BCAAs providing electrons to the respiratory chain and intermediates to the tricarboxylic acid cycle. Yet, the actual architecture of the degradation pathways of BCAAs is not well understood. In this study, gene network modeling in Arabidopsis and rice, and plant-prokaryote comparative genomics detected candidates for 3-methylglutaconyl-CoA hydratase (4.2.1.18), one of the missing plant enzymes of leucine catabolism. Alignments of these protein candidates sampled from various spermatophytes revealed non-homologous N-terminal extensions that are lacking in their bacterial counterparts, and green fluorescent protein-fusion experiments demonstrated that the Arabidopsis protein, product of gene At4g16800, is targeted to mitochondria. Recombinant At4g16800 catalyzed the dehydration of 3-hydroxymethylglutaryl-CoA into 3-methylglutaconyl-CoA, and displayed kinetic features similar to those of its prokaryotic homolog. When at4g16800 knockout plants were subjected to dark-induced carbon starvation, their rosette leaves displayed accelerated senescence as compared with control plants, and this phenotype was paralleled by a marked increase in the accumulation of free and total leucine, isoleucine and valine. The seeds of the at4g16800 mutant showed a similar accumulation of free BCAAs. These data suggest that 3-methylglutaconyl-CoA hydratase is not solely involved in the degradation of leucine, but is also a significant contributor to that of isoleucine and valine. Furthermore, evidence is shown that unlike the situation observed in Trypanosomatidae, leucine catabolism does not contribute to the formation of the terpenoid precursor mevalonate.

Identification of Putative Substrates of SEC2, a Chloroplast Inner Envelope Translocase
Li Y., Martin J.R., Aldama G.A., Fernadez D.E. and Cline K.
Plant Physiol, Oxford (2017) 173(4): 2121-2137. doi: 10.1104/pp.17.00012.
<Abstract>

Most chloroplast proteins are synthesized in the cytosol and imported into chloroplasts. Many imported proteins are further targeted to the thylakoid membrane and lumen by the SEC1, TAT, or SRP/ALB3 translocases. Others are targeted to the inner chloroplast envelope membrane by undescribed translocases. Recently, a second SEC system (SEC2) consisting of SCY2, SECE2, and SECA2 was found in the chloroplast envelope. Null mutants of SCY2 in Arabidopsis (Arabidopsis thaliana) exhibit a severe embryo-lethal phenotype. To investigate the function of the SEC2 system in plants, we used inducible RNA interference to knock down SCY2 in Arabidopsis. Seedlings cultured with inducer were chlorotic with aberrant chloroplasts and undeveloped thylakoids, indicating an essential role for SCY2 in chloroplast biogenesis beyond embryo development. In SCY2 down-regulated seedlings, several thylakoid membrane proteins, including SCY1, ALB3, and TATC, and inner envelope membrane proteins, including TIC40, TIC110, and FTSH12, were reduced substantially, suggesting that they may be SEC2 substrates. Additional insight was achieved by the in vitro reconstitution of protein integration into chloroplast membranes. The results show that SCY1 and ALB3 target directly to the thylakoid membrane and are likely independent of SEC2. FTSH12 was integrated into the envelope membrane in a coupled import-integration reaction that was impaired by the SECA inhibitor sodium azide. The stromal intermediate of TIC40 integrated into the envelope in a reaction that was largely inhibited when antibodies against epitope-tagged SCY2 or SECE2 were applied. These data demonstrate that the SEC2 translocase likely integrates a subset of inner envelope membrane proteins, such as FTSH12 and TIC40.

A new class of cyclin dependent kinase in Chlamydomonas is required for coupling cell size to cell division
Li Y., Liu D, López-Paz C., Olson B.J., Umen J.G.
eLife, Howard Hughes Medical Institute, Max Planck Society, and Wellcome Trust (2016) 25; 5: e10767. doi: 10.7554/eLife.10767
<Abstract>

Proliferating cells actively control their size by mechanisms that are poorly understood. The unicellular green alga Chlamydomonas reinhardtii divides by multiple fission, wherein a ‘counting’ mechanism couples mother cell-size to cell division number allowing production of uniform-sized daughters. We identified a sizer protein, CDKG1, that acts through the retinoblastoma (RB) tumor suppressor pathway as a D-cyclin-dependent RB kinase to regulate mitotic counting. Loss of CDKG1 leads to fewer mitotic divisions and large daughters, while mis-expression of CDKG1 causes supernumerous mitotic divisions and small daughters. The concentration of nuclear-localized CDKG1 in pre-mitotic cells is set by mother cell size, and its progressive dilution and degradation with each round of cell division may provide a link between mother cell-size and mitotic division number. Cell-size-dependent accumulation of limiting cell cycle regulators such as CDKG1 is a potentially general mechanism for size control.

The Sec2 translocase of the chloroplast inner envelope contains a unique and dedicated SECE2 component
Li Y., Singhal R., Taylor W. Isaiah., McMinn H.P., Chua X.Y., Cline K., and Fernandez D. E.
Plant J. (2015) 84: 647-658, DOI: 10.1111/tpj.13028
<Abstract>

Biogenesis of chloroplasts involves a series of protein trafficking events. Nuclear-encoded proteins are imported into the organelle, and then trafficked to various chloroplast locations by systems that are directly homologous to bacterial systems. Although the thylakoid-based systems have been studied extensively, much less is known about the systems that reside and function in the inner envelope membrane. One such system, the Sec2 system, is homologous to both the thylakoid-based Sec1 system and bacterial Sec systems, and may mediate both integration and translocation across the inner envelope. At a minimum, this system is expected to include three components, but only two, SCY2 and SECA2, have been identified in Arabidopsis. Bioinformatics and protein modeling were used to identify the protein encoded by At4g38490 as a candidate for the missing component (SECE2). Cellular localization, biochemistry, protein interaction assays in yeast, and co-immunoprecipitation experiments were used to establish that this protein is an integral membrane protein of the inner envelope, and specifically interacts with the SCY2 component in vivo. Sequence analyses indicated that SECE2 proteins are found in a variety of plants, and differ from the thylakoid SECE1 proteins in a stroma-exposed helical domain, which may contribute to their specificity. Finally, a genetic analysis indicated that SECE2 plays an essential role in plant growth and development.

The maize tapetum employs diverse mechanisms to synthesize and store proteins and flavonoids and transfer them to the pollen surface
Li Y., Suen D.F., Huang C.Y., Kung, S.Y. and Huang A.H.C.
Plant Physiol, Oxford (2012) 158: 1548-1561, DOI: 10.1104/pp.111.189241
<Abstract>

In anthers, the tapetum synthesizes and stores proteins and flavonoids, which will be transferred to the surface of adjacent microspores. The mechanism of synthesis, storage, and transfer of these pollen-coat materials in maize (Zea mays) differs completely from that reported in Arabidopsis (Arabidopsis thaliana), which stores major pollen-coat materials in tapetosomes and elaioplasts. On maize pollen, three proteins, glucanase, xylanase, and a novel protease, Zea mays pollen coat protease (ZmPCP), are predominant. During anther development, glucanase and xylanase transcripts appeared at a mid developmental stage, whereas protease transcript emerged at a late developmental stage. Protease and xylanase transcripts were present only in the anther tapetum of the plant, whereas glucanase transcript was distributed ubiquitously. ZmPCP belongs to the cysteine protease family but has no closely related paralogs. Its nascent polypeptide has a putative amino-terminal endoplasmic reticulum (ER)-targeting peptide and a propeptide. All three proteins were synthesized in the tapetum and were present on mature pollen after tapetum death. Electron microscopy of tapetum cells of mid to late developmental stages revealed small vacuoles distributed throughout the cytoplasm and numerous secretory vesicles concentrated near the locular side. Immunofluorescence microscopy and subcellular fractionation localized glucanase in ER-derived vesicles in the cytoplasm and the wall facing the locule, xylanase in the cytosol, protease in vacuoles, and flavonoids in subdomains of ER rather than in vacuoles. The nonoverlapping subcellular locations of the three proteins and flavonoids indicate distinct modes of their storage in tapetum cells and transfer to the pollen surface, which in turn reflect their respective functions in tapetum cells or the pollen surface.

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