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  • Gene Transcription as a Limiting Factor in Protein Production and Cell Growth. G3 (Bethesda, Md.) Metzl-Raz, E., Kafri, M., Yaakov, G., Barkai, N. 2020

    Abstract

    Cell growth is driven by the synthesis of proteins, genes, and other cellular components. Defining processes that limit biosynthesis rates is fundamental for understanding the determinants of cell physiology. Here, we analyze the consequences of engineering cells to express extremely high levels of mCherry proteins, as a tool to define limiting processes that fail to adapt upon increasing biosynthetic demands. Protein-burdened cells were transcriptionally and phenotypically similar to mutants of the Mediator, a transcription coactivator complex. However, our binding data suggest that the Mediator was not depleted from endogenous promoters. Burdened cells showed an overall increase in the abundance of the majority of endogenous transcripts, except for highly expressed genes. Our results, supported by mathematical modeling, suggest that wild-type cells transcribe highly expressed genes at the maximal possible rate, as defined by the transcription machinery's physical properties. We discuss the possible cellular benefit of maximal transcription rates to allow a coordinated optimization of cell size and cell growth.

    View details for DOI 10.1534/g3.120.401303

    View details for PubMedID 32694199

  • Uncovering targeting priority to yeast peroxisomes using an in-cell competition assay. Proceedings of the National Academy of Sciences of the United States of America Rosenthal, M., Metzl-Raz, E., Bürgi, J., Yifrach, E., Drwesh, L., Fadel, A., Peleg, Y., Rapaport, D., Wilmanns, M., Barkai, N., Schuldiner, M., Zalckvar, E. 2020

    Abstract

    Approximately half of eukaryotic proteins reside in organelles. To reach their correct destination, such proteins harbor targeting signals recognized by dedicated targeting pathways. It has been shown that differences in targeting signals alter the efficiency in which proteins are recognized and targeted. Since multiple proteins compete for any single pathway, such differences can affect the priority for which a protein is catered. However, to date the entire repertoire of proteins with targeting priority, and the mechanisms underlying it, have not been explored for any pathway. Here we developed a systematic tool to study targeting priority and used the Pex5-mediated targeting to yeast peroxisomes as a model. We titrated Pex5 out by expressing high levels of a Pex5-cargo protein and examined how the localization of each peroxisomal protein is affected. We found that while most known Pex5 cargo proteins were outcompeted, several cargo proteins were not affected, implying that they have high targeting priority. This priority group was dependent on metabolic conditions. We dissected the mechanism of priority for these proteins and suggest that targeting priority is governed by different parameters, including binding affinity of the targeting signal to the cargo factor, the number of binding interfaces to the cargo factor, and more. This approach can be modified to study targeting priority in various organelles, cell types, and organisms.

    View details for DOI 10.1073/pnas.1920078117

    View details for PubMedID 32817524

  • Principles of Systems Biology, No. 21 CELL SYSTEMS Cao, J., Packer, J., Waterston, R., Trapnell, C., Shendure, J., Rajaram, S., Wu, L. F., Altschuler, S. J., Liang, J., O'Brien, L., Eizenberg-Magar, I., Rimer, J., Friedman, N., Metzl-Raz, E., Kafri, M., Yaakov, G., Soifer, I., Gurvich, Y., Barkai, N., Mardinoglu, A., Ponten, F., Uhlen, M., Rahi, S., Cross, F. R., Baumgart, M., Noack, S. 2017; 5 (3): 158–60

    Abstract

    This month: relating single cells to populations (Cao/Packer, Wu/Altschuler, O'Brien, Friedman), an excess of ribosomes (Barkai), human pathology atlas (Uhlen), signatures of feedback (Rahi), and major genome redesign (Baumgart).

    View details for Web of Science ID 000411874500002

    View details for PubMedID 28957648

  • Principles of cellular resource allocation revealed by condition-dependent proteome profiling. eLife Metzl-Raz, E., Kafri, M., Yaakov, G., Soifer, I., Gurvich, Y., Barkai, N. 2017; 6

    Abstract

    Growing cells coordinate protein translation with metabolic rates. Central to this coordination is ribosome production. Ribosomes drive cell growth, but translation of ribosomal proteins competes with production of non-ribosomal proteins. Theory shows that cell growth is maximized when all expressed ribosomes are constantly translating. To examine whether budding yeast function at this limit of full ribosomal usage, we profiled the proteomes of cells growing in different environments. We find that cells produce excess ribosomal proteins, amounting to a constant ≈8% of the proteome. Accordingly, ≈25% of ribosomal proteins expressed in rapidly growing cells does not contribute to translation. Further, this fraction increases as growth rate decreases and these excess ribosomal proteins are employed when translation demands unexpectedly increase. We suggest that steadily growing cells prepare for conditions that demand increased translation by producing excess ribosomes, at the expense of lower steady-state growth rate.

    View details for DOI 10.7554/eLife.28034

    View details for PubMedID 28857745

    View details for PubMedCentralID PMC5578734

  • Rethinking cell growth models. FEMS yeast research Kafri, M., Metzl-Raz, E., Jonas, F., Barkai, N. 2016; 16 (7)

    Abstract

    The minimal description of a growing cell consists of self-replicating ribosomes translating the cellular proteome. While neglecting all other cellular components, this model provides key insights into the control and limitations of growth rate. It shows, for example, that growth rate is maximized when ribosomes work at full capacity, explains the linear relation between growth rate and the ribosome fraction of the proteome and defines the maximal possible growth rate. This ribosome-centered model also highlights the challenge of coordinating cell growth with related processes such as cell division or nutrient production. Coordination is promoted when ribosomes don't translate at maximal capacity, as it allows escaping strict exponential growth. Recent data support the notion that multiple cellular processes limit growth. In particular, increasing transcriptional demand may be as deleterious as increasing translational demand, depending on growth conditions. Consistent with the idea of trade-off, cells may forgo maximal growth to enable more efficient interprocess coordination and faster adaptation to changing conditions.

    View details for DOI 10.1093/femsyr/fow081

    View details for PubMedID 27650704

  • The Cost of Protein Production. Cell reports Kafri, M., Metzl-Raz, E., Jona, G., Barkai, N. 2016; 14 (1): 22–31

    Abstract

    The economy of protein production is central to cell physiology, being intimately linked with cell division rate and cell size. Attempts to model cellular physiology are limited by the scarcity of experimental data defining the molecular processes limiting protein expression. Here, we distinguish the relative contribution of gene transcription and protein translation to the slower proliferation of budding yeast producing excess levels of unneeded proteins. In contrast to widely held assumptions, rapidly growing cells are not universally limited by ribosome content. Rather, transcription dominates cost under some conditions (e.g., low phosphate), translation in others (e.g., low nitrogen), and both in other conditions (e.g., rich media). Furthermore, cells adapted to enforced protein production by becoming larger and increasing their endogenous protein levels, suggesting limited competition for common resources. We propose that rapidly growing cells do not exhaust their resources to maximize growth but maintain sufficient reserves to accommodate changing requirements.

    View details for DOI 10.1016/j.celrep.2015.12.015

    View details for PubMedID 26725116

    View details for PubMedCentralID PMC4709330

  • miR-142 orchestrates a network of actin cytoskeleton regulators during megakaryopoiesis. eLife Chapnik, E., Rivkin, N., Mildner, A., Beck, G., Pasvolsky, R., Metzl-Raz, E., Birger, Y., Amir, G., Tirosh, I., Porat, Z., Israel, L. L., Lellouche, E., Michaeli, S., Lellouche, J. M., Izraeli, S., Jung, S., Hornstein, E. 2014; 3: e01964

    Abstract

    Genome-encoded microRNAs (miRNAs) provide a posttranscriptional regulatory layer that controls the differentiation and function of various cellular systems, including hematopoietic cells. miR-142 is one of the most prevalently expressed miRNAs within the hematopoietic lineage. To address the in vivo functions of miR-142, we utilized a novel reporter and a loss-of-function mouse allele that we have recently generated. In this study, we show that miR-142 is broadly expressed in the adult hematopoietic system. Our data further reveal that miR-142 is critical for megakaryopoiesis. Genetic ablation of miR-142 caused impaired megakaryocyte maturation, inhibition of polyploidization, abnormal proplatelet formation, and thrombocytopenia. Finally, we characterized a network of miR-142-3p targets which collectively control actin filament homeostasis, thereby ensuring proper execution of actin-dependent proplatelet formation. Our study reveals a pivotal role for miR-142 activity in megakaryocyte maturation and function, and demonstrates a critical contribution of a single miRNA in orchestrating cytoskeletal dynamics and normal hemostasis.DOI: http://dx.doi.org/10.7554/eLife.01964.001.

    View details for DOI 10.7554/eLife.01964

    View details for PubMedID 24859754

    View details for PubMedCentralID PMC4067751

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