Michael Lanz

All Publications

• Genome concentration limits cell growth and modulates proteome composition in Escherichia coli. eLife Mäkelä, J., Papagiannakis, A., Lin, W. H., Lanz, M. C., Glenn, S., Swaffer, M., Marinov, G. K., Skotheim, J. M., Jacobs-Wagner, C. 2024; 13

  Abstract

  Defining the cellular factors that drive growth rate and proteome composition is essential for understanding and manipulating cellular systems. In bacteria, ribosome concentration is known to be a constraining factor of cell growth rate, while gene concentration is usually assumed not to be limiting. Here, using single-molecule tracking, quantitative single-cell microscopy, and modeling, we show that genome dilution in Escherichia coli cells arrested for DNA replication limits total RNA polymerase activity within physiological cell sizes across tested nutrient conditions. This rapid-onset limitation on bulk transcription results in sub-linear scaling of total active ribosomes with cell size and sub-exponential growth. Such downstream effects on bulk translation and cell growth are near-immediately detectable in a nutrient-rich medium, but delayed in nutrient-poor conditions, presumably due to cellular buffering activities. RNA sequencing and tandem-mass-tag mass spectrometry experiments further reveal that genome dilution remodels the relative abundance of mRNAs and proteins with cell size at a global level. Altogether, our findings indicate that chromosome concentration is a limiting factor of transcription and a global modulator of the transcriptome and proteome composition in E. coli. Experiments in Caulobacter crescentus and comparison with eukaryotic cell studies identify broadly conserved DNA concentration-dependent scaling principles of gene expression.

  View details for DOI 10.7554/eLife.97465

  View details for PubMedID 39714909

  View details for PubMedCentralID PMC11666246

• Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells. Nature structural & molecular biology Lanz, M. C., Zhang, S., Swaffer, M. P., Ziv, I., Gotz, L. H., Kim, J., McCarthy, F., Jarosz, D. F., Elias, J. E., Skotheim, J. M. 2024

  Abstract

  Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how cell size influences physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be compositionally different. In the present study, we utilize the natural heterogeneity of hepatocyte ploidy and yeast genetics to establish that the ploidy-to-cell size ratio is a highly conserved determinant of proteome composition. In both mammalian and yeast cells, genome dilution by cell growth elicits a starvation-like phenotype, suggesting that growth in large cells is restricted by genome concentration in a manner that mimics a limiting nutrient. Moreover, genome dilution explains some proteomic changes ascribed to yeast aging. Overall, our data indicate that genome concentration drives changes in cell composition independently of external environmental cues.

  View details for DOI 10.1038/s41594-024-01353-z

  View details for PubMedID 39048803

• Cell Size Contributes to Single-Cell Proteome Variation. Journal of proteome research Lanz, M. C., Fuentes Valenzuela, L., Elias, J. E., Skotheim, J. M. 2023

  Abstract

  Accurate measurements of the molecular composition of single cells will be necessary for understanding the relationship between gene expression and function in diverse cell types. One of the most important phenotypes that differs between cells is their size, which was recently shown to be an important determinant of proteome composition in populations of similarly sized cells. We, therefore, sought to test if the effects of the cell size on protein concentrations were also evident in single-cell proteomics data. Using the relative concentrations of a set of reference proteins to estimate a cell's DNA-to-cell volume ratio, we found that differences in the cell size explain a significant amount of cell-to-cell variance in two published single-cell proteome data sets.

  View details for DOI 10.1021/acs.jproteome.3c00441

  View details for PubMedID 37910793

• Increasing cell size remodels the proteome and promotes senescence. Molecular cell Lanz, M. C., Zatulovskiy, E., Swaffer, M. P., Zhang, L., Ilerten, I., Zhang, S., You, D. S., Marinov, G., McAlpine, P., Elias, J. E., Skotheim, J. M. 2022

  Abstract

  Cell size is tightly controlled in healthy tissues, but it is unclear how deviations in cell size affect cell physiology. To address this, we measured how the cell's proteome changes with increasing cell size. Size-dependent protein concentration changes are widespread and predicted by subcellular localization, size-dependent mRNA concentrations, and protein turnover. As proliferating cells grow larger, concentration changes typically associated with cellular senescence are increasingly pronounced, suggesting that large size may be a cause rather than just a consequence of cell senescence. Consistent with this hypothesis, larger cells are prone to replicative, DNA-damage-induced, and CDK4/6i-induced senescence. Size-dependent changes to the proteome, including those associated with senescence, are not observed when an increase in cell size is accompanied by an increase in ploidy. Together, our findings show how cell size could impact many aspects of cell physiology by remodeling the proteome and provide a rationale for cell size control and polyploidization.

  View details for DOI 10.1016/j.molcel.2022.07.017

  View details for PubMedID 35987199

• Whi5 is diluted and protein synthesis does not dramatically increase in pre-Start G1. Molecular biology of the cell Schmoller, K. M., Lanz, M. C., Kim, J., Koivomagi, M., Qu, Y., Tang, C., Kukhtevich, I. V., Schneider, R., Rudolf, F., Moreno, D. F., Aldea, M., Lucena, R., Skotheim, J. M. 2022; 33 (5): lt1

  View details for DOI 10.1091/mbc.E21-01-0029

  View details for PubMedID 35482510

• Delineation of proteome changes driven by cell size and growth rate. Frontiers in cell and developmental biology Zatulovskiy, E., Lanz, M. C., Zhang, S., McCarthy, F., Elias, J. E., Skotheim, J. M. 2022; 10: 980721

  Abstract

  Increasing cell size drives changes to the proteome, which affects cell physiology. As cell size increases, some proteins become more concentrated while others are diluted. As a result, the state of the cell changes continuously with increasing size. In addition to these proteomic changes, large cells have a lower growth rate (protein synthesis rate per unit volume). That both the cell's proteome and growth rate change with cell size suggests they may be interdependent. To test this, we used quantitative mass spectrometry to measure how the proteome changes in response to the mTOR inhibitor rapamycin, which decreases the cellular growth rate and has only a minimal effect on cell size. We found that large cell size and mTOR inhibition, both of which lower the growth rate of a cell, remodel the proteome in similar ways. This suggests that many of the effects of cell size are mediated by the size-dependent slowdown of the cellular growth rate. For example, the previously reported size-dependent expression of some senescence markers could reflect a cell's declining growth rate rather than its size per se. In contrast, histones and other chromatin components are diluted in large cells independently of the growth rate, likely so that they remain in proportion with the genome. Finally, size-dependent changes to the cell's growth rate and proteome composition are still apparent in cells continually exposed to a saturating dose of rapamycin, which indicates that cell size can affect the proteome independently of mTORC1 signaling. Taken together, our results clarify the dependencies between cell size, growth, mTOR activity, and the proteome remodeling that ultimately controls many aspects of cell physiology.

  View details for DOI 10.3389/fcell.2022.980721

  View details for PubMedID 36133920

• In-depth and 3-dimensional exploration of the budding yeast phosphoproteome EMBO REPORTS Lanz, M. C., Yugandhar, K., Gupta, S., Sanford, E. J., Faca, V. M., Vega, S., Joiner, A. N., Fromme, J., Yu, H., Smolka, M. B. 2021: e51121

  Abstract

  Phosphorylation is one of the most dynamic and widespread post-translational modifications regulating virtually every aspect of eukaryotic cell biology. Here, we assemble a dataset from 75 independent phosphoproteomic experiments performed in our laboratory using Saccharomyces cerevisiae. We report 30,902 phosphosites identified from cells cultured in a range of DNA damage conditions and/or arrested in distinct cell cycle stages. To generate a comprehensive resource for the budding yeast community, we aggregate our dataset with the Saccharomyces Genome Database and another recently published study, resulting in over 46,000 budding yeast phosphosites. With the goal of enhancing the identification of functional phosphorylation events, we perform computational positioning of phosphorylation sites on available 3D protein structures and systematically identify events predicted to regulate protein complex architecture. Results reveal hundreds of phosphorylation sites mapping to or near protein interaction interfaces, many of which result in steric or electrostatic "clashes" predicted to disrupt the interaction. With the advancement of Cryo-EM and the increasing number of available structures, our approach should help drive the functional and spatial exploration of the phosphoproteome.

  View details for DOI 10.15252/embr.202051121

  View details for Web of Science ID 000610988800001

  View details for PubMedID 33491328

  View details for PubMedCentralID PMC7857435