A thermodynamic paradigm for solution demixing inspired by nuclear transport in living cells

Living cells display a remarkable capacity to compartmentalize their functional biochemistry. A particularly fascinating example is the cell nucleus. Exchange of macromolecules between the nucleus and the surrounding cytoplasm does not involve traversing a lipid bilayer membrane. Instead, large protein channels known as nuclear pores cross the nuclear envelope and regulate the passage of other proteins and RNA molecules. Beyond simply gating diffusion, the system of nuclear pores and associated transport receptors is able to generate substantial concentration gradients, at the energetic expense of guanosine triphosphate (GTP) hydrolysis. In contrast to conventional approaches to demixing such as reverse osmosis or dialysis, the biological system operates continuously, without application of cyclic changes in pressure or solvent exchange. Abstracting the biological paradigm, we examine this transport system as a thermodynamic machine of solution demixing. Building on the construct of free energy transduction and biochemical kinetics, we find conditions for stable operation and optimization of the concentration gradients as a function of dissipation in the form of entropy production.Comment: 6+9 pages, 4+5 figures, to appear in Phys. Rev. Let

Nucleocytoplasmic transport: a thermodynamic mechanism

The nuclear pore supports molecular communication between cytoplasm and nucleus in eukaryotic cells. Selective transport of proteins is mediated by soluble receptors, whose regulation by the small GTPase Ran leads to cargo accumulation in, or depletion from the nucleus, i.e., nuclear import or nuclear export. We consider the operation of this transport system by a combined analytical and experimental approach. Provocative predictions of a simple model were tested using cell-free nuclei reconstituted in Xenopus egg extract, a system well suited to quantitative studies. We found that accumulation capacity is limited, so that introduction of one import cargo leads to egress of another. Clearly, the pore per se does not determine transport directionality. Moreover, different cargo reach a similar ratio of nuclear to cytoplasmic concentration in steady-state. The model shows that this ratio should in fact be independent of the receptor-cargo affinity, though kinetics may be strongly influenced. Numerical conservation of the system components highlights a conflict between the observations and the popular concept of transport cycles. We suggest that chemical partitioning provides a framework to understand the capacity to generate concentration gradients by equilibration of the receptor-cargo intermediary.Comment: in press at HFSP Journal, vol 3 16 text pages, 1 table, 4 figures, plus Supplementary Material include

Unraveling the multifaceted resilience of arsenic resistant bacterium Deinococcus indicus

Funding Information: This study was financially supported by the Portuguese Fundação para a Ciência e Tecnologia (FCT), grants PTDC/BIA-BQM/31317/2017, Project MOSTMICRO-ITQB with references UIDB/04612/2020 and UIDP/04612/2020, and LS4FUTURE Associated Laboratory (LA/P/0087/2020). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 857203. AG and BS are recipients of FCT grants SFRH/BD/06723/2020 and SFRH/BD/08066/2020, respectively. CR is recipient of FCT Institutional CEEC. Cryo-electron microscopy studies received partial support from the Weizmann Institute of Science (The Irving and Cherna Moskowitz Center for Nano and BioNano Imaging), and from the European Union (ERC-AdV grant, CryoSTEM, 101055413 to ME). This work benefited from access to the Weizmann Institute Electron Microscopy Unit, an Instruct-ERIC centre through the Access proposal PID: 19879. Funding Information: We would like to acknowledge the ALBA Synchrotron Light Facility with the collaboration of ALBA staff for the data collection of Di ArsC2 structures performed at BL13-XALOC beamline. The image analysis was made available thanks to the de Picciotto Cancer Cell Observatory In Memory of Wolfgang and Ruth Lesser of the MICC Life Sciences Core Facilities Weizmann Institute of Science Israel. Teresa Silva and Cristina Timóteo from the Microbial Cell Production and Protein Purification and Characterization Research facilities at ITQB-NOVA are acknowledged for providing the competent cells of Escherichia coli strains and to purify TEV protease. Publisher Copyright: Copyright © 2023 Gouveia, Salgueiro, Ranmar, Antunes, Kirchweger, Golani, Wolf, Elbaum, Matias and Romão.Arsenic (As) is a toxic heavy metal widely found in the environment that severely undermines the integrity of water resources. Bioremediation of toxic compounds is an appellative sustainable technology with a balanced cost-effective setup. To pave the way for the potential use of Deinococcus indicus, an arsenic resistant bacterium, as a platform for arsenic bioremediation, an extensive characterization of its resistance to cellular insults is paramount. A comparative analysis of D. indicus cells grown in two rich nutrient media conditions (M53 and TGY) revealed distinct resistance patterns when cells are subjected to stress via UV-C and methyl viologen (MV). Cells grown in M53 demonstrated higher resistance to both UV-C and MV. Moreover, cells grow to higher density upon exposure to 25 mM As(V) in M53 in comparison with TGY. This analysis is pivotal for the culture of microbial species in batch culture bioreactors for bioremediation purposes. We also demonstrate for the first time the presence of polyphosphate granules in D. indicus which are also found in a few Deinococcus species. To extend our analysis, we also characterized DiArsC2 (arsenate reductase) involved in arsenic detoxification and structurally determined different states, revealing the structural evidence for a catalytic cysteine triple redox system. These results contribute for our understanding into the D. indicus resistance mechanism against stress conditions.publishersversionpublishe

A tough 3D puzzle in the walnut shell

This article comments on: Antreich SJ, Xiao N, Huss JC, Gierlinger N. 2021. A belt for the cell: cellulosic wall thickenings and their role in morphogenesis of the 3D puzzle cells in walnut shells. Journal of Experimental Botany 72,4744–4756.</jats:p