Sáenz Lab Research Wiki
We study how membranes are built, regulated, and adapted — combining membrane biophysics, lipidomics, and synthetic genomics to connect molecular composition to cellular function. Our goal is to decode the principles that make a living membrane work, and use them to engineer cells with programmable physical behaviours. This wiki compiles our lab’s publications alongside earlier work and collaborations that built toward our current research program.
Sources
Sáenz Lab publications
Papers from the independent research group (2019–present).
Membrane biophysics and lipidome design
- Principles of membrane adaptation revealed through bacterial lipidome remodeling — Chwastek et al. 2020, Cell Reports
- [[functional-diversity-isoprenoid-lipids|Functional diversity of isoprenoid lipids in M. extorquens PA1]] — Rizk et al. 2021, Molecular Microbiology
- High-throughput measurements of viscosity in sub-micrometer-sized membrane systems — Chwastek et al. 2019, ChemBioChem
- Acyl chain unsaturation position modulates hopanoid and sterol ordering — Nguyen et al. 2024, Biophysical Journal
Minimal cell membrane biology
- A tuneable minimal cell membrane reveals that two lipid species suffice for life — Justice et al. 2024, Nature Communications
- [[temperature-lipidome-adaptation-minimal-cells|Temperature change elicits lipidome adaptation in M. mycoides and JCVI-syn3B]] — Safronova et al. 2024, Cell Reports
- Chemically defined lipid diets reveal lipidome remodeling versatility in minimal cells — Safronova et al. 2024, bioRxiv
- Metabolic heat flow from JCVI-Syn3B: lipidome-dependence of growth — Oertel et al. 2025, bioRxiv
RNA–lipid interactions
- Lipid membranes modulate RNA activity through sequence-dependent interactions — Czerniak & Sáenz 2022, PNAS
- Effects of lipid membranes on RNA catalytic activity and stability — Czerniak & Sáenz 2025, Biology of the Cell
- The secret life of RNA and lipids — Czerniak & Sáenz 2025, RNA Biology (review)
James’ PhD and postdoc publications
Work on hopanoid biology and biogeochemistry from the PhD (MIT-WHOI, 2004–2010) and postdoc (MPI-CBG, 2010–2017) that established the foundation for the lab’s current research.
- PhD thesis: Exploring bacterial membrane lipid distributions and roles — Sáenz 2010
- [[hopanoid-enrichment-drm-crocosphaera|Hopanoid enrichment in a detergent resistant membrane fraction of C. watsonii]] — Sáenz 2010, Organic Geochemistry
- BHP abundance and diversity along a river to ocean transect — Sáenz et al. 2011, Organic Geochemistry
- BHPs in marine suboxic and anoxic environments — Sáenz et al. 2011, Organic Geochemistry
- Hopanoids in marine cyanobacteria: phylogenetic distribution and biological role — Sáenz et al. 2012, Geobiology
- Anammox bacteria distribution in a subterranean estuary — Sáenz et al. 2012, Marine Chemistry
- Functional convergence of hopanoids and sterols in membrane ordering — Sáenz et al. 2012, PNAS
- Hopanoids as functional analogues of cholesterol in bacterial membranes — Sáenz et al. 2015, PNAS
Collaborative papers
Papers to which our group contributed expertise as co-authors. See individual pages for details on our contributions.
Hopanoid biology and biogeochemistry
- Hopanoid diversity across a tropical land-sea gradient — Pearson et al. 2009, Organic Geochemistry
- Adenosylhopane: first intermediate in hopanoid side chain biosynthesis — Bradley et al. 2010, Organic Geochemistry
- lipid stratigraphy in the Black Sea — Coolen et al. 2009, Earth and Planetary Science Letters
- Chemoautotrophy in the Cariaco Basin chemocline — Wakeham et al. 2012, Deep-Sea Research
- Hopanoids fortifying rhizobia against climate change — Tookmanian et al. 2021, mLife (review)
- [[hopanoids-robustness-bradyrhizobium|Hopanoids confer robustness in B. diazoefficiens]] — Tookmanian et al. 2022, mBio
Minimal cell and synthetic biology
- Fundamental behaviors emerge from simulations of a living minimal cell — Thornburg et al. 2022, Cell
- Prebiotic foam environments to oligomerize and accumulate RNA — Tekin et al. 2022, ChemBioChem
- A roadmap toward the synthesis of life — Kriebisch et al. 2025, Chem
Membrane biology and lipid signaling
- [[lps-structure-m-extorquens-methanol|LPS structure of M. extorquens and methanol resistance]] — Di Lorenzo et al. 2023, JACS Au
- Gill membrane permeabilities in teleosts and elasmobranchs — Hill et al. 2004
- Cholesterol and Lumacaftor impact CFTR folding — Alhadeff et al. 2023
- Effect of viscosity on microswimmers — Acemoglu et al. 2021
- [[eps-plant-abiotic-stress-m-extorquens|EPS role in plant abiotic stress: M. extorquens]] — Ramírez-Villacis et al. 2022
- MemPrep: organellar membrane isolation and lipid bilayer stress — Buyan et al. 2024
Entities
- Hopanoids — pentacyclic isoprenoidal membrane lipids; bacterial “sterol surrogates”
- Diplopterol — the simplest hopanoid; orders membranes analogously to cholesterol
- Bacteriohopanepolyols (BHPs) — extended side-chain hopanoids; biomarkers and membrane lipids
- Lipid A — conserved core of LPS; partner of hopanoids in bacterial outer membrane ordering
- [[crocosphaera-watsonii|Crocosphaera watsonii]] — nitrogen-fixing marine cyanobacterium; early model for hopanoid biology
- [[methylobacterium-extorquens|Methylobacterium extorquens]] — gram-negative methylotroph; in vivo model for hopanoid membrane function
- [[mycoplasma-mycoides|Mycoplasma mycoides]] — simple pathogen; parent of JCVI-Syn3 minimal cells; tuneable membrane model
- B — genomically minimal cells; platform for lipidome design studies
Concepts
- Lipid Ordering — how polycyclic isoprenoids create liquid-ordered phases in biological membranes
- Hopanoid–Sterol Functional Analogy — from structural similarity to demonstrated functional convergence
- Hopanoid Biomarkers — interpreting the sedimentary record of hopanoids and related lipids
- Lipidome Design Principles — minimal rules for building adaptive living membranes
- RNA–Lipid Interactions — sequence-dependent interactions between RNA and lipid membranes