About

Alexey Merz is a Professor in the Department of Biochemistry at the University of Washington. His research focuses on understanding how cells within human beings and other organisms are organized, with a particular interest in subcellular degradative organelles called endosomes and lysosomes. His laboratory aims to elucidate how these organelles are constructed at the molecular and biophysical levels, and how these mechanisms contribute to health and disease.

Research topics

• Biochemistry
• Biophysics
• Biology
• Chemistry
• Cell biology

Selected publications

• Expression of soluble Type IV Minor Pilins and isolation of a <i>Neisseria gonorrhoeae</i> PilI-PilJ subcomplex

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-09

  articleOpen accessSenior authorCorresponding

  Abstract Type IV pili and type II secretion systems assemble dynamic fibers used by bacteria and archaea for diverse functions. The pilus fiber is made up of major and minor pilin subunits containing a hydrophobic α-helical spine and a globular head. Purifying minor pilins is complicated by the hydrophobic α-helical spine, frequently present disulfide bonds, and low abundance within the fiber. These challenges have impeded structural and functional studies of pilin protomers. Here, we describe a method for expression and purification of soluble type IV pilin proteins from Escherichia coli . Signal peptidase I cleavage sites are engineered into the α-helix of the pilin proteins. This allows their globular domains to be purified from the periplasmic fraction. We used this method to obtain the Neisseria gonorrhoeae minor pilins PilI and PilK in soluble form. In a third case, where the minor pilin PilJ could not be obtained on its own, coexpression with PilI and purification of a PilI-PilJ heterodimer was possible. We suggest that PilI and PilJ form an obligate heterodimer that is essential for their function. Importance Type IV pili are essential to many bacteria responsible for disease. They can be found in both Gram-negative and Gram-positive bacteria, as well as archaea, making them likely present in the last common ancestor of all life on Earth. Despite their significance in a variety of species, there are large gaps in our understanding of the structure of these diverse biological machines. One roadblock to this research has been the difficulty of purifying the minor pilin proteins that serve different functions in the fiber. Here, we describe a novel method for the purification of these proteins and demonstrate the ability of this method to identify a protein-protein interaction between two minor pilins of Nesseria gonorrhoeae .

  PublisherDOI

• Sequential restriction of SNARE-mediated fusion by the COPII inner coat and SNARE chaperones

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-04

  articleOpen accessSenior authorCorresponding

  SNARE-mediated fusion requires assembly of four SNARE domains (R, Qa, Qb, and Qc) distributed across two membranes, with an SM (Sec1/Munc-18 family) chaperone catalyzing this assembly. We investigated topological requirements for the four SNAREs that mediate ER-Golgi fusion using in vitro assays. In the presence of the cognate SM Sly1, we find that only a single topology drives efficient fusion: the R SNARE on one membrane versus Qa, Qb, and Qc SNAREs on the other. These results prompted us to look upstream, at COPII-SNARE interactions. The assembled COPII coat is known to block fusion. We discovered that of five COPII core subunits, the Sar1 GTPase and Sec23/Sec24 subunits were necessary and sufficient to prevent fusion. When specific Sec24-SNARE interactions were disrupted, fusion was restored, suggesting that SNARE sequestration by COPII prevents fusion. These observations help to explain how appropriate fusion events are facilitated while inappropriate events are deterred.

  PublisherOA PDFDOI

• β-strand complementation within tip initiation complexes licenses assembly of diverse type IV filaments

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-15 · 1 citations

  articleOpen accessSenior authorCorresponding

  ABSTRACT PilC/PilY1 proteins are tip-located adhesins of type IV pili (T4P) that are critical for T4P function in diverse behaviors including twitching motility, DNA uptake, and host cell adhesion. PilC and PilY1 adhesins are proposed to interact with initiation complexes composed of minor pilins (PilIJK family proteins) to aid in initiation of T4P polymerization, but it has been unclear how PilC/PilY1 proteins promote fiber assembly. We combined structural modeling, genetic, and biochemical experiments using Neisseria gonorrhoeae and Acinetobacter baylyi to delineate how PilC/PilY1 control T4P assembly: a short peptide at the C-terminus of PilC/PilY1 initiates T4P assembly via β-strand complementation with PilK-family minor pilins. This β-strand is necessary and partially sufficient to trigger fiber assembly. In a working model, the PilK-PilC/PilY1 complex is recognized by a preformed PilI-PilJ heterodimer to form a quaternary “licensing complex” that then templates and initiates fiber assembly. In type II secretion systems (T2SS) lacking PilC/PilY1, PilK homologs directly incorporate the terminal β-strand provided by PilC/PilY1 in T4P. Moreover, phylogenetically distinct Tad T4P lack a canonical PilK homolog and instead contain a structurally similar minor pilin-like protein called TadG/CpaL that is important for fiber assembly. We show that CpaL of Caulobacter crescentus Tad T4P acts similarly to the T2SS PilK homolog to provide the C-terminal β-strand required for assembly. Our results explain how PilC/PilY1 can be retained on the fiber tip under enormous tensile loads generated during mechanical shear and T4P retraction and demonstrate how diverse T4P systems employ β-strand complementation to license fiber assembly. SIGNIFICANCE Prokaryotic type IV filaments are ancient, diverse, and broadly distributed nanomachines that assemble and retract to execute diverse microbial functions. They include type IV pili and type II secretion systems, mediating toxin secretion, motility, surface adhesion, biofilm formation, DNA uptake, and other functions. Here, we show that two widely conserved subunits of the tip, PilI and PilJ, form a module that recognizes the folding of a β-sheet in a third subunit, PilK. The final β-strand in this sheet can be supplied in trans by the last ∼10 aminoacyl residues of large PilC/PilY1 adhesins, or in cis by PilK itself. In a working model, this recognition results in formation of a PilIJK trimer, which then licenses fiber polymerization through a templating mechanism.

  PublisherDOI

• BPS2026 – Temperature at which yeast vacuole membranes undergo liquid-liquid phase separation as a function of time in the stationary stage (Tmix vs time)

  Biophysical Journal · 2026-02-01

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  PublisherDOI

• BPS2025 - Impact of replicative age on liquid-liquid phase separation in the yeast vacuole membrane

  Biophysical Journal · 2025-02-01

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  PublisherDOI

• SM protein Sly1 and a SNARE Habc domain promote membrane fusion through multiple mechanisms

  The Journal of Cell Biology · 2024-03-13 · 1 citations

  articleOpen accessSenior authorCorresponding

  SM proteins including Sly1 are essential cofactors of SNARE-mediated membrane fusion. Using SNARE and Sly1 mutants and chemically defined in vitro assays, we separate and assess proposed mechanisms through which Sly1 augments fusion: (i) opening the closed conformation of the Qa-SNARE Sed5; (ii) close-range tethering of vesicles to target organelles, mediated by the Sly1-specific regulatory loop; and (iii) nucleation of productive trans-SNARE complexes. We show that all three mechanisms are important and operate in parallel, and that close-range tethering promotes trans-complex assembly when cis-SNARE assembly is a competing process. Further, we demonstrate that the autoinhibitory N-terminal Habc domain of Sed5 has at least two positive activities: it is needed for correct Sed5 localization, and it directly promotes Sly1-dependent fusion. "Split Sed5," with Habc presented solely as a soluble fragment, can function both in vitro and in vivo. Habc appears to facilitate events leading to lipid mixing rather than promoting opening or stability of the fusion pore.

  PublisherOA PDFDOI

• Disordered hinge regions of the AP-3 adaptor complex promote vesicle budding from the late Golgi in yeast

  Journal of Cell Science · 2024-09-27 · 4 citations

  articleOpen access

  Vesicles bud from maturing Golgi cisternae in a programmed sequence. Budding is mediated by adaptors that recruit cargoes and facilitate vesicle biogenesis. In Saccharomyces cerevisiae, the AP-3 adaptor complex directs cargoes from the Golgi to the lysosomal vacuole. The AP-3 core consists of small and medium subunits complexed with two non-identical large subunits, β3 (Apl6) and δ (Apl5). The C-termini of β3 and δ were thought to be flexible hinges linking the core to ear domains that bind accessory proteins involved in vesicular transport. We found by computational modeling that the yeast β3 and δ hinges are intrinsically disordered and lack folded ear domains. When either hinge is truncated, AP-3 is recruited to the Golgi, but vesicle budding is impaired and cargoes normally sorted into the AP-3 pathway are mistargeted. This budding deficiency causes AP-3 to accumulate on ring-like Golgi structures adjacent to GGA adaptors that, in wild-type cells, bud vesicles downstream of AP-3 during Golgi maturation. Thus, each of the disordered hinges of yeast AP-3 has a crucial role in mediating transport vesicle formation at the Golgi.

  PublisherOA PDFDOI

• SNARE chaperone Sly1 directly mediates close-range vesicle tethering

  The Journal of Cell Biology · 2024 · 5 citations

  Senior authorCorresponding
  • Chemistry
  • Cell biology
  • Biophysics

  The essential Golgi protein Sly1 is a member of the Sec1/mammalian Unc-18 (SM) family of SNARE chaperones. Sly1 was originally identified through remarkable gain-of-function alleles that bypass requirements for diverse vesicle tethering factors. Employing genetic analyses and chemically defined reconstitutions of ER-Golgi fusion, we discovered that a loop conserved among Sly1 family members is not only autoinhibitory but also acts as a positive effector. An amphipathic lipid packing sensor (ALPS)-like helix within the loop directly binds high-curvature membranes. Membrane binding is required for relief of Sly1 autoinhibition and also allows Sly1 to directly tether incoming vesicles to the Qa-SNARE on the target organelle. The SLY1-20 mutation bypasses requirements for diverse tethering factors but loses this ability if the tethering activity is impaired. We propose that long-range tethers, including Golgins and multisubunit tethering complexes, hand off vesicles to Sly1, which then tethers at close range to initiate trans-SNARE complex assembly and fusion in the early secretory pathway.

  PublisherOA PDFDOI

• Abstract 1504: Septin filaments interact with AP-3 and are required for trafficking via the AP-3 pathway in budding yeast

  Journal of Biological Chemistry · 2023-01-01

  articleOpen access
  PublisherDOI

• Reversible, large-scale, liquid-liquid phase separation in living yeast membranes

  Biophysical Journal · 2023-02-01 · 1 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

Recent grants

• Dynamics of Endomembrane Docking and Fusion

  NIH · $6.1M · 2006–2025

• MECHANISMS OF AP-3 FUNCTION IN VESICLE FORMATION AND GOLGI MATURATION

  NIH · $1.9M · 2019–2024

• INNER CENTROMERE TARGETING OF THE CHROMOSOME PASSENGER COMPLEX

  NIH · $10.6M · 2011–2016

Frequent coauthors

• Rachael L. Plemel

  University of Washington

  20 shared

• Daniel P. Nickerson

  California State University, San Bernardino

  18 shared

• Mengtong Duan

  University of Washington

  15 shared

• Sarah L. Keller

  14 shared

• Braden T. Lobingier

  Oregon Health & Science University

  13 shared

• Caitlin E. Cornell

  University of California, Berkeley

  12 shared

• William Wickner

  Dartmouth College

  12 shared

• Magdalene So

  University of Arizona

  12 shared