Elife 84974 v2

RESEARCH ARTICLE
Scavenger receptor endocytosis controls

apical membrane morphogenesis in the
Drosophila airways
Ana Sofia Pinheiro1†, Vasilios Tsarouhas1*†, Kirsten André Senti1,2, Badrul Arefin1,3,
Christos Samakovlis1,4*
1
Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren
Institute, Stockholm University, Stockholm, Sweden; 2IMBA – Institute of Molecular
Biotechnology, Austrian Academy of Sciences, Vienna, Austria; 3Sahlgrenska
Academy, Gothenburg University, Gothenburg, Sweden; 4Cardiopulmonary Institute,
Justus Liebig University of Giessen, Giessen, Germany
Abstract The acquisition of distinct branch sizes and shapes is a central aspect in tubular organ
morphogenesis and function. In the Drosophila airway tree, the interplay of apical extracellular
matrix (ECM) components with the underlying membrane and cytoskeleton controls tube elonga-
tion, but the link between ECM composition with apical membrane morphogenesis and tube size
regulation is elusive. Here, we characterized Emp (epithelial membrane protein), a Drosophila CD36
homolog belonging to the scavenger receptor class B protein family. emp mutant embryos fail to
internalize the luminal chitin deacetylases Serp and Verm at the final stages of airway maturation and
*For correspondence: die at hatching with liquid filled airways. Emp localizes in apical epithelial membranes and shows
[email protected] (VT); cargo selectivity for LDLr-domain containing proteins. emp mutants also display over elongated
christos.samakovlis@scilifelab. tracheal tubes with increased levels of the apical proteins Crb, DE-cad, and phosphorylated Src
se (CS) (p-Src). We show that Emp associates with and organizes the βH-Spectrin cytoskeleton and is itself
†
These authors contributed confined by apical F-actin bundles. Overexpression or loss of its cargo protein Serp lead to abnormal
equally to this work apical accumulations of Emp and perturbations in p-Src levels. We propose that during morphogen-
Competing interest: The authors esis, Emp senses and responds to luminal cargo levels by initiating apical membrane endocytosis
declare that no competing along the longitudinal tube axis and thereby restricts airway elongation.
interests exist.
Funding: See page 21

Editor's evaluation
Received: 17 November 2022
In this important work, the authors convincingly show that the Drosophila scavenger receptor Emp
Preprinted: 05 December 2022
Accepted: 13 September 2023
(homologous to human CD36) senses and responds to the levels of its cargo apical ECM proteins
Published: 14 September 2023 and triggers the initiation of apical endocytosis, thereby regulating tube length via controlling
Crumbs and Src. This work will be of broad interest to cell and development biologists as well as
Reviewing Editor: Elisabeth cancer biologists.
Knust, Max-Planck Institute
of Molecular Cell Biology and
Genetics, Germany
‍ ‍Copyright Pinheiro, Tsarouhas

et al. This article is distributed
Introduction
The tube shapes in transporting organs like kidney, lung, and vascular system are precisely
under the terms of the Creative
Commons Attribution License, controlled to ensure optimal fluid flow and thereby, function. Failure in normal tube size acquisi-
which permits unrestricted use tion leads to cystic, stenotic, or winding tubes. The Drosophila respiratory network, the trachea,
and redistribution provided that provides a well-characterized system for the genetic dissection of tubular organ maturation. Like
the original author and source mammalian lungs, the trachea undergoes a precisely timed series of maturation events to convert
are credited. the nascent branches into functional airways. First, a transient secretion burst of luminal proteins
Pinheiro, Tsarouhas et al. eLife 2023;12:e84974. DOI: https://doi.org/10.7554/eLife.84974 1 of 24

Research article Developmental Biology
(Tsarouhas et al., 2007; Jayaram et al., 2008; Förster et al., 2010) initiates diametric tube expan-
sion. Luminal proteins assemble into a chitinous central rod and into a cuticular apical extracellular
matrix (aECM, taenidia), lining the apical membrane. After 10 hr, luminal material becomes rapidly
cleared from the tubes by massive endocytosis involving several endocytic pathways. Finally, a liquid
clearance pulse converts the tubes into functional airways (Tsarouhas et al., 2007). Genetic studies
suggested an instructive role of luminal chitin and proteins in tube growth coordination and termi-
nation. Mutations affecting chitin biosynthesis (kkv) or matrix assembly (knk, gasp) show irregular
tube shapes, diametric expansion and tube maturation defects (Moussian et al., 2006; Tiklová
et al., 2013; Öztürk-Çolak et al., 2016). Tube elongation is continuous during tracheal develop-
ment and its termination requires chitin biosynthesis and the secreted chitin deacetylases vermiform
(Verm) and serpentine (Serp) (Beitel and Krasnow, 2000; Luschnig et al., 2006; Wang et al., 2006;
Öztürk-Çolak et al., 2016). These luminal proteins presumably modify the structure and physical
properties of the aECM and thereby restrict tube elongation. In addition to the luminal matrix
pathway, components involved in the assembly of basolateral septate junctions (SJs) also restrict
tube elongation, through the regulation of the subcellular localization of Crumbs (Crb), a trans-
membrane protein that promotes expansion of the tracheal cell apical surface and tube elongation
(Laprise et al., 2010). More recently, the conserved non-receptor tyrosine kinase, Src oncogene
at 42A (Src42A) was found to promote axial elongation by controlling the apical cytoskeleton and
apical cell (Förster and Luschnig, 2012; Nelson et al., 2012; Öztürk-Çolak et al., 2016; Olivares-
Castiñeira and Llimargas, 2018). Additionally, Yorkie (Yki) and several components of the Hippo
pathway control tube elongation, along with transcription factors like Blimp-1 and Grainy head (Grh)
(Hemphälä et al., 2003; Robbins et al., 2014; Öztürk-Çolak et al., 2016; McSharry and Beitel,
2019; Skouloudaki et al., 2019). An appealing model suggests that the interaction between apical
membrane and aECM elasticity may influence apical cytoskeletal organization and thereby control
tube shapes (Dong et al., 2014). Although ECM integrity and the apical cytoskeleton appear crucial
in tube length regulation, it is unknown how ECM signals are perceived by the airway cells to regu-
late their shapes during tube maturation.
Scavenger receptors comprise a superfamily of cell surface membrane proteins that bind and inter-
nalize modified lipoproteins and various other types of ligands. Cluster of differentiation 36 (CD36)
belongs to class B scavenger receptor family, which includes scavenger receptor B1 (SRB1) and lyso-
somal integral membrane protein 2 (LIMP2). CD36 is expressed on the surface of many cell types
including epithelial, endothelial cells, and macrophages. Disruption of CD36 function in mice can lead
to inflammation, atherosclerosis, metabolic disorders, tumor growth, and metastasis (Chen et al.,
2008; Pascual et al., 2017; Wang et al., 2020). CD36 has several cargoes, including long-chain fatty
acids, oxidized LDL (ox-LDL), oxidized phospholipids and thrombospondin-1 (TSP-1) (Githaka et al.,
2016; Deng et al., 2022). In vitro imaging studies of macrophages and endothelial cells propose
that CD36 clustering at the cell surface upon engagement of multivalent ligands and in conjunction
with the cortical cytoskeleton triggers signal transduction and receptor–ligand complex endocytosis
(Jaqaman et al., 2011; Githaka et al., 2016). The activity of several signaling effectors, including the
Src family kinases, Fyn, Yes (Thorne et al., 2006; Zani et al., 2015) and the mitogen-activated kinases,
Jun-kinase (JNK) 1 and 2 (Rahaman et al., 2006) can be regulated by CD36. The Drosophila genome
includes a family of 14 CD36-like genes, with distinct tissue-specific expression patterns. The genetic
analysis of a few members in this class B scavenger receptor family implicated them in phagocytosis,
immune responses, and photoreceptor function (Philips et al., 2005; Stuart et al., 2005; Voolstra
et al., 2006). The Drosophila epithelial membrane protein (Emp) shows the highest similarity with
CD36 and is selectively expressed in embryonic epithelial tissues (Hart and Wilcox, 1993).
Here, we show that Emp is a selective receptor for internalization, endosomal targeting, and
tracheal luminal clearance of proteins with LDLr- domains. emp mutants display over elongated
tracheal tubes with increased levels of junctional Crb, DE-cad, and phospho-Src. Reduction of Src42A
in emp mutants, rescues the tube elongation phenotype indicating that Emp modulates junctional
p-Src42A levels to control apical membrane expansion and tube length. The organization of the beta-
heavy spectrin (βH-Spectrin) cytoskeletal network is compromised in emp mutants. Emp binds to
βH-Spectrin directly, suggesting that it provides a direct link between ECM, apical membrane, and
cytoskeleton during tube maturation process. Re-expression of human CD36 in emp mutants can
ameliorate the mutant tube phenotypes suggesting conserved functions of Emp.

Results
Emp is a selective scavenger receptor required for tube elongation and luminal protein clearance
emp (or CG2727 in Flybase) encodes a class-B scavenger receptor expressed in embryonic ecto-
dermal epithelial tissues including the tracheal system (Hart and Wilcox, 1993). To elucidate the
developmental functions of emp in the airways, a deletion mutant (empe3d1, referred as emp mutant
hereafter) was generated using the FLP/FRT recombinase system (Parks et al., 2004; Figure 1—
figure supplement 1A). PCR mapping of genomic DNA identified a 4.8-kb deletion encompassing
exon 2 in the CG2727 locus. Both immunofluorescence and western blots using a polyclonal anti-
serum against recombinant Emp (see Methods) (Figure 1—figure supplement 1B), failed to detect
Emp protein in emp mutants (Figure 1—figure supplement 1C, D). Similarly, quantitative Reverse
Transcription-Polymerase Chain Reaction (RT-PCR) of RNA extracted from late embryos showed a
strong reduction of emp RNA in the mutants (Figure 1—figure supplement 1E). emp homozygous
or Df(2R)BSC608/emp mutants were embryonic lethal with few escapers surviving to first instar larvae.
This embryonic lethality could be rescued by the re-expression of a transgenic emp construct using
the ectodermal driver 69BGal4. This suggests that the deletion generates a strong loss-of function
mutation in emp and does not affect any neighboring genes required for embryo viability. To examine
a potential role of Emp in airway maturation, we visualized the tracheal tubes during embryonic devel-
opment in wild-type and emp mutants. emp embryos at stage 16 showed a 30% over-elongation of
the dorsal trunk (DT) compared to the wild-type (Figure 1A), but showed no defects in tube diameter
(Figure 1—figure supplement 1F). emp mutants also failed to fill their airways with gas at hatching
(Figure 1H, Figure 1—figure supplement 1I). Both phenotypes could be rescued by re-expression
of emp in tracheal cells of the emp mutants (Figure 1A, B, H, Figure 1—figure supplement 1Ic).
These data indicate that Emp is required for normal tube elongation and gas-filling during embryonic
development. The survival of emp mutants overexpressing emp in the airways was limited to larval
stages, suggesting that the tracheal-specific re-expression of emp is not sufficient for larval or adult
survival. This suggests additional roles for Emp in other tissues. The human homolog of Emp, CD36
shares the overall protein architecture and 30% of amino acid identity with Emp (Figure 1—figure
supplement 1G, H). We generated a transgenic line expressing the coding sequence of human CD36
and drove its expression in fly airways to test if Emp and CD36 have conserved functions. We found
that both the tracheal length and gas-filling defects in emp mutants were partially reversed by tracheal
CD36 overexpression, arguing for a conserved function of CD36 (Figure 1A, B, H, Figure 1—figure
supplement 1Id).
To establish whether the failure of tracheal gas-filling originates from a defect in luminal protein
clearance, we stained wild-type and emp mutants for the luminal proteins Serp, Verm, and Gasp.
These secretory proteins were internalized from the lumen by late stage 17 in wild-type embryos. Serp
and Verm, but not Gasp were selectively retained in the emp DT airways (Figure 1C) suggesting a role
of Emp in the internalization of a subset of luminal proteins. To confirm the protein clearance pheno-
types, we generated emp mutants carrying btl>Serp-GFP or btl>Verm-GFP or btl>Gasp-mCherry
transgenes and analyzed them by live imaging from 17 h to 21 h after egg laying (AEL) (Figure 1D,
E). The three reporters were normally secreted into the lumen of both emp mutants and wild-type
embryos and at 19 hr they were cleared from the tubes of wild-type embryos. In emp mutants Gasp-
mCherry was also cleared from the lumen but the Serp-GFP and Verm-GFP reporters remained inside
the tube. This suggests that Emp acts as a selective endocytosis receptor during luminal protein
clearance. The unperturbed clearance of Gasp-Cherry suggested differential requirements for the
internalization of luminal proteins.
clathrin (chc1) null mutants show defects in luminal ANF-GFP clearance (Tsarouhas et al., 2007) and
tube length (Behr et al., 2007). We stained chc1 mutants for Serp, Verm, and Gasp and analyzed them
at late embryonic stages, when luminal clearance is completed in wild-type embryos. This analysis
showed that Serp and Verm were cleared, whereas Gasp clearance was selectively impaired in chc1
mutants (Figure 1F, G). This indicates that Emp is involved in a selective, clathrin-independent endo-
cytosis pathway internalizing Verm and Serp. Gasp endocytosis is clathrin dependent and presum-
ably involves an unidentified surface receptor. These genetic experiments suggest that Emp controls
tracheal tube elongation and luminal clearance of chitin deacetylases presumably by mediating their
endocytosis.

A Serp B
wild-type
emp e3d1
e3d1
emp ;btl>Emp
Relative tracheal length

e3d1
emp ;btl>CD36
C Serp Verm Gasp
wild-type stg
t late17
emp e3d1
D GaspFL- VermFL-GFP SerpFL-GFP E

mCherry
wild-type
e3d1
e
e3 d
d1
e3d1
emp
F Serp Verm Gasp H
wild-type stg 16
wild-type stg late 17
chc1 stg 16
chc1 stg late 17
Figure 1. empe3d1 mutants show over-elongation of the tracheal tubes and severe luminal clearance defect of Serp. (A) Images showing the dorsal
trunk (DT) of wild-type, empe3d1, empe3d1;btl>Emp, empe3d1;btl>CD36 embryos stained for the luminal marker Serp. (B) Graph showing the tracheal
DT length in wild-type embryos (n = 16), empe3d1 mutants (n = 17), empe3d1;btl>Emp (n = 19) and empe3d1;btl>CD36 (n = 15) embryos. (C) Confocal
images showing the DT of wild-type and empe3d1 mutant at late stage 17 embryos, stained for the endogenous luminal proteins Serp, Verm, and
Figure 1 continued on next page

Figure 1 continued
Gasp. (D) Confocal images showing the DT of live btl>GaspFL-mCherry (magenta), btl>VermFL-GFP and btl>SerpFL-GFP (green) in wild-type, and
empe3d1 mutant at 20.0 h AEL. (E) Plots showing the percentage of embryos with completion of luminal clearance in btl>VermFL-GFP (green, n = 59),
empe3d1;btl>VermFL-GFP (green, n = 37), btl>SerpFL-GFP (green, n = 58), empe3d1;btl>SerpFL-GFP (green, n = 15), btl>GaspFL-mCherry (magenta, n =
28) and empe3d1;btl>GaspFL-mCherry (magenta, n = 18). Representative confocal images showing the tracheal DT of wild-type (F) and chc1 (G) mutant
embryos, stained for the endogenous luminal markers Serp (magenta), Verm (yellow), and Gasp (green) before and after luminal clearance, stage 16 and
late stage 17 (n ≥ 8, for each genotype were analyzed). (H) Bar graph shows the percentage of embryos that fill with gas in wild-type (n = 177), empe3d1
(n = 182), empe3d1; btl>Emp (n = 119), empe3d1;btl>Emp-GFP (n = 178), and empe3d1; btl>CD36 (n = 70) embryos. Error bars denote standard error of the
mean (SEM), p > 0.05 not significant (ns), **p < 0.005, ***p < 0.0005, and ***p < 0.0001 (unpaired two-tailed t-tests). Scale bars, (A) 50 μm, (C, D) 10 μm,
and (F) 5 μm.
The online version of this article includes the following source data and figure supplement(s) for figure 1:
Figure supplement 1. Conserved function of Emp and its human homolog CD36.
Figure supplement 1—source data 1. This zip archive contains the raw unedited western blot shown in Figure 1—figure supplement 1.
Dynamic subcellular localization of Emp during tracheal development

To further elucidate Emp functions, we generated an antibody against its extracellular domain
(Figure 1—figure supplement 1B) and determined its subcellular localization by co-staining for
the previously characterized apical membrane proteins, Crb and Ptp10D, markers of adherens junc-
tions (DE-cad, pY) and septate epithelial junctions (Disc Large/Dlg, Coracle/Cora). During tracheal
branch elongation (stage 14–16), wild-type embryos showed an Emp enrichment in epithelial apical
membranes and in subapical cytoplasmic puncta (Figure 2A, B). Similar to the tracheal cells, Emp
showed apical localization, initially diffuse in dots in subapical regions and progressively more
defined at the apical cortical region in the epidermis, hindgut and tracheal terminal branches of stage
15–16 wild-type embryos (Figure 2—figure supplement 1A, B and Figure 2—figure supplement
2). During late stage 16 to early stage 17, Emp localization became predominantly restricted in the
junctional subapical region of tracheal, epidermal, and intestinal cells, where it colocalized with Crb,
DEcad-GFP, and Phospho-Src (Figure 2A, C and Figure 2—figure supplement 1A–C). The Emp
signal showed only weak colocalization with the SJ markers Coracle, Mtf, Dlg, and with the lateral
cytoskeleton marked by α-Spectrin (Figure 2—figure supplement 1A–C). The massive uptake of
luminal material correlates with the disassembly of apical actin bundles running along the transverse
tube axis. The diaphanous-like formin, DAAM and the type III receptor tyrosine phosphatases, Ptp4E
and Ptp10D, control the organization of F-actin bundles running along the perpendicular tube axis
in the Drosophila airways (Matusek et al., 2006; Tsarouhas et al., 2019). Mutations in Ptp10D4E
(Ptp10D and Ptp4E) or expression of a dominant negative form of DAAM (btl>C-DAAM) disrupt the
transverse actin bundle arrays and prematurely initiate luminal protein clearance. Similarly, Latrun-
culin A (Lat-A) injection in embryos destroys the actin bundles and leads to luminal protein uptake.
These experiments had suggested that the transverse F-actin bundles restrict the endocytic uptake of
luminal cargoes (Tsarouhas et al., 2019). We analyzed wild-type embryos over-expressing the GFP-
tagged actin-binding domain of moesin (btl>moe-GFP) in tracheal cells stained for Emp and GFP.
This showed low colocalization (r2 = 0.218, n = 5) suggesting distinct apical membrane domains of
Emp and actin bundles (GFP) (Figure 2—figure supplement 3A–D). We infer that Emp is predomi-
nantly localized in F-actin bundle-free membrane regions to promote the endocytosis and recycling
of selected luminal cargos along the longitudinal tube axis. Next, we tested whether the localization
of Emp may be altered in Ptp10D4E mutants and in embryos overexpressing the dominant negative
C-DAAM construct in the airways. Embryos of both genotypes showed premature translocation of
Emp to the airway cell junctions compared to wild-type (Figure 2D, E). This suggests, that similar to
luminal protein uptake, the relocation of Emp to the apical junctional region can be induced by the
premature disassembly of the actin bundles. Additionally, we analyzed the localization and intensity
of Emp and Crb protein stainings along the apical membrane in wild-type and btl>C-DAAM embryos.
DAAM inactivation increased the intensity of apical Emp punctate accumulations compared to wild-
type (Figure 2F, G), further arguing that the transverse actin bundles restrict Emp localization at the
apical membrane.
To test if a subset of the apical Emp puncta may correspond to endocytic vesicles, we analyzed
the localization of Emp relatively to several YFP-tagged Rab GTPases (YRab), expressed at endoge-
nous levels. Co-staining for Emp and GFP (Dunst et al., 2015) showed an overlap with YRab5 (early

Figure 2. Dynamic apical distribution of Emp during tube maturation. (A) Confocal images showing dorsal trunk
(DT) projections, from stage 14, 15, and 17 embryos, stained for Emp and Crb (Crumbs). (B) Confocal images
of the DT in wild-type embryos stained for Emp and Ptp10D. Inset denotes a region of the apical membrane
(arrowheads) with Emp and Ptp10D co-localization. (C) Confocal images of embryonic gut cells stained for Emp,

Figure 2 continued
p-Src, α-Spectrin (α-Spec), and 4′,6-diamidino-2-phenylindole ( DAPI) showing the subcellular localization of Emp
in stage 17. (D) DT projections, from stage 15, 16, and 17 of wild-type and Ptp4E10D (4E10D) stained for Emp.
(E) Confocal image-projections of the DT cortex (depth: 5.2 μm) in wild-type and btl>C-DAAM/+ (stage early-16)
embryos stained for Emp and Crb. Emp is prematurely enriched at the AJs in btl>C-DAAM/+, but not in wild-type
embryos (arrowheads). Images in insets are single longitudinal sections depicting the luminal borders of the tubes.
Note: btl>C-DAAM/+, displays irregular tubes with ellipsoid dilations. (F) Confocal images showing the tracheal
DT of wild-type and btl>C-DAAM/+ embryos stained for Emp and Crb. Insets show magnified regions of (F),
indicated by the white rectangles. The apical or basal sides of the tracheal cells are indicated. (G) Bar plot showing
the relative intensity of apical Emp puncta at DT (Tr8) in wild-type (n = 168 puncta, 5 embryos) and btl>C-DAAM
(n = 237 puncta, 6 embryos). Statistically significant shown in p-values, ***p < 0.0005 (unpaired two-tailed t-tests).
Scale bars, 5 μm (A, E, F) and 10 μm (B, C, D).
The online version of this article includes the following figure supplement(s) for figure 2:
Figure supplement 1. Emp localization.
Figure supplement 2. The apical localization of Emp in dorsal trunk (DT) and terminal branches.
Figure supplement 3. Low apical co-localization of Emp with the cortical actin bundles.
endosomes) and YRab7 (late endosomes) with the Emp positive cytoplasmic puncta. We also detected
weaker colocalization with YRab11 (recycling endosomes), (Figure 3A). Live imaging of embryos
expressing btl>Emp-GFP in the time interval of luminal protein clearance (early stage 17) showed
an increase of Emp intracellular puncta compared to stage 15 or late stage 17 embryos (Figure 2—
figure supplement 1D). Overall, these experiments suggest that the localization of Emp in the apical
membrane and endocytic vesicles is dynamic and influenced by actin bundle integrity. The timing of
the final, steady-state accumulation of Emp is controlled by PTP signaling.
Serp internalization and endosomal targeting requires Emp

The luminal retention of Serp in emp mutants and the partial localization of Emp with endosomal
markers led us to examine if Emp mediates the endosomal uptake and subsequent trafficking of
luminal Serp. We co-stained for endogenous YFP-tagged endosomal markers and Serp in wild-type
and emp mutant embryos. This analysis showed that intracellular Serp puncta co-stained for the
early endosomal marker Rab5 (Figure 3A–C; arrows, r2 = 0.29) and late endosomal marker, Rab7
(Figure 3A–C; arrows, r2 = 0.27) in wild-type embryos. In the emp mutants, the colocalization of Serp
with both early and late endocytic markers was significantly decreased (Figure 3B, C), suggesting that
Emp mediates Serp internalization and endosomal vesicle targeting.
In addition, the number of intracellular Serp puncta was reduced in emp mutant embryos compared
to wild-type (Figure 3—figure supplement 1A), whereas the total number of GFP puncta corre-
sponding to early and late endosomes remained unchanged (Figure 3—figure supplement 1B). The
large size of YRab7 vesicles appeared reduced in emp mutants, presumably due to impaired apical
internalization and targeting of cargoes to late endosomes. Because Emp also shares homology with
the mammalian lysosomal integral membrane protein-2 (LIMP-2) (Hart and Wilcox, 1993), we cannot
exclude an additional function of Emp in endo-lysosomal integrity and trafficking. Taken together, these
results suggest that Emp functions as a receptor for Serp internalization and endosomal targeting.
To further investigate Emp cargo specificity, we tested the luminal clearance of GFP constructs,
tagged with different domains of Serp in wild-type embryos and emp mutants (Figure 3D). We used
GFP constructs fused to either Serp-full-length or to the Serp-LDLr-domain (low-density lipoprotein
receptor-domain) or to the Serp-CBD-domain (chitin-binding domain) (Luschnig et al., 2006; Wang
et al., 2006) and examined their luminal secretion and clearance. The constructs were expressed
and similarly secreted into the tracheal tubes of wild-type and emp mutant embryos. The Serp-LDLr
reporter was cleared from the lumen efficiently as the full-length Serp-GFP but the CBD-GFP fusion
was retained in the tracheal lumen of 20% of wild-type embryos. Interestingly, both the Serp-GFP and
LDLr-GFP were retained in the lumen of emp mutants. These results suggest that the LDLr-domain of
Serp, targets GFP to Emp-mediated internalization. CBD-GFP clearance failed in only 40% of the emp
mutants suggesting that this cargo is also internalized by additional unknown receptors (Figure 3E,
F). To further test if the addition of the LDLr-domain is sufficient to target an unrelated protein for
Emp-mediated uptake, we fused the Serp LDLr-domain to the Gasp-mCherry protein, which does not

A YRab5 Serp Emp YRab5 Serp Emp
wild-type
YRab7 Serp Emp YRab7 Serp Emp
wild-type
YRab11 Serp Emp YRab11Serp Emp
wild-type
B YRab5 Serp YRab5 Serp C
empe3d1
YRab7 Serp YRab7 Serp
empe3d1
YRab11 Serp YRab11 Serp
empe3d1
D SP ChtB2 LDLr DA GFP FL

Serp - GFP SP ChtB2 ChtB2 ChtB2 mCherry
FL
Gasp - mCherry
LDLr LDLr
SP LDLr GFP Serp - GFP SP ChtB2 ChtB2 ChtB2 LDLr mCherry Gasp - mCherry
CBD
SP ChtB2 GFP Serp - GFP
E F
Figure 3. The endosomal localization of Serp is strongly reduced in empe3d1 mutants. (A) Confocal images of tracheal dorsal trunk (DT) of wild-type
embryos expressing endogenous tagged YFP-Rab (knock-in) proteins, YRab5, YRab7, and YRab11 stained with Emp, Serp, and GFP. Insets show
zoomed cross section views of the DT (y–z plane) of Emp co-localization with YRab5, YRab7, and YRab11, as indicated with red arrowheads. (B) Confocal
images showing the tracheal DT, stained for Serp and endogenous YRab5, YRab7, and YRab11 in empe3d1 mutant. (C) Scatter plots representing

Figure 3 continued
the co-localization between the YRabs and Serp in wild-type and in emp3ed1 mutants calculated by Pearson correlation coefficient (r2). (D) Schematic
representation of Serp and Gasp domain organization. The following abbreviations are used: SP, signal peptide (blue); LDLr, low-density lipoprotein
receptor (black); ChtB, chitin-binding domain (black); GFP (green); Cht BD2, chitin-binding domain (black); and mCherry (magenta). btl>SerpFL-
GFP represents the full length of Serp, btl>SerpLDLr-GFP represents the LDLr-domain of Serp, btl>SerpCBD-GFP expresses ChtB domain of Serp,
btl>GaspFL-mCherry represents the full-length Gasp protein and btl>GaspLDLr-mCherry represents the full-length Gasp protein with addition of
the LDLr-domain. (E) Confocal images showing the DT of live btl>SerpFL-GFP, btl>SerpLDL-GFP, btl>SerpCBD-GFP (green) embryos before (18.0 h
AEL) and after (20.0 h AEL) luminal protein clearance. btl>SerpCBD-GFP embryos show incomplete luminal GFP clearance compared to btl>SerpFL-
GFP or btl>SerpLDLr-GFP. (F) Plots showing the percentage of embryos with completion of luminal clearance in btl>SerpFL-GFP (green, n = 58);
empe3d1;btl>SerpFL-GFP (green, n = 15); btl>SerpLDLr-GFP (green, n = 3 2); empe3d1;btl>SerpLDLr-GFP (green, n = 26); btl>SerpCBD-GFP (green, n =
45); empe3d1; btl>SerpCBD-GFP (green, n = 28); btl>GaspFL-LDLr-mCherry (magenta, n = 57); and empe3d1;btl>GaspFL-LDLr-mCherry (magenta, n = 56),
from at least five independent experiments. The median (horizontal line) is shown in the plots with the data range from 25th to 75th percentile. Error
bars denote standard error of the mean (SEM), *p < 0.05, ** p < 0.01, and ***p < 0.0005 (unpaired two-tailed t-tests). Scale bars, 5 μm (A, B) and 10 μm
(E).
The online version of this article includes the following figure supplement(s) for figure 3:
Figure supplement 1. Quantification of Serp internalization.
require emp for its luminal clearance. As with the Serp-based constructs we analyzed the clearance
of GaspFL-mCherry and GaspFL+LDLr-mCherry in wild-type and emp mutant embryos. Both constructs
were normally cleared form the airways of wild-type embryos. However, btl>GaspFLFL+LDLr-mCherry,
but not btl>GaspFL-mCherry, was retained in the airways of emp embryos (Figure 3F). These data
suggest that the LDLr-domain can confer cargo specificity for Emp-mediated internalization. Loss of
function verm serp mutants or overexpression of Serp-GFP leads to over elongation of the tracheal
tubes (Luschnig et al., 2006; Wang et al., 2006). We thus examined the effects of Serp and Verm on
the levels and localization of Emp. btl>Serp-GFP overexpressing embryos showed increased punc-
tate accumulations of Emp and Crb at the apical cell surface compared to wild-type (Figure 4A).
Conversely, in vermex245,serpex7 double mutants, we detected more diffuse punctate cytoplasmic accu-
mulations for both Emp and Crb compared to wild-type (Figure 4A, B). To investigate whether the
changes in intensity and localization of Emp and Crb puncta upon Serp-GFP overexpression or verm
and serp deletion were due to changes in protein synthesis or stability we performed western blots
of mutant and wild-type embryos. The total protein levels of Crb and Emp did not change in the
mutants suggesting that the levels of luminal Serp control the punctate accumulation of Emp and Crb
at the apical membrane (Figure 4D–F). As expected, overexpression of Emp in the airways (btl>Emp)
increased the overall levels of cytoplasmic Emp, without a major influence on the accumulation of
Crb (Figure 4A–C). Overall, these data suggest that the levels of luminal cargo control the punctate
accumulation of Emp and Crb at the apical membrane. btl >Serp-GFP overexpression also causes
DT tube over-elongation. This phenotype is similar to the loss-of-function phenotype of verm serp
double mutants (Wang et al., 2006) and argues that deviations of the normal luminal Serp levels, too
low or too high, can similarly cause tube over-elongation. Measurements from the Tr5 to Tr10 showed
reduced DT elongation in emp;btl>Serp-GFP embryos compared to btl>Serp-GFP, suggesting that
Serp-GFP overexpression control the length of the Drosophila airways, at least partially, through Emp
(Figure 4G). Overall, these results suggest that Emp acts as a scavenger receptor for LDLr-domain
proteins, such as Serp, thereby facilitating their internalization through clathrin-independent endocy-
tosis. The levels of luminal Serp-GFP influence the localized apical membrane accumulation of Emp
and Crb and interfere with tube elongation.
Emp controls tube morphogenesis

Crb and DE-cad trafficking underlies the anisotropic growth of the apical surface and elongation of
Drosophila airways (Förster and Luschnig, 2012; Nelson et al., 2012). We first quantified the ratio of
longitudinal/transverse cell junction lengths (LCJ/TCJ) in emp mutants and wild-type embryos stained
for Crb. The longitudinal junction length and aspect ratio (LCJ/TCJ) of emp mutant tracheal cells
significantly increased, while the length of junctions along the transverse tube axis was not affected
(Figure 5A–C).
The selective accumulation of the apical polarity protein Crb at longitudinal junctions relates
to tube elongation (Olivares-Castiñeira and Llimargas, 2018). Consistent with this, we detected

A B C
FP
D
-G
7
rp
p ex
Se
p e3 FP
er
tl>
-G
,s
5
;b
pe
24
rp
d1
d1
ex
p e3
Se
-ty
rm
ild
l>
em
em
ve
bt
w
vermex245,serpex7 250 --
Crb
Emp
50 --
50 -- Tubulin
G 400
E F *** **
DT length um (tr5-10)
*
300
200
100
0
FP
P
)
p
ch
tl> -GF
em
-G
m
rp
p
X
er
Se
A
d1 S
A
p e3 tl>
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bt
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em
Figure 4. Serp-GFP overexpression induces apical Emp accumulations and tracheal over-elongation. (A) Confocal images stained for Emp and Crb, in
wild-type, btl>Serp-GFP, vermex245,serpex7 mutant, and btl>Emp embryos. Inset shows zoomed view of Emp and Crb signals. The arrows indicate the
accumulation of Emp and Crb in yz plane. Bar plots showing total fluorescence intensities of apical enriched Emp (B) or Crb (C) in wild-type (n = 15),
btl>Serp-GFP (n = 12), vermex245,serpex7 (n = 10) mutant, and btl>Emp (n = 7) embryos. (D) Representative western blot from protein lysates of wild-type,
empe3d1, btl>Serp-GFP, empe3d1;btl>Serp-GFP and vermex245,serpex7 mutants, blotted for Emp and α-Tubulin. (E) and (F) show the quantification of protein

Figure 4 continued
levels of Emp and Crb, respectively, based on four independent western blot experiments (n = 4). (G) Plots representing the length of the tracheal dorsal
trunk (DT) in µm (tr 5–10) from btl>CAAX-mcherry (control, n = 15), emp e3d1 (n = 10), btl>Serp-GFP (n = 37) and emp e3d1;btl>Serp-GFP (n = 29) embryos.
Statistical significance shown in p-values; ****p < 0.0001, ***p < 0.0005, **p < 0.01, *p < 0.05, and p > 0.05 not significant (ns) (unpaired two-tailed
t-tests). Scale bars, 5 μm.
Source data 1. This zip archive contains the raw unedited western blot shown in Figure 4D.
Figure supplement 1. Epithelial cell integrity is not affected in empe3d1 mutants.
increased Crb signals along the longitudinal but not transverse junctions in over-elongated tubes of
emp mutants (Figure 5D–F). Stainings for the AJ component DE-cad showed increased levels along
both longitudinal and transverse junctions in emp mutants (Figure 5D–F). To examine whether the
intensity differences may be due to changes in overall protein levels, we analyzed the relative protein
levels of Crb and DE-cad in emp mutants by western blots. We observed no significant difference in
total protein levels of Crb (Figure 5GI) or DE-cad (Figure 5H, J) in emp mutant embryos compared
to wild-type. These results suggest that Crb accumulates in LCJ and DE-cad in LCJs and TCJs in emp
mutants presumably due to defects in their endocytic uptake and trafficking. The relative LCJ vs. TCJ
intensities (Raw Intensity/Junctional length) of stainings for the AJs component α-CAT (α-Catenin) (Pai
et al., 1996) and the SJs protein Dlg (disc large) (Olivares-Castiñeira and Llimargas, 2018; Sharifk-
hodaei et al., 2019) were indistinguishable between emp and wild-type embryos (Figure 4—figure
supplement 1A–D), suggesting that intracellular junction components are intact in the mutants. Simi-
larly, a dextran leakage assay comparing paracellular junction integrity of wild-type, emp, and ATPα
mutant embryos showed that emp loss does not affect general SJ integrity (Figure 4—figure supple-
ment 1E). Overall, these results suggest that Emp function regulates the apical membrane levels of
Crb and DE-cad without majorly affecting junctional integrity or function.
Emp modulates the apical actin organization

Our analysis until now suggests that Emp is a scavenger receptor involved in the continuous, basal-
level trafficking of Serp during tube elongation and in its massive uptake during luminal protein clear-
ance. Since the organization of the transverse actin bundles restrict both tube elongation and the
timing of luminal protein clearance, we investigated the apical actin cytoskeleton in emp mutants. We
first examined the apical F-actin in DTs of late stage embryos by live imaging using btl>Moe-GFP. At
17.5 h AEL, at the time interval of airway protein clearance, emp mutants showed a more diffuse and
continuous apical actin bundle density compared to wild-type embryos (Figure 6A, B and Figure 6—
figure supplement 1E). We also detected higher apical accumulation of the dDAAM formin, in emp
mutants compared with wild-type embryos by antibody stainings. Stainings for Gasp that visualized
the forming taenidial of ECM, did not show detectable defects in chitin deposition in the emp mutants
(Figure 6C). These observations suggested that Emp modulates the actin bundle organization at the
apical membrane, presumably upon engagement with its luminal cargoes.
To identify proteins that might provide a direct connection between the cytoskeleton and Emp,
we used the cytoplasmic C-terminus of Emp (484–520 aa) as bait in a yeast two hybrid (Y2H) screen
at Hybrigenics. This uncovered three potential interacting proteins, CG32506 encoding a RabGAP
protein, CG34376 encoding a protein with a predicted Zinc Finger motif and βH-Spec/Kst (Figure 6D).
We further characterized the interaction with βH-Spec/Kst because of its established role in the apical
cytoskeleton organization in Drosophila epithelial tissues (Thomas and Williams, 1999; Phillips
and Thomas, 2006). The α- and β-heavy Spectrin subunits form tetramers, which assemble in two
dimensional networks together with actin underneath the apical plasma membranes. Additionally,
βH-Spec/Kst is required for the early steps and endocytic trafficking of V-ATPase in the brush border
of intestinal epithelial cells (Phillips and Thomas, 2006). We used a knock-in, fusion construct of Venus
into the kst locus to detect endogenous, βH-Spec/Kst together with Emp and α-Spectrin in epithe-
lial cells of the trachea and hindgut. As expected Kst-Venus colocalized with Emp apically, whereas
α-Spectrin was also detected along the lateral sides (Figure 6E and Figure 6—figure supplement
1D). To confirm the Emp binding to Kst and also map their interaction domains we used immuno-
precipitation experiments of tagged proteins in Drosophila S2 cells. We expressed V5-tagged Emp

B C
A
D Crb DEcad Crb DEcad

TCJ
LCJ
wild-type
empe3d1
E F
G H I J
d1
pe
pe
d1
e3
p
e3
p
-ty
-ty
em em
ild
ild
w
w
250 -- Crb
150 -- DE-cad
75 --
75 --
Lamin
Lamin
Figure 5. Emp modulates the Crb and DE-cad levels to control tracheal tube elongation. (A) and (B) bar plots showing the length (in μm) of longitudinal
and transverse cell axis, respectively, in wild-type and empe3d1 embryos. (C) Bar plots showing the aspect ratio, between longitudinal over transverse
axis (LCJ/TCJ) in wild-type (n = 30), and empe3d1 (n = 30), mutant embryos. ****p < 0.0001, ***p < 0.0005, and p > 0.05 not significant (ns) (unpaired
two-tailed t-tests). (D) Projection images of wild-type and empe3d1 mutant embryos, from stage 16, stained for Crb and DE-cadherin. (E) and (F) show

Figure 5 continued
quantifications of the fluorescence intensities of Crb and DE-Cadherin along longitudinal (E) and transverse (F) axis in wild-type (n = 78), and empe3d1 (n
= 66), mutants. ****p < 0.0001 and **p < 0.01 (Mann–Whitney test). Representative western blot from protein lysates of wild-type and empe3d1 mutants,
blotted with anti-Crb (G) or anti-DE-cad (H) and anti-Lamin (control). (I) and (J) are quantifications of Crb and DE-cad protein levels, respectively, based
on three independent western blot experiments (n = 3). Statistical significance shown in p-values; p > 0.05 not significant (ns) (unpaired two-tailed t-
tests). Scale bars, 5 μm.
The online version of this article includes the following source data for figure 5:
Source data 1. This zip archive contains the raw unedited western blot shown in Figure 5G, H.
and a series of constructs expressing different fragments of βH-Spec/Kst protein fused to the FLAG
epitope. We found that the intracellular C-terminus of Emp co-precipitates with the C-terminal region
of βH-Spec/Kst (Figure 6F) consistent with their interaction detected in the Y2H system. Additionally,
kst2 mutants show similar tracheal over elongation phenotypes with emp suggesting a functional
interaction between Emp and Kst (Figure 6—figure supplement 1A, B). To further test this, we
analyzed the localization and abundance of tagged βH-Spec/Kst in the airways of emp mutants. The
apical levels of βH-Spec/Kst were severely reduced, while Crb staining was increased and staining of
an unrelated apical protein Uninflatable remained unaffected in the emp mutants compared to the
wild-type (Figure 6G–I). The localization or levels of Emp were not noticeably affected in kst mutants
(Figure 6—figure supplement 1C). Together, these results indicate that the C-terminal intracellular
domain of Emp binds to apical βH-Spectrin (Kst) and controls the spectrin cytoskeleton presumably by
stabilizing βH-Spec/Kst. Additionally, in emp mutants the intensity and distribution of actin bundles is
distorted and the levels of the diaphanous-related formin, DAAM are increased.
Emp regulates Src phosphorylation

Src phosphorylation and activation are required for tracheal tube elongation and controls Crb accu-
mulation at the longitudinal cell junctions (Olivares-Castiñeira and Llimargas, 2018), and the Beitel
laboratory proposed that Src together with DAAM orient the directed membrane expansion during
tube elongation (Nelson et al., 2012). Since emp mutants showed higher Crb accumulation in longitu-
dinal junctions and an overall increase in the apical levels of DAAM, we compared Src phosphorylation
(p-Src) levels by immunostainings and by western blot in wild-type, emp mutants, btl>Serp-GFP and
emp;btl>Serp-GFP embryos (Figure 7A–C). The specificity of the p-Src419 antibody was first confirmed
by staining of src42A src64B double mutants (Figure 7—figure supplement 1A). Both immunos-
taining and western blot analysis showed increased p-Src levels in emp mutants compared to wild-
type (Figure 7A–C). Interestingly, p-Src levels were also increased in the verm serp double or verm
serp heterozygous (Figure 7—figure supplement 1C, D). Mutant embryos and decreased in wild-
type embryos overexpressing btl>Serp-GFP (Figure 7B) This decrease by Serp overexpression was
partly ameliorated in emp mutants (Figure 7A–C), suggesting that the effect of Serp-GFP overexpres-
sion on Src phosphorylation is, at least partly, mediated by Emp on the cell surface. We also detected
increased p-Src levels in total protein extract from emp and verm serp mutant embryos (Figure 7B)
suggesting that their interaction controls Src phosphorylation in other ectodermal tissues. In agree-
ment with this, neurons of the ventral neve cord in emp mutant embryos also showed increased
p-Src levels compared to wild-type (Figure 7—figure supplement 1B). To test if the increase in p-Src
levels in emp mutants underlies the apical membrane over-elongation defects, we performed genetic
interaction experiments between src42A and emp mutants. As expected, emp mutants showed over-
elongated tubes while the src42AE1 mutants showed short tubes (Nelson et al., 2012). The increase of
tube length in emp mutants was significantly suppressed in emp; src42AE1 embryos, where the levels
of Src protein were reduced (Figure 7D, E). Similarly, the increased apical accumulation of Crb and
DE-cad in emp mutants was partly restored by overexpression of a Src42ADN dominant negative form
(Src42ADN) in emp mutant embryos (Figure 7—figure supplement 1E–H). Previous work has shown
that changes in chitin synthesis or ECM integrity affects the levels of phosphorylated Src42A (pSrc) at
cell junctions (Öztürk-Çolak et al., 2016). Verm and Serp loss also causes p-Src upregulation and over-
elongation and we also show that Serp overexpression leads to p-Src downregulation as expected
(Figure 7B). Counter intuitively, Serp overexpression also results in tube over-elongation (Wang et al.,
2006). Although Src42A is necessary and sufficient for cell shape changes during tracheal tube elon-
gation (Förster and Luschnig, 2012; Nelson et al., 2012), this overexpression paradox could be

A B Longitudinal section
Longitudinal section
C'
C GASP GASP D
GASP
Longitudinal section C'' Emp
C-terminus
C'
βH Spectrin/Kst
empe3d1
4007bp
C' C'' 26bp 3475bp
Input
F
IP:Flag
1633-1903
1904-2632
2594-4097
1-1632
1633-1903
1904-2632
2594-4097
1-1632
Kst
Kst
Kst
Kst
NT
Kst
Kst
Kst
Kst
NT
100 --
100 --
Emp
Emp
1-1632 2594-4097
Kst * Kst
1-1632 2594-4097 150 -- *
Kst
150 -- * * Kst
1633-1903
* Kst
1904-2632 75 -- 1904-2632
75 -- * Kst
*
Kst
37 --
1633-1903 Tubulin
37 -- * Kst 50 --
G
H
Figure 6. Loss of Emp affects apical F-actin organization. (A) Confocal images showing live dorsal trunk (DT) of wild-type and empe3d1 mutant embryos
from 17.5 h AEL expressing the actin reporter btl>moe-GFP. (A’, A’’) zoomed views of areas indicated by the rectangular frames of (A) panel. (B)
Confocal images of dDAAM stainings in wild-type and empe3d1 mutant embryos. (B’, B’’) shows magnified regions of (B), indicated with white rectangle.
(C) Confocal images of GASP stainings showing the DT in wild-type and empe3d1 mutant embryos at stage 17. (C', C'') are magnified regions of the

Figure 6 continued
apical extracellular matrix (ECM) as indicated by the rectangular frames in (C) panel. (D) Schematic view of the interaction domain of Emp C-terminus
in 3475–4007 bp region of βH-Spectrin/Kst, as obtained by the Y2H screen. The tested Y2H prey-clones were covered the 26–4007 bps of the gene.
(E) Confocal images showing the DT of Kst-Venus expressing embryos (wild-type) stained for Emp, GFP (kst), and α-Spec (α-Spectrin). (F) Co-
immunoprecipitation of Flag-tagged Kst constructs from transfected S2 cells lysates, blotted with anti-Emp and anti-Flag. Input 2% is indicated. Red
stars (*) denote the coresponding Kst band. st band. (G) Confocal images showing endogenous Kst-Venus in the DT of wild-type and empe3d1 mutants,
stained for GFP (kst) and Uif (Uninflatable). (H) Bar plot showing Kst-GFP levels in wild-type (n = 5), and empe3d1 (n = 5), mutant embryos in relation to Uif.
(I) Confocal images showing wild-type and empe3d1 mutant embryos stained for GFP (kst) and Crb. Statistical significance shown in p-value, * p < 0.05
(unpaired two-tailed t-tests) (H). Scale bars, 5 μm (B, D, F, H) and 10 μm (A).
Source data 1. This zip archive contains the raw unedited western blots shown in Figure 6E.
Figure supplement 1. Tube elongation is defected in kst2 mutants.
explained by an indirect and src-independent effect of the overexpressed luminal Serp-GFP on tube
elongation.
Discussion
Emp, a CD36 homolog, is a selective scavenger receptor required for endocytosis of a subset of
luminal proteins. The endocytosis defects in emp mutants become most apparent during the massive
endocytosis wave that removes all secreted luminal components just before gas-filling of the airways.
Our comparison of the endocytosis requirements of Serp and Gasp together with the LDLr-domain
swap experiments defined a subset of Emp cargoes and indicates that the LDLr-domain targets
cargoes to Emp through clathrin-independent endocytosis. These selective requirements of Serp and
Gasp internalization are consistent with the view that the choice of endocytic route is a cargo-driven
process (Mettlen et al., 2018).
The machinery involved in class B scavenger receptor endocytosis have not been characterized
in Drosophila, but an important characteristic of all clathrin-independent endocytosis pathways is
their dependance on the dynamic control of actin polymerization to distort the plasma membrane
for cargo internalization (Mayor et al., 2014). Pioneering biochemical experiments suggested that
CD36 receptor clustering is essential for its internalization and signaling in response to multivalent
cargo binding. Single molecule tracking of CD36 in primary human macrophages showed that the
un-ligated receptor diffuses in linear confinement tracks set by the actin cytoskeleton. These diffusion
tracks enable clustering and internalization upon oxLDL-ligand addition (Jaqaman et al., 2011). Simi-
larly, in human endothelial cells the actin cytoskeleton is required for the increase of CD36 clustering
upon thrombospondin binding and Fyn, a Src-family kinase, activation (Githaka et al., 2016). These
studies argue that CD36 is confined in cytoskeletal tracks and cargo/ligand binding induces its clus-
tering and signaling ability. Similarly, to CD36, Emp function is also tightly connected with the apical
cytoskeleton. First, emp activity is confined in apical ‘macro’-domains along the longitudinal tube axis
by the transverse, DAAM-dependent actin filaments. Disruption of these filaments induces massive
endocytosis and re-localization of Emp. Additionally, the initially punctate Emp distribution along the
apical membrane becomes aggregated upon overexpression of luminal Serp, suggesting that LDLr-
domains on chitin-binding proteins induce Emp clustering. Apart from the Emp similarities to CD36,
our results also reveal an unexpected direct function of Emp in organizing the apical Spectrin and actin
cytoskeleton. The distribution of the DAAM-formin, the transverse actin bundle density and the apical
accumulation of Kst are all disrupted in emp mutants. Because we showed that the conserved C-ter-
minal intracellular domain of Emp binds directly to Kst, we propose that a central function of Emp,
and possibly CD36, is to also directly organize the epithelial cytoskeleton. This notion is supported
by the ability of human CD36 to partially rescue the emp mutant phenotypes when overexpressed in
the Drosophila airways.
How can a scavenger receptor restrict epithelial tube elongation? In the interval of embryonic
stages 13–16, regulated Src and DAAM activities promote tube elongation and the formation and
alignment of the transverse actin bundles (Matusek et al., 2006). These bundles inhibit Emp inter-
nalization and restrict Serp endocytosis and trafficking to the longitudinal tube axis. We showed
that Emp is directly linked to the apical βH-Spectrin cytoskeleton and is required for its assembly.

projections
projections
B C
FL
FP
-G
rp
7
FL
p ex
Se
FP
er
tl>
-G
,s
;b
5
pe
d1
d1
24
rp
p e3
p e3
ex
-ty
Se
rm
ild
em
em
l>
ve
bt
w
75 --
p-Src
50 --
50 -- Tubulin
D Verm E
wild-type
Relative tracheal length
empe3d1
src42AE1
empe3d1,src42AE1
Figure 7. Elevated p-Src levels in empe3d1 mutants. (A) Confocal images showing projection of the tracheal dorsal trunk (DT) of wild-type, empe3d1
mutants, btl>Serp-GFP and empe3d1;btl>Serp-GFP embryos at late stage 16 to early stage 17, stained for endogenous p-Src. (B) Representative western
blot from protein lysates of wild-type, empe3d1 mutants, btl>Serp-GFP, empe3d1;btl>Serp-GFP and verm,serp double mutant embryos, blotted with anti-
p-Src and anti-α-Tubulin. (C) Quantifications of p-Src protein levels based on three independent western blot experiments (n = 3). *p < 0.05 and **p <

Figure 7 continued
0.01 (unpaired two-tailed t-tests). (D) Representative images of tracheal length size (DT), in wild-type, empe3d1, src42AE1, and empe3d1,src42AE1 embryos
stained for the luminal marker Verm. (E) Plots show the quantification of tracheal DT length of wild-type (n = 6), empe3d1 (n = 7), src42AE1 (n = 10), and
empe3d1;src42AE1 (n = 7) embryos. Error bars denote standard error of the mean (SEM) wild-type, *p < 0.05, **p < 0.005, and ****p < 0.0001 (unpaired
two-tailed t-tests). Scale bars, 10 and 50 μm for images (A) and (D), respectively.
Source data 1. This zip archive contains the raw unprocessed western blots shown in Figure 7B.
Figure supplement 1. p-Src levels are increased in CNS of empe3d1 mutants.
This cytoskeletal organization might indirectly interfere with DAAM localization and presumably with
Src42A activation and function as also proposed by Nelson et al., 2012. These data suggest that
endocytosis of luminal proteins during tube elongation is controlled by at least two parallel path-
ways, one enabling Emp-endocytosis along the longitudinal tube axis and one restricting it along
the transverse axis. We hypothesize that in the bundle-free membrane domains, Emp associates
with Kst and presumably establishes an endocytosis domain, where Serp-mediated Emp clustering
leads to internalization (Figure 8A, B). A similar function for Kst enabling endocytosis and trafficking
of apical H+ V-ATPase has been proposed in the brush border of the larval Drosophila intestine,
where its anchoring to the membrane remains unknown. The luminal levels of chitin deacetylases,
like Serp, and other chitin modifying proteins are transcriptionally regulated (Yao et al., 2017) and
are predicted to control the biophysical properties of the apical ECM (Cui et al., 2016). We infer
that luminal Serp bound to chitin generates a multivalent ligand and is continuously recognized
and endocytosed by Emp selectively along the longitudinal tube axis. Together with the clustered
receptors, apical membrane and ‘passenger’ transmembrane proteins are expected to follow in the
Emp endocytic vesicles. The over-elongation defects in emp mutant airways can be explained by the
failure to balance elongation induced by Src activation with endocytosis of membrane and trans-
membrane regulators on the longitudinal tube axis (Figure 8A, B). Src42A phosphorylation levels
have been proposed as a feedback mechanism of the aECM to the underlying cells to modulate
proper cytoskeletal organization in airways (Öztürk-Çolak et al., 2016). Our work is complementary
to this mechanism and further argues that Emp senses and responds to the levels of specific ECM
cargoes by initiating apical membrane protein endocytosis and recycling during tube elongation.
After protein clearance, Emp and Crb accumulate at the subapical region of the longitudinal junc-
tions, where they could enable cytoskeletal interactions and the modulation of apical membrane
tension.
At the initiation of protein clearance, the transverse bundles are transiently resolved and luminal
proteins together with apical transmembrane proteins and membrane are massively internalized and
targeted for degradation or recycling to the junctional areas (Figure 8C). The mechanism of Crb recy-
cling in airway cells involves retromer components (Olivares-Castiñeira and Llimargas, 2017) but the
selective targeting mechanism to longitudinal junctions is still unknown. The re-localization of Emp to
the apical epithelial junctions during airway maturation is accompanied by massive alteration in Src
activity, which is not restricted to the tracheal system but is common to several ectodermal organs
including neurons. This suggests that scavenger receptor endocytosis has a general, but poorly under-
stood role, in embryonic morphogenesis of epithelial tissues. Our work on Emp provides an entry
toward elucidating the roles of scavenger receptor class B in development and pathogenesis.
Materials and methods

Drosophila strains
The empe3d1 null mutant was generated by FLP-FRT site-directed recombination using two piggyBac
elements (PBacWH#021071 and PBacRB#e0441541). Embryos trans-heterozygous for Df(2R)BSC08
and emp were lethal showing identical phenotypes to emp homozygous embryos (Supplementary
file 1). w1118 was used as the wild-type strain. In all experiments CyO and TM3 balancer strains carrying
dfd-GFP were used to identify the desired genotypes. Flies were raised at 25°C and 50% humidity,
with a 12-hr light–dark cycle.

Figure 8. The proposed model of Emp regulation. (A) 3D drawing shows the multicellular tube (dorsal trunk) of Drosophila airways. The annular ridges
of the apical extracellular matrix (ECM) are indicated in relation to the longitudinal elongation. LJ: Longitudinal junctions; TJ: transverse junctions. (B)
Schematic zoom of the apical ECM region (A) showing the formation of two apical domains in the membrane–cytoskeleton interface of tracheal cells
at 12–16 h AEL. Transverse F-actin bundles (white color zone) restrict apical Emp endocytosis along the transverse tube axis. In F-actin bundle-free

Figure 8 continued
membrane region (green color zone), Emp is associated with βH-Spectrin and Serp promotes Emp clustering leading to endocytosis and recycling of
Serp and others ‘passenger’ transmembrane proteins (i.e. Crb) along the longitudinal tube axis. (C) Drawing of the apical, SAR and AJ regions during
luminal protein clearance (18–19 h). Emp clears luminal Serp by endocytosis and trans-locates to the SAR/AJ to restrict p-Src42 activity and to control
DE-Cad, Crb levels at the SAR/AJ.
Molecular biology and transgenic flies

Complementary DNA (cDNA) encoding for Human CD36 (RC221976) was cloned using Hifi DNA
assembly kit (NEB E5520S) into the pJFRC-MUH vector (Addgene, plasmid 26213). bglII and XbaI
were used to clone the amplified PCR fragment. UAS-Emp transgene was generated by cloning the
cDNA sequencing of CG2727 by PCR amplification with primers containing EcoRI and KpnI. The UAS-
Gasp construct was generated by sequential cloning of Gasp cDNA using primers containing EcoRI
and XhoI. Further, LDLr-domain and mCherry were subcloned using enzymes XhoI and XbaI. The UAS-
SerpFL-GFP and UAS-SerpLDLr-GFP constructs were generated according to Luschnig et al., 2006, and
the UAS-SerpCBD-GFP was provided by S. Luschning. mCherry-Emp-V5His construct was cloned using
Hifi DNA assembly kit NEB E5520S into the pAc5.1/V5-His A vector (Invitrogen) using the following
enzymes Acc65I and XhoI. The different Kst constructs were generously provided by N. Tapon. All the
plasmids were confirmed by sequencing. Polyclonal antibody (anti-Emp) obtained by immunization
with bacterially expressed recombinant polypeptides corresponding to amino acids 46–460 of Emp-A.
Anti-sera obtained from immunized rats (Genscript).
Co-immunoprecipitation and western blot analysis

Drosophila S2 cell extracts and Co-IP were prepared as previously described (Tsarouhas et al.,
2019) and (Fletcher et al., 2015), respectively. The FLAG-tagged Kst constructs were provided
by Nic Tapon (Fletcher et al., 2015). For detection of purified proteins and associated complexes,
ChemiDoc XRS + system (Bio-Rad) was used. Western blots were probed with mouse anti-FLAG M2
(1:3000, Sigma, F3165), rat anti-Emp and rabbit anti-α-tubulin (1:2000, Cell Signaling, 11H10). For
western blot analysis, Drosophila embryos were collected 12–20 h AEL and lysed in 20 μl of lysis
buffer containing 50 mM HEPES (pH 7.6), 1 mM MgCl2, 1 mM ethylene glycol-bis(β-aminoethyl ether)-
N,N,N′,N′-tetraacetic acid (EGTA), 50 mM KCl, 1% NP40, Protease inhibitor cocktail tablets (Roche
#11697498001), and Phosphatase inhibitor cocktail 2 (Sigma-Aldrich #P5726). The lysates were centri-
fuged at maximum speed (30,060 × g) for 10 min at 4 °C. Protein loading buffer (50 mM Tris/HCl, pH
6.8, 2% sodium dodecyl sulfate (SDS), 5% glycerol, 0.002% bromophenol blue) was added to the
supernatant and samples were analyzed by SDS–polyacrylamide gel electrophoresis and immunoblot-
ting according to standard protocols, using the ChemiDoc XRS + system (Bio-Rad), after application
of the SuperSignal West Femto Maximum Sensitivity Substrate (Thermo Fisher Scientific, 34096). The
following primary antibodies were used at the indicated dilutions: rabbit anti-α-tubulin (1:2000, Cell
Signaling, 11H10), rabbit anti-Phospho-Src (1:750 Tyr418, Thermo Fisher), and Lamin ADL195 (1:100,
DSHB).
Quantification of western blots

For the western blot analysis, the actual signal intensity of each band of interest was estimated after
subtraction of the background using ImageJ/Fiji software. The values were then divided by the corre-
sponding intensity values of the loading control (α-tubulin or lamin).
Immunostaining
Embryos were dechorionated in 5% bleach and fixed for 20 min in 4% formaldehyde saturated in
heptane as described in Patel, 1994. The following antibodies were used: mouse anti-Ptp10D (1:10,
8B22F5, Developmental Studies Hybridoma Bank, DSHB), rabbit anti Phospho-Src (1:400, Tyr 419,
Thermo Fisher), mouse anti Dlg (1:100, 4F3 DSHB), mouse anti-Crb (1:10, Cq4 DSHB), mouse anti-
Coracle (1:100, C615.16 DSHB), DAAM antibody was a kind gift from József Mihály (Matusek et al.,
2006), rabbit anti-GFP (1:400, A11122, Thermo Scientific), chicken anti-GFP (1:400, abl3970, Abcam),
mouse GFP (1:200, JL-8, Clontech) gp anti-Verm (Wang et al., 2006), gp anti-Gasp (Tiklová et al.,
2013), mouse anti-Flag M2 (1:3000, Sigma, F3165), Serp antibody were provided by S. Luschning
(Luschnig et al., 2006). Secondary antibodies conjugated to Cy3 or Cy5 or Alexa Fluor-488 and -568

(Jackson Immunochemicals) were used and diluted as recommended by the manufacturer. For rat
anti-DE-Cad (1:50, DSHB) embryos were fixed with 4% paraformaldehyde (PFA)–heptane for 20 min.
Embryos expressing moe-GFP were dechorionated, devitellinized by hand and fixed in 4% PFA or
formaldehyde (methanol free) in phosphate-buffered saline–heptane or PEM (PIPES-EGTA-MgCl2)–
heptane mix, (PEM: 0.1 mM piperazine-N,N′-bis(2-ethanesulfonic acid) (PIPES) pH 6.9, 2.5 mM EGTA,
1 mM MgCl2) for 20 min. Embryos were de-hydrated and mounted in pure methyl-salicylate (Tran
et al., 2016). Stained embryos were imaged with an Airy-scan-equipped confocal microscope system
(Zeiss LSM 800, Carl Zeiss) using a Plan-Apo ×63/1.40 DIC oil immersion objective.
Yeast two-hybrid screen

The screen was carried out by HYBRIGENICS using a prey library constructed from RNA of embryos
that were 0–24 hr old. A fragment encoding the C-terminus domain of Emp (amino acids 484–520)
was inserted into the pB27 vector (N-LexA–bait-C fusion) and was used to screen 167 million clones.
qPCR
Embryos dechorionated in bleach, hand-sorted for GFP expression, collected in 300 ml of TRizol LS
Reagent and stored at −80°C until further use. For RNA extraction, the embryos were homogenized
in TRIzol LS Reagent using a 1.5-ml tube pestle and the total RNA was purified using the Direct-zol
RNA MicroPrep kit (R2060, Zymo Research). RNA was resuspended in RNase-free water and subse-
quently treated with DNAse I (AMPD1-1KT, Merk), for genomic DNA removal. Then 400 ng of RNA
was reverse transcribed using High-Capacity RNA to cDNA kit (4387406 Thermo Fisher). The cDNA
products were subsequently diluted 1:5 and 2 μl were used as a template in each qPCR reaction. qPCR
was performed using iTaq Universal SYBR Green Supermix (Bio-Rad). Generation of specific PCR prod-
ucts was confirmed by melting-curve analysis. Ct values for all genes were normalized to the levels of
Rp49. For data analysis, the delta-delta Ct values were applied. The sequences of primers used are
provided in Supplementary file 2.
Live imaging
Dechorionated embryos mounted in a glass-slide with a gas permeable membrane (Tsarouhas et al.,
2007). Widefield live imaging performed to analyze protein clearance and gas-filling on embryos as
described in Tsarouhas et al., 2019. For confocal live imaging, embryos were imaged with a scanning
confocal microscope (LSM 780, or 800 Carl Zeiss) equipped with an Argon and an HeNe 633 laser
using a C-Apochromat ×63/1.2 NA water objective. Z-stacks with a step size of 0.5–1.0 μm were taken
every 6 min over a 3–8 hr period. For high-resolution confocal live imaging, an Airy-scan-equipped
confocal microscope system (Zeiss LSM 800, Carl Zeiss) was used. Z-stacks (0.16–0.2 μm step size)
were taken every 15 min over a 2–4 hr period using a Plan-Apo 63 ×/1.40 DIC oil or a C-Apochromat
×63/1.2 NA water objective (Zeiss). Raw data were processed with the Airy-scan processing tool avail-
able on the Zen Black software version 2.3 (Carl Zeiss). Images were converted to tiff format using the
Zen Black or ImageJ/Fiji software.
Morphometric analysis
Tube length measurements were conducted in embryos stained for the luminal markers Verm or Serp.
Tracheal lengths were measured by tracing the length of the DT determined by the luminal markers
using the freehand line selection tool of ImageJ/Fiji software. For metamere length measurements,
we traced the DT length between the corresponding TC (transverse connective) branches. Longitu-
dinal and transverse cell junctions were defined according to the angles from the DT axis (angle = 0°).
Junctions with clear orientation angle 0° ± 30° or 90° ± 30° were defined as longitudinal or transverse,
respectively. The rate of gas-filling calculated as the percentage of embryos with gas-filled tracheae
divided by the total number of embryos analyzed.
Dextran injections
For dye-permeability assays, 10 kDa Dextran-TR (Thermo Fisher Scientific) was injected into late
stage 16 embryos (after the maturation of SJ) as described in Jayaram et al., 2008. Injections were
performed in a microinjection system (FemtoJet, Eppendorf) coupled to an inverted fluorescence
microscope (Cell Observer, Zeiss).

Quantification of fluorescence intensity

The total fluorescence intensity signal of Emp, Crb, DE-cad, Dlg, and α-Cat was measured with ImageJ
by manually drawing a 5-pixel line with the ‘Freehand Line tool’, over the junctional region of the
tracheal cells. The total fluorescence intensity in TCJ and LCJ of Crb and DE-cad was measured
according to Olivares- Castiñeira and Llimargas, 2018. Background signals of 5-pixel line were
subtracted from the intensities. For the quantification of fluorescent intensity on apical Emp positive
puncta, 0.75 μm2 squares on each puncture were defined as the regions of interests (ROIs). Mean
fluorescent intensity within these ROIs was measured in Fiji. These values were divided by the corre-
sponding fluorescence intensity observed in the ROI of the co-stained Crb puncta. Background signals
of 0.75 μm2 square-ROIs were subtracted from the intensities. Data collected from ImageJ were trans-
ferred to an Excel file for further analysis and plotting by GraphPad Prism.
Statistical analysis
Statistical analysis was carried out using two-tailed t-test for unpaired variables unless indicated. The
type of statistical test, n values and p-values are all provided in the figure legends. The experiments
were replicated three to six times. All statistical analyses were performed using GraphPad Prism 9.1.
The number of biological replicates for all the experiments is indicated in the figure legends. No
explicit power analysis was used to estimate sample sizes for each experiment.
Acknowledgements
We would like to thank Stefan Luschnig, Stefano De Renzis, Nic Tapon, Matthias Behr, the Bloom-
ington Drosophila Stock Center, the Drosophila Genomics Resource Center (DGRC; IN), and the
Developmental Studies Hybridoma Bank (DSHB; IA) for fly strains, clones, and antibodies. We thank
the fly community that isolated, characterized or distributed mutant strains or antibodies. Special
thanks to Flybase for the Drosophila genomic resources. We thank the Stockholm University Imaging
Facility (IFSU). We thank the former ERASMUS student Claudia’s Ctortecka, members of the M
Mannervik, C Samakovlis (particularly Ryo Matsuda), Q Dai, S Åström, and Y Engström laboratories for
comments and support during this project. This work was funded by the Swedish Research Council
and the Swedish Cancer Society to CS; by the Magn. Bergvalls stiftelse and O E och Edla Johanssons
vetenskapliga stiftelse to VT; and by the German Research Foundation (DFG), grant KFO309 (project
number 284237345) to CS.
Additional information
Funding
Funder Grant reference number Author
Vetenskapsrådet Christos Samakovlis
Cancerfonden Christos Samakovlis
O. E. och Edla Johanssons Vasilios Tsarouhas

Vetenskapliga Stiftelse
Magnus Bergvalls Stiftelse 2021-04453 Vasilios Tsarouhas
Deutsche KFO309 Christos Samakovlis

Forschungsgemeinschaft
The funders had no role in study design, data collection, and interpretation, or the
decision to submit the work for publication.
Author contributions
Ana Sofia Pinheiro, Data curation, Formal analysis, Validation, Investigation, Visualization, Method-
ology, Writing – original draft; Vasilios Tsarouhas, Data curation, Formal analysis, Supervision, Valida-
tion, Investigation, Visualization, Methodology, Writing – original draft, Writing – review and editing;
Kirsten André Senti, Conceptualization, Investigation; Badrul Arefin, Investigation; Christos Samakovlis,

Conceptualization, Data curation, Formal analysis, Supervision, Funding acquisition, Writing – original
draft, Project administration, Writing – review and editing
Author ORCIDs
Vasilios Tsarouhas ‍ ‍http://orcid.org/0000-0002-2933-1351
Badrul Arefin ‍ ‍https://orcid.org/0000-0003-1117-9125
Christos Samakovlis ‍ ‍https://orcid.org/0000-0002-9153-6040
Decision letter and Author response

Decision letter https://doi.org/10.7554/eLife.84974.sa1
Author response https://doi.org/10.7554/eLife.84974.sa2
Additional files
Supplementary files
• Supplementary file 1. The fly strains used in this study.
• Supplementary file 2. The sequences of primers used for qPCR analysis.
• MDAR checklist
Data availability
All data generated or analyzed during this study are included in the manuscript and supporting files.
Unprocessed western blots are provided as source data files in zip format.
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RESEARCH ARTICLE

Scavenger receptor endocytosis controls

Funding: See page 21

‍ ‍Copyright Pinheiro, Tsarouhas

Pinheiro, Tsarouhas et al. eLife 2023;12:e84974. DOI: https://doi.org/10.7554/eLife.84974  1 of 24

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Relative tracheal length

D GaspFL- VermFL-GFP SerpFL-GFP E

F Serp Verm Gasp H

wild-type stg late 17

chc1 stg late 17

Pinheiro, Tsarouhas et al. eLife 2023;12:e84974. DOI: https://doi.org/10.7554/eLife.84974  4 of 24

Dynamic subcellular localization of Emp during tracheal development

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Serp internalization and endosomal targeting requires Emp

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A YRab5 Serp Emp YRab5 Serp Emp

B YRab5 Serp YRab5 Serp C

D SP ChtB2 LDLr DA GFP FL

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Emp controls tube morphogenesis

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Emp modulates the apical actin organization

Pinheiro, Tsarouhas et al. eLife 2023;12:e84974. DOI: https://doi.org/10.7554/eLife.84974  11 of 24

D Crb DEcad Crb DEcad

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Emp regulates Src phosphorylation

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Materials and methods

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Molecular biology and transgenic flies

Co-immunoprecipitation and western blot analysis

Quantification of western blots

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Yeast two-hybrid screen

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Quantification of fluorescence intensity

Vetenskapsrådet Christos Samakovlis

Cancerfonden Christos Samakovlis

O. E. och Edla Johanssons Vasilios Tsarouhas

Magnus Bergvalls Stiftelse 2021-04453 Vasilios Tsarouhas

Deutsche KFO309 Christos Samakovlis

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Decision letter and Author response

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