The nuclear proteome of Trypanosoma brucei
The nuclear proteome of Trypanosoma brucei
Carina Goos 0 1
Mario Dejung 1
Christian J. Janzen 0 1
Falk Butter 1
Susanne Kramer 0 1
0 Department of Cell and Developmental Biology, Biocenter, University of WuÈ rzburg , Am Hubland, WuÈrzburg, Germany , 2 Institute of Molecular Biology (IMB) , Ackermannweg 4, Mainz , Germany
1 Editor: Patricia Talamas-Rohana, Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional , MEXICO
Trypanosoma brucei is a protozoan flagellate that is transmitted by tsetse flies into the mammalian bloodstream. The parasite has a huge impact on human health both directly by causing African sleeping sickness and indirectly, by infecting domestic cattle. The biology of trypanosomes involves some highly unusual, nuclear-localised processes. These include polycistronic transcription without classical promoters initiated from regions defined by histone variants, trans-splicing of all transcripts to the exon of a spliced leader RNA, transcription of some very abundant proteins by RNA polymerase I and antigenic variation, a switch in expression of the cell surface protein variants that allows the parasite to resist the immune system of its mammalian host. Here, we provide the nuclear proteome of procyclic Trypanosoma brucei, the stage that resides within the tsetse fly midgut. We have performed quantitative label-free mass spectrometry to score 764 significantly nuclear enriched proteins in comparison to whole cell lysates. A comparison with proteomes of several experimentally characterised nuclear and non-nuclear structures and pathways confirmed the high quality of the dataset: the proteome contains about 80% of all nuclear proteins and less than 2% false positives. Using motif enrichment, we found the amino acid sequence KRxR present in a large number of nuclear proteins. KRxR is a sub-motif of a classical eukaryotic monopartite nuclear localisation signal and could be responsible for nuclear localization of proteins in Kinetoplastida species. As a proof of principle, we have confirmed the nuclear localisation of six proteins with previously unknown localisation by expressing eYFP fusion proteins. While proteome data of several T. brucei organelles have been published, our nuclear proteome closes an important gap in knowledge to study trypanosome biology, in particular nuclearrelated processes.
Data Availability Statement: All relevant data are
within the paper and its Supporting Information
Funding: This work was supported by DFG, www.
dfg.de Kr4017/1-2 (SK). The funder had no role in
study design, data collection and analysis, decision
to publish, or preparation of the manuscript.
Competing interests: The authors have declared
that no competing interests exist.
Trypanosoma brucei is a protozoan, parasitic flagellate with a digenic life cycle that involves a
mammalian host and the tsetse fly insect vector. The parasite causes African sleeping sickness
as well as the related cattle disease Nagana and thus has a huge impact on human health.
Mainly affected are rural areas of sub-Saharan Africa; some of these belong to the poorest
regions in the world. Sleeping sickness is fatal if untreated and currently available drugs, in
particular against the late stages of the disease, are difficult to administer and extremely toxic.
Trypanosomes separated early in the eukaryotic lineage and evolved some interesting and in
some cases unique biological mechanisms. Many of these are in fact located in the nucleus. For
example the full reliance of the parasites on polycistronic transcription: tens to hundreds of
functionally unrelated genes are co-transcribed together and subsequently processed by the
addition of the intron of the spliced leader RNA in a trans-splicing reaction, which is coupled
to polyadenylation of the upstream gene [
Trypanosome research has been eased by the availability of a large number of proteomic
data. These are in particular important, since RNA and protein data poorly correlate, due to
the absence of transcriptional control. Proteomic studies have analysed the proteomes of the
different life cycle stages [2±4], changes during developmental differentiation [
] and the
parasite's phosphoproteome [
]. Additionally, different subcellular proteomes are available, for
example the proteome of the flagellum [
], the nuclear pores [
], the mitochondrion [
the cell surface [
] the mitochondrial importome [
] and the glysosome [
]; the later even
for different life cycle stages [
The nuclear proteome is still missing and we set out to fill the gap. We performed label-free
quantitative mass spectrometry of purified trypanosome nuclei and compared the protein
enrichment against whole cell lysates identifying 764 proteins significantly enriched in purified
nuclei. A comparison with the proteomes of known nuclear and non-nuclear structures
allowed us to estimate the number of false positive proteins to be less than 2% and the
completeness of the proteome to be about 80%. We found the motif KRxR, which is reminiscent of
a nuclear localisation signal (NLS), significantly enriched within our nuclear proteome.
Material and methods
Trypanosoma brucei Lister 427 procyclic cells were used throughout. All experiments were
performed with logarithmically growing trypanosomes at a cell density of less than 1·107 cells/ml.
The generation of transgenic trypanosomes was done using standard methods [
Purification of trypanosome nuclei
The purification protocol was based on the purification of trypanosome nuclei described in
]. For each purification, approximately 1·1010 procyclic cells at about 6·106 cells/ml were
cultivated in conical glass flasks (5 l volume) with gentle shaking. Cells were pelleted (1,700g,
10 min, 27ÊC) (swing out rotor 11650, Sigma 6-16K) and washed twice with SDM79 without
serum and heme. From now work was done on ice. Cells were resuspended in 20 ml lysis
] and disrupted by a POLYTRON1 homogenizer (PT 1200E, PT-DA 12/2 EC-E123,
Kinematica AG, Switzerland) for at least 5 minutes at 2/3 of its maximum speed. Cell lysis was
monitored by phase contrast and fluorescence microscopy, using DAPI staining for the
detection of nuclei and kinetoplasts; part of this sample was kept for mass spectrometry (whole cell
lysate, WCL). The cell lysate was underlaid with 10 ml underlay buffer [
] in a 30 ml COREX
(No. 8445) glass tube and centrifuged (10,500g, 20 min, 4ÊC, rotor HB-6 in a Sorvall R6 plus
centrifuge). The supernatant (containing mainly crude cytosol) was decanted and discarded.
The pellet was immediately resuspended in 8 ml resuspension buffer [
], followed by further
homogenisation with the POLYTRON1 (5 min, 2/3 of maximum speed) and loaded on a
three-step sucrose gradient (8 ml 2.01 M / 8 ml 2.1 M / 8 ml 2.3 M) in a Sorvall AH629 rotor
tube (PA, thinwall, 38.5 ml, No 253050). After ultracentrifugation (25,000 rpm, 3.5 h, 4ÊC,
Beckmann L7 centrifuge), the gradient was harvested from the top. The ring-shaped pellet at
the bottom of the tube was resuspended in 2 ml 2.3 M sucrose. Samples were stained with
DAPI and analysed microscopically. The pellet fraction contained the highest concentration in
nuclei and the lowest concentration in visible contaminants and was subsequently used for
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600 μl methanol, 150 μl chloroform and 450 μl water were added stepwise (with vigorous
vortexing after each step) to 200 μl (10%) of the pellet fraction or 100 μl of the whole cell lysate.
After centrifugation (5 min, 20,000 g), the upper, aqueous phase was discarded, and another
650 μl methanol was added (mixing by inversion). Proteins were pelleted by centrifugation (5
min, max. speed), resuspended in 100 μl 1 x NuPAGE LDS sample buffer (Thermo Fisher
Scientific) with 100 mM DTT and incubated at 70ÊC for 10 minutes. Afterwards the samples were
sonicated with the Bioruptor1 Plus sonication device (Diagenode, Belgium) (settings: high, 10
cycles, 30 sec ON /30 sec OFF).
The samples were in-gel digested and MS measurement was performed as previously
] with the following adaptations: the measurement time per sample was extended
to 240 min. The four replicates were analysed with MaxQuant version 22.214.171.124 [
standard settings except LFQ quantitation and match between runs was activated. The
trypanosome protein database TREU927 version 8.0 (11,567 entries) was downloaded from www.
]. Filtering for proteins only identified by site, potential contaminants and
reverse entries where conducted with custom R scripts. A second filter step is removing all
protein groups with no unique and less than two peptides. Also the protein needs to be
quantified in at least two samples in either NUC or WCL. Prior to imputation of missing LFQ values
with a beta distribution ranging from 0.1 to 0.2 percentile within each sample, the values were
log2 transformed. The mass spectrometry proteomics data have been deposited to the
ProteomeXchange Consortium via the PRIDE [
] partner repository with the dataset identifier
Expression of eYFP fusion proteins
All eYFP-fusion proteins (C-terminal tagging) were expressed from the endogenous locus,
using the plasmid pPOTv4 as PCR template, exactly as described in [
SDS page and Western blots
Proteins were separated on a 12% acrylamide gel. Western blots were performed according to
standard protocols. The histone H3 antibody is described in [
For microscopy, cells were washed in SDM79 without serum and heme and fixed at a density
of less than 1·107 cells/ml with 2.5% paraformaldehyde overnight at 4ÊC in suspension, washed
twice in PBS and stained with DAPI. Z-stack images (60 stacks at 100 nm distance) were taken
with a custom build TILL Photonics iMic microscope equipped with a sensicam camera
(PCO), deconvolved using Huygens Essential software (Scientific Volume Imaging B. V.,
Hilversum, The Netherlands) and are presented as z-stack projections or single plane images.
eYFP was monitored with the FRET-CFP/YFP-B-000 filter and DNA with the DAPI filter
(Chroma Technology CORP, Bellows Falls, VT).
Results and discussion
Purification of trypanosome nuclei
Nuclei of procyclic Trypanosoma brucei Lister 427 cells were purified in four independent
experiments essentially as described in [
]. Briefly, cells were mechanically lysed and the
insoluble material was isolated by centrifugation across a sucrose cushion and further
separated on a discontinuous sucrose gradient by ultracentrifugation (Fig 1A). Samples of the
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Fig 1. Purification of trypanosome nuclei. A) Schematics of the procedure. 1·1010 procyclic trypanosome
cells were mechanically lysed with a POLYTRON® homogenizer (whole cell lysate, WCL). The insoluble cell
fraction which includes the nuclei was separated from the soluble fraction via a sucrose cushion and further
separated on a discontinuous sucrose gradient. Various organelles and cell fragments accumulate at the
interfaces of the sucrose layers and are thus separated from the nuclei, which are found in the pellet fraction
(NUC). A typical picture of an ultracentrifugation tube after centrifugation is shown on the right. B) Samples of
whole cell lysates (WCL) and the nuclear fraction (NUC) were stained with DAPI and microscopically analysed. In
the NUC sample, isolated nuclei are clearly visible as ovoids and few other structures are present, such as
remnants of flagella (brightfield image). Nuclei are intact (native shape, nucleolus is visible by absence of DAPI
staining) and only few kinetoplasts are visible (DAPI image). In contrast, the WCL sample contains remnants of
whole cells, including both nuclei and kinetoplasts. Note that the samples were not fixed to the slide and moved
during imaging; the different channels do not completely overlap. The DAPI image is shown as deconvolved
zstack projections, the brightfield image is a single plane. C) Enrichment in histones in fraction NUC.
Coomassiestained gel loaded with 0.5% of the WCL fraction and 10% of the NUC fractions (upper panel). The arrows point
to the bands corresponding to histones. In addition, histone H3 was detected by western blot (lower panel, H3).
D) NES histogram: For each 0.2 NES range, the number of proteins is shown. The NES of 0.7 that was used in
this work to define a nuclear protein is shown as a red line.
gradient were stained with DAPI and analysed microscopically. The pellet fraction contained
the highest number of nuclei and little visible contaminants, such as kinetoplasts (disc-like
network of circular DNA inside the single trypanosome mitochondrion, visible in the DAPI
image) or flagella (visible in the brightfield image) (Fig 1B, right panels). This fraction will be
referred to as NUC (nuclear fraction). In each nuclear purification experiment, one control
sample was taken immediately after the mechanical lysis (whole cell lysate, WCL). As expected,
whole cell lysates contained whole cell remnants with both nuclei and kinetoplasts (Fig 1B, left
panels). Protein samples of the NUC and WCL fractions were analysed on a Coomassie-stained
gel and by western blot. Histones were highly enriched in the nuclear fraction in comparison to
whole cell lysates, while the amount of total proteins decreased (Fig 1C), in agreement with a
successful enrichment of nuclei. All samples (4 x NUC and 4 x WCL) were subjected to label free
quantitative (LFQ) mass spectrometry. 3447 protein groups were detected in at least 2 of the
samples, corresponding to more than a third of all proteins encoded by the T. brucei genome 
(S1A Table). The nuclear enrichment score (NES) of each protein group was determined as the
ratio of LFQ intensities of the nuclear fraction divided by the LFQ intensity of WCL. To this end,
LFQ values were transformed by log2 and the NES ranged from +7.7 to -9.2 (Fig 1D). The
significance of the enrichment was determined by Welch's t-test.
Threshold definitions and GO-term analysis
Our aim was to produce a high-confident list of nuclear proteins, with few false positives. A
comparison with experimentally validated non-nuclear compartments (described below) was
subsequently used to evaluate the chosen thresholds. Initially, all proteins with an NES below
0.7 or a p-value above 0.05 were removed from the list. The threshold of 0.7 was chosen
because it corresponded to a local minimum in the NES histogram (Fig 1D). This resulted in
760 candidate protein groups with nuclear localization. This cut-off is extremely stringent, as
even some of the histones were excluded. In fact, a very high abundance of a protein reduces
the difference between the nuclear LFQ and the total LFQ score. This was compensated in a
second step by adding all proteins to the list with an NES above 0.7 if they were among the top
20% abundant proteins, independent of the p-value. This added only four more proteins to the
list, but additional to Tb927.7.4180 and Tb927.11.2510 included two of the histones. Thus, the
final list of nuclear protein candidates contains 764 protein groups (S1B Table); 239 of these
are hypothetical proteins. For an initial quality control, we performed a Gene Ontology (GO)
enrichment analysis with the tool provided by TriTrypDB [
]. We found 79 GO-terms for
biological function more than 3-fold enriched within our 764 nuclear protein candidates in
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comparison to the whole genome (p-value <0.05) (S2 Table). These were almost exclusively
GO-terms describing various processes of nuclear DNA and RNA metabolism, for example
mRNA splicing, chromatin remodelling and transcription. There was only one exception,
namely a GO term enrichment in long-chain fatty acid biosynthesis (GO:0042759 and
GO:0001676), based on the presence of three fatty acid elongases (ELO1-3) in our nuclear
proteome in comparison to four in the total genome. Fatty acid elongases are known to localise to
the perinuclear region of the ER membrane in yeast [
] and this localisation appears
conserved for the T. brucei enzymes, as shown by expressing an eYFP fusion of ELO3 [
the presence of fatty acid elongases in the nuclear proteome is likely caused by a
co-purification of the nucleus-adjacent ER membrane.
The nuclear proteome contains less than 2% false positives
To estimate the number of non-nuclear proteins (false-positives) within our nuclear proteome,
the proteome was compared with six experimentally characterised, non-nuclear structures/
pathways: the lipid metabolism pathway [
], the flagellome [
], the mitochondrial proteome
] proteins that associate with the cilium transition zone [
], the glycosome [
] and the
cell surface [
] (Fig 2A).
There are 96 proteins described to be involved in T. brucei lipid metabolism based on
homology to yeast enzymes and/or experimental characterisation [
]. Of these, seven are
present in our nuclear proteome, including the three fatty acid elongases mentioned above
(S3A Table). Many of the lipid metabolism proteins that are absent from our nuclear proteome
localise to the ER, for example all enzymes involved in glycosylphosphatidylinositol (GPI)
biosynthesis. This indicates that the contamination of our nuclear proteome with ER proteins
seen in the GO-term enrichment analysis above is not a general phenomenon.
There are 331 proteins that were identified by mass spectrometry in purified flagella of T.
]. Of these, 16 are found in our nuclear proteome (S3B Table). However, for ten of
them, nuclear localisation was demonstrated by the expression of GFP-fusion proteins [
or by specific antibody staining . Three of the remaining six proteins are clear homologues
to proteins with nuclear localisation in other organisms, namely GLE2, Kre33 and ERB1.
Thus, the actual number of possible flagellar proteins in our nuclear proteome is not higher
than three (Tb927.5.940, Tb927.8.2290 and Tb927.3.5010).
The T. brucei mitochondrial proteome was determined from mitochondria enriched
]. The total mitochondrial proteome contains about 1000 proteins. For the
comparison with the nuclear proteome, we focussed on the 401 proteins that were assigned to
mitochondria with high confidence [
]. Of these 401 proteins, only four proteins are found in
our nuclear proteome (S3C Table). They are likely false positives in our nuclear proteome as
they are described by mitochondrial GO-terms and two of them are experimentally
characterised, one is an RNA editing component [
] and another is found in the small subunit of the
mitochondrial ribosome [
The proteome of the cilium transition zone was recently characterised [
]. As part of this
study, 68 proteins were successfully localised by eYFP tagging to several different non-nuclear
localisations (S3D Table). These included the cilium transition zone, the basal body, the
probasal body, the flagellar pocket collar, the Inv-like compartment (a region distally adjacent to
the transition zone), a longitudinal structure near the flagellum exit from the flagellar pocket,
the flagellum, the Golgi and combinations of these localisations. Notably, there was no overlap
between these 68 proteins and our nuclear proteome.
A proteome of the trypanosome glycosome was obtained by a combination of epitope
tagged glycosome purification and SILAC labelling [
]. This study identified 129 glycosomal
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Fig 2. Comparison of the nuclear proteome with known nuclear and non-nuclear structures. A) The
content of the nuclear proteome was compared with proteins involved in lipid metabolism, proteins of the
flagellar proteome, proteins identified with high confidence in mitochondria, proteins tagged as part of the
characterisation of the cilium transition zone, proteins of the glycosomal proteome and the cell surface
proteome. The number of proteins that are present in both proteomes is shown in the overlap of the circles. B)
The content of the nuclear proteome was compared with proteins of known nuclear structures: the nuclear
pores, the exosome, the kinetochores and the spliceosome. The number of proteins that are present in both
proteomes is shown in the overlap of the circles. C) The molecular weight of proteins from the known nuclear
structures characterised in B is shown, for proteins that are present in the nuclear proteome (left) and for
proteins that are absent from the nuclear proteome (right).
proteins with very high confidence. Accordingly, our nuclear proteome is contaminated with
up to three glycosomal proteins (Tb927.5.2590, Tb927.8.920, Tb927.9.15260) (S3E Table).
The cell surface proteome of procyclic trypanosomes was obtained by mass spectrometry
analysis of biotinylated surface proteins [
]. 198 unique protein groups, corresponding to 295
proteins, were identified (S3F Table). Of these, nine proteins are present in our nuclear
proteome. Six of these have strong experimental evidence for nuclear localisation [29±31]. This
leaves three proteins (all retrotransposon hot spot proteins, Tb927.1.120, Tb927.2.1330,
Tb927.2.470) that could be false positives in our nuclear proteome; the absence of Tb927.1.120
from the nucleus was shown [
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In summary, we have looked at 1162 unique proteins with non-nuclear localisation,
excluding duplicates present in more than one proteome. Of these, 20 are present in our nuclear
proteome and could therefore be false-positives, resulting in an estimated false positive rate of 1.7%.
The nuclear proteome contains about 80% of the nuclear proteins
To estimate the comprehensiveness of the nuclear proteome, we compared it with the content
of four well-characterised nuclear structures: the nuclear pores, the exosome, kinetochores and
the spliceosome (Fig 2B).
Two studies have identified 27 structural components of the nuclear pores, excluding
export factors [
] (S4A Table). The localisation of all proteins to a punctuate structure at
the nuclear rim was confirmed by GFP tagging, with the exception of TbNup59 and TbNup62
which failed tagging [
]. Our nuclear proteome contains 25 of these 27 proteins; only
TbNup75 and TbNup65 are absent.
The T. brucei exosome contains 11 known proteins [33±35] (S4B Table). Whether exosome
localisation is entirely or only partially nuclear has been debated in the past, mainly based on
contradictory results of cellular fractionation studies [
]. However, newer studies strongly
support the view that the majority or all of the exosome is nuclear: all functions of the T. brucei
exosome reported to date are nuclear [33,36±38] and eYFP tagging of the essential exosome
component Rrp6 clearly showed dominant nuclear localisation mainly at the rim of the
nucleolus with no or very little cytoplasmic fluorescence [
]. Of the 11 exosome proteins, ten were
present in our nuclear proteome; only RRP41B was absent due to a slightly too high p-value.
Two recent studies aimed to describe the trypanosome kinetochores and identified 20
kinetoplast kinetochore proteins (KKT1-20), seven kinetoplast kinetochore interacting proteins
(KKIP1-7)) and seven further nuclear proteins [
] (S4C Table). The nuclear localisation of
all 34 proteins was confirmed by eYFP tagging [
]. Of these 34 proteins, 27 were present in
our nuclear proteome. KKT1, KKT5, KKT10, KKT15, KKT16, KKIP5 and KKIP7 were absent.
The trypanosome spliceosome contains 59 known proteins, excluding all proteins that
co-purify with spliceosomal components without a known function in splicing ([
references herein) (S4D Table). For most proteins, the localisation to the nucleus was not
independently confirmed, but the trypanosome spliceosome is one of the best-characterised
trypanosome structures: spliceosomal proteins of the different spliceosomal complexes were
carefully identified by a combination of bioinformatics and tandem tag affinity purification
with four different bait proteins, by many labs ([
] and references herein). Note that
trypanosomes only have one heptameric Lsm complex, which is nuclear [
]. Of the known 59
spliceosomal proteins, 44 were present in our nuclear proteome. The 15 missing spliceosomal
proteins included mostly small Lsm and Sm proteins.
To summarize, of the 131 proteins with known nuclear localisation, 106 are present in our
nuclear proteome, corresponding to 80.9%. We therefore estimate the comprehensiveness of
our nuclear proteome to about 80%. To note, very small proteins are preferentially absent:
the average molecular weight of the nuclear proteins in our dataset (66 kDa) is significantly
higher than the average molecular weight of the missing nuclear proteins (37.4 kDa) (result of
unpaired, two-tailed students t-test = 0.01) (Fig 2C). Smaller proteins are more likely to be lost
during the purification procedure by leaking out of the nucleus and result in fewer unique
peptides detectable in the mass spectrometer.
Identification of novel nuclear proteins
To investigate whether our proteome data set can be used to localize previously
uncharacterized proteins, we expressed six proteins fused to eYFP from their endogenous loci [
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Fig 3. Validation of nuclear localisation by expressing eYFP fusion proteins. Six proteins of the nuclear proteome with previously unknown
localisation were expressed as eYFP fusion proteins from their endogenous loci. Representative images (single plane images of deconvolved
zstacks) are shown. The DNA of the nucleus and the kinetoplast was stained with DAPI.
were four hypothetical proteins (including one with a p-value slightly above the threshold),
one helicase and one GTPase activating protein with no available information about
localisation (Fig 3). The NES values of these six proteins ranged from 1.8 to 5. Three proteins
(Tb927.10.12030, Tb927.8.4800, Tb927.5.3940) were mainly in the nucleolus (visualised by the
absence of DAPI staining) in one case (Tb927.10.12030) there were additional spots in the
nucleoplasm. The GTPase activating protein (Tb927.10.7680) localised to a dot-like structure
at the nuclear periphery, highly reminiscent of nuclear pores. The two remaining proteins
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(Tb927.10.8160 and Tb927.8.2460) localised to the nuclear rim, but the pattern was less
spotlike and both proteins have predicted trans-membrane domains. This suggests localisation to
the nuclear membrane, albeit a localisation to the nucleus-adjacent membrane of the ER
cannot be excluded due to the limits of light microscopy.
The motif KRxR is highly enriched in the nuclear proteins
A motif search with DREME [
] revealed three small peptide-motifs significantly enriched
within or nuclear proteome: GSGKT, KRPR and KR[Q/E]R. The motif GSGKT is found in 31
proteins of the nuclear proteome (4.1%) and in 116 proteins (1.1%) of the total genome. The
relevance of this enrichment remains unclear. The remaining two motifs are a sub-motif of the
K[K/R]x[K/R] motif, which is the essential part of the monopartite classical nuclear
localisation signal (NLS) [
]. The only known T. brucei protein with such a classical, experimentally
characterised NLS is the LA protein; the sequence RGHKRSRE is both necessary and sufficient
to mediate nuclear localisation [
]. The motif KRxR is present in 398 of the 764 proteins of
the nuclear proteome at least once, thus in 52%. This represents a significant enrichment,
compared to 17.7% of all trypanosome proteins (1810 of 10244 coding genes in the TREU927
strain). The position between the two arginine residues can be filled by any amino acid, except
tryptophan. The most abundant amino acids at this position are arginine, proline, serine,
glutamate and glutamic acid (S1 Fig). These results indicate that about half of all nuclear proteins
could have a classical, monopartite NLS.
We propose that the KRxR motif can serve to predict nuclear localisation. It is present in 9
of the 25 known nuclear proteins that were absent from our nuclear proteome. Importantly,
the KRxR motif could help to identify proteins that shuttle between the nucleus and the
cytoplasm and have predominantly cytoplasmic localisation, as these are currently difficult to
identify. The most prominent group of shuttling proteins, the group of ribosomal proteins, is not
enriched in the KRxR motif and ribosomal proteins may thus use a different mechanism for
nuclear entry. Notably, the absence of the KRxR motif does not exclude a protein from being
nuclear. It is absent from almost half of all nuclear proteins and there are several other non
classical nuclear localisation signals in trypanosomes [
We provide a high-quality proteome of the T. brucei nucleus, which is about 80% complete
and contains less than 2% non-nuclear proteins. The KRxR motif is highly enriched in nuclear
proteins and could serve as a prediction tool for nuclear localisation. Nuclear proteins that are
absent from the proteome are often of small size, and the 2% contaminants are enriched for
proteins of the nucleus adjacent ER membrane. Note that the T. brucei nuclear proteome
contains mainly proteins with exclusive nuclear localisation: proteins that shuttle between the
cytoplasm and the nucleus with predominant cytoplasmic localisation are absent, as they are
not enriched in the nucleus in comparison to the whole cell lysate. Recently, the proteome of
the related kinetoplastid T. cruzi was determined and the number of nuclear proteins was in a
similar range [
Our proteome data adds one more tool to the available sources for the study of
trypanosome biology. Recently, TrypTag has started to systematically localise all T. brucei proteins
]. We believe that our data are complementary to the current efforts of TrypTag. It may
for example fill the gaps for the 10% of proteins that failed tagging or the fraction of the
successfully tagged proteins with too low expression levels (Sam Dean, University of Oxford, UK,
personal communication). Overall, our dataset will be useful to further untangle nuclear
processes in trypanosomes.
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tion of missing proteins).
S1 Fig. Frequency distribution of all amino acids at the position between the two arginine
residues of the KRxR motif, for both the nuclear proteome and the total T. brucei
proteS1 Table. A) List of all proteins that were detected by mass spectrometry. B) List of the
S2 Table. GO-term analysis for biological function with the nuclear proteome.
S3 Table. Lists of non-nuclear proteins, including overlaps with the nuclear proteome
(estimation of false positives).
S4 Table. Lists of nuclear proteins, including overlap with the nuclear proteome
(estimaWe thank Sam Dean (University of Oxford, UK) for discussions and ideas. Keith Gull
(University of Oxford, UK) is acknowledged for providing the Trypanosoma brucei Lister 427 procyclic
cells. SK thanks Markus Engstler (University of WuÈrzburg, Germany) for mentoring and
hosting the work.
Conceptualization: Christian J. Janzen, Falk Butter, Susanne Kramer.
Data curation: Carina Goos, Mario Dejung.
Formal analysis: Mario Dejung, Falk Butter.
Funding acquisition: Susanne Kramer.
Investigation: Carina Goos.
Methodology: Carina Goos, Mario Dejung, Falk Butter.
Project administration: Christian J. Janzen, Falk Butter, Susanne Kramer.
Supervision: Susanne Kramer.
Writing ± original draft: Susanne Kramer.
Writing ± review & editing: Carina Goos, Mario Dejung, Christian J. Janzen, Falk Butter,
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