TLR8 Protein
Background information:
TLR8, or Toll-Like Receptor 8, is a member of the Toll-Like Receptor cell family. They play a
pivotal role in pathogen recognition and activation of innate immunity. They are transmembrane
pattern recognition receptors, meaning they are specifically adapted to recognize and contain
certain harmful molecules, typically viral RNA. These pathogen-associated molecular patterns (
or PAMPs), activate intracellular
signaling pathways causing the
release of cytokines and type I
interferons (Cervantes et. al 2012).
Figure 1. TLR pathways. TLR7 and
8 recognize pathogenic molecules
and stimulate intracellular
communication to release
cytokines and interferons (Hemmi
H., Kaisho T. et al., 2002.)
http://www.invivogen.com/reviewtlr7-tlr8
TLR8 proteins are most commonly
found in lung cells in humans as
well as peripheral leukocytes
(Rimbach et. al 2015). There are
10 known functional TLRs in
Humans, and 12 in mice, 1-9 of
which are conserved in both species (Cervantes et. al 2012). Such high commonality between
species led us to believe there was a high chance of finding an ortholog in whale sharks.
Methods:
First ensembl.org was used to find the protein sequence of the human protein
ENSP00000312082. The protein sequence was then used as a query in a Blast against the
predicted whale shark protein. This blast was done using whaleshark.georgiaaquarium.org
(Galaxy server). The full predicted sequences of the top predicted protein hits were then found
individually using the Galaxy server and the top hit protein IDs. These were used as queries in
reciprocal protein BLASTs against the NCBI human protein database to determine if a homolog
had been found.
In order to find predicted orthologs in species other than the whale shark, the same human
protein sequence for ENSP00000312082 was used to blast against different species in the
NCBI blast server. Protein BLASTs were performed for the mouse, zebrafish, yeast, african
clawed frog and fruit fly. The default settings were used.
Searching for TLR7 in whale sharks:
Using the whale shark predicted protein database, the human protein TLR8 was used as a
query and the top hits are shown below (Figure 2). There were 5 hits with E-values below 1e-22.
However, the top hit, an E-value of 2e-154, has an E-value over one hundred times smaller than
any other hit.
ID
Predicted
Top hit E-value
Length
g45743.t1
635
2e-154
g48010.t1
244
3e-25
g36276.t1
926
7e-45
g29067.t1
640
3e-29
g19777.t1
326
2e-22
Figure 2- The best hits from a blast against the predicted whale shark protein sequence and the
human protein TLR8. The top hits based on E-value are shown here along with their ID
numbers and predicted length. The predicted lengths were found individually on the Galaxy
website using the fasta extract sequence tool and counting the number of amino acids within the
entire protein sequence.
The top hit (g45743.t1) was then used in a reciprocal pBLAST against the human protein
database. The top hit in the blast was the “toll-like receptor 8 isoform 1 [Homo sapian]” with an
E- value of 9e-161. This low E-value is indicative of an ortholog between the humans and whale
sharks.
Protein domains:
There are seven protein domains:protein domains:
IPR027175 TLR8
IPR000483 Cys-rich_flank_reg_C
IPR001611 Leu-rich_rpt
IPR000157 TIR_dom
IPR003591 Leu-rich_rpt_typical-subtyp
http://www.genecards.org/cgi-bin/carddisp.pl?gene=TLR8
Toll-like receptor 8 (TLR8) is a key component of innate and adaptive immunity [PMID:
16123302, PMID: 12032557, PMID: 16188996]. TLRs (Toll-like receptors) control host
immune response against pathogens through recognition of molecular patterns specific to
microorganisms. It acts via MYD88 and TRAF6, leading to NF-kappa-B activation, cytokine
secretion and the inflammatory response [PMID: 17932028]. TLR8 has been shown to
recognise different types of ligands such as viral or bacterial ssRNA, as well as small
synthetic molecules. Activation by ligands is species-specific, varying among non-rodents
and rodents [PMID: 14976262, PMID: 21949866].
Orthologs:
The human TLR8 protein sequence (AAZ95441.1) was used as a query sequence in an NCBI
BLAST against individual species protein sequence database. Several of these species, mice,
zebra fish, and african clawed frogs, all appear to have orthologs of the TLR8 gene. Note that
each species has an e-value so low it is represented as 0, indicating a high level of certainty in
the commonality of these sequences. Such results are not entirely unexpected, as TLR8
proteins are known to be found in mice as well as in whale sharks (Cervantes et. al 2012). This
suggests they are not exclusive to mammals or even terrestrial animals, and indicates a very
early common ancestor passed the protein or one similar onto these species.
Species
Name
ID
Length
E-value
Homo Sapiens
toll-like receptor
8 isoform 1
ref|NP_057694.2|
1059
0.0(NA)
Mouse
toll-like receptor
8 [Mus
musculus]
gb|AAK62677.1|
1032
0.0(NA)
Zebra Fish
PREDICTED:
toll-like receptor
8 [Danio rerio]
ref|XP_002665954
.4|
1019
0.0(NA)
African Clawed
Frog
PREDICTED:
toll-like receptor
8 [Xenopus
(Silurana)
tropicalis]
ref|XP_002933859
.1|
1037
0.0(NA)
Fruit Fly
CG7896
[Drosophila
melanogaster]
ref|NP_651754.1|
1392
3e-27
Yeast
adenylate
cyclase
[Saccharomyces
cerevisiae
S288c]
ref|NP_012529.3|
2026
3e-05
Table 1. Best hits with human TLR8 protein BLAST. The human TLR8 sequence was used in
protein BLASTs against individual species. Name, ID, length and E-value of the best hit from
each search is reported here.
Phylogeny:
The best hits from the protein searches were used to create a phylogenetic tree. From this tree
it is clear that this protein in humans is most closely related to that in mice and most distantly
related to the same protein in yeast.
Figure 3 - Phylogenetic Tree of the human TLR8 protein. The best hits from BLAST searches
were used in the ClustalW program to create a phylogenetic tree.
Conclusions:
References:
Cervantes, J. (2012). TLR8: The forgotten relative revindicated. Cellular & Molecular
Immunology, 9, 434–438-434–438. Retrieved April 2, 2015, from
http://www.nature.com/cmi/journal/v9/n6/full/cmi201238a.html
Rimbach, K., & Helm, M. (2015). 2'-O-Methylation within Bacterial RNA Acts as Suppressor of
TLR7/TLR8 Activation in Human Innate Immune Cells. Journal of Innate Immunity, 0(0), 1-12.
Hemmi H., Kaisho T. et al., 2002. Nat Immunol. 3(2):196-200.