| Literature DB >> 32998424 |
Navaneethaiyer Umasuthan1,2, Sdnk Bathige1,3, William Shanthakumar Thulasitha1,4, Minyoung Oh1,5, Jehee Lee1,6.
Abstract
CXCL8 (Entities:
Keywords: CXC chemokine; CXCL8; chemotaxis; genomic sequence arrangement; interleukin-8 (il-8); leukocyte proliferation; molecular profiling; promoter prediction analyses; transcriptional expression
Year: 2020 PMID: 32998424 PMCID: PMC7601086 DOI: 10.3390/biom10101382
Source DB: PubMed Journal: Biomolecules ISSN: 2218-273X
Figure 1Structures of genomic organization, transcript, and protein domain architecture for rock bream interleukin-8 (Ofcxcl8) homologs. (A,B) Genomic composition of Ofcxcl8s: Exons (E1-E3/E4) and untranslated sequences are indicated by black and cross-checked boxes, respectively, whereas introns are shown as black lines with the corresponding sizes (bp). Inset table shows the exon−intron composition and features of exon−intron boundaries. *, Intron sequences are shown in lower case. The acceptor and donor sites in intron sequences are bold-boxed. (C,D) Structure of the transcripts of Ofcxcl8 homologs: Size of coding sequences (CDS) and untranslated regions (UTRs) are shown. (E,F) The schematic diagram of rock bream CXCL8 proteins: Signal peptide (SP) is indicated by a blank box. SCY domain (CXC chemokine module; yellow), ELR motif variants (NSH or EMH; red), and CXC signature (CXC; purple) are color shaded. Four cysteine residues are marked. All motifs are shown in colors corresponding to Figure S1.
Figure 2Multiple amino acid alignment analysis of rock bream interleukin-8 homologs (OfCXCL8s) with other known teleost, chicken, and human CXCL8s generated by ClustalW with default parameters. Completely (100%) and strongly conserved residues are marked with an asterisk (*) and colon (:), respectively. Weak conservation is marked by a full stop (.). The N-terminal signal peptide is underlined. Conserved Cys residues are highlighted and marked with blue asterisks, and the disulfide bonds are shown. ELR-like motif and CXC signature are boxed and indicated. A Leu residue, which is proposed to be essential for the chemotactic activity [55], is shown with a downward arrow.
Homology indices of rock bream CXCL8s (OfCXCL8-L1 and OfCXCL8-L3) with known selected orthologs of other vertebrates.
| Taxonomy | Species | Accession No | Protein Name | OfCXCL8-L1 | Species | Accession No | Protein Name | OfCXCL8-L3 | ||
|---|---|---|---|---|---|---|---|---|---|---|
| I% | S% | I% | S% | |||||||
| Fish |
| AGR27882.1 | Interleukin-8 (OfCXCL8-L1) | 100.0 | 100.0 |
| AGR27882.1 | Interleukin-8 (OfCXCL8-L1) | 30.60 | 53.30 |
| Fish |
| ADK35757.1 | Interleukin-8 | 98.0 | 99.0 |
| ADK35757.1 | Interleukin-8 | 29.70 | 53.30 |
| Fish |
| AGR27883.1 | Interleukin-8 like (OfCXCL8-L3) | 30.6 | 53.3 |
| AGR27883.1 | Interleukin-8 like (OfCXCL8-L3) | 100.00 | 100.00 |
| Fish |
| AFK65606.1 | Interleukin-8 | 88.9 | 94.9 |
| QFG40053.1 | Interleukin-8 | 91.40 | 96.20 |
| Fish |
| CAM32186.1 | Interleukin-8 | 87.9 | 93.9 |
| XP_030285781.1 | Permeability factor 2 | 89.50 | 96.20 |
| Fish |
| ACQ99511.1 | Interleukin-8 | 86.9 | 94.9 |
| ASK51661.1 | Interleukin-8 | 89.50 | 95.20 |
| Fish |
| ADK35756.1 | Interleukin-8 | 85.0 | 92.0 |
| AKC57337.1 | Interleukin-8 | 87.60 | 94.30 |
| Fish |
| ACQ57874.1 | Interleukin-8 | 79.8 | 91.9 |
| XP_029943750.1 | Interleukin-8 | 81.90 | 89.50 |
| Fish |
| ABE47600.1 | Interleukin-8 | 60.6 | 77.6 |
| ACQ58275.1 | Interleukin-8 | 78.10 | 83.80 |
| Fish |
| XP_001342606.2 | Permeability factor 2 IF X1 | 58.6 | 76.5 |
| XP_001342606.2 | Permeability factor 2 IF X1 | 29.70 | 55.20 |
| Fish |
| AAO25640.1 | Interleukin-8 | 57.1 | 76.5 |
| CAF90539.1 | Unnamed protein * | 68.60 | 81.90 |
| Amphibia |
| XP_002942577.1 | Interleukin-8 | 39.3 | 60.0 |
| XP_002942577.1 | Interleukin-8 | 31.20 | 52.40 |
| Amphibia |
| AEB96252.1 | Interleukin-8 | 37.1 | 63.1 |
| AEB96252.1 | Interleukin-8 | 33.90 | 55.20 |
| Reptilia |
| XP_003230087.1 | Interleukin-8 | 41.2 | 65.0 |
| XP_003230087.1 | Interleukin-8 | 33.90 | 50.50 |
| Aves |
| NP_990349.1 | Interleukin-8 | 41.5 | 63.5 |
| NP_990349.1 | Interleukin-8 | 30.30 | 53.30 |
| Mammalia |
| NP_999032.1 | Interleukin-8 | 34.3 | 56.3 |
| NP_999032.1 | Interleukin-8 | 27.50 | 49.50 |
| Mammalia |
| NP_000575.1 | Interleukin-8 IF 1 | 34.7 | 57.6 |
| NP_000575.1 | Interleukin-8 IF 1 | 25.20 | 56.20 |
| Mammalia |
| NP_001075762.1 | Interleukin-8 | 33.0 | 56.4 |
| NP_001075762.1 | Interleukin-8 | 27.50 | 52.40 |
Matrix was generated by the MatGAT program using BLOSUM62 scoring matrix, maintaining the first gap penalty and extending gap penalty levels at 12 and 1, respectively. IF, isoform. * Blast hit showed that this is an interleukin-8 homolog and phylogeny analyses showed it belongs to lineage 3 (L3).
Figure 3Molecular phylogenetic tree of selected CXCL8 (IL-8) homologs from vertebrates. The evolutionary history was inferred by the Neighbor-Joining method, and the evolutionary distances were computed with the p-distance method using MEGA X. Major clusters are indicated with vertical bars. The values at the forks indicate the percentage of trees in which the grouping occurred after bootstrap 5000 replicates. The tree was drawn to scale. The GenBank accession numbers are given next to each species.
Figure 4Schematic representation and comparison of the genomic organization of cxcl8 (il-8) in vertebrates: (A) tetrapods and (B,C) teleosts. While the coding sequences (CDSs) are represented by cross-checked boxes, untranslated regions (UTRs) are indicated with plain boxes. Introns are presented as bent lines with intron numbers below. Sizes of exons are indicated below the boxes if they are conserved, and otherwise, a letter is placed (P, Q, X). For more information, including the accession numbers and size of exons/introns of each sequence, please refer to Table 2.
Inter-lineage genome organization and comparison of exon-intron structure for classic il-8 and novel il-8-like genes among vertebrate classes.
| Gene Symbol 1 | Accession Number/Reference | Organism | Exon 1 3 | Intron 1 | Exon 2 | Intron 2 | Exon 3 4 | Intron 3 | Exon 4 4 | Group | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 5′ UTR | CDSP | CDS | CDS | CDSX,Q | 3′ UTR | |||||||
|
| ENST00000307407 2 |
| 153 | 64 | 819 | 136 | 271 | 84 | 416 | 16 | 1252 | Mammals |
|
| ENSBTAT00000026275 2 |
| 70 | 64 | 1573 | 136 | 273 | 84 | 439 | 22 | 1105 | Mammals |
|
| ENSSSCT00000009807 2 |
| 83 | 64 | 1018 | 136 | 288 | 84 | 427 | 28 | 1093 | Mammals |
|
| ENSOCUT00000030077 2 |
| 265 | 64 | 516 | 136 | 269 | 84 | 448 | 22 | 1148 | Mammals |
|
| ENSGALT00000042745 2 |
| - |
| 774 | 136 | 642 | 84 | 568 | 31 | 2661 | Birds |
|
| XM_005498533 |
| 63 |
| 773 | 136 | 700 | 84 | 1249 | 31 | 169 | Birds |
|
| ENSACAT00000011352 2 |
| - | 64 | 993 | 136 | 265 |
| 339 | 32 | - | Reptiles |
|
| XM_004911120 |
| 81 | 64 | 263 |
| 676 |
| 1490 | 12 | 294 | Amphibians |
|
| This study |
| 200 | 67 | 194 | 133 | 146 | 87 | 142 | 10 | 358 | Fish |
|
| Laing et al. (2002) |
| - | 64 | 341 | 133 | 247 | 87 | 292 | 10 | - | Fish |
|
| ENSTRUT00000016751 2/NC_042301 |
| 137 | 64 | 107 | 133 | 93 | 87 | 106 | 12 | 365 | Fish |
|
| Wang et al. (2013) |
| - | 64 | 143 | 133 | 123 | 87 | 125 | 13 | - | Fish |
|
| EU007442/ Seppola et al. (2008) |
| 122 | 73 | 109 | 133 | 151 | 87 | 202 | 13 | 169 | Fish |
|
| JQ407041/ Li et al. (2013) |
| - | 52 | 168 | 133 | 149 | 87 | 682 | 13 | - | Fish |
|
| KP202400/ Mu et al. (2015) |
| 64 | 137 | 133 | 129 | 87 | 124 | 16 | - | Fish | |
|
| AJ421443/ Huising et al. (2003) |
| 81 | 58 | 117 | 133 | 126 | 88 | 148 | 19 | 247 | Fish |
|
| XM_003198892/NM_001327985 |
| 74 | 70 | 79 |
| 2660 |
| 2476 | 88 | 303 | Fish |
|
| Chen et al. (2005) |
| - | 67 | 87 |
| 153 |
| 164 | 73 | - | Fish |
|
| ENSTNIT000000059822 |
| - | 52 | 427 | 136 | 140 | 130 | - | - | - | Fish |
|
| NW_004531887/XM_004570701 |
| 46 | 52 | 1090 | 136 | 1252 |
| - | - | 413 | Fish |
|
| This study |
| 59 | 52 | 2202 | 136 | 2209 | 130 | - | - | 625 | Fish |
1 As provided in the respective database resource; 2 Ensembl accession number; 3 the first (Exon 1) and 4 last (Exon 3 or 4) have been divided into two parts (5′- or 3′-UTRs and CDS); exons and parts of exons composing the CDS of cxcl8 are gray shaded; the exons in CDS, those deviating from the generalized structure (Figure 4), are underlined; X, non-conserved exon (a segment in exon 4) in tetrapod cxcl8, P, Q, non-conserved exons (segments in exon 1 and 4, respectively) in classic cxcl8 of teleosts.
Figure 5Analysis of the putative promoter region of rock bream Ofcxcl8s: (A) Ofcxcl8-L1 and (B) Ofcxcl8-L3. The sequence numbers are relative to the predicted transcription-initiation site (TIS; +1), which is indicated by a bent-arrow. TATA box (or like) sequences preceding the transcription initiation site (TIS) are marked. Possible NF-κB/ NF-κB1, C/EBPα, C/EBPβ, Jun:Fos (AP1), and POU2F1 (Oct-1) binding sites are differentially marked and indicated below, with the directions whenever possible. The transcribed sequence up to translation start site (atg) is shown with gray shade (5′ UTR). Translation start site is boxed, and few translated aa are shown.
Figure 6Constitutive mRNA expression of rock bream cxcl8 (Ofcxcl8) homologs, Ofcxcl8-L1 and Ofcxcl8-L3, in tissues of healthy juveniles. Relative transcript level of Ofcxcl8s was examined in 11 tissues by SYBR green qPCR. Rock bream β-actin was chosen as the internal reference gene. The calculation was performed using the Livak method [51], and values were calibrated against mRNA level of Ofcxcl8-L3 in muscle. The results are reported as mean ± standard deviation (SD) of triplicates. Ms, muscle; Hk, head kidney; Br, brain; Kd, kidney; Ht, heart; Sp, spleen; Lv, liver; Sk, skin; Bl, blood (PBCs); It, intestine; Gl, gill. Different letters above bars (Ofcxcl8-L1, a-e and Ofcxcl8-L3, f-j) represent significant differences between tissue mRNA levels (one-way analysis of variance (ANOVA), Tukey’s post hoc test, p < 0.05).
Figure 7The temporal mRNA expression of rock bream cxcl8 (Ofcxcl8) homologs, Ofcxcl8-L1 and Ofcxcl8-L3, after flagellin (FLA-ST) injection detected by SYBR green qPCR in different tissues: (A) head kidney, (B) intestine, (C), kidney, (D) gills, (E) liver and (F) spleen. The relative mRNA level of both transcripts in each tissue was calculated by the comparative Ct method using β-actin as the reference gene. The fold-change in mRNA expression is presented as relative to mRNA level of PBS-injected group at each time point. Relative expression level in unchallenged (0 h) control was considered as the baseline (1). The vertical bars represent SD (n = 4). Statistical analysis was performed by one-way ANOVA, followed by Tukey’s post hoc test. The asterisk symbol (*) indicates the statistical difference in transcription when compared with untreated (0 h) control at p < 0.05.
Figure 8The temporal mRNA expression of rock bream cxcl8-L1 (Ofcxcl8-L1) and cxcl8-L3 (Ofcxcl8-L3) in spleen following immune challenges detected by SYBR green qPCR. The data refer to (A) LPS, (B) E. tarda, (C) S. iniae, (D) poly(I:C) and (E) RBIV. The vertical bars represent SD (n = 3). For details of the captions, please refer to Figure 7. The asterisk symbol (*) indicates the statistical difference in transcription when compared with untreated (0 h) control at p < 0.05.
Figure 9Functional characterization of recombinant OfCXCL8-L1 (rOfCXCL8-L1) and OfCXCL8-L3 (rOfCXCL8-L3) using biological assays. Kidney leukocytes were treated with three different concentrations of rOfCXCL8 proteins. The rMBP was used as a control in each assay with the same concentrations. (A) Chemotaxis assay was performed with Transwell to quantify the migrating leukocytes. Chemotactic index (ci) was estimated as the ratio between the number of cells migrated in response to rOfCXCL8 or rMBP and elution buffer (negative control). (B) Proliferation assay was performed by treating leukocytes with different concentrations of rOfCXCL8 or rMBP, and using WST-1 assay. The OD450 represents the degree of leukocyte proliferation. Data are presented as means ± SD (n = 3). Statistical analysis was performed by one-way ANOVA, followed by Tukey’s post hoc test. Significance difference between treatments with rOfCXCL8-L1 or rOfCXCL8-L3 and rMBP within a particular concentration of recombinant protein (rProtein) is indicated by an asterisk symbol (*) at p < 0.05.
Concise comparison of the properties of rock bream cxcl8s, Ofcxcl8-L1, and Ofcxcl8-L3, at different molecular levels.
| Characteristics |
|
| |
|---|---|---|---|
| Complimentary DNA | GenBank accession No. | KC522966 | KC522965 |
| Length of cDNA | 855 | 1002 | |
| 5′ UTR | 200 | 59 | |
| CDS (bp) | 297 | 318 | |
| 3′ UTR | 358 | 625 | |
| mRNA instability motif | 3 | 2 | |
| Polyadenylation signal | 831AATAAA836 | 986AATAAA991 | |
| Genome | Length of gDNA (bp) | 1337 | 5413 |
| Number of exons | 4 | 3 | |
| Number of introns | 3 | 2 | |
| Protein | Peptide (aa) | 98 | 105 |
| Molecular mass (Da) | 10,833 | 11,571.6 | |
| Theoretical | 8.78 | 8.95 | |
| Signal peptide | 1–23 | 1–18 | |
| SCY domain | 32-93 | 23-88 | |
| ELR-like motif | 32EMH34 | 27NSH29 | |
| CXC motif | 35CRC37 | 30CRC32 | |
| Invariant cysteines | 35, 37, 61, 78 | 30, 32, 57, 73 | |
| Highest homology | Mandarin fish IL-8 | Japanese sea bass IL-8 | |
| 5′-flanking region | Transcription factor binding sites | NF-κB/ NF-κB1, C/EBPα, C/EBPβ (NF-IL6), Jun:Fos (AP1) and POU2F1 (Oct-1) | |
| Transcripts | Dominant mRNA expression (qPCR) | gills, intestine, and PBCs | spleen and gills |
| Functional characteristics | Chemotaxis index (100 ng/µL) | ~130 (significant) | ~19 (not significant) |