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. 2023 Apr 6;18(4):e0283431.
doi: 10.1371/journal.pone.0283431. eCollection 2023.

Identification of GC-rich LAT genes in birds

Sarka Janusova  1   2 , Veronika Krchlikova  3 , Tomas Hron  3 , Daniel Elleder  3 , Ondrej Stepanek  1
Affiliations

Identification of GC-rich LAT genes in birds

Sarka Janusova et al. PLoS One. .

Abstract

Linker for activation of T cells (LAT) plays a key role in T-cell antigenic signaling in mammals. Accordingly, LAT orthologues were identified in the majority of vertebrates. However, LAT orthologues were not identified in most birds. In this study, we show that LAT gene is present in genomes of multiple extant birds. It was not properly assembled previously because of its GC-rich content. LAT expression is enriched in lymphoid organs in chicken. The analysis of the coding sequences revealed a strong conservation of key signaling motifs in LAT between chicken and human. Overall, our data indicate that mammalian and avian LAT genes are functional homologues with a common role in T-cell signaling.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Phylogenetic relationship of LAT genes from birds and other vertebrates.
The maximum likelihood tree was constructed from the newly identified avian LAT sequences together with selected orthologues from other vertebrates. Bootstrap support values (percent of 500 replicates) are shown above the branches. Species with newly identified LAT sequence are in bold. The scale bar above indicates the number of substitutions per site.
Fig 2
Fig 2. LAT gene exhibits a high GC content and long G/C stretches in birds.
Comparison of GC content and the presence of G/C stretches in LAT genes from birds and other vertebrates. Dot plot was generated based on the coding sequences of LAT gene from vertebrate species shown in Fig 1. GC content is plotted against average length of sequence stretches containing G or C nucleotides. G/C-stretch was defined as an undisrupted sequence of at least three consecutive G or C nucleotides [18]. To allow comparison with all annotated chicken genes, a histogram showing the distribution of average G/C-stretch length in the chicken RefSeq gene category is depicted by a gray line. Chicken RefSeq genes comprise the complete set of approximately six thousand chicken coding sequences longer than 299 nucleotides. The chicken (Gallus gallus) and American alligator (Alligator mississippiensis), which is the closest relative to birds from included reptile species, are highlighted by arrows.
Fig 3
Fig 3. cLAT contains conserved palmitoylation and signaling motifs.
The alignments of amino acid LAT sequences of human and chicken (A) and zebrafish and chicken (B) are shown. Conserved tyrosine residues are highlighted in black, glycine and/or aspartate at position 131 is highlighted in grey, conserved palmitoylated cysteines are in bold with black triangle, prolines in the proline-rich sequence (amino acids 30–100 of hLAT) are in red, proline-rich LCK-binding motif is highlighted in the hLAT sequence.
Fig 4
Fig 4. Expression of cLAT is enriched in immune-related organs.
The expression levels of cLAT mRNA was determined in silico from SRA data (see Methods). Immune-related organs are depicted by red bars.
See this image and copyright information in PMC

References

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