Distribution, organization an evolutionary history of La and LARPs in eukaryotes

Abstract

The fate of any cellular RNA is largely influenced by the nature and diversity of its interactions with various RNA-binding proteins (RBPs) leading to the formation of a biologically significant ribonucleoprotein (RNP) complex. La motif-containing proteins (composed of genuine La and La-related proteins (LARPs)) represent an evolutionary conserved family of RBPs that encompass a large range of crucial functions, involving coding and non-coding RNAs. In this work, we provide data that extend our previous knowledge on the distribution, organization and evolutionary history of this important protein family. Using a repertoire of 345 La motif-containing proteins from 135 species representing all major eukaryotic lineages, we were able to pinpoint many lineage-specific variations in the structural organization of La and LARPs and propose new evolutive scenarios to explain their modern genomic distribution.

Keywords: LARP; La-related proteins; RNA-binding proteins; evolution; genuine La.

Figure 1.

Distribution, phylogenetic relationships and structural organization of genuine La in eukaryotes. Full-length La protein sequences from the different eukaryotic lineages were aligned and used to construct the phylogenetic tree (with the exception of Alveolates La for which the La motif alone was used). Statistical supports of key nodes calculated with the approximate likelihood-ratio test are indicated. Scale bar indicates length of 0.1 substitution/site. For a description of species and protein sequences used, see Supplemental Table 1. Boxes on the right define how the different lineages were colour-coded. The grey shading is used to highlight the presence of two genuine La protein subgroups in Poaceae and Brassicaceae. Positions of the different conserved regions (on the Human La sequence (NP_003133.1)) are the following: La motif (10–91), RRM1 (110–185), RRM2 (232–326) and GK/R-repeats (332–361)

Figure 2.

Distribution, phylogenetic relationships and structural organization of LARP1 in eukaryotes. Only full-length LARP1 protein sequences from the different eukaryotic lineages were aligned and used to construct the phylogenetic tree. Statistical supports of key nodes calculated with the approximate likelihood-ratio test are indicated. Scale bar indicates length of 0.1 substitution/site. For a description of species and protein sequences used, see Supplemental Table 1. Boxes on the right define how the different lineages were colour-coded. The grey shading is used to highlight the presence of two LARP1 (LARP1A and LARP1B) subgroups in vertebrates. Positions of the different conserved regions (on the Human LARP1A sequence (NP_291029.2)) are the following: GR repeats (338–353), LaM (401–478), RRM (500–559), CR1 (603–687), CR2 (825–884) and DM15 (885–999). The RRM region, adjacent to the LaM, is conserved at the primary sequence level only in vertebrates. In other eukaryotes, its presence was inferred from secondary structure prediction only[2] and is represented by RRM*

Figure 3.

Distribution, phylogenetic relationships and structural organization of LARP4 in eukaryotes. Full-length LARP4 proteins from the different eukaryotic lineages were aligned and used to construct the phylogenetic tree. Statistical supports of key nodes calculated with the approximate likelihood-ratio test are indicated. Scale bar indicates length of 1 substitution/site. For a description of species and protein sequences used, see Supplemental Table 1. Boxes on the right define how the different lineages were colour-coded. The grey shading is used to distinguish between vertebrate LARP4As and LARP4Bs from other LARP4s. Positions of the different conserved regions (on the Human LARP4A sequence (NP_443111.4)) are the following: P2 (including the PAM2 w, 8–31), La (117–195), RRM (200–271), PMB (281–349), CR1 (477–489), CR2 (613–629). For LARP4B, sequence conservation was observed from the N-terminal end to the PAM2 w motif (Position 1 to 71 on the Human LARP4B sequence (NP_055970.1)) and is indicated as P2 +. A few invertebrate LARP4s have a consensus PAM2 motif (indicated by a green asterisk)[22] but overall this region is not conserved in invertebrates

Figure 4.

Distribution, phylogenetic relationships and structural organization of LARP6 in eukaryotes. Full-length LARP6 proteins from the different eukaryotic lineages were aligned and used to construct the phylogenetic tree. Statistical supports of key nodes calculated with the approximate likelihood-ratio test are indicated. Scale bar indicates length of 0.1 substitution/site. For a description of species and protein sequences used, see Supplemental Table 1. Boxes on the right define how the different lineages were colour-coded. The grey shading is used to distinguish between vertebrate LARP6As and LARP6Bs from other LARP6s. The green shading is used to highlight the presence of three plant specific LARP6 subgroups (LARP6A, B and C). Positions of the different conserved regions (on the Human LARP6 sequence (NP_060827.2)) are the following: La (90–169), RRM (185–275), LSA (467–482). Position of the Embryophyte specific GK/R conserved region (on the Arabidopsis thaliana LARP6C sequence (At3g19090)) is from amino acids 379 to 388

Figure 5.

Distribution, phylogenetic relationships and structural organization of LARP7 in eukaryotes. Full-length LARP7 proteins from the different eukaryotic lineages were aligned and used to construct the phylogenetic tree. The Fungi LARP7-related (Pof8) proteins were not used for the phylogenetic analysis since their homology with other LARP7 is limited to the short RRM2 region. Fungi LARP7-like La motif and RRM1 were only inferred from secondary structure predictions and are represented by La* and RRM1* in the corresponding cartoon. Statistical supports of key nodes calculated with the approximate likelihood-ratio test are indicated. Scale bar indicates length of 1 substitution/site. For a description of species and protein sequences used, see Supplemental Table 1. Boxes on the right define how the different lineages were colour-coded. Positions of the different conserved regions (on the Human LARP7 sequence (NP_056269)) are the following: La (40–111), RRM1 (124–199), RRM2 (450–558)

Figure 6.

Sequence alignment of Pof8 (LARP7-like) RRM2 from different Fungi lineages showing primary and secondary sequence conservation. The amino acids are coloured in blue based on their conservation. Experimentally determined positions of the S. Pombe Pof8 (SpPof8) secondary structure[39] are schematically represented above the alignment. For other sequences, secondary structure predictions, inferred using the Phyre2 software are superimposed. The origin of each sequence is colour-coded

Figure 7.

Diagrammatic representation of the LARP4 (A) and LARP6 (B) putative evolutionary scenarios. See the Discussion section for a description of the two scenarios