High content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm Olavius algarvensis

Abstract

Selenocysteine (Sec) and pyrrolysine (Pyl) are rare amino acids that are cotranslationally inserted into proteins and known as the 21st and 22nd amino acids in the genetic code. Sec and Pyl are encoded by UGA and UAG codons, respectively, which normally serve as stop signals. Herein, we report on unusually large selenoproteomes and pyrroproteomes in a symbiont metagenomic dataset of a marine gutless worm, Olavius algarvensis. We identified 99 selenoprotein genes that clustered into 30 families, including 17 new selenoprotein genes that belong to six families. In addition, several Pyl-containing proteins were identified in this dataset. Most selenoproteins and Pyl-containing proteins were present in a single deltaproteobacterium, delta1 symbiont, which contained the largest number of both selenoproteins and Pyl-containing proteins of any organism reported to date. Our data contrast with the previous observations that symbionts and host-associated bacteria either lose Sec utilization or possess a limited number of selenoproteins, and suggest that the environment in the gutless worm promotes Sec and Pyl utilization. Anaerobic conditions and consistent selenium supply might be the factors that support the use of amino acids that extend the genetic code.

Figure 1.

A schematic diagram of the search algorithm. Details of the search process are provided in Materials and methods section.

Figure 2.

Multiple sequence alignment of FrhD family. Conserved residues are highlighted. Sec (U) and the corresponding Cys (C) residues are shown in red and blue, respectively.

Figure 3.

Multiple sequence alignment of several known selenoprotein families containing new features. New Sec positions are shown in pink. Contigs containing these new features are also highlighted in green background. (A) Rhodanese-related sulfurtransferase; (B) F420-reducing hydrogenase, alpha subunit.

Figure 4.

Multiple sequence alignments of new selenoproteins and their Cys homologs. The alignments show Sec-flanking regions in detected proteins. Both selenoprotein sequences detected in the Olavius symbionts’ metagenome dataset and their Sec/Cys-containing homologs present in indicated organisms are shown. Conserved residues are highlighted. Predicted Sec (U) and the corresponding Cys (C) residues in other homologs are shown in red and blue, respectively.

Figure 5.

Predicted bacterial SECIS elements in representative sequences of new selenoprotein families. Only sequences downstream of in-frame UGA codons are shown. In-frame UGA codons and conserved guanosines in the apical loop are shown in red. (A) YHS domain protein, AASZ01000529; (B) Putative redox protein, AASZ01002486; (C) OS_HP1, AASZ01000351; (D) Conserved protein (COG1810), AASZ01000538; (E) OS_HP3, AASZ01001720.

Figure 6.

Occurrence of genes for Pyl-containing proteins and Pyl operon proteins in Olavius symbionts’ metagenomic sequences. The mtbB and mttB genes and other Pyl operon genes are shown by the indicated color scheme in contigs containing these genes.

Figure 7.

Multiple alignments of Pyl-flanking regions in methylamine methyltransferase families (MtbB and MttB). Pyl is shown by X and its location in the alignment is highlighted in red.

Figure 8.

Relationship among habitats, genome size, proteome size and selenoproteomes. Sec-containing organisms were classified into four groups based on different habitats: aquatic, host-associated, multiple and terrestrial. (A) Correlation between genome size and proteome size. (B) Correlation between proteome size and selenoproteomes. δ1 and δ4 symbionts are indicated in the figure.