Characterization of the Functional Domain of β2-Microglobulin from the Asian Seabass, Lates calcarifer

BACKGROUND: β2-Microglobulin (β(2)M) is the light chain of major histocompatibility class I (MHC I) that binds non-covalently with the α heavy chain. Both proteins attach to the antigen peptide, presenting a complex to the T cell to be destroyed via the immune mechanism. METHODOLOGY/PRINCIPAL FINDINGS: In this study, a cDNA sequence encoding β(2)M in the Asian seabass (Lates calcarifer) was identified and analyzed using in silico approaches to predict and characterize its functional domain. The β(2)M cDNA contains an open reading frame (ORF) of 351 bases with a coding capacity of 116 amino acids. A large portion of the protein consists of the IG constant domain (IGc1), similar to β(2)M sequences from other species studied thus far. Alignment of the IGc1 domains of β(2)M from L. calcarifer and other species shows a high degree of overall conservation. Seven amino acids were found to be conserved across taxa whereas conservation between L. calcarifer and other fish species was restricted to 14 amino acids at identical conserved positions. CONCLUSION/SIGNIFICANCE: As the L. calcarifer β(2)M protein analyzed in this study contains a functional domain similar to that of β(2)M proteins in other species, it can be postulated that the β(2)M proteins from L. calcarifer and other organisms are derived from a common ancestor and thus have a similar immune function. Interestingly, fish β(2)M genes could also be classified according to the ecological habitat of the species, i.e. whether it is from a freshwater, marine or euryhaline environment

Data on genome assembly and annotation of Marinobacter sp. strain CA1 isolated from indigenous diatom found in whiteleg shrimp pond in Malaysia

Marinobacter is a genus belonging to the class Gammaproteobacteria and the family Alteromonadaceae. This genus is a Gram-negative bacterium which can be found in a wide range of marine and saline water environments. Here, we present the genome sequence of Marinobacter sp. strain CA1 that was isolated from the indigenous diatom found in the whiteleg shrimp, Penaeus vannamei (Bonne 1931) pond in Malaysia. Genome sequencing was done using Pacbio and Illumina sequencing platforms. De novo hybrid assembly based on Pacbio long reads and high quality Illumina short reads yielded a complete circular chromosome with 4.7 M base pair (bp) in size. This genome was submitted to Genbank, NCBI database and can be accessed under accession number: NZ_CP071785 and the BioProject acession number PRJNA710741. This data could be useful for other studies on microalgae and bacteria interaction, and comparative genomics analysis of other Marinobacter species

Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates

Transferrin is a protein super-family involved in iron transport, a central process in cellular homeostasis. Throughout the evolution of vertebrates, transferrin members have diversified into distinct subfamilies including serotransferrin, ovotransferrin, lactoferrin, melanotransferrin, the inhibitor of carbonic anhydrase, pacifastin, and the major yolk protein in sea urchin. Previous phylogenetic analyses have established the branching order of the diverse transferrin subfamilies but were mostly focused on the transferrin repertoire present in mammals. Here, we conduct a comprehensive phylogenetic analysis of transferrin protein sequences in sequenced vertebrates, placing a special focus on the less-studied nonmammalian vertebrates. Our analyses uncover a novel transferrin clade present across fish, sauropsid, and amphibian genomes but strikingly absent from mammals. Our reconstructed scenario implies that this novel class emerged through a duplication event at the vertebrate ancestor, and that it was subsequently lost in the lineage leading to mammals. We detect footprints of accelerated evolution following the duplication event, which suggest positive selection and early functional divergence of this novel clade. Interestingly, the loss of this novel class of transferrin in mammals coincided with the divergence by duplication of lactoferrin and serotransferrin in this lineage. Altogether, our results provide novel insights on the evolution of iron-binding proteins in the various vertebrate groups.This work was supported by grants from the Malaysian Ministry of Science, Technology and Innovation (07-05-MGI-GMB009), the Spanish Ministry of Science and Innovation (BFU2009-09168), and Universiti Kebangsaan Malaysia (UKM-DLP-2011-027

NJ phylogenetic tree of β₂M protein sequences representing whole organisms.

<p>The phylogenetic tree shown is the collapsed tree of 55 sets of sequence data. This tree shows that β₂M sequences are clustered together according to their taxons. β₂M sequences from Eutheria are clustered together and consist of sequences from Primates, Equine, Rodents, Ruminants, SscQ07717, OcuP01885 and FcaQ5MGS7. Marsupials, Monotremes and Avians are the intermediate taxons between Eutheria and Fish. Amphibian Xla protein Q9IA97 is clustered together with Actinopterygii fishes while the outgroup in this tree is a cartilaginous fish Reg Q8AXA0. The divergence of fish and mammalian β₂M received a high bootstrap value (89) to support the reliability of this phylogenetic tree.</p

β₂M sequences used in this analysis.

<p>The 55 protein sequences used in this study were retrieved from the Swiss-Prot and Refseq databases. Protein ID shows the accession number of the sequence in the database while Protein Name is the protein name designated in this study. Equine, Rodents, Ruminants, Primates and Others are largely grouped as Eutheria.</p

Multiple sequence alignment of IGc1 domains.

<p>The alignment consists of IGc1 domain sequences from organisms of various taxa such as Eutheria, Marsupials, Monotremes, Avians, Chondrichthyes fish and Actinopterygii fishes. Lca is the <i>L. calcarifer</i> protein sequence and the conserved residues are marked by (*). S1, S2, S3, S4, S5, S6 and S7 indicate the regions of seven β strands in the IGc1 domain. Numbers at the top indicate amino acid positions. Information on the sequences is given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013159#pone-0013159-t001" target="_blank">Table 1</a>.</p

NJ phylogenetic tree of IGc1 domains present in β₂M protein sequences from fish.

<p>The phylogenetic tree shows that fish β₂M proteins are clustered according to the fish's ecological habitat, which may be fresh water, euryhaline or marine. The chicken sequence was used as the outgroup. Information on the sequences is given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013159#pone-0013159-t001" target="_blank">Table 1</a>.</p

Data of the first de novo transcriptome assembly of the inflorescence of Curcuma alismatifolia

Curcuma alismatifolia, is an Asian crop from Zingiberaceae family, popularly used as ornamental plant in floriculture industry of Thailand and Cambodia. Different varieties with a wide range of colors can be found in species. Until now, few breeding programs have been done on this species and most commercially important cultivars are hybrids that are propagated vegetatively. In spite of other flowering plants, there is still lack of transcriptomic-based data on the functions of genes related to flower color in C. alismatifolia. The raw data presented in this article provides information on new original transcriptome data of two cultivars of C. alismatifolia by Illumina Hiseq. 4000 RNA-Seq technology which is the first ever report about this plant. The data is accessible via European Nucleotide Archive (ENA) under project number PRJEB18956. Keywords: Curcuma alismatifolia, De novo, Illumina, RNA-Seq, Transcriptome assembl

Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates

Transferrin is a protein super-family involved in iron transport, a central process in cellular homeostasis. Throughout the evolution of vertebrates, transferrin members have diversified into distinct subfamilies including serotransferrin, ovotransferrin, lactoferrin, melanotransferrin, the inhibitor of carbonic anhydrase, pacifastin, and the major yolk protein in sea urchin. Previous phylogenetic analyses have established the branching order of the diverse transferrin subfamilies but were mostly focused on the transferrin repertoire present in mammals. Here, we conduct a comprehensive phylogenetic analysis of transferrin protein sequences in sequenced vertebrates, placing a special focus on the less-studied nonmammalian vertebrates. Our analyses uncover a novel transferrin clade present across fish, sauropsid, and amphibian genomes but strikingly absent from mammals. Our reconstructed scenario implies that this novel class emerged through a duplication event at the vertebrate ancestor, and that it was subsequently lost in the lineage leading to mammals. We detect footprints of accelerated evolution following the duplication event, which suggest positive selection and early functional divergence of this novel clade. Interestingly, the loss of this novel class of transferrin in mammals coincided with the divergence by duplication of lactoferrin and serotransferrin in this lineage. Altogether, our results provide novel insights on the evolution of iron-binding proteins in the various vertebrate groups.This work was supported by grants from the Malaysian Ministry of Science, Technology and Innovation (07-05-MGI-GMB009), the Spanish Ministry of Science and Innovation (BFU2009-09168), and Universiti Kebangsaan Malaysia (UKM-DLP-2011-027