Conserved intron positions in ancient protein modules

The polyphyletic origins of glycyl-tRNA synthetase and lysyl-tRNA synthetase and their implications

I analyzed the polyphyletic origin of glycyl-tRNA synthetase (GlyRS) and lysyl-tRNA synthetase (LysRS), making plausible the following implications. The fact that the genetic code needed to evolve aminoacyl-tRNA synthetases (ARSs) only very late would be in perfect agreement with a late origin, in the main phyletic lineages, of both GlyRS and LysRS. Indeed, as suggested by the coevolution theory, since the genetic code was structured by biosynthetic relationships between amino acids and as these occurred on tRNA-like molecules which were evidently already loaded with amino acids during its structuring, this made possible a late origin of ARSs. All this corroborates the coevolution theory of the origin of the genetic code to the detriment of theories which would instead predict an early intervention of the action of ARSs in organizing the genetic code. Furthermore, the assembly of the GlyRS and LysRS protein domains in main phyletic lineages is itself at least evidence of the possibility that ancestral genes were assembled using pieces of genetic material that coded these protein domains. This is in accordance with the exon theory of genes which postulates that ancestral exons coded for protein domains or modules that were assembled to form the first genes. This theory is exemplified precisely in the evolution of both GlyRS and LysRS which occurred through the assembly of protein domains in the main phyletic lineages, as analyzed here. Furthermore, this late assembly of protein domains of these proteins into the two main phyletic lineages, i.e. a polyphyletic origin of both GlyRS and LysRS, appears to corroborate the progenote evolutionary stage for both LUCA and at least the first part of the evolutionary stages of the ancestor of bacteria and that of archaea. Indeed, this polyphyletic origin would imply that the genetic code was still evolving because at least two ARSs, i.e. proteins that make the genetic code possible today, were still evolving. This would imply that the evolutionary stages involved were characterized not by cells but by protocells, that is, by progenotes because this is precisely the definition of a progenote. This conclusion would be strengthened by the observation that both GlyRS and LysRS originating in the phyletic lineages leading to bacteria and archaea, would demonstrate that, more generally, proteins were most likely still in rapid and progressive evolution. Namely, a polyphyletic origin of proteins which would qualify at least the initial phase of the evolutionary stage of the ancestor of bacteria and that of archaea as stages belonging to the progenote.

Genome-Wide Identification and Characterization of the Vacuolar H+-ATPase Subunit H Gene Family in Crop Plants

The vacuolar H⁺-ATPase (V-ATPase) plays many important roles in cell growth and in response to stresses in plants. The V-ATPase subunit H (VHA-H) is required to form a stable and active V-ATPase. Genome-wide analyses of VHA-H genes in crops contribute significantly to a systematic understanding of their functions. A total of 22 VHA-H genes were identified from 11 plants representing major crops including cotton, rice, millet, sorghum, rapeseed, maize, wheat, soybean, barley, potato, and beet. All of these VHA-H genes shared exon-intron structures similar to those of Arabidopsis thaliana. The C-terminal domain of VHA-H was shorter and more conserved than the N-terminal domain. The VHA-H gene was effectively used as a genetic marker to infer the phylogenetic relationships among plants, which were congruent with currently accepted taxonomic groupings. The VHA-H genes from six species of crops (Gossypium raimondii, Brassica napus, Glycine max, Solanum tuberosum, Triticum aestivum, and Zea mays) showed high gene structural diversity. This resulted from the gains and losses of introns. Seven VHA-H genes in six species of crops (Gossypium raimondii, Hordeum vulgare, Solanum tuberosum, Setaria italica, Triticum aestivum, and Zea mays) contained multiple transcript isoforms arising from alternative splicing. The study of cis-acting elements of gene promoters and RNA-seq gene expression patterns confirms the role of VHA-H genes as eco-enzymes. The gene structural diversity and proteomic diversity of VHA-H genes in our crop sampling facilitate understanding of their functional diversity, including stress responses and traits important for crop improvement.

Systems Identification and Characterization of Cell Wall Reassembly and Degradation Related Genes in Glycine max (L.) Merill, a Bioenergy Legume

Soybean is a promising biomass resource for generation of second-generation biofuels. Despite the utility of soybean cellulosic biomass and post-processing residues in biofuel generation, there is no comprehensive information available on cell wall loosening and degradation related gene families. In order to achieve enhanced lignocellulosic biomass with softened cell walls and reduced recalcitrance, it is important to identify genes involved in cell wall polymer loosening and degrading. Comprehensive genome-wide analysis of gene families involved in cell wall modifications is an efficient stratagem to find new candidate genes for soybean breeding for expanding biofuel industry. We report the identification of 505 genes distributed among 12 gene families related to cell wall loosening and degradation. 1262 tandem duplication events contributed towards expansion and diversification of studied gene families. We identified 687 Simple Sequence Repeat markers and 5 miRNA families distributed on 316 and 10 genes, respectively. Publically available microarray datasets were used to explore expression potential of identified genes in soybean plant developmental stages, 68 anatomical parts, abiotic and biotic stresses. Co-expression networks revealed transcriptional coordination of different gene families involved in cell wall loosening and degradation process.

Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era

BACKGROUND

The last eukaryotic common ancestor already had an amazingly complex cell possessing genomic and cellular features such as spliceosomal introns, mitochondria, cilia-dependent motility, and a cytoskeleton together with several intracellular transport systems. In contrast to the microtubule-based dyneins and kinesins, the actin-filament associated myosins are considerably divergent in extant eukaryotes and a unifying picture of their evolution has not yet emerged.

RESULTS

Here, we manually assembled and annotated 7852 myosins from 929 eukaryotes providing an unprecedented dense sequence and taxonomic sampling. For classification we complemented phylogenetic analyses with gene structure comparisons resulting in 79 distinct myosin classes. The intron pattern analysis and the taxonomic distribution of the classes suggest two myosins in the last eukaryotic common ancestor, a class-1 prototype and another myosin, which is most likely the ancestor of all other myosin classes. The sparse distribution of class-2 and class-4 myosins outside their major lineages contradicts their presence in the last eukaryotic common ancestor but instead strongly suggests early eukaryote-eukaryote horizontal gene transfer.

CONCLUSIONS

By correlating the evolution of myosin diversity with the history of Earth we found that myosin innovation occurred in independent major "burst" events in the major eukaryotic lineages. Most myosin inventions happened in the Mesoproterozoic era. In the late Neoproterozoic era, a process of extensive independent myosin loss began simultaneously with further eukaryotic diversification. Since the Cambrian explosion, myosin repertoire expansion is driven by lineage- and species-specific gene and genome duplications leading to subfunctionalization and fine-tuning of myosin functions.

Genome and transcriptome-wide analyses of cellulose synthase gene superfamily in soybean

The plant cellulose synthase gene superfamily belongs to the category of type-2 glycosyltransferases, and is involved in cellulose and hemicellulose biosynthesis. These enzymes are vital for maintaining cell-wall structural integrity throughout plant life. Here, we identified 78 putative cellulose synthases (CS) in the soybean genome. Phylogenetic analysis against 40 reference Arabidopsis CS genes clustered soybean CSs into seven major groups (CESA, CSL A, B, C, D, E and G), located on 19 chromosomes (except chromosome 18). Soybean CS expansion occurred in 66 duplication events. Additionally, we identified 95 simple sequence repeat makers related to 44 CSs. We next performed digital expression analysis using publically available datasets to understand potential CS functions in soybean. We found that CSs were highly expressed during soybean seed development, a pattern confirmed with an Affymatrix soybean IVT array and validated with RNA-seq profiles. Within CS groups, CESAs had higher relative expression than CSLs. Soybean CS models were designed based on maximum average RPKM values. Gene co-expression networks were developed to explore which CSs could work together in soybean. Finally, RT-PCR analysis confirmed the expression of 15 selected CSs during all four seed developmental stages.

PIECE 2.0: an update for the plant gene structure comparison and evolution database

PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. In the current version, we also added several new features: (i) a new viewer was developed to show phylogenetic trees displayed along with the structure of individual genes; (ii) genes in the phylogenetic tree can now be also grouped according to KOG (The annotation of Eukaryotic Orthologous Groups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) information on intronless genes are now included in the database; (iv) a statistical summary of global gene structure information for each species and its comparison with other species was added; and (v) an improved GSDraw tool was implemented in the web server to enhance the analysis and display of gene structure. The updated PIECE 2.0 database will be a valuable resource for the plant research community for the study of gene structure and evolution.

Alternative splicing acting as a bridge in evolution

BACKGROUND

Alternative splicing (AS) regulates diverse cellular and developmental functions through alternative protein structures of different isoforms. Alternative exons dominate AS in vertebrates; however, very little is known about the extent and function of AS in lower eukaryotes. To understand the role of introns in gene evolution, we examined AS from a green algal and five fungal genomes using a novel EST-based gene-modeling algorithm (COMBEST).

METHODS

AS from each genome was classified with COMBEST that maps EST sequences to genomes to build gene models. Various aspects of AS were analyzed through statistical methods. The interplay of intron 3n length, phase, coding property, and intron retention (RI) were examined with Chi-square testing.

RESULTS

With 3 to 834 times EST coverage, we identified up to 73% of AS in intron-containing genes and found preponderance of RI among 11 types of AS. The number of exons, expression level, and maximum intron length correlated with number of AS per gene (NAG), and intron-rich genes suppressed AS. Genes with AS were more ancient, and AS was conserved among fungal genomes. Among stopless introns, non-retained introns (NRI) avoided, but major RI preferred 3n length. In contrast, stop-containing introns showed uniform distribution among 3n, 3n+1, and 3n+2 lengths. We found a clue to the intron phase enigma: it was the coding function of introns involved in AS that dictates the intron phase bias.

CONCLUSIONS

Majority of AS is non-functional, and the extent of AS is suppressed for intron-rich genes. RI through 3n length, stop codon, and phase bias bridges the transition from functionless to functional alternative isoforms.

Reverse transcriptase and intron number evolution

BACKGROUND

Introns are universal in eukaryotic genomes and play important roles in transcriptional regulation, mRNA export to the cytoplasm, nonsense-mediated decay as both a regulatory and a splicing quality control mechanism, R-loop avoidance, alternative splicing, chromatin structure, and evolution by exon-shuffling.

METHODS

Sixteen complete fungal genomes were used 13 of which were sequenced and annotated by JGI. Ustilago maydis, Cryptococcus neoformans, and Coprinus cinereus (also named Coprinopsis cinerea) were from the Broad Institute. Gene models from JGI-annotated genomes were taken from the GeneCatalog track that contained the best representative gene models. Varying fractions of the GeneCatalog were manually curated by external users. For clarity, we used the JGI unique database identifier.

RESULTS

The last common ancestor of eukaryotes (LECA) has an estimated 6.4 coding exons per gene (EPG) and evolved into the diverse eukaryotic life forms, which is recapitulated by the development of a stem cell. We found a parallel between the simulated reverse transcriptase (RT)-mediated intron loss and the comparative analysis of 16 fungal genomes that spanned a wide range of intron density. Although footprints of RT (RTF) were dynamic, relative intron location (RIL) to the 5'-end of mRNA faithfully traced RT-mediated intron loss and revealed 7.7 EPG for LECA. The mode of exon length distribution was conserved in simulated intron loss, which was exemplified by the shared mode of 75 nt between fungal and Chlamydomonas genomes. The dominant ancient exon length was corroborated by the average exon length of the most intron-rich genes in fungal genomes and consistent with ancient protein modules being ~25 aa. Combined with the conservation of a protein length of 400 aa, the earliest ancestor of eukaryotes could have 16 EPG. During earlier evolution, Ascomycota's ancestor had significantly more 3'-biased RT-mediated intron loss that was followed by dramatic RTF loss. There was a down trend of EPG from more conserved to less conserved genes. Moreover, species-specific genes have higher exon-densities, shorter exons, and longer introns when compared to genes conserved at the phylum level. However, intron length in species-specific genes became shorter than that of genes conserved in all species after genomes experiencing drastic intron loss. The estimated EPG from the most frequent exon length is more than double that from the RIL method.

CONCLUSIONS

This implies significant intron loss during the very early period of eukaryotic evolution. De novo gene-birth contributes to shorter exons, longer introns, and higher exon-density in species-specific genes relative to conserved genes.

GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures

Background

All sequenced eukaryotic genomes have been shown to possess at least a few introns. This includes those unicellular organisms, which were previously suspected to be intron-less. Therefore, gene splicing must have been present at least in the last common ancestor of the eukaryotes. To explain the evolution of introns, basically two mutually exclusive concepts have been developed. The introns-early hypothesis says that already the very first protein-coding genes contained introns while the introns-late concept asserts that eukaryotic genes gained introns only after the emergence of the eukaryotic lineage. A very important aspect in this respect is the conservation of intron positions within homologous genes of different taxa.

Results

GenePainter is a standalone application for mapping gene structure information onto protein multiple sequence alignments. Based on the multiple sequence alignments the gene structures are aligned down to single nucleotides. GenePainter accounts for variable lengths in exons and introns, respects split codons at intron junctions and is able to handle sequencing and assembly errors, which are possible reasons for frame-shifts in exons and gaps in genome assemblies. Thus, even gene structures of considerably divergent proteins can properly be compared, as it is needed in phylogenetic analyses. Conserved intron positions can also be mapped to user-provided protein structures. For their visualization GenePainter provides scripts for the molecular graphics system PyMol.

Conclusions

GenePainter is a tool to analyse gene structure conservation providing various visualization options. A stable version of GenePainter for all operating systems as well as documentation and example data are available at http://www.motorprotein.de/genepainter.html.

SNP identification and allelic-specific PCR markers development for TaGW2, a gene linked to wheat kernel weight

TaGW2, an orthologous gene of rice OsGW2, has been associated with kernel width and weight of bread wheat (Triticum aestivum). Difference in TaGW2 coding sequence was not found among different wheat varieties in previous researches. In this study, we found eight exons and seven introns in TaGW2 with a full-length cDNA sequence of 1,275 bp, which contains a conserved function domain and seven splice sites that shared homology with rice OsGW2. A single T-base insertion in the eighth exon of TaGW2 on chromosome 6A was detected in a large-kernel wheat variety, Lankaodali. This insertion mutation reduces the coding protein sequence from normal 424 amino acids (~47.2 kDa) to 328 amino acids (~37.1 kDa) by truncating 96 amino acids. The result was validated by identifying histidine-tagged TaGW2 proteins encoded by both alleles of the mutant and the wild types in SDS-PAGE. Allele-specific PCR markers were developed based on the single nucleotide polymorphism (SNP) site. The SNP markers were genotyped for an F(2) segregation population from the cross of Lankaodali × Chinese Spring. Seed traits of F(2:3) families were evaluated in three different environments. The association analysis indicated that F(2:3) families with the mutated TaGW2 allele significantly increased kernel width (KW) and thousand-kernel weight (TKW), and slightly improved kernel length (KL). Using the SNP markers, another two varieties harbored the mutated TaGW2 allele were successfully identified from 22 additional wheat varieties, and they both have large KW and TKW. Cloning and sequencing of the gene further confirmed the functions of the mutated allele of TaGW2 in the two large kernel varieties. The results suggested that TaGW2 may negatively regulate kernel size variation, which shares the same function as OsGW2 in rice. The successful development of SNP markers provides a useful tool for improving kernel yield in wheat.

ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes

We have developed ExDom, a unique database for the comparative analysis of the exon-intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon-intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon-intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon-intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins. ExDom database is freely accessible at: http://66.170.16.154/ExDom/.

Functional evolutionary history of the mouse Fgf gene family

Fibroblast Growth Factors (FGFs) are polypeptides with diverse activities in development and physiology. The mammalian Fgf family can be divided into the intracellular Fgf11/12/13/14 subfamily (iFGFs), the hormone-like Fgf15/21/23 subfamily (hFGFs), and the canonical Fgf subfamilies, including Fgf1/2/5, Fgf3/4/6, Fgf7/10/22, Fgf8/17/18, and Fgf9/16/20. However, all Fgfs are evolutionarily related. We propose that an Fgf13-like gene is the ancestor of the iFgf subfamily and the most likely evolutionary ancestor of the entire Fgf family. Potential ancestors of the canonical and hFgf subfamilies, Fgf4-, Fgf5-, Fgf8-, Fgf9-, Fgf10-, and Fgf15-like, appear to have derived from an Fgf13-like ancestral gene. Canonical FGFs function in a paracrine manner, while hFGFs function in an endocrine manner. We conclude that the ancestral Fgfs for these subfamilies acquired this functional diversity before the evolution of vertebrates. During the evolution of early vertebrates, the Fgf subfamilies further expanded to contain three or four members in each subfamily.