Differential expression pattern of the four mitochondrial adenine nucleotide transporter ant genes and their roles during the development of Caenorhabditis elegans
Abstract:The adenine nucleotide transporter (ANT) mediates exchange of cytosolic ADP and mitochondrial ATP. Although most species contain more than one ANT family member, it is not known whether their roles in developmental processes are redundant or specific. Here, we show that the Caenorhabditis elegans genome encodes four candidate ant genes (ant-1.1, ant-1.2, ant-1.3, and ant-1.4). We have investigated their spatiotemporal expression patterns and discovered that, whereas ANT-1.1 is a ubiquitously expressed mitochon… Show more
“…(Supplementary Figure S5). In agreement with its mitochondrial localization, the subcellular localization of the GFP signal in these cells was mostly cytoplasmic and somewhat similar to that of the C. elegans mitochondrial adenine nucleotide transporter ANT-1.1 (36). Figure 5.OSGL-1::GFP localizes to mitochondria.…”
Yeast Qri7 and human OSGEPL are members of the orthologous Kae1(OSGEP)/YgjD protein family, the last class of universally conserved proteins without assigned function. Phylogenetic analyses indicate that the eukaryotic Qri7(OSGEPL) proteins originated from bacterial YgjD proteins. We have recently shown that the archaeal Kae1 protein is a DNA-binding protein that exhibits apurinic endonuclease activity in vitro. We show here that the Qri7/OSGEPL proteins localize in mitochondria and are involved in mitochondrial genome maintenance in two model eukaryotic organisms, Saccharomyces cerevisiae and Caenorhabditis elegans. Furthermore, S. cerevisiae Qri7 complements the loss of the bacterial YgjD protein in Escherichia coli, suggesting that Qri7/OSGEPL and YgjD proteins have retained similar functions in modern organisms. We suggest to name members of the Kae1(OSGEP)/YgjD family UGMP, for Universal Genome Maintenance Proteins.
“…(Supplementary Figure S5). In agreement with its mitochondrial localization, the subcellular localization of the GFP signal in these cells was mostly cytoplasmic and somewhat similar to that of the C. elegans mitochondrial adenine nucleotide transporter ANT-1.1 (36). Figure 5.OSGL-1::GFP localizes to mitochondria.…”
Yeast Qri7 and human OSGEPL are members of the orthologous Kae1(OSGEP)/YgjD protein family, the last class of universally conserved proteins without assigned function. Phylogenetic analyses indicate that the eukaryotic Qri7(OSGEPL) proteins originated from bacterial YgjD proteins. We have recently shown that the archaeal Kae1 protein is a DNA-binding protein that exhibits apurinic endonuclease activity in vitro. We show here that the Qri7/OSGEPL proteins localize in mitochondria and are involved in mitochondrial genome maintenance in two model eukaryotic organisms, Saccharomyces cerevisiae and Caenorhabditis elegans. Furthermore, S. cerevisiae Qri7 complements the loss of the bacterial YgjD protein in Escherichia coli, suggesting that Qri7/OSGEPL and YgjD proteins have retained similar functions in modern organisms. We suggest to name members of the Kae1(OSGEP)/YgjD family UGMP, for Universal Genome Maintenance Proteins.
“…ANT-1.1 is an essential mitochondrial adenine transporter that is ubiquitously expressed (Farina et al, 2008). Our data clearly discriminates between two classes of exon-exon junctions for ant-1.1 : on one hand three constitutive junctions for each of which ~6 million reads are found, and on the other hand 170 junctions supported by a number of reads ranging from 1 to 200,000.…”
ABSTRACT:Almost twenty years after the completion of the C. elegans genome sequence, gene structure annotation is still an ongoing process with new evidence for gene variants still being regularly uncovered by additional in-depth transcriptome studies. While alternative splice forms can allow a single gene to encode several functional isoforms the question of how much spurious splicing is tolerated is still heavily debated.Here we gathered a compendium of 1,682 publicly available C. elegans RNA-seq datasets to increase the dynamic range of detection of RNA isoforms and obtained robust measurements of the relative abundance of each splicing event. While most of the splicing reads come from reproducibly detected splicing events, a large fraction of purported junctions are only supported by a very low number of reads. We devised an automated curation method that takes into account the expression level of each gene to discriminate robust splicing events from potential biological noise.We found that rarely used splice sites disproportionately come from highly expressed genes and are significantly less conserved in other nematode genomes than splice sites with a higher usage frequency.Our increased detection power confirmed trans-splicing for at least 84% of C. elegans protein coding genes. The genes for which trans-splicing was not observed are overwhelmingly low expression genes, suggesting that the mechanism is pervasive but not full captured by organismwide RNA-Seq.We generated annotated gene models including quantitative exon usage information for the entire C. elegans genome. This allows users to visualize at a glance the relative expression of each isoform for their gene of interest. ! !
“…Experiments in the fruit fly Drosophila melanogaster demonstrate that lipid droplet associated proteins are required to support early development [2]. It is important to note that the fat accumulation defects are not necessarily direct effect of lipid droplets, for example, act-5 (RNAi) worms likely have poor nutrient absorption due to defects in intestinal microvilli [58]. A limitation of our study was that we identified relatively few lipid metabolism proteins.…”
Lipid droplets are cytoplasmic organelles that store neutral lipids for membrane synthesis and energy reserves. In this study, we characterized the lipid and protein composition of purified C. elegans lipid droplets. These lipid droplets are composed mainly of triacylglycerols, surrounded by a phospholipid monolayer composed primarily of phosphatidylcholine and phosphatidylethanolamine. The fatty acid composition of the triacylglycerols is rich in fatty acid species obtained from the dietary E. coli, including cyclopropane fatty acids and cis-vaccenic acid. Unlike other organisms, C. elegans lipid droplets contain very little cholesterol or cholesterol esters. Comparison of the lipid droplet proteomes of wild type and high-fat daf-2 mutant strains shows a very similar proteome in both strains, except that the most abundant protein in the C. elegans lipid droplet proteome, MDT-28, is relatively less abundant in lipid droplets isolated from daf-2 mutants. Functional analysis of lipid droplet proteins identified in our proteomic studies indicated an enrichment of proteins required for growth and fat homeostasis in C. elegans. Finally, we confirmed the localization of one of the newly identified lipid droplet proteins, ACS-4. We found that ACS-4 localizes to the surface of lipid droplets in the C. elegans intestine and skin. This study bolsters C. elegans as a model to study the dynamics and functions of lipid droplets in a multicellular organism.
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