Comparative structures and evolution of vertebrate lipase H (LIPH) genes and proteins: a relative of the phospholipase A1 gene families

Lipase H (LIPH) is a membrane-bound phospholipase generating 2-acyl lysophosphatidic acid (LPA) in the body. LPA is a lipid mediator required for maintaining homeostasis of diverse biological functions and in activating cell surface receptors such as P2Y5, which plays an essential role in hair growth. Bioinformatic methods were used to predict the amino acid sequences, secondary and tertiary structures, and gene locations for LIPH genes and encoded proteins using data from several vertebrate genome projects. Vertebrate LIPH genes contained ten coding exons transcribed on either the positive or negative DNA strands. Evidence is presented for duplicated LIPH genes for the chicken and zebra fish genomes. Vertebrate LIPH protein subunits shared 56–97 % sequence identities and exhibited sequence alignments and identities for key LIPH amino acid residues as well as extensive conservation of predicted secondary and tertiary structures with those previously reported for horse pancreatic lipase (LIPP), with ‘N-signal peptide’, ‘lipase,’ and ‘plat’ structural domains. Comparative studies of vertebrate LIPH sequences with other phospholipase A1-like lipases (LIPI and PS-PLA1), as well as vascular and pancreatic lipases, confirmed predictions for LIPH N-terminal signal peptides (residues 1–18); a conserved vertebrate LIPH N-glycosylation site (66NVT for human LIPH); active site ‘triad’ residues (Ser 154; Asp 178; His 248); disulfide bond residues (233–246; 270–281; 284–292; 427–446), and a ‘short’ 12 residue ‘active site lid’, which is comparable to other phospholipases examined. Phylogenetic analyses demonstrated the relationships and potential evolutionary origins of the vertebrate LIPH family of genes related to, but distinct from other phospholipase A1-like genes (LIPI and PS-PLA1), and from vascular lipase and pancreatic lipase gene families. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13205-012-0087-z) contains supplementary material, which is available to authorized users

Vertebrate endothelial lipase: comparative studies of an ancient gene and protein in vertebrate evolution

Endothelial lipase (gene: LIPG; enzyme: EL) is one of three members of the triglyceride lipase family that contributes to lipoprotein degradation within the circulation system and plays a major role in HDL metabolism in the body. In this study, in silico methods were used to predict the amino acid sequences, secondary and tertiary structures, and gene locations for LIPG genes and encoded proteins using data from several vertebrate genome projects. LIPG is located on human chromosome 18 and is distinct from other human 'neutral lipase' genes, hepatic lipase (gene: LIPC; enzyme: HL) and lipoprotein lipase (gene: LPL; enzyme: LPL) examined. Vertebrate LIPG genes usually contained 10 coding exons located on the positive strand for most primates, as well as for horse, bovine, opossum, platypus and frog genomes. The rat LIPG gene however contained only 9 coding exons apparently due to the presence of a 'stop' codon' within exon 9. Vertebrate EL protein subunits shared 58-97% sequence identity as compared with 38-45% sequence identities with human HL and LPL. Four previously reported human EL N-glycosylation sites were predominantly conserved among the 10 potential N-glycosylation sites observed for the vertebrate EL sequences examined. Sequence alignments and identities for key EL amino acid residues were observed as well as conservation of predicted secondary and tertiary structures with those previously reported for horse pancreatic lipase (PL) (Bourne et al. 1994). Several potential sites for regulating LIPG gene expression were observed including CpG islands near the LIPG gene promoter and a predicted microRNA binding site near the 3'-untranslated region. Promoter regions containing functional polymorphisms that regulate HDL cholesterol in baboons were conserved among primates but not retained between primates and rodents. Phylogenetic analyses examined the relationships and potential evolutionary origins of the vertebrate LIPG gene subfamily with other neutral triglyceride lipase gene families, LIPC and LPL. It is apparent that the triglyceride lipase ancestral gene for the vertebrate LIPG gene predated the appearance of fish during vertebrate evolution[500 million years ago.Full Tex

Far-Infrared Emission From E and E/S0 Galaxies

Studies of cold material through IRAS 60um and 100um observations indicated that half of ordinary E and E/S0 galaxies were detected above the 3 sigma level, indicating that cold gas is common, although no correlation was found between the optical and far- infrared fluxes. Most detections were near the instrumental threshold, and given an improved understanding of detection confidence, we reconsider the 60um and 100um detection rate. After excluding active galactic nuclei, peculiar systems, and background contamination, only 15 non-peculiar E and E/S0 galaxies from the RSA catalog are detected above the 98% confidence level, about 12% of the sample. An unusually high percentage of these 15 galaxies possess cold gas (HI, CO) and optical emission lines (Halpha), supporting the presence of gas cooler than 10E4 K. The 60um to 100um flux ratios imply a median dust temperature for the sample of 30 K, with a range of 23-38 K. These detections define the upper envelope of the optical to far-infrared relationship, F_fir propto F_B^0.24+/-0.08, showing that optically bright objects are also brighter in the infrared, although with considerable dispersion. A luminosity correlation is present with L_fir propto L_B^1.65+/-0.28, but the dust temperature is uncorrelated with luminosity. Models that contain large dust grains composed of amorphous carbon plus silicates come close to reproducing the typical 60um to 100um flux ratios, the far-infrared luminosity, and the L_fir - L_B relationship.Comment: 10 postscript pages, 2 tables, and 2 figure

Identification of baboon microRNAs expressed in liver and lymphocytes

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are small noncoding RNAs (~22 nucleotides) that regulate gene expression by cleaving mRNAs or inhibiting translation. The baboon is a well-characterized cardiovascular disease model; however, no baboon miRNAs have been identified. Evidence indicates that the baboon and human genomes are highly conserved; based on this conservation, we hypothesized that comparative genomic methods could be used to identify baboon miRNAs.</p> <p>Methods</p> <p>We employed an <it>in silico </it>comparative genomics approach and human miRNA arrays to identify baboon expressed miRNAs in liver (n = 6) and lymphocytes (n = 6). Expression profiles for selected miRNAs in multiple tissues were validated by RT-PCR.</p> <p>Results</p> <p>We identified <it>in silico </it>555 putative baboon pre-miRNAs, of which 41% exhibited 100% identity and an additional 58% shared more than 90% sequence identity with human pre-miRNAs. Some of these miRNAs are primate-specific and are clustered in the baboon genome like human miRNA clusters. We detected expression of 494 miRNAs on the microarray and validated expression of selected miRNAs in baboon liver and lymphocytes by RT-PCR. We also observed miRNA expression in additional tissues relevant to dyslipidemia and atherosclerosis. Approximately half of the miRNAs expressed on the array were not predicted <it>in silico </it>suggesting that we have identified novel baboon miRNAs, which could not be predicted using the current draft of the baboon genome.</p> <p>Conclusion</p> <p>We identified a subset of baboon miRNAs using a comparative genomic approach, identified additional baboon miRNAs using a human array and showed tissue-specific expression of baboon miRNAs. Our discovery of baboon miRNAs in liver and lymphocytes will provide resources for studies on the roles of miRNAs in dyslipidemia and atherosclerosis, and for translational studies.</p

Opossum carboxylesterases: sequences, phylogeny and evidence for CES gene duplication events predating the marsupial-eutherian common ancestor

Background Carboxylesterases (CES) perform diverse metabolic roles in mammalian organisms in the detoxification of a broad range of drugs and xenobiotics and may also serve in specific roles in lipid, cholesterol, pheromone and lung surfactant metabolism. Five CES families have been reported in mammals with human CES1 and CES2 the most extensively studied. Here we describe the genetics, expression and phylogeny of CES isozymes in the opossum and report on the sequences and locations of CES1, CES2 and CES6 'like' genes within two gene clusters on chromosome one. We also discuss the likely sequence of gene duplication events generating multiple CES genes during vertebrate evolution. Results We report a cDNA sequence for an opossum CES and present evidence for CES1 and CES2 like genes expressed in opossum liver and intestine and for distinct gene locations of five opossum CES genes,CES1, CES2.1, CES2.2, CES2.3 and CES6, on chromosome 1. Phylogenetic and sequence alignment studies compared the predicted amino acid sequences for opossum CES with those for human, mouse, chicken, frog, salmon and Drosophila CES gene products. Phylogenetic analyses produced congruent phylogenetic trees depicting a rapid early diversification into at least five distinct CES gene family clusters: CES2, CES1, CES7, CES3, and CES6. Molecular divergence estimates based on a Bayesian relaxed clock approach revealed an origin for the five mammalian CES gene families between 328-378 MYA. Conclusion The deduced amino acid sequence for an opossum cDNA was consistent with its identity as a mammalian CES2 gene product (designated CES2.1). Distinct gene locations for opossum CES1 (1: 446,222,550-446,274,850), three CES2 genes (1: 677,773,395-677,927,030) and a CES6 gene (1: 677,585,520-677,730,419) were observed on chromosome 1. Opossum CES1 and multiple CES2 genes were expressed in liver and intestine. Amino acid sequences for opossum CES1 and three CES2 gene products revealed conserved residues previously reported for human CES1 involved in catalysis, ligand binding, tertiary structure and organelle localization. Phylogenetic studies indicated the gene duplication events which generated ancestral mammalian CES genes predated the common ancestor for marsupial and eutherian mammals, and appear to coincide with the early diversification of tetrapods.Full Tex

Does Ocean Acidification Benefit Seagrasses in a Mesohaline Environment? A Mesocosm Experiment in the Northern Gulf of Mexico

Ocean acidification is thought to benefit seagrasses because of increased carbon dioxide (CO2) availability for photosynthesis. However, in order to truly assess ecological responses, effects of ocean acidification need to be investigated in a variety of coastal environments. We tested the hypothesis that ocean acidification would benefit seagrasses in the northern Gulf of Mexico, where the seagrasses Halodule wrightii and Ruppia maritima coexist in a fluctuating environment. To evaluate if benefits of ocean acidification could alter seagrass bed composition, cores of H. wrightii and R. maritima were placed alone or in combination into aquaria and maintained in an outdoor mesocosm. Half of the aquaria were exposed to either ambient (mean pH of 8.1 ± 0.04 SD on total scale) or high CO2 (mean pH 7.7 ± 0.05 SD on total scale) conditions. After 54 days of experimental exposure, the δ13C values were significantly lower in seagrass tissue in the high CO2 condition. This integration of a different carbon source (either: preferential use of CO2, gas from cylinder, or both) indicates that plants were not solely relying on stored energy reserves for growth. Yet, after 41 to 54 days, seagrass morphology, biomass, photo-physiology, metabolism, and carbon and nitrogen content in the high CO2 condition did not differ from those at ambient. There was also no indication of differences in traits between the homospecific or heterospecific beds. Findings support two plausible conclusions: (1) these seagrasses rely heavily on bicarbonate use and growth will not be stimulated by near future acidification conditions or (2) the mesohaline environment limited the beneficial impacts of increased CO2 availability