An ubiquitously expressed gene 3.5 kilobases upstream of the glycerol-3-phosphate dehydrogenase gene in mice.

While studying the organization of the mouse glycerol-phosphate dehydrogenase gene (Gdc-1 on chromosome 15), we identified a novel transcriptional unit located only 3.4 kilobases (kb) upstream of the 5' end of the Gdc-1 gene. This gene has been provisionally named D15Kz1. The unusual proximity of these two genes led us to investigate the pattern of expression and sequence characteristics of the new gene for comparison with those of Gdc-1. D15Kz1 was found to have transcripts of 3.2 and 3.4 kb in length. The 3.4-kb transcript was expressed at low levels in all tissues examined, whereas the 3.2-kb transcript was detected only in the cerebral cortex and the brown fat. D15Kz1 and Gdc-1 are not coordinately regulated, as evidenced by the characteristics of their expression in several tissues and in differentiating 3T3-F442A adipocyte cultures. A cDNA sequence of 3,105 bases isolated from an embryonal carcinoma lambda gt10 cDNA library had a large open reading frame of 461 amino acids at one end followed by 1.6 kb of sequence with multiple stop codons. Algorithms used to search the protein and nucleic acid data bases detected no significant sequence similarity to any other protein or gene. Southern blot analysis of genomic DNA using the D15Kz1 cDNA as a probe indicated that D15Kz1 is a single-copy gene in the mouse genome and that it is conserved in humans, rats, and chickens. This conservation of gene sequences suggests that D15Kz1 encodes a protein with an important cellular function.

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Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

Molecular Biology and Evolution ◽

10.1093/molbev/msu286 ◽

2014 ◽

Vol 32 (1) ◽

pp. 258-267 ◽

Cited By ~ 68

Author(s):

Bryan A. Moyers ◽

Jianzhi Zhang

Keyword(s):

Genome Evolution ◽

Sequence Similarity ◽

A Priori ◽

Critical Evaluation ◽

Age Groups ◽

Null Model ◽

New Gene ◽

Or Gene ◽

The Impact ◽

Gene Age

Phylostratigraphy is a method for dating the evolutionary emergence of a gene or gene family by identifying its homologs across the tree of life, typically by using BLAST searches. Applying this method to all genes in a species, or genomic phylostratigraphy, allows investigation of genome-wide patterns in new gene origination at different evolutionary times and thus has been extensively used. However, gene age estimation depends on the challenging task of detecting distant homologs via sequence similarity, which is expected to have differential accuracies for different genes. Here, we evaluate the accuracy of phylostratigraphy by realistic computer simulation with parameters estimated from genomic data, and investigate the impact of its error on findings of genome evolution. We show that 1) phylostratigraphy substantially underestimates gene age for a considerable fraction of genes, 2) the error is especially serious when the protein evolves rapidly, is short, and/or its most conserved block of sites is small, and 3) these errors create spurious nonuniform distributions of various gene properties among age groups, many of which cannot be predicted a priori. Given the high likelihood that conclusions about gene age are faulty, we advocate the use of realistic simulation to determine if observations from phylostratigraphy are explainable, at least qualitatively, by a null model of biased measurement, and in all cases, critical evaluation of results.

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SpCoel1: a sea urchin profilin gene expressed specifically in coelomocytes in response to injury.

Molecular Biology of the Cell ◽

10.1091/mbc.3.4.403 ◽

1992 ◽

Vol 3 (4) ◽

pp. 403-414 ◽

Cited By ~ 49

Author(s):

L C Smith ◽

R J Britten ◽

E H Davidson

Keyword(s):

Sea Urchin ◽

Sequence Similarity ◽

Single Copy ◽

Untranslated Regions ◽

Amino Acid Sequence Similarity ◽

Signal Transduction System ◽

Reading Frame ◽

Purple Sea Urchin ◽

Copy Gene ◽

External Injury

SpCoel1 is a single copy gene that is specifically expressed in most of the coelomocytes of the adult purple sea urchin, Strongylocentrotus purpuratus. The 4-kb transcript from this gene has a relatively short (426 nucleotide) open reading frame (ORF) with long 3' and 5' untranslated regions. The ORF encodes a protein that has strong amino acid sequence similarity to profilins from yeast to mammals. Transcript titrations of SpCoel1 show significant increases per coelomocyte in animals that have been physiologically challenged. Increases in transcript levels are of similar magnitudes between animals receiving different treatments, such as injuries from needle punctures or from injections of foreign cells. The evidence presented here implies a molecular mechanism by which this lower deuterostome defense system responds to external insult, viz that an external "injury signal" activates a signal transduction system, which in turn mediates the alterations in cytoskeletal state that are required for coelomocyte activation.

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EVIDENCE FOR A PREVIOUSLY UNIDENTIFIED UPSTREAM EXON IN THE HUMAN OESTROGEN RECEPTOR GENE.

Journal of Molecular Endocrinology ◽

10.1677/jme.0.0060111 ◽

1991 ◽

Vol 6 (1) ◽

pp. 111-115 ◽

Cited By ~ 80

Author(s):

M. Keaveney ◽

J. Klug ◽

M.T. Dawson ◽

P.V. Nestor ◽

J.G. Neilan ◽

...

Keyword(s):

Untranslated Region ◽

Oestrogen Receptor ◽

Human Gene ◽

Genomic Structure ◽

Receptor Gene ◽

Upstream Open Reading Frame ◽

Transcriptional Unit ◽

Reading Frame ◽

Or Gene ◽

Upstream Exon

ABSTRACT The presence of a previously unidentified exon upstream of the originally described human oestrogen receptor (hOR) gene is demonstrated. This is shown to be spliced to the 5′ untranslated region of the previously designated exon I. The resulting genomic structure of the human gene is thus in agreement with the structure of the mouse OR gene and highlights the conservation of an 18 amino acid upstream open-reading frame formed from the above splicing event. Taken in conjunction with previous publications this would suggest that the hOR gene is a complex transcriptional unit that contains two promoters.

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Gene organization and transcription of TED, a lepidopteran retrotransposon integrated within the baculovirus genome

Molecular and Cellular Biology ◽

10.1128/mcb.10.6.3067-3077.1990 ◽

1990 ◽

Vol 10 (6) ◽

pp. 3067-3077

Author(s):

P D Friesen ◽

M S Nissen

Keyword(s):

Trichoplusia Ni ◽

Sequence Similarity ◽

Single Copy ◽

Gene Organization ◽

Open Reading Frames ◽

Long Terminal Repeats ◽

Reading Frame ◽

Subsequent Activation ◽

Nuclear Polyhedrosis ◽

A Site

A single copy of the retrotransposon TED, from the moth Trichoplusia ni (a lepidopteran noctuid), was identified within the DNA genome of the baculovirus Autographa californica nuclear polyhedrosis virus. Determination of the complete nucleotide sequence (7,510 base pairs) of the integrated copy indicated that TED belongs to the family of retrotransposons that includes Drosophila melanogaster elements 17.6 and gypsy and thus represents the first nondipteran member of this invertebrate group to be identified. The internal portion of TED, flanked by long terminal repeats (LTRs), is composed of three long open reading frames comparable in size and location to the gag, pol, and env genes of the vertebrate retroviruses. Sequence similarity with the dipteran elements was the highest within individual domains of TED open reading frame 2 (pol region) that are also conserved among the retroviruses and encode protease, reverse transcriptase, and integrase functions, respectively. Mapping the 5' and 3' termini of TED RNAs indicated that the LTRs have a retroviral U3-R-U5 structural organization that is capable of directing the synthesis of transcripts that represent potential substrates for reverse transcription and intermediates in transposition. Abundant RNAs were also initiated from a site within the 5' LTR that matches the consensus motif for the promoter of late, hyperexpressed baculovirus genes. The presence of this viruslike promoter within TED and its subsequent activation only after integration within the viral genome suggest a possible symbiotic relationship with the baculovirus that could extend transposon host range.

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The human E48 antigen, highly homologous to the murine Ly-6 antigen ThB, is a GPI-anchored molecule apparently involved in keratinocyte cell-cell adhesion.

The Journal of Cell Biology ◽

10.1083/jcb.129.6.1677 ◽

1995 ◽

Vol 129 (6) ◽

pp. 1677-1689 ◽

Cited By ~ 92

Author(s):

R H Brakenhoff ◽

M Gerretsen ◽

E M Knippels ◽

M van Dijk ◽

H van Essen ◽

...

Keyword(s):

Cell Adhesion ◽

Core Protein ◽

Sequence Similarity ◽

Single Copy ◽

Chromosome 8 ◽

Expression Cloning ◽

Target Antigen ◽

Reading Frame ◽

Antigen A ◽

Cell Cell

The E48 antigen, a putative human homologue of the 20-kD protein present in desmosomal preparations of bovine muzzle, and formerly called desmoglein III (dg4), is a promising target antigen for antibody-based therapy of squamous cell carcinoma in man. To anticipate the effect of high antibody dose treatment, and to evaluate the possible biological involvement of the antigen in carcinogenesis, we set out to molecularly characterize the antigen. A cDNA clone encoding the E48 antigen was isolated by expression cloning in COS cells. Sequence analysis revealed that the clone contained an open reading frame of 128 amino acids, encoding a core protein of 13,286 kD. Database searching showed that the E48 antigen has a high level of sequence similarity with the mouse ThB antigen, a member of the Ly-6 antigen family. Phosphatidylinositol-specific (PI-specific) phospholipase-C treatment indicated that the E48 antigen is glycosylphosphatidylinositol-anchored (GPI-anchored) to the plasma membrane. The gene encoding the E48 antigen is a single copy gene, located on human chromosome 8 in the 8q24-qter region. The expression of the gene is confined to keratinocytes and squamous tumor cells. The putative mouse homologue, the ThB antigen, originally identified as an antigen on cells of the lymphocyte lineage, was shown to be highly expressed in squamous mouse epithelia. Moreover, the ThB expression level is in keratinocytes, in contrast to that in lymphocytes, not mouse strain related. Transfection of mouse SV40-polyoma transformed mouse NIH/3T3 cells with the E48 cDNA confirmed that the antigen is likely to be involved in cell-cell adhesion.

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Gene organization and transcription of TED, a lepidopteran retrotransposon integrated within the baculovirus genome.

Molecular and Cellular Biology ◽

10.1128/mcb.10.6.3067 ◽

1990 ◽

Vol 10 (6) ◽

pp. 3067-3077 ◽

Cited By ~ 80

Author(s):

P D Friesen ◽

M S Nissen

Keyword(s):

Trichoplusia Ni ◽

Sequence Similarity ◽

Single Copy ◽

Gene Organization ◽

Open Reading Frames ◽

Long Terminal Repeats ◽

Reading Frame ◽

Subsequent Activation ◽

Nuclear Polyhedrosis ◽

A Site

A single copy of the retrotransposon TED, from the moth Trichoplusia ni (a lepidopteran noctuid), was identified within the DNA genome of the baculovirus Autographa californica nuclear polyhedrosis virus. Determination of the complete nucleotide sequence (7,510 base pairs) of the integrated copy indicated that TED belongs to the family of retrotransposons that includes Drosophila melanogaster elements 17.6 and gypsy and thus represents the first nondipteran member of this invertebrate group to be identified. The internal portion of TED, flanked by long terminal repeats (LTRs), is composed of three long open reading frames comparable in size and location to the gag, pol, and env genes of the vertebrate retroviruses. Sequence similarity with the dipteran elements was the highest within individual domains of TED open reading frame 2 (pol region) that are also conserved among the retroviruses and encode protease, reverse transcriptase, and integrase functions, respectively. Mapping the 5' and 3' termini of TED RNAs indicated that the LTRs have a retroviral U3-R-U5 structural organization that is capable of directing the synthesis of transcripts that represent potential substrates for reverse transcription and intermediates in transposition. Abundant RNAs were also initiated from a site within the 5' LTR that matches the consensus motif for the promoter of late, hyperexpressed baculovirus genes. The presence of this viruslike promoter within TED and its subsequent activation only after integration within the viral genome suggest a possible symbiotic relationship with the baculovirus that could extend transposon host range.

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Primary structure of the mouse glycerol-3-phosphate dehydrogenase gene.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)67311-9 ◽

1986 ◽

Vol 261 (25) ◽

pp. 11779-11785

Author(s):

R C Ireland ◽

M A Kotarski ◽

L A Johnston ◽

U Stadler ◽

E Birkenmeier ◽

...

Keyword(s):

Primary Structure ◽

Dehydrogenase Gene ◽

Glycerol 3 Phosphate Dehydrogenase

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The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis

Plants ◽

10.3390/plants9121692 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1692

Author(s):

Li Gu ◽

Ting Su ◽

Ming-Tai An ◽

Guo-Xiong Hu

Keyword(s):

Phylogenetic Analysis ◽

Sequence Similarity ◽

Single Copy ◽

Structural Features ◽

Rrna Genes ◽

Trna Genes ◽

Sequencing Data ◽

High Sequence Similarity ◽

Plastid Genomes ◽

Cp Genome

Oreocharis esquirolii, a member of Gesneriaceae, is known as Thamnocharis esquirolii, which has been regarded a synonym of the former. The species is endemic to Guizhou, southwestern China, and is evaluated as vulnerable (VU) under the International Union for Conservation of Nature (IUCN) criteria. Until now, the sequence and genome information of O. esquirolii remains unknown. In this study, we assembled and characterized the complete chloroplast (cp) genome of O. esquirolii using Illumina sequencing data for the first time. The total length of the cp genome was 154,069 bp with a typical quadripartite structure consisting of a pair of inverted repeats (IRs) of 25,392 bp separated by a large single copy region (LSC) of 85,156 bp and a small single copy region (SSC) of18,129 bp. The genome comprised 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Thirty-one repeat sequences and 74 simple sequence repeats (SSRs) were identified. Genome alignment across five plastid genomes of Gesneriaceae indicated a high sequence similarity. Four highly variable sites (rps16-trnQ, trnS-trnG, ndhF-rpl32, and ycf 1) were identified. Phylogenetic analysis indicated that O. esquirolii grouped together with O. mileensis, supporting resurrection of the name Oreocharis esquirolii from Thamnocharisesquirolii. The complete cp genome sequence will contribute to further studies in molecular identification, genetic diversity, and phylogeny.

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Arabinanase A from Pseudomonas fluorescens subsp. cellulosa exhibits both an endo- and an exo- mode of action

Biochemical Journal ◽

10.1042/bj3230547 ◽

1997 ◽

Vol 323 (2) ◽

pp. 547-555 ◽

Cited By ~ 55

Author(s):

Vincent A. McKIE ◽

Gary W. BLACK ◽

Sarah J. MILLWARD-SADLER ◽

Geoffrey P. HAZLEWOOD ◽

Judith I. LAURIE ◽

...

Keyword(s):

Pseudomonas Fluorescens ◽

Mode Of Action ◽

Plant Cell Wall ◽

Catalytic Domain ◽

Genomic Library ◽

Glycosyl Hydrolase ◽

Single Copy ◽

Terminal Sequence ◽

Reading Frame ◽

Significant Release

Pseudomonas fluorescens subsp. cellulosa expressed arabinanase activity when grown on media supplemented with arabinan or arabinose. Arabinanase activity was not induced by the inclusion of other plant structural polysaccharides, and was repressed by the addition of glucose. The majority of the Pseudomonas arabinanase activity was extracellular. Screening of a genomic library of P. fluorescens subsp. cellulosa DNA constructed in Lambda ZAPII, for recombinants that hydrolysed Red-dyed arabinan, identified five arabinan-degrading plaques. Each of the phage contained the same Pseudomonas arabinanase gene, designated arbA, which was present as a single copy in the Pseudomonas genome. The nucleotide sequence of arbA revealed an open reading frame of 1041 bp encoding a protein, designated arabinanase A (ArbA), of Mr 39438. The N-terminal sequence of ArbA exhibited features typical of a prokaryotic signal peptide. Analysis of the primary structure of ArbA indicated that, unlike most Pseudomonas plant cell wall hydrolases, it did not contain linker sequences or have a modular structure, but consisted of a single catalytic domain. Sequence comparison between the Pseudomonas arabinanase and proteins in the SWISS-PROT database showed that ArbA exhibits greatest sequence identity with arabinanase A from Aspergillus niger, placing the enzyme in glycosyl hydrolase Family 43. The significance of the differing substrate specificities of enzymes in Family 43 is discussed. ArbA purifed from a recombinant strain of Escherichia coli had an Mr of 34000 and an N-terminal sequence identical to residues 32–51 of the deduced sequence of ArbA, and hydrolysed linear arabinan, carboxymethylarabinan and arabino-oligosaccharides. The enzyme displayed no activity against other plant structural polysaccharides, including branched sugar beet arabinan. ArbA produced almost exclusively arabinotriose from linear arabinan and appeared to hydrolyse arabino-oligosaccharides by successively releasing arabinotriose. ArbA and the Aspergillus arabinanase mediated a decrease in the viscosity of linear arabinan that was associated with a significant release of reducing sugar. We propose that ArbA is an arabinanase that exhibits both an endo- and an exo- mode of action.

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