The expression of rat homeobox-containing genes is developmentally regulated and tissue specific

Development ◽  
1988 ◽  
Vol 103 (3) ◽  
pp. 601-610
Author(s):  
M. Falzon ◽  
S.Y. Chung
Keyword(s):  
Amino Acid ◽  
Blot Analysis ◽  
Genomic Library ◽  
Sequence Similarity ◽  
Amino Acid Level ◽  
Single Copy ◽  
Developmentally Regulated ◽  
Tissue Specific ◽  
Rna Transcripts ◽  
Flanking Sequences

Seven rat homeobox-containing sequences have been isolated by screening a genomic library with a probe derived from a Drosophila antennapedia cDNA clone. The characterization of two of these homeobox-containing clones has been described (Falzon, M., Sanderson, N.D. and Chung, S. Y. (1987) Gene 54, 23–32). Sequence analysis of the remaining five homeobox regions reveals a 180 bp domain sharing 70–95% identity at the amino acid level with the homeodomain from the Drosophila antennapedia gene and with the homeodomains from other metazoan species. Genomic blot analysis shows that each of the homeobox-containing DNA segments is probably present in a single copy per haploid genome. Northern blot analysis of RNA transcripts indicates that the rat homeobox-containing sequences are expressed during embryogenesis and in newborn and adult tissues in a tissue-specific manner; RNA expression is predominantly detected in spinal cord and kidney. Moreover, the pattern of RNA transcripts observed is distinct for each homeobox sequence, indicating differential regulation. Among the seven rat homeobox-containing sequences, the flanking sequences of five of the clones have no obvious sequence similarity with previously published sequences of homeobox-containing genes from other species. Two of the rat clones have been identified as potential homologues to mouse homeobox-containing sequences. For both pairs, a high degree of amino acid conservation (greater than 95%) is observed within the homeodomain and its immediate flanking regions between the putative homologous genes in mouse and rat. This strengthens the assertion that some of the mammalian homeobox-containing genes encode highly conserved proteins and may serve important biological functions.

Salamander rods and cones contain distinct transducin alpha subunits

2000 ◽  
Vol 17 (6) ◽  
pp. 847-854 ◽  
Author(s):  
JAMES C. RYAN ◽  
SERGEY ZNOIKO ◽  
LIN XU ◽  
ROSALIE K. CROUCH ◽  
JIAN-XING MA
Keyword(s):  
Amino Acid ◽  
Blot Analysis ◽  
Cellular Localization ◽  
Amino Acid Level ◽  
Single Copy ◽  
Lower Vertebrate ◽  
Rods And Cones ◽  
Sequence Identity ◽  
Outer Segments ◽  
Cone Pigments

The mammalian retina is known to contain two distinct transducins that interact with their respective rod and cone pigments. However, there are no reports of a nonmammalian species having two distinct transducins. In the present study, we report the cloning and cellular localization of two transducin α subunits (Gαt) from the tiger salamander. Through degenerate polymerase chain reaction (PCR) and subsequent screening of a salamander retina cDNA library, we have identified two forms of Gαt. When compared to existing sequences in GenBank, the cloned subunits showed high similarity to rod and cone transducins. The salamander Gαt-1 has 91.2–93.7% amino acid sequence identity to mammalian rod Gαt subunits and 79.7–80.9% to mammalian cone Gαts. The salamander Gαt-2 has 86.2–87.9% sequence identity to mammalian cone Gαts and 78.9–80.9% to mammalian rod Gαts at the amino acid level. The Gαt-1 cDNA encodes 350 amino acids while the Gαt-2 cDNA encodes 354 residues, which is typical for rod and cone Gαts, respectively, and we thus identified the Gαt-1 as rod and Gαt-2 as cone Gαt. Sequences identified as effector binding sites and GTPase activity regions are highly conserved between the two subunits. Genomic Southern blot analysis showed that rod and cone Gαt subunits are both encoded by single-copy genes. Northern blot analysis identified retina-specific transcripts of 3.0 kb for rod Gαt and 2.6 kb for cone Gαt. Immunohistochemistry in the flat-mounted salamander retina demonstrated that rod Gαt is localized to rods, predominantly in the outer segments; similarly, cone Gαt is localized to cone outer segments. The results confirm that the two sequences encode rod and cone transducins and demonstrate that this lower vertebrate contains two distinct transducins that are localized specifically to rod and cone photoreceptors.

scholarly journals Cloning of Beauveria bassiana Chitinase Gene Bbchit1 and Its Application To Improve Fungal Strain Virulence

2005 ◽  
Vol 71 (1) ◽  
pp. 363-370 ◽  
Author(s):  
Weiguo Fang ◽  
Bo Leng ◽  
Yuehua Xiao ◽  
Kai Jin ◽  
Jincheng Ma ◽  
...  
Keyword(s):  
Amino Acid ◽  
Beauveria Bassiana ◽  
Entomopathogenic Fungi ◽  
Pathogenic Fungus ◽  
Amino Acid Level ◽  
Single Copy ◽  
Chitinase Gene ◽  
Streptomyces Avermitilis ◽  
Regulatory Sequence ◽  
Significant Similarity

ABSTRACT Entomopathogenic fungi can produce a series of chitinases, some of which act synergistically with proteases to degrade insect cuticle. However, chitinase involvement in insect fungus pathogenesis has not been fully characterized. In this paper, an endochitinase, Bbchit1, was purified to homogeneity from liquid cultures of Beauveria bassiana grown in a medium containing colloidal chitin. Bbchit1 had a molecular mass of about 33 kDa and pI of 5.4. Based on the N-terminal amino acid sequence, the chitinase gene, Bbchit1, and its upstream regulatory sequence were cloned. Bbchit1 was intronless, and there was a single copy in B. bassiana. Its regulatory sequence contained putative CreA/Crel carbon catabolic repressor binding domains, which was consistent with glucose suppression of Bbchit1. At the amino acid level, Bbchit1 showed significant similarity to a Streptomyces avermitilis putative endochitinase, a Streptomyces coelicolor putative chitinase, and Trichoderma harzianum endochitinase Chit36Y. However, Bbchit1 had very low levels of identity to other chitinase genes previously isolated from entomopathogenic fungi, indicating that Bbchit1 was a novel chitinase gene from an insect-pathogenic fungus. A gpd-Bbchit1 construct, in which Bbchit1 was driven by the Aspergiullus nidulans constitutive promoter, was transformed into the genome of B. bassiana, and three transformants that overproduced Bbchit1 were obtained. Insect bioassays revealed that overproduction of Bbchit1 enhanced the virulence of B. bassiana for aphids, as indicated by significantly lower 50% lethal concentrations and 50% lethal times of the transformants compared to the values for the wild-type strain.

scholarly journals Evidence for a Role of rpoE in Stressed and Unstressed Cells of Marine Vibrio angustumStrain S14

2000 ◽  
Vol 182 (24) ◽  
pp. 6964-6974 ◽  
Author(s):  
Erika Hild ◽  
Kathy Takayama ◽  
Rose-Marie Olsson ◽  
Staffan Kjelleberg
Keyword(s):  
Oxidative Stress ◽  
Blot Analysis ◽  
Type Strain ◽  
Wild Type Strain ◽  
Sequence Similarity ◽  
Temperature Shift ◽  
Optimal Growth ◽  
Single Copy ◽  
Carbon Starvation ◽  
Wild Type

ABSTRACT We report the cloning, sequencing, and characterization of therpoE homolog in Vibrio angustum S14. TherpoE gene encodes a protein with a predicted molecular mass of 19.4 kDa and has been demonstrated to be present as a single-copy gene by Southern blot analysis. The deduced amino acid sequence of RpoE is most similar to that of the RpoE homolog of Sphingomonas aromaticivorans, ς24, displaying sequence similarity and identity of 63 and 43%, respectively. Northern blot analysis demonstrated the induction of rpoE 6, 12, and 40 min after a temperature shift to 40°C. An rpoE mutant was constructed by gene disruption. There was no difference in viability during logarithmic growth, stationary phase, or carbon starvation between the wild type and the rpoE mutant strain. In contrast, survival of the mutant was impaired following heat shock during exponential growth, as well as after oxidative stress at 24 h of carbon starvation. The mutant exhibited microcolony formation during optimal growth temperatures (22 to 30°C), and cell area measurements revealed an increase in cell volume of the mutant during growth at 30°C, compared to the wild-type strain. Moreover, outer membrane and periplasmic space protein analysis demonstrated many alterations in the protein profiles for the mutant during growth and carbon starvation, as well as following oxidative stress, in comparison with the wild-type strain. It is thereby concluded that RpoE has an extracytoplasmic function and mediates a range of specific responses in stressed as well as unstressed cells of V. angustum S14.

scholarly journals Cloning and identification of tissue-specific expression of KCNN4 splice variants in rat colon

2010 ◽  
Vol 299 (2) ◽  
pp. C251-C263 ◽  
Author(s):  
Christian Barmeyer ◽  
Christoph Rahner ◽  
Youshan Yang ◽  
Frederick J. Sigworth ◽  
Henry J. Binder ◽  
...  
Keyword(s):  
Amino Acid ◽  
Splice Variants ◽  
Amino Acid Level ◽  
Distal Colon ◽  
Rat Colon ◽  
Membrane Expression ◽  
Specific Expression ◽  
Tissue Specific ◽  
Anion Secretion ◽  
Tissue Specific Expression

KCNN4 channels that provide the driving force for cAMP- and Ca2+-induced anion secretion are present in both apical and basolateral membranes of the mammalian colon. However, only a single KCNN4 has been cloned. This study was initiated to identify whether both apical and basolateral KCNN4 channels are encoded by the same or different isoforms. Reverse transcriptase-PCR (RT-PCR), real-time quantitative-PCR (RT-QPCR), and immunofluorescence studies were used to clone and identify tissue-specific expression of KCNN4 isoforms. Three distinct KCNN4 cDNAs that are designated as KCNN4a, KCNN4b, and KCNN4c encoding 425, 424, and 395 amino acid proteins, respectively, were isolated from the rat colon. KCNN4a differs from KCNN4b at both the nucleotide and the amino acid level with distinct 628 bp at the 3′-untranslated region and an additional glutamine at position 415, respectively. KCNN4c differs from KCNN4b by lacking the second exon that encodes a 29 amino acid motif. KCNN4a and KCNN4b/c are identified as smooth muscle- and epithelial cell-specific transcripts, respectively. KCNN4b and KCNN4c transcripts likely encode basolateral (40 kDa) and apical (37 kDa) membrane proteins in the distal colon, respectively. KCNN4c, which lacks the S2 transmembrane segment, requires coexpression of a large conductance K+ channel β-subunit for plasma membrane expression. The KCNN4 channel blocker TRAM-34 inhibits KCNN4b- and KCNN4c-mediated 86Rb (K+ surrogate) efflux with an apparent inhibitory constant of 0.6 ± 0.1 and 7.8 ± 0.4 μM, respectively. We conclude that apical and basolateral KCNN4 K+ channels that regulate K+ and anion secretion are encoded by distinct isoforms in colonic epithelial cells.

scholarly journals Developmentally Regulated Chromosome Fragmentation Linked to Imprecise Elimination of Repeated Sequences in Paramecia

2003 ◽  
Vol 2 (5) ◽  
pp. 1076-1090 ◽  
Author(s):  
Anne Le Mouël ◽  
Alain Butler ◽  
François Caron ◽  
Eric Meyer
Keyword(s):  
De Novo ◽  
Germ Line ◽  
Single Copy ◽  
Mendelian Inheritance ◽  
Direct Repeats ◽  
Developmentally Regulated ◽  
Chromosome Fragmentation ◽  
Dna Elimination ◽  
Flanking Sequences ◽  
Identical Cell

ABSTRACT The chromosomes of ciliates are fragmented at reproducible sites during the development of the polyploid somatic macronucleus, but the mechanisms involved appear to be quite diverse in different species. In Paramecium aurelia, the process is imprecise and results in de novo telomere addition at locally heterogeneous positions. To search for possible determinants of chromosome fragmentation, we have studied an ∼21-kb fragmentation region from the germ line genome of P. primaurelia. The mapping and sequencing of alternative macronuclear versions of the region show that two distinct multicopy elements, a minisatellite and a degenerate transposon copy, are eliminated by an imprecise mechanism leading either to chromosome fragmentation and the formation of new telomeres or to the rejoining of flanking sequences. Heterogeneous internal deletions occur between short direct repeats containing TA dinucleotides. The complex rearrangement patterns produced vary slightly among genetically identical cell lines, show non-Mendelian inheritance during sexual reproduction, and can be experimentally modified by transformation of the maternal macronucleus with homologous sequences. These results suggest that chromosome fragmentation in Paramecium is the consequence of imprecise DNA elimination events that are distinct from the precise excision of single-copy internal eliminated sequences and that target multicopy germ line sequences by homology-dependent epigenetic mechanisms.

scholarly journals Characterization of two developmentally regulated sea urchin U2 small nuclear RNA promoters: a common required TATA sequence and independent proximal and distal elements.

1992 ◽  
Vol 12 (2) ◽  
pp. 650-660 ◽  
Author(s):  
B Stefanovic ◽  
W F Marzluff
Keyword(s):  
Sea Urchin ◽  
Core Promoter ◽  
Sequence Similarity ◽  
Single Copy ◽  
Upstream Sequence ◽  
Small Nuclear Rna ◽  
Developmentally Regulated ◽  
Sequence Element ◽  
Nuclear Rna ◽  
Tata Sequence

The promoters of two U2 small nuclear RNA genes isolated from the sea urchin Lytechinus variegatus were mapped by microinjection of genes into sea urchin zygotes. One gene, LvU2E, is expressed only in oocytes and embryos and is found in a tandemly repeated gene set, while the other gene, LvU2L, is a single-copy gene and is expressed in embryos and somatic cells. The promoters each contain a TATA sequence at -25 which is required for expression, a proximal sequence element (PSE) centered at -55 required for expression, a sequence at -100 which couples the core promoter (PSE plus TATA box) to the upstream element, and an upstream sequence which stimulates expression fourfold. The PSE together with the TATA sequence is sufficient to determine the transcription start site. There is no sequence similarity between the -100 and PSE sequences of the two genes. The -100 sequences can be interchanged between the two genes. The LvU2E PSE functions in the context of the LvU2L gene, but the LvU2L PSE functions poorly in the context of the LvU2E gene.

scholarly journals A family of dynein genes in Drosophila melanogaster.

1994 ◽  
Vol 5 (1) ◽  
pp. 45-55 ◽  
Author(s):  
K Rasmusson ◽  
M Serr ◽  
J Gepner ◽  
I Gibbons ◽  
T S Hays
Keyword(s):  
Amino Acid ◽  
Heavy Chain ◽  
Amino Acid Level ◽  
Single Copy ◽  
Cytoplasmic Dynein ◽  
Amino Acid Identity ◽  
Chain Gene ◽  
Phosphate Binding ◽  
Atp Binding Site ◽  
Dynein Heavy Chain

We report the identification and initial characterization of seven Drosophila dynein heavy chain genes. Each gene is single copy and maps to a unique genomic location. Sequence analysis of partial clones reveals that each encodes a highly conserved portion of the putative dynein hydrolytic ATP-binding site in dyneins that includes a consensus phosphate-binding (P-loop) motif. One of the clones is derived from a Drosophila cytoplasmic dynein heavy chain gene, Dhc64C, that shows extensive amino acid identity to cytoplasmic dynein isoforms from other organisms. Two other Drosophila dynein clones are 85 and 90% identical at the amino acid level to the corresponding region of the beta heavy chain of sea urchin axonemal dynein. Probes for all seven of the dynein-related sequences hybridize to transcripts that are of the appropriate size, approximately 14 kilobases, to encode the characteristic high molecular weight dynein heavy chain polypeptides. The Dhc64C transcript is readily detected in RNA from ovaries, embryos, and testes. Transcripts from five of the six remaining genes are also detected in much lesser amounts in tissues other than testes. All but one of the dynein transcripts are expressed at comparable levels in testes suggesting their participation in flagellar axoneme assembly and motility.

scholarly journals Evidence for the existence of a pristanoyl-CoA oxidase gene in man

1997 ◽  
Vol 325 (3) ◽  
pp. 593-599 ◽  
Author(s):  
Johannes C. T. VANHOOREN ◽  
Peter MARYNEN ◽  
Guy P. MANNAERTS ◽  
Paul P. VAN VELDHOVEN
Keyword(s):  
Amino Acid ◽  
Northern Blot ◽  
Blot Analysis ◽  
Northern Blot Analysis ◽  
Developmental Stages ◽  
Genomic Library ◽  
Immunoblot Analysis ◽  
Human Tissues ◽  
Oxidase Gene ◽  
Activity Measurements

In the rat, 2-methyl branched fatty acids and the bile acid intermediates di- and tri-hydroxycoprostanic acids are desaturated by pristanoyl-CoA oxidase and trihydroxycoprostanoyl-CoA oxidase respectively. In the human, these compounds are oxidized by a single enzyme, branched-chain acyl-CoA oxidase, which according to its amino acid sequence is the human homologue of rat trihydroxycoprostanoyl-CoA oxidase. Pristanoyl-CoA oxidase is apparently absent from human tissues as indicated by immunoblot analysis [Van Veldhoven, Van Rompuy, Fransen, de Béthune and Mannaerts (1994) Eur. J. Biochem. 222, 795–801] and Northern-blot analysis [Vanhooren, Fransen, de Béthune, Baumgart, Baes, Torrekens, Van Leuven, Mannaerts and Van Veldhoven (1996) Eur. J. Biochem. 239, 302–309] of human tissues. In this paper we present evidence, however, that at least the gene for pristanoyl-CoA oxidase is present in the human. A human liver cDNA encoding a protein of 700 amino acids, showing 75% amino acid identity with rat pristanoyl-CoA oxidase and harbouring a peroxisomal C-terminal-targeting signal (SKL), was isolated. Bacterial expression of the cDNA resulted in a fusion protein that was cross-reactive with antibodies directed against rat pristanoyl-CoA oxidase and the C-terminal SKL sequence. Screening of a genomic library with the isolated cDNA as a probe resulted in a genomic clone in which four introns were localized. By means of fluorescence in situhybridization the gene for human pristanoyl-CoA oxidase was mapped at chromosome position 4p15.3. We conclude that a gene for pristanoyl-CoA oxidase is present in the human genome. The gene appears to be expressed to such a low extent in liver that its mRNA cannot be detected by routine Northern-blot analysis and that its product remains undetected by standard immunoblotting or by enzyme activity measurements. We speculate that the gene may be expressed under special (e.g. certain developmental stages) conditions or in certain specialized tissues not examined thus far.

scholarly journals A Rab4-like GTPase in Dictyostelium discoideum colocalizes with V-H(+)-ATPases in reticular membranes of the contractile vacuole complex and in lysosomes

1994 ◽  
Vol 107 (10) ◽  
pp. 2801-2812 ◽  
Author(s):  
J. Bush ◽  
K. Nolta ◽  
J. Rodriguez-Paris ◽  
N. Kaufmann ◽  
T. O'Halloran ◽  
...  
Keyword(s):  
Dictyostelium Discoideum ◽  
Blot Analysis ◽  
Mammalian Cells ◽  
Amino Acid Level ◽  
Single Copy ◽  
Contractile Vacuole ◽  
Western Blots ◽  
Atpase Subunit ◽  
Cell Extracts ◽  
Gradient Fractionation

In the course of screening a cDNA library for ras-related Dictyostelium discoideum genes, we cloned a 0.7 kb cDNA (rabD) encoding a putative protein that was 70% identical at the amino acid level to human Rab4. Rab4 is a small M(r) GTPase, which belongs to the Ras superfamily and functions to regulate endocytosis in mammalian cells. Southern blot analysis indicated that the rabD cDNA was encoded by a single copy gene while Northern blot analysis revealed that the rabD gene was expressed at relatively constant levels during growth and differentiation. Affinity-purified antibodies were prepared against a RabD fusion protein expressed in bacteria; the antibodies recognized a single 23 kDa polypeptide on western blots of cell extracts. Density gradient fractionation revealed that the RabD antigen co-distributed primarily with buoyant membranes rich in vacuolar protons pumps (V-H(+)-ATPases) and, to a lesser extent, with lysosomes. This result was confirmed by examining cell lines expressing an epitope-tagged version of RabD. Magnetically purified early endocytic vesicles and post-lysosomal vacuoles reacted more weakly with anti-RabD antibodies than did lysosomes. Other organelles were negative for RabD. Double-label indirect immunofluorescence microscopy revealed that RabD and the 100 kDa V-H(+)-ATPase subunit colocalized in a fine reticular network throughout the cytoplasm. This network was reminiscent of spongiomes, the tubular elements of the contractile vacuole system. Immunoelectron microscopy confirmed the presence of RabD in lysosome fractions and in the membranes rich in V-H(+)-ATPase. We conclude that a Rab4-like GTPase in D. discoideum is principally associated with the spongiomes of contractile vacuole complex.

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