Reducing the environmental sensitivity of yellow fluorescent protein. Mechanism and applications.

Yellow mutants of the green fluorescent protein (YFP) are crucial constituents of genetically encoded indicators of signal transduction and fusions to monitor protein-protein interactions. However, previous YFPs show excessive pH sensitivity, chloride interference, poor photostability, or poor expression at 37 degrees C. Protein evolution in Escherichia coli has produced a new YFP named Citrine, in which the mutation Q69M confers a much lower pK(a) (5.7) than for previous YFPs, indifference to chloride, twice the photostability of previous YFPs, and much better expression at 37 degrees C and in organelles. The halide resistance is explained by a 2.2-A x-ray crystal structure of Citrine, showing that the methionine side chain fills what was once a large halide-binding cavity adjacent to the chromophore. Insertion of calmodulin within Citrine or fusion of cyan fluorescent protein, calmodulin, a calmodulin-binding peptide and Citrine has generated improved calcium indicators. These chimeras can be targeted to multiple cellular locations and have permitted the first single-cell imaging of free [Ca(2+)] in the Golgi. Citrine is superior to all previous YFPs except when pH or halide sensitivity is desired and is particularly advantageous within genetically encoded fluorescent indicators of physiological signals.

Role of alternative splicing in generating isoform diversity among plasma membrane calcium pumps.

Calcium pumps of the plasma membrane (also known as plasma membrane Ca(2+)-ATPases or PMCAs) are responsible for the expulsion of Ca(2+) from the cytosol of all eukaryotic cells. Together with Na(+)/Ca(2+) exchangers, they are the major plasma membrane transport system responsible for the long-term regulation of the resting intracellular Ca(2+) concentration. Like the Ca(2+) pumps of the sarco/endoplasmic reticulum (SERCAs), which pump Ca(2+) from the cytosol into the endoplasmic reticulum, the PMCAs belong to the family of P-type primary ion transport ATPases characterized by the formation of an aspartyl phosphate intermediate during the reaction cycle. Mammalian PMCAs are encoded by four separate genes, and additional isoform variants are generated via alternative RNA splicing of the primary gene transcripts. The expression of different PMCA isoforms and splice variants is regulated in a developmental, tissue- and cell type-specific manner, suggesting that these pumps are functionally adapted to the physiological needs of particular cells and tissues. PMCAs 1 and 4 are found in virtually all tissues in the adult, whereas PMCAs 2 and 3 are primarily expressed in excitable cells of the nervous system and muscles. During mouse embryonic development, PMCA1 is ubiquitously detected from the earliest time points, and all isoforms show spatially overlapping but distinct expression patterns with dynamic temporal changes occurring during late fetal development. Alternative splicing affects two major locations in the plasma membrane Ca(2+) pump protein: the first intracellular loop and the COOH-terminal tail. These two regions correspond to major regulatory domains of the pumps. In the first cytosolic loop, the affected region is embedded between a putative G protein binding sequence and the site of phospholipid sensitivity, and in the COOH-terminal tail, splicing affects pump regulation by calmodulin, phosphorylation, and differential interaction with PDZ domain-containing anchoring and signaling proteins. Recent evidence demonstrating differential distribution, dynamic regulation of expression, and major functional differences between alternative splice variants suggests that these transporters play a more dynamic role than hitherto assumed in the spatial and temporal control of Ca(2+) signaling. The identification of mice carrying PMCA mutations that lead to diseases such as hearing loss and ataxia, as well as the corresponding phenotypes of genetically engineered PMCA "knockout" mice further support the concept of specific, nonredundant roles for each Ca(2+) pump isoform in cellular Ca(2+) regulation.

Biochemistry, mutagenesis, and oligomerization of DsRed, a red fluorescent protein from coral.

DsRed is a recently cloned 28-kDa fluorescent protein responsible for the red coloration around the oral disk of a coral of the Discosoma genus. DsRed has attracted tremendous interest as a potential expression tracer and fusion partner that would be complementary to the homologous green fluorescent protein from Aequorea, but very little is known of the biochemistry of DsRed. We now show that DsRed has a much higher extinction coefficient and quantum yield than previously reported, plus excellent resistance to pH extremes and photobleaching. In addition, its 583-nm emission maximum can be further shifted to 602 nm by mutation of Lys-83 to Met. However, DsRed has major drawbacks, such as strong oligomerization and slow maturation. Analytical ultracentrifugation proves DsRed to be an obligate tetramer in vitro, and fluorescence resonance energy transfer measurements and yeast two-hybrid assays verify oligomerization in live cells. Also, DsRed takes days to ripen fully from green to red in vitro or in vivo, and mutations such as Lys-83 to Arg prevent the color change. Many potential cell biological applications of DsRed will require suppression of the tetramerization and acceleration of the maturation.

Fas preassociation required for apoptosis signaling and dominant inhibition by pathogenic mutations.

Heterozygous mutations encoding abnormal forms of the death receptor Fas dominantly interfere with Fas-induced lymphocyte apoptosis in human autoimmune lymphoproliferative syndrome. This effect, rather than depending on ligand-induced receptor oligomerization, was found to stem from ligand- independent interaction of wild-type and mutant Fas receptors through a specific region in the extracellular domain. Preassociated Fas complexes were found in living cells by means of fluorescence resonance energy transfer between variants of green fluorescent protein. These results show that formation of preassociated receptor complexes is necessary for Fas signaling and dominant interference in human disease.

Recent advances in technology for measuring and manipulating cell signals.

Signal transduction research has made some glowing progress in the past 12 months. Recent advances in fluorescent proteins, small molecule fluorophores and imaging technology are generating new ways to investigate signal transduction.

Measurement of molecular interactions in living cells by fluorescence resonance energy transfer between variants of the green fluorescent protein.

Many signal transduction pathways operate through oligomerization of proteins into multi-subunit complexes. Although biochemical assays can identify potential protein-protein interactions, studying these interactions in living cells is more challenging. Fluorescence resonance energy transfer (FRET) has been used as a "spectroscopic ruler" to measure molecular proximity, but these methods have been limited by the need for chemical labeling of target proteins or labeled antibodies. We present methods for examining interactions between target proteins molecularly fused to cyan and yellow variants of the green fluorescent protein (GFP) by FRET in living cells. Flow cytometric and microscope-based methods are described that have been applied to a variety of interacting proteins.

Circular permutation and receptor insertion within green fluorescent proteins.

Many areas of biology and biotechnology have been revolutionized by the ability to label proteins genetically by fusion to the Aequorea green fluorescent protein (GFP). In previous fusions, the GFP has been treated as an indivisible entity, usually appended to the amino or carboxyl terminus of the host protein, occasionally inserted within the host sequence. The tightly interwoven, three-dimensional structure and intricate posttranslational self-modification required for chromophore formation would suggest that major rearrangements or insertions within GFP would prevent fluorescence. However, we now show that several rearrangements of GFPs, in which the amino and carboxyl portions are interchanged and rejoined with a short spacer connecting the original termini, still become fluorescent. These circular permutations have altered pKa values and orientations of the chromophore with respect to a fusion partner. Furthermore, certain locations within GFP tolerate insertion of entire proteins, and conformational changes in the insert can have profound effects on the fluorescence. For example, insertions of calmodulin or a zinc finger domain in place of Tyr-145 of a yellow mutant (enhanced yellow fluorescent protein) of GFP result in indicator proteins whose fluorescence can be enhanced severalfold upon metal binding. The calmodulin graft into enhanced yellow fluorescent protein can monitor cytosolic Ca(2+) in single mammalian cells. The tolerance of GFPs for circular permutations and insertions shows the folding process is surprisingly robust and offers a new strategy for creating genetically encodable, physiological indicators.

Developmental expression of the four plasma membrane calcium ATPase (Pmca) genes in the mouse.

The plasma membrane calcium ATPases are critical components in the regulation of cellular calcium homeostasis and signaling. In mammals, there are 4 Pmca genes, and information on the cellular and tissue distribution of their expression during development will provide insight into the regulation and possible function of each Pmca isoform. Using specific probes and in situ hybridization, we found that the four Pmca genes are expressed in spatially overlapping but distinct patterns in the mouse embryo. The dynamic temporal patterns of expression indicate that the individual isoforms are subject to both positive and negative regulation. The differential and restricted expression of Pmca genes supports the notion that they play unique functional roles in mammalian development.

Minimum CAG repeat in the human calmodulin-1 gene 5' untranslated region is required for full expression.

The human calmodulin-1 gene (hCALM1) contains a (CAG)7 repeat in its 5'-untranslated region (5'-UTR). We found this repeat to be stable and nonpolymorphic in the human population. To determine whether the repeat region affects hCALM1 expression and whether repeat expansions to numbers known to be associated with disease in other genes may alter expression, we tested luciferase reporter genes driven by the hCALM1 promoter and 5'-UTR containing 0, 7 (wild-type), 20, and 45 CAG repeats in human NT2/D1 teratoma cells. Interestingly, the repeat deletion, (CAG)0, decreased expression by 45%, while repeat expansions to (CAG)20 and (CAG)45, or the insertion of a scrambled (C,A,G)7 sequence did not alter gene expression. These data indicate (1) that the endogenous repeat element is required for full expression of hCALM1, and (2) that some triplet repeat expansions in the 5'-UTR of protein-coding genes may be well tolerated and even optimize gene expression.

mRNA expression of the four isoforms of the human plasma membrane Ca(2+)-ATPase in the human hippocampus.

Ca2+ dyshomeostasis is a contributing factor to the development and progression of neurodegenerative disease. Plasma membrane Ca(2+)-ATPases (PMCAs) are responsible for setting intracellular Ca2+ levels and may be involved in the dynamic processing of Ca2+ loads in normal and pathological conditions. In situ hybridization was employed to determine the expression pattern of the four human PMCA isoforms in the human hippocampus. PMCA1 and 3 mRNAs were weakly expressed throughout the hippocampal formation, whereas PMCA2 and 4 mRNA expression showed distinct regional differences, with increased levels in CA2 and the dentate gyrus. Differential expression of PMCA isoforms may reflect cellular differences in Ca(2+)-handling properties and provide a partial explanation for the differential susceptibility of hippocampal neurons to Ca(2+)-mediated cell death.

Change in plasma membrane Ca2(+)-ATPase splice-variant expression in response to a rise in intracellular Ca2+.

BACKGROUND: Most eukaryotic genes are divided into introns and exons. Upon transcription, the intronic segments are eliminated and the exonic sequences spliced together through a series of complex processing events. Alternative splicing refers to the optional inclusion or exclusion of specific exons in transcripts derived from a single gene, which leads to structural and functional changes in the encoded proteins. Although many components of the machinery directing the physical excision of introns and joining of exons have been elucidated in recent years, the signaling pathways regulating the activity of the machinery remain largely unexplored. RESULTS: A calcium-mediated signaling pathway regulates alternative splicing at a specific site of human plasma membrane calcium pump-2 transcripts. This site consists of three exons, which are differentially used in a tissue-specific manner. In IMR32 neuroblastoma cells, a transient elevation of intracellular calcium changed the predominant pattern from one in which all three exons are included to the coexpression of a variant including only the third exon. Western-blot analysis demonstrated that the newly expressed mRNAs are faithfully translated. Once induced, the new splicing pattern was maintained over multiple cell divisions. Protein synthesis was not required to induce the alternative splice change, indicating that all components necessary for a rapid cellular response are present in the cells. CONCLUSIONS: Calcium signaling exerts a direct influence on the regulation of alternative splicing. Notably, a calcium-mediated change in the expression of alternatively spliced variants of a calcium regulatory protein was discovered. The change in splicing occurs quickly, is persistent but reversible and leads to a corresponding change in protein expression. The specific nature in which differently spliced protein variants are expressed, and now the fact that their expression can be regulated by distinct intracellular signaling pathways, suggests that the regulation of alternative splicing by physiological stimuli is a widespread regulatory mechanism by which a cell may coordinate its responses to environmental cues.

Primary structure of human plasma membrane Ca(2+)-ATPase isoform 3.

The complete coding sequence of the human plasma membrane calcium ATPase (PMCA) isoform 3 was determined from overlapping genomic and cDNA clones. The cDNAs for the two major alternative splice variants 3a (3CII) and 3b (3CI) code for proteins of 1173 and 1220 amino-acid residues, respectively, which show 98% identity with the corresponding rat isoforms. On a multiple human tissue Northern blot, a major PMCA3 transcript of about 7 kb was detected exclusively in the brain, demonstrating the highly restricted pattern of expression of this isoform to human neuronal tissues. With the elucidation of the human PMCA3 primary structure, complete sequence information is now available for the entire family of human PMCA isoforms.

Expression of high- and low-affinity neurotrophin receptors on human transformed B lymphocytes.

We performed high-sensitivity flow cytometry and Western blotting to study the expression of the low-affinity NGF receptor (p75NGFR) and of the transmembrane tyrosine kinase (Trk) family of high-affinity receptors for the different neurotrophic factors on Epstein-Barr virus (EBV)-transformed human B lymphocytes. Reverse transcriptase (RT) polymerase chain reaction (PCR) with single and multiple sets of primers (multiplex RT-PCR) was used to survey the repertoire of neurotrophin receptor transcripts in this cell line. We demonstrated that transformed B cells express detectable levels of Trk b and its mRNA. Conversely, negative results were obtained for p75NGFR, Trk a, and Trk c. Exposure of EBV-transformed B lymphocytes to brain-derived neurotrophic factor (BDNF) triggered the phosphorylation of Trk b, as demonstrated by Western blots of cell lysates probed with monoclonal antibody against phosphotyrosine.

Transcript distribution of plasma membrane Ca2+ pump isoforms and splice variants in the human brain.

Plasma membrane calcium pumps (PMCAs) play a major role in the maintenance and fine regulation of the intracellular Ca2+ concentration. Fourteen subregions of the normal human brain were carefully dissected and analyzed by reverse transcriptase-polymerase chain reaction for the distribution of mRNAs corresponding to the four known PMCA genes as well as their alternative splicing products at two previously defined 'hotspots' A and C. All PMCA genes were found to be expressed in every brain subregion; however, consistent differences were found in the distribution of alternative splice options. The four cortical regions and hippocampus were characterized by the relative preference of variants that include an entire exon at site C and lead to the expression of isoforms of the a-type. Inferior olive and olfactory bulb showed a relative preponderance of the b-form 'default' types of alternative splicing at site C, and a decrease or even the lack of 'differentiated' forms such as variants 1a and 1c. At the N-terminal splice site A, the default x-type variants were predominant in all brain regions for PMCA 1, 3, and 4. By contrast, the pattern of PMCA2 variants was the most variable, ranging from the presence of the entire set of 2x, 2w, and 2z forms in inferior olive to the almost exclusive presence of form 2z (excluding all alternatively spliced sequences) in the four cortical regions, caudate, and hippocampus. Regional differences in the PMCA splice type distribution in normal human brain may correlate with different demands on the regulation of the set-point resting Ca2+ levels in these areas. Changes in these patterns may correlate with altered physiological states of the affected regions and/or reflect an (early) sign of Ca2+ dyshomeostasis characteristic of many neurodegenerative diseases.