Biomedical subjects
Publications and source records attributed to Eric Lam.
In this Genomics Era with a wealth of annotated sequence data, it is easy to pigeonhole a protein into a particular function. However, Noa Matarasso et al. recently found a vacuolar protease that can also function as a transcription factor. This work illustrates that a protein can serve multiple roles in a cell, raising intriguing questions as to the extent that genomic information can be deciphered de novo.
Fluorescent protein chromatin tagging as achieved by the lac operator/lac repressor system is useful to trace distinct chromatin domains in living eukaryotic nuclei. To interpret the data correctly, it is important to recognize influences of the tagging system on nuclear architecture of the host cells. Within an Arabidopsis line that carries lac operator/lac repressor/GFP transgenes, the transgene loci frequently associate with each other and with heterochromatic chromocenters. Accumulation of tagged fusion protein further enhances the association frequency. Independent experiments with a transgenic plant carrying another multi-copy transgene also revealed, independent of its transcriptional state, unusually high frequencies of association with each other and with heterochromatin. From these results we conclude that the lac operator/lac repressor chromatin tagging system may alter the spatial chromatin organization in the host nuclei (in particular when more than one insertion locus is present) and also that loci of homologous transgenic repeats associate more often with each other and with endogenous heterochromatin than normal euchromatic regions.
A binary vector amenable to high-throughput cloning was constructed for ethanol-inducible expression of double-stranded RNA (dsRNA) in plants. Silencing of a transgene encoding beta-glucuronidase (GUS) was then examined at RNA and protein levels in tobacco. Transient gene silencing could be effectively achieved in plants with higher expression levels of alcR (the ethanol sensor) after single application of 1% ethanol (v/v) through root drenching. GUS activities showed more dramatic pattern of loss and recovery in young leaves than in older leaves. Repeated ethanol treatment resulted in extended gene suppression and increased loss of GUS activities. Interestingly, recovery of GUS transcript level is dramatically earlier than that of GUS protein levels as measured by enzyme assays. These observations indicate that dsRNA-mediated gene silencing may occur through more stable translational inhibition in addition to reversible targeted RNA degradation.
Metacaspases in plants, fungi, and protozoa constitute new members of a conserved superfamily of caspase-related proteases. A yeast caspase-1 protein (Yca1p), which is the single metacaspase in Saccharomyces cerevisiae, was shown to mediate apoptosis triggered by oxidative stress or aging in yeast. To examine whether plant metacaspase genes are functionally related to YCA1, we carried out analyses of AtMCP1b and AtMCP2b, representing the two subtypes of the Arabidopsis metacaspase family, utilizing yeast strains with wild-type and the disrupted YCA1 gene (yca1Delta). Inducible expression of AtMCP1b and AtMCP2b significantly promoted yeast apoptosis-like cell death of both the wild-type and yca1Delta strains, relative to the vector controls, during oxidative stress and early aging process. Mutational analysis of the two AtMCPs revealed that their cell-death-inducing activities depend on their catalytic center cysteine residues as well as caspase-like processing. In addition, the phenotype induced by the expression of two AtMCPs was effectively prevented when the cells were pretreated with a broad-spectrum caspase inhibitor N-benzyloxycarbonyl-Val-Ala-Asp-fluoromethyl-ketone. These results suggest that the two subtypes of Arabidopsis metacaspases are functionally related to Yca1p with caspase-like characteristics. However, we found that bacterial and yeast extracts containing AtMCP1b, AtMCP2b, or Yca1p exhibit arginine/lysine-specific endopeptidase activities but cannot cleave caspase-specific substrates. Together, the results strongly implicate that expression of metacaspases could result in the activation of downstream protease(s) with caspase-like activities that are required to mediate cell death activation via oxidative stress in yeast. Metacaspases from higher plants may serve similar functions.
The molecular identity of the key executioners involved in controlling plant programmed cell death (PCD) has been elusive. In a recent paper published in Science, Hatsugai and coworkers reported that a well-characterized protease called VPE from the plant cell vacuole can cleave caspase-specific substrates and is required for cell death activation by tobacco mosaic virus. This work provides clear evidence for the importance of the vacuole in plant PCD and a novel regulatory function for this organelle as well as for VPE proteases.
Fluorescent chromatin tagging makes possible tracking of specific loci in vivo and in situ. Loci tagged by the lac operator (lacO)/GFP-LacI/Nuclear Localization Signal (NLS) system show rapid motility and constrained chromatin dynamics in somatic nuclei of a transgenic line, designated EL702C, in Arabidopsis thaliana. The tagged loci associated with each other significantly more often than expected at random, due to homologous pairing of the lacO tandem repeat arrays. Furthermore, these arrays associated significantly more often than average euchromatic regions with heterochromatic chromocenters (CCs). We show now that the inserted lacO array in this transgenic line became strongly methylated at CG sites in the T3 generation, which can be reversed upon transfer into the mutant backgrounds of decrease in DNA methylation 1 (ddm1) and methyltransferase 1 (met1). Concomitantly, the tagged loci showed lower association frequencies as compared with the transgenics in wild-type background, which is correlated with a significant decrease in allelic and ectopic pairing of the lacO repeat arrays as visualized by fluorescence in situ hybridization. In contrast, the preferential association of the lacO arrays with heterochromatin, locus mobility in somatic nuclei and transcription of neighboring transgenes were not altered by reduced DNA methylation in ddm1 and met1 backgrounds. Our results show that repeat arrays can activate hypermethylation of the inserted locus that correlates with high frequencies of homologous pairing in somatic cells. In contrast, the preferential association of these inserted arrays with CCs in plant cells occurs through another mechanism.
As an example of the cost-effective large-scale generation of small-interfering RNA (siRNAs), we have created transgenic tobacco plants that produce siRNAs targeted to the mRNA of the non-structural protein NS1 from the influenza A virus subtype H1N1. We have investigated if these siRNAs, specifically targeted to the 5'-portion of the NS1 transcripts (5mNS1), would suppress viral propagation in mammalian cells. Agroinfiltration of transgenic tobacco with an Agrobacterium strain harboring a 5mNS1-expressing binary vector caused a reduction in 5mNS1 transcripts in the siRNA-accumulating transgenic plants. Further, H1N1 infection of siRNA-transfected mammalian cells resulted in significant suppression of viral replication. These results demonstrate that plant-derived siRNAs can inhibit viral propagation through RNA interference and could potentially be applied in control of viral-borne diseases.
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BACKGROUND: This study was designed to compare ultrasonography, clinical findings, and radiography in the detection of rib and sternal fractures. METHODS: In a prospective study, 88 patients presenting consecutively to an emergency department with isolated blunt chest injury of mild to moderate force were recruited. RESULTS: Ultrasonography yielded a sensitivity of 80.3 (95% confidence interval [CI], 69.5-88.5) for detecting chest wall fractures compared with sensitivities of 26.0 (95% CI, 15.8-36.3) for clinical acumen and 23.7 (95% CI, 14.7-34.8) for radiography. CONCLUSION: Early ultrasonography is more accurate than clinical and radiologic evaluation at detecting rib and sternal fractures.
With the rapid development of sequencing technologies in the past decade, many eukaryotic genomes have been resolved at the primary sequence level. However, organization of the genome within nuclei and the principles that govern such properties remain largely unclear. Optimization of fluorescence probe-based hybridization technologies combined with new advances in the instrumentation for microscopy has steadily yielded more structural information on chromosome organization in eukaryote model systems. These studies provide static snapshots of the detailed organization of chromatin. More recently, the successful application of a chromatin tagging strategy utilizing auto fluorescent fusion proteins opened a new era of chromatin studies in which the dynamic organization of the genome can be tracked in near real time. This review focuses on these new approaches to studying chromatin organization and dynamics in plants, and on future prospects in unraveling the basic principle of chromosome organization.
Lecithin-cholesterol acyltransferase deficiency is frequently associated with hypertriglyceridemia (HTG) in animal models and humans. We investigated the mechanism of HTG in the ldlr-/- x lcat-/- (double knockout (dko)) mice using the ldlr-/- x lcat+/+ (knock-out (ko)) littermates as control. Mean fasting triglyceride (TG) levels in the dko mice were elevated 1.75-fold compared with their controls (p < 0.002). Both the very low density lipoprotein and the low density lipoprotein/intermediate density lipoprotein fractions separated by fast protein liquid chromatography were TG-enriched in the dko mice. In vitro lipolysis assay revealed that the dko mouse very low density lipoprotein (d < 1.019 g/ml) fraction separated by ultracentrifugation was a more efficient substrate for lipolysis by exogenous bovine lipoprotein lipase. Post-heparin lipoprotein lipase activity was reduced by 61% in the dko mice. Hepatic TG production rate, determined after intravenous Triton WR1339 injection, was increased 8-fold in the dko mice. Hepatic mRNA levels of sterol regulatory element binding protein-1 (srebp-1) and its target genes acetyl-CoA carboxylase-1 (acc-1), fatty acid synthase (fas), and stearoyl-CoA desaturase-1 (scd-1) were significantly elevated in the dko mice compared with the ko control. The hepatic mRNA levels of LXRalpha (lxralpha) and its target genes including angiopoietin-like protein 3 (angptl-3) in the dko mice were unchanged. Fasting glucose and insulin levels were reduced by 31 and 42%, respectively in the dko mice, in conjunction with a 49% reduction in hepatic pepck-1 mRNA (p = 0.014). Both the HTG and the improved fasting glucose phenotype seen in the dko mice are at least in part attributable to an up-regulation of the hepatic srebp-1c gene.
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In the current model of chromatin organization in the interphase cell nucleus, chromosomes are organized into territories. Although constrained diffusion of chromatin in interphase cells has been confirmed in all cell types examined, little is known about chromatin dynamics in plant interphase cells. In this work, we measured for the first time interphase chromatin dynamics in plants using the green-fluorescent-protein-mediated chromatin-tagging system. Moreover, we compared the dynamics of diploid guard cells and endoreduplicated pavement cells. The movement of tagged loci in live seedlings shows constrained behavior in both types of nuclei. However, we found that the apparent confinement area for tagged loci in pavement cells is over 6 times larger than it is in guard cells. These findings suggest that chromatin is anchored to some component of the nucleus and that this might be responsible for the different dynamics of chromatin diffusion between diploid cells and endoreduplicated cells.
The p35 protein from baculovirus is a broad-range caspase inhibitor and suppresses programmed cell death in animals. We report here the effects of transgenic expression in tobacco of the p35 protein during the hypersensitive response (HR). Expression of p35 causes partial inhibition of nonhost HR triggered by bacteria and gene-for-gene HR triggered by virus. Infection of p35-expressing tobacco plants with Tobacco mosaic virus (TMV) disrupts N-mediated disease resistance, causing systemic spreading of the virus within a resistant background. Mutant variants altered in aspartate residues within the loop region of p35 are inefficient substrates for caspases in vitro, and they do not suppress caspase proteolytic activity in animal systems. Tobacco plants expressing these mutant variants of the p35 protein do not show inhibition of HR cell death or enhanced virus systemic movement. Thus, HR inhibition and TMV systemic spreading phenotype in p35-expressing plants correlate with the ability of the p35 protein to suppress caspase activity in animal systems. In addition, a C-terminal truncated variant of p35 is unable to suppress cell death in animals as well as HR cell death in transgenic tobacco. Our results provide evidence for the participation of caspase-like proteases during the HR. In addition, they suggest that timely activation of cell death is necessary for effective TMV containment within the primary infection site.
Although it is now well documented that metazoans have evolved general transcription factor (GTF) variants to regulate their complex patterns of gene expression, there is so far no information regarding the existence of specific GTFs in plants. Here we report the characterization of a ubiquitously expressed gene that encodes a bona fide novel transcription factor IIB (TFIIB)-related protein in Arabidopsis thaliana. We have shown that this protein is the founding member of a plant-specific TFIIB-related protein family named pBrp (for plant-specific TFIIB-related protein). Surprisingly, in contrast to common GTFs that are localized in the nucleus, the bulk of pBrp proteins are bound to the cytoplasmic face of the plastid envelope, suggesting an organelle-specific function for this novel class of TFIIB-related protein. We show that pBrp proteins harbor conditional proteolytic signals that can target these proteins for rapid turnover by the proteasome-mediated protein degradation pathway. Interestingly, under conditions of proteasome inhibition, pBrp proteins accumulate in the nucleus. Together, our results suggest a possible involvement of these proteins in an intracellular signaling pathway between plastids and the nucleus. Our data provide the first evidence for an organelle-related evolution of the eukaryotic general transcription machinery.
One of the earliest signal transduction events that trigger the hypersensitive response (HR) of plants against pathogen attack is thought to be an alteration of proton flux across the plasma membrane (PM). However, no direct genetic evidence for the involvement of PM-localised proton channels or pumps in the induction of this response has been reported. We previously showed that expression of the bacterial proton pump bacterio-opsin (bO) in transgenic plants resulted in the spontaneous activation of the HR. Here we show that the bO protein is likely localised to the PM in transgenic tobacco plants. Furthermore, mutational analysis shows that induction of the HR by bO expression is dependent upon the capability of bO to translocate protons. Although bO functions as a light-driven proton pump in Halobacteria when assembled with retinal, we also show by mutational analysis that this chromophore binding is unnecessary for its in planta activity. Taken together, our results suggest that expression of bO in plants leads to the insertion of a passive proton channel into the PM. The activity of this channel in the PM results in spontaneous activation of cell death and HR-associated phenotypes including enhanced resistance to a broad spectrum of plant pathogens. Our work provides direct molecular evidence to support a working model in which alterations in ionic homeostasis at the level of the PM may work as one of the critical steps in the signalling pathway for the activation of the HR.
Transcription factors often belong to multigene families and their individual contribution in a particular regulatory network remains difficult to assess. We show here that specific members from a family of conserved Arabidopsis bZIP transcription factors, the TGA proteins, are regulated in their protein stability by developmental stage-specific proteolysis. Using GFP fusions of three different Arabidopsis TGA factors that represent members of distinct subclasses of the TGA factor family, we demonstrate that two of these TGA proteins are specifically targeted for proteolysis in mature leaf cells. Using a supershift gel mobility assay, we found evidence for similar regulation of the cognate proteins as compared to the GFP fusion proteins expressed under the cauliflower mosaic virus (CaMV) 35S promoter. Using various inhibitors, we showed that the expression of at least one of these three TGA factors could be stabilized by inhibition of proteasome-mediated proteolysis. This study indicates that TGA transcription factors may be regulated by distinct pathways of targeted proteolysis that can serve to modulate the contribution of specific members of a multigene family in complex regulatory pathways.
The control of subcellular localization of proteins and their interaction with other partners in vivo are important parameters that provide clues to their function and regulation. The ability to simultaneously track multiple protein species with high resolution should provide a valuable assay system to study and characterize various types of posttranslational control pathways. In this work, we established the system and a method involving "spectral profiling" for the resolution of four different fluorescent protein tags in the same viewing field using digital imaging technology. With these techniques, we have (a) developed new derivatives of mGFP5, which is commonly used in the plant field, that are about three times brighter; (b) demonstrated that four spectrally distinct fluorescent proteins (cyan, green, yellow, and red) that are fused to a transcription factor could be stably expressed in nuclei and distinguished in tobacco (Nicotiana tabacum) mesophyll cells; and (c) shown that interaction between partners of a dimeric transcription factor can be detected by measuring fluorescence resonance energy transfer. These technologies should help one to study protein-protein interactions efficiently, especially for nuclear proteins under in vivo conditions.