Post-transcriptional regulation of organ-specific expression of individual rbcS mRNAs in Lemna gibba

Aquatic Plant Genomics: Advances, Applications, and Prospects

Genomics is a discipline in genetics that studies the genome composition of organisms and the precise structure of genes and their expression and regulation. Genomics research has resolved many problems where other biological methods have failed. Here, we summarize advances in aquatic plant genomics with a focus on molecular markers, the genes related to photosynthesis and stress tolerance, comparative study of genomes and genome/transcriptome sequencing technology.

Unusual small subunit that is not expressed in photosynthetic cells alters the catalytic properties of rubisco in rice

Rubisco small subunits (RbcSs) are encoded by a nuclear multigene family in plants. Five RbcS genes, OsRbcS1, OsRbcS2, OsRbcS3, OsRbcS4, and OsRbcS5, have been identified in rice (Oryza sativa). Among them, the amino acid sequence of OsRbcS1 differs notably from those of other rice RbcSs. Phylogenetic analysis showed that OsRbcS1 is genetically distant from other rice RbcS genes and more closely related to RbcS from a fern and two woody plants. Reverse transcription-PCR and promoter β-glucuronidase analyses revealed that OsRbcS1 was not expressed in leaf blade, a major photosynthetic organ in rice, but was expressed in leaf sheath, culm, anther, and root central cylinder. In leaf blade of transgenic rice overexpressing OsRbcS1 and leaf sheath of nontransgenic rice, OsRbcS1 was incorporated into the Rubisco holoenzyme. Incorporation of OsRbcS1 into Rubisco increased the catalytic turnover rate and Km for CO2 of the enzyme and slightly decreased the specificity for CO2, indicating that the catalytic properties were shifted to those of a high-activity type Rubisco. The CO2 assimilation rate at low CO2 partial pressure was decreased in overexpression lines but was not changed under ambient and high CO2 partial pressure compared with nontransgenic rice. Although the Rubisco content was increased, Rubisco activation state was decreased in overexpression lines. These results indicate that the catalytic properties of Rubisco can be altered by ectopic expression of OsRbcS1, with substantial effects on photosynthetic performance in rice. We believe this is the first demonstration of organ-specific expression of individual members of the RbcS gene family resulting in marked effects on Rubisco catalytic activity.

RBCS1A and RBCS3B, two major members within the Arabidopsis RBCS multigene family, function to yield sufficient Rubisco content for leaf photosynthetic capacity

Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit (RBCS) is encoded by a nuclear RBCS multigene family in many plant species. The contribution of the RBCS multigenes to accumulation of Rubisco holoenzyme and photosynthetic characteristics remains unclear. T-DNA insertion mutants of RBCS1A (rbcs1a-1) and RBCS3B (rbcs3b-1) were isolated among the four Arabidopsis RBCS genes, and a double mutant (rbcs1a3b-1) was generated. RBCS1A mRNA was not detected in rbcs1a-1 and rbcs1a3b-1, while the RBCS3B mRNA level was suppressed to ∼20% of the wild-type level in rbcs3b-1 and rbcs1a3b-1 leaves. As a result, total RBCS mRNA levels declined to 52, 79, and 23% of the wild-type level in rbcs1a-1, rbcs3b-1, and rbcs1a3b-1, respectively. Rubisco contents showed declines similar to total RBCS mRNA levels, and the ratio of Rubisco-nitrogen to total nitrogen was 62, 78, and 40% of the wild-type level in rbcs1a-1, rbcs3b-1, and rbcs1a3b-1, respectively. The effects of RBCS1A and RBCS3B mutations in rbcs1a3b-1 were clearly additive. The rates of CO(2) assimilation at ambient CO(2) of 40 Pa were reduced with decreased Rubisco contents in the respective mutant leaves. Although the RBCS composition in the Rubisco holoenzyme changed, the CO(2) assimilation rates per unit of Rubisco content were the same irrespective of the genotype. These results clearly indicate that RBCS1A and RBCS3B contribute to accumulation of Rubisco in Arabidopsis leaves and that these genes work additively to yield sufficient Rubisco for photosynthetic capacity. It is also suggested that the RBCS composition in the Rubisco holoenzyme does not affect photosynthesis under the present ambient [CO(2)] conditions.

Differences in expression of the RBCS multigene family and rubisco protein content in various rice plant tissues at different growth stages

Four out of five members of the RBCS multigene family (OsRBCS2-OsRBCS5) were highly expressed in leaf blades of rice (Oryza sativa L.) irrespective of plant growth stage, whereas accumulation of all RBCS mRNAs in leaf sheaths, roots and developing spikelets was quite low. A highly positive correlation was observed between total RBCS and RBCL mRNA levels and Rubisco content at their maxima, irrespective of tissue and growth stage. The results indicate that the total RBCS mRNA level may be a primary determinant for maximal Rubisco protein content and that Rubisco gene expression is well coordinated through the whole life of rice.

Unique and overlapping expression patterns among members of photosynthesis-associated nuclear gene families in Arabidopsis

Light provides crucial positional information in plant development, and the morphogenetic processes that are orchestrated by light signals are triggered by changes of gene expression in response to variations in light parameters. Control of expression of members of the RbcS and Lhc families of photosynthesis-associated nuclear genes by light cues is a paradigm for light-regulated gene transcription, but high-resolution expression profiles for these gene families are lacking. In this study, we have investigated expression patterns of members of the RbcS and Lhc gene families in Arabidopsis (Arabidopsis thaliana) at the cellular level during undisturbed development and upon controlled interference of the light environment. Members of the RbcS and Lhc gene families are expressed in specialized territories, including root tip, leaf adaxial, abaxial, and epidermal domains, and with distinct chronologies, identifying successive stages of leaf mesophyll ontogeny. Defined spatial and temporal overlap of gene expression fields suggest that the light-harvesting and photosynthetic apparatus may have a different polypeptide composition in different cells and that such composition could change over time even within the same cell.

Light enhances the unfolded protein response as measured by BiP2 gene expression and the secretory GFP-2SC marker in Arabidopsis

Disruption of the protein-folding capacity in the ER induces the accumulation of unfolded proteins and ER stress, which activate the unfolded protein response (UPR). Although UPR has been extensively studied in yeast and mammals, much less is known about UPR and its relationship with light in plants. Here, we examined the effects of chemically induced UPR and light on a molecular marker of UPR (binding protein, BiP2, gene expression) and a secretory green fluorescent protein marker (GFP-2SC) that is trafficked from the ER to vacuole in Arabidopsis thaliana (L). UPR, which was induced by DTT and tunicamycin (TM), increased Bip2 mRNA levels and decreased the levels of microsomal and vacuolar forms of GFP-2SC. Treatment with protease inhibitors lessened the effects of DTT and TM on GFP-2SC, indicating the decrease in GFP levels partially involved protein degradation. Light treatments synergistically enhanced the decrease in GFP levels in both the ER and vacuole and induced the expression of UPR marker genes for BiP2 and protein disulfide isomerase (PDI, EC 5.3.4.1). DTT and TM treatments required light for maximal induction of the UPR. Light-induced UPR occurred during the daily dark to light cycle and when dark-adapted plants were exposed to light. We propose that light activates the UPR to increase the protein folding capacity in the ER to accommodate an increase in translation during dark to light transitions.

Transcriptome analysis reveals season-specific rbcS gene expression profiles in diploid perennial ryegrass (Lolium perenne L.)

Perennial ryegrass (Lolium perenne L.) is a major grass species used for forage and turf throughout the world, and gains by conventional breeding have reached a plateau. Perennial ryegrass is an outcrossing, self-incompatible diploid (2n = 2x = 14) with a relatively large genome (4067 Mbp/diploid genome; Evans, G.M., Rees, H., Snell, C.L. and Sun, S. (1972) The relation between nuclear DNA amount and the duration of the mitotic cycle. Chrom. Today, 3, 24-31). Using tissues sourced from active pastures during the peak of the autumn, winter, spring and summer seasons, we analysed the ryegrass transcriptome employing a Serial Analysis of Gene Expression (SAGE) protocol, with the dual goals of understanding the seasonal changes in perennial ryegrass gene expression and enhancing our ability to select genes for genetic manipulation. A total of 159,002 14-mer SAGE tags was sequenced and mapped to the perennial ryegrass DNA database, comprising methyl-filtered (GeneThresher) and expressed sequence tag (EST) sequences. The analysis of 14,559 unique SAGE tags, which were present more than once in our SAGE library, revealed 964, 1331, 346 and 131 exclusive transcripts to autumn, winter, spring and summer, respectively. Intriguingly, our analysis of the SAGE tags revealed season-specific expression profiles for the small subunit of ribulose-1,5-bisphosphate carboxylase (Rubisco), LprbcS. The transcript level for LprbcS was highest in spring, and then decreased gradually between summer and winter. Five different copies of LprbcS were revealed in ryegrass, with one possibly producing splice variant transcripts. Two highly expressed LprbcS genes were reported, one of which was not active in autumn. Another LprbcS gene showed an inverse expression profile to the autumn inactive LprbcS in a manner to compensate the expression level.

Untranslated regions from C4 amaranth AhRbcS1 mRNAs confer translational enhancement and preferential bundle sheath cell expression in transgenic C4 Flaveria bidentis

Many aspects of photosynthetic gene expression are posttranscriptionally regulated in C4 plants. To determine if RbcS mRNA untranslated regions (UTRs) in themselves could confer any characteristic C4 expression patterns, 5'- and 3'-UTRs of AhRbcS1 mRNA from the C4 dicot amaranth were linked to a gusA reporter gene. These were constitutively transcribed from a cauliflower mosaic virus promoter and assayed for posttranscriptional expression patterns in transgenic lines of the C4 dicot Flaveria bidentis. Three characteristic C4 expression patterns were conferred by heterologous AhRbcS1 UTRs in transgenic F. bidentis. First, the AhRbcS1 UTRs conferred strong translational enhancement of gusA expression, relative to control constructs lacking these UTRs. Second, while the UTRs did not appear to confer tissue-specific expression when analyzed by beta-glucuronidase activity assays, differences in gusA mRNA accumulation were observed in leaves, stems, and roots. Third, the AhRbcS1 UTRs conferred preferential gusA expression (enzyme activity and gusA mRNA accumulation) in leaf bundle sheath cells. AhRbcS1 UTR-mediated translational enhancement was also observed in transgenic C3 plants (tobacco [Nicotiana tabacum]) and in in vitro translation extracts. These mRNAs appear to be translated with different efficiencies in C4 versus C3 plants, indicating that processes determining overall translational efficiency may vary between these two categories of higher plants. Our findings suggest that the AhRbcS1 5'-UTR functions as a strong translational enhancer in leaves and other tissues, and may work synergistically with the 3'-UTR to modulate overall levels of Rubisco gene expression in different tissues and cell types of C4 plants.

Response of Arabidopsis to iron deficiency stress as revealed by microarray analysis

Gene expression in response to Fe deficiency was analyzed in Arabidopsis roots and shoots through the use of a cDNA collection representing at least 6,000 individual gene sequences. Arabidopsis seedlings were grown 1, 3, and 7 d in the absence of Fe, and gene expression in roots and shoots was investigated. Following confirmation of data and normalization methods, expression of several sequences encoding enzymes known to be affected by Fe deficiency was investigated by microarray analysis. Confirmation of literature reports, particularly for changes in enzyme activity, was not always possible, but changes in gene expression could be confirmed. An expression analysis of genes in glycolysis, the tricarboxylic acid cycle, and oxidative pentose phosphate pathway revealed an induction of several enzymes within 3 d of Fe-deficient growth, indicating an increase in respiration in response to Fe deficiency. In roots, transcription of sequences corresponding to enzymes of anaerobic respiration was also induced, whereas in shoots, the induction of several genes in gluconeogenesis, starch degradation, and phloem loading was observed. Thus, it seemed likely that the energy demand in roots required for the Fe deficiency response exceeded the capacity of oxidative phosphorylation, and an increase in carbon import and anaerobic respiration were required to maintain metabolism.

The tomato I-box binding factor LeMYBI is a member of a novel class of myb-like proteins

The RBCS3A gene of tomato belongs to a small gene family consisting of five members. Although the RBCS1, RBCS2 and RBCS3A promoters contain closely related cis regulatory sequences, the expression patterns of the genes are different. Whereas the RBCS1 and RBCS2 genes are expressed in both leaves and young fruit, the RBCS3A promoter is highly active in leaves, but not in young fruit. This lack of transcription could be due to a mutation in the RBCS3A promoter creating the so-called F-box, a protein binding site located between the activating cis elements, the I-box and G-box. In order to identify proteins that bind to the RBCS3A I-box/F-box region, the yeast one-hybrid system was used. One clone, LeMYBI was isolated which contains strong similarity to plant myb transcription factors. The encoded LeMYBI protein is at least 188 amino acids in length and contains two myb-like domains located at the amino terminus and close to the carboxy terminus, separated by a negatively charged domain. The protein contains a SHAQKYF amino acid signature motif in the second myb-like repeat, which is highly conserved in a number of recently identified plant myb-related genes, thus defining a new class of plant DNA-binding proteins. LeMYBI binds specifically to the I-box sequence of the RBCS1, RBCS2 and RBCS3A promoters, therefore representing the first cloned I-box binding factor. LeMYBI acts as a transcriptional activator in yeast and plants, and binds to the I-box with a DNA-binding domain located in the carboxyterminal domain.

The inflorescence architecture of Petunia hybrida is modified by the Arabidopsis thaliana Ap2 gene

We have introduced the Apetala2 (Ap2) gene of Arabidopsis thaliana into Petunia hybrida. Four out of 10 Ap2 transgenic plants flowered and exhibited an altered inflorescence architecture. Internode elongation suggests that the transition from the vegetative to the inflorescence phase does occur, although flower formation is delayed and the cymose branching pattern is not established. Instead, the inflorescence continues to produce bracts and eventually terminates in an aberrant flower with an excess of floral organs. New inflorescence branches then develop from the axillary meristems of the bracts, repeating the formation of a number of bracts before conversion into a terminal, aberrant flower. These results indicate that the Ap2 gene plays a role in the determination of inflorescence meristem identity, but not as a typical A-like function, adding to the existing doubt about the general role of Ap2 gene(s) in floral development.

Chimeric Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase/oxygenase containing a pea small subunit protein is compromised in carbamylation

A cDNA of pea (Pisum sativum L.) RbcS 3A, encoding a small subunit protein (S) of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), has been expressed in Arabidopsis thaliana under control of the cauliflower mosaic virus 35S promoter, and the transcript and mature S protein were detected. Specific antibodies revealed two protein spots for the four Arabidopsis S and one additional spot for pea S. Pea S in chimeric Rubisco amounted to 15 to 18% of all S, as judged by separation on two-dimensional isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels from partially purified enzyme preparations and quantitation of silver-stained protein spots. The chimeric enzyme had 11 +/- 1% fewer carbamylated sites and a 11 +/- 1% lower carboxylase activity than wild-type Arabidopsis Rubisco. Whereas pea S expression, preprotein transport, and processing and assembly resulted in a stable holoenzyme, the chimeric enzyme was reproducibly catalytically less efficient. We suggest that the presence of, on average, one foreign S per holoenzyme is responsible for the altered activity. In addition, higher-plant Rubisco, unlike the cyanobacterial enzyme, seems to have evolved species-specific interactions between S and the large subunit protein that are involved in carbamylation of the active site.

C4 Gene Expression in Photosynthetic and Nonphotosynthetic Leaf Regions of Amaranthus tricolor

Throughout most of its growth and development, Amaranthus tricolor produces fully green leaves. However, near the onset of flowering, unique leaves emerge that consist of three distinct color regions: green apices, yellow middle regions, and red basal regions. The green apices are identical to fully green leaves in terms of pigment composition, photosynthetic function, and C4 gene expression. The yellow and red regions possess greatly reduced levels of chlorophyll and they lack photosynthetic activity. The absence of photosynthetic capacity in the nongreen leaf regions was associated with three distinct alterations in C4 gene expression. First, there was a reduction in the translation of C4 polypeptides, and in the yellow regions synthesis of the ribulose-1,5-bisphosphate carboxylase small subunit occurred in the absence of large subunit synthesis. Second, there was a reduction in the relative transcription rates of two plastid-encoded photosynthetic genes, rbcL and psbA. Third, there was a loss of bundle-sheath cell-specific accumulation of the rbcL and RbcS mRNAs (but not the polypeptides, which remained bundle-sheath-specific). This study indicates that alterations in photosynthetic activity or developmental processes responsible for the loss of activity can influence C4 gene expression at multiple regulatory levels.

Tissue-Specific and Light-Mediated Expression of the C4 Photosynthetic NAD-Dependent Malic Enzyme of Amaranth Mitochondria

In the C4 dicotyledonous grain plant amaranth (Amaranthus hypochondriacus), a mitochondrial NAD-dependent malic enzyme (NAD-ME; EC 1.1.1.39) serves a specialized and essential role in photosynthetic carbon fixation. In this study we have examined specialized photosynthetic gene expression patterns for the NAD-ME [alpha] subunit. We show here that the [alpha] subunit gene is preferentially expressed in leaves and cotyledons (the most photosynthetically active tissues), and this expression is specific to the bundle-sheath cells of these tissues from the earliest stages of development. Synthesis of the [alpha] subunit polypeptide and accumulation of its corresponding mRNA are strongly light-dependent, but this regulation is also influenced by seedling development. In addition, light-dependent accumulation of the [alpha] subunit mRNA is regulated at transcriptional as well as posttranscriptional levels. Our findings demonstrate that the NAD-ME of amaranth has acquired numerous complex tissue-specific and light-mediated regulation patterns that define its specialized function as a key enzyme in the C4 photosynthetic pathway.

Control of mRNA stability in higher plants

The degradation rates of different mRNAs in higher plants can vary over a broad range and are regulated by a variety of endogenous and exogenous stimuli. During the past several years, efforts to better understand the control of mRNA stability in plants have increased considerably and this has led to improved methodologies and important mechanistic insights. In this review, we highlight some of the most interesting examples of plant transcripts that are controlled at the level of mRNA decay and discuss what has been learned from their study. Experiments that implicate or demonstrate the involvement of particular cis- and trans-acting factors in mRNA decay pathways are a major focus, as are those experiments that have led to mechanistic models. Emphasis is also placed on studies that address the relationship between translation and mRNA stability. Our current knowledge indicates that some of the determinants and pathways for mRNA decay may differ in plants compared to other eukaryotes, whereas others appear to be similar. This knowledge, coupled with the availability of biochemical, molecular and genetic approaches to elucidate plant mRNA decay mechanisms, should continue to lead to findings of novel and general significance.

Ontogenetic regulation and photoregulation of members of the Phaseolus vulgaris L. rbcS gene family

The rbcS1, 2 and 3 genes of Phaseolus vulgaris are identical in coding sequence and we have studied their expression using gene-specific probes derived from their 3' non-coding regions. The genes differ in their relative levels of expression but show only minor qualitative differences in their regulation. Transcripts of the three genes are undetectable in primary leaves in the imbibed seed, accumulate early in leaf expansion reaching a maximum 7-10 d after sowing and decrease to low levels by the time expansion is complete. Both dark-grown and light-grown primary leaves exhibit this ontogenetic pattern of expression, although the light-grown leaves have two to three times more rbcS transcripts. Light can over-ride the ontogenetic control of rbcS expression; for example, when 7-d-old dark-grown primary leaves are illuminated there is a 6- to 12-fold increase in the transcript levels of the rbcS genes. Transfer of illuminated leaves to darkness results in the loss of transcripts of all three genes, but rbcS2 transcripts persist in the dark-adapted leaves. Possible physiological mechanisms of the ontogenetic regulation of expression are discussed.

Organ-specific differential regulation of a promoter subfamily for the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit genes in tomato

The tomato (Lycopersicon esculentum) gene family for the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RBCS) has been investigated to determine the role of promoter regions and DNA-protein interactions in the differential organ-specific transcription of individual genes. Transgenic plants expressing RBCS-promoter-beta-glucuronidase fusion genes have confirmed that promoter fragments ranging from 0.6 to 3.0 kb of the RBCS1, RBCS2, and RBCS3A genes were sufficient to confer the temporal, organ-specific, and differential expression pattern observed for the endogenous genes. The individual temporal and organ-specific beta-glucuronidase enzyme activities closely reflect the qualitative and quantitative transcription activities of the respective RBCS genes, including the strongly reduced activity of RBCS3A (L.A. Wanner, W. Gruissem [1991] Plant Cell 3: 1289-1303). In particular, tissue-specific activity of all three promoters is similar in developing fruit, with high activity in the locular tissue and extremely reduced activity in the pericarp. This specific pattern of gene activity was further substantiated by in situ analysis of RBCS mRNA levels. Together, the data suggest an interesting correlation between RBCS gene activity and sink strength in different fruit tissues. DNA-protein interaction studies have revealed a novel fruit-specific DNA-binding protein called FBF that specifically interacts with a sequence element directly upstream of the G-box in the RBCS3A promoter. FBF binding thus correlates with the reduced activity of this promoter in developing tomato fruit, rendering it a candidate for a fruit-specific negative regulator of transcription in tomato.

Organ-Specific Stability of Two Lemna rbcS mRNAs Is Determined Primarily in the Nuclear Compartment

It has previously been shown that the organ-specific expression of two members of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (rbcS) gene family is post-transcriptionally regulated in Lemna gibba. While both small subunit genes encoding SSU1 and SSU5B were transcribed at comparable levels in root and frond nuclei, SSU1 mRNA accumulated to high levels in both roots and fronds in contrast to SSU5B mRNA, which was of very low abundance in the roots compared with the fronds. In this study, we have used two approaches to pinpoint the step(s) at which SSU1 and SSU5B mRNAs are differentially accumulated in these organs. In the first approach, total nuclear steady state mRNA was isolated from roots and fronds, and the amount of each transcript was measured by RNase protection assays and compared with the transcription rates in isolated nuclei. In the second approach, cordycepin was used to inhibit mRNA synthesis in Lemna fronds or roots, and the rate of decay of each mRNA was measured by RNA gel blot analysis or RNase protection assays. Our findings indicate that the differential accumulation of SSU1 and SSU5B mRNAs in the fronds versus the roots is determined primarily in the nuclear compartment. In addition, SSU1 was found to have a longer half-life in total steady state mRNA than SSU5B had in both organs. This feature probably accounts for SSU1 being the predominantly expressed family member.

Control of Arabidopsis flower and seed development by the homeotic gene APETALA2

APETALA2 (AP2) plays a central role in the establishment of the floral meristem, the specification of floral organ identity, and the regulation of floral homeotic gene expression in Arabidopsis. We show here that in addition to its functions during flower development, AP2 activity is also required during seed development. We isolated the AP2 gene and found that it encodes a putative nuclear protein that is distinguished by an essential 68-amino acid repeated motif, the AP2 domain. Consistent with its genetic functions, we determined that AP2 is expressed at the RNA level in all four types of floral organs--sepals, petals, stamens, and carpels--and in developing ovules. Thus, AP2 gene transcription does not appear to be spatially restricted by the floral homeotic gene AGAMOUS as predicted by previous studies. We also found that AP2 is expressed at the RNA level in the inflorescence meristem and in nonfloral organs, including leaf and stem. Taken together, our results suggest that AP2 represents a new class of plant regulatory proteins that may play a general role in the control of Arabidopsis development.

Control of Arabidopsis flower and seed development by the homeotic gene APETALA2

APETALA2 (AP2) plays a central role in the establishment of the floral meristem, the specification of floral organ identity, and the regulation of floral homeotic gene expression in Arabidopsis. We show here that in addition to its functions during flower development, AP2 activity is also required during seed development. We isolated the AP2 gene and found that it encodes a putative nuclear protein that is distinguished by an essential 68-amino acid repeated motif, the AP2 domain. Consistent with its genetic functions, we determined that AP2 is expressed at the RNA level in all four types of floral organs--sepals, petals, stamens, and carpels--and in developing ovules. Thus, AP2 gene transcription does not appear to be spatially restricted by the floral homeotic gene AGAMOUS as predicted by previous studies. We also found that AP2 is expressed at the RNA level in the inflorescence meristem and in nonfloral organs, including leaf and stem. Taken together, our results suggest that AP2 represents a new class of plant regulatory proteins that may play a general role in the control of Arabidopsis development.

Development and Environmental Stress Employ Different Mechanisms in the Expression of a Plant Gene Family

Ribulose bisphosphate carboxylase small subunit (RbcS) genes in the common ice plant, as in all higher plants, constitute a multigene family. We have measured transcription activity and steady state mRNA levels of individual members of the family, six RbcS genes, in the ice plant with emphasis on the transition from C3 photosynthesis to Crassulacean acid metabolism (CAM), which this plant undergoes during development and under environmental stress. Four RbcS genes are differentially expressed in leaves but are regulated in a coordinate fashion. A developmentally engrained, sharp decline in the steady state mRNA levels, which is observed during the juvenile-to-adult growth phase transition, coincides with the time interval when the C3-to-CAM switch occurs. Developmental down regulation of RbcS is due to down regulation of transcription. In contrast, NaCl stress specifically affected RbcS transcript accumulation post-transcriptionally, resulting in decreased RbcS mRNA levels. Antagonistic regulatory programs are apparent in stress/stress relief experiments. The results indicate complex controls, affecting both transcriptional and post-transcriptional processes, that act differentially during plant development, stress, and recovery from stress.

Post-transcriptional control of cell type-specific gene expression in bundle sheath and mesophyll chloroplasts of Amaranthus hypochondriacus

Plants that utilize the highly efficient C4 photosynthetic pathway possess two types of specialized leaf cells, the mesophyll and bundle sheath. In mature leaves of amaranth, a dicotyledonous C4 plant, ribulose 1,5-bisphosphate carboxylase (Rubisco) is localized specifically to the chloroplasts of bundle sheath cells, and is not present in the chloroplasts of mesophyll cells. The cell type-specific expression of the chloroplast-encoded Rubisco large subunit (rbcL) gene, and other representative chloroplastic genes, was investigated by using separated bundle sheath and mesophyll chloroplasts prepared from mature amaranth leaves. One-dimensional SDS-polyacrylamide gel electrophoresis revealed several differences in the polypeptide compositions of the two chloroplast types. Western analysis demonstrated that, as in the intact leaves, the Rubisco LSU polypeptide was present only in chloroplast preparations from bundle sheath cells. Pyruvate orthophosphate dikinase (PPdK), a nuclear-encoded chloroplastic enzyme, was found only in the mesophyll chloroplast preparations. rbcL mRNA was present only in the bundle sheath chloroplast preparations, whereas transcripts for the chloroplast-encoded psbA, psaA-B, and rpl2 genes were present in both chloroplast types. Although the rbcL message accumulated only in bundle sheath chloroplasts, run-on transcription analysis indicated that the rbcL gene was transcribed in both bundle sheath and mesophyll chloroplast preparations. Therefore, differential rbcL gene expression in the isolated C4 chloroplasts is regulated, at least in part, at the post-transcriptional level. Possibly this control is mediated by differential processing or stabilization of the rbcL transcript.

5'-upstream cis-elements and binding factor(s) potentially involved in light-regulated expression of a Brassica napus rbcS gene

The 5'-upstream region of a Brassica napus rbcS gene contains sequence elements that resemble the cis-regulatory elements described for other species. In band shift competition assays using whole-cell extracts and sets of deletion fragments we could assign protein binding to a region located 110-130 base pairs upstream of the transcription start site. DNase I protection experiments showed that the binding region is non-contiguous and reveals symmetry. On the non-coding strand, the sequence contains 5'-CAC-3' and 5'-GTGG-3' elements which together resemble the contiguous G-box core motif, CACGTGG, of other rbcS genes. The DNA-protein interaction was more efficient with extracts from light-grown than with those from dark-grown seedlings, indicating the possible involvement of light-regulated factors(s).

Expression dynamics of the tomato rbcS gene family during development

The tomato rbcS gene family is composed of five genes (rbcS1, 2, 3A, 3B, and 3C) that are differentially expressed during tomato development. Nuclear run-on transcription assays and RNA analysis were used to determine the contribution of transcriptional and post-transcriptional regulation to the accumulation of mRNA from the five rbcS genes in tomato seedlings, leaves, and fruit. We found that the qualitative pattern of mRNA accumulation is regulated at the transcriptional level and that, in general, there is a correlation of rates of rbcS transcription with overall rbcS mRNA abundance in fruit and leaves. Although transcriptional control is a primary determinant for rbcS gene expression in tomato, examination of relative transcription rates and mRNA accumulation of each rbcS gene demonstrated that there is also significant post-transcriptional control of rbcS gene expression during organ development. Individual rbcS mRNAs, which have highly conserved coding sequences and differ only in their 5' and 3' untranslated sequences, have different stabilities. We showed that both transcription and stability of individual rbcS mRNAs are altered in different organs and by the developmental program within these organs as well as by exposure to light. Together, the results provide a comprehensive analysis of the extent of transcriptional and post-transcriptional control that operates within the rbcS gene family during plant development.

Maize rbcS promoter activity depends on sequence elements not found in dicot rbcS promoters

Although the molecular mechanisms of dicot photosynthetic gene regulation have been pursued actively, comparable studies of monocot regulation have been slow to come forth. We show here that monocot (maize and wheat) but not dicot (pea, tobacco, and Arabidopsis) ribulose-1,5-bisphosphate carboxylase small subunit (rbcS) gene promoters are active in maize mesophyll protoplasts. The evolutionarily conserved GT and G boxes of dicot rbcS promoters are not essential for light-responsive expression in monocot leaf cells. Instead, at least six constitutive and light-sensitive regulatory elements are likely important for maize rbcS expression. Synergism between upstream and downstream promoter elements is required. Whereas in dicots, light triggers coupled leaf development and photosynthetic gene expression, in monocots, light regulation of rbcS is uncoupled from leaf development. Light regulation of maize rbcS may be divided into direct and indirect contributions mediated by different regulatory elements. Because wheat and maize rbcS promoters show sequence homologies and similar expression patterns in monocot and dicot leaf cells, it appears likely that monocots share conserved regulatory elements irrespective of whether they utilize the C3 or C4 pathway for carbon fixation.

Circadian Control of cab Gene Transcription and mRNA Accumulation in Arabidopsis

An intriguing property of many organisms is their ability to exhibit rhythmic cellular events that continue independently of environmental stimuli. These rhythmic processes are generated by an endogenous mechanism known as the biological clock. We wished to determine whether Arabidopsis thaliana will serve as a model plant system for a molecular genetic dissection of the circadian clock. To this end, we investigated the expression of Arabidopsis chlorophyll a/b-binding protein (cab) genes throughout the circadian cycle. Steady-state mRNA levels of the cab2 and cab3 genes showed a dramatic circadian cycling in plants shifted from light/dark cycles to constant darkness, whereas the cab1 mRNA level exhibited little or no cycling under the same conditions. Analysis of cab promoter fusions in transgenic tobacco revealed that both the cab1 and cab2 5[prime] upstream regions confer circadian-regulated expression on a chloramphenicol acetyltransferase (cat) reporter gene. In vitro nuclear run-on transcription assays also indicated that the transcription of the cab1 and cab2 genes is circadian regulated in Arabidopsis. Taken together, these data suggest that a post-transcriptional mechanism influences cab1 mRNA levels in Arabidopsis. The identification of circadian-regulated cis-acting elements in the cab1 and cab2 upstream regions will provide powerful tools for both molecular and genetic analysis of the higher plant circadian clock.

Circadian Control of cab Gene Transcription and mRNA Accumulation in Arabidopsis

An intriguing property of many organisms is their ability to exhibit rhythmic cellular events that continue independently of environmental stimuli. These rhythmic processes are generated by an endogenous mechanism known as the biological clock. We wished to determine whether Arabidopsis thaliana will serve as a model plant system for a molecular genetic dissection of the circadian clock. To this end, we investigated the expression of Arabidopsis chlorophyll a/b-binding protein (cab) genes throughout the circadian cycle. Steady-state mRNA levels of the cab2 and cab3 genes showed a dramatic circadian cycling in plants shifted from light/dark cycles to constant darkness, whereas the cab1 mRNA level exhibited little or no cycling under the same conditions. Analysis of cab promoter fusions in transgenic tobacco revealed that both the cab1 and cab2 5[prime] upstream regions confer circadian-regulated expression on a chloramphenicol acetyltransferase (cat) reporter gene. In vitro nuclear run-on transcription assays also indicated that the transcription of the cab1 and cab2 genes is circadian regulated in Arabidopsis. Taken together, these data suggest that a post-transcriptional mechanism influences cab1 mRNA levels in Arabidopsis. The identification of circadian-regulated cis-acting elements in the cab1 and cab2 upstream regions will provide powerful tools for both molecular and genetic analysis of the higher plant circadian clock.