Analysis of regulatory elements of the promoter and the 3' untranslated region of the maize Hrgp gene coding for a cell wall protein

Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression

Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.

An intronless form of the tobacco extensin gene terminator strongly enhances transient gene expression in plant leaves

KEY MESSAGE

We have found interesting features of a plant gene (extensin) 3' flanking region, including extremely efficient polyadenylation which greatly improves transient expression of transgenes when an intron is removed. Its use will greatly benefit studies of gene expression in plants, research in molecular biology, and applications for recombinant proteins. Plants are a promising platform for the production of recombinant proteins. To express high-value proteins in plants efficiently, the optimization of expression cassettes using appropriate regulatory sequences is critical. Here, we characterize the activity of the tobacco extensin (Ext) gene terminator by transient expression in Nicotiana benthamiana, tobacco, and lettuce. Ext is a member of the hydroxyproline-rich glycoprotein (HRGP) superfamily and constitutes the major protein component of cell walls. The present study demonstrates that the Ext terminator with its native intron removed increased transient gene expression up to 13.5-fold compared to previously established terminators. The enhanced transgene expression was correlated with increased mRNA accumulation and reduced levels of read-through transcripts, which could impair gene expression. Analysis of transcript 3'-ends found that the majority of polyadenylated transcripts were cleaved at a YA dinucleotide downstream from a canonical AAUAAA motif and a UG-rich region, both of which were found to be highly conserved among related extensin terminators. Deletion of either of these regions eliminated most of the activity of the terminator. Additionally, a 45 nt polypurine sequence ~ 175 nt upstream from the polyadenylation sites was found to also be necessary for the enhanced expression. We conclude that the use of Ext terminator has great potential to benefit the production of recombinant proteins in plants.

Grande retrotransposons contain an accessory gene in the unusually long 3'-internal region that encodes a nuclear protein transcribed from its own promoter

LTR retrotransposons are major components of plant genomes playing important roles in the evolution of their host genomes, for example, generating new genes or providing new promoters to existing genes. The Grande family of retrotransposons is present in Zea species and is characterized by an unusually long internal region due to the presence of a 7-kbp region between the gag-pol coding region and the 3'LTR. We demonstrate here that such unusual sequence is present in the great majority of Grande copies in maize genome. This region contains a gene, gene23, which is transcribed from its own promoter in antisense orientation to the gag-pol genes. The expression of gene23 is ubiquitous, and its promoter contains all the putative consensus sequences typical of eukaryotic promoters, being able to direct GUS expression in different plant species and organs. The coding region of gene23 is conserved in most Grande copies and encodes a protein rich in glycine, serine, and acidic amino acids that shows no significant similarity with any protein of known function. Nevertheless, the C- and N-terminal parts are rich in basic amino acids, and these are interspersed with other amino acids in its C-terminus, compatible with a putative DNA-binding function. It contains a nuclear localization signal KRKR motif in the N-terminus. Fusions to GFP demonstrate that this protein localizes in the nucleus. We discuss the possible origin of gene23 and the potential function of its encoded protein.

Functional analysis of a rice late pollen-abundant UDP-glucose pyrophosphorylase (OsUgp2) promoter

OsUgp2, a rice UDP-glucose pyrophosphorylase gene, has previously been shown to preferentially express in maturing pollens and plays an important role in pollen starch accumulation. Here, a 1943 bp promoter fragment (P1943) of OsUgp2 was characterized by 5' deletion and gain-of-function experiments. P1943 and its 5' deletion derivatives (P1495, P1005, P665 and P159) were fused to GUS reporter gene and stably introduced into rice plants. Histochemical analyses of different tissues and pollens at different developmental stages of the transgenic plants showed that P1943 could only direct GUS expression in binucleate pollens. P1495 and P1005 could still drive GUS expression in binucleate pollens but at a lower level. On the other hand, neither P665 nor P159 transformant exhibited any GUS activity in pollens. Gain-of-function analyses showed that the region (-1005 to -665 relative to translation start site) combined with a minimal CaMV 35S promoter could direct GUS expression in pollens. Further analysis of 5' deletion truncated at -952, -847 and -740 delimited a 53 bp region (-1005 to -952) essential for pollen-specific expression. The 53 bp sequence contains two motifs of TTTCT and TTTC, which were known to be pollen-specific cis-elements. In addition, the same P1943-GUS fusion construct was introduced into tobacco to analyze its specificity in dicotyledon. Interestingly, the GUS expression pattern in transgenic tobacco was quite different from that in rice. High level of GUS expression was detected in mature pollens as well as leaves, roots, sepals and stigmas. These findings suggested a complicated transcriptional regulation of OsUgp2.

Functional analysis of the DAT gene promoter using transient Catharanthus roseus and stable Nicotiana tabacum transformation systems

The Catharanthus roseus DAT gene encodes the enzyme acetyl-CoA:deacetylvindoline-4-O-acetyltransferase involved in the last step of the indole alkaloid pathway leading to vindoline. This gene is characterized by specific cell type expression in idioblasts and laticifers. To understand the specific transcriptional regulation mechanism(s) of DAT, several DAT promoter GUS constructs were cloned into pCAMBIA1305.1. Agroinfiltration of different explant types of C. roseus resulted in organ-specific accumulation of GUS, albeit at various levels. Heterologous accumulation of GUS in transgenic tobacco revealed both general and non-specific expression with the exception of a stomata-specific expression when 2.3 kb of the DAT promoter was coupled with a portion of the DAT ORF. These results suggest that in addition to the 2.3 kb upstream of the DAT transcriptional start site, additional cis-acting elements may be responsible for the specific spatial expression of DAT in vivo. Furthermore, hairy roots transformed with DAT promoter GUS constructs demonstrated GUS expression in root tissues (visualized through GUS enzyme activity), even though DAT is repressed in non-transformed roots.

Identification of a cis-regulatory element that acts in companion cell-specific expression of AtMT2B promoter through the use of Brassica vasculature and gene-gun-mediated transient assay

The molecular basis underlying the development, maintenance and function of companion cells in plants is largely unknown. The identification of several genes expressed specifically in companion cells implies the contribution of specific transcriptional elements to the identity of companion cells. However, less is known about the companion cell-specific transcriptional regulation of promoters. We established a novel assay method using gene-gun delivery of partially deleted promoters to string-containing vascular bundles excised from the petiole of Brassica napus for the rapid identification of cis-elements. To test this system, we analyzed the Arabidopsis METALLOTHIONEIN 2B (MT2B) gene, which is expressed in companion cells. The assay revealed a 49-bp region possessing two predicted cis-regulatory elements: a G-box and an evening element-related sequence (EEr), and EEr showed higher activity. We confirmed the reliability of the result with stable transformants harboring a deleted MT2B promoter:GUS transgene. The lack of EEr completely eliminated the MT2B-like expression, but the lack of G-box did not eliminate it. We conclude that EEr is a major cis-regulatory element of the MT2B promoter. Our method will help to explain the transcriptional background of companion cells through the rapid identification of cis-regulatory regions.

Positive selection and expression divergence following gene duplication in the sunflower CYCLOIDEA gene family

Members of the CYCLOIDEA (CYC)/TEOSINTE-BRANCHED1 (TB1) group of transcription factors have been implicated in the evolution of zygomorphic (i.e., bilaterally symmetric) flowers in Antirrhinum and Lotus and the loss of branching phenotype during the domestication of maize. The composite inflorescences of sunflower (Helianthus annuus L. Asteraceae) contain both zygomorphic and actinomorphic (i.e., radially symmetric) florets (rays and disks, respectively), and the cultivated sunflower has evolved an unbranched phenotype in response to domestication from its highly branched wild progenitor; hence, genes related to CYC/TB1 are of great interest in this study system. We identified 10 members of the CYC/TB1 gene family in sunflower, which is more than found in any other species investigated to date. Phylogenetic analysis indicates that these genes occur in 3 distinct clades, consistent with previous research in other eudicot species. A combination of dating the duplication events and linkage mapping indicates that only some of the duplications were associated with polyploidization. Cosegregation between CYC-like genes and branching-related quantitative trait loci suggest a minor, if any, role for these genes in conferring differences in branching. However, the expression patterns of one gene suggest a possible role in the development of ray versus disk florets. Molecular evolutionary analyses reveal that residues in the conserved domains were the targets of positive selection following gene duplication. Taken together, these results indicate that gene duplication and functional divergence have played a major role in diversification of the sunflower CYC gene family.

Functional analysis of a Douglas-fir metallothionein-like gene promoter: transient assays in zygotic and somatic embryos and stable transformation in transgenic tobacco

Douglas-fir (Pseudotsuga menziesii [Mirb] Franco) metallothionein (PmMT) cDNA encodes a novel cysteine- and serine-rich MT, indicating a new subtype or prototype MT from which other plant MTs may have evolved. A genomic library of Douglas-fir was screened using MT cDNA probes, and genomic sequences that mediate tissue-specific, temporal as well as inducible expression of the embryo-specific MT-gene were analyzed. The promoter region of the PmMT genomic clone (gPmMT) contained a hexameric G-box, two putative ethylene-responsive elements and an inverted repeat of a motif similar to the core metal regulatory element. Interestingly, comparison of the upstream region of Douglas-fir gPm2S1 and gPmMTa genes revealed a conserved motif, CATTATTGA, not found in any known angiosperm gene promoter. Chimeric gene constructs containing a series of deletions in the gPmMTa promoter fused to the uidA reporter gene were assayed in Douglas-fir and transgenic tobacco (Nicotiana tabacum L.). Transient-expression assays in Douglas-fir megagametophyte and zygotic embryos indicated that the sequence -190 to +88 of gPmMTa was sufficient to drive the expression of the reporter gene and that the 225-bp fragment (-677 to -453) contained sequences necessary for high-level expression. In transgenic tobacco seedlings the beta-glucuronidase activity was localized in the vacuolar tissue and proliferating tissue of the auxiliary buds and stem elongation zone. The gPmMTa promoter was not active in the seeds of transgenic tobacco or in the roots of seedlings up to 3 weeks old. Detailed studies of transient expression and stable transformation provided important information on evolutionary conservation as well as novel features found in the conifer promoter. This is the first report of an MT-like gene promoter from conifers.