Retroviruses must bypass the tight coupling of splicing and nuclear export of mRNA in their replication cycle because unspliced genomic RNA and incompletely spliced mRNA must be exported to the cytoplasm for packaging or translation. This process is mediated by a cis-acting constitutive transport element (CTE) for simple retroviruses and by the trans-acting viral protein Rev in concert with its response element (RRE) for complex retroviruses (e.g., HIV). Recently, we identified RNA helicase A (RHA) as a potential cellular cofactor for CTE. Here, we report that RHA also plays a role in Rev͞RRE-mediated gene expression and HIV replication. RHA binds weakly to HIV-1 RRE independently of Rev. Overexpression of RHA, but not of an RHA mutant lacking helicase activity, increased both Rev͞RRE-and CTEdependent gene expression and the levels of unspliced HIV mRNA. Microinjection of antibodies to RHA into nuclei dramatically inhibited both CTE-and Rev-dependent gene expression in human cells. Exogenous RHA cDNA, but not the mutant RHA, rescued this inhibition. We propose that RHA is required to release both CTE-and RRE-containing mRNA from spliceosomes before completion of splicing, thus freeing them for nuclear export.HIV uses complex regulatory mechanisms to control gene expression. Such mechanisms involve the interdigitation of viral and cellular elements. Rev (regulator of virion protein expression) is a trans-acting viral protein that recognizes a cis-acting RNA element, the Rev response element (RRE), on the viral genome (see ref. 1 for review). Extensive studies to date revealed that Rev͞RRE interaction facilitates the nuclear export of unspliced or singly spliced viral mRNA (2-4). However, Rev binding to RRE alone is insufficient. An activation domain on Rev, distinct from the RRE binding domain, is essential for function, presumably through binding of cellular effector molecules (2-6). This activator domain comprises a nuclear export signal (NES), which can be replaced functionally by the NES of some known export proteins (7-9). Several cellular proteins reportedly bind specifically to the Rev NES, including a nucleoporin-like protein called Rev activation domain-binding protein (10) or human Rev interacting protein (11), and the protein eIF-5A (12). More recently, Rev-NES was found to bind to the nuclear export receptor CRM-1͞exportin-1 (13, 14), and it is likely that this interaction bridges the indirect binding of Rev-NES to Rev activation domain-binding protein͞human Rev interacting protein (15,16). Cellular proteins involved in RNA splicing͞ processing also have been found to bind directly to RRE (17) or the Rev͞RRE complex (18). These proteins repressed Rev activity when overexpressed in cells. Other complex retroviruses, such as human T-cell leukemia virus and animal lentiviruses, also encode Rev-like proteins for post-transcriptional regulation (19).In contrast to complex retroviruses, simple retroviruses, such as the Mason-Pfizer monkey virus, do not encode a Rev-like protein, even though there ...

MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. This work investigated miRNAs in rice (Oryza sativa), an important food crop. High-throughput sequencing technology was used to reveal expression differences in miRNAs between superior and inferior spikelets in rice (japonica cultivar Xinfeng 2) at 18 d after fertilization. Totals of 351 and 312 known miRNAs were obtained from the superior and inferior spikelets, respectively. Analysis of the expression profiles of these miRNAs showed that 189 miRNAs were differentially expressed between superior spikelets and inferior spikelets. In addition, 43 novel miRNAs were identified mostly by the accumulation of miRNA*s expressed differentially between the superior and inferior spikelets. Further analysis with bioinformatics software and comparison with existing databases showed that these differentially expressed miRNAs may individually participate in regulating hormone metabolism, carbohydrate metabolic pathways, and cell division during rice grain development. The results indicate that the slow grain-filling and low grain weight of rice inferior spikelets are attributed partly to differences in expression and function between superior and inferior spikelet miRNAs.

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MicroRNAs (miRNAs) are upstream gene regulators of plant development and hormone homeostasis through their directed cleavage or translational repression of the target mRNAs, which may play crucial roles in rice grain filling and determining the final grain weight and yield. In this study, high-throughput sequencing was performed to survey the dynamic expressions of miRNAs and their corresponding target genes at five distinct developmental stages of grain filling. In total, 445 known miRNAs and 45 novel miRNAs were detected with most of them expressed in a developmental stage dependent manner, and the majority of known miRNAs, which increased gradually with rice grain filling, showed negatively related to the grain filling rate. Detailed expressional comparisons revealed a clear negative correlation between most miRNAs and their target genes. It was found that specific miRNA cohorts are expressed in a developmental stage dependent manner during grain filling and the known functions of these miRNAs are involved in plant hormone homeostasis and starch accumulation, indicating that the expression dynamics of these miRNAs might play key roles in regulating rice grain filling.

BackgroundThe inferior spikelets are defined to be those at portions where the grains receive less photosynthetic products during the seed development. The typical inferior spikelets are physically located on the proximal secondary branches in a rice panicle and traditionally characterized by a later flowering time and a slower grain-filling rate, compared to those so-called superior spikelets. Grains produced on the inferior spikelets are consequently under-developed and lighter in weight than those formed on the superior spikelets. MicroRNAs (miRNAs) are recognized as key players in regulating plant development through post-transcriptional gene regulations. We previously presented the evidence that miRNAs may influence grain-filling rate and played a role in determining the grain weight and yield in rice.ResultsIn this study, further analyses of the expressed small RNAs in superior and inferior spikelets were conducted at five distinct developmental stages of grain development. Totally, 457 known miRNAs and 13 novel miRNAs were analyzed, showing a differential expression of 141 known miRNAs between superior and inferior spikelets with higher expression levels of most miRNAs associated with the superior than the inferior spikelets during the early stage of grain filling. Genes targeted by those differentially expressed miRNAs (i.e. miR156, miR164, miR167, miR397, miR1861, and miR1867) were recognized to play roles in multiple developmental and signaling pathways related to plant hormone homeostasis and starch accumulation.ConclusionsOur data established a complicated link between miRNA dynamics and the traditional role of hormones in grain filling and development, providing new insights into the widely accepted concepts of the so-called superior and inferior spikelets in rice production.