Pollen tubes extend through pistil tissues and are guided to ovules where they release sperm for fertilization. Although pollen tubes can germinate and elongate in a synthetic medium, their trajectory is random and their growth rates are slower compared to growth in pistil tissues. Furthermore, interaction with the pistil renders pollen tubes competent to respond to guidance cues secreted by specialized cells within the ovule. The molecular basis for this potentiation of the pollen tube by the pistil remains uncharacterized. Using microarray analysis in Arabidopsis, we show that pollen tubes that have grown through stigma and style tissues of a pistil have a distinct gene expression profile and express a substantially larger fraction of the Arabidopsis genome than pollen grains or pollen tubes grown in vitro. Genes involved in signal transduction, transcription, and pollen tube growth are overrepresented in the subset of the Arabidopsis genome that is enriched in pistil-interacted pollen tubes, suggesting the possibility of a regulatory network that orchestrates gene expression as pollen tubes migrate through the pistil. Reverse genetic analysis of genes induced during pollen tube growth identified seven that had not previously been implicated in pollen tube growth. Two genes are required for pollen tube navigation through the pistil, and five genes are required for optimal pollen tube elongation in vitro. Our studies form the foundation for functional genomic analysis of the interactions between the pollen tube and the pistil, which is an excellent system for elucidation of novel modes of cell–cell interaction.
INTRODUCTIONThe BLAST algorithm was developed as a way to perform DNA and protein sequence similarity searches by an algorithm that is faster than FASTA but considered to be equally as sensitive. Both of these methods follow a heuristic (tried-and-true) method that almost always works to find related sequences in a database search, but does not have the underlying guarantee of an optimal solution like the dynamic programming algorithm. FASTA finds short common patterns in query and database sequences and joins these into an alignment. BLAST is similar to FASTA, but gains a further increase in speed by searching only for rarer, more significant patterns in nucleic acid and protein sequences. BLAST is very popular due to its availability on the World Wide Web through a large server at the National Center for Biotechnology Information (NCBI) and at many other sites. The BLAST algorithm has evolved to provide molecular biologists with a set of very powerful search tools that are freely available to run on many computer platforms. This article is intended to be a "user's guide" to the principles underlying BLAST.
ABSTRACr The recA and 1exA proteins of Eseherichia coli are involved in a complex regulatory circuit that allows the exression of a diverse set of functions after DNA damage or inhibition of DNA replication. Exponentially growing cells contain a low level of recA protein, and genetic evidence suggests that lexA protein is involved in its regulation, perhaps as a simple repressor. Recent models for recA derepression after DNA damage have suggested that an early event in this process is the proteolytic cleavage of lexA protein, leading to high-level expression of recA. We present several lines of evidence that the specific protease activity of the recA protein, previously described with the A repressor as substrate, is Escherichia coli exhibits a complex response to agents that damage DNA or inhibit DNA replication (1). A number of new cellular processes, including mutagenesis, prophage induction, and new DNA repair capacity, are expressed. These are sometimes called "SOS functions" because they ark believed to aid cell survival. Extensive genetic evidence indicates that expression of these processes is controlled by a regulatory system that involves the products of at least two unlinked genes, recA and lexA. The biochemical analysis of the recA and 1exA proteins has begun, and in this communication we report evidence for a direct interaction between the two proteins.The recA protein has recently been purified and extensively characterized in vitro. It exhibits at least two distinct sets of properties. First, it binds to single-or double-stranded DNA and to double-stranded DNA possessing internal or terminal single-stranded regions; it catalyzes assimilation of single-stranded DNA fragments into homologous duplex DNA, and when bound to single-stranded DNA it promotes unwinding of double-stranded homologous or nonhomologous DNA (2-7). These functions are believed to be important in DNA repair and in genetic recombination. It also exhibits DNA-dependent ATPase activity, which is probably involved with its DNAThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U. S. C. §1734 solely to indicate this fact. 3225 binding activities (2,8,9). Second, the recA protein is a highly specific protease (9-13). It cleaves the phage A repressor, inactivating its function, in a reaction requiring ATP and single-stranded DNA. A mutant form of the recA protein, the product of the tif-1 allele, is several-fold more active than is the wild-type protease in this reaction. In contrast, the biochemical function of the lexA protein is not yet known. Genetic evidence suggests a role in the regulation of the recA gene, perhaps as a simple repressor (14-16). We have recently identified the lexA3 mutant protein by radiolabeling techniques and studies with mutants (17) and have also shown that the wild-type lexA + protein is probably a protein with a mobility slightly different from that of the mutant protein in our electrophores...
Escherichia coli shows a pleiotropic response (the SOS response) to treatments that damage DNA or inhibit DNA replication. Previous evidence has suggested that the product of the lexA gene is involved in regulating the SOS response, perhaps as a repressor, and that it is sensitive to the recA protease. We show here that lexA protein is a repressor of at least two genes, recA and lexA. Purified protein bound specifically to the regulatory regions of the two genes, as judged by DNase I protection experiments, and it specifically inhibited in vitro transcription of both genes. The binding sites in recA and lexA were found to be about 20 base pairs (bp) and 40 bp long, respectively. The 40-bp sequence in lexA was composed of two adjacent 20-bp sequences, which had considerable homology to one another and to the corresponding recA sequence. These 20-bp sequences, which we term "SOS boxes," show considerable inverted repeat structure as well. These features suggest that each box represents a single repressor binding site. Finally, we found that purified lexA protein was a substrate for the recA protease in a reaction requiring ATP or an analogue, adenosine 5'-[gamma-thio]triphosphate, and denatured DNA.
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