Gene Networks replace Mendel’s Model

1. Gene NetworksreplaceMendel’s Model Dec. 6, 2005

2. DNA ReplicationBudd, M.E., et al. 2005. A network of multi-tasking proteins in the DNA replication fork preserves genome stability. PLoSGenetics 1:1.

3. Replication fork Lagging strand& DNA repair Another “system”of many genes Another “system”of many genes The Network Over 800 genes

4. Maize Streak Virus:genotypic contrasts Maize streak virus (MSV) is transcribed bidirectionally from an intergenic region and rightward transcription produces an RNA that encodes the coat protein. The intergenic region contains promoter elements required for rightward transcription including an upstream activating sequence (UAS) which endows the promoter with full activity in a maize transient expression system. The UAS contains two GC-rich repeats (GC boxes) and a long inverted repeat or hairpin with a loop harboring a TAATATTAC sequence common to all geminiviruses. Deletions through the UAS demonstrated the presence of an element, called the rightward promoter element (rpe1), which is responsible for transcriptional activation. Rpe1 includes the two GC-rich boxes, which are similar in sequence to Sp1 binding sites in mammalian cells, but not the conserved hairpin loop.

5. Viral genes affect host gene activity Cell-cycle, phase-specific activation of Maize streak virus promoters.Nikovics K, Simidjieva J, Peres A, Ayaydin F, Pasternak T, Davies JW, Boulton MI, Dudits D, Horvath GV.Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged.It is believed that geminiviral DNA replication is coupled to the cell-cycle regulatory complex of the plant cell and that the virus-early (complementary or C sense) gene products REP and REPA may be able to manipulate the regulation of the cycle. In this study, we examined expression from the promoters of Maize streak virus (MSV) in transgenic maize plants and cells to determine whether they showed cell-cycle specificity. Histochemical staining of plant roots containing "long and short" C-sense promoter sequences upstream of the GUS (beta-glucuronidase) reporter gene showed thatpromoter activity was restricted to the meristematic region of the roots and was enhanced by 2,4-dichlorophenoxy acetic acid (2,4-D) treatment. Analysis of reporter gene and cell-cycle-specific gene transcript levels coupled with flow cytometric data in synchronized transgenic maize cells revealed that all of the MSV promoters showed cell-cycle specificity. The coat protein gene promoter showed highest activity in early G2, whereas the C-sense promoter sequences produced two peaks of activity in the S and G2 cell-cycle phases.

6. Relationship to GMO crops: April 18, 2001 Comment by Dr. Joe Cummins Reply to comments on CaMV by Dr. Redinbaugh (not included here) The sense of Dr. Redinbaugh's comments on your question about the CaMV promoter is that since the promotor is not transcribed it cannot possibly participate in recombination with an RNA virus. That view point is, unfortunately, a narrow one and one that ignores the actual promoter first patented by Monsanto and later improved with enhancer and other elements under separate patents. The Monsanto patent : US5352605:Chimeric genes for transforming plant cells using viral promoters Fraley; Robert T. , Ballwin, MO Horsch; Robert B. , St. Louis, MO Rogers; Stephen G. , St. Louis, MO Applicant(s): Monsanto Company, St. Louis, MO Includes the untranscribed promoter and a polyadenylation signal that is transcribed but not translated. Downstream of the promoter there is an untranslated leader sequence of great importance. In DNA the CaMV promoter region is a hot spot for recombination and in the intact virus most recombination has been associated with RNA to DNA reverse transcription. Turning to RNA to RNA recombination in viruses the homology requirement may be specious, particularly one that ignores the leader sequence. Many times in the past the researchers and journal editors have preferred to consider alternative views about this issue. `Howard Temin, the discoverer of retroviruses, was a friend of mine and I recollect the difficulty of having clear alternatives considered against science dogma of the time. In conclusion, the virus group being considered is noted, according to the literature, for actively exchanging blocks of genes. In time interesting gene acquisition may be identified in the virus. Note that the virus acts as a transposon inducer. Continue the implications….

7. … and where next do the unexpected consequences appear? Back in 1994 when Calgene's GM Flavr Savr tomato was first commercialized Dr. Joseph Cummins, Professor Emeritus in genetics from the University of West-Ontario, Canada, warned the biotechnology community:"Probably the greatest threat from genetically altered crops is the insertion of modified virus and insect virus genes into crops. It has been shown in the laboratory that genetic recombination will create highly virulent new viruses from such constructions. Certainly the widely used cauliflower mosaic virus [CaMV] is a potentially dangerous gene. It is a pararetrovirus meaning that it multiplies by making DNA from RNA messages. It is very similar to the Hepatitis B virus and related to HIV."

8. Maize Streak Virus