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Major advances in sequencing technology has produced an avalanche of biological data over the past 12 years. The bottleneck in discovery has consequently shifted from data generation to data analysis. It raises the persistent, nagging question that a vanishingly small amount of the data is used to its full potential \cite{Lockhart_Winzeler_2000}.
One technique of gaining more insight from existing biological data could be crowdsourcing. Putting the many and varied eyes and hands of the general public to the purpose of mining, organizing or analyzing biological data has surfaced several times in bioinformatics \cite{Good_Su_2013} \cite{ld_Allison_Bonneau_et_al__2012}. Examples of problems approached by crowdsourcing include protein [ref] and RNA folding,
and both paid [ingenuity] and unpaid [refs] curation of literature.
Rather than engage
this a problem strictly as professionals, an Open Source DIY workshop was presented where scientists and the public could work together to tackle an introductory synthetic biology project resulting in a publishable outcome. The problem to be solved would need data from completely open sources, not require difficult analysis and ideally look at one or more typical bioinformatics data sources. Thus we decided to do a survey of plant translation initiation motifs which could be embodied as an open source parts list for controlling translation in metabolic engineering and synthetic biology efforts.
Plants offer many advantages as systems to do fine biological engineering [examples needed]. There is a paucity of published information, however, on how to control sets of genes working in concert. Use of small sequence motifs as ribosome binding site parts for synthetic biology
have has been proposed in bacteria [ \cite{Salis_Mirsky_Voigt_2009} see also: http://parts.igem.org/Ribosome_Binding_Sites/Prokaryotic/Constitutive/Anderson.] and
some similar parts have been produced for yeast [parts.igem.org]. So far the half dozen estimates of RBS parts in prokaryotic systems show that the translation of the gene can be reduced to 3% vs control, suggesting that RBS parts can be used to control
of gene expression in a synthetic biology effort.
Plants offer many advantages as systems to do fine biological engineers [examples needed]. But there is a paucity of published information however about how to control sets of genes working in concert. The
glowing plant project Glowing Plant Project has solicited parts from the DIYBio community [reference] and so an estimate of the power of
translational plant translation initiation motifs was conceived as a useful project.
Working meetings were posted through Counter Culture Labs and Berkeley Bio Labs (two groups with over 100 members each) on meetup.com and
met occurred regularly every week or two over the course of three months.
In eukaryotic cells, such as plants, the 5' cap of the mRNA transcript acts as the ribosome binding site. Another sequence within the mRNA, termed the Kozak sequence, acts as the signal for translation initiation. Additionally, some genes are encoded within the chloroplast genome. Due to the evolutionarily bacterial origins of the chloroplast, its transcripts contain distinct consensus sequences
compared in comparison to the transcripts from the nuclear genome. Thus, instead of the 5' cap, there is a short motif called the Shine-Delgarno sequence where the ribosome binds and then initiates translation generally 8 nucleotides downstream but in chloroplast the distance from the start codon to the Shine-Delgarno motif has been shown to vary. Although there has been some experimental work on ribosome binding sites and Kozak sequences in plants [refs, perhaps Lutcke et al EMBO J 1987], genomic surveys have not been performed.
Here we use
combine combined RNA- and protein expression data (publicly available) for both nuclear and chloroplast genes in order to describe the ribosome binding and translation initiation sequence motifs. These are initial results, but experimental confirmation of the motifs will follow.
