Chloroplast Research in the Genomic Age Presented by: Andrew Brian Raupp

1. Chloroplast Research in the Genomic Age Presented by: Andrew Brian Raupp Research conducted by: Dario Leister Abteilung f�r Pflanzenz�chtung und Ertragsphysiologie, Max-Planck-Institut f�r Z�chtungsforschung, Carl-von-Linn�-Weg 10, 50829, K�ln, Germany Trends in Genetics Volume 19, Issue 1 , January 2003, Pages 47-56

2. Interpretation This is an example of a literature review article, therefore �success� is based upon the clarity and comprehensiveness of the information compiled. The goal of the authors is to show the trends in chloroplast genomic research by tying together the various methods used into one paper. Papers such as this, make it easier to reference information when inquiring about a specific topic.

3. Abstract Chloroplast research takes significant advantage of genomics and genome sequencing, and a new picture is emerging of how the chloroplast functions and communicates with other cellular compartments. In terms of evolution, it is now known that only a fraction of the many proteins of cyanobacterial origin were rerouted to higher plant plastids. Reverse genetics, Forward Genetics and novel mutant screens are providing a growing catalogue of chloroplast protein�function relationships, and the characterization of plastid-to-nucleus signaling mutants reveals cell�organelle interactions. Recent advances in transcriptomics and proteomics of the chloroplast make this organelle one of the best understood of all plant cell compartments. 

4. Article Terminology cTPs (chloroplast transit peptides)- nucleus encoded proteins used by the vast majority of chloroplasts which require an N-terminal presequence Rubisco (ribulose biphosphate carboxylase)- most abundant enzyme in the world, involved in many plant pathways TAT (twin-arginine translocation)- a pathway which requires a TAT motif

5. Key Terms Cont� YCFs- Conserved ORFs (open reading frames) or gene types when followed by a # and written lowercase/noted in italics NPQ (Non-photochemical quenching)- a class of mutants which reflects the energy dissipated as heat following energization of the thylakoid membrane due to lumen acidifcation. Plastome- Chloroplast genome Nucleome- Nuclear genome

6. Arabidopsis Thaliana Description Arabidopsis thaliana (L.) Heynh. (thale cress) belongs to the Brassicaceae (Cruciferae) family . It is a small weed that is distributed widely around the world. Its small size and rapid life cycle have made it a very popular and useful model organism used in the modern plant biology.

7. Article-relevant Organisms Arabidopsis Thaliana* Maize Chlamydomonas

8. Arabidopsis Thaliana Genome The Arabidopsis genome was completely sequenced at the end of year 2000. It contains about 26000 genes, of which still less than half can be identified or given an assigned function. Several more or less coordinated efforts in the scientific community aim at learning the role and function of these unknown genes using various sophisticated methods.

9. Chloroplasts: Parts are of particular interest A plastid containing chlorophyll, developed only in cells exposed to the light. Central site of the photosynthetic process in plants Contained in the cytoplasm of plant cells.

10. Chloroplast Anatomy The smooth outer membrane is freely permeable which means molecules come in and out freely. The smooth inner membrane uses transporters, to regulate the passage in an out of the chloroplast The thykloid lumen is the cavity bounded by a plant cell wall. A thykloid is the structural unit of the grana in the chloroplasts of plant cells. It is a saclike membrane.

11. Evolutionary/Functionality Understanding by reading into the Plastome �As endosymbiotic remnants of a free-living cyanobacterial progenitor, plastids have, over evolutionary time, lost the vast majority of their genes. Indeed, depending on the organism, contemporary plastomes contain only 60�200 open reading frames (ORFs). The plastomes of green algae and flowering plants are remarkably similar in the sequences of their genes, whereas the organization of genes on the plastid chromosome differs drastically.�

12. Evolutionary/ Functionality Understanding by reading into the chloroplast Cont� �The vast majority of chloroplast proteins are nucleus-encoded and, with the exception of the outer envelope proteins, require N-terminal presequences, termed `chloroplast transit peptides' (cTPs), to target them to the chloroplast. Between 2100 and 3600 distinct proteins are estimated to be located in the Arabidopsis chloroplast� Other proteins such as TAT are also similarly examined.

13. Evolutionary/ Functionality Understanding by reading into the nucleome�

15. Why Study Mutations? One of the most important parts of� Arabidopsis is the generation of mutants (defects in genes). By identifying the mutation that affects the growth and development, or environmental adaptation of the plant, genes that are responsible for these traits can be identified.

16. Using Diverse methods In combination Reverse genetics- the traditional approach was to find a gene product and then try to identify the gene itself. In molecular genetics, the reverse has been done by identifying genes purely on the basis of their position in the genome with no knowledge of the gene product. This revolutionary approach is reverse genetics. Also called positional cloning. In this case, it is used to find nuclear genes encoding plasmid proteins, novel proteins involved in photosynthesis, small subunits of PSI and PSII, essential proteins and to learn more about Rubisco. (See distributed protocol for more details.)

17. Key Methodology Cont� Novel mutant screens- A screen is the analysis of different isolates for a given phenotype or property (like unusual growth, the level of a given enzyme, the presence of an interesting metabolite, the level of a particular antigen, or the presence of a region of DNA capable of hybridizing to a given probe). It should not be confused with a selection ,which is a demand for a given phenotype and is therefore orders of magnitude more "powerful". (See distributed protocol for more details.)

18. Key Methodology Cont� Transcriptomics- The genome-wide study of mRNA expression levels. Proteomics- The study of the full set of proteins encoded by a genome. previous methods used in combination, advances in software and equipment sensitivity increases have also improved plant cell understanding

19. Since Mutant screens have been quite successful, the goal is to be able to find the functions of as many as 1000 genes in the next decade Increase understanding of photosynthesis� role on plastid signaling The assignment of proteins to the chloroplasts subcompartments Future Implications/Outlook

20. http://images.google.com/images?q=arabidopsis+&hl=en&lr=&ie=UTF-8&oe=UTF-8&start=180&sa=N