Charting 2D Gels making use of the different Chlamydomonas databases available Christine Markert, Universität Jena

Outline Project: Mapping Thylakoid Proteins 2D-PAGE Databases Types Limitations

Thesis Project Comparison of different mutant strains Isolation of Thylakoids 2D-PAGE Mass Spectrometry Database Analysis  PROTEIN INFORMATION

Information of Interest Amino acid sequence Database Entry Annotation possible Modifications New Database Information

Types of Databases Assembled Lhc Proteins EST Databases Genomic Database (first release February 2003)

Protein dynamics of photosystem I and its light- harvesting antenna proteins in assembly and adaptation processes Variation of physiological conditions Mutant analysis (PSI defective) Functional Proteomics of Transmembrane Multiprotein Complexes

Data Mining Annotation of Database Genome  Introns Modifications (e.g. Phosphorylation) Homologues

Chlamydomonas reinhardtii is a unicellular green alga which swims with two flagella and has chloroplasts for photosynthesis. The genome is ~100 Mbp and is distributed in 17 chromosomes. The initial goal of the Chlamydomonas reinhardtii genome project is to generate EST sequences, and to date there are over 55,860 Chlamydomonas ESTs in GenBank. Because Chlamydomonas reinhardtii is quite GC rich (~65% G+C), we have begun a pilot project to sequence several BACs in collaboration with Dr. Susan K. Dutcher in the Department of Genetics at Washington University School of Medicine in St. Louis, Missouri. These BAC clones cover a region of ~600 kbp in the Chlamydomonas reinhardtii genome.Dr. Susan K. Dutcher The BAC library prepared by Pete Lefebvre in collaboration with Genome Systems (now IncyteGenomics) is available from IncyteGenomics. Requests for these BACs should be directed to Incyte GenomicsIncyte Genomics A table viewing the BAC clones being sequenced can be viewed at URL: In accord with the Bermuda Agreement and NHGRI policy, we are depositing all our human genomic sequence data into the High-Throughput Genomic Sequences (HTGS) division of GenBank as soon as a target large insert clone sequencing project can be assembled into contigs greater than 2 kb. The following BAC clones are being sequenced. This sequence data has been deposited into GenBank, and given accession numbers:High-Throughput Genomic Sequences (HTGS) division of GenBank

Status The current draft release, version 2.0 of the Chlamydomonas reinhardtii genome, was generated using the whole genome shotgun strategy, using only data generated here at the JGI. Gene models for this release are currently undergoing manual curation by members of the Chlamydomonas community.This massive effort began during the Chlamydomonas Jamboree, held at the JGI during the week of Dec 8th, Annotations can be viewed immediately from the protein pages as they become available. To search for genes that have manual annotations, please read the directions on our advanced search page. ReleaseThis assembly was constructed with JAZZ, the JGI assembler, capitalizing on paired-end sequencing reads. After trimming for vector and quality, 1.8 Million reads assembled into 3211 scaffolds totaling 125 Mbp. Roughly half of the genome is contained in 72 scaffolds, all of at least 504 Kb in length. Gene models have been updated using the depth of EST/cDNA information publicly available for C. reinhardtii. Future plansManual review of gene models will continue through the spring, and results will be discussed at a second Jamboree due to be scheduled this coming summer. Stanford will begin finishing the genome later this year. We will update this site once finishing efforts are complete. FundingThis work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.advanced search

Assembly C. reinhardtii release 2.0 assembled scaffolds (unmasked): chlre2.fasta.gz (29054 Kb) C. reinhardtii release 2.0 assembled scaffolds (masked): chlre2.allmasked.gz (28364 Kb) C. reinhardtii release 2.0 predicted proteins: proteins.finalModelsV2.fasta.gz (5009 Kb) chlre2.fasta.gz chlre2.allmasked.gz proteins.finalModelsV2.fasta.gz

SEARCH BY KOG ID SEARCH BY KOG KEYWORDCELLULAR PROCESSES AND SIGNALING SEARCH BY KOG IDSEARCH BY KOG KEYWORD MCell wall/membrane/envelope biogenesis 80 gene models NCell motility 6 gene models OPosttranslational modification, protein turnover, chaperones 712 gene models TSignal transduction mechanisms 666 gene models UIntracellular trafficking, secretion, and vesicular transport 308 gene models VDefense mechanisms 55 gene models WExtracellular structures 28 gene models YNuclear structure 33 gene models ZCytoskeleton 170 gene models Total Gene Count2058INFORMATION STORAGE AND PROCESSING 80 gene models 6 gene models 712 gene models 666 gene models 308 gene models 55 gene models 28 gene models 33 gene models 170 gene models ARNA processing and modification 319 gene models BChromatin structure and dynamics 239 gene models JTranslation, ribosomal structure and biogenesis 369 gene models KTranscription 304 gene models LReplication, recombination and repair 219 gene models Total Gene Count1450METABOLISM 319 gene models 239 gene models 369 gene models 304 gene models 219 gene models CEnergy production and conversion 255 gene models DCell cycle control, cell division, chromosome partitioning 199 gene models EAmino acid transport and metabolism 278 gene models FNucleotide transport and metabolism 111 gene models GCarbohydrate transport and metabolism 265 gene models HCoenzyme transport and metabolism 100 gene models ILipid transport and metabolism 232 gene models PInorganic ion transport and metabolism 203 gene models QSecondary metabolites biosynthesis, transport and catabolism 172 gene models Total Gene Count1815POORLY CHARACTERIZED 255 gene models 199 gene models 278 gene models 111 gene models 265 gene models 100 gene models 232 gene models 203 gene models 172 gene models RGeneral function prediction only 1057 gene models SFunction unknown 381 gene models Total Gene Count gene models 381 gene models

Summary

9 2D-map of Lhca proteins from C. reinhardtii