Keynote: Luis Serrano - M pneumoniae (Towards a... - ISMB/ECCB 2011

Fully understanding of Micoplasma pneumoniae - - Venkata P. Satagopam

Can we successfully analyze and integrate large number of data types in order to predict changes in system in face of any perturbation? Use case: M pneumoniae - Shannon McWeeney

It contains 689 ORFs + 44 RNSs , 10TFs, kinases and one phosphatase - Venkata P. Satagopam

10 TF ( classical) 2 kinases, 1 phosphatase, full chemical signaling repertoire - Shannon McWeeney

EM tomography used to get the cytoskeleton - Venkata P. Satagopam

Related papers from this work: Yus et al 2009; Güell et al 2009 - Shannon McWeeney

Metabolome - it was difficult to draw the metabolic network, mined last 20years of literature and final network contains 129 enzymes, 140 genes - Venkata P. Satagopam

Strong argument that structural analysis is key - Shannon McWeeney

Modeled using flux balance analysis (FBA) - Venkata P. Satagopam

Motabolomics analysis done using MS and NMR ... developed complete validated map, but missing parameters for reactions, regulatory loops, effect of post translational modifications, enzymes for reactions, - Venkata P. Satagopam

Transcriptome, initially used microarrays, then time-dependent tilling array, then did single strand sequencing - Venkata P. Satagopam

Expression profiling: ncRNA everywhere. expression appears to decay along the operon - "staircase behavior" - Barb Bryant

take home points non-coding RNA abundant; staircase behaviour of operons (steps coincide with end of gene in operon) ? of how this is regulated. - Shannon McWeeney

more than 1 promoter for one operon seems common - Shannon McWeeney

There is a whole huge world of translational regulation, and we "don't have a clue" - Barb Bryant

suggestion to replace operon model - Shannon McWeeney

Cool - there are different RNA polymerase complexes that recognize different operon-start locations; each one also recognizes particular stop signals, and so each may transcribe a different operon. - Barb Bryant

how to explain complexity with so few tf? - Shannon McWeeney

other proteins can act as TF - Shannon McWeeney

possible role of noncoding - Shannon McWeeney

found new putative RNA/DNA binding proteins - Venkata P. Satagopam

Tiny RNAs accurately mark the transcription start sites of genes, about 40 bases long. Have also been found in eukaryotes. Don't know function. - Barb Bryant

Summary - transcriptional complexity in M. pneumoniae could be explained by new TFs, ncRNA, tiny RNAs, new RNA/DNA binding proteins, etc. - Barb Bryant

Missing - who regulates the TFs and DNA binding proteins - Venkata P. Satagopam

Analysis of protein complexes - Sebestian Kuhner et al Science 326, 1235 (2009) - Venkata P. Satagopam

Electron tomography: can visualize large complexes. Allows you to count the number of complexes per cell. - Barb Bryant

Full quantification of proteins and transcripts to get copies per cell, with half-life modeling, and taking into consideration point in growth curve. From this, create full computer model. - Barb Bryant

Statistically more abundant proteins are more essential like Ecoli - Venkata P. Satagopam

Some mRNAs present at (way) less than 1 copy per cell. - Barb Bryant

Poor correlation between mRNA and proteins (~0.5) - Barb Bryant

low copy number of noise - low translation efficiency and long protein half-life eliminates noise - Venkata P. Satagopam

150 ribosomes, 400 promoters, 140 RNA polymerase - Venkata P. Satagopam

There are probably different ribosomes, with different subunit compositions. - Barb Bryant

protein/volume ratio is a magic number - a universal constant: 200 g/l. This is true for 3 bacteria -- is it true for human? - Barb Bryant

They have observed post-translational modifications, but we don't yet know how they are placed, or their function. - Barb Bryant

It's tough to convince students and post-docs to dive into the badly needed research on one or a few proteins when omics experiments are so much faster and often publishable in better journals. - Barb Bryant