Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes

Abstract

The analysis of proteomes from aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 cell cultures by liquid chromatography-mass spectrometry yielded approximately 6,500 high confidence peptides representing 1,675 gene products (39% of the predicted proteins). The identified proteins corresponded primarily to open reading frames (ORFs) contained within the two chromosomal elements of this bacterium, but a significant number were also observed from ORFs associated with 5 naturally occurring plasmids. Using the accurate mass and time (AMT) tag approach, comparative studies showed that a number of proteins were uniquely detected within the photosynthetic cell culture. The estimated abundances of proteins observed in both aerobic respiratory and photosynthetic grown cultures were compared to provide insights into bioenergetic models for both modes of growth. Additional emphasis was placed on gene products annotated as hypothetical to gain information as to their potential roles within these two growth conditions. Where possible, transcriptome and proteome data for R. sphaeroides obtained under the same culture conditions were also compared.

Fig. 1

A) Distribution of ~ 6500 peptides according to discriminant score that were identified by LC-MS/MS and subsequently detected by LC-FTICR. B) Plot of estimated percent false with increasing discriminant score for the PMT database. 90% of peptides detected by the LC-FTICR had discrimininant scores of 1.0, which inferred that the percentage of false positives from the application of the AMT approach was low.

Fig. 2

Functional categories assigned to predicted and identified proteins based on clusters of orthologous groups (COGS). Percentages were calculated from the number of identified proteins compared to the number of predicted proteins for a functional category. This comparison was made for all identified proteins and these proteins grouped by chromosome.

Fig. 3

Heat map comparison of calculated Z-scores for hypothetical proteins detected in the soluble and insoluble protein extracts. Calculated Z-scores are compared for data obtained from both proteome and transcriptome measurements. Proteins in qualitative agreement and disagreement with transcriptome measurements are bracketed.

Fig. 4

Heat map comparisons of Z-scores between proteins involved in electron transfer detected in either or both the soluble and insoluble sample preparations. Increasing intensity in the positive range represents abundances that are greater than the mean abundance derived from both culture conditions and sample preparations relative to the standard deviation associated with the mean. Decreasing intensity in the negative range represents abundances that are less than the mean abundance relative the standard deviation. A majority of proteins showed a greater affinity for the insoluble preparation. Z-score values for the aerobic and photosynthetic cell cultures also suggest the growth condition in which the protein was observed with the greatest abundance.