Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting

Abstract

Probing the intracellular proteome of Thermotoga maritima and Caldicellulosiruptor saccharolyticus in pure and co-culture affords a global investigation into the machinery and mechanisms enduring inside the bacterial thermophilic cell at the time of harvest. The second of a two part study, employing GeLC-MS2 a variety of proteins were confidently identified with <1% false discovery rate, and spectral counts for label-free relative quantification afforded indication of the dynamic proteome as a function of environmental stimuli. Almost 25% of the T. maritima proteome and 10% of the C. saccharolyticus proteome were identified. Through comparison of growth temperatures for T. maritima, a protein associated with chemotaxis was uniquely present in the sample cultivated at the non-optimal growth temperature. It is suspected that movement was induced due to the non-optimal condition as the organism may need to migrate in the culture to locate more nutrients. The inventory of C. saccharolyticus proteins identified in these studies and attributed to spectral counting, demonstrated that two CRISPR-associated proteins had increased expression in the pure culture versus the co-culture. Further focusing on this relationship, a C. saccharolyticus phage-shock protein was identified in the co-culture expanding a scenario that the co-culture had decreased antiviral resistance and accordingly an infection-related protein was present. Alterations in growth conditions of these bacterial thermophilic microorganisms offer a glimpse into the intricacy of microbial behavior and interaction.

Stable coexistence of two Caldicellulosiruptor species in a de novo constructed hydrogen-producing co-culture

“…Tm. maritima , to a pure culture of C. saccharolyticus triggers events causing the presence, absence and differential expression of protein species within the system [ 15 ]. Although the genome of C. saccharolyticus has been fully sequenced and annotated [ 34 ], it is difficult to examine for the presence of putative small peptide signaling molecules since signaling peptides are often products of genes encoding proteins less than 100 amino acids in length.…”

Quantitative proteomics in the field of microbiology

“…Further, the estimation of protein abundance has been performed in a large study of the substrate‐controlled succession of marine bacterioplankton populations in the North Sea . Assessment of spectral counts is also helpful in the determination of processes that occur during co‐cultivation of different species reflecting mechanisms of competition . Besides using spectral counting for the relative quantitative estimation of protein abundances, these values may also be used as additional information in studies aimed either at relative comparisons by metabolic labeling or protocol optimization .…”