A Functional Approach to Transcriptome Profiling: Linking Gene Expression Patterns to Metabolites that Matter

Abstract

Secondary metabolites or natural products have been isolated from many marine organisms. These metabolites often have important bioactive functions; however, very little information is available regarding the biosynthesis and regulation of many secondary metabolites. At a time when use of marine-derived metabolites is rapidly expanding in industry and pharmacological fields, a better understanding of the genetic mechanisms controlling secondary metabolite production is necessary. We review the recent development of a novel transcriptome profiling methodology that allows for rapid and high-throughput screening of changes in mRNA sequence pools. The application of genomics-based techniques and the integration of both biochemical and molecular data sets in marine organisms complement ongoing drug discovery efforts.

Proteomic profiling of healthy and diseased hybrid soft corals Sinularia maxima × S. polydactyla

“…Furthermore, these results indicate that shotgun proteomics can be utilized to identify the functional differences in proteins expressed by healthy and diseased individuals, providing a greater understanding of stress responses relative to data acquired in the more commonly used transcriptomic approaches (e.g. Hoover et al 2007). The data presented here represent a pilot-scale study that demonstrates the value of proteomics in research on marine diseases; future studies will focus on differential susceptibility to STLD between the parents and the hybrid, and how their proteomes mediate these processes.…”

Towards Commercial Production of Sponge Medicines

“…A targeted approach should be used to begin this complex study. Many marine natural products are terpenes [34] and thus a good start to investigate gene expression in sponges would be to focus on the mevalonate pathway, which is a known common terpene biosynthesis pathway [5]. …”

“…Because of the low concentrations inside the sponge the amount of sponge biomass needed will be very high [3,4]. To be able to increase the production per sponge, more knowledge is needed on the biosynthetic pathways and their regulation, which includes factors that induce production of the metabolites [5]. …”

Environmental and Molecular Mechanisms of Cold Adaptation in Polar Marine Invertebrates

“…In order to compare changes within embryos or larvae to changes in gene activities, a novel methodology based on reannealing kinetics is employed for the rapid, high-throughput, effi cient, and economical profi ling of the sequence complexity of a transcriptome (Marsh and Fielman, 2005;Hoover et al, 2007a;. Measuring renaturation rates of cDNA along a temperature gradient can provide information about the transcript sequence complexity of a nucleic acid pool sample.…”