Testing long-term (up to 4 weeks) RNAlater preservation of field collected animal-microbe symbioses at room temperature for metaproteomic analyses

ABSTRACT: When studying gene expression in microbe-animals symbioses collected in the field it is essential to quickly and efficiently preserve in situ symbiont and host gene expression patterns. One of the most commonly used sample preservation methods for samples targeted for proteomic analyses is flash freezing, however, liquid nitrogen or dry ice needed for flash freezing are often not available at remote field sites. We first tested if RNAlater allows to preserve proteins in animal-microbe symbioses as efficiently as flash freezing and without introducing issues with downstream processing (see PXD014591). Second, for the data in this PRIDE submission we tested if RNAlater preserves protein expression patterns over time at room temperature. We used the marine gutless oligochaete Olavius algarvensis as a test case. Olavius algarvensis lives in shallow water sediments off the coast of Elba, Italy. It has no digestive and excretory system and harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (Kleiner et al., 2012, PNAS 109(19):1173-82). For this dataset, we fixed a total of 33 worms and incubated them in RNAlater for up to 4 weeks. We then evaluated proteome preservation quality in terms of the number of identified proteins, abundances of individual proteins and potential biases against specific protein or taxonomic groups. Out of this 33 samples, eleven worms were incubated for 24 hours in RNAlater at 4°C (t0), while the other worms were incubated in RNAlater at room temperature (21-23°C) for additional 24 hours (t1, 6 worms), one week (t2, 8 worms), and four weeks (t3, 8 worms). We removed RNAlater from the worms after incubation and froze the samples at -80°C.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Olavius Algarvensis Gamma 3 Endosymbiont Olavius Algarvensis Chromatiales Bacterium Oalggamma1 Olavius Algarvensis Gamma 1 Endosymbiont Olavius Algarvensis Delta 4 Endosymbiont Spirochaeta Sp. Elba Olavius Algarvensis Sulfate-reducing Endosymbiont Olavius Algarvensis Spirochete Endosymbiont Olavius Algarvensis Delta 1 Endosymbiont

SUBMITTER: Marlene Jensen  

LAB HEAD: Dr. Manuel kleiner

PROVIDER: PXD014881 | Pride | 2021-11-03

REPOSITORIES: Pride