Multiomics study of a heterotardigrade, Echinisicus testudo, suggests the possibility of convergent evolution of abundant heat-soluble proteins in Tardigrada

Abstract

Background Many limno-terrestrial tardigrades can enter an ametabolic state, known as anhydrobiosis, upon desiccation, in which the animals can withstand extreme environments. Through genomics studies, molecular components of anhydrobiosis are beginning to be elucidated, such as the expansion of oxidative stress response genes, loss of stress signaling pathways, and gain of tardigrade-specific heat-soluble protein families designated CAHS and SAHS. However, to date, studies have predominantly investigated the class Eutardigrada, and molecular mechanisms in the remaining class, Heterotardigrada, still remains elusive. To address this gap in the research, we report a multiomics study of the heterotardigrade Echiniscus testudo, one of the most desiccation-tolerant species which is not yet culturable in laboratory conditions. Results In order to elucidate the molecular basis of anhydrobiosis in E. testudo, we employed a multi-omics strategy encompassing genome sequencing, differential transcriptomics, and proteomics. Using ultra-low input library sequencing protocol from a single specimen, we sequenced and assembled the 153.7 Mbp genome annotated using RNA-Seq data. None of the previously identified tardigrade-specific abundant heat-soluble genes was conserved, while the loss and expansion of existing pathways were partly shared. Furthermore, we identified two families novel abundant heat-soluble proteins, which we named E. testudo Abundant Heat Soluble (EtAHS), that are predicted to contain large stretches of disordered regions. Likewise the AHS families in eutardigrada, EtAHS shows structural changes from random coil to alphahelix as the water content was decreased in vitro. These characteristics of EtAHS proteins are analogous to those of CAHS in eutardigrades, while there is no conservation at the sequence level. Conclusions Our results suggest that Heterotardigrada have partly shared but distinct anhydrobiosis machinery compared with Eutardigrada, possibly due to convergent evolution within Tardigrada. (276/350).

Production of reactive oxygen species and involvement of bioprotectants during anhydrobiosis in the tardigrade Paramacrobiotus spatialis

“…The targeting of glutathione transferase ( gst ) had no effects on the motilities of injected animals at any time following rehydration. GSTs have been seen to exist in high copy number in several tardigrade species 25 , 71 , implying that P. spatialis may also have a high copy number of these genes. If this is the case, the knockdown of a single putative gene of gst might not be sufficient to perturb anhydrobiosis in this species.…”

“…Targeting superoxide dismutase ( sod ) via RNAi did not negatively affect the motility percentages of injected animals at any time of rehydration. Comparing the gene repertoire of different tardigrade species, the duplication of sod genes was observed as a common characteristic of anhydrobiotic tardigrades 25 , 71 . Since P. spatialis is a good anhydrobiont 10 , 48 , it is possible that its sod genes are duplicated as well, and therefore, the targeting of a single sod gene might not be enough to affect the motilities of injected tardigrades, even though the sod genes could play a useful role during desiccation.…”

Stress-dependent cell stiffening by tardigrade tolerance proteins through reversible formation of cytoskeleton-like filamentous network and gel-transition

“…These animals might possess another class of stress-dependent filament-forming proteins. Recently, a new heat-soluble protein family termed EtAHS was identified in E. testudo [20]. This protein family or other new ones are likely good candidates.…”

“…Through a search for LEA-like heat-soluble proteins that remain soluble even after boiling in tardigrades, we previously identified cytoplasmic-abundant heat-soluble (CAHS) proteins from one of the toughest tardigrade species, Ramazzottius varieornatus [15]. CAHS proteins exhibited almost no similarity with non-tardigrade proteins, and later genome and transcriptome analyses suggested that CAHS proteins are present only in eutardigrades, one of the major classes of the phylum Tardigrada [11,16,17,18,19,20]. Despite the absence of sequence similarity between CAHS proteins and LEA proteins, they share similar biochemical properties, e.g., high-hydrophilicity supporting heat-solubility and structural transition from the disordered state in hydration to a helix under desolvating or dehydrated conditions [12,15].…”

Deciphering the Biological Enigma—Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the Chironomid Polypedilum vanderplanki

“…The importance of antioxidant pathways has been emphasized in molecular [ 106 , 107 , 108 ] and omics analysis on anhydrobiosis [ 73 , 99 , 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 ]. The expression of superoxide dismutase (SOD), glutathione-S transferase (GST), and catalase is induced during desiccation in the tardigrade Hypsibius exemplaris (Gąsiorek, Stec, Morek and Michalczyk, 2018).…”