A novel filarial serine protease inhibitor (SPI) from the human parasitic nematode Onchocerca volvulus, Ov-SPI-1, was identified through the analysis of a molting third-stage larvae expressed sequence tag dataset. Subsequent analysis of the expressed sequence tag datasets of O. volvulus and other filariae identified four other members of this family. These proteins are related to the low molecular weight SPIs originally isolated from Ascaris suum where they are believed to protect the parasite from host intestinal proteases. The two Ov-spi transcripts are up-regulated in the molting larvae and adult stages of the development of the parasite. Recombinant Ov-SPI-1 is an active inhibitor of serine proteases, specifically elastase, chymotrypsin, and cathepsin G. Immunolocalization of the Ov-SPI proteins demonstrates that the endogenous proteins are localized to the basal layer of the cuticle of third-stage, molting third-stage, and fourth-stage larvae, the body channels and multivesicular bodies of third-stage larvae and the processed material found between the two cuticles during molting. In O. volvulus adult worms the Ov-SPI proteins are localized to the sperm and to eggshells surrounding the developing embryos. RNA interference targeting the Ov-spi genes resulted in the specific knockdown of the transcript levels of both Ov-spi-1 and Ov-spi-2, a loss of native proteins, and a significant reduction in both molting and viability of third-stage larvae. We suggest the Ov-SPI proteins play a vital role in nematode molting by controlling the activity of an endogenous serine protease(s). The localization data in adults also indicate that these inhibitors may be involved in other processes such as embryogenesis and spermatogenesis.The cuticle is an extracellular hydroskeleton that overlays the hypodermis of all nematodes. Most nematodes molt their cuticles four times during pre-adult development. Although being fairly inert and structurally robust, the cuticle is also permeable to small compounds and expands during growth periods between molts (1). A number of enzymes have been implicated in the shedding of old cuticles and the remodeling process that occurs as the new cuticle develops (2-8). Proteolytic enzymes have been shown to play a vital role in these processes, and inhibitor studies and rational cloning strategies have identified several nematode proteases whose functions are required for molting (9 -11).To identify novel filarial proteins involved in the molting process, we adopted a transcriptomics approach. Thousands of expressed sequence tags (ESTs) 4 have been sequenced from cDNA libraries constructed from the infective third-stage larvae (L3) and molting L3 (mL3) of the human filarial nematode Onchocerca volvulus (12, 13). Analysis of these datasets identified novel cysteine proteases involved in the molting process (14,15). Also identified in these analyses was an O. volvulus small molecular weight serine protease inhibitor (SPI) with similarities to other nematode SPI; Ascaris suum chymotrypsin/elastase in...