SUMMARY Small RNAs target invaders for silencing in the CRISPR-Cas pathways that protect bacteria and archaea from viruses and plasmids. The CRISPR RNAs (crRNAs) contain sequence elements acquired from invaders that guide CRISPR-associated (Cas) proteins back to the complementary invading DNA or RNA. Here, we have analyzed essential features of the crRNAs associated with the Cas RAMP module (Cmr) effector complex, which cleaves targeted RNAs. We show that Cmr crRNAs contain an 8-nucleotide 5’ sequence tag (also found on crRNAs associated with other CRISPR-Cas pathways) that is critical for crRNA function and can be used to engineer crRNAs that direct cleavage of novel targets. We also present data that indicates that the Cmr complex cleaves an endogenous complementary RNA in Pyrococcus furiosus, providing direct in vivo evidence of RNA targeting by the CRISPR-Cas system. Our findings indicate that the CRISPR RNA-Cmr protein pathway may be exploited to cleave RNAs of interest.

Apoptosis, or programmed cell death, is an endogenous cellular process whereby an external signal activates a metabolic pathway that results in cell death. This form of cell death appears to be a common feature in many biological processes where cell deletion is a mechanism for altering tissue structure and function. Historically, apoptosis has been studied using histological techniques; however, more recent interest has focused on analyzing this process at the biochemical level. A biochemical hallmark of apoptosis is a characteristic form of DNA degradation in which the genome is cleaved at internucleosomal sites, generating a 'ladder' of DNA fragments when analyzed by agarose gel electrophoresis. A number of assay systems have been developed to study this nuclease activity. For example, nuclease activity has been analyzed by measuring the release of endogenous DNA from apoptotic cells, by flow cytometric analysis of apoptotic cells and by analyzing in situ apoptotic nuclease activity in polyacrylamide gels containing DNA. Use of these assay systems has enabled investigators to study the signal transduction pathways that mediate apoptosis and to characterize the endonuclease itself. Future biochemical studies in this field will focus on isolating the genes and gene products that mediate apoptosis.

The CRISPR-Cas system provides many prokaryotes with acquired resistance to viruses and other mobile genetic elements. The core components of this defense system are small, host-encoded prokaryotic silencing (psi)RNAs and Cas (CRISPR-associated) proteins. Invader-derived sequences within the psiRNAs guide Cas effector proteins to recognize and silence invader nucleic acids. Critical for CRISPR-Cas defense is processing of the psiRNAs from the primary transcripts of the host CRISPR (clustered regularly interspaced short palindromic repeat) locus. Cas6, a previously identified endoribonuclease present in a wide range of prokaryotes with the CRISPR-Cas system, binds and cleaves within the repeat sequences that separate the individual invader targeting elements in the CRISPR locus transcript. In the present study, we investigated several key aspects of the mechanism of function of Cas6 in psiRNA biogenesis. RNA footprinting reveals that Pyrococcus furiosus Cas6 binds to a 7-nt (nucleotide) sequence near the 59 end of the CRISPR RNA repeat sequence, 14 nt upstream of the Cas6 cleavage site. In addition, analysis of the cleavage activity of P. furiosus Cas6 proteins with mutations at conserved residues suggests that a triad comprised of Tyr31, His46, and Lys52 plays a critical role in catalysis, consistent with a possible general acid-base RNA cleavage mechanism for Cas6. Finally, we show that P. furiosus Cas6 remains stably associated with its cleavage products, suggesting additional roles for Cas6 in psiRNA biogenesis.

Glucocorticoid-induced lymphocytolysis has been studied for many years; however, the mechanism of lymphoid cell death has not been elucidated. In this study we have investigated the effects of glucocorticoids on the lymphocyte genome using the rat thymocyte model. Adrenalectomized rats were injected ip with dexamethasone (DEX) and killed thereafter. The thymus gland was removed, and DNA was extracted from isolated thymocytes and then separated electrophoretically on 1.8% agarose gels. Administration of glucocorticoids in vivo resulted in the cleavage of lymphocyte DNA at internucleosomal intervals. Genomic DNA separated on agarose gels from DEX-treated rats appeared as a ladder of DNA fragments which were multiples of about 180 base pairs, while DNA from control rats appeared as a single high mol wt band. This cleavage of thymocyte DNA was a rapid effect of adrenal steroid treatment and occurred before cell death. Thymocyte DNA fragmentation increased with time after DEX treatment and the dose of half-maximal response in vivo was estimated to be about 1.8 X 10(-8) M. Internucleosomal cleavage of DNA was only observed in lymphoid tissues (thymus and spleen), but not in other glucocorticoid-sensitive tissues (kidney, liver, heart, brain, or testis). Treatment of rats with estrogen, androgen, or progestin failed to elicit thymocyte DNA degradation. Glucocorticoid-induced DNA cleavage was partly inhibited by the glucocorticoid antagonist RU 486 (17 beta-hydroxy-11 beta,4-dimethylaminophenyl-17 alpha-propynl-estra-4,9-diene-3-one). These findings suggest that glucocorticoids activate, via a receptor-mediated process, an endonuclease-like activity in lymphoid tissues which cleaves the lymphocyte genome at internucleosomal sites. Activation of this nuclease by glucocorticoids precedes lymphocytolysis and may represent the hormonal regulation of programmed cell death.

The radial spoke is a stable structural complex in the 9 ؉ 2 axoneme for the control of flagellar motility. However, the spokes in Chlamydomonas mutant pf24 are heterogeneous and unstable, whereas several spoke proteins are reduced differentially. To elucidate the defective mechanism, we clone RSP16, a prominent spoke protein diminished in pf24 axonemes. Unexpectedly, RSP16 is a novel HSP40 member of the DnaJ superfamily that assists chaperones in various protein-folding-related processes. Importantly, RSP16 is uniquely excluded from the 12S spoke precursor complex that is packaged in the cell body and transported toward the flagellar tip to be converted into mature 20S axonemal spokes. Rather, RSP16, transported separately, joins the precursor complex in flagella. Furthermore, RSP16 molecules in vitro and in flagella form homodimers, a characteristic required for the cochaperone activity of HSP40. We postulate that the spoke HSP40 operates as a cochaperone to assist chaperone machinery at the flagellar tip to actively convert the smaller spoke precursor and itself into the mature stable complex; failure of the interaction between the spoke HSP40 and its target polypeptide results in heterogeneous unstable radial spokes in pf24. INTRODUCTIONThe radial spoke is a conserved macromolecular complex required for regulation of bending in motile 9 ϩ 2 cilia and flagella (Smith and Yang, 2004). The T-shaped structure anchors to the nine outer doublets with a thin stalk, while its bulbous head contacts central pair apparatus periodically during the oscillatory beating (Warner and Satir, 1974;Goodenough and Heuser, 1985). It is hypothesized that this intermittent interaction with central pair apparatus enables the radial spokes to distribute "signals," originating from central pair apparatus, to subsets of outer doublets for localized control of dynein-driven microtubule sliding (Huang et al., 1982). Consistent with this "distributor" model, the central apparatus is asymmetric in structure (Dutcher et al., 1984;Goodenough and Heuser, 1985;Mitchell and Sale, 1999;Mitchell, 2003;Wargo and Smith, 2003; reviewed in Smith and Yang, 2004) and in some organisms central pair rotates once per beat cycle (reviewed by Omoto et al., 1999). The radial spoke is thought to be relatively rigid to endure physical force arising from the interaction with central pair (Warner and Satir, 1974;Goodenough and Heuser, 1985;Lindemann, 2003;Smith and Yang, 2004;Yang et al., 2004) and is extracted as a stable 20S complex of 23 polypeptides that resists disassembly even in buffers containing 0.6 M KI Patel-King et al., 2004). In addition to the mechanical properties, the radial spokes also contain proteins thought to be involved in chemical signaling through calcium or nucleotide binding (Patel-King et al., 2004;Yang et al., 2001Yang et al., , 2004. Based on these data and other studies, it has been postulated that the radial spoke operates as both mechano-and chemo-transducers reviewed by Smith and Yang, 2004).Among the most important issues is ...