A puzzling anomaly in the 4-mer composition of the giant pandoravirus genomes reveals a stringent new evolutionary selection process

International audienceThe Pandoraviridae is a rapidly growing family of giant viruses, all of which have been isolated using laboratory strains of Acanthamoeba. The genomes of ten distinct strains have been fully characterized, reaching up to 2.5 Mb in size. These double-stranded DNA genomes encode the largest of all known viral proteomes and are propagated in oblate virions that are among the largest ever-described (1.2 μm long and 0.5 μm wide). The evolutionary origin of these atypical viruses is the object of numerous speculations. Applying the Chaos Game Representation to the pandoravirus genome sequences, we discovered that the tetranucleotide (4-mer) "AGCT" is totally absent from the genomes of 2 strains (P. dulcis and P. quercus) and strongly underrepresented in others. Given the amazingly low probability of such an observation in the corresponding randomized sequences, we investigated its biological significance through a comprehensive study of the 4-mer compositions of all viral genomes. Our results indicate that "AGCT" was specifically eliminated during the evolution of the Pandoraviridae and that none of the previously proposed host-virus antagonistic relationships could explain this phenomenon. Unlike the three other families of giant viruses (Mimiviridae, Pithoviridae, Molliviridae) infecting the same Acanthamoeba host, the pandoraviruses exhibit a puzzling genomic anomaly suggesting a highly specific DNA editing in response to a new kind of strong evolutionary pressure.IMPORTANCE The recent years have seen the discovery of several families of giant DNA viruses all infecting the ubiquitous amoebozoa of the genus Acanthamoeba. With dsDNA genomes reaching 2.5 Mb in length packaged in oblate particles the size of a bacterium, the pandoraviruses are the most complex and largest viruses known as of today. In addition to their spectacular dimensions, the pandoraviruses encode the largest proportion of proteins without homolog in other organisms which are thought to result from a de novo gene creation process. While using comparative genomics to investigate the evolutionary forces responsible for the emergence of such an unusual giant virus family, we discovered a unique bias in the tetranucleotide composition of the pandoravirus genomes that can only result from an undescribed evolutionary process not encountered in any other microorganism

Revisiting Preimage Sampling for Lattices

Preimage Sampling is a fundamental process in lattice-based cryptography whose performance directly affects the one of the cryptographic mechanisms that rely on it. In 2012, Micciancio and Peikert proposed a new way of generating trapdoors (and an associated preimage sampling procedure) with very interesting features. Unfortunately, in some applications such as digital signatures, the performance may not be as competitive as other approaches like Fiat-Shamir with Aborts. We first revisit the Lyubashevsky-Wichs (LW) sampler for Micciancio-Peikert (MP) trapdoors which leverages rejection sampling but suffered from strong parameter requirements that hampered performance. We propose an improved analysis which yields much more compact parameters. This leads to gains on the preimage size of about 60% over the LW sampler, and up to 30% compared to the original MP sampling technique. It sheds a new light on the LW sampler hoping to open promising perspectives for the efficiency of advanced lattice-based constructions relying on such mechanisms. We then show that we can leverage the special shape of the resulting preimages to design the first lattice-based aggregate signature supporting public aggregation and that achieves relevant compression compared to the concatenation of individual signatures. Our scheme is proven secure in the aggregate chosen-key model coined by Boneh et al. in 2003, based on the well-studied assumptions Module Learning With Errors and Module Short Integer Solution

Lattice Signature with Efficient Protocols, Application to Anonymous Credentials

Digital signature is an essential primitive in cryptography, which can be used as the digital analogue of handwritten signatures but also as a building block for more complex systems. In the latter case, signatures with specific features are needed, so as to smoothly interact with the other components of the systems, such as zero-knowledge proofs. This has given rise to so-called signatures with efficient protocols, a versatile tool that has been used in countless applications. Designing such signatures is however quite difficult, in particular if one wishes to withstand quantum computing. We are indeed aware of only one post-quantum construction, proposed by Libert et al. at Asiacrypt\u2716, yielding very large signatures and proofs. In this paper, we propose a new construction that can be instantiated in both standard lattices and structured ones, resulting in each case in dramatic performance improvements. In particular, the size of a proof of message-signature possession, which is one of the main metrics for such schemes, can be brought down to less than 650 KB. As our construction retains all the features expected from signatures with efficient protocols, it can be used as a drop-in replacement in all systems using them, which mechanically improves their own performance, and has thus a direct impact on many applications. It can also be used to easily design new privacy-preserving mechanisms. As an example, we provide the first lattice-based anonymous credentials system

Practical Post-Quantum Signatures for Privacy

The transition to post-quantum cryptography has been an enormous challenge and effort for cryptographers over the last decade, with impressive results such as the future NIST standards. However, the latter has so far only considered central cryptographic mechanisms (signatures or KEM) and not more advanced ones, e.g., targeting privacy-preserving applications. Of particular interest is the family of solutions called blind signatures, group signatures and anonymous credentials, for which standards already exist, and which are deployed in billions of devices. Such a family does not have, at this stage, an efficient post-quantum counterpart although very recent works improved this state of affairs by offering two different alternatives: either one gets a system with rather large elements but a security proved under standard assumptions or one gets a more efficient system at the cost of ad-hoc interactive assumptions or weaker security models. Moreover, all these works have only considered size complexity without implementing the quite complex building blocks their systems are composed of. In other words, the practicality of such systems is still very hard to assess, which is a problem if one envisions a post-quantum transition for the corresponding systems/standards. In this work, we propose a construction of so-called signature with efficient protocols (SEP), which is the core of such privacy-preserving solutions. By revisiting the approach by Jeudy et al. (Crypto 2023) we manage to get the best of the two alternatives mentioned above, namely short sizes with no compromise on security. To demonstrate this, we plug our SEP in an anonymous credential system, achieving credentials of less than 80 KB. In parallel, we fully implemented our system, and in particular the complex zero-knowledge framework of Lyubashevsky et al. (Crypto\u2722), which has, to our knowledge, not be done so far. Our work thus not only improves the state-of-the-art on privacy-preserving solutions, but also significantly improves the understanding of efficiency and implications for deployment in real-world systems

Human-Phosphate-Binding-Protein inhibits HIV-1 gene transcription and replication

The Human Phosphate-Binding protein (HPBP) is a serendipitously discovered lipoprotein that binds phosphate with high affinity. HPBP belongs to the DING protein family, involved in various biological processes like cell cycle regulation. We report that HPBP inhibits HIV-1 gene transcription and replication in T cell line, primary peripherical blood lymphocytes and primary macrophages. We show that HPBP is efficient in naïve and HIV-1 AZT-resistant strains. Our results revealed HPBP as a new and potent anti HIV molecule that inhibits transcription of the virus, which has not yet been targeted by HAART and therefore opens new strategies in the treatment of HIV infection

Pandoravirus Celtis Illustrates the Microevolution Processes at Work in the Giant Pandoraviridae Genomes

With genomes of up to 2.7 Mb propagated in μm-long oblong particles and initially predicted to encode more than 2000 proteins, members of the Pandoraviridae family display the most extreme features of the known viral world. The mere existence of such giant viruses raises fundamental questions about their origin and the processes governing their evolution. A previous analysis of six newly available isolates, independently confirmed by a study including three others, established that the Pandoraviridae pan-genome is open, meaning that each new strain exhibits protein-coding genes not previously identified in other family members. With an average increment of about 60 proteins, the gene repertoire shows no sign of reaching a limit and remains largely coding for proteins without recognizable homologs in other viruses or cells (ORFans). To explain these results, we proposed that most new protein-coding genes were created de novo, from pre-existing non-coding regions of the G+C rich pandoravirus genomes. The comparison of the gene content of a new isolate, pandoravirus celtis, closely related (96% identical genome) to the previously described p. quercus is now used to test this hypothesis by studying genomic changes in a microevolution range. Our results confirm that the differences between these two similar gene contents mostly consist of protein-coding genes without known homologs, with statistical signatures close to that of intergenic regions. These newborn proteins are under slight negative selection, perhaps to maintain stable folds and prevent protein aggregation pending the eventual emergence of fitness-increasing functions. Our study also unraveled several insertion events mediated by a transposase of the hAT family, 3 copies of which are found in p. celtis and are presumably active. Members of the Pandoraviridae are presently the first viruses known to encode this type of transposase

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