Maf/ham1-like pyrophosphatases of non-canonical nucleotides are host-specific partners of viral RNA-dependent RNA polymerases

Abstract

Cassava brown streak disease (CBSD), dubbed the “Ebola of plants”, is a serious threat to food security in Africa caused by two viruses of the family Potyviridae: cassava brown streak virus (CBSV) and Ugandan (U)CBSV. Intriguingly, U/CBSV, along with another member of this family and one secoviridae, are the only known RNA viruses encoding a protein of the Maf/ham1-like family, a group of widespread pyrophosphatase of non-canonical nucleotides (ITPase) expressed by all living organisms. Despite the socio-economic impact of CDSD, the relevance and role of this atypical viral factor has not been yet established. Here, using an infectious cDNA clone and reverse genetics, we demonstrate that UCBSV requires the ITPase activity for infectivity in cassava, but not in the model plant Nicotiana benthamiana. HPLC-MS/MS experiments showed that, quite likely, this host-specific constraint is due to an unexpected high concentration of non-canonical nucleotides in cassava. Finally, protein analyses and experimental evolution of mutant viruses indicated that keeping a fraction of the yielded UCBSV ITPase covalently bound to the viral RNA-dependent RNA polymerase (RdRP) optimizes viral fitness, and this seems to be a feature shared by the other members of the Potyviridae family expressing Maf/ham1-like proteins. All in all, our work (i) reveals that the over-accumulation of non-canonical nucleotides in the host might have a key role in antiviral defense, and (ii) provides the first example of an RdRP-ITPase partnership, reinforcing the idea that RNA viruses are incredibly versatile at adaptation to different host setups.

Inosine triphosphate pyrophosphatase: A guardian of the cellular nucleotide pool and potential mediator of RNA function

“…ITPase in Ugandan cassava brown streak virus (UCBSV) is required for its infectivity of cassava, which contain high levels of noncanonical nucleotides. A fraction of UCBSV‐ITPase is covalently associated with the viral RNA polymerase NIb, consistent with its functioning to prevent misincorporation of noncanonical nucleotides during viral replication (Valli et al, 2022).…”

A mixed infection of ITPase-encoding potyvirid and secovirid in Mercurialis perennis: evidences for a convergent euphorbia-specific viral counterstrike

“…This fusion may ensure that an active ITPase dimer co-localizes with and protect the viral replicase. The production of both forms of ITPase is due to a weak proteolytic cleavage caused by a T in the last position of the cleavage site VDTQ/T, which is sub-optimally recognized by the protease Nla-Pro (Valli et al, 2022). Interestingly, a T is found at a similar position on the putative cleavage site preceding the MMV ITPase (Fig.…”

Cassava torrado-like virus encodes a gene that facilitates the mechanical transmission to Nicotiana benthamiana of Cassava virus X

“…CsTLV is an atypical member of the Secoviridae, containing a Maf/Ham1 domain located in RNA1 downstream of the RdRp domain (Leiva et al, 2022). Maf/HAM1 proteins are nucleoside triphosphate (NTP) pyrophosphatases that protect cells by hydrolyzing non-canonical NTPs, preventing their incorporation into DNA or RNA (Noskov et al, 1996;Mbanzibwa et al, 2009;Tomlinson et al, 2019;Valli et al, 2022). Recent results demonstrated that Maf/Ham1 domain is associated with the development of necrosis in N. benthamiana plants (Tomlinson et al, 2019) and Valli et al (2022) suggests that the HAM1 domain participates in viral replication because it might be covalently bound during CBSV and EuRV infections.…”