A clade of RHH proteins ubiquitous in Sulfolobales and their viruses regulates cell cycle progression

Abstract

Coupling of cell growth, genome replication and segregation and cell division is crucial for all living organisms, yet cell progression control is largely underexplored in archaea. In this work, we characterize a ribbon-helix-helix transcriptional regulator (gp21) of rudivirus SIRV2, which infects the hyperthermophilic crenarchaeon S. islandicus LAL14/1. This protein belongs to a clade of highly conserved proteins of the Sulfolobales with homologs in several families of crenarchaeal viruses. Overexpression of gp21 and other members of the clade including the host homolog SiL_0190, results in impairment of cell division, evidenced by growth retardation, cell enlargement and an increase in DNA content. Additionally, gp21 can either repress or induce the transcription of several genes involved in cell division, DNA replication and cellular metabolism. Both gp21 and its cellular homolog SiL_0190 bind to the motif AGTATTA present in the promoter of their target genes, which correspond to the regulatory motif previously identified in a subset of cyclic genes in S. acidocaldarius ccr-2 (Cell Cycle Regulon 2) box. We therefore rename this clade of proteins Ccr-2 and their binding motif as ccr-2 box. Our results suggest that Ccr-2 is a master regulator of the cell cycle that silences genes involved in cell division and drives progression to the S-phase in Sulfolobales, a function exploited by all known viruses to facilitate viral propagation.

Genomics, Transcriptomics, and Proteomics of SSV1 and Related Fusellovirus: A Minireview

“…It is noteworthy that around one-third of the genes in the core genome (5/17) are putative transcriptional regulators (A79, C80, C102, B115, and B129), and this holds true also for several genes of the shell- and cloud-genomes ( Figure 2 , green circles). These transcriptional factors have not been experimentally characterized, although a couple of studies address the role of regulators that do not belong to the core genes [ 33 , 42 , 43 , 44 , 45 , 46 , 47 ]. C80 is homologous to the host transcriptional regulator aCcr-1 (SSO_RS11690 in S. solfataricus P2), a global cell cycle regulator in the Sulfolobales.…”

“…Homologs of aCcr-1 are widespread in viruses infecting Sulfolobales and are thought to benefit virus replication by driving the cell into the S-phase of the cycle where DNA synthesis occurs. This ensures the presence of proteins and resources required for viral genome replication, which depends on the cellular machinery [ 47 ]. However, while the C80 homologs of SSV19–22 and ASSV1 have high sequence similarity to aCcr-1, the other members of the C80 cluster are divergent, cluster separately to aCcr-1 and consist of two different RHH-domains linked together, implying a functional difference [ 47 ].…”

“…This ensures the presence of proteins and resources required for viral genome replication, which depends on the cellular machinery [ 47 ]. However, while the C80 homologs of SSV19–22 and ASSV1 have high sequence similarity to aCcr-1, the other members of the C80 cluster are divergent, cluster separately to aCcr-1 and consist of two different RHH-domains linked together, implying a functional difference [ 47 ]. The prevailing presence of transcriptional factors in fuselloviruses suggests that transcriptional regulation of viral gene expression is critical to their infection, as illustrated by F55 (see below), a protein unique to SSV1 involved in the control of early gene expression after UV induction of viral replication [ 33 , 45 ].…”