This is a rendering of cis-acting replication element inspired by an image of common cre structure found in Coronavirus from a review paper by Sola et al., 2015[1]
Cis-acting replication elements (cre) bring together the 5′ and 3′ ends during replication of positive-sense single-stranded RNA viruses (for example Picornavirus, Flavivirus, Coronavirus, Togaviruses, Hepatitis C virus) and double-stranded RNA viruses (for example rotavirus and reovirus).[2]
Cre are regions of the viral RNA that act as regulatory signals for essential steps in the virus life cycle[3]. These regions typically fold into loop-like structures and are located in the protein-making part of the genome called the translated region or flanking these regions in parts of the genome called the untranslated region.[3][4]
These folded RNA structures interact with proteins from the virus or host to manage processes like making new viral proteins and replicating the virus’ genetic material.[5] The exact shape and role of these structures vary between different types of viruses.[5]
Function of cres in Viral Replication
Positive-Sense RNA Virus Replication
The replication process of some positive-sense RNA viruses (ie. enteroviruses) proceeds via protein-primed replication.[6] This refers to replication that requires the binding of a protein to the RNA to begin.[6] Viral protein genome-linked (VPg) plays the essential role of the protein primer that initiates the replication process in these viruses.[6][7] However, VPg only becomes an active primer when two uridine nucleotides are added to a tyrosine molecule located on the protein [7].The addition of two uridines to a tyrosine molecule is a process called uridylylation.[7] The uridylylation of the tyrosine molecule on VPg is guided by cres.[7] Once the two necessary uridines have been added, VPg is able to prime the initiation of viral replication.[7]
Cres also affect viral replication through RNA-RNA interactions, specifically interactions between the cre and other regions of the viral genome.[8] These complex and dynamic interactions are necessary for the efficient synthesis of viral DNA and ensure proper internal ribosome entry site (IRES) function.[8] The IRES allows for the recruitment of host ribosomes and the translation of the viral genome in a cap-independent manner.[9] This is an essential step in viral replication as a lot of positive-sense RNA viruses do not possess the chemical cap on the 5' end of their genome necessary for host ribosomes to translate their RNA into protein.[10] Cap-independent translation bypasses this problem, allowing the virus to generate the proteins it needs for replication.
Additionally, cres have been shown to interact with several different host proteins.[11] In Enterovirus A71, cres were shown to bind to the cellular factor insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) with a cooperative relationship. Cre-IGF2BP2 interaction resulted in the increase of both viral replication and IGF2BP2 expression.[12]
Function of cre in Coronavirus
Coronavirus is another example of a positive sense RNA virus that uses cres for many functions including RNA synthesis, transcription and virus particle formation.[13][14] Its single stranded genome contains 3 cre structures located at the 3’ end of the genome that does not produce protein and 5 at the 5’ end.[13] Studies investigating the possible RNA-RNA interactions in coronavirus have found that replication of the viral genome is initiated once the 5’ cre binds to the 3' end of the coronavirus genome.[15][16] This interaction enables the recruitment of RNA dependent RNA polymerase which is a protein used to make new RNA strands. Once RNA synthesis is complete cres are also used to package the viral genome into newly formed virus particles.[17]
Medical Applications of cre
Cre have been identified as attractive antiviral targets for the treatment of diseases caused by viral infections such as hepatitis.[18][19] In the context of Hepatitis B Virus, scientists have proposed the development of small molecules that could disrupt the binding of cres to the viral polymerase causing early replication inhibition.[19]
