Biology subjects

Akter, L.

Publications and source records attributed to Akter, L..

4 recordsLinked to original sources

bioRxiv2025

Nanopore sequencing-based measurement of paramyxovirus RNA editing reveals virus-specific differences in editing efficiency of mRNA, antigenome and genome

Paramyxovirus polymerase recognizes an RNA editing signal on the viral genome and transcribes mRNA in which guanine nucleotides are inserted in a template-independent manner. This enables the synthesis of multiple proteins from a single gene, which is important for viral growth. We developed a method to quantify RNA editing efficiency using Oxford Nanopore Technologies MinION platform. We performed sequence analysis of reverse transcription (RT)-PCR amplicons with the RNA editing sites in cells infected with Sendai virus (SeV) and canine distemper virus (CDV). By modifying RT primers, we simultaneously assessed RNA editing efficiency in mRNA, antigenome and genome. We observed distinct differences in mRNA editing efficiency between SeV and CDV. Notably, while RNA editing in SeV is confined to mRNA, in CDV it is also observed in antigenome/genome. (Anti)genomes harboring extra nucleotides may deviate from a multiple-of-six sequence, suggesting that RNAs not following the "Rule of Six" are produced in CDV-infected cells. HighlightsO_LIA method was established to quantify RNA editing efficiency in RNAs from paramyxovirus-infected cells using the MinION platform. C_LIO_LIRNA editing efficiency in mRNA differs between Sendai virus and canine distemper virus. C_LIO_LIAlthough RNA editing is confined to mRNA during Sendai virus infection, it is also observed in the antigenome and genome during canine distemper virus infection. C_LI

microbiology↗

bioRxiv2025

Draft genome sequences of four lactic acid bacteria from fermented chicken meat unveil biosynthetic gene clusters for antimicrobial compounds

Lactic acid bacteria play a crucial role in fermented food production and serve as important sources of antimicrobial peptides. This study reports four lactic acid bacteria strains, isolated from fermented chicken meat, which harbor biosynthetic gene clusters encoding antimicrobial compounds. These strains are classified within the genera Pediococcus and Lactiplantibacillus.

genomics↗

bioRxiv2025

Functional analysis of promoter element 2 within the viral polymerase gene of an emerging paramyxovirus, Sosuga virus

Paramyxovirus genomes carry bipartite promoters at the 3 ends of both their genome and antigenome, thereby initiating RNA synthesis, which requires the viral polymerase to recognize two elements: the primary promoter element 1 (PE1) and the secondary promoter element 2 (PE2). We have previously shown that the antigenomic PE2 (agPE2) in many viruses in the Rubulavirinae subfamily is located within the coding region of the viral RNA polymerase L gene. Sosuga virus (SOSV), belonging to the Rubulavirinae subfamily, is highly pathogenic to humans, thus necessitating high-level containment facilities for infectious virus research. The use of a minigenome system permits studies of viral RNA synthesis at lower biosafety levels. Because minigenomes of negative-strand RNA viruses generally comprise only the untranslated regions, agPE2 within the L coding region--such as those found in Rubulavirinae like SOSV--are typically omitted. However, generating an SOSV minigenome that retains agPE2 led to a pronounced increase in activity, enabling a detailed examination of the role of agPE2 in SOSV replication. In many Rubulavirinae, the agPE2 not only acts as a promoter but also encodes part of the L protein, resulting in a distinct motif at the C-terminus of the L protein. We have further shown that this motif is preserved even in Rubulavirinae that no longer contain the agPE2 within the L gene. ImportanceParamyxoviruses are classified into three major subfamilies: Orthoparamyxovirinae, Avulavirinae and Rubulavirinae. All paramyxovirus genomes and antigenomes possess bipartite promoters, comprising two elements: promoter element 1 (PE1) at the 3 end and promoter element 2 (PE2) located internally. We previously revealed that, in many Rubulavirinae, the antigenomic PE2 lies within the coding region of the viral RNA polymerase L gene. In this study, we used Sosuga virus, a member of the Rubulavirinae subfamily, to elucidate the role of antigenomic PE2 in viral replication. Because the PE2 region encodes part of the L protein, its presence leads to a distinctive motif at the C-terminus of L protein. Notably, this motif is conserved in all Rubulavirinae, including those that do not harbor the antigenomic PE2 within their L gene, indicating its importance in viral propagation.

microbiology↗

bioRxiv2024

Segment-specific promoter activity for RNA synthesis in the genome of Oz virus, genus Thogotovirus

Oz virus (OZV), a tick-borne, six-segmented negative-strand RNA virus in the genus Thogotovirus, caused a fatal human infection in Japan in 2023. To investigate mechanisms of viral RNA synthesis, we developed an OZV minigenome assay used in mammalian cells. Comparisons of promoter activities across six segments revealed that Segment 5 exhibited markedly lower promoter activity. Unlike the other segments forming a "distal duplex", a double-strand RNA beginning at the 11th nucleotide on the 5 end and the 10th on the 3, Segment 5 partially lacks this feature. Introducing a mutation in Segment 5 distal duplex resulted in a substantial increase in promoter activity. Further, we examined the promoter structures of other viruses in the genus Thogotovirus using public database. Thogoto virus Segment 1 also partially lacks a base pair in the distal duplex. In six-segmented RNA viruses, promoter activities are varied, with notable differences in activities likely existing among segments. HighlightsO_LIA minigenome assay was developed to elucidate the RNA synthesis mechanism of Oz virus. C_LIO_LISegment 5 of the Oz virus exhibits significantly lower promoter activity compared to other segments. C_LIO_LIThe distal duplex region formed by double-strand RNA at the genomic ends is essential for Oz virus RNA synthesis. C_LIO_LIPromoter activities in six-segmented RNA viruses are inherently variable among segments. C_LI

microbiology↗