Biology subjects

Kojima, S.

Publications and source records attributed to Kojima, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Interaction of FlhF, SRP-like GTPase with FliF, MS ring component assembling the initial structure of flagella in marine Vibrio

Vibrio alginolyticus forms a single flagellum at its cell pole. FlhF and FlhG are known to be the main proteins responsible for the polar formation of single flagellum. FlhF, which belongs to the signal recognition particle (SRP)-type GTPase family, localizes at the cell pole and initiates flagellar generation. In contrast, FlhG negatively regulates flagellar numbers. Furthermore, MS-ring formation in the flagellar basal body appears to be an initiation step for flagellar assembly. The MS-ring is formed by a single protein, FliF, which has two transmembrane (TM) segments and a large periplasmic region. We had shown that FlhF was required for the polar localization of Vibrio FliF, and FlhF facilitated MS-ring formation when FliF was overexpressed in E. coli cells. These results suggest that FlhF interacts with FliF to facilitate MS-ring formation. Here, we attempted to detect this interaction using Vibrio FliF fragments fused to a tag of Glutathione S-transferase (GST) in E. coli. We found that the N-terminal 108 residues of FliF, including the first TM segment and the periplasmic region, could pull FlhF down. In the first step, the SRP and its receptor are involved in the transport of membrane proteins to target them, which delivers them to the translocon. FlhF may have a similar or enhanced function as SRP, which binds to a region rich in hydrophobic residues. IMPORTANCEVibrio alginolyticus forms only a single flagellum at the cell pole by regulators of FlhF and FlhG. FlhF regulates positively the formation of flagella and is required for polar positioning of the flagellum. FliF, the two transmembrane (TM) segments and a large periplasmic region, forms the MS ring of flagellar basal body in the membrane. Previous studies suggest that FlhF interacts with FliF to facilitate MS ring formation at the cell pole, but the interaction has not been detected. Here, we show the evidence that FlhF interacts with FliF at residues including the first TM segment and following periplasmic region. The hydrophobic residues of this region seem to be important for the interaction.

microbiology↗

bioRxiv2022

Function and structure of FlaK, a master regulator of the polar flagellar genes in marine Vibrio

Vibrio alginolyticus has a flagellum at the cell pole, and the fla genes, involved in its formation, are hierarchically regulated in several classes. FlaK (also called FlrA) is an ortholog of Pseudomonas aeruginosa FleQ, an AAA+ ATPase that functions as a master regulator for all later fla genes. In this study, we conducted mutational analysis of FlaK to examine its ATPase activity, ability to form a multimeric structure, and function in flagellation. We cloned flaK and confirmed that its deletion caused a non-flagellated phenotype. We substituted amino acids at the ATP binding/hydrolysis site and performed putative subunit interfaces in a multimeric structure. Mutations in the aforementioned sites abolished both ATPase activity and the ability of FlaK to induce downstream flagellar gene expression. The L371E mutation, at the putative subunit interface, abolished flagellar gene expression but retained ATPase activity, suggesting that ATP hydrolysis is not sufficient for flagellar gene expression. We also found that FlhG, a negative flagellar biogenesis regulator, suppressed the ATPase activity of FlaK. The 20 FlhG C-terminal residues are critical for reducing FlaK ATPase activity. Chemical crosslinking and size exclusion chromatography revealed that FlaK mostly exists as a dimer in solution and can form multimers, independent of ATP. However, ATP induced the interaction between FlhG and FlaK to form a large complex. The in vivo effects of FlhG on FlaK, such as multimer formation and/or DNA binding, are important for gene regulation. IMPORTANCEFlaK is an NtrC-type activator of the AAA+ ATPase subfamily of {sigma}54-dependent promoters of flagellar genes. FlhG, a MinD-like ATPase, negatively regulates the polar flagellar number by collaborating with FlhF, an FtsY-like GTPase. We found that FlaK and FlhG interact in the presence of ATP, to form a large complex. Mutational analysis revealed the importance of FlaK ATPase activity in flagellar gene expression and provided a model of the Vibrio molecular mechanism that regulates the flagellar number.

microbiology↗

bioRxiv2022

A comprehensive list of the replication promoters of Bunyavirales reveals a unique promoter structure in Nairoviridae differing from other virus families

Bunyaviruses belong to the order Bunyavirales, the largest group of RNA viruses. They infect a wide variety of host species around the world, including plants, animals and humans, and pose a major threat to public health. Major families in the order Bunyavirales have tri-segmented negative-sense RNA genomes, the 5 and 3 ends of which form complementary strands that serve as a replication promoter. Elucidation of the mechanisms by which viral RNA-dependent RNA polymerase recognizes the promoter to initiates RNA synthesis is important for understanding viral replication and pathogenesis, and for developing antivirals. A list of replication promoter configuration patterns may provide details on the differences in the replication mechanisms among bunyaviruses. Here, by using public sequence data of all known bunyavirus species, we constructed a comprehensive list of the replication promoters comprising 40 nucleotides in both the 5 and 3 ends of the genome that form a specific complementary strand. We showed that among tri-segmented bunyaviruses, viruses belonging to the family Nairoviridae, including the highly pathogenic Crimean-Congo hemorrhagic fever virus, have evolved a GC-rich promoter structure that differs from that of other bunyaviruses. The unique promoter structure might be related to the large genome size of the family Nairoviridae among bunyaviruses. It is possible that the large genome architecture confers a pathogenic advantage. The promoter list provided in this report is expected to be useful for predicting virus family-specific replication mechanisms of segmented negative-sense RNA viruses.

microbiology↗

bioRxiv2022

Formation of multiple flagella caused by a mutation of the flagellar rotor protein FliM in Vibrio alginolyticus

The marine bacterium Vibrio alginolyticus forms only a single flagellum at the cell pole. In Vibrio, two proteins (GTPase FlhF and ATPase FlhG) regulate flagellar number at the cell pole. We previously isolated a mutant strain characterized as NMB155 that forms multiple flagella despite the absence of mutations in flhF and flhG. NMB155 also exhibited straight swimming without a directional change in flagellar rotation. Whole-genome sequencing of NMB155 identified an E9K mutation in FliM that is a component of the C-ring in the flagellar rotor. Mutations in FliM result in defects in flagellar formation (fla) and flagellar rotation (che or mot); however, there are few reports indicating that FliM mutations increase the number of flagella. Here, we determined that the E9K mutation confers the multi-flagellar phenotype and also the che phenotype. The co-expression of wild-type FliM and FliM-E9K indicated that they were competitive in regard to determining the flagellar number. It had been shown that the ATPase activity of FlhG corresponds to the flagellar number. We observed that the ATPase activity of FlhG was increased by the addition of FliM but not by the addition of FliM-E9K. This indicates that the N-terminal region of FliM that includes the E9 residue interacts with FlhG to increase its ATPase activity, and the E9K mutation may inhibit this interaction. We concluded that FliM downregulate FlhG activity to inhibit the formation of additional flagella. ImportanceThe flagellar rotor generates a driving force to rotate the flagellum and is not involved in controlling the number of flagella in Vibrio. However, we observed that the E9K mutation in the rotor protein FliM confers multiple flagella. Our findings reveal a novel regulatory mechanism controlling flagellar number.

microbiology↗

bioRxiv2022

Mobile elements in human population-specific genome and phenotype divergence

Mobile genetic elements (MEs) are heritable mutagens that contribute to divergence between lineages by recursively generating structural variants. ME variants (MEVs) are difficult to genotype, obscuring their impact on recent genome and trait diversification. We developed a tool that uses short-read sequence data to accurately genotype MEVs, enabling us to study them using statistical genetics methods in global human genomes. We observe population-specific differences in the distribution of Alu insertions that distinguish Japanese from other populations. We integrated MEVs with epigenomic and expression quantitative trait loci (eQTL) maps to determine how they impact traits. This reveals coherent patterns by which specific MEs regulate tissue-specific gene expression, including creating or attenuating enhancers and recruiting post-transcriptional regulators. We pinpoint MEVs as genetic causes of disease risk, including a LINE-1 insertion linked to keloid and other diseases of fibroblast inflammation, by introducing MEVs into the genome-wide association study (GWAS) framework. In addition to nominating previously-hidden MEVs as causes of human diseases, this work highlights MEs as accelerators of human population divergence and begins to decipher the semantics of MEs.

genetics↗

bioRxiv2022

Functional analysis of the N-terminal region of Vibrio FlhG, a MinD-type ATPase in flagellar number control

GTPase FlhF and ATPase FlhG are two key factors involved in regulating the flagellum number in Vibrio alginolyticus. FlhG is a paralog of the Escherichia coli cell division regulator MinD, which has a longer N-terminal region. Deleting the N-terminal region of FlhG results in cells with multiple flagella. The Q9A mutation in the DQAxxLR motif of the N-terminal region prevents it from activating the GTPase activity of FlhF in vitro and results in a multi-flagellation phenotype. The mutant FlhG protein was remarkably reduced compared to that of the wild-type protein in vivo. When the mutant FlhG was expressed at the same level as the wild-type FlhG, the number of flagella was restored to the wild-type level. Once synthesized in Vibrio cells, the N-terminal region mutation in FlhG seems not to affect the protein stability. We speculated that the flhG translation efficiency is decreased by N-terminal mutation. Our results suggest that the N-terminal region of FlhG controls the number of flagella by adjusting the FlhF activity and the amount of FlhG in vivo. We speculate that the regulation by FlhG, achieved through transcription by the master regulator FlaK, is affected by the mutations, resulting in reduced flagellar formation by FlhF.

biochemistry↗

bioRxiv2022

Frequency of a nucleotide overhang at the 5' end of hemorrhagic fever mammarenavirus genomes in public sequence data

Mammarenaviruses, such as Lassa virus and South American hemorrhagic fever (SAHF) virus, cause severe hemorrhagic fevers in humans, and pose major threats to public health. Mammarenaviruses consist of a bi-segmented negative-sense RNA genome in which the 5 and 3 ends form complementary strands that serve as a replication promoter. Some mammarenaviruses have a nucleotide overhang at the 5 genome end. By examining the complementarity of 5 and 3 genome ends using public mammarenavirus genome sequences, we found that the 5 guanine overhang (5-G overhang) was present more frequently in Lassa and SAHF viruses than in other viruses. The 5-G overhang in the Lassa and SAHF virus sequences was found to be restricted to the L and S segments, respectively. If the genome end sequence data in the public database are accurate, the 5-G overhang may be related to the high pathogenicity of mammarenaviruses in humans.

microbiology↗

bioRxiv2021

Hoop-like role of the cytosolic interface helix in Vibrio PomA, an ion-conducting membrane protein, in the bacterial flagellar motor

Vibrio has a polar flagellum driven by sodium ions for swimming. The force-generating stator unit consists of PomA and PomB. PomA contains four-transmembrane regions and a cytoplasmic domain of approximately 100 residues which interacts with the rotor protein, FliG, to be important for the force generation of rotation. The three-dimensional structure of the stator shows that the cytosolic interface (CI) helix of PomA is located parallel to the inner membrane. In this study, we investigated the function of CI helix and its role as stator. Systematic proline mutagenesis showed that residues K64, F66, and M67 were important for this function. The mutant stators did not assemble around the rotor. Moreover, the growth defect caused by PomB plug deletion was suppressed by these mutations. We speculate that the mutations affect the structure of the helices extending from TM3 and TM4 and reduce the structural stability of the stator complex. This study suggests that the helices parallel to the inner membrane play important roles in various processes, such as the hoop-like function in securing the stability of the stator complex and the ion conduction pathway, which may lead to the elucidation of the ion permeation and assembly mechanism of the stator. ImportanceBacteria have a motor embedded in the membrane to rotate flagella as screw for swimming. The motor is composed rotor and stator complexes. The interaction between the rotor and stator converts the electrochemical potential gradient across the membrane into motor torque. The stator functions as an ion channel and is composed of two membrane proteins, MotA and MotB for proton or PomA and PomB for sodium ion. Based on the structural data of stator, we systematically introduce the proline replacement mutations and found that the cytosolic interface (CI) helix which is located parallel to the inner membrane between the second and third transmembrane (TM) segments, performs a hoop-like function in securing the stability of the stator complex and the ion conduction pathway. The results of this study provide novel insights into the energy conversion mechanism of the flagellar motor and the general mechanism of the ion channel function.

biophysics↗

bioRxiv2021

Crosstalk between Flavonoids and the Plant Circadian Clock

Flavonoids are a well-known class of specialized metabolites that play key roles in plant development, reproduction, and survival. Flavonoids are also of considerable interest from the perspective of human health, both as phytonutrients and pharmaceuticals. RNA-Seq analysis of an Arabidopsis null allele for chalcone synthase (CHS), which catalyzes the first step in flavonoid biosynthesis, has uncovered evidence that these compounds influence the expression of circadian clock genes in plants. Analysis of promoter-luciferase constructs showed that the transcriptional activity of genes encoding two components of the central clock, CCA1 and TOC1, across the day/night cycle is altered in CHS-deficient seedlings. The effect of flavonoids on circadian function was furthermore reflected in photosynthetic activity, with chlorophyll cycling abolished in the mutant line. Analysis of a mutant lacking flavonoid 3-hydroxylase (F3H) activity, and thus able to synthesize mono- but not di-hydroxylated B-ring flavonoids, suggests that the latter are at least partially responsible, as further supported by the effects of quercetin on CCA1 promoter activity in wild-type seedlings. Collectively, these experiments point to a previously-unknown connection between flavonoids and circadian cycling in plants and open the way to better understanding of the molecular basis of flavonoid action.

plant biology↗

bioRxiv2021

ZomB is essential for chemotaxis of Vibrio alginolyticus by the rotational direction control of the polar flagellar motor

Bacteria exhibit chemotaxis by controlling flagellar rotation to move toward preferred places or away from non-preferred places. The change in rotation is triggered by the binding of the chemotaxis signaling protein CheY to the C-ring in the flagellar motor. Some specific bacteria, including Vibrio spp. and Shewanella spp. have a single transmembrane protein called ZomB. ZomB is essential for controlling the flagellar rotational direction in Shewanella putrefaciens and Vibrio parahaemolyticus. In this study, we confirmed that the zomB deletion results only in the counterclockwise (CCW) rotation of the motor in Vibrio alginolyticus as previously reported in other bacteria. We found that ZomB is not required for the clockwise (CW) rotation-fixing phenotype caused by mutations in fliG and fliM, and that ZomB is essential for CW rotation induced by overproduction of CheY. Purified ZomB proteins form multimers, indicating that ZomB functions as a complex. ZomB may interact with a protein involved in the flagellar rotation, stator proteins or rotor proteins. We found that ZomB is a new player in chemotaxis and is required for the rotational control in addition to CheY in Vibrio alginolyticus. ImportanceBacterial chemotaxis is performed by the control of the flagellar rotation. CheY and ZomB control the rotational direction of the flagellar motor in Vibrio spp. and Shewanella spp. In this study, we characterized ZomB in Vibrio alginolyticus, which is essential for the clockwise rotation of the motor.

microbiology↗

bioRxiv2021

Hidden viral sequences in public sequencing data and warning for future emerging diseases

RNA viruses cause numerous emerging diseases, mostly due to transmission from mammalian and avian reservoirs. Large-scale surveillance of RNA viral infections in these animals is a fundamental step for controlling viral infectious diseases. Metagenomic analysis is a powerful method for virus identification with low bias and has substantially contributed to the discovery of novel viruses. Deep sequencing data have been collected from diverse animals and accumulated in public databases, which can be valuable resources for identifying unknown viral sequences. Here, we screened for infections of 33 RNA viral families in publicly available mammalian and avian sequencing data and found approximately 900 hidden viral infections. We also discovered six nearly complete viral genomes in livestock, wild, and experimental animals: hepatovirus in a goat, hepeviruses in blind mole-rats and a galago, astrovirus in macaque monkeys, parechovirus in a cow, and pegivirus in tree shrews. Some of these viruses were phylogenetically close to human pathogenic viruses, suggesting the potential risk of causing disease in humans upon infection. Furthermore, the infections of five novel viruses were identified in several different individuals, indicating that their infections may have already spread in the natural host population. Our findings demonstrate the reusability of public sequencing data for surveying viral infections and identifying novel viral sequences, presenting a warning about a new threat of viral infectious disease to public health. ImportanceMonitoring the spread of viral infections and identifying novel viruses capable of infecting humans through animal reservoirs are necessary to control emerging viral diseases. Massive amounts of sequencing data collected from various animals are publicly available, and these data may contain sequences originating from a wide variety of viruses. Here, we analyzed more than 46,000 public sequencing data and identified approximately 900 hidden RNA viral infections in mammalian and avian samples. Some viruses discovered in this study were genetically similar to pathogens that cause hepatitis, diarrhea, or encephalitis in humans, suggesting the presence of new threats to public health. Our study demonstrates the effectiveness of reusing public sequencing data to identify known and unknown viral infections, indicating that future continuous monitoring of public sequencing data by metagenomic analyses would help prepare and mitigate future viral pandemics.

microbiology↗

bioRxiv2021

Function of the Vibrio PomB plug region based on the stator rotation model for bacterial flagellar motor

Bacterial flagella are the only real rotational motor organs in the biological world. The spiral-shaped flagellar filaments that extend from the cell surface rotate like a screw to create a propulsive force. The base of the flagellar filament has a protein motor consisting of a stator and a rotor embedded in the membrane. The motor part has stators composed of two types of membrane subunits, PomA(MotA) and PomB(MotB), which are energy converters coupled to the ion flow that assemble around the rotor. Recently, structures of the stator, in which two molecules of MotB stuck in the center of the MotA ring made of five molecules, were reported and a model in which the MotA ring rotates with respect to MotB, which is coupled to the influx of ions, was proposed. We focused on the Vibrio PomB plug region, which has been reported to control the activation of flagellar motors. We searched for the plug region, which is the interacting region, through site-directed photo-cross-linking and disulfide cross-linking experiments. Our results demonstrated that it interacts with the extracellular short loop region of PomA, which is between transmembrane 3 and 4. Although the motor halted following cross-linking, its function was recovered with a reducing reagent that disrupted the disulfide bond. Our results support the hypothesis, which has been inferred from the stator structure, that the plug region terminates the ion inflow by stopping the rotation of the rotor. ImportanceThe flagellar biological motor resembles a mechanical motor, which is composed of stator and rotor and where the rotational force is transmitted by gear-like movements. We hypothesized that the flagellar the rotation of stator that the pentamer of A subunits revolves around the axis of the B subunit dimer with ion flow. The plug region of the B subunit has been shown to regulate the ion flow. Herein, we demonstrated that the ion flow was terminated by the crosslinking between the plug region and the A subunit. These finding support the rotation hypothesis and explain the role of the plug region in terminating the rotation.

microbiology↗

bioRxiv2021

Endogenous retrovirus rewired the gene regulatory network shared between primordial germ cells and naïve pluripotent cells in hominoids

Although the gene regulatory network controlling germ cell development is critical for gamete integrity, this network has been substantially diversified during mammalian evolution. Here, we show that several hundred loci of LTR5_Hs, a hominoid-specific endogenous retrovirus (ERV), function as enhancers in both human primordial germ cells (PGCs) and naive pluripotent cells. PGCs and naive pluripotent cells exhibit a similar transcriptome signature, and the enhancers derived from LTR5_Hs contribute to establishing such similarity. LTR5_Hs appears to be activated by transcription factors critical in both cell types (KLF4, TFAP2C, NANOG, and CBFA2T2). Comparative transcriptome analysis between humans and macaques suggested that the expression of many genes in PGCs and naive pluripotent cells has been upregulated by LTR5_Hs insertions in the hominoid lineage. Together, this study suggests that LTR5_Hs insertions have rewired and finetuned the gene regulatory network shared between PGCs and naive pluripotent cells during hominoid evolution. TeaserA hominoid-specific ERV has rewired the gene regulatory network shared between PGCs and naive pluripotent cells.

genetics↗

bioRxiv2021

Site-directed crosslinking identifies the stator-rotor interaction surfaces in a hybrid bacterial flagellar motor

The bacterial flagellum is the motility organelle powered by a rotary motor. The rotor and stator elements of the motor are embedded in the cytoplasmic membrane. The stator units assemble around the rotor, and an ion flux (typically H+ or Na+) conducted through a channel of the stator induces conformational changes that generate rotor torque. Electrostatic interactions between the stator protein PomA in Vibrio (MotA in Escherichia coli) and the rotor protein FliG have been suggested by genetic analyses, but have not been demonstrated directly. Here, we used site-directed photo- and disulfide-crosslinking to provide direct evidence for the interaction. We introduced a UV-reactive amino acid, p-benzoyl-L-phenylalanine (pBPA), into the cytoplasmic region of PomA or the C-terminal region of FliG in intact cells. After UV irradiation, pBPA inserted at a number of positions formed a crosslink with FliG. PomA residue K89 gave the highest yield of crosslinks, suggesting that it is the PomA residue nearest to FliG. UV-induced crosslinking stopped motor rotation, and the isolated hook-basal body contained the crosslinked products. pBPA inserted to replace residues R281 or D288 in FliG formed crosslinks with the Escherichia coli stator protein, MotA. A cysteine residue introduced in place of PomA K89 formed disulfide crosslinks with cysteine inserted in place of FliG residues R281 and D288, and some other flanking positions. These results provide the first demonstration of direct physical interaction between specific residues in FliG and PomA/MotA.

microbiology↗

bioRxiv2021

Role of the N- and C-terminal regions of FliF, the MS ring component in Vibrio flagellar basal body

The MS ring is a part of the flagellar basal body and formed by 34 subunits of FliF, which consists of a large periplasmic region and two transmembrane segments connected to the N- and C-terminal regions facing the cytoplasm. A cytoplasmic protein, FlhF, which determines the position and number of the basal body, supports MS ring formation in the membrane. In this study, we constructed FliF deletion mutants that lack 30 or 50 residues at the N-terminus ({Delta}N30 and {Delta}N50), and 83 ({Delta}C83) or 110 residues ({Delta}C110) at the C-terminus. The N-terminal deletions were functional and conferred motility of Vibrio cells, whereas the C-terminal deletions were nonfunctional. The mutants were expressed in Escherichia coli to determine whether an MS ring could still be assembled. When co-expressing {Delta}N30FliF or {Delta}N50FliF with FlhF, fewer MS rings were observed than with the expression of wild-type FliF, in the MS ring fraction, suggesting that the N-terminus interacts with FlhF. MS ring formation is probably inefficient without an additional factor or FlhF. The deletion of the C-terminal cytoplasmic region did not affect the ability of FliF to form an MS ring because a similar number of MS rings were observed for {Delta}C83FliF as with wild-type FliF, although further deletion of the second transmembrane segment ({Delta}C110FliF) abolished it. These results suggest that the terminal regions of FliF have distinct roles; the N-terminal region for efficient MS ring formation and the C-terminal region for MS ring function. The second transmembrane segment is indispensable for MS ring assembly. ImportanceThe bacterial flagellum is a supramolecular architecture involved in cell motility. At the base of the flagella, a rotary motor that begins to construct an MS ring in the cytoplasmic membrane comprises 34 transmembrane proteins (FliF). Here, we investigated the roles of the N and C terminal regions of FliF, which are MS rings. Unexpectedly, the cytoplasmic regions of FliF are not indispensable for the formation of the MS ring, but the N-terminus appears to assist in ring formation through recruitment of FlhF, which is essential for flagellar formation. The C-terminus is essential for motor formation or function.

microbiology↗

bioRxiv2020

One hundred million years history of bornavirus infections hidden in vertebrate genomes

Although viruses have threatened our ancestors for millions of years, prehistoric epidemics of viruses are largely unknown. Endogenous bornavirus-like elements (EBLs) are ancient viral sequences that have been integrated into animal genomes. These elements can be used as molecular fossil records to trace past bornaviral infections. In this study, we systematically identified EBLs in vertebrate genomes and revealed the history of bornavirus infections over nearly 100 million years. We found that ancient bornaviral infections have occurred in diverse vertebrate lineages, especially in primate ancestors. Phylogenetic analyses indicated that primate ancestors had been infected with various bornaviral lineages during evolution. Moreover, EBLs in primate genomes formed clades according to their integration ages, suggesting that epidemic lineages of bornaviruses had changed chronologically. However, we found that some bornaviral lineages coexisted with primate ancestors and underwent repeated endogenizations for tens of millions of years. Furthermore, this viral lineage that coexisted with primate ancestors was also endogenized in some ancestral bats. Notably, the geographic distributions of these bat ancestors have been reported to overlap with the migration route of primate ancestors, suggesting that long-term virus-host coexistence could have expanded the geographic distributions of the viral lineage and might have spread their infections to new hosts. Thus, our findings describe hidden virus-host co-evolutionary history over geological timescales, including chronological change in epidemic bornaviral lineages, long-term virus-host coexistence, and expansion of viral infections.

microbiology↗

bioRxiv2020

Virus-derived variation in diverse human genomes

Acquisition of genetic material from viruses by their hosts can generate inter-host structural genome variation. We developed computational tools enabling us to study virus-derived structural variants (SVs) in population-scale whole genome sequencing (WGS) datasets and applied them to 3,332 humans. Although SVs had already been cataloged in these subjects, we found previously-overlooked virus-derived SVs. We detected somatic SVs present in the sequenced lymphoblastoid cell lines (LCLs) derived from squirrel monkey retrovirus (SMRV), human immunodeficiency virus 1 (HIV-1), and human T lymphotropic virus (HTLV-1); these variants are attributable to infection of LCLs or their progenitor cells and may impact gene expression results and the biosafety of experiments using these cells. In addition, we detected new heritable SVs derived from human herpesvirus 6 (HHV-6) and human endogenous retrovirus-K (HERV-K). We report the first solo-DR HHV-6 that likely to reflects rearrangement of a known full-length endogenous HHV-6. We used linkage disequilibrium between single nucleotide variants (SNVs) and variants in reads that align to HERV-K, which often cannot be mapped uniquely using conventional short-read sequencing analysis methods, to locate previously-unknown polymorphic HERV-K loci. Some of these loci are tightly linked to trait-associated SNVs, some are in complex genome regions inaccessible to prior methods, and some contain novel HERV-K haplotypes likely derived from gene conversion from an unknown source or introgression. These tools and results broaden our perspective on the coevolution between viruses and humans, including ongoing virus-to-human gene transfer contributing to genetic variation between humans.

genetics↗

bioRxiv2020

Identifications of novel avian and mammalian deltaviruses filled the large evolutionally gaps and revealed inter-family transmission of deltaviruses

Hepatitis delta virus (HDV) is a satellite virus that requires hepadnavirus envelope proteins for its transmission. Although recent studies identified HDV-related deltaviruses in certain animals, the evolution of deltaviruses, such as the origin of HDV and the mechanism of its coevolution with its helper viruses, is unknown, mainly because of the phylogenetic gaps among deltaviruses. Here we identified novel deltaviruses of passerine birds, woodchucks, and white-tailed deer by extensive database searches and molecular surveillance. Phylogenetic and molecular epidemiological analyses suggest that HDV originated from mammalian deltaviruses and the past interspecies transmission of mammalian and passerine deltaviruses. Further, metaviromic and experimental analyses suggest that the satellite-helper relationship between HDV and hepadnavirus was established after the divergence of the HDV lineage from non-HDV mammalian deltaviruses. Our findings enhance our understanding of deltavirus evolution, diversity, and transmission, indicating the importance of further surveillance for deltaviruses.

microbiology↗