Structure of Adenovirus Type 21 Knob in Complex with CD46 Reveals Key Differences in Receptor Contacts among Species B Adenoviruses

The complement regulation protein CD46 is the primary attachment receptor for most species B adenoviruses (Ads). However, significant variability exists in sequence and structure among species B Ads in the CD46-binding regions, correlating with differences in affinity. Here, we report a structure-function analysis of the interaction of the species B Ad21 knob with the two N-terminal repeats SCR1 and SCR2 of CD46, CD46-D2. We have determined the structures of the Ad21 knob in its unliganded form as well as in complex with CD46-D2, and we compare the interactions with those observed for the Ad11 knob-CD46-D2 complex. Surface plasmon resonance measurements demonstrate that the affinity of Ad21 knobs for CD46-D2 is 22-fold lower than that of the Ad11 knob. The superposition of the Ad21 and Ad11 knob structures in complex with CD46-D2 reveals a substantially different binding mode, providing an explanation for the weaker binding affinity of the Ad21 knob for its receptor. A critical difference in both complex structures is that a key interaction point, the DG loop, protrudes more in the Ad21 knob than in the Ad11 knob. Therefore, the protruding DG loop does not allow CD46-D2 to approach the core of the Ad21 knob as closely as in the Ad11 knob-CD46-D2 complex. In addition, the engagement of CD46-D2 induces a conformational change in the DG loop in the Ad21 knob but not in the Ad11 knob. Our results contribute to a more profound understanding of the CD46-binding mechanism of species B Ads and have relevance for the design of more efficient gene delivery vectors.The 52 human adenovirus (Ad) serotypes are divided into seven species (species A to G) (20). Species B Ads are of interest, as they cause severe infections of the respiratory tract, urinary tract, and kidney as well as multiorgan system failure and death in immunocompromised patients (2, 23, 24). Species B Ads can be further grouped into subspecies B1 (Ad3, Ad7, Ad16, Ad21, and Ad50) and subspecies B2 (Ad11, Ad14, Ad34, and Ad35). Viruses in the two subspecies differ in their tropisms: while most B1 viruses cause ocular and/or acute respiratory tract infections, the B2 viruses primarily cause persistent infections of the urinary tract as well as eye infections, meningitis, and infections of the gastrointestinal tract (10, 11, 43). The subspecies B1 Ad21, which is the subject of this study, recently caused outbreaks of acute respiratory disease (28).Adenoviruses have a nonenveloped icosahedral capsid with a linear double-stranded DNA (46). The major capsid proteins are the hexon, the penton base, and the fiber. The trimeric fiber protein, which protrudes from each of the 12 capsid vertices, consists of three distinct domains: an N-terminal tail, an elongated shaft, and a globular knob. The knob mediates cellular attachment to the primary receptors CD46 (16, 26, 38), coxsackievirus and adenovirus receptor (CAR) (36), and sialic acid (3). Virus attachment is followed by internalization into the host cell via clathrin-coated endocytosis and macropinocytosis, triggered by αv integrins (17, 27, 45).The species B adenovirus receptor CD46 is a member of a family of proteins that regulate complement activation and are constructed mainly from short consensus repeat (SCR) domains (25). The extracellular portion of CD46 contains four such domains (SCR1 to SCR4), and structural and functional analyses have established that interactions with Ad knobs require only the SCR1 and SCR2 domains (34). The four SCR domains are followed by a 25-amino-acid sequence that is rich in serine, threonine, and proline (the STP region); a single transmembrane segment; and a short cytoplasmic tail. Structural information is currently limited to the N-terminal CD46 domains SCR1 and SCR2. The crystal structure of a fragment comprising these two domains revealed a pronounced kink between the two repeats and some flexibility at the domain interface (7). The protein is expressed on all human cells with the exception of erythrocytes. CD46 acts as a cofactor for factor I, a serine protease that blocks further recruitment of the membrane attack complex by cleaving C3b and C4b (25, 40).CD46 is also a receptor for many other pathogens, including measles virus, human herpesvirus 6, Neisseria gonorrhoeae, Neisseria meningitidis, and group A streptococci (8, 13, 22, 30, 37).The structural analysis of the Ad11 knob in complex with the SCR1-SCR2 fragment of CD46 (CD46-D2) showed that engagement by the knob triggers a conformational change in CD46, producing an elongated, nearly linear conformation that differs substantially from the kinked conformation of the unliganded receptor (34). Furthermore, the structure of this complex provided an explanation for the previously observed critical role of Ad11 knob residue Arg279 in CD46 binding. Earlier mutagenesis studies demonstrated that a mutation of Arg279 to glutamine abolishes binding to CD46-D2 (18). Although the structure of the complex showed that Arg279 does not contact the receptor directly, its side chain lies parallel to that of the CD46-contacting residue Arg280. Stacking interactions between the guanidinium groups of Arg279 and Arg280, resulting in an arginine sandwich, likely play a central role in determining receptor specificity (33), and the mutation of Arg279 is thought to prevent Arg280 from forming contacts with CD46 (18).Although it also uses CD46 as a receptor, the Ad21 knob does not contain an arginine sandwich, as the residue corresponding to Arg279 in Ad11 is a serine. Therefore, the mode of binding of the Ad21 knob to CD46 is likely distinct from that observed for Ad11, consistent with the observation that previously reported mutational studies failed to determine a central binding motif among species B Ads (32, 44). The Ad21 and Ad11 knobs exhibit low sequence identity, especially at the surface loops that mediate binding to CD46 in Ad11. We therefore used a combination of structural and functional studies to establish the mechanism of Ad21 knob binding to CD46-D2. Our structural analysis reveals substantial differences in the numbers and types of contacts between the complexes of Ad11 and Ad21 with CD46-D2 and also in the relative orientations of CD46-D2 and its contacting knobs. Furthermore, our analysis allows the comparison of structural features of the Ad21 and Ad35 knobs, which are closely related in sequence yet also display significantly different CD46-D2-binding properties as well as different tissue tropisms. Thus, our findings result in a significantly enhanced understanding of the interactions between species B Ads and CD46.In addition to their role as pathogens, species B Ads serve as widely used gene delivery vectors, as they can transduce a broad range of possible target cells that are normally poorly permissive to other Ads, such as hematopoietic stem cells, dendritic cells, and malignant tumor cells (19, 41). Therefore, our results should also guide efforts to improve the gene delivery properties of these viruses.     

Mutational Analysis of the Avian Adenovirus CELO, Which Provides a Basis for Gene Delivery Vectors

The avian adenovirus CELO is being developed as a gene transfer tool. Using homologous recombination in Escherichia coli, the CELO genome was screened for regions that could be deleted and would tolerate the insertion of a marker gene (luciferase or enhanced green fluorescent protein). For each mutant genome, the production of viable virus able to deliver the transgene to target cells was monitored. A series of mutants in the genome identified a set of open reading frames that could be deleted but which must be supplied in trans for virus replication. A region of the genome which is dispensable for viral replication and allows the insertion of an expression cassette was identified and a vector based on this mutation was evaluated as a gene delivery reagent. Transduction of avian cells occurs at 10- to 100-fold greater efficiency (per virus particle) than with an adenovirus type 5 (Ad5)-based vector carrying the same expression cassette. Most important for gene transfer applications, the CELO vector transduced mammalian cells as efficiently as an Ad5 vector. The CELO vector is exceptionally stable, can be grown inexpensively in chicken embryos, and provides a useful alternative to Ad5-based vectors.     

An Adenovirus Type 5 Mutant with the Preterminal Protein Gene Deleted Efficiently Provides Helper Functions for the Production of Recombinant Adeno-Associated Virus

Production of recombinant adeno-associated virus (rAAV) requires helper functions that have routinely been provided by infection of the producer cells with adenovirus. Complete removal and/or inactivation of progeny adenovirus, present in such rAAV preparations, presents significant difficulty. Here, we report that an adenovirus type 5 (Ad5) mutant with the preterminal protein (pTP) gene deleted can provide helper function for the growth of rAAV. At high multiplicity, Ad5dl308_ΔpTP was as efficient as the phenotypically wild-type Ad5dl309 in permitting growth of rAAV. Use of Ad5dl308_ΔpTP, which is incapable of replication in the absence of complementation for pTP, as a helper avoids the need to remove contaminating adenovirus infectious activity by heat inactivation or by purification. Comparison of the transducing ability of rAAV generated with either Ad5dl308_ΔpTP or Ad5dl309 as a helper demonstrated that the heat inactivation protocol generally used does not remove all of the helper Ad5dl309 function.     

表达猪圆环病毒2型Cap蛋白重组复制缺陷型人5型腺病毒的构建及小鼠免疫试验

构建表达猪圆环病毒2型Cap蛋白重组复制缺陷型人5型腺病毒,评价其对小鼠免疫效果。本研究将编码PCV2Cap蛋白的ORF2克隆到腺病毒表达系统穿梭质粒,构建了重组穿梭质粒pacAd5CMV-Cap。将被限制性内切酶PacI线性化后的骨架质粒和重组穿梭质粒共转染HEK293AD细胞,两者在真核细胞内同源重组并包装出携带PCV2-Cap基因的复制缺陷型重组人5型腺病毒,命名为rAd5-Cap;以同样方法重组获得了不含任何靶基因的野生型重组腺病毒wt-rAd5。病毒增殖稳定后,rAd5-Cap与wt-rAd5滴度可达到108.5 TCID50/mL左右;一步增殖实验证明,相对于wt-rAd5,rAd5-Cap中Cap基因的引入几乎没有给重组腺病毒增殖造成影响。RT-PCR和间接免疫荧光实验显示,rAd5-Cap能够有效介导PCV2Cap蛋白在真核细胞HEK293AD细胞中表达。以107 TCID50的rAd5-Cap肌肉注射接种小鼠,14d后小鼠血清中产生可检测水平的针对Cap蛋白的体液免疫应答,并且至少在免疫后28d之前抗体水平持续加强。对重组腺病毒的分子生物学鉴定和在小鼠上的初步免疫试验结果表明,重组腺病毒rAd5-Cap可介导Cap蛋白在真核细胞中的表达,并且表达的靶蛋白具有较好的免疫原性,为进一步将其开发成新型PCV2疫苗奠定了基础。     

Footprint Analysis of the RAG Protein Recombination Signal Sequence Complex for V(D)J Type Recombination

We have studied the interaction between recombination signal sequences (RSSs) and protein products of the truncated forms of recombination-activating genes (RAG) by gel mobility shift, DNase I footprinting, and methylation interference assays. Methylation interference with dimethyl sulfate demonstrated that binding was blocked by methylation in the nonamer at the second-position G residue in the bottom strand and at the sixth- and seventh-position A residues in the top strand. DNase I footprinting experiments demonstrated that RAG1 alone, or even a RAG1 homeodomain peptide, gave footprint patterns very similar to those obtained with the RAG1-RAG2 complex. In the heptamer, partial methylation interference was observed at the sixth-position A residue in the bottom strand. In DNase I footprinting, the heptamer region was weakly protected in the bottom strand by RAG1. The effects of RSS mutations on RAG binding were evaluated by DNA footprinting. Comparison of the RAG-RSS footprint data with the published Hin model confirmed the notion that sequence-specific RSS-RAG interaction takes place primarily between the Hin domain of the RAG1 protein and adjacent major and minor grooves of the nonamer DNA.     

Transformation Potentials of the Noninfectious (Defective) Component in Pools of Adenoviruses Type 12 and Simian Adenovirus 7

Pools of adenovirus 12 and simian adenovirus 7 were separated into four or five fractions by density gradient centrifugation in cesium chloride. Each fraction was analyzed for total in vitro infectivity units, total transformation activity, and for total virus particle (VP) content. Two major subpopulations were separated with mean densities of 1.30 +/- 0.02 and 1.34 +/- 0.02 g/ml, respectively. Virions in the 1.34 g/ml range were highly infectious (10(2) to 10(3) VP per infectivity unit) in contrast to virions at 1.30 g/ml density (10(4) to 10(5) VP per infectivity units). Transformation capacity was evenly distributed throughout fractions of both viruses, indicating that genetically incomplete or defective virus particles were not deficient in their ability to induce transformation. The average VP per transformation unit for adenovirus 12 (2.85 x 10(6)) and for simian adenovirus 7 (4.00 x 10(6)) did not vary significantly from fraction to fraction. These values were obtained with optimal input multiplicities of 16 to 64 VP per cell. At higher multiplicities the apparent increase in VP per transformation unit was attributable to the viral cytocidal effect on hamster cells. These studies revealed that quantitation of in vitro transformation based on VP multiplicities was more reliable than on the basis of infectious units. These estimates were independent of method of virus production, extraction, and purification.     

Genetic Analysis of Human Adenovirus Type 7 Strains Circulating in Different Parts of China

To investigate the molecular epidemiology and genetic variation of human adenovirus type 7(HAdV-7) in children with acute respiratory infections(ARI) in China. HAdV-7-positive respiratory samples collected from children with ARI in Beijing, Shijiazhuang, Wenzhou and Guangzhou from 2014–2018 were selected for gene amplification and sequence analysis. Fifty-seven HAdV-7 clinical strains with hexon, penton base and fiber gene sequences were obtained. Meanwhile17 strains were selected randomly from different cities for whole genome sequencing. Phylogenetic and variation analyses were performed based on the obtained sequences, HAdV-7 prototype strain Gomen(AY594255), vaccine strains(AY495969 and AY594256) and representative sequences of strains. The phylogenetic trees constructed based on whole genome sequences, major capsid protein genes(hexon, penton base and fiber) and the early genes(E1, E2, E3 and E4) were not completely consistent. The HAdV-7 strains obtained in this study always clustered with most of the circulating strains worldwide from the 1980 s to the present. Compared with the HAdV-7 prototype strain Gomen(AY594255), some amino acid mutations in loop1 and loop2 of hexon and the RGD loop region of the penton base gene were observed. Recombination analysis showed that partial regions of 55 k Da protein and 100 kDa hexon-assembly associated protein genes among all HAdV-7 strains in this study were from HAdV-16 and HAdV-3, respectively. Our study demonstrated the molecular evolution characteristics of HAdV-7 strains circulating in China and provided basic reference data for the prevention, control and vaccine development of HAdV-7.     

Evidence for Extensive Resistance Gene Transfer among Bacteroides spp. and among Bacteroides and Other Genera in the Human Colon

Transfer of antibiotic resistance genes by conjugation is thought to play an important role in the spread of resistance. Yet virtually no information is available about the extent to which such horizontal transfers occur in natural settings. In this paper, we show that conjugal gene transfer has made a major contribution to increased antibiotic resistance in Bacteroides species, a numerically predominant group of human colonic bacteria. Over the past 3 decades, carriage of the tetracycline resistance gene, tetQ, has increased from about 30% to more than 80% of strains. Alleles of tetQ in different Bacteroides species, with one exception, were 96 to 100% identical at the DNA sequence level, as expected if horizontal gene transfer was responsible for their spread. Southern blot analyses showed further that transfer of tetQ was mediated by a conjugative transposon (CTn) of the CTnDOT type. Carriage of two erythromycin resistance genes, ermF and ermG, rose from <2 to 23% and accounted for about 70% of the total erythromycin resistances observed. Carriage of tetQ and the erm genes was the same in isolates taken from healthy people with no recent history of antibiotic use as in isolates obtained from patients with Bacteroides infections. This finding indicates that resistance transfer is occurring in the community and not just in clinical environments. The high percentage of strains that are carrying these resistance genes in people who are not taking antibiotics is consistent with the hypothesis that once acquired, these resistance genes are stably maintained in the absence of antibiotic selection. Six recently isolated strains carried ermB genes. Two were identical to erm(B)-P from Clostridium perfringens, and the other four had only one to three mismatches. The nine strains with ermG genes had DNA sequences that were more than 99% identical to the ermG of Bacillus sphaericus. Evidently, there is a genetic conduit open between gram-positive bacteria, including bacteria that only pass through the human colon, and the gram-negative Bacteroides species. Our results support the hypothesis that extensive gene transfer occurs among bacteria in the human colon, both within the genus Bacteroides and among Bacteroides species and gram-positive bacteria.     

Molecular Mechanisms of Recombination Restriction in the Envelope Gene of the Human Immunodeficiency Virus

The ability of pathogens to escape the host''s immune response is crucial for the establishment of persistent infections and can influence virulence. Recombination has been observed to contribute to this process by generating novel genetic variants. Although distinctive recombination patterns have been described in many viral pathogens, little is known about the influence of biases in the recombination process itself relative to selective forces acting on newly formed recombinants. Understanding these influences is important for determining how recombination contributes to pathogen genome and proteome evolution. Most previous research on recombination-driven protein evolution has focused on relatively simple proteins, usually in the context of directed evolution experiments. Here, we study recombination in the envelope gene of HIV-1 between primary isolates belonging to subtypes that recombine naturally in the HIV/AIDS pandemic. By characterizing the early steps in the generation of recombinants, we provide novel insights into the evolutionary forces that shape recombination patterns within viral populations. Specifically, we show that the combined effects of mechanistic processes that determine the locations of recombination breakpoints across the HIV-1 envelope gene, and purifying selection acting against dysfunctional recombinants, can explain almost the entire distribution of breakpoints found within this gene in nature. These constraints account for the surprising paucity of recombination breakpoints found in infected individuals within this highly variable gene. Thus, the apparent randomness of HIV evolution via recombination may in fact be relatively more predictable than anticipated. In addition, the dominance of purifying selection in localized areas of the HIV genome defines regions where functional constraints on recombinants appear particularly strong, pointing to vulnerable aspects of HIV biology.     

Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination

The development of an effective human immunodeficiency virus type 1 (HIV-1) vaccine is likely to depend on knowledge of circulating variants of genes other than the commonly sequenced gag and env genes. In addition, full-genome data are particularly limited for HIV-1 subtype C, currently the most commonly transmitted subtype in India and worldwide. Likewise, little is known about sequence variation of HIV-1 in India, the country facing the largest burden of HIV worldwide. Therefore, the objective of this study was to clone and characterize the complete genome of HIV-1 from seroconverters infected with subtype C variants in India. Cocultured HIV-1 isolates were obtained from six seroincident individuals from Pune, India, and virtually full-length HIV-1 genomes were amplified, cloned, and sequenced from each. Sequence analysis revealed that five of the six genomes were of subtype C, while one was a mosaic of subtypes A and C, with multiple breakpoints in env, nef, and the 3′ long terminal repeat as determined by both maximal χ² analysis and phylogenetic bootstrapping. Sequences were compared for preservation of known cytotoxic T lymphocyte (CTL) epitopes. Compared with those of the HIV-1_LAI sequence, 38% of well-defined CTL epitopes were identical. The proportion of nonconservative substitutions for Env, at 61%, was higher (P < 0.001) than those for Gag (24%), Pol (18%), and Nef (32%). Therefore, characterized CTL epitopes demonstrated substantial differences from subtype B laboratory strains, which were most pronounced in Env. Because these clones were obtained from Indian seroconverters, they are likely to facilitate vaccine-related efforts in India by providing potential antigens for vaccine candidates as well as for assays of vaccine responsiveness.     

Genetic Analysis of the Saccharomyces Cerevisiae Rho3 Gene, Encoding a Rho-Type Small Gtpase, Provides Evidence for a Role in Bud Formation

RHO3 encodes a Rho-type small GTPase of the yeast Saccharomyces cerevisiae. We isolated temperature-sensitive alleles and a dominant active allele of RHO3. Ts(-) rho3 cells lost cell polarity during bud formation and grew more isotropically than wild-type cells at nonpermissive temperatures. In contrast, cells carrying a dominant active mutant RHO3 displayed cold sensitivity, and the cells became elongated and bent, often at the position where actin patches were concentrated. These phenotypes of the rho3 mutants strongly suggest that RHO3 is involved in directing the growing points during bud formation. In addition, we found that SRO6, previously isolated as a multicopy suppressor of rho3, is the same as SEC4. The sec4-2 mutation was synthetic lethal with temperature-sensitive rho3 mutations and suppressed the cold sensitivity caused by a dominant active mutant RHO3. The genetic interactions between RHO3 and SEC4, taken together with the fact that the Rab-type GTPase Sec4p is required to fuse secretory vesicles together with plasma membrane for exocytosis, support a model in which the Rho3p pathway modulates morphogenesis during bud growth via directing organization of the actin cytoskeleton and the position of the secretory machinery for exocytosis.     

Analysis of a Recombination Hotspot for Gene Conversion Occurring at the His2 Gene of Saccharomyces Cerevisiae

The properties of gene conversion as measured in fungi that generate asci containing all the products of meiosis imply that meiotic recombination initiates at specific sites. The HIS2 gene of Saccharomyces cerevisiae displays a high frequency of gene conversion, indicating that it is a recombination hotspot. The HIS2 gene was cloned and sequenced, and the cloned DNA was used to make several different types of alterations in the yeast chromosome by transformation; these alterations were used to determine the location of the sequences necessary for the high levels of meiotic conversion observed at HIS2. Previous work indicated that the gene conversion polarity gradient is high at the 3' end of the gene, and that the promoter of the gene is not necessary for the high frequency of conversion observed. Data presented here suggest that at least some of the sequences necessary for high levels of conversion at HIS2 are located over 700 bp downstream of the end of the coding region, extend over (at least) several hundred base pairs, and may be quite complex, perhaps involving chromatin structure. Additional data indicate that multiple single base heterologies within a 1-kb interval contribute little to the frequency of gene conversion. This contrasts with other reports about the role of heterologies at the MAT locus.