Redefining high risk multiple myeloma with an APOBEC/Inflammation-based classifier

Graphical Abstract

Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer

A prominent source of mutation in cancer is single-stranded DNA cytosine deamination by cellular APOBEC3 enzymes, which results in signature C-to-T and C-to-G mutations in TCA and TCT motifs. Although multiple enzymes have been implicated, reports conflict and it is unclear which protein(s) are responsible. Here we report the development of a selectable system to quantify genome mutation and demonstrate its utility by comparing the mutagenic activities of three leading candidates-APOBEC3A, APOBEC3B, and APOBEC3H. The human cell line, HAP1, is engineered to express the thymidine kinase (TK) gene of HSV-1, which confers sensitivity to ganciclovir. Expression of APOBEC3A and APOBEC3B, but not catalytic mutant controls or APOBEC3H, triggers increased frequencies of TK mutation and similar TC-biased cytosine mutation profiles in the selectable TK reporter gene. Whole genome sequences from independent clones enabled an analysis of thousands of single base substitution mutations and extraction of local sequence preferences with APOBEC3A preferring YTCW motifs 70% of the time and APOBEC3B 50% of the time (Y = C/T; W = A/T). Signature comparisons with breast tumor whole genome sequences indicate that most malignancies manifest intermediate percentages of APOBEC3 signature mutations in YTCW motifs, mostly between 50 and 70%, suggesting that both enzymes contribute in a combinatorial manner to the overall mutation landscape. Although the vast majority of APOBEC3A- and APOBEC3B-induced single base substitution mutations occur outside of predicted chromosomal DNA hairpin structures, whole genome sequence analyses and supporting biochemical studies also indicate that both enzymes are capable of deaminating the single-stranded loop regions of DNA hairpins at elevated rates. These studies combine to help resolve a long-standing etiologic debate on the source of APOBEC3 signature mutations in cancer and indicate that future diagnostic and therapeutic efforts should focus on both APOBEC3A and APOBEC3B.

APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer

The single-stranded DNA cytosine-to-uracil deaminase APOBEC3B is an antiviral protein implicated in cancer. However, its substrates in cells are not fully delineated. Here APOBEC3B proteomics reveal interactions with a surprising number of R-loop factors. Biochemical experiments show APOBEC3B binding to R-loops in cells and in vitro. Genetic experiments demonstrate R-loop increases in cells lacking APOBEC3B and decreases in cells overexpressing APOBEC3B. Genome-wide analyses show major changes in the overall landscape of physiological and stimulus-induced R-loops with thousands of differentially altered regions, as well as binding of APOBEC3B to many of these sites. APOBEC3 mutagenesis impacts genes overexpressed in tumors and splice factor mutant tumors preferentially, and APOBEC3-attributed kataegis are enriched in RTCW motifs consistent with APOBEC3B deamination. Taken together with the fact that APOBEC3B binds single-stranded DNA and RNA and preferentially deaminates DNA, these results support a mechanism in which APOBEC3B regulates R-loops and contributes to R-loop mutagenesis in cancer.

Primary mucosal melanomas of the head and neck are characterised by overexpression of the DNA mutating enzyme APOBEC3B

AIMS

Primary head/neck mucosal melanomas (MMs) are rare and exhibit aggressive biologic behaviour and elevated mutational loads. The molecular mechanisms responsible for high genomic instability observed in head/neck MMs remain elusive. The DNA cytosine deaminase APOBEC3B (A3B) constitutes a major endogenous source of mutation in human cancer. A3B-related mutations are identified through C-to-T/-G base substitutions in 5'-TCA/T motifs. Herein, we present immunohistochemical and genomic data supportive of a role for A3B in head/neck MMs.

METHODS AND RESULTS

A3B protein levels were assessed in oral (n = 13) and sinonasal (n = 13) melanomas, and oral melanocytic nevi (n = 13) by immunohistochemistry using a custom rabbit α-A3B mAb (5210-87-13). Heterogeneous, selective-to-diffuse, nuclear only, A3B immunopositivity was observed in 12 of 13 (92.3%) oral melanomas (H-score range = 9-72, median = 40) and 8 of 13 (62%) sinonasal melanomas (H-score range = 1-110, median = 24). Two cases negative for A3B showed prominent cytoplasmic staining consistent with A3G. A3B protein levels were significantly higher in oral and sinonasal MMs than intraoral melanocytic nevi (P < 0.0001 and P = 0.0022, respectively), which were A3B-negative (H-score range = 1-8, median = 4). A3B levels, however, did not differ significantly between oral and sinonasal tumours (P > 0.99). NGS performed in 10 sinonasal MMs revealed missense NRAS mutations in 50% of the studied cases and one each KIT and HRAS mutations. Publicly available whole-genome sequencing (WGS) data disclosed that the number of C-to-T mutations and APOBEC3 enrichment score were markedly elevated in head/neck MMs (n = 2).

CONCLUSION

The above data strongly indicate a possible role for the mutagenic enzyme A3B in head/neck melanomagenesis, but not benign melanocytic neoplasms.

Abstract 925: A genetically engineered mouse model for carcinogenesis by the human enzyme APOBEC3B

Introduction: Advanced DNA sequencing technologies have revealed a substantial endogenous source of mutations in cancers, the human DNA-mutating enzyme APOBEC3B (A3B). This protein changes DNA cytosines into uracils (C-to-U), which can become “immortalized” in the genome as C-to-T or C-to-G mutations depending on how each uracil lesion is processed. However, mice lack analogous carcinogenic A3 enzymes, which makes a definitive cause-and-effect model of A3-induced carcinogenesis difficult to establish.

Results: Using C57BL/6 mice, we have generated a novel genetically engineered mouse model (GEMM) expressing the human protein A3B, where it is driven constitutively from the Rosa26 locus in combination with the strong synthetic CAG promoter. Importantly, tumor-free survival data suggest that CAG A3B mice develop tumors at an increased rate compared to wild-type mice. These CAG A3B mice develop predominantly lymphoid neoplasms including B- and T-cell lymphomas and marked splenomegaly, and less frequently lung and liver cancers. Using immunohistochemical and whole-genome sequencing techniques, we have further characterized the tumors arising in these novel GEMMs. The above analyses thus far have revealed that A3B is actively driving tumor formation, as seen by an enrichment of canonical APOBEC-related mutations in these cancers.

Conclusion: Overall, the CAG A3B mice are the first GEMMs demonstrating the potential for A3B to drive tumor formation in vivo, with a predilection towards blood malignancies. They will be an invaluable tool for characterizing A3B-driven mutational processes in an organism and testing novel therapeutic strategies against APOBEC-induced cancer initiation and progression.

Citation Format: Cameron C. Durfee, Prokopios P. Argyris, Matthew C. Jarvis, Rena Levin-Klein, Emily K. Law, Reuben S. Harris. A genetically engineered mouse model for carcinogenesis by the human enzyme APOBEC3B [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 925.

Abstract P5-12-01: Apobec mutation signature in breast cancer explained by combinatorial action of apobec3a and apobec3b

Background: Mutations drive the initiation and progression of cancer. A leading druggable source of mutation in cancer is enzymatic deamination of single-stranded DNA cytosines by cellular APOBEC3 enzymes. Cytosine-to-uracil deamination can result in a variety of different mutational outcomes including DNA breakage and chromosomal aberrations as well as single base substitution mutations. The latter are comprised of C-to-T and C-to-G mutations in TCA or TCT trinucleotides and attributable to the intrinsic preference of several APOBEC3 family members for binding to these motifs. This mutation pattern, commonly called the “APOBEC signature”, is evident in approximately one-quarter of primary breast tumors and one-third of metastatic breast tumors. Although multiple APOBEC3 enzymes have been implicated as a source of this signature in breast cancer (namely, APOBEC3A, APOBEC3B, and APOBEC3H), the literature is full of conflicting views and it is not clear which of these enzymes contributes most significantly to the mutational landscape of breast cancer. Methods: The near-haploid human cell line, HAP1, was engineered to express the HSV-1 TK gene as a mutation reporter. Candidate APOBEC3 enzymes were expressed individually and confirmed by immunoblotting and activity assays. DNA breakage was measured directly by COMET assays and DNA damage responses indirectly by phosphorylated gamma-H2AX staining. Mutation frequencies were quantified by assaying rates of drug resistance, and mutation patterns were analyzed by sequencing locally in TK and globally across whole genomes. Results: APOBEC3A and APOBEC3B both caused significant increases in chromosomal DNA breakage and DNA damage responses. These enzymes also elevated drug resistance mutation frequencies. In contrast, expression of active APOBEC3H or catalytic mutant derivatives of APOBEC3A and APOBEC3B failed to trigger increases beyond normal spontaneous levels. Interestingly, APOBEC3A and APOBEC3B both inflicted mutation signatures that were indistinguishable locally in TK and globally across whole genomes. The vast majority of these APOBEC signature mutations were dispersed (non-kataegic) and not associated with obvious mesoscale chromosomal features such as single-stranded loop regions of stem-loop structures. Computational comparisons of the broader pentanucleotide APOBEC3A and APOBEC3B mutation signatures and those extracted from 794 primary breast tumor genomes (ICGC cohort) revealed an APOBEC3A-biased subset, an APOBEC3B-biased subset, and a larger group of tumors best explained by combinatorial action of both of these enzymes. Conclusions: Our results indicate that APOBEC3A and APOBEC3B contribute combinatorially in most instances to the observed APOBEC mutation signature in breast cancer. These results provide a framework for developing diagnostic and therapeutic approaches for APOBEC-positive breast cancer.

Citation Format: Reuben S Harris, Matthew C Jarvis, Michael A Carpenter, Margaret R Brown, Prokopios P Argyris, William Brown, Douglas Yee. Apobec mutation signature in breast cancer explained by combinatorial action of apobec3a and apobec3b [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-12-01.

APOBEC3A catalyzes mutation and drives carcinogenesis in vivo

The APOBEC3 family of antiviral DNA cytosine deaminases is implicated as the second largest source of mutation in cancer. This mutational process may be a causal driver or inconsequential passenger to the overall tumor phenotype. We show that human APOBEC3A expression in murine colon and liver tissues increases tumorigenesis. All other APOBEC3 family members, including APOBEC3B, fail to promote liver tumor formation. Tumor DNA sequences from APOBEC3A-expressing animals display hallmark APOBEC signature mutations in TCA/T motifs. Bioinformatic comparisons of the observed APOBEC3A mutation signature in murine tumors, previously reported APOBEC3A and APOBEC3B mutation signatures in yeast, and reanalyzed APOBEC mutation signatures in human tumor datasets support cause-and-effect relationships for APOBEC3A-catalyzed deamination and mutagenesis in driving multiple human cancers.

Characterization of the mechanism by which the RB/E2F pathway controls expression of the cancer genomic DNA deaminase APOBEC3B

APOBEC3B (A3B)-catalyzed DNA cytosine deamination contributes to the overall mutational landscape in breast cancer. Molecular mechanisms responsible for A3B upregulation in cancer are poorly understood. Here we show that a single E2F cis-element mediates repression in normal cells and that expression is activated by its mutational disruption in a reporter construct or the endogenous A3B gene. The same E2F site is required for A3B induction by polyomavirus T antigen indicating a shared molecular mechanism. Proteomic and biochemical experiments demonstrate the binding of wildtype but not mutant E2F promoters by repressive PRC1.6/E2F6 and DREAM/E2F4 complexes. Knockdown and overexpression studies confirm the involvement of these repressive complexes in regulating A3B expression. Altogether, these studies demonstrate that A3B expression is suppressed in normal cells by repressive E2F complexes and that viral or mutational disruption of this regulatory network triggers overexpression in breast cancer and provides fuel for tumor evolution.

The DNA Cytosine Deaminase APOBEC3B is a Molecular Determinant of Platinum Responsiveness in Clear Cell Ovarian Cancer

PURPOSE

Clear cell ovarian carcinoma (CCOC) is an aggressive disease that often demonstrates resistance to standard chemotherapies. Approximately 25% of patients with CCOC show a strong APOBEC mutation signature. Here, we determine which APOBEC3 enzymes are expressed in CCOC, establish clinical correlates, and identify a new biomarker for detection and intervention.

EXPERIMENTAL DESIGNS

APOBEC3 expression was analyzed by IHC and qRT-PCR in a pilot set of CCOC specimens (n = 9 tumors). The IHC analysis of APOBEC3B was extended to a larger cohort to identify clinical correlates (n = 48). Dose-response experiments with platinum-based drugs in CCOC cell lines and carboplatin treatment of patient-derived xenografts (PDXs) were done to address mechanistic linkages.

RESULTS

One DNA deaminase, APOBEC3B, is overexpressed in a formidable subset of CCOC tumors and is low or absent in normal ovarian and fallopian tube epithelial tissues. High APOBEC3B expression associates with improved progression-free survival (P = 0.026) and moderately with overall survival (P = 0.057). Cell-based studies link APOBEC3B activity and subsequent uracil processing to sensitivity to cisplatin and carboplatin. PDX studies extend this mechanistic relationship to CCOC tissues.

CONCLUSIONS

These studies demonstrate that APOBEC3B is overexpressed in a subset of CCOC and, contrary to initial expectations, associated with improved (not worse) clinical outcomes. A likely molecular explanation is that APOBEC3B-induced DNA damage sensitizes cells to additional genotoxic stress by cisplatin. Thus, APOBEC3B is a molecular determinant and a candidate predictive biomarker of the therapeutic response to platinum-based chemotherapy. These findings may have broader translational relevance, as APOBEC3B is overexpressed in many different cancer types.

A Conserved Mechanism of APOBEC3 Relocalization by Herpesviral Ribonucleotide Reductase Large Subunits

An integral part of the antiviral innate immune response is the APOBEC3 family of single-stranded DNA cytosine deaminases, which inhibits virus replication through deamination-dependent and -independent activities. Viruses have evolved mechanisms to counteract these enzymes, such as HIV-1 Vif-mediated formation of a ubiquitin ligase to degrade virus-restrictive APOBEC3 enzymes. A new example is Epstein-Barr virus (EBV) ribonucleotide reductase (RNR)-mediated inhibition of cellular APOBEC3B (A3B). The large subunit of the viral RNR, BORF2, causes A3B relocalization from the nucleus to cytoplasmic bodies and thereby protects viral DNA during lytic replication. Here, we use coimmunoprecipitation and immunofluorescence microscopy approaches to ask whether this mechanism is shared with the closely related gammaherpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) and the more distantly related alphaherpesvirus herpes simplex virus 1 (HSV-1). The large RNR subunit of KSHV, open reading frame 61 (ORF61), coprecipitated multiple APOBEC3s, including A3B and APOBEC3A (A3A). KSHV ORF61 also caused relocalization of these two enzymes to perinuclear bodies (A3B) and to oblong cytoplasmic structures (A3A). The large RNR subunit of HSV-1, ICP6, also coprecipitated A3B and A3A and was sufficient to promote the relocalization of these enzymes from nuclear to cytoplasmic compartments. HSV-1 infection caused similar relocalization phenotypes that required ICP6. However, unlike the infectivity defects previously reported for BORF2-null EBV, ICP6 mutant HSV-1 showed normal growth rates and plaque phenotypes. Combined, these results indicate that both gamma- and alphaherpesviruses use a conserved RNR-dependent mechanism to relocalize A3B and A3A and furthermore suggest that HSV-1 possesses at least one additional mechanism to neutralize these antiviral enzymes.IMPORTANCE The APOBEC3 family of DNA cytosine deaminases constitutes a vital innate immune defense against a range of different viruses. A novel counterrestriction mechanism has recently been uncovered for the gammaherpesvirus EBV, in which a subunit of the viral protein known to produce DNA building blocks (ribonucleotide reductase) causes A3B to relocalize from the nucleus to the cytosol. Here, we extend these observations with A3B to include a closely related gammaherpesvirus, KSHV, and a more distantly related alphaherpesvirus, HSV-1. These different viral ribonucleotide reductases also caused relocalization of A3A, which is 92% identical to A3B. These studies are important because they suggest a conserved mechanism of APOBEC3 evasion by large double-stranded DNA herpesviruses. Strategies to block this host-pathogen interaction may be effective for treating infections caused by these herpesviruses.

The deaminase APOBEC3B triggers the death of cells lacking uracil DNA glycosylase

Human cells express up to 9 active DNA cytosine deaminases with functions in adaptive and innate immunity. Many cancers manifest an APOBEC mutation signature and APOBEC3B (A3B) is likely the main enzyme responsible. Although significant numbers of APOBEC signature mutations accumulate in tumor genomes, the majority of APOBEC-catalyzed uracil lesions are probably counteracted in an error-free manner by the uracil base excision repair pathway. Here, we show that A3B-expressing cells can be selectively killed by inhibiting uracil DNA glycosylase 2 (UNG) and that this synthetic lethal phenotype requires functional mismatch repair (MMR) proteins and p53. UNG knockout human 293 and MCF10A cells elicit an A3B-dependent death. This synthetic lethal phenotype is dependent on A3B catalytic activity and reversible by UNG complementation. A3B expression in UNG-null cells causes a buildup of genomic uracil, and the ensuing lethality requires processing of uracil lesions (likely U/G mispairs) by MSH2 and MLH1 (likely noncanonical MMR). Cancer cells expressing high levels of endogenous A3B and functional p53 can also be killed by expressing an UNG inhibitor. Taken together, UNG-initiated base excision repair is a major mechanism counteracting genomic mutagenesis by A3B, and blocking UNG is a potential strategy for inducing the selective death of tumors.

HIV-1 restriction by endogenous APOBEC3G in the myeloid cell line THP-1

HIV-1 replication in CD4-positive T lymphocytes requires counteraction of multiple different innate antiviral mechanisms. Macrophage cells are also thought to provide a reservoir for HIV-1 replication but less is known in this cell type about virus restriction and counteraction mechanisms. Many studies have combined to demonstrate roles for APOBEC3D, APOBEC3F, APOBEC3G and APOBEC3H in HIV-1 restriction and mutation in CD4-positive T lymphocytes, whereas the APOBEC enzymes involved in HIV-1 restriction in macrophages have yet to be delineated fully. We show that multiple APOBEC3 genes including APOBEC3G are expressed in myeloid cell lines such as THP-1. Vif-deficient HIV-1 produced from THP-1 is less infectious than Vif-proficient virus, and proviral DNA resulting from such Vif-deficient infections shows strong G to A mutation biases in the dinucleotide motif preferred by APOBEC3G. Moreover, Vif mutant viruses with selective sensitivity to APOBEC3G show Vif null-like infectivity levels and similarly strong APOBEC3G-biased mutation spectra. Importantly, APOBEC3G-null THP-1 cells yield Vif-deficient particles with significantly improved infectivities and proviral DNA with background levels of G to A hypermutation. These studies combine to indicate that APOBEC3G is the main HIV-1 restricting APOBEC3 family member in THP-1 cells.

Evolution of rotavirus C in humans and several domestic animal species

Rotavirus C (RVC) causes enteric disease in multiple species, including humans, swine, bovines, and canines. To date, the evolutionary relationships of RVC populations circulating in different host species are poorly understood, owing to the low availability of genetic sequence data. To address this gap, we sequenced 45 RVC complete genomes from swine samples collected in the United States and Mexico. A phylogenetic analysis of each genome segment indicates that RVC populations have been evolving independently in human, swine, canine, and bovine hosts for at least the last century, with inter-species transmission events occurring deep in the phylogenetic tree, and none in the last 100 years. Bovine and canine RVC populations clustered together nine of the 11 gene segments, indicating a shared common ancestor centuries ago. The evolutionary relationships of RVC in humans and swine were more complex, due to the extensive genetic diversity and multiple RVC clades identified in pigs, which were not structured geographically. Topological differences between trees inferred for different genome segments occurred frequently, including at nodes deep in the tree, indicating that RVC's evolutionary history includes multiple reassortment events that occurred a long time ago. Overall, we find that RVC is evolving within host-defined lineages, but the evolutionary history of RVC is more complex than previously recognized due to the high genetic diversity of RVC in swine, with a common ancestor dating back centuries. Pigs may act as a reservoir host for RVC, and a source of the lineages identified in other species, including humans, but additional sequencing is needed to understand the full diversity of this understudied pathogen across multiple host species.

Epstein-Barr virus BORF2 inhibits cellular APOBEC3B to preserve viral genome integrity

The APOBEC family of single-stranded (ss)DNA cytosine deaminases provides innate immunity against virus and transposon replication^1–4. A well-studied mechanism is APOBEC3G restriction of HIV-1, which is counteracted by a virus-encoded degradation mechanism^1–4. Accordingly, most work has focused on retroviruses with obligate ssDNA replication intermediates and it is unclear whether large double-stranded (ds)DNA viruses may be similarly susceptible to restriction. Here, we show that the large dsDNA herpesvirus Epstein-Barr virus (EBV), which is the causative agent of infectious mononucleosis and multiple cancers⁵, utilizes a two-pronged approach to counteract restriction by APOBEC3B. The large subunit of the EBV ribonucleotide reductase, BORF2^6,7, bound to APOBEC3B in proteomics studies and immunoprecipitation experiments. Mutagenesis mapped the interaction to the APOBEC3B catalytic domain, and biochemical studies demonstrated that BORF2 stoichiometrically inhibits APOBEC3B DNA cytosine deaminase activity. BORF2 also caused a dramatic relocalization of nuclear APOBEC3B to perinuclear bodies. Upon lytic reactivation, BORF2-null viruses were susceptible to APOBEC3B-mediated deamination as evidenced by lower viral titers, lower infectivity, and hypermutation. The Kaposi’s sarcoma herpesvirus (KSHV) homolog, ORF61, also bound APOBEC3B and mediated relocalization. These data support a model in which the genomic integrity of human γ-herpesviruses is maintained by active neutralization of the antiviral enzyme APOBEC3B.

Mutation Signatures Including APOBEC in Cancer Cell Lines

Background:

Multiple endogenous and exogenous sources of DNA damage contribute to the overall mutation burden in cancer, with distinct and overlapping combinations contributing to each cancer type. Many mutation sources result in characteristic mutation signatures, which can be deduced from tumor genomic DNA sequences. Examples include spontaneous hydrolytic deamination of methyl-cytosine bases in CG motifs (AGEING signature) and C-to-T and C-to-G mutations in 5'-TC(A/T) motifs (APOBEC signature).

Methods:

The deconstructSigs R package was used to analyze single-base substitution mutation signatures in more than 1000 cancer cell lines. Two additional approaches were used to analyze the APOBEC mutation signature.

Results:

Most cell lines show evidence for multiple mutation signatures. For instance, the AGEING signature, which is the largest source of mutation in most primary tumors, predominates in the majority of cancer cell lines. The APOBEC mutation signature is enriched in cancer cell lines from breast, lung, head/neck, bladder, and cervical cancers, where this signature also comprises a large fraction of all mutations.

Conclusions:

The single-base substitution mutation signatures of cancer cell lines often reflect those of the original tumors from which they are derived. Cancer cell lines with enrichments for distinct mutation signatures such as APOBEC have the potential to become model systems for fundamental research on the underlying mechanisms and for advancing clinical strategies to exploit these processes.

Genotypic and epitope characteristics of group A porcine rotavirus strains circulating in Canada

Surveillance of Rotavirus A (RVA) infections in North America swine populations are limited and not performed over a significant time period to properly assess the diversity of RVA strains in swine. The VP7 (G) and VP4 (P) genes of 32 Canadian RVA strains, circulating between 2009 and 2015 were sequenced, identifying the G3P[13], G5P[7], G9P[7], G9[13], and G9[19] genotype combinations. The Canadian RVA strains were compared to the RVA strains present in the swine ProSystems RCE rotavirus vaccine. The comparison revealed multiple amino acid differences in the G and P antigenic epitopes, regardless of the G and P genotypes but specifically in the Canadian G3, P[13] and P[19] genotypes. Our study further contributes to the characterization of RVA's evolution and disease mitigation among swine, which may optimize target vaccine design, thereby minimizing RVA disease in this economically important animal population.

Complete Genome Sequence of Porcine Epidemic Diarrhea Virus Strain COL/Cundinamarca/2014 from Colombia

Porcine epidemic diarrhea virus (PEDV) has been found throughout Europe and Asia, and has emerged in North and South America. A whole genome sequence was obtained from a paraffin-embedded tissue sample from the Instituto Colombiano Agropecuario (ICA), Colombia through Next Generation Sequencing techniques to further understand the evolution of PEDV.

Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus

Porcine epidemic diarrhea virus (PEDV) has caused severe economic losses both recently in the United States (US) and historically throughout Europe and Asia. Traditionally, analysis of the spike gene has been used to determine phylogenetic relationships between PEDV strains. We determined the complete genomes of 93 PEDV field samples from US swine and analyzed the data in conjunction with complete genome sequences available from GenBank (n=126) to determine the most variable genomic areas. Our results indicate high levels of variation within the ORF1 and spike regions while the C-terminal domains of structural genes were highly conserved. Analysis of the Receptor Binding Domains in the spike gene revealed a limited number of amino acid substitutions in US strains compared to Asian strains. Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. These finding suggest that significant genetic events outside of the spike region have contributed to the evolution of PEDV.

Modelling polymer interactions of the 'molecular Velcro' type in wood under mechanical stress

Trees withstand wind and snow loads by synthesising wood that varies greatly in mechanical properties: flexible in twigs and in the stem of the sapling, and rigid in the outer part of the mature stem. The 'molecular Velcro' model of Keckes et al. [2003. Cell-wall recovery after irreversible deformation of wood. Nat. Mater. 2, 810-814] permits the simulation of the tensile properties of water-saturated wood as found in living trees. A basic feature of this model is the presence of non-covalent interactions between hemicellulose chains attached to adjacent cellulose microfibrils, which are disrupted above a threshold level of interfibrillar shear. However, other evidence does not confirm the importance of hemicellulose-hemicellulose association in the cohesion of the interfibrillar matrix. Here, we present an alternative model in which hemicellulose chains bridging continuously from one microfibril aggregate (macrofibril) to the next provide most of the cohesion. We show that such hemicellulose bridges exist and that the stripping of the bridging chains from the cellulose surfaces under the tensile stress component normal to the macrofibrils can provide an alternative triggering mechanism for shear deformation between one macrofibril and the next. When one macrofibril then slides past another, a domain of the wood cell wall can extend but simultaneously it twists until the spacing between macrofibrils is reduced again and contact through hemicelluloses bridges is restored. Overall deformation therefore takes place through a series of local stick-slip events involving temporary twisting of small domains within the wood cell wall. Modelled load-deformation curves for this modified 'molecular Velcro' model are similar, although not identical, to those for the original model. However, the mechanism is different and more consistent with current views of the structure of wood cell walls, providing a framework within which the developmental control of rigidity in wood synthesised in different parts of a tree may be considered.

Lignification in relation to the biennial growth habit in brassicas

The forage brassicas are a useful model system for the study of wood formation because the thickened cell walls of their vascular tissue can vary widely in lignin content. Solid-state 13C NMR spectroscopy was used to quantify lignin, and determine features of its structure, in the vascular cell walls of forage rape (Brassica napus L.), and Thousandhead and marrowstem cultivars of kale (Brassica oleracea L. var. acephala). During the first season of vegetative growth, lignin levels in these cell walls remained low in the upper part of the stems despite the physical resemblance of this tissue to wood. The extended flowering stems produced in the following year were thinner and their vascular tissue contained much more strongly lignified cell walls. The structure of the lignin was typical of angiosperm wood. It showed only small variations in syringyl/guaiacyl ratio, but this ratio increased with lignin content and thus with the proportion of the lignin that was associated with secondary cell-wall layers.

Developmental regulation of pectic epitopes during potato tuberisation

We show, by immunogold labelling, that potato (Solanum tuberosum L. cv Karnico) pectic epitopes are developmentally regulated within regions of the stolon, in addition to showing tissue-specific differences in abundance and localisation. The (1-->4)-beta-D-galactan and (1-->5)-alpha-arabinan epitopes demarcate two distinct zones within stolons; galactans are enriched in primary walls of elongating cells proximal to the stolon hook, whilst arabinans predominate in younger cells distal to the hook. Low-methoxyl homogalacturonan epitopes are concentrated in the middle lamella and show a proximo-distal gradient in stolons similar to that of galactans, whilst high-methoxyl homogalacturonan is uniformly abundant. Calcium pectate is restricted to the middle lamella at cell corners and pit fields. Calcium-binding sites are uniformly present in stolon cell walls, but their total density is reduced and they become localised to a few cell corners in mature tubers, as determined by image-electron energy loss spectroscopy. During the transition from elongation growth to isodiametric expansion during tuberisation of the stolon hook, there were no detectable changes in pectic epitope abundance or localisation. As tubers matured, all epitopes increased in abundance in parenchymal cell walls, except for calcium pectate. We conclude that potentially significant changes in pectic composition occur as young cells distal to the stolon hook move into the zone of cell elongation proximal to the hook.

Altered middle lamella homogalacturonan and disrupted deposition of (1-->5)-alpha-L-arabinan in the pericarp of Cnr, a ripening mutant of tomato

Cnr (colorless non-ripening) is a pleiotropic tomato (Lycopersicon esculentum) fruit ripening mutant with altered tissue properties including weaker cell-to-cell contacts in the pericarp (A.J. Thompson, M. Tor, C.S. Barry, J. Vrebalov, C. Orfila, M.C. Jarvis, J.J. Giovannoni, D. Grierson, G.B. Seymour [1999] Plant Physiol 120: 383-390). Whereas the genetic basis of the Cnr mutation is being identified by molecular analyses, here we report the identification of cell biological factors underlying the Cnr texture phenotype. In comparison with wild type, ripe-stage Cnr fruits have stronger, non-swollen cell walls (CW) throughout the pericarp and extensive intercellular space in the inner pericarp. Using electron energy loss spectroscopy imaging of calcium-binding capacity and anti-homogalacturonan (HG) antibody probes (PAM1 and JIM5) we demonstrate that maturation processes involving middle lamella HG are altered in Cnr fruit, resulting in the absence or a low level of HG-/calcium-based cell adhesion. We also demonstrate that the deposition of (1-->5)-alpha-L-arabinan is disrupted in Cnr pericarp CW and that this disruption occurs prior to fruit ripening. The relationship between the disruption of (1-->5)-alpha-L-arabinan deposition in pericarp CW and the Cnr phenotype is discussed.

A definition for dietary fibre

The objective of this paper is to present a definition for dietary fibre based on recent advances that have taken place not only in human nutrition but also in plant cell-wall science and animal nutrition. We propose a physiologically based framework definition but, recognizing the diversity of dietary fibre, we have proposed further classifications within this framework. We also suggest that dietary fibre be removed from the carbohydrate group of nutrients because some compounds defined as dietary fibre are not chemically carbohydrates. The definition and classification system clearly highlight areas where further studies are needed.

Interconversion of the Ialpha and Ibeta crystalline forms of cellulose by bending

Bending cellulose in a plane normal to the hydrogen-bonded sheets of chains causes a longitudinal displacement of the sheets with respect to one another. The magnitude of this displacement is shown to be sufficient to interconvert the Ialpha and Ibeta forms of cellulose within a bending angle of 39 degrees when the curvature of the sheets of chains comprising the microfibril is modelled as a series of concentric circular arcs. Bending through an angle of 90 degrees is more than sufficient to convert the Ialpha form into Ibeta and back again. Cellulose microfibrils emerging from the cellulose synthase complex in the plasma membrane must bend sharply before they can lie parallel with the inner face of the cell wall. The scale of the changes induced by bending is sufficient to ensure that whatever crystal form would be expected from the geometry of the biosynthetic complex, it is likely be radically altered before the cellulose is incorporated into the cell wall.

Molecular and genetic characterization of a novel pleiotropic tomato-ripening mutant

In this paper we describe a novel, dominant pleiotropic tomato (Lycopersicon esculentum)-ripening mutation, Cnr (colorless nonripening). This mutant occurred spontaneously in a commercial population. Cnr has a phenotype that is quite distinct from that of the other pleiotropic tomato-ripening mutants and is characterized by fruit that show greatly reduced ethylene production, an inhibition of softening, a yellow skin, and a nonpigmented pericarp. The ripening-related biosynthesis of carotenoid pigments was abolished in the pericarp tissue. The pericarp also showed a significant reduction in cell-to-cell adhesion, with cell separation occurring when blocks of tissue were incubated in water alone. The mutant phenotype was not reversed by exposure to exogenous ethylene. Crosses with other mutant lines and the use of a restriction fragment length polymorphism marker demonstrated that Cnr was not allelic with the pleiotropic ripening mutants nor, alc, rin, Nr, Gr, and Nr-2. The gene has been mapped to the top of chromosome 2, also indicating that it is distinct from the other pleiotropic ripening mutants. We undertook the molecular characterization of Cnr by examining the expression of a panel of ripening-related genes in the presence and absence of exogenous ethylene. The pattern of gene expression in Cnr was related to, but differed from, that of several of the other well-characterized mutants. We discuss here the possible relationships among nor, Cnr, and rin in a putative ripening signal cascade.

Polymer mobility in cell walls of cucumber hypocotyls

Cell walls were prepared from the growing region of cucumber (Cucumis sativus) hypocotyls and examined by solid-state 13C NMR spectroscopy, in both enzymically active and inactivated states. The rigidity of individual polymer segments within the hydrated cell walls was assessed from the proton magnetic relaxation parameter, T2, and from the kinetics of cross-polarisation from 1H to 13C. The microfibrils, including most of the xyloglucan in the cell wall, as well as cellulose, behaved as very rigid solids. A minor xyloglucan fraction, which may correspond to cross-links between microfibrils, shared a lower level of rigidity with some of the pectic galacturonan. Other pectins, including most of the galactan side-chain residues of rhamnogalacturonan I, were much more mobile and behaved in a manner intermediate between the solid and liquid states. The only difference observed between the enzymically active and inactive cell walls, was the loss of a highly mobile, methyl-esterified galacturonan fraction, as the result of pectinesterase activity.

Fine structure in cellulose microfibrils: NMR evidence from onion and quince

It has been controversial for many years whether in the cellulose of higher plants, the microfibrils are aggregates of 'elementary fibrils', which have been suggested to be about 3.5 nm in diameter. Solid-state NMR spectroscopy was used to examine two celluloses whose fibril diameters had been established by electron microscopy: onion (8-10 nm, but containing 40% of xyloglucan as well as cellulose) and quince (2 nm cellulose core). Both of these forms of cellulose contained crystalline units of similar size, as estimated from the ratio of surface to interior chains, and the time required for proton magnetisation to diffuse from the surface to the interior. It is suggested that the onion microfibrils must therefore be constructed from a number of cellulose subunits 2 nm in diameter, smaller than the 'elementary fibrils' envisaged previously. The size of these subunits would permit a hexagonal arrangement resembling the cellulose synthase complex.

Structural analysis of cyclamen seed xyloglucan oligosaccharides using cellulase digestion and spectroscopic methods

Xyloglucan polymers have been isolated from cyclamen seeds and characterized by both liquid and CP-MAS 13C NMR spectroscopy. Treatment of the polysaccharides with cellulase from Trichoderma viride afforded XG oligomers which have been studied with both mass spectrometry and NMR spectroscopy. The repeating unit in the intact polymers and the most abundant hydrolysis product correspond to the Gal1 Xyl3 Glc4 (XXLG) fragment. However, detection of notable amounts of Xyl3 Glc4 (XXXG) and Gal2 Xyl3 Glc4 (XLLG) indicates that the galactose distribution in xyloglucan from cyclamen is irregular. FAB-MS analysis of a new derivative, prepared by forming the glycosamine of m-tetrafluoroethoxy aniline, has led to unambiguous sequence information for the XXLG oligomer.

Control of thickness of collenchyma cell walls by pectins

Near-isotropic stresses were generated within collenchyma cell walls of celery (Apium graveolens L.) by exchanging K(+) for Ca(2+) ions, varying the ionic strength and de-esterifying the pectic carboxyl groups, treatments that changed the free-charge density of the pectic polysaccharides. The collenchyma strands swelled radially with increasing free-charge density but there was very little longitudinal swelling. Depolymerising the pectins by β-elimination also induced much more radial than longitudinal swelling. Supported by earlier work on Nitella, these results indicate that pectins control the interlamellar spacing in cell walls and hold them together across their thickness, particularly against turgor stresses tending to delaminate the walls at the cell corners.

Direct observation of cell wall structure in living plant tissues by solid-state C NMR spectroscopy

Solid-state (13)C nuclear magnetic resonance (NMR) spectra of the following intact plant tissues were recorded by the crosspolarization magic-angle spinning technique: celery (Apium graveolens L.) collenchyma; carob bean (Ceratonia siliqua L.), fenugreek (Trigonella foenum-graecum L.), and nasturtium (Tropaeolum majus L.) endosperm; and lupin (Lupinus polyphyllus Lindl.) seed cotyledons. All these tissues had thickened cell walls which allowed them to withstand the centrifugal forces of magic angle spinning and which, except in the case of lupin seeds, dominated the NMR spectra. The celery collenchyma cell walls gave spectra typical of dicot primary cell walls. The carob bean and fenugreek seed spectra were dominated by resonances from galactomannans, which showed little sign of crystalline order. Resonances from beta(1,4')-d galactan were visible in the lupin seed spectrum, but there was much interference from protein. The nasturtium seed spectrum was largely derived from a xyloglucan, in which the conformation of the glucan core chain appeared to be intermediate between the solution form and solid forms of cellulose.

A survey of the pectic content of nonlignified monocot cell walls

The primary cell walls of graminaceous monocots were known to have a low content of pectin compared to those of dicots, but it was uncertain how widespread this feature was within the monocots as a whole. Nonlignified cell walls were therefore prepared from 33 monocot species for determination of their pectin content. It was not possible to solubilize intact pectins quantitatively from the cell walls, and the pectin content was assessed from three criteria: the total uronic acid content; the content of alpha-(1,4')-D-galacturonan isolated by partial hydrolysis and characterized by electrophoresis and degradation by purified polygalacturonase; and the proportion of neutral residues in a representative pectic fraction solubilized by sequential beta-elimination and N,N,N'N'-cyclohexanediaminetetraacetic acid extraction. Low galacturonan contents were restricted to species from the Gramineae, Cyperaceae, Juncaceae, and Restionaceae. Other species related to these had intermediate galacturonan contents, and the remainder of the monocots examined had high galacturonan contents comparable with those of dicots. The other criteria of pectin content showed the same pattern.

The proportion of calcium-bound pectin in plant cell walls

The amount of pectin held in cell walls by ionic bonds only was determined by extraction with cyclohexanediamine tetraacetic acid (CDTA) at room temperature, to remove calcium ions without degrading the galacturonan chains. Enzymic degradation was avoided by extracting the cell walls with phenol-acetic acid-water during preparation. From cell walls of celery petioles, cress hypocotyls and tomato and cucumber pericarp CDTA extracted 64-100 mg g(-1) pectin, leaving 80-167 mg g(-1) uronic acid in the residue. An additional extraction at high ionic strength was used to make the galacturonan chains more flexible and thus detach any pectins held by steric interactions, but the amount released in this way was small. Most of the residual uronic acid polymers could be extracted by cold alkali and remained soluble on neutralisation, showing that it was not water-insolubility that prevented their extraction with CDTA. Covalent bonding was thought more likely.

The polysaccharide structure of potato cell walls: Chemical fractionation

Cell walls of potato tubers were fractionated by successive extraction with various reagents. A slightly degraded pectic fraction with 77% galacturonic acid was extracted in hot, oxalate-citrate buffer at pH 4. A further, major pectic fraction with 38% galacturonic acid was extracted in cold 0.1 M Na2CO3 with little apparent degradation. These two pectic fractions together made up 52% of the cell wall. Most of the oxalate-citrate fraction could alternatively be extracted with cold acetate-N,N',N'-tetracetic acid (CDTA) buffer, a non-degradative extractant which nevertheless removed essentially all the calcium ions. This fraction was therefore probably held only by calcium binding, and the remainder of the pectins by covalent bonds. Electrophoresis showed that both pectic fractions contained a range of molecular types differing in composition, with a high arabinose: galactose ratio as well as much galacturonic acid in the most extractable fractions. From methylation data, the main side-chains were 1,4'-linked galactans and 1,5'-linked arabinans, with smaller quantities of covalently attached xyloglucan. Extraction with NaOH-borate removed a small hemicellulose fraction and some cellulose. The main hemicelluloses were apparently a galactoxyloglucan, a mannan or glucomannan and an arabinogalactan.