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Order Patatavirales
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
Figure 29.2 shows the genomic structure of the Potyviridae family members. As summarized by Wylie et al. (2017), the genomes range from 8.2–11.3 kb, with an average size of 9.7 kb. The most genomes are monopartite, but those of members of the genus Bymovirus are bipartite. The genomes have a VPg of about 24 kDa, which is covalently linked to the 5′- end, while the 3′-terminus is polyadenylated. The encoded large polyprotein is self-cleaved into a set of functional proteins, and the gene order is generally conserved throughout the family.
Molecular Genetic Approaches to Obesity
Published in Claude Bouchard, The Genetics of Obesity, 2020
Streamson C. Chua, Rudolph L. Leibel
Comparative gene mapping between mammals has revealed a striking degree of homology in both chromosomal cytology and gene organization. The most extensive comparisons have been made between man and mouse. In man, over 2300 genes have been mapped and over 10,000 loci defined by DNA markers.16–17 Over 3000 loci (genes, DNA markers) have been mapped in the mouse,18 and more than 600 loci homologous between mouse and man have been identified.19 The mouse is particularly useful in the molecular genetic analysis of single and polygene phenotypes because of the availability of inbred strains, extensive classical genetic resources (phenotype analysis, linkage maps, recombinant inbred strains), and the ability to manipulate the genome using transgenic techniques. The extent of homology between mouse and human genomes ranges from single-locus gene identities to conservations of groups of genes within a region in which gene order may or may not be conserved.
Dynamics of Immunoglobulin and T-cell Receptor Genes Recombinations During Lymphocyte Development
Published in Gérard Chaouat, The Immunology of the Fetus, 2020
Daniele Primi, Evelyne Jouvin-Marche, Raphael A. Clynes, Jean-Pierre Marolleau, Carine Gris, Kenneth B. Marcu, Pierre-André Cazenave
M24T and M24Bm also displayed an unusual γ locus rearrangement. The TcR locus is composed of four known CTγ genes (CTγ1, CTγ2, CTγ3, and CTγ4) and four known VTγ families (VVTγ1, VTγ4, VTγ5, and VTγ6). Each VTγ family has a single member, except for VTγ1, which consists of three genes (VTγ1.1, VTγ1.2, amd VTγ1.3). The analysis of a large panel of T-cells has revealed that: (1) VTγ4, VTγ5, and VTγ6 each rearrange to CTγ1; (2) VTγ1.2 rearranges to CTγ2; (3) VTγ1.1 rearranges to CTγ4; and (4) VTγ3 is linked to CTγ3, which is a pseudogene.30-47 In M24T and M24Bm, both germ-line copies of the CTγ1 gene are replaced by a rearranged 16-kg band. Since the 16-kb rearranged CTγ1 band also hybridized to a VTγ1 probe, this probably represents a VTγ1 to CTγ1 recombination. This would constitute the first example of a γ chain rearrangement that does not follow their clustered gene order because members of the VTγ1 family have only been found to recombine with CTγ2 and CTγ4.47,48 The ability of VTγ genes to rearrange outside their cluster could represent a new important source of diversity for the products of the TcRγ genes.
Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health
Published in Gut Microbes, 2021
Jessica C. Ezeji, Daven K. Sarikonda, Austin Hopperton, Hailey L. Erkkila, Daniel E. Cohen, Sandra P. Martinez, Fabio Cominelli, Tomomi Kuwahara, Armand E. K. Dichosa, Caryn E. Good, Michael R. Jacobs, Mikhail Khoretonenko, Alida Veloo, Alexander Rodriguez-Palacios
Elegantly, Quaiser et al.132 showed through Blast searches that the major capsid protein VP1 sequences from the assembled viral wetland genomes showed similarities to VP1 proteins encoded in the P. merdae and P. distasonis genomes.2 The Parabacteroides VP1 genes show that genes encoding for homolog VP2 and VP4 genes (other capsular phage proteins) were juxtaposed next to the bacterial VP1 genes, supporting the presence of a prophage Microviridae in both Parabacteroides species. Comparing their organization, the identified prophage regions flanking the VP1 gene (5 kbp) were extracted from the genomes and considered circular for analysis, using the VP1 gene as an arbitrary start. Synteny analysis showed, remarkably, that the prophages have the same gene order in such bacteria (P. distasonis: VP1-ORF1-ORF2-ORF3-VP2-VP4, and P. merdae: VP1-ORF1-VP2-VP4) suggesting that both have a common functional prophage ancestor. The gene coding for the arbitrarily assigned protein ORF1 downstream of VP1 in both bacteria were specific to each prophage and did not match to genes from other Microviridae or in NCBI non-redundant databases. This strengthens the hypothesis that these prophages represent a distinct subfamily of Microviridae, suggesting the relevance of this genus and species in water sources previously described.
Identification of a growth factor required for culturing specific fastidious oral bacteria
Published in Journal of Oral Microbiology, 2023
Pallavi Murugkar, Eric Dimise, Eric Stewart, Stéphane N. Viala, Jon Clardy, Floyd E. Dewhirst, Kim Lewis
To determine if other strains of P. pasteri, or strains of other oral species in the genera Porphyromonas and Tannerella, had complete or incomplete menaquinone synthesis pathways, we examined 93 genomes available in the NCBI database, representing 11 oral taxa. The analysis found an operon, composed of menBCDEF, that was either present or absent in each genome. In the 5-gene operon, the gene order was always menFDBCE. The last two genes in the synthetic pathway, menA and ubiE, were present in all genomes but were scattered in the genomes as individual genes. The genome of P. pasteri type strain JCM 30531 and Forsyth strain F0450 lacked the operon for the early pathway as did strain P. pasteri KLE1280. The genomes of all strains of Porphyromonas asaccharolytica, Porphyromonas uenonis and T. forsythia contained the full pathway. P. gingivalis was unique in having some strains with and some strains without the complete pathway. Interestingly, among the 64 strains of P. gingivalis, 31% contained the full pathway while the others had incomplete pathways. Porphyromonas catoniae, Porphyromonas endodontalis, Porphyromonas sp. HMT-275, Porphyromonas sp. HMT-278, Tannerella sp. HMT-286 and Tannerella sp. HMT-808 had incomplete pathways. In P. gingivalis and T. forsythia genomes, each of the genes in the 5-gene operon shared 94–98% identity with those in genomes from other strains of these two species. However, the genes in the operon from P. gingivalis and T. forsythia are only distantly related, <73%, to homologous genes in the 5-gene operon from P. asaccharolytica and P. uenonis. It would therefore appear that this 5-gene operon is gained or lost through horizontal gene transfer rather than passed vertically. Results from this analysis are summarized in Table 3 and a full listing of the proteins identified for each of the 93 strains is available as supplementary Table S1.