scholarly journals Altered 3D chromatin structure permits inversional recombination at the IgH locus

2020 ◽  
Vol 6 (33) ◽  
pp. eaaz8850
Author(s):  
Xiang Qiu ◽  
Fei Ma ◽  
Mingming Zhao ◽  
Yaqiang Cao ◽  
Lillian Shipp ◽  
...  
Keyword(s):  
Regulatory Sequence ◽  
Gene Products ◽  
Dna Rearrangement ◽  
Wild Type ◽  
Gene Assembly ◽  
Igh Locus ◽  
Recombination Activating Gene ◽  
3D Chromatin Structure ◽  
Rag 1 ◽  
And Inversion

Immunoglobulin heavy chain (IgH) genes are assembled by two sequential DNA rearrangement events that are initiated by recombination activating gene products (RAG) 1 and 2. Diversity (DH) gene segments rearrange first, followed by variable (VH) gene rearrangements. Here, we provide evidence that each rearrangement step is guided by different rules of engagement between rearranging gene segments. DH gene segments, which recombine by deletion of intervening DNA, must be located within a RAG1/2 scanning domain for efficient recombination. In the absence of intergenic control region 1, a regulatory sequence that delineates the RAG scanning domain on wild-type IgH alleles, VH and DH gene segments can recombine with each other by both deletion and inversion of intervening DNA. We propose that VH gene segments find their targets by distinct mechanisms from those that apply to DH gene segments. These distinctions may underlie differential allelic choice associated with each step of IgH gene assembly.

scholarly journals Commitment to the B Lymphoid Lineage Occurs before DH-JH Recombination

1999 ◽  
Vol 189 (4) ◽  
pp. 735-740 ◽  
Author(s):  
David Allman ◽  
Jin Li ◽  
Richard R. Hardy
Keyword(s):  
Polymerase Chain Reaction Analysis ◽  
Mouse Bone Marrow ◽  
B Lymphopoiesis ◽  
Lymphoid Lineage ◽  
Igh Locus ◽  
Recombination Activating Gene ◽  
Polymerase Chain ◽  
Rag 1 ◽  
B Lineage ◽  
B Lymphoid

Lineage commitment in B lymphopoiesis remains poorly understood due to the inability to clearly define newly committed B lineage progenitors and their multipotential descendants. We examined the potential of three recently described progenitor populations in adult mouse bone marrow to differentiate into each hematopoietic lineage. The earliest of these, termed fraction (Fr.) A0, exhibited myeloid, erythroid, and B and T lymphoid progenitor activity and included individual cells with myeloid/B lymphoid potential. In sharp contrast, two later populations, termed Frs. A1 and A2 and characterized by surface B220 expression and transcription of the germline immunoglobulin heavy chain (IgH) locus, lacked progenitor activity for all hematopoietic lineages except B lymphocytes. These observations, together with single cell polymerase chain reaction analysis showing a lack of DHJH rearrangements in each population and experiments showing identical precursor potentials when these populations were derived from recombination activating gene (Rag)-1−/− and JH−/− mice, demonstrate that commitment to the B lymphoid lineage occurs before and independently of VHDHJH recombination.

Identification of a baculovirus polyhedron formation mutant with a novel phenotype

1996 ◽  
Vol 54 ◽  
pp. 796-797
Author(s):  
James M. Slavicek ◽  
Melissa J. Mercer ◽  
Mary Ellen Kelly
Keyword(s):  
Viral Gene ◽  
Gene Products ◽  
Type Number ◽  
Infection Cycle ◽  
Wild Type ◽  
Protein Matrix ◽  
Insect Midgut ◽  
Viral Particles ◽  
Budded Virus ◽  
Viral Form

Nucleopolyhedroviruses (NPV, family Baculoviridae) produce two morphological forms, a budded virus form and a viral form that is occluded into a paracrystalline protein matrix. This structure is termed a polyhedron and is composed primarily of the protein polyhedrin. Insects are infected by NPVs after ingestion of the polyhedron and release of the occluded virions through dissolution of the polyhedron in the alkaline environment of the insect midgut. Early after infection the budded virus form is produced. It buds through the plasma membrane and then infects other cells. Later in the infection cycle the occluded form of the virus is generated (reviewed by Blissard and Rohrmann, 1990).The processes of polyhedron formation and virion occlusion are likely to involve a number of viral gene products. However, only two genes, the polyhedrin gene and 25K FP gene, have been identified to date that are necessary for the wild type number of polyhedra to be formed and viral particles occluded.

scholarly journals MALE-SPECIFIC LETHAL MUTATIONS OF DROSOPHILA MELANOGASTER. II. PARAMETERS OF GENE ACTION DURING MALE DEVELOPMENT

Genetics ◽  
1983 ◽  
Vol 105 (4) ◽  
pp. 881-896
Author(s):  
John M Belote
Keyword(s):  
Growth Patterns ◽  
Gene Products ◽  
Wild Type ◽  
Linked Gene ◽  
Lethal Mutations ◽  
Male Specific Lethal ◽  
A Cell ◽  
Type Gene ◽  
Diploid Cells ◽  
Male Specific

ABSTRACT The male-specific lethal mutations (msl's) identify loci whose wild-type gene products are essential for male, but not female, viability. Earlier studies in which X-linked gene activities were monitored in msl/msl male larvae demonstrated that these genes are responsible for setting and/or maintaining the level of X chromosome transcription in males (i.e., they are necessary for proper dosage compensation). The present study examines several important questions concerning their mode of action during development—The results of an examination of the effects of an msl-1 deficiency on male-lethal phase and female viability suggest that this mutation is an amorph, or a severe hypomorph. The effects of rendering a fly mutant for more than one male-lethal mutation were also examined. Multiply mutant flies were no more severely affected than singly mutant ones. A gynandromorph analysis revealed that the male-limited lethality associated with msl-2 has no single lethal focus. Somatic clones of homozygous msl-2 cells were initiated at various times during development by X-ray-induced mitotic recombination. An examination of the viability, growth patterns and morphology of marked clones demonstrated that: (1) msl-2  + acts in a cell autonomous manner, (2) msl-2  + function is required not only in larval (polytene) cells as was shown in previous work but is also needed in the diploid cells that give rise to adult structures, (3) the msl-2  + gene is needed fairly late in development and perhaps continuously, (4) the msl-2 mutation does not affect sexual differentiation.

Multiple GCD genes required for repression of GCN4, a transcriptional activator of amino acid biosynthetic genes in Saccharomyces cerevisiae

1986 ◽  
Vol 6 (11) ◽  
pp. 3990-3998
Author(s):  
S Harashima ◽  
A G Hinnebusch
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Lacz Gene ◽  
Gene Products ◽  
Wild Type ◽  
Double Mutation ◽  
Double Stranded Rna ◽  
Amino Acid Availability ◽  
Genes Encoding ◽  
New Alleles

GCN4 encodes a positive regulator of multiple unlinked genes encoding amino acid biosynthetic enzymes in Saccharomyces cerevisiae. Expression of GCN4 is coupled to amino acid availability by a control mechanism involving GCD1 as a negative effector and GCN1, GCN2, and GCN3 as positive effectors of GCN4 expression. We used reversion of a gcn2 gcn3 double mutation to isolate new alleles of GCD1 and mutations in four additional GCD genes which we designate GCD10, GCD11, GCD12, and GCD13. All of the mutations lead to constitutive derepression of HIS4 transcription in the absence of the GCN2+ and GCN3+ alleles. By contrast, the gcd mutations require the wild-type GCN4 allele for their derepressing effect, suggesting that each acts by influencing the level of GCN4 activity in the cell. Consistent with this interpretation, mutations in each GCD gene lead to constitutive derepression of a GCN4::lacZ gene fusion. Thus, at least five gene products are required to maintain the normal repressed level of GCN4 expression in nonstarvation conditions. Interestingly, the gcd mutations are pleiotropic and also affect growth rate in nonstarvation conditions. In addition, certain alleles lead to a loss of M double-stranded RNA required for the killer phenotype. This pleiotropy suggests that the GCD gene products contribute to an essential cellular function, in addition to, or in conjunction with, their role in GCN4 regulation.

scholarly journals Somatic Hypermutation in the Absence of DNA-Dependent Protein Kinase Catalytic Subunit (DNA-Pkcs) or Recombination-Activating Gene (Rag)1 Activity

2000 ◽  
Vol 192 (10) ◽  
pp. 1509-1514 ◽  
Author(s):  
Mats Bemark ◽  
Julian E. Sale ◽  
Hye-Jung Kim ◽  
Claudia Berek ◽  
Ruth A. Cosgrove ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Somatic Hypermutation ◽  
Cell Receptor ◽  
Catalytic Subunit ◽  
Antigen Receptors ◽  
End Joining ◽  
Dependent Protein Kinase ◽  
Recombination Activating Gene ◽  
Dependent Protein ◽  
Rag 1

Somatic hypermutation and isotype switch recombination occur in germinal center B cells, are linked to transcription, and are similarly affected by deficiency in MutS homologue (MSH)2. Class-switch recombination is abrogated by disruption of genes encoding components of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs)/Ku complex and likely involves nonhomologous end joining (NHEJ). That somatic hypermutation might also be associated with end joining is suggested by its association with the creation of deletions, duplications, and sites accessible to terminal transferase. However, a requirement for NHEJ in the mutation process has not been demonstrated. Here we show that somatic mutation in mice deficient in NHEJ can be tested by introduction of rearranged immunoglobulin and T cell receptor transgenes: the transgene combination not only permits reconstitution of peripheral lymphoid compartments but also allows formation of germinal centers, despite the wholly monoclonal nature of the lymphocyte antigen receptors in these animals. Using this strategy, we confirm that somatic hypermutation like class-switching can occur in the absence of recombination-activating gene (RAG)1 but show that the two processes differ in that hypermutation can proceed essentially unaffected by deficiency in DNA-PKcs activity.

scholarly journals Identification and Functional Analysis of the Gene Cluster for l-Arabinose Utilization in Corynebacterium glutamicum

2009 ◽  
Vol 75 (11) ◽  
pp. 3419-3429 ◽  
Author(s):  
Hideo Kawaguchi ◽  
Miho Sasaki ◽  
Alain A. Vertès ◽  
Masayuki Inui ◽  
Hideaki Yukawa
Keyword(s):  
Growth Rate ◽  
Corynebacterium Glutamicum ◽  
Gene Cluster ◽  
Wild Type Strain ◽  
Transcriptional Regulator ◽  
Transcriptional Unit ◽  
Gene Products ◽  
Wild Type ◽  
Mutant Cells ◽  
Arabinose Isomerase

ABSTRACT Corynebacterium glutamicum ATCC 31831 grew on l-arabinose as the sole carbon source at a specific growth rate that was twice that on d-glucose. The gene cluster responsible for l-arabinose utilization comprised a six-cistron transcriptional unit with a total length of 7.8 kb. Three l-arabinose-catabolizing genes, araA (encoding l-arabinose isomerase), araB (l-ribulokinase), and araD (l-ribulose-5-phosphate 4-epimerase), comprised the araBDA operon, upstream of which three other genes, araR (LacI-type transcriptional regulator), araE (l-arabinose transporter), and galM (putative aldose 1-epimerase), were present in the opposite direction. Inactivation of the araA, araB, or araD gene eliminated growth on l-arabinose, and each of the gene products was functionally homologous to its Escherichia coli counterpart. Moreover, compared to the wild-type strain, an araE disruptant exhibited a >80% decrease in the growth rate at a lower concentration of l-arabinose (3.6 g liter−1) but not at a higher concentration of l-arabinose (40 g liter−1). The expression of the araBDA operon and the araE gene was l-arabinose inducible and negatively regulated by the transcriptional regulator AraR. Disruption of araR eliminated the repression in the absence of l-arabinose. Expression of the regulon was not repressed by d-glucose, and simultaneous utilization of l-arabinose and d-glucose was observed in aerobically growing wild-type and araR deletion mutant cells. The regulatory mechanism of the l-arabinose regulon is, therefore, distinct from the carbon catabolite repression mechanism in other bacteria.

scholarly journals Mutants of Listeria monocytogenes Defective in In Vitro Invasion and Cell-to-Cell Spreading Still Invade and Proliferate in Hepatocytes of Neutropenic Mice

2000 ◽  
Vol 68 (2) ◽  
pp. 912-914 ◽  
Author(s):  
Rui Appelberg ◽  
Irene S. Leal
Keyword(s):  
Monoclonal Antibody ◽  
Listeria Monocytogenes ◽  
Cell Spreading ◽  
Histologic Examination ◽  
Gene Products ◽  
Wild Type ◽  
In Vitro Invasion ◽  
Parenchymal Cells ◽  
Type Strains

ABSTRACT Listeria monocytogenes mutants defective in theactA gene, the plcB gene, and theinlA and inlB genes were less virulent when injected intravenously into BALB/c mice. The growth of these strains as well as of the virulent wild-type strains was increased by treating mice with a neutrophil-specific depleting monoclonal antibody, RB6-8C5. Histologic examination of the livers of the treated animals showed intrahepatocytic proliferation of the listeriae in all cases. Our data show that more than one pathway exists that allows L. monocytogenes to invade parenchymal cells. One pathway most likely involves the actA and plcB gene products, and a second one probably involves the internalins.

scholarly journals Yersinia pestis YbtU and YbtT Are Involved in Synthesis of the Siderophore Yersiniabactin but Have Different Effects on Regulation

2000 ◽  
Vol 68 (8) ◽  
pp. 4452-4461 ◽  
Author(s):  
Valerie A. Geoffroy ◽  
Jacqueline D. Fetherston ◽  
Robert D. Perry
Keyword(s):  
Yersinia Pestis ◽  
Iron Transport ◽  
Significant Loss ◽  
Gene Products ◽  
Galactosidase Activity ◽  
Wild Type ◽  
Iron Deficient ◽  
High Pathogenicity ◽  
Mutant Strains ◽  
Culture Supernatants

ABSTRACT One prerequisite for the virulence of Yersinia pestis, causative agent of bubonic plague, is the yersiniabactin (Ybt) siderophore-dependent iron transport system that is encoded within a high-pathogenicity island (HPI) within the pgm locus of theY. pestis chromosome. Several gene products within the HPI have demonstrated functions in the synthesis or transport of Ybt. Here we examine the roles of ybtU and ybtT. In-frame mutations in ybtT or ybtU yielded strains defective in siderophore production. Mutant strains were unable to grow on iron-deficient media at 37°C but could be cross-fed by culture supernatants from a Ybt-producing strain of Y. pestis. TheybtU mutant failed to express four indicator Ybt proteins (HMWP1, HMWP2, YbtE, and Psn), a pattern similar to those for otherybt biosynthetic mutants. In contrast, strains carrying mutations in ybtT or ybtS (a previously identified gene required for Ybt biosynthesis) produced all four proteins at wild-type levels under iron-deprived conditions. To assess the effects of ybtT, -U, and -Smutations on transcription of ybt genes, reporter plasmids with ybtP or psn promoters controllinglacZ expression were introduced into these mutants. Normal iron-regulated β-galactosidase activity was observed in theybtT and ybtS mutants, whereas a significant loss of expression occurred in the ΔybtU strain. These results show that ybtT and ybtU genes are involved in the biosynthesis of the Ybt siderophore and that aybtU mutation but not ybtT or ybtSmutations affects transcription from the ybtP andpsn promoters.

scholarly journals Effects of Nonpolar Mutations in Each of the Seven Bacillus subtilis mrp Genes Suggest Complex Interactions among the Gene Products in Support of Na+ and Alkali but Not Cholate Resistance

2000 ◽  
Vol 182 (20) ◽  
pp. 5663-5670 ◽  
Author(s):  
Masahiro Ito ◽  
Arthur A. Guffanti ◽  
Wei Wang ◽  
Terry A. Krulwich
Keyword(s):  
Bacillus Subtilis ◽  
Membrane Vesicles ◽  
Alkali Resistance ◽  
Gene Products ◽  
Wild Type ◽  
Upstream Gene ◽  
Complex Interactions ◽  
Low Levels ◽  
The Individual ◽  
Secondary Membrane

ABSTRACT The Bacillus subtilis mrp (multiple resistance and pH) operon supports Na+ and alkali resistance via an Na+/H+ antiport, as well as cholate efflux and resistance. Among the individual mutants with nonpolar mutations in each of the seven mrp genes, only the mrpFmutant exhibited cholate sensitivity and a cholate efflux defect that were complemented by expression of the deleted gene in trans. Expression of mrpF in the mrp null (VKN1) strain also restored cholate transport and increased Na+ efflux, indicating that MrpF does not require even low levels of other mrp gene expression for its own function. In contrast to MrpF, MrpA function had earlier seemed to depend upon at least modest expression of other mrp genes, i.e., mrpA restored Na+ resistance and efflux to strain VK6 (a polar mrpA mutant which expresses low levels of mrpB to -G) but not to the null strain VKN1. In a wild-type background, each nonpolar mutation in individual mrp genes caused profound Na+sensitivity at both pH 7.0 and 8.3. The mrpA andmrpD mutants were particularly sensitive to alkaline pH even without added Na+. While transport assays in membrane vesicles from selected strains indicated that MrpA-dependent antiport can occur by a secondary, proton motive force-dependent mechanism, the requirement for multiple mrp gene products suggests that there are features of energization, function, or stabilization that differ from typical secondary membrane transporters. Northern analyses indicated regulatory relationships among mrp genes as well. All the mrp mutants, especially the mrpA,-B, -D, -E, and -G mutants, had elevated levels of mrp RNA relative to the wild type. Expression of an upstream gene, maeN, that encodes an Na+/malate symporter, was coordinately regulated withmrp, although it is not part of the operon.

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