Chapter 3 Genes encoding the immunoglobulin variable regions

1987 ◽  
pp. 81-109 ◽  
Author(s):  
Peter H. Brodeur
Keyword(s):  
Variable Regions ◽  
Genes Encoding

scholarly journals Genomic comparison of archaeal conjugative plasmids fromSulfolobus

Archaea ◽  
2004 ◽  
Vol 1 (4) ◽  
pp. 231-239 ◽  
Author(s):  
Bo Greve ◽  
Susanne Jensen ◽  
Kim Brügger ◽  
Wolfram Zillig ◽  
Roger A. Garrett
Keyword(s):  
Sequence Similarity ◽  
Comparative Sequence Analysis ◽  
Genomic Comparison ◽  
Variable Regions ◽  
Integrase Gene ◽  
Significant Sequence Similarity ◽  
Genes Encoding ◽  
Putative Origin ◽  
Main Components ◽  
Intercellular Exchange

All of the known self-transmissable plasmids of the Archaea have been found in the genusSulfolobus. To gain more insight into archaeal conjugative processes, four newly isolated self-transmissable plasmids, pKEF9, pHVE14, pARN3 and pARN4, were sequenced and subjected to a comparative sequence analysis with two earlier sequenced plasmids, pNOB8 and pING1. The analyses revealed three conserved and functionally distinct sections in the genomes. Section A is considered to encode the main components of the conjugative apparatus, where two genes show low but significant sequence similarity to sections of genes encoding bacterial conjugative proteins. A putative origin of replication is located in section B, which is highly conserved in sequence and contains several perfect and imperfect direct and inverted repeats. Further downstream, in section C, an operon encoding six to nine smaller proteins is implicated in the initiation and regulation of replication. Each plasmid carries an integrase gene of the type that does not partition on integration, and there is strong evidence for their integration into host chromosomes, where they may facilitate intercellular exchange of chromosomal genes. Two plasmids contain hexameric short regularly spaced repeats (SRSR), which have been implicated in plasmid maintenance, and each plasmid carries multiple recombination motifs, concentrated in the variable regions, which likely provide sites for genomic rearrangements.

Sequence heterogeneity of the small subunit ribosomal RNA genes among Blastocystis isolates

Parasitology ◽  
2003 ◽  
Vol 126 (1) ◽  
pp. 1-9 ◽  
Author(s):  
N. ARISUE ◽  
T. HASHIMOTO ◽  
H. YOSHIKAWA
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Reconstruction ◽  
Small Subunit ◽  
Higher Order ◽  
Variable Regions ◽  
Small Subunit Ribosomal Rna ◽  
Statistical Confidence ◽  
Sequence Patterns ◽  
Genes Encoding ◽  
Morphological Identity

Genes encoding small subunit ribosomal RNA (SSUrRNA) of 16 Blastocystis isolates from humans and other animals were amplified by the polymerase chain reaction, and the corresponding fragments were cloned and sequenced. Alignment of these sequences with the previously reported ones indicated the presence of 7 different sequence patterns in the highly variable regions of the small subunit ribosomal RNA. Phylogenetic reconstruction analysis using Proteromonas lacertae as the outgroup clearly demonstrated that the 7 groups with the different sequence patterns are separated to form independent clades, 5 of which consisted of the Blastocystis isolates from both humans (B. hominis) and other animals. The presence of 3 higher order clades was also clearly supported in the phylogenetic tree. However, a relationship among the 4 groups including these 3 higher order clades was not settled with statistical confidence. The remarkable heterogeneity of small subunit ribosomal RNAs among different Blastocystis isolates found in this study confirmed, with sequence-based evidence, that these organisms are genetically highly divergent in spite of their morphological identity. The highly variable small subunit ribosomal RNA regions among the distinct groups will provide useful information for the development of group-specific diagnostic primers.

Germ line variable regions that match hypermutated sequences in genes encoding murine anti-hapten antibodies.

Genetics ◽  
1992 ◽  
Vol 132 (3) ◽  
pp. 799-811 ◽  
Author(s):  
V David ◽  
N L Folk ◽  
N Maizels
Keyword(s):  
Germinal Center ◽  
Germ Line ◽  
Somatic Hypermutation ◽  
Germinal Centers ◽  
Kappa Light Chain ◽  
Variable Regions ◽  
Genes Encoding ◽  
Mutagenic Process ◽  
Antigen Selection ◽  
Mutational Process

Abstract We asked whether there are germ line immunoglobulin variable (V) segments that match sites of hypermutation in V regions encoding murine antibodies. Murine germ line DNA was probed with a panel of short deoxyoligonucleotides identical in sequence to segments of hypermutated V regions from hybridomas generated in the BALB/c response to the hapten 2-phenyloxazolone (Ox). Germ line sequences that match mutations in both heavy and kappa light chain V regions were identified, and clones of some of these germ line V segments were obtained. Comparison of these clones with hypermutated V regions revealed regions of identity ranging in size from 7 to over 50 nucleotides. In an effort to separate the effects of antigen selection from the mutagenic process, we also searched for matches to a panel of silent mutations in VH regions from germinal center B cells. Fourteen silent mutations occur among a collection of 36 hypermutated VH regions from two separate germinal centers of C57BL/6 mice stimulated with the hapten 4-hydroxy-3-nitrophenyl. Matches to nine of these silent mutations can be found among published sequences of C57BL/6 VH regions of the J558 family. Taken together, these data are consistent with the possibility that a template-dependent mutational process, like gene conversion, may contribute to somatic hypermutation.

scholarly journals Full-length genome sequences of two SARS-like coronaviruses in horseshoe bats and genetic variation analysis

2006 ◽  
Vol 87 (11) ◽  
pp. 3355-3359 ◽  
Author(s):  
Wuze Ren ◽  
Wendong Li ◽  
Meng Yu ◽  
Pei Hao ◽  
Yuan Zhang ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Variation Analysis ◽  
Genome Sequences ◽  
Variable Regions ◽  
Additional Group ◽  
Genes Encoding ◽  
Palm Civet ◽  
Group 2 ◽  
Horseshoe Bat ◽  
Full Length Genome

Bats were recently identified as natural reservoirs of SARS-like coronavirus (SL-CoV) or SARS coronavirus-like virus. These viruses, together with SARS coronaviruses (SARS-CoV) isolated from human and palm civet, form a distinctive cluster within the group 2 coronaviruses of the genus Coronavirus, tentatively named group 2b (G2b). In this study, complete genome sequences of two additional group 2b coronaviruses (G2b-CoVs) were determined from horseshoe bat Rhinolophus ferrumequinum (G2b-CoV Rf1) and Rhinolophus macrotis (G2b-CoV Rm1). The bat G2b-CoV isolates have an identical genome organization and share an overall genome sequence identity of 88–92 % among themselves and between them and the human/civet isolates. The most variable regions are located in the genes encoding nsp3, ORF3a, spike protein and ORF8 when bat and human/civet G2b-CoV isolates are compared. Genetic analysis demonstrated that a diverse G2b-CoV population exists in the bat habitat and has evolved from a common ancestor of SARS-CoV.

scholarly journals Denaturing Gradient Gel Electrophoresis Analysis of 16S Ribosomal DNA Amplicons To Monitor Changes in Fecal Bacterial Populations of Weaning Pigs after Introduction of Lactobacillus reuteri Strain MM53

2000 ◽  
Vol 66 (11) ◽  
pp. 4705-4714 ◽  
Author(s):  
Joyce M. Simpson ◽  
Vance J. McCracken ◽  
H. Rex Gaskins ◽  
Roderick I. Mackie
Keyword(s):  
16S Rdna ◽  
Gel Electrophoresis ◽  
Lactobacillus Reuteri ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Populations ◽  
Variable Regions ◽  
Select Group ◽  
Genes Encoding ◽  
Gradient Gel Electrophoresis ◽  
Weaning Pigs

ABSTRACT The diversity and stability of the fecal bacterial microbiota in weaning pigs was studied after introduction of an exogenousLactobacillus reuteri strain, MM53, using a combination of cultivation and techniques based on genes encoding 16S rRNA (16S rDNA). Piglets (n = 9) were assigned to three treatment groups (control, daily dosed, and 4th-day dosed), and fresh fecal samples were collected daily. Dosed animals received 2.5 × 1010 CFU of antibiotic-resistant L. reuteriMM53 daily or every 4th day. Mean Lactobacillus counts for the three groups ranged from 1 × 109 to 4 × 109 CFU/g of feces. Enumeration of strain L. reuteri MM53 on MRS agar (Difco) plates containing streptomycin and rifampin showed that the introduced strain fluctuated between 8 × 103 and 5 × 106 CFU/g of feces in the two dosed groups. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments, with primers specific for variable regions 1 and 3 (V1 and V3), was used to profile complexity of fecal bacterial populations. Analysis of DGGE banding profiles indicated that each individual maintained a unique fecal bacterial population that was stable over time, suggesting a strong host influence. In addition, individual DGGE patterns could be separated into distinct time-dependent clusters. Primers designed specifically to restrict DGGE analysis to a select group of lactobacilli allowed examination of interspecies relationships and abundance. Based on relative band migration distance and sequence determination, L. reuteriwas distinguishable within the V1 region 16S rDNA gene patterns. Daily fluctuations in specific bands within these profiles were observed, which revealed an antagonistic relationship between L. reuteri MM53 (band V1-3) and another indigenousLactobacillus assemblage (band V1-6).

scholarly journals Transferable Denitrification Capability of Thermus thermophilus

2013 ◽  
Vol 80 (1) ◽  
pp. 19-28 ◽  
Author(s):  
Laura Alvarez ◽  
Carlos Bricio ◽  
Alba Blesa ◽  
Aurelio Hidalgo ◽  
José Berenguer
Keyword(s):  
Thermus Thermophilus ◽  
Electron Acceptors ◽  
Complex Iii ◽  
Variable Regions ◽  
Continuous Growth ◽  
Content Type ◽  
New Class ◽  
Extrachromosomal Elements ◽  
Chromosomal Genes ◽  
Genes Encoding

ABSTRACTLaboratory-adapted strains ofThermusspp. have been shown to require oxygen for growth, including the model strainsT. thermophilusHB27 and HB8. In contrast, many isolates of this species that have not been intensively grown under laboratory conditions keep the capability to grow anaerobically with one or more electron acceptors. The use of nitrogen oxides, especially nitrate, as electron acceptors is one of the most widespread capabilities among these facultative strains. In this process, nitrate is reduced to nitrite by a reductase (Nar) that also functions as electron transporter toward nitrite and nitric oxide reductases when nitrate is scarce, effectively replacing respiratory complex III. In manyT. thermophilusdenitrificant strains, most electrons for Nar are provided by a new class of NADH dehydrogenase (Nrc). The ability to reduce nitrite to NO and subsequently to N2O by the corresponding Nir and Nor reductases is also strain specific. The genes encoding the capabilities for nitrate (nar) and nitrite (nirandnor) respiration are easily transferred betweenT. thermophilusstrains by natural competence or by a conjugation-like process and may be easily lost upon continuous growth under aerobic conditions. The reason for this instability is apparently related to the fact that these metabolic capabilities are encoded in gene cluster islands, which are delimited by insertion sequences and integrated within highly variable regions of easily transferable extrachromosomal elements. Together with the chromosomal genes, these plasmid-associated genetic islands constitute the extended pangenome ofT. thermophilusthat provides this species with an enhanced capability to adapt to changing environments.

scholarly journals Bacteroides fragilistype VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species

2016 ◽  
Vol 113 (13) ◽  
pp. 3627-3632 ◽  
Author(s):  
Maria Chatzidaki-Livanis ◽  
Naama Geva-Zatorsky ◽  
Laurie E. Comstock
Keyword(s):  
Secretion Systems ◽  
Human Gut ◽  
Variable Regions ◽  
Type Vi Secretion ◽  
Genes Encoding ◽  
T6ss Locus ◽  
Integrative Conjugative Elements ◽  
Mutation Analyses ◽  
Competition Assays

Type VI secretion systems (T6SSs) are multiprotein complexes best studied in Gram-negative pathogens where they have been shown to inhibit or kill prokaryotic or eukaryotic cells and are often important for virulence. We recently showed that T6SS loci are also widespread in symbiotic human gut bacteria of the order Bacteroidales, and that these T6SS loci segregate into three distinct genetic architectures (GA). GA1 and GA2 loci are present on conserved integrative conjugative elements (ICE) and are transferred and shared among diverse human gut Bacteroidales species. GA3 loci are not contained on conserved ICE and are confined toBacteroides fragilis. Unlike GA1 and GA2 T6SS loci, most GA3 loci do not encode identifiable effector and immunity proteins. Here, we studied GA3 T6SSs and show that they antagonize most human gut Bacteroidales strains analyzed, except forB. fragilisstrains with the same T6SS locus. A combination of mutation analyses,trans-protection analyses, and in vitro competition assays, allowed us to identify novel effector and immunity proteins of GA3 loci. These proteins are not orthologous to known proteins, do not contain identified motifs, and most have numerous predicted transmembrane domains. Because the genes encoding effector and immunity proteins are contained in two variable regions of GA3 loci, GA3 T6SSs of the speciesB. fragilisare likely the source of numerous novel effector and immunity proteins. Importantly, we show that the GA3 T6SS of strain 638R is functional in the mammalian gut and provides a competitive advantage to this organism.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

Sign in / Sign up

Export Citation Format

Share Document