scholarly journals Interaction between Kb and Q4 gene sequences generates the Kbm6 mutation

1986 ◽  
Vol 6 (2) ◽  
pp. 645-652
Author(s):  
J Geliebter ◽  
R A Zeff ◽  
D H Schulze ◽  
L R Pease ◽  
E H Weiss ◽  
...  

Genetic interaction as a mechanism for the generation of mutations is suggested by recurrent, multiple nucleotide substitutions that are identical to nucleotide sequences elsewhere in the genome. We have sequenced the mutant K gene from the bm6 mouse, which is one of a series of eight closely related, yet independently occurring mutants known collectively as the "bg series." Two changes from the Kb gene are found, positioned 15 nucleotides apart: an A-to-T change and a T-to-C change in the codons corresponding to amino acids 116 and 121, resulting in Tyr-to-Phe and Cys-to-Arg substitutions, respectively. Hybridization analysis with an oligonucleotide specific for the altered Kbm6 sequence identifies one donor gene, Q4, located in the Qa region of the H-2 complex. The two altered nucleotides that differentiate Kbm6 and Kb are present in Q4 in a region where Kb and Q4 are otherwise identical for 95 nucleotides, delineating the maximum genetic transfer between the two genes. Because the Kbm6 mutation arose in an homozygous mouse these data indicate that the Q4 gene contains the only donor sequence and demonstrates that Q-region gene sequences can interact with the Kb gene to generate variant K molecules.

1986 ◽  
Vol 6 (2) ◽  
pp. 645-652 ◽  
Author(s):  
J Geliebter ◽  
R A Zeff ◽  
D H Schulze ◽  
L R Pease ◽  
E H Weiss ◽  
...  

Genetic interaction as a mechanism for the generation of mutations is suggested by recurrent, multiple nucleotide substitutions that are identical to nucleotide sequences elsewhere in the genome. We have sequenced the mutant K gene from the bm6 mouse, which is one of a series of eight closely related, yet independently occurring mutants known collectively as the "bg series." Two changes from the Kb gene are found, positioned 15 nucleotides apart: an A-to-T change and a T-to-C change in the codons corresponding to amino acids 116 and 121, resulting in Tyr-to-Phe and Cys-to-Arg substitutions, respectively. Hybridization analysis with an oligonucleotide specific for the altered Kbm6 sequence identifies one donor gene, Q4, located in the Qa region of the H-2 complex. The two altered nucleotides that differentiate Kbm6 and Kb are present in Q4 in a region where Kb and Q4 are otherwise identical for 95 nucleotides, delineating the maximum genetic transfer between the two genes. Because the Kbm6 mutation arose in an homozygous mouse these data indicate that the Q4 gene contains the only donor sequence and demonstrates that Q-region gene sequences can interact with the Kb gene to generate variant K molecules.


2009 ◽  
Vol 43 (1) ◽  
pp. 203-205 ◽  
Author(s):  
Chetan Kumar ◽  
K. Sekar

The identification of sequence (amino acids or nucleotides) motifs in a particular order in biological sequences has proved to be of interest. This paper describes a computing server,SSMBS, which can locate and display the occurrences of user-defined biologically important sequence motifs (a maximum of five) present in a specific order in protein and nucleotide sequences. While the server can efficiently locate motifs specified using regular expressions, it can also find occurrences of long and complex motifs. The computation is carried out by an algorithm developed using the concepts of quantifiers in regular expressions. The web server is available to users around the clock at http://dicsoft1.physics.iisc.ernet.in/ssmbs/.


Genome ◽  
2004 ◽  
Vol 47 (4) ◽  
pp. 732-741 ◽  
Author(s):  
Wolfgang Staiber

The origin of germline-limited chromosomes (Ks) as descendants of somatic chromosomes (Ss) and their structural evolution was recently elucidated in the chironomid Acricotopus. The Ks consist of large S-homologous sections and of heterochromatic segments containing germline-specific, highly repetitive DNA sequences. Less is known about the molecular evolution and features of the sequences in the S-homologous K sections. More information about this was received by comparing homologous gene sequences of Ks and Ss. Genes for 5.8S, 18S, 28S, and 5S ribosomal RNA were choosen for the comparison and therefore isolated first by PCR from somatic DNA of Acricotopus and sequenced. Specific K DNA was collected by microdissection of monopolar moving K complements from differential gonial mitoses and was then amplified by degenerate oligonucleotide primer (DOP)-PCR. With the sequence data of the somatic rDNAs, the homologous 5.8S and 5S rDNA sequences were isolated by PCR from the DOP-PCR sequence pool of the Ks. In addition, a number of K DOP-PCR sequences were directly cloned and analysed. One K clone contained a section of a putative N-acetyltransferase gene. Compared with its homolog from the Ss, the sequence exhibited few nucleotide substitutions (99.2% sequence identity). The same was true for the 5.8S and 5S sequences from Ss and Ks (97.5%–100% identity). This supports the idea that the S-homologous K sequences may be conserved and do not evolve independently from their somatic homologs. Possible mechanisms effecting such conservation of S-derived sequences in the Ks are discussed.Key words: microdissection, DOP-PCR, germline-limited chromosomes, molecular evolution.


2001 ◽  
Vol 183 (13) ◽  
pp. 4040-4051 ◽  
Author(s):  
Walter M. Yuan ◽  
Guillaume D. Gentil ◽  
Allen D. Budde ◽  
Sally A. Leong

ABSTRACT Ustilago maydis, the causal agent of corn smut disease, acquires and transports ferric ion by producing the extracellular, cyclic peptide, hydroxamate siderophores ferrichrome and ferrichrome A. Ferrichrome biosynthesis likely proceeds by hydroxylation and acetylation of l-ornithine, and later steps likely involve covalently bound thioester intermediates on a multimodular, nonribosomal peptide synthetase. sid1 encodesl-ornithine N 5-oxygenase, which catalyzes hydroxylation of l-ornithine, the first committed step of ferrichrome and ferrichrome A biosynthesis in U. maydis. In this report we characterize sid2, another biosynthetic gene in the pathway, by gene complementation, gene replacement, DNA sequence, and Northern hybridization analysis. Nucleotide sequencing has revealed that sid2 is located 3.7 kb upstream of sid1 and encodes an intronless polypeptide of 3,947 amino acids with three iterated modules of an approximate length of 1,000 amino acids each. Multiple motifs characteristic of the nonribosomal peptide synthetase protein family were identified in each module. A corresponding iron-regulated sid2 transcript of 11 kb was detected by Northern hybridization analysis. By contrast, constitutive accumulation of this large transcript was observed in a mutant carrying a disruption of urbs1, a zinc finger, GATA family transcription factor previously shown to regulate siderophore biosynthesis in Ustilago. Multiple GATA motifs are present in the intergenic region between sid1 and sid2, suggesting bidirectional transcription regulation by urbs1of this pathway. Indeed, mutation of two of these motifs, known to be important to regulation of sid1, altered the differential regulation of sid2 by iron.


1957 ◽  
Vol 5 (3) ◽  
pp. 305 ◽  
Author(s):  
MJD White

Moraba scurra Rehn shows inversion polymorphism in two different chromosome pairs, ."CD" and "EF". Each of these systems produces a heterotic effect on male viability. The cytological polymorphism of the CD pair is present in almost all populations except in the south-western part of the distribution area of the species (Tumut, N.S.W., to Merton, Vic.), where only the Standard sequence is present. Some populations have the Standard CD much more frequent than the Blundell CD, while in other localities the relationship is reversed and in five colonies a third sequence, Molonglo, was found, either replacing Standard or coexisting with Standard and Blundell. The cytological polymorphism of the EF chromosome is distributed rather irregularly throughout the geographic area occupied by the species. Many populations have only the Standard type of EF chromosome and even in those which also contain the Tidbinbilla sequence the latter is always greatly outnumbered by Standard. In populations containing both cytological polymorphisms, these are apparently not combined at random, there being a genetic interaction between them, as far as the viability of the males is concerned. This interaction leads to a deficiency of Bl/Bl, St/St individuals and to a further deficiency of genotypes in which Tidbinbilla coexists with the Standard CD chromosome, either in the heterozygous or the homozygous condition. On the assumption that the overall selective values of these genotypes are generally similar to their effects on male viability, those populations which possess both heterotic mechanisms must have a complex balanced polymorphism, involving equilibria between the alternative gene sequences of the two different chromosome pairs, as well as between those of the same pair.


2002 ◽  
Vol 83 (6) ◽  
pp. 1477-1482 ◽  
Author(s):  
Kyoji Hagiwara ◽  
Shujing Rao ◽  
Simon W. Scott ◽  
Gerald R. Carner

The complete nucleotide sequences of genomic segments S1, S3 and S4 from Bombyx mori cypovirus 1 (BmCPV-1) have been determined. The segments consisted of 4190, 3846 and 3262 nucleotides encoding putative proteins of 1333, 1239 and 1058 amino acids with molecular masses of approximately 148, 140 and 120 kDa (p148, p140 and p120, respectively). All segments possess a single open reading frame. Homology searches showed that all three proteins have homologies to proteins of Rice ragged stunt virus, a member of the genus Oryzavirus within the family Reoviridae. Partial homologies of p140 to structural proteins in other viruses were also found. The predicted molecular masses and the homologies with structural proteins in other viruses lead us to suggest that S1, S3 and S4 encode the capsid proteins VP1, VP3, and VP4, respectively, of BmCPV-1.


Cell ◽  
1984 ◽  
Vol 36 (3) ◽  
pp. 681-688 ◽  
Author(s):  
John G. Flanagan ◽  
Marie-Paule Lefranc ◽  
Terence H. Rabbitts

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2644-2644
Author(s):  
Daxing Zhu ◽  
Chen Lossos ◽  
Jennifer R Chapman-Fredricks ◽  
Julie M Mattews ◽  
Offiong F Ikpatt ◽  
...  

Abstract Abstract 2644 Mucosa-associated lymphoid tissue (MALT) lymphomas are the most common lymphomas in the ocular adnexa. Similar to extranodular MALT lymphomas in other tissues, ocular adnexa MALT lymphomas (OAMALTL) are frequently characterized by an indolent clinical course and often remain localized for many years. While chronic infection (e. g. Helicobacter pylori) or autoimmune diseases (e.g. Hashimoto's thyroiditis and Sjogren's syndrome) frequently precede and predispose patients to develop MALT lymphomas in the stomach, thyroid and salivary glands, respectively, the etiology and pathogenesis of OAMALTL are still controversial. An Italian group and investigators from several other geographic regions demonstrated Chlamydia psittaci (C. psittaci) DNA present in OAMALTL, suggesting that this pathogen may be implicated in the development of these lymphomas. However, similar studies performed by us and other investigators on US-based patients have failed to corroborate this finding. Furthermore, DNA from other bacteria was also not detected by us, thus not supporting a bacterial etiology in US-based patients. Since non-bacterial antigens may predispose patients to OAMALTL, we have examined immunoglubulin (Ig) heavy chain variable region (VH) usage and mutations in the largest to date cohort of C psittaci negative OAMALTL originating from a single institution. DNA was extracted by standard techniques from 68 fresh OAMALTL tissues and used for direct PCR or PCR followed by cloning and sequencing using family specific VH leader and JH primers. To control for potential PCR error, all patient samples were evaluated by 2 independent PCR reactions and sequencing and only cases with identical CDR3 regions in the independent PCR runs were defined as clonal. Using this definition, clonal rearranged VHDJH sequences were identified in 44 (64.7%) tumors originating from the orbit (19), conjunctivae (19) and lacrimal gland (6). Forty seven clonal VH gene sequences were detected (3 of the patients had 2 clonal sequences) with 46 potentially functional and 1 harboring an out-of-frame junction with a stop codon. In 14 (31.8%) cases the PCR product could be sequenced directly, whereas in 30 (68.2%) cases PCR amplicons had to be subcloned to identify the VH gene. The 46 potentially functional VH were derived from 4 of the 7 human VH gene families with the following distribution: VH1, 13.1%; VH2, 2.2%; VH3, 39.1%; VH4, 45.6%, demonstrating a biased overrepresentation of the VH4 gene family (p=0.001). The most frequently encountered genes were VH4-34 (n=8), VH3-30 (n=6), VH3-23 (n=5) and VH4-30 (n=4). VH4-34 represented 17% of all the potentially functional VH genes identified in this study in contrast to its usage in 4–7% in adult peripheral B lymphocytes. Only 3 VH gene sequences were unmutated. The average percent homology to the germ line sequence in the 43 functional mutated sequences was 93.2% (range 71.5–99.6). Multinomial algorithm for antigen selection revealed evidence for positive selection in the CDR in 15 sequences, negative selection in the FR in 17 sequences, and selection in both CDR and FR (in the same sequence) in 7 sequences. Selection analysis using the focused binomial test demonstrated evidence of selection in the FR in 12 sequences and in the CDR in only 4 sequences. Selection was detected in 5 of the 8 functional VH4-34 sequences. Analysis of the tumor-derived CDR3 sequences revealed low similarity and an absence of stereotyped sequences with no homology to antibacterial and other previously published antibodies. The average CDR3 isoelectric point was 5.91±1.89 (SD). The average CDR3 length was 15.73±13.62 (SD) amino acids, with 19 sequences harboring 15–19 amino acids and 7 CDR3 sequences longer than 19 amino acids. Intraclonal variation was assessed by extensive molecular cloning in 8 potentially functional VH gene isolates from 8 randomly selected tumor specimens. Confirmed ongoing mutations were detected in the 6 of the 8 analyzed sequences. Overall our findings demonstrate that C. psittaci negative OAMALTL exhibit biased usage of VH families and genes with evidence for intraclonal heterogeneity and antigen selection in multiple tumors, implicating immunological stimulation in the pathogenesis of these lymphomas. The nature of the antigens potentially playing role in these processes is currently unknown and requires further studies. Disclosures: No relevant conflicts of interest to declare.


Genome ◽  
2008 ◽  
Vol 51 (7) ◽  
pp. 511-523 ◽  
Author(s):  
L. E. Sáenz de Miera ◽  
J. Ramos ◽  
M. Pérez de la Vega

Convicilins, a set of seed storage proteins, differ from vicilins, a related group of seed storage proteins, mainly because of the presence of the N-terminal extension, an additional sequence of amino acids in the sequence corresponding to the first exon. Convicilins have been described only in species of the legume tribe Vicieae. One or two genes for convicilins have been identified in most species of this tribe. The genus Pisum is the main exception, since two genes have been identified in most of its species. Thirty-four new convicilin gene sequences from 29 different species ( Lathyrus , Lens , Pisum, and Vicia spp.) have been analyzed here. Convicilin gene sequences are generally organized in 6 exons, but in some instances one of the internal introns (2nd or 4th) is lost. In these 29 species, the N-terminal extension is formed by a stretch of 99 to 196 amino acids particularly rich in polar and charged amino acids (on average, it contains 29.43% glutamic acid and 15.38% arginine residues). This N-terminal extension has the characteristics of an intrinsically unstructured region (IUR), one of the categories of protein “degenerate sequences”. A comparative analysis indicates that the N-terminal extension sequence has evolved faster than the surrounding sequence, which is common to all vicilins, and it evolved mainly through a series of duplications of short internal sequences and triplet expansions, the predominant one being GAA. This agrees with the evolution of IURs, which is faster than the evolution of surrounding sequences and is mainly due to replication slippage and unequal crossover recombination. Alternative maximum-likelihood trees of phylogenetic relationships among the 29 Vicieae species based on the convicilin exon sequences are presented and discussed.


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