scholarly journals Genes Essential for Nod Factor Production and Nodulation Are Located on a Symbiotic Amplicon (AMPRtrCFN299pc60) in Rhizobium tropici

1998 ◽  
Vol 180 (11) ◽  
pp. 2866-2874 ◽  
Author(s):  
Patrick Mavingui ◽  
Toon Laeremans ◽  
Margarita Flores ◽  
David Romero ◽  
Esperanza Martínez-Romero ◽  
...  
Keyword(s):  
Insertion Sequence ◽  
Gene Dosage ◽  
Kanamycin Resistance ◽  
Nod Factors ◽  
Rhizobium Tropici ◽  
Resistance Marker ◽  
Nod Factor ◽  
Origins Of Replication ◽  
Symbiotic Plasmid

ABSTRACT Amplifiable DNA regions (amplicons) have been identified in the genome of Rhizobium etli. Here we report the isolation and molecular characterization of a symbiotic amplicon of Rhizobium tropici. To search for symbiotic amplicons, a cartridge containing a kanamycin resistance marker that responds to gene dosage and conditional origins of replication and transfer was inserted in the nodulation region of the symbiotic plasmid (pSym) of R. tropici CFN299. Derivatives harboring amplifications were selected by increasing the concentration of kanamycin in the cell culture. The amplified DNA region was mobilized into Escherichia coli and then into Agrobacterium tumefaciens. The 60-kb symbiotic amplicon, which we termed AMPRtrCFN299pc60, contains several nodulation and nitrogen fixation genes and is flanked by a novel insertion sequence ISRtr1. Amplification of AMPRtrCFN299pc60 through homologous recombination between ISRtr1 repeats increased the amount of Nod factors. Strikingly, the conjugal transfer of the amplicon into a plasmidlessA. tumefaciens strain confers on the transconjugant the ability to produce R. tropici Nod factors and to nodulatePhaseolus vulgaris, indicating that R. tropicigenes essential for the nodulation process are confined to an ampliable DNA region of the pSym.

Regulation of Nod factor sulphation genes in Rhizobium tropici CIAT899

2001 ◽  
Vol 47 (6) ◽  
pp. 574-579 ◽  
Author(s):  
Hamid Manyani ◽  
Carolina Sousa ◽  
María-Eugenia Soria Díaz ◽  
Antonio Gil-Serrano ◽  
Manuel Megías
Keyword(s):  
Wide Spectrum ◽  
Constitutive Expression ◽  
Upstream Region ◽  
Broad Host Range ◽  
Nod Factors ◽  
Rhizobium Tropici ◽  
Free Living ◽  
Nod Factor ◽  
Symbiotic Plasmid ◽  
Transcriptional Fusions

Rhizobium tropici CIAT899 is a tropical symbiont able to nodulate various legumes such as Leucaena, Phaseolus, and Macroptilium. Broad host range of this species is related to its Nod factors wide spectrum. R. tropici contains Nod factors sulphation nod genes, nodHPQ genes, which control nodulation efficiency in Leucaena. To study nodHPQ regulation, we carried out different interposon insertions in its upstream region. One of these generated interruptions, nodI mutant produced nonsulphated Nod factors suggesting a possible dependence of these genes on nodI upstream region. Moreover, analysis results of lacZ transcriptional fusions with these genes in symbiotic plasmid showed dependence of these genes on NodD protein. In order to determine nodHPQ organization, we studied the effect of interposon insertion upstream of each lacZ transcriptional fusion, and the data obtained was used to indicate that nodHPQ belong to the nodABCSUIJ operon. However, comparison between nodP::lacZ β-galactosidase activity in the symbiotic plasmid and in the pHM500 plasmid (containing nodHPQ genes) suggested constitutive expression in free living, and flavonoid inducible expression in symbiotic conditions. Constitutive nodHPQ expression may play a role in bacterial house-keeping metabolism. On the other hand, the transference of R. tropici nodHPQ genes to other rhizobia that do not present sulphated substitutions demonstrated that NodH protein sulphotransference is specific to C6 at the reducing end.Key words: Nod factors, nodHPQ genes, Rhizobium tropici, nod-box.

scholarly journals Isolation and Characterization of a Native Composite Transposon, Tn14751, Carrying 17.4 Kilobases of Corynebacterium glutamicum Chromosomal DNA

2005 ◽  
Vol 71 (1) ◽  
pp. 407-416 ◽  
Author(s):  
Masayuki Inui ◽  
Yota Tsuge ◽  
Nobuaki Suzuki ◽  
Alain A. Vert�s ◽  
Hideaki Yukawa
Keyword(s):  
Corynebacterium Glutamicum ◽  
Insertion Sequence ◽  
Kanamycin Resistance ◽  
Chromosomal Dna ◽  
Kanamycin Resistance Cassette ◽  
Isolation And Characterization ◽  
Genes Encoding ◽  
Genome Scale ◽  
Random Insertion

ABSTRACT A native composite transposon was isolated from Corynebacterium glutamicum ATCC 14751. This transposon comprises two functional copies of a corynebacterial IS31831-like insertion sequence organized as converging terminal inverted repeats. This novel 20.3-kb element, Tn14751, carries 17.4 kb of C. glutamicum chromosomal DNA containing various genes, including genes involved in purine biosynthesis but not genes related to bacterial warfare, such as genes encoding mediators of antibiotic resistance or extracellular toxins. A derivative of this element carrying a kanamycin resistance cassette, minicomposite Tn14751, transposed into the genome of C. glutamicum at an efficiency of 1.8 � 102 transformants per μg of DNA. Random insertion of the Tn14751 derivative carrying the kanamycin resistance cassette into the chromosome was verified by Southern hybridization. This work paves the way for realization of the concept of minimum genome factories in the search for metabolic engineering via genome-scale directed evolution through a combination of random and directed approaches.

scholarly journals Phaseolus vulgaris Recognizes Azorhizobium caulinodans Nod Factors with a Variety of Chemical Substituents

1999 ◽  
Vol 12 (9) ◽  
pp. 820-824 ◽  
Author(s):  
T. Laeremans ◽  
C. Snoeck ◽  
J. Mariën ◽  
C. Verreth ◽  
E. Martínez-Romero ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Host Plant ◽  
Wide Spectrum ◽  
Nod Factors ◽  
Azorhizobium Caulinodans ◽  
Rhizobium Tropici ◽  
Nod Factor ◽  
Mutant Strains

Phaseolus vulgaris is a promiscuous host plant that can be nodulated by many different rhizobia representing a wide spectrum of Nod factors. In this study, we introduced the Rhizobium tropici CFN299 Nod factor sulfation genes nodHPQ into Azorhizobium caulinodans. The A. caulinodans transconjugants produce Nod factors that are mostly if not all sulfated and often with an arabinosyl residue as the reducing end glycosylation. Using A. caulinodans mutant strains, affected in reducing end decorations, and their respective transconjugants in a bean nodulation assay, we demonstrated that bean nodule induction efficiency, in decreasing order, is modulated by the Nod factor reducing end decorations fucose, arabinose or sulfate, and hydrogen.

scholarly journals Structural and Functional Characterization of IS1358 from Vibrio cholerae

1998 ◽  
Vol 180 (23) ◽  
pp. 6101-6106 ◽  
Author(s):  
Sandrine Dumontier ◽  
Patrick Trieu-Cuot ◽  
Patrick Berche
Keyword(s):  
Vibrio Cholerae ◽  
Insertion Sequence ◽  
Functional Characterization ◽  
Insertion Site ◽  
Kanamycin Resistance ◽  
Conjugative Plasmid ◽  
Multiple Copies ◽  
Dna Fragment ◽  
El Tor

ABSTRACT The new epidemic serovar O139 of Vibrio cholerae has emerged from the pandemic serovar O1 biotype El Tor through the replacement of a 22-kbp DNA region by a 40-kbp O139-specific DNA fragment. This O139-specific DNA fragment contains an insertion sequence that was described previously (U. H. Stroeher, K. E. Jedani, B. K. Dredge, R. Morona, M. H. Brown, L. E. Karageorgos, J. M. Albert, and P. A. Manning, Proc. Natl. Acad. Sci. USA 92:10374–10378, 1995) and designated IS1358 O139. We studied the distribution of the IS1358 element in strains from various serovars by Southern analysis. Its presence was detected in strains from serovars O1, O2, O22, O139, and O155 but not in strains from serovars O15, O39, and O141. Furthermore, IS1358 was present in multiple copies in strains from serovars O2, O22, and O155. We cloned and sequenced four copies of IS1358 from V. cholerae O22 and one copy from V. cholerae O155. A comparison of their nucleotide sequences with those of O1 and O139 showed that they were almost identical. We constructed a transposon consisting of a kanamycin resistance gene flanked by two directly oriented copies of IS1358 to study the functionality of this element. Transposition of this element from a nonmobilizable plasmid onto the conjugative plasmid pOX38-Gen was detected in an Escherichia coli recA donor at a frequency of 1.2 × 10−8. Sequence analysis revealed that IS1358 duplicates 10 bp at its insertion site.

scholarly journals Characterization of Caenorhabditis elegans Homologs of the Down Syndrome Candidate Gene DYRK1A

Genetics ◽  
2003 ◽  
Vol 163 (2) ◽  
pp. 571-580 ◽  
Author(s):  
William B Raich ◽  
Celine Moorman ◽  
Clay O Lacefield ◽  
Jonah Lehrer ◽  
Dusan Bartsch ◽  
...  
Keyword(s):  
Down Syndrome ◽  
Caenorhabditis Elegans ◽  
Trisomy 21 ◽  
Gene Dosage ◽  
Inducible Promoters ◽  
C Elegans ◽  
Dual Specificity ◽  
Specificity Protein

Abstract The pathology of trisomy 21/Down syndrome includes cognitive and memory deficits. Increased expression of the dual-specificity protein kinase DYRK1A kinase (DYRK1A) appears to play a significant role in the neuropathology of Down syndrome. To shed light on the cellular role of DYRK1A and related genes we identified three DYRK/minibrain-like genes in the genome sequence of Caenorhabditis elegans, termed mbk-1, mbk-2, and hpk-1. We found these genes to be widely expressed and to localize to distinct subcellular compartments. We isolated deletion alleles in all three genes and show that loss of mbk-1, the gene most closely related to DYRK1A, causes no obvious defects, while another gene, mbk-2, is essential for viability. The overexpression of DYRK1A in Down syndrome led us to examine the effects of overexpression of its C. elegans ortholog mbk-1. We found that animals containing additional copies of the mbk-1 gene display behavioral defects in chemotaxis toward volatile chemoattractants and that the extent of these defects correlates with mbk-1 gene dosage. Using tissue-specific and inducible promoters, we show that additional copies of mbk-1 can impair olfaction cell-autonomously in mature, fully differentiated neurons and that this impairment is reversible. Our results suggest that increased gene dosage of human DYRK1A in trisomy 21 may disrupt the function of fully differentiated neurons and that this disruption is reversible.

Insertion Sequence Based Molecular Characterization of Burkholderia mallei NCTC 3709 Strain

2014 ◽  
Vol 38 (2) ◽  
pp. 99-102
Author(s):  
Chandan Prakash ◽  
P. Das ◽  
B. V. Sunil Kumar ◽  
Bincy Joseph ◽  
Vidya Singh ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Insertion Sequence ◽  
Burkholderia Mallei

scholarly journals Identification and characterization of Fep15, a new selenocysteine-containing member of the Sep15 protein family

2006 ◽  
Vol 394 (3) ◽  
pp. 575-579 ◽  
Author(s):  
Sergey V. Novoselov ◽  
Deame Hua ◽  
Alexey V. Lobanov ◽  
Vadim N. Gladyshev
Keyword(s):  
Mammalian Cells ◽  
Insertion Sequence ◽  
Phylogenetic Analyses ◽  
Dependent Manner ◽  
Putative Active Site ◽  
A Genome ◽  
Sequence Elements ◽  
Identification And Characterization ◽  
Insertion Sequence Elements

Sec (selenocysteine) is a rare amino acid in proteins. It is co-translationally inserted into proteins at UGA codons with the help of SECIS (Sec insertion sequence) elements. A full set of selenoproteins within a genome, known as the selenoproteome, is highly variable in different organisms. However, most of the known eukaryotic selenoproteins are represented in the mammalian selenoproteome. In addition, many of these selenoproteins have cysteine orthologues. Here, we describe a new selenoprotein, designated Fep15, which is distantly related to members of the 15 kDa selenoprotein (Sep15) family. Fep15 is absent in mammals, can be detected only in fish and is present in these organisms only in the selenoprotein form. In contrast with other members of the Sep15 family, which contain a putative active site composed of Sec and cysteine, Fep15 has only Sec. When transiently expressed in mammalian cells, Fep15 incorporated Sec in an SECIS- and SBP2 (SECIS-binding protein 2)-dependent manner and was targeted to the endoplasmic reticulum by its N-terminal signal peptide. Phylogenetic analyses of Sep15 family members suggest that Fep15 evolved by gene duplication.

scholarly journals Dynamics of Genome Architecture in Rhizobium sp. Strain NGR234

2002 ◽  
Vol 184 (1) ◽  
pp. 171-176 ◽  
Author(s):  
Patrick Mavingui ◽  
Margarita Flores ◽  
Xianwu Guo ◽  
Guillermo Dávila ◽  
Xavier Perret ◽  
...  
Keyword(s):  
Large Scale ◽  
Insertion Sequence ◽  
Biological Significance ◽  
Genome Architecture ◽  
Bacterial Genomes ◽  
Symbiotic Plasmid ◽  
Sequence Elements ◽  
Dynamic Structures ◽  
Genome Analyses ◽  
Insertion Sequence Elements

ABSTRACT Bacterial genomes are usually partitioned in several replicons, which are dynamic structures prone to mutation and genomic rearrangements, thus contributing to genome evolution. Nevertheless, much remains to be learned about the origins and dynamics of the formation of bacterial alternative genomic states and their possible biological consequences. To address these issues, we have studied the dynamics of the genome architecture in Rhizobium sp. strain NGR234 and analyzed its biological significance. NGR234 genome consists of three replicons: the symbiotic plasmid pNGR234a (536,165 bp), the megaplasmid pNGR234b (>2,000 kb), and the chromosome (>3,700 kb). Here we report that genome analyses of cell siblings showed the occurrence of large-scale DNA rearrangements consisting of cointegrations and excisions between the three replicons. As a result, four new genomic architectures have emerged. Three consisted of the cointegrates between two replicons: chromosome-pNGR234a, chromosome-pNGR234b, and pNGR234a-pNGR234b. The other consisted of a cointegrate of the three replicons (chromosome-pNGR234a-pNGR234b). Cointegration and excision of pNGR234a with either the chromosome or pNGR234b were studied and found to proceed via a Campbell-type mechanism, mediated by insertion sequence elements. We provide evidence showing that changes in the genome architecture did not alter the growth and symbiotic proficiency of Rhizobium derivatives.

scholarly journals Characterization of IS46, an insertion sequence found on two IncN plasmids.

1984 ◽  
Vol 159 (2) ◽  
pp. 472-481 ◽  
Author(s):  
A M Brown ◽  
G M Coupland ◽  
N S Willetts
Keyword(s):  
Insertion Sequence
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