Denitrification in Sinorhizobium meliloti

2011 ◽  
Vol 39 (6) ◽  
pp. 1886-1889 ◽  
Author(s):  
María J. Torres ◽  
María I. Rubia ◽  
Eulogio J. Bedmar ◽  
María J. Delgado
Keyword(s):  
Dna Sequences ◽  
Bradyrhizobium Japonicum ◽  
Sinorhizobium Meliloti ◽  
Current Knowledge ◽  
Gene Products ◽  
Free Living ◽  
Symbiotic Plasmid ◽  
Meliloti Strain ◽  
Complete Set ◽  
Denitrification Genes

Denitrification is the complete reduction of nitrate or nitrite to N2, via the intermediates nitric oxide (NO) and nitrous oxide (N2O), and is coupled to energy conservation and growth under O2-limiting conditions. In Bradyrhizobium japonicum, this process occurs through the action of the napEDABC, nirK, norCBQD and nosRZDFYLX gene products. DNA sequences showing homology with nap, nirK, nor and nos genes have been found in the genome of the symbiotic plasmid pSymA of Sinorhizobium meliloti strain 1021. Whole-genome transcriptomic analyses have demonstrated that S. meliloti denitrification genes are induced under micro-oxic conditions. Furthermore, S. meliloti has also been shown to possess denitrifying activities in both free-living and symbiotic forms. Despite possessing and expressing the complete set of denitrification genes, S. meliloti is considered a partial denitrifier since it does not grow under anaerobic conditions with nitrate or nitrite as terminal electron acceptors. In the present paper, we show that, under micro-oxic conditions, S. meliloti is able to grow by using nitrate or nitrite as respiratory substrates, which indicates that, in contrast with anaerobic denitrifiers, O2 is necessary for denitrification by S. meliloti. Current knowledge of the regulation of S. meliloti denitrification genes is also included.

scholarly journals New Recombination Methods for Sinorhizobium meliloti Genetics

2004 ◽  
Vol 70 (5) ◽  
pp. 2806-2815 ◽  
Author(s):  
Brent L. House ◽  
Michael W. Mortimer ◽  
Michael L. Kahn
Keyword(s):  
Dna Sequences ◽  
Sinorhizobium Meliloti ◽  
Bacterial Genome ◽  
Considerable Time ◽  
Deletion Mutations ◽  
Flp Recombinase ◽  
Symbiotic Plasmid ◽  
Cloning Method ◽  
Improved Methods

ABSTRACT The availability of bacterial genome sequences has created a need for improved methods for sequence-based functional analysis to facilitate moving from annotated DNA sequence to genetic materials for analyzing the roles that postulated genes play in bacterial phenotypes. A powerful cloning method that uses lambda integrase recombination to clone and manipulate DNA sequences has been adapted for use with the gram-negative α-proteobacterium Sinorhizobium meliloti in two ways that increase the utility of the system. Adding plasmid oriT sequences to a set of vehicles allows the plasmids to be transferred to S. meliloti by conjugation and also allows cloned genes to be recombined from one plasmid to another in vivo by a pentaparental mating protocol, saving considerable time and expense. In addition, vehicles that contain yeast Flp recombinase target recombination sequences allow the construction of deletion mutations where the end points of the deletions are located at the ends of the cloned genes. Several deletions were constructed in a cluster of 60 genes on the symbiotic plasmid (pSymA) of S. meliloti, predicted to code for a denitrification pathway. The mutations do not affect the ability of the bacteria to form nitrogen-fixing nodules on Medicago sativa (alfalfa) roots.

Experimental evidence for plasmid-bornenor-nirgenes inSinorhizobium melilotiJJ1c10

2004 ◽  
Vol 50 (9) ◽  
pp. 657-667 ◽  
Author(s):  
Yiu-Kwok Chan ◽  
Wayne A McCormick
Keyword(s):  
Nitric Oxide ◽  
Nitrous Oxide ◽  
Sinorhizobium Meliloti ◽  
Nitrite Reduction ◽  
Nucleotide Sequence Analysis ◽  
Gene Products ◽  
Oxide Reduction ◽  
Accessory Gene ◽  
Genes Encoding ◽  
Denitrification Genes

In denitrification, nir and nor genes are respectively required for the sequential dissimilatory reduction of nitrite and nitric oxide to form nitrous oxide. Their location on the pSymA megaplasmid of Sinorhizobium meliloti was confirmed by Southern hybridization of its clones with specific structural gene probes for nirK and norCB. A 20-kb region of pSymA containing the nor-nir genes was delineated by nucleotide sequence analysis. These genes were linked to the nap genes encoding periplasmic proteins involved in nitrate reduction. The nor-nir-nap segment is situated within 30 kb downstream from the nos genes encoding nitrous oxide reduction, with a fix cluster intervening between nir and nos. Most of these predicted nor-nir and accessory gene products are highly homologous with those of related proteobacterial denitrifiers. Functional tests of Tn5 mutants confirmed the requirement of the nirV product and 1 unidentified protein for nitrite reduction as well as the norB-D products and another unidentified protein for nitric oxide reduction. Overall comparative analysis of the derived amino acid sequences of the S. meliloti gene products suggested a close relationship between this symbiotic N2fixer and the free-living non-N2-fixing denitrifier Pseudomonas G-179, despite differences in their genetic organization. This relationship may be due to lateral gene transfer of denitrification genes from a common donor followed by rearrangement and recombination of these genes.Key words: denitrification genes, nitric oxide reductase, nitrite reductase, Rhizobiaceae, Sinorhizobium meliloti.

scholarly journals Molecular cloning and chromosomal localization of DNA sequences associated with a human DNA repair gene.

1985 ◽  
Vol 5 (2) ◽  
pp. 398-405 ◽  
Author(s):  
J S Rubin ◽  
V R Prideaux ◽  
H F Willard ◽  
A M Dulhanty ◽  
G F Whitmore ◽  
...  
Keyword(s):  
Dna Repair ◽  
Dna Sequences ◽  
Chromosomal Localization ◽  
Excision Repair ◽  
Repair Process ◽  
Human Cells ◽  
Gene Products ◽  
Repair Gene ◽  
Human Dna ◽  
Dna Repair Gene

The genes and gene products involved in the mammalian DNA repair processes have yet to be identified. Toward this end we made use of a number of DNA repair-proficient transformants that were generated after transfection of DNA from repair-proficient human cells into a mutant hamster line that is defective in the initial incision step of the excision repair process. In this report, biochemical evidence is presented that demonstrates that these transformants are repair proficient. In addition, we describe the molecular identification and cloning of unique DNA sequences closely associated with the transfected human DNA repair gene and demonstrate the presence of homologous DNA sequences in human cells and in the repair-proficient DNA transformants. The chromosomal location of these sequences was determined by using a panel of rodent-human somatic cell hybrids. Both unique DNA sequences were found to be on human chromosome 19.

The complete denitrification pathway of the symbiotic, nitrogen-fixing bacterium Bradyrhizobium japonicum

2005 ◽  
Vol 33 (1) ◽  
pp. 141-144 ◽  
Author(s):  
E.J. Bedmar ◽  
E.F. Robles ◽  
M.J. Delgado
Keyword(s):  
Nitric Oxide ◽  
Nitrous Oxide ◽  
Bradyrhizobium Japonicum ◽  
Mutational Analysis ◽  
Control Level ◽  
Gene Clusters ◽  
Alternative Form ◽  
Nitrate Respiration ◽  
Regulatory Cascade ◽  
Denitrification Genes

Denitrification is an alternative form of respiration in which bacteria sequentially reduce nitrate or nitrite to nitrogen gas by the intermediates nitric oxide and nitrous oxide when oxygen concentrations are limiting. In Bradyrhizobium japonicum, the N2-fixing microsymbiont of soya beans, denitrification depends on the napEDABC, nirK, norCBQD, and nosRZDFYLX gene clusters encoding nitrate-, nitrite-, nitric oxide- and nitrous oxide-reductase respectively. Mutational analysis of the B. japonicum nap genes has demonstrated that the periplasmic nitrate reductase is the only enzyme responsible for nitrate respiration in this bacterium. Regulatory studies using transcriptional lacZ fusions to the nirK, norCBQD and nosRZDFYLX promoter region indicated that microaerobic induction of these promoters is dependent on the fixLJ and fixK2 genes whose products form the FixLJ–FixK2 regulatory cascade. Besides FixK2, another protein, nitrite and nitric oxide respiratory regulator, has been shown to be required for N-oxide regulation of the B. japonicum nirK and norCBQD genes. Thus nitrite and nitric oxide respiratory regulator adds to the FixLJ–FixK2 cascade an additional control level which integrates the N-oxide signal that is critical for maximal induction of the B. japonicum denitrification genes. However, the identity of the signalling molecule and the sensing mechanism remains unknown.

scholarly journals Bradyrhizobium japonicum NnrR, a Denitrification Regulator, Expands the FixLJ-FixK2 Regulatory Cascade

2003 ◽  
Vol 185 (13) ◽  
pp. 3978-3982 ◽  
Author(s):  
Socorro Mesa ◽  
Eulogio J. Bedmar ◽  
Astrid Chanfon ◽  
Hauke Hennecke ◽  
Hans-Martin Fischer
Keyword(s):  
Bradyrhizobium Japonicum ◽  
Control Level ◽  
Nitric Oxide Reductase ◽  
Regulatory Cascade ◽  
Additional Control ◽  
Mutant Strains ◽  
Genes Encoding ◽  
Maximal Induction ◽  
Nitrate And Nitrite ◽  
Denitrification Genes

ABSTRACT In Bradyrhizobium japonicum, a gene named nnrR was identified which encodes a protein with high similarity to FNR/CRP-type transcriptional regulators. Mutant strains carrying an nnrR null mutation were unable to grow anaerobically in the presence of nitrate or nitrite, and they lacked both nitrate and nitrite reductase activities. Anaerobic activation of an nnrR′-′lacZ fusion required FixLJ and FixK2. In turn, N oxide-mediated induction of nir and nor genes encoding nitrite and nitric oxide reductase, respectively, depended on NnrR. Thus, NnrR expands the FixLJ-FixK2 regulatory cascade by an additional control level which integrates the N oxide signal required for maximal induction of the denitrification genes.

scholarly journals Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021

2001 ◽  
Vol 98 (17) ◽  
pp. 9877-9882 ◽  
Author(s):  
D. Capela ◽  
F. Barloy-Hubler ◽  
J. Gouzy ◽  
G. Bothe ◽  
F. Ampe ◽  
...  
Keyword(s):  
Sinorhizobium Meliloti ◽  
Chromosome Sequence ◽  
Meliloti Strain

scholarly journals Horizontal gene transfer of a unique nif island drives convergent evolution of free-living N2-fixing Bradyrhizobium

2021 ◽  
Author(s):  
Jinjin Tao ◽  
Sishuo Wang ◽  
Tianhua Liao ◽  
Haiwei Luo
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Agricultural Research ◽  
Current Knowledge ◽  
Gene Clusters ◽  
Soil Samples ◽  
Genomic Context ◽  
Free Living ◽  
Phylogenomic Analyses ◽  
Conserved Gene

SummaryThe alphaproteobacterial genus Bradyrhizobium has been best known as N2-fixing members that nodulate legumes, supported by the nif and nod gene clusters. Recent environmental surveys show that Bradyrhizobium represents one of the most abundant free-living bacterial lineages in the world’s soils. However, our understanding of Bradyrhizobium comes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88 Bradyrhizobium strains derived from diverse soil samples, including both nif-carrying and non-nif-carrying free-living (nod free) members. Phylogenomic analyses of these and 252 publicly available Bradyrhizobium genomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, the nif phylogeny shows that all nif-carrying free-living members comprise a cluster which branches off earlier than most symbiotic lineages. These results indicate that horizontal gene transfer (HGT) promotes nif expansion among the free-living Bradyrhizobium and that the free-living nif cluster represents a more ancestral version compared to that in symbiotic lineages. Further evidence for this rampant HGT is that the nif in free-living members consistently co-locate with several important genes involved in coping with oxygen tension which are missing from symbiotic members, and that while in free-living Bradyrhizobium nif and the co-locating genes show a highly conserved gene order, they each have distinct genomic context. Given the dominance of Bradyrhizobium in world’s soils, our findings have implications for global nitrogen cycles and agricultural research.

Plasmid replicons of Rhizobium

2005 ◽  
Vol 33 (1) ◽  
pp. 157-158 ◽  
Author(s):  
L.C. Crossman
Keyword(s):  
Short Review ◽  
Nitrogen Fixing ◽  
Rhizobium Etli ◽  
Free Living ◽  
Leguminous Plants ◽  
Symbiotic Plasmid ◽  
Rhizobium Spp ◽  
Plasmid Replicons ◽  
Rhizobium Sp

Rhizobium spp. are found in soil. They are both free-living and found symbiotically associated with the nodules of leguminous plants. Traditionally, studies have focused on the association of these organisms with plants in nitrogen-fixing nodules, since this is regarded as the most important role of these bacteria in the environment. Rhizobium sp. are known to possess several replicons. Some, like the Rhizobium etli symbiotic plasmid p42d and the plasmid pNGR234b of Rhizobium NGR234, have been sequenced and characterized. The plasmids from these organisms are the focus of this short review.

scholarly journals The Novel Genes emmABC Are Associated with Exopolysaccharide Production, Motility, Stress Adaptation, and Symbiosis in Sinorhizobium meliloti

2009 ◽  
Vol 191 (19) ◽  
pp. 5890-5900 ◽  
Author(s):  
Jennifer Morris ◽  
Juan E. González
Keyword(s):  
Sinorhizobium Meliloti ◽  
Genetic Factors ◽  
Leguminous Plant ◽  
The Novel ◽  
Two Component System ◽  
Cell Component ◽  
Plant Host ◽  
Free Living ◽  
Novel Genes ◽  
Exopolysaccharide Production

ABSTRACT The nitrogen-fixing symbiont Sinorhizobium meliloti senses and responds to constantly changing environmental conditions as it makes its way through the soil in search of its leguminous plant host, Medicago sativa (alfalfa). As a result, this bacterium regulates various aspects of its physiology in order to respond appropriately to stress, starvation, and competition. For example, exopolysaccharide production, which has been shown to play an important role in the ability of S. meliloti to successfully invade its host, also helps the bacterium withstand osmotic changes and other environmental stresses. In an effort to further elucidate the intricate regulation of this important cell component, we set out to identify genetic factors that may affect its production. Here we characterize novel genes that encode a small protein (EmmA) and a putative two-component system (EmmB-EmmC). A mutation in any of these genes leads to increased production of the symbiotically important exopolysaccharide succinoglycan. In addition, emm mutants display membrane-associated defects, are nonmotile, and are unable to form an optimal symbiosis with alfalfa, suggesting that these novel genes may play a greater role in the overall fitness of S. meliloti both during the free-living stage and in its association with its host.

Biodiversity of intertidal marine flatworms (Polycladida, Platyhelminthes) in southeastern Australia

Zootaxa ◽  
2021 ◽  
Vol 5024 (1) ◽  
pp. 1-63
Author(s):  
JORGE RODRÍGUEZ ◽  
PAT A. HUTCHINGS ◽  
JANE E. WILLIAMSON
Keyword(s):  
Dna Sequences ◽  
New South ◽  
Marine Biota ◽  
Free Living ◽  
Marine Fauna ◽  
Southeastern Australia ◽  
Marine Habitats ◽  
South Wales ◽  
Molecular Sequencing ◽  
Insight Into

Flatworms of the Order Polycladida are a group of free-living invertebrates found in a diversity of marine habitats, with over 800 species described worldwide. Marine flatworms are a conspicuous component of Australia’s marine fauna yet have received little attention. Less than 30 scientific articles have been published on Australian marine flatworms since 1855, of which only nine include species from southeastern Australia. Here, the biodiversity and distribution of species belonging to the Order Polycladida inhabiting intertidal rocky beaches in southeastern Australian waters were identified and analysed. Sampling was conducted at low tide along the coasts of New South Wales and Victoria. Collected samples were serially sectioned for comparative anatomical studies, and tissue was removed from each individual for molecular sequencing and analyses. Both nuclear and mitochondrial DNA sequences were obtained and used as an additional source of evidence for the description of new species as well as providing further insight into the phylogenetic relationships between them. A total of 20 species, six of which are new (e.g., Eulatocestus australis sp. nov.), and a new genus (Parabolia gen. nov.) have been described, as well as two new records for Australia (e.g., Stylochoplana clara Kato, 1937) have been identified increasing our knowledge of this important component of the Australian marine biota.  

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