Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti

Genome ◽  
2009 ◽  
Vol 52 (10) ◽  
pp. 862-875 ◽  
Author(s):  
Hong Guo ◽  
Sheng Sun ◽  
Bertrand Eardly ◽  
Turlough Finan ◽  
Jianping Xu
Keyword(s):  
Genome Size ◽  
Sinorhizobium Meliloti ◽  
Distribution Patterns ◽  
Pulse Field ◽  
Size Difference ◽  
Whole Genome ◽  
Nitrogen Fixing ◽  
Genome Variation ◽  
Pulse Field Gel Electrophoresis ◽  
A Genome

Differences in genome size and gene content are among the most important signatures of microbial adaptation and genome evolution. Here, we investigated the patterns of genome variation among 10 natural strains of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti , using pulse field gel electrophoresis (PFGE) and whole-genome microarray hybridizations. Our PFGE analysis showed a genome size range of 6.45–7.01 Mbp, with the greatest variation arising from the pSymA replicon, followed by pSymB; no size difference was evident among the chromosomes. Consistent with this pattern of size differences, 41.2% of open reading frames (ORFs) on pSymA were variably absent/present, followed by 12.7% on pSymB and 3.7% on the chromosome. However, the ORFs that were variably duplicated were more evenly distributed among the three replicons: 11.0%, 16.5%, and 15.3% of ORFs on pSymA, pSymB, and the chromosome, respectively. Among the 10 strains, the percentage of ORFs that were absent ranged from 1.51% to 6.35%, and the percentage of ORFs that were duplicated ranged from 0.27% to 8.56%. Our analyses showed that host plants, geographic origins, multilocus enzyme electrophoretic types, and replicon sizes had little influence on the distribution patterns of absent or duplicated ORFs. The proportions of ORFs that were either variably absent/present or variably duplicated differed greatly among the functional categories, for each of the three replicons as well as for the whole genome. Interestingly, we observed positive correlations among the three replicons in the number of absent ORFs as well as the number of duplicated ORFs, consistent with coordinated gene gains and losses in this important bacterium in nature.

scholarly journals Novel DNA Sequences from Natural Strains of the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti

2005 ◽  
Vol 71 (11) ◽  
pp. 7130-7138 ◽  
Author(s):  
Hong Guo ◽  
Sheng Sun ◽  
Turlough M. Finan ◽  
Jianping Xu
Keyword(s):  
Genome Size ◽  
Dna Sequences ◽  
Sinorhizobium Meliloti ◽  
Representational Difference Analysis ◽  
Gene Gain ◽  
Enzyme Electrophoresis ◽  
Dna Fragments ◽  
Nitrogen Fixing ◽  
Ecological Specialization ◽  
A Genome

ABSTRACT Variation in genome size and content is common among bacterial strains. Identifying these naturally occurring differences can accelerate our understanding of bacterial attributes, such as ecological specialization and genome evolution. In this study, we used representational difference analysis to identify potentially novel sequences not present in the sequenced laboratory strain Rm1021 of the nitrogen-fixing bacterium Sinorhizobium meliloti. Using strain Rm1021 as the driver and the type strain of S. meliloti ATCC 9930, which has a genome size ∼370 kilobases bigger than that of strain Rm1021, as the tester, we identified several groups of sequences in the ATCC 9930 genome not present in strain Rm1021. Among the 85 novel DNA fragments examined, 55 showed no obvious homologs anywhere in the public databases. Of the remaining 30 sequences, 24 contained homologs to the Rm1021 genome as well as unique segments not found in Rm1021, 3 contained sequences homologous to those published for another S. meliloti strain but absent in Rm1021, 2 contained sequences homologous to other symbiotic nitrogen-fixing bacteria (Rhizobium etli and Bradyrhizobium japonicum), and 1 contained a sequence homologous to a gene in a non-nitrogen-fixing species, Pseudomonas sp. NK87. Using PCR, we assayed the distribution of 12 of the above 85 novel sequences in a collection of 59 natural S. meliloti strains. The distribution varied widely among the 12 novel DNA fragments, from 1.7% to 72.9%. No apparent correlation was found between the distribution of these novel DNA sequences and their genotypes obtained using multilocus enzyme electrophoresis. Our results suggest potentially high rates of gene gain and loss in S. meliloti genomes.

scholarly journals Comparison of the Microsatellite Distribution Patterns in the Genomes of Euarchontoglires at the Taxonomic Level

2021 ◽  
Vol 12 ◽  
Author(s):  
Xuhao Song ◽  
Tingbang Yang ◽  
Xinyi Zhang ◽  
Ying Yuan ◽  
Xianghui Yan ◽  
...  
Keyword(s):  
Genome Size ◽  
Gc Content ◽  
Distribution Patterns ◽  
Functional Roles ◽  
Tree Shrews ◽  
Copy Numbers ◽  
Genome Wide ◽  
A Genome ◽  
Dinucleotide Motif ◽  
Evolution Of Mammals

Microsatellite or simple sequence repeat (SSR) instability within genes can induce genetic variation. The SSR signatures remain largely unknown in different clades within Euarchontoglires, one of the most successful mammalian radiations. Here, we conducted a genome-wide characterization of microsatellite distribution patterns at different taxonomic levels in 153 Euarchontoglires genomes. Our results showed that the abundance and density of the SSRs were significantly positively correlated with primate genome size, but no significant relationship with the genome size of rodents was found. Furthermore, a higher level of complexity for perfect SSR (P-SSR) attributes was observed in rodents than in primates. The most frequent type of P-SSR was the mononucleotide P-SSR in the genomes of primates, tree shrews, and colugos, while mononucleotide or dinucleotide motif types were dominant in the genomes of rodents and lagomorphs. Furthermore, (A)n was the most abundant motif in primate genomes, but (A)n, (AC)n, or (AG)n was the most abundant motif in rodent genomes which even varied within the same genus. The GC content and the repeat copy numbers of P-SSRs varied in different species when compared at different taxonomic levels, reflecting underlying differences in SSR mutation processes. Notably, the CDSs containing P-SSRs were categorized by functions and pathways using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations, highlighting their roles in transcription regulation. Generally, this work will aid future studies of the functional roles of the taxonomic features of microsatellites during the evolution of mammals in Euarchontoglires.

scholarly journals A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 245 ◽  
Author(s):  
Jan-Philip Schlüter ◽  
Jan Reinkensmeier ◽  
Svenja Daschkey ◽  
Elena Evguenieva-Hackenberg ◽  
Stefan Janssen ◽  
...  
Keyword(s):  
Sinorhizobium Meliloti ◽  
Nitrogen Fixing ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Survey

scholarly journals Complete Genome Sequence of Sinorhizobium meliloti Bacteriophage HMSP1-Susan

2018 ◽  
Vol 6 (18) ◽  
pp. e01450-17 ◽  
Author(s):  
Brennon Fleagle ◽  
Aldina Imamovic ◽  
Silvia Toledo ◽  
Madison Couves ◽  
Autumn Jensen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sinorhizobium Meliloti ◽  
Gc Content ◽  
Nitrogen Fixing ◽  
Coding Sequences ◽  
A Genome

ABSTRACT Sinorhiozbium bacteriophage HMSP1-Susan has a genome of 51,963 bp in size, with a GC content of 52.5%. It contains 97 putative coding sequences; 83% of these coding sequences (CDS) encode proteins classified as hypothetical or having unknown functions. HMSP1 has limited homology to previously reported viruses and likely represents a new phage that infects this nitrogen-fixing bacterium.

scholarly journals The Prevalence of Virulence Determinants and Antibiotic Resistance Patterns in Methicillin—Resistant Staphylococcus aureus in a Nursing Home in Poland

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 427
Author(s):  
Martyna Kasela ◽  
Agnieszka Grzegorczyk ◽  
Bożena Nowakowicz-Dębek ◽  
Anna Malm
Keyword(s):  
Staphylococcus Aureus ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Variable Number Tandem Repeat ◽  
Multidrug Resistant ◽  
Variable Number ◽  
Pulse Field ◽  
Virulence Determinants ◽  
Gene Encoding ◽  
Methicillin Resistant ◽  
Pulse Field Gel Electrophoresis

Nursing homes (NH) contribute to the regional spread of methicillin-resistant Staphylococcus aureus (MRSA). Moreover, residents are vulnerable to the colonization and subsequent infection of MRSA etiology. We aimed at investigating the molecular and phenotypic characteristics of 21 MRSA collected from the residents and personnel in an NH (Lublin, Poland) during 2018. All MRSA were screened for 20 genes encoding virulence determinants (sea-see, eta, etb, tst, lukS-F-PV, eno, cna, ebpS, fib, bbp, fnbA, fnbB, icaADBC) and for resistance to 18 antimicrobials. To establish the relatedness and clonal complexes of MRSA in NH we applied multiple-locus variable-number tandem-repeat fingerprinting (MLVF), pulse field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) typing. We identified four sequence types (ST) among two clonal complexes (CC): ST (CC22) known as EMRSA-15 as well as three novel STs—ST6295 (CC8), ST6293 (CC8) and ST6294. All tested MRSA were negative for sec, eta, etb, lukS-F-PV, bbp and ebpS genes. The most prevalent gene encoding toxin was sed (52.4%; n = 11/21), and adhesins were eno and fnbA (100%). Only 9.5% (n = 2/21) of MRSA were classified as multidrug-resistant. The emergence of novel MRSA with a unique virulence and the presence of epidemic clone EMRSA-15 creates challenges for controlling the spread of MRSA in NH.

scholarly journals The Location of Substitutions and Bacterial Genome Arrangements

2020 ◽  
Author(s):  
Daniella F Lato ◽  
G Brian Golding
Keyword(s):  
Sinorhizobium Meliloti ◽  
Bacterial Genome ◽  
Evolutionary Analysis ◽  
Origin Of Replication ◽  
Ancestral Reconstruction ◽  
Molecular Change ◽  
E Coli ◽  
A Genome ◽  
The Impact ◽  
Molecular Evolutionary Analysis

Abstract Increasing evidence supports the notion that different regions of a genome have unique rates of molecular change. This variation is particularly evident in bacterial genomes where previous studies have reported gene expression and essentiality tend to decrease, while substitution rates usually increases with increasing distance from the origin of replication. Genomic reorganization such as rearrangements occur frequently in bacteria and allow for the introduction and restructuring of genetic content, creating gradients of molecular traits along genomes. Here, we explore the interplay of these phenomena by mapping substitutions to the genomes of Escherichia coli, Bacillus subtilis, Streptomyces, and Sinorhizobium meliloti, quantifying how many substitutions have occurred at each position in the genome. Preceding work indicates that substitution rate significantly increases with distance from the origin. Using a larger sample size and accounting for genome rearrangements through ancestral reconstruction, our analysis demonstrates that the correlation between the number of substitutions and distance from the origin of replication is often significant but small and inconsistent in direction. Some replicons had a significantly decreasing trend (E. coli and the chromosome of S. meliloti), while others showed the opposite significant trend (B. subtilis, Streptomyces, pSymA and pSymB in S. meliloti). dN, dS and ω were examined across all genes and there was no significant correlation between those values and distance from the origin. This study highlights the impact that genomic rearrangements and location have on molecular trends in some bacteria, illustrating the importance of considering spatial trends in molecular evolutionary analysis. Assuming that molecular trends are exclusively in one direction can be problematic.

scholarly journals A Genome-Scale Metabolic Model of Anabaena 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers

Metabolites ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 168
Author(s):  
John I. Hendry ◽  
Hoang V. Dinh ◽  
Debolina Sarkar ◽  
Lin Wang ◽  
Anindita Bandyopadhyay ◽  
...  
Keyword(s):  
Electron Transport ◽  
Pyruvate Decarboxylase ◽  
Metabolic Model ◽  
Cell Types ◽  
Economic Feasibility ◽  
Nitrogen Fixing ◽  
Design Algorithm ◽  
A Genome ◽  
Anabaena Sp ◽  
Genome Scale

Nitrogen fixing-cyanobacteria can significantly improve the economic feasibility of cyanobacterial production processes by eliminating the requirement for reduced nitrogen. Anabaena sp. ATCC 33047 is a marine, heterocyst forming, nitrogen fixing cyanobacteria with a very short doubling time of 3.8 h. We developed a comprehensive genome-scale metabolic (GSM) model, iAnC892, for this organism using annotations and content obtained from multiple databases. iAnC892 describes both the vegetative and heterocyst cell types found in the filaments of Anabaena sp. ATCC 33047. iAnC892 includes 953 unique reactions and accounts for the annotation of 892 genes. Comparison of iAnC892 reaction content with the GSM of Anabaena sp. PCC 7120 revealed that there are 109 reactions including uptake hydrogenase, pyruvate decarboxylase, and pyruvate-formate lyase unique to iAnC892. iAnC892 enabled the analysis of energy production pathways in the heterocyst by allowing the cell specific deactivation of light dependent electron transport chain and glucose-6-phosphate metabolizing pathways. The analysis revealed the importance of light dependent electron transport in generating ATP and NADPH at the required ratio for optimal N2 fixation. When used alongside the strain design algorithm, OptForce, iAnC892 recapitulated several of the experimentally successful genetic intervention strategies that over produced valerolactam and caprolactam precursors.

scholarly journals Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luz K. Medina-Cordoba ◽  
Aroon T. Chande ◽  
Lavanya Rishishwar ◽  
Leonard W. Mayer ◽  
Lina C. Valderrama-Aguirre ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Nitrogen Fixation ◽  
Plant Growth ◽  
Phosphate Solubilization ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Promising Tool ◽  
A Genome ◽  
Plant Growth Promoting ◽  
Growth Promoting

AbstractPrevious studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems.

scholarly journals Draft Genome Sequence of the Nitrogen-Fixing and Hormogonia-Inducing CyanobacteriumNostoc cycadaeStrain WK-1, Isolated from the Coralloid Roots ofCycas revoluta

2018 ◽  
Vol 6 (7) ◽  
Author(s):  
Yu Kanesaki ◽  
Masaki Hirose ◽  
Yuu Hirose ◽  
Takatomo Fujisawa ◽  
Yasukazu Nakamura ◽  
...  
Keyword(s):  
Host Plant ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nitrogen Fixing ◽  
Coralloid Roots ◽  
Cycas Revoluta

ABSTRACTWe report here the whole-genome sequence ofNostoc cycadaestrain WK-1, which was isolated from cyanobacterial colonies growing in the coralloid roots of the gymnospermCycas revoluta. It can provide valuable resources to study the mutualistic relationships and the syntrophic metabolisms between the cyanobacterial symbiont and the host plant,C. revoluta.

scholarly journals DNA Genome Size Affects the Stability of the Adenovirus Virion

2008 ◽  
Vol 83 (4) ◽  
pp. 2025-2028 ◽  
Author(s):  
Adam C. Smith ◽  
Kathy L. Poulin ◽  
Robin J. Parks
Keyword(s):  
Genome Size ◽  
Critical Role ◽  
Heat Stability ◽  
Helper Virus ◽  
Heat Inactivation ◽  
Similar Relationship ◽  
Viral Dna ◽  
A Genome ◽  
The Stability ◽  
Replication Defective Adenovirus

ABSTRACT Replication-defective adenovirus (Ad) vectors can vary considerably in genome length, but whether this affects virion stability has not been investigated. Helper-dependent Ad vectors with a genome size of ∼30 kb were 100-fold more sensitive to heat inactivation than their parental helper virus (>36 kb), and increasing the genome size of the vector significantly improved heat stability. A similar relationship between genome size and stability existed for Ad with early region 1 deleted. Loss of infectivity was due to release of vertex proteins, followed by disintegration of the capsid. Thus, not only does the viral DNA encode all of the heritable information essential for virus replication, it also plays a critical role in maintaining capsid strength and integrity.

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