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Zhang K, Wang Y, Zhang Y, Shan X. Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina. BMC Genom Data 2024; 25:6. [PMID: 38218810 PMCID: PMC10788020 DOI: 10.1186/s12863-024-01191-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/04/2024] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND Hemerocallis citrina Baroni is a traditional vegetable crop widely cultivated in eastern Asia for its high edible, medicinal, and ornamental value. The phenomenon of codon usage bias (CUB) is prevalent in various genomes and provides excellent clues for gaining insight into organism evolution and phylogeny. Comprehensive analysis of the CUB of mitochondrial (mt) genes can provide rich genetic information for improving the expression efficiency of exogenous genes and optimizing molecular-assisted breeding programmes in H. citrina. RESULTS Here, the CUB patterns in the mt genome of H. citrina were systematically analyzed, and the possible factors shaping CUB were further evaluated. Composition analysis of codons revealed that the overall GC (GCall) and GC at the third codon position (GC3) contents of mt genes were lower than 50%, presenting a preference for A/T-rich nucleotides and A/T-ending codons in H. citrina. The high values of the effective number of codons (ENC) are indicative of fairly weak CUB. Significant correlations of ENC with the GC3 and codon counts were observed, suggesting that not only compositional constraints but also gene length contributed greatly to CUB. Combined ENC-plot, neutrality plot, and Parity rule 2 (PR2)-plot analyses augmented the inference that the CUB patterns of the H. citrina mitogenome can be attributed to multiple factors. Natural selection, mutation pressure, and other factors might play a major role in shaping the CUB of mt genes, although natural selection is the decisive factor. Moreover, we identified a total of 29 high-frequency codons and 22 optimal codons, which exhibited a consistent preference for ending in A/T. Subsequent relative synonymous codon usage (RSCU)-based cluster and mt protein coding gene (PCG)-based phylogenetic analyses suggested that H. citrina is close to Asparagus officinalis, Chlorophytum comosum, Allium cepa, and Allium fistulosum in evolutionary terms, reflecting a certain correlation between CUB and evolutionary relationships. CONCLUSIONS There is weak CUB in the H. citrina mitogenome that is subject to the combined effects of multiple factors, especially natural selection. H. citrina was found to be closely related to Asparagus officinalis, Chlorophytum comosum, Allium cepa, and Allium fistulosum in terms of their evolutionary relationships as well as the CUB patterns of their mitogenomes. Our findings provide a fundamental reference for further studies on genetic modification and phylogenetic evolution in H. citrina.
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Affiliation(s)
- Kun Zhang
- College of Agriculture and Life Sciences, Shanxi Datong University, Datong, Shanxi, China.
- Key Laboratory of Organic Dry Farming for Special Crops in Datong City, Datong, Shanxi, China.
| | - Yiheng Wang
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yue Zhang
- College of Agriculture and Life Sciences, Shanxi Datong University, Datong, Shanxi, China
| | - Xiaofei Shan
- College of Agriculture and Life Sciences, Shanxi Datong University, Datong, Shanxi, China
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Xu J, Wang Y, Liu F, Duan G, Yang H. Genome mining reveals the prevalence and extensive diversity of toxin-antitoxin systems in Staphylococcus aureus. Front Microbiol 2023; 14:1165981. [PMID: 37293231 PMCID: PMC10244574 DOI: 10.3389/fmicb.2023.1165981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/28/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction Staphylococcus aureus (S. aureus) is a highly pathogenic and adaptable Gram-positive bacterium that exhibits persistence in various environments. The toxin-antitoxin (TA) system plays a crucial role in the defense mechanism of bacterial pathogens, allowing them to survive in stressful conditions. While TA systems in clinical pathogens have been extensively studied, there is limited knowledge regarding the diversity and evolutionary complexities of TA systems in S. aureus. Methods We conducted a comprehensive in silico survey using 621 publicly available S. aureus isolates. We employed bioinformatic search and prediction tools, including SLING, TADB2.0, and TASmania, to identify TA systems within the genomes of S. aureus. Results Our analysis revealed a median of seven TA systems per genome, with three type II TA groups (HD, HD_3, and YoeB) being present in over 80% of the strains. Additionally, we observed that TA genes were predominantly encoded in the chromosomal DNA, with some TA systems also found within the Staphylococcal Cassette Chromosomal mec (SCCmec) genomic islands. Discussion This study provides a comprehensive overview of the diversity and prevalence of TA systems in S. aureus. The findings enhance our understanding of these putative TA genes and their potential implications in S. aureus ecology and disease management. Moreover, this knowledge could guide the development of novel antimicrobial strategies.
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Affiliation(s)
| | | | | | | | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou, China
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3
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Martinez-Gutierrez CA, Aylward FO. Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales. PLoS Genet 2022; 18:e1010220. [PMID: 35605022 PMCID: PMC9166353 DOI: 10.1371/journal.pgen.1010220] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/03/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022] Open
Abstract
The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider the potential bias introduced by the shared ancestry of many lineages, which is critical when using species as data points because of the potential dependence on residuals. In this study, we investigated the genome size distributions across a broad diversity of bacteria and archaea to evaluate if this trait is phylogenetically conserved at broad phylogenetic scales. After model fit, Pagel's lambda indicated a strong phylogenetic signal in genome size data, suggesting that the diversification of this trait is influenced by shared evolutionary histories. We used a phylogenetic generalized least-squares analysis (PGLS) to test whether phylogeny influences the predictability of genome size from dN/dS ratios and 16S copy number, two variables that have been previously linked to genome size. These results confirm that failure to account for evolutionary history can lead to biased interpretations of genome size predictors. Overall, our results indicate that although bacteria and archaea can rapidly gain and lose genetic material through gene transfers and deletions, respectively, phylogenetic signal for genome size distributions can still be recovered at broad phylogenetic scales that should be taken into account when inferring the drivers of genome size evolution.
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Affiliation(s)
| | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, United States of America
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Eltarahony M, Ibrahim A, El-shall H, Ibrahim E, Althobaiti F, Fayad E. Antibacterial, Antifungal and Antibiofilm Activities of Silver Nanoparticles Supported by Crude Bioactive Metabolites of Bionanofactories Isolated from Lake Mariout. Molecules 2021; 26:3027. [PMID: 34069487 PMCID: PMC8161313 DOI: 10.3390/molecules26103027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/24/2022] Open
Abstract
Lake Mariout is one of the polluted coastal marine ecosystems in Egypt which is considered to be a reservoir of serious effluents from different anthropogenic activities. Such selective pressure enforces indigenous microbial populations to acquire new advantageous themes. Thus, in this study, two Streptomyces strains were screened, from Lake Mariout's sediment for bioreduction of 5 mM AgNO3. Both strains were identified molecularly; their biochemical and physiological characterization revealed their ability to secrete bioactive metabolites with antagonistic activity. The cultural and incubation conditions influencing AgNPs productivity were evaluated. Subsequently, the physicochemical properties of the biofabricated AgNPs were pursued. UV-Vis spectroscopy detected surface plasmon resonance at range 458-422 nm. XRD indicated crystalline, pure, face-centered cubic AgNPs; EDX demonstrated strong silver signal at 3.5 keV. Besides, FT-IR and TGA analysis unveiled self-stabilization and functionalization of AgNPs by bioorganic molecules. However, electron microscopy micrographs depicted numerous uniform spherical AgNPs (1.17-13.3 nm). Potent bactericidal and fungicide activity were recorded by zone of inhibition assay at 50 μg/mL. Further, the antibiofilm activity was exerted in a dose-dependent manner. Moreover, the conjugation of AgNPs with the crude bioactive metabolites of both bionanofactories ameliorated the antimicrobial potency, reflecting a synergistic efficiency versus examined pathogens (free-living and biofilm).
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Affiliation(s)
- Marwa Eltarahony
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Alexandria, Egypt; (H.E.-s.); (E.I.)
| | - Amany Ibrahim
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Hadeel El-shall
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Alexandria, Egypt; (H.E.-s.); (E.I.)
| | - Eman Ibrahim
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Alexandria, Egypt; (H.E.-s.); (E.I.)
| | - Fayez Althobaiti
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (F.A.); (E.F.)
| | - Eman Fayad
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (F.A.); (E.F.)
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Rajamanickam K, Yang J, Chidambaram SB, Sakharkar MK. Enhancing Drug Efficacy against Mastitis Pathogens-An In Vitro Pilot Study in Staphylococcus aureus and Staphylococcus epidermidis. Animals (Basel) 2020; 10:E2117. [PMID: 33203170 PMCID: PMC7696410 DOI: 10.3390/ani10112117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Bovine mastitis is one of the major infectious diseases in dairy cattle, resulting in large economic loss due to decreased milk production and increased production cost to the dairy industry. Antibiotics are commonly used to prevent/treat bovine mastitis infections. However, increased antibiotic resistance and consumers' concern regarding antibiotic overuse make it prudent and urgent to develop novel therapeutic protocols for this disease. MATERIALS AND METHODS Potential druggable targets were found in 20 mastitis-causing pathogens and conserved and unique targets were identified. Bacterial strains Staphylococcus aureus (ATCC 29213, and two clinical isolates CI 1 and CI 2) and Staphylococcus epidermidis (ATCC 12228, and two clinical isolates CI 1 and CI 2) were used in the present study for validation of an effective drug combination. RESULTS In the current study, we identified the common and the unique druggable targets for twenty mastitis-causing pathogens using an integrative approach. Furthermore, we showed that phosphorylcholine, a drug for a unique target gamma-hemolysin component B in Staphylococcus aureus, and ceftiofur, the mostly used veterinary antibiotic that is FDA approved for treating mastitis infections, exhibit a synergistic effect against S. aureus and a strong additive effect against Staphylococcus epidermidis in vitro. CONCLUSION Based on the data generated in this study, we propose that combination therapy with drugs that work synergistically against conserved and unique targets can help increase efficacy and lower the usage of antibiotics for treating bacterial infections. However, these data need further validations in animal models of infection.
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Affiliation(s)
- Karthic Rajamanickam
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada; (K.R.); (J.Y.)
| | - Jian Yang
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada; (K.R.); (J.Y.)
| | - Saravana Babu Chidambaram
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research (JSS AHER), Mysuru-570015, Karnataka, India;
| | - Meena Kishore Sakharkar
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada; (K.R.); (J.Y.)
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Molecular insights into the genome dynamics and interactions between core and acquired genomes of Vibrio cholerae. Proc Natl Acad Sci U S A 2020; 117:23762-23773. [PMID: 32873641 DOI: 10.1073/pnas.2006283117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial species are hosts to horizontally acquired mobile genetic elements (MGEs), which encode virulence, toxin, antimicrobial resistance, and other metabolic functions. The bipartite genome of Vibrio cholerae harbors sporadic and conserved MGEs that contribute in the disease development and survival of the pathogens. For a comprehensive understanding of dynamics of MGEs in the bacterial genome, we engineered the genome of V. cholerae and examined in vitro and in vivo stability of genomic islands (GIs), integrative conjugative elements (ICEs), and prophages. Recombinant vectors carrying the integration module of these GIs, ICE and CTXΦ, helped us to understand the efficiency of integrations of MGEs in the V. cholerae chromosome. We have deleted more than 250 acquired genes from 6 different loci in the V. cholerae chromosome and showed contribution of CTX prophage in the essentiality of SOS response master regulator LexA, which is otherwise not essential for viability in other bacteria, including Escherichia coli In addition, we observed that the core genome-encoded RecA helps CTXΦ to bypass V. cholerae immunity and allow it to replicate in the host bacterium in the presence of similar prophage in the chromosome. Finally, our proteomics analysis reveals the importance of MGEs in modulating the levels of cellular proteome. This study engineered the genome of V. cholerae to remove all of the GIs, ICEs, and prophages and revealed important interactions between core and acquired genomes.
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Leon-Velarde CG, Jun JW, Skurnik M. Yersinia Phages and Food Safety. Viruses 2019; 11:E1105. [PMID: 31795231 PMCID: PMC6950378 DOI: 10.3390/v11121105] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022] Open
Abstract
One of the human- and animal-pathogenic species in genus Yersinia is Yersinia enterocolitica, a food-borne zoonotic pathogen that causes enteric infections, mesenteric lymphadenitis, and sometimes sequelae such as reactive arthritis and erythema nodosum. Y. enterocolitica is able to proliferate at 4 C, making it dangerous if contaminated food products are stored under refrigeration. The most common source of Y. enterocolitica is raw pork meat. Microbiological detection of the bacteria from food products is hampered by its slow growth rate as other bacteria overgrow it. Bacteriophages can be exploited in several ways to increase food safety with regards to contamination by Y. enterocolitica. For example, Yersinia phages could be useful in keeping the contamination of food products under control, or, alternatively, the specificity of the phages could be exploited in developing rapid and sensitive diagnostic tools for the identification of the bacteria in food products. In this review, we will discuss the present state of the research on these topics.
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Affiliation(s)
- Carlos G. Leon-Velarde
- Agriculture and Food Laboratory, Laboratory Services Division, University of Guelph, Guelph, ON N1H 8J7, Canada;
| | - Jin Woo Jun
- Department of Aquaculture, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea;
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 HY Helsinki, Finland
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, 00029 HUS Helsinki, Finland
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8
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He Y, Tian S, Tian P. Fundamental asymmetry of insertions and deletions in genomes size evolution. J Theor Biol 2019; 482:109983. [PMID: 31445016 DOI: 10.1016/j.jtbi.2019.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/18/2019] [Accepted: 08/21/2019] [Indexed: 12/01/2022]
Abstract
The origin of large genomes that underlies the long standing "C-value enigma" is only partially explained by selfish DNA. We investigated insertions and deletions (indels) of nucleotides and discussed their relevance in size evolution of random biological sequences (RBS) and genomes. By developing a probabilistic model of RBS based on size evolution of expandable sites in a thought perfect genome, it was found that insertion bias engenders exponential increase of average RBS sizes. When combined with existing large segments of genome that are not subject to selection pressure (e.g. selfish DNA), such insertion bias results in explosive expansion of genomes, and therefore helps explain the "C value enigma" besides selfish DNA. Such increase of RBS size is caused by the fundamental asymmetry of indels, with insertions result in more available sites and deletions result in less deletable nucleotides. In qualitative agreement with the size distribution of known genomes, tails of RBS size distributions exhibit exponential decay with probabilities of larger RBS segments being smaller. Unsurprisingly, a slight deletion bias (higher deletions probabilities) results in a slow decrease of average RBS size and may lead to their eventual vanishing. Contrary to intuition, strictly balanced insertion and deletion results in linearly increasing instead of completely fixed RBS size. Nonetheless, such slow linear increase of average RBS sizes with time are small in magnitude and are consequently not influential on genome size evolution, and certainly not a major contributor for the "C-value enigma". Our model suggested that insertion bias of nucleotides may provide complementary explanation for large genomes besides selfish DNA. The fundamental indel asymmetry is applicable for all forms of genomic insertions and deletions. Long-lasting exponential increase of genome size present energy and material requirement that is impossible to sustain. We therefore concluded that if there were explosively accelerating expansion caused by significant effective insertion bias for any survival species, it must have occurred sporadically. Our model also provided an explanation for the observed proportional evolution of genome size.
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Affiliation(s)
- Yang He
- School of Life Sciences, Jilin University Changchun, 2699 Qianjin Street, China 130012
| | - Suyan Tian
- Division of Clinical Epidemiology, First Hospital of The Jilin University, 71 Xinmin Street, Changchun, China, 130021.
| | - Pu Tian
- School of Life Sciences and MOE Key laboratory of Molecular Enzymology and Engineering, Jilin University 2699 Qianjin Street, Changchun, China 130012.
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Abstract
Bacterial chromosomes harbour a unique origin of bidirectional replication, oriC. They are almost always circular, with replication terminating in a region diametrically opposite to oriC, the terminus. The oriC-terminus organisation is reflected by the orientation of the genes and by the disposition of DNA-binding protein motifs implicated in the coordination of chromosome replication and segregation with cell division. Correspondingly, the E. coli and B. subtilis model bacteria possess a replication fork trap system, Tus/ter and RTP/ter, respectively, which enforces replication termination in the terminus region. Here, we show that tus and rtp are restricted to four clades of bacteria, suggesting that tus was recently domesticated from a plasmid gene. We further demonstrate that there is no replication fork system in Vibrio cholerae, a bacterium closely related to E. coli. Marker frequency analysis showed that replication forks originating from ectopic origins were not blocked in the terminus region of either of the two V. cholerae chromosomes, but progressed normally until they encountered an opposite fork. As expected, termination synchrony of the two chromosomes is disrupted by these ectopic origins. Finally, we show that premature completion of the primary chromosome replication did not modify the choreography of segregation of its terminus region.
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Moldovan MA. Prokaryotic and Mitochondrial Linear Genomes: Their Genesis, Evolutionary Significance, and the Problem of Replicating Chromosome Ends. Mol Biol 2019. [DOI: 10.1134/s0026893319020122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Kono N, Tomita M, Arakawa K. Accelerated Laboratory Evolution Reveals the Influence of Replication on the GC Skew in Escherichia coli. Genome Biol Evol 2018; 10:3110-3117. [PMID: 30371772 PMCID: PMC6263442 DOI: 10.1093/gbe/evy237] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2018] [Indexed: 12/13/2022] Open
Abstract
Most bacterial genomes display contrasting strand asymmetry in a variety of features, such as nucleotide composition and gene orientation, of the two replichores separated by the replication origin and terminus. The cause for the polarization is often attributed to mutations arising from the asymmetric replication machinery. Notably, a base compositional bias known as a GC skew is focused on as a footprint of the bacterial genome evolution driven by DNA replication. Previously, although a replication driven mutation pattern responsible for the GC skew formation or the related mathematical models have been well reported, an exact impact of the replication-related elements on the genomic structure is yet actively debated, and not confirmed experimentally. However, the GC skew formation is very time consuming and challenging in the laboratory. We, therefore, used cytosine deaminase as a DNA mutator, and by monitoring the mutations during an accelerated laboratory evolution procedure with Illumina sequencing, we enabled the trial and error of the GC skew formation in high resolution. Using this technology, we succeeded in reconfirming the influence of bacterial replication machinery on the genomic structure at high resolution.
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Affiliation(s)
- Nobuaki Kono
- Institute for Advanced Biosciences, Keio University
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12
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Dent D. Non-nodular Endophytic Bacterial Symbiosis and the Nitrogen Fixation of Gluconacetobacter diazotrophicus. Symbiosis 2018. [DOI: 10.5772/intechopen.75813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Barros-Carvalho GA, Van Sluys MA, Lopes FM. An Efficient Approach to Explore and Discriminate Anomalous Regions in Bacterial Genomes Based on Maximum Entropy. J Comput Biol 2017; 24:1125-1133. [PMID: 28570142 DOI: 10.1089/cmb.2017.0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recently, there has been an increase in the number of whole bacterial genomes sequenced, mainly due to the advancing of next-generation sequencing technologies. In face of this, there is a need to provide new analytical alternatives that can follow this advance. Given our current knowledge about the genomic plasticity of bacteria and that those genomic regions can uncover important features about this microorganism, our goal was to develop a fast methodology based on maximum entropy (ME) to guide the researcher to regions that could be prioritized during the analysis. This methodology was compared with other available methods. In addition, ME was applied to eight different bacterial genera. The methodology consists of two main steps: processing the nucleotide sequence and ME calculation. We applied ME to Xanthomonas axonopodis pv. citri 306 (XAC) and Xanthomonas campestris pv. campestris ATCC 33913 (XCC), both of which have their anomalous regions well documented. We then compared our results against those from Alien Hunter, HGT-DB, Islander, IslandPath, and SIGI-HMM. ME was shown to be superior in terms of efficiency and analysis duration. Besides, ME only needs the genome sequence in FASTA format as input. The proposed strategy based on ME is able to help in bacterial genome exploration. This is a simple and fast strategy for individual genomes in comparison with other available methods, without relying on previous annotation and alignments. This methodology can also be a new option in the early stages of analysis of newly sequenced bacterial genomes.
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Affiliation(s)
- Gesiele Almeida Barros-Carvalho
- 1 Institute of Mathematics and Statistics, University of São Paulo , São Paulo, Brazil .,2 GaTE Lab, Department of Botany, Institute of Bioscience, University of São Paulo , São Paulo, Brazil
| | - Marie-Anne Van Sluys
- 2 GaTE Lab, Department of Botany, Institute of Bioscience, University of São Paulo , São Paulo, Brazil
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Lynch M, Ackerman MS, Gout JF, Long H, Sung W, Thomas WK, Foster PL. Genetic drift, selection and the evolution of the mutation rate. Nat Rev Genet 2017; 17:704-714. [PMID: 27739533 DOI: 10.1038/nrg.2016.104] [Citation(s) in RCA: 452] [Impact Index Per Article: 64.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
As one of the few cellular traits that can be quantified across the tree of life, DNA-replication fidelity provides an excellent platform for understanding fundamental evolutionary processes. Furthermore, because mutation is the ultimate source of all genetic variation, clarifying why mutation rates vary is crucial for understanding all areas of biology. A potentially revealing hypothesis for mutation-rate evolution is that natural selection primarily operates to improve replication fidelity, with the ultimate limits to what can be achieved set by the power of random genetic drift. This drift-barrier hypothesis is consistent with comparative measures of mutation rates, provides a simple explanation for the existence of error-prone polymerases and yields a formal counter-argument to the view that selection fine-tunes gene-specific mutation rates.
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Affiliation(s)
- Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Matthew S Ackerman
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Jean-Francois Gout
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Hongan Long
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Way Sung
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Patricia L Foster
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
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15
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Lee H, Doak TG, Popodi E, Foster PL, Tang H. Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli. Nucleic Acids Res 2016; 44:7109-19. [PMID: 27431326 PMCID: PMC5009759 DOI: 10.1093/nar/gkw647] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/08/2016] [Indexed: 12/27/2022] Open
Abstract
A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 × 10(-4) insertions per genome per generation and the rate of IS homologous recombination is 4.5 × 10(-5) recombinations per genome per generation. These events are mostly contributed by the IS elements IS1, IS2, IS5 and IS186 Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS186 target-sites, 5'-GGGG(N6/N7)CCCC-3'. We also detected 48 long deletions not involving IS elements.
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Affiliation(s)
- Heewook Lee
- School of Informatics and Computing, Indiana University, Bloomington, IN 47401, USA Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington, IN 47401, USA National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47401, USA
| | - Ellen Popodi
- Department of Biology, Indiana University, Bloomington, IN 47401, USA
| | - Patricia L Foster
- Department of Biology, Indiana University, Bloomington, IN 47401, USA
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, IN 47401, USA
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Bakhshi F, Pilehchian Langroudi R, Eimani BG. Enhanced expression of recombinant beta toxin of Clostridium perfringens type B using a commercially available Escherichia coli strain. ACTA ACUST UNITED AC 2016; 83:a1136. [PMID: 27380656 PMCID: PMC6238768 DOI: 10.4102/ojvr.v83i1.1136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/25/2016] [Accepted: 03/31/2016] [Indexed: 11/16/2022]
Abstract
Clostridium perfringens beta toxin is only produced by types B and C and plays an important role in many human and animal diseases, causing fatal conditions that originate in the intestines. We compared the expression of C. perfringens type B vaccine strain recombinant beta toxin gene in the Escherichia coli strains RosettaTM(DE3) and BL21(DE3). The beta toxin gene was extracted from pJETβ and ligated with pET22b(+). pET22β was transformed into E. coli strains BL21(DE3) and RosettaTM(DE3). Recombinant protein was expressed as a soluble protein after isopropyl β-D-1-thiogalactopyranoside (IPTG) induction in strain RosettaTM(DE3) but not in BL21(DE3). Expression was optimised by growing recombinant cells at 37 °C and at an induction of 0.5 mM, 1 mM, 1.5 mM IPTG. Expression was evaluated using sodium dodecyl sulfate Polyacrylamide gel electrophoresis (SDS-PAGE). The recombinant protein was purified via Ni-NTA and was analysed using western blot. We concluded that E. coli strain RosettaTM(DE3) can enhance the expression of C. perfringens recombinant beta toxin.
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Affiliation(s)
| | - Reza Pilehchian Langroudi
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Alborz, Karaj.
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Mariscal C, Doolittle WF. Eukaryotes first: how could that be? Philos Trans R Soc Lond B Biol Sci 2016; 370:20140322. [PMID: 26323754 DOI: 10.1098/rstb.2014.0322] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In the half century since the formulation of the prokaryote : eukaryote dichotomy, many authors have proposed that the former evolved from something resembling the latter, in defiance of common (and possibly common sense) views. In such 'eukaryotes first' (EF) scenarios, the last universal common ancestor is imagined to have possessed significantly many of the complex characteristics of contemporary eukaryotes, as relics of an earlier 'progenotic' period or RNA world. Bacteria and Archaea thus must have lost these complex features secondarily, through 'streamlining'. If the canonical three-domain tree in which Archaea and Eukarya are sisters is accepted, EF entails that Bacteria and Archaea are convergently prokaryotic. We ask what this means and how it might be tested.
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Affiliation(s)
- Carlos Mariscal
- Departments of Philosophy, Dalhousie University, PO Box 15000, Halifax, Nova Scotia, Canada B3H 4R2 Biochemistry and Molecular Biology, Dalhousie University, PO Box 15000, Halifax, Nova Scotia, Canada B3H 4R2
| | - W Ford Doolittle
- Biochemistry and Molecular Biology, Dalhousie University, PO Box 15000, Halifax, Nova Scotia, Canada B3H 4R2
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Xu W, Xing T, Zhao M, Yin X, Xia G, Wang M. Synonymous codon usage bias in plant mitochondrial genes is associated with intron number and mirrors species evolution. PLoS One 2015; 10:e0131508. [PMID: 26110418 PMCID: PMC4481540 DOI: 10.1371/journal.pone.0131508] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/03/2015] [Indexed: 11/21/2022] Open
Abstract
Synonymous codon usage bias (SCUB) is a common event that a non-uniform usage of codons often occurs in nearly all organisms. We previously found that SCUB is correlated with both intron number and exon position in the plant nuclear genome but not in the plastid genome; SCUB in both nuclear and plastid genome can mirror the evolutionary specialization. However, how about the rules in the mitochondrial genome has not been addressed. Here, we present an analysis of SCUB in the mitochondrial genome, based on 24 plant species ranging from algae to land plants. The frequencies of NNA and NNT (A- and T-ending codons) are higher than those of NNG and NNC, with the strongest preference in bryophytes and the weakest in land plants, suggesting an association between SCUB and plant evolution. The preference for NNA and NNT is more evident in genes harboring a greater number of introns in land plants, but the bias to NNA and NNT exhibits even among exons. The pattern of SCUB in the mitochondrial genome differs in some respects to that present in both the nuclear and plastid genomes.
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Affiliation(s)
- Wenjing Xu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China
| | - Tian Xing
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China
| | - Mingming Zhao
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China
| | - Xunhao Yin
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China
- * E-mail:
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Qi Y, Xu W, Xing T, Zhao M, Li N, Yan L, Xia G, Wang M. Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity. Evol Bioinform Online 2015; 11:65-77. [PMID: 25922569 PMCID: PMC4395140 DOI: 10.4137/ebo.s22566] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/22/2015] [Accepted: 02/22/2015] [Indexed: 01/26/2023] Open
Abstract
Synonymous codon usage bias (SCUB) is the nonuniform usage of codons, occurring often in nearly all organisms. Our previous study found that SCUB is correlated with intron number, is unequal among exons in the plant nuclear genome, and mirrors evolutionary specialization. However, whether this rule exists in the plastid genome has not been addressed. Here, we present an analysis of SCUB in the plastid genomes of 25 species from lower to higher plants (algae, bryophytes, pteridophytes, gymnosperms, and spermatophytes). We found NNA and NNT (A- and T-ending codons) are preferential in the plastid genomes of all plants. Interestingly, this preference is heterogeneous among taxonomies of plants, with the strongest preference in bryophytes and the weakest in pteridophytes, suggesting an association between SCUB and plant evolution. In addition, SCUB frequencies are consistent among genes with varied introns and among exons, indicating that the bias of NNA and NNT is unrelated to either intron number or exon position. Further, SCUB is associated with DNA methylation–induced conversion of cytosine to thymine in the vascular plants but not in algae or bryophytes. These data demonstrate that these SCUB profiles in the plastid genome are distinctly different compared with the nuclear genome.
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Affiliation(s)
- Yueying Qi
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
| | - Wenjing Xu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
| | - Tian Xing
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
| | - Mingming Zhao
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
| | - Nana Li
- Shandong Center of Crop Germplasm Resources, Jinan 250100,Shandong, China
| | - Li Yan
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
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López-Madrigal S, Latorre A, Moya A, Gil R. The link between independent acquisition of intracellular gamma-endosymbionts and concerted evolution in Tremblaya princeps. Front Microbiol 2015; 6:642. [PMID: 26161080 PMCID: PMC4479817 DOI: 10.3389/fmicb.2015.00642] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/12/2015] [Indexed: 02/05/2023] Open
Abstract
Many insect species establish mutualistic symbiosis with intracellular bacteria that complement their unbalanced diets. The betaproteobacterium "Candidatus Tremblaya" maintains an ancient symbiosis with mealybugs (Hemiptera: Pseudococcidae), which are classified in subfamilies Phenacoccinae and Pseudococcinae. Most Phenacoccinae mealybugs have "Candidatus Tremblaya phenacola" as their unique endosymbiont, while most Pseudococcinae mealybugs show a nested symbiosis (a bacterial symbiont placed inside another one) where every "Candidatus Tremblaya princeps" cell harbors several cells of a gammaproteobacterium. Genomic characterization of the endosymbiotic consortium from Planococcus citri, composed by "Ca. Tremblaya princeps" and "Candidatus Moranella endobia," unveiled several atypical features of the former's genome, including the concerted evolution of paralogous loci. Its comparison with the genome of "Ca. Tremblaya phenacola" PAVE, single endosymbiont of Phenacoccus avenae, suggests that the atypical reductive evolution of "Ca. Tremblaya princeps" could be linked to the acquisition of "Ca. Moranella endobia," which possess an almost complete set of genes encoding proteins involved in homologous recombination. In order to test this hypothesis, we performed comparative genomics between "Ca. Tremblaya phenacola" and "Ca. Tremblaya princeps" and searched for the co-occurrence of concerted evolution and homologous recombination genes in endosymbiotic consortia from four unexplored mealybug species, Dysmicoccus boninsis, Planococcus ficus, Pseudococcus longispinus, and Pseudococcus viburni. Our results support a link between concerted evolution and nested endosymbiosis.
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Affiliation(s)
- Sergio López-Madrigal
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain
- Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) – Salud PúblicaValència, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain
- Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) – Salud PúblicaValència, Spain
| | - Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain
- *Correspondence: Rosario Gil, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, C/Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
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Challacombe J, Kuske C. Mobile genetic elements in the bacterial phylum Acidobacteria. Mob Genet Elements 2014; 2:179-183. [PMID: 23087842 PMCID: PMC3469429 DOI: 10.4161/mge.21943] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Analysis of the genome of Candidatus Solibacter usitatus Ellin6076, a member of the phylum Acidobacteria, revealed a large number of genes associated with mobile genetic elements. These genes encoded transposases, insertion sequence elements and phage integrases. When the amino acid sequences of the mobile element-associated genes were compared, many of them had high (90–100%) amino acid sequence identities, suggesting that these genes may have recently duplicated and dispersed throughout the genome. Although phage integrase encoding genes were prevalent in the Can. S. usitatus Ellin6076 genome, no intact prophage regions were found. This suggests that the Can. S. usitatus Ellin6076 large genome arose by horizontal gene transfer via ancient bacteriophage and/or plasmid-mediated transduction, followed by widespread small-scale gene duplications, resulting in an increased number of paralogs encoding traits that could provide selective metabolic, defensive and regulatory advantages in the soil environment. Here we examine the mobile element repertoire of Can. S. usitatus Ellin6076 in comparison to other genomes from the Acidobacteria phylum, reviewing published studies and contributing some new analyses. We also discuss the presence and potential roles of mobile elements in members of this phylum that inhabit a variety of environments.
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Affiliation(s)
- Jean Challacombe
- Los Alamos National Laboratory; Bioscience Division; Los Alamos NM USA
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22
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Han MV. Characterizing gene movements between chromosomes in Drosophila. Fly (Austin) 2014; 6:121-5. [DOI: 10.4161/fly.20144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Demarre G, Galli E, Muresan L, Paly E, David A, Possoz C, Barre FX. Differential management of the replication terminus regions of the two Vibrio cholerae chromosomes during cell division. PLoS Genet 2014; 10:e1004557. [PMID: 25255436 PMCID: PMC4177673 DOI: 10.1371/journal.pgen.1004557] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 06/25/2014] [Indexed: 12/04/2022] Open
Abstract
The replication terminus region (Ter) of the unique chromosome of most bacteria locates at mid-cell at the time of cell division. In several species, this localization participates in the necessary coordination between chromosome segregation and cell division, notably for the selection of the division site, the licensing of the division machinery assembly and the correct alignment of chromosome dimer resolution sites. The genome of Vibrio cholerae, the agent of the deadly human disease cholera, is divided into two chromosomes, chrI and chrII. Previous fluorescent microscopy observations suggested that although the Ter regions of chrI and chrII replicate at the same time, chrII sister termini separated before cell division whereas chrI sister termini were maintained together at mid-cell, which raised questions on the management of the two chromosomes during cell division. Here, we simultaneously visualized the location of the dimer resolution locus of each of the two chromosomes. Our results confirm the late and early separation of chrI and chrII Ter sisters, respectively. They further suggest that the MatP/matS macrodomain organization system specifically delays chrI Ter sister separation. However, TerI loci remain in the vicinity of the cell centre in the absence of MatP and a genetic assay specifically designed to monitor the relative frequency of sister chromatid contacts during constriction suggest that they keep colliding together until the very end of cell division. In contrast, we found that even though it is not able to impede the separation of chrII Ter sisters before septation, the MatP/matS macrodomain organization system restricts their movement within the cell and permits their frequent interaction during septum constriction. The genome of Vibrio cholerae is divided into two circular chromosomes, chrI and chrII. ChrII is derived from a horizontally acquired mega-plasmid, which raised questions on the necessary coordination of the processes that ensure its segregation with the cell division cycle. Here, we show that the MatP/matS macrodomain organization system impedes the separation of sister copies of the terminus region of chrI before the initiation of septum constriction. In its absence, however, chrI sister termini remain sufficiently close to mid-cell to be processed by the FtsK cell division translocase. In contrast, we show that MatP cannot impede the separation of chrII sister termini before constriction. However, it restricts their movements within the cell, which allows for their processing by FtsK at the time of cell division. These results suggest that multiple redundant factors, including MatP in the enterobacteriaceae and the Vibrios, ensure that sister copies of the terminus region of bacterial chromosomes remain sufficiently close to mid-cell to be processed by FtsK.
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Affiliation(s)
- Gaëlle Demarre
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Elisa Galli
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Leila Muresan
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Evelyne Paly
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Ariane David
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Christophe Possoz
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - François-Xavier Barre
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- * E-mail:
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Puigbò P, Lobkovsky AE, Kristensen DM, Wolf YI, Koonin EV. Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes. BMC Biol 2014; 12:66. [PMID: 25141959 PMCID: PMC4166000 DOI: 10.1186/s12915-014-0066-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/31/2014] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species. RESULTS We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, 'open' supergenomes. CONCLUSIONS Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.
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Baumgart M, Unthan S, Rückert C, Sivalingam J, Grünberger A, Kalinowski J, Bott M, Noack S, Frunzke J. Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 for use as a platform strain for basic research and industrial biotechnology. Appl Environ Microbiol 2013; 79:6006-15. [PMID: 23892752 PMCID: PMC3811366 DOI: 10.1128/aem.01634-13] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Accepted: 07/17/2013] [Indexed: 11/20/2022] Open
Abstract
The activity of bacteriophages and phage-related mobile elements is a major source for genome rearrangements and genetic instability of their bacterial hosts. The genome of the industrial amino acid producer Corynebacterium glutamicum ATCC 13032 contains three prophages (CGP1, CGP2, and CGP3) of so far unknown functionality. Several phage genes are regularly expressed, and the large prophage CGP3 (∼190 kbp) has recently been shown to be induced under certain stress conditions. Here, we present the construction of MB001, a prophage-free variant of C. glutamicum ATCC 13032 with a 6% reduced genome. This strain does not show any unfavorable properties during extensive phenotypic characterization under various standard and stress conditions. As expected, we observed improved growth and fitness of MB001 under SOS-response-inducing conditions that trigger CGP3 induction in the wild-type strain. Further studies revealed that MB001 has a significantly increased transformation efficiency and produced about 30% more of the heterologous model protein enhanced yellow fluorescent protein (eYFP), presumably as a consequence of an increased plasmid copy number. These effects were attributed to the loss of the restriction-modification system (cg1996-cg1998) located within CGP3. The deletion of the prophages without any negative effect results in a novel platform strain for metabolic engineering and represents a useful step toward the construction of a C. glutamicum chassis genome of strain ATCC 13032 for biotechnological applications and synthetic biology.
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Affiliation(s)
- Meike Baumgart
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Simon Unthan
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | | | - Jasintha Sivalingam
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | | | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
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Synonymous codon usage bias is correlative to intron number and shows disequilibrium among exons in plants. BMC Genomics 2013; 14:56. [PMID: 23350908 PMCID: PMC3576282 DOI: 10.1186/1471-2164-14-56] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 01/18/2013] [Indexed: 01/15/2023] Open
Abstract
Background Evidence has been assembled to suggest synonymous codon usage bias (SCUB) has close relationship with intron. However, the relationship (if any) between SCUB and intron number as well as exon position is at present rather unclear. Results To explore this relationship, the sequences of a set of genes containing between zero and nine introns was extracted from the published genome sequences of three algal species, one moss, one fern and six angiosperms (three monocotyledonous species and three dicotyledonous species). In the algal genomes, the frequency of synonymous codons of the form NNG/NNC (codons with G and C at the third position) was positively related to intron number, but that of NNA/NNT was inversely correlated; the opposite was the case in the land plant genomes. The frequency of NNC/NNG was higher and that of NNA/NNT lower in two terminal exons than in the interstitial exons in the land plant genes, but the rule showed to be opposite in the algal genes. SCUB patterns in the interstitial and two terminal exons mirror the different evolutionary relationships between these plant species, while the first exon shows the highest level of conservation is therefore concluded to be the one which experiences the heaviest selection pressure. The phenomenon of SCUB may also be related to DNA methylation induced conversion of CG to AT. Conclusions These data provide some evidence of linkage between SCUB, the evolution of introns and DNA methylation, which brings about a new perspective for understanding how genomic variation is created during plant evolution.
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27
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The influence of ATP-dependent proteases on a variety of nucleoid-associated processes. J Struct Biol 2012; 179:181-92. [PMID: 22683345 DOI: 10.1016/j.jsb.2012.05.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/24/2012] [Accepted: 05/26/2012] [Indexed: 01/07/2023]
Abstract
ATP-dependent proteases are crucial components of all living cells and are involved in a variety of responses to physiological and environmental changes. Nucleoids are dynamic nucleoprotein complexes present in bacteria and eukaryotic organelles (mitochondria and plastids) and are the place where the majority of cellular responses to stress begin. These structures are actively remodeled in reaction to changing environmental and physiological conditions. The levels of nucleoid protein components (e.g. DNA-stabilizing proteins, transcription factors, replication proteins) therefore have to be continually regulated. ATP-dependent proteases have all the characteristics needed to fulfill this requirement. Some of them bind nucleic acids, but above all, they control and maintain the level of many DNA-binding proteins. In this review we will discuss the roles of the Lon, ClpAP, ClpXP, HslUV and FtsH proteases in the maintenance, stability, transcription and repair of DNA in eubacterial and mitochondrial nucleoids.
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Diversity analysis of streptomycetes and associated phosphotranspherase genes in soil. PLoS One 2012; 7:e35756. [PMID: 22540003 PMCID: PMC3335164 DOI: 10.1371/journal.pone.0035756] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 03/26/2012] [Indexed: 11/23/2022] Open
Abstract
An attempt was made to verify the observation that Streptomyces griseus was prevalent in soil based on isolation work. A genus-specific PCR was developed for Streptomyces based on the housekeeping gene atpD and used to investigate species diversity within selected soils. The presence of S. griseus was investigated to determine coexistence of resistance-only streptomycin phosphotransferase (strA) in the same soil as streptomycin producers. Two additional PCR-based assays were developed; one specific for strA in association with production, the other for more diverse strA and other related phosphotranferases. Both the S. griseus atpD and strA genes were below the PCR detection limit in all soils examined. A number of more diverse phosphotransferase genes were amplified, a minority of which may be associated with streptomycin production. We conclude that neither streptomycin producers nor S. griseus are prevalent in the fresh or chitin and starch-amended soils examined (less than 0.1% of soil actinobacteria). One of the soil sites had received plantomycin (active ingredient: streptomycin) and diversity studies suggested that this altered the streptomycete populations present in the soil.
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Genome engineering in Vibrio cholerae: a feasible approach to address biological issues. PLoS Genet 2012; 8:e1002472. [PMID: 22253612 PMCID: PMC3257285 DOI: 10.1371/journal.pgen.1002472] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 11/24/2011] [Indexed: 01/10/2023] Open
Abstract
Although bacteria with multipartite genomes are prevalent, our knowledge of the mechanisms maintaining their genome is very limited, and much remains to be learned about the structural and functional interrelationships of multiple chromosomes. Owing to its bi-chromosomal genome architecture and its importance in public health, Vibrio cholerae, the causative agent of cholera, has become a preferred model to study bacteria with multipartite genomes. However, most in vivo studies in V. cholerae have been hampered by its genome architecture, as it is difficult to give phenotypes to a specific chromosome. This difficulty was surmounted using a unique and powerful strategy based on massive rearrangement of prokaryotic genomes. We developed a site-specific recombination-based engineering tool, which allows targeted, oriented, and reciprocal DNA exchanges. Using this genetic tool, we obtained a panel of V. cholerae mutants with various genome configurations: one with a single chromosome, one with two chromosomes of equal size, and one with both chromosomes controlled by identical origins. We used these synthetic strains to address several biological questions--the specific case of the essentiality of Dam methylation in V. cholerae and the general question concerning bacteria carrying circular chromosomes--by looking at the effect of chromosome size on topological issues. In this article, we show that Dam, RctB, and ParA2/ParB2 are strictly essential for chrII origin maintenance, and we formally demonstrate that the formation of chromosome dimers increases exponentially with chromosome size.
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Wang Y, Yang JK, Lee OO, Li TG, Al-Suwailem A, Danchin A, Qian PY. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments. PLoS One 2011; 6:e29149. [PMID: 22216192 PMCID: PMC3244439 DOI: 10.1371/journal.pone.0029149] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 11/21/2011] [Indexed: 11/18/2022] Open
Abstract
The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed.
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Affiliation(s)
- Yong Wang
- KAUST Global Collaborative Research, Division of Life Sciences, Hong Kong, University of Science and Technology, Clear Water Bay, Hong Kong, China
- Institute of Oceanography, Chinese Academy of Sciences, Qingdao, China
| | - Jiang Ke Yang
- KAUST Global Collaborative Research, Division of Life Sciences, Hong Kong, University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - On On Lee
- KAUST Global Collaborative Research, Division of Life Sciences, Hong Kong, University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Tie Gang Li
- King Abdullah University of Science and Technology, Thuwal, The Kingdom of Saudi Arabia
| | - Abdulaziz Al-Suwailem
- King Abdullah University of Science and Technology, Thuwal, The Kingdom of Saudi Arabia
| | | | - Pei-Yuan Qian
- KAUST Global Collaborative Research, Division of Life Sciences, Hong Kong, University of Science and Technology, Clear Water Bay, Hong Kong, China
- * E-mail:
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Kvist S, Narechania A, Oceguera-Figueroa A, Fuks B, Siddall ME. Phylogenomics of Reichenowia parasitica, an alphaproteobacterial endosymbiont of the freshwater leech Placobdella parasitica. PLoS One 2011; 6:e28192. [PMID: 22132238 PMCID: PMC3223239 DOI: 10.1371/journal.pone.0028192] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Accepted: 11/02/2011] [Indexed: 01/30/2023] Open
Abstract
Although several commensal alphaproteobacteria form close relationships with plant hosts where they aid in (e.g.,) nitrogen fixation and nodulation, only a few inhabit animal hosts. Among these, Reichenowia picta, R. ornata and R. parasitica, are currently the only known mutualistic, alphaproteobacterial endosymbionts to inhabit leeches. These bacteria are harbored in the epithelial cells of the mycetomal structures of their freshwater leech hosts, Placobdella spp., and these structures have no other obvious function than housing bacterial symbionts. However, the function of the bacterial symbionts has remained unclear. Here, we focused both on exploring the genomic makeup of R. parasitica and on performing a robust phylogenetic analysis, based on more data than previous hypotheses, to test its position among related bacteria. We sequenced a combined pool of host and symbiont DNA from 36 pairs of mycetomes and performed an in silico separation of the different DNA pools through subtractive scaffolding. The bacterial contigs were compared to 50 annotated bacterial genomes and the genome of the freshwater leech Helobdella robusta using a BLASTn protocol. Further, amino acid sequences inferred from the contigs were used as queries against the 50 bacterial genomes to establish orthology. A total of 358 orthologous genes were used for the phylogenetic analyses. In part, results suggest that R. parasitica possesses genes coding for proteins related to nitrogen fixation, iron/vitamin B translocation and plasmid survival. Our results also indicate that R. parasitica interacts with its host in part by transmembrane signaling and that several of its genes show orthology across Rhizobiaceae. The phylogenetic analyses support the nesting of R. parasitica within the Rhizobiaceae, as sister to a group containing Agrobacterium and Rhizobium species.
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Affiliation(s)
- Sebastian Kvist
- Richard Gilder Graduate School, American Museum of Natural History, New York, New York, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Alejandro Oceguera-Figueroa
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
- Department of Biology, The Graduate Center, The City University of New York, New York, New York, United States of America
| | - Bella Fuks
- Long Island University Brooklyn Campus, Brooklyn, New York, United States of America
| | - Mark E. Siddall
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
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Abstract
Despite substantial attention from theoreticians, the evolutionary mechanisms that drive intra- and interspecific variation in the mutation rate remain unclear. It has often been argued that mutation rates associated with the major replicative polymerases have been driven down to their physiological limits, defined as the point at which further enhancement in replication fidelity incurs a cost in terms of reproductive output, but no evidence in support of this argument has emerged for cellular organisms. Here, it is suggested that the lower barrier to mutation rate evolution may ultimately be defined not by molecular limitations but by the power of random genetic drift. As the mutation rate is reduced to a very low level, a point will eventually be reached at which the small advantage of any further reduction is overwhelmed by the power of drift. This hypothesis is consistent with a number of observations, including the inverse relationship between the per-site mutation rate and genome size in microbes, the negative scaling between the per-site mutation rate and effective population size in eukaryotes, and the elevated error rates associated with less frequently deployed polymerases and repair pathways.
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Kurup K, Mary S, Rafi ZA. Intergenics: A tool for extraction of intergenicregions. Bioinformation 2010; 5:83-4. [PMID: 21364785 PMCID: PMC3040482 DOI: 10.6026/97320630005083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 08/26/2010] [Indexed: 11/23/2022] Open
Abstract
For the past one decade, there has been considerable explosion of interest in searching novel regulatory elements in the intergenic region between the protein coding regions. The microbial genomes are the most exploited in terms of intergenic (noncoding) regions due to its less complexity. We think, the increasing pace of genome sequencing calls for a tool which will be useful for the extraction of intergenic regions. IntergenicS (Intergenic Sequence) is a tool which can extract the intergenic regions of microbial genomes at NCBI. All the unannotated regions between annotated protein coding genes and noncoding RNA genes can be extracted. It also deals with the calculation of GC base composition of the intergenic regions. This will be a useful tool for the analysis of noncoding regions of both bacterial and archael genomes.
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Affiliation(s)
- Kavitha Kurup
- Centre of excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University, Madurai 625 021, Tamil Nadu, India
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Gil R, Latorre A, Moya A. Evolution of Prokaryote-Animal Symbiosis from a Genomics Perspective. (ENDO)SYMBIOTIC METHANOGENIC ARCHAEA 2010. [DOI: 10.1007/978-3-642-13615-3_11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Pradella S, Päuker O, Petersen J. Genome organisation of the marine Roseobacter clade member Marinovum algicola. Arch Microbiol 2009; 192:115-26. [PMID: 20039020 DOI: 10.1007/s00203-009-0535-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 11/10/2009] [Accepted: 12/09/2009] [Indexed: 11/30/2022]
Abstract
The Roseobacter clade, belonging to the family Rhodobacteraceae of the class Alphaproteobacteria, is one of the major bacterial groups in marine environments. A remarkable wealth of diverse large plasmids has been detected in members of this lineage. Here, we analysed the genome structure and extrachromosomal DNA content of four strains of the roseobacter species Marinovum algicola by pulsed-field gel electrophoresis. They were originally isolated from toxic dinoflagellates and possess multireplicon genomes with sizes between 5.20 and 5.35 Mb. In addition to the single circular chromosomes (3.60-3.74 Mb), whose organisation seem to be conserved, 9 to 12 extrachromosomal replicons have been detected for each strain. This number is unprecedented for roseobacters and proposes a sophisticated regulation of replication and partitioning to ensure stable maintenance. The plasmid lengths range from 7 to 477 kb and our analyses document a circular conformation for all but one of them, which might represent a linear plasmid-like prophage. In striking contrast to other roseobacters, up to one-third of the genomic information (1.75 Mb) is plasmid borne in Marinovum algicola. The plasmid patterns of some strains are conspicuously different, indicating that recombination and conjugative gene transfer are dominant mechanisms for microevolution within the Roseobacter clade.
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Affiliation(s)
- Silke Pradella
- German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany.
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Merhej V, Royer-Carenzi M, Pontarotti P, Raoult D. Massive comparative genomic analysis reveals convergent evolution of specialized bacteria. Biol Direct 2009; 4:13. [PMID: 19361336 PMCID: PMC2688493 DOI: 10.1186/1745-6150-4-13] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 04/10/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome size and gene content in bacteria are associated with their lifestyles. Obligate intracellular bacteria (i.e., mutualists and parasites) have small genomes that derived from larger free-living bacterial ancestors; however, the different steps of bacterial specialization from free-living to intracellular lifestyle have not been studied comprehensively. The growing number of available sequenced genomes makes it possible to perform a statistical comparative analysis of 317 genomes from bacteria with different lifestyles. RESULTS Compared to free-living bacteria, host-dependent bacteria exhibit fewer rRNA genes, more split rRNA operons and fewer transcriptional regulators, linked to slower growth rates. We found a function-dependent and non-random loss of the same 100 orthologous genes in all obligate intracellular bacteria. Thus, we showed that obligate intracellular bacteria from different phyla are converging according to their lifestyle. Their specialization is an irreversible phenomenon characterized by translation modification and massive gene loss, including the loss of transcriptional regulators. Although both mutualists and parasites converge by genome reduction, these obligate intracellular bacteria have lost distinct sets of genes in the context of their specific host associations: mutualists have significantly more genes that enable nutrient provisioning whereas parasites have genes that encode Types II, IV, and VI secretion pathways. CONCLUSION Our findings suggest that gene loss, rather than acquisition of virulence factors, has been a driving force in the adaptation of parasites to eukaryotic cells. This comparative genomic analysis helps to explore the strategies by which obligate intracellular genomes specialize to particular host-associations and contributes to advance our knowledge about the mechanisms of bacterial evolution.
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Affiliation(s)
- Vicky Merhej
- Faculty of Medicine, Unit for Research on Emergent and Tropical Infectious Diseases, CNRS-IRD UMR 6236 IFR48, University of the Mediterranean, Marseilles, France.
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Krupka M, Raska M, Belakova J, Horynova M, Novotny R, Weigl E. Biological aspects of Lyme disease spirochetes: unique bacteria of the Borrelia burgdorferi species group. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2008; 151:175-86. [PMID: 18345249 DOI: 10.5507/bp.2007.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Borrelia burgdorferi sensu lato is a group of at least twelve closely related species some of which are responsible for Lyme disease, the most frequent zoonosis in Europe and the USA. Many of the biological features of Borrelia are unique in prokaryotes and very interesting not only from the medical viewpoint but also from the view of molecular biology. METHODS Relevant recent articles were searched using PubMed and Google search tools. RESULTS AND CONCLUSION This is a review of the biological, genetic and physiological features of the spirochete species group, Borrelia burgdorferi sensu lato. In spite of a lot of recent articles focused on B. burgdorferi sensu lato, many features of Borrelia biology remain obscure. It is one of the main reasons for persisting problems with prevention, diagnosis and therapy of Lyme disease. The aim of the review is to summarize ongoing current knowledge into a lucid and comprehensible form.
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Affiliation(s)
- Michal Krupka
- Department of Immunology, Faculty of Medicine, Palacky University, Olomouc, Czech Republic.
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Val ME, Kennedy SP, Karoui ME, Bonné L, Chevalier F, Barre FX. FtsK-dependent dimer resolution on multiple chromosomes in the pathogen Vibrio cholerae. PLoS Genet 2008; 4:e1000201. [PMID: 18818731 PMCID: PMC2533119 DOI: 10.1371/journal.pgen.1000201] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 08/18/2008] [Indexed: 11/18/2022] Open
Abstract
Unlike most bacteria, Vibrio cholerae harbors two distinct, nonhomologous circular chromosomes (chromosome I and II). Many features of chromosome II are plasmid-like, which raised questions concerning its chromosomal nature. Plasmid replication and segregation are generally not coordinated with the bacterial cell cycle, further calling into question the mechanisms ensuring the synchronous management of chromosome I and II. Maintenance of circular replicons requires the resolution of dimers created by homologous recombination events. In Escherichia coli, chromosome dimers are resolved by the addition of a crossover at a specific site, dif, by two tyrosine recombinases, XerC and XerD. The process is coordinated with cell division through the activity of a DNA translocase, FtsK. Many E. coli plasmids also use XerCD for dimer resolution. However, the process is FtsK-independent. The two chromosomes of the V. cholerae N16961 strain carry divergent dimer resolution sites, dif1 and dif2. Here, we show that V. cholerae FtsK controls the addition of a crossover at dif1 and dif2 by a common pair of Xer recombinases. In addition, we show that specific DNA motifs dictate its orientation of translocation, the distribution of these motifs on chromosome I and chromosome II supporting the idea that FtsK translocation serves to bring together the resolution sites carried by a dimer at the time of cell division. Taken together, these results suggest that the same FtsK-dependent mechanism coordinates dimer resolution with cell division for each of the two V. cholerae chromosomes. Chromosome II dimer resolution thus stands as a bona fide chromosomal process. During proliferation, DNA synthesis, chromosome segregation, and cell division must be coordinated to ensure the stable inheritance of the genetic material. In eukaryotes, this is achieved by checkpoint mechanisms that delay certain steps until others are completed. No such temporal separation exists in bacteria, which can undergo overlapping replication cycles. The eukaryotic cell cycle is particularly well suited to the management of multiple chromosomes, with the same replication initiation and segregation machineries operating on all the chromosomes, while the bacterial cell cycle is linked to genomes of less complexity, most bacteria harboring a single chromosome. The discovery of bacteria harboring multiple circular chromosomes, such as V. cholerae, raised therefore a considerable interest for the mechanisms ensuring the synchronous management of different replicons. Here, we took advantage of our knowledge of chromosome dimer resolution, the only bacterial segregation process for which coordination with cell division is well understood, to investigate one of the mechanisms ensuring the synchronous management of the smaller, plasmid-like, and larger, chromosome-like, replicons of V. cholerae.
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Affiliation(s)
- Marie-Eve Val
- CNRS, Centre de Génétique Moléculaire, UPR 2167, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- Université Pierre et Marie Curie, Paris 6, Paris, France
| | - Sean P. Kennedy
- CNRS, Centre de Génétique Moléculaire, UPR 2167, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- Université Pierre et Marie Curie, Paris 6, Paris, France
| | - Meriem El Karoui
- INRA, Unité des Bactéries Lactiques et Pathogènes Opportunistes, UR888, Jouy en Josas, France
| | - Laetitia Bonné
- CNRS, Centre de Génétique Moléculaire, UPR 2167, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- Université Pierre et Marie Curie, Paris 6, Paris, France
| | - Fabien Chevalier
- CNRS, Centre de Génétique Moléculaire, UPR 2167, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- Université Pierre et Marie Curie, Paris 6, Paris, France
| | - François-Xavier Barre
- CNRS, Centre de Génétique Moléculaire, UPR 2167, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- Université Pierre et Marie Curie, Paris 6, Paris, France
- * E-mail:
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Guzmán E, Romeu A, Garcia-Vallve S. Completely sequenced genomes of pathogenic bacteria: a review. Enferm Infecc Microbiol Clin 2008; 26:88-98. [PMID: 18341921 DOI: 10.1157/13115544] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Six out of ten completely sequenced bacterial genomes are pathogenic or opportunistic bacteria. The genome sequence of at least one strain of all the principal pathogenic bacteria will soon be available. This information should enable us to identify genes that encode virulence factors. As these genes are potential targets for drugs and vaccines, their identification should have considerable repercussions on prevention, diagnosis, and treatment of the main bacterial infectious diseases. Comparison of genome sequences of several strains of the same species should allow identification of the genetic clues responsible for the differing behavior of related bacterial pathogens. This article reviews the genomes from pathogenic bacteria that have been or are currently being sequenced, describes the main tasks to be accomplished after a genome sequence becomes available, and discusses the benefits of having the genome sequence of bacterial pathogens.
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Affiliation(s)
- Eduard Guzmán
- Institut Català de la Salut, Area Bàsica de Salut, Tarragona, Spain.
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Sakharkar KR, Chow VTK. Microbial genomics: rhetoric or reality? Indian J Microbiol 2008; 48:156-62. [PMID: 23100710 DOI: 10.1007/s12088-008-0025-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Accepted: 05/30/2008] [Indexed: 11/27/2022] Open
Abstract
The availability of complete genome sequences of many bacterial species is facilitating numerous computational approaches for understanding bacterial genomes. One of the major incentives behind the genome sequencing of many pathogenic bacteria is the desire to better understand their diversity and to develop new approaches for controlling human diseases caused by these microorganisms. This task has become even more urgent with the rapid evolution of antibiotic resistance among many bacterial pathogens. Novel drug targets are required in order to design new antimicrobials against antibiotic-resistant pathogens. The complete genome sequences of an ever increasing number of pathogenic microbes constitute an invaluable resource and provide lead information on potential drug targets. This review focuses on in silico analyses of microbial genomes, their host-specific adaptations, with specific reference to genome architecture, design, evolution, and trends in computational identification of microbial drug targets. These trends underscore the utility of genomic data for systematic in silico drug target identification in the post-genomic era.
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Affiliation(s)
- Kishore R Sakharkar
- Human Genome Laboratory, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, 117 597 Singapore
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Abstract
Although organisms with linear chromosomes must solve the problem of fully replicating their chromosome ends, this chromosome configuration has emerged repeatedly during bacterial evolution and is evident in three divergent bacterial phyla. The benefit usually ascribed to this topology is the ability to boost genetic variation through increased recombination. But because numerous processes can impact linkage disequilibrium, such an effect is difficult to assess by comparing across bacterial taxa that possess different chromosome topologies. To test directly the contribution of chromosome architecture to genetic diversity and recombination, we examined sequence variation in strains of Agrobacterium Biovar 1, which are unique among sequenced bacteria in having both a circular and a linear chromosome. Whereas the allelic diversity among strains is generated principally by mutations, intragenic recombination is higher within genes situated on the circular chromosome. In contrast, recombination between genes is, on average, higher on the linear chromosome, but it occurs at the same rate as that observed between genes mapping to the distal portion of the circular chromosome. Collectively, our findings indicate that chromosome topology does not contribute significantly to either allelic or genotypic diversity and that the evolution of linear chromosomes is not based on a facility to recombine.
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Quantitative determination of gene strand bias in prokaryotic genomes. Genomics 2007; 90:733-40. [DOI: 10.1016/j.ygeno.2007.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 07/09/2007] [Accepted: 07/23/2007] [Indexed: 11/19/2022]
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Cooper A, Layton R, Owens L, Ketheesan N, Govan B. Evidence for the classification of a crayfish pathogen as a member of the genus Coxiella. Lett Appl Microbiol 2007; 45:558-63. [PMID: 17908227 DOI: 10.1111/j.1472-765x.2007.02240.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS The study aimed to provide characterization of a potential new species of Coxiella, identified following a series of outbreaks of disease in Australian native freshwater crayfish. METHODS AND RESULTS PCR primers designed for amplification of Coxiella burnetii genes including 16S rDNA, com1 and sodB were used to amplify homologues in the Coxiella-like crayfish pathogen. Products were then cloned and sequenced. The organism demonstrated a high degree of sequence homology in the highly conserved 16S rDNA (96%) and sodB (99%) genes, as well as the Coxiella sp. specific com1 (100%) gene. Regions flanking the sodB coding sequence demonstrated homology to C. burnetii antioxidant AhpC/Tsa family protein and dihydrodipicolinate reductase gene. CONCLUSIONS The degree of homology between the genes selected and flanking regions suggested the two organisms were sufficiently closely related to belong to the same genus. SIGNIFICANCE AND IMPACT OF THE STUDY This study provided evidence for a potential new species in the currently monospecific genus Coxiella, with the only described member being C. burnetii, a category B biological warfare agent.
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Affiliation(s)
- A Cooper
- Faculty of Medicine Health & Molecular Sciences, School of Veterinary and Biomedical Sciences, James Cook University, Townsville, Queensland, Australia
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Vara Prasad JVN. New oxazolidinones. Curr Opin Microbiol 2007; 10:454-60. [PMID: 17928263 DOI: 10.1016/j.mib.2007.08.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 08/03/2007] [Indexed: 11/17/2022]
Abstract
Due to the emergence of resistance to known antibiotics to various organisms, for example, Staphylococcus, Streptococcus, Enterococci, and Pseudomonas there is a renewed interest in the discovery of new antibacterials. Oxazolidinones, totally synthetic class of novel antibacterials, possess activity against drug-resistant Gram-positive pathogens, especially MRSA. Linezolid, the first approved drug from this class, has shown a great promise in saving lives of many patients by acting against drug-resistant Gram-positive organisms. However, its use is somewhat limited because of its myelotoxicity when used long term (>21 days). Various research groups are active in this area either to improve myelotoxicity profile of linezolid or to expand the spectrum of activity of linezolid. In spite of active research in this area, the discovery of an oxazolidinone possessing improved myelotoxicity compared to linezolid, linezolid-like efficacy, and PK remains challenging.
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Affiliation(s)
- J V N Vara Prasad
- Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA.
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Larsen J, Kuhnert P, Frey J, Christensen H, Bisgaard M, Olsen JE. Analysis of gene order data supports vertical inheritance of the leukotoxin operon and genome rearrangements in the 5' flanking region in genus Mannheimia. BMC Evol Biol 2007; 7:184. [PMID: 17915007 PMCID: PMC2228313 DOI: 10.1186/1471-2148-7-184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2007] [Accepted: 10/03/2007] [Indexed: 12/30/2022] Open
Abstract
Background The Mannheimia subclades belong to the same bacterial genus, but have taken divergent paths toward their distinct lifestyles. For example, M. haemolytica + M. glucosida are potential pathogens of the respiratory tract in the mammalian suborder Ruminantia, whereas M. ruminalis, the supposed sister group, lives as a commensal in the ovine rumen. We have tested the hypothesis that vertical inheritance of the leukotoxin (lktCABD) operon has occurred from the last common ancestor of genus Mannheimia to any ancestor of the diverging subclades by exploring gene order data. Results We examined the gene order in the 5' flanking region of the leukotoxin operon and found that the 5' flanking gene strings, hslVU-lapB-artJ-lktC and xylAB-lktC, are peculiar to M. haemolytica + M. glucosida and M. granulomatis, respectively, whereas the gene string hslVU-lapB-lktC is present in M. ruminalis, the supposed sister group of M. haemolytica + M. glucosida, and in the most ancient subclade M. varigena. In M. granulomatis, we found remnants of the gene string hslVU-lapB-lktC in the xylB-lktC intergenic region. Conclusion These observations indicate that the gene string hslVU-lapB-lktC is more ancient than the hslVU-lapB-artJ-lktC and xylAB-lktC gene strings. The presence of (remnants of) the ancient gene string hslVU-lapB-lktC among any subclades within genus Mannheimia supports that it has been vertically inherited from the last common ancestor of genus Mannheimia to any ancestor of the diverging subclades, thus reaffirming the hypothesis of vertical inheritance of the leukotoxin operon. The presence of individual 5' flanking regions in M. haemolytica + M. glucosida and M. granulomatis reflects later genome rearrangements within each subclade. The evolution of the novel 5' flanking region in M. haemolytica + M. glucosida resulted in transcriptional coupling between the divergently arranged artJ and lkt promoters. We propose that the chimeric promoter have led to high level expression of the leukotoxin operon which could explain the increased potential of certain M. haemolytica + M. glucosida strains to cause a particular type of infection.
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Affiliation(s)
- Jesper Larsen
- Department of Veterinary Pathobiology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, University of Berne, Länggass-Strasse 122, CH-3012 Berne, Switzerland
| | - Joachim Frey
- Institute of Veterinary Bacteriology, University of Berne, Länggass-Strasse 122, CH-3012 Berne, Switzerland
| | - Henrik Christensen
- Department of Veterinary Pathobiology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Magne Bisgaard
- Department of Veterinary Pathobiology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - John E Olsen
- Department of Veterinary Pathobiology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
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Prozorov AA. Regularities of the location of genes having different functions and of some other nucleotide sequences in the bacterial chromosome. Microbiology (Reading) 2007. [DOI: 10.1134/s0026261707040017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Hu J, Zhao X, Yu J. Replication-associated purine asymmetry may contribute to strand-biased gene distribution. Genomics 2007; 90:186-94. [PMID: 17532183 DOI: 10.1016/j.ygeno.2007.04.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2006] [Revised: 03/09/2007] [Accepted: 04/02/2007] [Indexed: 11/19/2022]
Abstract
Among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased. Several hypotheses explaining this strand-biased gene distribution (SGD) have been proposed, but none have been tested or supported by sufficient data analyses. In this work we have analyzed 211 prokaryotic genomes in terms of compositional strand asymmetries and the presence or absence of polC and have found that SGD correlates not only with polC, but also with purine asymmetry (PAS). Furthermore, SGD, PAS, and polC are all features associated with a group of low-GC, gram-positive bacteria (Firmicutes). We conclude that PAS is a characteristic of organisms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC and dnaE, which may play a direct role in the maintenance of SGD.
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Affiliation(s)
- Jianfei Hu
- College of Life Sciences, Peking University, Beijing 100871, China.
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48
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Hu B, Yang G, Zhao W, Zhang Y, Zhao J. MreB is important for cell shape but not for chromosome segregation of the filamentous cyanobacterium Anabaena sp. PCC 7120. Mol Microbiol 2007; 63:1640-52. [PMID: 17367385 DOI: 10.1111/j.1365-2958.2007.05618.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
MreB is a bacterial actin that plays important roles in determination of cell shape and chromosome partitioning in Escherichia coli and Caulobacter crescentus. In this study, the mreB from the filamentous cyanobacterium Anabaena sp. PCC 7120 was inactivated. Although the mreB null mutant showed a drastic change in cell shape, its growth rate, cell division and the filament length were unaltered. Thus, MreB in Anabaena maintains cell shape but is not required for chromosome partitioning. The wild type and the mutant had eight and 10 copies of chromosomes per cell respectively. We demonstrated that DNA content in two daughter cells after cell division in both strains was not always identical. The ratios of DNA content in two daughter cells had a Gaussian distribution with a standard deviation much larger than a value expected if the DNA content in two daughter cells were identical, suggesting that chromosome partitioning is a random process. The multiple copies of chromosomes in cyanobacteria are likely required for chromosome random partitioning in cell division.
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Affiliation(s)
- Bin Hu
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
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49
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Pumbwe L, Wareham DW, Aduse-Opoku J, Brazier JS, Wexler HM. Genetic analysis of mechanisms of multidrug resistance in a clinical isolate of Bacteroides fragilis. Clin Microbiol Infect 2007; 13:183-189. [PMID: 17328731 DOI: 10.1111/j.1469-0691.2006.01620.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study investigated the mechanisms of multidrug resistance (MDR) in an isolate of Bacteroides fragilis (WI1) from a patient with anaerobic sepsis. The MDR of WI1 affected susceptibility to beta-lactams, clindamycin, fluoroquinolones, metronidazole and tetracycline. In addition to its 5.31-Mb chromosome, WI1 possessed two low-copy-number plasmids, pHagl (5.6 kb) and pHag2 (9.9 kb), that were absent from B. fragilis NCTC 9343. Restriction digestion with EcoRV, HindIII and SstI, combined with DNA sequencing, revealed that pHAG2 contained a tet(Q) gene at base position 3689 that resided on the conjugative transposon CTn341. Genes cfiA (encoding a metallo-beta-lactamase) and erm(F) (encoding a macrolide-lincosamide-streptogramin B resistance determinant) were also found in WI1, but were absent from B. fragilis NCTC 9343. Nitrocefin hydrolysis revealed that WI1 had high beta-lactamase activity. Sequencing of the gyrA quinolone resistance-determining region revealed a mutation causing a Ser82 --> Phe substitution, and comparative quantitative real-time RT-PCR revealed that the cfiA, erm(F) and tet(Q) genes were all expressed in WI1. In addition, the resistance-nodulation-division efflux pump genes bmeB9 and bmeB15 were significantly over-expressed (12.30 +/- 0.42-fold and 3541.1 +/- 95.4-fold, respectively), and the efflux pump inhibitors carbonyl cyanide m-chlorophenylhydrazone and reserpine significantly increased the susceptibility of the isolate to several unrelated antibiotics (p <0.005). These data suggested that WI1 was highly multidrug-resistant because of the additive effects of chromosome- and plasmid-encoded resistance determinants.
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Affiliation(s)
- L Pumbwe
- Greater Los Angeles Veterans Administration Healthcare Systems, Los Angeles, CA, USA; Department of Medicine, University of California, Los Angeles, CA, USA
| | - D W Wareham
- Department of Microbiology, Barts and The London NHS Trust; Centre for Infectious Disease, Institute of Cell and Molecular Science, Queen Mary's School of Medicine and Dentistry, University of London, London
| | - J Aduse-Opoku
- Centre for Infectious Disease, Institute of Cell and Molecular Science, Queen Mary's School of Medicine and Dentistry, University of London, London
| | - J S Brazier
- Anaerobe Reference Laboratory, National Public Health Service Microbiology Cardiff, University Hospital of Wales, Cardiff, UK
| | - H M Wexler
- Greater Los Angeles Veterans Administration Healthcare Systems, Los Angeles, CA, USA; Department of Medicine, University of California, Los Angeles, CA, USA.
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50
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Tanaka K, Urbanczyk H, Matsui H, Sawada H, Suzuki K. Construction of physical map and mapping of chromosomal virulence genes of the biovar 3 Agrobacterium (Rhizobium vitis) strain K-Ag-1. Genes Genet Syst 2007; 81:373-80. [PMID: 17283382 DOI: 10.1266/ggs.81.373] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Most plant pathogenic Agrobacterium strains have been classified into three biovars, "biovar 1 (A. tumefaciens; Rhizobium radiobacter), biovar 2 (A. rhizogenes; R. rhizogenes) and biovar 3 (A. vitis; R. vitis)". The bacteria possess diverse types of genomic organization depending on the biovar. Previous genomic physical maps indicated difference in location of rDNA and chromosomally-coded virulence genes between biovar 1 and 2 genomes. In order to understand biovar 3 genome and its evolution in relation to the biovar 1, 2 and 3 genomes, we constructed physical map of a pathogenic biovar 3 strain K-Ag-1 in this study. Its genome consisted of two circular chromosomes (3.6 and 1.1 Mbp in length), and three plasmids (560, 230 and 70 kbp). Gene mapping based on the physical map showed presence of two rDNA loci in the larger chromosome and at least one rDNA locus in the smaller chromosome. Six chromosomal virulence genes, namely chvA, chvD, chvE, glgP, exoC and ros were found in the larger chromosome and not in the smaller chromosome. The location of rDNA loci is similar with that of biovar 1 genome, whereas the location of chromosomal virulence genes is similar with that of biovar 2 genome despite of the closer 16S-rRNA based phylogenetic relation of biovar 3 with biovar 1 than with biovar 2. Genomic PFGE RFLP analysis revealed that the K-Ag-1 strain, which was isolated on a kiwifruit plant in Japan, has the closest intra-species relation with two strains isolated from grapevine plants in Japan among eight biovar 3 strains examined. This datum suggests that the line of the strain is a major one in biovar 3 in Japan. Evolution of the genome of the strain is discussed based on the data.
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Affiliation(s)
- Katsuyuki Tanaka
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima 739-8526, Japan.
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