Novel tRNA gene organization in the 16S-23S intergenic spacer of the Streptococcus pneumoniae rRNA gene cluster.

Abstract Background The mitogenomes of 12 teleost fish of the bothid family (order Pleuronectiformes) indicated that the genomic-scale rearrangements characterized in previous work. A novel mechanism of genomic rearrangement called the Dimer-Mitogenome and Non-Random Loss (DMNL) model was used to account for the rearrangement found in one of these bothids, Crossorhombus azureus. Results The 18,170 bp mitogenome of G. polyophthalmus contains 37 genes, two control regions (CRs), and the origin of replication of the L-strand (OL). This mitogenome is characterized by genomic-scale rearrangements: genes located on the L-strand are grouped in an 8-gene cluster (Q-A-C-Y-S1-ND6-E-P) that does not include tRNA-N; genes found on the H-strand are grouped together (F-12S … CytB-T) except for tRNA-D that was translocated inside the 8-gene L-strand cluster. Compared to non-rearranged mitogenomes of teleost fishes, gene organization in the mitogenome of G. polyophthalmus and in that of the other 12 bothids characterized thus far is very similar. These rearrangements could be sorted into four types (Type I, II, III and IV), differing in the particular combination of the CR, tRNA-D gene and 8-gene cluster and the shuffling of tRNA-V. The DMNL model was used to account for all but one gene rearrangement found in all 13 bothid mitogenomes. Translocation of tRNA-D most likely occurred after the DMNL process in 10 bothid mitogenomes and could have occurred either before or after DMNL in the three other species. During the DMNL process, the tRNA-N gene was retained rather than the expected tRNA-N′ gene. tRNA-N appears to assist in or act as OL function when the OL secondary structure could not be formed from intergenic sequences. A striking finding was that each of the non-transcribed genes has degenerated to a shorter intergenic spacer during the DMNL process. These findings highlight a rare phenomenon in teleost fish. Conclusions This result provides significant evidence to support the existence of dynamic dimeric mitogenomes and the DMNL model as the mechanism of gene rearrangement in bothid mitogenomes, which not only promotes the understanding of mitogenome structural diversity, but also sheds light on mechanisms of mitochondrial genome rearrangement and replication.

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Characterization of a Polycyclic Aromatic Hydrocarbon Degradation Gene Cluster in a Phenanthrene-Degrading Acidovorax Strain

Applied and Environmental Microbiology ◽

10.1128/aem.01955-08 ◽

2009 ◽

Vol 75 (9) ◽

pp. 2613-2620 ◽

Cited By ~ 77

Author(s):

David R. Singleton ◽

Liza Guzmán Ramirez ◽

Michael D. Aitken

Keyword(s):

Polycyclic Aromatic Hydrocarbon ◽

Aromatic Hydrocarbon ◽

Gene Cluster ◽

Large Subunit ◽

Gene Organization ◽

Stable Isotope Probing ◽

Rrna Gene ◽

Gene Transcript ◽

Phenanthrene Degradation ◽

Polycyclic Aromatic

ABSTRACT Acidovorax sp. strain NA3 was isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soil that had been treated in a bioreactor and enriched with phenanthrene. The 16S rRNA gene of the isolate possessed 99.8 to 99.9% similarity to the dominant sequences recovered during a previous stable-isotope probing experiment with [U-13C]phenanthrene on the same soil (D. R. Singleton, S. N. Powell, R. Sangaiah, A. Gold, L. M. Ball, and M. D. Aitken, Appl. Environ. Microbiol. 71:1202-1209, 2005). The strain grew on phenanthrene as a sole carbon and energy source and could mineralize 14C from a number of partially labeled PAHs, including naphthalene, phenanthrene, chrysene, benz[a]anthracene, and benzo[a]pyrene, but not pyrene or fluoranthene. Southern hybridizations of a genomic fosmid library with a fragment of the large subunit of the ring-hydroxylating dioxygenase gene from a naphthalene-degrading Pseudomonas strain detected the presence of PAH degradation genes subsequently determined to be highly similar in both nucleotide sequence and gene organization to an uncharacterized Alcaligenes faecalis gene cluster. The genes were localized to the chromosome of strain NA3. To test for gene induction by selected compounds, RNA was extracted from amended cultures and reverse transcribed, and cDNA associated with the enzymes involved in the first three steps of phenanthrene degradation was quantified by quantitative real-time PCR. Expression of each of the genes was induced most strongly by phenanthene and to a lesser extent by naphthalene, but other tested PAHs and PAH metabolites had negligible effects on gene transcript levels.

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Mechanisms of Gene Rearrangement in 13 Bothids Based on Comparison with a Newly Completed Mitogenome of the Threespot Flounder, Grammatobothus polyophthalmus (Pleuronectiformes: Bothidae)

10.21203/rs.2.9891/v2 ◽

2019 ◽

Author(s):

Hairong Luo ◽

Xiaoyu Kong ◽

Shixi Chen ◽

Wei Shi

Keyword(s):

Gene Cluster ◽

Teleost Fish ◽

Gene Rearrangement ◽

Genome Rearrangement ◽

Intergenic Spacer ◽

Gene Organization ◽

N Gene ◽

Type I ◽

Intergenic Sequences ◽

Genomic Scale

Abstract Background: The previously characterized mitogenomes of 12 teleost fish of the bothid family (order Pleuronectiformes) indicated that the genomic-scale rearrangements occurred in this teleost lineage. A novel mechanism of genomic rearrangement called the Dimer-Mitogenome and Non-Random Loss (DMNL) model was used to account for the rearrangement found in one of these bothids, Crossorhombus azureus. Results: The 18170 bp mitogenome of G. polyophthalmus contains 37 genes, two control regions (CRs), and the origin of replication of the L-strand (OL). This mitogenome is characterized by genomic-scale rearrangements: genes located on the L-strand are grouped in an 8-gene cluster (Q-A-C-Y-S1-ND6-E-P) that does not include tRNA-N; genes found on the H-strand are grouped together (F-12S … CytB-T) except for tRNA-D that was translocated inside the 8-gene L-strand cluster. Compared to non-rearranged mitogenomes of teleost fishes, gene organization in the mitogenome of G. polyophthalmus and in that of the other 12 bothids characterized thus far is very similar. These rearrangements could be sorted into four types (Type I, II, III and IV), differing in the particular combination of the CR, tRNA-D gene and 8-gene cluster and the shuffling of tRNA-V. The DMNL model was used to account for all but one gene rearrangement found in all 13 bothid mitogenomes. Translocation of tRNA-D most likely occurred after the DMNL process in 10 bothid mitogenomes and could have occurred either before or after DMNL in the three other species. During the DMNL process, the tRNA-N gene was retained rather than the expected tRNA-N′ gene. tRNA-N appears to assist in or act as OL function when the OL secondary structure could not be formed from intergenic sequences. A striking finding was that each of the non-transcribed genes has degenerated to a shorter intergenic spacer during the DMNL process. These findings highlight a rare phenomenon in teleost fish. Conclusions: This result provides significant evidence to support the existence of dynamic dimeric mitogenomes and the DMNL model as the mechanism of gene rearrangement in bothid mitogenomes, which not only promotes the understanding of mitogenome structural diversity, but also sheds light on mechanisms of mitochondrial genome rearrangement and replication.

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Mechanisms of Gene Rearrangement in 13 Bothids Based on Comparison with a Newly Completed Mitogenome of the Threespot Flounder, Grammatobothus polyophthalmus (Pleuronectiformes: Bothidae)

10.21203/rs.2.9891/v3 ◽

2019 ◽

Author(s):

Hairong Luo ◽

Xiaoyu Kong ◽

Shixi Chen ◽

Wei Shi

Keyword(s):

Gene Cluster ◽

Teleost Fish ◽

Gene Rearrangement ◽

Genome Rearrangement ◽

Intergenic Spacer ◽

Gene Organization ◽

N Gene ◽

Type I ◽

Intergenic Sequences ◽

Genomic Scale

Abstract Background: The previously characterized mitogenomes of 12 teleost fish of the bothid family (order Pleuronectiformes) indicated that the genomic-scale rearrangements occurred in this teleost lineage. A novel mechanism of genomic rearrangement called the Dimer-Mitogenome and Non-Random Loss (DMNL) model was used to account for the rearrangement found in one of these bothids, Crossorhombus azureus. Results: The 18170 bp mitogenome of G. polyophthalmus contains 37 genes, two control regions (CRs), and the origin of replication of the L-strand (OL). This mitogenome is characterized by genomic-scale rearrangements: genes located on the L-strand are grouped in an 8-gene cluster (Q-A-C-Y-S1-ND6-E-P) that does not include tRNA-N; genes found on the H-strand are grouped together (F-12S … CytB-T) except for tRNA-D that was translocated inside the 8-gene L-strand cluster. Compared to non-rearranged mitogenomes of teleost fishes, gene organization in the mitogenome of G. polyophthalmus and in that of the other 12 bothids characterized thus far is very similar. These rearrangements could be sorted into four types (Type I, II, III and IV), differing in the particular combination of the CR, tRNA-D gene and 8-gene cluster and the shuffling of tRNA-V. The DMNL model was used to account for all but one gene rearrangement found in all 13 bothid mitogenomes. Translocation of tRNA-D most likely occurred after the DMNL process in 10 bothid mitogenomes and could have occurred either before or after DMNL in the three other species. During the DMNL process, the tRNA-N gene was retained rather than the expected tRNA-N′ gene. tRNA-N appears to assist in or act as OL function when the OL secondary structure could not be formed from intergenic sequences. A striking finding was that each of the non-transcribed genes has degenerated to a shorter intergenic spacer during the DMNL process. These findings highlight a rare phenomenon in teleost fish. Conclusions: This result provides significant evidence to support the existence of dynamic dimeric mitogenomes and the DMNL model as the mechanism of gene rearrangement in bothid mitogenomes, which not only promotes the understanding of mitogenome structural diversity, but also sheds light on mechanisms of mitochondrial genome rearrangement and replication.

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Exploring tRNA gene cluster in archaea

10.1101/370668 ◽

2018 ◽

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Gene Cluster ◽

Trna Gene ◽

Gene Clusters ◽

Gene Organization ◽

Trna Genes ◽

Genomic Analyses ◽

Living Organisms

AbstractShared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organization of tRNA genes as clusters, but this trait has not been explored in archaea domain. Here, based on analyses of complete and draft archaeal genomes, we demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene cluster was identified at least in three Archaea class, Halobacteria, Methanobacteria and Methanomicrobia from Euryarchaeota supergroup. Genomic analyses also revealed evidence of tRNA gene cluster associated with mobile genetic elements and horizontal gene transfer inter/intra-domain. The presence of tRNA gene clusters in the three domain of life suggests a role of this type of tRNA gene organization in the biology of the living organisms.

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Heterogeneity in the Intergenic Spacer Region (IGS) of the Ribosomal RNA Gene Cluster Among Syrian Pyrenophora graminea Isolates

Cereal Research Communications ◽

10.1007/bf03543335 ◽

2004 ◽

Vol 32 (4) ◽

pp. 459-464 ◽

Cited By ~ 3

Author(s):

M. Jawhar ◽

B. Tóth ◽

M. I. E. Arabi

Keyword(s):

Gene Cluster ◽

Ribosomal Rna ◽

Intergenic Spacer ◽

Ribosomal Rna Gene ◽

Intergenic Spacer Region ◽

Pyrenophora Graminea

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Identification of the kinanthraquinone biosynthetic gene cluster by expression of an atypical response regulator

Bioscience Biotechnology and Biochemistry ◽

10.1093/bbb/zbaa082 ◽

2021 ◽

Vol 85 (3) ◽

pp. 714-721

Author(s):

Risa Takao ◽

Katsuyuki Sakai ◽

Hiroyuki Koshino ◽

Hiroyuki Osada ◽

Shunji Takahashi

Keyword(s):

Heterologous Expression ◽

Gene Cluster ◽

Secondary Metabolite ◽

Response Regulator ◽

Bac Library ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Gene Organization ◽

Biosynthetic Gene ◽

Streptomyces Sp

ABSTRACT Recent advances in genome sequencing have revealed a variety of secondary metabolite biosynthetic gene clusters in actinomycetes. Understanding the biosynthetic mechanism controlling secondary metabolite production is important for utilizing these gene clusters. In this study, we focused on the kinanthraquinone biosynthetic gene cluster, which has not been identified yet in Streptomyces sp. SN-593. Based on chemical structure, 5 type II polyketide synthase gene clusters were listed from the genome sequence of Streptomyces sp. SN-593. Among them, a candidate gene cluster was selected by comparing the gene organization with grincamycin, which is synthesized through an intermediate similar to kinanthraquinone. We initially utilized a BAC library for subcloning the kiq gene cluster, performed heterologous expression in Streptomyces lividans TK23, and identified the production of kinanthraquinone and kinanthraquinone B. We also found that heterologous expression of kiqA, which belongs to the DNA-binding response regulator OmpR family, dramatically enhanced the production of kinanthraquinones.

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Characterization of Fusarium spp. isolates by PCR-RFLP analysis of the intergenic spacer region of the rRNA gene (rDNA)

International Journal of Food Microbiology ◽

10.1016/j.ijfoodmicro.2005.09.005 ◽

2006 ◽

Vol 106 (3) ◽

pp. 297-306 ◽

Cited By ~ 36

Author(s):

A. Llorens ◽

M.J. Hinojo ◽

R. Mateo ◽

M.T. González-Jaén ◽

F.M. Valle-Algarra ◽

...

Keyword(s):

Intergenic Spacer ◽

Rflp Analysis ◽

Rrna Gene ◽

Fusarium Spp ◽

Intergenic Spacer Region ◽

Pcr Rflp

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The Western Progression of Lyme Disease: Infectious and NonclonalBorrelia burgdorferi Sensu LatoPopulations in Grand Forks County, North Dakota

Applied and Environmental Microbiology ◽

10.1128/aem.02422-14 ◽

2014 ◽

Vol 81 (1) ◽

pp. 48-58 ◽

Cited By ~ 12

Author(s):

Brandee L. Stone ◽

Nathan M. Russart ◽

Robert A. Gaultney ◽

Angela M. Floden ◽

Jefferson A. Vaughan ◽

...

Keyword(s):

Lyme Disease ◽

16S Rrna ◽

16S Rrna Gene ◽

North Dakota ◽

Intergenic Spacer ◽

Rrna Gene ◽

Content Type ◽

Intergenic Spacer Region ◽

Grand Forks ◽

The 16S Rrna Gene

ABSTRACTScant attention has been paid to Lyme disease,Borrelia burgdorferi,Ixodes scapularis, or reservoirs in eastern North Dakota despite the fact that it borders high-risk counties in Minnesota. Recent reports ofB. burgdorferiandI. scapularisin North Dakota, however, prompted a more detailed examination. Spirochetes cultured from the hearts of five rodents trapped in Grand Forks County, ND, were identified asB. burgdorferi sensu latothrough sequence analyses of the 16S rRNA gene, the 16S rRNA gene-ileTintergenic spacer region,flaB,ospA,ospC, andp66. OspC typing revealed the presence of groups A, B, E, F, L, and I. Two rodents were concurrently carrying multiple OspC types. Multilocus sequence typing suggested the eastern North Dakota strains are most closely related to those found in neighboring regions of the upper Midwest and Canada. BALB/c mice were infected withB. burgdorferiisolate M3 (OspC group B) by needle inoculation or tick bite. Tibiotarsal joints and ear pinnae were culture positive, andB. burgdorferiM3 was detected by quantitative PCR (qPCR) in the tibiotarsal joints, hearts, and ear pinnae of infected mice. Uninfected larvalI. scapularisticks were able to acquireB. burgdorferiM3 from infected mice; M3 was maintained inI. scapularisduring the molt from larva to nymph; and further, M3 was transmitted from infectedI. scapularisnymphs to naive mice, as evidenced by cultures and qPCR analyses. These results demonstrate that isolate M3 is capable of disseminated infection by both artificial and natural routes of infection. This study confirms the presence of unique (nonclonal) and infectiousB. burgdorferipopulations in eastern North Dakota.

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Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

BioMed Research International ◽

10.1155/2014/480170 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 9

Author(s):

Sonia Ciccazzo ◽

Alfonso Esposito ◽

Eleonora Rolli ◽

Stefan Zerbe ◽

Daniele Daffonchio ◽

...

Keyword(s):

High Altitude ◽

Developmental Stage ◽

Bacterial Communities ◽

Developmental Stages ◽

Gene Diversity ◽

Intergenic Spacer ◽

Intermediate Stage ◽

Plant Colonization ◽

Early Developmental Stage ◽

Rrna Gene

The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P<0.05) on 16S rRNA gene diversity revealed significant differences (P<0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

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