scholarly journals Genera specific distribution of DEAD-box RNA helicases in cyanobacteria

2021 ◽  
Vol 7 (3) ◽  
Author(s):  
Denise S. Whitford ◽  
Brendan T. Whitman ◽  
George W. Owttrim
Keyword(s):  
Phylogenetic Analysis ◽  
Rna Helicase ◽  
Evolutionary Divergence ◽  
Sequence Motif ◽  
Rna Helicases ◽  
Homologous Proteins ◽  
Content Type ◽  
Conserved Sequence ◽  
Link Type ◽  
Dead Box

Although RNA helicases are essentially ubiquitous and perform roles in all stages of RNA metabolism, phylogenetic analysis of the DEAD (Asp-Glu-Ala-Asp)-box RNA helicase family in a single phylum has not been performed. Here, we performed a phylogenetic analysis on DEAD-box helicases from all currently available cyanobacterial genomes, comprising a total of 362 helicase protein sequences from 280 strains. DEAD-box helicases belonging to three distinct clades were observed. Two clades, the CsdA (cold shock DEAD-box A)-like and RhlE (RNA helicase E)-like helicases, cluster with the homologous proteins from Escherichia coli . The third clade, the CrhR (cyanobacterial RNA helicase Redox)-like helicases, is unique to cyanobacteria and characterized by a conserved sequence motif in the C-terminal extension. Restricted distribution is observed across cyanobacterial diversity with respect to both helicase type and strain. CrhR-like and CsdA-like helicases essentially never occur together, while RhlE always occurs with either a CrhR-like or CsdA-like helicase. CrhR-like and RhlE-like proteins occurred in filamentous cyanobacteria of the orders Nostocales , Oscillatoriales and Synechococcales . Similarly, CsdA- and RhlE-like proteins are restricted to unicellular cyanobacteria of the genera Cyanobium and Synechococcus . In addition, the unexpected occurrence of RhlE in two Synechococcus strains suggests recent acquisition and evolutionary divergence. This study, therefore, raises physiological and evolutionary questions as to why DEAD-box RNA helicases encoded in cyanobacterial lineages display restricted distributions, suggesting niches that require either CrhR or CsdA RNA helicase activity but not both. Extensive conservation of gene synteny surrounding the previously described rimO–crhR operon is also observed, indicating a role in the maintenance of photosynthesis. The analysis provides insights into the evolution, origin and dissemination of sequences within a single gene family to yield divergent functional roles.

scholarly journals Association of the Cold Shock DEAD-Box RNA Helicase RhlE to the RNA Degradosome in Caulobacter crescentus

2017 ◽  
Vol 199 (13) ◽  
Author(s):  
Angel A. Aguirre ◽  
Alexandre M. Vicente ◽  
Steven W. Hardwick ◽  
Daniela M. Alvelos ◽  
Ricardo R. Mazzon ◽  
...  
Keyword(s):  
Low Temperature ◽  
Caulobacter Crescentus ◽  
Immunoblot Analysis ◽  
Rna Helicase ◽  
Rnase E ◽  
Rna Helicases ◽  
Content Type ◽  
Dead Box ◽  
Rna Degradosome ◽  
The Dead

ABSTRACT In diverse bacterial lineages, multienzyme assemblies have evolved that are central elements of RNA metabolism and RNA-mediated regulation. The aquatic Gram-negative bacterium Caulobacter crescentus, which has been a model system for studying the bacterial cell cycle, has an RNA degradosome assembly that is formed by the endoribonuclease RNase E and includes the DEAD-box RNA helicase RhlB. Immunoprecipitations of extracts from cells expressing an epitope-tagged RNase E reveal that RhlE, another member of the DEAD-box helicase family, associates with the degradosome at temperatures below those optimum for growth. Phenotype analyses of rhlE, rhlB, and rhlE rhlB mutant strains show that RhlE is important for cell fitness at low temperature and its role may not be substituted by RhlB. Transcriptional and translational fusions of rhlE to the lacZ reporter gene and immunoblot analysis of an epitope-tagged RhlE indicate that its expression is induced upon temperature decrease, mainly through posttranscriptional regulation. RNase E pulldown assays show that other proteins, including the transcription termination factor Rho, a second DEAD-box RNA helicase, and ribosomal protein S1, also associate with the degradosome at low temperature. The results suggest that the RNA degradosome assembly can be remodeled with environmental change to alter its repertoire of helicases and other accessory proteins. IMPORTANCE DEAD-box RNA helicases are often present in the RNA degradosome complex, helping unwind secondary structures to facilitate degradation. Caulobacter crescentus is an interesting organism to investigate degradosome remodeling with change in temperature, because it thrives in freshwater bodies and withstands low temperature. In this study, we show that at low temperature, the cold-induced DEAD-box RNA helicase RhlE is recruited to the RNA degradosome, along with other helicases and the Rho protein. RhlE is essential for bacterial fitness at low temperature, and its function may not be complemented by RhlB, although RhlE is able to complement for rhlB loss. These results suggest that RhlE has a specific role in the degradosome at low temperature, potentially improving adaptation to this condition.

scholarly journals The embryonic RNA helicase gene (ERH): a new member of the DEAD box family of RNA helicases

1995 ◽  
Vol 308 (3) ◽  
pp. 839-846 ◽  
Author(s):  
J Sowden ◽  
W Putt ◽  
K Morrison ◽  
R Beddington ◽  
Y Edwards
Keyword(s):  
Expression Profile ◽  
Sequence Similarity ◽  
Rna Helicase ◽  
Chromosome 1 ◽  
Rna Helicases ◽  
High Sequence Similarity ◽  
Dead Box ◽  
Isolation And Characterization ◽  
Helicase Gene ◽  
The Dead

DEAD box proteins share several highly conserved motifs including the characteristic Asp-Glu-Ala-Asp (D-E-A-D in the amino acid single-letter code) motif and have established or putative ATP-dependent RNA helicase activity. These proteins are implicated in a range of cellular processes that involve regulation of RNA function, including translation initiation, RNA splicing and ribosome assembly. Here we describe the isolation and characterization of an embryonic RNA helicase gene, ERH, which maps to mouse chromosome 1 and encodes a new member of the DEAD box family of proteins. The predicted ERH protein shows high sequence similarity to the testes-specific mouse PL10 and to the maternally acting Xenopus An3 helicase proteins. The ERH expression profile is similar, to that of An3, which localizes to the animal hemisphere of oocytes and is abundantly expressed in the embryo. ERH is expressed in oocytes and is a ubiquitous mRNA in the 9 days-post-conception embryo, and at later stages of development shows a more restricted pattern of expression in brain and kidney. The similarities in sequence and in expression profile suggest that ERH is the murine equivalent of the Xenopus An3 gene, and we propose that ERH plays a role in translational activation of mRNA in the oocyte and early embryo.

scholarly journals Marinomonas mangrovi sp. nov., isolated from mangrove sediment

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1537-1541 ◽  
Author(s):  
De-Chao Zhang ◽  
Rosa Margesin
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Mangrove Sediment ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Content Sharing ◽  
Link Type ◽  
Curved Rods ◽  
Sequence Similarities

A Gram-stain-negative, Na+-requiring bacterial strain, designated B20-1T, was isolated from soil of the root system of mangrove forest. Cells were curved rods and motile by means of a polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B20-1T belonged to the genus Marinomonas , sharing highest sequence similarities with Marinomonas rhizomae IVIA-Po-145T (97.6 %), Marinomonas dokdonensis DSW10-10T (97.0 %) and Marinomonas foliarum IVIA-Po-155T (96.9 %). The predominant cellular fatty acids of strain B20-1T were C10 : 0 3-OH, C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. Phosphatidylethanolamine and phosphatidylglycerol were identified as the predominant phospholipids. The predominant ubiquinone was Q-8. The genomic DNA G+C content of strain B20-1T was 46.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Marinomonas mangrovi sp. nov., is proposed with B20-1T ( = DSM 28136T = LMG 28077T) as the type strain.

Sphingomonas indica sp. nov., isolated from hexachlorocyclohexane (HCH)-contaminated soil

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2997-3002 ◽  
Author(s):  
Neha Niharika ◽  
Swati Jindal ◽  
Jasvinder Kaur ◽  
Rup Lal
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Total Dna ◽  
Physiological Tests

A bacterial strain, designated Dd16T, was isolated from a hexachlorocyclohexane (HCH) dumpsite at Lucknow, India. Cells of strain Dd16T were Gram-stain-negative, non-motile, rod-shaped and yellow-pigmented. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Sphingomonas in the family Sphingomonadaceae , as it showed highest sequence similarity to Sphingomonas asaccharolytica IFO 15499T (95.36 %), Sphingosinicella vermicomposti YC7378T (95.30), ‘Sphingomonas humi’ PB323 (95.20 %), Sphingomonas sanxanigenens NX02T (95.14 %) and Sphingomonas desiccabilis CP1DT (95.00 %). The major fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) C14 : 0 2-OH, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipid profile of strain Dd16T also corresponded to those reported for species of the genus Sphingomonas (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, and a sphingoglycolipid), again supporting its identification as a member of the genus Sphingomonas . The predominant respiratory quinone was ubiquinone Q10, and sym-homospermidine was the major polyamine observed. The total DNA G+C content of strain Dd16T was 65.8 mol%. The results obtained on the basis of phenotypic characteristics and phylogenetic analysis and after biochemical and physiological tests, clearly distinguished strain Dd16T from closely related members of the genus Sphingomonas . Thus, strain Dd16T represents a novel species of the genus Sphingomonas for which the name Sphingomonas indica sp. nov. is proposed. The type strain is Dd16T ( = DSM 25434T = CCM 7882T).

scholarly journals Characterization and Genomic Analysis of ValSw3-3, a New Siphoviridae Bacteriophage Infecting Vibrio alginolyticus

2020 ◽  
Vol 94 (10) ◽  
Author(s):  
Ling Chen ◽  
Quan Liu ◽  
Jiqiang Fan ◽  
Tingwei Yan ◽  
Haoran Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
In Silico ◽  
Bacterial Infections ◽  
Phage Therapy ◽  
Gc Content ◽  
Vibrio Alginolyticus ◽  
Lytic Bacteriophage ◽  
Sequence Alignments ◽  
Content Type ◽  
Link Type

ABSTRACT A novel lytic bacteriophage, ValSw3-3, which efficiently infects pathogenic strains of Vibrio alginolyticus, was isolated from sewage water and characterized by microbiological and in silico genomic analyses. Transmission electron microscopy indicated that ValSw3-3 has the morphology of siphoviruses. This phage can infect four species in the Vibrio genus and has a latent period of 15 min and a burst size of 95 ± 2 PFU/infected bacterium. Genome sequencing results show that ValSw3-3 has a 39,846-bp double-stranded DNA genome with a GC content of 43.1%. The similarity between the genome sequences of ValSw3-3 and those of other phages recorded in the GenBank database was below 50% (42%), suggesting that ValSw3-3 significantly differs from previously reported phages at the DNA level. Multiple genome comparisons and phylogenetic analysis based on the major capsid protein revealed that phage ValSw3-3 is grouped in a clade with five other phages, including Listonella phage phiHSIC (GenBank accession no. NC_006953.1), Vibrio phage P23 (MK097141.1), Vibrio phage pYD8-B (NC_021561.1), Vibrio phage 2E1 (KX507045.1), and Vibrio phage 12G5 (HQ632860.1), and is distinct from all known genera within the Siphoviridae family that have been ratified by the International Committee on Taxonomy of Viruses (ICTV). An in silico proteomic comparison of diverse phages from the Siphoviridae family supported this clustering result and suggested that ValSw3-3, phiHSIC, P23, pYD8-B, 2E1, and 12G5 should be classified as a novel genus cluster of Siphoviridae. A subsequent analysis of core genes also revealed the common genes shared within this new cluster. Overall, these results provide a characterization of Vibrio phage ValSw3-3 and support our proposal of a new viral genus within the family Siphoviridae. IMPORTANCE Phage therapy has been considered a potential alternative to antibiotic therapy in treating bacterial infections. For controlling the vibriosis-causing pathogen Vibrio alginolyticus, well-documented phage candidates are still lacking. Here, we characterize a novel lytic Vibrio phage, ValSw3-3, based on its morphology, host range and infectivity, growth characteristics, stability under various conditions, and genomic features. Our results show that ValSw3-3 could be a potent candidate for phage therapy to treat V. alginolyticus infections due to its stronger infectivity and better pH and thermal stability than those of previously reported Vibrio phages. Moreover, genome sequence alignments, phylogenetic analysis, in silico proteomic comparison, and core gene analysis all support that this novel phage, ValSw3-3, and five unclassified phages form a clade distant from those of other known genera ratified by the ICTV. Thus, we propose a new viral genus within the Siphoviridae family to accommodate this clade, with ValSw3-3 as a representative member.

Methanospirillum psychrodurum sp. nov., isolated from wetland soil

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 638-641 ◽  
Author(s):  
Liguang Zhou ◽  
Xiaoli Liu ◽  
Xiuzhu Dong
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Wetland Soil ◽  
Rrna Gene ◽  
Lower Growth ◽  
Content Type ◽  
Link Type ◽  
Hydrogenotrophic Methanogenesis

A psychrotolerant methanogenic strain, X-18T, was isolated from the soil of the Madoi wetland at Qinghai, Tibetan plateau, China. Cells were wavy rods (11–62 µm long) with blunt tapered ends and Gram-stain-negative. Strain X-18T grew strictly anaerobically and produced methane exclusively from H2/CO2. Growth occurred in the temperature range of 4–32 °C and optimally at 25 °C. Growth pH ranged from 6.5 to 8.0 and the optimum was 7.0. The G+C content of the genomic DNA of strain X-18T was 44.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and the alpha subunit of methyl-coenzyme M reductase indicated that strain X-18T was affiliated to the genus Methanospirillum and was most closely related to Methanospirillum lacunae Ki8-1T, with 96.3 % 16S rRNA gene sequence similarity. However, strain X-18T could be distinguished from the existing species of the genus Methanospirillum by its lower growth temperature and obligate hydrogenotrophic methanogenesis. On the basis of phenotypic characteristics and phylogenetic analysis, strain X-18T represents a novel species of the genus Methanospirillum , for which the name Methanospirillum psychrodurum sp. nov. is proposed and strain X-18T is assigned as the type strain ( = CGMCC 1.5186T = JCM 19216T).

Paracoccus huijuniae sp. nov., an amide pesticide-degrading bacterium isolated from activated sludge of a wastewater biotreatment system

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1132-1137 ◽  
Author(s):  
Li-Na Sun ◽  
Jun Zhang ◽  
Soon-Wo Kwon ◽  
Jian He ◽  
Shun-Gui Zhou ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Type Species ◽  
Amide Bond ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A facultatively anaerobic, non-spore-forming, non-motile, catalase- and oxidase-positive, Gram-reaction-negative, coccoid to short rod-shaped strain, designated FLN-7T, was isolated from activated sludge of a wastewater biotreatment facility. The strain was able to hydrolyse amide pesticides (e.g. diflubenzuron, propanil, chlorpropham and dimethoate) through amide bond cleavage. Strain FLN-7T grew at 4–42 °C (optimum 28 °C), at pH 5.0–8.0 (optimum pH 7.0) and with 0–5.0 % (w/v) NaCl (optimum 1.0 %). The major respiratory quinone was ubiquinone-10. The major cellular fatty acid was C18 : 1ω7c. The genomic DNA G+C content of strain FLN-7T was 66.4±0.5 mol%. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine and an unidentified glycolipid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain FLN-7T was a member of the genus Paracoccus and showed highest 16S rRNA gene sequence similarities with Paracoccus aminovorans JCM 7685T (99.2 %), P. denitrificans DSM 413T (97.8 %), P. yeei CDC G1212T (97.3 %) and P. thiocyanatus THI 011T (97.1 %). Strain FLN-7T showed low DNA–DNA relatedness with P. aminovorans KACC 12261T (36.5±3.4 %), P. denitrificans KACC 12251T (30.5±2.6 %), P. yeei CCUG 46822T (26.2±2.4 %) and P. thiocyanatus KACC 13901T (15.5±0.9 %). Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition and biochemical characteristics, strain FLN-7T was clearly distinguished from all recognized species of the genus Paracoccus and should be classified in a novel species, for which the name Paracoccus huijuniae sp. nov. is proposed. The type strain is FLN-7T ( = KACC 16242T  = ACCC 05690T).

Luteimonas huabeiensis sp. nov., isolated from stratum water

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3352-3357 ◽  
Author(s):  
Gang Wu ◽  
Yang Liu ◽  
Qing Li ◽  
Huijing Du ◽  
Jing You ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Physiological And Biochemical Characteristics ◽  
Taxonomic Approach ◽  
Type Strains ◽  
Physiological And Biochemical

A yellow-coloured bacterial strain, designated HB2T, isolated from stratum water was investigated using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was a member of the genus Luteimonas , its three closest neighbours being Luteimonas aquatica BCRC 17731T (97.5 % similarity), Luteimonas marina JCM 12488T (97.3 %) and Luteimonas aestuarii DSM 19680T (96.9 %). Strain HB2T could clearly be distinguished from these type strains based on phylogenetic analysis, DNA–DNA hybridization, fatty acid composition and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strain HB2T represents a novel species of the genus Luteimonas , for which the name Luteimonas huabeiensis sp. nov. is proposed. The type strain is HB2T ( = DSM 26429T = CICC 11005sT).

Sphingobacterium caeni sp. nov., isolated from activated sludge

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2260-2264 ◽  
Author(s):  
Li-Na Sun ◽  
Jun Zhang ◽  
Qing Chen ◽  
Jian He ◽  
Shun-Peng Li
Keyword(s):  
Phylogenetic Analysis ◽  
Activated Sludge ◽  
Dna Hybridization ◽  
Type Species ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach ◽  
Ph Range

The taxonomic status of a bacterium, strain DC-8T, isolated from activated sludge, was determined using a polyphasic taxonomic approach. The cells of strain DC-8T were Gram-negative, non-motile, non-spore-forming and rod-shaped. The isolate grew at temperature range of 10–40 °C (optimum 30–35 °C), pH range of 5.0–10.0 (optimum 6.5–8.0) and NaCl concentrations of 0–5 % (optimum 0–1 %). The predominant menaquinone of strain DC-8T was MK-7 and major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 39.7 %), iso-C15 : 0 (33.7 %) and C16 : 0 (5.2 %). The DNA G+C content was 39.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain DC-8T was a member of the genus Sphingobacterium . Strain DC-8T shared the highest similarity with Sphingobacterium siyangense SY1T (98.4 %), Sphingobacterium multivorum IAM 14316T (98.3 %), Sphingobacterium canadense CR11T (98.0 %) and Sphingobacterium detergens 6.2ST (97.9 %) and shared less than 97 % similarity with other members of the genus Sphingobacterium . DNA–DNA hybridization experiments showed that the DNA–DNA relatedness values between strain DC-8T and its closest phylogenetic neighbours were below 70 %. Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain DC-8T was clearly distinguished from all recognized species of the genus Sphingobacterium and should be classified as a representative of a novel species of the genus Sphingobacterium , for which the name Sphingobacterium caeni sp. nov. is proposed. The type strain is DC-8T ( = CCTCC AB 2012020T = KACC 16850T).

Mycobacterium parakoreense sp. nov., a slowly growing non-chromogenic species related to Mycobacterium koreense , isolated from a human clinical specimen

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2301-2308 ◽  
Author(s):  
Byoung-Jun Kim ◽  
Seok-Hyun Hong ◽  
Hee-Kyung Yu ◽  
Young-Gil Park ◽  
Joseph Jeong ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sputum Sample ◽  
Clinical Specimen ◽  
Mycolic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A previously undescribed, slowly growing, non-chromogenic Mycobacterium strain (299T) was isolated from the sputum sample of a patient with a symptomatic pulmonary infection. Phenotypically, strain 299T was generally similar to Mycobacterium koreense DSM 45576T and Mycobacterium triviale ATCC 23292T. The 16S rRNA gene sequence of strain 299T was similar to that of M. koreense DSM 45576T (GenBank accession no. AY734996, 99.5 % similarity); however, it differed substantially from that of M. triviale ATCC 23292T (X88924, 98.2 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 299T clustered together with M. koreense DSM 45576T and M. triviale ATCC 23292T, supported by high bootstrapping values (99 %). Unique mycolic acid profiles and phylogenetic analysis based on two different chronometer molecules, the hsp65 and rpoB genes, strongly supported the taxonomic status of this strain as representing a distinct species. These data support the conclusion that strain 299T represents a novel mycobacterial species, for which the name Mycobacterium parakoreense sp. nov. is proposed. The type strain is 299T ( = DSM 45575T = KCTC 19818T).

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